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gezelter |
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2006-01-16 10:26 gezelter |
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* configure: Testing commit |
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2006-01-13 16:57 chuckv |
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* src/: UseTheForce/SC_FF.cpp, |
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applications/nanoparticleBuilder/sphericalNanoparticle.cpp, |
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io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals. |
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Handled by forceField now. |
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2006-01-13 14:17 chuckv |
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* src/io/Globals.cpp: Added NPAT to Globals integrators. |
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2006-01-13 11:33 gezelter |
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* Makefile: [no log message] |
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2006-01-13 11:26 gezelter |
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* Makefile: testing to make sure GNU make is the make that was used |
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to build OOPSE |
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2006-01-13 10:48 gezelter |
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* configure, ac-tools/configure.in: changed compiler search order |
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2006-01-12 19:09 chuckv |
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* forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc, |
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samples/metals/Sutton-Chen/Au_bulk.in, |
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samples/metals/Sutton-Chen/Au_bulk_QSC.md, |
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samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen |
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units |
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2006-01-12 16:16 gezelter |
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* LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some |
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version info and the copyright date |
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2006-01-12 15:52 gezelter |
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* src/config.h.in: added some missing checks for header files |
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(particularly zlib.h), used autoheader to help generate config.h.in |
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2006-01-12 15:51 gezelter |
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* configure, ac-tools/configure.in: added some missing checks for |
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header files (particularly zlib.h) |
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2006-01-12 15:19 gezelter |
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* make/Makefile.in: fixed a dependency problem for the Executable |
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builds |
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2006-01-12 15:02 gezelter |
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* samples/gbljtest/Makefile: Missing Makefile in this sample |
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directory |
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2006-01-12 15:01 gezelter |
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* make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile: |
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Old makefile.in no longer required |
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2006-01-12 15:01 gezelter |
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* forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff |
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needs to be installed |
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72 |
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2006-01-12 14:56 chuckv |
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* src/io/DumpWriter.cpp: Changed formating. |
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76 |
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2006-01-12 11:47 chrisfen |
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* samples/water/tip4p/tp4.md, |
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src/UseTheForce/DarkSide/electrostatic.F90, |
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src/UseTheForce/DarkSide/electrostatic_interface.F90, |
81 |
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src/UseTheForce/DarkSide/electrostatic_interface.h, |
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src/brains/SimInfo.cpp: unifying function name in electrostatics |
83 |
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84 |
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2006-01-12 11:04 tim |
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* samples/metals/: EAM/nanoparticle/Makefile, |
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EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile, |
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Sutton-Chen/Makefile: fix make install problem for metals samples |
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2006-01-12 10:22 tim |
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* make/Makefile.in: remove samples/metals from install list. |
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94 |
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2006-01-12 09:31 tim |
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* src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not |
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handle multiple line macro, just convert multiple line macro into |
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single line macro. |
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2006-01-11 23:13 chrisfen |
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102 |
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* src/: UseTheForce/DarkSide/electrostatic.F90, |
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UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some |
104 |
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changes to electrostatics for shifted-potential and shifted-force |
105 |
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with mono and multipoles |
106 |
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107 |
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2006-01-11 18:04 gezelter |
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109 |
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* src/config.h.in, src/UseTheForce/doForces_interface.h, |
110 |
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src/UseTheForce/DarkSide/atype_interface.h, |
111 |
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src/UseTheForce/DarkSide/eam_interface.h, |
112 |
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src/UseTheForce/DarkSide/electrostatic_interface.h, |
113 |
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src/UseTheForce/DarkSide/fForceOptions_interface.h, |
114 |
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src/UseTheForce/DarkSide/gb_interface.h, |
115 |
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src/UseTheForce/DarkSide/lj_interface.h, |
116 |
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src/UseTheForce/DarkSide/shapes_interface.h, |
117 |
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src/UseTheForce/DarkSide/simParallel_interface.h, |
118 |
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src/UseTheForce/DarkSide/simulation_interface.h, |
119 |
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src/UseTheForce/DarkSide/sticky_interface.h, |
120 |
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src/UseTheForce/DarkSide/suttonchen_interface.h, |
121 |
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src/UseTheForce/DarkSide/switcheroo_interface.h, |
122 |
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src/mdParser/MDParser.g, src/profiling/mdProfile.cpp, |
123 |
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src/utils/fError.c, configure, make/Makefile.in: autoconf |
124 |
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modernization and cruft removal |
125 |
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126 |
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2006-01-11 18:04 gezelter |
127 |
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128 |
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* ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf |
129 |
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modernization and cruft-removal |
130 |
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131 |
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2006-01-11 17:50 tim |
132 |
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133 |
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* src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix |
134 |
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some error messages |
135 |
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136 |
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2006-01-11 14:01 tim |
137 |
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138 |
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* src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp, |
139 |
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io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp, |
140 |
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types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp, |
141 |
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types/TorsionStamp.hpp, utils/OOPSEException.hpp, |
142 |
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utils/StringUtils.hpp: instead of printing to std::cout, throwing |
143 |
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an exception when error is found. |
144 |
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145 |
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2006-01-11 13:41 gezelter |
146 |
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147 |
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* src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling |
148 |
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error |
149 |
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150 |
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2006-01-10 17:55 chuckv |
151 |
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152 |
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* forceFields/SuttonChen.frc: Changed conversion factor. |
153 |
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154 |
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2006-01-10 16:14 chuckv |
155 |
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156 |
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* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
157 |
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src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be |
158 |
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working now. |
159 |
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160 |
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2006-01-09 17:22 chuckv |
161 |
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162 |
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* src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC |
163 |
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164 |
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2006-01-09 17:14 tim |
165 |
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166 |
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* src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp, |
167 |
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StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
168 |
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StaticPropsCmd.h: fixing RhoZ |
169 |
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170 |
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2006-01-09 14:26 chuckv |
171 |
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172 |
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* forceFields/SuttonChen.frc, |
173 |
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samples/metals/Sutton-Chen/Au_bulk_SC.md, |
174 |
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src/io/LennardJonesAtomTypesSectionParser.cpp, |
175 |
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src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to |
176 |
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section parsers. |
177 |
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178 |
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2006-01-09 14:11 tim |
179 |
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180 |
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* src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp, |
181 |
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utils/StringUtils.hpp: replace isType<int> with isInteger |
182 |
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183 |
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2006-01-06 16:15 tim |
184 |
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185 |
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* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra |
186 |
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forceFieldOptions from SC_FF |
187 |
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188 |
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2006-01-06 15:27 chuckv |
189 |
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190 |
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* forceFields/SuttonChen.frc: Add force file. |
191 |
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192 |
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2005-12-31 17:42 chuckv |
193 |
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194 |
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* src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer |
195 |
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segfaults or produces 0 potential, but rather produces Inf for the |
196 |
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potential. Progress.... |
197 |
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198 |
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2005-12-30 18:15 chuckv |
199 |
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200 |
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* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
201 |
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src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
202 |
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src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp, |
203 |
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src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More |
204 |
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Sutton-Chen bug fixes. |
205 |
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206 |
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2005-12-30 16:25 tim |
207 |
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208 |
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* src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range |
209 |
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potential return from fortran is already accumulated, it should not |
210 |
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be accumulated again; nGroupTypesCol is not initialized; |
211 |
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GroupMaxCutoffCol is not allocated; |
212 |
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213 |
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2005-12-30 10:32 tim |
214 |
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215 |
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* make/Makefile.in, src/brains/SimCreator.cpp: In order to compile |
216 |
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MPI version, we need to cast const char* to void* for |
217 |
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stringstream.str(); Previous Makefile use bjects of single version |
218 |
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to make the MPI library; |
219 |
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220 |
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2005-12-29 19:18 chuckv |
221 |
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222 |
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* make/Makefile.in, samples/metals/Makefile, |
223 |
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src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
224 |
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src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes. |
225 |
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Almost there... |
226 |
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227 |
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2005-12-29 15:19 chuckv |
228 |
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229 |
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* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in |
230 |
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forcefield. |
231 |
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232 |
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2005-12-29 15:07 chuckv |
233 |
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234 |
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* samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile, |
235 |
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metals.md: added files for sutton-chen |
236 |
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237 |
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2005-12-29 11:37 chuckv |
238 |
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239 |
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* samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile, |
240 |
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metals.md: More cvs changing. |
241 |
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242 |
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2005-12-29 11:34 chuckv |
243 |
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244 |
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* samples/metals/Au_nanoparticle.in: More moving... |
245 |
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246 |
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2005-12-29 11:33 chuckv |
247 |
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248 |
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* samples/metals/EAM/nanoparticle/: |
249 |
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Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md, |
250 |
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Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More |
251 |
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changes to directory structure. |
252 |
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253 |
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2005-12-29 11:21 chuckv |
254 |
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255 |
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* samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md, |
256 |
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Au_bulk_voter.md, Makefile, metals.md: More Directory changes... |
257 |
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258 |
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2005-12-29 11:17 chuckv |
259 |
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260 |
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* samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in, |
261 |
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Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md, |
262 |
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Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of |
263 |
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directory structure |
264 |
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265 |
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2005-12-29 11:03 chuckv |
266 |
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267 |
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* src/: UseTheForce/DarkSide/fForceOptions_interface.F90, |
268 |
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brains/SimCreator.cpp: Fixed issue with symbol naming and added |
269 |
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call to set force options in SimCreator. |
270 |
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271 |
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2005-12-28 16:44 chuckv |
272 |
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273 |
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* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More |
274 |
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changes to forcefield options. |
275 |
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276 |
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2005-12-28 16:42 chuckv |
277 |
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278 |
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* src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options |
279 |
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passed to fortran. |
280 |
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281 |
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2005-12-23 18:04 chuckv |
282 |
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283 |
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* src/: UseTheForce/DarkSide/fForceOptions_interface.h, |
284 |
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io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option |
285 |
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changes. |
286 |
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287 |
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2005-12-16 16:52 tim |
288 |
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289 |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
290 |
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src/config.h.in, src/UseTheForce/DarkSide/gb.F90, |
291 |
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src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp, |
292 |
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src/openbabel/chains.cpp, src/openbabel/chiral.cpp, |
293 |
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src/openbabel/data.cpp, src/openbabel/fingerprint.cpp, |
294 |
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src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp, |
295 |
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src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp, |
296 |
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src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp, |
297 |
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src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp, |
298 |
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src/openbabel/obbond.cpp, src/openbabel/oberror.cpp, |
299 |
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src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp, |
300 |
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src/openbabel/obutil.cpp, src/openbabel/patty.cpp, |
301 |
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src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp, |
302 |
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src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp, |
303 |
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src/openbabel/ring.cpp, src/openbabel/rotor.cpp, |
304 |
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src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp, |
305 |
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src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed |
306 |
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__FUNCTION__ to __func__ to match C99 standard, and then added an |
307 |
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autoconf test to check for __func__ usability. Changed some |
308 |
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default compile flags for the Sun architecture |
309 |
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310 |
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2005-12-16 14:01 gezelter |
311 |
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312 |
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* ac-tools/AC_CXX_HAVE_STL.m4: added the STL check |
313 |
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314 |
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2005-12-16 13:55 tim |
315 |
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316 |
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* src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor |
317 |
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change to build oopse under solaris |
318 |
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319 |
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2005-12-16 13:26 tim |
320 |
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321 |
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* src/: brains/SimCreator.cpp, io/Globals.cpp, |
322 |
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types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library |
323 |
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came with SUN compiler does not have a conforming std::use_facet, |
324 |
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define a macro to handle it. Adding exception handling to |
325 |
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SimCreator. |
326 |
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327 |
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2005-12-16 10:53 gezelter |
328 |
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329 |
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* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
330 |
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GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom |
331 |
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which was living inside the GB particle. No alien-like ripping out |
332 |
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of the stomach was required. |
333 |
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334 |
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2005-12-15 21:57 tim |
335 |
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336 |
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* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
337 |
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MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
338 |
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MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: |
339 |
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replace grammar for numerical parsing |
340 |
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341 |
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2005-12-15 16:43 gezelter |
342 |
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343 |
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* src/UseTheForce/doForces.F90: fixed a cutoff bug |
344 |
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345 |
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2005-12-15 09:48 gezelter |
346 |
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347 |
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* src/antlr/: CharScanner.hpp, config.hpp: Removing compiler |
348 |
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dependencies and replacing them with real autoconf checks |
349 |
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350 |
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2005-12-15 09:47 gezelter |
351 |
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352 |
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* configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4, |
353 |
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ac-tools/configure.in, src/config.h.in: Adding checks for various |
354 |
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features used by ANTLR |
355 |
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356 |
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2005-12-14 13:02 tim |
357 |
|
|
|
358 |
|
|
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
359 |
|
|
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
360 |
|
|
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a |
361 |
|
|
nasty negative integer parsing problem by refining the grammar |
362 |
|
|
|
363 |
|
|
2005-12-12 14:32 gezelter |
364 |
|
|
|
365 |
|
|
* src/: UseTheForce/doForces_interface.F90, |
366 |
|
|
UseTheForce/doForces_interface.h, |
367 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
368 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
369 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
370 |
|
|
brains/MoleculeCreator.cpp, brains/SimInfo.cpp, |
371 |
|
|
math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made |
372 |
|
|
some minor changes to allow compilation with the portland group |
373 |
|
|
compilers |
374 |
|
|
|
375 |
|
|
2005-12-10 11:54 tim |
376 |
|
|
|
377 |
|
|
* src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation |
378 |
|
|
problem for icc7 |
379 |
|
|
|
380 |
|
|
2005-12-09 16:18 gezelter |
381 |
|
|
|
382 |
|
|
* src/utils/CaseConversion.hpp: added missing include |
383 |
|
|
|
384 |
|
|
2005-12-09 12:11 gezelter |
385 |
|
|
|
386 |
|
|
* configure, ac-tools/aclocal.m4: added some checks for pathscale |
387 |
|
|
compiler |
388 |
|
|
|
389 |
|
|
2005-12-08 17:05 gezelter |
390 |
|
|
|
391 |
|
|
* src/io/ForceFieldOptions.cpp: added copyright |
392 |
|
|
|
393 |
|
|
2005-12-08 17:04 gezelter |
394 |
|
|
|
395 |
|
|
* src/UseTheForce/doForces.F90: added info printout |
396 |
|
|
|
397 |
|
|
2005-12-08 17:04 gezelter |
398 |
|
|
|
399 |
|
|
* configure, ac-tools/configure.in: added pathscale |
400 |
|
|
|
401 |
|
|
2005-12-08 10:38 chuckv |
402 |
|
|
|
403 |
|
|
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp, |
404 |
|
|
UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp, |
405 |
|
|
UseTheForce/SHAPES_FF.cpp, io/BendTypesSectionParser.cpp, |
406 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
407 |
|
|
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
408 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
409 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
410 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, |
411 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
412 |
|
|
io/GayBerneAtomTypesSectionParser.cpp, |
413 |
|
|
io/GayBerneAtomTypesSectionParser.hpp, |
414 |
|
|
io/MultipoleAtomTypesSectionParser.cpp, |
415 |
|
|
io/MultipoleAtomTypesSectionParser.hpp, |
416 |
|
|
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
417 |
|
|
io/ShapeAtomTypesSectionParser.cpp, |
418 |
|
|
io/ShapeAtomTypesSectionParser.hpp, |
419 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
420 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
421 |
|
|
io/StickyPowerAtomTypesSectionParser.cpp, |
422 |
|
|
io/StickyPowerAtomTypesSectionParser.hpp, |
423 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp: |
424 |
|
|
Wow thats alot o' files. Now passing forceFieldOptions to all of |
425 |
|
|
the parsers. |
426 |
|
|
|
427 |
|
|
2005-12-07 18:10 chuckv |
428 |
|
|
|
429 |
|
|
* src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp, |
430 |
|
|
SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things.... |
431 |
|
|
Started adding support for ForceOptions to section parsers. |
432 |
|
|
|
433 |
|
|
2005-12-07 18:01 gezelter |
434 |
|
|
|
435 |
|
|
* src/UseTheForce/DarkSide/gb_interface.h: [no log message] |
436 |
|
|
|
437 |
|
|
2005-12-07 18:00 chuckv |
438 |
|
|
|
439 |
|
|
* src/io/: LennardJonesAtomTypesSectionParser.cpp, |
440 |
|
|
LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to |
441 |
|
|
section parser |
442 |
|
|
|
443 |
|
|
2005-12-07 14:58 chuckv |
444 |
|
|
|
445 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90, |
446 |
|
|
lj_interface.h, suttonchen.F90, suttonchen_interface.F90, |
447 |
|
|
suttonchen_interface.h: Removed geometric distance mixing from |
448 |
|
|
individual modules and now use force options to detemine what the |
449 |
|
|
deal is. |
450 |
|
|
|
451 |
|
|
2005-12-07 14:46 chuckv |
452 |
|
|
|
453 |
|
|
* src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90: |
454 |
|
|
Further fixes for compiler issues. |
455 |
|
|
|
456 |
|
|
2005-12-07 14:44 chuckv |
457 |
|
|
|
458 |
|
|
* src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue. |
459 |
|
|
|
460 |
|
|
2005-12-07 14:38 chuckv |
461 |
|
|
|
462 |
|
|
* src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90, |
463 |
|
|
fForceOptions_interface.F90, fForceOptions_interface.h: Added |
464 |
|
|
support for fortran force options. |
465 |
|
|
|
466 |
|
|
2005-12-06 16:01 tim |
467 |
|
|
|
468 |
|
|
* src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion |
469 |
|
|
|
470 |
|
|
2005-12-06 14:26 chuckv |
471 |
|
|
|
472 |
|
|
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC. |
473 |
|
|
|
474 |
|
|
2005-12-06 12:53 chuckv |
475 |
|
|
|
476 |
|
|
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
477 |
|
|
GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned |
478 |
|
|
crystal |
479 |
|
|
|
480 |
|
|
2005-12-06 12:52 chuckv |
481 |
|
|
|
482 |
|
|
* src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for |
483 |
|
|
dumpwriter. |
484 |
|
|
|
485 |
|
|
2005-12-06 11:49 tim |
486 |
|
|
|
487 |
|
|
* samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md, |
488 |
|
|
argon/ar864.md, argon/argonNVT.md, argon/lj.md, |
489 |
|
|
dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md, |
490 |
|
|
dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md, |
491 |
|
|
gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md, |
492 |
|
|
gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md, |
493 |
|
|
lipid/5x5.md, lipid/lipid.md, lipid/water.md, |
494 |
|
|
metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md, |
495 |
|
|
metals/Au_bulk_voter.md, metals/Au_nanoparticle.md, |
496 |
|
|
metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md, |
497 |
|
|
minimizer/water.md, shape/linear.md, |
498 |
|
|
thermoIntegration/liquid/ssde.md, |
499 |
|
|
thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md, |
500 |
|
|
thermoIntegration/solid/water.md, water/dimer/cl.md, |
501 |
|
|
water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md, |
502 |
|
|
water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md, |
503 |
|
|
water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md, |
504 |
|
|
water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md, |
505 |
|
|
water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md, |
506 |
|
|
water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md, |
507 |
|
|
water/tip3p_ice/tp3.md, water/tip3p_ice/water.md, |
508 |
|
|
water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md, |
509 |
|
|
zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated |
510 |
|
|
keywords from samples |
511 |
|
|
|
512 |
|
|
2005-12-05 18:37 tim |
513 |
|
|
|
514 |
|
|
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp, |
515 |
|
|
Globals.cpp, Makefile: Fix parsing error in OptionSectionParser |
516 |
|
|
|
517 |
|
|
2005-12-05 17:23 gezelter |
518 |
|
|
|
519 |
|
|
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp, |
520 |
|
|
UseTheForce/Makefile, brains/Register.cpp, |
521 |
|
|
io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding |
522 |
|
|
handler for CLAY force field |
523 |
|
|
|
524 |
|
|
2005-12-05 16:45 chuckv |
525 |
|
|
|
526 |
|
|
* src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug |
527 |
|
|
in openbabel. |
528 |
|
|
|
529 |
|
|
2005-12-05 14:10 tim |
530 |
|
|
|
531 |
|
|
* src/types/MoleculeStamp.cpp: reformat error message |
532 |
|
|
|
533 |
|
|
2005-12-05 14:07 gezelter |
534 |
|
|
|
535 |
|
|
* forceFields/CLAYFF.frc: Adding .frc file for CLAYFF |
536 |
|
|
|
537 |
|
|
2005-12-05 13:23 tim |
538 |
|
|
|
539 |
|
|
* src/: types/AtomStamp.cpp, types/AtomStamp.hpp, |
540 |
|
|
types/BendStamp.hpp, types/MoleculeStamp.cpp, |
541 |
|
|
types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp: |
542 |
|
|
adding more checking for topology |
543 |
|
|
|
544 |
|
|
2005-12-02 17:37 gezelter |
545 |
|
|
|
546 |
|
|
* src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon |
547 |
|
|
removal |
548 |
|
|
|
549 |
|
|
2005-12-02 17:37 gezelter |
550 |
|
|
|
551 |
|
|
* src/config.h.in: We've made big changes. This isn't 2.0 anymore. |
552 |
|
|
|
553 |
|
|
2005-12-02 17:37 gezelter |
554 |
|
|
|
555 |
|
|
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
556 |
|
|
GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md, |
557 |
|
|
traditional.md: removing deprecated nAtoms and nComponents lines |
558 |
|
|
|
559 |
|
|
2005-12-02 15:34 tim |
560 |
|
|
|
561 |
|
|
* src/selection/SelectionToken.cpp: adding SelectionToken.cpp |
562 |
|
|
|
563 |
|
|
2005-12-02 15:18 tim |
564 |
|
|
|
565 |
|
|
* src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding |
566 |
|
|
FragmentStamp |
567 |
|
|
|
568 |
|
|
2005-12-02 15:11 gezelter |
569 |
|
|
|
570 |
|
|
* src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no |
571 |
|
|
longer thrown with consts (fixes compilation bug on the Mac). |
572 |
|
|
|
573 |
|
|
2005-12-02 15:10 gezelter |
574 |
|
|
|
575 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious |
576 |
|
|
printing out of timestep |
577 |
|
|
|
578 |
|
|
2005-12-02 15:10 gezelter |
579 |
|
|
|
580 |
|
|
* src/brains/ForceManager.cpp: Got rid of spurious printing out of |
581 |
|
|
junk |
582 |
|
|
|
583 |
|
|
2005-12-02 15:10 gezelter |
584 |
|
|
|
585 |
|
|
* make/Makefile.in: Change build process for libOOPSE.a so that the |
586 |
|
|
libraries aren't unpacked. libOOPSE.a is now made directly from |
587 |
|
|
the object files |
588 |
|
|
|
589 |
|
|
2005-12-02 15:09 gezelter |
590 |
|
|
|
591 |
|
|
* configure, ac-tools/configure.in: added check for egrep (grep -E) |
592 |
|
|
needed for new build of libOOPSE.a |
593 |
|
|
|
594 |
|
|
2005-12-02 13:43 tim |
595 |
|
|
|
596 |
|
|
* src/types/DataHolder.hpp: adding DataHolder |
597 |
|
|
|
598 |
|
|
2005-12-02 12:01 gezelter |
599 |
|
|
|
600 |
|
|
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
601 |
|
|
GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test |
602 |
|
|
case for the cutoff policies |
603 |
|
|
|
604 |
|
|
2005-12-02 10:38 tim |
605 |
|
|
|
606 |
|
|
* make/Makefile.in: update Makefile |
607 |
|
|
|
608 |
|
|
2005-12-02 10:38 tim |
609 |
|
|
|
610 |
|
|
* src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp, |
611 |
|
|
antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp, |
612 |
|
|
antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp, |
613 |
|
|
antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp, |
614 |
|
|
antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp, |
615 |
|
|
antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp, |
616 |
|
|
antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp, |
617 |
|
|
antlr/CharScanner.cpp, antlr/CharScanner.hpp, |
618 |
|
|
antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp, |
619 |
|
|
antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp, |
620 |
|
|
antlr/CommonASTWithHiddenTokens.cpp, |
621 |
|
|
antlr/CommonASTWithHiddenTokens.hpp, |
622 |
|
|
antlr/CommonHiddenStreamToken.cpp, |
623 |
|
|
antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp, |
624 |
|
|
antlr/CommonToken.hpp, antlr/IOException.hpp, |
625 |
|
|
antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp, |
626 |
|
|
antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp, |
627 |
|
|
antlr/Makefile, antlr/MismatchedCharException.cpp, |
628 |
|
|
antlr/MismatchedCharException.hpp, |
629 |
|
|
antlr/MismatchedTokenException.cpp, |
630 |
|
|
antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp, |
631 |
|
|
antlr/NoViableAltException.hpp, |
632 |
|
|
antlr/NoViableAltForCharException.cpp, |
633 |
|
|
antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp, |
634 |
|
|
antlr/Parser.hpp, antlr/ParserSharedInputState.hpp, |
635 |
|
|
antlr/RecognitionException.cpp, antlr/RecognitionException.hpp, |
636 |
|
|
antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp, |
637 |
|
|
antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp, |
638 |
|
|
antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp, |
639 |
|
|
antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp, |
640 |
|
|
antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp, |
641 |
|
|
antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp, |
642 |
|
|
antlr/TokenStreamHiddenTokenFilter.cpp, |
643 |
|
|
antlr/TokenStreamHiddenTokenFilter.hpp, |
644 |
|
|
antlr/TokenStreamIOException.hpp, |
645 |
|
|
antlr/TokenStreamRecognitionException.hpp, |
646 |
|
|
antlr/TokenStreamRetryException.hpp, |
647 |
|
|
antlr/TokenStreamRewriteEngine.cpp, |
648 |
|
|
antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp, |
649 |
|
|
antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp, |
650 |
|
|
antlr/TreeParser.cpp, antlr/TreeParser.hpp, |
651 |
|
|
antlr/TreeParserSharedInputState.hpp, antlr/config.hpp, |
652 |
|
|
applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
653 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
654 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
655 |
|
|
constraints/ZconstraintForceManager.cpp, |
656 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp, |
657 |
|
|
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
658 |
|
|
io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp, |
659 |
|
|
io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile, |
660 |
|
|
io/ZConsReader.cpp, io/interface.c, io/make_nodes.c, |
661 |
|
|
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, |
662 |
|
|
io/parse_interface.h, io/parse_me.h, io/parse_tree.c, |
663 |
|
|
io/parse_tree.h, mdParser/FilenameObserver.cpp, |
664 |
|
|
mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp, |
665 |
|
|
mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g, |
666 |
|
|
mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp, |
667 |
|
|
mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g, |
668 |
|
|
mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp, |
669 |
|
|
mdParser/Makefile, mdParser/SimplePreprocessor.hpp, |
670 |
|
|
openbabel/obconversion.cpp, openbabel/oopseformat.cpp, |
671 |
|
|
openbabel/xyzformat.cpp, primitives/RigidBody.cpp, |
672 |
|
|
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
673 |
|
|
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
674 |
|
|
selection/Makefile, selection/NameFinder.cpp, |
675 |
|
|
selection/NameFinder.hpp, selection/SelectionCompiler.hpp, |
676 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
677 |
|
|
selection/SelectionManager.hpp, selection/SelectionToken.hpp, |
678 |
|
|
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp, |
679 |
|
|
types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp, |
680 |
|
|
types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp, |
681 |
|
|
types/Component.cpp, types/Component.hpp, |
682 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
683 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile, |
684 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
685 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
686 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
687 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp, |
688 |
|
|
types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp, |
689 |
|
|
utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp, |
690 |
|
|
utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp, |
691 |
|
|
utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the |
692 |
|
|
Link --> List Return of the Oject-Oriented replace yacc/lex parser |
693 |
|
|
with antlr parser |
694 |
|
|
|
695 |
|
|
2005-11-30 16:00 chuckv |
696 |
|
|
|
697 |
|
|
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to |
698 |
|
|
calculate rho(Z) to calculate density profiles for water slabs. |
699 |
|
|
|
700 |
|
|
2005-11-29 17:54 chuckv |
701 |
|
|
|
702 |
|
|
* configure, ac-tools/configure.in: added checks for some functions |
703 |
|
|
to configure script |
704 |
|
|
|
705 |
|
|
2005-11-22 20:05 chuckv |
706 |
|
|
|
707 |
|
|
* src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp, |
708 |
|
|
obbond.cpp: Changed file names that conflict w/ oopse file name |
709 |
|
|
object files. |
710 |
|
|
|
711 |
|
|
2005-11-21 17:59 gezelter |
712 |
|
|
|
713 |
|
|
* src/utils/residentMem.c: compilation bug |
714 |
|
|
|
715 |
|
|
2005-11-21 17:59 gezelter |
716 |
|
|
|
717 |
|
|
* src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp |
718 |
|
|
|
719 |
|
|
2005-11-21 17:59 gezelter |
720 |
|
|
|
721 |
|
|
* src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes |
722 |
|
|
|
723 |
|
|
2005-11-21 17:59 gezelter |
724 |
|
|
|
725 |
|
|
* src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation |
726 |
|
|
issue |
727 |
|
|
|
728 |
|
|
2005-11-21 17:58 gezelter |
729 |
|
|
|
730 |
|
|
* src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90, |
731 |
|
|
doForces_interface.F90, doForces_interface.h, fForceOptions.h, |
732 |
|
|
notifyCutoffs.F90, notifyCutoffs_interface.F90, |
733 |
|
|
notifyCutoffs_interface.h, DarkSide/LJ.F90, |
734 |
|
|
DarkSide/electrostatic.F90, DarkSide/gb.F90, |
735 |
|
|
DarkSide/suttonchen.F90: Cutoff mixing fixes have been made. |
736 |
|
|
|
737 |
|
|
2005-11-21 11:22 tim |
738 |
|
|
|
739 |
|
|
* src/io/ParamConstraint.cpp: Adding ParamConstraint.cpp |
740 |
|
|
|
741 |
|
|
2005-11-21 09:59 tim |
742 |
|
|
|
743 |
|
|
* forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt, |
744 |
|
|
atomtyp.txt, bondtyp.txt, element.txt, extable.txt, |
745 |
|
|
isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt, |
746 |
|
|
resdata.txt, torlib.txt, types.txt: adding openbabel data files |
747 |
|
|
|
748 |
|
|
2005-11-18 15:17 tim |
749 |
|
|
|
750 |
|
|
* src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp: |
751 |
|
|
adding support for soft linking |
752 |
|
|
|
753 |
|
|
2005-11-18 15:17 tim |
754 |
|
|
|
755 |
|
|
* make/Makefile.in: Adding support for soft linking |
756 |
|
|
|
757 |
|
|
2005-11-18 12:50 gezelter |
758 |
|
|
|
759 |
|
|
* make/Makefile.in: Adding linking stuff |
760 |
|
|
|
761 |
|
|
2005-11-18 11:38 tim |
762 |
|
|
|
763 |
|
|
* make/Makefile.in, src/applications/atom2mdin/Makefile, |
764 |
|
|
src/applications/atom2mdin/atom2mdin.cpp, |
765 |
|
|
src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: |
766 |
|
|
rename mdinConverter to atom2mdin |
767 |
|
|
|
768 |
|
|
2005-11-17 15:44 gezelter |
769 |
|
|
|
770 |
|
|
* src/openbabel/obconversion.cpp: fixed a bug |
771 |
|
|
|
772 |
|
|
2005-11-17 15:39 gezelter |
773 |
|
|
|
774 |
|
|
* configure: Adding some config checks for OpenBabel codes we are |
775 |
|
|
using |
776 |
|
|
|
777 |
|
|
2005-11-17 15:39 gezelter |
778 |
|
|
|
779 |
|
|
* ac-tools/configure.in: Adding some checks for OpenBabel code |
780 |
|
|
|
781 |
|
|
2005-11-17 15:39 gezelter |
782 |
|
|
|
783 |
|
|
* src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel |
784 |
|
|
|
785 |
|
|
2005-11-17 15:38 gezelter |
786 |
|
|
|
787 |
|
|
* src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp, |
788 |
|
|
bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp, |
789 |
|
|
fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp, |
790 |
|
|
obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp, |
791 |
|
|
patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp, |
792 |
|
|
residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp: |
793 |
|
|
Unifying config.h stuff and making sure the OpenBabel codes can |
794 |
|
|
find our default (and environment variable) Force Field |
795 |
|
|
directories. |
796 |
|
|
|
797 |
|
|
2005-11-17 13:35 tim |
798 |
|
|
|
799 |
|
|
* src/io/ForceFieldOptions.hpp: adding ForceFieldOptions |
800 |
|
|
|
801 |
|
|
2005-11-16 18:10 tim |
802 |
|
|
|
803 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
804 |
|
|
brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, |
805 |
|
|
brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, |
806 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
807 |
|
|
io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp, |
808 |
|
|
io/OptionSectionParser.hpp, io/ParamConstraint.hpp, |
809 |
|
|
io/SectionParser.hpp, io/SectionParserManager.cpp, |
810 |
|
|
io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp, |
811 |
|
|
math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp, |
812 |
|
|
primitives/Bend.hpp, primitives/GhostBend.cpp, |
813 |
|
|
primitives/GhostBend.hpp, primitives/GhostTorsion.cpp, |
814 |
|
|
primitives/GhostTorsion.hpp, primitives/Torsion.cpp, |
815 |
|
|
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
816 |
|
|
primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp, |
817 |
|
|
types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp, |
818 |
|
|
types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp, |
819 |
|
|
types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser |
820 |
|
|
get compiled |
821 |
|
|
|
822 |
|
|
2005-11-16 16:37 chuckv |
823 |
|
|
|
824 |
|
|
* src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp, |
825 |
|
|
io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp, |
826 |
|
|
UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField |
827 |
|
|
optional parameters.... |
828 |
|
|
|
829 |
|
|
2005-11-16 16:22 tim |
830 |
|
|
|
831 |
|
|
* src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp, |
832 |
|
|
fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp, |
833 |
|
|
gromos96format.cpp, gromos96format.hpp, oopseformat.cpp, |
834 |
|
|
oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp, |
835 |
|
|
povrayformat.hpp, smilesformat.cpp, smilesformat.hpp, |
836 |
|
|
tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp: |
837 |
|
|
adding more readers/writers |
838 |
|
|
|
839 |
|
|
2005-11-16 16:20 tim |
840 |
|
|
|
841 |
|
|
* make/Makefile.in: adding openbabel |
842 |
|
|
|
843 |
|
|
2005-11-16 16:20 tim |
844 |
|
|
|
845 |
|
|
* src/brains/: Register.cpp, Register.hpp: register openbabel |
846 |
|
|
readers/writers |
847 |
|
|
|
848 |
|
|
2005-11-16 14:57 chrisfen |
849 |
|
|
|
850 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: included shifted |
851 |
|
|
potential self term |
852 |
|
|
|
853 |
|
|
2005-11-16 14:57 chrisfen |
854 |
|
|
|
855 |
|
|
* samples/water/spce/spce.md: just some parameters |
856 |
|
|
|
857 |
|
|
2005-11-16 14:42 tim |
858 |
|
|
|
859 |
|
|
* src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp, |
860 |
|
|
babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp, |
861 |
|
|
bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp, |
862 |
|
|
chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp, |
863 |
|
|
data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp, |
864 |
|
|
fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp, |
865 |
|
|
isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp, |
866 |
|
|
matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp, |
867 |
|
|
obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp, |
868 |
|
|
oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp, |
869 |
|
|
obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp, |
870 |
|
|
patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp, |
871 |
|
|
phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp, |
872 |
|
|
ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp, |
873 |
|
|
snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp, |
874 |
|
|
tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp, |
875 |
|
|
types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp, |
876 |
|
|
zipstreamimpl.hpp: adding openbabel |
877 |
|
|
|
878 |
|
|
2005-11-15 14:42 chrisfen |
879 |
|
|
|
880 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary |
881 |
|
|
commented code |
882 |
|
|
|
883 |
|
|
2005-11-15 14:04 chrisfen |
884 |
|
|
|
885 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the |
886 |
|
|
charge-charge interactions a bit... |
887 |
|
|
|
888 |
|
|
2005-11-15 14:03 chrisfen |
889 |
|
|
|
890 |
|
|
* samples/water/spce/: spce.md, water.md: just playing |
891 |
|
|
|
892 |
|
|
2005-11-15 11:38 chrisfen |
893 |
|
|
|
894 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the |
895 |
|
|
shifted_potential case |
896 |
|
|
|
897 |
|
|
2005-11-15 11:37 chrisfen |
898 |
|
|
|
899 |
|
|
* samples/: argon/500.md, water/spce/spce.md, water/spce/water.md: |
900 |
|
|
just playing around - we need to refresh all the samples sometime |
901 |
|
|
soon... |
902 |
|
|
|
903 |
|
|
2005-11-15 11:18 chuckv |
904 |
|
|
|
905 |
|
|
* src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made |
906 |
|
|
preforce calc public in suttonchen. |
907 |
|
|
|
908 |
|
|
2005-11-15 11:05 chuckv |
909 |
|
|
|
910 |
|
|
* src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to |
911 |
|
|
SimInfo |
912 |
|
|
|
913 |
|
|
2005-11-15 11:01 chuckv |
914 |
|
|
|
915 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h, |
916 |
|
|
DarkSide/simulation.F90: Added Sutton-Chen to force loop... |
917 |
|
|
|
918 |
|
|
2005-11-15 10:34 chuckv |
919 |
|
|
|
920 |
|
|
* forceFields/Makefile: Added sutton-chen to makefile. |
921 |
|
|
|
922 |
|
|
2005-11-14 17:20 chuckv |
923 |
|
|
|
924 |
|
|
* src/UseTheForce/DarkSide/: suttonchen.F90, |
925 |
|
|
suttonchen_interface.h: Build Fixes for sutton-chen. |
926 |
|
|
|
927 |
|
|
2005-11-14 17:03 chuckv |
928 |
|
|
|
929 |
|
|
* src/io/Makefile: Missed makefile for sutton-chen. |
930 |
|
|
|
931 |
|
|
2005-11-14 17:03 chuckv |
932 |
|
|
|
933 |
|
|
* src/UseTheForce/: Makefile, DarkSide/Makefile, |
934 |
|
|
DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff |
935 |
|
|
|
936 |
|
|
2005-11-14 16:29 chuckv |
937 |
|
|
|
938 |
|
|
* src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp, |
939 |
|
|
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
940 |
|
|
UseTheForce/DarkSide/suttonchen.F90, |
941 |
|
|
UseTheForce/DarkSide/suttonchen_interface.F90, |
942 |
|
|
UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp, |
943 |
|
|
brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp, |
944 |
|
|
types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to |
945 |
|
|
fix do_forces to use Sutton-Chen. |
946 |
|
|
|
947 |
|
|
2005-11-11 12:21 chrisfen |
948 |
|
|
|
949 |
|
|
* src/UseTheForce/DarkSide/: fSwitchingFunctionType.h, |
950 |
|
|
switcheroo_interface.F90, switcheroo_interface.h: Forgot to add |
951 |
|
|
some files |
952 |
|
|
|
953 |
|
|
2005-11-11 10:22 chrisfen |
954 |
|
|
|
955 |
|
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp, |
956 |
|
|
io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial |
957 |
|
|
switching function option |
958 |
|
|
|
959 |
|
|
2005-11-11 10:21 chrisfen |
960 |
|
|
|
961 |
|
|
* src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a |
962 |
|
|
5th order polynomial switching function |
963 |
|
|
|
964 |
|
|
2005-11-11 10:21 chrisfen |
965 |
|
|
|
966 |
|
|
* samples/water/ssd/ssd.md: playing with switching functions again |
967 |
|
|
|
968 |
|
|
2005-11-11 10:21 chrisfen |
969 |
|
|
|
970 |
|
|
* samples/argon/500.md: playing with switching functions |
971 |
|
|
|
972 |
|
|
2005-11-08 19:11 chuckv |
973 |
|
|
|
974 |
|
|
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force |
975 |
|
|
files for Sutton-Chen and Quantum Sutton-Chen |
976 |
|
|
|
977 |
|
|
2005-11-08 08:32 chrisfen |
978 |
|
|
|
979 |
|
|
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp, |
980 |
|
|
DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and |
981 |
|
|
ability to output forces and torques |
982 |
|
|
|
983 |
|
|
2005-11-08 08:32 chrisfen |
984 |
|
|
|
985 |
|
|
* src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for |
986 |
|
|
output of forces and torques |
987 |
|
|
|
988 |
|
|
2005-11-08 08:31 chrisfen |
989 |
|
|
|
990 |
|
|
* src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90: |
991 |
|
|
Working on shifted_force... |
992 |
|
|
|
993 |
|
|
2005-11-08 08:31 chrisfen |
994 |
|
|
|
995 |
|
|
* samples/water/: spce/spce.md, ssde/ssde.md: Just testing... |
996 |
|
|
|
997 |
|
|
2005-11-03 18:22 chrisfen |
998 |
|
|
|
999 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly |
1000 |
|
|
commented section |
1001 |
|
|
|
1002 |
|
|
2005-11-03 18:12 chrisfen |
1003 |
|
|
|
1004 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, |
1005 |
|
|
UseTheForce/DarkSide/fElectrostaticScreeningMethod.h, |
1006 |
|
|
UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp, |
1007 |
|
|
io/Globals.cpp, io/Globals.hpp: improvements in shifted-force |
1008 |
|
|
|
1009 |
|
|
2005-11-03 18:11 chrisfen |
1010 |
|
|
|
1011 |
|
|
* samples/water/spce/spce.md: mmm... damped shifted force... |
1012 |
|
|
|
1013 |
|
|
2005-11-03 18:06 chuckv |
1014 |
|
|
|
1015 |
|
|
* src/UseTheForce/DarkSide/suttonchen.F90: More work on SC. |
1016 |
|
|
|
1017 |
|
|
2005-11-02 18:50 chuckv |
1018 |
|
|
|
1019 |
|
|
* src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen. |
1020 |
|
|
|
1021 |
|
|
2005-11-02 16:01 chrisfen |
1022 |
|
|
|
1023 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
1024 |
|
|
removed some test code |
1025 |
|
|
|
1026 |
|
|
2005-11-02 15:45 chrisfen |
1027 |
|
|
|
1028 |
|
|
* src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the |
1029 |
|
|
screening method header |
1030 |
|
|
|
1031 |
|
|
2005-11-02 15:36 chrisfen |
1032 |
|
|
|
1033 |
|
|
* src/brains/SimInfo.cpp: again, changing how we deal with |
1034 |
|
|
summation and screening methods |
1035 |
|
|
|
1036 |
|
|
2005-11-02 15:36 chrisfen |
1037 |
|
|
|
1038 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, |
1039 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
1040 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
1041 |
|
|
UseTheForce/DarkSide/fElectrostaticSummationMethod.h, |
1042 |
|
|
io/Globals.cpp, io/Globals.hpp: changing how we deal with summation |
1043 |
|
|
and screening methods |
1044 |
|
|
|
1045 |
|
|
2005-11-02 15:35 chrisfen |
1046 |
|
|
|
1047 |
|
|
* src/UseTheForce/doForces.F90: debug stuff for rf removed |
1048 |
|
|
|
1049 |
|
|
2005-11-01 18:32 chuckv |
1050 |
|
|
|
1051 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
1052 |
|
|
UseTheForce/DarkSide/atype_interface.F90, |
1053 |
|
|
UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp, |
1054 |
|
|
types/AtomTypeProperties.h: Added suppport to atypes for MEAM and |
1055 |
|
|
sutton-chen |
1056 |
|
|
|
1057 |
|
|
2005-11-01 14:24 chrisfen |
1058 |
|
|
|
1059 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
1060 |
|
|
removed some testing code... |
1061 |
|
|
|
1062 |
|
|
2005-11-01 14:14 chrisfen |
1063 |
|
|
|
1064 |
|
|
* src/: brains/Register.cpp, brains/SimInfo.cpp, |
1065 |
|
|
brains/fSimulation.h, integrators/IntegratorFactory.hpp, |
1066 |
|
|
io/Globals.cpp: fixed a capitalization problem with NPT integrator |
1067 |
|
|
initialization |
1068 |
|
|
|
1069 |
|
|
2005-11-01 14:13 chrisfen |
1070 |
|
|
|
1071 |
|
|
* src/applications/oopse/oopse.cpp: nothing |
1072 |
|
|
|
1073 |
|
|
2005-11-01 14:09 chrisfen |
1074 |
|
|
|
1075 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
1076 |
|
|
DarkSide/simulation.F90: still fixing up wolf... |
1077 |
|
|
|
1078 |
|
|
2005-11-01 13:29 chuckv |
1079 |
|
|
|
1080 |
|
|
* src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In |
1081 |
|
|
process of adding sutton-chen forcefield. |
1082 |
|
|
|
1083 |
|
|
2005-10-26 18:32 chrisfen |
1084 |
|
|
|
1085 |
|
|
* src/brains/SimInfo.cpp: changed the default switching radius to |
1086 |
|
|
85% of rcut |
1087 |
|
|
|
1088 |
|
|
2005-10-26 18:31 chrisfen |
1089 |
|
|
|
1090 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks |
1091 |
|
|
to be working now - for charges and dipoles alike |
1092 |
|
|
|
1093 |
|
|
2005-10-26 18:31 chrisfen |
1094 |
|
|
|
1095 |
|
|
* src/UseTheForce/doForces.F90: reaction field looks to be working |
1096 |
|
|
now |
1097 |
|
|
|
1098 |
|
|
2005-10-26 18:30 chrisfen |
1099 |
|
|
|
1100 |
|
|
* samples/water/ssdrf/water.md: added a test molecule |
1101 |
|
|
|
1102 |
|
|
2005-10-26 18:30 chrisfen |
1103 |
|
|
|
1104 |
|
|
* forceFields/DUFF2.frc: added a test atom type |
1105 |
|
|
|
1106 |
|
|
2005-10-24 09:06 chrisfen |
1107 |
|
|
|
1108 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole |
1109 |
|
|
reaction field - don't know if it works... |
1110 |
|
|
|
1111 |
|
|
2005-10-23 16:08 chrisfen |
1112 |
|
|
|
1113 |
|
|
* src/: UseTheForce/doForces.F90, |
1114 |
|
|
UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp: |
1115 |
|
|
streamlined reaction field for dipoles (now a good bit faster) and |
1116 |
|
|
added reaction field for charges - still need to do charge-dipole |
1117 |
|
|
RF |
1118 |
|
|
|
1119 |
|
|
2005-10-23 16:07 chrisfen |
1120 |
|
|
|
1121 |
|
|
* samples/water/ssdrf/ssdrf.md: minor changes when testing reaction |
1122 |
|
|
field |
1123 |
|
|
|
1124 |
|
|
2005-10-23 16:06 chrisfen |
1125 |
|
|
|
1126 |
|
|
* samples/water/spce/spce.md: reaction field now works for charges |
1127 |
|
|
|
1128 |
|
|
2005-10-20 15:27 tim |
1129 |
|
|
|
1130 |
|
|
* src/primitives/Torsion.cpp: Fix the other branch of force |
1131 |
|
|
calculation in Torision.cpp |
1132 |
|
|
|
1133 |
|
|
2005-10-19 14:24 chrisfen |
1134 |
|
|
|
1135 |
|
|
* src/: UseTheForce/doForces.F90, |
1136 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
1137 |
|
|
UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp, |
1138 |
|
|
brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals |
1139 |
|
|
toUpper problems - these changes should fix those... |
1140 |
|
|
|
1141 |
|
|
2005-10-19 14:23 chrisfen |
1142 |
|
|
|
1143 |
|
|
* samples/water/ssdrf/ssdrf.md: nothing |
1144 |
|
|
|
1145 |
|
|
2005-10-19 12:03 gezelter |
1146 |
|
|
|
1147 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in |
1148 |
|
|
GayBerne |
1149 |
|
|
|
1150 |
|
|
2005-10-19 11:49 tim |
1151 |
|
|
|
1152 |
|
|
* src/: UseTheForce/DarkSide/fInteractionMap.h, |
1153 |
|
|
brains/ForceManager.cpp: fix an index mismathcing between c and |
1154 |
|
|
fortran |
1155 |
|
|
|
1156 |
|
|
2005-10-18 18:03 gezelter |
1157 |
|
|
|
1158 |
|
|
* samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added |
1159 |
|
|
samples for the cutoff methods that Yang Zheng has been working on |
1160 |
|
|
|
1161 |
|
|
2005-10-18 16:13 gezelter |
1162 |
|
|
|
1163 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques |
1164 |
|
|
and a rotation matrix bug |
1165 |
|
|
|
1166 |
|
|
2005-10-18 16:13 gezelter |
1167 |
|
|
|
1168 |
|
|
* samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md, |
1169 |
|
|
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
1170 |
|
|
added a few GB test cases |
1171 |
|
|
|
1172 |
|
|
2005-10-18 16:13 gezelter |
1173 |
|
|
|
1174 |
|
|
* forceFields/DUFF2.frc: Fixing GB parameters |
1175 |
|
|
|
1176 |
|
|
2005-10-18 13:36 kdaily |
1177 |
|
|
|
1178 |
|
|
* forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne |
1179 |
|
|
type |
1180 |
|
|
|
1181 |
|
|
2005-10-18 10:01 chrisfen |
1182 |
|
|
|
1183 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
1184 |
|
|
UseTheForce/DarkSide/Makefile, |
1185 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
1186 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
1187 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
1188 |
|
|
UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged |
1189 |
|
|
reaction field with electrostatics.F90 |
1190 |
|
|
|
1191 |
|
|
2005-10-17 18:13 tim |
1192 |
|
|
|
1193 |
|
|
* src/: brains/ForceManager.cpp, brains/Stats.cpp, |
1194 |
|
|
brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp, |
1195 |
|
|
io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp, |
1196 |
|
|
io/StatWriter.hpp: Customized StatWriter is working |
1197 |
|
|
|
1198 |
|
|
2005-10-17 17:42 kdaily |
1199 |
|
|
|
1200 |
|
|
* src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver |
1201 |
|
|
paper |
1202 |
|
|
|
1203 |
|
|
2005-10-17 16:47 gezelter |
1204 |
|
|
|
1205 |
|
|
* src/UseTheForce/DarkSide/gb.F90: bugtracking gb |
1206 |
|
|
|
1207 |
|
|
2005-10-17 14:24 tim |
1208 |
|
|
|
1209 |
|
|
* src/io/ParamConstraint.hpp: Another bug fix |
1210 |
|
|
|
1211 |
|
|
2005-10-17 14:22 tim |
1212 |
|
|
|
1213 |
|
|
* src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace |
1214 |
|
|
issues in Globals |
1215 |
|
|
|
1216 |
|
|
2005-10-17 14:12 gezelter |
1217 |
|
|
|
1218 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90, |
1219 |
|
|
UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90, |
1220 |
|
|
UseTheForce/DarkSide/gb_interface.F90, |
1221 |
|
|
UseTheForce/DarkSide/gb_interface.h, |
1222 |
|
|
io/GayBerneAtomTypesSectionParser.cpp, |
1223 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
1224 |
|
|
changing GB architecture |
1225 |
|
|
|
1226 |
|
|
2005-10-17 14:12 gezelter |
1227 |
|
|
|
1228 |
|
|
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, |
1229 |
|
|
gbRotRoundZ.in: Adding samples for gb tests |
1230 |
|
|
|
1231 |
|
|
2005-10-16 22:06 tim |
1232 |
|
|
|
1233 |
|
|
* src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy |
1234 |
|
|
a string to event's err_msg, there are still tons of memory |
1235 |
|
|
leaking problem in Globals |
1236 |
|
|
|
1237 |
|
|
2005-10-16 19:51 tim |
1238 |
|
|
|
1239 |
|
|
* src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change |
1240 |
|
|
error message in Globals |
1241 |
|
|
|
1242 |
|
|
2005-10-14 16:43 tim |
1243 |
|
|
|
1244 |
|
|
* src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for |
1245 |
|
|
parameters are working now |
1246 |
|
|
|
1247 |
|
|
2005-10-14 11:43 gezelter |
1248 |
|
|
|
1249 |
|
|
* samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests |
1250 |
|
|
|
1251 |
|
|
2005-10-14 11:05 gezelter |
1252 |
|
|
|
1253 |
|
|
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, |
1254 |
|
|
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
1255 |
|
|
Adding some Gay Berne tests |
1256 |
|
|
|
1257 |
|
|
2005-10-14 11:05 gezelter |
1258 |
|
|
|
1259 |
|
|
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some |
1260 |
|
|
cutoff tests |
1261 |
|
|
|
1262 |
|
|
2005-10-14 10:44 kdaily |
1263 |
|
|
|
1264 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, |
1265 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, |
1266 |
|
|
src/UseTheForce/DarkSide/gb_interface.F90, |
1267 |
|
|
src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne |
1268 |
|
|
LJ |
1269 |
|
|
|
1270 |
|
|
2005-10-14 09:48 tim |
1271 |
|
|
|
1272 |
|
|
* src/io/ParamConstraint.hpp: Adding Parameter Constraint class |
1273 |
|
|
|
1274 |
|
|
2005-10-14 09:18 chrisfen |
1275 |
|
|
|
1276 |
|
|
* samples/thermoIntegration/liquid/ssde.md, |
1277 |
|
|
samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp, |
1278 |
|
|
src/restraints/Restraints.cpp: added default restraint spring |
1279 |
|
|
constants into Globals |
1280 |
|
|
|
1281 |
|
|
2005-10-13 17:26 tim |
1282 |
|
|
|
1283 |
|
|
* src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
1284 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp, |
1285 |
|
|
constraints/ZconstraintForceManager.cpp, |
1286 |
|
|
integrators/Integrator.cpp, integrators/NPT.cpp, |
1287 |
|
|
integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp, |
1288 |
|
|
io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp, |
1289 |
|
|
minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp, |
1290 |
|
|
restraints/ThermoIntegrationForceManager.cpp, |
1291 |
|
|
visitors/ZconsVisitor.cpp: rewrite Globals |
1292 |
|
|
|
1293 |
|
|
2005-10-12 16:57 chuckv |
1294 |
|
|
|
1295 |
|
|
* src/brains/ForceManager.cpp: Fix to forceManager to pass |
1296 |
|
|
potential array to fortran. |
1297 |
|
|
|
1298 |
|
|
2005-10-12 16:00 gezelter |
1299 |
|
|
|
1300 |
|
|
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't |
1301 |
|
|
remember what we did |
1302 |
|
|
|
1303 |
|
|
2005-10-12 16:00 gezelter |
1304 |
|
|
|
1305 |
|
|
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
1306 |
|
|
DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h, |
1307 |
|
|
DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90, |
1308 |
|
|
DarkSide/sticky.F90: simplifying long range potential array |
1309 |
|
|
|
1310 |
|
|
2005-10-12 16:00 gezelter |
1311 |
|
|
|
1312 |
|
|
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new |
1313 |
|
|
cutoff methods |
1314 |
|
|
|
1315 |
|
|
2005-10-12 16:00 gezelter |
1316 |
|
|
|
1317 |
|
|
* forceFields/DUFF2.frc: Messing with 2-point water models |
1318 |
|
|
|
1319 |
|
|
2005-10-12 15:22 chuckv |
1320 |
|
|
|
1321 |
|
|
* src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran |
1322 |
|
|
interface now expects an array for pot. |
1323 |
|
|
|
1324 |
|
|
2005-10-12 15:18 chuckv |
1325 |
|
|
|
1326 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/gb.F90, |
1327 |
|
|
DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for |
1328 |
|
|
calculation of potential. |
1329 |
|
|
|
1330 |
|
|
2005-10-12 14:55 chuckv |
1331 |
|
|
|
1332 |
|
|
* src/UseTheForce/doForces.F90: More changes to MPI potential |
1333 |
|
|
calculations. |
1334 |
|
|
|
1335 |
|
|
2005-10-12 13:59 chuckv |
1336 |
|
|
|
1337 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90, |
1338 |
|
|
DarkSide/eam.F90, DarkSide/electrostatic.F90, |
1339 |
|
|
DarkSide/fInteractionMap.h, DarkSide/force_globals.F90, |
1340 |
|
|
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky |
1341 |
|
|
Breaky: Add Support for seperating potential contributions. |
1342 |
|
|
|
1343 |
|
|
2005-10-11 17:00 chuckv |
1344 |
|
|
|
1345 |
|
|
* src/UseTheForce/doForces.F90: Free some variables that weren't |
1346 |
|
|
freed before. |
1347 |
|
|
|
1348 |
|
|
2005-10-11 16:59 chuckv |
1349 |
|
|
|
1350 |
|
|
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
1351 |
|
|
GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod |
1352 |
|
|
builder --twinned. |
1353 |
|
|
|
1354 |
|
|
2005-10-11 16:57 chuckv |
1355 |
|
|
|
1356 |
|
|
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
1357 |
|
|
nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, |
1358 |
|
|
nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp, |
1359 |
|
|
sphericalNanoparticle.hpp: Added code for nanoparticle builder to |
1360 |
|
|
cvs. |
1361 |
|
|
|
1362 |
|
|
2005-10-10 16:34 chuckv |
1363 |
|
|
|
1364 |
|
|
* src/UseTheForce/doForces.F90: Bug fix, undeclared local variable |
1365 |
|
|
in MPI. |
1366 |
|
|
|
1367 |
|
|
2005-10-10 16:20 chuckv |
1368 |
|
|
|
1369 |
|
|
* src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column |
1370 |
|
|
indexing of groupToGtype. We now have two seperate maps |
1371 |
|
|
groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer |
1372 |
|
|
that is set to groupToGtypeRow in the single processor version. |
1373 |
|
|
|
1374 |
|
|
2005-10-06 13:44 chrisfen |
1375 |
|
|
|
1376 |
|
|
* samples/water/: dimer/water.md, spce/water.md, ssd/water.md, |
1377 |
|
|
ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md, |
1378 |
|
|
tip3p_ice/water.md, tip4p/water.md: fixing up the samples |
1379 |
|
|
|
1380 |
|
|
2005-10-05 16:12 tim |
1381 |
|
|
|
1382 |
|
|
* src/primitives/RigidBody.cpp: There is still something wrong with |
1383 |
|
|
inertia tensor projection |
1384 |
|
|
|
1385 |
|
|
2005-10-05 14:35 tim |
1386 |
|
|
|
1387 |
|
|
* src/primitives/RigidBody.cpp: erase output of inertia tensor. |
1388 |
|
|
There is still something wrong with current implementation. |
1389 |
|
|
|
1390 |
|
|
2005-10-05 14:34 tim |
1391 |
|
|
|
1392 |
|
|
* src/brains/MoleculeCreator.cpp: fix a bug in creating |
1393 |
|
|
cutoffGroup. When cutoffGroup is turned off, there is a mismatch |
1394 |
|
|
between group and center of mass array |
1395 |
|
|
|
1396 |
|
|
2005-10-05 14:12 tim |
1397 |
|
|
|
1398 |
|
|
* src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup. |
1399 |
|
|
When cutoffGroup is turned off, there is a mismatch between group |
1400 |
|
|
and center of mass array |
1401 |
|
|
|
1402 |
|
|
2005-10-04 14:34 chrisfen |
1403 |
|
|
|
1404 |
|
|
* src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying |
1405 |
|
|
mass ratio bug that results in simulation failure with massless |
1406 |
|
|
particles |
1407 |
|
|
|
1408 |
|
|
2005-10-04 14:33 chrisfen |
1409 |
|
|
|
1410 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on |
1411 |
|
|
wolf |
1412 |
|
|
|
1413 |
|
|
2005-10-04 14:32 chrisfen |
1414 |
|
|
|
1415 |
|
|
* samples/water/dimer/two.md, samples/water/dimer/water.md, |
1416 |
|
|
samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md, |
1417 |
|
|
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some |
1418 |
|
|
random changes when testing |
1419 |
|
|
|
1420 |
|
|
2005-10-03 10:54 tim |
1421 |
|
|
|
1422 |
|
|
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in |
1423 |
|
|
projecting the inertia tensor of directional atom in rigibody into |
1424 |
|
|
rigidbody's body frame (previous commit is wrong) |
1425 |
|
|
|
1426 |
|
|
2005-10-03 09:31 tim |
1427 |
|
|
|
1428 |
|
|
* src/primitives/RigidBody.cpp: fix a bug in projecting the inertia |
1429 |
|
|
tensor of directional atom in rigibody into rigidbody's body frame |
1430 |
|
|
|
1431 |
|
|
2005-09-28 13:47 chrisfen |
1432 |
|
|
|
1433 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: working on wolf |
1434 |
|
|
|
1435 |
|
|
2005-09-28 13:46 chrisfen |
1436 |
|
|
|
1437 |
|
|
* samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md, |
1438 |
|
|
dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md, |
1439 |
|
|
ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md, |
1440 |
|
|
tip4p/tp4.md: fixed some samples |
1441 |
|
|
|
1442 |
|
|
2005-09-28 13:46 chrisfen |
1443 |
|
|
|
1444 |
|
|
* ChangeLog: updated |
1445 |
|
|
|
1446 |
chrisfen |
2337 |
2005-09-28 11:55 tim |
1447 |
|
|
|
1448 |
|
|
* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid |
1449 |
|
|
divergence in rotation matrix to quaternion transformation |
1450 |
|
|
|
1451 |
|
|
2005-09-28 11:32 gezelter |
1452 |
|
|
|
1453 |
|
|
* src/primitives/RigidBody.cpp: Rotation matrix multiplication |
1454 |
|
|
order error |
1455 |
|
|
|
1456 |
|
|
2005-09-28 11:32 gezelter |
1457 |
|
|
|
1458 |
|
|
* src/io/DumpReader.cpp: tracking down quaternion bug |
1459 |
|
|
|
1460 |
|
|
2005-09-28 11:32 gezelter |
1461 |
|
|
|
1462 |
|
|
* forceFields/DUFF2.frc: Added DIP atom types for 2-point water |
1463 |
|
|
model |
1464 |
|
|
|
1465 |
|
|
2005-09-27 15:02 tim |
1466 |
|
|
|
1467 |
|
|
* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix |
1468 |
|
|
to quaternion |
1469 |
|
|
|
1470 |
|
|
2005-09-26 13:38 chuckv |
1471 |
|
|
|
1472 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc |
1473 |
|
|
7 so derfc is external. Other compilers should treat erfc as |
1474 |
|
|
intrinsic. |
1475 |
|
|
|
1476 |
|
|
2005-09-26 12:07 chuckv |
1477 |
|
|
|
1478 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc |
1479 |
|
|
and declared it to be external to fix issure with ifc7. Hopefully |
1480 |
|
|
this will not cause a problem with other compilers where derfc is |
1481 |
|
|
an intrinsic function. |
1482 |
|
|
|
1483 |
|
|
2005-09-26 11:42 chuckv |
1484 |
|
|
|
1485 |
|
|
* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype |
1486 |
|
|
in simulation module. We needed a seperate receive buffer. |
1487 |
|
|
|
1488 |
|
|
2005-09-26 10:58 chuckv |
1489 |
|
|
|
1490 |
|
|
* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added |
1491 |
|
|
support for skinThickness keyword to Globals. |
1492 |
|
|
|
1493 |
|
|
2005-09-26 10:56 tim |
1494 |
|
|
|
1495 |
|
|
* src/io/DumpReader.cpp: fix a typo in DumpReader |
1496 |
|
|
|
1497 |
|
|
2005-09-26 09:27 chrisfen |
1498 |
|
|
|
1499 |
|
|
* samples/: minimizer/tip4p_two.md, |
1500 |
|
|
thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, |
1501 |
|
|
water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, |
1502 |
|
|
water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, |
1503 |
|
|
water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, |
1504 |
|
|
water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, |
1505 |
|
|
water/tip4p/tp4.md: fixing up some samples |
1506 |
|
|
|
1507 |
|
|
2005-09-24 12:39 chrisfen |
1508 |
|
|
|
1509 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now |
1510 |
|
|
roughly the same speed as the old version when using dipoles |
1511 |
|
|
|
1512 |
|
|
energies are now exactly the same between the old version of OOPSE |
1513 |
|
|
and this version |
1514 |
|
|
|
1515 |
|
|
2005-09-24 12:38 chrisfen |
1516 |
|
|
|
1517 |
|
|
* samples/water/ssdrf/ssdrf.md: turned rf on |
1518 |
|
|
|
1519 |
|
|
2005-09-23 15:31 chuckv |
1520 |
|
|
|
1521 |
|
|
* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the |
1522 |
|
|
skin thickness and hardcode listSkin to be 1.0. We now get listskin |
1523 |
|
|
from skin. This will get fixed to where we can manually set skin |
1524 |
|
|
thickness. |
1525 |
|
|
|
1526 |
|
|
2005-09-22 13:50 gezelter |
1527 |
|
|
|
1528 |
|
|
* src/math/derfc.F90: added error function |
1529 |
|
|
|
1530 |
|
|
2005-09-21 19:08 chuckv |
1531 |
|
|
|
1532 |
|
|
* src/integrators/Velocitizer.cpp: Removed print statement for |
1533 |
|
|
angular momentum and inertia tensor from velocitizer. |
1534 |
|
|
|
1535 |
|
|
2005-09-21 19:04 chuckv |
1536 |
|
|
|
1537 |
|
|
* src/integrators/Velocitizer.cpp: Removed print statements for |
1538 |
|
|
remove angular momentum. |
1539 |
|
|
|
1540 |
|
|
2005-09-21 18:45 chuckv |
1541 |
|
|
|
1542 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ |
1543 |
|
|
(say we are using EAM), we probably shouldn't rebuild the LJ mixing |
1544 |
|
|
map. |
1545 |
|
|
|
1546 |
|
|
2005-09-21 15:59 tim |
1547 |
|
|
|
1548 |
|
|
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: |
1549 |
|
|
DumpReader using pure c++ io |
1550 |
|
|
|
1551 |
|
|
2005-09-21 12:20 chrisfen |
1552 |
|
|
|
1553 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a |
1554 |
|
|
defaultCutoff bug (HEMES!) |
1555 |
|
|
|
1556 |
|
|
2005-09-20 17:13 gezelter |
1557 |
|
|
|
1558 |
|
|
* make/Makefile.in: libz additions |
1559 |
|
|
|
1560 |
|
|
2005-09-20 17:03 gezelter |
1561 |
|
|
|
1562 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1563 |
|
|
src/config.h.in: added check for zlib in configure |
1564 |
|
|
|
1565 |
|
|
2005-09-20 16:22 tim |
1566 |
|
|
|
1567 |
|
|
* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, |
1568 |
|
|
gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter |
1569 |
|
|
|
1570 |
|
|
2005-09-20 11:22 tim |
1571 |
|
|
|
1572 |
|
|
* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding |
1573 |
|
|
testcase for zipstream |
1574 |
|
|
|
1575 |
|
|
2005-09-20 10:41 tim |
1576 |
|
|
|
1577 |
|
|
* src/io/zipstream.hpp: adding zipstream.hpp |
1578 |
|
|
|
1579 |
|
|
2005-09-20 10:34 chrisfen |
1580 |
|
|
|
1581 |
|
|
* samples/: dipole/splitInWater.md, dipole/split_SSD.md, |
1582 |
|
|
dipole/twoSplitDipole.md, minimizer/ssdEM.md, |
1583 |
|
|
minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, |
1584 |
|
|
zcons/zconsMoving.md: fixed up some sample md files |
1585 |
|
|
|
1586 |
|
|
2005-09-19 18:21 chrisfen |
1587 |
|
|
|
1588 |
|
|
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
1589 |
|
|
src/UseTheForce/doForces.F90, |
1590 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
1591 |
|
|
src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, |
1592 |
|
|
src/brains/fSimulation.h: Fixed bugs in reaction field, now it |
1593 |
|
|
appears as though it really is working... |
1594 |
|
|
|
1595 |
chrisfen |
2310 |
2005-09-18 15:45 chrisfen |
1596 |
|
|
|
1597 |
|
|
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
1598 |
|
|
src/UseTheForce/doForces.F90, |
1599 |
|
|
src/UseTheForce/doForces_interface.F90, |
1600 |
|
|
src/UseTheForce/doForces_interface.h, |
1601 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
1602 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.h, |
1603 |
|
|
src/brains/SimInfo.cpp: reaction field seems to work now, still |
1604 |
|
|
need to do some testing... |
1605 |
|
|
|
1606 |
chrisfen |
2309 |
2005-09-16 18:04 chuckv |
1607 |
|
|
|
1608 |
|
|
* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed |
1609 |
|
|
dump files. |
1610 |
|
|
|
1611 |
|
|
2005-09-16 16:07 chrisfen |
1612 |
|
|
|
1613 |
|
|
* src/: UseTheForce/doForces_interface.F90, |
1614 |
|
|
UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a |
1615 |
|
|
bug that ifc missed... |
1616 |
|
|
|
1617 |
|
|
2005-09-16 15:36 chrisfen |
1618 |
|
|
|
1619 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
1620 |
|
|
fixing some summation method issues |
1621 |
|
|
|
1622 |
|
|
2005-09-16 14:35 chrisfen |
1623 |
|
|
|
1624 |
|
|
* src/brains/SimInfo.cpp: fixed a capitalization error |
1625 |
|
|
|
1626 |
|
|
2005-09-16 14:34 chrisfen |
1627 |
|
|
|
1628 |
|
|
* src/UseTheForce/: fElectrostaticSummationMethod.h, |
1629 |
|
|
DarkSide/fElectrostaticSummationMethod.h: moved a header file |
1630 |
|
|
around |
1631 |
|
|
|
1632 |
|
|
2005-09-16 14:00 chrisfen |
1633 |
|
|
|
1634 |
|
|
* src/: UseTheForce/DarkSide/electrostatic_interface.F90, |
1635 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there |
1636 |
|
|
are known issues - particularly with reaction field... |
1637 |
|
|
|
1638 |
|
|
2005-09-16 11:07 chrisfen |
1639 |
|
|
|
1640 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
1641 |
|
|
io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking |
1642 |
|
|
(cutting out the old way to do reaction field) |
1643 |
|
|
|
1644 |
|
|
2005-09-15 17:05 gezelter |
1645 |
|
|
|
1646 |
|
|
* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, |
1647 |
|
|
fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, |
1648 |
|
|
DarkSide/electrostatic_interface.F90, |
1649 |
|
|
DarkSide/electrostatic_interface.h: Working on adding WOLF |
1650 |
|
|
|
1651 |
|
|
2005-09-15 14:17 tim |
1652 |
|
|
|
1653 |
|
|
* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame |
1654 |
|
|
is called without calling getNFrames |
1655 |
|
|
|
1656 |
|
|
2005-09-15 08:47 chrisfen |
1657 |
|
|
|
1658 |
|
|
* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header |
1659 |
|
|
|
1660 |
|
|
2005-09-14 21:48 chuckv |
1661 |
|
|
|
1662 |
|
|
* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was |
1663 |
|
|
not initialized after creation. When maxval(gtypeMaxCutoff) was |
1664 |
|
|
called, the largest random garbage value was returned from the |
1665 |
|
|
array. |
1666 |
|
|
|
1667 |
|
|
2005-09-14 19:14 chrisfen |
1668 |
|
|
|
1669 |
|
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, |
1670 |
|
|
io/Globals.hpp: changes to include the coulombicCorrection selector |
1671 |
|
|
|
1672 |
|
|
2005-09-14 19:13 chrisfen |
1673 |
|
|
|
1674 |
|
|
* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, |
1675 |
|
|
reactionField.F90: added in the undamped wolf, in the process of |
1676 |
|
|
doing the damped wolf |
1677 |
|
|
|
1678 |
|
|
2005-09-14 19:13 chrisfen |
1679 |
|
|
|
1680 |
|
|
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
1681 |
|
|
doForces_interface.h, notifyCutoffs.F90: some changes to activate |
1682 |
|
|
the coulombicCorrection selector |
1683 |
|
|
|
1684 |
|
|
2005-09-14 19:11 chrisfen |
1685 |
|
|
|
1686 |
|
|
* samples/water/dimer/: cl.in, cl.md, water.md: just some testing |
1687 |
|
|
|
1688 |
|
|
2005-09-14 19:11 chrisfen |
1689 |
|
|
|
1690 |
|
|
* samples/argon/: 500.in, 500.md: Equilibrated the sample |
1691 |
|
|
|
1692 |
|
|
2005-09-14 19:10 chrisfen |
1693 |
|
|
|
1694 |
|
|
* forceFields/DUFF2.frc: re-added Cl- and Na+ |
1695 |
|
|
|
1696 |
|
|
2005-09-14 15:31 chuckv |
1697 |
|
|
|
1698 |
|
|
* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup |
1699 |
|
|
eamAtypes instead of assuming a 1-1 correspondence to atypes. |
1700 |
|
|
|
1701 |
|
|
2005-09-14 15:28 gezelter |
1702 |
|
|
|
1703 |
|
|
* src/UseTheForce/doForces.F90: fix to put back calculation of r in |
1704 |
|
|
do_prepair |
1705 |
|
|
|
1706 |
|
|
2005-09-14 14:02 gezelter |
1707 |
|
|
|
1708 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the |
1709 |
|
|
createMixingMap routine. It should now set doShift correctly |
1710 |
|
|
|
1711 |
|
|
2005-09-07 17:44 chuckv |
1712 |
|
|
|
1713 |
|
|
* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. |
1714 |
|
|
|
1715 |
|
|
2005-09-07 17:23 chuckv |
1716 |
|
|
|
1717 |
|
|
* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi |
1718 |
|
|
logical variables |
1719 |
|
|
|
1720 |
|
|
2005-09-07 17:08 gezelter |
1721 |
|
|
|
1722 |
|
|
* src/UseTheForce/doForces.F90: bugfix on the grouptype finding |
1723 |
|
|
algorithm |
1724 |
|
|
|
1725 |
|
|
2005-09-07 15:46 gezelter |
1726 |
|
|
|
1727 |
|
|
* src/: UseTheForce/doForces.F90, |
1728 |
|
|
UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, |
1729 |
|
|
UseTheForce/notifyCutoffs_interface.F90, |
1730 |
|
|
UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, |
1731 |
|
|
io/Globals.cpp, io/Globals.hpp: adding c-side interface to change |
1732 |
|
|
cutoff Policy |
1733 |
|
|
|
1734 |
|
|
2005-09-07 14:18 gezelter |
1735 |
|
|
|
1736 |
|
|
* src/UseTheForce/doForces.F90: Some bug hunting |
1737 |
|
|
|
1738 |
|
|
2005-09-07 14:18 gezelter |
1739 |
|
|
|
1740 |
|
|
* samples/argon/argonNVT.md: Just a longer test |
1741 |
|
|
|
1742 |
|
|
2005-09-06 12:32 chuckv |
1743 |
|
|
|
1744 |
|
|
* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap |
1745 |
|
|
etc.. |
1746 |
|
|
|
1747 |
|
|
2005-09-01 17:56 gezelter |
1748 |
|
|
|
1749 |
|
|
* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to |
1750 |
|
|
zero |
1751 |
|
|
|
1752 |
|
|
2005-09-01 15:17 gezelter |
1753 |
|
|
|
1754 |
|
|
* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote |
1755 |
|
|
createGtypeCutoffMap |
1756 |
|
|
|
1757 |
|
|
2005-08-30 13:23 chrisfen |
1758 |
|
|
|
1759 |
|
|
* src/: UseTheForce/doForces.F90, |
1760 |
|
|
UseTheForce/doForces_interface.F90, |
1761 |
|
|
UseTheForce/doForces_interface.h, |
1762 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
1763 |
|
|
UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, |
1764 |
|
|
brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some |
1765 |
|
|
changes for implementing the wolf potential |
1766 |
|
|
|
1767 |
|
|
2005-08-26 17:39 chrisfen |
1768 |
|
|
|
1769 |
|
|
* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut |
1770 |
|
|
|
1771 |
|
|
2005-08-26 16:30 chrisfen |
1772 |
|
|
|
1773 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/eam.F90, |
1774 |
|
|
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added |
1775 |
|
|
some probably nonfunctional get*cut routines |
1776 |
|
|
|
1777 |
|
|
2005-08-26 15:34 chuckv |
1778 |
|
|
|
1779 |
|
|
* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. |
1780 |
|
|
|
1781 |
|
|
2005-08-26 11:36 gezelter |
1782 |
|
|
|
1783 |
|
|
* src/UseTheForce/doForces.F90: fixing some of the problems in the |
1784 |
|
|
interactionHash and gtypeCutoff routines |
1785 |
|
|
|
1786 |
|
|
2005-08-17 10:26 gezelter |
1787 |
|
|
|
1788 |
|
|
* src/UseTheForce/: doForces.F90, fCutoffPolicy.h, |
1789 |
|
|
DarkSide/simulation.F90: added fCutoffPolicy.h |
1790 |
|
|
|
1791 |
|
|
2005-08-11 16:04 gezelter |
1792 |
|
|
|
1793 |
|
|
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in |
1794 |
|
|
progress |
1795 |
|
|
|
1796 |
|
|
2005-08-10 14:17 gezelter |
1797 |
|
|
|
1798 |
|
|
* src/primitives/StuntDouble.hpp: putting spaceballs back where |
1799 |
|
|
they belong |
1800 |
|
|
|
1801 |
|
|
2005-08-09 17:33 gezelter |
1802 |
|
|
|
1803 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard |
1804 |
|
|
Jones module |
1805 |
|
|
|
1806 |
|
|
2005-08-09 17:33 gezelter |
1807 |
|
|
|
1808 |
|
|
* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky |
1809 |
|
|
|
1810 |
|
|
2005-08-09 14:40 chuckv |
1811 |
|
|
|
1812 |
|
|
* src/UseTheForce/doForces.F90: In process of re-write for group |
1813 |
|
|
based cutoff.... |
1814 |
|
|
|
1815 |
|
|
2005-07-29 14:38 gezelter |
1816 |
|
|
|
1817 |
|
|
* src/UseTheForce/doForces.F90: fixes in progress |
1818 |
|
|
|
1819 |
|
|
2005-07-29 12:34 tim |
1820 |
|
|
|
1821 |
|
|
* src/UseTheForce/doForces.F90: fix a bug which does not update |
1822 |
|
|
me_i and me_j correctly |
1823 |
|
|
|
1824 |
|
|
2005-07-28 17:12 chuckv |
1825 |
|
|
|
1826 |
|
|
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed |
1827 |
|
|
cutoffs... Segfaults nicely now... |
1828 |
|
|
|
1829 |
|
|
2005-07-20 12:04 gezelter |
1830 |
|
|
|
1831 |
|
|
* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text |
1832 |
|
|
error messages from pathscale compiler |
1833 |
|
|
|
1834 |
|
|
2005-07-13 11:48 tim |
1835 |
|
|
|
1836 |
|
|
* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in |
1837 |
|
|
<functional> |
1838 |
|
|
|
1839 |
|
|
2005-07-13 10:54 tim |
1840 |
|
|
|
1841 |
|
|
* src/: UseTheForce/fSwitchingFunction.h, |
1842 |
|
|
UseTheForce/mpiComponentPlan.h, |
1843 |
|
|
UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, |
1844 |
|
|
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
1845 |
|
|
io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, |
1846 |
|
|
io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, |
1847 |
|
|
io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, |
1848 |
|
|
utils/simError.c, utils/simError.h: replace c++ style comment in c |
1849 |
|
|
files |
1850 |
|
|
|
1851 |
|
|
2005-07-03 15:53 chuckv |
1852 |
|
|
|
1853 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
1854 |
|
|
UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added |
1855 |
|
|
subroutine to set cuttoff for Interaction map and function in |
1856 |
|
|
simulation.F90 to determine if a particular atype is present in a |
1857 |
|
|
simulation. |
1858 |
|
|
|
1859 |
|
|
2005-06-28 08:58 gezelter |
1860 |
|
|
|
1861 |
|
|
* src/UseTheForce/doForces.F90: [no log message] |
1862 |
|
|
|
1863 |
|
|
2005-06-27 17:21 chuckv |
1864 |
|
|
|
1865 |
|
|
* src/UseTheForce/doForces.F90: More breaking and destruction of |
1866 |
|
|
force code. Does not build at this point... |
1867 |
|
|
|
1868 |
|
|
2005-06-27 16:01 gezelter |
1869 |
|
|
|
1870 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, |
1871 |
|
|
UseTheForce/DarkSide/fInteractionMap.h, |
1872 |
|
|
UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: |
1873 |
|
|
Breaky breaky! |
1874 |
|
|
|
1875 |
|
|
2005-06-20 11:03 gezelter |
1876 |
|
|
|
1877 |
|
|
* samples/water/ssd/ssd.md, |
1878 |
|
|
src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a |
1879 |
|
|
simulation |
1880 |
|
|
|
1881 |
|
|
2005-06-13 13:25 tim |
1882 |
|
|
|
1883 |
|
|
* src/: applications/staticProps/DensityPlot.cpp, |
1884 |
|
|
applications/staticProps/DensityPlot.hpp, |
1885 |
|
|
applications/staticProps/SCDOrderParameter.cpp, |
1886 |
|
|
applications/staticProps/StaticProps.cpp, |
1887 |
|
|
io/AtomTypesSectionParser.cpp: working version of DensityPlot |
1888 |
|
|
|
1889 |
|
|
2005-05-31 17:31 chuckv |
1890 |
|
|
|
1891 |
|
|
* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to |
1892 |
|
|
remove angular momentum. |
1893 |
|
|
|
1894 |
|
|
2005-05-31 12:34 chuckv |
1895 |
|
|
|
1896 |
|
|
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in |
1897 |
|
|
typo in nanorodBuilder. |
1898 |
|
|
|
1899 |
|
|
2005-05-30 09:01 chuckv |
1900 |
|
|
|
1901 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
1902 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
1903 |
|
|
brains/Stats.hpp, integrators/Velocitizer.cpp, |
1904 |
|
|
integrators/Velocitizer.hpp: Added method to remove system angular |
1905 |
|
|
momentum to velocitizer and added method to calculate system |
1906 |
|
|
angular momentum to siminfo. |
1907 |
|
|
|
1908 |
|
|
2005-05-29 16:16 chrisfen |
1909 |
|
|
|
1910 |
|
|
* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed |
1911 |
|
|
balance from the Darkside (files) |
1912 |
|
|
|
1913 |
|
|
2005-05-29 16:15 chrisfen |
1914 |
|
|
|
1915 |
|
|
* src/UseTheForce/doForces.F90: Removed balance from doForces |
1916 |
|
|
|
1917 |
|
|
2005-05-29 16:15 chrisfen |
1918 |
|
|
|
1919 |
|
|
* samples/water/tap/: tap.in, tap.md: Updated tap sample |
1920 |
|
|
|
1921 |
|
|
2005-05-29 16:15 chrisfen |
1922 |
|
|
|
1923 |
|
|
* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap |
1924 |
|
|
dimer for testing purposes |
1925 |
|
|
|
1926 |
|
|
2005-05-29 16:14 chrisfen |
1927 |
|
|
|
1928 |
|
|
* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It |
1929 |
|
|
was apparently wiped earlier this month... |
1930 |
|
|
|
1931 |
|
|
2005-05-29 16:13 chrisfen |
1932 |
|
|
|
1933 |
|
|
* ChangeLog: ran make cvslog |
1934 |
|
|
|
1935 |
chrisfen |
2246 |
2005-05-28 19:16 tim |
1936 |
|
|
|
1937 |
|
|
* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
1938 |
|
|
AtomNameVisitor |
1939 |
|
|
|
1940 |
|
|
2005-05-28 19:09 tim |
1941 |
|
|
|
1942 |
|
|
* src/integrators/Integrator.cpp: dding resetIntegrator |
1943 |
|
|
|
1944 |
|
|
2005-05-28 19:06 tim |
1945 |
|
|
|
1946 |
|
|
* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
1947 |
|
|
NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
1948 |
|
|
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
1949 |
|
|
resetIntegrator |
1950 |
|
|
|
1951 |
|
|
2005-05-27 16:11 tim |
1952 |
|
|
|
1953 |
|
|
* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
1954 |
|
|
Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
1955 |
|
|
SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
1956 |
|
|
StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
1957 |
|
|
StaticProps |
1958 |
|
|
|
1959 |
|
|
2005-05-26 23:41 tim |
1960 |
|
|
|
1961 |
|
|
* src/: applications/staticProps/Makefile, |
1962 |
|
|
applications/staticProps/P2OrderParameter.cpp, |
1963 |
|
|
applications/staticProps/P2OrderParameter.hpp, |
1964 |
|
|
applications/staticProps/StaticProps.cpp, |
1965 |
|
|
applications/staticProps/StaticProps.ggo, |
1966 |
|
|
applications/staticProps/StaticPropsCmd.c, |
1967 |
|
|
applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
1968 |
|
|
utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
1969 |
|
|
|
1970 |
|
|
2005-05-26 17:45 tim |
1971 |
|
|
|
1972 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
1973 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
1974 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
1975 |
|
|
applications/staticProps/Makefile, |
1976 |
|
|
applications/staticProps/P2OrderParameter.cpp, |
1977 |
|
|
applications/staticProps/P2OrderParameter.hpp, |
1978 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
1979 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
1980 |
|
|
applications/staticProps/StaticAnalyser.hpp, |
1981 |
|
|
applications/staticProps/StaticProps.cpp, |
1982 |
|
|
applications/staticProps/StaticProps.ggo, |
1983 |
|
|
applications/staticProps/StaticPropsCmd.c, |
1984 |
|
|
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
1985 |
|
|
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
1986 |
|
|
AtomNameVisitor to convert atom name to its base name; |
1987 |
|
|
wrappingvisitor now wrap back to the center of the mass; adding |
1988 |
|
|
P2OrderParameter into StaticProps |
1989 |
|
|
|
1990 |
|
|
2005-05-22 16:36 chuckv |
1991 |
|
|
|
1992 |
gezelter |
2568 |
* src/: applications/nanoRodBuilder/Geometry.cpp, |
1993 |
|
|
applications/nanoRodBuilder/GeometryBuilder.cpp, |
1994 |
|
|
applications/nanoRodBuilder/GeometryFactory.cpp, |
1995 |
|
|
applications/nanoRodBuilder/GeometryFactory.hpp, |
1996 |
|
|
applications/nanoRodBuilder/nanorodBuilder.cpp, |
1997 |
|
|
integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
1998 |
chrisfen |
2246 |
tensor. |
1999 |
|
|
|
2000 |
|
|
2005-05-22 16:05 tim |
2001 |
|
|
|
2002 |
|
|
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
2003 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
2004 |
|
|
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
2005 |
|
|
printPressureTensor |
2006 |
|
|
|
2007 |
|
|
2005-05-20 14:27 tim |
2008 |
|
|
|
2009 |
|
|
* src/integrators/NPrT.cpp: NPrT in progress |
2010 |
|
|
|
2011 |
|
|
2005-05-20 11:01 tim |
2012 |
|
|
|
2013 |
|
|
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
2014 |
|
|
utils/OOPSEConstant.hpp: NPrT in progress |
2015 |
|
|
|
2016 |
|
|
2005-05-19 16:31 tim |
2017 |
|
|
|
2018 |
|
|
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
2019 |
|
|
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
2020 |
|
|
io/Globals.hpp: NPAT is working |
2021 |
|
|
|
2022 |
|
|
2005-05-19 10:49 tim |
2023 |
|
|
|
2024 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
2025 |
|
|
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
2026 |
|
|
|
2027 |
|
|
2005-05-18 23:28 tim |
2028 |
|
|
|
2029 |
|
|
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
2030 |
|
|
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
2031 |
|
|
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
2032 |
|
|
|
2033 |
|
|
2005-05-18 14:06 chrisfen |
2034 |
|
|
|
2035 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
2036 |
|
|
some tap changes |
2037 |
|
|
|
2038 |
|
|
2005-05-18 13:31 chrisfen |
2039 |
|
|
|
2040 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
2041 |
|
|
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
2042 |
|
|
in the first solvation shell for tap |
2043 |
|
|
|
2044 |
|
|
2005-05-18 07:35 chrisfen |
2045 |
|
|
|
2046 |
|
|
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
2047 |
|
|
for testing purposes |
2048 |
|
|
|
2049 |
|
|
2005-05-17 17:35 chrisfen |
2050 |
|
|
|
2051 |
|
|
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
2052 |
|
|
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
2053 |
|
|
src/UseTheForce/doForces.F90, |
2054 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
2055 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
2056 |
|
|
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
2057 |
|
|
correcting changes to the previous merge that were not caught |
2058 |
|
|
|
2059 |
chrisfen |
2229 |
2005-05-16 23:20 chuckv |
2060 |
|
|
|
2061 |
|
|
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
2062 |
|
|
Fixed merge issues between Kyle and Chris so OOPSE will actually |
2063 |
|
|
build. |
2064 |
|
|
|
2065 |
|
|
2005-05-16 22:46 kdaily |
2066 |
|
|
|
2067 |
|
|
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
2068 |
|
|
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
2069 |
|
|
|
2070 |
|
|
2005-05-16 21:08 kdaily |
2071 |
|
|
|
2072 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
2073 |
|
|
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
2074 |
|
|
src/types/DirectionalAtomType.cpp, |
2075 |
|
|
src/types/DirectionalAtomType.hpp: added gb |
2076 |
|
|
|
2077 |
|
|
2005-05-13 15:36 chrisfen |
2078 |
|
|
|
2079 |
|
|
* forceFields/DUFF2.frc: Better tap |
2080 |
|
|
|
2081 |
|
|
2005-05-12 14:43 chrisfen |
2082 |
|
|
|
2083 |
|
|
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
2084 |
|
|
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
2085 |
|
|
src/applications/dump2Xyz/Dump2XYZ.cpp, |
2086 |
|
|
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
2087 |
|
|
Need to parametrize. |
2088 |
|
|
|
2089 |
|
|
2005-05-11 18:15 chuckv |
2090 |
|
|
|
2091 |
|
|
* src/: io/ShapeAtomTypesSectionParser.cpp, |
2092 |
|
|
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
2093 |
|
|
build issues under ifc7. |
2094 |
|
|
|
2095 |
|
|
2005-05-09 17:07 chuckv |
2096 |
|
|
|
2097 |
|
|
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
2098 |
|
|
builder changes. |
2099 |
|
|
|
2100 |
|
|
2005-05-05 10:06 chrisfen |
2101 |
|
|
|
2102 |
|
|
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
2103 |
|
|
to TAP |
2104 |
|
|
|
2105 |
|
|
2005-05-05 09:47 chrisfen |
2106 |
|
|
|
2107 |
|
|
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
2108 |
|
|
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
2109 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
2110 |
|
|
src/UseTheForce/DarkSide/atype.F90, |
2111 |
|
|
src/UseTheForce/DarkSide/atype_interface.F90, |
2112 |
|
|
src/UseTheForce/DarkSide/simulation.F90, |
2113 |
|
|
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
2114 |
|
|
src/brains/fSimulation.h, src/io/Makefile, |
2115 |
|
|
src/io/StickyAtomTypesSectionParser.cpp, |
2116 |
|
|
src/io/StickyPowerAtomTypesSectionParser.cpp, |
2117 |
|
|
src/io/StickyPowerAtomTypesSectionParser.hpp, |
2118 |
|
|
src/types/AtomType.cpp, src/types/AtomType.hpp, |
2119 |
|
|
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
2120 |
|
|
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
2121 |
|
|
not parametrized, but OOPSE will now let me run it... |
2122 |
|
|
|
2123 |
|
|
2005-05-03 17:55 chuckv |
2124 |
|
|
|
2125 |
|
|
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
2126 |
|
|
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
2127 |
|
|
Adding support for generic geometry to nanorodbuilder. |
2128 |
|
|
|
2129 |
|
|
2005-05-03 12:55 chuckv |
2130 |
|
|
|
2131 |
|
|
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
2132 |
|
|
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
2133 |
|
|
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
2134 |
|
|
|
2135 |
|
|
2005-04-29 14:16 gezelter |
2136 |
|
|
|
2137 |
|
|
* make/Makefile.in: [no log message] |
2138 |
|
|
|
2139 |
|
|
2005-04-29 11:26 chrisfen |
2140 |
|
|
|
2141 |
|
|
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
2142 |
|
|
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
2143 |
|
|
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
2144 |
|
|
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
2145 |
|
|
samples/water/tip4p/water.md: Added TIP4P-Ew |
2146 |
|
|
|
2147 |
|
|
2005-04-27 19:24 chuckv |
2148 |
|
|
|
2149 |
|
|
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
2150 |
|
|
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
2151 |
|
|
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
2152 |
|
|
nanoRodBuilder.... |
2153 |
|
|
|
2154 |
|
|
2005-04-27 15:13 chrisfen |
2155 |
|
|
|
2156 |
|
|
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
2157 |
|
|
src/UseTheForce/DarkSide/atype.F90, |
2158 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
2159 |
|
|
src/UseTheForce/DarkSide/shapes_interface.F90, |
2160 |
|
|
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
2161 |
|
|
write statements and am closer to a working shapes |
2162 |
|
|
|
2163 |
|
|
2005-04-22 16:57 chuckv |
2164 |
|
|
|
2165 |
|
|
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
2166 |
|
|
|
2167 |
|
|
2005-04-22 16:52 tim |
2168 |
|
|
|
2169 |
|
|
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
2170 |
|
|
Trim.hpp: adding CharClassificationFunctor to fix the locale |
2171 |
|
|
problem of c++ |
2172 |
|
|
|
2173 |
|
|
2005-04-21 09:12 chrisfen |
2174 |
|
|
|
2175 |
|
|
* samples/shape/Shapes.frc, samples/shape/linear.in, |
2176 |
|
|
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
2177 |
|
|
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
2178 |
|
|
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
2179 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
2180 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
2181 |
|
|
src/UseTheForce/DarkSide/shapes_interface.F90, |
2182 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
2183 |
|
|
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
2184 |
|
|
src/io/Makefile, src/io/SectionParser.cpp, |
2185 |
|
|
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
2186 |
|
|
src/io/ShapeAtomTypesSectionParser.cpp, |
2187 |
|
|
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
2188 |
|
|
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
2189 |
|
|
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
2190 |
|
|
bounds overwrite (I think...). At least the parser loads the |
2191 |
|
|
forcefield fine... |
2192 |
|
|
|
2193 |
|
|
2005-04-18 10:44 chrisfen |
2194 |
|
|
|
2195 |
|
|
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
2196 |
|
|
Mac (capitalization confusion of filenames) |
2197 |
|
|
|
2198 |
|
|
2005-04-17 22:50 chrisfen |
2199 |
|
|
|
2200 |
|
|
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
2201 |
|
|
UseTheForce/Shapes_FF.cpp, |
2202 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
2203 |
|
|
io/ShapeAtomTypesSectionParser.cpp, |
2204 |
|
|
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
2205 |
|
|
|
2206 |
|
|
2005-04-15 17:43 gezelter |
2207 |
|
|
|
2208 |
|
|
* README: gmake in case people forget |
2209 |
|
|
|
2210 |
|
|
2005-04-15 17:40 gezelter |
2211 |
|
|
|
2212 |
|
|
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
2213 |
|
|
banner. Vanity. |
2214 |
|
|
|
2215 |
|
|
2005-04-15 17:22 gezelter |
2216 |
|
|
|
2217 |
|
|
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
2218 |
|
|
in banner (and version numbers in config.h) |
2219 |
|
|
|
2220 |
|
|
2005-04-15 17:22 gezelter |
2221 |
|
|
|
2222 |
|
|
* ChangeLog, LICENSE, README: Documentation changes |
2223 |
|
|
|
2224 |
gezelter |
2205 |
2005-04-15 17:03 gezelter |
2225 |
|
|
|
2226 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2227 |
|
|
UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
2228 |
|
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
2229 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
2230 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
2231 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
2232 |
|
|
UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
2233 |
|
|
UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
2234 |
|
|
UseTheForce/notifyCutoffs.F90, |
2235 |
|
|
UseTheForce/notifyCutoffs_interface.F90, |
2236 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
2237 |
|
|
UseTheForce/DarkSide/atype.F90, |
2238 |
|
|
UseTheForce/DarkSide/atype_interface.F90, |
2239 |
|
|
UseTheForce/DarkSide/eam.F90, |
2240 |
|
|
UseTheForce/DarkSide/eam_interface.F90, |
2241 |
|
|
UseTheForce/DarkSide/eam_interface.h, |
2242 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
2243 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
2244 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
2245 |
|
|
UseTheForce/DarkSide/force_globals.F90, |
2246 |
|
|
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
2247 |
|
|
UseTheForce/DarkSide/lj_interface.F90, |
2248 |
|
|
UseTheForce/DarkSide/lj_interface.h, |
2249 |
|
|
UseTheForce/DarkSide/neighborLists.F90, |
2250 |
|
|
UseTheForce/DarkSide/reactionField.F90, |
2251 |
|
|
UseTheForce/DarkSide/shapes.F90, |
2252 |
|
|
UseTheForce/DarkSide/shapes_interface.F90, |
2253 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
2254 |
|
|
UseTheForce/DarkSide/simParallel.F90, |
2255 |
|
|
UseTheForce/DarkSide/simParallel_interface.F90, |
2256 |
|
|
UseTheForce/DarkSide/simParallel_interface.h, |
2257 |
|
|
UseTheForce/DarkSide/simulation.F90, |
2258 |
|
|
UseTheForce/DarkSide/simulation_interface.F90, |
2259 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
2260 |
|
|
UseTheForce/DarkSide/sticky.F90, |
2261 |
|
|
UseTheForce/DarkSide/sticky_interface.F90, |
2262 |
|
|
UseTheForce/DarkSide/sticky_interface.h, |
2263 |
|
|
UseTheForce/DarkSide/switcheroo.F90, |
2264 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
2265 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
2266 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
2267 |
|
|
applications/dynamicProps/CrossTimeCorrFunc.cpp, |
2268 |
|
|
applications/dynamicProps/CrossTimeCorrFunc.hpp, |
2269 |
|
|
applications/dynamicProps/DipoleCorrFunc.cpp, |
2270 |
|
|
applications/dynamicProps/DipoleCorrFunc.hpp, |
2271 |
|
|
applications/dynamicProps/DynamicProps.cpp, |
2272 |
|
|
applications/dynamicProps/DynamicPropsCmd.c, |
2273 |
|
|
applications/dynamicProps/DynamicPropsCmd.h, |
2274 |
|
|
applications/dynamicProps/FrameTimeCorrFunc.hpp, |
2275 |
|
|
applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
2276 |
|
|
applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
2277 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
2278 |
|
|
applications/dynamicProps/RCorrFunc.hpp, |
2279 |
|
|
applications/dynamicProps/TimeCorrFunc.cpp, |
2280 |
|
|
applications/dynamicProps/TimeCorrFunc.hpp, |
2281 |
|
|
applications/dynamicProps/VCorrFunc.cpp, |
2282 |
|
|
applications/dynamicProps/VCorrFunc.hpp, |
2283 |
|
|
applications/nanoRodBuilder/GeometryBuilder.cpp, |
2284 |
|
|
applications/nanoRodBuilder/GeometryBuilder.hpp, |
2285 |
|
|
applications/nanoRodBuilder/nanorodBuilder.cpp, |
2286 |
|
|
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
2287 |
|
|
applications/nanoRodBuilder/nanorodBuilderCmd.h, |
2288 |
|
|
applications/oopse/oopse.cpp, |
2289 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
2290 |
|
|
applications/simpleBuilder/simpleBuilderCmd.c, |
2291 |
|
|
applications/simpleBuilder/simpleBuilderCmd.h, |
2292 |
|
|
applications/staticProps/GofAngle2.cpp, |
2293 |
|
|
applications/staticProps/GofAngle2.hpp, |
2294 |
|
|
applications/staticProps/GofR.cpp, |
2295 |
|
|
applications/staticProps/GofR.hpp, |
2296 |
|
|
applications/staticProps/GofRAngle.cpp, |
2297 |
|
|
applications/staticProps/GofRAngle.hpp, |
2298 |
|
|
applications/staticProps/GofXyz.cpp, |
2299 |
|
|
applications/staticProps/GofXyz.hpp, |
2300 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
2301 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
2302 |
|
|
applications/staticProps/StaticProps.cpp, |
2303 |
|
|
applications/staticProps/StaticPropsCmd.c, |
2304 |
|
|
applications/staticProps/StaticPropsCmd.h, |
2305 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
2306 |
|
|
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
2307 |
|
|
brains/Exclude.hpp, brains/ForceManager.cpp, |
2308 |
|
|
brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
2309 |
|
|
brains/MoleculeCreator.hpp, brains/Register.cpp, |
2310 |
|
|
brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
2311 |
|
|
brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
2312 |
|
|
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
2313 |
|
|
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
2314 |
|
|
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
2315 |
|
|
brains/fSimulation.h, constraints/ConstraintElem.hpp, |
2316 |
|
|
constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
2317 |
|
|
constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
2318 |
|
|
constraints/ZconstraintForceManager.cpp, |
2319 |
|
|
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
2320 |
|
|
integrators/DLM.hpp, integrators/Integrator.cpp, |
2321 |
|
|
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
2322 |
|
|
integrators/IntegratorFactory.cpp, |
2323 |
|
|
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
2324 |
|
|
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
2325 |
|
|
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
2326 |
|
|
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
2327 |
|
|
integrators/NVT.cpp, integrators/NVT.hpp, |
2328 |
|
|
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
2329 |
|
|
integrators/Velocitizer.hpp, |
2330 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
2331 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
2332 |
|
|
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
2333 |
|
|
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
2334 |
|
|
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
2335 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
2336 |
|
|
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
2337 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
2338 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
2339 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
2340 |
|
|
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
2341 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
2342 |
|
|
io/Globals.cpp, io/Globals.hpp, |
2343 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, |
2344 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
2345 |
|
|
io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
2346 |
|
|
io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
2347 |
|
|
io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
2348 |
|
|
io/SectionParser.cpp, io/SectionParser.hpp, |
2349 |
|
|
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
2350 |
|
|
io/StatWriter.cpp, io/StatWriter.hpp, |
2351 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
2352 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
2353 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
2354 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
2355 |
|
|
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
2356 |
|
|
io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
2357 |
|
|
io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
2358 |
|
|
io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
2359 |
|
|
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
2360 |
|
|
lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
2361 |
|
|
lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
2362 |
|
|
lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
2363 |
|
|
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
2364 |
|
|
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
2365 |
|
|
math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
2366 |
|
|
math/Quaternion.hpp, math/RandNumGen.hpp, |
2367 |
|
|
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
2368 |
|
|
math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
2369 |
|
|
math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
2370 |
|
|
math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
2371 |
|
|
minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
2372 |
|
|
minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
2373 |
|
|
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
2374 |
|
|
minimizers/MinimizerFactory.hpp, |
2375 |
|
|
minimizers/MinimizerParameterSet.cpp, |
2376 |
|
|
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
2377 |
|
|
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
2378 |
|
|
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
2379 |
|
|
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
2380 |
|
|
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
2381 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
2382 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
2383 |
|
|
primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
2384 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp, |
2385 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
2386 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
2387 |
|
|
primitives/Torsion.cpp, primitives/Torsion.hpp, |
2388 |
|
|
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
2389 |
|
|
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
2390 |
|
|
profiling/timing.F90, restraints/Restraints.cpp, |
2391 |
|
|
restraints/Restraints.hpp, |
2392 |
|
|
restraints/ThermoIntegrationForceManager.cpp, |
2393 |
|
|
restraints/ThermoIntegrationForceManager.hpp, |
2394 |
|
|
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
2395 |
|
|
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
2396 |
|
|
selection/NameFinder.cpp, selection/NameFinder.hpp, |
2397 |
|
|
selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
2398 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
2399 |
|
|
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
2400 |
|
|
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
2401 |
|
|
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
2402 |
|
|
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
2403 |
|
|
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
2404 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
2405 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
2406 |
|
|
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
2407 |
|
|
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
2408 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
2409 |
|
|
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
2410 |
|
|
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
2411 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, |
2412 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
2413 |
|
|
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
2414 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
2415 |
|
|
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
2416 |
|
|
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
2417 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
2418 |
|
|
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
2419 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
2420 |
|
|
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
2421 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
2422 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
2423 |
|
|
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
2424 |
|
|
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
2425 |
|
|
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
2426 |
|
|
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
2427 |
|
|
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
2428 |
|
|
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
2429 |
|
|
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
2430 |
|
|
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
2431 |
|
|
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
2432 |
|
|
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
2433 |
|
|
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
2434 |
|
|
utils/residentMem.h, utils/simError.c, utils/simError.h, |
2435 |
|
|
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
2436 |
|
|
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
2437 |
|
|
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
2438 |
|
|
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
2439 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
2440 |
|
|
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
2441 |
|
|
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
2442 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
2443 |
|
|
been drafted to perform our indentation services |
2444 |
|
|
|
2445 |
|
|
2005-04-15 17:03 gezelter |
2446 |
|
|
|
2447 |
|
|
* configure, ac-tools/configure.in: Jedi mind-trick warning |
2448 |
|
|
messages have been added to make users ignore CGAL. |
2449 |
|
|
|
2450 |
|
|
2005-04-15 13:41 tim |
2451 |
|
|
|
2452 |
|
|
* make/Makefile.in: fix make install |
2453 |
|
|
|
2454 |
|
|
2005-04-15 13:41 tim |
2455 |
|
|
|
2456 |
|
|
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
2457 |
|
|
add Makefile of samples |
2458 |
|
|
|
2459 |
|
|
2005-04-15 13:33 tim |
2460 |
|
|
|
2461 |
|
|
* samples/: lipid/Makefile, water/dimer/Makefile, |
2462 |
|
|
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
2463 |
|
|
installed correctly |
2464 |
|
|
|
2465 |
|
|
2005-04-14 16:41 gezelter |
2466 |
|
|
|
2467 |
|
|
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
2468 |
|
|
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
2469 |
|
|
scripts/filepp, scripts/filepp.in: configure now searches for perl |
2470 |
|
|
to use with filepp |
2471 |
|
|
|
2472 |
gezelter |
2199 |
2005-04-14 16:20 gezelter |
2473 |
tim |
2102 |
|
2474 |
gezelter |
2199 |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
2475 |
|
|
MoLocator |
2476 |
|
|
|
2477 |
|
|
2005-04-14 14:12 gezelter |
2478 |
|
|
|
2479 |
|
|
* LICENSE: [no log message] |
2480 |
|
|
|
2481 |
|
|
2005-04-14 11:10 chuckv |
2482 |
|
|
|
2483 |
|
|
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
2484 |
|
|
nanorodbuilder now exit's when libCGAL is not present. |
2485 |
|
|
|
2486 |
|
|
2005-04-14 10:20 tim |
2487 |
|
|
|
2488 |
|
|
* src/io/make_nodes.h: fix one more warning message in make_nodes |
2489 |
|
|
|
2490 |
|
|
2005-04-13 18:36 chuckv |
2491 |
|
|
|
2492 |
|
|
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
2493 |
|
|
interface name for SGI Compiler |
2494 |
|
|
|
2495 |
|
|
2005-04-13 18:29 chrisfen |
2496 |
|
|
|
2497 |
|
|
* samples/water/ssde/ssde.md: oops... bad sample |
2498 |
|
|
|
2499 |
|
|
2005-04-13 18:00 chuckv |
2500 |
|
|
|
2501 |
|
|
* src/config.h.in: Change typo in CGAL. |
2502 |
|
|
|
2503 |
|
|
2005-04-13 17:43 tim |
2504 |
|
|
|
2505 |
|
|
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
2506 |
|
|
selection/SelectionCompiler.hpp: fix some warning messages |
2507 |
|
|
|
2508 |
|
|
2005-04-13 17:30 gezelter |
2509 |
|
|
|
2510 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
2511 |
|
|
make/Makefile.in, src/config.h.in, |
2512 |
|
|
src/applications/nanoRodBuilder/Makefile, |
2513 |
|
|
src/applications/nanoRodBuilder/Makefile.in, |
2514 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
2515 |
|
|
checks |
2516 |
|
|
|
2517 |
|
|
2005-04-13 15:36 chuckv |
2518 |
|
|
|
2519 |
|
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
2520 |
|
|
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
2521 |
|
|
DarkSide/electrostatic_interface.F90, |
2522 |
|
|
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
2523 |
|
|
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
2524 |
|
|
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
2525 |
|
|
destroy methods for Fortran modules. |
2526 |
|
|
|
2527 |
|
|
2005-04-13 15:17 chuckv |
2528 |
|
|
|
2529 |
|
|
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
2530 |
|
|
shapes_interface.h: Added destroy method to clean up memory |
2531 |
|
|
|
2532 |
|
|
2005-04-13 13:41 tim |
2533 |
|
|
|
2534 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
2535 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
2536 |
|
|
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
2537 |
|
|
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
2538 |
|
|
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
2539 |
|
|
fixed |
2540 |
|
|
|
2541 |
|
|
2005-04-12 17:44 chuckv |
2542 |
|
|
|
2543 |
|
|
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
2544 |
|
|
for nanoRodBuilder. |
2545 |
|
|
|
2546 |
|
|
2005-04-12 17:42 tim |
2547 |
|
|
|
2548 |
|
|
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
2549 |
|
|
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
2550 |
|
|
and simpleBuilder(forget to delete lattice) |
2551 |
|
|
|
2552 |
|
|
2005-04-12 17:33 tim |
2553 |
|
|
|
2554 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
2555 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
2556 |
|
|
refactory lattice |
2557 |
|
|
|
2558 |
|
|
2005-04-12 17:07 tim |
2559 |
|
|
|
2560 |
|
|
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
2561 |
|
|
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
2562 |
|
|
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
2563 |
|
|
LatticeFactory and LatticeCreator |
2564 |
|
|
|
2565 |
|
|
2005-04-12 16:58 tim |
2566 |
|
|
|
2567 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
2568 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
2569 |
|
|
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
2570 |
|
|
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
2571 |
|
|
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
2572 |
|
|
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
2573 |
|
|
|
2574 |
|
|
2005-04-12 16:28 gezelter |
2575 |
|
|
|
2576 |
|
|
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
2577 |
|
|
vector_class.F90: cleaned up vector_class memory leak fix by |
2578 |
|
|
deallocating in reverse order of how we allocated. Also migrated |
2579 |
|
|
MoLocator into utils directory |
2580 |
|
|
|
2581 |
|
|
2005-04-12 16:27 gezelter |
2582 |
|
|
|
2583 |
|
|
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
2584 |
|
|
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
2585 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
2586 |
|
|
directory |
2587 |
|
|
|
2588 |
|
|
2005-04-12 16:27 gezelter |
2589 |
|
|
|
2590 |
|
|
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
2591 |
|
|
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
2592 |
|
|
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
2593 |
|
|
nanoRodBuilder/LatticeCreator.hpp, |
2594 |
|
|
nanoRodBuilder/LatticeFactory.cpp, |
2595 |
|
|
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
2596 |
|
|
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
2597 |
|
|
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
2598 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
2599 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
2600 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
2601 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
2602 |
|
|
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
2603 |
|
|
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
2604 |
|
|
these files are now redundant |
2605 |
|
|
|
2606 |
|
|
2005-04-12 16:27 gezelter |
2607 |
|
|
|
2608 |
|
|
* src/UseTheForce/DarkSide/: atype_interface.F90, |
2609 |
|
|
atype_interface.h: cleaned up memory leak fix |
2610 |
|
|
|
2611 |
|
|
2005-04-12 16:26 gezelter |
2612 |
|
|
|
2613 |
|
|
* make/Makefile.in: added lattice subdirectory |
2614 |
|
|
|
2615 |
|
|
2005-04-12 15:57 chrisfen |
2616 |
|
|
|
2617 |
|
|
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
2618 |
|
|
a space by accident |
2619 |
|
|
|
2620 |
|
|
2005-04-12 15:56 chrisfen |
2621 |
|
|
|
2622 |
|
|
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
2623 |
|
|
quadrupole sample |
2624 |
|
|
|
2625 |
|
|
2005-04-12 15:56 chrisfen |
2626 |
|
|
|
2627 |
|
|
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
2628 |
|
|
samples |
2629 |
|
|
|
2630 |
|
|
2005-04-12 13:30 tim |
2631 |
|
|
|
2632 |
|
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
2633 |
|
|
type in fortran side |
2634 |
|
|
|
2635 |
|
|
2005-04-12 12:45 chuckv |
2636 |
|
|
|
2637 |
|
|
* src/utils/vector_class.F90: Further changes to vector_class |
2638 |
|
|
destroy function. |
2639 |
|
|
|
2640 |
|
|
2005-04-12 12:39 chuckv |
2641 |
|
|
|
2642 |
|
|
* src/utils/vector_class.F90: Fixed pointer memory leak in |
2643 |
|
|
vector_class. |
2644 |
|
|
|
2645 |
|
|
2005-04-12 12:12 chuckv |
2646 |
|
|
|
2647 |
|
|
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
2648 |
|
|
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
2649 |
|
|
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
2650 |
|
|
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
2651 |
|
|
|
2652 |
|
|
2005-04-12 09:24 chrisfen |
2653 |
|
|
|
2654 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
2655 |
|
|
output |
2656 |
|
|
|
2657 |
|
|
2005-04-11 19:29 chuckv |
2658 |
|
|
|
2659 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
2660 |
|
|
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
2661 |
|
|
|
2662 |
|
|
2005-04-11 19:28 chuckv |
2663 |
|
|
|
2664 |
|
|
* src/utils/vector_class.F90: Added code to delete vector. |
2665 |
|
|
|
2666 |
|
|
2005-04-11 16:58 tim |
2667 |
|
|
|
2668 |
|
|
* src/io/basic_ifstrstream.hpp: avoid multiple inherit in |
2669 |
|
|
basic_ifstrstream |
2670 |
|
|
|
2671 |
|
|
2005-04-11 16:37 chuckv |
2672 |
|
|
|
2673 |
|
|
* make/Makefile.in, |
2674 |
|
|
src/applications/nanoRodBuilder/BaseLattice.cpp, |
2675 |
|
|
src/applications/nanoRodBuilder/BaseLattice.hpp, |
2676 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
2677 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
2678 |
|
|
src/applications/nanoRodBuilder/Lattice.cpp, |
2679 |
|
|
src/applications/nanoRodBuilder/Lattice.hpp, |
2680 |
|
|
src/applications/nanoRodBuilder/LatticeCreator.cpp, |
2681 |
|
|
src/applications/nanoRodBuilder/LatticeCreator.hpp, |
2682 |
|
|
src/applications/nanoRodBuilder/LatticeFactory.cpp, |
2683 |
|
|
src/applications/nanoRodBuilder/LatticeFactory.hpp, |
2684 |
|
|
src/applications/nanoRodBuilder/Makefile, |
2685 |
|
|
src/applications/nanoRodBuilder/MoLocator.cpp, |
2686 |
|
|
src/applications/nanoRodBuilder/MoLocator.hpp, |
2687 |
|
|
src/applications/nanoRodBuilder/nanoBuilder.ggo, |
2688 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
2689 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.ggo, |
2690 |
|
|
src/applications/nanoRodBuilder/nanorodBuilderCmd.c, |
2691 |
|
|
src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing |
2692 |
|
|
nanoRodBuilder application (may not work yet). ((Doesn't work |
2693 |
|
|
yet.)) (((May never work....))) |
2694 |
|
|
|
2695 |
|
|
2005-04-11 15:54 tim |
2696 |
|
|
|
2697 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete |
2698 |
|
|
prepareVisitor in Dump2XYZ |
2699 |
|
|
|
2700 |
|
|
2005-04-11 15:19 chrisfen |
2701 |
|
|
|
2702 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixing of the |
2703 |
|
|
quadrupoles. look! it's divide by 3 like stone says! |
2704 |
|
|
|
2705 |
|
|
2005-04-11 15:18 chrisfen |
2706 |
|
|
|
2707 |
|
|
* forceFields/DUFF2.frc: fixing of the quadrupoles |
2708 |
|
|
|
2709 |
|
|
2005-04-11 15:16 tim |
2710 |
|
|
|
2711 |
|
|
* src/selection/Token.hpp: change the parameter name in |
2712 |
|
|
constructors |
2713 |
|
|
|
2714 |
|
|
2005-04-11 14:49 gezelter |
2715 |
|
|
|
2716 |
|
|
* make/Makefile.in: One more bug fix for GNU make versions < 3.80 |
2717 |
|
|
|
2718 |
|
|
2005-04-11 14:06 gezelter |
2719 |
|
|
|
2720 |
|
|
* make/Makefile.in: Fixed the uc and lc functions for GNU make |
2721 |
|
|
versions < 3.80 |
2722 |
|
|
|
2723 |
|
|
2005-04-11 11:13 gezelter |
2724 |
|
|
|
2725 |
|
|
* make/Makefile.in, src/UseTheForce/Makefile, |
2726 |
|
|
src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added |
2727 |
|
|
some stuff to clean out module files during "make clean" |
2728 |
|
|
|
2729 |
|
|
2005-04-08 17:13 chrisfen |
2730 |
|
|
|
2731 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: quadrupole |
2732 |
|
|
interactions should be working with a remaining question of |
2733 |
|
|
interaction magnitude |
2734 |
|
|
|
2735 |
|
|
2005-04-08 17:12 chrisfen |
2736 |
|
|
|
2737 |
|
|
* samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with |
2738 |
|
|
samples |
2739 |
|
|
|
2740 |
|
|
2005-04-08 13:48 chrisfen |
2741 |
|
|
|
2742 |
|
|
* samples/water/ssd/ssd.md: oops... messed up a sample |
2743 |
|
|
|
2744 |
|
|
2005-04-08 09:43 chrisfen |
2745 |
|
|
|
2746 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix |
2747 |
|
|
charge-dipole interactions |
2748 |
|
|
|
2749 |
|
|
2005-04-08 09:42 chrisfen |
2750 |
|
|
|
2751 |
|
|
* samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, |
2752 |
|
|
ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole |
2753 |
|
|
|
2754 |
|
|
2005-04-08 09:41 chrisfen |
2755 |
|
|
|
2756 |
|
|
* forceFields/DUFF2.frc: added Cl- and Na+ |
2757 |
|
|
|
2758 |
|
|
2005-04-06 18:59 tim |
2759 |
|
|
|
2760 |
|
|
* src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser |
2761 |
|
|
|
2762 |
|
|
2005-04-05 18:09 tim |
2763 |
|
|
|
2764 |
|
|
* src/selection/: NameFinder.cpp, SelectionCompiler.cpp, |
2765 |
|
|
SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' |
2766 |
|
|
in atom type name;clean the code a little bit |
2767 |
|
|
|
2768 |
|
|
2005-03-29 16:00 tim |
2769 |
|
|
|
2770 |
|
|
* src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug |
2771 |
|
|
in converting rotation matrix to quaternion |
2772 |
|
|
|
2773 |
|
|
2005-03-28 17:41 tim |
2774 |
|
|
|
2775 |
|
|
* src/visitors/LipidTransVisitor.cpp: fixed the wrapping |
2776 |
|
|
|
2777 |
|
|
2005-03-28 17:30 tim |
2778 |
|
|
|
2779 |
|
|
* src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do |
2780 |
|
|
the wrapping |
2781 |
|
|
|
2782 |
|
|
2005-03-28 10:54 tim |
2783 |
|
|
|
2784 |
|
|
* src/applications/staticProps/GofXyz.cpp: fix a bug in getting the |
2785 |
|
|
dimension of histogram |
2786 |
|
|
|
2787 |
|
|
2005-03-22 11:38 tim |
2788 |
|
|
|
2789 |
|
|
* make/Makefile.in, src/applications/dump2Xyz/Makefile, |
2790 |
|
|
src/applications/dynamicProps/Makefile, |
2791 |
|
|
src/applications/oopse/Makefile, |
2792 |
|
|
src/applications/simpleBuilder/Makefile, |
2793 |
|
|
src/applications/staticProps/Makefile: avoid building parallel |
2794 |
|
|
executable for dump2XYZ, simpleBuilder, staticProps and |
2795 |
|
|
dynamicProps |
2796 |
|
|
|
2797 |
|
|
2005-03-21 17:34 chrisfen |
2798 |
|
|
|
2799 |
|
|
* forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the |
2800 |
|
|
forcefield files |
2801 |
|
|
|
2802 |
|
|
2005-03-21 15:51 chrisfen |
2803 |
|
|
|
2804 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
2805 |
|
|
DarkSide/reactionField.F90: Make sure electrostatic_module provides |
2806 |
|
|
data for reaction_field |
2807 |
|
|
|
2808 |
|
|
2005-03-21 15:50 chrisfen |
2809 |
|
|
|
2810 |
|
|
* forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE |
2811 |
|
|
WILL CHANGE THIS BACK, RIGHT? |
2812 |
|
|
|
2813 |
|
|
2005-03-21 14:23 gezelter |
2814 |
|
|
|
2815 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: constant back to |
2816 |
|
|
correct value |
2817 |
|
|
|
2818 |
|
|
2005-03-21 14:22 gezelter |
2819 |
|
|
|
2820 |
|
|
* make/Makefile.in: fixed an install-related bug. |
2821 |
|
|
$(InstallCommand) had been set to $(InstallData) |
2822 |
|
|
|
2823 |
|
|
2005-03-15 09:21 gezelter |
2824 |
|
|
|
2825 |
|
|
* src/integrators/Integrator.cpp: VelocityVerletIntegrator already |
2826 |
|
|
deletes and Nullifies restWriter, so Integrator shouldn't do it. |
2827 |
|
|
|
2828 |
|
|
2005-03-15 09:20 gezelter |
2829 |
|
|
|
2830 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos |
2831 |
|
|
|
2832 |
|
|
2005-03-13 02:39 gezelter |
2833 |
|
|
|
2834 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: first run at |
2835 |
|
|
charge-quadrupole interactions |
2836 |
|
|
|
2837 |
|
|
2005-03-12 14:12 chrisfen |
2838 |
|
|
|
2839 |
|
|
* samples/: Makefile.in, thermoIntegration/liquid/Makefile, |
2840 |
|
|
thermoIntegration/solid/Makefile: forgot a couple of makefiles |
2841 |
|
|
|
2842 |
|
|
2005-03-12 14:05 chrisfen |
2843 |
|
|
|
2844 |
|
|
* samples/thermoIntegration/liquid/ssde.in, |
2845 |
|
|
samples/thermoIntegration/liquid/ssde.md, |
2846 |
|
|
samples/thermoIntegration/liquid/water.md, |
2847 |
|
|
samples/thermoIntegration/solid/idealCrystal.in, |
2848 |
|
|
samples/thermoIntegration/solid/ssde.in, |
2849 |
|
|
samples/thermoIntegration/solid/ssde.md, |
2850 |
|
|
samples/thermoIntegration/solid/ssde.zang0, |
2851 |
|
|
samples/thermoIntegration/solid/water.md, |
2852 |
|
|
samples/water/tip3p_ice/tp3.md, |
2853 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
2854 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: added some |
2855 |
|
|
samples |
2856 |
|
|
|
2857 |
|
|
2005-03-11 12:50 tim |
2858 |
|
|
|
2859 |
|
|
* src/: brains/SimCreator.cpp, |
2860 |
|
|
io/MultipoleAtomTypesSectionParser.cpp: fix a typo in |
2861 |
|
|
MultipoleAtomTypesSectionParser |
2862 |
|
|
|
2863 |
|
|
2005-03-11 10:55 tim |
2864 |
|
|
|
2865 |
|
|
* src/brains/SimInfo.cpp: pairs inside cutoff group should not be |
2866 |
|
|
excluded |
2867 |
|
|
|
2868 |
|
|
2005-03-11 10:53 gezelter |
2869 |
|
|
|
2870 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for |
2871 |
|
|
quadrupoles |
2872 |
|
|
|
2873 |
|
|
2005-03-11 10:52 gezelter |
2874 |
|
|
|
2875 |
|
|
* forceFields/DUFF2.frc: quadrupoles for SSD models |
2876 |
|
|
|
2877 |
|
|
2005-03-11 10:00 tim |
2878 |
|
|
|
2879 |
|
|
* ChangeLog, doc/SelectionExpression.html, |
2880 |
|
|
doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, |
2881 |
|
|
doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, |
2882 |
|
|
src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, |
2883 |
|
|
src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, |
2884 |
|
|
src/selection/TokenMap.cpp: clean up SimInfo; modify the images of |
2885 |
|
|
SelectionExpression.html |
2886 |
|
|
|
2887 |
|
|
2005-03-10 19:43 chrisfen |
2888 |
|
|
|
2889 |
tim |
2116 |
* samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, |
2890 |
|
|
src/io/RestReader.cpp, src/restraints/Restraints.cpp, |
2891 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in |
2892 |
|
|
MPI restraints |
2893 |
|
|
|
2894 |
gezelter |
2199 |
2005-03-10 18:56 tim |
2895 |
tim |
2116 |
|
2896 |
|
|
* doc/SelectionExpression.html, src/brains/SimInfo.cpp, |
2897 |
|
|
src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody |
2898 |
|
|
and cutoff group |
2899 |
|
|
|
2900 |
gezelter |
2199 |
2005-03-10 17:06 gezelter |
2901 |
tim |
2116 |
|
2902 |
|
|
* src/types/MorseBondType.hpp: fixed a doxygen problem |
2903 |
|
|
|
2904 |
gezelter |
2199 |
2005-03-10 16:51 gezelter |
2905 |
tim |
2116 |
|
2906 |
|
|
* samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with |
2907 |
|
|
the split dipole test cases |
2908 |
|
|
|
2909 |
gezelter |
2199 |
2005-03-10 16:51 gezelter |
2910 |
tim |
2116 |
|
2911 |
|
|
* doc/SelectionExpression.html: updated some documentation |
2912 |
|
|
|
2913 |
gezelter |
2199 |
2005-03-10 15:40 gezelter |
2914 |
tim |
2116 |
|
2915 |
|
|
* src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, |
2916 |
|
|
Makefile: LinkedList removal project starts now |
2917 |
|
|
|
2918 |
gezelter |
2199 |
2005-03-10 15:28 tim |
2919 |
tim |
2116 |
|
2920 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
2921 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: |
2922 |
|
|
using map to replace link list |
2923 |
|
|
|
2924 |
gezelter |
2199 |
2005-03-10 14:11 tim |
2925 |
tim |
2116 |
|
2926 |
|
|
* samples/dipole/: splitInWater.in, splitInWater.md: adding test |
2927 |
|
|
case of split dipole |
2928 |
|
|
|
2929 |
gezelter |
2199 |
2005-03-10 14:10 chrisfen |
2930 |
tim |
2116 |
|
2931 |
|
|
* samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, |
2932 |
|
|
src/io/RestWriter.cpp, |
2933 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now |
2934 |
|
|
builds... |
2935 |
|
|
|
2936 |
gezelter |
2199 |
2005-03-10 13:44 tim |
2937 |
tim |
2116 |
|
2938 |
|
|
* samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, |
2939 |
|
|
split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: |
2940 |
|
|
adding test case for split dipole |
2941 |
|
|
|
2942 |
gezelter |
2199 |
2005-03-10 12:54 gezelter |
2943 |
tim |
2116 |
|
2944 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side |
2945 |
|
|
support for split dipoles |
2946 |
|
|
|
2947 |
gezelter |
2199 |
2005-03-10 11:27 chrisfen |
2948 |
tim |
2116 |
|
2949 |
|
|
* samples/water/tip3p_ice/tp3.md, |
2950 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixes to |
2951 |
|
|
restraints |
2952 |
|
|
|
2953 |
gezelter |
2199 |
2005-03-10 11:15 chrisfen |
2954 |
tim |
2116 |
|
2955 |
|
|
* samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, |
2956 |
|
|
src/UseTheForce/ForceFields.hpp, |
2957 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints |
2958 |
|
|
|
2959 |
gezelter |
2199 |
2005-03-10 11:14 tim |
2960 |
tim |
2116 |
|
2961 |
|
|
* ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, |
2962 |
|
|
src/io/MultipoleAtomTypesSectionParser.cpp, |
2963 |
|
|
src/selection/SelectionEvaluator.cpp: minor change |
2964 |
|
|
|
2965 |
gezelter |
2199 |
2005-03-10 10:10 chrisfen |
2966 |
tim |
2116 |
|
2967 |
tim |
2102 |
* make/Makefile.in, samples/water/tip3p_ice/tp3.md, |
2968 |
|
|
src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, |
2969 |
|
|
src/integrators/Integrator.cpp, src/integrators/Integrator.hpp, |
2970 |
|
|
src/integrators/VelocityVerletIntegrator.cpp, |
2971 |
|
|
src/integrators/VelocityVerletIntegrator.hpp, |
2972 |
|
|
src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp, |
2973 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp, |
2974 |
|
|
src/io/RestReader.hpp, src/io/RestWriter.cpp, |
2975 |
|
|
src/io/RestWriter.hpp, src/io/RestraintReader.cpp, |
2976 |
|
|
src/io/RestraintWriter.cpp, src/restraints/Makefile, |
2977 |
|
|
src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, |
2978 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp, |
2979 |
|
|
src/restraints/ThermoIntegrationForceManager.hpp: First commit of |
2980 |
|
|
the new restraints code |
2981 |
|
|
|
2982 |
gezelter |
2199 |
2005-03-09 13:48 tim |
2983 |
tim |
2102 |
|
2984 |
|
|
* src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding |
2985 |
|
|
IndexFinder |
2986 |
|
|
|
2987 |
gezelter |
2199 |
2005-03-09 13:46 tim |
2988 |
tim |
2102 |
|
2989 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.ggo, |
2990 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
2991 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
2992 |
|
|
selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: |
2993 |
|
|
fix compilation issue |
2994 |
|
|
|
2995 |
gezelter |
2199 |
2005-03-09 12:58 tim |
2996 |
tim |
2102 |
|
2997 |
|
|
* forceFields/DUFF2.frc, scripts/filepp, |
2998 |
|
|
src/UseTheForce/EAM_FF.cpp, |
2999 |
|
|
src/io/MultipoleAtomTypesSectionParser.cpp, |
3000 |
|
|
src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug |
3001 |
|
|
in SectionParser (lineNo is not updated) |
3002 |
|
|
|
3003 |
gezelter |
2199 |
2005-03-09 12:30 tim |
3004 |
tim |
2102 |
|
3005 |
|
|
* src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, |
3006 |
|
|
applications/dump2Xyz/Dump2XYZ.ggo, |
3007 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
3008 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp, |
3009 |
|
|
brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp, |
3010 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
3011 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
3012 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile, |
3013 |
|
|
io/MultipoleAtomTypesSectionParser.cpp, |
3014 |
|
|
io/MultipoleAtomTypesSectionParser.hpp, |
3015 |
|
|
io/SectionParserManager.cpp, selection/Makefile, |
3016 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
3017 |
|
|
types/AtomType.cpp, types/DirectionalAtomType.cpp, |
3018 |
|
|
visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp, |
3019 |
|
|
visitors/OtherVisitor.hpp: adding IndexFinder which is used to |
3020 |
|
|
select the molecules; Seperate ElectrostaticAtomTypesSectionParser |
3021 |
|
|
into ChargeAtomTypesSectionParser and |
3022 |
|
|
MultipoleAtomTypesSectionParser;remove print dipole option from |
3023 |
|
|
Dump2XYZ; |
3024 |
|
|
|
3025 |
gezelter |
2199 |
2005-03-09 12:28 tim |
3026 |
tim |
2102 |
|
3027 |
|
|
* forceFields/DUFF2.frc: change the format of DUFF2 |
3028 |
|
|
|
3029 |
gezelter |
2199 |
2005-03-09 10:44 gezelter |
3030 |
tim |
2102 |
|
3031 |
|
|
* src/UseTheForce/DarkSide/: electrostatic.F90, |
3032 |
|
|
electrostatic_interface.F90, electrostatic_interface.h: new |
3033 |
|
|
electrostatic module |
3034 |
|
|
|
3035 |
gezelter |
2199 |
2005-03-09 09:26 gezelter |
3036 |
tim |
2102 |
|
3037 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
3038 |
|
|
DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole |
3039 |
|
|
and fixed quadrupole stuff |
3040 |
|
|
|
3041 |
gezelter |
2199 |
2005-03-09 09:25 gezelter |
3042 |
tim |
2102 |
|
3043 |
|
|
* src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines |
3044 |
|
|
for outdated charge and dipole interfaces |
3045 |
|
|
|
3046 |
gezelter |
2199 |
2005-03-08 16:08 gezelter |
3047 |
tim |
2102 |
|
3048 |
|
|
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, |
3049 |
|
|
mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun |
3050 |
|
|
charge-dipole test cases |
3051 |
|
|
|
3052 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
3053 |
tim |
2102 |
|
3054 |
|
|
* src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, |
3055 |
|
|
OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a |
3056 |
|
|
strange icc8 bug (we think). |
3057 |
|
|
|
3058 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
3059 |
tim |
2102 |
|
3060 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! |
3061 |
|
|
|
3062 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
3063 |
tim |
2102 |
|
3064 |
|
|
* src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic |
3065 |
|
|
Unification Project |
3066 |
|
|
|
3067 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
3068 |
tim |
2102 |
|
3069 |
|
|
* src/io/Globals.cpp: Dunno |
3070 |
|
|
|
3071 |
gezelter |
2199 |
2005-03-08 16:06 gezelter |
3072 |
tim |
2102 |
|
3073 |
|
|
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using |
3074 |
|
|
OOPSE_itoa and checking a NULL left over from the LinkedList days |
3075 |
|
|
|
3076 |
gezelter |
2199 |
2005-03-08 16:06 gezelter |
3077 |
tim |
2102 |
|
3078 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
3079 |
|
|
atype_interface.F90, atype_interface.h, charge.F90, |
3080 |
|
|
charge_interface.F90, charge_interface.h, dipole.F90, |
3081 |
|
|
dipole_interface.F90, dipole_interface.h: electrostatic unification |
3082 |
|
|
project fixed an uninitialized variable in Lennard Jones mixing map |
3083 |
|
|
|
3084 |
gezelter |
2199 |
2005-03-08 16:05 gezelter |
3085 |
tim |
2102 |
|
3086 |
|
|
* src/UseTheForce/doForces.F90: electrostatic unification project |
3087 |
|
|
|
3088 |
gezelter |
2199 |
2005-03-08 16:05 gezelter |
3089 |
tim |
2102 |
|
3090 |
|
|
* samples/water/dimer/: two.md, water.md: making some cool test |
3091 |
|
|
cases |
3092 |
|
|
|
3093 |
gezelter |
2199 |
2005-03-08 16:05 gezelter |
3094 |
tim |
2102 |
|
3095 |
|
|
* forceFields/DUFF2.frc: Added a charge for Chlorine |
3096 |
|
|
|
3097 |
gezelter |
2199 |
2005-03-07 17:39 tim |
3098 |
tim |
2102 |
|
3099 |
|
|
* src/: brains/SimInfo.cpp, io/DumpReader.cpp, |
3100 |
|
|
math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, |
3101 |
|
|
primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: |
3102 |
|
|
Fixing a bug in BitSet.cpp |
3103 |
|
|
|
3104 |
gezelter |
2199 |
2005-03-04 10:28 gezelter |
3105 |
tim |
2102 |
|
3106 |
|
|
* src/config.h.in: Cleaning up config.h.in by adding comments |
3107 |
|
|
|
3108 |
gezelter |
2199 |
2005-03-04 10:28 gezelter |
3109 |
tim |
2102 |
|
3110 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in, |
3111 |
|
|
src/brains/SimCreator.cpp: SPRNG eradication project |
3112 |
|
|
|
3113 |
gezelter |
2199 |
2005-03-03 09:40 tim |
3114 |
tim |
2102 |
|
3115 |
|
|
* src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the |
3116 |
|
|
missing atom type problem) |
3117 |
|
|
|
3118 |
gezelter |
2199 |
2005-03-02 11:29 tim |
3119 |
tim |
2102 |
|
3120 |
|
|
* src/math/RandNumGen.hpp: adding base class of Random Number |
3121 |
|
|
generator |
3122 |
|
|
|
3123 |
gezelter |
2199 |
2005-03-02 11:28 tim |
3124 |
tim |
2102 |
|
3125 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
3126 |
|
|
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in |
3127 |
|
|
Velocitizer is not initialized which causes a seg fault |
3128 |
|
|
|
3129 |
gezelter |
2199 |
2005-03-02 10:36 tim |
3130 |
tim |
2102 |
|
3131 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
3132 |
|
|
integrators/Velocitizer.hpp, math/Makefile, |
3133 |
|
|
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
3134 |
|
|
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp, |
3135 |
|
|
math/SeqRandNumGen.hpp: remove default parameter from |
3136 |
|
|
MersenneTwister.hpp which causes all kinds of trouble. Refactory |
3137 |
|
|
random number generator |
3138 |
|
|
|
3139 |
gezelter |
2199 |
2005-03-02 02:32 tim |
3140 |
tim |
2102 |
|
3141 |
|
|
* test/math/testRandNumGen.cpp: Adding unit test for random number |
3142 |
|
|
generator |
3143 |
|
|
|
3144 |
gezelter |
2199 |
2005-03-01 18:17 tim |
3145 |
tim |
2102 |
|
3146 |
|
|
* src/brains/Thermo.hpp: fixed a file inclusion problem |
3147 |
|
|
|
3148 |
gezelter |
2199 |
2005-03-01 18:17 tim |
3149 |
tim |
2102 |
|
3150 |
|
|
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
3151 |
|
|
OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, |
3152 |
|
|
ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, |
3153 |
|
|
RandNumGenTestCase.hpp: fixed compilation problem |
3154 |
|
|
|
3155 |
gezelter |
2199 |
2005-03-01 18:02 tim |
3156 |
tim |
2102 |
|
3157 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
3158 |
|
|
integrators/Velocitizer.hpp, math/Makefile, |
3159 |
|
|
math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp, |
3160 |
|
|
math/ParallelRandNumGen.hpp, math/mt19937ar.c, |
3161 |
|
|
math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand |
3162 |
|
|
|
3163 |
gezelter |
2199 |
2005-03-01 18:00 tim |
3164 |
tim |
2102 |
|
3165 |
|
|
* test/math/: Makefile, ParallelandNumGenTestCase.cpp, |
3166 |
|
|
ParallelandNumGenTestCase.hpp: Change the name of test case |
3167 |
|
|
|
3168 |
gezelter |
2199 |
2005-03-01 16:00 tim |
3169 |
tim |
2102 |
|
3170 |
|
|
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
3171 |
|
|
OOPSERandNumGenTestCase.hpp: adding testcase for random number |
3172 |
|
|
generator |
3173 |
|
|
|
3174 |
gezelter |
2199 |
2005-03-01 15:10 tim |
3175 |
tim |
2102 |
|
3176 |
|
|
* src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, |
3177 |
|
|
integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, |
3178 |
|
|
math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp, |
3179 |
|
|
math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp, |
3180 |
|
|
math/Vector3.hpp, minimizers/MinimizerCreator.hpp, |
3181 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
3182 |
|
|
utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, |
3183 |
|
|
visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 |
3184 |
|
|
|
3185 |
gezelter |
2199 |
2005-03-01 14:11 tim |
3186 |
tim |
2102 |
|
3187 |
|
|
* src/: brains/SimCreator.cpp, brains/SimInfo.hpp, |
3188 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
3189 |
|
|
math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding |
3190 |
|
|
OOPSERandNumGen |
3191 |
|
|
|
3192 |
gezelter |
2199 |
2005-03-01 10:44 gezelter |
3193 |
tim |
2102 |
|
3194 |
|
|
* make/Makefile.in: Fixed the damned build problem with the |
3195 |
|
|
libraries not being removed in make clean and make distclean (at |
3196 |
|
|
least we think it is fixed). |
3197 |
|
|
|
3198 |
gezelter |
2199 |
2005-03-01 10:26 gezelter |
3199 |
tim |
2102 |
|
3200 |
|
|
* src/math/MersenneTwister.hpp: Making small modifications to allow |
3201 |
|
|
for use on MPI machines |
3202 |
|
|
|
3203 |
gezelter |
2199 |
2005-03-01 09:45 tim |
3204 |
tim |
2102 |
|
3205 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, |
3206 |
|
|
integrators/Velocitizer.cpp, io/DumpReader.cpp, |
3207 |
|
|
math/MersenneTwister.hpp: adding MersenneTwister random number |
3208 |
|
|
generator |
3209 |
|
|
|
3210 |
gezelter |
2199 |
2005-02-28 22:55 tim |
3211 |
tim |
2102 |
|
3212 |
|
|
* src/math/MersenneTwister.hpp: Adding a modified version of |
3213 |
|
|
MersenneTwister.hpp |
3214 |
|
|
|
3215 |
gezelter |
2199 |
2005-02-28 12:24 tim |
3216 |
tim |
2102 |
|
3217 |
|
|
* doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, |
3218 |
|
|
definition.jpg: selection expression |
3219 |
|
|
|
3220 |
gezelter |
2199 |
2005-02-25 16:22 tim |
3221 |
tim |
2102 |
|
3222 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, |
3223 |
|
|
UseTheForce/DarkSide/lj_interface.F90, |
3224 |
|
|
UseTheForce/DarkSide/lj_interface.h, |
3225 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, |
3226 |
|
|
types/AtomType.hpp: adding soft potential to LJ Module |
3227 |
|
|
|
3228 |
gezelter |
2199 |
2005-02-25 11:38 tim |
3229 |
tim |
2102 |
|
3230 |
|
|
* doc/SelectionExpression.html: adding documentation for selection |
3231 |
|
|
expression |
3232 |
|
|
|
3233 |
gezelter |
2199 |
2005-02-24 15:55 tim |
3234 |
tim |
2102 |
|
3235 |
|
|
* src/: applications/simpleBuilder/simpleBuilder.cpp, |
3236 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, |
3237 |
|
|
io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp: |
3238 |
|
|
adding basic_teebuf which can operate on multiple stream |
3239 |
|
|
simutaneously. |
3240 |
|
|
|
3241 |
gezelter |
2199 |
2005-02-22 14:26 chrisfen |
3242 |
tim |
2102 |
|
3243 |
gezelter |
2199 |
* samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf |
3244 |
|
|
sample |
3245 |
|
|
|
3246 |
|
|
2005-02-22 13:56 tim |
3247 |
|
|
|
3248 |
tim |
2102 |
* src/: UseTheForce/DarkSide/reactionField.F90, |
3249 |
|
|
primitives/RigidBody.cpp: reactionfield get fixed |
3250 |
|
|
|
3251 |
gezelter |
2199 |
2005-02-21 11:57 tim |
3252 |
tim |
2102 |
|
3253 |
|
|
* src/: applications/staticProps/GofRAngle.cpp, |
3254 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix |
3255 |
|
|
a bug in GofRAngle |
3256 |
|
|
|
3257 |
gezelter |
2199 |
2005-02-21 10:28 tim |
3258 |
tim |
2102 |
|
3259 |
|
|
* src/primitives/Molecule.cpp: Fix for compilation on the Sun |
3260 |
|
|
|
3261 |
gezelter |
2199 |
2005-02-21 10:22 tim |
3262 |
tim |
2102 |
|
3263 |
|
|
* src/utils/next_combination.hpp: fix for compilation on the Sun |
3264 |
|
|
|
3265 |
gezelter |
2199 |
2005-02-21 10:21 tim |
3266 |
tim |
2102 |
|
3267 |
|
|
* src/utils/GenericData.hpp: fix problem in sun |
3268 |
|
|
|
3269 |
gezelter |
2199 |
2005-02-18 18:07 tim |
3270 |
tim |
2102 |
|
3271 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
3272 |
|
|
applications/dump2Xyz/Dump2XYZ.ggo, |
3273 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
3274 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
3275 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
3276 |
|
|
applications/staticProps/GofXyz.cpp, |
3277 |
|
|
applications/staticProps/GofXyz.hpp, |
3278 |
|
|
applications/staticProps/StaticProps.cpp, |
3279 |
|
|
applications/staticProps/StaticProps.ggo, |
3280 |
|
|
applications/staticProps/StaticPropsCmd.c, |
3281 |
|
|
applications/staticProps/StaticPropsCmd.h, |
3282 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
3283 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
3284 |
|
|
visitors/Makefile: adding LipidTransVisitor, GofXyz is working now |
3285 |
|
|
|
3286 |
gezelter |
2199 |
2005-02-18 10:58 gezelter |
3287 |
tim |
2102 |
|
3288 |
|
|
* src/brains/Register.cpp: Corrected filename collision for EAM on |
3289 |
|
|
Mac OS X |
3290 |
|
|
|
3291 |
gezelter |
2199 |
2005-02-18 10:58 gezelter |
3292 |
tim |
2102 |
|
3293 |
|
|
* src/applications/oopse/oopse.cpp: Updated copyright information |
3294 |
|
|
|
3295 |
gezelter |
2199 |
2005-02-18 10:58 gezelter |
3296 |
tim |
2102 |
|
3297 |
|
|
* src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, |
3298 |
|
|
Makefile: corrected filename collision for EAM on operating systems |
3299 |
|
|
which are not case sensitive (aka Mac OS X) |
3300 |
|
|
|
3301 |
gezelter |
2199 |
2005-02-17 15:15 tim |
3302 |
tim |
2102 |
|
3303 |
|
|
* src/applications/staticProps/GofXyz.cpp: more bug get fixed |
3304 |
|
|
|
3305 |
gezelter |
2199 |
2005-02-17 14:50 tim |
3306 |
tim |
2102 |
|
3307 |
|
|
* src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug |
3308 |
|
|
in GofXyz |
3309 |
|
|
|
3310 |
gezelter |
2199 |
2005-02-17 14:09 tim |
3311 |
tim |
2102 |
|
3312 |
|
|
* src/applications/staticProps/RadialDistrFunc.hpp: make |
3313 |
|
|
processHistogram non-abstrct function |
3314 |
|
|
|
3315 |
gezelter |
2199 |
2005-02-17 13:41 tim |
3316 |
tim |
2102 |
|
3317 |
|
|
* src/applications/staticProps/GofXyz.cpp: [no log message] |
3318 |
|
|
|
3319 |
gezelter |
2199 |
2005-02-17 13:30 tim |
3320 |
tim |
2102 |
|
3321 |
|
|
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
3322 |
|
|
GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: |
3323 |
|
|
finish GofXyz |
3324 |
|
|
|
3325 |
gezelter |
2199 |
2005-02-17 11:21 tim |
3326 |
tim |
2102 |
|
3327 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, |
3328 |
|
|
GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial |
3329 |
|
|
distribution function |
3330 |
|
|
|
3331 |
gezelter |
2199 |
2005-02-17 10:23 tim |
3332 |
tim |
2102 |
|
3333 |
|
|
* src/utils/BitSet.hpp: forget the const correctness for BitSet |
3334 |
|
|
|
3335 |
gezelter |
2199 |
2005-02-17 10:18 tim |
3336 |
tim |
2102 |
|
3337 |
|
|
* src/: brains/BlockSnapshotManager.cpp, |
3338 |
|
|
selection/DistanceFinder.cpp: The change of interface of BitSet |
3339 |
|
|
cause a bug in SelectionEvaluation |
3340 |
|
|
|
3341 |
gezelter |
2199 |
2005-02-16 16:13 tim |
3342 |
tim |
2102 |
|
3343 |
|
|
* src/utils/residentMem.c: return residentMem in byte |
3344 |
|
|
|
3345 |
gezelter |
2199 |
2005-02-16 16:00 tim |
3346 |
tim |
2102 |
|
3347 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix |
3348 |
|
|
a bug in writing out the value of cosang |
3349 |
|
|
|
3350 |
gezelter |
2199 |
2005-02-16 15:43 tim |
3351 |
tim |
2102 |
|
3352 |
|
|
* src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to |
3353 |
|
|
estimate avaliable memory |
3354 |
|
|
|
3355 |
gezelter |
2199 |
2005-02-16 15:30 tim |
3356 |
tim |
2102 |
|
3357 |
|
|
* src/: applications/staticProps/GofAngle2.cpp, |
3358 |
|
|
applications/staticProps/GofAngle2.hpp, |
3359 |
|
|
applications/staticProps/GofR.cpp, |
3360 |
|
|
applications/staticProps/GofR.hpp, |
3361 |
|
|
applications/staticProps/GofRAngle.cpp, |
3362 |
|
|
applications/staticProps/GofRAngle.hpp, |
3363 |
|
|
applications/staticProps/GofXyz.cpp, |
3364 |
|
|
applications/staticProps/GofXyz.hpp, |
3365 |
|
|
applications/staticProps/StaticProps.cpp, |
3366 |
|
|
applications/staticProps/StaticProps.ggo, |
3367 |
|
|
applications/staticProps/StaticPropsCmd.c, |
3368 |
|
|
applications/staticProps/StaticPropsCmd.h, |
3369 |
|
|
brains/BlockSnapshotManager.cpp: change the default bin number |
3370 |
|
|
|
3371 |
gezelter |
2199 |
2005-02-16 14:36 tim |
3372 |
tim |
2102 |
|
3373 |
|
|
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
3374 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
3375 |
|
|
applications/dynamicProps/TimeCorrFunc.cpp, |
3376 |
|
|
applications/dynamicProps/VCorrFunc.cpp, |
3377 |
|
|
applications/staticProps/GofAngle2.cpp, |
3378 |
|
|
applications/staticProps/GofR.cpp, |
3379 |
|
|
applications/staticProps/GofR.hpp, |
3380 |
|
|
applications/staticProps/GofRAngle.cpp, |
3381 |
|
|
applications/staticProps/GofRAngle.hpp, |
3382 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
3383 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
3384 |
|
|
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
3385 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output |
3386 |
|
|
files;fix the problem of counting in staticProps |
3387 |
|
|
|
3388 |
gezelter |
2199 |
2005-02-15 14:39 tim |
3389 |
tim |
2102 |
|
3390 |
|
|
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
3391 |
|
|
BlockSnapshotManager |
3392 |
|
|
|
3393 |
gezelter |
2199 |
2005-02-15 14:36 tim |
3394 |
tim |
2102 |
|
3395 |
|
|
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
3396 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
3397 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
3398 |
|
|
selection/SelectionEvaluator.cpp: BlockSnapshotManager is using |
3399 |
|
|
reference counting now |
3400 |
|
|
|
3401 |
gezelter |
2199 |
2005-02-15 12:49 tim |
3402 |
tim |
2102 |
|
3403 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
3404 |
|
|
replace std::make_pair by VariablesType::value_type to make Sun |
3405 |
|
|
Compiler happy |
3406 |
|
|
|
3407 |
gezelter |
2199 |
2005-02-15 12:35 tim |
3408 |
tim |
2102 |
|
3409 |
|
|
* src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to |
3410 |
|
|
TokenMap, using TokenMapType::value_type instead of std::make_pair |
3411 |
|
|
to make Sun compiler happy |
3412 |
|
|
|
3413 |
gezelter |
2199 |
2005-02-15 12:24 tim |
3414 |
tim |
2102 |
|
3415 |
|
|
* src/applications/staticProps/: GofRAngle.cpp, |
3416 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps |
3417 |
|
|
|
3418 |
gezelter |
2199 |
2005-02-15 12:11 tim |
3419 |
tim |
2102 |
|
3420 |
|
|
* src/: applications/staticProps/GofR.cpp, |
3421 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
3422 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
3423 |
|
|
brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding |
3424 |
|
|
#ifdef __RWSTD to make sun compiler happy (2) fix pair density |
3425 |
|
|
calculation problem when two selections intersect with each other |
3426 |
|
|
|
3427 |
gezelter |
2199 |
2005-02-15 10:24 gezelter |
3428 |
tim |
2102 |
|
3429 |
|
|
* src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy |
3430 |
|
|
xlc++ |
3431 |
|
|
|
3432 |
gezelter |
2199 |
2005-02-15 10:17 gezelter |
3433 |
tim |
2102 |
|
3434 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
3435 |
|
|
src/utils/residentMem.c: [no log message] |
3436 |
|
|
|
3437 |
gezelter |
2199 |
2005-02-15 01:17 gezelter |
3438 |
tim |
2102 |
|
3439 |
|
|
* src/utils/residentMem.c: bug fix for null termination |
3440 |
|
|
|
3441 |
gezelter |
2199 |
2005-02-15 01:11 gezelter |
3442 |
tim |
2102 |
|
3443 |
|
|
* configure, ac-tools/configure.in, src/utils/residentMem.c: |
3444 |
|
|
bugfixing residentMem |
3445 |
|
|
|
3446 |
gezelter |
2199 |
2005-02-15 00:59 gezelter |
3447 |
tim |
2102 |
|
3448 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
3449 |
|
|
src/utils/residentMem.c: bugfixes for residentMem on LINUX |
3450 |
|
|
|
3451 |
gezelter |
2199 |
2005-02-15 00:08 gezelter |
3452 |
tim |
2102 |
|
3453 |
|
|
* src/utils/Makefile.in: added residentMem |
3454 |
|
|
|
3455 |
gezelter |
2199 |
2005-02-15 00:05 gezelter |
3456 |
tim |
2102 |
|
3457 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in, |
3458 |
|
|
src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, |
3459 |
|
|
src/utils/residentMem.h: modifications to estimate memory in use by |
3460 |
|
|
other processes autoconf fixes ps syntax checking config.h file |
3461 |
|
|
cleaning |
3462 |
|
|
|
3463 |
gezelter |
2199 |
2005-02-14 18:26 gezelter |
3464 |
tim |
2102 |
|
3465 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in: ps niceness |
3466 |
|
|
|
3467 |
gezelter |
2199 |
2005-02-14 18:16 gezelter |
3468 |
tim |
2102 |
|
3469 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps |
3470 |
|
|
strangeness |
3471 |
|
|
|
3472 |
gezelter |
2199 |
2005-02-14 14:42 tim |
3473 |
tim |
2102 |
|
3474 |
|
|
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
3475 |
|
|
BlockSnapshotManager.hpp |
3476 |
|
|
|
3477 |
gezelter |
2199 |
2005-02-14 13:51 tim |
3478 |
tim |
2102 |
|
3479 |
|
|
* src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, |
3480 |
|
|
StaticPropsCmd.c: default length for staticProps is 1/2 smallest |
3481 |
|
|
length of first frame |
3482 |
|
|
|
3483 |
gezelter |
2199 |
2005-02-14 13:12 tim |
3484 |
tim |
2102 |
|
3485 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: fix a bug in |
3486 |
|
|
VelocityVerletIntegrator : last frame is written twice |
3487 |
|
|
|
3488 |
gezelter |
2199 |
2005-02-14 12:57 tim |
3489 |
tim |
2102 |
|
3490 |
|
|
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
3491 |
|
|
brains/SimInfo.cpp, primitives/RigidBody.cpp, |
3492 |
|
|
primitives/StuntDouble.hpp: begin bug fix |
3493 |
|
|
|
3494 |
gezelter |
2199 |
2005-02-14 12:35 tim |
3495 |
tim |
2102 |
|
3496 |
|
|
* src/applications/dynamicProps/: CorrelationFunction.cpp, |
3497 |
|
|
CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, |
3498 |
|
|
CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp, |
3499 |
|
|
DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile, |
3500 |
|
|
ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp, |
3501 |
|
|
RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, |
3502 |
|
|
VCorrFunc.hpp: refactory CorrelationFunction |
3503 |
|
|
|
3504 |
gezelter |
2199 |
2005-02-14 10:18 gezelter |
3505 |
tim |
2102 |
|
3506 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: bug fix |
3507 |
|
|
and start of switch for type of correlation function |
3508 |
|
|
|
3509 |
gezelter |
2199 |
2005-02-13 16:18 tim |
3510 |
tim |
2102 |
|
3511 |
|
|
* src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in |
3512 |
|
|
calculating bytes per stuntdouble |
3513 |
|
|
|
3514 |
gezelter |
2199 |
2005-02-13 16:03 tim |
3515 |
tim |
2102 |
|
3516 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: more fix |
3517 |
|
|
|
3518 |
gezelter |
2199 |
2005-02-13 15:57 tim |
3519 |
tim |
2102 |
|
3520 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: fixed a |
3521 |
|
|
bug in CorrelationFunction |
3522 |
|
|
|
3523 |
gezelter |
2199 |
2005-02-13 15:36 tim |
3524 |
tim |
2102 |
|
3525 |
|
|
* src/: applications/staticProps/GofR.cpp, |
3526 |
|
|
applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a |
3527 |
|
|
bug in SimInfo::getCutoff() |
3528 |
|
|
|
3529 |
gezelter |
2199 |
2005-02-13 15:08 tim |
3530 |
tim |
2102 |
|
3531 |
|
|
* make/Makefile.in: adding staticProps and dynamicProps into |
3532 |
|
|
Makefile.in |
3533 |
|
|
|
3534 |
gezelter |
2199 |
2005-02-13 15:05 tim |
3535 |
tim |
2102 |
|
3536 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
3537 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
3538 |
|
|
applications/staticProps/StaticProps.cpp, |
3539 |
|
|
applications/staticProps/StaticProps.ggo, |
3540 |
|
|
applications/staticProps/StaticPropsCmd.c, |
3541 |
|
|
applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp, |
3542 |
|
|
brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length |
3543 |
|
|
defaults to the cutoff radius |
3544 |
|
|
|
3545 |
gezelter |
2199 |
2005-02-13 14:14 tim |
3546 |
tim |
2102 |
|
3547 |
|
|
* src/utils/Algorithm.hpp: adding Algorithm.hpp |
3548 |
|
|
|
3549 |
gezelter |
2199 |
2005-02-13 14:10 tim |
3550 |
tim |
2102 |
|
3551 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
3552 |
|
|
applications/dynamicProps/CorrelationFunction.cpp, |
3553 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
3554 |
|
|
applications/dynamicProps/DynamicProps.cpp, |
3555 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
3556 |
|
|
integrators/Integrator.cpp, integrators/Integrator.hpp, |
3557 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
3558 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp, |
3559 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp, |
3560 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, |
3561 |
|
|
visitors/OtherVisitor.cpp: dynamicProps get built |
3562 |
|
|
|
3563 |
gezelter |
2199 |
2005-02-13 10:56 tim |
3564 |
tim |
2102 |
|
3565 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
3566 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
3567 |
|
|
brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in |
3568 |
|
|
progress |
3569 |
|
|
|
3570 |
gezelter |
2199 |
2005-02-13 03:04 tim |
3571 |
tim |
2102 |
|
3572 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.hpp, |
3573 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
3574 |
|
|
brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
3575 |
|
|
brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more |
3576 |
|
|
work in dynamicProps |
3577 |
|
|
|
3578 |
gezelter |
2199 |
2005-02-13 02:25 tim |
3579 |
tim |
2102 |
|
3580 |
|
|
* src/applications/dynamicProps/DynamicProps.cpp: adding |
3581 |
|
|
dynamicProps |
3582 |
|
|
|
3583 |
gezelter |
2199 |
2005-02-13 02:14 tim |
3584 |
tim |
2102 |
|
3585 |
|
|
* src/applications/dynamicProps/: DynamicPropsCmd.c, |
3586 |
|
|
DynamicPropsCmd.h: adding command line option to DynamicProps |
3587 |
|
|
|
3588 |
gezelter |
2199 |
2005-02-13 02:13 tim |
3589 |
tim |
2102 |
|
3590 |
|
|
* src/applications/dynamicProps/: DynamicProps.ggo, Makefile: |
3591 |
|
|
adding command line option for DynamicProps |
3592 |
|
|
|
3593 |
gezelter |
2199 |
2005-02-13 01:57 tim |
3594 |
tim |
2102 |
|
3595 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
3596 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
3597 |
|
|
applications/dynamicProps/DipoleCorrFunc.cpp, |
3598 |
|
|
applications/dynamicProps/DipoleCorrFunc.hpp, |
3599 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
3600 |
|
|
applications/dynamicProps/RCorrFunc.hpp, |
3601 |
|
|
applications/dynamicProps/VCorrFunc.cpp, |
3602 |
|
|
applications/dynamicProps/VCorrFunc.hpp, |
3603 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
3604 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
3605 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
3606 |
|
|
brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
3607 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding |
3608 |
|
|
dynamicProps |
3609 |
|
|
|
3610 |
gezelter |
2199 |
2005-02-12 15:09 tim |
3611 |
tim |
2102 |
|
3612 |
|
|
* src/selection/SelectionManager.cpp: adding SelectionManager.cpp |
3613 |
|
|
|
3614 |
gezelter |
2199 |
2005-02-11 17:41 tim |
3615 |
tim |
2102 |
|
3616 |
|
|
* src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one |
3617 |
|
|
more constructor to Snapshot to create customized DataStorage |
3618 |
|
|
|
3619 |
gezelter |
2199 |
2005-02-11 17:39 tim |
3620 |
tim |
2102 |
|
3621 |
|
|
* src/selection/: DistanceFinder.hpp, Makefile, |
3622 |
|
|
SelectionManager.hpp: adding beginSelected, nextSelected method to |
3623 |
|
|
SelectionManager |
3624 |
|
|
|
3625 |
gezelter |
2199 |
2005-02-11 17:36 tim |
3626 |
tim |
2102 |
|
3627 |
|
|
* src/config.h.in, configure: adding support for physmem |
3628 |
|
|
|
3629 |
gezelter |
2199 |
2005-02-11 17:35 tim |
3630 |
tim |
2102 |
|
3631 |
|
|
* ac-tools/configure.in: adding supprot for physmem |
3632 |
|
|
|
3633 |
gezelter |
2199 |
2005-02-11 17:35 tim |
3634 |
tim |
2102 |
|
3635 |
|
|
* src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding |
3636 |
|
|
physmem |
3637 |
|
|
|
3638 |
gezelter |
2199 |
2005-02-10 17:37 tim |
3639 |
tim |
2102 |
|
3640 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
3641 |
|
|
GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, |
3642 |
|
|
GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
3643 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
3644 |
|
|
StaticPropsCmd.h: more work in StaticProps |
3645 |
|
|
|
3646 |
gezelter |
2199 |
2005-02-10 13:14 tim |
3647 |
tim |
2102 |
|
3648 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
3649 |
|
|
GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, |
3650 |
|
|
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp, |
3651 |
|
|
Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
3652 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
3653 |
|
|
StaticPropsCmd.h: change the filenames |
3654 |
|
|
|
3655 |
gezelter |
2199 |
2005-02-10 09:15 tim |
3656 |
tim |
2102 |
|
3657 |
|
|
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
3658 |
|
|
GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, |
3659 |
|
|
RadialDistrFunc.hpp: adding GofRAngle |
3660 |
|
|
|
3661 |
gezelter |
2199 |
2005-02-09 13:21 tim |
3662 |
tim |
2102 |
|
3663 |
|
|
* src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some |
3664 |
|
|
useless files |
3665 |
|
|
|
3666 |
gezelter |
2199 |
2005-02-09 13:12 tim |
3667 |
tim |
2102 |
|
3668 |
|
|
* src/applications/staticProps/: GofR.cpp, Makefile, |
3669 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress |
3670 |
|
|
|
3671 |
gezelter |
2199 |
2005-02-09 12:08 tim |
3672 |
tim |
2102 |
|
3673 |
|
|
* src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, |
3674 |
|
|
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, |
3675 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR |
3676 |
|
|
|
3677 |
gezelter |
2199 |
2005-02-07 17:39 tim |
3678 |
tim |
2102 |
|
3679 |
|
|
* src/primitives/Molecule.hpp: add getRigidBodyAt function into |
3680 |
|
|
Molecule class |
3681 |
|
|
|
3682 |
gezelter |
2199 |
2005-02-07 17:38 tim |
3683 |
tim |
2102 |
|
3684 |
|
|
* src/applications/dump2Xyz/Dump2XYZCmd.c: update help info |
3685 |
|
|
|
3686 |
gezelter |
2199 |
2005-02-07 17:36 tim |
3687 |
tim |
2102 |
|
3688 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
3689 |
|
|
SelectionCompiler.cpp: support select internal index selection, for |
3690 |
|
|
example, select DMPC.3 |
3691 |
|
|
|
3692 |
gezelter |
2199 |
2005-02-07 16:11 tim |
3693 |
tim |
2102 |
|
3694 |
|
|
* src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update |
3695 |
|
|
help info for Dump2XYZ |
3696 |
|
|
|
3697 |
gezelter |
2199 |
2005-02-07 15:39 chrisfen |
3698 |
tim |
2102 |
|
3699 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
3700 |
|
|
selection librarys added |
3701 |
|
|
|
3702 |
gezelter |
2199 |
2005-02-07 15:31 tim |
3703 |
tim |
2102 |
|
3704 |
|
|
* src/selection/Makefile, make/Makefile.in: adding Makefile |
3705 |
|
|
|
3706 |
gezelter |
2199 |
2005-02-07 15:20 chrisfen |
3707 |
tim |
2102 |
|
3708 |
|
|
* src/utils/wildcards.hpp: issue commented out in wildcards |
3709 |
|
|
|
3710 |
gezelter |
2199 |
2005-02-07 15:06 tim |
3711 |
tim |
2102 |
|
3712 |
|
|
* src/selection/SelectionEvaluator.cpp: forget to reset the pc |
3713 |
|
|
which cause reevaluate return NULL |
3714 |
|
|
|
3715 |
gezelter |
2199 |
2005-02-07 14:14 tim |
3716 |
tim |
2102 |
|
3717 |
|
|
* src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, |
3718 |
|
|
SimSnapshotManager.hpp: fix a bug in determing the global index for |
3719 |
|
|
rigidbodies |
3720 |
|
|
|
3721 |
gezelter |
2199 |
2005-02-07 14:13 tim |
3722 |
tim |
2102 |
|
3723 |
|
|
* src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change |
3724 |
|
|
in Bitset |
3725 |
|
|
|
3726 |
gezelter |
2199 |
2005-02-07 14:13 tim |
3727 |
tim |
2102 |
|
3728 |
|
|
* src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, |
3729 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
3730 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, |
3731 |
|
|
TokenMap.cpp: selection library is working |
3732 |
|
|
|
3733 |
gezelter |
2199 |
2005-02-04 17:46 tim |
3734 |
tim |
2102 |
|
3735 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor |
3736 |
|
|
|
3737 |
gezelter |
2199 |
2005-02-04 17:45 tim |
3738 |
tim |
2102 |
|
3739 |
|
|
* src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor |
3740 |
|
|
and XYZVisitor now use selection library |
3741 |
|
|
|
3742 |
gezelter |
2199 |
2005-02-04 17:44 tim |
3743 |
tim |
2102 |
|
3744 |
|
|
* src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: |
3745 |
|
|
adding SelectionManager into SimInfo |
3746 |
|
|
|
3747 |
gezelter |
2199 |
2005-02-04 17:43 tim |
3748 |
tim |
2102 |
|
3749 |
|
|
* src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, |
3750 |
|
|
Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of |
3751 |
|
|
selection library |
3752 |
|
|
|
3753 |
gezelter |
2199 |
2005-02-04 17:42 tim |
3754 |
tim |
2102 |
|
3755 |
|
|
* src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change |
3756 |
|
|
in BitSet |
3757 |
|
|
|
3758 |
gezelter |
2199 |
2005-02-04 17:41 tim |
3759 |
tim |
2102 |
|
3760 |
|
|
* src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing |
3761 |
|
|
implementation |
3762 |
|
|
|
3763 |
gezelter |
2199 |
2005-02-04 17:39 tim |
3764 |
tim |
2102 |
|
3765 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
3766 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
3767 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
3768 |
|
|
SelectionManager.hpp, Token.hpp: half of the selection utility is |
3769 |
|
|
working need to debug within keyword and atomproperty keyword |
3770 |
|
|
|
3771 |
gezelter |
2199 |
2005-02-04 00:42 tim |
3772 |
tim |
2102 |
|
3773 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp: selection library |
3774 |
|
|
get built |
3775 |
|
|
|
3776 |
gezelter |
2199 |
2005-02-04 00:42 tim |
3777 |
tim |
2102 |
|
3778 |
|
|
* src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet |
3779 |
|
|
|
3780 |
gezelter |
2199 |
2005-02-04 00:26 tim |
3781 |
tim |
2102 |
|
3782 |
|
|
* src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: |
3783 |
|
|
remove some useless files |
3784 |
|
|
|
3785 |
gezelter |
2199 |
2005-02-03 23:57 tim |
3786 |
tim |
2102 |
|
3787 |
|
|
* src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, |
3788 |
|
|
selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: |
3789 |
|
|
adding wildcard class; NameFinder is finished |
3790 |
|
|
|
3791 |
gezelter |
2199 |
2005-02-03 18:14 tim |
3792 |
tim |
2102 |
|
3793 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
3794 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
3795 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
3796 |
|
|
SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in |
3797 |
|
|
selection library |
3798 |
|
|
|
3799 |
gezelter |
2199 |
2005-02-03 09:04 tim |
3800 |
tim |
2102 |
|
3801 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
3802 |
|
|
selection in progress |
3803 |
|
|
|
3804 |
gezelter |
2199 |
2005-02-02 18:13 tim |
3805 |
tim |
2102 |
|
3806 |
|
|
* src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, |
3807 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, |
3808 |
|
|
Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in |
3809 |
|
|
progress, except SelectionEvaluator, other files are compiled |
3810 |
|
|
|
3811 |
gezelter |
2199 |
2005-02-02 18:12 tim |
3812 |
tim |
2102 |
|
3813 |
|
|
* src/utils/: Makefile.in, any.hpp: adding boost::any |
3814 |
|
|
|
3815 |
gezelter |
2199 |
2005-02-02 07:51 tim |
3816 |
tim |
2102 |
|
3817 |
|
|
* src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp |
3818 |
|
|
|
3819 |
gezelter |
2199 |
2005-02-01 17:49 tim |
3820 |
tim |
2102 |
|
3821 |
|
|
* src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, |
3822 |
|
|
selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, |
3823 |
|
|
selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, |
3824 |
|
|
selection/Token.hpp: Selection in progress |
3825 |
|
|
|
3826 |
gezelter |
2199 |
2005-02-01 01:55 tim |
3827 |
tim |
2102 |
|
3828 |
|
|
* src/: selection/SelectionCompiler.hpp, |
3829 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
3830 |
|
|
selection/SelectionManager.hpp, selection/Token.hpp, |
3831 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp: adding selection library |
3832 |
|
|
|
3833 |
gezelter |
2199 |
2005-01-26 10:26 tim |
3834 |
tim |
2102 |
|
3835 |
|
|
* src/integrators/: Integrator.cpp, Integrator.hpp, |
3836 |
|
|
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget |
3837 |
|
|
to add eorWriter |
3838 |
|
|
|
3839 |
gezelter |
2199 |
2005-01-26 10:15 tim |
3840 |
tim |
2102 |
|
3841 |
|
|
* src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: |
3842 |
|
|
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the |
3843 |
|
|
wrong column of electroframe |
3844 |
|
|
|
3845 |
gezelter |
2199 |
2005-01-25 16:59 tim |
3846 |
tim |
2102 |
|
3847 |
|
|
* src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in |
3848 |
|
|
SimInfo, use number of cutoff stamp as counter to loop over |
3849 |
|
|
rigidbody stamp |
3850 |
|
|
|
3851 |
gezelter |
2199 |
2005-01-25 12:45 tim |
3852 |
tim |
2102 |
|
3853 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
3854 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
3855 |
|
|
integrators/DLM.cpp, io/AtomTypesSectionParser.cpp, |
3856 |
|
|
io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, |
3857 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp, |
3858 |
|
|
io/EAMAtomTypesSectionParser.cpp, |
3859 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp, |
3860 |
|
|
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
3861 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
3862 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
3863 |
|
|
math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp, |
3864 |
|
|
primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp, |
3865 |
|
|
primitives/GhostTorsion.hpp, primitives/Makefile, |
3866 |
|
|
primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete |
3867 |
|
|
section parser's error message (2) add GhostTorsion (3) accumulate |
3868 |
|
|
inertial tensor from the directional atoms before calculate |
3869 |
|
|
rigidbody's inertial tensor |
3870 |
|
|
|
3871 |
gezelter |
2199 |
2005-01-17 17:17 tim |
3872 |
tim |
2102 |
|
3873 |
|
|
* forceFields/DUFF2.frc: forget to set dipole for lipid head group |
3874 |
|
|
|
3875 |
gezelter |
2199 |
2005-01-17 11:58 tim |
3876 |
tim |
2102 |
|
3877 |
|
|
* src/integrators/NVT.cpp: fix a bug in loading initial extended |
3878 |
|
|
system parameters |
3879 |
|
|
|
3880 |
gezelter |
2199 |
2005-01-17 11:05 tim |
3881 |
tim |
2102 |
|
3882 |
|
|
* src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT |
3883 |
|
|
|
3884 |
gezelter |
2199 |
2005-01-14 17:02 tim |
3885 |
tim |
2102 |
|
3886 |
|
|
* src/UseTheForce/WATER.cpp: remove WATER.cpp |
3887 |
|
|
|
3888 |
gezelter |
2199 |
2005-01-14 16:37 tim |
3889 |
tim |
2102 |
|
3890 |
|
|
* forceFields/Makefile: sync Makefile |
3891 |
|
|
|
3892 |
gezelter |
2199 |
2005-01-14 16:13 gezelter |
3893 |
tim |
2102 |
|
3894 |
|
|
* make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, |
3895 |
|
|
src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, |
3896 |
|
|
src/applications/dump2Xyz/Makefile, |
3897 |
|
|
src/applications/oopse/Makefile, |
3898 |
|
|
src/applications/simpleBuilder/Makefile, src/brains/Makefile, |
3899 |
|
|
src/constraints/Makefile, src/integrators/Makefile, |
3900 |
|
|
src/io/Makefile, src/math/Makefile, src/minimizers/Makefile, |
3901 |
|
|
src/primitives/Makefile, src/profiling/Makefile, |
3902 |
|
|
src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in, |
3903 |
|
|
src/visitors/Makefile: moved Package variable into subdirectory |
3904 |
|
|
makefiles to speed up the building process |
3905 |
|
|
|
3906 |
gezelter |
2199 |
2005-01-14 15:48 gezelter |
3907 |
tim |
2102 |
|
3908 |
|
|
* src/applications/oopse/oopse.cpp: Fixed publication details in |
3909 |
|
|
banner |
3910 |
|
|
|
3911 |
gezelter |
2199 |
2005-01-14 15:48 gezelter |
3912 |
tim |
2102 |
|
3913 |
|
|
* src/UseTheForce/DarkSide/: simParallel_interface.F90, |
3914 |
|
|
simParallel_interface.h: added dummy subroutine to avoid empty |
3915 |
|
|
unit, synchronized this dummy routine between C and fortran |
3916 |
|
|
|
3917 |
gezelter |
2199 |
2005-01-14 15:31 gezelter |
3918 |
tim |
2102 |
|
3919 |
|
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, |
3920 |
|
|
notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, |
3921 |
|
|
DarkSide/Makefile, DarkSide/atype.F90, |
3922 |
|
|
DarkSide/atype_interface.F90, DarkSide/charge.F90, |
3923 |
|
|
DarkSide/charge_interface.F90, DarkSide/dipole.F90, |
3924 |
|
|
DarkSide/dipole_interface.F90, DarkSide/eam.F90, |
3925 |
|
|
DarkSide/eam_interface.F90, DarkSide/gb.F90, |
3926 |
|
|
DarkSide/gb_interface.F90, DarkSide/lj_interface.F90, |
3927 |
|
|
DarkSide/shapes.F90, DarkSide/shapes_interface.F90, |
3928 |
|
|
DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90, |
3929 |
|
|
DarkSide/simulation.F90, DarkSide/simulation_interface.F90, |
3930 |
|
|
DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating |
3931 |
|
|
modules and C/Fortran interface subroutines |
3932 |
|
|
|
3933 |
gezelter |
2199 |
2005-01-14 15:15 gezelter |
3934 |
tim |
2102 |
|
3935 |
|
|
* configure, ac-tools/aclocal.m4: more fixes for gnugetopt |
3936 |
|
|
|
3937 |
gezelter |
2199 |
2005-01-14 15:09 gezelter |
3938 |
tim |
2102 |
|
3939 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
3940 |
|
|
src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt |
3941 |
|
|
|
3942 |
gezelter |
2199 |
2005-01-14 11:49 tim |
3943 |
tim |
2102 |
|
3944 |
|
|
* src/: io/EAMAtomTypesSectionParser.cpp, |
3945 |
|
|
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
3946 |
|
|
utils/StringUtils.hpp: using c library to do conversion instead of |
3947 |
|
|
using iostream due to a bug in libstdc++(GCC 3.2) |
3948 |
|
|
|
3949 |
gezelter |
2199 |
2005-01-13 21:40 tim |
3950 |
tim |
2102 |
|
3951 |
|
|
* src/brains/SimSetup.cpp: no message |
3952 |
|
|
|
3953 |
gezelter |
2199 |
2005-01-13 20:56 tim |
3954 |
tim |
2102 |
|
3955 |
|
|
* src/primitives/Molecule.hpp: fix a bug in global index |
3956 |
|
|
|
3957 |
gezelter |
2199 |
2005-01-13 20:04 tim |
3958 |
tim |
2102 |
|
3959 |
|
|
* src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include |
3960 |
|
|
Integrator.hpp in Minimizer |
3961 |
|
|
|
3962 |
gezelter |
2199 |
2005-01-13 17:14 gezelter |
3963 |
tim |
2102 |
|
3964 |
|
|
* src/utils/Makefile: compile getopt and getopt1 if we need to |
3965 |
|
|
|
3966 |
gezelter |
2199 |
2005-01-13 16:56 gezelter |
3967 |
tim |
2102 |
|
3968 |
|
|
* make/Makefile.in: template flags |
3969 |
|
|
|
3970 |
gezelter |
2199 |
2005-01-13 16:48 gezelter |
3971 |
tim |
2102 |
|
3972 |
|
|
* src/applications/oopse/Makefile: formatting |
3973 |
|
|
|
3974 |
gezelter |
2199 |
2005-01-13 16:48 gezelter |
3975 |
tim |
2102 |
|
3976 |
|
|
* make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir |
3977 |
|
|
target |
3978 |
|
|
|
3979 |
gezelter |
2199 |
2005-01-13 14:40 tim |
3980 |
tim |
2102 |
|
3981 |
|
|
* src/: UseTheForce/fSwitchingFunction.h, |
3982 |
|
|
UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, |
3983 |
|
|
math/Makefile, math/RectMatrix.hpp, math/Vector.hpp, |
3984 |
|
|
primitives/RigidBody.cpp, types/AtomTypeProperties.h, |
3985 |
|
|
types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform |
3986 |
|
|
|
3987 |
gezelter |
2199 |
2005-01-13 13:26 tim |
3988 |
tim |
2102 |
|
3989 |
|
|
* make/Makefile.in: change the order of linking (object file comes |
3990 |
|
|
first and then follow by user built library) |
3991 |
|
|
|
3992 |
gezelter |
2199 |
2005-01-12 18:24 tim |
3993 |
tim |
2102 |
|
3994 |
|
|
* src/io/DumpWriter.cpp: remove useless debug info |
3995 |
|
|
|
3996 |
gezelter |
2199 |
2005-01-12 18:21 tim |
3997 |
tim |
2102 |
|
3998 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix |
3999 |
|
|
|
4000 |
gezelter |
2199 |
2005-01-12 18:17 tim |
4001 |
tim |
2102 |
|
4002 |
|
|
* make/: Makefile.in, Makefile.in: missing tab |
4003 |
|
|
|
4004 |
gezelter |
2199 |
2005-01-12 18:15 tim |
4005 |
tim |
2102 |
|
4006 |
|
|
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor |
4007 |
|
|
get fixed |
4008 |
|
|
|
4009 |
gezelter |
2199 |
2005-01-12 17:40 gezelter |
4010 |
tim |
2102 |
|
4011 |
|
|
* make/Makefile.in, src/UseTheForce/DUFF.cpp, |
4012 |
|
|
src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, |
4013 |
|
|
src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp, |
4014 |
|
|
src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, |
4015 |
|
|
src/UseTheForce/ForceFieldCreator.hpp, |
4016 |
|
|
src/UseTheForce/ForceFieldFactory.cpp, |
4017 |
|
|
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp, |
4018 |
|
|
src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp, |
4019 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h, |
4020 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
4021 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
4022 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
4023 |
|
|
src/UseTheForce/notifyCutoffs.F90, |
4024 |
|
|
src/UseTheForce/notifyCutoffs_interface.h, |
4025 |
|
|
src/UseTheForce/DarkSide/LJ.F90, |
4026 |
|
|
src/UseTheForce/DarkSide/atype.F90, |
4027 |
|
|
src/UseTheForce/DarkSide/atype_interface.h, |
4028 |
|
|
src/UseTheForce/DarkSide/charge.F90, |
4029 |
|
|
src/UseTheForce/DarkSide/charge_interface.h, |
4030 |
|
|
src/UseTheForce/DarkSide/dipole.F90, |
4031 |
|
|
src/UseTheForce/DarkSide/dipole_interface.h, |
4032 |
|
|
src/UseTheForce/DarkSide/eam.F90, |
4033 |
|
|
src/UseTheForce/DarkSide/eam_interface.h, |
4034 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
4035 |
|
|
src/UseTheForce/DarkSide/gb.F90, |
4036 |
|
|
src/UseTheForce/DarkSide/gb_interface.h, |
4037 |
|
|
src/UseTheForce/DarkSide/lj_interface.h, |
4038 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
4039 |
|
|
src/UseTheForce/DarkSide/reactionField.F90, |
4040 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
4041 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
4042 |
|
|
src/UseTheForce/DarkSide/simParallel.F90, |
4043 |
|
|
src/UseTheForce/DarkSide/simParallel_interface.h, |
4044 |
|
|
src/UseTheForce/DarkSide/simulation.F90, |
4045 |
|
|
src/UseTheForce/DarkSide/simulation_interface.h, |
4046 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
4047 |
|
|
src/UseTheForce/DarkSide/sticky_interface.h, |
4048 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90, |
4049 |
|
|
src/applications/Makedepend, src/applications/quickLate.c, |
4050 |
|
|
src/applications/dump2Xyz/Dump2XYZ.cpp, |
4051 |
|
|
src/applications/oopse/oopse.cpp, |
4052 |
|
|
src/applications/simpleBuilder/BaseLattice.cpp, |
4053 |
|
|
src/applications/simpleBuilder/BaseLattice.hpp, |
4054 |
|
|
src/applications/simpleBuilder/Lattice.cpp, |
4055 |
|
|
src/applications/simpleBuilder/Lattice.hpp, |
4056 |
|
|
src/applications/simpleBuilder/LatticeCreator.cpp, |
4057 |
|
|
src/applications/simpleBuilder/LatticeCreator.hpp, |
4058 |
|
|
src/applications/simpleBuilder/LatticeFactory.cpp, |
4059 |
|
|
src/applications/simpleBuilder/LatticeFactory.hpp, |
4060 |
|
|
src/applications/simpleBuilder/MoLocator.cpp, |
4061 |
|
|
src/applications/simpleBuilder/MoLocator.hpp, |
4062 |
|
|
src/applications/simpleBuilder/simpleBuilder.cpp, |
4063 |
|
|
src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, |
4064 |
|
|
src/brains/Exclude.cpp, src/brains/Exclude.hpp, |
4065 |
|
|
src/brains/ForceManager.cpp, src/brains/ForceManager.hpp, |
4066 |
|
|
src/brains/Makefile, src/brains/Migrator.hpp, |
4067 |
|
|
src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp, |
4068 |
|
|
src/brains/Register.cpp, src/brains/Register.hpp, |
4069 |
|
|
src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, |
4070 |
|
|
src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
4071 |
|
|
src/brains/SimModel.hpp, src/brains/SimSetup.hpp, |
4072 |
|
|
src/brains/SimSnapshotManager.cpp, |
4073 |
|
|
src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp, |
4074 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
4075 |
|
|
src/brains/SkipList.hpp, src/brains/Snapshot.cpp, |
4076 |
|
|
src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, |
4077 |
|
|
src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp, |
4078 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
4079 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
4080 |
|
|
src/constraints/AbstractClasses.hpp, |
4081 |
|
|
src/constraints/ConstraintElem.hpp, |
4082 |
|
|
src/constraints/ConstraintPair.hpp, src/constraints/Makefile, |
4083 |
|
|
src/constraints/Rattle.cpp, src/constraints/Rattle.hpp, |
4084 |
|
|
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
4085 |
|
|
src/constraints/ZconsStruct.hpp, |
4086 |
|
|
src/constraints/ZconstraintForceManager.cpp, |
4087 |
|
|
src/constraints/ZconstraintForceManager.hpp, |
4088 |
|
|
src/integrators/AbstractClasses.hpp, |
4089 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp, |
4090 |
|
|
src/integrators/DLM.hpp, src/integrators/Integrator.cpp, |
4091 |
|
|
src/integrators/Integrator.hpp, |
4092 |
|
|
src/integrators/IntegratorCreator.hpp, |
4093 |
|
|
src/integrators/IntegratorFactory.cpp, |
4094 |
|
|
src/integrators/IntegratorFactory.hpp, src/integrators/Makefile, |
4095 |
|
|
src/integrators/NPT.cpp, src/integrators/NPT.hpp, |
4096 |
|
|
src/integrators/NPTf.cpp, src/integrators/NPTf.hpp, |
4097 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTi.hpp, |
4098 |
|
|
src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp, |
4099 |
|
|
src/integrators/NVE.cpp, src/integrators/NVE.hpp, |
4100 |
|
|
src/integrators/NVT.cpp, src/integrators/NVT.hpp, |
4101 |
|
|
src/integrators/RotationAlgorithm.hpp, |
4102 |
|
|
src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, |
4103 |
|
|
src/integrators/VelocityVerletIntegrator.cpp, |
4104 |
|
|
src/integrators/VelocityVerletIntegrator.hpp, |
4105 |
|
|
src/io/AtomTypesSectionParser.cpp, |
4106 |
|
|
src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp, |
4107 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
4108 |
|
|
src/io/BendTypesSectionParser.cpp, |
4109 |
|
|
src/io/BendTypesSectionParser.hpp, |
4110 |
|
|
src/io/BondTypesSectionParser.cpp, |
4111 |
|
|
src/io/BondTypesSectionParser.hpp, |
4112 |
|
|
src/io/DirectionalAtomTypesSectionParser.cpp, |
4113 |
|
|
src/io/DirectionalAtomTypesSectionParser.hpp, |
4114 |
|
|
src/io/DumpReader.cpp, src/io/DumpReader.hpp, |
4115 |
|
|
src/io/DumpWriter.cpp, src/io/DumpWriter.hpp, |
4116 |
|
|
src/io/EAMAtomTypesSectionParser.cpp, |
4117 |
|
|
src/io/EAMAtomTypesSectionParser.hpp, |
4118 |
|
|
src/io/ElectrostaticAtomTypesSectionParser.cpp, |
4119 |
|
|
src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp, |
4120 |
|
|
src/io/Globals.hpp, src/io/InitializeFromFile.cpp, |
4121 |
|
|
src/io/LennardJonesAtomTypesSectionParser.cpp, |
4122 |
|
|
src/io/LennardJonesAtomTypesSectionParser.hpp, |
4123 |
|
|
src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp, |
4124 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
4125 |
|
|
src/io/Makefile, src/io/SectionParser.cpp, |
4126 |
|
|
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
4127 |
|
|
src/io/SectionParserManager.hpp, src/io/StatWriter.cpp, |
4128 |
|
|
src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp, |
4129 |
|
|
src/io/StickyAtomTypesSectionParser.hpp, |
4130 |
|
|
src/io/TorsionTypesSectionParser.cpp, |
4131 |
|
|
src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp, |
4132 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
4133 |
|
|
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
4134 |
|
|
src/io/interface.c, src/io/make_nodes.c, src/io/make_nodes.h, |
4135 |
|
|
src/io/mpiBASS.c, src/io/mpiBASS.h, src/io/node_list.h, |
4136 |
|
|
src/io/parse_interface.h, src/io/parse_me.h, src/io/parse_tree.c, |
4137 |
|
|
src/io/parse_tree.h, src/math/ChebyshevPolynomials.cpp, |
4138 |
|
|
src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c, |
4139 |
|
|
src/math/MatVec3.h, src/math/Polynomial.hpp, |
4140 |
|
|
src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp, |
4141 |
|
|
src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp, |
4142 |
|
|
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
4143 |
|
|
src/math/Vector.hpp, src/math/Vector3.hpp, |
4144 |
|
|
src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp, |
4145 |
|
|
src/minimizers/CGFamilyMinimizer.cpp, |
4146 |
|
|
src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile, |
4147 |
|
|
src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp, |
4148 |
|
|
src/minimizers/MinimizerCreator.hpp, |
4149 |
|
|
src/minimizers/MinimizerFactory.cpp, |
4150 |
|
|
src/minimizers/MinimizerFactory.hpp, |
4151 |
|
|
src/minimizers/MinimizerParameterSet.cpp, |
4152 |
|
|
src/minimizers/MinimizerParameterSet.hpp, |
4153 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
4154 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
4155 |
|
|
src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp, |
4156 |
|
|
src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp, |
4157 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
4158 |
|
|
src/primitives/Bend.cpp, src/primitives/Bend.hpp, |
4159 |
|
|
src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp, |
4160 |
|
|
src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp, |
4161 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
4162 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
4163 |
|
|
src/primitives/GhostBend.hpp, src/primitives/Makefile, |
4164 |
|
|
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
4165 |
|
|
src/primitives/RigidBody.cpp, src/primitives/RigidBody.hpp, |
4166 |
|
|
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
4167 |
|
|
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
4168 |
|
|
src/primitives/Torsion.hpp, src/primitives/TorsionExtensions.cpp, |
4169 |
|
|
src/primitives/UreyBradleyBend.cpp, |
4170 |
|
|
src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, |
4171 |
|
|
src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp, |
4172 |
|
|
src/types/AtomStamp.hpp, src/types/AtomType.cpp, |
4173 |
|
|
src/types/AtomType.hpp, src/types/AtomTypeProperties.h, |
4174 |
|
|
src/types/BendStamp.cpp, src/types/BendStamp.hpp, |
4175 |
|
|
src/types/BendType.hpp, src/types/BondStamp.cpp, |
4176 |
|
|
src/types/BondStamp.hpp, src/types/BondType.hpp, |
4177 |
|
|
src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp, |
4178 |
|
|
src/types/Component.cpp, src/types/Component.hpp, |
4179 |
|
|
src/types/CubicBendType.hpp, src/types/CubicBondType.hpp, |
4180 |
|
|
src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp, |
4181 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp, |
4182 |
|
|
src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, |
4183 |
|
|
src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, |
4184 |
|
|
src/types/MakeStamps.cpp, src/types/MakeStamps.hpp, |
4185 |
|
|
src/types/Makefile, src/types/MoleculeStamp.cpp, |
4186 |
|
|
src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp, |
4187 |
|
|
src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp, |
4188 |
|
|
src/types/PolynomialBondType.hpp, |
4189 |
|
|
src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, |
4190 |
|
|
src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, |
4191 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
4192 |
|
|
src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, |
4193 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
4194 |
|
|
src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, |
4195 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
4196 |
|
|
src/utils/GenericData.hpp, src/utils/GenericFactory.hpp, |
4197 |
|
|
src/utils/LocalIndexManager.hpp, src/utils/Makefile, |
4198 |
|
|
src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp, |
4199 |
|
|
src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp, |
4200 |
|
|
src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp, |
4201 |
|
|
src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp, |
4202 |
|
|
src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp, |
4203 |
|
|
src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp, |
4204 |
|
|
src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp, |
4205 |
|
|
src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp, |
4206 |
|
|
src/utils/Utility.cpp, src/utils/Utility.hpp, |
4207 |
|
|
src/utils/definitions.F90, src/utils/fError.c, |
4208 |
|
|
src/utils/next_combination.hpp, src/utils/oopseMPI.F90, |
4209 |
|
|
src/utils/simError.c, src/utils/simError.h, src/utils/status.F90, |
4210 |
|
|
src/utils/vector_class.F90, src/visitors/AtomData.hpp, |
4211 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
4212 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
4213 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
4214 |
|
|
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
4215 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
4216 |
|
|
src/visitors/ZconsVisitor.hpp: merging new_design branch into |
4217 |
|
|
OOPSE-2.0 |
4218 |
|
|
|
4219 |
gezelter |
2199 |
2005-01-12 13:13 tim |
4220 |
tim |
2102 |
|
4221 |
|
|
* src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, |
4222 |
|
|
utils/TypeContainer.hpp: forget to include <algorithm> |
4223 |
|
|
|
4224 |
gezelter |
2199 |
2005-01-12 12:25 tim |
4225 |
tim |
2102 |
|
4226 |
|
|
* forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, |
4227 |
|
|
newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force |
4228 |
|
|
fields |
4229 |
|
|
|
4230 |
gezelter |
2199 |
2005-01-12 12:14 tim |
4231 |
tim |
2102 |
|
4232 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
4233 |
|
|
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
4234 |
|
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
4235 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
4236 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
4237 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
4238 |
|
|
UseTheForce/doForces.F90, UseTheForce/doForces_interface.h, |
4239 |
|
|
UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, |
4240 |
|
|
UseTheForce/notifyCutoffs.F90, |
4241 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
4242 |
|
|
UseTheForce/DarkSide/atype.F90, |
4243 |
|
|
UseTheForce/DarkSide/atype_interface.h, |
4244 |
|
|
UseTheForce/DarkSide/charge.F90, |
4245 |
|
|
UseTheForce/DarkSide/charge_interface.h, |
4246 |
|
|
UseTheForce/DarkSide/dipole.F90, |
4247 |
|
|
UseTheForce/DarkSide/dipole_interface.h, |
4248 |
|
|
UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h, |
4249 |
|
|
UseTheForce/DarkSide/force_globals.F90, |
4250 |
|
|
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
4251 |
|
|
UseTheForce/DarkSide/lj_interface.h, |
4252 |
|
|
UseTheForce/DarkSide/neighborLists.F90, |
4253 |
|
|
UseTheForce/DarkSide/reactionField.F90, |
4254 |
|
|
UseTheForce/DarkSide/shapes.F90, |
4255 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
4256 |
|
|
UseTheForce/DarkSide/simParallel.F90, |
4257 |
|
|
UseTheForce/DarkSide/simParallel_interface.h, |
4258 |
|
|
UseTheForce/DarkSide/simulation.F90, |
4259 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
4260 |
|
|
UseTheForce/DarkSide/sticky.F90, |
4261 |
|
|
UseTheForce/DarkSide/sticky_interface.h, |
4262 |
|
|
UseTheForce/DarkSide/switcheroo.F90, |
4263 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
4264 |
|
|
applications/simpleBuilder/BaseLattice.cpp, |
4265 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
4266 |
|
|
applications/simpleBuilder/Lattice.cpp, |
4267 |
|
|
applications/simpleBuilder/Lattice.hpp, |
4268 |
|
|
applications/simpleBuilder/LatticeCreator.cpp, |
4269 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
4270 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
4271 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
4272 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
4273 |
|
|
applications/simpleBuilder/MoLocator.hpp, |
4274 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
4275 |
|
|
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
4276 |
|
|
brains/Exclude.hpp, brains/ForceManager.cpp, |
4277 |
|
|
brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp, |
4278 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
4279 |
|
|
brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp, |
4280 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
4281 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
4282 |
|
|
brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp, |
4283 |
|
|
brains/Snapshot.cpp, brains/Snapshot.hpp, |
4284 |
|
|
brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp, |
4285 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h, |
4286 |
|
|
constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, |
4287 |
|
|
constraints/Rattle.cpp, constraints/Rattle.hpp, |
4288 |
|
|
constraints/ZconsStruct.hpp, |
4289 |
|
|
constraints/ZconstraintForceManager.cpp, |
4290 |
|
|
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
4291 |
|
|
integrators/DLM.hpp, integrators/Integrator.cpp, |
4292 |
|
|
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
4293 |
|
|
integrators/IntegratorFactory.cpp, |
4294 |
|
|
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
4295 |
|
|
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
4296 |
|
|
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
4297 |
|
|
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
4298 |
|
|
integrators/NVT.cpp, integrators/NVT.hpp, |
4299 |
|
|
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
4300 |
|
|
integrators/Velocitizer.hpp, |
4301 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
4302 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
4303 |
|
|
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
4304 |
|
|
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
4305 |
|
|
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
4306 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
4307 |
|
|
io/BondTypesSectionParser.hpp, |
4308 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
4309 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
4310 |
|
|
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
4311 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
4312 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
4313 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp, |
4314 |
|
|
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
4315 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
4316 |
|
|
io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp, |
4317 |
|
|
io/SectionParser.cpp, io/SectionParser.hpp, |
4318 |
|
|
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
4319 |
|
|
io/StatWriter.cpp, io/StatWriter.hpp, |
4320 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
4321 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
4322 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
4323 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
4324 |
|
|
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/interface.c, |
4325 |
|
|
io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, |
4326 |
|
|
io/node_list.h, io/parse_interface.h, io/parse_me.h, |
4327 |
|
|
io/parse_tree.c, io/parse_tree.h, math/ChebyshevPolynomials.cpp, |
4328 |
|
|
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
4329 |
|
|
math/Polynomial.hpp, math/Quaternion.hpp, |
4330 |
|
|
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
4331 |
|
|
math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp, |
4332 |
|
|
math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp, |
4333 |
|
|
math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp, |
4334 |
|
|
minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp, |
4335 |
|
|
minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp, |
4336 |
|
|
minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp, |
4337 |
|
|
minimizers/MinimizerParameterSet.cpp, |
4338 |
|
|
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
4339 |
|
|
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
4340 |
|
|
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
4341 |
|
|
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
4342 |
|
|
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
4343 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
4344 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
4345 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp, |
4346 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
4347 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
4348 |
|
|
primitives/Torsion.cpp, primitives/Torsion.hpp, |
4349 |
|
|
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
4350 |
|
|
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
4351 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp, |
4352 |
|
|
types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp, |
4353 |
|
|
types/AtomType.hpp, types/AtomTypeProperties.h, |
4354 |
|
|
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
4355 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
4356 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
4357 |
|
|
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
4358 |
|
|
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
4359 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
4360 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp, |
4361 |
|
|
types/FixedBondType.hpp, types/HarmonicBendType.hpp, |
4362 |
|
|
types/HarmonicBondType.hpp, types/MakeStamps.cpp, |
4363 |
|
|
types/MakeStamps.hpp, types/MoleculeStamp.cpp, |
4364 |
|
|
types/MoleculeStamp.hpp, types/MorseBondType.hpp, |
4365 |
|
|
types/OplsTorsionType.hpp, types/PolynomialBendType.hpp, |
4366 |
|
|
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
4367 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp, |
4368 |
|
|
types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp, |
4369 |
|
|
types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp, |
4370 |
|
|
types/ShapeAtomType.hpp, types/TorsionStamp.cpp, |
4371 |
|
|
types/TorsionStamp.hpp, types/TorsionType.hpp, |
4372 |
|
|
types/UreyBradleyBendType.hpp, types/ZconStamp.cpp, |
4373 |
|
|
types/ZconStamp.hpp, utils/GenericData.hpp, |
4374 |
|
|
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
4375 |
|
|
utils/MemoryUtils.hpp, utils/NumericConstant.hpp, |
4376 |
|
|
utils/OOPSEConstant.hpp, utils/PropertyMap.cpp, |
4377 |
|
|
utils/PropertyMap.hpp, utils/StringTokenizer.cpp, |
4378 |
|
|
utils/StringTokenizer.hpp, utils/StringUtils.cpp, |
4379 |
|
|
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
4380 |
|
|
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
4381 |
|
|
utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90, |
4382 |
|
|
utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90, |
4383 |
|
|
utils/simError.c, utils/simError.h, utils/status.F90, |
4384 |
|
|
utils/vector_class.F90, visitors/AtomData.hpp, |
4385 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp, |
4386 |
|
|
visitors/BaseVisitor.hpp, visitors/CompositeVisitor.cpp, |
4387 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
4388 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
4389 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
4390 |
|
|
visitors/ZconsVisitor.hpp: change license |
4391 |
|
|
|
4392 |
gezelter |
2199 |
2005-01-12 12:14 tim |
4393 |
tim |
2102 |
|
4394 |
|
|
* src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on |
4395 |
|
|
branch new_design. |
4396 |
|
|
|
4397 |
gezelter |
2199 |
2005-01-11 16:03 tim |
4398 |
tim |
2102 |
|
4399 |
|
|
* src/: constraints/ZconstraintForceManager.cpp, |
4400 |
|
|
constraints/ZconstraintForceManager.hpp, |
4401 |
|
|
minimizers/MinimizerParameterSet.cpp, |
4402 |
|
|
minimizers/MinimizerParameterSet.hpp: change const static double |
4403 |
|
|
data member to const double |
4404 |
|
|
|
4405 |
gezelter |
2199 |
2005-01-11 15:50 tim |
4406 |
tim |
2102 |
|
4407 |
|
|
* src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: |
4408 |
|
|
|
4409 |
gezelter |
2199 |
2005-01-11 15:39 tim |
4410 |
tim |
2102 |
|
4411 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: |
4412 |
|
|
change data type from logical to integer in AtomTypeProperties.h |
4413 |
|
|
|
4414 |
gezelter |
2199 |
2005-01-11 11:36 tim |
4415 |
tim |
2102 |
|
4416 |
|
|
* forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding |
4417 |
|
|
new format of EAM force field |
4418 |
|
|
|
4419 |
gezelter |
2199 |
2005-01-11 11:24 tim |
4420 |
tim |
2102 |
|
4421 |
|
|
* src/UseTheForce/DUFF.cpp: change default name of DUFF force field |
4422 |
|
|
to DUFF2.frc |
4423 |
|
|
|
4424 |
gezelter |
2199 |
2005-01-11 11:23 tim |
4425 |
tim |
2102 |
|
4426 |
|
|
* forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to |
4427 |
|
|
DUFF2.frc |
4428 |
|
|
|
4429 |
gezelter |
2199 |
2005-01-11 11:09 tim |
4430 |
tim |
2102 |
|
4431 |
|
|
* make/Makefile.in: adding constraints and minimizers into |
4432 |
|
|
Makefile.in |
4433 |
|
|
|
4434 |
gezelter |
2199 |
2005-01-11 11:03 tim |
4435 |
tim |
2102 |
|
4436 |
|
|
* src/io/: ChargeAtomTypesSectionParser.cpp, |
4437 |
|
|
ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, |
4438 |
|
|
DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless |
4439 |
|
|
files |
4440 |
|
|
|
4441 |
gezelter |
2199 |
2005-01-11 10:59 tim |
4442 |
tim |
2102 |
|
4443 |
|
|
* src/io/ZConsWriter.cpp: [no log message] |
4444 |
|
|
|
4445 |
gezelter |
2199 |
2005-01-11 10:53 tim |
4446 |
tim |
2102 |
|
4447 |
|
|
* src/UseTheForce/EAM.cpp: minor fix |
4448 |
|
|
|
4449 |
gezelter |
2199 |
2005-01-11 10:52 tim |
4450 |
tim |
2102 |
|
4451 |
tim |
2116 |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
4452 |
|
|
on branch new_design. |
4453 |
|
|
|
4454 |
gezelter |
2199 |
2005-01-11 10:52 tim |
4455 |
tim |
2116 |
|
4456 |
tim |
2102 |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
4457 |
|
|
on branch new_design. |
4458 |
|
|
|
4459 |
gezelter |
2199 |
2005-01-11 10:52 tim |
4460 |
tim |
2102 |
|
4461 |
|
|
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
4462 |
|
|
|
4463 |
gezelter |
2199 |
2005-01-11 10:47 tim |
4464 |
tim |
2102 |
|
4465 |
|
|
* make/Makefile.in: forget a '$' sign |
4466 |
|
|
|
4467 |
gezelter |
2199 |
2005-01-11 10:46 tim |
4468 |
tim |
2102 |
|
4469 |
|
|
* make/Makefile.in: missing tab in rules |
4470 |
|
|
|
4471 |
gezelter |
2199 |
2005-01-10 17:04 tim |
4472 |
tim |
2102 |
|
4473 |
|
|
* src/: UseTheForce/ForceFieldCreator.cpp, |
4474 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
4475 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
4476 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
4477 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
4478 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile, |
4479 |
|
|
brains/Register.cpp, brains/Register.hpp, |
4480 |
|
|
integrators/IntegratorCreator.cpp, |
4481 |
|
|
integrators/IntegratorCreator.hpp, |
4482 |
|
|
integrators/IntegratorFactory.cpp, |
4483 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
4484 |
|
|
integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp, |
4485 |
|
|
minimizers/Makefile, minimizers/MinimizerCreator.cpp, |
4486 |
|
|
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
4487 |
|
|
minimizers/MinimizerFactory.hpp: create a register module to |
4488 |
|
|
register force fields, integrators and minimizers |
4489 |
|
|
|
4490 |
gezelter |
2199 |
2005-01-10 17:04 tim |
4491 |
tim |
2102 |
|
4492 |
|
|
* src/brains/Register.cpp: file Register.cpp was initially added on |
4493 |
|
|
branch new_design. |
4494 |
|
|
|
4495 |
gezelter |
2199 |
2005-01-10 17:04 tim |
4496 |
tim |
2102 |
|
4497 |
|
|
* src/brains/Register.hpp: file Register.hpp was initially added on |
4498 |
|
|
branch new_design. |
4499 |
|
|
|
4500 |
gezelter |
2199 |
2005-01-10 15:52 tim |
4501 |
tim |
2102 |
|
4502 |
|
|
* src/: UseTheForce/ForceFieldFactory.cpp, |
4503 |
|
|
applications/oopse/oopse.cpp, brains/ForceManager.hpp, |
4504 |
|
|
constraints/ZconstraintForceManager.cpp, |
4505 |
|
|
constraints/ZconstraintForceManager.hpp, |
4506 |
|
|
integrators/IntegratorFactory.cpp, |
4507 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp, |
4508 |
|
|
io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp, |
4509 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint |
4510 |
|
|
method is working now |
4511 |
|
|
|
4512 |
gezelter |
2199 |
2005-01-10 13:05 tim |
4513 |
tim |
2102 |
|
4514 |
|
|
* src/: constraints/ConstraintElem.hpp, |
4515 |
|
|
constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, |
4516 |
|
|
constraints/ZconstraintForceManager.cpp, |
4517 |
|
|
constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp, |
4518 |
|
|
io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
4519 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in |
4520 |
|
|
zconstraint |
4521 |
|
|
|
4522 |
gezelter |
2199 |
2005-01-10 13:05 tim |
4523 |
tim |
2102 |
|
4524 |
|
|
* src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was |
4525 |
|
|
initially added on branch new_design. |
4526 |
|
|
|
4527 |
gezelter |
2199 |
2005-01-07 16:50 tim |
4528 |
tim |
2102 |
|
4529 |
tim |
2116 |
* src/constraints/ZconstraintForceManager.cpp: file |
4530 |
|
|
ZconstraintForceManager.cpp was initially added on branch |
4531 |
|
|
new_design. |
4532 |
|
|
|
4533 |
gezelter |
2199 |
2005-01-07 16:50 tim |
4534 |
tim |
2116 |
|
4535 |
|
|
* src/constraints/ZconstraintForceManager.hpp: file |
4536 |
|
|
ZconstraintForceManager.hpp was initially added on branch |
4537 |
|
|
new_design. |
4538 |
|
|
|
4539 |
gezelter |
2199 |
2005-01-07 16:50 tim |
4540 |
tim |
2116 |
|
4541 |
tim |
2102 |
* src/: applications/simpleBuilder/BaseLattice.hpp, |
4542 |
|
|
applications/simpleBuilder/Lattice.hpp, |
4543 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
4544 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
4545 |
|
|
applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp, |
4546 |
|
|
constraints/ConstraintElem.hpp, constraints/Makefile, |
4547 |
|
|
constraints/ZConstraint.cpp, constraints/ZconsData.hpp, |
4548 |
|
|
constraints/ZconstraintForceManager.cpp, |
4549 |
|
|
constraints/ZconstraintForceManager.hpp, |
4550 |
|
|
integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, |
4551 |
|
|
utils/NumericConstant.hpp: ZConstraintForceManager in progress |
4552 |
|
|
|
4553 |
gezelter |
2199 |
2005-01-07 16:50 tim |
4554 |
tim |
2102 |
|
4555 |
|
|
* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was |
4556 |
|
|
initially added on branch new_design. |
4557 |
|
|
|
4558 |
gezelter |
2199 |
2005-01-06 17:31 tim |
4559 |
tim |
2102 |
|
4560 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
4561 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
4562 |
|
|
constraints/ConstraintPair.hpp, integrators/Integrator.cpp, |
4563 |
|
|
integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp, |
4564 |
|
|
io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: |
4565 |
|
|
constraint is almost working |
4566 |
|
|
|
4567 |
gezelter |
2199 |
2005-01-05 19:36 tim |
4568 |
tim |
2102 |
|
4569 |
|
|
* src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is |
4570 |
|
|
working |
4571 |
|
|
|
4572 |
gezelter |
2199 |
2005-01-05 19:16 tim |
4573 |
tim |
2102 |
|
4574 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
4575 |
|
|
applications/oopse/oopse.cpp, |
4576 |
|
|
applications/simpleBuilder/BaseLattice.cpp, |
4577 |
|
|
applications/simpleBuilder/Lattice.cpp, |
4578 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
4579 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
4580 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
4581 |
|
|
applications/simpleBuilder/MoLocator.hpp, |
4582 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
4583 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp, |
4584 |
|
|
minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder |
4585 |
|
|
in progress |
4586 |
|
|
|
4587 |
gezelter |
2199 |
2005-01-05 12:35 tim |
4588 |
tim |
2102 |
|
4589 |
|
|
* src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp |
4590 |
|
|
was initially added on branch new_design. |
4591 |
|
|
|
4592 |
gezelter |
2199 |
2005-01-05 12:35 tim |
4593 |
tim |
2102 |
|
4594 |
tim |
2116 |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
4595 |
|
|
added on branch new_design. |
4596 |
|
|
|
4597 |
gezelter |
2199 |
2005-01-05 12:35 tim |
4598 |
tim |
2116 |
|
4599 |
tim |
2102 |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
4600 |
|
|
Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, |
4601 |
|
|
MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, |
4602 |
|
|
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, |
4603 |
|
|
SDMinimizer.hpp: minimizer in progress |
4604 |
|
|
|
4605 |
gezelter |
2199 |
2005-01-05 12:35 tim |
4606 |
tim |
2102 |
|
4607 |
tim |
2116 |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
4608 |
|
|
was initially added on branch new_design. |
4609 |
tim |
2102 |
|
4610 |
gezelter |
2199 |
2005-01-05 12:35 tim |
4611 |
tim |
2102 |
|
4612 |
tim |
2116 |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
4613 |
tim |
2102 |
was initially added on branch new_design. |
4614 |
|
|
|
4615 |
gezelter |
2199 |
2005-01-05 12:35 tim |
4616 |
tim |
2102 |
|
4617 |
tim |
2116 |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
4618 |
tim |
2102 |
was initially added on branch new_design. |
4619 |
|
|
|
4620 |
gezelter |
2199 |
2005-01-05 12:35 tim |
4621 |
tim |
2102 |
|
4622 |
|
|
* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially |
4623 |
|
|
added on branch new_design. |
4624 |
|
|
|
4625 |
gezelter |
2199 |
2005-01-04 17:18 tim |
4626 |
tim |
2102 |
|
4627 |
|
|
* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
4628 |
|
|
brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, |
4629 |
|
|
brains/Thermo.cpp, constraints/ConstraintPair.hpp, |
4630 |
|
|
constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp, |
4631 |
|
|
integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp, |
4632 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp, |
4633 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in |
4634 |
|
|
progress |
4635 |
|
|
|
4636 |
gezelter |
2199 |
2005-01-04 17:18 tim |
4637 |
tim |
2102 |
|
4638 |
tim |
2116 |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
4639 |
|
|
initially added on branch new_design. |
4640 |
tim |
2102 |
|
4641 |
gezelter |
2199 |
2005-01-04 17:18 tim |
4642 |
tim |
2102 |
|
4643 |
|
|
* src/minimizers/MinimizerParameterSet.cpp: file |
4644 |
|
|
MinimizerParameterSet.cpp was initially added on branch new_design. |
4645 |
|
|
|
4646 |
gezelter |
2199 |
2005-01-04 17:18 tim |
4647 |
tim |
2102 |
|
4648 |
|
|
* src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was |
4649 |
|
|
initially added on branch new_design. |
4650 |
|
|
|
4651 |
gezelter |
2199 |
2005-01-04 17:18 tim |
4652 |
tim |
2102 |
|
4653 |
tim |
2116 |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
4654 |
|
|
was initially added on branch new_design. |
4655 |
|
|
|
4656 |
gezelter |
2199 |
2005-01-04 17:18 tim |
4657 |
tim |
2116 |
|
4658 |
|
|
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
4659 |
|
|
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
4660 |
|
|
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
4661 |
|
|
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
4662 |
|
|
|
4663 |
gezelter |
2199 |
2005-01-04 17:18 tim |
4664 |
tim |
2116 |
|
4665 |
tim |
2102 |
* src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on |
4666 |
|
|
branch new_design. |
4667 |
|
|
|
4668 |
gezelter |
2199 |
2004-12-20 15:50 chuckv |
4669 |
tim |
2102 |
|
4670 |
|
|
* make/Makefile.in: Fixed Makefile test bug under OSX and possibly |
4671 |
|
|
other BSD's, replaced test -f *.mod with ls function since BSD test |
4672 |
|
|
apparently doesn't support wildcards. |
4673 |
|
|
|
4674 |
gezelter |
2199 |
2004-12-20 15:36 tim |
4675 |
tim |
2102 |
|
4676 |
|
|
* make/Makefile.in: fix a test command incompatiable problem |
4677 |
|
|
|
4678 |
gezelter |
2199 |
2004-12-20 14:49 tim |
4679 |
tim |
2102 |
|
4680 |
|
|
* src/integrators/NPTi.cpp: NPT is working now |
4681 |
|
|
|
4682 |
gezelter |
2199 |
2004-12-16 14:20 tim |
4683 |
tim |
2102 |
|
4684 |
|
|
* src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the |
4685 |
|
|
invalid stamp id |
4686 |
|
|
|
4687 |
gezelter |
2199 |
2004-12-16 14:00 tim |
4688 |
tim |
2102 |
|
4689 |
|
|
* forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, |
4690 |
|
|
newEAM.u6.frc: adding new EAM force field files |
4691 |
|
|
|
4692 |
gezelter |
2199 |
2004-12-16 13:55 tim |
4693 |
tim |
2102 |
|
4694 |
|
|
* src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays |
4695 |
|
|
in EAM parameter file is incorrect |
4696 |
|
|
|
4697 |
gezelter |
2199 |
2004-12-16 12:27 tim |
4698 |
tim |
2102 |
|
4699 |
|
|
* src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
4700 |
|
|
brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, |
4701 |
|
|
utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM |
4702 |
|
|
|
4703 |
gezelter |
2199 |
2004-12-15 17:34 tim |
4704 |
tim |
2102 |
|
4705 |
|
|
* src/: applications/simpleBuilder/BaseLattice.cpp, |
4706 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
4707 |
|
|
applications/simpleBuilder/Lattice.cpp, |
4708 |
|
|
applications/simpleBuilder/Lattice.hpp, |
4709 |
|
|
applications/simpleBuilder/LatticeCreator.cpp, |
4710 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
4711 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
4712 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
4713 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
4714 |
|
|
io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream |
4715 |
|
|
|
4716 |
gezelter |
2199 |
2004-12-15 16:07 tim |
4717 |
tim |
2102 |
|
4718 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
4719 |
|
|
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, |
4720 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: |
4721 |
|
|
add EAM Force Field |
4722 |
|
|
|
4723 |
gezelter |
2199 |
2004-12-15 14:40 tim |
4724 |
tim |
2102 |
|
4725 |
|
|
* src/applications/oopse/oopse.cpp: add more force fields |
4726 |
|
|
|
4727 |
gezelter |
2199 |
2004-12-15 11:44 tim |
4728 |
tim |
2102 |
|
4729 |
|
|
* src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget |
4730 |
|
|
to call All_reduce in MPI version) |
4731 |
|
|
|
4732 |
gezelter |
2199 |
2004-12-15 11:13 tim |
4733 |
tim |
2102 |
|
4734 |
|
|
* src/: brains/SimCreator.cpp, brains/SimInfo.cpp, |
4735 |
|
|
io/DumpReader.cpp: MPI in NVE is working |
4736 |
|
|
|
4737 |
gezelter |
2199 |
2004-12-14 16:57 tim |
4738 |
tim |
2102 |
|
4739 |
|
|
* src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. |
4740 |
|
|
Master nodes does not brocast the total number of frames |
4741 |
|
|
|
4742 |
gezelter |
2199 |
2004-12-14 14:08 tim |
4743 |
tim |
2102 |
|
4744 |
|
|
* src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, |
4745 |
|
|
integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
4746 |
|
|
minimizers/CGFamilyMinimizer.cpp, |
4747 |
|
|
minimizers/MinimizerParameterSet.hpp, |
4748 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
4749 |
|
|
minimizers/SDMinimizer.cpp: more fix in MPI version |
4750 |
|
|
|
4751 |
gezelter |
2199 |
2004-12-13 17:30 tim |
4752 |
tim |
2102 |
|
4753 |
|
|
* src/: UseTheForce/DarkSide/simParallel.F90, |
4754 |
|
|
applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
4755 |
|
|
brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp, |
4756 |
|
|
integrators/DLM.cpp, integrators/Integrator.cpp, |
4757 |
|
|
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
4758 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp, |
4759 |
|
|
io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp, |
4760 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp, |
4761 |
|
|
io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, |
4762 |
|
|
math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp, |
4763 |
|
|
primitives/RigidBody.cpp, primitives/StuntDouble.cpp, |
4764 |
|
|
primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp, |
4765 |
|
|
utils/LocalIndexManager.hpp, utils/PropertyMap.cpp, |
4766 |
|
|
utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version |
4767 |
|
|
is built |
4768 |
|
|
|
4769 |
gezelter |
2199 |
2004-12-10 13:41 tim |
4770 |
tim |
2102 |
|
4771 |
|
|
* src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp |
4772 |
|
|
|
4773 |
gezelter |
2199 |
2004-12-10 11:14 tim |
4774 |
tim |
2102 |
|
4775 |
|
|
* src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, |
4776 |
|
|
primitives/StuntDouble.hpp: forget to zero out the torque. Sticky |
4777 |
|
|
and Dipole is working now |
4778 |
|
|
|
4779 |
gezelter |
2199 |
2004-12-09 18:15 tim |
4780 |
tim |
2102 |
|
4781 |
|
|
* src/: UseTheForce/DarkSide/dipole.F90, |
4782 |
|
|
UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: |
4783 |
|
|
fix an index problem in eFrame matrix |
4784 |
|
|
|
4785 |
gezelter |
2199 |
2004-12-09 18:09 tim |
4786 |
tim |
2102 |
|
4787 |
|
|
* src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when |
4788 |
|
|
initializing the new Charge AtomType |
4789 |
|
|
|
4790 |
gezelter |
2199 |
2004-12-09 16:15 tim |
4791 |
tim |
2102 |
|
4792 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, |
4793 |
|
|
types/DirectionalAtomType.cpp: sticky module get compiled |
4794 |
|
|
|
4795 |
gezelter |
2199 |
2004-12-09 15:43 gezelter |
4796 |
tim |
2102 |
|
4797 |
|
|
* src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, |
4798 |
|
|
reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for |
4799 |
|
|
GB |
4800 |
|
|
|
4801 |
gezelter |
2199 |
2004-12-09 15:42 gezelter |
4802 |
tim |
2102 |
|
4803 |
|
|
* src/UseTheForce/doForces.F90: u_l -> eFrame |
4804 |
|
|
|
4805 |
gezelter |
2199 |
2004-12-09 15:27 gezelter |
4806 |
tim |
2102 |
|
4807 |
|
|
* src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky |
4808 |
|
|
module now has the option for multiple sticky types |
4809 |
|
|
|
4810 |
gezelter |
2199 |
2004-12-09 15:27 gezelter |
4811 |
tim |
2102 |
|
4812 |
|
|
* src/UseTheForce/doForces.F90: sticky |
4813 |
|
|
|
4814 |
gezelter |
2199 |
2004-12-09 11:22 tim |
4815 |
tim |
2102 |
|
4816 |
|
|
* src/integrators/: NPT.cpp, NVT.cpp: fix an interface |
4817 |
|
|
inconsistency in lab2Bidy |
4818 |
|
|
|
4819 |
gezelter |
2199 |
2004-12-09 10:45 tim |
4820 |
tim |
2102 |
|
4821 |
|
|
* src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug |
4822 |
|
|
in calculating torque in rigid body |
4823 |
|
|
|
4824 |
gezelter |
2199 |
2004-12-08 15:37 tim |
4825 |
tim |
2102 |
|
4826 |
|
|
* src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, |
4827 |
|
|
brains/SnapShot.cpp, brains/Snapshot.hpp, |
4828 |
|
|
integrators/Integrator.cpp, |
4829 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: |
4830 |
|
|
fix a parsing bug in ElectroStaticAtomTypesSectionParser |
4831 |
|
|
|
4832 |
gezelter |
2199 |
2004-12-08 12:03 tim |
4833 |
tim |
2102 |
|
4834 |
|
|
* src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane |
4835 |
|
|
in NVT is working |
4836 |
|
|
|
4837 |
gezelter |
2199 |
2004-12-07 18:08 tim |
4838 |
tim |
2102 |
|
4839 |
|
|
* src/: UseTheForce/Makefile, brains/SimInfo.hpp, |
4840 |
|
|
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
4841 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, |
4842 |
|
|
io/DumpWriter.cpp: NPT in progress |
4843 |
|
|
|
4844 |
gezelter |
2199 |
2004-12-07 09:43 tim |
4845 |
tim |
2102 |
|
4846 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.hpp: [no log |
4847 |
|
|
message] |
4848 |
|
|
|
4849 |
gezelter |
2199 |
2004-12-07 00:12 tim |
4850 |
tim |
2102 |
|
4851 |
|
|
* src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in |
4852 |
|
|
UseInitXSstate |
4853 |
|
|
|
4854 |
gezelter |
2199 |
2004-12-07 00:00 tim |
4855 |
tim |
2102 |
|
4856 |
|
|
* src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message |
4857 |
|
|
|
4858 |
gezelter |
2199 |
2004-12-06 23:47 tim |
4859 |
tim |
2102 |
|
4860 |
|
|
* src/types/DirectionalAtomType.cpp: [no log message] |
4861 |
|
|
|
4862 |
gezelter |
2199 |
2004-12-06 21:18 tim |
4863 |
tim |
2102 |
|
4864 |
|
|
* forceFields/newDUFF.frc: merge WATER force field into DUFF |
4865 |
|
|
|
4866 |
gezelter |
2199 |
2004-12-06 20:33 tim |
4867 |
tim |
2102 |
|
4868 |
|
|
* forceFields/newDUFF.frc: change the force constant of bonds |
4869 |
|
|
|
4870 |
gezelter |
2199 |
2004-12-06 18:29 tim |
4871 |
tim |
2102 |
|
4872 |
|
|
* src/: UseTheForce/DarkSide/charge.F90, |
4873 |
|
|
UseTheForce/DarkSide/charge_interface.h, |
4874 |
|
|
UseTheForce/DarkSide/dipole.F90, |
4875 |
|
|
UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: |
4876 |
|
|
fix atom type ident in Charge and Dipole Module |
4877 |
|
|
|
4878 |
gezelter |
2199 |
2004-12-06 17:56 tim |
4879 |
tim |
2102 |
|
4880 |
|
|
* src/primitives/Torsion.cpp: butane is working now |
4881 |
|
|
|
4882 |
gezelter |
2199 |
2004-12-06 15:15 tim |
4883 |
tim |
2102 |
|
4884 |
|
|
* src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, |
4885 |
|
|
primitives/Bond.hpp, primitives/Torsion.cpp: short range |
4886 |
|
|
interaction for butane is correct.Still something wrong with long |
4887 |
|
|
range one |
4888 |
|
|
|
4889 |
gezelter |
2199 |
2004-12-05 23:49 tim |
4890 |
tim |
2102 |
|
4891 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
4892 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
4893 |
|
|
io/BendTypesSectionParser.cpp, math/Polynomial.hpp, |
4894 |
|
|
primitives/Atom.hpp, utils/NumericConstant.hpp, |
4895 |
|
|
utils/TypeContainer.hpp: fix a bug in Exclude List |
4896 |
|
|
|
4897 |
gezelter |
2199 |
2004-12-05 17:21 tim |
4898 |
tim |
2102 |
|
4899 |
|
|
* forceFields/newDUFF.frc: minor fix in DUFF |
4900 |
|
|
|
4901 |
gezelter |
2199 |
2004-12-05 17:02 tim |
4902 |
tim |
2102 |
|
4903 |
|
|
* src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, |
4904 |
|
|
utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: |
4905 |
|
|
fix a bug in filling MolMembership |
4906 |
|
|
|
4907 |
gezelter |
2199 |
2004-12-05 12:12 tim |
4908 |
tim |
2102 |
|
4909 |
|
|
* forceFields/newDUFF.frc: minor fix in force field file |
4910 |
|
|
|
4911 |
gezelter |
2199 |
2004-12-05 12:09 tim |
4912 |
tim |
2102 |
|
4913 |
|
|
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
4914 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp |
4915 |
|
|
|
4916 |
gezelter |
2199 |
2004-12-04 15:09 tim |
4917 |
tim |
2102 |
|
4918 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, |
4919 |
|
|
math/Vector3.hpp: NVE is working now, get the same result as |
4920 |
|
|
OOPSE-1.0 |
4921 |
|
|
|
4922 |
gezelter |
2199 |
2004-12-04 14:29 tim |
4923 |
tim |
2102 |
|
4924 |
|
|
* src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy |
4925 |
|
|
|
4926 |
gezelter |
2199 |
2004-12-04 14:24 gezelter |
4927 |
tim |
2102 |
|
4928 |
|
|
* src/primitives/: Bend.cpp, Torsion.cpp: What? |
4929 |
|
|
|
4930 |
gezelter |
2199 |
2004-12-04 14:24 gezelter |
4931 |
tim |
2102 |
|
4932 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion |
4933 |
|
|
|
4934 |
gezelter |
2199 |
2004-12-04 00:24 tim |
4935 |
tim |
2102 |
|
4936 |
|
|
* src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, |
4937 |
|
|
integrators/Integrator.hpp, |
4938 |
|
|
integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp, |
4939 |
|
|
utils/TypeContainer.hpp: NVE conserved energy, however, potential |
4940 |
|
|
is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf |
4941 |
|
|
and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, |
4942 |
|
|
dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step |
4943 |
|
|
4 EAM Step 5 Shape Step 6 Constraint & Restraint |
4944 |
|
|
|
4945 |
gezelter |
2199 |
2004-12-03 19:01 tim |
4946 |
tim |
2102 |
|
4947 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, |
4948 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, |
4949 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
4950 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
4951 |
|
|
io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, |
4952 |
|
|
energy of NVE is not conserved |
4953 |
|
|
|
4954 |
gezelter |
2199 |
2004-12-03 17:36 tim |
4955 |
tim |
2102 |
|
4956 |
|
|
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
4957 |
|
|
primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running |
4958 |
|
|
|
4959 |
gezelter |
2199 |
2004-12-03 16:30 tim |
4960 |
tim |
2102 |
|
4961 |
|
|
* src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, |
4962 |
|
|
brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, |
4963 |
|
|
integrators/NVE.cpp, primitives/Molecule.cpp, |
4964 |
|
|
primitives/Molecule.hpp, primitives/StuntDouble.hpp, |
4965 |
|
|
primitives/Torsion.hpp: more missing function get implemented |
4966 |
|
|
|
4967 |
gezelter |
2199 |
2004-12-03 15:30 tim |
4968 |
tim |
2102 |
|
4969 |
|
|
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, |
4970 |
|
|
SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo |
4971 |
|
|
|
4972 |
gezelter |
2199 |
2004-12-03 12:59 tim |
4973 |
tim |
2102 |
|
4974 |
|
|
* src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
4975 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
4976 |
|
|
integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp, |
4977 |
|
|
io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp, |
4978 |
|
|
io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, |
4979 |
|
|
utils/TypeContainer.hpp: begin to fix bugs |
4980 |
|
|
|
4981 |
gezelter |
2199 |
2004-12-02 19:26 tim |
4982 |
tim |
2102 |
|
4983 |
tim |
2116 |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
4984 |
|
|
new_design. |
4985 |
|
|
|
4986 |
gezelter |
2199 |
2004-12-02 19:26 tim |
4987 |
tim |
2116 |
|
4988 |
tim |
2102 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
4989 |
|
|
UseTheForce/ForceFieldCreator.cpp, |
4990 |
|
|
UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, |
4991 |
|
|
integrators/IntegratorCreator.cpp, |
4992 |
|
|
integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp, |
4993 |
|
|
io/SectionParserManager.hpp, utils/Makefile, |
4994 |
|
|
utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a |
4995 |
|
|
bug in countTokens in StringTokenizer |
4996 |
|
|
|
4997 |
gezelter |
2199 |
2004-12-02 19:06 tim |
4998 |
tim |
2102 |
|
4999 |
|
|
* forceFields/newDUFF.frc: minor fix |
5000 |
|
|
|
5001 |
gezelter |
2199 |
2004-12-02 18:15 tim |
5002 |
tim |
2102 |
|
5003 |
|
|
* forceFields/newDUFF.frc: new ForceField format |
5004 |
|
|
|
5005 |
gezelter |
2199 |
2004-12-02 17:15 tim |
5006 |
tim |
2102 |
|
5007 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
5008 |
|
|
UseTheForce/ForceFieldCreator.cpp, |
5009 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
5010 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
5011 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
5012 |
|
|
applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp, |
5013 |
|
|
integrators/IntegratorCreator.hpp, |
5014 |
|
|
integrators/IntegratorFactory.cpp, |
5015 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
5016 |
|
|
integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp, |
5017 |
|
|
integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
5018 |
|
|
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
5019 |
|
|
integrators/NVT.cpp, integrators/NVT.hpp, |
5020 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
5021 |
|
|
types/Makefile: refine factory pattern to make it initialized |
5022 |
|
|
correctly |
5023 |
|
|
|
5024 |
gezelter |
2199 |
2004-12-02 17:15 tim |
5025 |
tim |
2102 |
|
5026 |
|
|
* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp |
5027 |
|
|
was initially added on branch new_design. |
5028 |
|
|
|
5029 |
gezelter |
2199 |
2004-12-02 17:15 tim |
5030 |
tim |
2102 |
|
5031 |
tim |
2116 |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
5032 |
|
|
was initially added on branch new_design. |
5033 |
|
|
|
5034 |
gezelter |
2199 |
2004-12-02 17:15 tim |
5035 |
tim |
2116 |
|
5036 |
|
|
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
5037 |
|
|
was initially added on branch new_design. |
5038 |
|
|
|
5039 |
gezelter |
2199 |
2004-12-02 17:15 tim |
5040 |
tim |
2116 |
|
5041 |
|
|
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
5042 |
|
|
was initially added on branch new_design. |
5043 |
|
|
|
5044 |
gezelter |
2199 |
2004-12-02 11:53 tim |
5045 |
tim |
2116 |
|
5046 |
tim |
2102 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, |
5047 |
|
|
types/DirectionalAtomType.cpp, types/Makefile: oopse get built |
5048 |
|
|
|
5049 |
gezelter |
2199 |
2004-12-02 11:04 tim |
5050 |
tim |
2102 |
|
5051 |
|
|
* src/: applications/simpleBuilder/LatticeCreator.cpp, |
5052 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
5053 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
5054 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
5055 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp, |
5056 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
5057 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, |
5058 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
5059 |
|
|
brains/SnapshotManager.hpp, brains/Stats.cpp, |
5060 |
|
|
constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp, |
5061 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, |
5062 |
|
|
io/basic_ifstrstream.hpp, primitives/Bend.hpp, |
5063 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
5064 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
5065 |
|
|
types/OplsTorsionType.hpp, types/ShapeAtomType.hpp, |
5066 |
|
|
utils/PropertyMap.hpp, utils/TypeContainer.hpp, |
5067 |
|
|
visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp, |
5068 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
5069 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
5070 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still |
5071 |
|
|
have two linking problem |
5072 |
|
|
|
5073 |
gezelter |
2199 |
2004-12-02 00:17 tim |
5074 |
tim |
2102 |
|
5075 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
5076 |
|
|
applications/simpleBuilder/Lattice.cpp, |
5077 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
5078 |
|
|
constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp, |
5079 |
|
|
io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp, |
5080 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp, |
5081 |
|
|
restraints/Restraints.cpp, visitors/AtomVisitor.cpp, |
5082 |
|
|
visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, |
5083 |
|
|
visitors/ZconsVisitor.cpp: change endl to std::endl |
5084 |
|
|
|
5085 |
gezelter |
2199 |
2004-12-02 00:14 tim |
5086 |
tim |
2102 |
|
5087 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
5088 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
5089 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
5090 |
|
|
applications/simpleBuilder/Lattice.hpp, |
5091 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
5092 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
5093 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
5094 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
5095 |
|
|
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
5096 |
|
|
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
5097 |
|
|
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
5098 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
5099 |
|
|
visitors/RigidBodyVisitor.hpp: minor fix |
5100 |
|
|
|
5101 |
gezelter |
2199 |
2004-12-02 00:09 tim |
5102 |
tim |
2102 |
|
5103 |
|
|
* src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: |
5104 |
|
|
remove StreamTokenizer |
5105 |
|
|
|
5106 |
gezelter |
2199 |
2004-12-02 00:06 tim |
5107 |
tim |
2102 |
|
5108 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
5109 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
5110 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp, |
5111 |
|
|
io/ZConsWriter.cpp, math/randomSPRNG.cpp, |
5112 |
|
|
restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using |
5113 |
|
|
namespace std in .cpp file |
5114 |
|
|
|
5115 |
gezelter |
2199 |
2004-12-02 00:04 tim |
5116 |
tim |
2102 |
|
5117 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
5118 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
5119 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
5120 |
|
|
applications/simpleBuilder/Lattice.cpp, |
5121 |
|
|
applications/simpleBuilder/Lattice.hpp, |
5122 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
5123 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
5124 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
5125 |
|
|
applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp, |
5126 |
|
|
brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp, |
5127 |
|
|
io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
5128 |
|
|
minimizers/MinimizerParameterSet.hpp, |
5129 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
5130 |
|
|
minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp, |
5131 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp, |
5132 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
5133 |
|
|
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
5134 |
|
|
utils/GenericData.hpp, visitors/CompositeVisitor.cpp, |
5135 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
5136 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding |
5137 |
|
|
qulified name prefix std |
5138 |
|
|
|
5139 |
gezelter |
2199 |
2004-12-01 23:55 tim |
5140 |
tim |
2102 |
|
5141 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
5142 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
5143 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
5144 |
|
|
applications/simpleBuilder/Lattice.hpp, |
5145 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
5146 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
5147 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
5148 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
5149 |
|
|
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
5150 |
|
|
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
5151 |
|
|
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
5152 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
5153 |
|
|
visitors/RigidBodyVisitor.hpp: replace string by std::string |
5154 |
|
|
|
5155 |
gezelter |
2199 |
2004-12-01 22:12 tim |
5156 |
tim |
2102 |
|
5157 |
|
|
* make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, |
5158 |
|
|
src/applications/simpleBuilder/BaseLattice.hpp, |
5159 |
|
|
src/applications/simpleBuilder/Lattice.hpp, |
5160 |
|
|
src/applications/simpleBuilder/LatticeCreator.hpp, |
5161 |
|
|
src/applications/simpleBuilder/LatticeFactory.hpp, |
5162 |
|
|
src/applications/simpleBuilder/MoLocator.hpp, |
5163 |
|
|
src/brains/SimInfo.cpp, src/brains/SkipList.hpp, |
5164 |
|
|
src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp, |
5165 |
|
|
src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp, |
5166 |
|
|
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
5167 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp, |
5168 |
|
|
src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp, |
5169 |
|
|
src/utils/Makefile, src/utils/StringUtils.cpp, |
5170 |
|
|
src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp, |
5171 |
|
|
src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp, |
5172 |
|
|
src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp, |
5173 |
|
|
test/brains/RigidBody.cpp: replace misuse of using namespace std in |
5174 |
|
|
header files |
5175 |
|
|
|
5176 |
gezelter |
2199 |
2004-12-01 21:23 tim |
5177 |
tim |
2102 |
|
5178 |
|
|
* src/: primitives/Atom.hpp, primitives/RigidBody.hpp, |
5179 |
|
|
primitives/StuntDouble.hpp, utils/TypeContainer.hpp, |
5180 |
|
|
utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: |
5181 |
|
|
begin to fix linking problem |
5182 |
|
|
|
5183 |
gezelter |
2199 |
2004-12-01 21:08 tim |
5184 |
tim |
2102 |
|
5185 |
|
|
* src/: applications/oopse/oopse.cpp, brains/Stats.cpp, |
5186 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, |
5187 |
|
|
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
5188 |
|
|
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
5189 |
|
|
integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp, |
5190 |
|
|
math/SquareMatrix3.hpp, primitives/Atom.hpp, |
5191 |
|
|
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
5192 |
|
|
utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, |
5193 |
|
|
still has some linking problem |
5194 |
|
|
|
5195 |
gezelter |
2199 |
2004-12-01 19:26 tim |
5196 |
tim |
2102 |
|
5197 |
|
|
* src/: integrators/NVT.cpp, integrators/NVT.hpp, |
5198 |
|
|
utils/OOPSEConstant.hpp: NVT get built |
5199 |
|
|
|
5200 |
gezelter |
2199 |
2004-12-01 19:09 tim |
5201 |
tim |
2102 |
|
5202 |
tim |
2116 |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
5203 |
|
|
branch new_design. |
5204 |
tim |
2102 |
|
5205 |
gezelter |
2199 |
2004-12-01 19:09 tim |
5206 |
tim |
2102 |
|
5207 |
tim |
2116 |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
5208 |
|
|
branch new_design. |
5209 |
|
|
|
5210 |
gezelter |
2199 |
2004-12-01 19:09 tim |
5211 |
tim |
2116 |
|
5212 |
tim |
2102 |
* src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, |
5213 |
|
|
brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
5214 |
|
|
brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, |
5215 |
|
|
integrators/Integrator.hpp, integrators/Makefile, |
5216 |
|
|
integrators/NVE.cpp, integrators/NVE.hpp, |
5217 |
|
|
integrators/RotationAlgorithm.hpp, |
5218 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
5219 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE |
5220 |
|
|
get built |
5221 |
|
|
|
5222 |
gezelter |
2199 |
2004-12-01 19:09 tim |
5223 |
tim |
2102 |
|
5224 |
tim |
2116 |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
5225 |
|
|
was initially added on branch new_design. |
5226 |
tim |
2102 |
|
5227 |
gezelter |
2199 |
2004-12-01 17:45 tim |
5228 |
tim |
2102 |
|
5229 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, |
5230 |
|
|
integrators/IntegratorFactory.cpp, |
5231 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
5232 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
5233 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
5234 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp, |
5235 |
|
|
io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, |
5236 |
|
|
io/StatWriter.hpp: rename DumpWrite to DumpWriter |
5237 |
|
|
|
5238 |
gezelter |
2199 |
2004-12-01 17:45 tim |
5239 |
tim |
2102 |
|
5240 |
|
|
* src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on |
5241 |
|
|
branch new_design. |
5242 |
|
|
|
5243 |
gezelter |
2199 |
2004-12-01 15:05 tim |
5244 |
tim |
2102 |
|
5245 |
|
|
* src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, |
5246 |
|
|
io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, |
5247 |
|
|
utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp, |
5248 |
|
|
visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp, |
5249 |
|
|
visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, |
5250 |
|
|
visitors/ZconsVisitor.hpp: visitors get built |
5251 |
|
|
|
5252 |
gezelter |
2199 |
2004-12-01 14:32 chrisfen |
5253 |
tim |
2102 |
|
5254 |
|
|
* samples/water/tip3p_ice/tp3.md: fixed a sample |
5255 |
|
|
|
5256 |
gezelter |
2199 |
2004-12-01 14:10 tim |
5257 |
tim |
2102 |
|
5258 |
|
|
* src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, |
5259 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
5260 |
|
|
src/types/AtomType.hpp, src/utils/Utility.hpp, |
5261 |
|
|
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
5262 |
|
|
src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: |
5263 |
|
|
spell check |
5264 |
|
|
|
5265 |
gezelter |
2199 |
2004-12-01 13:42 tim |
5266 |
tim |
2102 |
|
5267 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
5268 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
5269 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp, |
5270 |
|
|
primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp, |
5271 |
|
|
primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator |
5272 |
|
|
and constraint, other directories get built |
5273 |
|
|
|
5274 |
gezelter |
2199 |
2004-12-01 12:38 tim |
5275 |
tim |
2102 |
|
5276 |
|
|
* src/: brains/DataStorage.cpp, brains/DataStorage.hpp, |
5277 |
|
|
brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
5278 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
5279 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, |
5280 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
5281 |
|
|
primitives/GhostBend.cpp, primitives/RigidBody.cpp, |
5282 |
|
|
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
5283 |
|
|
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
5284 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
5285 |
|
|
refactory AtomType |
5286 |
|
|
|
5287 |
gezelter |
2199 |
2004-11-30 22:11 tim |
5288 |
tim |
2102 |
|
5289 |
|
|
* src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change |
5290 |
|
|
|
5291 |
gezelter |
2199 |
2004-11-30 21:30 tim |
5292 |
tim |
2102 |
|
5293 |
|
|
* src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change |
5294 |
|
|
NumericConstant |
5295 |
|
|
|
5296 |
gezelter |
2199 |
2004-11-30 21:24 tim |
5297 |
tim |
2102 |
|
5298 |
|
|
* src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, |
5299 |
|
|
primitives/RigidBody.cpp: minor fix |
5300 |
|
|
|
5301 |
gezelter |
2199 |
2004-11-30 18:14 tim |
5302 |
tim |
2102 |
|
5303 |
|
|
* src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
5304 |
|
|
io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, |
5305 |
|
|
io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io |
5306 |
|
|
get built, next is integrator |
5307 |
|
|
|
5308 |
gezelter |
2199 |
2004-11-30 17:43 tim |
5309 |
tim |
2102 |
|
5310 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
5311 |
|
|
UseTheForce/ForceField.hpp, brains/SimCreator.cpp, |
5312 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
5313 |
|
|
io/BASS_interface.cpp, primitives/StuntDouble.hpp, |
5314 |
|
|
utils/StringUtils.hpp: brains get built |
5315 |
|
|
|
5316 |
gezelter |
2199 |
2004-11-30 15:50 tim |
5317 |
tim |
2102 |
|
5318 |
|
|
* src/: brains/ForceManager.cpp, brains/Makefile, |
5319 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
5320 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
5321 |
|
|
utils/StringUtils.hpp: brains get built, io is next |
5322 |
|
|
|
5323 |
gezelter |
2199 |
2004-11-30 14:58 tim |
5324 |
tim |
2102 |
|
5325 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
5326 |
|
|
brains/ForceManager.cpp, brains/ForceManager.hpp, |
5327 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.hpp, |
5328 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, |
5329 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
5330 |
|
|
brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp, |
5331 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, |
5332 |
|
|
math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo |
5333 |
|
|
|
5334 |
gezelter |
2199 |
2004-11-30 14:58 tim |
5335 |
tim |
2102 |
|
5336 |
tim |
2116 |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
5337 |
|
|
added on branch new_design. |
5338 |
|
|
|
5339 |
gezelter |
2199 |
2004-11-30 12:54 tim |
5340 |
tim |
2116 |
|
5341 |
tim |
2102 |
* src/: primitives/Bend.hpp, primitives/Bond.hpp, |
5342 |
|
|
primitives/StuntDouble.hpp, primitives/Torsion.hpp, |
5343 |
|
|
utils/LocalIndexManager.hpp: more get fixed |
5344 |
|
|
|
5345 |
gezelter |
2199 |
2004-11-30 00:03 tim |
5346 |
tim |
2102 |
|
5347 |
tim |
2116 |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
5348 |
|
|
initially added on branch new_design. |
5349 |
|
|
|
5350 |
gezelter |
2199 |
2004-11-30 00:03 tim |
5351 |
tim |
2116 |
|
5352 |
tim |
2102 |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
5353 |
|
|
LocalndexManager.hpp to LocalIndexManager.hpp |
5354 |
|
|
|
5355 |
gezelter |
2199 |
2004-11-29 23:43 tim |
5356 |
tim |
2102 |
|
5357 |
|
|
* src/: io/BendTypesSectionParser.cpp, |
5358 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
5359 |
|
|
io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp, |
5360 |
|
|
io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp, |
5361 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
5362 |
|
|
types/PolynomialTorsionType.hpp: Section Parsers get compiled |
5363 |
|
|
|
5364 |
gezelter |
2199 |
2004-11-29 23:14 tim |
5365 |
tim |
2102 |
|
5366 |
|
|
* src/: io/BendTypesSectionParser.cpp, |
5367 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
5368 |
|
|
io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp, |
5369 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor |
5370 |
|
|
fixed |
5371 |
|
|
|
5372 |
gezelter |
2199 |
2004-11-29 22:49 tim |
5373 |
tim |
2102 |
|
5374 |
|
|
* src/: io/TorsionTypesSectionParser.cpp, |
5375 |
|
|
io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, |
5376 |
|
|
types/CubicTorsionType.hpp, types/PolynomialBendType.hpp, |
5377 |
|
|
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
5378 |
|
|
types/QuarticTorsionType.hpp: minor fixed |
5379 |
|
|
|
5380 |
gezelter |
2199 |
2004-11-29 22:32 tim |
5381 |
tim |
2102 |
|
5382 |
|
|
* src/: io/TorsionTypesSectionParser.cpp, |
5383 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
5384 |
|
|
types/PolynomialTorsionType.hpp: #inlcude statement can not be |
5385 |
|
|
embedded |
5386 |
|
|
|
5387 |
gezelter |
2199 |
2004-11-29 16:42 tim |
5388 |
tim |
2102 |
|
5389 |
|
|
* test/math/: Makefile, PolynomialTestCase.cpp, |
5390 |
|
|
PolynomialTestCase.hpp: add PolynomialTestCase |
5391 |
|
|
|
5392 |
gezelter |
2199 |
2004-11-29 16:42 tim |
5393 |
tim |
2102 |
|
5394 |
|
|
* src/math/Polynomial.hpp: Polynomial passes unit test |
5395 |
|
|
|
5396 |
gezelter |
2199 |
2004-11-29 15:03 tim |
5397 |
tim |
2102 |
|
5398 |
|
|
* src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename |
5399 |
|
|
QuarticTorsion.hpp to QuarticTorsionType.hpp |
5400 |
|
|
|
5401 |
gezelter |
2199 |
2004-11-29 15:03 tim |
5402 |
tim |
2102 |
|
5403 |
|
|
* src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was |
5404 |
|
|
initially added on branch new_design. |
5405 |
|
|
|
5406 |
gezelter |
2199 |
2004-11-29 14:56 tim |
5407 |
tim |
2102 |
|
5408 |
|
|
* src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was |
5409 |
|
|
initially added on branch new_design. |
5410 |
|
|
|
5411 |
gezelter |
2199 |
2004-11-29 14:56 tim |
5412 |
tim |
2102 |
|
5413 |
|
|
* src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add |
5414 |
|
|
CubicTorsionType and QuarticTorsionType |
5415 |
|
|
|
5416 |
gezelter |
2199 |
2004-11-29 14:56 tim |
5417 |
tim |
2102 |
|
5418 |
|
|
* src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was |
5419 |
|
|
initially added on branch new_design. |
5420 |
|
|
|
5421 |
gezelter |
2199 |
2004-11-29 13:00 tim |
5422 |
tim |
2102 |
|
5423 |
|
|
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
5424 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
5425 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get |
5426 |
|
|
fixed |
5427 |
|
|
|
5428 |
gezelter |
2199 |
2004-11-29 12:59 tim |
5429 |
tim |
2102 |
|
5430 |
|
|
* src/utils/Trim.hpp: file Trim.hpp was initially added on branch |
5431 |
|
|
new_design. |
5432 |
|
|
|
5433 |
gezelter |
2199 |
2004-11-29 12:59 tim |
5434 |
tim |
2102 |
|
5435 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim |
5436 |
|
|
Algorithm for std::string |
5437 |
|
|
|
5438 |
gezelter |
2199 |
2004-11-29 10:52 tim |
5439 |
tim |
2102 |
|
5440 |
|
|
* src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove |
5441 |
|
|
some useless files |
5442 |
|
|
|
5443 |
gezelter |
2199 |
2004-11-29 10:50 tim |
5444 |
tim |
2102 |
|
5445 |
|
|
* src/io/: BondTypesSectionParser.cpp, |
5446 |
|
|
ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, |
5447 |
|
|
ElectrostaticAtomTypesSectionParser.cpp, |
5448 |
|
|
HarmonicBondTypesSectionParser.cpp, |
5449 |
|
|
HarmonicBondTypesSectionParser.hpp, |
5450 |
|
|
LennardJonesAtomTypesSectionParser.cpp, Makefile, |
5451 |
|
|
SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, |
5452 |
|
|
StickyAtomTypesSectionParser.hpp: more files get fixed |
5453 |
|
|
|
5454 |
gezelter |
2199 |
2004-11-29 10:27 tim |
5455 |
tim |
2102 |
|
5456 |
|
|
* src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, |
5457 |
|
|
DirectionalAtomTypesSectionParser.cpp, |
5458 |
|
|
EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp, |
5459 |
|
|
Makefile, SectionParser.cpp, SectionParser.hpp, |
5460 |
|
|
SectionParserManager.cpp, SectionParserManager.hpp: part of io get |
5461 |
|
|
built |
5462 |
|
|
|
5463 |
gezelter |
2199 |
2004-11-29 09:49 tim |
5464 |
tim |
2102 |
|
5465 |
|
|
* src/types/UreyBradleyBendType.hpp: types get built |
5466 |
|
|
|
5467 |
gezelter |
2199 |
2004-11-29 09:40 tim |
5468 |
tim |
2102 |
|
5469 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: |
5470 |
|
|
types get built |
5471 |
|
|
|
5472 |
gezelter |
2199 |
2004-11-25 21:13 tim |
5473 |
tim |
2102 |
|
5474 |
|
|
* src/: UseTheForce/ForceField.hpp, |
5475 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, |
5476 |
|
|
types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some |
5477 |
|
|
files |
5478 |
|
|
|
5479 |
gezelter |
2199 |
2004-11-25 15:18 tim |
5480 |
tim |
2102 |
|
5481 |
tim |
2116 |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
5482 |
|
|
initially added on branch new_design. |
5483 |
|
|
|
5484 |
gezelter |
2199 |
2004-11-25 15:18 tim |
5485 |
tim |
2116 |
|
5486 |
tim |
2102 |
* src/: io/AtomTypesSectionParser.cpp, |
5487 |
|
|
io/BondTypesSectionParser.cpp, |
5488 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
5489 |
|
|
types/QuadraticBendType.hpp, types/QuadraticBondType.hpp, |
5490 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some |
5491 |
|
|
files |
5492 |
|
|
|
5493 |
gezelter |
2199 |
2004-11-25 15:18 tim |
5494 |
tim |
2102 |
|
5495 |
|
|
* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was |
5496 |
|
|
initially added on branch new_design. |
5497 |
|
|
|
5498 |
gezelter |
2199 |
2004-11-24 17:12 tim |
5499 |
tim |
2102 |
|
5500 |
|
|
* src/: io/AtomTypesSectionParser.cpp, |
5501 |
|
|
io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, |
5502 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
5503 |
|
|
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
5504 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
5505 |
|
|
io/DipoleAtomTypesSectionParser.cpp, |
5506 |
|
|
io/DipoleAtomTypesSectionParser.hpp, |
5507 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
5508 |
|
|
io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp, |
5509 |
|
|
io/EAMAtomTypesSectionParser.hpp, |
5510 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
5511 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, |
5512 |
|
|
io/HarmonicBondTypesSectionParser.hpp, |
5513 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, |
5514 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile, |
5515 |
|
|
io/SectionParser.hpp, io/SectionParserManager.hpp, |
5516 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
5517 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
5518 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
5519 |
|
|
utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built |
5520 |
|
|
|
5521 |
gezelter |
2199 |
2004-11-24 16:33 tim |
5522 |
tim |
2102 |
|
5523 |
|
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, |
5524 |
|
|
ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, |
5525 |
|
|
LJFF.cpp, Makefile: UseTheForce get built |
5526 |
|
|
|
5527 |
gezelter |
2199 |
2004-11-24 15:55 tim |
5528 |
tim |
2102 |
|
5529 |
|
|
* src/: math/RectMatrix.hpp, primitives/Bend.cpp, |
5530 |
|
|
primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, |
5531 |
|
|
primitives/Makefile, primitives/Molecule.cpp, |
5532 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
5533 |
|
|
primitives/StuntDouble.hpp, primitives/Torsion.cpp, |
5534 |
|
|
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
5535 |
|
|
primitives/UreyBradleyBend.hpp: types and primitives get built |
5536 |
|
|
|
5537 |
gezelter |
2199 |
2004-11-24 14:49 tim |
5538 |
tim |
2102 |
|
5539 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
5540 |
|
|
StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint |
5541 |
|
|
StringTokenizerTestCase |
5542 |
|
|
|
5543 |
gezelter |
2199 |
2004-11-24 14:49 tim |
5544 |
tim |
2102 |
|
5545 |
|
|
* src/utils/: GenericData.hpp, StringTokenizer.cpp, |
5546 |
|
|
StringTokenizer.hpp: StringTokenizer passes unit test |
5547 |
|
|
|
5548 |
gezelter |
2199 |
2004-11-24 13:20 tim |
5549 |
tim |
2102 |
|
5550 |
|
|
* ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, |
5551 |
|
|
src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: |
5552 |
|
|
change Makefile |
5553 |
|
|
|
5554 |
gezelter |
2199 |
2004-11-24 13:06 chrisfen |
5555 |
tim |
2102 |
|
5556 |
|
|
* src/io/RestraintReader.cpp: improved restraints - mpi should work |
5557 |
|
|
fine |
5558 |
|
|
|
5559 |
gezelter |
2199 |
2004-11-24 13:06 chrisfen |
5560 |
tim |
2102 |
|
5561 |
|
|
* src/integrators/Integrator.cpp: improved restraints |
5562 |
|
|
|
5563 |
gezelter |
2199 |
2004-11-24 13:05 chrisfen |
5564 |
tim |
2102 |
|
5565 |
|
|
* samples/water/tip3p_ice/tp3.md: oops... |
5566 |
|
|
|
5567 |
gezelter |
2199 |
2004-11-24 12:42 tim |
5568 |
tim |
1779 |
|
5569 |
|
|
* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
5570 |
|
|
brains/DataStorage.hpp, brains/SimCreator.cpp, |
5571 |
|
|
brains/SimCreator.hpp, integrators/Integrator.hpp, |
5572 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
5573 |
|
|
primitives/DirectionalAtom.cpp: add SetForceManager method to |
5574 |
|
|
integrator |
5575 |
|
|
|
5576 |
gezelter |
2199 |
2004-11-23 18:12 tim |
5577 |
tim |
1779 |
|
5578 |
|
|
* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
5579 |
|
|
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
5580 |
|
|
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
5581 |
|
|
integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, |
5582 |
|
|
integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, |
5583 |
|
|
integrators/NVT.hpp, integrators/Velocitizer.cpp, |
5584 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
5585 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
5586 |
|
|
types/UreyBradleyBendType.hpp: refactory NPT integrator |
5587 |
|
|
|
5588 |
gezelter |
2199 |
2004-11-23 17:50 chrisfen |
5589 |
tim |
1779 |
|
5590 |
|
|
* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
5591 |
|
|
Restraints should work in parallel now |
5592 |
|
|
|
5593 |
gezelter |
2199 |
2004-11-23 17:48 chrisfen |
5594 |
tim |
1779 |
|
5595 |
|
|
* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
5596 |
|
|
brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
5597 |
|
|
integrators/Integrator.cpp, integrators/Integrator.hpp, |
5598 |
|
|
io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, |
5599 |
|
|
io/RestraintReader.cpp, io/RestraintWriter.cpp, |
5600 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
5601 |
|
|
to restraints |
5602 |
|
|
|
5603 |
gezelter |
2199 |
2004-11-23 17:47 chrisfen |
5604 |
tim |
1779 |
|
5605 |
|
|
* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
5606 |
|
|
return to the original on next commit |
5607 |
|
|
|
5608 |
gezelter |
2199 |
2004-11-23 12:53 tim |
5609 |
tim |
1779 |
|
5610 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
5611 |
|
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
5612 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
5613 |
|
|
io/ChargeAtomTypesSectionParser.cpp, |
5614 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, |
5615 |
|
|
io/EAMAtomTypesSectionParser.cpp, |
5616 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
5617 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
5618 |
|
|
io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
5619 |
|
|
utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
5620 |
|
|
|
5621 |
gezelter |
2199 |
2004-11-23 12:53 tim |
5622 |
tim |
1779 |
|
5623 |
|
|
* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
5624 |
|
|
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
5625 |
|
|
branch new_design. |
5626 |
|
|
|
5627 |
gezelter |
2199 |
2004-11-23 12:53 tim |
5628 |
tim |
1779 |
|
5629 |
tim |
2116 |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
5630 |
|
|
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
5631 |
|
|
branch new_design. |
5632 |
tim |
1779 |
|
5633 |
gezelter |
2199 |
2004-11-23 01:03 tim |
5634 |
tim |
1779 |
|
5635 |
|
|
* src/: io/EAMAtomTypesSectionParser.cpp, |
5636 |
|
|
io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
5637 |
|
|
types/AtomType.hpp, types/DirectionalAtomType.cpp, |
5638 |
|
|
types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
5639 |
|
|
|
5640 |
gezelter |
2199 |
2004-11-23 01:03 tim |
5641 |
tim |
1779 |
|
5642 |
tim |
2116 |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
5643 |
|
|
was initially added on branch new_design. |
5644 |
|
|
|
5645 |
gezelter |
2199 |
2004-11-23 01:03 tim |
5646 |
tim |
2116 |
|
5647 |
tim |
1779 |
* src/io/EAMAtomTypesSectionParser.hpp: file |
5648 |
|
|
EAMAtomTypesSectionParser.hpp was initially added on branch |
5649 |
|
|
new_design. |
5650 |
|
|
|
5651 |
gezelter |
2199 |
2004-11-23 01:03 tim |
5652 |
tim |
1779 |
|
5653 |
tim |
2116 |
* src/io/EAMAtomTypesSectionParser.cpp: file |
5654 |
|
|
EAMAtomTypesSectionParser.cpp was initially added on branch |
5655 |
|
|
new_design. |
5656 |
tim |
1779 |
|
5657 |
gezelter |
2199 |
2004-11-22 23:35 tim |
5658 |
tim |
1779 |
|
5659 |
tim |
2116 |
* src/io/TorsionTypesSectionParser.hpp: file |
5660 |
|
|
TorsionTypesSectionParser.hpp was initially added on branch |
5661 |
tim |
1779 |
new_design. |
5662 |
|
|
|
5663 |
gezelter |
2199 |
2004-11-22 23:35 tim |
5664 |
tim |
1779 |
|
5665 |
|
|
* src/io/BendTypesSectionParser.hpp: file |
5666 |
|
|
BendTypesSectionParser.hpp was initially added on branch |
5667 |
|
|
new_design. |
5668 |
|
|
|
5669 |
gezelter |
2199 |
2004-11-22 23:35 tim |
5670 |
tim |
1779 |
|
5671 |
|
|
* src/io/BondTypesSectionParser.hpp: file |
5672 |
|
|
BondTypesSectionParser.hpp was initially added on branch |
5673 |
|
|
new_design. |
5674 |
|
|
|
5675 |
gezelter |
2199 |
2004-11-22 23:35 tim |
5676 |
tim |
1779 |
|
5677 |
tim |
2116 |
* src/io/BondTypesSectionParser.cpp: file |
5678 |
|
|
BondTypesSectionParser.cpp was initially added on branch |
5679 |
tim |
1779 |
new_design. |
5680 |
|
|
|
5681 |
gezelter |
2199 |
2004-11-22 23:35 tim |
5682 |
tim |
1779 |
|
5683 |
tim |
2116 |
* src/io/TorsionTypesSectionParser.cpp: file |
5684 |
|
|
TorsionTypesSectionParser.cpp was initially added on branch |
5685 |
tim |
1779 |
new_design. |
5686 |
|
|
|
5687 |
gezelter |
2199 |
2004-11-22 23:35 tim |
5688 |
tim |
1779 |
|
5689 |
|
|
* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
5690 |
|
|
BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
5691 |
|
|
TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add |
5692 |
|
|
BondTypesSectionParser, BendTypesSectionParser and |
5693 |
|
|
TorsionTypeSectionParser |
5694 |
|
|
|
5695 |
gezelter |
2199 |
2004-11-22 23:35 tim |
5696 |
tim |
1779 |
|
5697 |
tim |
2116 |
* src/io/BendTypesSectionParser.cpp: file |
5698 |
|
|
BendTypesSectionParser.cpp was initially added on branch |
5699 |
|
|
new_design. |
5700 |
|
|
|
5701 |
gezelter |
2199 |
2004-11-22 18:04 tim |
5702 |
tim |
2116 |
|
5703 |
tim |
1779 |
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
5704 |
|
|
DUFF and EAM |
5705 |
|
|
|
5706 |
gezelter |
2199 |
2004-11-22 18:02 tim |
5707 |
tim |
1779 |
|
5708 |
tim |
2116 |
* src/io/: DirectionalAtomTypesParser.hpp, |
5709 |
|
|
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
5710 |
|
|
|
5711 |
gezelter |
2199 |
2004-11-22 18:02 tim |
5712 |
tim |
2116 |
|
5713 |
tim |
1779 |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
5714 |
|
|
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
5715 |
|
|
new_design. |
5716 |
|
|
|
5717 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5718 |
tim |
1779 |
|
5719 |
tim |
2116 |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
5720 |
|
|
DipoleAtomTypesSectionParser.hpp was initially added on branch |
5721 |
|
|
new_design. |
5722 |
tim |
1779 |
|
5723 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5724 |
tim |
1779 |
|
5725 |
tim |
2116 |
* src/io/AtomTypesSectionParser.hpp: file |
5726 |
|
|
AtomTypesSectionParser.hpp was initially added on branch |
5727 |
tim |
1779 |
new_design. |
5728 |
|
|
|
5729 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5730 |
tim |
1779 |
|
5731 |
|
|
* src/io/HarmonicBondTypesSectionParser.hpp: file |
5732 |
|
|
HarmonicBondTypesSectionParser.hpp was initially added on branch |
5733 |
|
|
new_design. |
5734 |
|
|
|
5735 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5736 |
tim |
1779 |
|
5737 |
tim |
2116 |
* src/io/StickyAtomTypesSectionParser.cpp: file |
5738 |
|
|
StickyAtomTypesSectionParser.cpp was initially added on branch |
5739 |
tim |
1779 |
new_design. |
5740 |
|
|
|
5741 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5742 |
tim |
1779 |
|
5743 |
tim |
2116 |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
5744 |
|
|
LennardJonesAtomTypesSectionParser.hpp was initially added on |
5745 |
|
|
branch new_design. |
5746 |
|
|
|
5747 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5748 |
tim |
2116 |
|
5749 |
|
|
* src/io/HarmonicBondTypesSectionParser.cpp: file |
5750 |
|
|
HarmonicBondTypesSectionParser.cpp was initially added on branch |
5751 |
|
|
new_design. |
5752 |
|
|
|
5753 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5754 |
tim |
2116 |
|
5755 |
tim |
2102 |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
5756 |
|
|
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
5757 |
|
|
new_design. |
5758 |
|
|
|
5759 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5760 |
tim |
2102 |
|
5761 |
tim |
2116 |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
5762 |
|
|
was initially added on branch new_design. |
5763 |
|
|
|
5764 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5765 |
tim |
2116 |
|
5766 |
|
|
* src/io/AtomTypesSectionParser.cpp: file |
5767 |
|
|
AtomTypesSectionParser.cpp was initially added on branch |
5768 |
|
|
new_design. |
5769 |
|
|
|
5770 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5771 |
tim |
2116 |
|
5772 |
|
|
* src/io/ChargeAtomTypesSectionParser.cpp: file |
5773 |
|
|
ChargeAtomTypesSectionParser.cpp was initially added on branch |
5774 |
|
|
new_design. |
5775 |
|
|
|
5776 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5777 |
tim |
2116 |
|
5778 |
|
|
* src/io/DipoleAtomTypesSectionParser.cpp: file |
5779 |
|
|
DipoleAtomTypesSectionParser.cpp was initially added on branch |
5780 |
|
|
new_design. |
5781 |
|
|
|
5782 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5783 |
tim |
2116 |
|
5784 |
tim |
2102 |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
5785 |
|
|
LennardJonesAtomTypesSectionParser.cpp was initially added on |
5786 |
tim |
1779 |
branch new_design. |
5787 |
|
|
|
5788 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5789 |
tim |
1779 |
|
5790 |
tim |
2116 |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
5791 |
|
|
ChargeAtomTypesSectionParser.hpp was initially added on branch |
5792 |
tim |
1779 |
new_design. |
5793 |
|
|
|
5794 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5795 |
tim |
1779 |
|
5796 |
tim |
2116 |
* src/io/StickyAtomTypesSectionParser.hpp: file |
5797 |
|
|
StickyAtomTypesSectionParser.hpp was initially added on branch |
5798 |
|
|
new_design. |
5799 |
|
|
|
5800 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5801 |
tim |
2116 |
|
5802 |
|
|
* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
5803 |
|
|
added on branch new_design. |
5804 |
|
|
|
5805 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5806 |
tim |
2116 |
|
5807 |
tim |
2102 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
5808 |
|
|
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
5809 |
|
|
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
5810 |
|
|
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
5811 |
|
|
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
5812 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
5813 |
|
|
io/DipoleAtomTypesSectionParser.cpp, |
5814 |
|
|
io/DipoleAtomTypesSectionParser.hpp, |
5815 |
|
|
io/DirectionalAtomTypesParser.hpp, |
5816 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
5817 |
|
|
io/HarmonicBondTypesSectionParser.cpp, |
5818 |
|
|
io/HarmonicBondTypesSectionParser.hpp, |
5819 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, |
5820 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
5821 |
|
|
io/SectionParser.hpp, io/SectionParserManager.cpp, |
5822 |
|
|
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
5823 |
|
|
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
5824 |
|
|
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
5825 |
|
|
utils/GenericData.hpp: adding section parsers |
5826 |
|
|
|
5827 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5828 |
tim |
2102 |
|
5829 |
tim |
2116 |
* src/io/DirectionalAtomTypesParser.hpp: file |
5830 |
|
|
DirectionalAtomTypesParser.hpp was initially added on branch |
5831 |
tim |
1779 |
new_design. |
5832 |
|
|
|
5833 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5834 |
tim |
1779 |
|
5835 |
tim |
2102 |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
5836 |
tim |
1779 |
was initially added on branch new_design. |
5837 |
|
|
|
5838 |
gezelter |
2199 |
2004-11-22 15:55 tim |
5839 |
tim |
1779 |
|
5840 |
tim |
2116 |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
5841 |
|
|
added on branch new_design. |
5842 |
tim |
1779 |
|
5843 |
gezelter |
2199 |
2004-11-19 17:12 tim |
5844 |
tim |
1779 |
|
5845 |
tim |
2116 |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
5846 |
tim |
1779 |
added on branch new_design. |
5847 |
|
|
|
5848 |
gezelter |
2199 |
2004-11-19 17:12 tim |
5849 |
tim |
1779 |
|
5850 |
|
|
* src/: brains/SimState.cpp, brains/SimState.hpp, |
5851 |
|
|
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
5852 |
|
|
types/FixedBondType.hpp: remove more useless files |
5853 |
|
|
|
5854 |
gezelter |
2199 |
2004-11-19 16:47 tim |
5855 |
tim |
2102 |
|
5856 |
tim |
1779 |
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
5857 |
|
|
integrators/Integrator.cpp, applications/Makedepend: remove more |
5858 |
|
|
useless files |
5859 |
|
|
|
5860 |
gezelter |
2199 |
2004-11-19 16:38 tim |
5861 |
tim |
1779 |
|
5862 |
tim |
2116 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
5863 |
|
|
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
5864 |
|
|
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
5865 |
|
|
integrators/NVT.hpp: refactory integrator |
5866 |
|
|
|
5867 |
gezelter |
2199 |
2004-11-19 16:38 tim |
5868 |
tim |
2116 |
|
5869 |
tim |
1779 |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
5870 |
|
|
branch new_design. |
5871 |
|
|
|
5872 |
gezelter |
2199 |
2004-11-19 16:38 tim |
5873 |
tim |
1779 |
|
5874 |
tim |
2116 |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
5875 |
|
|
branch new_design. |
5876 |
tim |
1779 |
|
5877 |
gezelter |
2199 |
2004-11-19 16:38 tim |
5878 |
tim |
1779 |
|
5879 |
|
|
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
5880 |
|
|
branch new_design. |
5881 |
|
|
|
5882 |
gezelter |
2199 |
2004-11-19 16:38 tim |
5883 |
tim |
1779 |
|
5884 |
tim |
2116 |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
5885 |
|
|
on branch new_design. |
5886 |
tim |
1779 |
|
5887 |
gezelter |
2199 |
2004-11-19 16:38 tim |
5888 |
tim |
1779 |
|
5889 |
tim |
2116 |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
5890 |
tim |
1779 |
branch new_design. |
5891 |
|
|
|
5892 |
gezelter |
2199 |
2004-11-19 15:37 tim |
5893 |
tim |
2102 |
|
5894 |
tim |
2116 |
* forceFields/newDUFF.frc: new DUFF forcefield |
5895 |
tim |
2102 |
|
5896 |
gezelter |
2199 |
2004-11-19 15:23 tim |
5897 |
tim |
1779 |
|
5898 |
tim |
2116 |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
5899 |
|
|
branch new_design. |
5900 |
tim |
1779 |
|
5901 |
gezelter |
2199 |
2004-11-19 15:23 tim |
5902 |
tim |
1779 |
|
5903 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
5904 |
|
|
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
5905 |
|
|
utils/TypeContainer.hpp: add EAM |
5906 |
|
|
|
5907 |
gezelter |
2199 |
2004-11-19 15:23 tim |
5908 |
tim |
1779 |
|
5909 |
|
|
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
5910 |
|
|
branch new_design. |
5911 |
|
|
|
5912 |
gezelter |
2199 |
2004-11-19 13:02 tim |
5913 |
tim |
2102 |
|
5914 |
tim |
1779 |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
5915 |
|
|
error checking |
5916 |
|
|
|
5917 |
gezelter |
2199 |
2004-11-19 12:56 tim |
5918 |
tim |
1779 |
|
5919 |
tim |
2116 |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
5920 |
tim |
1779 |
was initially added on branch new_design. |
5921 |
|
|
|
5922 |
gezelter |
2199 |
2004-11-19 12:56 tim |
5923 |
tim |
1779 |
|
5924 |
tim |
2116 |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
5925 |
tim |
1779 |
was initially added on branch new_design. |
5926 |
|
|
|
5927 |
gezelter |
2199 |
2004-11-19 12:56 tim |
5928 |
tim |
1779 |
|
5929 |
|
|
* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
5930 |
|
|
added on branch new_design. |
5931 |
|
|
|
5932 |
gezelter |
2199 |
2004-11-19 12:56 tim |
5933 |
tim |
1779 |
|
5934 |
|
|
* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
5935 |
|
|
UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
5936 |
|
|
UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, |
5937 |
|
|
integrators/IntegratorFactory.cpp, |
5938 |
|
|
integrators/IntegratorFactory.hpp, integrators/NVE.hpp, |
5939 |
|
|
integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, |
5940 |
|
|
utils/StringTokenizer.cpp: DUFF is almost done except error |
5941 |
|
|
checking |
5942 |
|
|
|
5943 |
gezelter |
2199 |
2004-11-18 19:11 tim |
5944 |
tim |
1779 |
|
5945 |
|
|
* src/UseTheForce/DUFF.cpp: adding DUFF parser |
5946 |
|
|
|
5947 |
gezelter |
2199 |
2004-11-18 18:26 tim |
5948 |
tim |
1779 |
|
5949 |
tim |
2116 |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
5950 |
|
|
initially added on branch new_design. |
5951 |
|
|
|
5952 |
gezelter |
2199 |
2004-11-18 18:26 tim |
5953 |
tim |
2116 |
|
5954 |
tim |
1779 |
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
5955 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
5956 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
5957 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
5958 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
5959 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
5960 |
|
|
types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, |
5961 |
|
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
5962 |
|
|
DUFF parser |
5963 |
|
|
|
5964 |
gezelter |
2199 |
2004-11-18 16:42 tim |
5965 |
tim |
2102 |
|
5966 |
tim |
1779 |
* forceFields/newDUFF.frc: adding new format DUFF force field |
5967 |
|
|
|
5968 |
gezelter |
2199 |
2004-11-18 10:57 chrisfen |
5969 |
tim |
1779 |
|
5970 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
5971 |
|
|
slowed down the force loop |
5972 |
|
|
|
5973 |
gezelter |
2199 |
2004-11-18 00:42 tim |
5974 |
tim |
1779 |
|
5975 |
tim |
2116 |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
5976 |
tim |
1779 |
initially added on branch new_design. |
5977 |
|
|
|
5978 |
gezelter |
2199 |
2004-11-18 00:42 tim |
5979 |
tim |
1779 |
|
5980 |
tim |
2116 |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
5981 |
tim |
1779 |
initially added on branch new_design. |
5982 |
|
|
|
5983 |
gezelter |
2199 |
2004-11-18 00:42 tim |
5984 |
tim |
1779 |
|
5985 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
5986 |
|
|
primitives/Bend.cpp, utils/NumericConstant.cpp, |
5987 |
|
|
utils/NumericConstant.hpp: Adding NumericConstant class |
5988 |
|
|
|
5989 |
gezelter |
2199 |
2004-11-17 23:16 tim |
5990 |
tim |
1779 |
|
5991 |
|
|
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
5992 |
|
|
UseTheForce/ForceFields.hpp: remove more junk files |
5993 |
|
|
|
5994 |
gezelter |
2199 |
2004-11-17 23:12 tim |
5995 |
tim |
1779 |
|
5996 |
|
|
* src/: brains/ForceFields.cpp, brains/SimSetup.cpp, |
5997 |
|
|
brains/SimSetup.hpp, constraints/AbstractClasses.hpp, |
5998 |
|
|
integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, |
5999 |
|
|
primitives/AbstractClasses.hpp, primitives/Bond.cpp, |
6000 |
|
|
primitives/BondExtensions.cpp, primitives/SRI.hpp, |
6001 |
|
|
primitives/TorsionExtensions.cpp: remove some junk files |
6002 |
|
|
|
6003 |
gezelter |
2199 |
2004-11-17 23:07 tim |
6004 |
tim |
1779 |
|
6005 |
|
|
* src/primitives/BendExtensions.cpp: remove some junk files |
6006 |
|
|
|
6007 |
gezelter |
2199 |
2004-11-17 23:04 tim |
6008 |
tim |
1779 |
|
6009 |
|
|
* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, |
6010 |
|
|
QuadraticBondType.hpp: refine QudraticBond |
6011 |
|
|
|
6012 |
gezelter |
2199 |
2004-11-17 22:57 tim |
6013 |
tim |
1779 |
|
6014 |
|
|
* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp |
6015 |
|
|
|
6016 |
gezelter |
2199 |
2004-11-17 22:57 tim |
6017 |
tim |
1779 |
|
6018 |
|
|
* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was |
6019 |
|
|
initially added on branch new_design. |
6020 |
|
|
|
6021 |
gezelter |
2199 |
2004-11-17 16:47 tim |
6022 |
tim |
1779 |
|
6023 |
tim |
2116 |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
6024 |
|
|
was initially added on branch new_design. |
6025 |
|
|
|
6026 |
gezelter |
2199 |
2004-11-17 16:47 tim |
6027 |
tim |
2116 |
|
6028 |
tim |
1779 |
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
6029 |
|
|
added on branch new_design. |
6030 |
|
|
|
6031 |
gezelter |
2199 |
2004-11-17 16:47 tim |
6032 |
tim |
1779 |
|
6033 |
tim |
2116 |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
6034 |
|
|
added on branch new_design. |
6035 |
|
|
|
6036 |
gezelter |
2199 |
2004-11-17 16:47 tim |
6037 |
tim |
2116 |
|
6038 |
tim |
1779 |
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
6039 |
|
|
initially added on branch new_design. |
6040 |
|
|
|
6041 |
gezelter |
2199 |
2004-11-17 16:47 tim |
6042 |
tim |
1779 |
|
6043 |
tim |
2116 |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
6044 |
tim |
1779 |
initially added on branch new_design. |
6045 |
|
|
|
6046 |
gezelter |
2199 |
2004-11-17 16:47 tim |
6047 |
tim |
1779 |
|
6048 |
tim |
2116 |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
6049 |
tim |
1779 |
initially added on branch new_design. |
6050 |
|
|
|
6051 |
gezelter |
2199 |
2004-11-17 16:47 tim |
6052 |
tim |
1779 |
|
6053 |
|
|
* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially |
6054 |
|
|
added on branch new_design. |
6055 |
|
|
|
6056 |
gezelter |
2199 |
2004-11-17 16:47 tim |
6057 |
tim |
1779 |
|
6058 |
|
|
* src/: math/ChebyshevPolynomials.cpp, |
6059 |
|
|
math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, |
6060 |
|
|
primitives/Bend.hpp, primitives/GhostBend.cpp, |
6061 |
|
|
primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, |
6062 |
|
|
primitives/UreyBradleyBend.hpp, types/BondType.hpp, |
6063 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
6064 |
|
|
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
6065 |
|
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
6066 |
|
|
UreyBradleyBend and GhostBend |
6067 |
|
|
|
6068 |
gezelter |
2199 |
2004-11-17 13:58 tim |
6069 |
tim |
2102 |
|
6070 |
tim |
1779 |
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
6071 |
|
|
was initially added on branch new_design. |
6072 |
|
|
|
6073 |
gezelter |
2199 |
2004-11-17 13:58 tim |
6074 |
tim |
1779 |
|
6075 |
|
|
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
6076 |
|
|
was initially added on branch new_design. |
6077 |
|
|
|
6078 |
gezelter |
2199 |
2004-11-17 13:58 tim |
6079 |
tim |
1779 |
|
6080 |
|
|
* src/: math/ChebyshevPolynomials.cpp, |
6081 |
|
|
math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, |
6082 |
|
|
primitives/Bond.hpp, types/CharmmTorsionType.hpp, |
6083 |
|
|
types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, |
6084 |
|
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
6085 |
|
|
stuff and Chebyshev Polynomial |
6086 |
|
|
|
6087 |
gezelter |
2199 |
2004-11-17 13:58 tim |
6088 |
tim |
1779 |
|
6089 |
tim |
2116 |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
6090 |
tim |
1779 |
initially added on branch new_design. |
6091 |
|
|
|
6092 |
gezelter |
2199 |
2004-11-17 01:37 tim |
6093 |
tim |
1779 |
|
6094 |
tim |
2116 |
* src/types/PolynomialTorsionType.hpp: file |
6095 |
|
|
PolynomialTorsionType.hpp was initially added on branch new_design. |
6096 |
tim |
1779 |
|
6097 |
gezelter |
2199 |
2004-11-17 01:37 tim |
6098 |
tim |
1779 |
|
6099 |
|
|
* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was |
6100 |
|
|
initially added on branch new_design. |
6101 |
|
|
|
6102 |
gezelter |
2199 |
2004-11-17 01:37 tim |
6103 |
tim |
1779 |
|
6104 |
|
|
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
6105 |
|
|
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
6106 |
|
|
types/BondType.hpp, types/CharmmTorsionType.cpp, |
6107 |
|
|
types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, |
6108 |
|
|
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
6109 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
6110 |
|
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp, |
6111 |
|
|
utils/StringTokenizer.hpp: add PolynomialBondType, |
6112 |
|
|
PolynomialBendType, PolynomialTorsionType, HarmonicBendType and |
6113 |
|
|
CharmmTorsionType. Need to refine the design and add document for |
6114 |
|
|
them |
6115 |
|
|
|
6116 |
gezelter |
2199 |
2004-11-17 01:37 tim |
6117 |
tim |
1779 |
|
6118 |
tim |
2116 |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
6119 |
|
|
initially added on branch new_design. |
6120 |
|
|
|
6121 |
gezelter |
2199 |
2004-11-17 01:37 tim |
6122 |
tim |
2116 |
|
6123 |
|
|
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
6124 |
|
|
initially added on branch new_design. |
6125 |
|
|
|
6126 |
gezelter |
2199 |
2004-11-17 01:37 tim |
6127 |
tim |
2116 |
|
6128 |
|
|
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
6129 |
|
|
initially added on branch new_design. |
6130 |
|
|
|
6131 |
gezelter |
2199 |
2004-11-16 20:11 tim |
6132 |
tim |
2116 |
|
6133 |
tim |
1779 |
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
6134 |
|
|
TorsionType.hpp: add PolynomialBondType |
6135 |
|
|
|
6136 |
gezelter |
2199 |
2004-11-16 20:11 tim |
6137 |
tim |
1779 |
|
6138 |
|
|
* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was |
6139 |
|
|
initially added on branch new_design. |
6140 |
|
|
|
6141 |
gezelter |
2199 |
2004-11-16 18:20 tim |
6142 |
tim |
1779 |
|
6143 |
|
|
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
6144 |
|
|
on branch new_design. |
6145 |
|
|
|
6146 |
gezelter |
2199 |
2004-11-16 18:20 tim |
6147 |
tim |
1779 |
|
6148 |
tim |
2116 |
* src/math/Polynomial.hpp: Adding Polynomial class |
6149 |
tim |
1779 |
|
6150 |
gezelter |
2199 |
2004-11-16 17:04 gezelter |
6151 |
tim |
1779 |
|
6152 |
|
|
* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially |
6153 |
|
|
added on branch new_design. |
6154 |
|
|
|
6155 |
gezelter |
2199 |
2004-11-16 17:04 gezelter |
6156 |
tim |
1779 |
|
6157 |
tim |
2116 |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
6158 |
|
|
initially added on branch new_design. |
6159 |
|
|
|
6160 |
gezelter |
2199 |
2004-11-16 17:04 gezelter |
6161 |
tim |
2116 |
|
6162 |
tim |
1779 |
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
6163 |
|
|
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
6164 |
|
|
|
6165 |
gezelter |
2199 |
2004-11-16 15:36 tim |
6166 |
tim |
1779 |
|
6167 |
|
|
* src/: primitives/Bend.cpp, primitives/Bend.hpp, |
6168 |
|
|
primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, |
6169 |
|
|
types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and |
6170 |
|
|
TorsionType |
6171 |
|
|
|
6172 |
gezelter |
2199 |
2004-11-15 21:07 tim |
6173 |
tim |
1779 |
|
6174 |
tim |
2116 |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
6175 |
|
|
branch new_design. |
6176 |
|
|
|
6177 |
gezelter |
2199 |
2004-11-15 21:07 tim |
6178 |
tim |
2116 |
|
6179 |
tim |
1779 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
6180 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
6181 |
|
|
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
6182 |
|
|
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
6183 |
|
|
|
6184 |
gezelter |
2199 |
2004-11-15 18:00 tim |
6185 |
tim |
1779 |
|
6186 |
tim |
2116 |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
6187 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
6188 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
6189 |
|
|
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
6190 |
|
|
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
6191 |
tim |
1779 |
|
6192 |
gezelter |
2199 |
2004-11-15 18:00 tim |
6193 |
tim |
1779 |
|
6194 |
|
|
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
6195 |
|
|
was initially added on branch new_design. |
6196 |
|
|
|
6197 |
gezelter |
2199 |
2004-11-15 18:00 tim |
6198 |
tim |
1779 |
|
6199 |
tim |
2116 |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
6200 |
|
|
was initially added on branch new_design. |
6201 |
|
|
|
6202 |
gezelter |
2199 |
2004-11-15 18:00 tim |
6203 |
tim |
2116 |
|
6204 |
tim |
2102 |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
6205 |
|
|
branch new_design. |
6206 |
tim |
1779 |
|
6207 |
gezelter |
2199 |
2004-11-15 13:02 tim |
6208 |
tim |
1779 |
|
6209 |
tim |
2116 |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
6210 |
|
|
initially added on branch new_design. |
6211 |
tim |
1779 |
|
6212 |
gezelter |
2199 |
2004-11-15 13:02 tim |
6213 |
tim |
1779 |
|
6214 |
|
|
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
6215 |
|
|
branch new_design. |
6216 |
|
|
|
6217 |
gezelter |
2199 |
2004-11-15 13:02 tim |
6218 |
tim |
1779 |
|
6219 |
|
|
* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on |
6220 |
|
|
branch new_design. |
6221 |
|
|
|
6222 |
gezelter |
2199 |
2004-11-15 13:02 tim |
6223 |
tim |
1779 |
|
6224 |
|
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
6225 |
|
|
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
6226 |
|
|
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
6227 |
|
|
io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, |
6228 |
|
|
DumpWriter.Next Step is LJFF and integrators |
6229 |
|
|
|
6230 |
gezelter |
2199 |
2004-11-13 00:08 tim |
6231 |
tim |
1779 |
|
6232 |
|
|
* src/: brains/ForceManager.cpp, brains/ForceManager.hpp, |
6233 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
6234 |
|
|
brains/SimInfo.hpp, primitives/Molecule.cpp, |
6235 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, |
6236 |
|
|
refactory, refactory |
6237 |
|
|
|
6238 |
gezelter |
2199 |
2004-11-12 17:43 tim |
6239 |
tim |
1779 |
|
6240 |
|
|
* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, |
6241 |
|
|
StringTokenizer.cpp: bug fix in hasMoreTokens |
6242 |
|
|
|
6243 |
gezelter |
2199 |
2004-11-12 17:28 tim |
6244 |
tim |
1779 |
|
6245 |
|
|
* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was |
6246 |
|
|
initially added on branch new_design. |
6247 |
|
|
|
6248 |
gezelter |
2199 |
2004-11-12 17:28 tim |
6249 |
tim |
1779 |
|
6250 |
|
|
* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding |
6251 |
|
|
StringUtils, a c-style strtok like class, need unit test |
6252 |
|
|
|
6253 |
gezelter |
2199 |
2004-11-12 12:40 tim |
6254 |
tim |
1779 |
|
6255 |
|
|
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
6256 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
6257 |
|
|
brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test |
6258 |
|
|
|
6259 |
gezelter |
2199 |
2004-11-12 02:05 tim |
6260 |
tim |
1779 |
|
6261 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
6262 |
|
|
primitives/CutoffGroup.hpp, primitives/Molecule.cpp: |
6263 |
|
|
MoleculeCreator forget to create CutoffGroups for free atoms |
6264 |
|
|
|
6265 |
gezelter |
2199 |
2004-11-12 01:19 tim |
6266 |
tim |
1779 |
|
6267 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
6268 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
6269 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
6270 |
|
|
io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: |
6271 |
|
|
OOPSE = Object-Obfuscated Parallel Simulation Engine |
6272 |
|
|
|
6273 |
gezelter |
2199 |
2004-11-11 16:48 chrisfen |
6274 |
tim |
1779 |
|
6275 |
|
|
* samples/water/tip3p_ice/tp3.md: working sample |
6276 |
|
|
|
6277 |
gezelter |
2199 |
2004-11-11 16:47 chrisfen |
6278 |
tim |
1779 |
|
6279 |
|
|
* src/restraints/Restraints.cpp: working towards parallel |
6280 |
|
|
restraints |
6281 |
|
|
|
6282 |
gezelter |
2199 |
2004-11-11 16:47 chrisfen |
6283 |
tim |
1779 |
|
6284 |
|
|
* src/integrators/Integrator.cpp: Commented out some write |
6285 |
|
|
statements |
6286 |
|
|
|
6287 |
gezelter |
2199 |
2004-11-11 16:46 chrisfen |
6288 |
tim |
1779 |
|
6289 |
|
|
* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some |
6290 |
|
|
write statements |
6291 |
|
|
|
6292 |
gezelter |
2199 |
2004-11-11 16:46 chrisfen |
6293 |
tim |
1779 |
|
6294 |
|
|
* samples/water/tip3p_ice/tp3.md: Fun with ice |
6295 |
|
|
|
6296 |
gezelter |
2199 |
2004-11-11 11:41 tim |
6297 |
tim |
1779 |
|
6298 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
6299 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
6300 |
|
|
brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, |
6301 |
|
|
brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, |
6302 |
|
|
io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove |
6303 |
|
|
useless mpiSimulation |
6304 |
|
|
|
6305 |
gezelter |
2199 |
2004-11-11 11:41 tim |
6306 |
tim |
1779 |
|
6307 |
|
|
* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on |
6308 |
|
|
branch new_design. |
6309 |
|
|
|
6310 |
gezelter |
2199 |
2004-11-10 17:50 tim |
6311 |
tim |
1779 |
|
6312 |
|
|
* src/: brains/ForceManager.cpp, brains/SimInfo.cpp, |
6313 |
|
|
brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, |
6314 |
|
|
integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo |
6315 |
|
|
|
6316 |
gezelter |
2199 |
2004-11-10 17:01 tim |
6317 |
tim |
1779 |
|
6318 |
|
|
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
6319 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
6320 |
|
|
brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
6321 |
|
|
brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, |
6322 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
6323 |
|
|
io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, |
6324 |
|
|
visitors/AtomVisitor.cpp: another painful day (1) SimCreator, |
6325 |
|
|
SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom |
6326 |
|
|
File will be removed) (3) ForceField (at least LJ) and BondType, |
6327 |
|
|
BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & |
6328 |
|
|
Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint |
6329 |
|
|
|
6330 |
gezelter |
2199 |
2004-11-10 09:52 tim |
6331 |
tim |
1779 |
|
6332 |
|
|
* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a |
6333 |
|
|
configurable StatWriter |
6334 |
|
|
|
6335 |
gezelter |
2199 |
2004-11-10 09:52 tim |
6336 |
tim |
1779 |
|
6337 |
|
|
* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on |
6338 |
|
|
branch new_design. |
6339 |
|
|
|
6340 |
gezelter |
2199 |
2004-11-09 21:58 tim |
6341 |
tim |
1779 |
|
6342 |
|
|
* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation |
6343 |
|
|
in progress |
6344 |
|
|
|
6345 |
gezelter |
2199 |
2004-11-09 18:11 tim |
6346 |
tim |
1779 |
|
6347 |
tim |
2116 |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
6348 |
|
|
added on branch new_design. |
6349 |
|
|
|
6350 |
gezelter |
2199 |
2004-11-09 18:11 tim |
6351 |
tim |
2116 |
|
6352 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: file |
6353 |
|
|
VelocityVerletIntegrator.cpp was initially added on branch |
6354 |
|
|
new_design. |
6355 |
|
|
|
6356 |
gezelter |
2199 |
2004-11-09 18:11 tim |
6357 |
tim |
2116 |
|
6358 |
tim |
1779 |
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
6359 |
|
|
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
6360 |
|
|
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
6361 |
|
|
brains/mpiSimulation.hpp, integrators/Integrator.hpp, |
6362 |
|
|
integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, |
6363 |
|
|
integrators/VelocityVerletIntegrator.hpp: adding ForceManager |
6364 |
|
|
|
6365 |
gezelter |
2199 |
2004-11-09 18:11 tim |
6366 |
tim |
1779 |
|
6367 |
|
|
* src/brains/ForceManager.hpp: file ForceManager.hpp was initially |
6368 |
|
|
added on branch new_design. |
6369 |
|
|
|
6370 |
gezelter |
2199 |
2004-11-09 18:11 tim |
6371 |
tim |
1779 |
|
6372 |
|
|
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
6373 |
|
|
branch new_design. |
6374 |
|
|
|
6375 |
gezelter |
2199 |
2004-11-08 20:08 tim |
6376 |
tim |
2102 |
|
6377 |
tim |
1779 |
* src/integrators/VelocityVerletIntegrator.hpp: file |
6378 |
|
|
VelocityVerletIntegrator.hpp was initially added on branch |
6379 |
|
|
new_design. |
6380 |
|
|
|
6381 |
gezelter |
2199 |
2004-11-08 20:08 tim |
6382 |
tim |
1779 |
|
6383 |
tim |
2116 |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
6384 |
|
|
branch new_design. |
6385 |
|
|
|
6386 |
gezelter |
2199 |
2004-11-08 20:08 tim |
6387 |
tim |
2116 |
|
6388 |
tim |
1779 |
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
6389 |
|
|
integrators/Integrator.hpp, integrators/NVE.hpp, |
6390 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
6391 |
|
|
utils/TypeContainer.hpp: More to break |
6392 |
|
|
|
6393 |
gezelter |
2199 |
2004-11-06 00:21 tim |
6394 |
tim |
2102 |
|
6395 |
tim |
1779 |
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
6396 |
|
|
added on branch new_design. |
6397 |
|
|
|
6398 |
gezelter |
2199 |
2004-11-06 00:21 tim |
6399 |
tim |
1779 |
|
6400 |
|
|
* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, |
6401 |
|
|
UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, |
6402 |
|
|
utils/TypeContainer.hpp, utils/next_combination.hpp: adding |
6403 |
|
|
ForceField and TypeContainer classes |
6404 |
|
|
|
6405 |
gezelter |
2199 |
2004-11-05 18:38 tim |
6406 |
tim |
1779 |
|
6407 |
tim |
2116 |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
6408 |
|
|
initially added on branch new_design. |
6409 |
|
|
|
6410 |
gezelter |
2199 |
2004-11-05 18:38 tim |
6411 |
tim |
2116 |
|
6412 |
tim |
1779 |
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
6413 |
|
|
initially added on branch new_design. |
6414 |
|
|
|
6415 |
gezelter |
2199 |
2004-11-05 18:38 tim |
6416 |
tim |
1779 |
|
6417 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
6418 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
6419 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
6420 |
|
|
brains/SimInfo.hpp, primitives/Molecule.hpp, |
6421 |
|
|
utils/LocalndexManager.hpp: Fix Exclude class etc. |
6422 |
|
|
|
6423 |
gezelter |
2199 |
2004-11-05 16:45 chrisfen |
6424 |
tim |
2102 |
|
6425 |
tim |
1779 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
6426 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the |
6427 |
|
|
linear visitor |
6428 |
|
|
|
6429 |
gezelter |
2199 |
2004-11-05 16:04 chrisfen |
6430 |
tim |
1779 |
|
6431 |
|
|
* src/UseTheForce/DarkSide/shapes.F90: current status of the |
6432 |
|
|
debugging process |
6433 |
|
|
|
6434 |
gezelter |
2199 |
2004-11-05 16:04 chrisfen |
6435 |
tim |
1779 |
|
6436 |
|
|
* make/Makefile.in: included visitors and minimizer |
6437 |
|
|
|
6438 |
gezelter |
2199 |
2004-11-05 16:03 chrisfen |
6439 |
tim |
1779 |
|
6440 |
|
|
* ChangeLog: new changes |
6441 |
|
|
|
6442 |
gezelter |
2199 |
2004-11-04 21:56 tim |
6443 |
tim |
1701 |
|
6444 |
chrisfen |
1714 |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
6445 |
|
|
primitives/Molecule.hpp: Pain...... |
6446 |
tim |
1712 |
|
6447 |
gezelter |
2199 |
2004-11-04 15:55 tim |
6448 |
chrisfen |
1714 |
|
6449 |
|
|
* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
6450 |
|
|
src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
6451 |
|
|
src/brains/Stats.hpp: time to break SimSetup |
6452 |
|
|
|
6453 |
gezelter |
2199 |
2004-11-04 15:51 gezelter |
6454 |
chrisfen |
1714 |
|
6455 |
|
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
6456 |
|
|
classes in progress |
6457 |
|
|
|
6458 |
gezelter |
2199 |
2004-11-04 14:48 tim |
6459 |
tim |
1712 |
|
6460 |
|
|
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
6461 |
tim |
1701 |
branch new_design. |
6462 |
|
|
|
6463 |
gezelter |
2199 |
2004-11-04 14:48 tim |
6464 |
tim |
1712 |
|
6465 |
|
|
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
6466 |
|
|
branch new_design. |
6467 |
|
|
|
6468 |
gezelter |
2199 |
2004-11-04 14:48 tim |
6469 |
tim |
1712 |
|
6470 |
tim |
2116 |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
6471 |
|
|
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
6472 |
|
|
class |
6473 |
|
|
|
6474 |
gezelter |
2199 |
2004-11-04 11:22 gezelter |
6475 |
tim |
2116 |
|
6476 |
tim |
1712 |
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
6477 |
|
|
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
6478 |
|
|
linearAxis are virtual in StuntDouble, but are implemented by |
6479 |
|
|
DirectionalAtom and RigidBody In StuntDouble, they should return |
6480 |
|
|
false and "-1" but there should be logic to figure them out in the |
6481 |
|
|
other two classes |
6482 |
|
|
|
6483 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
6484 |
tim |
1712 |
|
6485 |
|
|
* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
6486 |
|
|
remember what I did |
6487 |
|
|
|
6488 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
6489 |
tim |
1712 |
|
6490 |
|
|
* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
6491 |
|
|
|
6492 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
6493 |
tim |
1712 |
|
6494 |
|
|
* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
6495 |
|
|
in the entry_plug so that it only is set if the atoms really are in |
6496 |
|
|
the simulation |
6497 |
|
|
|
6498 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
6499 |
tim |
1712 |
|
6500 |
|
|
* samples/water/ssd/ssd.md: testing force fields |
6501 |
|
|
|
6502 |
gezelter |
2199 |
2004-11-04 11:19 gezelter |
6503 |
tim |
1712 |
|
6504 |
|
|
* samples/shape/linear.in: testing shapes |
6505 |
|
|
|
6506 |
gezelter |
2199 |
2004-11-03 14:56 tim |
6507 |
tim |
1712 |
|
6508 |
|
|
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
6509 |
|
|
class(similar as SimSetup) |
6510 |
|
|
|
6511 |
gezelter |
2199 |
2004-11-03 14:56 tim |
6512 |
tim |
1712 |
|
6513 |
|
|
* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
6514 |
|
|
added on branch new_design. |
6515 |
|
|
|
6516 |
gezelter |
2199 |
2004-11-03 14:56 tim |
6517 |
chrisfen |
1714 |
|
6518 |
|
|
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
6519 |
|
|
added on branch new_design. |
6520 |
|
|
|
6521 |
gezelter |
2199 |
2004-11-03 13:00 tim |
6522 |
tim |
1712 |
|
6523 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
6524 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
6525 |
|
|
UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, |
6526 |
|
|
brains/DataStorage.hpp, primitives/Atom.hpp, |
6527 |
|
|
primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
6528 |
|
|
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
6529 |
|
|
compiled. Still a long way to go ...... |
6530 |
|
|
|
6531 |
gezelter |
2199 |
2004-11-03 11:08 tim |
6532 |
tim |
1712 |
|
6533 |
|
|
* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
6534 |
|
|
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
6535 |
|
|
src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, |
6536 |
|
|
src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, |
6537 |
|
|
src/io/ZConsReader.cpp, src/primitives/Bend.cpp, |
6538 |
|
|
src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, |
6539 |
|
|
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
6540 |
|
|
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
6541 |
|
|
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
6542 |
|
|
src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, |
6543 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
6544 |
|
|
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
6545 |
|
|
|
6546 |
gezelter |
2199 |
2004-11-02 17:41 tim |
6547 |
tim |
1712 |
|
6548 |
tim |
2116 |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
6549 |
|
|
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
6550 |
|
|
Need unit test |
6551 |
chrisfen |
1714 |
|
6552 |
gezelter |
2199 |
2004-11-02 17:41 tim |
6553 |
chrisfen |
1714 |
|
6554 |
tim |
1712 |
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
6555 |
|
|
initially added on branch new_design. |
6556 |
|
|
|
6557 |
gezelter |
2199 |
2004-11-02 17:41 tim |
6558 |
tim |
1712 |
|
6559 |
tim |
2116 |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
6560 |
|
|
branch new_design. |
6561 |
tim |
1712 |
|
6562 |
gezelter |
2199 |
2004-11-02 11:59 tim |
6563 |
tim |
1712 |
|
6564 |
tim |
2116 |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
6565 |
|
|
branch new_design. |
6566 |
|
|
|
6567 |
gezelter |
2199 |
2004-11-02 11:59 tim |
6568 |
tim |
2116 |
|
6569 |
tim |
2102 |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
6570 |
|
|
SimSnapshotManager.hpp: SimModel in progress |
6571 |
tim |
1712 |
|
6572 |
gezelter |
2199 |
2004-11-02 10:28 chrisfen |
6573 |
tim |
1701 |
|
6574 |
|
|
* src/: UseTheForce/DarkSide/shapes.F90, |
6575 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
6576 |
|
|
looks like it's working |
6577 |
|
|
|
6578 |
gezelter |
2199 |
2004-11-02 10:27 tim |
6579 |
tim |
1701 |
|
6580 |
tim |
2116 |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
6581 |
|
|
functions for dealing with memory issue |
6582 |
|
|
|
6583 |
gezelter |
2199 |
2004-11-02 10:27 tim |
6584 |
tim |
2116 |
|
6585 |
tim |
2102 |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
6586 |
|
|
added on branch new_design. |
6587 |
tim |
1701 |
|
6588 |
gezelter |
2199 |
2004-11-02 10:23 tim |
6589 |
tim |
1701 |
|
6590 |
|
|
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
6591 |
|
|
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
6592 |
|
|
SimModel(something similar as SimInfo) |
6593 |
|
|
|
6594 |
gezelter |
2199 |
2004-11-01 17:52 tim |
6595 |
tim |
1701 |
|
6596 |
|
|
* src/: applications/simpleBuilder/MoLocator.hpp, |
6597 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
6598 |
|
|
brains/DataStorage.hpp, brains/ForceFields.cpp, |
6599 |
|
|
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, |
6600 |
|
|
constraints/ZConstraint.cpp, integrators/Integrator.cpp, |
6601 |
|
|
integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, |
6602 |
|
|
math/SquareMatrix3.hpp, math/Vector3.hpp, |
6603 |
|
|
minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, |
6604 |
|
|
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
6605 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp, |
6606 |
|
|
primitives/RigidBody.hpp, primitives/Torsion.hpp, |
6607 |
|
|
restraints/Restraints.cpp, types/TorsionType.hpp, |
6608 |
|
|
utils/PropertyMap.hpp, utils/StringTokenizer.hpp, |
6609 |
|
|
visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, |
6610 |
|
|
visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
6611 |
|
|
RigidBody and StuntDouble classes get compiled |
6612 |
|
|
|
6613 |
gezelter |
2199 |
2004-11-01 16:40 tim |
6614 |
tim |
1701 |
|
6615 |
tim |
2116 |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
6616 |
|
|
on branch new_design. |
6617 |
|
|
|
6618 |
gezelter |
2199 |
2004-11-01 16:40 tim |
6619 |
tim |
2116 |
|
6620 |
tim |
2102 |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
6621 |
|
|
branch new_design. |
6622 |
tim |
1701 |
|
6623 |
gezelter |
2199 |
2004-11-01 16:40 tim |
6624 |
tim |
1701 |
|
6625 |
|
|
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
6626 |
|
|
branch new_design. |
6627 |
|
|
|
6628 |
gezelter |
2199 |
2004-11-01 16:40 tim |
6629 |
tim |
1701 |
|
6630 |
tim |
2116 |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
6631 |
|
|
version of Bond, Bend and Torsion. |
6632 |
tim |
1701 |
|
6633 |
gezelter |
2199 |
2004-11-01 16:37 tim |
6634 |
tim |
1701 |
|
6635 |
|
|
* src/types/BendType.hpp: file BendType.hpp was initially added on |
6636 |
|
|
branch new_design. |
6637 |
|
|
|
6638 |
gezelter |
2199 |
2004-11-01 16:37 tim |
6639 |
tim |
1701 |
|
6640 |
tim |
2116 |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
6641 |
|
|
BondType, BendType, TorsionType |
6642 |
tim |
1701 |
|
6643 |
gezelter |
2199 |
2004-11-01 16:37 tim |
6644 |
tim |
1701 |
|
6645 |
|
|
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
6646 |
|
|
added on branch new_design. |
6647 |
|
|
|
6648 |
gezelter |
2199 |
2004-11-01 16:37 tim |
6649 |
tim |
1701 |
|
6650 |
tim |
2116 |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
6651 |
|
|
branch new_design. |
6652 |
tim |
1701 |
|
6653 |
gezelter |
2199 |
2004-11-01 15:15 tim |
6654 |
tim |
1701 |
|
6655 |
|
|
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
6656 |
|
|
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
6657 |
|
|
GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, |
6658 |
|
|
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
6659 |
|
|
break, break and break..... |
6660 |
|
|
|
6661 |
gezelter |
2199 |
2004-11-01 14:57 tim |
6662 |
tim |
1701 |
|
6663 |
|
|
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
6664 |
|
|
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
6665 |
|
|
StuntDouble.hpp: these core classes get compiled |
6666 |
|
|
|
6667 |
gezelter |
2199 |
2004-10-29 17:37 tim |
6668 |
tim |
1701 |
|
6669 |
|
|
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
6670 |
|
|
class |
6671 |
|
|
|
6672 |
gezelter |
2199 |
2004-10-29 17:28 chrisfen |
6673 |
tim |
1701 |
|
6674 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
6675 |
|
|
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
6676 |
|
|
types/ShapeAtomType.cpp: still debugging |
6677 |
|
|
|
6678 |
gezelter |
2199 |
2004-10-29 17:28 chrisfen |
6679 |
tim |
1701 |
|
6680 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
6681 |
|
|
shapes rcut calculator added |
6682 |
|
|
|
6683 |
gezelter |
2199 |
2004-10-29 17:27 chrisfen |
6684 |
tim |
1701 |
|
6685 |
|
|
* samples/shape/linear.md: shorter run |
6686 |
|
|
|
6687 |
gezelter |
2199 |
2004-10-29 15:54 tim |
6688 |
tim |
1701 |
|
6689 |
|
|
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
6690 |
|
|
|
6691 |
gezelter |
2199 |
2004-10-29 11:22 tim |
6692 |
tim |
1701 |
|
6693 |
|
|
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
6694 |
|
|
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
6695 |
|
|
some deprecated files |
6696 |
|
|
|
6697 |
gezelter |
2199 |
2004-10-29 11:20 tim |
6698 |
tim |
1701 |
|
6699 |
|
|
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
6700 |
|
|
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
6701 |
|
|
More painful reconstruction is coming !!! |
6702 |
|
|
|
6703 |
gezelter |
2199 |
2004-10-28 17:34 tim |
6704 |
tim |
1701 |
|
6705 |
|
|
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
6706 |
|
|
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
6707 |
|
|
test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, |
6708 |
|
|
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
6709 |
|
|
DirectionalAtom and RigidBody |
6710 |
|
|
|
6711 |
gezelter |
2199 |
2004-10-28 17:26 tim |
6712 |
tim |
1701 |
|
6713 |
|
|
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
6714 |
|
|
src/applications/simpleBuilder/MoLocator.cpp, |
6715 |
|
|
src/applications/simpleBuilder/Vector3d.hpp, |
6716 |
|
|
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
6717 |
|
|
remove old Vector3d.hpp from application/simpleBuilder |
6718 |
|
|
|
6719 |
gezelter |
2199 |
2004-10-28 16:42 tim |
6720 |
tim |
1701 |
|
6721 |
|
|
* src/utils/next_combination.hpp: Minor change in next_combination |
6722 |
|
|
|
6723 |
gezelter |
2199 |
2004-10-28 16:28 tim |
6724 |
tim |
1681 |
|
6725 |
|
|
* src/utils/next_combination.hpp, |
6726 |
|
|
test/utils/NextCombinationTestCase.cpp, |
6727 |
|
|
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
6728 |
|
|
|
6729 |
gezelter |
2199 |
2004-10-28 16:11 tim |
6730 |
tim |
1681 |
|
6731 |
|
|
* src/utils/next_combination.hpp: change documentation of |
6732 |
|
|
next_combination.hpp |
6733 |
|
|
|
6734 |
gezelter |
2199 |
2004-10-28 15:41 tim |
6735 |
tim |
1681 |
|
6736 |
|
|
* ChangeLog, src/utils/next_combination.hpp, |
6737 |
|
|
test/utils/NextCombinationTestCase.cpp, |
6738 |
|
|
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
6739 |
|
|
|
6740 |
gezelter |
2199 |
2004-10-28 15:01 tim |
6741 |
tim |
1681 |
|
6742 |
|
|
* src/utils/next_combination.hpp: adding replace wildcard function |
6743 |
|
|
|
6744 |
gezelter |
2199 |
2004-10-28 14:33 tim |
6745 |
tim |
1681 |
|
6746 |
|
|
* src/utils/next_combination.hpp: Minor change |
6747 |
|
|
|
6748 |
gezelter |
2199 |
2004-10-28 14:06 tim |
6749 |
tim |
1677 |
|
6750 |
|
|
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
6751 |
|
|
src/applications/simpleBuilder/simpleBuilder.cpp, |
6752 |
|
|
src/utils/next_combination.hpp, test/utils/Makefile, |
6753 |
|
|
test/utils/NextCombinationTestCase.cpp, |
6754 |
|
|
test/utils/ReplaceWildCardTestCase.cpp, |
6755 |
|
|
test/utils/next_combination.hpp: STL next_permutation like |
6756 |
|
|
next_combination is working |
6757 |
|
|
|
6758 |
gezelter |
2199 |
2004-10-28 12:22 chrisfen |
6759 |
tim |
1677 |
|
6760 |
|
|
* src/UseTheForce/WATER.cpp: fix of setDipoles |
6761 |
|
|
|
6762 |
gezelter |
2199 |
2004-10-28 12:20 gezelter |
6763 |
tim |
1677 |
|
6764 |
|
|
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
6765 |
|
|
shapeFile |
6766 |
|
|
|
6767 |
gezelter |
2199 |
2004-10-28 12:20 gezelter |
6768 |
tim |
1677 |
|
6769 |
|
|
* samples/shape/linear.md: forgot the orientation line |
6770 |
|
|
|
6771 |
gezelter |
2199 |
2004-10-28 11:56 gezelter |
6772 |
tim |
1677 |
|
6773 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
6774 |
|
|
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
6775 |
|
|
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
6776 |
|
|
declaration foo |
6777 |
|
|
|
6778 |
gezelter |
2199 |
2004-10-28 11:55 gezelter |
6779 |
tim |
1677 |
|
6780 |
|
|
* samples/lipid/5x5.md: uncommented .in line |
6781 |
|
|
|
6782 |
gezelter |
2199 |
2004-10-28 10:42 tim |
6783 |
tim |
1677 |
|
6784 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
6785 |
|
|
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
6786 |
|
|
in progress |
6787 |
|
|
|
6788 |
gezelter |
2199 |
2004-10-28 10:15 tim |
6789 |
tim |
1677 |
|
6790 |
|
|
* test/utils/: NextCombinationTestCase.cpp, |
6791 |
|
|
NextCombinationTestCase.hpp: adding next_combination test case |
6792 |
|
|
|
6793 |
gezelter |
2199 |
2004-10-28 10:02 tim |
6794 |
tim |
1677 |
|
6795 |
|
|
* test/utils/next_combination.hpp: STL Compatible combination |
6796 |
|
|
sequence generator |
6797 |
|
|
|
6798 |
gezelter |
2199 |
2004-10-28 01:23 tim |
6799 |
tim |
1677 |
|
6800 |
|
|
* test/utils/: GenerateCombination.hpp, |
6801 |
|
|
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
6802 |
|
|
|
6803 |
gezelter |
2199 |
2004-10-28 01:16 tim |
6804 |
tim |
1677 |
|
6805 |
|
|
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
6806 |
|
|
next_combination function. |
6807 |
|
|
|
6808 |
gezelter |
2199 |
2004-10-27 22:27 tim |
6809 |
tim |
1677 |
|
6810 |
|
|
* test/utils/ReplaceWildCard.hpp: no message |
6811 |
|
|
|
6812 |
gezelter |
2199 |
2004-10-27 22:14 tim |
6813 |
tim |
1677 |
|
6814 |
|
|
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
6815 |
|
|
ReplaceWildCard(recursive version) is working, need refactoring. An |
6816 |
|
|
iterative version is on the way |
6817 |
|
|
|
6818 |
gezelter |
2199 |
2004-10-27 21:28 tim |
6819 |
tim |
1677 |
|
6820 |
|
|
* test/utils/: Makefile, ReplaceWildCard.hpp, |
6821 |
|
|
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
6822 |
|
|
|
6823 |
gezelter |
2199 |
2004-10-27 21:08 tim |
6824 |
tim |
1677 |
|
6825 |
|
|
* test/utils/: ReplaceWildCardTestCase.cpp, |
6826 |
|
|
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
6827 |
|
|
|
6828 |
gezelter |
2199 |
2004-10-27 18:17 tim |
6829 |
tim |
1677 |
|
6830 |
|
|
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
6831 |
|
|
test |
6832 |
|
|
|
6833 |
gezelter |
2199 |
2004-10-27 01:25 tim |
6834 |
tim |
1677 |
|
6835 |
|
|
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
6836 |
|
|
char matching is on the way |
6837 |
|
|
|
6838 |
gezelter |
2199 |
2004-10-27 01:07 tim |
6839 |
tim |
1677 |
|
6840 |
|
|
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
6841 |
|
|
|
6842 |
gezelter |
2199 |
2004-10-26 22:00 gezelter |
6843 |
tim |
1674 |
|
6844 |
|
|
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
6845 |
|
|
|
6846 |
gezelter |
2199 |
2004-10-26 21:20 gezelter |
6847 |
tim |
1674 |
|
6848 |
|
|
* src/UseTheForce/ForceFields.hpp: subclass foo |
6849 |
|
|
|
6850 |
gezelter |
2199 |
2004-10-26 21:16 gezelter |
6851 |
tim |
1674 |
|
6852 |
|
|
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
6853 |
|
|
string conversion |
6854 |
|
|
|
6855 |
gezelter |
2199 |
2004-10-26 19:01 gezelter |
6856 |
tim |
1674 |
|
6857 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
6858 |
|
|
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
6859 |
|
|
brains/SimSetup.hpp: char* -> string |
6860 |
|
|
|
6861 |
gezelter |
2199 |
2004-10-26 17:25 gezelter |
6862 |
tim |
1674 |
|
6863 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
6864 |
|
|
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
6865 |
|
|
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
6866 |
|
|
isXXX |
6867 |
|
|
|
6868 |
gezelter |
2199 |
2004-10-26 17:25 gezelter |
6869 |
tim |
1674 |
|
6870 |
|
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
6871 |
|
|
define name collision |
6872 |
|
|
|
6873 |
gezelter |
2199 |
2004-10-26 17:24 gezelter |
6874 |
tim |
1674 |
|
6875 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
6876 |
|
|
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
6877 |
|
|
UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
6878 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
6879 |
|
|
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
6880 |
|
|
forcefield refactoring for shapes |
6881 |
|
|
|
6882 |
gezelter |
2199 |
2004-10-26 17:24 gezelter |
6883 |
tim |
1677 |
|
6884 |
|
|
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
6885 |
|
|
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
6886 |
|
|
linear.md, linear.shape, toluene.shape: adding sample shape |
6887 |
|
|
directory |
6888 |
|
|
|
6889 |
gezelter |
2199 |
2004-10-26 17:19 tim |
6890 |
tim |
1674 |
|
6891 |
|
|
* ChangeLog, src/brains/DataStorage.cpp, |
6892 |
|
|
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
6893 |
|
|
test/brains/DataStorageTestCase.cpp, |
6894 |
|
|
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
6895 |
|
|
DataStorage passes unit test |
6896 |
|
|
|
6897 |
gezelter |
2199 |
2004-10-26 13:03 chrisfen |
6898 |
tim |
1674 |
|
6899 |
|
|
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
6900 |
|
|
Changes to help advance shapes |
6901 |
|
|
|
6902 |
gezelter |
2199 |
2004-10-26 13:02 chrisfen |
6903 |
tim |
1674 |
|
6904 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
6905 |
|
|
Shapes force field reader |
6906 |
|
|
|
6907 |
gezelter |
2199 |
2004-10-26 12:28 tim |
6908 |
tim |
1674 |
|
6909 |
|
|
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
6910 |
|
|
SnapshotTestCase in progress |
6911 |
|
|
|
6912 |
gezelter |
2199 |
2004-10-25 17:46 tim |
6913 |
tim |
1648 |
|
6914 |
|
|
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
6915 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
6916 |
|
|
src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
6917 |
|
|
test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
6918 |
|
|
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
6919 |
|
|
and Vector classes |
6920 |
|
|
|
6921 |
gezelter |
2199 |
2004-10-25 12:03 tim |
6922 |
tim |
1644 |
|
6923 |
|
|
* ChangeLog, src/utils/GenericFactory.hpp, |
6924 |
|
|
test/utils/GenericFactoryTestCase.cpp, |
6925 |
|
|
test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
6926 |
|
|
GenericFactory Test Case. GenericFactory now can bed used to creat |
6927 |
|
|
ForcefieldFactory and IntegratorFactory etc. |
6928 |
|
|
|
6929 |
gezelter |
2199 |
2004-10-24 23:08 tim |
6930 |
tim |
1644 |
|
6931 |
|
|
* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
6932 |
|
|
brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
6933 |
|
|
brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
6934 |
|
|
get reconstructed |
6935 |
|
|
|
6936 |
gezelter |
2199 |
2004-10-24 02:55 tim |
6937 |
tim |
1644 |
|
6938 |
|
|
* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
6939 |
|
|
|
6940 |
gezelter |
2199 |
2004-10-23 18:09 tim |
6941 |
tim |
1644 |
|
6942 |
|
|
* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
6943 |
|
|
StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
6944 |
|
|
RigidBody.cpp: Refactoring in progress |
6945 |
|
|
|
6946 |
gezelter |
2199 |
2004-10-22 18:09 tim |
6947 |
tim |
1643 |
|
6948 |
|
|
* ChangeLog, src/brains/Snapshot.hpp, |
6949 |
|
|
src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
6950 |
|
|
test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
6951 |
|
|
test/brains/StuntDouble.hpp: more work in Snapshot |
6952 |
|
|
|
6953 |
gezelter |
2199 |
2004-10-22 17:59 chrisfen |
6954 |
tim |
1643 |
|
6955 |
|
|
* src/: UseTheForce/LJFF.cpp, |
6956 |
|
|
UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
6957 |
|
|
god! It runs and conserves energy! |
6958 |
|
|
|
6959 |
gezelter |
2199 |
2004-10-22 17:54 chrisfen |
6960 |
tim |
1643 |
|
6961 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
6962 |
|
|
|
6963 |
gezelter |
2199 |
2004-10-22 17:53 chrisfen |
6964 |
tim |
1643 |
|
6965 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
6966 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
6967 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
6968 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
6969 |
|
|
breakey |
6970 |
|
|
|
6971 |
gezelter |
2199 |
2004-10-22 17:53 chrisfen |
6972 |
tim |
1643 |
|
6973 |
|
|
* make/Makefile.in: compiler flags |
6974 |
|
|
|
6975 |
gezelter |
2199 |
2004-10-22 16:20 gezelter |
6976 |
tim |
1643 |
|
6977 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
6978 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
6979 |
|
|
brains/fSimulation.h, types/AtomType.hpp, |
6980 |
|
|
types/DirectionalAtomType.hpp: fixey fixey |
6981 |
|
|
|
6982 |
gezelter |
2199 |
2004-10-22 15:22 gezelter |
6983 |
tim |
1643 |
|
6984 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
6985 |
|
|
charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
6986 |
|
|
lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
6987 |
|
|
fortran files and c/Fortran interfaces |
6988 |
|
|
|
6989 |
gezelter |
2199 |
2004-10-22 15:21 gezelter |
6990 |
tim |
1643 |
|
6991 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
6992 |
|
|
DirectionalAtomType.hpp, Makefile: More on AtomType and |
6993 |
|
|
DirectionalAtomType |
6994 |
|
|
|
6995 |
gezelter |
2199 |
2004-10-22 09:47 gezelter |
6996 |
tim |
1639 |
|
6997 |
|
|
* src/types/AtomType.hpp: Adding AtomType |
6998 |
|
|
|
6999 |
gezelter |
2199 |
2004-10-21 16:31 tim |
7000 |
tim |
1639 |
|
7001 |
|
|
* ChangeLog, src/brains/Snapshot.hpp, |
7002 |
|
|
src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
7003 |
|
|
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
7004 |
|
|
src/math/Vector.hpp, src/math/Vector3.hpp, |
7005 |
|
|
test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
7006 |
|
|
Snapshot and SnapshotManager in progress |
7007 |
|
|
|
7008 |
gezelter |
2199 |
2004-10-21 16:30 tim |
7009 |
tim |
1639 |
|
7010 |
|
|
* test/brains/: BrainsTest.cpp, Makefile, |
7011 |
|
|
SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
7012 |
|
|
SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
7013 |
|
|
Snapshot and snapshotManager. |
7014 |
|
|
|
7015 |
gezelter |
2199 |
2004-10-21 15:15 gezelter |
7016 |
tim |
1630 |
|
7017 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
7018 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
7019 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
7020 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
7021 |
|
|
UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
7022 |
|
|
UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
7023 |
|
|
brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
7024 |
|
|
Fixey Fixey. |
7025 |
|
|
|
7026 |
gezelter |
2199 |
2004-10-21 11:32 tim |
7027 |
tim |
1630 |
|
7028 |
|
|
* src/utils/GenericData.cpp, src/utils/Makefile, |
7029 |
|
|
test/utils/Makefile, test/utils/UtilTest: remove some junk files |
7030 |
|
|
|
7031 |
gezelter |
2199 |
2004-10-21 11:24 tim |
7032 |
tim |
1630 |
|
7033 |
|
|
* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
7034 |
|
|
|
7035 |
gezelter |
2199 |
2004-10-21 11:22 tim |
7036 |
tim |
1630 |
|
7037 |
|
|
* ChangeLog, src/brains/SimSetup.cpp, |
7038 |
|
|
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
7039 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
7040 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
7041 |
|
|
src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
7042 |
|
|
src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
7043 |
|
|
src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
7044 |
|
|
src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
7045 |
|
|
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
7046 |
|
|
src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
7047 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
7048 |
|
|
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
7049 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
7050 |
|
|
src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
7051 |
|
|
GenericData |
7052 |
|
|
|
7053 |
gezelter |
2199 |
2004-10-21 10:25 chuckv |
7054 |
tim |
1630 |
|
7055 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
7056 |
|
|
module. |
7057 |
|
|
|
7058 |
gezelter |
2199 |
2004-10-21 10:24 chuckv |
7059 |
tim |
1630 |
|
7060 |
|
|
* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
7061 |
|
|
fortran lj module. |
7062 |
|
|
|
7063 |
gezelter |
2199 |
2004-10-20 17:54 tim |
7064 |
tim |
1625 |
|
7065 |
|
|
* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
7066 |
|
|
test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
7067 |
|
|
test/utils/PropertyMapTestCase.cpp, |
7068 |
|
|
test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
7069 |
|
|
GenericData and PropertyMap pass unit test. |
7070 |
|
|
|
7071 |
gezelter |
2199 |
2004-10-20 16:52 gezelter |
7072 |
tim |
1622 |
|
7073 |
|
|
* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
7074 |
|
|
DarkSide/sticky_interface.h: fixed a fortran name problem |
7075 |
|
|
|
7076 |
gezelter |
2199 |
2004-10-20 16:38 tim |
7077 |
tim |
1622 |
|
7078 |
|
|
* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
7079 |
|
|
GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
7080 |
|
|
UtilTest, UtilTest.cpp: adding generic data test case |
7081 |
|
|
|
7082 |
gezelter |
2199 |
2004-10-20 16:16 chuckv |
7083 |
tim |
1622 |
|
7084 |
|
|
* configure, ac-tools/aclocal.m4, |
7085 |
|
|
src/UseTheForce/DarkSide/Makefile, |
7086 |
|
|
src/UseTheForce/DarkSide/mpiSimulation.F90, |
7087 |
|
|
src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
7088 |
|
|
src/UseTheForce/DarkSide/simParallel.F90, |
7089 |
|
|
src/UseTheForce/DarkSide/simParallel_interface.h, |
7090 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
7091 |
|
|
Fortran/C++ interface de-obfuscation project appears to be |
7092 |
|
|
complete! Woo hoo! |
7093 |
|
|
|
7094 |
gezelter |
2199 |
2004-10-20 15:47 chuckv |
7095 |
tim |
1622 |
|
7096 |
|
|
* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
7097 |
|
|
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
7098 |
|
|
continues |
7099 |
|
|
|
7100 |
gezelter |
2199 |
2004-10-20 15:46 chuckv |
7101 |
tim |
1622 |
|
7102 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
7103 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
7104 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
7105 |
|
|
UseTheForce/doForces_interface.h, |
7106 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
7107 |
|
|
UseTheForce/DarkSide/atype_interface.h, |
7108 |
|
|
UseTheForce/DarkSide/eam_interface.h, |
7109 |
|
|
UseTheForce/DarkSide/gb_interface.h, |
7110 |
|
|
UseTheForce/DarkSide/mpiSimulation_interface.h, |
7111 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
7112 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
7113 |
|
|
UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
7114 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
7115 |
|
|
de-obfuscation project (It is a very long story) |
7116 |
|
|
|
7117 |
gezelter |
2199 |
2004-10-20 13:07 tim |
7118 |
tim |
1622 |
|
7119 |
|
|
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
7120 |
|
|
test/math/SquareMatrix3TestCase.cpp, |
7121 |
|
|
test/math/SquareMatrixTestCase.cpp, |
7122 |
|
|
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
7123 |
|
|
|
7124 |
gezelter |
2199 |
2004-10-20 00:52 tim |
7125 |
tim |
1616 |
|
7126 |
|
|
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
7127 |
|
|
SnapshotManager in design phase |
7128 |
|
|
|
7129 |
gezelter |
2199 |
2004-10-19 23:54 gezelter |
7130 |
tim |
1616 |
|
7131 |
|
|
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
7132 |
|
|
problem prevented linking |
7133 |
|
|
|
7134 |
gezelter |
2199 |
2004-10-19 23:54 gezelter |
7135 |
tim |
1616 |
|
7136 |
|
|
* src/UseTheForce/Shapes_FF.cpp: fixed include |
7137 |
|
|
|
7138 |
gezelter |
2199 |
2004-10-19 23:26 gezelter |
7139 |
tim |
1616 |
|
7140 |
|
|
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
7141 |
|
|
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
7142 |
|
|
more fortran name mangling |
7143 |
|
|
|
7144 |
gezelter |
2199 |
2004-10-19 23:23 gezelter |
7145 |
tim |
1616 |
|
7146 |
|
|
* src/profiling/timing.F90: yet more fortran renaming |
7147 |
|
|
|
7148 |
gezelter |
2199 |
2004-10-19 23:19 gezelter |
7149 |
tim |
1616 |
|
7150 |
|
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
7151 |
|
|
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
7152 |
|
|
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
7153 |
|
|
wrappers.F90: Fortran name cleanup continues |
7154 |
|
|
|
7155 |
gezelter |
2199 |
2004-10-19 23:12 gezelter |
7156 |
tim |
1616 |
|
7157 |
|
|
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
7158 |
|
|
broken fortran stuff |
7159 |
|
|
|
7160 |
gezelter |
2199 |
2004-10-19 23:02 gezelter |
7161 |
tim |
1616 |
|
7162 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
7163 |
|
|
atype_interface.h, atype_module.F90, atype_module_interface.h, |
7164 |
|
|
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
7165 |
|
|
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
7166 |
|
|
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
7167 |
|
|
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
7168 |
|
|
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
7169 |
|
|
mpiSimulation_interface.h, mpiSimulation_module.F90, |
7170 |
|
|
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
7171 |
|
|
shapes_interface.h, shapes_module.h, simulation.F90, |
7172 |
|
|
simulation_interface.h, simulation_module.F90, |
7173 |
|
|
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
7174 |
|
|
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
7175 |
|
|
name sanity on the fortran side |
7176 |
|
|
|
7177 |
gezelter |
2199 |
2004-10-19 19:18 tim |
7178 |
tim |
1616 |
|
7179 |
|
|
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
7180 |
|
|
|
7181 |
gezelter |
2199 |
2004-10-19 18:01 tim |
7182 |
tim |
1616 |
|
7183 |
|
|
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
7184 |
|
|
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
7185 |
|
|
except diagonalize(), all of functions in math library pass the |
7186 |
|
|
test |
7187 |
|
|
|
7188 |
gezelter |
2199 |
2004-10-19 17:43 chuckv |
7189 |
tim |
1616 |
|
7190 |
|
|
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
7191 |
|
|
C-fortran interface functions. |
7192 |
|
|
|
7193 |
gezelter |
2199 |
2004-10-19 17:37 chuckv |
7194 |
tim |
1616 |
|
7195 |
|
|
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
7196 |
|
|
eam_module_inteface.h, gb_module_interface.h, |
7197 |
|
|
mpisimulation_module_interface.h, simulation_module_interface.h, |
7198 |
|
|
sticky_pair_module_interface.h: Added correct prototypes for |
7199 |
|
|
C-fortran interface functions. |
7200 |
|
|
|
7201 |
gezelter |
2199 |
2004-10-19 16:28 tim |
7202 |
tim |
1616 |
|
7203 |
|
|
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
7204 |
|
|
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
7205 |
|
|
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
7206 |
|
|
test/math/RectMatrixTestCase.cpp, |
7207 |
|
|
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
7208 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
7209 |
|
|
bugs get fixed at math library |
7210 |
|
|
|
7211 |
gezelter |
2199 |
2004-10-19 15:43 chuckv |
7212 |
tim |
1616 |
|
7213 |
|
|
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
7214 |
|
|
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
7215 |
|
|
DarkSide/mpisimulation_module_interface.h, |
7216 |
|
|
DarkSide/simulation_module_interface.h, |
7217 |
|
|
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
7218 |
|
|
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
7219 |
|
|
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
7220 |
|
|
DarkSide/simulation_module.F90, do_Forces.F90, |
7221 |
|
|
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
7222 |
|
|
notifycutoffs_module_interface.h: Added new files for fortran |
7223 |
|
|
interface. |
7224 |
|
|
|
7225 |
gezelter |
2199 |
2004-10-19 15:43 gezelter |
7226 |
tim |
1616 |
|
7227 |
|
|
* src/UseTheForce/Makefile: regressing |
7228 |
|
|
|
7229 |
gezelter |
2199 |
2004-10-19 15:40 gezelter |
7230 |
tim |
1616 |
|
7231 |
|
|
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
7232 |
|
|
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
7233 |
|
|
working on shapes for portability |
7234 |
|
|
|
7235 |
gezelter |
2199 |
2004-10-19 15:40 gezelter |
7236 |
tim |
1616 |
|
7237 |
|
|
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
7238 |
|
|
|
7239 |
gezelter |
2199 |
2004-10-19 13:21 chrisfen |
7240 |
tim |
1616 |
|
7241 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
7242 |
|
|
findBegin |
7243 |
|
|
|
7244 |
gezelter |
2199 |
2004-10-18 23:34 tim |
7245 |
tim |
1603 |
|
7246 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
7247 |
|
|
are fixed in Vector class |
7248 |
|
|
|
7249 |
gezelter |
2199 |
2004-10-18 23:28 tim |
7250 |
tim |
1603 |
|
7251 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
7252 |
|
|
some bugs in RectMatrixTestCase |
7253 |
|
|
|
7254 |
gezelter |
2199 |
2004-10-18 23:21 tim |
7255 |
tim |
1603 |
|
7256 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
7257 |
|
|
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
7258 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
7259 |
|
|
test/math/VectorTestCase.hpp: implement more test cases |
7260 |
|
|
|
7261 |
gezelter |
2199 |
2004-10-18 18:13 tim |
7262 |
tim |
1603 |
|
7263 |
|
|
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
7264 |
|
|
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
7265 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
7266 |
|
|
src/utils/StringTokenizer.hpp, test/math/Makefile, |
7267 |
|
|
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
7268 |
|
|
tests on math library |
7269 |
|
|
|
7270 |
gezelter |
2199 |
2004-10-18 16:03 tim |
7271 |
tim |
1603 |
|
7272 |
|
|
* test/math/: Makefile, QuaternionTestCase.cpp, |
7273 |
|
|
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
7274 |
|
|
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
7275 |
|
|
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
7276 |
|
|
more testing units |
7277 |
|
|
|
7278 |
gezelter |
2199 |
2004-10-18 12:07 tim |
7279 |
tim |
1603 |
|
7280 |
|
|
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
7281 |
|
|
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
7282 |
|
|
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
7283 |
|
|
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
7284 |
|
|
|
7285 |
gezelter |
2199 |
2004-10-18 11:30 gezelter |
7286 |
tim |
1603 |
|
7287 |
|
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
7288 |
|
|
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
7289 |
|
|
\phi) |
7290 |
|
|
|
7291 |
gezelter |
2199 |
2004-10-18 11:29 gezelter |
7292 |
tim |
1603 |
|
7293 |
|
|
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
7294 |
|
|
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
7295 |
|
|
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
7296 |
|
|
Shapes into OOPSE |
7297 |
|
|
|
7298 |
gezelter |
2199 |
2004-10-18 10:21 gezelter |
7299 |
tim |
1603 |
|
7300 |
|
|
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
7301 |
|
|
|
7302 |
gezelter |
2199 |
2004-10-18 00:23 tim |
7303 |
tim |
1603 |
|
7304 |
|
|
* test/math/VectorTestCase.hpp: adding vector test case |
7305 |
|
|
|
7306 |
gezelter |
2199 |
2004-10-18 00:23 tim |
7307 |
tim |
1603 |
|
7308 |
|
|
* src/utils/GenericFactory.hpp: adding generic factory and vector |
7309 |
|
|
test case |
7310 |
|
|
|
7311 |
gezelter |
2199 |
2004-10-16 20:19 tim |
7312 |
tim |
1594 |
|
7313 |
|
|
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
7314 |
|
|
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
7315 |
|
|
progress |
7316 |
|
|
|
7317 |
gezelter |
2199 |
2004-10-15 20:31 tim |
7318 |
tim |
1594 |
|
7319 |
|
|
* src/math/Quaternion.hpp: add quaternion class |
7320 |
|
|
|
7321 |
gezelter |
2199 |
2004-10-15 16:11 tim |
7322 |
tim |
1594 |
|
7323 |
|
|
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
7324 |
|
|
IfstrstreamTestCase.hpp: adding test file |
7325 |
|
|
|
7326 |
gezelter |
2199 |
2004-10-15 16:10 tim |
7327 |
tim |
1594 |
|
7328 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
7329 |
|
|
|
7330 |
gezelter |
2199 |
2004-10-15 15:42 tim |
7331 |
tim |
1594 |
|
7332 |
|
|
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
7333 |
|
|
|
7334 |
gezelter |
2199 |
2004-10-15 15:35 tim |
7335 |
tim |
1594 |
|
7336 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
7337 |
|
|
|
7338 |
gezelter |
2199 |
2004-10-15 15:34 tim |
7339 |
tim |
1594 |
|
7340 |
|
|
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
7341 |
|
|
namespace oopse |
7342 |
|
|
|
7343 |
gezelter |
2199 |
2004-10-15 14:38 chuckv |
7344 |
tim |
1594 |
|
7345 |
|
|
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
7346 |
|
|
XLF and XLC. |
7347 |
|
|
|
7348 |
gezelter |
2199 |
2004-10-15 13:28 tim |
7349 |
tim |
1594 |
|
7350 |
|
|
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
7351 |
|
|
adding ifstrstream test case |
7352 |
|
|
|
7353 |
gezelter |
2199 |
2004-10-15 13:20 tim |
7354 |
tim |
1594 |
|
7355 |
|
|
* src/io/basic_ifstrstream.hpp: fix include |
7356 |
|
|
|
7357 |
gezelter |
2199 |
2004-10-15 13:18 tim |
7358 |
tim |
1594 |
|
7359 |
|
|
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
7360 |
|
|
|
7361 |
gezelter |
2199 |
2004-10-15 13:17 tim |
7362 |
tim |
1594 |
|
7363 |
|
|
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
7364 |
|
|
|
7365 |
gezelter |
2199 |
2004-10-15 13:16 tim |
7366 |
tim |
1594 |
|
7367 |
|
|
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
7368 |
|
|
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
7369 |
|
|
|
7370 |
gezelter |
2199 |
2004-10-15 10:37 tim |
7371 |
tim |
1594 |
|
7372 |
|
|
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
7373 |
|
|
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
7374 |
|
|
|
7375 |
gezelter |
2199 |
2004-10-15 10:20 tim |
7376 |
tim |
1594 |
|
7377 |
|
|
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
7378 |
|
|
|
7379 |
gezelter |
2199 |
2004-10-15 10:19 tim |
7380 |
tim |
1594 |
|
7381 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
7382 |
|
|
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
7383 |
|
|
SquareMatrixTestCase class |
7384 |
|
|
|
7385 |
gezelter |
2199 |
2004-10-15 02:52 tim |
7386 |
tim |
1594 |
|
7387 |
|
|
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
7388 |
|
|
|
7389 |
gezelter |
2199 |
2004-10-14 18:28 tim |
7390 |
tim |
1594 |
|
7391 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
7392 |
|
|
Vector.hpp: math library in progress |
7393 |
|
|
|
7394 |
gezelter |
2199 |
2004-10-14 18:27 tim |
7395 |
tim |
1594 |
|
7396 |
|
|
* src/io/FileReader.hpp: FileReader in progress |
7397 |
|
|
|
7398 |
gezelter |
2199 |
2004-10-13 18:53 tim |
7399 |
tim |
1594 |
|
7400 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
7401 |
|
|
test in isOrthogonal of SquareMatrix is failed by some reasons |
7402 |
|
|
|
7403 |
gezelter |
2199 |
2004-10-13 17:28 tim |
7404 |
tim |
1594 |
|
7405 |
|
|
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
7406 |
|
|
class |
7407 |
|
|
|
7408 |
gezelter |
2199 |
2004-10-13 17:27 tim |
7409 |
tim |
1594 |
|
7410 |
|
|
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
7411 |
|
|
RectMatrixTestCase.hpp: adding testing unit |
7412 |
|
|
|
7413 |
gezelter |
2199 |
2004-10-13 17:24 tim |
7414 |
tim |
1594 |
|
7415 |
|
|
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
7416 |
|
|
|
7417 |
gezelter |
2199 |
2004-10-13 01:51 tim |
7418 |
tim |
1594 |
|
7419 |
|
|
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
7420 |
|
|
Vector3.hpp: refactory vector and matrix classes |
7421 |
|
|
|
7422 |
gezelter |
2199 |
2004-10-13 01:50 tim |
7423 |
tim |
1594 |
|
7424 |
|
|
* src/math/Vector3d.hpp: Remove some Makefile.in |
7425 |
|
|
|
7426 |
gezelter |
2199 |
2004-10-12 18:57 tim |
7427 |
tim |
1594 |
|
7428 |
|
|
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
7429 |
|
|
Matrix3x3d.hpp |
7430 |
|
|
|
7431 |
gezelter |
2199 |
2004-10-12 14:08 tim |
7432 |
tim |
1594 |
|
7433 |
|
|
* doc/: cppstyle.html, style.css: adding c++ coding style |
7434 |
|
|
|
7435 |
gezelter |
2199 |
2004-10-11 17:15 tim |
7436 |
tim |
1594 |
|
7437 |
|
|
* src/: constraints/AbstractClasses.hpp, |
7438 |
|
|
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
7439 |
|
|
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
7440 |
|
|
|
7441 |
gezelter |
2199 |
2004-10-11 16:54 tim |
7442 |
tim |
1594 |
|
7443 |
|
|
* scripts/filepp: fix a bug in filepp |
7444 |
|
|
|
7445 |
gezelter |
2199 |
2004-10-11 16:13 tim |
7446 |
tim |
1594 |
|
7447 |
|
|
* make/Makefile.in: using filepp to generate dependencies instead |
7448 |
|
|
of compilers |
7449 |
|
|
|
7450 |
gezelter |
2199 |
2004-10-11 16:10 tim |
7451 |
tim |
1594 |
|
7452 |
|
|
* scripts/filepp: filepp can be used to generate dependencies for |
7453 |
|
|
c/c++ now |
7454 |
|
|
|
7455 |
gezelter |
2199 |
2004-10-11 13:40 tim |
7456 |
tim |
1594 |
|
7457 |
|
|
* make/Makefile.in: remove -module from F90Options |
7458 |
|
|
|
7459 |
gezelter |
2199 |
2004-10-11 13:01 tim |
7460 |
tim |
1594 |
|
7461 |
|
|
* make/Makefile.in: adding rules to move fortran 90 module to |
7462 |
|
|
target directory |
7463 |
|
|
|
7464 |
gezelter |
2199 |
2004-10-11 10:43 gezelter |
7465 |
tim |
1594 |
|
7466 |
|
|
* make/Makefile.in: fixed makefile.in |
7467 |
|
|
|
7468 |
gezelter |
2199 |
2004-10-11 09:51 tim |
7469 |
tim |
1594 |
|
7470 |
|
|
* scripts/filepp: remove "use bytes" which causes problem in sgi |
7471 |
|
|
machine |
7472 |
|
|
|
7473 |
gezelter |
2199 |
2004-10-11 09:26 tim |
7474 |
tim |
1594 |
|
7475 |
|
|
* forceFields/Makefile: add Makefile |
7476 |
|
|
|
7477 |
gezelter |
2199 |
2004-10-11 09:23 tim |
7478 |
tim |
1594 |
|
7479 |
|
|
* samples/: water/dimer/Makefile, water/spce/Makefile, |
7480 |
|
|
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
7481 |
|
|
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
7482 |
|
|
directory |
7483 |
|
|
|
7484 |
gezelter |
2199 |
2004-10-11 09:23 tim |
7485 |
tim |
1594 |
|
7486 |
gezelter |
2199 |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
7487 |
|
|
Makefile |
7488 |
tim |
1594 |
|
7489 |
gezelter |
2199 |
2004-10-09 01:01 tim |
7490 |
tim |
1594 |
|
7491 |
gezelter |
2199 |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
7492 |
|
|
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
7493 |
|
|
Remove some Makefile.in |
7494 |
|
|
|
7495 |
|
|
2004-10-08 18:15 tim |
7496 |
|
|
|
7497 |
tim |
1594 |
* make/Makefile.in: [no log message] |
7498 |
|
|
|
7499 |
gezelter |
2199 |
2004-10-08 17:51 tim |
7500 |
tim |
1594 |
|
7501 |
|
|
* make/Makefile.in: fix make install |
7502 |
|
|
|
7503 |
gezelter |
2199 |
2004-10-08 17:10 tim |
7504 |
tim |
1594 |
|
7505 |
|
|
* make/Makefile.in: adding make install |
7506 |
|
|
|
7507 |
gezelter |
2199 |
2004-10-08 17:04 tim |
7508 |
tim |
1594 |
|
7509 |
gezelter |
2199 |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
7510 |
|
|
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
7511 |
|
|
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
7512 |
tim |
1594 |
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
7513 |
|
|
water/ssde/Makefile, water/ssde/Makefile.in, |
7514 |
|
|
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
7515 |
|
|
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
7516 |
|
|
zcons/Makefile.in: add Makefile to sample directory |
7517 |
|
|
|
7518 |
gezelter |
2199 |
2004-10-06 18:03 gezelter |
7519 |
tim |
1594 |
|
7520 |
|
|
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
7521 |
|
|
stuff |
7522 |
|
|
|
7523 |
gezelter |
2199 |
2004-10-06 18:03 gezelter |
7524 |
tim |
1594 |
|
7525 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
7526 |
|
|
make/Doxyfile, src/applications/getopt.c, |
7527 |
|
|
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
7528 |
|
|
build fixes |
7529 |
|
|
|
7530 |
gezelter |
2199 |
2004-10-06 17:20 tim |
7531 |
tim |
1594 |
|
7532 |
|
|
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
7533 |
|
|
|
7534 |
gezelter |
2199 |
2004-10-06 17:19 tim |
7535 |
tim |
1594 |
|
7536 |
|
|
* scripts/filepp: filepp can handle different fortran module case |
7537 |
|
|
and suffix |
7538 |
|
|
|
7539 |
gezelter |
2199 |
2004-10-06 16:27 gezelter |
7540 |
tim |
1594 |
|
7541 |
|
|
* src/restraints/Restraints.cpp: Chris doesn't know about the |
7542 |
|
|
OOPSE-2.0 directory structure yet |
7543 |
|
|
|
7544 |
gezelter |
2199 |
2004-10-06 16:27 gezelter |
7545 |
tim |
1594 |
|
7546 |
|
|
* ChangeLog: Yeah yeah, we'lll get around to it later |
7547 |
|
|
|
7548 |
gezelter |
2199 |
2004-10-06 16:22 gezelter |
7549 |
gezelter |
1490 |
|
7550 |
tim |
1594 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
7551 |
|
|
make/Makefile.in: cleaning up build process |
7552 |
gezelter |
1490 |
|
7553 |
gezelter |
2199 |
2004-10-06 15:01 chrisfen |
7554 |
tim |
1594 |
|
7555 |
|
|
* src/restraints/Restraints.cpp: made the file reading in |
7556 |
|
|
restraints more intelligent - no longer gives uninformative seg |
7557 |
|
|
faults |
7558 |
|
|
|
7559 |
gezelter |
2199 |
2004-10-06 14:55 gezelter |
7560 |
tim |
1594 |
|
7561 |
|
|
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
7562 |
|
|
|
7563 |
gezelter |
2199 |
2004-10-06 14:51 gezelter |
7564 |
gezelter |
1490 |
|
7565 |
tim |
1594 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
7566 |
|
|
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
7567 |
gezelter |
1490 |
|
7568 |
gezelter |
2199 |
2004-10-06 13:53 tim |
7569 |
tim |
1594 |
|
7570 |
|
|
* make/: Makefile, Makefile.in: fix make statistics |
7571 |
|
|
|
7572 |
gezelter |
2199 |
2004-10-06 13:18 tim |
7573 |
tim |
1594 |
|
7574 |
|
|
* make/: Makefile, Makefile.in: adding GNU make functions to |
7575 |
|
|
combine all of the static libraries to a big library |
7576 |
|
|
|
7577 |
gezelter |
2199 |
2004-10-05 17:57 tim |
7578 |
tim |
1594 |
|
7579 |
|
|
* make/: Makefile, Makefile.in: adding shared library flag |
7580 |
|
|
|
7581 |
gezelter |
2199 |
2004-10-05 14:37 tim |
7582 |
tim |
1594 |
|
7583 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
7584 |
|
|
UseTheForce/mpiSimulation_module.F90, |
7585 |
|
|
UseTheForce/DarkSide/Makefile, |
7586 |
|
|
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
7587 |
|
|
mpiSimulation_module to DarkSide |
7588 |
|
|
|
7589 |
gezelter |
2199 |
2004-10-05 14:35 tim |
7590 |
tim |
1594 |
|
7591 |
|
|
* make/: Makefile, Makefile.in: building MPI version;using static |
7592 |
|
|
library instead of shared library |
7593 |
|
|
|
7594 |
gezelter |
2199 |
2004-10-05 09:14 tim |
7595 |
tim |
1594 |
|
7596 |
|
|
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
7597 |
|
|
to filepp |
7598 |
|
|
|
7599 |
gezelter |
2199 |
2004-10-04 15:56 tim |
7600 |
tim |
1594 |
|
7601 |
|
|
* make/: Makefile, Makefile.in: add make cvslog |
7602 |
|
|
|
7603 |
gezelter |
2199 |
2004-10-04 11:24 gezelter |
7604 |
tim |
1594 |
|
7605 |
|
|
* make/: Makefile, Makefile.in: more work on the parallel build |
7606 |
|
|
|
7607 |
gezelter |
2199 |
2004-10-04 11:06 gezelter |
7608 |
tim |
1594 |
|
7609 |
|
|
* make/: Makefile, Makefile.in: changes to backport declare flags |
7610 |
|
|
|
7611 |
gezelter |
2199 |
2004-10-04 10:27 gezelter |
7612 |
tim |
1594 |
|
7613 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
7614 |
|
|
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
7615 |
|
|
shapes |
7616 |
|
|
|
7617 |
gezelter |
2199 |
2004-10-01 23:40 tim |
7618 |
tim |
1594 |
|
7619 |
|
|
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
7620 |
|
|
|
7621 |
gezelter |
2199 |
2004-10-01 23:22 tim |
7622 |
tim |
1594 |
|
7623 |
|
|
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
7624 |
|
|
|
7625 |
gezelter |
2199 |
2004-10-01 16:59 tim |
7626 |
tim |
1594 |
|
7627 |
|
|
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
7628 |
|
|
|
7629 |
gezelter |
2199 |
2004-10-01 16:22 gezelter |
7630 |
gezelter |
1490 |
|
7631 |
tim |
1594 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
7632 |
|
|
few minor build changes |
7633 |
gezelter |
1490 |
|
7634 |
gezelter |
2199 |
2004-10-01 16:11 tim |
7635 |
tim |
1594 |
|
7636 |
|
|
* scripts/filepp: adding fortran90 make dependency tool |
7637 |
|
|
|
7638 |
gezelter |
2199 |
2004-09-30 10:41 tim |
7639 |
tim |
1594 |
|
7640 |
|
|
* make/: Makefile, Makefile.in: make clean is smart enough to only |
7641 |
|
|
remove object files belong to current package. turn off silent |
7642 |
|
|
mode |
7643 |
|
|
|
7644 |
gezelter |
2199 |
2004-09-29 16:55 tim |
7645 |
tim |
1594 |
|
7646 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
7647 |
|
|
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
7648 |
|
|
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
7649 |
|
|
brains/Makedepend, brains/Makefile, constraints/Makefile, |
7650 |
|
|
integrators/Makefile, io/Makefile, math/Makefile, |
7651 |
|
|
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
7652 |
|
|
restraints/Makefile, types/Makefile, utils/Makefile, |
7653 |
|
|
visitors/Makefile: define DEV_ROOT as relative path |
7654 |
|
|
|
7655 |
gezelter |
2199 |
2004-09-29 16:54 tim |
7656 |
tim |
1594 |
|
7657 |
|
|
* make/: Makefile, Makefile.in: get the relative path by shell |
7658 |
|
|
script |
7659 |
|
|
|
7660 |
gezelter |
2199 |
2004-09-29 16:32 tim |
7661 |
tim |
1594 |
|
7662 |
|
|
* make/Makefile: eliminate DEV_ROOT by relative path |
7663 |
|
|
|
7664 |
gezelter |
2199 |
2004-09-29 13:37 tim |
7665 |
tim |
1594 |
|
7666 |
|
|
* make/Makefile.in: add PackageLibs; fix dependency rule |
7667 |
|
|
|
7668 |
gezelter |
2199 |
2004-09-29 12:57 gezelter |
7669 |
gezelter |
1490 |
|
7670 |
gezelter |
1536 |
* configure, ac-tools/configure.in: updates |
7671 |
gezelter |
1490 |
|
7672 |
gezelter |
2199 |
2004-09-29 12:56 gezelter |
7673 |
tim |
1594 |
|
7674 |
chrisfen |
2337 |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
7675 |
tim |
1594 |
|
7676 |
gezelter |
2199 |
2004-09-29 12:46 tim |
7677 |
gezelter |
1490 |
|
7678 |
gezelter |
1536 |
* Makefile: If makefile does not exist, print error message |
7679 |
gezelter |
1490 |
|
7680 |
gezelter |
2199 |
2004-09-29 12:12 tim |
7681 |
tim |
1594 |
|
7682 |
|
|
* make/: Make.conf.in, Makefile: fix dependencies rule |
7683 |
|
|
|
7684 |
gezelter |
2199 |
2004-09-29 10:58 gezelter |
7685 |
gezelter |
1490 |
|
7686 |
tim |
1594 |
* Makefile, make/Makefile: still working on build process |
7687 |
gezelter |
1490 |
|
7688 |
gezelter |
2199 |
2004-09-29 10:00 tim |
7689 |
tim |
1594 |
|
7690 |
|
|
* make/Makefile: add print statment to rules |
7691 |
|
|
|
7692 |
gezelter |
2199 |
2004-09-29 09:59 tim |
7693 |
tim |
1594 |
|
7694 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
7695 |
|
|
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
7696 |
|
|
applications/simpleBuilder/Makefile, brains/Makefile, |
7697 |
|
|
constraints/Makefile, integrators/Makefile, io/Makefile, |
7698 |
|
|
math/Makefile, minimizers/Makefile, primitives/Makefile, |
7699 |
|
|
profiling/Makefile, restraints/Makefile, types/Makefile, |
7700 |
|
|
utils/Makefile, visitors/Makefile: change Makefile to relative path |
7701 |
|
|
|
7702 |
gezelter |
2199 |
2004-09-28 21:55 tim |
7703 |
tim |
1594 |
|
7704 |
|
|
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
7705 |
|
|
which cause headache in bulding libutils |
7706 |
|
|
|
7707 |
gezelter |
2199 |
2004-09-28 18:24 tim |
7708 |
tim |
1594 |
|
7709 |
|
|
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
7710 |
|
|
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
7711 |
|
|
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
7712 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
7713 |
|
|
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
7714 |
|
|
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
7715 |
|
|
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
7716 |
|
|
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
7717 |
|
|
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
7718 |
|
|
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
7719 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
7720 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
7721 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
7722 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
7723 |
|
|
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
7724 |
|
|
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
7725 |
|
|
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
7726 |
|
|
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
7727 |
|
|
change directory structure of application. Every executable file is |
7728 |
|
|
replaced in seperate directory |
7729 |
|
|
|
7730 |
gezelter |
2199 |
2004-09-28 17:15 gezelter |
7731 |
tim |
1594 |
|
7732 |
|
|
* lib/dummy: Keep that lib around, please. |
7733 |
|
|
|
7734 |
gezelter |
2199 |
2004-09-28 17:14 gezelter |
7735 |
gezelter |
1490 |
|
7736 |
tim |
1594 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
7737 |
|
|
starting a configure version |
7738 |
gezelter |
1490 |
|
7739 |
gezelter |
2199 |
2004-09-28 16:08 tim |
7740 |
tim |
1594 |
|
7741 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
7742 |
|
|
UseTheForce/DarkSide/Makefile, |
7743 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
7744 |
|
|
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
7745 |
|
|
brains/Makefile, brains/simulation_module.F90: move fortran files |
7746 |
|
|
around to solve dependency problem |
7747 |
|
|
|
7748 |
gezelter |
2199 |
2004-09-28 15:43 tim |
7749 |
gezelter |
1490 |
|
7750 |
tim |
1594 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
7751 |
|
|
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
7752 |
|
|
src/applications/Makedepend, src/applications/Makefile, |
7753 |
|
|
src/brains/Makedepend, src/brains/simulation_module.F90, |
7754 |
|
|
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
7755 |
|
|
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
7756 |
|
|
src/utils/Makefile: [no log message] |
7757 |
gezelter |
1490 |
|
7758 |
gezelter |
2199 |
2004-09-28 15:41 tim |
7759 |
tim |
1594 |
|
7760 |
|
|
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
7761 |
|
|
problem |
7762 |
|
|
|
7763 |
gezelter |
2199 |
2004-09-28 11:13 tim |
7764 |
tim |
1594 |
|
7765 |
|
|
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
7766 |
|
|
src/io/Makefile: add yacc and lex rules |
7767 |
|
|
|
7768 |
gezelter |
2199 |
2004-09-27 15:24 tim |
7769 |
tim |
1594 |
|
7770 |
|
|
* make/Makefile: adding include path to F90Options |
7771 |
|
|
|
7772 |
gezelter |
2199 |
2004-09-27 15:13 tim |
7773 |
tim |
1594 |
|
7774 |
|
|
* make/Makefile: change suffix from .cc to .cpp |
7775 |
|
|
|
7776 |
gezelter |
2199 |
2004-09-24 11:27 tim |
7777 |
tim |
1594 |
|
7778 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
7779 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
7780 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
7781 |
|
|
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
7782 |
|
|
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
7783 |
|
|
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
7784 |
|
|
UseTheForce/DarkSide/calc_LJ_FF.F90, |
7785 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
7786 |
|
|
UseTheForce/DarkSide/switch_module.F90, |
7787 |
|
|
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
7788 |
|
|
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
7789 |
|
|
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
7790 |
|
|
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
7791 |
|
|
applications/MoLocator.cpp, applications/MoLocator.hpp, |
7792 |
|
|
applications/cmdline.c, applications/nanoBuilder.cpp, |
7793 |
|
|
applications/oopse.cpp, applications/simpleBuilder.cpp, |
7794 |
|
|
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
7795 |
|
|
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
7796 |
|
|
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
7797 |
|
|
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
7798 |
|
|
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
7799 |
|
|
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
7800 |
|
|
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
7801 |
|
|
integrators/Integrator.hpp, integrators/NPT.cpp, |
7802 |
|
|
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
7803 |
|
|
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
7804 |
|
|
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
7805 |
|
|
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
7806 |
|
|
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
7807 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
7808 |
|
|
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
7809 |
|
|
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
7810 |
|
|
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
7811 |
|
|
math/MatVec3.h, math/randomSPRNG.cpp, |
7812 |
|
|
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
7813 |
|
|
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
7814 |
|
|
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
7815 |
|
|
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
7816 |
|
|
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
7817 |
|
|
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
7818 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
7819 |
|
|
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
7820 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
7821 |
|
|
primitives/RigidBody.hpp, primitives/SRI.hpp, |
7822 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
7823 |
|
|
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
7824 |
|
|
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
7825 |
|
|
restraints/Restraints.hpp, types/AtomStamp.cpp, |
7826 |
|
|
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
7827 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
7828 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
7829 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, |
7830 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
7831 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
7832 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
7833 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
7834 |
|
|
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
7835 |
|
|
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
7836 |
|
|
utils/simError.c, visitors/AtomVisitor.cpp, |
7837 |
|
|
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
7838 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
7839 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
7840 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
7841 |
|
|
visitors/ZconsVisitor.hpp: change the #include in source files |
7842 |
|
|
|
7843 |
gezelter |
2199 |
2004-09-23 23:16 gezelter |
7844 |
gezelter |
1490 |
|
7845 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
7846 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
7847 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
7848 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
7849 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
7850 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
7851 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
7852 |
|
|
src/UseTheForce/fForceField.h, |
7853 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
7854 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
7855 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
7856 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
7857 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
7858 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
7859 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
7860 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
7861 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
7862 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
7863 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
7864 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
7865 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
7866 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
7867 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
7868 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
7869 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
7870 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
7871 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
7872 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
7873 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
7874 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
7875 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
7876 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
7877 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
7878 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
7879 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
7880 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
7881 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
7882 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
7883 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
7884 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
7885 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
7886 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
7887 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
7888 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
7889 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
7890 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
7891 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
7892 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
7893 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
7894 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
7895 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
7896 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
7897 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
7898 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
7899 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
7900 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
7901 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
7902 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
7903 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
7904 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
7905 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
7906 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
7907 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
7908 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
7909 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
7910 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
7911 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
7912 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
7913 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
7914 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
7915 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
7916 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
7917 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
7918 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
7919 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
7920 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
7921 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
7922 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
7923 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
7924 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
7925 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
7926 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
7927 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
7928 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
7929 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
7930 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
7931 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
7932 |
|
|
src/utils/simError.c, src/utils/simError.h, |
7933 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
7934 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
7935 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
7936 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
7937 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
7938 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
7939 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
7940 |
chrisfen |
2337 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
7941 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
7942 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
7943 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
7944 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
7945 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
7946 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
7947 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
7948 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
7949 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
7950 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
7951 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
7952 |
|
|
src/applications/LatticeCreator.cpp, |
7953 |
|
|
src/applications/LatticeCreator.hpp, |
7954 |
|
|
src/applications/LatticeFactory.cpp, |
7955 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
7956 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
7957 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
7958 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
7959 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
7960 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
7961 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
7962 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
7963 |
|
|
src/applications/simpleBuilder.ggo, |
7964 |
|
|
src/applications/simpleBuilderCmd.c, |
7965 |
|
|
src/integrators/AbstractClasses.hpp, |
7966 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
7967 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
7968 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
7969 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
7970 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
7971 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
7972 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
7973 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
7974 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
7975 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
7976 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
7977 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
7978 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
7979 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
7980 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
7981 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
7982 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
7983 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
7984 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
7985 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
7986 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
7987 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
7988 |
gezelter |
2199 |
samples/argon/500.in, samples/argon/500.md, |
7989 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
7990 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
7991 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
7992 |
tim |
1594 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
7993 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
7994 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
7995 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
7996 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
7997 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
7998 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
7999 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
8000 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
8001 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
8002 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
8003 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
8004 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
8005 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
8006 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
8007 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
8008 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
8009 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
8010 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
8011 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
8012 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
8013 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
8014 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
8015 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
8016 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
8017 |
gezelter |
1490 |
|
8018 |
gezelter |
2199 |
2004-09-23 23:16 gezelter |
8019 |
gezelter |
1490 |
|
8020 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
8021 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
8022 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
8023 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
8024 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
8025 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
8026 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
8027 |
|
|
src/UseTheForce/fForceField.h, |
8028 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
8029 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
8030 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
8031 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
8032 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
8033 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
8034 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
8035 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
8036 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
8037 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
8038 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
8039 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
8040 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
8041 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
8042 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
8043 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
8044 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
8045 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
8046 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
8047 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
8048 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
8049 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
8050 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
8051 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
8052 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
8053 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
8054 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
8055 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
8056 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
8057 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
8058 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
8059 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
8060 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
8061 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
8062 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
8063 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
8064 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
8065 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
8066 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
8067 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
8068 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
8069 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
8070 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
8071 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
8072 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
8073 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
8074 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
8075 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
8076 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
8077 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
8078 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
8079 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
8080 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
8081 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
8082 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
8083 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
8084 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
8085 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
8086 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
8087 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
8088 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
8089 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
8090 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
8091 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
8092 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
8093 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
8094 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
8095 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
8096 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
8097 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
8098 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
8099 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
8100 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
8101 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
8102 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
8103 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
8104 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
8105 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
8106 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
8107 |
|
|
src/utils/simError.c, src/utils/simError.h, |
8108 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
8109 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
8110 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
8111 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
8112 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
8113 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
8114 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
8115 |
chrisfen |
2337 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
8116 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
8117 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
8118 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
8119 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
8120 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
8121 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
8122 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
8123 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
8124 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
8125 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
8126 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
8127 |
|
|
src/applications/LatticeCreator.cpp, |
8128 |
|
|
src/applications/LatticeCreator.hpp, |
8129 |
|
|
src/applications/LatticeFactory.cpp, |
8130 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
8131 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
8132 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
8133 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
8134 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
8135 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
8136 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
8137 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
8138 |
|
|
src/applications/simpleBuilder.ggo, |
8139 |
|
|
src/applications/simpleBuilderCmd.c, |
8140 |
|
|
src/integrators/AbstractClasses.hpp, |
8141 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
8142 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
8143 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
8144 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
8145 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
8146 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
8147 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
8148 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
8149 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
8150 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
8151 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
8152 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
8153 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
8154 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
8155 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
8156 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
8157 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
8158 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
8159 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
8160 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
8161 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
8162 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
8163 |
gezelter |
2199 |
samples/argon/500.in, samples/argon/500.md, |
8164 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
8165 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
8166 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
8167 |
tim |
1594 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
8168 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
8169 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
8170 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
8171 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
8172 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
8173 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
8174 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
8175 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
8176 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
8177 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
8178 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
8179 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
8180 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
8181 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
8182 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
8183 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
8184 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
8185 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
8186 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
8187 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
8188 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
8189 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
8190 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
8191 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Initial revision |
8192 |
gezelter |
1490 |
|