1 |
mmeineke |
705 |
2003-08-18 15:59 chuckv |
2 |
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3 |
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* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
4 |
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latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
5 |
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sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
6 |
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Nanobuilder still broke. |
7 |
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8 |
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2003-08-15 14:24 tim |
9 |
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10 |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, |
11 |
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libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
12 |
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libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
13 |
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libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, |
14 |
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libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
15 |
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Method |
16 |
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17 |
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2003-08-14 11:16 tim |
18 |
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19 |
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* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
20 |
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with average force substraction strategy |
21 |
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22 |
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2003-08-13 16:20 chuckv |
23 |
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24 |
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* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
25 |
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profiling code -DPROFILE. |
26 |
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27 |
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2003-08-13 14:21 tim |
28 |
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29 |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, |
30 |
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libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
31 |
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libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
32 |
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potential & z-contraint method |
33 |
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34 |
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2003-08-12 16:44 mmeineke |
35 |
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36 |
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* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
37 |
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libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
38 |
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libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
39 |
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libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really |
40 |
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annoying bug in Directional Atom, where mu was getting written to |
41 |
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pseudorandom memory location. |
42 |
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43 |
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2003-08-12 14:56 tim |
44 |
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45 |
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* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
46 |
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libBASS/Globals.hpp, libmdtools/Atom.hpp, |
47 |
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libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
48 |
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libmdtools/SimSetup.cpp: debugging globals |
49 |
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50 |
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2003-08-12 13:40 gezelter |
51 |
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52 |
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* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
53 |
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and new atypes in LJFF |
54 |
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55 |
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2003-08-12 13:15 gezelter |
56 |
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57 |
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* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
58 |
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stuff... |
59 |
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60 |
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2003-08-12 13:14 chuckv |
61 |
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62 |
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* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
63 |
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64 |
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2003-08-12 13:04 chuckv |
65 |
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66 |
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* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
67 |
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Missed del of files before. |
68 |
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69 |
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2003-08-12 13:03 chuckv |
70 |
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71 |
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* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
72 |
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message] |
73 |
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74 |
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2003-08-12 13:01 chuckv |
75 |
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76 |
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* utils/sysbuilder/Makefile: commit makefile |
77 |
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78 |
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2003-08-12 12:51 tim |
79 |
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80 |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, |
81 |
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libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
82 |
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libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
83 |
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libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
84 |
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harmonical potential to z-constraint method |
85 |
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86 |
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2003-08-11 17:31 chuckv |
87 |
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88 |
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* utils/Makefile: Changed makefile to only build quicklate. |
89 |
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90 |
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2003-08-11 17:25 chuckv |
91 |
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92 |
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* ac-tools/configure.in: added utils/sysbuilder to be built. |
93 |
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94 |
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2003-08-11 17:12 chuckv |
95 |
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96 |
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* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
97 |
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bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
98 |
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sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, |
99 |
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sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, |
100 |
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sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, |
101 |
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sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, |
102 |
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sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, |
103 |
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sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, |
104 |
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sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged |
105 |
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sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
106 |
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with new atom allocation in libmdtools. |
107 |
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108 |
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2003-08-11 14:41 tim |
109 |
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110 |
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* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
111 |
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moving zconstraint molecules to specified positions |
112 |
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113 |
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2003-08-11 14:39 tim |
114 |
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115 |
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* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
116 |
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117 |
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2003-08-11 14:38 mmeineke |
118 |
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119 |
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* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
120 |
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libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
121 |
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libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, |
122 |
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libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c, |
123 |
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libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h, |
124 |
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libBASS/node_list.h, libBASS/parse_interface.h, |
125 |
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libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
126 |
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into the BASS language syntax. |
127 |
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128 |
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2003-08-11 13:29 mmeineke |
129 |
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130 |
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* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
131 |
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degrees of freedom to account for zConstreints |
132 |
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133 |
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2003-08-08 16:22 chuckv |
134 |
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135 |
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* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
136 |
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libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
137 |
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samples/metals/Au.bass: EAM works...... Neighbor list also |
138 |
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works..... |
139 |
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140 |
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2003-08-08 13:32 mmeineke |
141 |
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142 |
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* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
143 |
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moved frameCount's functionality into DumpReader. also split props |
144 |
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into staticProps and dynamicProps. (currently only have |
145 |
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staticProps) |
146 |
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147 |
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2003-08-08 12:48 mmeineke |
148 |
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149 |
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* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
150 |
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instance of Atom::setZ and Atom::getZ in ZConstaint. |
151 |
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152 |
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2003-08-07 16:47 mmeineke |
153 |
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154 |
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* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
155 |
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DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
156 |
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GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, |
157 |
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SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, |
158 |
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SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
159 |
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configuration from SimState rather than arrays from Atom |
160 |
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161 |
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2003-08-06 19:47 chuckv |
162 |
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163 |
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* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
164 |
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libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
165 |
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libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
166 |
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samples/metals/Au.bass: Bug fixes for eam... |
167 |
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168 |
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2003-08-01 11:18 tim |
169 |
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170 |
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* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
171 |
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Z-Constraint |
172 |
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173 |
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2003-07-31 14:59 tim |
174 |
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175 |
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* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
176 |
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libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
177 |
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libmdtools/ZConstraint.cpp: add index range checking into |
178 |
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ZConstraint |
179 |
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|
180 |
tim |
660 |
2003-07-31 10:38 tim |
181 |
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182 |
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* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
183 |
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to the globals |
184 |
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185 |
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2003-07-31 10:35 tim |
186 |
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187 |
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* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
188 |
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Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
189 |
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NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
190 |
|
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SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
191 |
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Added Z constraint. |
192 |
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193 |
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2003-07-30 16:17 chuckv |
194 |
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195 |
mmeineke |
705 |
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
196 |
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libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
197 |
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libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
198 |
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samples/metals/Au.bass: More bug fixes for eam. |
199 |
tim |
660 |
|
200 |
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2003-07-29 11:32 mmeineke |
201 |
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202 |
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* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
203 |
mmeineke |
705 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
204 |
|
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props/frameCount.c, props/frameCount.h, props/props.cpp, |
205 |
|
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src/Makefile: working on the props code |
206 |
tim |
660 |
|
207 |
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2003-07-29 11:32 mmeineke |
208 |
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209 |
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* libBASS/Globals.cpp: [no log message] |
210 |
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211 |
mmeineke |
705 |
2003-07-25 15:05 chuckv |
212 |
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213 |
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* samples/metals/: Au.bass, metals.mdl: Added bass models for |
214 |
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metals |
215 |
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216 |
tim |
660 |
2003-07-25 15:00 chuckv |
217 |
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218 |
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* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
219 |
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notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
220 |
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221 |
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2003-07-24 16:22 chuckv |
222 |
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223 |
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* ac-tools/configure.in: Changed configure to look for both upper |
224 |
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and lower cass .mod files |
225 |
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226 |
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2003-07-24 14:57 chuckv |
227 |
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228 |
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* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
229 |
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eam and do_forces. |
230 |
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231 |
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2003-07-23 17:13 chuckv |
232 |
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233 |
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* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
234 |
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force_globals.F90, simulation_module.F90, status_module.F90: |
235 |
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Finished most code for eam.... |
236 |
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237 |
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2003-07-22 16:49 mmeineke |
238 |
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239 |
|
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* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
240 |
|
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function to the DumpReader. It should now save the start of each |
241 |
|
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frame in a vector. |
242 |
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243 |
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2003-07-22 15:05 mmeineke |
244 |
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245 |
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* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
246 |
|
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to read dump files |
247 |
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248 |
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2003-07-22 14:54 tim |
249 |
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250 |
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* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
251 |
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Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
252 |
|
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NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
253 |
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message] |
254 |
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255 |
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2003-07-22 11:41 mmeineke |
256 |
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257 |
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* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
258 |
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SimSetup.cpp: Fixed a current time initialization bug in |
259 |
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InitFromFile. |
260 |
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261 |
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2003-07-21 16:27 mmeineke |
262 |
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263 |
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* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
264 |
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Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
265 |
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friends to accomadate random file access |
266 |
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267 |
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2003-07-21 11:23 mmeineke |
268 |
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269 |
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* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
270 |
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one sets it. |
271 |
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272 |
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2003-07-21 11:23 mmeineke |
273 |
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274 |
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* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
275 |
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ReadWrite.hpp: fixed Initializefrom file to start the simulation |
276 |
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from the time specified in the init file. |
277 |
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278 |
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2003-07-17 16:49 gezelter |
279 |
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280 |
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* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
281 |
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DumpReader.cpp: Started work on a DumpReader |
282 |
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283 |
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2003-07-17 15:38 gezelter |
284 |
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285 |
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* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
286 |
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287 |
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2003-07-17 15:32 gezelter |
288 |
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289 |
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* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
290 |
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libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
291 |
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Changes for SSD/E |
292 |
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293 |
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2003-07-17 14:38 mmeineke |
294 |
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295 |
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* libmdtools/do_Forces.F90: commented out an eam line |
296 |
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297 |
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2003-07-17 14:32 chuckv |
298 |
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299 |
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* libmdtools/atype_module.F90: fixed spelling issue |
300 |
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301 |
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2003-07-17 14:29 chuckv |
302 |
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303 |
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* libmdtools/: fInfo.c, status_module.F90: added info module |
304 |
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305 |
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2003-07-17 14:25 chuckv |
306 |
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307 |
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* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
308 |
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atype_module.F90, calc_eam.F90, do_Forces.F90, |
309 |
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fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
310 |
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mpiSimulation_module.F90: Added massive changes for eam.... |
311 |
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312 |
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2003-07-16 16:49 chuckv |
313 |
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314 |
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* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
315 |
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316 |
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2003-07-16 16:30 mmeineke |
317 |
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318 |
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* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
319 |
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SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
320 |
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calc_reaction_field.F90, do_Forces.F90, fSimulation.h, |
321 |
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fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
322 |
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neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, |
323 |
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wrappers.F90: Changed how cutoffs were handled from C. Now |
324 |
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notifyCutoffs in Fortran notifies those who need the information of |
325 |
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any changes to cutoffs. |
326 |
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327 |
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2003-07-16 12:35 gezelter |
328 |
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329 |
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* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
330 |
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quickLate is now somewhat more intelligent about periodic |
331 |
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boundaries and wrapping. |
332 |
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333 |
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2003-07-16 11:40 chuckv |
334 |
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335 |
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* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
336 |
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337 |
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2003-07-16 10:34 mmeineke |
338 |
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339 |
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* scripts/cleanSrc: added a quick wipe-and-update script for quick |
340 |
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rebuilds on BoB |
341 |
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342 |
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2003-07-15 21:11 gezelter |
343 |
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344 |
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* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
345 |
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SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
346 |
|
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fixes for box changes |
347 |
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348 |
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2003-07-15 17:29 mmeineke |
349 |
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350 |
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* libmdtools/simulation_module.F90: removed some debugging print |
351 |
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statements. |
352 |
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|
|
353 |
|
|
2003-07-15 17:22 mmeineke |
354 |
|
|
|
355 |
|
|
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
356 |
|
|
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
357 |
|
|
do_forces. Rrf was not being used in the neighborlist correctly. |
358 |
|
|
rcut was conssistently being set lowere than Rrf causing the dipole |
359 |
|
|
cutoff region to be to small. Also led to the removal of the taper |
360 |
|
|
region to buffer the dipole cutoff. |
361 |
|
|
|
362 |
|
|
2003-07-15 16:34 mmeineke |
363 |
|
|
|
364 |
|
|
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
365 |
|
|
fixing ssd bug |
366 |
|
|
|
367 |
|
|
2003-07-15 14:56 gezelter |
368 |
|
|
|
369 |
|
|
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
370 |
|
|
for the NPT ensembles |
371 |
|
|
|
372 |
|
|
2003-07-15 13:52 mmeineke |
373 |
|
|
|
374 |
|
|
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
375 |
|
|
simSetup |
376 |
|
|
|
377 |
|
|
2003-07-15 12:57 mmeineke |
378 |
|
|
|
379 |
|
|
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
380 |
|
|
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
381 |
|
|
fixed some bugs, Changed entry_plug to info where appropriate |
382 |
|
|
|
383 |
|
|
2003-07-15 12:25 chuckv |
384 |
|
|
|
385 |
|
|
* utils/sysBuild.ggo: added more command line arguments |
386 |
|
|
|
387 |
|
|
2003-07-15 12:11 gezelter |
388 |
|
|
|
389 |
|
|
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
390 |
|
|
Fixing force field line |
391 |
|
|
|
392 |
|
|
2003-07-15 12:10 gezelter |
393 |
|
|
|
394 |
|
|
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
395 |
|
|
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
396 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
397 |
|
|
tensor |
398 |
|
|
|
399 |
|
|
2003-07-15 10:50 gezelter |
400 |
|
|
|
401 |
|
|
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
402 |
|
|
|
403 |
|
|
2003-07-15 10:42 gezelter |
404 |
|
|
|
405 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
406 |
|
|
removed old outdated code |
407 |
|
|
|
408 |
|
|
2003-07-15 09:45 gezelter |
409 |
|
|
|
410 |
|
|
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
411 |
|
|
|
412 |
|
|
2003-07-15 09:28 gezelter |
413 |
|
|
|
414 |
|
|
* libmdtools/Molecule.cpp: removing get_vx |
415 |
|
|
|
416 |
|
|
2003-07-14 22:28 gezelter |
417 |
|
|
|
418 |
|
|
* libmdtools/NPTfm.cpp: Added NPTfm |
419 |
|
|
|
420 |
|
|
2003-07-14 22:27 gezelter |
421 |
|
|
|
422 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
423 |
|
|
Bugfix in NPTim, fixes for NPTfm |
424 |
|
|
|
425 |
|
|
2003-07-14 22:08 gezelter |
426 |
|
|
|
427 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
428 |
|
|
Checking in changes for NPTim |
429 |
|
|
|
430 |
|
|
2003-07-14 18:06 gezelter |
431 |
|
|
|
432 |
|
|
* utils/Makefile: Broken SysBuilder |
433 |
|
|
|
434 |
|
|
2003-07-14 18:06 gezelter |
435 |
|
|
|
436 |
|
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
437 |
|
|
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
438 |
|
|
for samples |
439 |
|
|
|
440 |
|
|
2003-07-14 18:06 gezelter |
441 |
|
|
|
442 |
|
|
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
443 |
|
|
debugging write statements |
444 |
|
|
|
445 |
|
|
2003-07-14 17:38 gezelter |
446 |
|
|
|
447 |
|
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
448 |
|
|
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
449 |
|
|
|
450 |
|
|
2003-07-14 16:48 mmeineke |
451 |
|
|
|
452 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
453 |
|
|
and set routines to Atom and DirectionalAtom |
454 |
|
|
|
455 |
|
|
2003-07-14 16:35 chuckv |
456 |
|
|
|
457 |
|
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
458 |
|
|
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
459 |
|
|
that takes different cmd line arguments. |
460 |
|
|
|
461 |
|
|
2003-07-14 16:28 mmeineke |
462 |
|
|
|
463 |
|
|
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
464 |
|
|
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
465 |
|
|
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
466 |
|
|
were not being updated |
467 |
|
|
|
468 |
|
|
2003-07-14 10:04 gezelter |
469 |
|
|
|
470 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
471 |
|
|
NPTim |
472 |
|
|
|
473 |
|
|
2003-07-14 09:55 mmeineke |
474 |
|
|
|
475 |
|
|
* forceFields/DUFF.frc: Switched the bond in the force field back |
476 |
|
|
to constrained, to preserve energy |
477 |
|
|
|
478 |
|
|
2003-07-11 17:34 mmeineke |
479 |
|
|
|
480 |
|
|
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
481 |
|
|
Integrator.hpp: working on som integrator bugs |
482 |
|
|
|
483 |
|
|
2003-07-11 10:26 gezelter |
484 |
|
|
|
485 |
|
|
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
486 |
|
|
to worry about all the strtok() calls in our code |
487 |
|
|
|
488 |
|
|
2003-07-11 09:49 gezelter |
489 |
|
|
|
490 |
|
|
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
491 |
|
|
|
492 |
|
|
2003-07-10 20:15 gezelter |
493 |
|
|
|
494 |
|
|
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
495 |
|
|
eor. |
496 |
|
|
|
497 |
|
|
2003-07-10 17:15 mmeineke |
498 |
|
|
|
499 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
500 |
|
|
SimInfo.cpp, Thermo.cpp: fixed some bugs |
501 |
|
|
|
502 |
|
|
2003-07-10 14:53 chuckv |
503 |
|
|
|
504 |
|
|
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
505 |
|
|
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
506 |
|
|
nanoBuilder and a general Lattice builder. |
507 |
|
|
|
508 |
|
|
2003-07-10 12:10 gezelter |
509 |
|
|
|
510 |
|
|
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
511 |
|
|
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
512 |
|
|
|
513 |
|
|
2003-07-09 17:14 mmeineke |
514 |
|
|
|
515 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
516 |
|
|
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
517 |
|
|
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
518 |
|
|
caclulation of HmatInverse. |
519 |
|
|
|
520 |
|
|
2003-07-09 10:34 mmeineke |
521 |
|
|
|
522 |
|
|
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
523 |
|
|
|
524 |
|
|
2003-07-09 10:33 mmeineke |
525 |
|
|
|
526 |
|
|
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
527 |
|
|
|
528 |
|
|
2003-07-09 08:56 gezelter |
529 |
|
|
|
530 |
|
|
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
531 |
|
|
|
532 |
|
|
2003-07-09 08:56 gezelter |
533 |
|
|
|
534 |
|
|
* libBASS/Globals.cpp: Removed Qmass |
535 |
|
|
|
536 |
|
|
2003-07-08 21:15 gezelter |
537 |
|
|
|
538 |
|
|
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
539 |
|
|
and NPTi |
540 |
|
|
|
541 |
|
|
2003-07-08 20:41 gezelter |
542 |
|
|
|
543 |
|
|
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
544 |
|
|
|
545 |
|
|
2003-07-08 16:10 gezelter |
546 |
|
|
|
547 |
|
|
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
548 |
|
|
|
549 |
|
|
2003-07-08 16:06 gezelter |
550 |
|
|
|
551 |
|
|
* libmdtools/NPTi.cpp: fixed box scaling |
552 |
|
|
|
553 |
|
|
2003-07-08 15:56 gezelter |
554 |
|
|
|
555 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
556 |
|
|
SimInfo.hpp, Thermo.cpp: NPTi |
557 |
|
|
|
558 |
|
|
2003-07-03 14:41 mmeineke |
559 |
|
|
|
560 |
|
|
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
561 |
|
|
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
562 |
|
|
scripts in the makefiles |
563 |
|
|
|
564 |
|
|
2003-07-02 16:26 mmeineke |
565 |
|
|
|
566 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
567 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
568 |
|
|
libmdtools/Makefile, libmdtools/ReadWrite.hpp, |
569 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
570 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
571 |
|
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, |
572 |
|
|
utils/Makefile: fixed the bugs introduced by switching the periodic |
573 |
|
|
box to a matrix |
574 |
|
|
|
575 |
|
|
2003-07-01 17:39 gezelter |
576 |
|
|
|
577 |
|
|
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
578 |
|
|
|
579 |
|
|
2003-07-01 17:29 gezelter |
580 |
|
|
|
581 |
|
|
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
582 |
|
|
|
583 |
|
|
2003-07-01 16:33 mmeineke |
584 |
|
|
|
585 |
|
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
586 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
587 |
|
|
the box matrix to everything. |
588 |
|
|
|
589 |
|
|
2003-06-30 17:03 mmeineke |
590 |
|
|
|
591 |
|
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
592 |
|
|
src/oopse.cpp: |
593 |
|
|
Updated the ChangeLog, and Converted most of the SImInfo to use |
594 |
|
|
non-Isotropic boxes. wrapVector needs to be finished. |
595 |
|
|
|
596 |
mmeineke |
568 |
2003-06-25 16:12 mmeineke |
597 |
|
|
|
598 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
599 |
|
|
to Harmonic bonds in the DUFF frc file |
600 |
|
|
|
601 |
|
|
fixed constraints. |
602 |
|
|
|
603 |
|
|
2003-06-25 16:11 mmeineke |
604 |
|
|
|
605 |
|
|
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
606 |
|
|
the DUFF frc file |
607 |
|
|
|
608 |
|
|
2003-06-24 17:51 gezelter |
609 |
|
|
|
610 |
|
|
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
611 |
|
|
|
612 |
|
|
2003-06-24 14:57 mmeineke |
613 |
|
|
|
614 |
|
|
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
615 |
|
|
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
616 |
|
|
the DUFF forcefield and BondExtensions.cpp |
617 |
|
|
|
618 |
|
|
2003-06-23 16:24 mmeineke |
619 |
|
|
|
620 |
|
|
* libmdtools/Integrator.cpp: Doing some work to debug the |
621 |
|
|
constraint code. |
622 |
|
|
|
623 |
|
|
2003-06-20 15:50 gezelter |
624 |
|
|
|
625 |
|
|
* libmdtools/Integrator.hpp: NPT fix |
626 |
|
|
|
627 |
|
|
2003-06-20 15:29 mmeineke |
628 |
|
|
|
629 |
|
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
630 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
631 |
|
|
libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
632 |
|
|
libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
633 |
|
|
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
634 |
|
|
integrator and NVT seem to be working now. |
635 |
|
|
|
636 |
|
|
2003-06-20 11:49 gezelter |
637 |
|
|
|
638 |
|
|
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
639 |
|
|
|
640 |
|
|
2003-06-19 17:02 mmeineke |
641 |
|
|
|
642 |
|
|
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
643 |
|
|
forceFields/LJ_FF.frc, forceFields/Makefile, |
644 |
|
|
forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
645 |
|
|
libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
646 |
|
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
647 |
|
|
libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
648 |
|
|
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
649 |
|
|
forcefield names. |
650 |
|
|
|
651 |
|
|
2003-06-19 14:21 mmeineke |
652 |
|
|
|
653 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
654 |
|
|
finished the basics of the integrator and SimSetup.cpp |
655 |
|
|
|
656 |
|
|
2003-06-19 14:11 mmeineke |
657 |
|
|
|
658 |
|
|
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
659 |
|
|
up / get it to work with the new Integrator. |
660 |
|
|
|
661 |
|
|
2003-06-18 17:20 mmeineke |
662 |
|
|
|
663 |
|
|
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
664 |
|
|
output times. |
665 |
|
|
|
666 |
|
|
2003-06-17 16:56 mmeineke |
667 |
|
|
|
668 |
|
|
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
669 |
|
|
fro the ghost Bend in TraPPE_Ex |
670 |
|
|
|
671 |
|
|
some work on the integrator. ( incomplete) |
672 |
|
|
|
673 |
|
|
2003-06-17 16:55 mmeineke |
674 |
|
|
|
675 |
|
|
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
676 |
|
|
Bend in TraPPE_Ex |
677 |
|
|
|
678 |
|
|
2003-06-04 16:06 mmeineke |
679 |
|
|
|
680 |
|
|
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
681 |
|
|
constrainB to the Symplectic integrator |
682 |
|
|
|
683 |
|
|
2003-05-30 16:32 mmeineke |
684 |
|
|
|
685 |
|
|
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
686 |
|
|
the basic integrator. |
687 |
|
|
|
688 |
|
|
bilayerSys.cpp altered for building tb3. |
689 |
|
|
|
690 |
|
|
2003-05-30 16:31 mmeineke |
691 |
|
|
|
692 |
|
|
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
693 |
|
|
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
694 |
|
|
modifiying Symplectic to become the basic integrator. |
695 |
|
|
|
696 |
|
|
2003-05-30 15:19 mmeineke |
697 |
|
|
|
698 |
|
|
* libmdtools/Integrator.hpp: added some member variables for |
699 |
|
|
position, velocity, etc. |
700 |
|
|
|
701 |
|
|
2003-05-30 14:07 mmeineke |
702 |
|
|
|
703 |
|
|
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
704 |
|
|
is now derived from Integrator |
705 |
|
|
|
706 |
|
|
2003-05-20 11:44 mmeineke |
707 |
|
|
|
708 |
|
|
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
709 |
|
|
|
710 |
|
|
2003-05-17 11:57 mmeineke |
711 |
|
|
|
712 |
|
|
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
713 |
|
|
working |
714 |
|
|
|
715 |
|
|
2003-05-16 16:37 mmeineke |
716 |
|
|
|
717 |
|
|
* utils/bilayerSys.cpp: still working on the bilayer code |
718 |
|
|
|
719 |
|
|
2003-05-16 09:28 mmeineke |
720 |
|
|
|
721 |
|
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
722 |
|
|
work to overhaul sysbuild. |
723 |
|
|
|
724 |
|
|
2003-05-13 16:23 mmeineke |
725 |
|
|
|
726 |
|
|
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
727 |
|
|
|
728 |
|
|
2003-05-13 15:47 mmeineke |
729 |
|
|
|
730 |
|
|
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
731 |
|
|
beadLipid/water.mdl: Added bead lipid model to the sample directory |
732 |
|
|
|
733 |
|
|
2003-05-13 15:34 mmeineke |
734 |
|
|
|
735 |
|
|
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
736 |
|
|
the Trappe extended force field |
737 |
|
|
|
738 |
|
|
2003-05-13 12:01 mmeineke |
739 |
|
|
|
740 |
|
|
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
741 |
|
|
TraPPe_Ex forceField |
742 |
|
|
|
743 |
|
|
2003-05-09 14:51 mmeineke |
744 |
|
|
|
745 |
|
|
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
746 |
|
|
there were some duplicate entries |
747 |
|
|
|
748 |
|
|
added a two chain lipid to the lipid.mdl in sample |
749 |
|
|
|
750 |
|
|
2003-05-09 14:51 mmeineke |
751 |
|
|
|
752 |
|
|
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
753 |
|
|
there were some duplicate entries |
754 |
|
|
|
755 |
|
|
2003-05-09 11:56 mmeineke |
756 |
|
|
|
757 |
|
|
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
758 |
|
|
configure script |
759 |
|
|
|
760 |
|
|
added the CH branching group to the TraPPE_Ex fource field |
761 |
|
|
|
762 |
|
|
2003-05-09 11:55 mmeineke |
763 |
|
|
|
764 |
|
|
* ac-tools/configure.in: added the utils subdirectory to the |
765 |
|
|
configure script |
766 |
|
|
|
767 |
|
|
2003-04-25 11:02 mmeineke |
768 |
|
|
|
769 |
|
|
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
770 |
|
|
bilayer builder |
771 |
|
|
|
772 |
|
|
2003-04-24 21:00 mmeineke |
773 |
|
|
|
774 |
|
|
* libmdtools/f_verlet_constrained.F90: added a new test for |
775 |
|
|
constraint failure |
776 |
|
|
|
777 |
|
|
2003-04-17 16:54 mmeineke |
778 |
|
|
|
779 |
|
|
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
780 |
|
|
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
781 |
|
|
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
782 |
|
|
build our systems |
783 |
|
|
|
784 |
|
|
2003-04-16 16:11 mmeineke |
785 |
|
|
|
786 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
787 |
|
|
|
788 |
|
|
2003-04-15 16:47 mmeineke |
789 |
|
|
|
790 |
|
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
791 |
|
|
and sysBuild both will build now. woot! |
792 |
|
|
|
793 |
|
|
2003-04-15 16:20 mmeineke |
794 |
|
|
|
795 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
796 |
|
|
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
797 |
|
|
|
798 |
|
|
sysBuild still need to write the bass file. |
799 |
|
|
|
800 |
|
|
MoLocator.cpp is currently empty |
801 |
|
|
|
802 |
|
|
2003-04-15 15:40 chuckv |
803 |
|
|
|
804 |
|
|
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
805 |
|
|
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
806 |
|
|
forceFields/pdu3.eam, forceFields/ptu3.eam, |
807 |
|
|
libmdtools/ForceFields.hpp: Added eam force files... |
808 |
|
|
|
809 |
|
|
2003-04-15 11:37 chuckv |
810 |
|
|
|
811 |
|
|
* libmdtools/EAM_FF.cpp: More eam work. |
812 |
|
|
|
813 |
|
|
2003-04-14 16:22 mmeineke |
814 |
|
|
|
815 |
|
|
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
816 |
|
|
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
817 |
|
|
working on the system builder |
818 |
|
|
|
819 |
|
|
2003-04-14 16:16 chuckv |
820 |
|
|
|
821 |
|
|
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
822 |
|
|
ordering on NVT calculation in integrators. |
823 |
|
|
|
824 |
|
|
2003-04-14 14:51 mmeineke |
825 |
|
|
|
826 |
|
|
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
827 |
|
|
obj/placeHolder: working on a system builder |
828 |
|
|
|
829 |
|
|
2003-04-14 14:04 mmeineke |
830 |
|
|
|
831 |
|
|
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
832 |
|
|
|
833 |
|
|
added sysBuild to the utils Makefile |
834 |
|
|
|
835 |
|
|
2003-04-14 14:03 mmeineke |
836 |
|
|
|
837 |
|
|
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
838 |
|
|
Ghost bends to the TraPPE_Ex forceField |
839 |
|
|
|
840 |
|
|
2003-04-14 13:19 chuckv |
841 |
|
|
|
842 |
|
|
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
843 |
|
|
|
844 |
|
|
2003-04-11 13:46 mmeineke |
845 |
|
|
|
846 |
|
|
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
847 |
|
|
simulation_module.F90: fixed a memory bug in Fortran, where |
848 |
|
|
molMembershipArray was declared nLocal instead of nGlobal. |
849 |
|
|
|
850 |
|
|
2003-04-11 10:16 gezelter |
851 |
|
|
|
852 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
853 |
|
|
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
854 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
855 |
|
|
for NPT |
856 |
|
|
|
857 |
|
|
2003-04-10 15:08 mmeineke |
858 |
|
|
|
859 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
860 |
|
|
globalIndex counter to Molecule |
861 |
|
|
|
862 |
|
|
2003-04-10 11:35 gezelter |
863 |
|
|
|
864 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
865 |
|
|
ConstantStress |
866 |
|
|
|
867 |
|
|
2003-04-10 11:27 mmeineke |
868 |
|
|
|
869 |
|
|
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
870 |
|
|
caused a miscalculation of nLocal. |
871 |
|
|
|
872 |
|
|
2003-04-10 11:21 mmeineke |
873 |
|
|
|
874 |
|
|
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
875 |
|
|
do_Forces.F90: fixed a bug in symplectic, where presure was only |
876 |
|
|
being calculated the first time through. |
877 |
|
|
|
878 |
|
|
2003-04-09 11:20 chuckv |
879 |
|
|
|
880 |
|
|
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
881 |
|
|
file |
882 |
|
|
|
883 |
|
|
2003-04-09 08:59 gezelter |
884 |
|
|
|
885 |
|
|
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
886 |
|
|
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
887 |
|
|
|
888 |
|
|
2003-04-08 23:06 gezelter |
889 |
|
|
|
890 |
|
|
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
891 |
|
|
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
892 |
|
|
SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
893 |
|
|
Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
894 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90, |
895 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
896 |
|
|
NVT |
897 |
|
|
|
898 |
|
|
2003-04-08 17:38 chuckv |
899 |
|
|
|
900 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
901 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
902 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
903 |
|
|
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
904 |
|
|
(kinda)... |
905 |
|
|
|
906 |
|
|
2003-04-08 16:35 gezelter |
907 |
|
|
|
908 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
909 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
910 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
911 |
|
|
|
912 |
|
|
2003-04-08 12:16 chuckv |
913 |
|
|
|
914 |
|
|
* libmdtools/: do_Forces.F90, neighborLists.F90, |
915 |
|
|
simulation_module.F90: Moved expand neighborlist to init_FF. |
916 |
|
|
|
917 |
|
|
2003-04-08 10:20 chuckv |
918 |
|
|
|
919 |
|
|
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
920 |
|
|
NVT |
921 |
|
|
|
922 |
|
|
2003-04-08 09:39 gezelter |
923 |
|
|
|
924 |
|
|
* libmdtools/Verlet.cpp: fixes for nvt / npt |
925 |
|
|
|
926 |
|
|
2003-04-08 09:34 gezelter |
927 |
|
|
|
928 |
|
|
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
929 |
|
|
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
930 |
|
|
|
931 |
|
|
2003-04-08 07:50 gezelter |
932 |
|
|
|
933 |
|
|
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
934 |
|
|
|
935 |
|
|
2003-04-08 07:44 gezelter |
936 |
|
|
|
937 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
938 |
|
|
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
939 |
|
|
NVT and NPT ensembles |
940 |
|
|
|
941 |
|
|
2003-04-07 16:42 gezelter |
942 |
|
|
|
943 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
944 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
945 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
946 |
|
|
|
947 |
|
|
2003-04-07 16:20 mmeineke |
948 |
|
|
|
949 |
|
|
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
950 |
|
|
portion of SSD. |
951 |
|
|
|
952 |
|
|
2003-04-07 16:16 mmeineke |
953 |
|
|
|
954 |
|
|
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
955 |
|
|
doing some testing in sticky through Symplectic. |
956 |
|
|
|
957 |
|
|
2003-04-07 15:51 gezelter |
958 |
|
|
|
959 |
|
|
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
960 |
|
|
|
961 |
|
|
2003-04-07 15:50 chuckv |
962 |
|
|
|
963 |
|
|
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
964 |
|
|
tau and virial. |
965 |
|
|
|
966 |
|
|
2003-04-07 15:06 mmeineke |
967 |
|
|
|
968 |
|
|
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
969 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
970 |
|
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
971 |
|
|
src/Makefile: bug fixes |
972 |
|
|
|
973 |
|
|
2003-04-07 11:56 gezelter |
974 |
|
|
|
975 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
976 |
|
|
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
977 |
|
|
Many fixes to add extended system |
978 |
|
|
|
979 |
|
|
2003-04-07 09:30 gezelter |
980 |
|
|
|
981 |
|
|
* src/Makefile: Fixed a bug caused by my experimentation |
982 |
|
|
|
983 |
|
|
2003-04-07 09:30 gezelter |
984 |
|
|
|
985 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
986 |
|
|
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
987 |
|
|
Added ExtendedSystem infrastructure for NPT and NVT calculations |
988 |
|
|
|
989 |
|
|
2003-04-07 09:30 gezelter |
990 |
|
|
|
991 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
992 |
|
|
|
993 |
|
|
2003-04-04 23:07 gezelter |
994 |
|
|
|
995 |
|
|
* src/Makefile: final mods to try a fortran compiler |
996 |
|
|
|
997 |
|
|
2003-04-04 22:39 gezelter |
998 |
|
|
|
999 |
|
|
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
1000 |
|
|
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
1001 |
|
|
|
1002 |
|
|
2003-04-04 21:56 gezelter |
1003 |
|
|
|
1004 |
|
|
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
1005 |
|
|
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
1006 |
|
|
|
1007 |
|
|
2003-04-04 21:45 gezelter |
1008 |
|
|
|
1009 |
|
|
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
1010 |
|
|
fixes to fortran wrappers |
1011 |
|
|
|
1012 |
|
|
2003-04-04 17:22 chuckv |
1013 |
|
|
|
1014 |
|
|
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1015 |
|
|
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
1016 |
|
|
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
1017 |
|
|
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
1018 |
|
|
smarter, fortran gets dumber... |
1019 |
|
|
|
1020 |
|
|
2003-04-04 14:57 mmeineke |
1021 |
|
|
|
1022 |
|
|
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
1023 |
|
|
neighborLists.F90: fixed a memory read bug in neighborlist |
1024 |
|
|
|
1025 |
|
|
2003-04-04 14:47 gezelter |
1026 |
|
|
|
1027 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
1028 |
|
|
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
1029 |
|
|
|
1030 |
|
|
2003-04-04 14:16 gezelter |
1031 |
|
|
|
1032 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
1033 |
|
|
SimInfo.hpp: Fixes for ExtendedSystem |
1034 |
|
|
|
1035 |
|
|
2003-04-03 20:57 gezelter |
1036 |
|
|
|
1037 |
|
|
* libmdtools/ExtendedSystem.hpp: Added extended system header |
1038 |
|
|
|
1039 |
|
|
2003-04-03 20:57 gezelter |
1040 |
|
|
|
1041 |
|
|
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
1042 |
|
|
for extended system code |
1043 |
|
|
|
1044 |
|
|
2003-04-03 18:49 gezelter |
1045 |
|
|
|
1046 |
|
|
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
1047 |
|
|
extendedsystem |
1048 |
|
|
|
1049 |
|
|
2003-04-03 17:19 mmeineke |
1050 |
|
|
|
1051 |
|
|
* libmdtools/Molecule.hpp: added some little fixes here and there. |
1052 |
|
|
|
1053 |
|
|
2003-04-03 17:01 mmeineke |
1054 |
|
|
|
1055 |
|
|
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
1056 |
|
|
initialize bug. |
1057 |
|
|
|
1058 |
|
|
2003-04-03 16:12 mmeineke |
1059 |
|
|
|
1060 |
|
|
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
1061 |
|
|
little things like deleteing unused variables and such. |
1062 |
|
|
|
1063 |
|
|
2003-04-03 15:57 mmeineke |
1064 |
|
|
|
1065 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
1066 |
|
|
simError.h also some fixes to Molecule.hpp |
1067 |
|
|
|
1068 |
|
|
2003-04-03 15:57 mmeineke |
1069 |
|
|
|
1070 |
|
|
* libBASS/simError.h: a few fixes to simError.h |
1071 |
|
|
|
1072 |
|
|
2003-04-03 15:21 mmeineke |
1073 |
|
|
|
1074 |
|
|
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
1075 |
|
|
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
1076 |
|
|
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
1077 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
1078 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
1079 |
|
|
src/Makefile, src/oopse.cpp: fixed some small things with |
1080 |
|
|
simError.h |
1081 |
|
|
|
1082 |
|
|
2003-04-03 15:19 gezelter |
1083 |
|
|
|
1084 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
1085 |
|
|
|
1086 |
|
|
2003-04-03 14:58 gezelter |
1087 |
|
|
|
1088 |
|
|
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
1089 |
|
|
now) |
1090 |
|
|
|
1091 |
|
|
2003-04-03 08:42 gezelter |
1092 |
|
|
|
1093 |
|
|
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
1094 |
|
|
Changed Readme, added some files |
1095 |
|
|
|
1096 |
|
|
2003-04-02 17:19 mmeineke |
1097 |
|
|
|
1098 |
|
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
1099 |
|
|
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
1100 |
|
|
dipoles mostly work, but there is a memory leak somewhere. |
1101 |
|
|
|
1102 |
|
|
2003-04-02 10:01 mmeineke |
1103 |
|
|
|
1104 |
|
|
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
1105 |
|
|
the proper atomIdents. |
1106 |
|
|
|
1107 |
|
|
2003-04-01 11:50 chuckv |
1108 |
|
|
|
1109 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
1110 |
|
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
1111 |
|
|
samples/argon/argon.bass: more bug fixes.... |
1112 |
|
|
|
1113 |
|
|
2003-04-01 11:49 mmeineke |
1114 |
|
|
|
1115 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
1116 |
|
|
DumpWriter to be more robust to errors. also added a little |
1117 |
|
|
namespace to InitFromFile to wrap it's helper functions in MPI |
1118 |
|
|
|
1119 |
|
|
2003-03-31 17:09 chuckv |
1120 |
|
|
|
1121 |
|
|
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
1122 |
|
|
not zeroed. |
1123 |
|
|
|
1124 |
|
|
2003-03-31 16:50 chuckv |
1125 |
|
|
|
1126 |
|
|
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
1127 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
1128 |
|
|
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
1129 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1130 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
1131 |
|
|
samples/alkane/butane.bass: Fixes in MPI force calc and in |
1132 |
|
|
Trappe_Ex parsing. |
1133 |
|
|
|
1134 |
|
|
2003-03-28 17:34 chuckv |
1135 |
|
|
|
1136 |
|
|
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
1137 |
|
|
|
1138 |
|
|
2003-03-28 16:45 chuckv |
1139 |
|
|
|
1140 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
1141 |
|
|
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
1142 |
|
|
routines. |
1143 |
|
|
|
1144 |
|
|
2003-03-28 14:33 mmeineke |
1145 |
|
|
|
1146 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
1147 |
|
|
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
1148 |
|
|
bug where the Excludes were not being created properly |
1149 |
|
|
|
1150 |
|
|
2003-03-28 14:30 chuckv |
1151 |
|
|
|
1152 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
1153 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
1154 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
1155 |
|
|
and debugging mpi read write from file. |
1156 |
|
|
|
1157 |
|
|
2003-03-28 10:28 mmeineke |
1158 |
|
|
|
1159 |
|
|
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
1160 |
|
|
interactions in Trappe |
1161 |
|
|
|
1162 |
|
|
2003-03-27 18:33 chuckv |
1163 |
|
|
|
1164 |
|
|
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
1165 |
|
|
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
1166 |
|
|
|
1167 |
|
|
2003-03-27 17:16 mmeineke |
1168 |
|
|
|
1169 |
|
|
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
1170 |
|
|
excludes were not being initialized |
1171 |
|
|
|
1172 |
|
|
2003-03-27 16:52 mmeineke |
1173 |
|
|
|
1174 |
|
|
* src/Makefile: [no log message] |
1175 |
|
|
|
1176 |
|
|
2003-03-27 16:52 mmeineke |
1177 |
|
|
|
1178 |
|
|
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
1179 |
|
|
|
1180 |
|
|
2003-03-27 16:07 mmeineke |
1181 |
|
|
|
1182 |
|
|
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
1183 |
|
|
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
1184 |
|
|
Verlet.cpp: fixed the compile time bugs, Source builds and links |
1185 |
|
|
|
1186 |
|
|
2003-03-27 15:48 mmeineke |
1187 |
|
|
|
1188 |
|
|
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
1189 |
|
|
more bugs. |
1190 |
|
|
|
1191 |
|
|
2003-03-27 15:40 mmeineke |
1192 |
|
|
|
1193 |
|
|
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
1194 |
|
|
|
1195 |
|
|
2003-03-27 15:39 mmeineke |
1196 |
|
|
|
1197 |
|
|
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
1198 |
|
|
|
1199 |
|
|
2003-03-27 15:36 mmeineke |
1200 |
|
|
|
1201 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
1202 |
|
|
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
1203 |
|
|
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
1204 |
|
|
|
1205 |
|
|
2003-03-27 15:12 mmeineke |
1206 |
|
|
|
1207 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
1208 |
|
|
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
1209 |
|
|
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
1210 |
|
|
to. will now attempt to compile. |
1211 |
|
|
|
1212 |
|
|
2003-03-27 14:21 mmeineke |
1213 |
|
|
|
1214 |
|
|
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
1215 |
|
|
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
1216 |
|
|
updating SimSetup to initialize and use the new MPI division of |
1217 |
|
|
labour, and Molecule class |
1218 |
|
|
|
1219 |
|
|
2003-03-27 12:55 mmeineke |
1220 |
|
|
|
1221 |
|
|
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
1222 |
|
|
use Molecule |
1223 |
|
|
|
1224 |
|
|
2003-03-27 12:32 mmeineke |
1225 |
|
|
|
1226 |
|
|
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
1227 |
|
|
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
1228 |
|
|
converted to the new Molecule model. TraPPE_Ex is currently being |
1229 |
|
|
updated. SimSetups routines are writtten, but not yet called. |
1230 |
|
|
|
1231 |
|
|
2003-03-27 10:07 gezelter |
1232 |
|
|
|
1233 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
1234 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
1235 |
|
|
numbering in MPI |
1236 |
|
|
|
1237 |
|
|
2003-03-27 09:30 mmeineke |
1238 |
|
|
|
1239 |
|
|
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
1240 |
|
|
|
1241 |
|
|
2003-03-26 20:49 gezelter |
1242 |
|
|
|
1243 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
1244 |
|
|
fileio for MPI |
1245 |
|
|
|
1246 |
|
|
2003-03-26 18:14 gezelter |
1247 |
|
|
|
1248 |
|
|
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
1249 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
1250 |
|
|
fixes many bug fixes |
1251 |
|
|
|
1252 |
|
|
2003-03-26 17:24 gezelter |
1253 |
|
|
|
1254 |
|
|
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
1255 |
|
|
sequence of atoms on the other processors. Node 0 now fires |
1256 |
|
|
potatoes at other processors to get them to send french fries back. |
1257 |
|
|
|
1258 |
|
|
2003-03-26 17:02 mmeineke |
1259 |
|
|
|
1260 |
|
|
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
1261 |
|
|
making the molecules is in place. ForceField needs to be updated |
1262 |
|
|
next. |
1263 |
|
|
|
1264 |
|
|
2003-03-26 16:54 mmeineke |
1265 |
|
|
|
1266 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
1267 |
|
|
the "static" bugs in Atom and Exclude |
1268 |
|
|
|
1269 |
|
|
2003-03-26 16:50 mmeineke |
1270 |
|
|
|
1271 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
1272 |
|
|
SimSetup.cpp: still working on the SimSetup routine. also fixed |
1273 |
|
|
some things in Exclude.hpp |
1274 |
|
|
|
1275 |
|
|
2003-03-26 16:24 gezelter |
1276 |
|
|
|
1277 |
|
|
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
1278 |
|
|
|
1279 |
|
|
2003-03-26 16:23 gezelter |
1280 |
|
|
|
1281 |
|
|
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
1282 |
|
|
and Exclude list |
1283 |
|
|
|
1284 |
|
|
2003-03-26 16:04 gezelter |
1285 |
|
|
|
1286 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
1287 |
|
|
delete ranges of atoms |
1288 |
|
|
|
1289 |
|
|
2003-03-26 15:45 mmeineke |
1290 |
|
|
|
1291 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
1292 |
|
|
with static arrays similar to the Atom class |
1293 |
|
|
|
1294 |
|
|
2003-03-26 15:22 mmeineke |
1295 |
|
|
|
1296 |
|
|
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
1297 |
|
|
overhauling the molecule class to contain it's own bonds, bends, |
1298 |
|
|
and torsions. |
1299 |
|
|
|
1300 |
|
|
may god have mercy on my soul. |
1301 |
|
|
|
1302 |
|
|
2003-03-26 14:34 chuckv |
1303 |
|
|
|
1304 |
|
|
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
1305 |
|
|
|
1306 |
|
|
2003-03-26 13:02 gezelter |
1307 |
|
|
|
1308 |
|
|
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
1309 |
|
|
mpiSimulation.hpp: MPI stuff for passing out molecules |
1310 |
|
|
|
1311 |
|
|
2003-03-26 11:12 chuckv |
1312 |
|
|
|
1313 |
|
|
* libmdtools/mpiSimulation.cpp: working on load balancing |
1314 |
|
|
|
1315 |
|
|
2003-03-26 10:37 chuckv |
1316 |
|
|
|
1317 |
|
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
1318 |
|
|
samples/argon/argon.bass: Fixes for Parallel thermalization |
1319 |
|
|
|
1320 |
|
|
2003-03-26 09:55 mmeineke |
1321 |
|
|
|
1322 |
|
|
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
1323 |
|
|
THermo.cpp |
1324 |
|
|
|
1325 |
|
|
2003-03-25 17:54 chuckv |
1326 |
|
|
|
1327 |
|
|
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
1328 |
|
|
of potential energy and temperature. |
1329 |
|
|
|
1330 |
|
|
2003-03-25 09:29 mmeineke |
1331 |
|
|
|
1332 |
|
|
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
1333 |
|
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
1334 |
|
|
|
1335 |
|
|
2003-03-25 09:29 mmeineke |
1336 |
|
|
|
1337 |
|
|
* libBASS/MPIobj/dummy: added dummy files to keep the build |
1338 |
|
|
deirectories from being pruned. |
1339 |
|
|
|
1340 |
|
|
2003-03-24 20:07 gezelter |
1341 |
|
|
|
1342 |
|
|
* samples/Makefile: moving tests to samples |
1343 |
|
|
|
1344 |
|
|
2003-03-24 20:06 gezelter |
1345 |
|
|
|
1346 |
|
|
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
1347 |
|
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
1348 |
|
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
1349 |
|
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
1350 |
|
|
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
1351 |
|
|
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
1352 |
|
|
samples |
1353 |
|
|
|
1354 |
|
|
2003-03-24 19:51 gezelter |
1355 |
|
|
|
1356 |
|
|
* ac-tools/configure.in: Tests are becoming samples |
1357 |
|
|
|
1358 |
|
|
2003-03-24 19:46 gezelter |
1359 |
|
|
|
1360 |
|
|
* ac-tools/Make.conf.in: Added makefiles in tests directories |
1361 |
|
|
|
1362 |
|
|
2003-03-24 16:55 gezelter |
1363 |
|
|
|
1364 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, |
1365 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, |
1366 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, |
1367 |
|
|
libmdtools/calc_reaction_field.F90, |
1368 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
1369 |
|
|
libmdtools/simulation_module.F90: electrostatic changes for dipole |
1370 |
|
|
/ RF separation |
1371 |
|
|
|
1372 |
|
|
2003-03-24 13:33 mmeineke |
1373 |
|
|
|
1374 |
|
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
1375 |
|
|
do_Forces.F90: little bug fixes here and there |
1376 |
|
|
|
1377 |
|
|
2003-03-24 10:26 mmeineke |
1378 |
|
|
|
1379 |
|
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
1380 |
|
|
where short range interactions were not being calculated. |
1381 |
|
|
|
1382 |
|
|
removed some debug print statements |
1383 |
|
|
|
1384 |
|
|
2003-03-21 17:11 chuckv |
1385 |
|
|
|
1386 |
|
|
* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, |
1387 |
|
|
do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: |
1388 |
|
|
various write statements for debugging |
1389 |
|
|
|
1390 |
|
|
2003-03-21 16:26 chuckv |
1391 |
|
|
|
1392 |
|
|
* forceFields/Makefile: added links to the makefile in forceFields |
1393 |
|
|
|
1394 |
|
|
2003-03-21 15:52 gezelter |
1395 |
|
|
|
1396 |
|
|
* ac-tools/Make.conf.in, ac-tools/configure.in, |
1397 |
|
|
libmdtools/Makefile: Fixed F_MACH_DEP bug |
1398 |
|
|
|
1399 |
|
|
2003-03-21 15:37 gezelter |
1400 |
|
|
|
1401 |
|
|
* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, |
1402 |
|
|
ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, |
1403 |
|
|
libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, |
1404 |
|
|
src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, |
1405 |
|
|
autoconf fixes |
1406 |
|
|
|
1407 |
gezelter |
385 |
2003-03-21 14:58 gezelter |
1408 |
mmeineke |
377 |
|
1409 |
gezelter |
385 |
* LICENSE: Added license file |
1410 |
|
|
|
1411 |
|
|
2003-03-21 14:55 gezelter |
1412 |
|
|
|
1413 |
|
|
* forceFields/Makefile: Fixed makefile |
1414 |
|
|
|
1415 |
|
|
2003-03-21 14:49 gezelter |
1416 |
|
|
|
1417 |
|
|
* forceFields/Makefile: Makefile for forceFields |
1418 |
|
|
|
1419 |
|
|
2003-03-21 14:42 gezelter |
1420 |
|
|
|
1421 |
|
|
* README: Readme changes |
1422 |
|
|
|
1423 |
|
|
2003-03-21 12:52 mmeineke |
1424 |
|
|
|
1425 |
|
|
* src/Makefile: [no log message] |
1426 |
|
|
|
1427 |
|
|
2003-03-21 12:52 mmeineke |
1428 |
|
|
|
1429 |
|
|
* libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends |
1430 |
|
|
|
1431 |
|
|
2003-03-21 12:42 mmeineke |
1432 |
|
|
|
1433 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
1434 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
1435 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
1436 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
1437 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
1438 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
1439 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
1440 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
1441 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
1442 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
1443 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
1444 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
1445 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
1446 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
1447 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
1448 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
1449 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
1450 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
1451 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
1452 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
1453 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
1454 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
1455 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
1456 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
1457 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
1458 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
1459 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
1460 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
1461 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
1462 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
1463 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
1464 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
1465 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
1466 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
1467 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1468 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1469 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
1470 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
1471 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
1472 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
1473 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
1474 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
1475 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
1476 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
1477 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
1478 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
1479 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
1480 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
1481 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
1482 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
1483 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
1484 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
1485 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
1486 |
|
|
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
1487 |
|
|
Tree |
1488 |
|
|
|
1489 |
|
|
2003-03-21 12:42 mmeineke |
1490 |
|
|
|
1491 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
1492 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
1493 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
1494 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
1495 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
1496 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
1497 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
1498 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
1499 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
1500 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
1501 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
1502 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
1503 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
1504 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
1505 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
1506 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
1507 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
1508 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
1509 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
1510 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
1511 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
1512 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
1513 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
1514 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
1515 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
1516 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
1517 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
1518 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
1519 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
1520 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
1521 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
1522 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
1523 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
1524 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
1525 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1526 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1527 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
1528 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
1529 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
1530 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
1531 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
1532 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
1533 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
1534 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
1535 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
1536 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
1537 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
1538 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
1539 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
1540 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
1541 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
1542 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
1543 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
1544 |
|
|
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
1545 |
|
|
revision |
1546 |
|
|
|