1 |
tim |
1255 |
2004-06-09 11:16 tim |
2 |
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3 |
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* libmdtools/: ConstraintAlgorithm.hpp, ConstraintElement.hpp, |
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Euler3.cpp, Euler3.hpp, Integrator.hpp, Make.dep, Makefile.in, |
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Mat3x3d.cpp, Mat3x3d.hpp, Quaternion.cpp, Quaternion.hpp, |
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Rattle.cpp, Rattle.hpp, RigidBody.cpp, RigidBody.hpp, Roll.cpp, |
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Roll.hpp, Shake.cpp, Shake.hpp, Vector3d.cpp, Vector3d.hpp: 1. |
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adding some useful math classes(Mat3x3d, Vector3d, Quaternion, |
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Euler3) these classes use anonymous union and struct to support |
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double[3], double[3][3] and double[4] 2. adding roll constraint |
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algorithm |
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2004-06-08 11:49 gezelter |
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15 |
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* libmdtools/: NPT.cpp, NPTf.cpp, StuntDouble.cpp, Thermo.cpp: |
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Fixed a bug in NPTf (vScale was declared in the cpp file in |
17 |
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addition to the declaration in Integrator.hpp file) |
18 |
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19 |
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2004-06-07 09:26 gezelter |
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21 |
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* libBASS/Globals.cpp, libmdtools/AtomVisitor.cpp, |
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libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.hpp, |
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libmdtools/ConstraintIterator.hpp, |
24 |
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libmdtools/ConstraintManager.hpp, libmdtools/ConstraintPair.hpp, |
25 |
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libmdtools/DirectionalAtom.cpp, libmdtools/DumpReader.cpp, |
26 |
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libmdtools/DumpWriter.cpp, libmdtools/MatVec3.c, |
27 |
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libmdtools/MatVec3.h, libmdtools/StreamTokenizer.hpp, |
28 |
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libmdtools/ZConsReader.cpp: Fixes from gcc -Wall |
29 |
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30 |
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2004-06-07 09:09 chrisfen |
31 |
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32 |
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* libmdtools/Thermo.cpp: Dan cleaned up the pressure calculation a |
33 |
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bit... Got rid of some unnecessary lines of code in Thermo.cpp |
34 |
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35 |
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2004-06-04 16:00 gezelter |
36 |
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37 |
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* libmdtools/: ConstraintIterator.hpp, OOPSEMinimizer.cpp, |
38 |
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StuntDouble.cpp: small bugfixes |
39 |
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40 |
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2004-06-04 15:29 tim |
41 |
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42 |
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* libmdtools/Integrator.hpp: [no log message] |
43 |
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44 |
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2004-06-04 14:30 tim |
45 |
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46 |
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* ChangeLog, libmdtools/CallbackFunctor.cpp, |
47 |
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libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.cpp, |
48 |
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libmdtools/ConstraintAlgorithm.hpp, libmdtools/Integrator.hpp, |
49 |
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libmdtools/OOPSEMinimizer.cpp, libmdtools/Rattle.hpp, |
50 |
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libmdtools/Shake.hpp, libmdtools/ShakeMin.cpp, |
51 |
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libmdtools/ShakeMin.hpp: constraint algorithm for minimization is |
52 |
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working |
53 |
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54 |
tim |
1248 |
2004-06-04 11:23 gezelter |
55 |
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56 |
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* forceFields/charmm27.vdw: Moved to SHAPES |
57 |
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58 |
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2004-06-04 11:23 gezelter |
59 |
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60 |
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* forceFields/: LJ.vdw, amber99.vdw, gaff.vdw, oplsaal.vdw: [no log |
61 |
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message] |
62 |
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63 |
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2004-06-04 09:59 gezelter |
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65 |
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* libmdtools/: notifyCutoffs.F90, status_module.F90, wrappers.F90: |
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More work on Fortran side of error handler |
67 |
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68 |
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2004-06-04 09:59 gezelter |
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70 |
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* configure, ac-tools/aclocal.m4: fixed a typo in autoconf script |
71 |
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72 |
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2004-06-04 09:35 gezelter |
73 |
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74 |
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* libmdtools/: Makefile.in, fInfo.c, status_module.F90: Unifying |
75 |
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the error handlers |
76 |
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77 |
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2004-06-04 09:17 gezelter |
78 |
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79 |
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* libBASS/: MemberStamp.cpp, MemberStamp.hpp: Not used anymore |
80 |
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81 |
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2004-06-04 09:11 gezelter |
82 |
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83 |
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* libBASS/: config.h.in, fError.c: forgot to add these |
84 |
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85 |
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2004-06-03 22:15 tim |
86 |
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87 |
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* ChangeLog, libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
88 |
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libmdtools/CallbackFunctor.cpp, libmdtools/ConstraintAlgorithm.cpp, |
89 |
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libmdtools/ConstraintManager.cpp, libmdtools/GenericData.cpp, |
90 |
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libmdtools/GenericData.hpp, libmdtools/Integrator.cpp, |
91 |
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libmdtools/Integrator.hpp, libmdtools/Make.dep, |
92 |
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libmdtools/Makefile.in, libmdtools/Molecule.cpp, |
93 |
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libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NVT.cpp, |
94 |
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libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, |
95 |
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libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
96 |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
97 |
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libmdtools/SimSetup.cpp, libmdtools/StuntDouble.cpp, |
98 |
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libmdtools/StuntDouble.hpp, utils/Vector3.hpp: new rattle algorithm |
99 |
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is working |
100 |
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101 |
tim |
1234 |
2004-06-03 21:38 gezelter |
102 |
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103 |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
104 |
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libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c, |
105 |
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libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in, |
106 |
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libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for |
107 |
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fortran access to SimError |
108 |
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109 |
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2004-06-03 16:51 tim |
110 |
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111 |
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* libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp, |
112 |
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ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp, |
113 |
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ConstraintElement.cpp, ConstraintElement.hpp, |
114 |
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ConstraintIterator.hpp, ConstraintManager.cpp, |
115 |
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ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp, |
116 |
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Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new |
117 |
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implementation of constraint |
118 |
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119 |
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2004-06-03 16:06 tim |
120 |
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121 |
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* libmdtools/DumpWriter.cpp: fixed a bug which only writes out the |
122 |
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first atom of a molecule |
123 |
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124 |
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2004-06-03 15:02 gezelter |
125 |
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126 |
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* libmdtools/SimSetup.cpp: Fixed groupOffset bug |
127 |
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128 |
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2004-06-03 15:02 gezelter |
129 |
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130 |
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* ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for |
131 |
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autoconf |
132 |
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133 |
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2004-06-02 13:28 gezelter |
134 |
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135 |
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* samples/: argon/Makefile, minimizer/argon/Makefile: Shouldn't |
136 |
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have been in CVS |
137 |
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138 |
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2004-06-02 13:28 gezelter |
139 |
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140 |
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* samples/: argon/Makefile, minimizer/argon/Makefile: Why is this |
141 |
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in CVS? |
142 |
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143 |
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2004-06-02 13:27 gezelter |
144 |
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145 |
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* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep, |
146 |
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Makefile.in, WATER.cpp: formatting error messages, dependency fixes |
147 |
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148 |
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2004-06-02 13:27 gezelter |
149 |
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150 |
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* libBASS/simError.h: starting fortran-usable version of simError |
151 |
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152 |
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2004-06-02 09:56 chrisfen |
153 |
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154 |
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* samples/: argon/Makefile, minimizer/argon/Makefile: Probably |
155 |
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shouldn't be in CVS |
156 |
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157 |
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2004-06-02 09:56 chrisfen |
158 |
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159 |
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* libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp, |
160 |
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Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes, |
161 |
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removed writeRaw |
162 |
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163 |
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2004-06-02 09:56 chrisfen |
164 |
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165 |
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* libBASS/simError.c: Formatting Changes |
166 |
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167 |
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2004-06-02 09:21 gezelter |
168 |
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169 |
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* libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp: |
170 |
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severity levels in simError |
171 |
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172 |
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2004-06-01 16:45 gezelter |
173 |
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174 |
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* libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90, |
175 |
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do_Forces.F90, mpiSimulation.cpp, neighborLists.F90, |
176 |
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simulation_module.F90: Bug fix (fixes of skipList and neighbor list |
177 |
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under MPI) |
178 |
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179 |
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2004-06-01 16:44 gezelter |
180 |
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181 |
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* libBASS/MoleculeStamp.cpp: Bug fix (memory leak) |
182 |
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183 |
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2004-06-01 13:43 gezelter |
184 |
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185 |
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* samples/: argon/argon.bass, minimizer/argon/argon.bass: Testing |
186 |
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187 |
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2004-06-01 13:42 gezelter |
188 |
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189 |
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* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
190 |
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SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp, |
191 |
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mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90: |
192 |
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Cutoff Groups for MPI |
193 |
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194 |
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2004-06-01 13:07 chrisfen |
195 |
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196 |
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* libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in |
197 |
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useLiquidThermInt routine in ForceFields.cpp |
198 |
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199 |
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2004-06-01 12:15 chrisfen |
200 |
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201 |
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* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
202 |
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SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate |
203 |
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solid and liquid thermodynamic integration routines |
204 |
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205 |
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2004-06-01 10:57 tim |
206 |
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207 |
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* libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in |
208 |
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progress |
209 |
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210 |
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2004-06-01 09:27 chrisfen |
211 |
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212 |
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* libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt |
213 |
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keyword and changed useThermInt to useSolidThermInt |
214 |
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215 |
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2004-06-01 09:21 chrisfen |
216 |
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217 |
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* libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate |
218 |
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solid and liquid thermodynamic integration routines |
219 |
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220 |
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2004-05-28 10:21 gezelter |
221 |
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222 |
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* libmdtools/do_Forces.F90: bugfix starting |
223 |
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224 |
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2004-05-27 15:06 chrisfen |
225 |
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226 |
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* libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in |
227 |
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Integrator.cpp where it called writeRaw() when useThermInt = |
228 |
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false... |
229 |
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230 |
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2004-05-27 14:51 tim |
231 |
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232 |
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* ChangeLog, libmdtools/do_Forces.F90, |
233 |
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libmdtools/simulation_module.F90: Bug fix for SkipList |
234 |
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235 |
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2004-05-27 14:26 gezelter |
236 |
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237 |
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* libmdtools/SimSetup.cpp: bugfix in simsetup? |
238 |
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239 |
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2004-05-27 13:59 gezelter |
240 |
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241 |
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* libmdtools/: DumpReader.cpp, DumpWriter.cpp, |
242 |
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InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp, |
243 |
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ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp, |
244 |
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mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp, |
245 |
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mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90: |
246 |
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Cutoff group changes under MPI |
247 |
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248 |
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2004-05-27 11:20 gezelter |
249 |
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250 |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for |
251 |
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xlc++ |
252 |
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253 |
tim |
1206 |
2004-05-27 10:31 tim |
254 |
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255 |
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* libmdtools/SimInfo.cpp: groupList new bases on global index of |
256 |
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atoms |
257 |
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258 |
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2004-05-27 10:21 gezelter |
259 |
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260 |
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* src/: oopse.cpp, oose.cpp: Modified the nifty banner |
261 |
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262 |
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2004-05-27 10:21 gezelter |
263 |
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264 |
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* libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: |
265 |
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Fixed off-by-one error in groupStartRow and groupStartCol |
266 |
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267 |
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2004-05-26 19:48 tim |
268 |
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269 |
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* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, |
270 |
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libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
271 |
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libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
272 |
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libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, |
273 |
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libmdtools/calc_charge_charge.F90, |
274 |
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libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
275 |
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libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
276 |
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libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
277 |
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libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, |
278 |
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libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, |
279 |
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libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
280 |
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libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
281 |
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libmdtools/simulation_module.F90: in the progress of fixing MPI |
282 |
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version of cutoff group |
283 |
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284 |
tim |
1198 |
2004-05-26 11:41 gezelter |
285 |
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286 |
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* libmdtools/do_Forces.F90: Compacted all of the 8 copies of the |
287 |
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force loop into one. |
288 |
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289 |
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2004-05-24 17:24 gezelter |
290 |
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291 |
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* libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
292 |
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293 |
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2004-05-24 16:23 chrisfen |
294 |
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295 |
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* libmdtools/Restraints.cpp: Removed unnecessary variables and |
296 |
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changed error messages in Restraints.cpp |
297 |
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298 |
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2004-05-24 16:03 gezelter |
299 |
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300 |
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* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
301 |
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calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
302 |
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calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
303 |
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for stress / pressure tensor by cutoff group |
304 |
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305 |
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2004-05-22 15:55 chrisfen |
306 |
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307 |
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* libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... |
308 |
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Too many arguements in a function call. |
309 |
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310 |
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2004-05-22 13:17 chrisfen |
311 |
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312 |
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* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
313 |
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useThermInt. |
314 |
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315 |
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2004-05-22 13:16 chrisfen |
316 |
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317 |
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* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
318 |
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ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
319 |
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Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
320 |
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SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
321 |
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StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
322 |
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code. |
323 |
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324 |
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2004-05-21 10:58 gezelter |
325 |
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326 |
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* libmdtools/: do_Forces.F90, simulation_module.F90: Major changes |
327 |
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to skipThisPair for efficiency |
328 |
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329 |
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2004-05-21 09:22 gezelter |
330 |
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331 |
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* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
332 |
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forceFields/amber99.vdw, forceFields/charmm27.vdw, |
333 |
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forceFields/gaff.vdw, forceFields/oplsaal.vdw, |
334 |
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samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes |
335 |
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for SHAPES potential |
336 |
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337 |
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2004-05-20 15:27 chrisfen |
338 |
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339 |
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* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
340 |
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included the bass keywords |
341 |
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342 |
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2004-05-20 15:24 chrisfen |
343 |
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344 |
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* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
345 |
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Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
346 |
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Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
347 |
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additions... Restraints.cpp and .hpp were included for restraining |
348 |
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particles in thermodynamic integration. By including these, |
349 |
|
|
changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, |
350 |
|
|
StatWriter, and possibly some other files. Two bass keywords were |
351 |
|
|
also added for performing thermodynamic integration: a lambda value |
352 |
|
|
one and a k power one. |
353 |
|
|
|
354 |
|
|
2004-05-13 16:08 gezelter |
355 |
|
|
|
356 |
|
|
* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
357 |
|
|
|
358 |
|
|
2004-05-12 17:01 tim |
359 |
|
|
|
360 |
|
|
* samples/: argon/Makefile, argon/argonEM.bass, |
361 |
|
|
argon/init_argon.eor, minimizer/argon/Makefile, |
362 |
|
|
minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, |
363 |
|
|
minimizer/water/Makefile, minimizer/water/Makefile.in, |
364 |
|
|
minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, |
365 |
|
|
minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, |
366 |
|
|
minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add |
367 |
|
|
minimizer sample |
368 |
|
|
|
369 |
|
|
2004-05-12 16:54 gezelter |
370 |
|
|
|
371 |
|
|
* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
372 |
|
|
compilation |
373 |
|
|
|
374 |
|
|
2004-05-12 15:54 gezelter |
375 |
|
|
|
376 |
|
|
* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
377 |
|
|
for compilation under Mac OS X with IBM's xl compilers |
378 |
|
|
|
379 |
|
|
2004-05-12 15:14 gezelter |
380 |
|
|
|
381 |
|
|
* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
382 |
|
|
|
383 |
|
|
2004-05-12 15:14 gezelter |
384 |
|
|
|
385 |
|
|
* libmdtools/LJFF.cpp: Removed an extraneous write |
386 |
|
|
|
387 |
|
|
2004-05-12 15:13 gezelter |
388 |
|
|
|
389 |
|
|
* libBASS/simError.h: Starting to change the error model |
390 |
|
|
|
391 |
|
|
2004-05-12 14:45 gezelter |
392 |
|
|
|
393 |
|
|
* utils/Dump2XYZ.cpp: const char* fix |
394 |
|
|
|
395 |
|
|
2004-05-12 14:44 gezelter |
396 |
|
|
|
397 |
|
|
* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
398 |
|
|
src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
399 |
|
|
write statements |
400 |
|
|
|
401 |
|
|
2004-05-12 11:38 tim |
402 |
|
|
|
403 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
404 |
|
|
ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
405 |
|
|
SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
406 |
|
|
massratio from simState, creat cutoff group forevery atom which |
407 |
|
|
does not belong to cutoff group defined at mdl file |
408 |
|
|
|
409 |
|
|
2004-05-12 10:58 gezelter |
410 |
|
|
|
411 |
|
|
* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
412 |
|
|
CutoffGroup |
413 |
|
|
|
414 |
|
|
2004-05-12 10:35 gezelter |
415 |
|
|
|
416 |
|
|
* samples/water/water.mdl: Added the cutoff Groups to the default |
417 |
|
|
water.mdl file |
418 |
|
|
|
419 |
|
|
2004-05-12 10:02 tim |
420 |
|
|
|
421 |
|
|
* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
422 |
|
|
fixed a bug in CutoffGroup::getCOM() |
423 |
|
|
|
424 |
tim |
1164 |
2004-05-12 09:29 gezelter |
425 |
|
|
|
426 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
427 |
|
|
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
428 |
|
|
samples/water/ssd.bass: bug fixes for cutoffGroups |
429 |
|
|
|
430 |
|
|
2004-05-11 17:28 tim |
431 |
|
|
|
432 |
|
|
* utils/Vector3.hpp: adding generic Vector3 class |
433 |
|
|
|
434 |
|
|
2004-05-11 16:44 tim |
435 |
|
|
|
436 |
|
|
* libmdtools/Integrator.hpp: adding instantiation of |
437 |
|
|
Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8 |
438 |
|
|
|
439 |
|
|
2004-05-11 16:31 gezelter |
440 |
|
|
|
441 |
|
|
* libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, |
442 |
|
|
calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, |
443 |
|
|
calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: |
444 |
|
|
Fortran-side changes for group-based cutoffs |
445 |
|
|
|
446 |
|
|
2004-05-11 16:20 tim |
447 |
|
|
|
448 |
|
|
* libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp |
449 |
|
|
|
450 |
|
|
2004-05-11 16:14 tim |
451 |
|
|
|
452 |
|
|
* libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, |
453 |
|
|
SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix |
454 |
|
|
anoter one in CutoffGroup which causes seg fault |
455 |
|
|
|
456 |
|
|
2004-05-11 15:33 tim |
457 |
|
|
|
458 |
|
|
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
459 |
|
|
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
460 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup |
461 |
|
|
into OOPSE |
462 |
|
|
|
463 |
|
|
2004-05-11 15:07 gezelter |
464 |
|
|
|
465 |
|
|
* libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup |
466 |
|
|
|
467 |
tim |
1157 |
2004-05-11 11:00 gezelter |
468 |
|
|
|
469 |
|
|
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
470 |
|
|
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
471 |
|
|
use the simplified cutoff stuff in the BASS library |
472 |
|
|
|
473 |
|
|
2004-05-10 23:21 gezelter |
474 |
|
|
|
475 |
|
|
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
476 |
|
|
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
477 |
|
|
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
478 |
|
|
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
479 |
|
|
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
480 |
|
|
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
481 |
|
|
Also restructured the plethora of cutoff radii into one |
482 |
|
|
cutoffRadius and one switchingRadius. Also removed the |
483 |
|
|
useMolecularCutoffs keyword |
484 |
|
|
|
485 |
|
|
2004-05-10 15:28 tim |
486 |
|
|
|
487 |
|
|
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
488 |
|
|
DumpWriter |
489 |
|
|
|
490 |
tim |
1152 |
2004-05-07 16:36 gezelter |
491 |
|
|
|
492 |
|
|
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
493 |
|
|
for fortran group-based switching function |
494 |
|
|
|
495 |
|
|
2004-05-07 16:35 gezelter |
496 |
|
|
|
497 |
|
|
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
498 |
|
|
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
499 |
|
|
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
500 |
|
|
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
501 |
|
|
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
502 |
|
|
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
503 |
|
|
simulation_module.F90: Many changes to get group-based cutoffs to |
504 |
|
|
work |
505 |
|
|
|
506 |
|
|
2004-05-01 13:52 tim |
507 |
|
|
|
508 |
|
|
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
509 |
|
|
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
510 |
|
|
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
511 |
|
|
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
512 |
|
|
libmdtools/fortranWrapDefines.hpp, |
513 |
|
|
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
514 |
|
|
|
515 |
tim |
1144 |
2004-04-29 11:03 tim |
516 |
|
|
|
517 |
|
|
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
518 |
|
|
calc_charge_charge when using molecular cutoff |
519 |
|
|
|
520 |
tim |
1143 |
2004-04-28 21:11 tim |
521 |
|
|
|
522 |
|
|
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
523 |
|
|
unmatched c/fortran interface |
524 |
|
|
|
525 |
|
|
2004-04-28 18:09 tim |
526 |
|
|
|
527 |
|
|
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
528 |
|
|
keep the previous position of cantilever in SMD |
529 |
|
|
|
530 |
tim |
1141 |
2004-04-28 17:34 tim |
531 |
|
|
|
532 |
|
|
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
533 |
|
|
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
534 |
|
|
in Molecule.cpp which initialize massRatio before creat the array. |
535 |
|
|
fix two bugs in ZconsVisitor |
536 |
|
|
|
537 |
|
|
2004-04-28 17:06 gezelter |
538 |
|
|
|
539 |
|
|
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
540 |
|
|
Adding molecular cutoffs |
541 |
|
|
|
542 |
|
|
2004-04-28 16:39 gezelter |
543 |
|
|
|
544 |
|
|
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
545 |
|
|
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
546 |
|
|
molecular cutoffs |
547 |
|
|
|
548 |
|
|
2004-04-28 16:39 gezelter |
549 |
|
|
|
550 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
551 |
|
|
Globals |
552 |
|
|
|
553 |
tim |
1140 |
2004-04-27 11:26 tim |
554 |
|
|
|
555 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
556 |
|
|
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
557 |
|
|
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
558 |
|
|
molecule and massRation into atom class |
559 |
|
|
|
560 |
|
|
2004-04-26 16:16 mmeineke |
561 |
|
|
|
562 |
|
|
* libBASS/Globals.cpp: modified the defaults for the system init |
563 |
|
|
time and system init state. |
564 |
|
|
|
565 |
|
|
2004-04-26 09:29 gezelter |
566 |
|
|
|
567 |
|
|
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
568 |
|
|
calc_charge_charge.F90 |
569 |
|
|
|
570 |
|
|
2004-04-23 23:31 tim |
571 |
|
|
|
572 |
|
|
* ChangeLog, libmdtools/AtomVisitor.cpp, |
573 |
|
|
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
574 |
|
|
reaction field correction to charge-charge interaction |
575 |
|
|
|
576 |
tim |
1132 |
2004-04-22 16:33 tim |
577 |
|
|
|
578 |
|
|
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
579 |
|
|
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
580 |
|
|
calculation of pressure tensor |
581 |
|
|
|
582 |
|
|
2004-04-22 09:55 tim |
583 |
|
|
|
584 |
|
|
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
585 |
|
|
another bug in InitFromFile. MPI verion of OOPSE is working again |
586 |
|
|
|
587 |
|
|
2004-04-21 22:29 tim |
588 |
|
|
|
589 |
|
|
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
590 |
|
|
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
591 |
|
|
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
592 |
|
|
bugs in MPI version of InitfromFile and one unmatch MPI command in |
593 |
|
|
DumpWriter |
594 |
|
|
|
595 |
|
|
2004-04-21 00:32 tim |
596 |
|
|
|
597 |
|
|
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
598 |
|
|
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
599 |
|
|
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
600 |
|
|
useless files |
601 |
|
|
|
602 |
|
|
2004-04-20 11:56 tim |
603 |
|
|
|
604 |
|
|
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
605 |
|
|
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
606 |
|
|
velocitize at thermo |
607 |
|
|
|
608 |
|
|
2004-04-20 00:39 tim |
609 |
|
|
|
610 |
|
|
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
611 |
|
|
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
612 |
|
|
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
613 |
|
|
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
614 |
|
|
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
615 |
|
|
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
616 |
|
|
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
617 |
|
|
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
618 |
|
|
|
619 |
|
|
2004-04-19 17:13 gezelter |
620 |
|
|
|
621 |
|
|
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
622 |
|
|
Thermo.cpp: Fixed a charge bug |
623 |
|
|
|
624 |
tim |
1126 |
2004-04-19 15:54 tim |
625 |
|
|
|
626 |
|
|
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
627 |
|
|
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
628 |
|
|
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
629 |
|
|
a bug in CompositeVisitor which cause the double counting problem |
630 |
|
|
|
631 |
|
|
2004-04-19 12:44 tim |
632 |
|
|
|
633 |
|
|
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
634 |
|
|
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
635 |
|
|
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
636 |
|
|
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
637 |
|
|
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
638 |
|
|
Dump2XYZ is almost working except atoms in rigidbody are double |
639 |
|
|
counted |
640 |
|
|
|
641 |
|
|
2004-04-18 22:52 tim |
642 |
|
|
|
643 |
|
|
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
644 |
|
|
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
645 |
|
|
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
646 |
|
|
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
647 |
|
|
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
648 |
|
|
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
649 |
|
|
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
650 |
|
|
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
651 |
|
|
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
652 |
|
|
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
653 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
654 |
|
|
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
655 |
|
|
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
656 |
|
|
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
657 |
|
|
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
658 |
|
|
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
659 |
|
|
implement of quickLate using visitor and composite pattern |
660 |
|
|
|
661 |
tim |
1118 |
2004-04-15 17:15 tim |
662 |
|
|
|
663 |
|
|
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
664 |
|
|
exclude list |
665 |
|
|
|
666 |
|
|
2004-04-15 11:18 tim |
667 |
|
|
|
668 |
|
|
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
669 |
|
|
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
670 |
|
|
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
671 |
|
|
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
672 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
673 |
|
|
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
674 |
|
|
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
675 |
|
|
whole bunch of bugs :-) |
676 |
|
|
|
677 |
tim |
1113 |
2004-04-14 12:20 chrisfen |
678 |
|
|
|
679 |
|
|
* forceFields/WATER.frc: Added the WATER.frc force field |
680 |
|
|
|
681 |
|
|
2004-04-14 11:32 gezelter |
682 |
|
|
|
683 |
|
|
* libmdtools/Molecule.cpp: fixed for get_potential |
684 |
|
|
|
685 |
|
|
2004-04-14 10:37 tim |
686 |
|
|
|
687 |
|
|
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
688 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
689 |
|
|
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
690 |
|
|
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
691 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
692 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
693 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
694 |
|
|
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
695 |
|
|
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
696 |
|
|
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
697 |
|
|
Change DumpWriter and InitFromFile |
698 |
|
|
|
699 |
|
|
2004-04-13 11:26 gezelter |
700 |
|
|
|
701 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
702 |
|
|
molecules can keep track of their own IntegrableObjects (and |
703 |
|
|
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
704 |
|
|
RigidBodies (which was done incorrectly before). |
705 |
|
|
|
706 |
|
|
2004-04-13 11:25 gezelter |
707 |
|
|
|
708 |
|
|
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
709 |
|
|
(will back out momentarily) |
710 |
|
|
|
711 |
|
|
2004-04-13 10:10 gezelter |
712 |
|
|
|
713 |
|
|
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
714 |
|
|
Those were old. |
715 |
|
|
|
716 |
|
|
2004-04-13 10:09 gezelter |
717 |
|
|
|
718 |
|
|
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
719 |
|
|
to add IntegrableObjects |
720 |
|
|
|
721 |
|
|
2004-04-12 16:02 gezelter |
722 |
|
|
|
723 |
|
|
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
724 |
|
|
|
725 |
|
|
2004-04-12 15:32 gezelter |
726 |
|
|
|
727 |
|
|
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
728 |
|
|
test run |
729 |
|
|
|
730 |
|
|
2004-04-12 15:32 gezelter |
731 |
|
|
|
732 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
733 |
|
|
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
734 |
|
|
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
735 |
|
|
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
736 |
|
|
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
737 |
|
|
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
738 |
|
|
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
739 |
|
|
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
740 |
|
|
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
741 |
|
|
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
742 |
|
|
(Somewhat extensive) |
743 |
|
|
|
744 |
|
|
2004-04-12 15:31 gezelter |
745 |
|
|
|
746 |
|
|
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
747 |
|
|
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
748 |
|
|
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
749 |
|
|
Changes for RigidBody dynamics |
750 |
|
|
|
751 |
tim |
1108 |
2004-03-17 09:22 tim |
752 |
|
|
|
753 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
754 |
|
|
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
755 |
|
|
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
756 |
|
|
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
757 |
tim |
1113 |
does not sound a good choice, next commit will seperate SMD and |
758 |
tim |
1108 |
ZConstraint |
759 |
|
|
|
760 |
|
|
2004-03-16 14:22 tim |
761 |
|
|
|
762 |
|
|
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
763 |
|
|
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
764 |
|
|
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
765 |
|
|
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
766 |
|
|
now can support sequential moving. Refactorying is needed to |
767 |
|
|
support SMD in ZConstraint |
768 |
|
|
|
769 |
tim |
1091 |
2004-03-02 15:32 tim |
770 |
|
|
|
771 |
|
|
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
772 |
|
|
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
773 |
|
|
support large file |
774 |
|
|
|
775 |
|
|
2004-03-01 16:17 tim |
776 |
|
|
|
777 |
|
|
* utils/zsub.cpp: Fix a couple of bugs in zsub |
778 |
|
|
|
779 |
|
|
2004-03-01 15:01 tim |
780 |
|
|
|
781 |
|
|
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
782 |
|
|
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
783 |
|
|
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
784 |
|
|
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
785 |
|
|
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
786 |
|
|
program which can be used to replace atom type for zconstraint into |
787 |
|
|
OOPSE |
788 |
|
|
|
789 |
tim |
1074 |
2004-02-24 11:36 tim |
790 |
|
|
|
791 |
|
|
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
792 |
|
|
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
793 |
|
|
message] |
794 |
|
|
|
795 |
tim |
1066 |
2004-02-24 10:49 tim |
796 |
|
|
|
797 |
|
|
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
798 |
|
|
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
799 |
|
|
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
800 |
|
|
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
801 |
|
|
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
802 |
|
|
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
803 |
|
|
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
804 |
|
|
|
805 |
|
|
2004-02-24 10:44 tim |
806 |
|
|
|
807 |
|
|
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
808 |
|
|
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
809 |
|
|
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
810 |
|
|
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
811 |
|
|
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
812 |
|
|
compose to implement Minimizer both versions are working |
813 |
|
|
|
814 |
|
|
2004-02-17 14:23 tim |
815 |
|
|
|
816 |
|
|
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
817 |
|
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
818 |
|
|
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
819 |
|
|
libmdtools/MinimizerParameterSet.hpp, |
820 |
|
|
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
821 |
|
|
to remove the constraint force along bond direction |
822 |
|
|
|
823 |
tim |
1057 |
2004-02-10 16:33 tim |
824 |
|
|
|
825 |
|
|
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
826 |
|
|
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
827 |
|
|
single version of energy minimization is working. |
828 |
|
|
|
829 |
|
|
2004-02-09 15:38 mmeineke |
830 |
|
|
|
831 |
|
|
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
832 |
|
|
the massive memory overusage by OOPSE |
833 |
|
|
|
834 |
|
|
2004-02-09 09:48 chrisfen |
835 |
|
|
|
836 |
|
|
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
837 |
|
|
hardwired LJ_rcut |
838 |
|
|
|
839 |
tim |
1046 |
2004-02-06 19:14 tim |
840 |
|
|
|
841 |
|
|
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
842 |
|
|
message] |
843 |
|
|
|
844 |
|
|
2004-02-06 16:37 tim |
845 |
|
|
|
846 |
|
|
* ChangeLog, libBASS/Globals.cpp, |
847 |
|
|
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
848 |
|
|
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
849 |
|
|
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
850 |
|
|
energy minimization for argon is working, need to add constraint |
851 |
|
|
|
852 |
tim |
1035 |
2004-02-06 14:05 tim |
853 |
|
|
|
854 |
|
|
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
855 |
|
|
one more file into Makefile.in |
856 |
|
|
|
857 |
|
|
2004-02-06 13:58 tim |
858 |
|
|
|
859 |
|
|
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
860 |
|
|
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
861 |
|
|
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
862 |
|
|
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
863 |
|
|
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
864 |
|
|
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
865 |
|
|
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
866 |
|
|
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
867 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
868 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
869 |
|
|
some lines into global.cpp to make it work with energy minimization |
870 |
|
|
|
871 |
tim |
1031 |
2004-02-04 17:26 tim |
872 |
|
|
|
873 |
|
|
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
874 |
|
|
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
875 |
|
|
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
876 |
|
|
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
877 |
|
|
Single version of conjugate gradient with golden search linesearch |
878 |
|
|
pass a couple of functions test. Brent's algorithm is still broken |
879 |
|
|
|
880 |
|
|
2004-02-03 17:54 tim |
881 |
|
|
|
882 |
|
|
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
883 |
|
|
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
884 |
|
|
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
885 |
|
|
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
886 |
|
|
|
887 |
|
|
2004-02-03 15:47 tim |
888 |
|
|
|
889 |
|
|
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
890 |
|
|
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
891 |
|
|
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
892 |
|
|
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
893 |
|
|
SteepestDescent.hpp: [no log message] |
894 |
|
|
|
895 |
|
|
2004-02-03 15:43 tim |
896 |
|
|
|
897 |
|
|
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
898 |
|
|
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
899 |
|
|
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
900 |
|
|
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
901 |
|
|
constraint class |
902 |
|
|
|
903 |
|
|
2004-02-03 12:10 tim |
904 |
|
|
|
905 |
|
|
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
906 |
|
|
|
907 |
|
|
2004-02-03 10:21 tim |
908 |
|
|
|
909 |
|
|
* ChangeLog, libmdtools/Minimizer1D.cpp, |
910 |
|
|
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
911 |
|
|
|
912 |
tim |
1005 |
2004-02-02 15:29 tim |
913 |
|
|
|
914 |
|
|
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
915 |
|
|
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
916 |
|
|
Adding GoldenSection and Brent LineSearch Method |
917 |
|
|
|
918 |
|
|
2004-01-30 16:47 tim |
919 |
|
|
|
920 |
|
|
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
921 |
|
|
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
922 |
|
|
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
923 |
|
|
MinimizerBase instead of a functor to do line seach |
924 |
|
|
|
925 |
|
|
2004-01-30 10:00 chrisfen |
926 |
|
|
|
927 |
|
|
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
928 |
|
|
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
929 |
|
|
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
930 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
931 |
|
|
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
932 |
|
|
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
933 |
|
|
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
934 |
|
|
has a working WATER.cpp forcefield and parser. This involved |
935 |
|
|
changes to WATER.cpp and ForceFields amoung other files. One |
936 |
|
|
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
937 |
|
|
This will be removed on the next commit... |
938 |
|
|
|
939 |
|
|
2004-01-29 18:00 gezelter |
940 |
|
|
|
941 |
|
|
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
942 |
|
|
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
943 |
|
|
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
944 |
|
|
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
945 |
|
|
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
946 |
|
|
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
947 |
|
|
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
948 |
|
|
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
949 |
|
|
member list fixes for rigid bodies |
950 |
|
|
|
951 |
|
|
2004-01-29 16:44 tim |
952 |
|
|
|
953 |
|
|
* libmdtools/MinimizerParameterSet.hpp: Adding |
954 |
|
|
MinimizerParameterSet class. |
955 |
|
|
|
956 |
|
|
2004-01-28 17:44 tim |
957 |
|
|
|
958 |
|
|
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
959 |
|
|
NLModel0 and NLModel1 |
960 |
|
|
|
961 |
|
|
2004-01-28 15:40 tim |
962 |
|
|
|
963 |
|
|
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
964 |
|
|
of NLModel |
965 |
|
|
|
966 |
|
|
2004-01-27 15:34 gezelter |
967 |
|
|
|
968 |
|
|
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
969 |
|
|
water.mdl file, updated ssd.bass to use new SSD name |
970 |
|
|
|
971 |
|
|
2004-01-27 15:34 gezelter |
972 |
|
|
|
973 |
|
|
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
974 |
|
|
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
975 |
|
|
stuff |
976 |
|
|
|
977 |
|
|
2004-01-27 14:39 gezelter |
978 |
|
|
|
979 |
|
|
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
980 |
|
|
|
981 |
|
|
2004-01-27 14:39 gezelter |
982 |
|
|
|
983 |
|
|
* samples/metals/Au.bass: Longer run time to test gold in MPI |
984 |
|
|
|
985 |
|
|
2004-01-27 14:38 gezelter |
986 |
|
|
|
987 |
tim |
1198 |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer |
988 |
|
|
run time to test argon |
989 |
tim |
1005 |
|
990 |
|
|
2004-01-27 14:38 gezelter |
991 |
|
|
|
992 |
|
|
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
993 |
|
|
changes to do new rigidBody scheme a copy of WATER.cpp from this |
994 |
|
|
morning |
995 |
|
|
|
996 |
|
|
2004-01-27 14:37 gezelter |
997 |
|
|
|
998 |
|
|
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
999 |
|
|
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
1000 |
|
|
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
1001 |
|
|
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
1002 |
|
|
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
1003 |
|
|
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
1004 |
|
|
do new rigidBody scheme |
1005 |
|
|
|
1006 |
|
|
2004-01-27 14:15 tim |
1007 |
|
|
|
1008 |
|
|
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
1009 |
|
|
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
1010 |
|
|
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
1011 |
|
|
constraint for Nonlinear Optimization Model |
1012 |
|
|
|
1013 |
|
|
2004-01-26 17:01 gezelter |
1014 |
|
|
|
1015 |
|
|
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
1016 |
|
|
Euler angles for orientation instead of unit vectors required |
1017 |
|
|
changes in MoLocator |
1018 |
|
|
|
1019 |
|
|
2004-01-26 16:53 gezelter |
1020 |
|
|
|
1021 |
|
|
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
1022 |
|
|
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
1023 |
|
|
water/water.mdl: Changed orientation lines from unit vectors to |
1024 |
|
|
euler angles |
1025 |
|
|
|
1026 |
|
|
2004-01-26 16:52 gezelter |
1027 |
|
|
|
1028 |
|
|
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
1029 |
|
|
|
1030 |
|
|
2004-01-26 16:45 gezelter |
1031 |
|
|
|
1032 |
|
|
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
1033 |
|
|
use Euler angles in the following order: phi, theta, psi Removed |
1034 |
|
|
the ability to set orientation using a unit vector |
1035 |
|
|
|
1036 |
|
|
2004-01-26 16:26 gezelter |
1037 |
|
|
|
1038 |
|
|
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
1039 |
|
|
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
1040 |
|
|
Euler angles in the following order: phi, theta, psi Removed the |
1041 |
|
|
ability to set orientation using a unit vector |
1042 |
|
|
|
1043 |
|
|
2004-01-26 13:52 gezelter |
1044 |
|
|
|
1045 |
|
|
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
1046 |
|
|
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
1047 |
|
|
|
1048 |
|
|
2004-01-22 12:34 chrisfen |
1049 |
|
|
|
1050 |
|
|
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
1051 |
|
|
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
1052 |
|
|
Corrected spelling in several directories, and stated WATER.cpp |
1053 |
|
|
|
1054 |
|
|
2004-01-21 17:16 tim |
1055 |
|
|
|
1056 |
|
|
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
1057 |
|
|
NLOPModel.hpp: constraint class in energy minimization |
1058 |
|
|
|
1059 |
|
|
2004-01-20 15:34 tim |
1060 |
|
|
|
1061 |
|
|
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
1062 |
|
|
|
1063 |
|
|
2004-01-20 15:32 tim |
1064 |
|
|
|
1065 |
|
|
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
1066 |
|
|
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
1067 |
|
|
|
1068 |
|
|
2004-01-19 16:17 gezelter |
1069 |
|
|
|
1070 |
|
|
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
1071 |
|
|
more user-friendly |
1072 |
|
|
|
1073 |
|
|
2004-01-19 13:51 chrisfen |
1074 |
|
|
|
1075 |
|
|
* forceFields/DUFF.frc: Updated the default water to SSD/E |
1076 |
|
|
|
1077 |
|
|
2004-01-19 13:36 tim |
1078 |
|
|
|
1079 |
|
|
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
1080 |
|
|
time, status time, thermal time and reset time are not divisible by |
1081 |
|
|
dt |
1082 |
|
|
|
1083 |
|
|
2004-01-19 11:10 gezelter |
1084 |
|
|
|
1085 |
|
|
* third-party/Makefile.in: Added a bunch of dummy targets so make |
1086 |
|
|
won't complain |
1087 |
|
|
|
1088 |
|
|
2004-01-19 11:10 gezelter |
1089 |
|
|
|
1090 |
|
|
* samples/lipid/5x5.bass: Fixed old bass file |
1091 |
|
|
|
1092 |
|
|
2004-01-19 11:09 gezelter |
1093 |
|
|
|
1094 |
|
|
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
1095 |
|
|
required a change in how the MoleculeStamps are used by divideLabor |
1096 |
|
|
in mpiSimulation.cpp |
1097 |
|
|
|
1098 |
|
|
2004-01-19 11:08 gezelter |
1099 |
|
|
|
1100 |
|
|
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
1101 |
|
|
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
1102 |
|
|
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
1103 |
|
|
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
1104 |
|
|
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
1105 |
|
|
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
1106 |
|
|
|
1107 |
|
|
2004-01-16 16:55 tim |
1108 |
|
|
|
1109 |
|
|
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
1110 |
|
|
eor file |
1111 |
|
|
|
1112 |
|
|
2004-01-16 16:51 mmeineke |
1113 |
|
|
|
1114 |
|
|
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
1115 |
|
|
write eor files |
1116 |
|
|
|
1117 |
|
|
2004-01-16 10:01 mmeineke |
1118 |
|
|
|
1119 |
|
|
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
1120 |
|
|
initialization of the AtomStruct |
1121 |
|
|
|
1122 |
|
|
2004-01-15 16:57 chuckv |
1123 |
|
|
|
1124 |
|
|
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
1125 |
|
|
|
1126 |
|
|
2004-01-15 10:51 gezelter |
1127 |
|
|
|
1128 |
|
|
* ac-tools/aclocal.m4: Changes for altivec |
1129 |
|
|
|
1130 |
|
|
2004-01-15 09:22 gezelter |
1131 |
|
|
|
1132 |
|
|
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
1133 |
|
|
|
1134 |
|
|
2004-01-14 23:33 gezelter |
1135 |
|
|
|
1136 |
|
|
* libmdtools/do_Forces.F90: changes for charge charge interactions |
1137 |
|
|
|
1138 |
|
|
2004-01-14 20:14 gezelter |
1139 |
|
|
|
1140 |
|
|
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
1141 |
|
|
notifyCutoffs.F90: More work for adding charges |
1142 |
|
|
|
1143 |
|
|
2004-01-14 17:41 gezelter |
1144 |
|
|
|
1145 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1146 |
|
|
src/Makefile.in: autoconf fixes |
1147 |
|
|
|
1148 |
|
|
2004-01-14 11:28 mmeineke |
1149 |
|
|
|
1150 |
|
|
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
1151 |
|
|
|
1152 |
|
|
2004-01-14 10:48 gezelter |
1153 |
|
|
|
1154 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1155 |
|
|
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
1156 |
|
|
changes for icc8 |
1157 |
|
|
|
1158 |
|
|
2004-01-13 18:01 gezelter |
1159 |
|
|
|
1160 |
|
|
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
1161 |
|
|
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
1162 |
|
|
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
1163 |
|
|
Changes for adding direct charge-charge interactions (with |
1164 |
|
|
switching function) |
1165 |
|
|
|
1166 |
|
|
2004-01-13 17:34 gezelter |
1167 |
|
|
|
1168 |
|
|
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
1169 |
|
|
oopseMPI_module.F90: Some changes for new MPI organization and |
1170 |
|
|
direct charge-charge interactions |
1171 |
|
|
|
1172 |
|
|
2004-01-13 17:11 tim |
1173 |
|
|
|
1174 |
|
|
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
1175 |
|
|
|
1176 |
|
|
2004-01-13 16:22 tim |
1177 |
|
|
|
1178 |
|
|
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
1179 |
|
|
|
1180 |
|
|
2004-01-13 15:35 tim |
1181 |
|
|
|
1182 |
|
|
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
1183 |
|
|
eor file whenever it is used instead of rewinding it |
1184 |
|
|
|
1185 |
|
|
2004-01-13 15:04 tim |
1186 |
|
|
|
1187 |
|
|
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
1188 |
|
|
of writeFrame |
1189 |
|
|
|
1190 |
|
|
2004-01-13 10:46 tim |
1191 |
|
|
|
1192 |
|
|
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
1193 |
|
|
Merge the code of writeFinal and writeDump; |
1194 |
|
|
Adding sortingIndex into DumpWriter; |
1195 |
|
|
Fix a bug of writing last frame twice in integrator |
1196 |
|
|
|
1197 |
|
|
2004-01-12 17:54 tim |
1198 |
|
|
|
1199 |
|
|
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
1200 |
|
|
a bug in copying string |
1201 |
|
|
|
1202 |
tim |
927 |
2004-01-12 15:37 tim |
1203 |
|
|
|
1204 |
|
|
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
1205 |
tim |
1198 |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: |
1206 |
|
|
Dumpwriter only write out the atoms on master nodes |
1207 |
tim |
927 |
|
1208 |
tim |
926 |
2004-01-10 04:46 tim |
1209 |
|
|
|
1210 |
|
|
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
1211 |
|
|
roll it back fix a bug of copying string to a pointer Still have |
1212 |
|
|
Seg fault, it looks like a random MPI seg fault in totalview |
1213 |
|
|
|
1214 |
tim |
920 |
2004-01-09 21:15 tim |
1215 |
|
|
|
1216 |
|
|
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
1217 |
|
|
|
1218 |
|
|
2004-01-09 15:29 gezelter |
1219 |
|
|
|
1220 |
|
|
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
1221 |
|
|
|
1222 |
|
|
2004-01-08 17:25 chuckv |
1223 |
|
|
|
1224 |
|
|
* libmdtools/DumpWriter.cpp: A work in progress... |
1225 |
|
|
|
1226 |
|
|
2004-01-08 13:59 gezelter |
1227 |
|
|
|
1228 |
|
|
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
1229 |
|
|
case |
1230 |
|
|
|
1231 |
|
|
2004-01-08 13:13 mmeineke |
1232 |
|
|
|
1233 |
|
|
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
1234 |
|
|
state bug. |
1235 |
|
|
|
1236 |
|
|
2004-01-08 13:05 gezelter |
1237 |
|
|
|
1238 |
|
|
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
1239 |
|
|
|
1240 |
|
|
2004-01-08 12:57 mmeineke |
1241 |
|
|
|
1242 |
|
|
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
1243 |
|
|
exstended state bug |
1244 |
|
|
|
1245 |
|
|
2004-01-08 12:40 gezelter |
1246 |
|
|
|
1247 |
|
|
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
1248 |
|
|
|
1249 |
|
|
2004-01-08 10:44 mmeineke |
1250 |
|
|
|
1251 |
|
|
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
1252 |
|
|
XS state info flag |
1253 |
|
|
|
1254 |
|
|
2004-01-07 14:26 tim |
1255 |
|
|
|
1256 |
|
|
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
1257 |
tim |
1198 |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass, |
1258 |
|
|
samples/water/ssd.bass: Fixed a bug of sending message from master |
1259 |
|
|
node to itself in DumpWriter.cpp and InitializeFromFile.cpp |
1260 |
tim |
920 |
|
1261 |
|
|
2004-01-06 14:49 chuckv |
1262 |
|
|
|
1263 |
|
|
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
1264 |
|
|
performance fixes in the dipole dipole and reaction field code |
1265 |
|
|
|
1266 |
|
|
2004-01-06 13:54 chuckv |
1267 |
|
|
|
1268 |
|
|
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
1269 |
|
|
little more sane |
1270 |
|
|
|
1271 |
|
|
2004-01-05 17:49 chuckv |
1272 |
|
|
|
1273 |
|
|
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1274 |
|
|
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
1275 |
|
|
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
1276 |
|
|
performance by reducing spurious function calls |
1277 |
|
|
|
1278 |
|
|
2004-01-05 17:18 chuckv |
1279 |
|
|
|
1280 |
|
|
* libmdtools/do_Forces.F90: mangling forces even further |
1281 |
|
|
|
1282 |
|
|
2004-01-05 17:18 chuckv |
1283 |
|
|
|
1284 |
|
|
* configure, ac-tools/configure.in: mpich mucking |
1285 |
|
|
|
1286 |
|
|
2004-01-05 17:12 chuckv |
1287 |
|
|
|
1288 |
|
|
* libmdtools/do_Forces.F90: mangled do_forces... |
1289 |
|
|
|
1290 |
|
|
2004-01-05 16:00 chuckv |
1291 |
|
|
|
1292 |
|
|
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
1293 |
|
|
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
1294 |
|
|
lookup |
1295 |
|
|
|
1296 |
chuckv |
894 |
2003-12-29 14:56 chuckv |
1297 |
gezelter |
760 |
|
1298 |
chuckv |
894 |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
1299 |
|
|
third-party directory for code not written by us. Also added |
1300 |
|
|
Mersenne Twister random number generator code. This will eventually |
1301 |
|
|
replace sprng as the random number generator used by OOPSE. |
1302 |
|
|
|
1303 |
|
|
2003-12-22 16:26 chuckv |
1304 |
|
|
|
1305 |
|
|
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
1306 |
|
|
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
1307 |
|
|
Fixes to profile code. |
1308 |
|
|
|
1309 |
|
|
2003-12-19 15:36 mmeineke |
1310 |
|
|
|
1311 |
|
|
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
1312 |
|
|
timing.F90, timing.f90: More profiling fixes. |
1313 |
|
|
|
1314 |
|
|
2003-12-19 15:19 chuckv |
1315 |
|
|
|
1316 |
|
|
* libmdtools/timing.f90: Another change for MPI in timing. |
1317 |
|
|
|
1318 |
|
|
2003-12-19 15:17 chuckv |
1319 |
|
|
|
1320 |
|
|
* libmdtools/timing.f90: Small update to timing in MPI |
1321 |
|
|
|
1322 |
|
|
2003-12-19 13:53 mmeineke |
1323 |
|
|
|
1324 |
|
|
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
1325 |
|
|
profiling commands work now. Will start adding PROFILE ifdefs into |
1326 |
|
|
the code |
1327 |
|
|
|
1328 |
|
|
2003-12-19 12:25 mmeineke |
1329 |
|
|
|
1330 |
|
|
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
1331 |
|
|
some profiling routines |
1332 |
|
|
|
1333 |
|
|
2003-12-19 10:12 mmeineke |
1334 |
|
|
|
1335 |
|
|
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
1336 |
|
|
and GofRomega |
1337 |
|
|
|
1338 |
|
|
additional work on randomBilayer |
1339 |
|
|
|
1340 |
|
|
2003-12-19 10:12 mmeineke |
1341 |
|
|
|
1342 |
|
|
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
1343 |
|
|
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
1344 |
|
|
GofRomega |
1345 |
|
|
|
1346 |
|
|
2003-12-18 16:47 mmeineke |
1347 |
|
|
|
1348 |
|
|
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
1349 |
|
|
some profile functionality |
1350 |
|
|
|
1351 |
|
|
2003-12-18 15:46 chuckv |
1352 |
|
|
|
1353 |
|
|
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
1354 |
|
|
Added functions for simple profiling in fortran. |
1355 |
|
|
|
1356 |
|
|
2003-12-17 15:13 chuckv |
1357 |
|
|
|
1358 |
|
|
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
1359 |
|
|
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
1360 |
|
|
rho_col were scattered into the same array. Unfortunately, MPI |
1361 |
|
|
zeros the array between scatters so half of the sum was being lost. |
1362 |
|
|
Fixed by added a temp array for column scatter, then sum loop over |
1363 |
|
|
nlocal. |
1364 |
|
|
|
1365 |
|
|
2003-12-16 15:49 mmeineke |
1366 |
|
|
|
1367 |
|
|
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
1368 |
|
|
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
1369 |
|
|
gofRomega. both need to be debugged and tested. |
1370 |
|
|
|
1371 |
|
|
2003-12-12 10:42 gezelter |
1372 |
|
|
|
1373 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1374 |
|
|
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
1375 |
|
|
gradients (to do minimizations) |
1376 |
|
|
|
1377 |
|
|
2003-12-12 10:33 mmeineke |
1378 |
|
|
|
1379 |
|
|
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
1380 |
|
|
header |
1381 |
|
|
|
1382 |
|
|
2003-12-10 11:52 mmeineke |
1383 |
|
|
|
1384 |
|
|
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
1385 |
|
|
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
1386 |
|
|
randomBilayer to the build. Also move the random bilayer builder |
1387 |
|
|
from bilayerSys to randomBilayer |
1388 |
|
|
|
1389 |
|
|
2003-11-25 10:44 mmeineke |
1390 |
|
|
|
1391 |
|
|
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
1392 |
|
|
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
1393 |
|
|
TB3 in DUFF.frc |
1394 |
|
|
|
1395 |
|
|
2003-11-21 15:09 mmeineke |
1396 |
|
|
|
1397 |
|
|
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
1398 |
|
|
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
1399 |
|
|
message in SimInfo. Added a more informative error message in |
1400 |
|
|
InitializeFromFile |
1401 |
|
|
|
1402 |
|
|
2003-11-21 15:07 mmeineke |
1403 |
|
|
|
1404 |
|
|
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
1405 |
|
|
ing in the GofR,CosTheta |
1406 |
|
|
|
1407 |
|
|
2003-11-21 14:31 chrisfen |
1408 |
|
|
|
1409 |
|
|
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
1410 |
|
|
a bug in SimInfo ordering of radii |
1411 |
|
|
|
1412 |
|
|
2003-11-11 12:20 mmeineke |
1413 |
|
|
|
1414 |
|
|
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
1415 |
|
|
a min function. |
1416 |
|
|
|
1417 |
|
|
2003-11-10 16:50 mmeineke |
1418 |
|
|
|
1419 |
|
|
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
1420 |
|
|
reordered the rcut/ecr/boxSize initialization |
1421 |
|
|
|
1422 |
|
|
removed the rcut/ecr shrink and grow algorithm. the simulation will |
1423 |
|
|
now exit when it runs into rcut or ecr. |
1424 |
|
|
|
1425 |
|
|
2003-11-07 16:46 chuckv |
1426 |
|
|
|
1427 |
|
|
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
1428 |
|
|
oopseMPI_module.F90: Added support for compiling fortran without |
1429 |
|
|
use of mpich modules. We use mpif.h instead.: |
1430 |
|
|
|
1431 |
|
|
2003-11-07 12:09 mmeineke |
1432 |
|
|
|
1433 |
|
|
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
1434 |
|
|
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
1435 |
|
|
the atom loop in the NPT family of integrators. |
1436 |
|
|
|
1437 |
|
|
2003-11-06 17:01 mmeineke |
1438 |
|
|
|
1439 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
1440 |
|
|
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
1441 |
|
|
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1442 |
|
|
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
1443 |
|
|
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
1444 |
|
|
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
1445 |
|
|
* useIntiTime => useInitialTime |
1446 |
|
|
|
1447 |
|
|
2003-11-06 14:24 mmeineke |
1448 |
|
|
|
1449 |
|
|
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
1450 |
|
|
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
1451 |
|
|
parse_tree.h: fixed the includes in the Make.dep |
1452 |
|
|
|
1453 |
|
|
2003-11-06 14:11 mmeineke |
1454 |
|
|
|
1455 |
|
|
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1456 |
|
|
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
1457 |
|
|
new-templateless branch to the main trunk. |
1458 |
|
|
|
1459 |
|
|
bug Fixes include: * fixed the switching function from ortho to |
1460 |
|
|
non-ortho box. !!!!! THis was responsible for all of the |
1461 |
|
|
sudden deaths we saw. * some formating in the string when we |
1462 |
|
|
write out the extended system state. * added NPT.cpp to the |
1463 |
|
|
makefile.in |
1464 |
|
|
|
1465 |
|
|
2003-11-06 13:20 mmeineke |
1466 |
|
|
|
1467 |
|
|
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
1468 |
|
|
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
1469 |
|
|
bug. The box was not switching between orthorhombic and |
1470 |
|
|
non-orthorhombic wrapping correctly. we added a fabs() to |
1471 |
|
|
the check.which should fix it. |
1472 |
|
|
|
1473 |
|
|
2003-11-05 14:16 mmeineke |
1474 |
|
|
|
1475 |
|
|
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
1476 |
|
|
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
1477 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1478 |
|
|
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
1479 |
|
|
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
1480 |
|
|
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
1481 |
|
|
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
1482 |
|
|
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
1483 |
|
|
some work on trying to find the compression bug |
1484 |
|
|
|
1485 |
|
|
2003-11-03 17:07 mmeineke |
1486 |
|
|
|
1487 |
|
|
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
1488 |
|
|
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
1489 |
|
|
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
1490 |
|
|
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
1491 |
|
|
most of standard template library from OOPSE. |
1492 |
|
|
|
1493 |
|
|
2003-10-31 16:06 mmeineke |
1494 |
|
|
|
1495 |
|
|
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1496 |
|
|
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
1497 |
|
|
SimSetup.cpp: started work on template removal. |
1498 |
|
|
|
1499 |
|
|
2003-10-31 13:28 mmeineke |
1500 |
|
|
|
1501 |
|
|
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
1502 |
|
|
added template stuff to the Maikefile template |
1503 |
|
|
|
1504 |
|
|
little changes to some printf format statements |
1505 |
|
|
|
1506 |
|
|
2003-10-31 13:28 mmeineke |
1507 |
|
|
|
1508 |
|
|
* libBASS/Makefile.in: added template stuff to the Maikefile |
1509 |
|
|
template |
1510 |
|
|
|
1511 |
|
|
2003-10-30 13:59 gezelter |
1512 |
|
|
|
1513 |
|
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
1514 |
|
|
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
1515 |
|
|
rList problems |
1516 |
|
|
|
1517 |
|
|
2003-10-30 09:11 gezelter |
1518 |
|
|
|
1519 |
|
|
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
1520 |
|
|
queried before q0 was allocated. |
1521 |
|
|
|
1522 |
|
|
2003-10-29 15:41 mmeineke |
1523 |
|
|
|
1524 |
|
|
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
1525 |
|
|
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
1526 |
|
|
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
1527 |
|
|
in bass.l |
1528 |
|
|
|
1529 |
|
|
fixed a little bug in the first time step, regarding the setting of |
1530 |
|
|
ecr and est in fortran |
1531 |
|
|
|
1532 |
|
|
2003-10-29 15:40 mmeineke |
1533 |
|
|
|
1534 |
|
|
* libBASS/BASSlex.l: fixed a stdlib.h include error |
1535 |
|
|
|
1536 |
|
|
2003-10-29 12:55 mmeineke |
1537 |
|
|
|
1538 |
|
|
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1539 |
|
|
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
1540 |
|
|
rcut is setup, as well as additional debugging comments. |
1541 |
|
|
|
1542 |
|
|
2003-10-29 09:28 gezelter |
1543 |
|
|
|
1544 |
|
|
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
1545 |
|
|
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
1546 |
|
|
templates |
1547 |
|
|
|
1548 |
|
|
2003-10-28 22:16 gezelter |
1549 |
|
|
|
1550 |
|
|
* src/Makefile.in: Refixed broken makefile |
1551 |
|
|
|
1552 |
|
|
2003-10-28 22:06 gezelter |
1553 |
|
|
|
1554 |
|
|
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
1555 |
|
|
fixes |
1556 |
|
|
|
1557 |
|
|
2003-10-28 19:19 tim |
1558 |
|
|
|
1559 |
|
|
* ChangeLog, libmdtools/AbstractClasses.hpp, |
1560 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
1561 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1562 |
|
|
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
1563 |
|
|
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
1564 |
|
|
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
1565 |
tim |
1198 |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi |
1566 |
|
|
and eta to the comment line of dump file. |
1567 |
chuckv |
894 |
|
1568 |
|
|
2003-10-28 17:25 mmeineke |
1569 |
|
|
|
1570 |
|
|
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
1571 |
|
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1572 |
|
|
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
1573 |
|
|
how c calls fortran. All function pointers and fortran calls are |
1574 |
|
|
rigidly typecast now. |
1575 |
|
|
|
1576 |
|
|
2003-10-28 15:42 gezelter |
1577 |
|
|
|
1578 |
|
|
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
1579 |
|
|
Portability fixes |
1580 |
|
|
|
1581 |
|
|
2003-10-28 15:09 gezelter |
1582 |
|
|
|
1583 |
|
|
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
1584 |
|
|
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
1585 |
|
|
src/Makefile.in: Compatibility fixes |
1586 |
|
|
|
1587 |
|
|
2003-10-28 12:08 mmeineke |
1588 |
|
|
|
1589 |
|
|
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
1590 |
|
|
started work on template removal |
1591 |
|
|
|
1592 |
|
|
2003-10-28 12:04 gezelter |
1593 |
|
|
|
1594 |
|
|
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
1595 |
|
|
trying to understand extern "C" stuff for pointers |
1596 |
|
|
|
1597 |
|
|
2003-10-28 11:20 gezelter |
1598 |
|
|
|
1599 |
|
|
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
1600 |
|
|
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
1601 |
|
|
|
1602 |
|
|
2003-10-28 11:03 gezelter |
1603 |
|
|
|
1604 |
|
|
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
1605 |
|
|
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
1606 |
|
|
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
1607 |
|
|
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
1608 |
|
|
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1609 |
|
|
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
1610 |
|
|
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
1611 |
|
|
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
1612 |
|
|
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
1613 |
|
|
more portable c header stuff Also, mod file fixes and portability |
1614 |
|
|
changes Some fortran changes will need to be reversed. |
1615 |
|
|
|
1616 |
|
|
2003-10-28 11:03 gezelter |
1617 |
|
|
|
1618 |
|
|
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
1619 |
|
|
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
1620 |
|
|
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
1621 |
|
|
portable c header stuff Also, mod file fixes and portability |
1622 |
|
|
changes |
1623 |
|
|
|
1624 |
|
|
2003-10-28 11:02 gezelter |
1625 |
|
|
|
1626 |
|
|
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
1627 |
|
|
stuff |
1628 |
|
|
|
1629 |
|
|
2003-10-27 18:00 gezelter |
1630 |
|
|
|
1631 |
|
|
* Makefile.in, configure, ac-tools/aclocal.m4, |
1632 |
|
|
ac-tools/configure.in, ac-tools/fortran90.m4, |
1633 |
|
|
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
1634 |
|
|
|
1635 |
|
|
2003-10-27 17:08 mmeineke |
1636 |
|
|
|
1637 |
tim |
837 |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1638 |
chuckv |
894 |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
1639 |
|
|
added routines for the sysbuilder to work with simSetup |
1640 |
|
|
|
1641 |
|
|
remved the QuickBass routines, and had all parsing go through |
1642 |
|
|
SimSetup. LatticeBilayer is in complete working order now. |
1643 |
|
|
|
1644 |
|
|
2003-10-27 17:07 mmeineke |
1645 |
|
|
|
1646 |
|
|
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
1647 |
|
|
routines for the sysbuilder to work with simSetup |
1648 |
|
|
|
1649 |
|
|
2003-10-27 11:20 gezelter |
1650 |
|
|
|
1651 |
|
|
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
1652 |
|
|
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
1653 |
|
|
|
1654 |
tim |
926 |
2003-10-24 17:17 mmeineke |
1655 |
chuckv |
894 |
|
1656 |
|
|
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1657 |
tim |
837 |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
1658 |
|
|
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
1659 |
|
|
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
1660 |
|
|
overhauled latticeBilayer into its own program. Removed sysBuild |
1661 |
|
|
from the Makefile |
1662 |
|
|
|
1663 |
tim |
926 |
2003-10-24 12:36 gezelter |
1664 |
tim |
837 |
|
1665 |
|
|
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
1666 |
|
|
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
1667 |
|
|
builder |
1668 |
|
|
|
1669 |
tim |
926 |
2003-10-24 12:35 gezelter |
1670 |
tim |
837 |
|
1671 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
1672 |
|
|
merge problem |
1673 |
|
|
|
1674 |
tim |
926 |
2003-10-23 14:57 mmeineke |
1675 |
tim |
837 |
|
1676 |
|
|
* samples/metals/Makefile.in: added eam ForceField files to the |
1677 |
|
|
init |
1678 |
|
|
|
1679 |
|
|
fixed an eam mpi parmeter setup bug |
1680 |
|
|
|
1681 |
|
|
added the init file to the makefile |
1682 |
|
|
|
1683 |
tim |
926 |
2003-10-23 14:57 mmeineke |
1684 |
tim |
837 |
|
1685 |
|
|
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
1686 |
|
|
to the init |
1687 |
|
|
|
1688 |
|
|
fixed an eam mpi parmeter setup bug |
1689 |
|
|
|
1690 |
tim |
926 |
2003-10-23 14:57 mmeineke |
1691 |
tim |
837 |
|
1692 |
|
|
* forceFields/Makefile.in: added eam ForceField files to the init |
1693 |
|
|
|
1694 |
tim |
926 |
2003-10-22 16:17 mmeineke |
1695 |
tim |
837 |
|
1696 |
|
|
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
1697 |
|
|
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
1698 |
|
|
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
1699 |
|
|
no box skew allowed. |
1700 |
|
|
|
1701 |
tim |
926 |
2003-10-21 14:33 mmeineke |
1702 |
tim |
837 |
|
1703 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1704 |
|
|
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
1705 |
|
|
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
1706 |
|
|
* useInitTime = false: sets the origin time to 0.0 regardless |
1707 |
|
|
of the time stamp in the .init file * default=> useInitTime = |
1708 |
|
|
true; |
1709 |
|
|
|
1710 |
tim |
926 |
2003-10-17 16:19 mmeineke |
1711 |
tim |
837 |
|
1712 |
|
|
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
1713 |
|
|
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1714 |
|
|
staticProps.cpp, obj/placeholder: added the staticProps directory |
1715 |
|
|
to the build list for both configure and configure.in |
1716 |
|
|
|
1717 |
|
|
fixed a number of bugs in the staticProps code. gofr is now |
1718 |
|
|
working. |
1719 |
|
|
|
1720 |
tim |
926 |
2003-10-17 16:18 mmeineke |
1721 |
tim |
837 |
|
1722 |
|
|
* ac-tools/configure.in: added the staticProps directory to the |
1723 |
|
|
build list for both configure and configure.in |
1724 |
|
|
|
1725 |
tim |
926 |
2003-10-17 16:17 mmeineke |
1726 |
tim |
837 |
|
1727 |
|
|
* configure: added the staticProps directory to the build list |
1728 |
|
|
|
1729 |
tim |
926 |
2003-10-16 14:16 mmeineke |
1730 |
tim |
837 |
|
1731 |
|
|
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
1732 |
|
|
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
1733 |
|
|
use linked lists instead of a vector. |
1734 |
|
|
|
1735 |
|
|
Fixed the makefile to build DumpReader.cpp |
1736 |
|
|
|
1737 |
|
|
Removed a comment output in Exclude.cpp |
1738 |
|
|
|
1739 |
|
|
Modified DumpWriter and Integrator to write an eor file every time |
1740 |
|
|
a frame is written. This lets the .eor file represent the last |
1741 |
|
|
written frame of a simulation. |
1742 |
|
|
|
1743 |
tim |
926 |
2003-10-10 12:10 mmeineke |
1744 |
tim |
837 |
|
1745 |
tim |
1005 |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1746 |
|
|
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1747 |
|
|
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1748 |
|
|
staticProps.cpp: removed the props directory, and moved everything |
1749 |
|
|
over to staticProps |
1750 |
tim |
837 |
|
1751 |
tim |
926 |
2003-10-09 17:09 mmeineke |
1752 |
tim |
837 |
|
1753 |
tim |
1005 |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1754 |
tim |
837 |
a position where it will compile and run first runs. |
1755 |
|
|
|
1756 |
tim |
926 |
2003-10-04 13:46 chuckv |
1757 |
tim |
837 |
|
1758 |
|
|
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
1759 |
|
|
samples/metals/Au.bass: Fixed bug in calc_eam. |
1760 |
|
|
|
1761 |
tim |
926 |
2003-10-04 13:08 chuckv |
1762 |
tim |
837 |
|
1763 |
|
|
* samples/metals/init_au.in: added Au init file for eam. |
1764 |
|
|
|
1765 |
tim |
926 |
2003-10-03 17:11 mmeineke |
1766 |
tim |
837 |
|
1767 |
|
|
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1768 |
|
|
entahlpy from the statwriter and thermo. |
1769 |
|
|
|
1770 |
tim |
926 |
2003-10-03 17:02 mmeineke |
1771 |
tim |
837 |
|
1772 |
|
|
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1773 |
|
|
statements in simError |
1774 |
|
|
|
1775 |
|
|
added a function to get the maxCutoff |
1776 |
|
|
|
1777 |
tim |
926 |
2003-10-03 17:01 mmeineke |
1778 |
tim |
837 |
|
1779 |
|
|
* libBASS/simError.c: changed the formating ogf the error |
1780 |
|
|
statements in simError |
1781 |
|
|
|
1782 |
tim |
926 |
2003-09-30 11:00 mmeineke |
1783 |
tim |
920 |
|
1784 |
tim |
837 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1785 |
|
|
f90Flags so they are no longer overwritten by the compiler. |
1786 |
|
|
|
1787 |
tim |
926 |
2003-09-29 17:06 mmeineke |
1788 |
tim |
837 |
|
1789 |
|
|
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
1790 |
|
|
for conifig.in |
1791 |
|
|
|
1792 |
|
|
fixed wrappers to extern "C" |
1793 |
|
|
|
1794 |
tim |
926 |
2003-09-29 17:06 mmeineke |
1795 |
tim |
837 |
|
1796 |
|
|
* ac-tools/configure.in: added mpif90 mod check back same for |
1797 |
|
|
conifig.in |
1798 |
|
|
|
1799 |
tim |
926 |
2003-09-29 17:05 mmeineke |
1800 |
tim |
837 |
|
1801 |
|
|
* configure: added mpif90 mod check back |
1802 |
|
|
|
1803 |
tim |
926 |
2003-09-29 16:16 mmeineke |
1804 |
tim |
837 |
|
1805 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1806 |
|
|
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
1807 |
|
|
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
1808 |
|
|
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
1809 |
|
|
libBASS/ZconStamp.cpp, libBASS/simError.c, |
1810 |
|
|
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
1811 |
|
|
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
1812 |
|
|
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
1813 |
|
|
found with SUN's SUNWspro.s1s7 |
1814 |
|
|
|
1815 |
tim |
926 |
2003-09-29 12:38 mmeineke |
1816 |
tim |
837 |
|
1817 |
|
|
* libmdtools/GenericData.hpp: light change in syntax. no |
1818 |
|
|
signifigant change. |
1819 |
|
|
|
1820 |
tim |
926 |
2003-09-25 16:17 mmeineke |
1821 |
tim |
837 |
|
1822 |
|
|
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1823 |
|
|
additional remarks from icc -w3 (extra verbose output) |
1824 |
|
|
|
1825 |
tim |
926 |
2003-09-25 14:27 mmeineke |
1826 |
tim |
837 |
|
1827 |
|
|
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1828 |
|
|
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1829 |
|
|
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1830 |
|
|
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1831 |
|
|
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1832 |
|
|
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1833 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1834 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1835 |
|
|
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1836 |
|
|
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1837 |
|
|
gcc -Wall and g++ -Wall |
1838 |
|
|
|
1839 |
tim |
926 |
2003-09-25 13:54 gezelter |
1840 |
tim |
837 |
|
1841 |
|
|
* configure, ac-tools/configure.in: fixed a bug in configure |
1842 |
|
|
|
1843 |
tim |
926 |
2003-09-25 11:42 gezelter |
1844 |
tim |
837 |
|
1845 |
|
|
* Makefile.in, configure, ac-tools/aclocal.m4, |
1846 |
|
|
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
1847 |
|
|
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
1848 |
|
|
fixes for configure |
1849 |
|
|
|
1850 |
tim |
926 |
2003-09-24 14:34 mmeineke |
1851 |
tim |
837 |
|
1852 |
|
|
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
1853 |
|
|
that it is called before the first Statistics are written. |
1854 |
|
|
|
1855 |
tim |
926 |
2003-09-23 15:36 gezelter |
1856 |
tim |
837 |
|
1857 |
|
|
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
1858 |
|
|
bunch of Make.dep files to CVS |
1859 |
|
|
|
1860 |
tim |
926 |
2003-09-23 15:34 mmeineke |
1861 |
tim |
837 |
|
1862 |
|
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
1863 |
|
|
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
1864 |
|
|
|
1865 |
|
|
Some small syntax cleaning in NPTfm and SimSetup |
1866 |
|
|
|
1867 |
tim |
926 |
2003-09-22 18:07 tim |
1868 |
tim |
837 |
|
1869 |
|
|
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1870 |
|
|
SimInfo.hpp: fix bug in calculating maxCutoff |
1871 |
|
|
|
1872 |
tim |
926 |
2003-09-22 16:23 mmeineke |
1873 |
tim |
837 |
|
1874 |
|
|
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
1875 |
|
|
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
1876 |
|
|
Converted NPTf to work with the NPT base class. |
1877 |
|
|
|
1878 |
|
|
Removed NPTfm and NPTim from cvs |
1879 |
|
|
|
1880 |
tim |
926 |
2003-09-19 15:00 mmeineke |
1881 |
tim |
837 |
|
1882 |
|
|
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1883 |
|
|
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
1884 |
|
|
class. NPTi is up to date. NPTf is not. |
1885 |
|
|
|
1886 |
tim |
926 |
2003-09-19 11:03 mmeineke |
1887 |
tim |
837 |
|
1888 |
|
|
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
1889 |
|
|
makefile |
1890 |
|
|
|
1891 |
tim |
926 |
2003-09-19 11:01 gezelter |
1892 |
tim |
837 |
|
1893 |
|
|
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
1894 |
|
|
|
1895 |
tim |
926 |
2003-09-19 11:01 gezelter |
1896 |
tim |
837 |
|
1897 |
|
|
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
1898 |
|
|
(nearly) conserved quantities for both NPTi and NPTf |
1899 |
|
|
|
1900 |
tim |
926 |
2003-09-19 10:20 mmeineke |
1901 |
tim |
837 |
|
1902 |
|
|
* utils/Makefile.in: fixed a typo in the makefile. |
1903 |
|
|
|
1904 |
tim |
926 |
2003-09-19 09:55 gezelter |
1905 |
tim |
837 |
|
1906 |
|
|
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
1907 |
|
|
samples/water/ssd.bass: [no log message] |
1908 |
|
|
|
1909 |
tim |
926 |
2003-09-19 09:22 tim |
1910 |
tim |
837 |
|
1911 |
|
|
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
1912 |
|
|
|
1913 |
tim |
926 |
2003-09-17 09:22 mmeineke |
1914 |
tim |
837 |
|
1915 |
|
|
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
1916 |
|
|
work with constraints. |
1917 |
|
|
|
1918 |
tim |
926 |
2003-09-16 15:02 tim |
1919 |
tim |
837 |
|
1920 |
|
|
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
1921 |
|
|
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
1922 |
|
|
|
1923 |
|
|
fixed conserved quantity in NPT (Still some small bug) |
1924 |
|
|
|
1925 |
|
|
NPTi appears very stable. |
1926 |
|
|
|
1927 |
tim |
926 |
2003-09-15 11:52 tim |
1928 |
tim |
837 |
|
1929 |
|
|
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
1930 |
|
|
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
1931 |
|
|
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
1932 |
|
|
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1933 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
1934 |
|
|
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
1935 |
|
|
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1936 |
|
|
statWriter fix bug of vector wrapping at NPTi |
1937 |
|
|
|
1938 |
tim |
926 |
2003-09-12 11:20 gezelter |
1939 |
tim |
920 |
|
1940 |
tim |
837 |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1941 |
|
|
Makefile.in |
1942 |
|
|
|
1943 |
tim |
926 |
2003-09-12 11:20 gezelter |
1944 |
tim |
837 |
|
1945 |
|
|
* ChangeLog: Entered changes for configure into ChangeLog |
1946 |
|
|
|
1947 |
tim |
926 |
2003-09-09 15:35 mmeineke |
1948 |
tim |
920 |
|
1949 |
gezelter |
760 |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
1950 |
|
|
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
1951 |
|
|
|
1952 |
|
|
added two new NPT integrators, they still need work. |
1953 |
|
|
|
1954 |
tim |
926 |
2003-09-09 15:34 mmeineke |
1955 |
gezelter |
760 |
|
1956 |
|
|
* ChangeLog: updated the ChangeLog |
1957 |
|
|
|
1958 |
tim |
926 |
2003-09-05 17:45 gezelter |
1959 |
gezelter |
760 |
|
1960 |
|
|
* libmdtools/Make.dep: dependency on config.h |
1961 |
|
|
|
1962 |
tim |
926 |
2003-09-05 17:36 gezelter |
1963 |
gezelter |
760 |
|
1964 |
|
|
* configure, ac-tools/aclocal.m4: fixed sprng problem |
1965 |
|
|
|
1966 |
tim |
926 |
2003-09-05 16:29 gezelter |
1967 |
gezelter |
760 |
|
1968 |
|
|
* samples/metals/Makefile.in: New Makefile for metals sample |
1969 |
|
|
|
1970 |
tim |
926 |
2003-09-05 16:27 gezelter |
1971 |
gezelter |
760 |
|
1972 |
|
|
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
1973 |
|
|
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
1974 |
|
|
forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
1975 |
|
|
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
1976 |
|
|
libBASS/Makefile.in, libmdtools/Integrator.hpp, |
1977 |
|
|
libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
1978 |
|
|
libmdtools/Makefile, libmdtools/Makefile.in, |
1979 |
|
|
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
1980 |
|
|
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
1981 |
|
|
libmdtools/fortranWrappers.cpp, |
1982 |
|
|
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
1983 |
|
|
libmdtools/simulation_module.F90, samples/Makefile, |
1984 |
|
|
samples/Makefile.in, samples/alkane/Makefile, |
1985 |
|
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
1986 |
|
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
1987 |
tim |
1198 |
samples/minimizer/argon/Makefile, |
1988 |
|
|
samples/minimizer/argon/Makefile.in, |
1989 |
|
|
samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, |
1990 |
|
|
samples/beadLipid/Makefile.in, samples/lipid/Makefile, |
1991 |
|
|
samples/lipid/Makefile.in, samples/water/Makefile, |
1992 |
|
|
samples/water/Makefile.in, src/Makefile, src/Makefile.in, |
1993 |
|
|
utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, |
1994 |
|
|
utils/sysbuilder/Makefile.in: Changes to autoconf / configure |
1995 |
|
|
method of configuring OOPSE |
1996 |
gezelter |
760 |
|
1997 |
tim |
926 |
2003-09-04 16:48 mmeineke |
1998 |
mmeineke |
754 |
|
1999 |
|
|
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
2000 |
|
|
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
2001 |
|
|
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
2002 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
2003 |
|
|
added resetTime to the Global namespace. |
2004 |
|
|
|
2005 |
|
|
added ability to reset the integrators in the NVT and NPT family. |
2006 |
|
|
|
2007 |
tim |
926 |
2003-09-04 16:48 mmeineke |
2008 |
mmeineke |
754 |
|
2009 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
2010 |
|
|
namespace. |
2011 |
|
|
|
2012 |
tim |
926 |
2003-09-02 09:30 tim |
2013 |
mmeineke |
754 |
|
2014 |
|
|
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
2015 |
|
|
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
2016 |
|
|
PolicyByMass |
2017 |
|
|
|
2018 |
tim |
926 |
2003-08-28 16:09 tim |
2019 |
mmeineke |
754 |
|
2020 |
|
|
* ChangeLog, libmdtools/GenericData.cpp, |
2021 |
|
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
2022 |
|
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
2023 |
|
|
|
2024 |
tim |
926 |
2003-08-27 14:23 tim |
2025 |
tim |
920 |
|
2026 |
tim |
736 |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
2027 |
|
|
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
2028 |
|
|
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
2029 |
|
|
turn on the optimization flag, it causes a seg fault |
2030 |
|
|
|
2031 |
tim |
926 |
2003-08-27 11:25 gezelter |
2032 |
tim |
736 |
|
2033 |
|
|
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
2034 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
2035 |
|
|
stress tensor parallel bug. |
2036 |
|
|
|
2037 |
tim |
926 |
2003-08-27 11:16 tim |
2038 |
tim |
736 |
|
2039 |
|
|
* ChangeLog, libmdtools/DUFF.cpp, |
2040 |
|
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
2041 |
|
|
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
2042 |
|
|
molMembershipList use global index instead of local index |
2043 |
|
|
|
2044 |
tim |
926 |
2003-08-26 15:37 tim |
2045 |
tim |
727 |
|
2046 |
|
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
2047 |
|
|
mpiSimulation.cpp: set default force substraction policy to |
2048 |
|
|
PolicyByMass |
2049 |
|
|
|
2050 |
tim |
926 |
2003-08-26 15:29 tim |
2051 |
tim |
727 |
|
2052 |
|
|
* libmdtools/Integrator.cpp: [no log message] |
2053 |
|
|
|
2054 |
tim |
926 |
2003-08-26 15:13 mmeineke |
2055 |
tim |
727 |
|
2056 |
|
|
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
2057 |
|
|
Statwriter and Dumpwriter to handle files larger than 2 gb. |
2058 |
|
|
|
2059 |
|
|
commented out some print statements in Zconstraint |
2060 |
|
|
|
2061 |
|
|
hard coding some system init into bilayer.sys |
2062 |
|
|
|
2063 |
tim |
926 |
2003-08-26 15:12 mmeineke |
2064 |
tim |
727 |
|
2065 |
|
|
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
2066 |
|
|
added define statemewnt to Statwriter and Dumpwriter to handle |
2067 |
|
|
files larger than 2 gb. |
2068 |
|
|
|
2069 |
|
|
commented out some print statements in Zconstraint |
2070 |
|
|
|
2071 |
tim |
926 |
2003-08-26 15:02 tim |
2072 |
tim |
727 |
|
2073 |
|
|
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
2074 |
|
|
and check the seed which is specified by user at least contains 9 |
2075 |
|
|
digits |
2076 |
|
|
|
2077 |
tim |
926 |
2003-08-26 13:32 mmeineke |
2078 |
tim |
727 |
|
2079 |
|
|
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
2080 |
|
|
|
2081 |
|
|
Fixed a bug in MPI_DUFF. The atom block type was not being properly |
2082 |
|
|
constucted in MPI. (The MPI struct had 6 doubles declared versus |
2083 |
|
|
the actual 11) |
2084 |
|
|
|
2085 |
tim |
926 |
2003-08-26 13:30 mmeineke |
2086 |
tim |
727 |
|
2087 |
|
|
* Makefile: changed the Makefiel a litle. |
2088 |
|
|
|
2089 |
tim |
926 |
2003-08-25 17:17 gezelter |
2090 |
tim |
727 |
|
2091 |
|
|
* utils/sysbuilder/Makefile: More FreeBSD fixes |
2092 |
|
|
|
2093 |
tim |
926 |
2003-08-25 16:51 gezelter |
2094 |
tim |
727 |
|
2095 |
|
|
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
2096 |
|
|
libmdtools/Makefile, src/Makefile: [no log message] |
2097 |
|
|
|
2098 |
tim |
926 |
2003-08-22 15:04 mmeineke |
2099 |
tim |
727 |
|
2100 |
|
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
2101 |
|
|
frequency of output dumps. |
2102 |
|
|
|
2103 |
tim |
926 |
2003-08-20 17:23 tim |
2104 |
tim |
727 |
|
2105 |
|
|
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
2106 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
2107 |
|
|
libmdtools/mpiSimulation.cpp: user can setup seed in bass file now, |
2108 |
|
|
if he does not specify any value for seed, oopse will take the |
2109 |
|
|
value of seconds of system time as seed |
2110 |
|
|
|
2111 |
tim |
926 |
2003-08-20 14:42 mmeineke |
2112 |
tim |
727 |
|
2113 |
|
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
2114 |
|
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
2115 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimState.cpp, |
2116 |
|
|
utils/sysbuilder/bilayerSys.cpp: updated the Changelog. |
2117 |
|
|
|
2118 |
|
|
added some bug fixes for setting the random number generator seed |
2119 |
|
|
value. |
2120 |
|
|
|
2121 |
|
|
fixed a bug where ghostbend atom b was not being set. ( recent bug |
2122 |
|
|
from SimState conversion) |
2123 |
|
|
|
2124 |
tim |
926 |
2003-08-20 14:41 mmeineke |
2125 |
tim |
727 |
|
2126 |
|
|
* libBASS/Globals.hpp: updated the Changelog. |
2127 |
|
|
|
2128 |
|
|
added some bug fixes for setting the random number generator seed |
2129 |
|
|
value. |
2130 |
|
|
|
2131 |
tim |
926 |
2003-08-20 14:41 mmeineke |
2132 |
tim |
727 |
|
2133 |
|
|
* ChangeLog: updated the Changelog. |
2134 |
|
|
|
2135 |
tim |
926 |
2003-08-20 14:11 tim |
2136 |
tim |
727 |
|
2137 |
|
|
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
2138 |
|
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
2139 |
|
|
bend class |
2140 |
|
|
|
2141 |
tim |
926 |
2003-08-20 10:13 mmeineke |
2142 |
tim |
727 |
|
2143 |
|
|
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
2144 |
|
|
make links. added -f to ln -s. |
2145 |
|
|
|
2146 |
tim |
926 |
2003-08-20 09:50 tim |
2147 |
tim |
727 |
|
2148 |
|
|
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
2149 |
|
|
|
2150 |
tim |
926 |
2003-08-20 09:34 tim |
2151 |
tim |
727 |
|
2152 |
|
|
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
2153 |
|
|
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
2154 |
|
|
printing |
2155 |
|
|
|
2156 |
tim |
926 |
2003-08-18 15:59 chuckv |
2157 |
mmeineke |
705 |
|
2158 |
|
|
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
2159 |
|
|
latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
2160 |
|
|
sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
2161 |
|
|
Nanobuilder still broke. |
2162 |
|
|
|
2163 |
tim |
926 |
2003-08-15 14:24 tim |
2164 |
mmeineke |
705 |
|
2165 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
2166 |
|
|
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
2167 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
2168 |
|
|
libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, |
2169 |
|
|
libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
2170 |
|
|
Method |
2171 |
|
|
|
2172 |
tim |
926 |
2003-08-14 11:16 tim |
2173 |
mmeineke |
705 |
|
2174 |
|
|
* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
2175 |
|
|
with average force substraction strategy |
2176 |
|
|
|
2177 |
tim |
926 |
2003-08-13 16:20 chuckv |
2178 |
mmeineke |
705 |
|
2179 |
|
|
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
2180 |
|
|
profiling code -DPROFILE. |
2181 |
|
|
|
2182 |
tim |
926 |
2003-08-13 14:21 tim |
2183 |
mmeineke |
705 |
|
2184 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
2185 |
|
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
2186 |
|
|
libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
2187 |
|
|
potential & z-contraint method |
2188 |
|
|
|
2189 |
tim |
926 |
2003-08-12 16:44 mmeineke |
2190 |
mmeineke |
705 |
|
2191 |
|
|
* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
2192 |
|
|
libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
2193 |
|
|
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
2194 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really |
2195 |
|
|
annoying bug in Directional Atom, where mu was getting written to |
2196 |
|
|
pseudorandom memory location. |
2197 |
|
|
|
2198 |
tim |
926 |
2003-08-12 14:56 tim |
2199 |
mmeineke |
705 |
|
2200 |
|
|
* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
2201 |
|
|
libBASS/Globals.hpp, libmdtools/Atom.hpp, |
2202 |
|
|
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
2203 |
|
|
libmdtools/SimSetup.cpp: debugging globals |
2204 |
|
|
|
2205 |
tim |
926 |
2003-08-12 13:40 gezelter |
2206 |
mmeineke |
705 |
|
2207 |
|
|
* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
2208 |
|
|
and new atypes in LJFF |
2209 |
|
|
|
2210 |
tim |
926 |
2003-08-12 13:15 gezelter |
2211 |
mmeineke |
705 |
|
2212 |
|
|
* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
2213 |
|
|
stuff... |
2214 |
|
|
|
2215 |
tim |
926 |
2003-08-12 13:14 chuckv |
2216 |
mmeineke |
705 |
|
2217 |
|
|
* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
2218 |
|
|
|
2219 |
tim |
926 |
2003-08-12 13:04 chuckv |
2220 |
mmeineke |
705 |
|
2221 |
|
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
2222 |
|
|
Missed del of files before. |
2223 |
|
|
|
2224 |
tim |
926 |
2003-08-12 13:03 chuckv |
2225 |
mmeineke |
705 |
|
2226 |
|
|
* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
2227 |
|
|
message] |
2228 |
|
|
|
2229 |
tim |
926 |
2003-08-12 13:01 chuckv |
2230 |
mmeineke |
705 |
|
2231 |
|
|
* utils/sysbuilder/Makefile: commit makefile |
2232 |
|
|
|
2233 |
tim |
926 |
2003-08-12 12:51 tim |
2234 |
mmeineke |
705 |
|
2235 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
2236 |
|
|
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
2237 |
|
|
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
2238 |
|
|
libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
2239 |
|
|
harmonical potential to z-constraint method |
2240 |
|
|
|
2241 |
tim |
926 |
2003-08-11 17:31 chuckv |
2242 |
mmeineke |
705 |
|
2243 |
|
|
* utils/Makefile: Changed makefile to only build quicklate. |
2244 |
|
|
|
2245 |
tim |
926 |
2003-08-11 17:25 chuckv |
2246 |
mmeineke |
705 |
|
2247 |
|
|
* ac-tools/configure.in: added utils/sysbuilder to be built. |
2248 |
|
|
|
2249 |
tim |
926 |
2003-08-11 17:12 chuckv |
2250 |
mmeineke |
705 |
|
2251 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
2252 |
|
|
bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
2253 |
|
|
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, |
2254 |
|
|
sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, |
2255 |
|
|
sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, |
2256 |
|
|
sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, |
2257 |
|
|
sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, |
2258 |
|
|
sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, |
2259 |
|
|
sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged |
2260 |
|
|
sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
2261 |
|
|
with new atom allocation in libmdtools. |
2262 |
|
|
|
2263 |
tim |
926 |
2003-08-11 14:41 tim |
2264 |
mmeineke |
705 |
|
2265 |
|
|
* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
2266 |
|
|
moving zconstraint molecules to specified positions |
2267 |
|
|
|
2268 |
tim |
926 |
2003-08-11 14:39 tim |
2269 |
mmeineke |
705 |
|
2270 |
|
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
2271 |
|
|
|
2272 |
tim |
926 |
2003-08-11 14:38 mmeineke |
2273 |
mmeineke |
705 |
|
2274 |
|
|
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
2275 |
|
|
libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
2276 |
|
|
libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, |
2277 |
|
|
libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c, |
2278 |
|
|
libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h, |
2279 |
|
|
libBASS/node_list.h, libBASS/parse_interface.h, |
2280 |
|
|
libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
2281 |
|
|
into the BASS language syntax. |
2282 |
|
|
|
2283 |
tim |
926 |
2003-08-11 13:29 mmeineke |
2284 |
mmeineke |
705 |
|
2285 |
|
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
2286 |
|
|
degrees of freedom to account for zConstreints |
2287 |
|
|
|
2288 |
tim |
926 |
2003-08-08 16:22 chuckv |
2289 |
mmeineke |
705 |
|
2290 |
|
|
* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
2291 |
|
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
2292 |
|
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
2293 |
|
|
works..... |
2294 |
|
|
|
2295 |
tim |
926 |
2003-08-08 12:48 mmeineke |
2296 |
tim |
920 |
|
2297 |
mmeineke |
705 |
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
2298 |
|
|
instance of Atom::setZ and Atom::getZ in ZConstaint. |
2299 |
|
|
|
2300 |
tim |
926 |
2003-08-07 16:47 mmeineke |
2301 |
mmeineke |
705 |
|
2302 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
2303 |
|
|
DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
2304 |
|
|
GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, |
2305 |
|
|
SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, |
2306 |
|
|
SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
2307 |
|
|
configuration from SimState rather than arrays from Atom |
2308 |
|
|
|
2309 |
tim |
926 |
2003-08-06 19:47 chuckv |
2310 |
mmeineke |
705 |
|
2311 |
|
|
* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
2312 |
|
|
libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
2313 |
|
|
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
2314 |
|
|
samples/metals/Au.bass: Bug fixes for eam... |
2315 |
|
|
|
2316 |
tim |
926 |
2003-08-01 11:18 tim |
2317 |
mmeineke |
705 |
|
2318 |
|
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
2319 |
|
|
Z-Constraint |
2320 |
|
|
|
2321 |
tim |
926 |
2003-07-31 14:59 tim |
2322 |
mmeineke |
705 |
|
2323 |
|
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2324 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
2325 |
|
|
libmdtools/ZConstraint.cpp: add index range checking into |
2326 |
|
|
ZConstraint |
2327 |
|
|
|
2328 |
tim |
926 |
2003-07-31 10:38 tim |
2329 |
tim |
660 |
|
2330 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
2331 |
|
|
to the globals |
2332 |
|
|
|
2333 |
tim |
926 |
2003-07-31 10:35 tim |
2334 |
tim |
660 |
|
2335 |
|
|
* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
2336 |
|
|
Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
2337 |
|
|
NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
2338 |
|
|
SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
2339 |
|
|
Added Z constraint. |
2340 |
|
|
|
2341 |
tim |
926 |
2003-07-30 16:17 chuckv |
2342 |
tim |
660 |
|
2343 |
mmeineke |
705 |
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
2344 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
2345 |
|
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
2346 |
|
|
samples/metals/Au.bass: More bug fixes for eam. |
2347 |
tim |
660 |
|
2348 |
tim |
926 |
2003-07-29 11:32 mmeineke |
2349 |
tim |
660 |
|
2350 |
|
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
2351 |
tim |
1005 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
2352 |
|
|
working on the props code |
2353 |
tim |
660 |
|
2354 |
tim |
926 |
2003-07-29 11:32 mmeineke |
2355 |
tim |
660 |
|
2356 |
|
|
* libBASS/Globals.cpp: [no log message] |
2357 |
|
|
|
2358 |
tim |
926 |
2003-07-25 15:05 chuckv |
2359 |
mmeineke |
705 |
|
2360 |
|
|
* samples/metals/: Au.bass, metals.mdl: Added bass models for |
2361 |
|
|
metals |
2362 |
|
|
|
2363 |
tim |
926 |
2003-07-25 15:00 chuckv |
2364 |
tim |
660 |
|
2365 |
|
|
* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
2366 |
|
|
notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
2367 |
|
|
|
2368 |
tim |
926 |
2003-07-24 16:22 chuckv |
2369 |
tim |
660 |
|
2370 |
|
|
* ac-tools/configure.in: Changed configure to look for both upper |
2371 |
|
|
and lower cass .mod files |
2372 |
|
|
|
2373 |
tim |
926 |
2003-07-24 14:57 chuckv |
2374 |
tim |
660 |
|
2375 |
|
|
* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
2376 |
|
|
eam and do_forces. |
2377 |
|
|
|
2378 |
tim |
926 |
2003-07-23 17:13 chuckv |
2379 |
tim |
660 |
|
2380 |
|
|
* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
2381 |
|
|
force_globals.F90, simulation_module.F90, status_module.F90: |
2382 |
|
|
Finished most code for eam.... |
2383 |
|
|
|
2384 |
tim |
926 |
2003-07-22 16:49 mmeineke |
2385 |
tim |
660 |
|
2386 |
|
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
2387 |
|
|
function to the DumpReader. It should now save the start of each |
2388 |
|
|
frame in a vector. |
2389 |
|
|
|
2390 |
tim |
926 |
2003-07-22 15:05 mmeineke |
2391 |
tim |
660 |
|
2392 |
|
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
2393 |
|
|
to read dump files |
2394 |
|
|
|
2395 |
tim |
926 |
2003-07-22 14:54 tim |
2396 |
tim |
660 |
|
2397 |
|
|
* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
2398 |
|
|
Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
2399 |
|
|
NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
2400 |
|
|
message] |
2401 |
|
|
|
2402 |
tim |
926 |
2003-07-22 11:41 mmeineke |
2403 |
tim |
660 |
|
2404 |
|
|
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
2405 |
|
|
SimSetup.cpp: Fixed a current time initialization bug in |
2406 |
|
|
InitFromFile. |
2407 |
|
|
|
2408 |
tim |
926 |
2003-07-21 16:27 mmeineke |
2409 |
tim |
660 |
|
2410 |
|
|
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
2411 |
|
|
Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
2412 |
|
|
friends to accomadate random file access |
2413 |
|
|
|
2414 |
tim |
926 |
2003-07-21 11:23 mmeineke |
2415 |
tim |
660 |
|
2416 |
|
|
* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
2417 |
|
|
one sets it. |
2418 |
|
|
|
2419 |
tim |
926 |
2003-07-21 11:23 mmeineke |
2420 |
tim |
660 |
|
2421 |
|
|
* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
2422 |
|
|
ReadWrite.hpp: fixed Initializefrom file to start the simulation |
2423 |
|
|
from the time specified in the init file. |
2424 |
|
|
|
2425 |
tim |
926 |
2003-07-17 16:49 gezelter |
2426 |
tim |
660 |
|
2427 |
|
|
* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
2428 |
|
|
DumpReader.cpp: Started work on a DumpReader |
2429 |
|
|
|
2430 |
tim |
926 |
2003-07-17 15:38 gezelter |
2431 |
tim |
660 |
|
2432 |
|
|
* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
2433 |
|
|
|
2434 |
tim |
926 |
2003-07-17 15:32 gezelter |
2435 |
tim |
660 |
|
2436 |
|
|
* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
2437 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
2438 |
|
|
Changes for SSD/E |
2439 |
|
|
|
2440 |
tim |
926 |
2003-07-17 14:38 mmeineke |
2441 |
tim |
660 |
|
2442 |
|
|
* libmdtools/do_Forces.F90: commented out an eam line |
2443 |
|
|
|
2444 |
tim |
926 |
2003-07-17 14:32 chuckv |
2445 |
tim |
660 |
|
2446 |
|
|
* libmdtools/atype_module.F90: fixed spelling issue |
2447 |
|
|
|
2448 |
tim |
926 |
2003-07-17 14:29 chuckv |
2449 |
tim |
660 |
|
2450 |
|
|
* libmdtools/: fInfo.c, status_module.F90: added info module |
2451 |
|
|
|
2452 |
tim |
926 |
2003-07-17 14:25 chuckv |
2453 |
tim |
660 |
|
2454 |
|
|
* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
2455 |
|
|
atype_module.F90, calc_eam.F90, do_Forces.F90, |
2456 |
|
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
2457 |
|
|
mpiSimulation_module.F90: Added massive changes for eam.... |
2458 |
|
|
|
2459 |
tim |
926 |
2003-07-16 16:49 chuckv |
2460 |
tim |
660 |
|
2461 |
|
|
* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
2462 |
|
|
|
2463 |
tim |
926 |
2003-07-16 16:30 mmeineke |
2464 |
tim |
660 |
|
2465 |
|
|
* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
2466 |
|
|
SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
2467 |
|
|
calc_reaction_field.F90, do_Forces.F90, fSimulation.h, |
2468 |
|
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
2469 |
|
|
neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, |
2470 |
|
|
wrappers.F90: Changed how cutoffs were handled from C. Now |
2471 |
|
|
notifyCutoffs in Fortran notifies those who need the information of |
2472 |
|
|
any changes to cutoffs. |
2473 |
|
|
|
2474 |
tim |
926 |
2003-07-16 12:35 gezelter |
2475 |
tim |
660 |
|
2476 |
|
|
* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
2477 |
|
|
quickLate is now somewhat more intelligent about periodic |
2478 |
|
|
boundaries and wrapping. |
2479 |
|
|
|
2480 |
tim |
926 |
2003-07-16 11:40 chuckv |
2481 |
tim |
660 |
|
2482 |
|
|
* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
2483 |
|
|
|
2484 |
tim |
926 |
2003-07-16 10:34 mmeineke |
2485 |
tim |
660 |
|
2486 |
|
|
* scripts/cleanSrc: added a quick wipe-and-update script for quick |
2487 |
|
|
rebuilds on BoB |
2488 |
|
|
|
2489 |
tim |
926 |
2003-07-15 21:11 gezelter |
2490 |
tim |
660 |
|
2491 |
|
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
2492 |
|
|
SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
2493 |
|
|
fixes for box changes |
2494 |
|
|
|
2495 |
tim |
926 |
2003-07-15 17:29 mmeineke |
2496 |
tim |
660 |
|
2497 |
|
|
* libmdtools/simulation_module.F90: removed some debugging print |
2498 |
|
|
statements. |
2499 |
|
|
|
2500 |
tim |
926 |
2003-07-15 17:22 mmeineke |
2501 |
tim |
660 |
|
2502 |
|
|
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
2503 |
|
|
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
2504 |
|
|
do_forces. Rrf was not being used in the neighborlist correctly. |
2505 |
|
|
rcut was conssistently being set lowere than Rrf causing the dipole |
2506 |
|
|
cutoff region to be to small. Also led to the removal of the taper |
2507 |
|
|
region to buffer the dipole cutoff. |
2508 |
|
|
|
2509 |
tim |
926 |
2003-07-15 16:34 mmeineke |
2510 |
tim |
660 |
|
2511 |
|
|
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
2512 |
|
|
fixing ssd bug |
2513 |
|
|
|
2514 |
tim |
926 |
2003-07-15 14:56 gezelter |
2515 |
tim |
660 |
|
2516 |
|
|
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
2517 |
|
|
for the NPT ensembles |
2518 |
|
|
|
2519 |
tim |
926 |
2003-07-15 13:52 mmeineke |
2520 |
tim |
660 |
|
2521 |
|
|
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
2522 |
|
|
simSetup |
2523 |
|
|
|
2524 |
tim |
926 |
2003-07-15 12:57 mmeineke |
2525 |
tim |
660 |
|
2526 |
|
|
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
2527 |
|
|
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
2528 |
|
|
fixed some bugs, Changed entry_plug to info where appropriate |
2529 |
|
|
|
2530 |
tim |
926 |
2003-07-15 12:25 chuckv |
2531 |
tim |
660 |
|
2532 |
|
|
* utils/sysBuild.ggo: added more command line arguments |
2533 |
|
|
|
2534 |
tim |
926 |
2003-07-15 12:11 gezelter |
2535 |
tim |
660 |
|
2536 |
|
|
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
2537 |
|
|
Fixing force field line |
2538 |
|
|
|
2539 |
tim |
926 |
2003-07-15 12:10 gezelter |
2540 |
tim |
660 |
|
2541 |
|
|
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
2542 |
|
|
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
2543 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
2544 |
|
|
tensor |
2545 |
|
|
|
2546 |
tim |
926 |
2003-07-15 10:50 gezelter |
2547 |
tim |
660 |
|
2548 |
|
|
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
2549 |
|
|
|
2550 |
tim |
926 |
2003-07-15 10:42 gezelter |
2551 |
tim |
660 |
|
2552 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
2553 |
|
|
removed old outdated code |
2554 |
|
|
|
2555 |
tim |
926 |
2003-07-15 09:45 gezelter |
2556 |
tim |
660 |
|
2557 |
|
|
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
2558 |
|
|
|
2559 |
tim |
926 |
2003-07-15 09:28 gezelter |
2560 |
tim |
660 |
|
2561 |
|
|
* libmdtools/Molecule.cpp: removing get_vx |
2562 |
|
|
|
2563 |
tim |
926 |
2003-07-14 22:28 gezelter |
2564 |
tim |
660 |
|
2565 |
|
|
* libmdtools/NPTfm.cpp: Added NPTfm |
2566 |
|
|
|
2567 |
tim |
926 |
2003-07-14 22:27 gezelter |
2568 |
tim |
660 |
|
2569 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
2570 |
|
|
Bugfix in NPTim, fixes for NPTfm |
2571 |
|
|
|
2572 |
tim |
926 |
2003-07-14 22:08 gezelter |
2573 |
tim |
660 |
|
2574 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
2575 |
|
|
Checking in changes for NPTim |
2576 |
|
|
|
2577 |
tim |
926 |
2003-07-14 18:06 gezelter |
2578 |
tim |
660 |
|
2579 |
|
|
* utils/Makefile: Broken SysBuilder |
2580 |
|
|
|
2581 |
tim |
926 |
2003-07-14 18:06 gezelter |
2582 |
tim |
660 |
|
2583 |
|
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
2584 |
tim |
1198 |
argon/init_argon.eor, minimizer/argon/argon.bass, |
2585 |
|
|
minimizer/argon/init_argon.eor, lipid/init_5x5.eor, |
2586 |
|
|
water/init_ssd.eor: Fixes for samples |
2587 |
tim |
660 |
|
2588 |
tim |
926 |
2003-07-14 18:06 gezelter |
2589 |
tim |
660 |
|
2590 |
|
|
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
2591 |
|
|
debugging write statements |
2592 |
|
|
|
2593 |
tim |
926 |
2003-07-14 17:38 gezelter |
2594 |
tim |
660 |
|
2595 |
|
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
2596 |
|
|
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
2597 |
|
|
|
2598 |
tim |
926 |
2003-07-14 16:48 mmeineke |
2599 |
tim |
660 |
|
2600 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
2601 |
|
|
and set routines to Atom and DirectionalAtom |
2602 |
|
|
|
2603 |
tim |
926 |
2003-07-14 16:35 chuckv |
2604 |
tim |
660 |
|
2605 |
|
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
2606 |
|
|
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
2607 |
|
|
that takes different cmd line arguments. |
2608 |
|
|
|
2609 |
tim |
926 |
2003-07-14 16:28 mmeineke |
2610 |
tim |
660 |
|
2611 |
|
|
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
2612 |
|
|
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
2613 |
|
|
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
2614 |
|
|
were not being updated |
2615 |
|
|
|
2616 |
tim |
926 |
2003-07-14 10:04 gezelter |
2617 |
tim |
660 |
|
2618 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
2619 |
|
|
NPTim |
2620 |
|
|
|
2621 |
tim |
926 |
2003-07-14 09:55 mmeineke |
2622 |
tim |
660 |
|
2623 |
|
|
* forceFields/DUFF.frc: Switched the bond in the force field back |
2624 |
|
|
to constrained, to preserve energy |
2625 |
|
|
|
2626 |
tim |
926 |
2003-07-11 17:34 mmeineke |
2627 |
tim |
660 |
|
2628 |
|
|
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
2629 |
|
|
Integrator.hpp: working on som integrator bugs |
2630 |
|
|
|
2631 |
tim |
926 |
2003-07-11 10:26 gezelter |
2632 |
tim |
660 |
|
2633 |
|
|
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
2634 |
|
|
to worry about all the strtok() calls in our code |
2635 |
|
|
|
2636 |
tim |
926 |
2003-07-11 09:49 gezelter |
2637 |
tim |
660 |
|
2638 |
|
|
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
2639 |
|
|
|
2640 |
tim |
926 |
2003-07-10 20:15 gezelter |
2641 |
tim |
660 |
|
2642 |
|
|
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
2643 |
|
|
eor. |
2644 |
|
|
|
2645 |
tim |
926 |
2003-07-10 17:15 mmeineke |
2646 |
tim |
660 |
|
2647 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
2648 |
|
|
SimInfo.cpp, Thermo.cpp: fixed some bugs |
2649 |
|
|
|
2650 |
tim |
926 |
2003-07-10 14:53 chuckv |
2651 |
tim |
660 |
|
2652 |
|
|
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
2653 |
|
|
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
2654 |
|
|
nanoBuilder and a general Lattice builder. |
2655 |
|
|
|
2656 |
tim |
926 |
2003-07-10 12:10 gezelter |
2657 |
tim |
660 |
|
2658 |
|
|
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
2659 |
|
|
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
2660 |
|
|
|
2661 |
tim |
926 |
2003-07-09 17:14 mmeineke |
2662 |
tim |
660 |
|
2663 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
2664 |
|
|
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
2665 |
|
|
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
2666 |
|
|
caclulation of HmatInverse. |
2667 |
|
|
|
2668 |
tim |
926 |
2003-07-09 10:34 mmeineke |
2669 |
tim |
660 |
|
2670 |
|
|
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
2671 |
|
|
|
2672 |
tim |
926 |
2003-07-09 10:33 mmeineke |
2673 |
tim |
660 |
|
2674 |
|
|
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
2675 |
|
|
|
2676 |
tim |
926 |
2003-07-09 08:56 gezelter |
2677 |
tim |
660 |
|
2678 |
|
|
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
2679 |
|
|
|
2680 |
tim |
926 |
2003-07-09 08:56 gezelter |
2681 |
tim |
660 |
|
2682 |
|
|
* libBASS/Globals.cpp: Removed Qmass |
2683 |
|
|
|
2684 |
tim |
926 |
2003-07-08 21:15 gezelter |
2685 |
tim |
660 |
|
2686 |
|
|
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
2687 |
|
|
and NPTi |
2688 |
|
|
|
2689 |
tim |
926 |
2003-07-08 20:41 gezelter |
2690 |
tim |
660 |
|
2691 |
|
|
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
2692 |
|
|
|
2693 |
tim |
926 |
2003-07-08 16:10 gezelter |
2694 |
tim |
660 |
|
2695 |
|
|
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
2696 |
|
|
|
2697 |
tim |
926 |
2003-07-08 16:06 gezelter |
2698 |
tim |
660 |
|
2699 |
|
|
* libmdtools/NPTi.cpp: fixed box scaling |
2700 |
|
|
|
2701 |
tim |
926 |
2003-07-08 15:56 gezelter |
2702 |
tim |
660 |
|
2703 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
2704 |
|
|
SimInfo.hpp, Thermo.cpp: NPTi |
2705 |
|
|
|
2706 |
tim |
926 |
2003-07-03 14:41 mmeineke |
2707 |
tim |
660 |
|
2708 |
|
|
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
2709 |
|
|
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
2710 |
|
|
scripts in the makefiles |
2711 |
|
|
|
2712 |
tim |
926 |
2003-07-02 16:26 mmeineke |
2713 |
tim |
660 |
|
2714 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
2715 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
2716 |
|
|
libmdtools/Makefile, libmdtools/ReadWrite.hpp, |
2717 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2718 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
2719 |
|
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, |
2720 |
|
|
utils/Makefile: fixed the bugs introduced by switching the periodic |
2721 |
|
|
box to a matrix |
2722 |
|
|
|
2723 |
tim |
926 |
2003-07-01 17:39 gezelter |
2724 |
tim |
660 |
|
2725 |
|
|
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
2726 |
|
|
|
2727 |
tim |
926 |
2003-07-01 17:29 gezelter |
2728 |
tim |
660 |
|
2729 |
|
|
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
2730 |
|
|
|
2731 |
tim |
926 |
2003-07-01 16:33 mmeineke |
2732 |
tim |
660 |
|
2733 |
|
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
2734 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
2735 |
|
|
the box matrix to everything. |
2736 |
|
|
|
2737 |
tim |
926 |
2003-06-30 17:03 mmeineke |
2738 |
tim |
660 |
|
2739 |
|
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2740 |
|
|
src/oopse.cpp: |
2741 |
|
|
Updated the ChangeLog, and Converted most of the SImInfo to use |
2742 |
|
|
non-Isotropic boxes. wrapVector needs to be finished. |
2743 |
|
|
|
2744 |
tim |
926 |
2003-06-25 16:12 mmeineke |
2745 |
mmeineke |
568 |
|
2746 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
2747 |
|
|
to Harmonic bonds in the DUFF frc file |
2748 |
|
|
|
2749 |
|
|
fixed constraints. |
2750 |
|
|
|
2751 |
tim |
926 |
2003-06-25 16:11 mmeineke |
2752 |
mmeineke |
568 |
|
2753 |
|
|
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
2754 |
|
|
the DUFF frc file |
2755 |
|
|
|
2756 |
tim |
926 |
2003-06-24 17:51 gezelter |
2757 |
mmeineke |
568 |
|
2758 |
|
|
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
2759 |
|
|
|
2760 |
tim |
926 |
2003-06-24 14:57 mmeineke |
2761 |
mmeineke |
568 |
|
2762 |
|
|
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
2763 |
|
|
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
2764 |
|
|
the DUFF forcefield and BondExtensions.cpp |
2765 |
|
|
|
2766 |
tim |
926 |
2003-06-23 16:24 mmeineke |
2767 |
mmeineke |
568 |
|
2768 |
|
|
* libmdtools/Integrator.cpp: Doing some work to debug the |
2769 |
|
|
constraint code. |
2770 |
|
|
|
2771 |
tim |
926 |
2003-06-20 15:50 gezelter |
2772 |
mmeineke |
568 |
|
2773 |
|
|
* libmdtools/Integrator.hpp: NPT fix |
2774 |
|
|
|
2775 |
tim |
926 |
2003-06-20 15:29 mmeineke |
2776 |
mmeineke |
568 |
|
2777 |
|
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
2778 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
2779 |
|
|
libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
2780 |
|
|
libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
2781 |
|
|
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
2782 |
|
|
integrator and NVT seem to be working now. |
2783 |
|
|
|
2784 |
tim |
926 |
2003-06-20 11:49 gezelter |
2785 |
mmeineke |
568 |
|
2786 |
|
|
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
2787 |
|
|
|
2788 |
tim |
926 |
2003-06-19 17:02 mmeineke |
2789 |
mmeineke |
568 |
|
2790 |
|
|
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
2791 |
|
|
forceFields/LJ_FF.frc, forceFields/Makefile, |
2792 |
|
|
forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
2793 |
|
|
libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
2794 |
|
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
2795 |
|
|
libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
2796 |
|
|
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
2797 |
|
|
forcefield names. |
2798 |
|
|
|
2799 |
tim |
926 |
2003-06-19 14:21 mmeineke |
2800 |
mmeineke |
568 |
|
2801 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
2802 |
|
|
finished the basics of the integrator and SimSetup.cpp |
2803 |
|
|
|
2804 |
tim |
926 |
2003-06-19 14:11 mmeineke |
2805 |
mmeineke |
568 |
|
2806 |
|
|
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
2807 |
|
|
up / get it to work with the new Integrator. |
2808 |
|
|
|
2809 |
tim |
926 |
2003-06-18 17:20 mmeineke |
2810 |
mmeineke |
568 |
|
2811 |
|
|
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
2812 |
|
|
output times. |
2813 |
|
|
|
2814 |
tim |
926 |
2003-06-17 16:56 mmeineke |
2815 |
mmeineke |
568 |
|
2816 |
|
|
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
2817 |
|
|
fro the ghost Bend in TraPPE_Ex |
2818 |
|
|
|
2819 |
|
|
some work on the integrator. ( incomplete) |
2820 |
|
|
|
2821 |
tim |
926 |
2003-06-17 16:55 mmeineke |
2822 |
mmeineke |
568 |
|
2823 |
|
|
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
2824 |
|
|
Bend in TraPPE_Ex |
2825 |
|
|
|
2826 |
tim |
926 |
2003-06-04 16:06 mmeineke |
2827 |
mmeineke |
568 |
|
2828 |
|
|
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
2829 |
|
|
constrainB to the Symplectic integrator |
2830 |
|
|
|
2831 |
tim |
926 |
2003-05-30 16:32 mmeineke |
2832 |
mmeineke |
568 |
|
2833 |
|
|
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
2834 |
|
|
the basic integrator. |
2835 |
|
|
|
2836 |
|
|
bilayerSys.cpp altered for building tb3. |
2837 |
|
|
|
2838 |
tim |
926 |
2003-05-30 16:31 mmeineke |
2839 |
mmeineke |
568 |
|
2840 |
|
|
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
2841 |
|
|
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
2842 |
|
|
modifiying Symplectic to become the basic integrator. |
2843 |
|
|
|
2844 |
tim |
926 |
2003-05-30 15:19 mmeineke |
2845 |
mmeineke |
568 |
|
2846 |
|
|
* libmdtools/Integrator.hpp: added some member variables for |
2847 |
|
|
position, velocity, etc. |
2848 |
|
|
|
2849 |
tim |
926 |
2003-05-30 14:07 mmeineke |
2850 |
mmeineke |
568 |
|
2851 |
|
|
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
2852 |
|
|
is now derived from Integrator |
2853 |
|
|
|
2854 |
tim |
926 |
2003-05-20 11:44 mmeineke |
2855 |
mmeineke |
568 |
|
2856 |
|
|
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
2857 |
|
|
|
2858 |
tim |
926 |
2003-05-17 11:57 mmeineke |
2859 |
mmeineke |
568 |
|
2860 |
|
|
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
2861 |
|
|
working |
2862 |
|
|
|
2863 |
tim |
926 |
2003-05-16 16:37 mmeineke |
2864 |
mmeineke |
568 |
|
2865 |
|
|
* utils/bilayerSys.cpp: still working on the bilayer code |
2866 |
|
|
|
2867 |
tim |
926 |
2003-05-16 09:28 mmeineke |
2868 |
mmeineke |
568 |
|
2869 |
|
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
2870 |
|
|
work to overhaul sysbuild. |
2871 |
|
|
|
2872 |
tim |
926 |
2003-05-13 16:23 mmeineke |
2873 |
mmeineke |
568 |
|
2874 |
|
|
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
2875 |
|
|
|
2876 |
tim |
926 |
2003-05-13 15:47 mmeineke |
2877 |
mmeineke |
568 |
|
2878 |
|
|
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
2879 |
|
|
beadLipid/water.mdl: Added bead lipid model to the sample directory |
2880 |
|
|
|
2881 |
tim |
926 |
2003-05-13 15:34 mmeineke |
2882 |
mmeineke |
568 |
|
2883 |
|
|
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
2884 |
|
|
the Trappe extended force field |
2885 |
|
|
|
2886 |
tim |
926 |
2003-05-13 12:01 mmeineke |
2887 |
mmeineke |
568 |
|
2888 |
|
|
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
2889 |
|
|
TraPPe_Ex forceField |
2890 |
|
|
|
2891 |
tim |
926 |
2003-05-09 14:51 mmeineke |
2892 |
mmeineke |
568 |
|
2893 |
|
|
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
2894 |
|
|
there were some duplicate entries |
2895 |
|
|
|
2896 |
|
|
added a two chain lipid to the lipid.mdl in sample |
2897 |
|
|
|
2898 |
tim |
926 |
2003-05-09 14:51 mmeineke |
2899 |
mmeineke |
568 |
|
2900 |
|
|
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
2901 |
|
|
there were some duplicate entries |
2902 |
|
|
|
2903 |
tim |
926 |
2003-05-09 11:56 mmeineke |
2904 |
mmeineke |
568 |
|
2905 |
|
|
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
2906 |
|
|
configure script |
2907 |
|
|
|
2908 |
|
|
added the CH branching group to the TraPPE_Ex fource field |
2909 |
|
|
|
2910 |
tim |
926 |
2003-05-09 11:55 mmeineke |
2911 |
mmeineke |
568 |
|
2912 |
|
|
* ac-tools/configure.in: added the utils subdirectory to the |
2913 |
|
|
configure script |
2914 |
|
|
|
2915 |
tim |
926 |
2003-04-25 11:02 mmeineke |
2916 |
mmeineke |
568 |
|
2917 |
|
|
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
2918 |
|
|
bilayer builder |
2919 |
|
|
|
2920 |
tim |
926 |
2003-04-24 21:00 mmeineke |
2921 |
mmeineke |
568 |
|
2922 |
|
|
* libmdtools/f_verlet_constrained.F90: added a new test for |
2923 |
|
|
constraint failure |
2924 |
|
|
|
2925 |
tim |
926 |
2003-04-17 16:54 mmeineke |
2926 |
mmeineke |
568 |
|
2927 |
|
|
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
2928 |
|
|
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
2929 |
|
|
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
2930 |
|
|
build our systems |
2931 |
|
|
|
2932 |
tim |
926 |
2003-04-16 16:11 mmeineke |
2933 |
mmeineke |
568 |
|
2934 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
2935 |
|
|
|
2936 |
tim |
926 |
2003-04-15 16:47 mmeineke |
2937 |
mmeineke |
568 |
|
2938 |
|
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
2939 |
|
|
and sysBuild both will build now. woot! |
2940 |
|
|
|
2941 |
tim |
926 |
2003-04-15 16:20 mmeineke |
2942 |
mmeineke |
568 |
|
2943 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
2944 |
|
|
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
2945 |
|
|
|
2946 |
|
|
sysBuild still need to write the bass file. |
2947 |
|
|
|
2948 |
|
|
MoLocator.cpp is currently empty |
2949 |
|
|
|
2950 |
tim |
926 |
2003-04-15 15:40 chuckv |
2951 |
mmeineke |
568 |
|
2952 |
|
|
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
2953 |
|
|
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
2954 |
|
|
forceFields/pdu3.eam, forceFields/ptu3.eam, |
2955 |
|
|
libmdtools/ForceFields.hpp: Added eam force files... |
2956 |
|
|
|
2957 |
tim |
926 |
2003-04-15 11:37 chuckv |
2958 |
mmeineke |
568 |
|
2959 |
|
|
* libmdtools/EAM_FF.cpp: More eam work. |
2960 |
|
|
|
2961 |
tim |
926 |
2003-04-14 16:22 mmeineke |
2962 |
mmeineke |
568 |
|
2963 |
|
|
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
2964 |
|
|
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
2965 |
|
|
working on the system builder |
2966 |
|
|
|
2967 |
tim |
926 |
2003-04-14 16:16 chuckv |
2968 |
mmeineke |
568 |
|
2969 |
|
|
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
2970 |
|
|
ordering on NVT calculation in integrators. |
2971 |
|
|
|
2972 |
tim |
926 |
2003-04-14 14:51 mmeineke |
2973 |
mmeineke |
568 |
|
2974 |
|
|
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
2975 |
|
|
obj/placeHolder: working on a system builder |
2976 |
|
|
|
2977 |
tim |
926 |
2003-04-14 14:04 mmeineke |
2978 |
mmeineke |
568 |
|
2979 |
|
|
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
2980 |
|
|
|
2981 |
|
|
added sysBuild to the utils Makefile |
2982 |
|
|
|
2983 |
tim |
926 |
2003-04-14 14:03 mmeineke |
2984 |
mmeineke |
568 |
|
2985 |
|
|
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
2986 |
|
|
Ghost bends to the TraPPE_Ex forceField |
2987 |
|
|
|
2988 |
tim |
926 |
2003-04-14 13:19 chuckv |
2989 |
mmeineke |
568 |
|
2990 |
|
|
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
2991 |
|
|
|
2992 |
tim |
926 |
2003-04-11 13:46 mmeineke |
2993 |
mmeineke |
568 |
|
2994 |
|
|
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
2995 |
|
|
simulation_module.F90: fixed a memory bug in Fortran, where |
2996 |
|
|
molMembershipArray was declared nLocal instead of nGlobal. |
2997 |
|
|
|
2998 |
tim |
926 |
2003-04-11 10:16 gezelter |
2999 |
mmeineke |
568 |
|
3000 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
3001 |
|
|
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
3002 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
3003 |
|
|
for NPT |
3004 |
|
|
|
3005 |
tim |
926 |
2003-04-10 15:08 mmeineke |
3006 |
mmeineke |
568 |
|
3007 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
3008 |
|
|
globalIndex counter to Molecule |
3009 |
|
|
|
3010 |
tim |
926 |
2003-04-10 11:35 gezelter |
3011 |
mmeineke |
568 |
|
3012 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
3013 |
|
|
ConstantStress |
3014 |
|
|
|
3015 |
tim |
926 |
2003-04-10 11:27 mmeineke |
3016 |
mmeineke |
568 |
|
3017 |
|
|
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
3018 |
|
|
caused a miscalculation of nLocal. |
3019 |
|
|
|
3020 |
tim |
926 |
2003-04-10 11:21 mmeineke |
3021 |
mmeineke |
568 |
|
3022 |
|
|
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
3023 |
|
|
do_Forces.F90: fixed a bug in symplectic, where presure was only |
3024 |
|
|
being calculated the first time through. |
3025 |
|
|
|
3026 |
tim |
926 |
2003-04-09 11:20 chuckv |
3027 |
mmeineke |
568 |
|
3028 |
|
|
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
3029 |
|
|
file |
3030 |
|
|
|
3031 |
tim |
926 |
2003-04-09 08:59 gezelter |
3032 |
mmeineke |
568 |
|
3033 |
|
|
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
3034 |
|
|
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
3035 |
|
|
|
3036 |
tim |
926 |
2003-04-08 23:06 gezelter |
3037 |
mmeineke |
568 |
|
3038 |
|
|
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
3039 |
|
|
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
3040 |
|
|
SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
3041 |
|
|
Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
3042 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90, |
3043 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
3044 |
|
|
NVT |
3045 |
|
|
|
3046 |
tim |
926 |
2003-04-08 17:38 chuckv |
3047 |
mmeineke |
568 |
|
3048 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
3049 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
3050 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
3051 |
|
|
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
3052 |
|
|
(kinda)... |
3053 |
|
|
|
3054 |
tim |
926 |
2003-04-08 16:35 gezelter |
3055 |
mmeineke |
568 |
|
3056 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
3057 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
3058 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
3059 |
|
|
|
3060 |
tim |
926 |
2003-04-08 12:16 chuckv |
3061 |
mmeineke |
568 |
|
3062 |
|
|
* libmdtools/: do_Forces.F90, neighborLists.F90, |
3063 |
|
|
simulation_module.F90: Moved expand neighborlist to init_FF. |
3064 |
|
|
|
3065 |
tim |
926 |
2003-04-08 10:20 chuckv |
3066 |
mmeineke |
568 |
|
3067 |
|
|
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
3068 |
|
|
NVT |
3069 |
|
|
|
3070 |
tim |
926 |
2003-04-08 09:39 gezelter |
3071 |
mmeineke |
568 |
|
3072 |
|
|
* libmdtools/Verlet.cpp: fixes for nvt / npt |
3073 |
|
|
|
3074 |
tim |
926 |
2003-04-08 09:34 gezelter |
3075 |
mmeineke |
568 |
|
3076 |
|
|
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
3077 |
|
|
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
3078 |
|
|
|
3079 |
tim |
926 |
2003-04-08 07:50 gezelter |
3080 |
mmeineke |
568 |
|
3081 |
|
|
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
3082 |
|
|
|
3083 |
tim |
926 |
2003-04-08 07:44 gezelter |
3084 |
mmeineke |
568 |
|
3085 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
3086 |
|
|
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
3087 |
|
|
NVT and NPT ensembles |
3088 |
|
|
|
3089 |
tim |
926 |
2003-04-07 16:42 gezelter |
3090 |
mmeineke |
568 |
|
3091 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
3092 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
3093 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
3094 |
|
|
|
3095 |
tim |
926 |
2003-04-07 16:20 mmeineke |
3096 |
mmeineke |
568 |
|
3097 |
|
|
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
3098 |
|
|
portion of SSD. |
3099 |
|
|
|
3100 |
tim |
926 |
2003-04-07 16:16 mmeineke |
3101 |
mmeineke |
568 |
|
3102 |
|
|
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
3103 |
|
|
doing some testing in sticky through Symplectic. |
3104 |
|
|
|
3105 |
tim |
926 |
2003-04-07 15:51 gezelter |
3106 |
mmeineke |
568 |
|
3107 |
|
|
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
3108 |
|
|
|
3109 |
tim |
926 |
2003-04-07 15:50 chuckv |
3110 |
mmeineke |
568 |
|
3111 |
|
|
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
3112 |
|
|
tau and virial. |
3113 |
|
|
|
3114 |
tim |
926 |
2003-04-07 15:06 mmeineke |
3115 |
mmeineke |
568 |
|
3116 |
|
|
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
3117 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
3118 |
|
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
3119 |
|
|
src/Makefile: bug fixes |
3120 |
|
|
|
3121 |
tim |
926 |
2003-04-07 11:56 gezelter |
3122 |
mmeineke |
568 |
|
3123 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
3124 |
|
|
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
3125 |
|
|
Many fixes to add extended system |
3126 |
|
|
|
3127 |
tim |
926 |
2003-04-07 09:30 gezelter |
3128 |
mmeineke |
568 |
|
3129 |
|
|
* src/Makefile: Fixed a bug caused by my experimentation |
3130 |
|
|
|
3131 |
tim |
926 |
2003-04-07 09:30 gezelter |
3132 |
mmeineke |
568 |
|
3133 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
3134 |
|
|
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
3135 |
|
|
Added ExtendedSystem infrastructure for NPT and NVT calculations |
3136 |
|
|
|
3137 |
tim |
926 |
2003-04-07 09:30 gezelter |
3138 |
mmeineke |
568 |
|
3139 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
3140 |
|
|
|
3141 |
|
|
2003-04-04 23:07 gezelter |
3142 |
|
|
|
3143 |
|
|
* src/Makefile: final mods to try a fortran compiler |
3144 |
|
|
|
3145 |
|
|
2003-04-04 22:39 gezelter |
3146 |
|
|
|
3147 |
|
|
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
3148 |
|
|
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
3149 |
|
|
|
3150 |
|
|
2003-04-04 21:56 gezelter |
3151 |
|
|
|
3152 |
|
|
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
3153 |
|
|
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
3154 |
|
|
|
3155 |
|
|
2003-04-04 21:45 gezelter |
3156 |
|
|
|
3157 |
|
|
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
3158 |
|
|
fixes to fortran wrappers |
3159 |
|
|
|
3160 |
|
|
2003-04-04 17:22 chuckv |
3161 |
|
|
|
3162 |
|
|
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
3163 |
|
|
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
3164 |
|
|
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
3165 |
|
|
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
3166 |
|
|
smarter, fortran gets dumber... |
3167 |
|
|
|
3168 |
|
|
2003-04-04 14:57 mmeineke |
3169 |
|
|
|
3170 |
|
|
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
3171 |
|
|
neighborLists.F90: fixed a memory read bug in neighborlist |
3172 |
|
|
|
3173 |
|
|
2003-04-04 14:47 gezelter |
3174 |
|
|
|
3175 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
3176 |
|
|
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
3177 |
|
|
|
3178 |
|
|
2003-04-04 14:16 gezelter |
3179 |
|
|
|
3180 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
3181 |
|
|
SimInfo.hpp: Fixes for ExtendedSystem |
3182 |
|
|
|
3183 |
|
|
2003-04-03 20:57 gezelter |
3184 |
|
|
|
3185 |
|
|
* libmdtools/ExtendedSystem.hpp: Added extended system header |
3186 |
|
|
|
3187 |
|
|
2003-04-03 20:57 gezelter |
3188 |
|
|
|
3189 |
|
|
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
3190 |
|
|
for extended system code |
3191 |
|
|
|
3192 |
|
|
2003-04-03 18:49 gezelter |
3193 |
|
|
|
3194 |
|
|
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
3195 |
|
|
extendedsystem |
3196 |
|
|
|
3197 |
|
|
2003-04-03 17:19 mmeineke |
3198 |
|
|
|
3199 |
|
|
* libmdtools/Molecule.hpp: added some little fixes here and there. |
3200 |
|
|
|
3201 |
|
|
2003-04-03 17:01 mmeineke |
3202 |
|
|
|
3203 |
|
|
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
3204 |
|
|
initialize bug. |
3205 |
|
|
|
3206 |
|
|
2003-04-03 16:12 mmeineke |
3207 |
|
|
|
3208 |
|
|
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
3209 |
|
|
little things like deleteing unused variables and such. |
3210 |
|
|
|
3211 |
|
|
2003-04-03 15:57 mmeineke |
3212 |
|
|
|
3213 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
3214 |
|
|
simError.h also some fixes to Molecule.hpp |
3215 |
|
|
|
3216 |
|
|
2003-04-03 15:57 mmeineke |
3217 |
|
|
|
3218 |
|
|
* libBASS/simError.h: a few fixes to simError.h |
3219 |
|
|
|
3220 |
|
|
2003-04-03 15:21 mmeineke |
3221 |
|
|
|
3222 |
|
|
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
3223 |
|
|
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
3224 |
|
|
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
3225 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
3226 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
3227 |
|
|
src/Makefile, src/oopse.cpp: fixed some small things with |
3228 |
|
|
simError.h |
3229 |
|
|
|
3230 |
|
|
2003-04-03 15:19 gezelter |
3231 |
|
|
|
3232 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
3233 |
|
|
|
3234 |
|
|
2003-04-03 14:58 gezelter |
3235 |
|
|
|
3236 |
|
|
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
3237 |
|
|
now) |
3238 |
|
|
|
3239 |
|
|
2003-04-03 08:42 gezelter |
3240 |
|
|
|
3241 |
|
|
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
3242 |
|
|
Changed Readme, added some files |
3243 |
|
|
|
3244 |
|
|
2003-04-02 17:19 mmeineke |
3245 |
|
|
|
3246 |
|
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
3247 |
|
|
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
3248 |
|
|
dipoles mostly work, but there is a memory leak somewhere. |
3249 |
|
|
|
3250 |
|
|
2003-04-02 10:01 mmeineke |
3251 |
|
|
|
3252 |
|
|
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
3253 |
|
|
the proper atomIdents. |
3254 |
|
|
|
3255 |
|
|
2003-04-01 11:50 chuckv |
3256 |
|
|
|
3257 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
3258 |
|
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
3259 |
tim |
1198 |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more |
3260 |
|
|
bug fixes.... |
3261 |
mmeineke |
568 |
|
3262 |
|
|
2003-04-01 11:49 mmeineke |
3263 |
|
|
|
3264 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
3265 |
|
|
DumpWriter to be more robust to errors. also added a little |
3266 |
|
|
namespace to InitFromFile to wrap it's helper functions in MPI |
3267 |
|
|
|
3268 |
|
|
2003-03-31 17:09 chuckv |
3269 |
|
|
|
3270 |
|
|
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
3271 |
|
|
not zeroed. |
3272 |
|
|
|
3273 |
|
|
2003-03-31 16:50 chuckv |
3274 |
|
|
|
3275 |
|
|
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
3276 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
3277 |
|
|
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
3278 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
3279 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
3280 |
|
|
samples/alkane/butane.bass: Fixes in MPI force calc and in |
3281 |
|
|
Trappe_Ex parsing. |
3282 |
|
|
|
3283 |
|
|
2003-03-28 17:34 chuckv |
3284 |
|
|
|
3285 |
|
|
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
3286 |
|
|
|
3287 |
|
|
2003-03-28 16:45 chuckv |
3288 |
|
|
|
3289 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
3290 |
|
|
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
3291 |
|
|
routines. |
3292 |
|
|
|
3293 |
|
|
2003-03-28 14:33 mmeineke |
3294 |
|
|
|
3295 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
3296 |
|
|
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
3297 |
|
|
bug where the Excludes were not being created properly |
3298 |
|
|
|
3299 |
|
|
2003-03-28 14:30 chuckv |
3300 |
|
|
|
3301 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
3302 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
3303 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
3304 |
|
|
and debugging mpi read write from file. |
3305 |
|
|
|
3306 |
|
|
2003-03-28 10:28 mmeineke |
3307 |
|
|
|
3308 |
|
|
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
3309 |
|
|
interactions in Trappe |
3310 |
|
|
|
3311 |
|
|
2003-03-27 18:33 chuckv |
3312 |
|
|
|
3313 |
|
|
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
3314 |
|
|
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
3315 |
|
|
|
3316 |
|
|
2003-03-27 17:16 mmeineke |
3317 |
|
|
|
3318 |
|
|
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
3319 |
|
|
excludes were not being initialized |
3320 |
|
|
|
3321 |
|
|
2003-03-27 16:52 mmeineke |
3322 |
|
|
|
3323 |
|
|
* src/Makefile: [no log message] |
3324 |
|
|
|
3325 |
|
|
2003-03-27 16:52 mmeineke |
3326 |
|
|
|
3327 |
|
|
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
3328 |
|
|
|
3329 |
|
|
2003-03-27 16:07 mmeineke |
3330 |
|
|
|
3331 |
|
|
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
3332 |
|
|
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
3333 |
|
|
Verlet.cpp: fixed the compile time bugs, Source builds and links |
3334 |
|
|
|
3335 |
|
|
2003-03-27 15:48 mmeineke |
3336 |
|
|
|
3337 |
|
|
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
3338 |
|
|
more bugs. |
3339 |
|
|
|
3340 |
|
|
2003-03-27 15:40 mmeineke |
3341 |
|
|
|
3342 |
|
|
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
3343 |
|
|
|
3344 |
|
|
2003-03-27 15:39 mmeineke |
3345 |
|
|
|
3346 |
|
|
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
3347 |
|
|
|
3348 |
|
|
2003-03-27 15:36 mmeineke |
3349 |
|
|
|
3350 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
3351 |
|
|
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
3352 |
|
|
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
3353 |
|
|
|
3354 |
|
|
2003-03-27 15:12 mmeineke |
3355 |
|
|
|
3356 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
3357 |
|
|
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
3358 |
|
|
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
3359 |
|
|
to. will now attempt to compile. |
3360 |
|
|
|
3361 |
|
|
2003-03-27 14:21 mmeineke |
3362 |
|
|
|
3363 |
|
|
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
3364 |
|
|
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
3365 |
|
|
updating SimSetup to initialize and use the new MPI division of |
3366 |
|
|
labour, and Molecule class |
3367 |
|
|
|
3368 |
|
|
2003-03-27 12:55 mmeineke |
3369 |
|
|
|
3370 |
|
|
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
3371 |
|
|
use Molecule |
3372 |
|
|
|
3373 |
|
|
2003-03-27 12:32 mmeineke |
3374 |
|
|
|
3375 |
|
|
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
3376 |
|
|
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
3377 |
|
|
converted to the new Molecule model. TraPPE_Ex is currently being |
3378 |
|
|
updated. SimSetups routines are writtten, but not yet called. |
3379 |
|
|
|
3380 |
|
|
2003-03-27 10:07 gezelter |
3381 |
|
|
|
3382 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
3383 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
3384 |
|
|
numbering in MPI |
3385 |
|
|
|
3386 |
|
|
2003-03-27 09:30 mmeineke |
3387 |
|
|
|
3388 |
|
|
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
3389 |
|
|
|
3390 |
|
|
2003-03-26 20:49 gezelter |
3391 |
|
|
|
3392 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
3393 |
|
|
fileio for MPI |
3394 |
|
|
|
3395 |
|
|
2003-03-26 18:14 gezelter |
3396 |
|
|
|
3397 |
|
|
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
3398 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
3399 |
|
|
fixes many bug fixes |
3400 |
|
|
|
3401 |
|
|
2003-03-26 17:24 gezelter |
3402 |
|
|
|
3403 |
|
|
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
3404 |
|
|
sequence of atoms on the other processors. Node 0 now fires |
3405 |
|
|
potatoes at other processors to get them to send french fries back. |
3406 |
|
|
|
3407 |
|
|
2003-03-26 17:02 mmeineke |
3408 |
|
|
|
3409 |
|
|
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
3410 |
|
|
making the molecules is in place. ForceField needs to be updated |
3411 |
|
|
next. |
3412 |
|
|
|
3413 |
|
|
2003-03-26 16:54 mmeineke |
3414 |
|
|
|
3415 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
3416 |
|
|
the "static" bugs in Atom and Exclude |
3417 |
|
|
|
3418 |
|
|
2003-03-26 16:50 mmeineke |
3419 |
|
|
|
3420 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
3421 |
|
|
SimSetup.cpp: still working on the SimSetup routine. also fixed |
3422 |
|
|
some things in Exclude.hpp |
3423 |
|
|
|
3424 |
|
|
2003-03-26 16:24 gezelter |
3425 |
|
|
|
3426 |
|
|
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
3427 |
|
|
|
3428 |
|
|
2003-03-26 16:23 gezelter |
3429 |
|
|
|
3430 |
|
|
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
3431 |
|
|
and Exclude list |
3432 |
|
|
|
3433 |
|
|
2003-03-26 16:04 gezelter |
3434 |
|
|
|
3435 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
3436 |
|
|
delete ranges of atoms |
3437 |
|
|
|
3438 |
|
|
2003-03-26 15:45 mmeineke |
3439 |
|
|
|
3440 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
3441 |
|
|
with static arrays similar to the Atom class |
3442 |
|
|
|
3443 |
|
|
2003-03-26 15:22 mmeineke |
3444 |
|
|
|
3445 |
|
|
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
3446 |
|
|
overhauling the molecule class to contain it's own bonds, bends, |
3447 |
|
|
and torsions. |
3448 |
|
|
|
3449 |
|
|
may god have mercy on my soul. |
3450 |
|
|
|
3451 |
|
|
2003-03-26 14:34 chuckv |
3452 |
|
|
|
3453 |
|
|
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
3454 |
|
|
|
3455 |
|
|
2003-03-26 13:02 gezelter |
3456 |
|
|
|
3457 |
|
|
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
3458 |
|
|
mpiSimulation.hpp: MPI stuff for passing out molecules |
3459 |
|
|
|
3460 |
|
|
2003-03-26 11:12 chuckv |
3461 |
|
|
|
3462 |
|
|
* libmdtools/mpiSimulation.cpp: working on load balancing |
3463 |
|
|
|
3464 |
|
|
2003-03-26 10:37 chuckv |
3465 |
|
|
|
3466 |
|
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
3467 |
tim |
1198 |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes |
3468 |
|
|
for Parallel thermalization |
3469 |
mmeineke |
568 |
|
3470 |
|
|
2003-03-26 09:55 mmeineke |
3471 |
|
|
|
3472 |
|
|
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
3473 |
|
|
THermo.cpp |
3474 |
|
|
|
3475 |
|
|
2003-03-25 17:54 chuckv |
3476 |
|
|
|
3477 |
|
|
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
3478 |
|
|
of potential energy and temperature. |
3479 |
|
|
|
3480 |
|
|
2003-03-25 09:29 mmeineke |
3481 |
|
|
|
3482 |
tim |
1031 |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
3483 |
|
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
3484 |
mmeineke |
568 |
|
3485 |
|
|
2003-03-25 09:29 mmeineke |
3486 |
|
|
|
3487 |
|
|
* libBASS/MPIobj/dummy: added dummy files to keep the build |
3488 |
|
|
deirectories from being pruned. |
3489 |
|
|
|
3490 |
|
|
2003-03-24 20:07 gezelter |
3491 |
|
|
|
3492 |
tim |
1005 |
* samples/Makefile: moving tests to samples |
3493 |
mmeineke |
568 |
|
3494 |
|
|
2003-03-24 20:06 gezelter |
3495 |
|
|
|
3496 |
tim |
1005 |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
3497 |
|
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
3498 |
|
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
3499 |
|
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
3500 |
tim |
1198 |
lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, |
3501 |
|
|
minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, |
3502 |
|
|
minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, |
3503 |
|
|
water/ssd.bass, water/water.mdl: moved tests to samples |
3504 |
mmeineke |
568 |
|
3505 |
|
|
2003-03-24 19:51 gezelter |
3506 |
|
|
|
3507 |
|
|
* ac-tools/configure.in: Tests are becoming samples |
3508 |
|
|
|
3509 |
|
|
2003-03-24 19:46 gezelter |
3510 |
|
|
|
3511 |
tim |
1005 |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
3512 |
mmeineke |
568 |
|
3513 |
|
|
2003-03-24 16:55 gezelter |
3514 |
|
|
|
3515 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, |
3516 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, |
3517 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, |
3518 |
|
|
libmdtools/calc_reaction_field.F90, |
3519 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
3520 |
|
|
libmdtools/simulation_module.F90: electrostatic changes for dipole |
3521 |
|
|
/ RF separation |
3522 |
|
|
|
3523 |
|
|
2003-03-24 13:33 mmeineke |
3524 |
|
|
|
3525 |
|
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
3526 |
|
|
do_Forces.F90: little bug fixes here and there |
3527 |
|
|
|
3528 |
|
|
2003-03-24 10:26 mmeineke |
3529 |
|
|
|
3530 |
|
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
3531 |
|
|
where short range interactions were not being calculated. |
3532 |
|
|
|
3533 |
|
|
removed some debug print statements |
3534 |
|
|
|
3535 |
|
|
2003-03-21 17:11 chuckv |
3536 |
|
|
|
3537 |
|
|
* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, |
3538 |
|
|
do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: |
3539 |
|
|
various write statements for debugging |
3540 |
|
|
|
3541 |
|
|
2003-03-21 16:26 chuckv |
3542 |
|
|
|
3543 |
|
|
* forceFields/Makefile: added links to the makefile in forceFields |
3544 |
|
|
|
3545 |
|
|
2003-03-21 15:52 gezelter |
3546 |
|
|
|
3547 |
|
|
* ac-tools/Make.conf.in, ac-tools/configure.in, |
3548 |
|
|
libmdtools/Makefile: Fixed F_MACH_DEP bug |
3549 |
|
|
|
3550 |
|
|
2003-03-21 15:37 gezelter |
3551 |
|
|
|
3552 |
|
|
* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, |
3553 |
|
|
ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, |
3554 |
|
|
libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, |
3555 |
|
|
src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, |
3556 |
|
|
autoconf fixes |
3557 |
|
|
|
3558 |
gezelter |
385 |
2003-03-21 14:58 gezelter |
3559 |
mmeineke |
377 |
|
3560 |
gezelter |
385 |
* LICENSE: Added license file |
3561 |
|
|
|
3562 |
|
|
2003-03-21 14:55 gezelter |
3563 |
|
|
|
3564 |
|
|
* forceFields/Makefile: Fixed makefile |
3565 |
|
|
|
3566 |
|
|
2003-03-21 14:49 gezelter |
3567 |
|
|
|
3568 |
|
|
* forceFields/Makefile: Makefile for forceFields |
3569 |
|
|
|
3570 |
|
|
2003-03-21 14:42 gezelter |
3571 |
|
|
|
3572 |
|
|
* README: Readme changes |
3573 |
|
|
|
3574 |
|
|
2003-03-21 12:52 mmeineke |
3575 |
|
|
|
3576 |
|
|
* src/Makefile: [no log message] |
3577 |
|
|
|
3578 |
|
|
2003-03-21 12:52 mmeineke |
3579 |
|
|
|
3580 |
|
|
* libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends |
3581 |
|
|
|
3582 |
|
|
2003-03-21 12:42 mmeineke |
3583 |
|
|
|
3584 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
3585 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
3586 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
3587 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
3588 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
3589 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
3590 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
3591 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
3592 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
3593 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
3594 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
3595 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
3596 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
3597 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
3598 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
3599 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
3600 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
3601 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
3602 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
3603 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
3604 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
3605 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
3606 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
3607 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
3608 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
3609 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
3610 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
3611 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
3612 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
3613 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
3614 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
3615 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
3616 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
3617 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
3618 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
3619 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
3620 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
3621 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
3622 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
3623 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
3624 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
3625 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
3626 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
3627 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
3628 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
3629 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
3630 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
3631 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
3632 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
3633 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
3634 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3635 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3636 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3637 |
tim |
1248 |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3638 |
|
|
revision |
3639 |
gezelter |
385 |
|
3640 |
|
|
2003-03-21 12:42 mmeineke |
3641 |
|
|
|
3642 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
3643 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
3644 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
3645 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
3646 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
3647 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
3648 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
3649 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
3650 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
3651 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
3652 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
3653 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
3654 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
3655 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
3656 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
3657 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
3658 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
3659 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
3660 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
3661 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
3662 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
3663 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
3664 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
3665 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
3666 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
3667 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
3668 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
3669 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
3670 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
3671 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
3672 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
3673 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
3674 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
3675 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
3676 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
3677 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
3678 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
3679 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
3680 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
3681 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
3682 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
3683 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
3684 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
3685 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
3686 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
3687 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
3688 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
3689 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
3690 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
3691 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
3692 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3693 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3694 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3695 |
tim |
1248 |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
3696 |
|
|
Tree |
3697 |
gezelter |
385 |
|