1 |
tim |
1118 |
2004-04-15 17:15 tim |
2 |
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3 |
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* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
4 |
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exclude list |
5 |
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6 |
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2004-04-15 11:18 tim |
7 |
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8 |
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* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
9 |
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libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
10 |
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libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
11 |
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libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
12 |
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libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
13 |
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libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
14 |
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libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
15 |
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whole bunch of bugs :-) |
16 |
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17 |
tim |
1113 |
2004-04-14 12:20 chrisfen |
18 |
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19 |
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* forceFields/WATER.frc: Added the WATER.frc force field |
20 |
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21 |
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2004-04-14 11:32 gezelter |
22 |
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23 |
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* libmdtools/Molecule.cpp: fixed for get_potential |
24 |
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25 |
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2004-04-14 10:37 tim |
26 |
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27 |
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* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
28 |
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libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
29 |
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libmdtools/Integrator.hpp, libmdtools/Make.dep, |
30 |
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libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
31 |
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libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
32 |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
33 |
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libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
34 |
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libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
35 |
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libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
36 |
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libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
37 |
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Change DumpWriter and InitFromFile |
38 |
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39 |
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2004-04-13 11:26 gezelter |
40 |
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41 |
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* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
42 |
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molecules can keep track of their own IntegrableObjects (and |
43 |
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RigidBodies). Also a bug-fix so that SimInfo can keep track of |
44 |
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RigidBodies (which was done incorrectly before). |
45 |
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46 |
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2004-04-13 11:25 gezelter |
47 |
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48 |
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* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
49 |
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(will back out momentarily) |
50 |
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51 |
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2004-04-13 10:10 gezelter |
52 |
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53 |
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* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
54 |
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Those were old. |
55 |
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56 |
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2004-04-13 10:09 gezelter |
57 |
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58 |
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* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
59 |
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to add IntegrableObjects |
60 |
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61 |
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2004-04-12 16:02 gezelter |
62 |
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63 |
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* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
64 |
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65 |
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2004-04-12 15:32 gezelter |
66 |
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67 |
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* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
68 |
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test run |
69 |
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70 |
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2004-04-12 15:32 gezelter |
71 |
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72 |
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* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
73 |
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DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
74 |
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DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
75 |
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ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
76 |
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Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
77 |
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MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
78 |
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NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
79 |
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SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
80 |
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SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
81 |
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WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
82 |
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(Somewhat extensive) |
83 |
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84 |
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2004-04-12 15:31 gezelter |
85 |
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86 |
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* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
87 |
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libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
88 |
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utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
89 |
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Changes for RigidBody dynamics |
90 |
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91 |
tim |
1108 |
2004-03-17 09:22 tim |
92 |
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93 |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
94 |
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libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
95 |
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libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
96 |
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libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
97 |
tim |
1113 |
does not sound a good choice, next commit will seperate SMD and |
98 |
tim |
1108 |
ZConstraint |
99 |
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100 |
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2004-03-16 14:22 tim |
101 |
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102 |
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* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
103 |
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libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
104 |
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libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
105 |
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libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
106 |
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now can support sequential moving. Refactorying is needed to |
107 |
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support SMD in ZConstraint |
108 |
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109 |
tim |
1091 |
2004-03-02 15:32 tim |
110 |
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111 |
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* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
112 |
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StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
113 |
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support large file |
114 |
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115 |
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2004-03-01 16:17 tim |
116 |
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117 |
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* utils/zsub.cpp: Fix a couple of bugs in zsub |
118 |
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119 |
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2004-03-01 15:01 tim |
120 |
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121 |
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* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
122 |
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libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
123 |
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libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
124 |
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utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
125 |
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utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
126 |
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program which can be used to replace atom type for zconstraint into |
127 |
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OOPSE |
128 |
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129 |
tim |
1074 |
2004-02-24 11:36 tim |
130 |
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131 |
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* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
132 |
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libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
133 |
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message] |
134 |
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135 |
tim |
1066 |
2004-02-24 10:49 tim |
136 |
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137 |
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* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
138 |
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Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
139 |
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ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
140 |
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Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
141 |
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NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
142 |
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OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
143 |
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SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
144 |
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145 |
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2004-02-24 10:44 tim |
146 |
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147 |
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* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
148 |
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Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
149 |
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MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
150 |
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OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
151 |
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SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
152 |
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compose to implement Minimizer both versions are working |
153 |
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154 |
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2004-02-17 14:23 tim |
155 |
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156 |
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* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
157 |
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libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
158 |
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libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
159 |
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libmdtools/MinimizerParameterSet.hpp, |
160 |
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libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
161 |
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to remove the constraint force along bond direction |
162 |
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163 |
tim |
1057 |
2004-02-10 16:33 tim |
164 |
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165 |
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* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
166 |
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libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
167 |
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single version of energy minimization is working. |
168 |
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169 |
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2004-02-09 15:38 mmeineke |
170 |
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171 |
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* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
172 |
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the massive memory overusage by OOPSE |
173 |
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174 |
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2004-02-09 09:48 chrisfen |
175 |
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176 |
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* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
177 |
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hardwired LJ_rcut |
178 |
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179 |
tim |
1046 |
2004-02-06 19:14 tim |
180 |
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181 |
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* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
182 |
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message] |
183 |
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184 |
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2004-02-06 16:37 tim |
185 |
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186 |
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* ChangeLog, libBASS/Globals.cpp, |
187 |
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libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
188 |
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libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
189 |
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libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
190 |
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energy minimization for argon is working, need to add constraint |
191 |
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192 |
tim |
1035 |
2004-02-06 14:05 tim |
193 |
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194 |
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* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
195 |
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one more file into Makefile.in |
196 |
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197 |
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2004-02-06 13:58 tim |
198 |
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199 |
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* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
200 |
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libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
201 |
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libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
202 |
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libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
203 |
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libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
204 |
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libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
205 |
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libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
206 |
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libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
207 |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
208 |
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libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
209 |
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some lines into global.cpp to make it work with energy minimization |
210 |
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211 |
tim |
1031 |
2004-02-04 17:26 tim |
212 |
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213 |
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* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
214 |
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Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
215 |
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Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
216 |
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NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
217 |
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Single version of conjugate gradient with golden search linesearch |
218 |
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pass a couple of functions test. Brent's algorithm is still broken |
219 |
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220 |
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2004-02-03 17:54 tim |
221 |
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222 |
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* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
223 |
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Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
224 |
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NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
225 |
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SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
226 |
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227 |
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2004-02-03 15:47 tim |
228 |
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229 |
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* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
230 |
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ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
231 |
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NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
232 |
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SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
233 |
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SteepestDescent.hpp: [no log message] |
234 |
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235 |
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2004-02-03 15:43 tim |
236 |
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237 |
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* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
238 |
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Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
239 |
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MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
240 |
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NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
241 |
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constraint class |
242 |
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243 |
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2004-02-03 12:10 tim |
244 |
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245 |
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* libmdtools/Functor.hpp: Functor.hpp pass unit test |
246 |
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247 |
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2004-02-03 10:21 tim |
248 |
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249 |
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* ChangeLog, libmdtools/Minimizer1D.cpp, |
250 |
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libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
251 |
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252 |
tim |
1005 |
2004-02-02 15:29 tim |
253 |
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254 |
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* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
255 |
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Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
256 |
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Adding GoldenSection and Brent LineSearch Method |
257 |
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258 |
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2004-01-30 16:47 tim |
259 |
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260 |
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* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
261 |
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MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
262 |
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NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
263 |
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MinimizerBase instead of a functor to do line seach |
264 |
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265 |
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2004-01-30 10:00 chrisfen |
266 |
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267 |
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* forceFields/Makefile.in, libmdtools/Atom.cpp, |
268 |
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libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
269 |
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libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
270 |
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libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
271 |
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libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
272 |
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libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
273 |
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libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
274 |
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has a working WATER.cpp forcefield and parser. This involved |
275 |
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changes to WATER.cpp and ForceFields amoung other files. One |
276 |
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important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
277 |
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This will be removed on the next commit... |
278 |
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279 |
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2004-01-29 18:00 gezelter |
280 |
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281 |
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* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
282 |
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libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
283 |
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libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
284 |
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libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
285 |
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libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
286 |
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libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
287 |
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libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
288 |
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libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
289 |
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member list fixes for rigid bodies |
290 |
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291 |
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2004-01-29 16:44 tim |
292 |
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293 |
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* libmdtools/MinimizerParameterSet.hpp: Adding |
294 |
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MinimizerParameterSet class. |
295 |
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296 |
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2004-01-28 17:44 tim |
297 |
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298 |
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* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
299 |
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NLModel0 and NLModel1 |
300 |
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301 |
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2004-01-28 15:40 tim |
302 |
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303 |
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* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
304 |
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of NLModel |
305 |
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306 |
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2004-01-27 15:34 gezelter |
307 |
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308 |
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* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
309 |
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water.mdl file, updated ssd.bass to use new SSD name |
310 |
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311 |
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2004-01-27 15:34 gezelter |
312 |
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313 |
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* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
314 |
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MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
315 |
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stuff |
316 |
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317 |
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2004-01-27 14:39 gezelter |
318 |
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319 |
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* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
320 |
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321 |
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2004-01-27 14:39 gezelter |
322 |
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323 |
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* samples/metals/Au.bass: Longer run time to test gold in MPI |
324 |
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325 |
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2004-01-27 14:38 gezelter |
326 |
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|
|
327 |
|
|
* samples/argon/argon.bass: Longer run time to test argon |
328 |
|
|
|
329 |
|
|
2004-01-27 14:38 gezelter |
330 |
|
|
|
331 |
|
|
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
332 |
|
|
changes to do new rigidBody scheme a copy of WATER.cpp from this |
333 |
|
|
morning |
334 |
|
|
|
335 |
|
|
2004-01-27 14:37 gezelter |
336 |
|
|
|
337 |
|
|
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
338 |
|
|
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
339 |
|
|
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
340 |
|
|
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
341 |
|
|
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
342 |
|
|
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
343 |
|
|
do new rigidBody scheme |
344 |
|
|
|
345 |
|
|
2004-01-27 14:15 tim |
346 |
|
|
|
347 |
|
|
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
348 |
|
|
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
349 |
|
|
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
350 |
|
|
constraint for Nonlinear Optimization Model |
351 |
|
|
|
352 |
|
|
2004-01-26 17:01 gezelter |
353 |
|
|
|
354 |
|
|
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
355 |
|
|
Euler angles for orientation instead of unit vectors required |
356 |
|
|
changes in MoLocator |
357 |
|
|
|
358 |
|
|
2004-01-26 16:53 gezelter |
359 |
|
|
|
360 |
|
|
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
361 |
|
|
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
362 |
|
|
water/water.mdl: Changed orientation lines from unit vectors to |
363 |
|
|
euler angles |
364 |
|
|
|
365 |
|
|
2004-01-26 16:52 gezelter |
366 |
|
|
|
367 |
|
|
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
368 |
|
|
|
369 |
|
|
2004-01-26 16:45 gezelter |
370 |
|
|
|
371 |
|
|
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
372 |
|
|
use Euler angles in the following order: phi, theta, psi Removed |
373 |
|
|
the ability to set orientation using a unit vector |
374 |
|
|
|
375 |
|
|
2004-01-26 16:26 gezelter |
376 |
|
|
|
377 |
|
|
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
378 |
|
|
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
379 |
|
|
Euler angles in the following order: phi, theta, psi Removed the |
380 |
|
|
ability to set orientation using a unit vector |
381 |
|
|
|
382 |
|
|
2004-01-26 13:52 gezelter |
383 |
|
|
|
384 |
|
|
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
385 |
|
|
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
386 |
|
|
|
387 |
|
|
2004-01-22 12:34 chrisfen |
388 |
|
|
|
389 |
|
|
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
390 |
|
|
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
391 |
|
|
Corrected spelling in several directories, and stated WATER.cpp |
392 |
|
|
|
393 |
|
|
2004-01-21 17:16 tim |
394 |
|
|
|
395 |
|
|
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
396 |
|
|
NLOPModel.hpp: constraint class in energy minimization |
397 |
|
|
|
398 |
|
|
2004-01-20 15:34 tim |
399 |
|
|
|
400 |
|
|
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
401 |
|
|
|
402 |
|
|
2004-01-20 15:32 tim |
403 |
|
|
|
404 |
|
|
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
405 |
|
|
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
406 |
|
|
|
407 |
|
|
2004-01-19 16:17 gezelter |
408 |
|
|
|
409 |
|
|
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
410 |
|
|
more user-friendly |
411 |
|
|
|
412 |
|
|
2004-01-19 13:51 chrisfen |
413 |
|
|
|
414 |
|
|
* forceFields/DUFF.frc: Updated the default water to SSD/E |
415 |
|
|
|
416 |
|
|
2004-01-19 13:36 tim |
417 |
|
|
|
418 |
|
|
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
419 |
|
|
time, status time, thermal time and reset time are not divisible by |
420 |
|
|
dt |
421 |
|
|
|
422 |
|
|
2004-01-19 11:10 gezelter |
423 |
|
|
|
424 |
|
|
* third-party/Makefile.in: Added a bunch of dummy targets so make |
425 |
|
|
won't complain |
426 |
|
|
|
427 |
|
|
2004-01-19 11:10 gezelter |
428 |
|
|
|
429 |
|
|
* samples/lipid/5x5.bass: Fixed old bass file |
430 |
|
|
|
431 |
|
|
2004-01-19 11:09 gezelter |
432 |
|
|
|
433 |
|
|
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
434 |
|
|
required a change in how the MoleculeStamps are used by divideLabor |
435 |
|
|
in mpiSimulation.cpp |
436 |
|
|
|
437 |
|
|
2004-01-19 11:08 gezelter |
438 |
|
|
|
439 |
|
|
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
440 |
|
|
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
441 |
|
|
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
442 |
|
|
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
443 |
|
|
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
444 |
|
|
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
445 |
|
|
|
446 |
|
|
2004-01-16 16:55 tim |
447 |
|
|
|
448 |
|
|
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
449 |
|
|
eor file |
450 |
|
|
|
451 |
|
|
2004-01-16 16:51 mmeineke |
452 |
|
|
|
453 |
|
|
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
454 |
|
|
write eor files |
455 |
|
|
|
456 |
|
|
2004-01-16 10:01 mmeineke |
457 |
|
|
|
458 |
|
|
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
459 |
|
|
initialization of the AtomStruct |
460 |
|
|
|
461 |
|
|
2004-01-15 16:57 chuckv |
462 |
|
|
|
463 |
|
|
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
464 |
|
|
|
465 |
|
|
2004-01-15 10:51 gezelter |
466 |
|
|
|
467 |
|
|
* ac-tools/aclocal.m4: Changes for altivec |
468 |
|
|
|
469 |
|
|
2004-01-15 09:22 gezelter |
470 |
|
|
|
471 |
|
|
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
472 |
|
|
|
473 |
|
|
2004-01-14 23:33 gezelter |
474 |
|
|
|
475 |
|
|
* libmdtools/do_Forces.F90: changes for charge charge interactions |
476 |
|
|
|
477 |
|
|
2004-01-14 20:14 gezelter |
478 |
|
|
|
479 |
|
|
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
480 |
|
|
notifyCutoffs.F90: More work for adding charges |
481 |
|
|
|
482 |
|
|
2004-01-14 17:41 gezelter |
483 |
|
|
|
484 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
485 |
|
|
src/Makefile.in: autoconf fixes |
486 |
|
|
|
487 |
|
|
2004-01-14 11:28 mmeineke |
488 |
|
|
|
489 |
|
|
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
490 |
|
|
|
491 |
|
|
2004-01-14 10:48 gezelter |
492 |
|
|
|
493 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
494 |
|
|
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
495 |
|
|
changes for icc8 |
496 |
|
|
|
497 |
|
|
2004-01-13 18:01 gezelter |
498 |
|
|
|
499 |
|
|
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
500 |
|
|
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
501 |
|
|
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
502 |
|
|
Changes for adding direct charge-charge interactions (with |
503 |
|
|
switching function) |
504 |
|
|
|
505 |
|
|
2004-01-13 17:34 gezelter |
506 |
|
|
|
507 |
|
|
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
508 |
|
|
oopseMPI_module.F90: Some changes for new MPI organization and |
509 |
|
|
direct charge-charge interactions |
510 |
|
|
|
511 |
|
|
2004-01-13 17:11 tim |
512 |
|
|
|
513 |
|
|
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
514 |
|
|
|
515 |
|
|
2004-01-13 16:22 tim |
516 |
|
|
|
517 |
|
|
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
518 |
|
|
|
519 |
|
|
2004-01-13 15:35 tim |
520 |
|
|
|
521 |
|
|
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
522 |
|
|
eor file whenever it is used instead of rewinding it |
523 |
|
|
|
524 |
|
|
2004-01-13 15:04 tim |
525 |
|
|
|
526 |
|
|
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
527 |
|
|
of writeFrame |
528 |
|
|
|
529 |
|
|
2004-01-13 10:46 tim |
530 |
|
|
|
531 |
|
|
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
532 |
|
|
Merge the code of writeFinal and writeDump; |
533 |
|
|
Adding sortingIndex into DumpWriter; |
534 |
|
|
Fix a bug of writing last frame twice in integrator |
535 |
|
|
|
536 |
|
|
2004-01-12 17:54 tim |
537 |
|
|
|
538 |
|
|
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
539 |
|
|
a bug in copying string |
540 |
|
|
|
541 |
tim |
927 |
2004-01-12 15:37 tim |
542 |
|
|
|
543 |
|
|
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
544 |
|
|
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
545 |
|
|
master nodes |
546 |
|
|
|
547 |
tim |
926 |
2004-01-10 04:46 tim |
548 |
|
|
|
549 |
|
|
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
550 |
|
|
roll it back fix a bug of copying string to a pointer Still have |
551 |
|
|
Seg fault, it looks like a random MPI seg fault in totalview |
552 |
|
|
|
553 |
tim |
920 |
2004-01-09 21:15 tim |
554 |
|
|
|
555 |
|
|
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
556 |
|
|
|
557 |
|
|
2004-01-09 15:29 gezelter |
558 |
|
|
|
559 |
|
|
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
560 |
|
|
|
561 |
|
|
2004-01-08 17:25 chuckv |
562 |
|
|
|
563 |
|
|
* libmdtools/DumpWriter.cpp: A work in progress... |
564 |
|
|
|
565 |
|
|
2004-01-08 13:59 gezelter |
566 |
|
|
|
567 |
|
|
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
568 |
|
|
case |
569 |
|
|
|
570 |
|
|
2004-01-08 13:13 mmeineke |
571 |
|
|
|
572 |
|
|
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
573 |
|
|
state bug. |
574 |
|
|
|
575 |
|
|
2004-01-08 13:05 gezelter |
576 |
|
|
|
577 |
|
|
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
578 |
|
|
|
579 |
|
|
2004-01-08 12:57 mmeineke |
580 |
|
|
|
581 |
|
|
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
582 |
|
|
exstended state bug |
583 |
|
|
|
584 |
|
|
2004-01-08 12:40 gezelter |
585 |
|
|
|
586 |
|
|
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
587 |
|
|
|
588 |
|
|
2004-01-08 10:44 mmeineke |
589 |
|
|
|
590 |
|
|
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
591 |
|
|
XS state info flag |
592 |
|
|
|
593 |
|
|
2004-01-07 14:26 tim |
594 |
|
|
|
595 |
|
|
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
596 |
|
|
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
597 |
|
|
sending message from master node to itself in DumpWriter.cpp and |
598 |
|
|
InitializeFromFile.cpp |
599 |
|
|
|
600 |
|
|
2004-01-06 14:49 chuckv |
601 |
|
|
|
602 |
|
|
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
603 |
|
|
performance fixes in the dipole dipole and reaction field code |
604 |
|
|
|
605 |
|
|
2004-01-06 13:54 chuckv |
606 |
|
|
|
607 |
|
|
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
608 |
|
|
little more sane |
609 |
|
|
|
610 |
|
|
2004-01-05 17:49 chuckv |
611 |
|
|
|
612 |
|
|
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
613 |
|
|
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
614 |
|
|
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
615 |
|
|
performance by reducing spurious function calls |
616 |
|
|
|
617 |
|
|
2004-01-05 17:18 chuckv |
618 |
|
|
|
619 |
|
|
* libmdtools/do_Forces.F90: mangling forces even further |
620 |
|
|
|
621 |
|
|
2004-01-05 17:18 chuckv |
622 |
|
|
|
623 |
|
|
* configure, ac-tools/configure.in: mpich mucking |
624 |
|
|
|
625 |
|
|
2004-01-05 17:12 chuckv |
626 |
|
|
|
627 |
|
|
* libmdtools/do_Forces.F90: mangled do_forces... |
628 |
|
|
|
629 |
|
|
2004-01-05 16:00 chuckv |
630 |
|
|
|
631 |
|
|
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
632 |
|
|
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
633 |
|
|
lookup |
634 |
|
|
|
635 |
chuckv |
894 |
2003-12-29 14:56 chuckv |
636 |
gezelter |
760 |
|
637 |
chuckv |
894 |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
638 |
|
|
third-party directory for code not written by us. Also added |
639 |
|
|
Mersenne Twister random number generator code. This will eventually |
640 |
|
|
replace sprng as the random number generator used by OOPSE. |
641 |
|
|
|
642 |
|
|
2003-12-22 16:26 chuckv |
643 |
|
|
|
644 |
|
|
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
645 |
|
|
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
646 |
|
|
Fixes to profile code. |
647 |
|
|
|
648 |
|
|
2003-12-19 15:36 mmeineke |
649 |
|
|
|
650 |
|
|
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
651 |
|
|
timing.F90, timing.f90: More profiling fixes. |
652 |
|
|
|
653 |
|
|
2003-12-19 15:19 chuckv |
654 |
|
|
|
655 |
|
|
* libmdtools/timing.f90: Another change for MPI in timing. |
656 |
|
|
|
657 |
|
|
2003-12-19 15:17 chuckv |
658 |
|
|
|
659 |
|
|
* libmdtools/timing.f90: Small update to timing in MPI |
660 |
|
|
|
661 |
|
|
2003-12-19 13:53 mmeineke |
662 |
|
|
|
663 |
|
|
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
664 |
|
|
profiling commands work now. Will start adding PROFILE ifdefs into |
665 |
|
|
the code |
666 |
|
|
|
667 |
|
|
2003-12-19 12:25 mmeineke |
668 |
|
|
|
669 |
|
|
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
670 |
|
|
some profiling routines |
671 |
|
|
|
672 |
|
|
2003-12-19 10:12 mmeineke |
673 |
|
|
|
674 |
|
|
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
675 |
|
|
and GofRomega |
676 |
|
|
|
677 |
|
|
additional work on randomBilayer |
678 |
|
|
|
679 |
|
|
2003-12-19 10:12 mmeineke |
680 |
|
|
|
681 |
|
|
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
682 |
|
|
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
683 |
|
|
GofRomega |
684 |
|
|
|
685 |
|
|
2003-12-18 16:47 mmeineke |
686 |
|
|
|
687 |
|
|
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
688 |
|
|
some profile functionality |
689 |
|
|
|
690 |
|
|
2003-12-18 15:46 chuckv |
691 |
|
|
|
692 |
|
|
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
693 |
|
|
Added functions for simple profiling in fortran. |
694 |
|
|
|
695 |
|
|
2003-12-17 15:13 chuckv |
696 |
|
|
|
697 |
|
|
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
698 |
|
|
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
699 |
|
|
rho_col were scattered into the same array. Unfortunately, MPI |
700 |
|
|
zeros the array between scatters so half of the sum was being lost. |
701 |
|
|
Fixed by added a temp array for column scatter, then sum loop over |
702 |
|
|
nlocal. |
703 |
|
|
|
704 |
|
|
2003-12-16 15:49 mmeineke |
705 |
|
|
|
706 |
|
|
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
707 |
|
|
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
708 |
|
|
gofRomega. both need to be debugged and tested. |
709 |
|
|
|
710 |
|
|
2003-12-12 10:42 gezelter |
711 |
|
|
|
712 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
713 |
|
|
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
714 |
|
|
gradients (to do minimizations) |
715 |
|
|
|
716 |
|
|
2003-12-12 10:33 mmeineke |
717 |
|
|
|
718 |
|
|
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
719 |
|
|
header |
720 |
|
|
|
721 |
|
|
2003-12-10 11:52 mmeineke |
722 |
|
|
|
723 |
|
|
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
724 |
|
|
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
725 |
|
|
randomBilayer to the build. Also move the random bilayer builder |
726 |
|
|
from bilayerSys to randomBilayer |
727 |
|
|
|
728 |
|
|
2003-11-25 10:44 mmeineke |
729 |
|
|
|
730 |
|
|
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
731 |
|
|
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
732 |
|
|
TB3 in DUFF.frc |
733 |
|
|
|
734 |
|
|
2003-11-21 15:09 mmeineke |
735 |
|
|
|
736 |
|
|
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
737 |
|
|
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
738 |
|
|
message in SimInfo. Added a more informative error message in |
739 |
|
|
InitializeFromFile |
740 |
|
|
|
741 |
|
|
2003-11-21 15:07 mmeineke |
742 |
|
|
|
743 |
|
|
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
744 |
|
|
ing in the GofR,CosTheta |
745 |
|
|
|
746 |
|
|
2003-11-21 14:31 chrisfen |
747 |
|
|
|
748 |
|
|
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
749 |
|
|
a bug in SimInfo ordering of radii |
750 |
|
|
|
751 |
|
|
2003-11-11 12:20 mmeineke |
752 |
|
|
|
753 |
|
|
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
754 |
|
|
a min function. |
755 |
|
|
|
756 |
|
|
2003-11-10 16:50 mmeineke |
757 |
|
|
|
758 |
|
|
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
759 |
|
|
reordered the rcut/ecr/boxSize initialization |
760 |
|
|
|
761 |
|
|
removed the rcut/ecr shrink and grow algorithm. the simulation will |
762 |
|
|
now exit when it runs into rcut or ecr. |
763 |
|
|
|
764 |
|
|
2003-11-07 16:46 chuckv |
765 |
|
|
|
766 |
|
|
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
767 |
|
|
oopseMPI_module.F90: Added support for compiling fortran without |
768 |
|
|
use of mpich modules. We use mpif.h instead.: |
769 |
|
|
|
770 |
|
|
2003-11-07 12:09 mmeineke |
771 |
|
|
|
772 |
|
|
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
773 |
|
|
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
774 |
|
|
the atom loop in the NPT family of integrators. |
775 |
|
|
|
776 |
|
|
2003-11-06 17:01 mmeineke |
777 |
|
|
|
778 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
779 |
|
|
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
780 |
|
|
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
781 |
|
|
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
782 |
|
|
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
783 |
|
|
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
784 |
|
|
* useIntiTime => useInitialTime |
785 |
|
|
|
786 |
|
|
2003-11-06 14:24 mmeineke |
787 |
|
|
|
788 |
|
|
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
789 |
|
|
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
790 |
|
|
parse_tree.h: fixed the includes in the Make.dep |
791 |
|
|
|
792 |
|
|
2003-11-06 14:11 mmeineke |
793 |
|
|
|
794 |
|
|
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
795 |
|
|
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
796 |
|
|
new-templateless branch to the main trunk. |
797 |
|
|
|
798 |
|
|
bug Fixes include: * fixed the switching function from ortho to |
799 |
|
|
non-ortho box. !!!!! THis was responsible for all of the |
800 |
|
|
sudden deaths we saw. * some formating in the string when we |
801 |
|
|
write out the extended system state. * added NPT.cpp to the |
802 |
|
|
makefile.in |
803 |
|
|
|
804 |
|
|
2003-11-06 13:20 mmeineke |
805 |
|
|
|
806 |
|
|
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
807 |
|
|
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
808 |
|
|
bug. The box was not switching between orthorhombic and |
809 |
|
|
non-orthorhombic wrapping correctly. we added a fabs() to |
810 |
|
|
the check.which should fix it. |
811 |
|
|
|
812 |
|
|
2003-11-05 14:16 mmeineke |
813 |
|
|
|
814 |
|
|
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
815 |
|
|
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
816 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
817 |
|
|
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
818 |
|
|
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
819 |
|
|
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
820 |
|
|
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
821 |
|
|
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
822 |
|
|
some work on trying to find the compression bug |
823 |
|
|
|
824 |
|
|
2003-11-03 17:07 mmeineke |
825 |
|
|
|
826 |
|
|
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
827 |
|
|
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
828 |
|
|
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
829 |
|
|
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
830 |
|
|
most of standard template library from OOPSE. |
831 |
|
|
|
832 |
|
|
2003-10-31 16:06 mmeineke |
833 |
|
|
|
834 |
|
|
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
835 |
|
|
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
836 |
|
|
SimSetup.cpp: started work on template removal. |
837 |
|
|
|
838 |
|
|
2003-10-31 13:28 mmeineke |
839 |
|
|
|
840 |
|
|
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
841 |
|
|
added template stuff to the Maikefile template |
842 |
|
|
|
843 |
|
|
little changes to some printf format statements |
844 |
|
|
|
845 |
|
|
2003-10-31 13:28 mmeineke |
846 |
|
|
|
847 |
|
|
* libBASS/Makefile.in: added template stuff to the Maikefile |
848 |
|
|
template |
849 |
|
|
|
850 |
|
|
2003-10-30 13:59 gezelter |
851 |
|
|
|
852 |
|
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
853 |
|
|
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
854 |
|
|
rList problems |
855 |
|
|
|
856 |
|
|
2003-10-30 09:11 gezelter |
857 |
|
|
|
858 |
|
|
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
859 |
|
|
queried before q0 was allocated. |
860 |
|
|
|
861 |
|
|
2003-10-29 15:41 mmeineke |
862 |
|
|
|
863 |
|
|
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
864 |
|
|
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
865 |
|
|
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
866 |
|
|
in bass.l |
867 |
|
|
|
868 |
|
|
fixed a little bug in the first time step, regarding the setting of |
869 |
|
|
ecr and est in fortran |
870 |
|
|
|
871 |
|
|
2003-10-29 15:40 mmeineke |
872 |
|
|
|
873 |
|
|
* libBASS/BASSlex.l: fixed a stdlib.h include error |
874 |
|
|
|
875 |
|
|
2003-10-29 12:55 mmeineke |
876 |
|
|
|
877 |
|
|
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
878 |
|
|
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
879 |
|
|
rcut is setup, as well as additional debugging comments. |
880 |
|
|
|
881 |
|
|
2003-10-29 09:28 gezelter |
882 |
|
|
|
883 |
|
|
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
884 |
|
|
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
885 |
|
|
templates |
886 |
|
|
|
887 |
|
|
2003-10-28 22:16 gezelter |
888 |
|
|
|
889 |
|
|
* src/Makefile.in: Refixed broken makefile |
890 |
|
|
|
891 |
|
|
2003-10-28 22:06 gezelter |
892 |
|
|
|
893 |
|
|
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
894 |
|
|
fixes |
895 |
|
|
|
896 |
|
|
2003-10-28 19:19 tim |
897 |
|
|
|
898 |
|
|
* ChangeLog, libmdtools/AbstractClasses.hpp, |
899 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
900 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
901 |
|
|
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
902 |
|
|
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
903 |
|
|
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
904 |
|
|
samples/water/ssd.bass: add chi and eta to the comment line of dump |
905 |
|
|
file. |
906 |
|
|
|
907 |
|
|
2003-10-28 17:25 mmeineke |
908 |
|
|
|
909 |
|
|
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
910 |
|
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
911 |
|
|
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
912 |
|
|
how c calls fortran. All function pointers and fortran calls are |
913 |
|
|
rigidly typecast now. |
914 |
|
|
|
915 |
|
|
2003-10-28 15:42 gezelter |
916 |
|
|
|
917 |
|
|
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
918 |
|
|
Portability fixes |
919 |
|
|
|
920 |
|
|
2003-10-28 15:09 gezelter |
921 |
|
|
|
922 |
|
|
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
923 |
|
|
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
924 |
|
|
src/Makefile.in: Compatibility fixes |
925 |
|
|
|
926 |
|
|
2003-10-28 12:08 mmeineke |
927 |
|
|
|
928 |
|
|
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
929 |
|
|
started work on template removal |
930 |
|
|
|
931 |
|
|
2003-10-28 12:04 gezelter |
932 |
|
|
|
933 |
|
|
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
934 |
|
|
trying to understand extern "C" stuff for pointers |
935 |
|
|
|
936 |
|
|
2003-10-28 11:20 gezelter |
937 |
|
|
|
938 |
|
|
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
939 |
|
|
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
940 |
|
|
|
941 |
|
|
2003-10-28 11:03 gezelter |
942 |
|
|
|
943 |
|
|
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
944 |
|
|
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
945 |
|
|
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
946 |
|
|
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
947 |
|
|
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
948 |
|
|
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
949 |
|
|
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
950 |
|
|
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
951 |
|
|
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
952 |
|
|
more portable c header stuff Also, mod file fixes and portability |
953 |
|
|
changes Some fortran changes will need to be reversed. |
954 |
|
|
|
955 |
|
|
2003-10-28 11:03 gezelter |
956 |
|
|
|
957 |
|
|
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
958 |
|
|
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
959 |
|
|
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
960 |
|
|
portable c header stuff Also, mod file fixes and portability |
961 |
|
|
changes |
962 |
|
|
|
963 |
|
|
2003-10-28 11:02 gezelter |
964 |
|
|
|
965 |
|
|
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
966 |
|
|
stuff |
967 |
|
|
|
968 |
|
|
2003-10-27 18:00 gezelter |
969 |
|
|
|
970 |
|
|
* Makefile.in, configure, ac-tools/aclocal.m4, |
971 |
|
|
ac-tools/configure.in, ac-tools/fortran90.m4, |
972 |
|
|
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
973 |
|
|
|
974 |
|
|
2003-10-27 17:08 mmeineke |
975 |
|
|
|
976 |
tim |
837 |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
977 |
chuckv |
894 |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
978 |
|
|
added routines for the sysbuilder to work with simSetup |
979 |
|
|
|
980 |
|
|
remved the QuickBass routines, and had all parsing go through |
981 |
|
|
SimSetup. LatticeBilayer is in complete working order now. |
982 |
|
|
|
983 |
|
|
2003-10-27 17:07 mmeineke |
984 |
|
|
|
985 |
|
|
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
986 |
|
|
routines for the sysbuilder to work with simSetup |
987 |
|
|
|
988 |
|
|
2003-10-27 11:20 gezelter |
989 |
|
|
|
990 |
|
|
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
991 |
|
|
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
992 |
|
|
|
993 |
tim |
926 |
2003-10-24 17:17 mmeineke |
994 |
chuckv |
894 |
|
995 |
|
|
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
996 |
tim |
837 |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
997 |
|
|
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
998 |
|
|
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
999 |
|
|
overhauled latticeBilayer into its own program. Removed sysBuild |
1000 |
|
|
from the Makefile |
1001 |
|
|
|
1002 |
tim |
926 |
2003-10-24 12:36 gezelter |
1003 |
tim |
837 |
|
1004 |
|
|
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
1005 |
|
|
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
1006 |
|
|
builder |
1007 |
|
|
|
1008 |
tim |
926 |
2003-10-24 12:35 gezelter |
1009 |
tim |
837 |
|
1010 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
1011 |
|
|
merge problem |
1012 |
|
|
|
1013 |
tim |
926 |
2003-10-23 14:57 mmeineke |
1014 |
tim |
837 |
|
1015 |
|
|
* samples/metals/Makefile.in: added eam ForceField files to the |
1016 |
|
|
init |
1017 |
|
|
|
1018 |
|
|
fixed an eam mpi parmeter setup bug |
1019 |
|
|
|
1020 |
|
|
added the init file to the makefile |
1021 |
|
|
|
1022 |
tim |
926 |
2003-10-23 14:57 mmeineke |
1023 |
tim |
837 |
|
1024 |
|
|
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
1025 |
|
|
to the init |
1026 |
|
|
|
1027 |
|
|
fixed an eam mpi parmeter setup bug |
1028 |
|
|
|
1029 |
tim |
926 |
2003-10-23 14:57 mmeineke |
1030 |
tim |
837 |
|
1031 |
|
|
* forceFields/Makefile.in: added eam ForceField files to the init |
1032 |
|
|
|
1033 |
tim |
926 |
2003-10-22 16:17 mmeineke |
1034 |
tim |
837 |
|
1035 |
|
|
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
1036 |
|
|
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
1037 |
|
|
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
1038 |
|
|
no box skew allowed. |
1039 |
|
|
|
1040 |
tim |
926 |
2003-10-21 14:33 mmeineke |
1041 |
tim |
837 |
|
1042 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1043 |
|
|
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
1044 |
|
|
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
1045 |
|
|
* useInitTime = false: sets the origin time to 0.0 regardless |
1046 |
|
|
of the time stamp in the .init file * default=> useInitTime = |
1047 |
|
|
true; |
1048 |
|
|
|
1049 |
tim |
926 |
2003-10-17 16:19 mmeineke |
1050 |
tim |
837 |
|
1051 |
|
|
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
1052 |
|
|
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1053 |
|
|
staticProps.cpp, obj/placeholder: added the staticProps directory |
1054 |
|
|
to the build list for both configure and configure.in |
1055 |
|
|
|
1056 |
|
|
fixed a number of bugs in the staticProps code. gofr is now |
1057 |
|
|
working. |
1058 |
|
|
|
1059 |
tim |
926 |
2003-10-17 16:18 mmeineke |
1060 |
tim |
837 |
|
1061 |
|
|
* ac-tools/configure.in: added the staticProps directory to the |
1062 |
|
|
build list for both configure and configure.in |
1063 |
|
|
|
1064 |
tim |
926 |
2003-10-17 16:17 mmeineke |
1065 |
tim |
837 |
|
1066 |
|
|
* configure: added the staticProps directory to the build list |
1067 |
|
|
|
1068 |
tim |
926 |
2003-10-16 14:16 mmeineke |
1069 |
tim |
837 |
|
1070 |
|
|
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
1071 |
|
|
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
1072 |
|
|
use linked lists instead of a vector. |
1073 |
|
|
|
1074 |
|
|
Fixed the makefile to build DumpReader.cpp |
1075 |
|
|
|
1076 |
|
|
Removed a comment output in Exclude.cpp |
1077 |
|
|
|
1078 |
|
|
Modified DumpWriter and Integrator to write an eor file every time |
1079 |
|
|
a frame is written. This lets the .eor file represent the last |
1080 |
|
|
written frame of a simulation. |
1081 |
|
|
|
1082 |
tim |
926 |
2003-10-10 12:10 mmeineke |
1083 |
tim |
837 |
|
1084 |
tim |
1005 |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1085 |
|
|
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1086 |
|
|
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1087 |
|
|
staticProps.cpp: removed the props directory, and moved everything |
1088 |
|
|
over to staticProps |
1089 |
tim |
837 |
|
1090 |
tim |
926 |
2003-10-09 17:09 mmeineke |
1091 |
tim |
837 |
|
1092 |
tim |
1005 |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1093 |
tim |
837 |
a position where it will compile and run first runs. |
1094 |
|
|
|
1095 |
tim |
926 |
2003-10-04 13:46 chuckv |
1096 |
tim |
837 |
|
1097 |
|
|
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
1098 |
|
|
samples/metals/Au.bass: Fixed bug in calc_eam. |
1099 |
|
|
|
1100 |
tim |
926 |
2003-10-04 13:08 chuckv |
1101 |
tim |
837 |
|
1102 |
|
|
* samples/metals/init_au.in: added Au init file for eam. |
1103 |
|
|
|
1104 |
tim |
926 |
2003-10-03 17:11 mmeineke |
1105 |
tim |
837 |
|
1106 |
|
|
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1107 |
|
|
entahlpy from the statwriter and thermo. |
1108 |
|
|
|
1109 |
tim |
926 |
2003-10-03 17:02 mmeineke |
1110 |
tim |
837 |
|
1111 |
|
|
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1112 |
|
|
statements in simError |
1113 |
|
|
|
1114 |
|
|
added a function to get the maxCutoff |
1115 |
|
|
|
1116 |
tim |
926 |
2003-10-03 17:01 mmeineke |
1117 |
tim |
837 |
|
1118 |
|
|
* libBASS/simError.c: changed the formating ogf the error |
1119 |
|
|
statements in simError |
1120 |
|
|
|
1121 |
tim |
926 |
2003-09-30 11:00 mmeineke |
1122 |
tim |
920 |
|
1123 |
tim |
837 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1124 |
|
|
f90Flags so they are no longer overwritten by the compiler. |
1125 |
|
|
|
1126 |
tim |
926 |
2003-09-29 17:06 mmeineke |
1127 |
tim |
837 |
|
1128 |
|
|
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
1129 |
|
|
for conifig.in |
1130 |
|
|
|
1131 |
|
|
fixed wrappers to extern "C" |
1132 |
|
|
|
1133 |
tim |
926 |
2003-09-29 17:06 mmeineke |
1134 |
tim |
837 |
|
1135 |
|
|
* ac-tools/configure.in: added mpif90 mod check back same for |
1136 |
|
|
conifig.in |
1137 |
|
|
|
1138 |
tim |
926 |
2003-09-29 17:05 mmeineke |
1139 |
tim |
837 |
|
1140 |
|
|
* configure: added mpif90 mod check back |
1141 |
|
|
|
1142 |
tim |
926 |
2003-09-29 16:16 mmeineke |
1143 |
tim |
837 |
|
1144 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1145 |
|
|
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
1146 |
|
|
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
1147 |
|
|
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
1148 |
|
|
libBASS/ZconStamp.cpp, libBASS/simError.c, |
1149 |
|
|
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
1150 |
|
|
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
1151 |
|
|
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
1152 |
|
|
found with SUN's SUNWspro.s1s7 |
1153 |
|
|
|
1154 |
tim |
926 |
2003-09-29 12:38 mmeineke |
1155 |
tim |
837 |
|
1156 |
|
|
* libmdtools/GenericData.hpp: light change in syntax. no |
1157 |
|
|
signifigant change. |
1158 |
|
|
|
1159 |
tim |
926 |
2003-09-25 16:17 mmeineke |
1160 |
tim |
837 |
|
1161 |
|
|
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1162 |
|
|
additional remarks from icc -w3 (extra verbose output) |
1163 |
|
|
|
1164 |
tim |
926 |
2003-09-25 14:27 mmeineke |
1165 |
tim |
837 |
|
1166 |
|
|
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1167 |
|
|
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1168 |
|
|
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1169 |
|
|
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1170 |
|
|
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1171 |
|
|
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1172 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1173 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1174 |
|
|
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1175 |
|
|
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1176 |
|
|
gcc -Wall and g++ -Wall |
1177 |
|
|
|
1178 |
tim |
926 |
2003-09-25 13:54 gezelter |
1179 |
tim |
837 |
|
1180 |
|
|
* configure, ac-tools/configure.in: fixed a bug in configure |
1181 |
|
|
|
1182 |
tim |
926 |
2003-09-25 11:42 gezelter |
1183 |
tim |
837 |
|
1184 |
|
|
* Makefile.in, configure, ac-tools/aclocal.m4, |
1185 |
|
|
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
1186 |
|
|
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
1187 |
|
|
fixes for configure |
1188 |
|
|
|
1189 |
tim |
926 |
2003-09-24 14:34 mmeineke |
1190 |
tim |
837 |
|
1191 |
|
|
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
1192 |
|
|
that it is called before the first Statistics are written. |
1193 |
|
|
|
1194 |
tim |
926 |
2003-09-23 15:36 gezelter |
1195 |
tim |
837 |
|
1196 |
|
|
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
1197 |
|
|
bunch of Make.dep files to CVS |
1198 |
|
|
|
1199 |
tim |
926 |
2003-09-23 15:34 mmeineke |
1200 |
tim |
837 |
|
1201 |
|
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
1202 |
|
|
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
1203 |
|
|
|
1204 |
|
|
Some small syntax cleaning in NPTfm and SimSetup |
1205 |
|
|
|
1206 |
tim |
926 |
2003-09-22 18:07 tim |
1207 |
tim |
837 |
|
1208 |
|
|
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1209 |
|
|
SimInfo.hpp: fix bug in calculating maxCutoff |
1210 |
|
|
|
1211 |
tim |
926 |
2003-09-22 16:23 mmeineke |
1212 |
tim |
837 |
|
1213 |
|
|
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
1214 |
|
|
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
1215 |
|
|
Converted NPTf to work with the NPT base class. |
1216 |
|
|
|
1217 |
|
|
Removed NPTfm and NPTim from cvs |
1218 |
|
|
|
1219 |
tim |
926 |
2003-09-19 15:00 mmeineke |
1220 |
tim |
837 |
|
1221 |
|
|
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1222 |
|
|
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
1223 |
|
|
class. NPTi is up to date. NPTf is not. |
1224 |
|
|
|
1225 |
tim |
926 |
2003-09-19 11:03 mmeineke |
1226 |
tim |
837 |
|
1227 |
|
|
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
1228 |
|
|
makefile |
1229 |
|
|
|
1230 |
tim |
926 |
2003-09-19 11:01 gezelter |
1231 |
tim |
837 |
|
1232 |
|
|
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
1233 |
|
|
|
1234 |
tim |
926 |
2003-09-19 11:01 gezelter |
1235 |
tim |
837 |
|
1236 |
|
|
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
1237 |
|
|
(nearly) conserved quantities for both NPTi and NPTf |
1238 |
|
|
|
1239 |
tim |
926 |
2003-09-19 10:20 mmeineke |
1240 |
tim |
837 |
|
1241 |
|
|
* utils/Makefile.in: fixed a typo in the makefile. |
1242 |
|
|
|
1243 |
tim |
926 |
2003-09-19 09:55 gezelter |
1244 |
tim |
837 |
|
1245 |
|
|
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
1246 |
|
|
samples/water/ssd.bass: [no log message] |
1247 |
|
|
|
1248 |
tim |
926 |
2003-09-19 09:22 tim |
1249 |
tim |
837 |
|
1250 |
|
|
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
1251 |
|
|
|
1252 |
tim |
926 |
2003-09-17 09:22 mmeineke |
1253 |
tim |
837 |
|
1254 |
|
|
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
1255 |
|
|
work with constraints. |
1256 |
|
|
|
1257 |
tim |
926 |
2003-09-16 15:02 tim |
1258 |
tim |
837 |
|
1259 |
|
|
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
1260 |
|
|
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
1261 |
|
|
|
1262 |
|
|
fixed conserved quantity in NPT (Still some small bug) |
1263 |
|
|
|
1264 |
|
|
NPTi appears very stable. |
1265 |
|
|
|
1266 |
tim |
926 |
2003-09-15 11:52 tim |
1267 |
tim |
837 |
|
1268 |
|
|
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
1269 |
|
|
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
1270 |
|
|
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
1271 |
|
|
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1272 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
1273 |
|
|
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
1274 |
|
|
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1275 |
|
|
statWriter fix bug of vector wrapping at NPTi |
1276 |
|
|
|
1277 |
tim |
926 |
2003-09-12 11:20 gezelter |
1278 |
tim |
920 |
|
1279 |
tim |
837 |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1280 |
|
|
Makefile.in |
1281 |
|
|
|
1282 |
tim |
926 |
2003-09-12 11:20 gezelter |
1283 |
tim |
837 |
|
1284 |
|
|
* ChangeLog: Entered changes for configure into ChangeLog |
1285 |
|
|
|
1286 |
tim |
926 |
2003-09-09 15:35 mmeineke |
1287 |
tim |
920 |
|
1288 |
gezelter |
760 |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
1289 |
|
|
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
1290 |
|
|
|
1291 |
|
|
added two new NPT integrators, they still need work. |
1292 |
|
|
|
1293 |
tim |
926 |
2003-09-09 15:34 mmeineke |
1294 |
gezelter |
760 |
|
1295 |
|
|
* ChangeLog: updated the ChangeLog |
1296 |
|
|
|
1297 |
tim |
926 |
2003-09-05 17:45 gezelter |
1298 |
gezelter |
760 |
|
1299 |
|
|
* libmdtools/Make.dep: dependency on config.h |
1300 |
|
|
|
1301 |
tim |
926 |
2003-09-05 17:36 gezelter |
1302 |
gezelter |
760 |
|
1303 |
|
|
* configure, ac-tools/aclocal.m4: fixed sprng problem |
1304 |
|
|
|
1305 |
tim |
926 |
2003-09-05 16:29 gezelter |
1306 |
gezelter |
760 |
|
1307 |
|
|
* samples/metals/Makefile.in: New Makefile for metals sample |
1308 |
|
|
|
1309 |
tim |
926 |
2003-09-05 16:27 gezelter |
1310 |
gezelter |
760 |
|
1311 |
|
|
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
1312 |
|
|
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
1313 |
|
|
forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
1314 |
|
|
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
1315 |
|
|
libBASS/Makefile.in, libmdtools/Integrator.hpp, |
1316 |
|
|
libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
1317 |
|
|
libmdtools/Makefile, libmdtools/Makefile.in, |
1318 |
|
|
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
1319 |
|
|
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
1320 |
|
|
libmdtools/fortranWrappers.cpp, |
1321 |
|
|
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
1322 |
|
|
libmdtools/simulation_module.F90, samples/Makefile, |
1323 |
|
|
samples/Makefile.in, samples/alkane/Makefile, |
1324 |
|
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
1325 |
|
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
1326 |
|
|
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
1327 |
|
|
samples/lipid/Makefile, samples/lipid/Makefile.in, |
1328 |
|
|
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
1329 |
|
|
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
1330 |
|
|
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
1331 |
|
|
autoconf / configure method of configuring OOPSE |
1332 |
|
|
|
1333 |
tim |
926 |
2003-09-04 16:48 mmeineke |
1334 |
mmeineke |
754 |
|
1335 |
|
|
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
1336 |
|
|
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
1337 |
|
|
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
1338 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
1339 |
|
|
added resetTime to the Global namespace. |
1340 |
|
|
|
1341 |
|
|
added ability to reset the integrators in the NVT and NPT family. |
1342 |
|
|
|
1343 |
tim |
926 |
2003-09-04 16:48 mmeineke |
1344 |
mmeineke |
754 |
|
1345 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
1346 |
|
|
namespace. |
1347 |
|
|
|
1348 |
tim |
926 |
2003-09-02 09:30 tim |
1349 |
mmeineke |
754 |
|
1350 |
|
|
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
1351 |
|
|
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
1352 |
|
|
PolicyByMass |
1353 |
|
|
|
1354 |
tim |
926 |
2003-08-28 16:09 tim |
1355 |
mmeineke |
754 |
|
1356 |
|
|
* ChangeLog, libmdtools/GenericData.cpp, |
1357 |
|
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
1358 |
|
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
1359 |
|
|
|
1360 |
tim |
926 |
2003-08-27 14:23 tim |
1361 |
tim |
920 |
|
1362 |
tim |
736 |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
1363 |
|
|
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
1364 |
|
|
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
1365 |
|
|
turn on the optimization flag, it causes a seg fault |
1366 |
|
|
|
1367 |
tim |
926 |
2003-08-27 11:25 gezelter |
1368 |
tim |
736 |
|
1369 |
|
|
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
1370 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
1371 |
|
|
stress tensor parallel bug. |
1372 |
|
|
|
1373 |
tim |
926 |
2003-08-27 11:16 tim |
1374 |
tim |
736 |
|
1375 |
|
|
* ChangeLog, libmdtools/DUFF.cpp, |
1376 |
|
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
1377 |
|
|
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
1378 |
|
|
molMembershipList use global index instead of local index |
1379 |
|
|
|
1380 |
tim |
926 |
2003-08-26 15:37 tim |
1381 |
tim |
727 |
|
1382 |
|
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
1383 |
|
|
mpiSimulation.cpp: set default force substraction policy to |
1384 |
|
|
PolicyByMass |
1385 |
|
|
|
1386 |
tim |
926 |
2003-08-26 15:29 tim |
1387 |
tim |
727 |
|
1388 |
|
|
* libmdtools/Integrator.cpp: [no log message] |
1389 |
|
|
|
1390 |
tim |
926 |
2003-08-26 15:13 mmeineke |
1391 |
tim |
727 |
|
1392 |
|
|
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
1393 |
|
|
Statwriter and Dumpwriter to handle files larger than 2 gb. |
1394 |
|
|
|
1395 |
|
|
commented out some print statements in Zconstraint |
1396 |
|
|
|
1397 |
|
|
hard coding some system init into bilayer.sys |
1398 |
|
|
|
1399 |
tim |
926 |
2003-08-26 15:12 mmeineke |
1400 |
tim |
727 |
|
1401 |
|
|
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
1402 |
|
|
added define statemewnt to Statwriter and Dumpwriter to handle |
1403 |
|
|
files larger than 2 gb. |
1404 |
|
|
|
1405 |
|
|
commented out some print statements in Zconstraint |
1406 |
|
|
|
1407 |
tim |
926 |
2003-08-26 15:02 tim |
1408 |
tim |
727 |
|
1409 |
|
|
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
1410 |
|
|
and check the seed which is specified by user at least contains 9 |
1411 |
|
|
digits |
1412 |
|
|
|
1413 |
tim |
926 |
2003-08-26 13:32 mmeineke |
1414 |
tim |
727 |
|
1415 |
|
|
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
1416 |
|
|
|
1417 |
|
|
Fixed a bug in MPI_DUFF. The atom block type was not being properly |
1418 |
|
|
constucted in MPI. (The MPI struct had 6 doubles declared versus |
1419 |
|
|
the actual 11) |
1420 |
|
|
|
1421 |
tim |
926 |
2003-08-26 13:30 mmeineke |
1422 |
tim |
727 |
|
1423 |
|
|
* Makefile: changed the Makefiel a litle. |
1424 |
|
|
|
1425 |
tim |
926 |
2003-08-25 17:17 gezelter |
1426 |
tim |
727 |
|
1427 |
|
|
* utils/sysbuilder/Makefile: More FreeBSD fixes |
1428 |
|
|
|
1429 |
tim |
926 |
2003-08-25 16:51 gezelter |
1430 |
tim |
727 |
|
1431 |
|
|
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
1432 |
|
|
libmdtools/Makefile, src/Makefile: [no log message] |
1433 |
|
|
|
1434 |
tim |
926 |
2003-08-22 15:04 mmeineke |
1435 |
tim |
727 |
|
1436 |
|
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
1437 |
|
|
frequency of output dumps. |
1438 |
|
|
|
1439 |
tim |
926 |
2003-08-20 17:23 tim |
1440 |
tim |
727 |
|
1441 |
|
|
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
1442 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1443 |
|
|
libmdtools/mpiSimulation.cpp: user can setup seed in bass file now, |
1444 |
|
|
if he does not specify any value for seed, oopse will take the |
1445 |
|
|
value of seconds of system time as seed |
1446 |
|
|
|
1447 |
tim |
926 |
2003-08-20 14:42 mmeineke |
1448 |
tim |
727 |
|
1449 |
|
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1450 |
|
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
1451 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimState.cpp, |
1452 |
|
|
utils/sysbuilder/bilayerSys.cpp: updated the Changelog. |
1453 |
|
|
|
1454 |
|
|
added some bug fixes for setting the random number generator seed |
1455 |
|
|
value. |
1456 |
|
|
|
1457 |
|
|
fixed a bug where ghostbend atom b was not being set. ( recent bug |
1458 |
|
|
from SimState conversion) |
1459 |
|
|
|
1460 |
tim |
926 |
2003-08-20 14:41 mmeineke |
1461 |
tim |
727 |
|
1462 |
|
|
* libBASS/Globals.hpp: updated the Changelog. |
1463 |
|
|
|
1464 |
|
|
added some bug fixes for setting the random number generator seed |
1465 |
|
|
value. |
1466 |
|
|
|
1467 |
tim |
926 |
2003-08-20 14:41 mmeineke |
1468 |
tim |
727 |
|
1469 |
|
|
* ChangeLog: updated the Changelog. |
1470 |
|
|
|
1471 |
tim |
926 |
2003-08-20 14:11 tim |
1472 |
tim |
727 |
|
1473 |
|
|
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
1474 |
|
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
1475 |
|
|
bend class |
1476 |
|
|
|
1477 |
tim |
926 |
2003-08-20 10:13 mmeineke |
1478 |
tim |
727 |
|
1479 |
|
|
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
1480 |
|
|
make links. added -f to ln -s. |
1481 |
|
|
|
1482 |
tim |
926 |
2003-08-20 09:50 tim |
1483 |
tim |
727 |
|
1484 |
|
|
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
1485 |
|
|
|
1486 |
tim |
926 |
2003-08-20 09:34 tim |
1487 |
tim |
727 |
|
1488 |
|
|
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
1489 |
|
|
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
1490 |
|
|
printing |
1491 |
|
|
|
1492 |
tim |
926 |
2003-08-18 15:59 chuckv |
1493 |
mmeineke |
705 |
|
1494 |
|
|
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
1495 |
|
|
latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
1496 |
|
|
sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
1497 |
|
|
Nanobuilder still broke. |
1498 |
|
|
|
1499 |
tim |
926 |
2003-08-15 14:24 tim |
1500 |
mmeineke |
705 |
|
1501 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1502 |
|
|
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
1503 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
1504 |
|
|
libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, |
1505 |
|
|
libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
1506 |
|
|
Method |
1507 |
|
|
|
1508 |
tim |
926 |
2003-08-14 11:16 tim |
1509 |
mmeineke |
705 |
|
1510 |
|
|
* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
1511 |
|
|
with average force substraction strategy |
1512 |
|
|
|
1513 |
tim |
926 |
2003-08-13 16:20 chuckv |
1514 |
mmeineke |
705 |
|
1515 |
|
|
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
1516 |
|
|
profiling code -DPROFILE. |
1517 |
|
|
|
1518 |
tim |
926 |
2003-08-13 14:21 tim |
1519 |
mmeineke |
705 |
|
1520 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1521 |
|
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
1522 |
|
|
libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
1523 |
|
|
potential & z-contraint method |
1524 |
|
|
|
1525 |
tim |
926 |
2003-08-12 16:44 mmeineke |
1526 |
mmeineke |
705 |
|
1527 |
|
|
* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
1528 |
|
|
libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1529 |
|
|
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
1530 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really |
1531 |
|
|
annoying bug in Directional Atom, where mu was getting written to |
1532 |
|
|
pseudorandom memory location. |
1533 |
|
|
|
1534 |
tim |
926 |
2003-08-12 14:56 tim |
1535 |
mmeineke |
705 |
|
1536 |
|
|
* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
1537 |
|
|
libBASS/Globals.hpp, libmdtools/Atom.hpp, |
1538 |
|
|
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
1539 |
|
|
libmdtools/SimSetup.cpp: debugging globals |
1540 |
|
|
|
1541 |
tim |
926 |
2003-08-12 13:40 gezelter |
1542 |
mmeineke |
705 |
|
1543 |
|
|
* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
1544 |
|
|
and new atypes in LJFF |
1545 |
|
|
|
1546 |
tim |
926 |
2003-08-12 13:15 gezelter |
1547 |
mmeineke |
705 |
|
1548 |
|
|
* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
1549 |
|
|
stuff... |
1550 |
|
|
|
1551 |
tim |
926 |
2003-08-12 13:14 chuckv |
1552 |
mmeineke |
705 |
|
1553 |
|
|
* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
1554 |
|
|
|
1555 |
tim |
926 |
2003-08-12 13:04 chuckv |
1556 |
mmeineke |
705 |
|
1557 |
|
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
1558 |
|
|
Missed del of files before. |
1559 |
|
|
|
1560 |
tim |
926 |
2003-08-12 13:03 chuckv |
1561 |
mmeineke |
705 |
|
1562 |
|
|
* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
1563 |
|
|
message] |
1564 |
|
|
|
1565 |
tim |
926 |
2003-08-12 13:01 chuckv |
1566 |
mmeineke |
705 |
|
1567 |
|
|
* utils/sysbuilder/Makefile: commit makefile |
1568 |
|
|
|
1569 |
tim |
926 |
2003-08-12 12:51 tim |
1570 |
mmeineke |
705 |
|
1571 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1572 |
|
|
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
1573 |
|
|
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
1574 |
|
|
libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
1575 |
|
|
harmonical potential to z-constraint method |
1576 |
|
|
|
1577 |
tim |
926 |
2003-08-11 17:31 chuckv |
1578 |
mmeineke |
705 |
|
1579 |
|
|
* utils/Makefile: Changed makefile to only build quicklate. |
1580 |
|
|
|
1581 |
tim |
926 |
2003-08-11 17:25 chuckv |
1582 |
mmeineke |
705 |
|
1583 |
|
|
* ac-tools/configure.in: added utils/sysbuilder to be built. |
1584 |
|
|
|
1585 |
tim |
926 |
2003-08-11 17:12 chuckv |
1586 |
mmeineke |
705 |
|
1587 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
1588 |
|
|
bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
1589 |
|
|
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, |
1590 |
|
|
sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, |
1591 |
|
|
sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, |
1592 |
|
|
sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, |
1593 |
|
|
sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, |
1594 |
|
|
sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, |
1595 |
|
|
sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged |
1596 |
|
|
sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
1597 |
|
|
with new atom allocation in libmdtools. |
1598 |
|
|
|
1599 |
tim |
926 |
2003-08-11 14:41 tim |
1600 |
mmeineke |
705 |
|
1601 |
|
|
* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
1602 |
|
|
moving zconstraint molecules to specified positions |
1603 |
|
|
|
1604 |
tim |
926 |
2003-08-11 14:39 tim |
1605 |
mmeineke |
705 |
|
1606 |
|
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
1607 |
|
|
|
1608 |
tim |
926 |
2003-08-11 14:38 mmeineke |
1609 |
mmeineke |
705 |
|
1610 |
|
|
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
1611 |
|
|
libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
1612 |
|
|
libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, |
1613 |
|
|
libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c, |
1614 |
|
|
libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h, |
1615 |
|
|
libBASS/node_list.h, libBASS/parse_interface.h, |
1616 |
|
|
libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
1617 |
|
|
into the BASS language syntax. |
1618 |
|
|
|
1619 |
tim |
926 |
2003-08-11 13:29 mmeineke |
1620 |
mmeineke |
705 |
|
1621 |
|
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
1622 |
|
|
degrees of freedom to account for zConstreints |
1623 |
|
|
|
1624 |
tim |
926 |
2003-08-08 16:22 chuckv |
1625 |
mmeineke |
705 |
|
1626 |
|
|
* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
1627 |
|
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
1628 |
|
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
1629 |
|
|
works..... |
1630 |
|
|
|
1631 |
tim |
926 |
2003-08-08 12:48 mmeineke |
1632 |
tim |
920 |
|
1633 |
mmeineke |
705 |
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
1634 |
|
|
instance of Atom::setZ and Atom::getZ in ZConstaint. |
1635 |
|
|
|
1636 |
tim |
926 |
2003-08-07 16:47 mmeineke |
1637 |
mmeineke |
705 |
|
1638 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
1639 |
|
|
DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
1640 |
|
|
GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, |
1641 |
|
|
SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, |
1642 |
|
|
SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
1643 |
|
|
configuration from SimState rather than arrays from Atom |
1644 |
|
|
|
1645 |
tim |
926 |
2003-08-06 19:47 chuckv |
1646 |
mmeineke |
705 |
|
1647 |
|
|
* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
1648 |
|
|
libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
1649 |
|
|
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
1650 |
|
|
samples/metals/Au.bass: Bug fixes for eam... |
1651 |
|
|
|
1652 |
tim |
926 |
2003-08-01 11:18 tim |
1653 |
mmeineke |
705 |
|
1654 |
|
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
1655 |
|
|
Z-Constraint |
1656 |
|
|
|
1657 |
tim |
926 |
2003-07-31 14:59 tim |
1658 |
mmeineke |
705 |
|
1659 |
|
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1660 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1661 |
|
|
libmdtools/ZConstraint.cpp: add index range checking into |
1662 |
|
|
ZConstraint |
1663 |
|
|
|
1664 |
tim |
926 |
2003-07-31 10:38 tim |
1665 |
tim |
660 |
|
1666 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
1667 |
|
|
to the globals |
1668 |
|
|
|
1669 |
tim |
926 |
2003-07-31 10:35 tim |
1670 |
tim |
660 |
|
1671 |
|
|
* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
1672 |
|
|
Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
1673 |
|
|
NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
1674 |
|
|
SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
1675 |
|
|
Added Z constraint. |
1676 |
|
|
|
1677 |
tim |
926 |
2003-07-30 16:17 chuckv |
1678 |
tim |
660 |
|
1679 |
mmeineke |
705 |
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
1680 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
1681 |
|
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
1682 |
|
|
samples/metals/Au.bass: More bug fixes for eam. |
1683 |
tim |
660 |
|
1684 |
tim |
926 |
2003-07-29 11:32 mmeineke |
1685 |
tim |
660 |
|
1686 |
|
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
1687 |
tim |
1005 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
1688 |
|
|
working on the props code |
1689 |
tim |
660 |
|
1690 |
tim |
926 |
2003-07-29 11:32 mmeineke |
1691 |
tim |
660 |
|
1692 |
|
|
* libBASS/Globals.cpp: [no log message] |
1693 |
|
|
|
1694 |
tim |
926 |
2003-07-25 15:05 chuckv |
1695 |
mmeineke |
705 |
|
1696 |
|
|
* samples/metals/: Au.bass, metals.mdl: Added bass models for |
1697 |
|
|
metals |
1698 |
|
|
|
1699 |
tim |
926 |
2003-07-25 15:00 chuckv |
1700 |
tim |
660 |
|
1701 |
|
|
* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
1702 |
|
|
notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
1703 |
|
|
|
1704 |
tim |
926 |
2003-07-24 16:22 chuckv |
1705 |
tim |
660 |
|
1706 |
|
|
* ac-tools/configure.in: Changed configure to look for both upper |
1707 |
|
|
and lower cass .mod files |
1708 |
|
|
|
1709 |
tim |
926 |
2003-07-24 14:57 chuckv |
1710 |
tim |
660 |
|
1711 |
|
|
* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
1712 |
|
|
eam and do_forces. |
1713 |
|
|
|
1714 |
tim |
926 |
2003-07-23 17:13 chuckv |
1715 |
tim |
660 |
|
1716 |
|
|
* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
1717 |
|
|
force_globals.F90, simulation_module.F90, status_module.F90: |
1718 |
|
|
Finished most code for eam.... |
1719 |
|
|
|
1720 |
tim |
926 |
2003-07-22 16:49 mmeineke |
1721 |
tim |
660 |
|
1722 |
|
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
1723 |
|
|
function to the DumpReader. It should now save the start of each |
1724 |
|
|
frame in a vector. |
1725 |
|
|
|
1726 |
tim |
926 |
2003-07-22 15:05 mmeineke |
1727 |
tim |
660 |
|
1728 |
|
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
1729 |
|
|
to read dump files |
1730 |
|
|
|
1731 |
tim |
926 |
2003-07-22 14:54 tim |
1732 |
tim |
660 |
|
1733 |
|
|
* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
1734 |
|
|
Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
1735 |
|
|
NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
1736 |
|
|
message] |
1737 |
|
|
|
1738 |
tim |
926 |
2003-07-22 11:41 mmeineke |
1739 |
tim |
660 |
|
1740 |
|
|
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
1741 |
|
|
SimSetup.cpp: Fixed a current time initialization bug in |
1742 |
|
|
InitFromFile. |
1743 |
|
|
|
1744 |
tim |
926 |
2003-07-21 16:27 mmeineke |
1745 |
tim |
660 |
|
1746 |
|
|
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
1747 |
|
|
Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
1748 |
|
|
friends to accomadate random file access |
1749 |
|
|
|
1750 |
tim |
926 |
2003-07-21 11:23 mmeineke |
1751 |
tim |
660 |
|
1752 |
|
|
* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
1753 |
|
|
one sets it. |
1754 |
|
|
|
1755 |
tim |
926 |
2003-07-21 11:23 mmeineke |
1756 |
tim |
660 |
|
1757 |
|
|
* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
1758 |
|
|
ReadWrite.hpp: fixed Initializefrom file to start the simulation |
1759 |
|
|
from the time specified in the init file. |
1760 |
|
|
|
1761 |
tim |
926 |
2003-07-17 16:49 gezelter |
1762 |
tim |
660 |
|
1763 |
|
|
* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
1764 |
|
|
DumpReader.cpp: Started work on a DumpReader |
1765 |
|
|
|
1766 |
tim |
926 |
2003-07-17 15:38 gezelter |
1767 |
tim |
660 |
|
1768 |
|
|
* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
1769 |
|
|
|
1770 |
tim |
926 |
2003-07-17 15:32 gezelter |
1771 |
tim |
660 |
|
1772 |
|
|
* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
1773 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
1774 |
|
|
Changes for SSD/E |
1775 |
|
|
|
1776 |
tim |
926 |
2003-07-17 14:38 mmeineke |
1777 |
tim |
660 |
|
1778 |
|
|
* libmdtools/do_Forces.F90: commented out an eam line |
1779 |
|
|
|
1780 |
tim |
926 |
2003-07-17 14:32 chuckv |
1781 |
tim |
660 |
|
1782 |
|
|
* libmdtools/atype_module.F90: fixed spelling issue |
1783 |
|
|
|
1784 |
tim |
926 |
2003-07-17 14:29 chuckv |
1785 |
tim |
660 |
|
1786 |
|
|
* libmdtools/: fInfo.c, status_module.F90: added info module |
1787 |
|
|
|
1788 |
tim |
926 |
2003-07-17 14:25 chuckv |
1789 |
tim |
660 |
|
1790 |
|
|
* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
1791 |
|
|
atype_module.F90, calc_eam.F90, do_Forces.F90, |
1792 |
|
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1793 |
|
|
mpiSimulation_module.F90: Added massive changes for eam.... |
1794 |
|
|
|
1795 |
tim |
926 |
2003-07-16 16:49 chuckv |
1796 |
tim |
660 |
|
1797 |
|
|
* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
1798 |
|
|
|
1799 |
tim |
926 |
2003-07-16 16:30 mmeineke |
1800 |
tim |
660 |
|
1801 |
|
|
* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
1802 |
|
|
SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1803 |
|
|
calc_reaction_field.F90, do_Forces.F90, fSimulation.h, |
1804 |
|
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1805 |
|
|
neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, |
1806 |
|
|
wrappers.F90: Changed how cutoffs were handled from C. Now |
1807 |
|
|
notifyCutoffs in Fortran notifies those who need the information of |
1808 |
|
|
any changes to cutoffs. |
1809 |
|
|
|
1810 |
tim |
926 |
2003-07-16 12:35 gezelter |
1811 |
tim |
660 |
|
1812 |
|
|
* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
1813 |
|
|
quickLate is now somewhat more intelligent about periodic |
1814 |
|
|
boundaries and wrapping. |
1815 |
|
|
|
1816 |
tim |
926 |
2003-07-16 11:40 chuckv |
1817 |
tim |
660 |
|
1818 |
|
|
* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
1819 |
|
|
|
1820 |
tim |
926 |
2003-07-16 10:34 mmeineke |
1821 |
tim |
660 |
|
1822 |
|
|
* scripts/cleanSrc: added a quick wipe-and-update script for quick |
1823 |
|
|
rebuilds on BoB |
1824 |
|
|
|
1825 |
tim |
926 |
2003-07-15 21:11 gezelter |
1826 |
tim |
660 |
|
1827 |
|
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
1828 |
|
|
SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
1829 |
|
|
fixes for box changes |
1830 |
|
|
|
1831 |
tim |
926 |
2003-07-15 17:29 mmeineke |
1832 |
tim |
660 |
|
1833 |
|
|
* libmdtools/simulation_module.F90: removed some debugging print |
1834 |
|
|
statements. |
1835 |
|
|
|
1836 |
tim |
926 |
2003-07-15 17:22 mmeineke |
1837 |
tim |
660 |
|
1838 |
|
|
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1839 |
|
|
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
1840 |
|
|
do_forces. Rrf was not being used in the neighborlist correctly. |
1841 |
|
|
rcut was conssistently being set lowere than Rrf causing the dipole |
1842 |
|
|
cutoff region to be to small. Also led to the removal of the taper |
1843 |
|
|
region to buffer the dipole cutoff. |
1844 |
|
|
|
1845 |
tim |
926 |
2003-07-15 16:34 mmeineke |
1846 |
tim |
660 |
|
1847 |
|
|
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
1848 |
|
|
fixing ssd bug |
1849 |
|
|
|
1850 |
tim |
926 |
2003-07-15 14:56 gezelter |
1851 |
tim |
660 |
|
1852 |
|
|
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
1853 |
|
|
for the NPT ensembles |
1854 |
|
|
|
1855 |
tim |
926 |
2003-07-15 13:52 mmeineke |
1856 |
tim |
660 |
|
1857 |
|
|
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
1858 |
|
|
simSetup |
1859 |
|
|
|
1860 |
tim |
926 |
2003-07-15 12:57 mmeineke |
1861 |
tim |
660 |
|
1862 |
|
|
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
1863 |
|
|
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
1864 |
|
|
fixed some bugs, Changed entry_plug to info where appropriate |
1865 |
|
|
|
1866 |
tim |
926 |
2003-07-15 12:25 chuckv |
1867 |
tim |
660 |
|
1868 |
|
|
* utils/sysBuild.ggo: added more command line arguments |
1869 |
|
|
|
1870 |
tim |
926 |
2003-07-15 12:11 gezelter |
1871 |
tim |
660 |
|
1872 |
|
|
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
1873 |
|
|
Fixing force field line |
1874 |
|
|
|
1875 |
tim |
926 |
2003-07-15 12:10 gezelter |
1876 |
tim |
660 |
|
1877 |
|
|
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
1878 |
|
|
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
1879 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
1880 |
|
|
tensor |
1881 |
|
|
|
1882 |
tim |
926 |
2003-07-15 10:50 gezelter |
1883 |
tim |
660 |
|
1884 |
|
|
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
1885 |
|
|
|
1886 |
tim |
926 |
2003-07-15 10:42 gezelter |
1887 |
tim |
660 |
|
1888 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
1889 |
|
|
removed old outdated code |
1890 |
|
|
|
1891 |
tim |
926 |
2003-07-15 09:45 gezelter |
1892 |
tim |
660 |
|
1893 |
|
|
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
1894 |
|
|
|
1895 |
tim |
926 |
2003-07-15 09:28 gezelter |
1896 |
tim |
660 |
|
1897 |
|
|
* libmdtools/Molecule.cpp: removing get_vx |
1898 |
|
|
|
1899 |
tim |
926 |
2003-07-14 22:28 gezelter |
1900 |
tim |
660 |
|
1901 |
|
|
* libmdtools/NPTfm.cpp: Added NPTfm |
1902 |
|
|
|
1903 |
tim |
926 |
2003-07-14 22:27 gezelter |
1904 |
tim |
660 |
|
1905 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
1906 |
|
|
Bugfix in NPTim, fixes for NPTfm |
1907 |
|
|
|
1908 |
tim |
926 |
2003-07-14 22:08 gezelter |
1909 |
tim |
660 |
|
1910 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
1911 |
|
|
Checking in changes for NPTim |
1912 |
|
|
|
1913 |
tim |
926 |
2003-07-14 18:06 gezelter |
1914 |
tim |
660 |
|
1915 |
|
|
* utils/Makefile: Broken SysBuilder |
1916 |
|
|
|
1917 |
tim |
926 |
2003-07-14 18:06 gezelter |
1918 |
tim |
660 |
|
1919 |
|
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
1920 |
|
|
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
1921 |
|
|
for samples |
1922 |
|
|
|
1923 |
tim |
926 |
2003-07-14 18:06 gezelter |
1924 |
tim |
660 |
|
1925 |
|
|
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
1926 |
|
|
debugging write statements |
1927 |
|
|
|
1928 |
tim |
926 |
2003-07-14 17:38 gezelter |
1929 |
tim |
660 |
|
1930 |
|
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
1931 |
|
|
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
1932 |
|
|
|
1933 |
tim |
926 |
2003-07-14 16:48 mmeineke |
1934 |
tim |
660 |
|
1935 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
1936 |
|
|
and set routines to Atom and DirectionalAtom |
1937 |
|
|
|
1938 |
tim |
926 |
2003-07-14 16:35 chuckv |
1939 |
tim |
660 |
|
1940 |
|
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
1941 |
|
|
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
1942 |
|
|
that takes different cmd line arguments. |
1943 |
|
|
|
1944 |
tim |
926 |
2003-07-14 16:28 mmeineke |
1945 |
tim |
660 |
|
1946 |
|
|
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
1947 |
|
|
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
1948 |
|
|
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
1949 |
|
|
were not being updated |
1950 |
|
|
|
1951 |
tim |
926 |
2003-07-14 10:04 gezelter |
1952 |
tim |
660 |
|
1953 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
1954 |
|
|
NPTim |
1955 |
|
|
|
1956 |
tim |
926 |
2003-07-14 09:55 mmeineke |
1957 |
tim |
660 |
|
1958 |
|
|
* forceFields/DUFF.frc: Switched the bond in the force field back |
1959 |
|
|
to constrained, to preserve energy |
1960 |
|
|
|
1961 |
tim |
926 |
2003-07-11 17:34 mmeineke |
1962 |
tim |
660 |
|
1963 |
|
|
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
1964 |
|
|
Integrator.hpp: working on som integrator bugs |
1965 |
|
|
|
1966 |
tim |
926 |
2003-07-11 10:26 gezelter |
1967 |
tim |
660 |
|
1968 |
|
|
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
1969 |
|
|
to worry about all the strtok() calls in our code |
1970 |
|
|
|
1971 |
tim |
926 |
2003-07-11 09:49 gezelter |
1972 |
tim |
660 |
|
1973 |
|
|
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
1974 |
|
|
|
1975 |
tim |
926 |
2003-07-10 20:15 gezelter |
1976 |
tim |
660 |
|
1977 |
|
|
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
1978 |
|
|
eor. |
1979 |
|
|
|
1980 |
tim |
926 |
2003-07-10 17:15 mmeineke |
1981 |
tim |
660 |
|
1982 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
1983 |
|
|
SimInfo.cpp, Thermo.cpp: fixed some bugs |
1984 |
|
|
|
1985 |
tim |
926 |
2003-07-10 14:53 chuckv |
1986 |
tim |
660 |
|
1987 |
|
|
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
1988 |
|
|
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
1989 |
|
|
nanoBuilder and a general Lattice builder. |
1990 |
|
|
|
1991 |
tim |
926 |
2003-07-10 12:10 gezelter |
1992 |
tim |
660 |
|
1993 |
|
|
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
1994 |
|
|
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
1995 |
|
|
|
1996 |
tim |
926 |
2003-07-09 17:14 mmeineke |
1997 |
tim |
660 |
|
1998 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
1999 |
|
|
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
2000 |
|
|
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
2001 |
|
|
caclulation of HmatInverse. |
2002 |
|
|
|
2003 |
tim |
926 |
2003-07-09 10:34 mmeineke |
2004 |
tim |
660 |
|
2005 |
|
|
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
2006 |
|
|
|
2007 |
tim |
926 |
2003-07-09 10:33 mmeineke |
2008 |
tim |
660 |
|
2009 |
|
|
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
2010 |
|
|
|
2011 |
tim |
926 |
2003-07-09 08:56 gezelter |
2012 |
tim |
660 |
|
2013 |
|
|
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
2014 |
|
|
|
2015 |
tim |
926 |
2003-07-09 08:56 gezelter |
2016 |
tim |
660 |
|
2017 |
|
|
* libBASS/Globals.cpp: Removed Qmass |
2018 |
|
|
|
2019 |
tim |
926 |
2003-07-08 21:15 gezelter |
2020 |
tim |
660 |
|
2021 |
|
|
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
2022 |
|
|
and NPTi |
2023 |
|
|
|
2024 |
tim |
926 |
2003-07-08 20:41 gezelter |
2025 |
tim |
660 |
|
2026 |
|
|
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
2027 |
|
|
|
2028 |
tim |
926 |
2003-07-08 16:10 gezelter |
2029 |
tim |
660 |
|
2030 |
|
|
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
2031 |
|
|
|
2032 |
tim |
926 |
2003-07-08 16:06 gezelter |
2033 |
tim |
660 |
|
2034 |
|
|
* libmdtools/NPTi.cpp: fixed box scaling |
2035 |
|
|
|
2036 |
tim |
926 |
2003-07-08 15:56 gezelter |
2037 |
tim |
660 |
|
2038 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
2039 |
|
|
SimInfo.hpp, Thermo.cpp: NPTi |
2040 |
|
|
|
2041 |
tim |
926 |
2003-07-03 14:41 mmeineke |
2042 |
tim |
660 |
|
2043 |
|
|
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
2044 |
|
|
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
2045 |
|
|
scripts in the makefiles |
2046 |
|
|
|
2047 |
tim |
926 |
2003-07-02 16:26 mmeineke |
2048 |
tim |
660 |
|
2049 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
2050 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
2051 |
|
|
libmdtools/Makefile, libmdtools/ReadWrite.hpp, |
2052 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2053 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
2054 |
|
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, |
2055 |
|
|
utils/Makefile: fixed the bugs introduced by switching the periodic |
2056 |
|
|
box to a matrix |
2057 |
|
|
|
2058 |
tim |
926 |
2003-07-01 17:39 gezelter |
2059 |
tim |
660 |
|
2060 |
|
|
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
2061 |
|
|
|
2062 |
tim |
926 |
2003-07-01 17:29 gezelter |
2063 |
tim |
660 |
|
2064 |
|
|
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
2065 |
|
|
|
2066 |
tim |
926 |
2003-07-01 16:33 mmeineke |
2067 |
tim |
660 |
|
2068 |
|
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
2069 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
2070 |
|
|
the box matrix to everything. |
2071 |
|
|
|
2072 |
tim |
926 |
2003-06-30 17:03 mmeineke |
2073 |
tim |
660 |
|
2074 |
|
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2075 |
|
|
src/oopse.cpp: |
2076 |
|
|
Updated the ChangeLog, and Converted most of the SImInfo to use |
2077 |
|
|
non-Isotropic boxes. wrapVector needs to be finished. |
2078 |
|
|
|
2079 |
tim |
926 |
2003-06-25 16:12 mmeineke |
2080 |
mmeineke |
568 |
|
2081 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
2082 |
|
|
to Harmonic bonds in the DUFF frc file |
2083 |
|
|
|
2084 |
|
|
fixed constraints. |
2085 |
|
|
|
2086 |
tim |
926 |
2003-06-25 16:11 mmeineke |
2087 |
mmeineke |
568 |
|
2088 |
|
|
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
2089 |
|
|
the DUFF frc file |
2090 |
|
|
|
2091 |
tim |
926 |
2003-06-24 17:51 gezelter |
2092 |
mmeineke |
568 |
|
2093 |
|
|
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
2094 |
|
|
|
2095 |
tim |
926 |
2003-06-24 14:57 mmeineke |
2096 |
mmeineke |
568 |
|
2097 |
|
|
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
2098 |
|
|
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
2099 |
|
|
the DUFF forcefield and BondExtensions.cpp |
2100 |
|
|
|
2101 |
tim |
926 |
2003-06-23 16:24 mmeineke |
2102 |
mmeineke |
568 |
|
2103 |
|
|
* libmdtools/Integrator.cpp: Doing some work to debug the |
2104 |
|
|
constraint code. |
2105 |
|
|
|
2106 |
tim |
926 |
2003-06-20 15:50 gezelter |
2107 |
mmeineke |
568 |
|
2108 |
|
|
* libmdtools/Integrator.hpp: NPT fix |
2109 |
|
|
|
2110 |
tim |
926 |
2003-06-20 15:29 mmeineke |
2111 |
mmeineke |
568 |
|
2112 |
|
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
2113 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
2114 |
|
|
libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
2115 |
|
|
libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
2116 |
|
|
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
2117 |
|
|
integrator and NVT seem to be working now. |
2118 |
|
|
|
2119 |
tim |
926 |
2003-06-20 11:49 gezelter |
2120 |
mmeineke |
568 |
|
2121 |
|
|
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
2122 |
|
|
|
2123 |
tim |
926 |
2003-06-19 17:02 mmeineke |
2124 |
mmeineke |
568 |
|
2125 |
|
|
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
2126 |
|
|
forceFields/LJ_FF.frc, forceFields/Makefile, |
2127 |
|
|
forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
2128 |
|
|
libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
2129 |
|
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
2130 |
|
|
libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
2131 |
|
|
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
2132 |
|
|
forcefield names. |
2133 |
|
|
|
2134 |
tim |
926 |
2003-06-19 14:21 mmeineke |
2135 |
mmeineke |
568 |
|
2136 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
2137 |
|
|
finished the basics of the integrator and SimSetup.cpp |
2138 |
|
|
|
2139 |
tim |
926 |
2003-06-19 14:11 mmeineke |
2140 |
mmeineke |
568 |
|
2141 |
|
|
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
2142 |
|
|
up / get it to work with the new Integrator. |
2143 |
|
|
|
2144 |
tim |
926 |
2003-06-18 17:20 mmeineke |
2145 |
mmeineke |
568 |
|
2146 |
|
|
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
2147 |
|
|
output times. |
2148 |
|
|
|
2149 |
tim |
926 |
2003-06-17 16:56 mmeineke |
2150 |
mmeineke |
568 |
|
2151 |
|
|
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
2152 |
|
|
fro the ghost Bend in TraPPE_Ex |
2153 |
|
|
|
2154 |
|
|
some work on the integrator. ( incomplete) |
2155 |
|
|
|
2156 |
tim |
926 |
2003-06-17 16:55 mmeineke |
2157 |
mmeineke |
568 |
|
2158 |
|
|
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
2159 |
|
|
Bend in TraPPE_Ex |
2160 |
|
|
|
2161 |
tim |
926 |
2003-06-04 16:06 mmeineke |
2162 |
mmeineke |
568 |
|
2163 |
|
|
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
2164 |
|
|
constrainB to the Symplectic integrator |
2165 |
|
|
|
2166 |
tim |
926 |
2003-05-30 16:32 mmeineke |
2167 |
mmeineke |
568 |
|
2168 |
|
|
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
2169 |
|
|
the basic integrator. |
2170 |
|
|
|
2171 |
|
|
bilayerSys.cpp altered for building tb3. |
2172 |
|
|
|
2173 |
tim |
926 |
2003-05-30 16:31 mmeineke |
2174 |
mmeineke |
568 |
|
2175 |
|
|
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
2176 |
|
|
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
2177 |
|
|
modifiying Symplectic to become the basic integrator. |
2178 |
|
|
|
2179 |
tim |
926 |
2003-05-30 15:19 mmeineke |
2180 |
mmeineke |
568 |
|
2181 |
|
|
* libmdtools/Integrator.hpp: added some member variables for |
2182 |
|
|
position, velocity, etc. |
2183 |
|
|
|
2184 |
tim |
926 |
2003-05-30 14:07 mmeineke |
2185 |
mmeineke |
568 |
|
2186 |
|
|
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
2187 |
|
|
is now derived from Integrator |
2188 |
|
|
|
2189 |
tim |
926 |
2003-05-20 11:44 mmeineke |
2190 |
mmeineke |
568 |
|
2191 |
|
|
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
2192 |
|
|
|
2193 |
tim |
926 |
2003-05-17 11:57 mmeineke |
2194 |
mmeineke |
568 |
|
2195 |
|
|
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
2196 |
|
|
working |
2197 |
|
|
|
2198 |
tim |
926 |
2003-05-16 16:37 mmeineke |
2199 |
mmeineke |
568 |
|
2200 |
|
|
* utils/bilayerSys.cpp: still working on the bilayer code |
2201 |
|
|
|
2202 |
tim |
926 |
2003-05-16 09:28 mmeineke |
2203 |
mmeineke |
568 |
|
2204 |
|
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
2205 |
|
|
work to overhaul sysbuild. |
2206 |
|
|
|
2207 |
tim |
926 |
2003-05-13 16:23 mmeineke |
2208 |
mmeineke |
568 |
|
2209 |
|
|
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
2210 |
|
|
|
2211 |
tim |
926 |
2003-05-13 15:47 mmeineke |
2212 |
mmeineke |
568 |
|
2213 |
|
|
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
2214 |
|
|
beadLipid/water.mdl: Added bead lipid model to the sample directory |
2215 |
|
|
|
2216 |
tim |
926 |
2003-05-13 15:34 mmeineke |
2217 |
mmeineke |
568 |
|
2218 |
|
|
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
2219 |
|
|
the Trappe extended force field |
2220 |
|
|
|
2221 |
tim |
926 |
2003-05-13 12:01 mmeineke |
2222 |
mmeineke |
568 |
|
2223 |
|
|
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
2224 |
|
|
TraPPe_Ex forceField |
2225 |
|
|
|
2226 |
tim |
926 |
2003-05-09 14:51 mmeineke |
2227 |
mmeineke |
568 |
|
2228 |
|
|
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
2229 |
|
|
there were some duplicate entries |
2230 |
|
|
|
2231 |
|
|
added a two chain lipid to the lipid.mdl in sample |
2232 |
|
|
|
2233 |
tim |
926 |
2003-05-09 14:51 mmeineke |
2234 |
mmeineke |
568 |
|
2235 |
|
|
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
2236 |
|
|
there were some duplicate entries |
2237 |
|
|
|
2238 |
tim |
926 |
2003-05-09 11:56 mmeineke |
2239 |
mmeineke |
568 |
|
2240 |
|
|
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
2241 |
|
|
configure script |
2242 |
|
|
|
2243 |
|
|
added the CH branching group to the TraPPE_Ex fource field |
2244 |
|
|
|
2245 |
tim |
926 |
2003-05-09 11:55 mmeineke |
2246 |
mmeineke |
568 |
|
2247 |
|
|
* ac-tools/configure.in: added the utils subdirectory to the |
2248 |
|
|
configure script |
2249 |
|
|
|
2250 |
tim |
926 |
2003-04-25 11:02 mmeineke |
2251 |
mmeineke |
568 |
|
2252 |
|
|
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
2253 |
|
|
bilayer builder |
2254 |
|
|
|
2255 |
tim |
926 |
2003-04-24 21:00 mmeineke |
2256 |
mmeineke |
568 |
|
2257 |
|
|
* libmdtools/f_verlet_constrained.F90: added a new test for |
2258 |
|
|
constraint failure |
2259 |
|
|
|
2260 |
tim |
926 |
2003-04-17 16:54 mmeineke |
2261 |
mmeineke |
568 |
|
2262 |
|
|
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
2263 |
|
|
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
2264 |
|
|
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
2265 |
|
|
build our systems |
2266 |
|
|
|
2267 |
tim |
926 |
2003-04-16 16:11 mmeineke |
2268 |
mmeineke |
568 |
|
2269 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
2270 |
|
|
|
2271 |
tim |
926 |
2003-04-15 16:47 mmeineke |
2272 |
mmeineke |
568 |
|
2273 |
|
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
2274 |
|
|
and sysBuild both will build now. woot! |
2275 |
|
|
|
2276 |
tim |
926 |
2003-04-15 16:20 mmeineke |
2277 |
mmeineke |
568 |
|
2278 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
2279 |
|
|
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
2280 |
|
|
|
2281 |
|
|
sysBuild still need to write the bass file. |
2282 |
|
|
|
2283 |
|
|
MoLocator.cpp is currently empty |
2284 |
|
|
|
2285 |
tim |
926 |
2003-04-15 15:40 chuckv |
2286 |
mmeineke |
568 |
|
2287 |
|
|
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
2288 |
|
|
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
2289 |
|
|
forceFields/pdu3.eam, forceFields/ptu3.eam, |
2290 |
|
|
libmdtools/ForceFields.hpp: Added eam force files... |
2291 |
|
|
|
2292 |
tim |
926 |
2003-04-15 11:37 chuckv |
2293 |
mmeineke |
568 |
|
2294 |
|
|
* libmdtools/EAM_FF.cpp: More eam work. |
2295 |
|
|
|
2296 |
tim |
926 |
2003-04-14 16:22 mmeineke |
2297 |
mmeineke |
568 |
|
2298 |
|
|
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
2299 |
|
|
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
2300 |
|
|
working on the system builder |
2301 |
|
|
|
2302 |
tim |
926 |
2003-04-14 16:16 chuckv |
2303 |
mmeineke |
568 |
|
2304 |
|
|
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
2305 |
|
|
ordering on NVT calculation in integrators. |
2306 |
|
|
|
2307 |
tim |
926 |
2003-04-14 14:51 mmeineke |
2308 |
mmeineke |
568 |
|
2309 |
|
|
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
2310 |
|
|
obj/placeHolder: working on a system builder |
2311 |
|
|
|
2312 |
tim |
926 |
2003-04-14 14:04 mmeineke |
2313 |
mmeineke |
568 |
|
2314 |
|
|
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
2315 |
|
|
|
2316 |
|
|
added sysBuild to the utils Makefile |
2317 |
|
|
|
2318 |
tim |
926 |
2003-04-14 14:03 mmeineke |
2319 |
mmeineke |
568 |
|
2320 |
|
|
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
2321 |
|
|
Ghost bends to the TraPPE_Ex forceField |
2322 |
|
|
|
2323 |
tim |
926 |
2003-04-14 13:19 chuckv |
2324 |
mmeineke |
568 |
|
2325 |
|
|
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
2326 |
|
|
|
2327 |
tim |
926 |
2003-04-11 13:46 mmeineke |
2328 |
mmeineke |
568 |
|
2329 |
|
|
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
2330 |
|
|
simulation_module.F90: fixed a memory bug in Fortran, where |
2331 |
|
|
molMembershipArray was declared nLocal instead of nGlobal. |
2332 |
|
|
|
2333 |
tim |
926 |
2003-04-11 10:16 gezelter |
2334 |
mmeineke |
568 |
|
2335 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
2336 |
|
|
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
2337 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
2338 |
|
|
for NPT |
2339 |
|
|
|
2340 |
tim |
926 |
2003-04-10 15:08 mmeineke |
2341 |
mmeineke |
568 |
|
2342 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
2343 |
|
|
globalIndex counter to Molecule |
2344 |
|
|
|
2345 |
tim |
926 |
2003-04-10 11:35 gezelter |
2346 |
mmeineke |
568 |
|
2347 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
2348 |
|
|
ConstantStress |
2349 |
|
|
|
2350 |
tim |
926 |
2003-04-10 11:27 mmeineke |
2351 |
mmeineke |
568 |
|
2352 |
|
|
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
2353 |
|
|
caused a miscalculation of nLocal. |
2354 |
|
|
|
2355 |
tim |
926 |
2003-04-10 11:21 mmeineke |
2356 |
mmeineke |
568 |
|
2357 |
|
|
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
2358 |
|
|
do_Forces.F90: fixed a bug in symplectic, where presure was only |
2359 |
|
|
being calculated the first time through. |
2360 |
|
|
|
2361 |
tim |
926 |
2003-04-09 11:20 chuckv |
2362 |
mmeineke |
568 |
|
2363 |
|
|
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
2364 |
|
|
file |
2365 |
|
|
|
2366 |
tim |
926 |
2003-04-09 08:59 gezelter |
2367 |
mmeineke |
568 |
|
2368 |
|
|
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
2369 |
|
|
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
2370 |
|
|
|
2371 |
tim |
926 |
2003-04-08 23:06 gezelter |
2372 |
mmeineke |
568 |
|
2373 |
|
|
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
2374 |
|
|
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
2375 |
|
|
SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
2376 |
|
|
Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
2377 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90, |
2378 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
2379 |
|
|
NVT |
2380 |
|
|
|
2381 |
tim |
926 |
2003-04-08 17:38 chuckv |
2382 |
mmeineke |
568 |
|
2383 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
2384 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
2385 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
2386 |
|
|
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
2387 |
|
|
(kinda)... |
2388 |
|
|
|
2389 |
tim |
926 |
2003-04-08 16:35 gezelter |
2390 |
mmeineke |
568 |
|
2391 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
2392 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
2393 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
2394 |
|
|
|
2395 |
tim |
926 |
2003-04-08 12:16 chuckv |
2396 |
mmeineke |
568 |
|
2397 |
|
|
* libmdtools/: do_Forces.F90, neighborLists.F90, |
2398 |
|
|
simulation_module.F90: Moved expand neighborlist to init_FF. |
2399 |
|
|
|
2400 |
tim |
926 |
2003-04-08 10:20 chuckv |
2401 |
mmeineke |
568 |
|
2402 |
|
|
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
2403 |
|
|
NVT |
2404 |
|
|
|
2405 |
tim |
926 |
2003-04-08 09:39 gezelter |
2406 |
mmeineke |
568 |
|
2407 |
|
|
* libmdtools/Verlet.cpp: fixes for nvt / npt |
2408 |
|
|
|
2409 |
tim |
926 |
2003-04-08 09:34 gezelter |
2410 |
mmeineke |
568 |
|
2411 |
|
|
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
2412 |
|
|
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
2413 |
|
|
|
2414 |
tim |
926 |
2003-04-08 07:50 gezelter |
2415 |
mmeineke |
568 |
|
2416 |
|
|
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
2417 |
|
|
|
2418 |
tim |
926 |
2003-04-08 07:44 gezelter |
2419 |
mmeineke |
568 |
|
2420 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
2421 |
|
|
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
2422 |
|
|
NVT and NPT ensembles |
2423 |
|
|
|
2424 |
tim |
926 |
2003-04-07 16:42 gezelter |
2425 |
mmeineke |
568 |
|
2426 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
2427 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
2428 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
2429 |
|
|
|
2430 |
tim |
926 |
2003-04-07 16:20 mmeineke |
2431 |
mmeineke |
568 |
|
2432 |
|
|
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
2433 |
|
|
portion of SSD. |
2434 |
|
|
|
2435 |
tim |
926 |
2003-04-07 16:16 mmeineke |
2436 |
mmeineke |
568 |
|
2437 |
|
|
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
2438 |
|
|
doing some testing in sticky through Symplectic. |
2439 |
|
|
|
2440 |
tim |
926 |
2003-04-07 15:51 gezelter |
2441 |
mmeineke |
568 |
|
2442 |
|
|
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
2443 |
|
|
|
2444 |
tim |
926 |
2003-04-07 15:50 chuckv |
2445 |
mmeineke |
568 |
|
2446 |
|
|
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
2447 |
|
|
tau and virial. |
2448 |
|
|
|
2449 |
tim |
926 |
2003-04-07 15:06 mmeineke |
2450 |
mmeineke |
568 |
|
2451 |
|
|
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
2452 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
2453 |
|
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
2454 |
|
|
src/Makefile: bug fixes |
2455 |
|
|
|
2456 |
tim |
926 |
2003-04-07 11:56 gezelter |
2457 |
mmeineke |
568 |
|
2458 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
2459 |
|
|
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
2460 |
|
|
Many fixes to add extended system |
2461 |
|
|
|
2462 |
tim |
926 |
2003-04-07 09:30 gezelter |
2463 |
mmeineke |
568 |
|
2464 |
|
|
* src/Makefile: Fixed a bug caused by my experimentation |
2465 |
|
|
|
2466 |
tim |
926 |
2003-04-07 09:30 gezelter |
2467 |
mmeineke |
568 |
|
2468 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
2469 |
|
|
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
2470 |
|
|
Added ExtendedSystem infrastructure for NPT and NVT calculations |
2471 |
|
|
|
2472 |
tim |
926 |
2003-04-07 09:30 gezelter |
2473 |
mmeineke |
568 |
|
2474 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
2475 |
|
|
|
2476 |
|
|
2003-04-04 23:07 gezelter |
2477 |
|
|
|
2478 |
|
|
* src/Makefile: final mods to try a fortran compiler |
2479 |
|
|
|
2480 |
|
|
2003-04-04 22:39 gezelter |
2481 |
|
|
|
2482 |
|
|
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
2483 |
|
|
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
2484 |
|
|
|
2485 |
|
|
2003-04-04 21:56 gezelter |
2486 |
|
|
|
2487 |
|
|
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
2488 |
|
|
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
2489 |
|
|
|
2490 |
|
|
2003-04-04 21:45 gezelter |
2491 |
|
|
|
2492 |
|
|
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
2493 |
|
|
fixes to fortran wrappers |
2494 |
|
|
|
2495 |
|
|
2003-04-04 17:22 chuckv |
2496 |
|
|
|
2497 |
|
|
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
2498 |
|
|
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
2499 |
|
|
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
2500 |
|
|
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
2501 |
|
|
smarter, fortran gets dumber... |
2502 |
|
|
|
2503 |
|
|
2003-04-04 14:57 mmeineke |
2504 |
|
|
|
2505 |
|
|
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
2506 |
|
|
neighborLists.F90: fixed a memory read bug in neighborlist |
2507 |
|
|
|
2508 |
|
|
2003-04-04 14:47 gezelter |
2509 |
|
|
|
2510 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
2511 |
|
|
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
2512 |
|
|
|
2513 |
|
|
2003-04-04 14:16 gezelter |
2514 |
|
|
|
2515 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
2516 |
|
|
SimInfo.hpp: Fixes for ExtendedSystem |
2517 |
|
|
|
2518 |
|
|
2003-04-03 20:57 gezelter |
2519 |
|
|
|
2520 |
|
|
* libmdtools/ExtendedSystem.hpp: Added extended system header |
2521 |
|
|
|
2522 |
|
|
2003-04-03 20:57 gezelter |
2523 |
|
|
|
2524 |
|
|
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
2525 |
|
|
for extended system code |
2526 |
|
|
|
2527 |
|
|
2003-04-03 18:49 gezelter |
2528 |
|
|
|
2529 |
|
|
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
2530 |
|
|
extendedsystem |
2531 |
|
|
|
2532 |
|
|
2003-04-03 17:19 mmeineke |
2533 |
|
|
|
2534 |
|
|
* libmdtools/Molecule.hpp: added some little fixes here and there. |
2535 |
|
|
|
2536 |
|
|
2003-04-03 17:01 mmeineke |
2537 |
|
|
|
2538 |
|
|
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
2539 |
|
|
initialize bug. |
2540 |
|
|
|
2541 |
|
|
2003-04-03 16:12 mmeineke |
2542 |
|
|
|
2543 |
|
|
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
2544 |
|
|
little things like deleteing unused variables and such. |
2545 |
|
|
|
2546 |
|
|
2003-04-03 15:57 mmeineke |
2547 |
|
|
|
2548 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
2549 |
|
|
simError.h also some fixes to Molecule.hpp |
2550 |
|
|
|
2551 |
|
|
2003-04-03 15:57 mmeineke |
2552 |
|
|
|
2553 |
|
|
* libBASS/simError.h: a few fixes to simError.h |
2554 |
|
|
|
2555 |
|
|
2003-04-03 15:21 mmeineke |
2556 |
|
|
|
2557 |
|
|
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
2558 |
|
|
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
2559 |
|
|
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
2560 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
2561 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
2562 |
|
|
src/Makefile, src/oopse.cpp: fixed some small things with |
2563 |
|
|
simError.h |
2564 |
|
|
|
2565 |
|
|
2003-04-03 15:19 gezelter |
2566 |
|
|
|
2567 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
2568 |
|
|
|
2569 |
|
|
2003-04-03 14:58 gezelter |
2570 |
|
|
|
2571 |
|
|
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
2572 |
|
|
now) |
2573 |
|
|
|
2574 |
|
|
2003-04-03 08:42 gezelter |
2575 |
|
|
|
2576 |
|
|
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
2577 |
|
|
Changed Readme, added some files |
2578 |
|
|
|
2579 |
|
|
2003-04-02 17:19 mmeineke |
2580 |
|
|
|
2581 |
|
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
2582 |
|
|
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
2583 |
|
|
dipoles mostly work, but there is a memory leak somewhere. |
2584 |
|
|
|
2585 |
|
|
2003-04-02 10:01 mmeineke |
2586 |
|
|
|
2587 |
|
|
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
2588 |
|
|
the proper atomIdents. |
2589 |
|
|
|
2590 |
|
|
2003-04-01 11:50 chuckv |
2591 |
|
|
|
2592 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
2593 |
|
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
2594 |
|
|
samples/argon/argon.bass: more bug fixes.... |
2595 |
|
|
|
2596 |
|
|
2003-04-01 11:49 mmeineke |
2597 |
|
|
|
2598 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
2599 |
|
|
DumpWriter to be more robust to errors. also added a little |
2600 |
|
|
namespace to InitFromFile to wrap it's helper functions in MPI |
2601 |
|
|
|
2602 |
|
|
2003-03-31 17:09 chuckv |
2603 |
|
|
|
2604 |
|
|
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
2605 |
|
|
not zeroed. |
2606 |
|
|
|
2607 |
|
|
2003-03-31 16:50 chuckv |
2608 |
|
|
|
2609 |
|
|
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
2610 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
2611 |
|
|
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
2612 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
2613 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
2614 |
|
|
samples/alkane/butane.bass: Fixes in MPI force calc and in |
2615 |
|
|
Trappe_Ex parsing. |
2616 |
|
|
|
2617 |
|
|
2003-03-28 17:34 chuckv |
2618 |
|
|
|
2619 |
|
|
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
2620 |
|
|
|
2621 |
|
|
2003-03-28 16:45 chuckv |
2622 |
|
|
|
2623 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
2624 |
|
|
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
2625 |
|
|
routines. |
2626 |
|
|
|
2627 |
|
|
2003-03-28 14:33 mmeineke |
2628 |
|
|
|
2629 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
2630 |
|
|
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
2631 |
|
|
bug where the Excludes were not being created properly |
2632 |
|
|
|
2633 |
|
|
2003-03-28 14:30 chuckv |
2634 |
|
|
|
2635 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
2636 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
2637 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
2638 |
|
|
and debugging mpi read write from file. |
2639 |
|
|
|
2640 |
|
|
2003-03-28 10:28 mmeineke |
2641 |
|
|
|
2642 |
|
|
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
2643 |
|
|
interactions in Trappe |
2644 |
|
|
|
2645 |
|
|
2003-03-27 18:33 chuckv |
2646 |
|
|
|
2647 |
|
|
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
2648 |
|
|
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
2649 |
|
|
|
2650 |
|
|
2003-03-27 17:16 mmeineke |
2651 |
|
|
|
2652 |
|
|
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
2653 |
|
|
excludes were not being initialized |
2654 |
|
|
|
2655 |
|
|
2003-03-27 16:52 mmeineke |
2656 |
|
|
|
2657 |
|
|
* src/Makefile: [no log message] |
2658 |
|
|
|
2659 |
|
|
2003-03-27 16:52 mmeineke |
2660 |
|
|
|
2661 |
|
|
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
2662 |
|
|
|
2663 |
|
|
2003-03-27 16:07 mmeineke |
2664 |
|
|
|
2665 |
|
|
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
2666 |
|
|
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
2667 |
|
|
Verlet.cpp: fixed the compile time bugs, Source builds and links |
2668 |
|
|
|
2669 |
|
|
2003-03-27 15:48 mmeineke |
2670 |
|
|
|
2671 |
|
|
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
2672 |
|
|
more bugs. |
2673 |
|
|
|
2674 |
|
|
2003-03-27 15:40 mmeineke |
2675 |
|
|
|
2676 |
|
|
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
2677 |
|
|
|
2678 |
|
|
2003-03-27 15:39 mmeineke |
2679 |
|
|
|
2680 |
|
|
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
2681 |
|
|
|
2682 |
|
|
2003-03-27 15:36 mmeineke |
2683 |
|
|
|
2684 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
2685 |
|
|
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
2686 |
|
|
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
2687 |
|
|
|
2688 |
|
|
2003-03-27 15:12 mmeineke |
2689 |
|
|
|
2690 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
2691 |
|
|
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
2692 |
|
|
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
2693 |
|
|
to. will now attempt to compile. |
2694 |
|
|
|
2695 |
|
|
2003-03-27 14:21 mmeineke |
2696 |
|
|
|
2697 |
|
|
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
2698 |
|
|
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
2699 |
|
|
updating SimSetup to initialize and use the new MPI division of |
2700 |
|
|
labour, and Molecule class |
2701 |
|
|
|
2702 |
|
|
2003-03-27 12:55 mmeineke |
2703 |
|
|
|
2704 |
|
|
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
2705 |
|
|
use Molecule |
2706 |
|
|
|
2707 |
|
|
2003-03-27 12:32 mmeineke |
2708 |
|
|
|
2709 |
|
|
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
2710 |
|
|
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
2711 |
|
|
converted to the new Molecule model. TraPPE_Ex is currently being |
2712 |
|
|
updated. SimSetups routines are writtten, but not yet called. |
2713 |
|
|
|
2714 |
|
|
2003-03-27 10:07 gezelter |
2715 |
|
|
|
2716 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
2717 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
2718 |
|
|
numbering in MPI |
2719 |
|
|
|
2720 |
|
|
2003-03-27 09:30 mmeineke |
2721 |
|
|
|
2722 |
|
|
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
2723 |
|
|
|
2724 |
|
|
2003-03-26 20:49 gezelter |
2725 |
|
|
|
2726 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
2727 |
|
|
fileio for MPI |
2728 |
|
|
|
2729 |
|
|
2003-03-26 18:14 gezelter |
2730 |
|
|
|
2731 |
|
|
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
2732 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
2733 |
|
|
fixes many bug fixes |
2734 |
|
|
|
2735 |
|
|
2003-03-26 17:24 gezelter |
2736 |
|
|
|
2737 |
|
|
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
2738 |
|
|
sequence of atoms on the other processors. Node 0 now fires |
2739 |
|
|
potatoes at other processors to get them to send french fries back. |
2740 |
|
|
|
2741 |
|
|
2003-03-26 17:02 mmeineke |
2742 |
|
|
|
2743 |
|
|
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
2744 |
|
|
making the molecules is in place. ForceField needs to be updated |
2745 |
|
|
next. |
2746 |
|
|
|
2747 |
|
|
2003-03-26 16:54 mmeineke |
2748 |
|
|
|
2749 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
2750 |
|
|
the "static" bugs in Atom and Exclude |
2751 |
|
|
|
2752 |
|
|
2003-03-26 16:50 mmeineke |
2753 |
|
|
|
2754 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
2755 |
|
|
SimSetup.cpp: still working on the SimSetup routine. also fixed |
2756 |
|
|
some things in Exclude.hpp |
2757 |
|
|
|
2758 |
|
|
2003-03-26 16:24 gezelter |
2759 |
|
|
|
2760 |
|
|
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
2761 |
|
|
|
2762 |
|
|
2003-03-26 16:23 gezelter |
2763 |
|
|
|
2764 |
|
|
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
2765 |
|
|
and Exclude list |
2766 |
|
|
|
2767 |
|
|
2003-03-26 16:04 gezelter |
2768 |
|
|
|
2769 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
2770 |
|
|
delete ranges of atoms |
2771 |
|
|
|
2772 |
|
|
2003-03-26 15:45 mmeineke |
2773 |
|
|
|
2774 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
2775 |
|
|
with static arrays similar to the Atom class |
2776 |
|
|
|
2777 |
|
|
2003-03-26 15:22 mmeineke |
2778 |
|
|
|
2779 |
|
|
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
2780 |
|
|
overhauling the molecule class to contain it's own bonds, bends, |
2781 |
|
|
and torsions. |
2782 |
|
|
|
2783 |
|
|
may god have mercy on my soul. |
2784 |
|
|
|
2785 |
|
|
2003-03-26 14:34 chuckv |
2786 |
|
|
|
2787 |
|
|
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
2788 |
|
|
|
2789 |
|
|
2003-03-26 13:02 gezelter |
2790 |
|
|
|
2791 |
|
|
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
2792 |
|
|
mpiSimulation.hpp: MPI stuff for passing out molecules |
2793 |
|
|
|
2794 |
|
|
2003-03-26 11:12 chuckv |
2795 |
|
|
|
2796 |
|
|
* libmdtools/mpiSimulation.cpp: working on load balancing |
2797 |
|
|
|
2798 |
|
|
2003-03-26 10:37 chuckv |
2799 |
|
|
|
2800 |
|
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
2801 |
|
|
samples/argon/argon.bass: Fixes for Parallel thermalization |
2802 |
|
|
|
2803 |
|
|
2003-03-26 09:55 mmeineke |
2804 |
|
|
|
2805 |
|
|
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
2806 |
|
|
THermo.cpp |
2807 |
|
|
|
2808 |
|
|
2003-03-25 17:54 chuckv |
2809 |
|
|
|
2810 |
|
|
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
2811 |
|
|
of potential energy and temperature. |
2812 |
|
|
|
2813 |
|
|
2003-03-25 09:29 mmeineke |
2814 |
|
|
|
2815 |
tim |
1031 |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
2816 |
|
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
2817 |
mmeineke |
568 |
|
2818 |
|
|
2003-03-25 09:29 mmeineke |
2819 |
|
|
|
2820 |
|
|
* libBASS/MPIobj/dummy: added dummy files to keep the build |
2821 |
|
|
deirectories from being pruned. |
2822 |
|
|
|
2823 |
|
|
2003-03-24 20:07 gezelter |
2824 |
|
|
|
2825 |
tim |
1005 |
* samples/Makefile: moving tests to samples |
2826 |
mmeineke |
568 |
|
2827 |
|
|
2003-03-24 20:06 gezelter |
2828 |
|
|
|
2829 |
tim |
1005 |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
2830 |
|
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
2831 |
|
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
2832 |
|
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
2833 |
|
|
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
2834 |
|
|
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
2835 |
|
|
samples |
2836 |
mmeineke |
568 |
|
2837 |
|
|
2003-03-24 19:51 gezelter |
2838 |
|
|
|
2839 |
|
|
* ac-tools/configure.in: Tests are becoming samples |
2840 |
|
|
|
2841 |
|
|
2003-03-24 19:46 gezelter |
2842 |
|
|
|
2843 |
tim |
1005 |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
2844 |
mmeineke |
568 |
|
2845 |
|
|
2003-03-24 16:55 gezelter |
2846 |
|
|
|
2847 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, |
2848 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, |
2849 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, |
2850 |
|
|
libmdtools/calc_reaction_field.F90, |
2851 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
2852 |
|
|
libmdtools/simulation_module.F90: electrostatic changes for dipole |
2853 |
|
|
/ RF separation |
2854 |
|
|
|
2855 |
|
|
2003-03-24 13:33 mmeineke |
2856 |
|
|
|
2857 |
|
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
2858 |
|
|
do_Forces.F90: little bug fixes here and there |
2859 |
|
|
|
2860 |
|
|
2003-03-24 10:26 mmeineke |
2861 |
|
|
|
2862 |
|
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
2863 |
|
|
where short range interactions were not being calculated. |
2864 |
|
|
|
2865 |
|
|
removed some debug print statements |
2866 |
|
|
|
2867 |
|
|
2003-03-21 17:11 chuckv |
2868 |
|
|
|
2869 |
|
|
* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, |
2870 |
|
|
do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: |
2871 |
|
|
various write statements for debugging |
2872 |
|
|
|
2873 |
|
|
2003-03-21 16:26 chuckv |
2874 |
|
|
|
2875 |
|
|
* forceFields/Makefile: added links to the makefile in forceFields |
2876 |
|
|
|
2877 |
|
|
2003-03-21 15:52 gezelter |
2878 |
|
|
|
2879 |
|
|
* ac-tools/Make.conf.in, ac-tools/configure.in, |
2880 |
|
|
libmdtools/Makefile: Fixed F_MACH_DEP bug |
2881 |
|
|
|
2882 |
|
|
2003-03-21 15:37 gezelter |
2883 |
|
|
|
2884 |
|
|
* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, |
2885 |
|
|
ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, |
2886 |
|
|
libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, |
2887 |
|
|
src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, |
2888 |
|
|
autoconf fixes |
2889 |
|
|
|
2890 |
gezelter |
385 |
2003-03-21 14:58 gezelter |
2891 |
mmeineke |
377 |
|
2892 |
gezelter |
385 |
* LICENSE: Added license file |
2893 |
|
|
|
2894 |
|
|
2003-03-21 14:55 gezelter |
2895 |
|
|
|
2896 |
|
|
* forceFields/Makefile: Fixed makefile |
2897 |
|
|
|
2898 |
|
|
2003-03-21 14:49 gezelter |
2899 |
|
|
|
2900 |
|
|
* forceFields/Makefile: Makefile for forceFields |
2901 |
|
|
|
2902 |
|
|
2003-03-21 14:42 gezelter |
2903 |
|
|
|
2904 |
|
|
* README: Readme changes |
2905 |
|
|
|
2906 |
|
|
2003-03-21 12:52 mmeineke |
2907 |
|
|
|
2908 |
|
|
* src/Makefile: [no log message] |
2909 |
|
|
|
2910 |
|
|
2003-03-21 12:52 mmeineke |
2911 |
|
|
|
2912 |
|
|
* libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends |
2913 |
|
|
|
2914 |
|
|
2003-03-21 12:42 mmeineke |
2915 |
|
|
|
2916 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
2917 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
2918 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
2919 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
2920 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
2921 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
2922 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
2923 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
2924 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
2925 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
2926 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
2927 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
2928 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
2929 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
2930 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
2931 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
2932 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
2933 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
2934 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
2935 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
2936 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
2937 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
2938 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
2939 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
2940 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
2941 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
2942 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
2943 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
2944 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
2945 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
2946 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
2947 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
2948 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
2949 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
2950 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2951 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
2952 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
2953 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
2954 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
2955 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
2956 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
2957 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
2958 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
2959 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
2960 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
2961 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
2962 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
2963 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
2964 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
2965 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
2966 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
2967 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
2968 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
2969 |
tim |
1118 |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
2970 |
|
|
Tree |
2971 |
gezelter |
385 |
|
2972 |
|
|
2003-03-21 12:42 mmeineke |
2973 |
|
|
|
2974 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
2975 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
2976 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
2977 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
2978 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
2979 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
2980 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
2981 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
2982 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
2983 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
2984 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
2985 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
2986 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
2987 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
2988 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
2989 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
2990 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
2991 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
2992 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
2993 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
2994 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
2995 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
2996 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
2997 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
2998 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
2999 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
3000 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
3001 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
3002 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
3003 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
3004 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
3005 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
3006 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
3007 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
3008 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
3009 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
3010 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
3011 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
3012 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
3013 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
3014 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
3015 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
3016 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
3017 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
3018 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
3019 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
3020 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
3021 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
3022 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
3023 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
3024 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3025 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3026 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3027 |
tim |
1118 |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3028 |
|
|
revision |
3029 |
gezelter |
385 |
|