| 1 |
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2004-10-06 16:22 gezelter |
| 2 |
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| 3 |
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* configure, ac-tools/configure.in, ac-tools/fortran90.m4: cleaning |
| 4 |
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up build process |
| 5 |
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|
| 6 |
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2004-10-06 14:51 gezelter |
| 7 |
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|
| 8 |
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* LICENSE, MPIobj/dummy: Cleaning up a bit |
| 9 |
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| 10 |
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2004-10-01 16:22 gezelter |
| 11 |
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| 12 |
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* Makefile, ac-tools/aclocal.m4: A few minor build changes |
| 13 |
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|
| 14 |
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2004-09-29 12:57 gezelter |
| 15 |
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| 16 |
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* configure, ac-tools/configure.in: updates |
| 17 |
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| 18 |
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2004-09-29 12:46 tim |
| 19 |
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| 20 |
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* Makefile: If makefile does not exist, print error message |
| 21 |
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| 22 |
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2004-09-29 10:58 gezelter |
| 23 |
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| 24 |
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* Makefile: still working on build process |
| 25 |
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| 26 |
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2004-09-28 17:14 gezelter |
| 27 |
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* Makefile, configure, ac-tools/configure.in: starting a configure |
| 29 |
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version |
| 30 |
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| 31 |
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2004-09-28 15:43 tim |
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* Makefile: [no log message] |
| 34 |
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| 35 |
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2004-09-23 23:16 gezelter |
| 36 |
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| 37 |
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* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 38 |
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ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 39 |
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ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 40 |
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ac-tools/install-sh, ac-tools/shtool: Import of OOPSE v. 2.0 |
| 41 |
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| 42 |
< |
2004-09-23 23:16 gezelter |
| 43 |
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| 44 |
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* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 45 |
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ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 46 |
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ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 47 |
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ac-tools/install-sh, ac-tools/shtool: Initial revision |
| 1 |
> |
2004-11-24 12:42 tim |
| 2 |
> |
|
| 3 |
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* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
| 4 |
> |
brains/DataStorage.hpp, brains/SimCreator.cpp, |
| 5 |
> |
brains/SimCreator.hpp, integrators/Integrator.hpp, |
| 6 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 7 |
> |
primitives/DirectionalAtom.cpp: add SetForceManager method to |
| 8 |
> |
integrator |
| 9 |
> |
|
| 10 |
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2004-11-23 18:12 tim |
| 11 |
> |
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| 12 |
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* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
| 13 |
> |
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
| 14 |
> |
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
| 15 |
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integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, |
| 16 |
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integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, |
| 17 |
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integrators/NVT.hpp, integrators/Velocitizer.cpp, |
| 18 |
> |
integrators/VelocityVerletIntegrator.cpp, |
| 19 |
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integrators/VelocityVerletIntegrator.hpp, |
| 20 |
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types/UreyBradleyBendType.hpp: refactory NPT integrator |
| 21 |
> |
|
| 22 |
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2004-11-23 17:50 chrisfen |
| 23 |
> |
|
| 24 |
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* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
| 25 |
> |
Restraints should work in parallel now |
| 26 |
> |
|
| 27 |
> |
2004-11-23 17:48 chrisfen |
| 28 |
> |
|
| 29 |
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* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 30 |
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brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
| 31 |
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integrators/Integrator.cpp, integrators/Integrator.hpp, |
| 32 |
> |
io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, |
| 33 |
> |
io/RestraintReader.cpp, io/RestraintWriter.cpp, |
| 34 |
> |
restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
| 35 |
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to restraints |
| 36 |
> |
|
| 37 |
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2004-11-23 17:47 chrisfen |
| 38 |
> |
|
| 39 |
> |
* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
| 40 |
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return to the original on next commit |
| 41 |
> |
|
| 42 |
> |
2004-11-23 12:53 tim |
| 43 |
> |
|
| 44 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 45 |
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UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 46 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
| 47 |
> |
io/ChargeAtomTypesSectionParser.cpp, |
| 48 |
> |
io/DirectionalAtomTypesSectionParser.hpp, |
| 49 |
> |
io/EAMAtomTypesSectionParser.cpp, |
| 50 |
> |
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 51 |
> |
io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
| 52 |
> |
io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
| 53 |
> |
utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
| 54 |
> |
|
| 55 |
> |
2004-11-23 12:53 tim |
| 56 |
> |
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| 57 |
> |
* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
| 58 |
> |
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
| 59 |
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branch new_design. |
| 60 |
> |
|
| 61 |
> |
2004-11-23 12:53 tim |
| 62 |
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| 63 |
> |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
| 64 |
> |
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
| 65 |
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branch new_design. |
| 66 |
> |
|
| 67 |
> |
2004-11-23 01:03 tim |
| 68 |
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| 69 |
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* src/: io/EAMAtomTypesSectionParser.cpp, |
| 70 |
> |
io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
| 71 |
> |
types/AtomType.hpp, types/DirectionalAtomType.cpp, |
| 72 |
> |
types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
| 73 |
> |
|
| 74 |
> |
2004-11-23 01:03 tim |
| 75 |
> |
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| 76 |
> |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
| 77 |
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was initially added on branch new_design. |
| 78 |
> |
|
| 79 |
> |
2004-11-23 01:03 tim |
| 80 |
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| 81 |
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* src/io/EAMAtomTypesSectionParser.hpp: file |
| 82 |
> |
EAMAtomTypesSectionParser.hpp was initially added on branch |
| 83 |
> |
new_design. |
| 84 |
> |
|
| 85 |
> |
2004-11-23 01:03 tim |
| 86 |
> |
|
| 87 |
> |
* src/io/EAMAtomTypesSectionParser.cpp: file |
| 88 |
> |
EAMAtomTypesSectionParser.cpp was initially added on branch |
| 89 |
> |
new_design. |
| 90 |
> |
|
| 91 |
> |
2004-11-22 23:35 tim |
| 92 |
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| 93 |
> |
* src/io/TorsionTypesSectionParser.hpp: file |
| 94 |
> |
TorsionTypesSectionParser.hpp was initially added on branch |
| 95 |
> |
new_design. |
| 96 |
> |
|
| 97 |
> |
2004-11-22 23:35 tim |
| 98 |
> |
|
| 99 |
> |
* src/io/BendTypesSectionParser.hpp: file |
| 100 |
> |
BendTypesSectionParser.hpp was initially added on branch |
| 101 |
> |
new_design. |
| 102 |
> |
|
| 103 |
> |
2004-11-22 23:35 tim |
| 104 |
> |
|
| 105 |
> |
* src/io/BondTypesSectionParser.hpp: file |
| 106 |
> |
BondTypesSectionParser.hpp was initially added on branch |
| 107 |
> |
new_design. |
| 108 |
> |
|
| 109 |
> |
2004-11-22 23:35 tim |
| 110 |
> |
|
| 111 |
> |
* src/io/BondTypesSectionParser.cpp: file |
| 112 |
> |
BondTypesSectionParser.cpp was initially added on branch |
| 113 |
> |
new_design. |
| 114 |
> |
|
| 115 |
> |
2004-11-22 23:35 tim |
| 116 |
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|
| 117 |
> |
* src/io/TorsionTypesSectionParser.cpp: file |
| 118 |
> |
TorsionTypesSectionParser.cpp was initially added on branch |
| 119 |
> |
new_design. |
| 120 |
> |
|
| 121 |
> |
2004-11-22 23:35 tim |
| 122 |
> |
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| 123 |
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* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
| 124 |
> |
BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
| 125 |
> |
TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add |
| 126 |
> |
BondTypesSectionParser, BendTypesSectionParser and |
| 127 |
> |
TorsionTypeSectionParser |
| 128 |
> |
|
| 129 |
> |
2004-11-22 23:35 tim |
| 130 |
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|
| 131 |
> |
* src/io/BendTypesSectionParser.cpp: file |
| 132 |
> |
BendTypesSectionParser.cpp was initially added on branch |
| 133 |
> |
new_design. |
| 134 |
> |
|
| 135 |
> |
2004-11-22 18:04 tim |
| 136 |
> |
|
| 137 |
> |
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
| 138 |
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DUFF and EAM |
| 139 |
> |
|
| 140 |
> |
2004-11-22 18:02 tim |
| 141 |
> |
|
| 142 |
> |
* src/io/: DirectionalAtomTypesParser.hpp, |
| 143 |
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DirectionalAtomTypesSectionParser.hpp: adding section parsers |
| 144 |
> |
|
| 145 |
> |
2004-11-22 18:02 tim |
| 146 |
> |
|
| 147 |
> |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
| 148 |
> |
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
| 149 |
> |
new_design. |
| 150 |
> |
|
| 151 |
> |
2004-11-22 15:55 tim |
| 152 |
> |
|
| 153 |
> |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
| 154 |
> |
DipoleAtomTypesSectionParser.hpp was initially added on branch |
| 155 |
> |
new_design. |
| 156 |
> |
|
| 157 |
> |
2004-11-22 15:55 tim |
| 158 |
> |
|
| 159 |
> |
* src/io/AtomTypesSectionParser.hpp: file |
| 160 |
> |
AtomTypesSectionParser.hpp was initially added on branch |
| 161 |
> |
new_design. |
| 162 |
> |
|
| 163 |
> |
2004-11-22 15:55 tim |
| 164 |
> |
|
| 165 |
> |
* src/io/HarmonicBondTypesSectionParser.hpp: file |
| 166 |
> |
HarmonicBondTypesSectionParser.hpp was initially added on branch |
| 167 |
> |
new_design. |
| 168 |
> |
|
| 169 |
> |
2004-11-22 15:55 tim |
| 170 |
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|
| 171 |
> |
* src/io/StickyAtomTypesSectionParser.cpp: file |
| 172 |
> |
StickyAtomTypesSectionParser.cpp was initially added on branch |
| 173 |
> |
new_design. |
| 174 |
> |
|
| 175 |
> |
2004-11-22 15:55 tim |
| 176 |
> |
|
| 177 |
> |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
| 178 |
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LennardJonesAtomTypesSectionParser.hpp was initially added on |
| 179 |
> |
branch new_design. |
| 180 |
> |
|
| 181 |
> |
2004-11-22 15:55 tim |
| 182 |
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|
| 183 |
> |
* src/io/HarmonicBondTypesSectionParser.cpp: file |
| 184 |
> |
HarmonicBondTypesSectionParser.cpp was initially added on branch |
| 185 |
> |
new_design. |
| 186 |
> |
|
| 187 |
> |
2004-11-22 15:55 tim |
| 188 |
> |
|
| 189 |
> |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
| 190 |
> |
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
| 191 |
> |
new_design. |
| 192 |
> |
|
| 193 |
> |
2004-11-22 15:55 tim |
| 194 |
> |
|
| 195 |
> |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
| 196 |
> |
was initially added on branch new_design. |
| 197 |
> |
|
| 198 |
> |
2004-11-22 15:55 tim |
| 199 |
> |
|
| 200 |
> |
* src/io/AtomTypesSectionParser.cpp: file |
| 201 |
> |
AtomTypesSectionParser.cpp was initially added on branch |
| 202 |
> |
new_design. |
| 203 |
> |
|
| 204 |
> |
2004-11-22 15:55 tim |
| 205 |
> |
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| 206 |
> |
* src/io/ChargeAtomTypesSectionParser.cpp: file |
| 207 |
> |
ChargeAtomTypesSectionParser.cpp was initially added on branch |
| 208 |
> |
new_design. |
| 209 |
> |
|
| 210 |
> |
2004-11-22 15:55 tim |
| 211 |
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| 212 |
> |
* src/io/DipoleAtomTypesSectionParser.cpp: file |
| 213 |
> |
DipoleAtomTypesSectionParser.cpp was initially added on branch |
| 214 |
> |
new_design. |
| 215 |
> |
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| 216 |
> |
2004-11-22 15:55 tim |
| 217 |
> |
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| 218 |
> |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
| 219 |
> |
LennardJonesAtomTypesSectionParser.cpp was initially added on |
| 220 |
> |
branch new_design. |
| 221 |
> |
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| 222 |
> |
2004-11-22 15:55 tim |
| 223 |
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| 224 |
> |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
| 225 |
> |
ChargeAtomTypesSectionParser.hpp was initially added on branch |
| 226 |
> |
new_design. |
| 227 |
> |
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| 228 |
> |
2004-11-22 15:55 tim |
| 229 |
> |
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| 230 |
> |
* src/io/StickyAtomTypesSectionParser.hpp: file |
| 231 |
> |
StickyAtomTypesSectionParser.hpp was initially added on branch |
| 232 |
> |
new_design. |
| 233 |
> |
|
| 234 |
> |
2004-11-22 15:55 tim |
| 235 |
> |
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| 236 |
> |
* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
| 237 |
> |
added on branch new_design. |
| 238 |
> |
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| 239 |
> |
2004-11-22 15:55 tim |
| 240 |
> |
|
| 241 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
| 242 |
> |
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
| 243 |
> |
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
| 244 |
> |
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
| 245 |
> |
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 246 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
| 247 |
> |
io/DipoleAtomTypesSectionParser.cpp, |
| 248 |
> |
io/DipoleAtomTypesSectionParser.hpp, |
| 249 |
> |
io/DirectionalAtomTypesParser.hpp, |
| 250 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
| 251 |
> |
io/HarmonicBondTypesSectionParser.cpp, |
| 252 |
> |
io/HarmonicBondTypesSectionParser.hpp, |
| 253 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, |
| 254 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
| 255 |
> |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
| 256 |
> |
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
| 257 |
> |
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
| 258 |
> |
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
| 259 |
> |
utils/GenericData.hpp: adding section parsers |
| 260 |
> |
|
| 261 |
> |
2004-11-22 15:55 tim |
| 262 |
> |
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| 263 |
> |
* src/io/DirectionalAtomTypesParser.hpp: file |
| 264 |
> |
DirectionalAtomTypesParser.hpp was initially added on branch |
| 265 |
> |
new_design. |
| 266 |
> |
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| 267 |
> |
2004-11-22 15:55 tim |
| 268 |
> |
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| 269 |
> |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
| 270 |
> |
was initially added on branch new_design. |
| 271 |
> |
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| 272 |
> |
2004-11-22 15:55 tim |
| 273 |
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| 274 |
> |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
| 275 |
> |
added on branch new_design. |
| 276 |
> |
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| 277 |
> |
2004-11-19 17:12 tim |
| 278 |
> |
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| 279 |
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* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
| 280 |
> |
added on branch new_design. |
| 281 |
> |
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| 282 |
> |
2004-11-19 17:12 tim |
| 283 |
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| 284 |
> |
* src/: brains/SimState.cpp, brains/SimState.hpp, |
| 285 |
> |
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
| 286 |
> |
types/FixedBondType.hpp: remove more useless files |
| 287 |
> |
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| 288 |
> |
2004-11-19 16:47 tim |
| 289 |
> |
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| 290 |
> |
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
| 291 |
> |
integrators/Integrator.cpp, applications/Makedepend: remove more |
| 292 |
> |
useless files |
| 293 |
> |
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| 294 |
> |
2004-11-19 16:38 tim |
| 295 |
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| 296 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 297 |
> |
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
| 298 |
> |
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
| 299 |
> |
integrators/NVT.hpp: refactory integrator |
| 300 |
> |
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| 301 |
> |
2004-11-19 16:38 tim |
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> |
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| 303 |
> |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
| 304 |
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branch new_design. |
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| 306 |
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2004-11-19 16:38 tim |
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* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
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branch new_design. |
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| 311 |
> |
2004-11-19 16:38 tim |
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* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
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branch new_design. |
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2004-11-19 16:38 tim |
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* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
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on branch new_design. |
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| 321 |
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2004-11-19 16:38 tim |
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* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
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branch new_design. |
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| 326 |
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2004-11-19 15:37 tim |
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* forceFields/newDUFF.frc: new DUFF forcefield |
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| 330 |
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2004-11-19 15:23 tim |
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| 332 |
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* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
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branch new_design. |
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2004-11-19 15:23 tim |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
| 338 |
> |
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
| 339 |
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utils/TypeContainer.hpp: add EAM |
| 340 |
> |
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| 341 |
> |
2004-11-19 15:23 tim |
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* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
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branch new_design. |
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2004-11-19 13:02 tim |
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| 348 |
> |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
| 349 |
> |
error checking |
| 350 |
> |
|
| 351 |
> |
2004-11-19 12:56 tim |
| 352 |
> |
|
| 353 |
> |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
| 354 |
> |
was initially added on branch new_design. |
| 355 |
> |
|
| 356 |
> |
2004-11-19 12:56 tim |
| 357 |
> |
|
| 358 |
> |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
| 359 |
> |
was initially added on branch new_design. |
| 360 |
> |
|
| 361 |
> |
2004-11-19 12:56 tim |
| 362 |
> |
|
| 363 |
> |
* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
| 364 |
> |
added on branch new_design. |
| 365 |
> |
|
| 366 |
> |
2004-11-19 12:56 tim |
| 367 |
> |
|
| 368 |
> |
* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
| 369 |
> |
UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
| 370 |
> |
UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, |
| 371 |
> |
integrators/IntegratorFactory.cpp, |
| 372 |
> |
integrators/IntegratorFactory.hpp, integrators/NVE.hpp, |
| 373 |
> |
integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, |
| 374 |
> |
utils/StringTokenizer.cpp: DUFF is almost done except error |
| 375 |
> |
checking |
| 376 |
> |
|
| 377 |
> |
2004-11-18 19:11 tim |
| 378 |
> |
|
| 379 |
> |
* src/UseTheForce/DUFF.cpp: adding DUFF parser |
| 380 |
> |
|
| 381 |
> |
2004-11-18 18:26 tim |
| 382 |
> |
|
| 383 |
> |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
| 384 |
> |
initially added on branch new_design. |
| 385 |
> |
|
| 386 |
> |
2004-11-18 18:26 tim |
| 387 |
> |
|
| 388 |
> |
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
| 389 |
> |
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
| 390 |
> |
integrators/VelocityVerletIntegrator.cpp, |
| 391 |
> |
integrators/VelocityVerletIntegrator.hpp, |
| 392 |
> |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 393 |
> |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
| 394 |
> |
types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, |
| 395 |
> |
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
| 396 |
> |
DUFF parser |
| 397 |
> |
|
| 398 |
> |
2004-11-18 16:42 tim |
| 399 |
> |
|
| 400 |
> |
* forceFields/newDUFF.frc: adding new format DUFF force field |
| 401 |
> |
|
| 402 |
> |
2004-11-18 10:57 chrisfen |
| 403 |
> |
|
| 404 |
> |
* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
| 405 |
> |
slowed down the force loop |
| 406 |
> |
|
| 407 |
> |
2004-11-18 00:42 tim |
| 408 |
> |
|
| 409 |
> |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
| 410 |
> |
initially added on branch new_design. |
| 411 |
> |
|
| 412 |
> |
2004-11-18 00:42 tim |
| 413 |
> |
|
| 414 |
> |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
| 415 |
> |
initially added on branch new_design. |
| 416 |
> |
|
| 417 |
> |
2004-11-18 00:42 tim |
| 418 |
> |
|
| 419 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
| 420 |
> |
primitives/Bend.cpp, utils/NumericConstant.cpp, |
| 421 |
> |
utils/NumericConstant.hpp: Adding NumericConstant class |
| 422 |
> |
|
| 423 |
> |
2004-11-17 23:16 tim |
| 424 |
> |
|
| 425 |
> |
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
| 426 |
> |
UseTheForce/ForceFields.hpp: remove more junk files |
| 427 |
> |
|
| 428 |
> |
2004-11-17 23:12 tim |
| 429 |
> |
|
| 430 |
> |
* src/: brains/ForceFields.cpp, brains/SimSetup.cpp, |
| 431 |
> |
brains/SimSetup.hpp, constraints/AbstractClasses.hpp, |
| 432 |
> |
integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, |
| 433 |
> |
primitives/AbstractClasses.hpp, primitives/Bond.cpp, |
| 434 |
> |
primitives/BondExtensions.cpp, primitives/SRI.hpp, |
| 435 |
> |
primitives/TorsionExtensions.cpp: remove some junk files |
| 436 |
> |
|
| 437 |
> |
2004-11-17 23:07 tim |
| 438 |
> |
|
| 439 |
> |
* src/primitives/BendExtensions.cpp: remove some junk files |
| 440 |
> |
|
| 441 |
> |
2004-11-17 23:04 tim |
| 442 |
> |
|
| 443 |
> |
* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, |
| 444 |
> |
QuadraticBondType.hpp: refine QudraticBond |
| 445 |
> |
|
| 446 |
> |
2004-11-17 22:57 tim |
| 447 |
> |
|
| 448 |
> |
* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp |
| 449 |
> |
|
| 450 |
> |
2004-11-17 22:57 tim |
| 451 |
> |
|
| 452 |
> |
* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was |
| 453 |
> |
initially added on branch new_design. |
| 454 |
> |
|
| 455 |
> |
2004-11-17 16:47 tim |
| 456 |
> |
|
| 457 |
> |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
| 458 |
> |
was initially added on branch new_design. |
| 459 |
> |
|
| 460 |
> |
2004-11-17 16:47 tim |
| 461 |
> |
|
| 462 |
> |
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
| 463 |
> |
added on branch new_design. |
| 464 |
> |
|
| 465 |
> |
2004-11-17 16:47 tim |
| 466 |
> |
|
| 467 |
> |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
| 468 |
> |
added on branch new_design. |
| 469 |
> |
|
| 470 |
> |
2004-11-17 16:47 tim |
| 471 |
> |
|
| 472 |
> |
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
| 473 |
> |
initially added on branch new_design. |
| 474 |
> |
|
| 475 |
> |
2004-11-17 16:47 tim |
| 476 |
> |
|
| 477 |
> |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
| 478 |
> |
initially added on branch new_design. |
| 479 |
> |
|
| 480 |
> |
2004-11-17 16:47 tim |
| 481 |
> |
|
| 482 |
> |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
| 483 |
> |
initially added on branch new_design. |
| 484 |
> |
|
| 485 |
> |
2004-11-17 16:47 tim |
| 486 |
> |
|
| 487 |
> |
* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially |
| 488 |
> |
added on branch new_design. |
| 489 |
> |
|
| 490 |
> |
2004-11-17 16:47 tim |
| 491 |
> |
|
| 492 |
> |
* src/: math/ChebyshevPolynomials.cpp, |
| 493 |
> |
math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, |
| 494 |
> |
primitives/Bend.hpp, primitives/GhostBend.cpp, |
| 495 |
> |
primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, |
| 496 |
> |
primitives/UreyBradleyBend.hpp, types/BondType.hpp, |
| 497 |
> |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
| 498 |
> |
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
| 499 |
> |
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
| 500 |
> |
UreyBradleyBend and GhostBend |
| 501 |
> |
|
| 502 |
> |
2004-11-17 13:58 tim |
| 503 |
> |
|
| 504 |
> |
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
| 505 |
> |
was initially added on branch new_design. |
| 506 |
> |
|
| 507 |
> |
2004-11-17 13:58 tim |
| 508 |
> |
|
| 509 |
> |
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
| 510 |
> |
was initially added on branch new_design. |
| 511 |
> |
|
| 512 |
> |
2004-11-17 13:58 tim |
| 513 |
> |
|
| 514 |
> |
* src/: math/ChebyshevPolynomials.cpp, |
| 515 |
> |
math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, |
| 516 |
> |
primitives/Bond.hpp, types/CharmmTorsionType.hpp, |
| 517 |
> |
types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, |
| 518 |
> |
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
| 519 |
> |
stuff and Chebyshev Polynomial |
| 520 |
> |
|
| 521 |
> |
2004-11-17 13:58 tim |
| 522 |
> |
|
| 523 |
> |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
| 524 |
> |
initially added on branch new_design. |
| 525 |
> |
|
| 526 |
> |
2004-11-17 01:37 tim |
| 527 |
> |
|
| 528 |
> |
* src/types/PolynomialTorsionType.hpp: file |
| 529 |
> |
PolynomialTorsionType.hpp was initially added on branch new_design. |
| 530 |
> |
|
| 531 |
> |
2004-11-17 01:37 tim |
| 532 |
> |
|
| 533 |
> |
* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was |
| 534 |
> |
initially added on branch new_design. |
| 535 |
> |
|
| 536 |
> |
2004-11-17 01:37 tim |
| 537 |
> |
|
| 538 |
> |
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
| 539 |
> |
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
| 540 |
> |
types/BondType.hpp, types/CharmmTorsionType.cpp, |
| 541 |
> |
types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, |
| 542 |
> |
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
| 543 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 544 |
> |
types/PolynomialTorsionType.hpp, types/TorsionType.hpp, |
| 545 |
> |
utils/StringTokenizer.hpp: add PolynomialBondType, |
| 546 |
> |
PolynomialBendType, PolynomialTorsionType, HarmonicBendType and |
| 547 |
> |
CharmmTorsionType. Need to refine the design and add document for |
| 548 |
> |
them |
| 549 |
> |
|
| 550 |
> |
2004-11-17 01:37 tim |
| 551 |
> |
|
| 552 |
> |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
| 553 |
> |
initially added on branch new_design. |
| 554 |
> |
|
| 555 |
> |
2004-11-17 01:37 tim |
| 556 |
> |
|
| 557 |
> |
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
| 558 |
> |
initially added on branch new_design. |
| 559 |
> |
|
| 560 |
> |
2004-11-17 01:37 tim |
| 561 |
> |
|
| 562 |
> |
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
| 563 |
> |
initially added on branch new_design. |
| 564 |
> |
|
| 565 |
> |
2004-11-16 20:11 tim |
| 566 |
> |
|
| 567 |
> |
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
| 568 |
> |
TorsionType.hpp: add PolynomialBondType |
| 569 |
> |
|
| 570 |
> |
2004-11-16 20:11 tim |
| 571 |
> |
|
| 572 |
> |
* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was |
| 573 |
> |
initially added on branch new_design. |
| 574 |
> |
|
| 575 |
> |
2004-11-16 18:20 tim |
| 576 |
> |
|
| 577 |
> |
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
| 578 |
> |
on branch new_design. |
| 579 |
> |
|
| 580 |
> |
2004-11-16 18:20 tim |
| 581 |
> |
|
| 582 |
> |
* src/math/Polynomial.hpp: Adding Polynomial class |
| 583 |
> |
|
| 584 |
> |
2004-11-16 17:04 gezelter |
| 585 |
> |
|
| 586 |
> |
* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially |
| 587 |
> |
added on branch new_design. |
| 588 |
> |
|
| 589 |
> |
2004-11-16 17:04 gezelter |
| 590 |
> |
|
| 591 |
> |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
| 592 |
> |
initially added on branch new_design. |
| 593 |
> |
|
| 594 |
> |
2004-11-16 17:04 gezelter |
| 595 |
> |
|
| 596 |
> |
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
| 597 |
> |
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
| 598 |
> |
|
| 599 |
> |
2004-11-16 15:36 tim |
| 600 |
> |
|
| 601 |
> |
* src/: primitives/Bend.cpp, primitives/Bend.hpp, |
| 602 |
> |
primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, |
| 603 |
> |
types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and |
| 604 |
> |
TorsionType |
| 605 |
> |
|
| 606 |
> |
2004-11-15 21:07 tim |
| 607 |
> |
|
| 608 |
> |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
| 609 |
> |
branch new_design. |
| 610 |
> |
|
| 611 |
> |
2004-11-15 21:07 tim |
| 612 |
> |
|
| 613 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 614 |
> |
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
| 615 |
> |
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
| 616 |
> |
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
| 617 |
> |
|
| 618 |
> |
2004-11-15 18:00 tim |
| 619 |
> |
|
| 620 |
> |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 621 |
> |
UseTheForce/ForceFieldFactory.cpp, |
| 622 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
| 623 |
> |
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
| 624 |
> |
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
| 625 |
> |
|
| 626 |
> |
2004-11-15 18:00 tim |
| 627 |
> |
|
| 628 |
> |
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
| 629 |
> |
was initially added on branch new_design. |
| 630 |
> |
|
| 631 |
> |
2004-11-15 18:00 tim |
| 632 |
> |
|
| 633 |
> |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
| 634 |
> |
was initially added on branch new_design. |
| 635 |
> |
|
| 636 |
> |
2004-11-15 18:00 tim |
| 637 |
> |
|
| 638 |
> |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
| 639 |
> |
branch new_design. |
| 640 |
> |
|
| 641 |
> |
2004-11-15 13:02 tim |
| 642 |
> |
|
| 643 |
> |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
| 644 |
> |
initially added on branch new_design. |
| 645 |
> |
|
| 646 |
> |
2004-11-15 13:02 tim |
| 647 |
> |
|
| 648 |
> |
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
| 649 |
> |
branch new_design. |
| 650 |
> |
|
| 651 |
> |
2004-11-15 13:02 tim |
| 652 |
> |
|
| 653 |
> |
* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on |
| 654 |
> |
branch new_design. |
| 655 |
> |
|
| 656 |
> |
2004-11-15 13:02 tim |
| 657 |
> |
|
| 658 |
> |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 659 |
> |
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
| 660 |
> |
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
| 661 |
> |
io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, |
| 662 |
> |
DumpWriter.Next Step is LJFF and integrators |
| 663 |
> |
|
| 664 |
> |
2004-11-13 00:08 tim |
| 665 |
> |
|
| 666 |
> |
* src/: brains/ForceManager.cpp, brains/ForceManager.hpp, |
| 667 |
> |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 668 |
> |
brains/SimInfo.hpp, primitives/Molecule.cpp, |
| 669 |
> |
primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, |
| 670 |
> |
refactory, refactory |
| 671 |
> |
|
| 672 |
> |
2004-11-12 17:43 tim |
| 673 |
> |
|
| 674 |
> |
* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, |
| 675 |
> |
StringTokenizer.cpp: bug fix in hasMoreTokens |
| 676 |
> |
|
| 677 |
> |
2004-11-12 17:28 tim |
| 678 |
> |
|
| 679 |
> |
* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was |
| 680 |
> |
initially added on branch new_design. |
| 681 |
> |
|
| 682 |
> |
2004-11-12 17:28 tim |
| 683 |
> |
|
| 684 |
> |
* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding |
| 685 |
> |
StringUtils, a c-style strtok like class, need unit test |
| 686 |
> |
|
| 687 |
> |
2004-11-12 12:40 tim |
| 688 |
> |
|
| 689 |
> |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 690 |
> |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 691 |
> |
brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test |
| 692 |
> |
|
| 693 |
> |
2004-11-12 02:05 tim |
| 694 |
> |
|
| 695 |
> |
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 696 |
> |
primitives/CutoffGroup.hpp, primitives/Molecule.cpp: |
| 697 |
> |
MoleculeCreator forget to create CutoffGroups for free atoms |
| 698 |
> |
|
| 699 |
> |
2004-11-12 01:19 tim |
| 700 |
> |
|
| 701 |
> |
* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
| 702 |
> |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 703 |
> |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 704 |
> |
io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: |
| 705 |
> |
OOPSE = Object-Obfuscated Parallel Simulation Engine |
| 706 |
> |
|
| 707 |
> |
2004-11-11 16:48 chrisfen |
| 708 |
> |
|
| 709 |
> |
* samples/water/tip3p_ice/tp3.md: working sample |
| 710 |
> |
|
| 711 |
> |
2004-11-11 16:47 chrisfen |
| 712 |
> |
|
| 713 |
> |
* src/restraints/Restraints.cpp: working towards parallel |
| 714 |
> |
restraints |
| 715 |
> |
|
| 716 |
> |
2004-11-11 16:47 chrisfen |
| 717 |
> |
|
| 718 |
> |
* src/integrators/Integrator.cpp: Commented out some write |
| 719 |
> |
statements |
| 720 |
> |
|
| 721 |
> |
2004-11-11 16:46 chrisfen |
| 722 |
> |
|
| 723 |
> |
* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some |
| 724 |
> |
write statements |
| 725 |
> |
|
| 726 |
> |
2004-11-11 16:46 chrisfen |
| 727 |
> |
|
| 728 |
> |
* samples/water/tip3p_ice/tp3.md: Fun with ice |
| 729 |
> |
|
| 730 |
> |
2004-11-11 11:41 tim |
| 731 |
> |
|
| 732 |
> |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 733 |
> |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 734 |
> |
brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, |
| 735 |
> |
brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, |
| 736 |
> |
io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove |
| 737 |
> |
useless mpiSimulation |
| 738 |
> |
|
| 739 |
> |
2004-11-11 11:41 tim |
| 740 |
> |
|
| 741 |
> |
* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on |
| 742 |
> |
branch new_design. |
| 743 |
> |
|
| 744 |
> |
2004-11-10 17:50 tim |
| 745 |
> |
|
| 746 |
> |
* src/: brains/ForceManager.cpp, brains/SimInfo.cpp, |
| 747 |
> |
brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, |
| 748 |
> |
integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo |
| 749 |
> |
|
| 750 |
> |
2004-11-10 17:01 tim |
| 751 |
> |
|
| 752 |
> |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
| 753 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
| 754 |
> |
brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 755 |
> |
brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, |
| 756 |
> |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
| 757 |
> |
io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, |
| 758 |
> |
visitors/AtomVisitor.cpp: another painful day (1) SimCreator, |
| 759 |
> |
SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom |
| 760 |
> |
File will be removed) (3) ForceField (at least LJ) and BondType, |
| 761 |
> |
BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & |
| 762 |
> |
Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint |
| 763 |
> |
|
| 764 |
> |
2004-11-10 09:52 tim |
| 765 |
> |
|
| 766 |
> |
* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a |
| 767 |
> |
configurable StatWriter |
| 768 |
> |
|
| 769 |
> |
2004-11-10 09:52 tim |
| 770 |
> |
|
| 771 |
> |
* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on |
| 772 |
> |
branch new_design. |
| 773 |
> |
|
| 774 |
> |
2004-11-09 21:58 tim |
| 775 |
> |
|
| 776 |
> |
* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation |
| 777 |
> |
in progress |
| 778 |
> |
|
| 779 |
> |
2004-11-09 18:11 tim |
| 780 |
> |
|
| 781 |
> |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
| 782 |
> |
added on branch new_design. |
| 783 |
> |
|
| 784 |
> |
2004-11-09 18:11 tim |
| 785 |
> |
|
| 786 |
> |
* src/integrators/VelocityVerletIntegrator.cpp: file |
| 787 |
> |
VelocityVerletIntegrator.cpp was initially added on branch |
| 788 |
> |
new_design. |
| 789 |
> |
|
| 790 |
> |
2004-11-09 18:11 tim |
| 791 |
> |
|
| 792 |
> |
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
| 793 |
> |
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 794 |
> |
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
| 795 |
> |
brains/mpiSimulation.hpp, integrators/Integrator.hpp, |
| 796 |
> |
integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, |
| 797 |
> |
integrators/VelocityVerletIntegrator.hpp: adding ForceManager |
| 798 |
> |
|
| 799 |
> |
2004-11-09 18:11 tim |
| 800 |
> |
|
| 801 |
> |
* src/brains/ForceManager.hpp: file ForceManager.hpp was initially |
| 802 |
> |
added on branch new_design. |
| 803 |
> |
|
| 804 |
> |
2004-11-09 18:11 tim |
| 805 |
> |
|
| 806 |
> |
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
| 807 |
> |
branch new_design. |
| 808 |
> |
|
| 809 |
> |
2004-11-08 20:08 tim |
| 810 |
> |
|
| 811 |
> |
* src/integrators/VelocityVerletIntegrator.hpp: file |
| 812 |
> |
VelocityVerletIntegrator.hpp was initially added on branch |
| 813 |
> |
new_design. |
| 814 |
> |
|
| 815 |
> |
2004-11-08 20:08 tim |
| 816 |
> |
|
| 817 |
> |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
| 818 |
> |
branch new_design. |
| 819 |
> |
|
| 820 |
> |
2004-11-08 20:08 tim |
| 821 |
> |
|
| 822 |
> |
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
| 823 |
> |
integrators/Integrator.hpp, integrators/NVE.hpp, |
| 824 |
> |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
| 825 |
> |
utils/TypeContainer.hpp: More to break |
| 826 |
> |
|
| 827 |
> |
2004-11-06 00:21 tim |
| 828 |
> |
|
| 829 |
> |
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
| 830 |
> |
added on branch new_design. |
| 831 |
> |
|
| 832 |
> |
2004-11-06 00:21 tim |
| 833 |
> |
|
| 834 |
> |
* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, |
| 835 |
> |
UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, |
| 836 |
> |
utils/TypeContainer.hpp, utils/next_combination.hpp: adding |
| 837 |
> |
ForceField and TypeContainer classes |
| 838 |
> |
|
| 839 |
> |
2004-11-05 18:38 tim |
| 840 |
> |
|
| 841 |
> |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
| 842 |
> |
initially added on branch new_design. |
| 843 |
> |
|
| 844 |
> |
2004-11-05 18:38 tim |
| 845 |
> |
|
| 846 |
> |
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
| 847 |
> |
initially added on branch new_design. |
| 848 |
> |
|
| 849 |
> |
2004-11-05 18:38 tim |
| 850 |
> |
|
| 851 |
> |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 852 |
> |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 853 |
> |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 854 |
> |
brains/SimInfo.hpp, primitives/Molecule.hpp, |
| 855 |
> |
utils/LocalndexManager.hpp: Fix Exclude class etc. |
| 856 |
> |
|
| 857 |
> |
2004-11-05 16:45 chrisfen |
| 858 |
> |
|
| 859 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 860 |
> |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the |
| 861 |
> |
linear visitor |
| 862 |
> |
|
| 863 |
> |
2004-11-05 16:04 chrisfen |
| 864 |
> |
|
| 865 |
> |
* src/UseTheForce/DarkSide/shapes.F90: current status of the |
| 866 |
> |
debugging process |
| 867 |
> |
|
| 868 |
> |
2004-11-05 16:04 chrisfen |
| 869 |
> |
|
| 870 |
> |
* make/Makefile.in: included visitors and minimizer |
| 871 |
> |
|
| 872 |
> |
2004-11-05 16:03 chrisfen |
| 873 |
> |
|
| 874 |
> |
* ChangeLog: new changes |
| 875 |
> |
|
| 876 |
> |
2004-11-04 21:56 tim |
| 877 |
> |
|
| 878 |
> |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
| 879 |
> |
primitives/Molecule.hpp: Pain...... |
| 880 |
> |
|
| 881 |
> |
2004-11-04 15:55 tim |
| 882 |
> |
|
| 883 |
> |
* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
| 884 |
> |
src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
| 885 |
> |
src/brains/Stats.hpp: time to break SimSetup |
| 886 |
> |
|
| 887 |
> |
2004-11-04 15:51 gezelter |
| 888 |
> |
|
| 889 |
> |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
| 890 |
> |
classes in progress |
| 891 |
> |
|
| 892 |
> |
2004-11-04 14:48 tim |
| 893 |
> |
|
| 894 |
> |
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
| 895 |
> |
branch new_design. |
| 896 |
> |
|
| 897 |
> |
2004-11-04 14:48 tim |
| 898 |
> |
|
| 899 |
> |
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
| 900 |
> |
branch new_design. |
| 901 |
> |
|
| 902 |
> |
2004-11-04 14:48 tim |
| 903 |
> |
|
| 904 |
> |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
| 905 |
> |
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
| 906 |
> |
class |
| 907 |
> |
|
| 908 |
> |
2004-11-04 11:22 gezelter |
| 909 |
> |
|
| 910 |
> |
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 911 |
> |
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
| 912 |
> |
linearAxis are virtual in StuntDouble, but are implemented by |
| 913 |
> |
DirectionalAtom and RigidBody In StuntDouble, they should return |
| 914 |
> |
false and "-1" but there should be logic to figure them out in the |
| 915 |
> |
other two classes |
| 916 |
> |
|
| 917 |
> |
2004-11-04 11:20 gezelter |
| 918 |
> |
|
| 919 |
> |
* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
| 920 |
> |
remember what I did |
| 921 |
> |
|
| 922 |
> |
2004-11-04 11:20 gezelter |
| 923 |
> |
|
| 924 |
> |
* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
| 925 |
> |
|
| 926 |
> |
2004-11-04 11:20 gezelter |
| 927 |
> |
|
| 928 |
> |
* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
| 929 |
> |
in the entry_plug so that it only is set if the atoms really are in |
| 930 |
> |
the simulation |
| 931 |
> |
|
| 932 |
> |
2004-11-04 11:20 gezelter |
| 933 |
> |
|
| 934 |
> |
* samples/water/ssd/ssd.md: testing force fields |
| 935 |
> |
|
| 936 |
> |
2004-11-04 11:19 gezelter |
| 937 |
> |
|
| 938 |
> |
* samples/shape/linear.in: testing shapes |
| 939 |
> |
|
| 940 |
> |
2004-11-03 14:56 tim |
| 941 |
> |
|
| 942 |
> |
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
| 943 |
> |
class(similar as SimSetup) |
| 944 |
> |
|
| 945 |
> |
2004-11-03 14:56 tim |
| 946 |
> |
|
| 947 |
> |
* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
| 948 |
> |
added on branch new_design. |
| 949 |
> |
|
| 950 |
> |
2004-11-03 14:56 tim |
| 951 |
> |
|
| 952 |
> |
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
| 953 |
> |
added on branch new_design. |
| 954 |
> |
|
| 955 |
> |
2004-11-03 13:00 tim |
| 956 |
> |
|
| 957 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 958 |
> |
UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
| 959 |
> |
UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, |
| 960 |
> |
brains/DataStorage.hpp, primitives/Atom.hpp, |
| 961 |
> |
primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
| 962 |
> |
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
| 963 |
> |
compiled. Still a long way to go ...... |
| 964 |
> |
|
| 965 |
> |
2004-11-03 11:08 tim |
| 966 |
> |
|
| 967 |
> |
* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
| 968 |
> |
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
| 969 |
> |
src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, |
| 970 |
> |
src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, |
| 971 |
> |
src/io/ZConsReader.cpp, src/primitives/Bend.cpp, |
| 972 |
> |
src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, |
| 973 |
> |
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
| 974 |
> |
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
| 975 |
> |
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
| 976 |
> |
src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, |
| 977 |
> |
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
| 978 |
> |
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
| 979 |
> |
|
| 980 |
> |
2004-11-02 17:41 tim |
| 981 |
> |
|
| 982 |
> |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
| 983 |
> |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
| 984 |
> |
Need unit test |
| 985 |
> |
|
| 986 |
> |
2004-11-02 17:41 tim |
| 987 |
> |
|
| 988 |
> |
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
| 989 |
> |
initially added on branch new_design. |
| 990 |
> |
|
| 991 |
> |
2004-11-02 17:41 tim |
| 992 |
> |
|
| 993 |
> |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
| 994 |
> |
branch new_design. |
| 995 |
> |
|
| 996 |
> |
2004-11-02 11:59 tim |
| 997 |
> |
|
| 998 |
> |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
| 999 |
> |
branch new_design. |
| 1000 |
> |
|
| 1001 |
> |
2004-11-02 11:59 tim |
| 1002 |
> |
|
| 1003 |
> |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
| 1004 |
> |
SimSnapshotManager.hpp: SimModel in progress |
| 1005 |
> |
|
| 1006 |
> |
2004-11-02 10:28 chrisfen |
| 1007 |
> |
|
| 1008 |
> |
* src/: UseTheForce/DarkSide/shapes.F90, |
| 1009 |
> |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
| 1010 |
> |
looks like it's working |
| 1011 |
> |
|
| 1012 |
> |
2004-11-02 10:27 tim |
| 1013 |
> |
|
| 1014 |
> |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
| 1015 |
> |
functions for dealing with memory issue |
| 1016 |
> |
|
| 1017 |
> |
2004-11-02 10:27 tim |
| 1018 |
> |
|
| 1019 |
> |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
| 1020 |
> |
added on branch new_design. |
| 1021 |
> |
|
| 1022 |
> |
2004-11-02 10:23 tim |
| 1023 |
> |
|
| 1024 |
> |
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
| 1025 |
> |
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
| 1026 |
> |
SimModel(something similar as SimInfo) |
| 1027 |
> |
|
| 1028 |
> |
2004-11-01 17:52 tim |
| 1029 |
> |
|
| 1030 |
> |
* src/: applications/simpleBuilder/MoLocator.hpp, |
| 1031 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
| 1032 |
> |
brains/DataStorage.hpp, brains/ForceFields.cpp, |
| 1033 |
> |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, |
| 1034 |
> |
constraints/ZConstraint.cpp, integrators/Integrator.cpp, |
| 1035 |
> |
integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, |
| 1036 |
> |
math/SquareMatrix3.hpp, math/Vector3.hpp, |
| 1037 |
> |
minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, |
| 1038 |
> |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
| 1039 |
> |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
| 1040 |
> |
primitives/RigidBody.hpp, primitives/Torsion.hpp, |
| 1041 |
> |
restraints/Restraints.cpp, types/TorsionType.hpp, |
| 1042 |
> |
utils/PropertyMap.hpp, utils/StringTokenizer.hpp, |
| 1043 |
> |
visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, |
| 1044 |
> |
visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
| 1045 |
> |
RigidBody and StuntDouble classes get compiled |
| 1046 |
> |
|
| 1047 |
> |
2004-11-01 16:40 tim |
| 1048 |
> |
|
| 1049 |
> |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
| 1050 |
> |
on branch new_design. |
| 1051 |
> |
|
| 1052 |
> |
2004-11-01 16:40 tim |
| 1053 |
> |
|
| 1054 |
> |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
| 1055 |
> |
branch new_design. |
| 1056 |
> |
|
| 1057 |
> |
2004-11-01 16:40 tim |
| 1058 |
> |
|
| 1059 |
> |
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
| 1060 |
> |
branch new_design. |
| 1061 |
> |
|
| 1062 |
> |
2004-11-01 16:40 tim |
| 1063 |
> |
|
| 1064 |
> |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
| 1065 |
> |
version of Bond, Bend and Torsion. |
| 1066 |
> |
|
| 1067 |
> |
2004-11-01 16:37 tim |
| 1068 |
> |
|
| 1069 |
> |
* src/types/BendType.hpp: file BendType.hpp was initially added on |
| 1070 |
> |
branch new_design. |
| 1071 |
> |
|
| 1072 |
> |
2004-11-01 16:37 tim |
| 1073 |
> |
|
| 1074 |
> |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
| 1075 |
> |
BondType, BendType, TorsionType |
| 1076 |
> |
|
| 1077 |
> |
2004-11-01 16:37 tim |
| 1078 |
> |
|
| 1079 |
> |
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
| 1080 |
> |
added on branch new_design. |
| 1081 |
> |
|
| 1082 |
> |
2004-11-01 16:37 tim |
| 1083 |
> |
|
| 1084 |
> |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
| 1085 |
> |
branch new_design. |
| 1086 |
> |
|
| 1087 |
> |
2004-11-01 15:15 tim |
| 1088 |
> |
|
| 1089 |
> |
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
| 1090 |
> |
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 1091 |
> |
GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, |
| 1092 |
> |
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
| 1093 |
> |
break, break and break..... |
| 1094 |
> |
|
| 1095 |
> |
2004-11-01 14:57 tim |
| 1096 |
> |
|
| 1097 |
> |
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
| 1098 |
> |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
| 1099 |
> |
StuntDouble.hpp: these core classes get compiled |
| 1100 |
> |
|
| 1101 |
> |
2004-10-29 17:37 tim |
| 1102 |
> |
|
| 1103 |
> |
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
| 1104 |
> |
class |
| 1105 |
> |
|
| 1106 |
> |
2004-10-29 17:28 chrisfen |
| 1107 |
> |
|
| 1108 |
> |
* src/: UseTheForce/DarkSide/atype.F90, |
| 1109 |
> |
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
| 1110 |
> |
types/ShapeAtomType.cpp: still debugging |
| 1111 |
> |
|
| 1112 |
> |
2004-10-29 17:28 chrisfen |
| 1113 |
> |
|
| 1114 |
> |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
| 1115 |
> |
shapes rcut calculator added |
| 1116 |
> |
|
| 1117 |
> |
2004-10-29 17:27 chrisfen |
| 1118 |
> |
|
| 1119 |
> |
* samples/shape/linear.md: shorter run |
| 1120 |
> |
|
| 1121 |
> |
2004-10-29 15:54 tim |
| 1122 |
> |
|
| 1123 |
> |
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
| 1124 |
> |
|
| 1125 |
> |
2004-10-29 11:22 tim |
| 1126 |
> |
|
| 1127 |
> |
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
| 1128 |
> |
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
| 1129 |
> |
some deprecated files |
| 1130 |
> |
|
| 1131 |
> |
2004-10-29 11:20 tim |
| 1132 |
> |
|
| 1133 |
> |
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
| 1134 |
> |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
| 1135 |
> |
More painful reconstruction is coming !!! |
| 1136 |
> |
|
| 1137 |
> |
2004-10-28 17:34 tim |
| 1138 |
> |
|
| 1139 |
> |
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
| 1140 |
> |
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
| 1141 |
> |
test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, |
| 1142 |
> |
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
| 1143 |
> |
DirectionalAtom and RigidBody |
| 1144 |
> |
|
| 1145 |
> |
2004-10-28 17:26 tim |
| 1146 |
> |
|
| 1147 |
> |
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
| 1148 |
> |
src/applications/simpleBuilder/MoLocator.cpp, |
| 1149 |
> |
src/applications/simpleBuilder/Vector3d.hpp, |
| 1150 |
> |
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
| 1151 |
> |
remove old Vector3d.hpp from application/simpleBuilder |
| 1152 |
> |
|
| 1153 |
> |
2004-10-28 16:42 tim |
| 1154 |
> |
|
| 1155 |
> |
* src/utils/next_combination.hpp: Minor change in next_combination |
| 1156 |
> |
|
| 1157 |
> |
2004-10-28 16:28 tim |
| 1158 |
> |
|
| 1159 |
> |
* src/utils/next_combination.hpp, |
| 1160 |
> |
test/utils/NextCombinationTestCase.cpp, |
| 1161 |
> |
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
| 1162 |
> |
|
| 1163 |
> |
2004-10-28 16:11 tim |
| 1164 |
> |
|
| 1165 |
> |
* src/utils/next_combination.hpp: change documentation of |
| 1166 |
> |
next_combination.hpp |
| 1167 |
> |
|
| 1168 |
> |
2004-10-28 15:41 tim |
| 1169 |
> |
|
| 1170 |
> |
* ChangeLog, src/utils/next_combination.hpp, |
| 1171 |
> |
test/utils/NextCombinationTestCase.cpp, |
| 1172 |
> |
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
| 1173 |
> |
|
| 1174 |
> |
2004-10-28 15:01 tim |
| 1175 |
> |
|
| 1176 |
> |
* src/utils/next_combination.hpp: adding replace wildcard function |
| 1177 |
> |
|
| 1178 |
> |
2004-10-28 14:33 tim |
| 1179 |
> |
|
| 1180 |
> |
* src/utils/next_combination.hpp: Minor change |
| 1181 |
> |
|
| 1182 |
> |
2004-10-28 14:06 tim |
| 1183 |
> |
|
| 1184 |
> |
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
| 1185 |
> |
src/applications/simpleBuilder/simpleBuilder.cpp, |
| 1186 |
> |
src/utils/next_combination.hpp, test/utils/Makefile, |
| 1187 |
> |
test/utils/NextCombinationTestCase.cpp, |
| 1188 |
> |
test/utils/ReplaceWildCardTestCase.cpp, |
| 1189 |
> |
test/utils/next_combination.hpp: STL next_permutation like |
| 1190 |
> |
next_combination is working |
| 1191 |
> |
|
| 1192 |
> |
2004-10-28 12:22 chrisfen |
| 1193 |
> |
|
| 1194 |
> |
* src/UseTheForce/WATER.cpp: fix of setDipoles |
| 1195 |
> |
|
| 1196 |
> |
2004-10-28 12:20 gezelter |
| 1197 |
> |
|
| 1198 |
> |
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
| 1199 |
> |
shapeFile |
| 1200 |
> |
|
| 1201 |
> |
2004-10-28 12:20 gezelter |
| 1202 |
> |
|
| 1203 |
> |
* samples/shape/linear.md: forgot the orientation line |
| 1204 |
> |
|
| 1205 |
> |
2004-10-28 11:56 gezelter |
| 1206 |
> |
|
| 1207 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 1208 |
> |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
| 1209 |
> |
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
| 1210 |
> |
declaration foo |
| 1211 |
> |
|
| 1212 |
> |
2004-10-28 11:55 gezelter |
| 1213 |
> |
|
| 1214 |
> |
* samples/lipid/5x5.md: uncommented .in line |
| 1215 |
> |
|
| 1216 |
> |
2004-10-28 10:42 tim |
| 1217 |
> |
|
| 1218 |
> |
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
| 1219 |
> |
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
| 1220 |
> |
in progress |
| 1221 |
> |
|
| 1222 |
> |
2004-10-28 10:15 tim |
| 1223 |
> |
|
| 1224 |
> |
* test/utils/: NextCombinationTestCase.cpp, |
| 1225 |
> |
NextCombinationTestCase.hpp: adding next_combination test case |
| 1226 |
> |
|
| 1227 |
> |
2004-10-28 10:02 tim |
| 1228 |
> |
|
| 1229 |
> |
* test/utils/next_combination.hpp: STL Compatible combination |
| 1230 |
> |
sequence generator |
| 1231 |
> |
|
| 1232 |
> |
2004-10-28 01:23 tim |
| 1233 |
> |
|
| 1234 |
> |
* test/utils/: GenerateCombination.hpp, |
| 1235 |
> |
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
| 1236 |
> |
|
| 1237 |
> |
2004-10-28 01:16 tim |
| 1238 |
> |
|
| 1239 |
> |
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
| 1240 |
> |
next_combination function. |
| 1241 |
> |
|
| 1242 |
> |
2004-10-27 22:27 tim |
| 1243 |
> |
|
| 1244 |
> |
* test/utils/ReplaceWildCard.hpp: no message |
| 1245 |
> |
|
| 1246 |
> |
2004-10-27 22:14 tim |
| 1247 |
> |
|
| 1248 |
> |
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
| 1249 |
> |
ReplaceWildCard(recursive version) is working, need refactoring. An |
| 1250 |
> |
iterative version is on the way |
| 1251 |
> |
|
| 1252 |
> |
2004-10-27 21:28 tim |
| 1253 |
> |
|
| 1254 |
> |
* test/utils/: Makefile, ReplaceWildCard.hpp, |
| 1255 |
> |
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
| 1256 |
> |
|
| 1257 |
> |
2004-10-27 21:08 tim |
| 1258 |
> |
|
| 1259 |
> |
* test/utils/: ReplaceWildCardTestCase.cpp, |
| 1260 |
> |
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
| 1261 |
> |
|
| 1262 |
> |
2004-10-27 18:17 tim |
| 1263 |
> |
|
| 1264 |
> |
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
| 1265 |
> |
test |
| 1266 |
> |
|
| 1267 |
> |
2004-10-27 01:25 tim |
| 1268 |
> |
|
| 1269 |
> |
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
| 1270 |
> |
char matching is on the way |
| 1271 |
> |
|
| 1272 |
> |
2004-10-27 01:07 tim |
| 1273 |
> |
|
| 1274 |
> |
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
| 1275 |
> |
|
| 1276 |
> |
2004-10-26 22:00 gezelter |
| 1277 |
> |
|
| 1278 |
> |
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
| 1279 |
> |
|
| 1280 |
> |
2004-10-26 21:20 gezelter |
| 1281 |
> |
|
| 1282 |
> |
* src/UseTheForce/ForceFields.hpp: subclass foo |
| 1283 |
> |
|
| 1284 |
> |
2004-10-26 21:16 gezelter |
| 1285 |
> |
|
| 1286 |
> |
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
| 1287 |
> |
string conversion |
| 1288 |
> |
|
| 1289 |
> |
2004-10-26 19:01 gezelter |
| 1290 |
> |
|
| 1291 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 1292 |
> |
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
| 1293 |
> |
brains/SimSetup.hpp: char* -> string |
| 1294 |
> |
|
| 1295 |
> |
2004-10-26 17:25 gezelter |
| 1296 |
> |
|
| 1297 |
> |
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
| 1298 |
> |
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
| 1299 |
> |
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
| 1300 |
> |
isXXX |
| 1301 |
> |
|
| 1302 |
> |
2004-10-26 17:25 gezelter |
| 1303 |
> |
|
| 1304 |
> |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
| 1305 |
> |
define name collision |
| 1306 |
> |
|
| 1307 |
> |
2004-10-26 17:24 gezelter |
| 1308 |
> |
|
| 1309 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 1310 |
> |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
| 1311 |
> |
UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
| 1312 |
> |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 1313 |
> |
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
| 1314 |
> |
forcefield refactoring for shapes |
| 1315 |
> |
|
| 1316 |
> |
2004-10-26 17:24 gezelter |
| 1317 |
> |
|
| 1318 |
> |
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
| 1319 |
> |
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
| 1320 |
> |
linear.md, linear.shape, toluene.shape: adding sample shape |
| 1321 |
> |
directory |
| 1322 |
> |
|
| 1323 |
> |
2004-10-26 17:19 tim |
| 1324 |
> |
|
| 1325 |
> |
* ChangeLog, src/brains/DataStorage.cpp, |
| 1326 |
> |
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
| 1327 |
> |
test/brains/DataStorageTestCase.cpp, |
| 1328 |
> |
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
| 1329 |
> |
DataStorage passes unit test |
| 1330 |
> |
|
| 1331 |
> |
2004-10-26 13:03 chrisfen |
| 1332 |
> |
|
| 1333 |
> |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
| 1334 |
> |
Changes to help advance shapes |
| 1335 |
> |
|
| 1336 |
> |
2004-10-26 13:02 chrisfen |
| 1337 |
> |
|
| 1338 |
> |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
| 1339 |
> |
Shapes force field reader |
| 1340 |
> |
|
| 1341 |
> |
2004-10-26 12:28 tim |
| 1342 |
> |
|
| 1343 |
> |
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
| 1344 |
> |
SnapshotTestCase in progress |
| 1345 |
> |
|
| 1346 |
> |
2004-10-25 17:46 tim |
| 1347 |
> |
|
| 1348 |
> |
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 1349 |
> |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
| 1350 |
> |
src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
| 1351 |
> |
test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
| 1352 |
> |
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
| 1353 |
> |
and Vector classes |
| 1354 |
> |
|
| 1355 |
> |
2004-10-25 12:03 tim |
| 1356 |
> |
|
| 1357 |
> |
* ChangeLog, src/utils/GenericFactory.hpp, |
| 1358 |
> |
test/utils/GenericFactoryTestCase.cpp, |
| 1359 |
> |
test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
| 1360 |
> |
GenericFactory Test Case. GenericFactory now can bed used to creat |
| 1361 |
> |
ForcefieldFactory and IntegratorFactory etc. |
| 1362 |
> |
|
| 1363 |
> |
2004-10-24 23:08 tim |
| 1364 |
> |
|
| 1365 |
> |
* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
| 1366 |
> |
brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
| 1367 |
> |
brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
| 1368 |
> |
get reconstructed |
| 1369 |
> |
|
| 1370 |
> |
2004-10-24 02:55 tim |
| 1371 |
> |
|
| 1372 |
> |
* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
| 1373 |
> |
|
| 1374 |
> |
2004-10-23 18:09 tim |
| 1375 |
> |
|
| 1376 |
> |
* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
| 1377 |
> |
StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
| 1378 |
> |
RigidBody.cpp: Refactoring in progress |
| 1379 |
> |
|
| 1380 |
> |
2004-10-22 18:09 tim |
| 1381 |
> |
|
| 1382 |
> |
* ChangeLog, src/brains/Snapshot.hpp, |
| 1383 |
> |
src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
| 1384 |
> |
test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
| 1385 |
> |
test/brains/StuntDouble.hpp: more work in Snapshot |
| 1386 |
> |
|
| 1387 |
> |
2004-10-22 17:59 chrisfen |
| 1388 |
> |
|
| 1389 |
> |
* src/: UseTheForce/LJFF.cpp, |
| 1390 |
> |
UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
| 1391 |
> |
god! It runs and conserves energy! |
| 1392 |
> |
|
| 1393 |
> |
2004-10-22 17:54 chrisfen |
| 1394 |
> |
|
| 1395 |
> |
* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
| 1396 |
> |
|
| 1397 |
> |
2004-10-22 17:53 chrisfen |
| 1398 |
> |
|
| 1399 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 1400 |
> |
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
| 1401 |
> |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 1402 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
| 1403 |
> |
breakey |
| 1404 |
> |
|
| 1405 |
> |
2004-10-22 17:53 chrisfen |
| 1406 |
> |
|
| 1407 |
> |
* make/Makefile.in: compiler flags |
| 1408 |
> |
|
| 1409 |
> |
2004-10-22 16:20 gezelter |
| 1410 |
> |
|
| 1411 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 1412 |
> |
UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
| 1413 |
> |
brains/fSimulation.h, types/AtomType.hpp, |
| 1414 |
> |
types/DirectionalAtomType.hpp: fixey fixey |
| 1415 |
> |
|
| 1416 |
> |
2004-10-22 15:22 gezelter |
| 1417 |
> |
|
| 1418 |
> |
* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
| 1419 |
> |
charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
| 1420 |
> |
lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
| 1421 |
> |
fortran files and c/Fortran interfaces |
| 1422 |
> |
|
| 1423 |
> |
2004-10-22 15:21 gezelter |
| 1424 |
> |
|
| 1425 |
> |
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
| 1426 |
> |
DirectionalAtomType.hpp, Makefile: More on AtomType and |
| 1427 |
> |
DirectionalAtomType |
| 1428 |
> |
|
| 1429 |
> |
2004-10-22 09:47 gezelter |
| 1430 |
> |
|
| 1431 |
> |
* src/types/AtomType.hpp: Adding AtomType |
| 1432 |
> |
|
| 1433 |
> |
2004-10-21 16:31 tim |
| 1434 |
> |
|
| 1435 |
> |
* ChangeLog, src/brains/Snapshot.hpp, |
| 1436 |
> |
src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
| 1437 |
> |
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
| 1438 |
> |
src/math/Vector.hpp, src/math/Vector3.hpp, |
| 1439 |
> |
test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
| 1440 |
> |
Snapshot and SnapshotManager in progress |
| 1441 |
> |
|
| 1442 |
> |
2004-10-21 16:30 tim |
| 1443 |
> |
|
| 1444 |
> |
* test/brains/: BrainsTest.cpp, Makefile, |
| 1445 |
> |
SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
| 1446 |
> |
SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
| 1447 |
> |
Snapshot and snapshotManager. |
| 1448 |
> |
|
| 1449 |
> |
2004-10-21 15:15 gezelter |
| 1450 |
> |
|
| 1451 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 1452 |
> |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 1453 |
> |
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
| 1454 |
> |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 1455 |
> |
UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
| 1456 |
> |
UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
| 1457 |
> |
brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
| 1458 |
> |
Fixey Fixey. |
| 1459 |
> |
|
| 1460 |
> |
2004-10-21 11:32 tim |
| 1461 |
> |
|
| 1462 |
> |
* src/utils/GenericData.cpp, src/utils/Makefile, |
| 1463 |
> |
test/utils/Makefile, test/utils/UtilTest: remove some junk files |
| 1464 |
> |
|
| 1465 |
> |
2004-10-21 11:24 tim |
| 1466 |
> |
|
| 1467 |
> |
* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
| 1468 |
> |
|
| 1469 |
> |
2004-10-21 11:22 tim |
| 1470 |
> |
|
| 1471 |
> |
* ChangeLog, src/brains/SimSetup.cpp, |
| 1472 |
> |
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
| 1473 |
> |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 1474 |
> |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 1475 |
> |
src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
| 1476 |
> |
src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
| 1477 |
> |
src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
| 1478 |
> |
src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
| 1479 |
> |
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
| 1480 |
> |
src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 1481 |
> |
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
| 1482 |
> |
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
| 1483 |
> |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 1484 |
> |
src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
| 1485 |
> |
GenericData |
| 1486 |
> |
|
| 1487 |
> |
2004-10-21 10:25 chuckv |
| 1488 |
> |
|
| 1489 |
> |
* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
| 1490 |
> |
module. |
| 1491 |
> |
|
| 1492 |
> |
2004-10-21 10:24 chuckv |
| 1493 |
> |
|
| 1494 |
> |
* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
| 1495 |
> |
fortran lj module. |
| 1496 |
> |
|
| 1497 |
> |
2004-10-20 17:54 tim |
| 1498 |
> |
|
| 1499 |
> |
* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
| 1500 |
> |
test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
| 1501 |
> |
test/utils/PropertyMapTestCase.cpp, |
| 1502 |
> |
test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
| 1503 |
> |
GenericData and PropertyMap pass unit test. |
| 1504 |
> |
|
| 1505 |
> |
2004-10-20 16:52 gezelter |
| 1506 |
> |
|
| 1507 |
> |
* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
| 1508 |
> |
DarkSide/sticky_interface.h: fixed a fortran name problem |
| 1509 |
> |
|
| 1510 |
> |
2004-10-20 16:38 tim |
| 1511 |
> |
|
| 1512 |
> |
* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
| 1513 |
> |
GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
| 1514 |
> |
UtilTest, UtilTest.cpp: adding generic data test case |
| 1515 |
> |
|
| 1516 |
> |
2004-10-20 16:16 chuckv |
| 1517 |
> |
|
| 1518 |
> |
* configure, ac-tools/aclocal.m4, |
| 1519 |
> |
src/UseTheForce/DarkSide/Makefile, |
| 1520 |
> |
src/UseTheForce/DarkSide/mpiSimulation.F90, |
| 1521 |
> |
src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
| 1522 |
> |
src/UseTheForce/DarkSide/simParallel.F90, |
| 1523 |
> |
src/UseTheForce/DarkSide/simParallel_interface.h, |
| 1524 |
> |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
| 1525 |
> |
Fortran/C++ interface de-obfuscation project appears to be |
| 1526 |
> |
complete! Woo hoo! |
| 1527 |
> |
|
| 1528 |
> |
2004-10-20 15:47 chuckv |
| 1529 |
> |
|
| 1530 |
> |
* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
| 1531 |
> |
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
| 1532 |
> |
continues |
| 1533 |
> |
|
| 1534 |
> |
2004-10-20 15:46 chuckv |
| 1535 |
> |
|
| 1536 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 1537 |
> |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 1538 |
> |
UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
| 1539 |
> |
UseTheForce/doForces_interface.h, |
| 1540 |
> |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
| 1541 |
> |
UseTheForce/DarkSide/atype_interface.h, |
| 1542 |
> |
UseTheForce/DarkSide/eam_interface.h, |
| 1543 |
> |
UseTheForce/DarkSide/gb_interface.h, |
| 1544 |
> |
UseTheForce/DarkSide/mpiSimulation_interface.h, |
| 1545 |
> |
UseTheForce/DarkSide/shapes_interface.h, |
| 1546 |
> |
UseTheForce/DarkSide/simulation_interface.h, |
| 1547 |
> |
UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
| 1548 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
| 1549 |
> |
de-obfuscation project (It is a very long story) |
| 1550 |
> |
|
| 1551 |
> |
2004-10-20 13:07 tim |
| 1552 |
> |
|
| 1553 |
> |
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
| 1554 |
> |
test/math/SquareMatrix3TestCase.cpp, |
| 1555 |
> |
test/math/SquareMatrixTestCase.cpp, |
| 1556 |
> |
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
| 1557 |
> |
|
| 1558 |
> |
2004-10-20 00:52 tim |
| 1559 |
> |
|
| 1560 |
> |
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
| 1561 |
> |
SnapshotManager in design phase |
| 1562 |
> |
|
| 1563 |
> |
2004-10-19 23:54 gezelter |
| 1564 |
> |
|
| 1565 |
> |
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
| 1566 |
> |
problem prevented linking |
| 1567 |
> |
|
| 1568 |
> |
2004-10-19 23:54 gezelter |
| 1569 |
> |
|
| 1570 |
> |
* src/UseTheForce/Shapes_FF.cpp: fixed include |
| 1571 |
> |
|
| 1572 |
> |
2004-10-19 23:26 gezelter |
| 1573 |
> |
|
| 1574 |
> |
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
| 1575 |
> |
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
| 1576 |
> |
more fortran name mangling |
| 1577 |
> |
|
| 1578 |
> |
2004-10-19 23:23 gezelter |
| 1579 |
> |
|
| 1580 |
> |
* src/profiling/timing.F90: yet more fortran renaming |
| 1581 |
> |
|
| 1582 |
> |
2004-10-19 23:19 gezelter |
| 1583 |
> |
|
| 1584 |
> |
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
| 1585 |
> |
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
| 1586 |
> |
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
| 1587 |
> |
wrappers.F90: Fortran name cleanup continues |
| 1588 |
> |
|
| 1589 |
> |
2004-10-19 23:12 gezelter |
| 1590 |
> |
|
| 1591 |
> |
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
| 1592 |
> |
broken fortran stuff |
| 1593 |
> |
|
| 1594 |
> |
2004-10-19 23:02 gezelter |
| 1595 |
> |
|
| 1596 |
> |
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
| 1597 |
> |
atype_interface.h, atype_module.F90, atype_module_interface.h, |
| 1598 |
> |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
| 1599 |
> |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
| 1600 |
> |
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
| 1601 |
> |
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
| 1602 |
> |
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
| 1603 |
> |
mpiSimulation_interface.h, mpiSimulation_module.F90, |
| 1604 |
> |
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
| 1605 |
> |
shapes_interface.h, shapes_module.h, simulation.F90, |
| 1606 |
> |
simulation_interface.h, simulation_module.F90, |
| 1607 |
> |
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
| 1608 |
> |
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
| 1609 |
> |
name sanity on the fortran side |
| 1610 |
> |
|
| 1611 |
> |
2004-10-19 19:18 tim |
| 1612 |
> |
|
| 1613 |
> |
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
| 1614 |
> |
|
| 1615 |
> |
2004-10-19 18:01 tim |
| 1616 |
> |
|
| 1617 |
> |
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 1618 |
> |
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
| 1619 |
> |
except diagonalize(), all of functions in math library pass the |
| 1620 |
> |
test |
| 1621 |
> |
|
| 1622 |
> |
2004-10-19 17:43 chuckv |
| 1623 |
> |
|
| 1624 |
> |
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
| 1625 |
> |
C-fortran interface functions. |
| 1626 |
> |
|
| 1627 |
> |
2004-10-19 17:37 chuckv |
| 1628 |
> |
|
| 1629 |
> |
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
| 1630 |
> |
eam_module_inteface.h, gb_module_interface.h, |
| 1631 |
> |
mpisimulation_module_interface.h, simulation_module_interface.h, |
| 1632 |
> |
sticky_pair_module_interface.h: Added correct prototypes for |
| 1633 |
> |
C-fortran interface functions. |
| 1634 |
> |
|
| 1635 |
> |
2004-10-19 16:28 tim |
| 1636 |
> |
|
| 1637 |
> |
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
| 1638 |
> |
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
| 1639 |
> |
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
| 1640 |
> |
test/math/RectMatrixTestCase.cpp, |
| 1641 |
> |
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
| 1642 |
> |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
| 1643 |
> |
bugs get fixed at math library |
| 1644 |
> |
|
| 1645 |
> |
2004-10-19 15:43 chuckv |
| 1646 |
> |
|
| 1647 |
> |
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
| 1648 |
> |
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
| 1649 |
> |
DarkSide/mpisimulation_module_interface.h, |
| 1650 |
> |
DarkSide/simulation_module_interface.h, |
| 1651 |
> |
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
| 1652 |
> |
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
| 1653 |
> |
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
| 1654 |
> |
DarkSide/simulation_module.F90, do_Forces.F90, |
| 1655 |
> |
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
| 1656 |
> |
notifycutoffs_module_interface.h: Added new files for fortran |
| 1657 |
> |
interface. |
| 1658 |
> |
|
| 1659 |
> |
2004-10-19 15:43 gezelter |
| 1660 |
> |
|
| 1661 |
> |
* src/UseTheForce/Makefile: regressing |
| 1662 |
> |
|
| 1663 |
> |
2004-10-19 15:40 gezelter |
| 1664 |
> |
|
| 1665 |
> |
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
| 1666 |
> |
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
| 1667 |
> |
working on shapes for portability |
| 1668 |
> |
|
| 1669 |
> |
2004-10-19 15:40 gezelter |
| 1670 |
> |
|
| 1671 |
> |
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
| 1672 |
> |
|
| 1673 |
> |
2004-10-19 13:21 chrisfen |
| 1674 |
> |
|
| 1675 |
> |
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
| 1676 |
> |
findBegin |
| 1677 |
> |
|
| 1678 |
> |
2004-10-18 23:34 tim |
| 1679 |
> |
|
| 1680 |
> |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
| 1681 |
> |
are fixed in Vector class |
| 1682 |
> |
|
| 1683 |
> |
2004-10-18 23:28 tim |
| 1684 |
> |
|
| 1685 |
> |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
| 1686 |
> |
some bugs in RectMatrixTestCase |
| 1687 |
> |
|
| 1688 |
> |
2004-10-18 23:21 tim |
| 1689 |
> |
|
| 1690 |
> |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
| 1691 |
> |
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
| 1692 |
> |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
| 1693 |
> |
test/math/VectorTestCase.hpp: implement more test cases |
| 1694 |
> |
|
| 1695 |
> |
2004-10-18 18:13 tim |
| 1696 |
> |
|
| 1697 |
> |
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
| 1698 |
> |
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 1699 |
> |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
| 1700 |
> |
src/utils/StringTokenizer.hpp, test/math/Makefile, |
| 1701 |
> |
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
| 1702 |
> |
tests on math library |
| 1703 |
> |
|
| 1704 |
> |
2004-10-18 16:03 tim |
| 1705 |
> |
|
| 1706 |
> |
* test/math/: Makefile, QuaternionTestCase.cpp, |
| 1707 |
> |
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
| 1708 |
> |
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
| 1709 |
> |
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
| 1710 |
> |
more testing units |
| 1711 |
> |
|
| 1712 |
> |
2004-10-18 12:07 tim |
| 1713 |
> |
|
| 1714 |
> |
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
| 1715 |
> |
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
| 1716 |
> |
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
| 1717 |
> |
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
| 1718 |
> |
|
| 1719 |
> |
2004-10-18 11:30 gezelter |
| 1720 |
> |
|
| 1721 |
> |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
| 1722 |
> |
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
| 1723 |
> |
\phi) |
| 1724 |
> |
|
| 1725 |
> |
2004-10-18 11:29 gezelter |
| 1726 |
> |
|
| 1727 |
> |
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
| 1728 |
> |
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
| 1729 |
> |
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
| 1730 |
> |
Shapes into OOPSE |
| 1731 |
> |
|
| 1732 |
> |
2004-10-18 10:21 gezelter |
| 1733 |
> |
|
| 1734 |
> |
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
| 1735 |
> |
|
| 1736 |
> |
2004-10-18 00:23 tim |
| 1737 |
> |
|
| 1738 |
> |
* test/math/VectorTestCase.hpp: adding vector test case |
| 1739 |
> |
|
| 1740 |
> |
2004-10-18 00:23 tim |
| 1741 |
> |
|
| 1742 |
> |
* src/utils/GenericFactory.hpp: adding generic factory and vector |
| 1743 |
> |
test case |
| 1744 |
> |
|
| 1745 |
> |
2004-10-16 20:19 tim |
| 1746 |
> |
|
| 1747 |
> |
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
| 1748 |
> |
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
| 1749 |
> |
progress |
| 1750 |
> |
|
| 1751 |
> |
2004-10-15 20:31 tim |
| 1752 |
> |
|
| 1753 |
> |
* src/math/Quaternion.hpp: add quaternion class |
| 1754 |
> |
|
| 1755 |
> |
2004-10-15 16:11 tim |
| 1756 |
> |
|
| 1757 |
> |
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
| 1758 |
> |
IfstrstreamTestCase.hpp: adding test file |
| 1759 |
> |
|
| 1760 |
> |
2004-10-15 16:10 tim |
| 1761 |
> |
|
| 1762 |
> |
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
| 1763 |
> |
|
| 1764 |
> |
2004-10-15 15:42 tim |
| 1765 |
> |
|
| 1766 |
> |
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
| 1767 |
> |
|
| 1768 |
> |
2004-10-15 15:35 tim |
| 1769 |
> |
|
| 1770 |
> |
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
| 1771 |
> |
|
| 1772 |
> |
2004-10-15 15:34 tim |
| 1773 |
> |
|
| 1774 |
> |
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
| 1775 |
> |
namespace oopse |
| 1776 |
> |
|
| 1777 |
> |
2004-10-15 14:38 chuckv |
| 1778 |
> |
|
| 1779 |
> |
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
| 1780 |
> |
XLF and XLC. |
| 1781 |
> |
|
| 1782 |
> |
2004-10-15 13:28 tim |
| 1783 |
> |
|
| 1784 |
> |
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
| 1785 |
> |
adding ifstrstream test case |
| 1786 |
> |
|
| 1787 |
> |
2004-10-15 13:20 tim |
| 1788 |
> |
|
| 1789 |
> |
* src/io/basic_ifstrstream.hpp: fix include |
| 1790 |
> |
|
| 1791 |
> |
2004-10-15 13:18 tim |
| 1792 |
> |
|
| 1793 |
> |
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
| 1794 |
> |
|
| 1795 |
> |
2004-10-15 13:17 tim |
| 1796 |
> |
|
| 1797 |
> |
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
| 1798 |
> |
|
| 1799 |
> |
2004-10-15 13:16 tim |
| 1800 |
> |
|
| 1801 |
> |
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
| 1802 |
> |
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
| 1803 |
> |
|
| 1804 |
> |
2004-10-15 10:37 tim |
| 1805 |
> |
|
| 1806 |
> |
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
| 1807 |
> |
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
| 1808 |
> |
|
| 1809 |
> |
2004-10-15 10:20 tim |
| 1810 |
> |
|
| 1811 |
> |
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
| 1812 |
> |
|
| 1813 |
> |
2004-10-15 10:19 tim |
| 1814 |
> |
|
| 1815 |
> |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
| 1816 |
> |
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
| 1817 |
> |
SquareMatrixTestCase class |
| 1818 |
> |
|
| 1819 |
> |
2004-10-15 02:52 tim |
| 1820 |
> |
|
| 1821 |
> |
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
| 1822 |
> |
|
| 1823 |
> |
2004-10-14 18:28 tim |
| 1824 |
> |
|
| 1825 |
> |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
| 1826 |
> |
Vector.hpp: math library in progress |
| 1827 |
> |
|
| 1828 |
> |
2004-10-14 18:27 tim |
| 1829 |
> |
|
| 1830 |
> |
* src/io/FileReader.hpp: FileReader in progress |
| 1831 |
> |
|
| 1832 |
> |
2004-10-13 18:53 tim |
| 1833 |
> |
|
| 1834 |
> |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
| 1835 |
> |
test in isOrthogonal of SquareMatrix is failed by some reasons |
| 1836 |
> |
|
| 1837 |
> |
2004-10-13 17:28 tim |
| 1838 |
> |
|
| 1839 |
> |
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
| 1840 |
> |
class |
| 1841 |
> |
|
| 1842 |
> |
2004-10-13 17:27 tim |
| 1843 |
> |
|
| 1844 |
> |
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
| 1845 |
> |
RectMatrixTestCase.hpp: adding testing unit |
| 1846 |
> |
|
| 1847 |
> |
2004-10-13 17:24 tim |
| 1848 |
> |
|
| 1849 |
> |
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
| 1850 |
> |
|
| 1851 |
> |
2004-10-13 01:51 tim |
| 1852 |
> |
|
| 1853 |
> |
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
| 1854 |
> |
Vector3.hpp: refactory vector and matrix classes |
| 1855 |
> |
|
| 1856 |
> |
2004-10-13 01:50 tim |
| 1857 |
> |
|
| 1858 |
> |
* src/math/Vector3d.hpp: Remove some Makefile.in |
| 1859 |
> |
|
| 1860 |
> |
2004-10-12 18:57 tim |
| 1861 |
> |
|
| 1862 |
> |
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
| 1863 |
> |
Matrix3x3d.hpp |
| 1864 |
> |
|
| 1865 |
> |
2004-10-12 14:08 tim |
| 1866 |
> |
|
| 1867 |
> |
* doc/: cppstyle.html, style.css: adding c++ coding style |
| 1868 |
> |
|
| 1869 |
> |
2004-10-11 17:15 tim |
| 1870 |
> |
|
| 1871 |
> |
* src/: constraints/AbstractClasses.hpp, |
| 1872 |
> |
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
| 1873 |
> |
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
| 1874 |
> |
|
| 1875 |
> |
2004-10-11 16:54 tim |
| 1876 |
> |
|
| 1877 |
> |
* scripts/filepp: fix a bug in filepp |
| 1878 |
> |
|
| 1879 |
> |
2004-10-11 16:13 tim |
| 1880 |
> |
|
| 1881 |
> |
* make/Makefile.in: using filepp to generate dependencies instead |
| 1882 |
> |
of compilers |
| 1883 |
> |
|
| 1884 |
> |
2004-10-11 16:10 tim |
| 1885 |
> |
|
| 1886 |
> |
* scripts/filepp: filepp can be used to generate dependencies for |
| 1887 |
> |
c/c++ now |
| 1888 |
> |
|
| 1889 |
> |
2004-10-11 13:40 tim |
| 1890 |
> |
|
| 1891 |
> |
* make/Makefile.in: remove -module from F90Options |
| 1892 |
> |
|
| 1893 |
> |
2004-10-11 13:01 tim |
| 1894 |
> |
|
| 1895 |
> |
* make/Makefile.in: adding rules to move fortran 90 module to |
| 1896 |
> |
target directory |
| 1897 |
> |
|
| 1898 |
> |
2004-10-11 10:43 gezelter |
| 1899 |
> |
|
| 1900 |
> |
* make/Makefile.in: fixed makefile.in |
| 1901 |
> |
|
| 1902 |
> |
2004-10-11 09:51 tim |
| 1903 |
> |
|
| 1904 |
> |
* scripts/filepp: remove "use bytes" which causes problem in sgi |
| 1905 |
> |
machine |
| 1906 |
> |
|
| 1907 |
> |
2004-10-11 09:26 tim |
| 1908 |
> |
|
| 1909 |
> |
* forceFields/Makefile: add Makefile |
| 1910 |
> |
|
| 1911 |
> |
2004-10-11 09:23 tim |
| 1912 |
> |
|
| 1913 |
> |
* samples/: water/dimer/Makefile, water/spce/Makefile, |
| 1914 |
> |
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
| 1915 |
> |
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
| 1916 |
> |
directory |
| 1917 |
> |
|
| 1918 |
> |
2004-10-11 09:23 tim |
| 1919 |
> |
|
| 1920 |
> |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
| 1921 |
> |
Makefile |
| 1922 |
> |
|
| 1923 |
> |
2004-10-09 01:01 tim |
| 1924 |
> |
|
| 1925 |
> |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
| 1926 |
> |
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
| 1927 |
> |
Remove some Makefile.in |
| 1928 |
> |
|
| 1929 |
> |
2004-10-08 18:15 tim |
| 1930 |
> |
|
| 1931 |
> |
* make/Makefile.in: [no log message] |
| 1932 |
> |
|
| 1933 |
> |
2004-10-08 17:51 tim |
| 1934 |
> |
|
| 1935 |
> |
* make/Makefile.in: fix make install |
| 1936 |
> |
|
| 1937 |
> |
2004-10-08 17:10 tim |
| 1938 |
> |
|
| 1939 |
> |
* make/Makefile.in: adding make install |
| 1940 |
> |
|
| 1941 |
> |
2004-10-08 17:04 tim |
| 1942 |
> |
|
| 1943 |
> |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
| 1944 |
> |
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
| 1945 |
> |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
| 1946 |
> |
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
| 1947 |
> |
water/ssde/Makefile, water/ssde/Makefile.in, |
| 1948 |
> |
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
| 1949 |
> |
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
| 1950 |
> |
zcons/Makefile.in: add Makefile to sample directory |
| 1951 |
> |
|
| 1952 |
> |
2004-10-06 18:03 gezelter |
| 1953 |
> |
|
| 1954 |
> |
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
| 1955 |
> |
stuff |
| 1956 |
> |
|
| 1957 |
> |
2004-10-06 18:03 gezelter |
| 1958 |
> |
|
| 1959 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1960 |
> |
make/Doxyfile, src/applications/getopt.c, |
| 1961 |
> |
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
| 1962 |
> |
build fixes |
| 1963 |
> |
|
| 1964 |
> |
2004-10-06 17:20 tim |
| 1965 |
> |
|
| 1966 |
> |
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
| 1967 |
> |
|
| 1968 |
> |
2004-10-06 17:19 tim |
| 1969 |
> |
|
| 1970 |
> |
* scripts/filepp: filepp can handle different fortran module case |
| 1971 |
> |
and suffix |
| 1972 |
> |
|
| 1973 |
> |
2004-10-06 16:27 gezelter |
| 1974 |
> |
|
| 1975 |
> |
* src/restraints/Restraints.cpp: Chris doesn't know about the |
| 1976 |
> |
OOPSE-2.0 directory structure yet |
| 1977 |
> |
|
| 1978 |
> |
2004-10-06 16:27 gezelter |
| 1979 |
> |
|
| 1980 |
> |
* ChangeLog: Yeah yeah, we'lll get around to it later |
| 1981 |
> |
|
| 1982 |
> |
2004-10-06 16:22 gezelter |
| 1983 |
> |
|
| 1984 |
> |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 1985 |
> |
make/Makefile.in: cleaning up build process |
| 1986 |
> |
|
| 1987 |
> |
2004-10-06 15:01 chrisfen |
| 1988 |
> |
|
| 1989 |
> |
* src/restraints/Restraints.cpp: made the file reading in |
| 1990 |
> |
restraints more intelligent - no longer gives uninformative seg |
| 1991 |
> |
faults |
| 1992 |
> |
|
| 1993 |
> |
2004-10-06 14:55 gezelter |
| 1994 |
> |
|
| 1995 |
> |
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
| 1996 |
> |
|
| 1997 |
> |
2004-10-06 14:51 gezelter |
| 1998 |
> |
|
| 1999 |
> |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
| 2000 |
> |
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
| 2001 |
> |
|
| 2002 |
> |
2004-10-06 13:53 tim |
| 2003 |
> |
|
| 2004 |
> |
* make/: Makefile, Makefile.in: fix make statistics |
| 2005 |
> |
|
| 2006 |
> |
2004-10-06 13:18 tim |
| 2007 |
> |
|
| 2008 |
> |
* make/: Makefile, Makefile.in: adding GNU make functions to |
| 2009 |
> |
combine all of the static libraries to a big library |
| 2010 |
> |
|
| 2011 |
> |
2004-10-05 17:57 tim |
| 2012 |
> |
|
| 2013 |
> |
* make/: Makefile, Makefile.in: adding shared library flag |
| 2014 |
> |
|
| 2015 |
> |
2004-10-05 14:37 tim |
| 2016 |
> |
|
| 2017 |
> |
* src/: Makefile, UseTheForce/Makefile, |
| 2018 |
> |
UseTheForce/mpiSimulation_module.F90, |
| 2019 |
> |
UseTheForce/DarkSide/Makefile, |
| 2020 |
> |
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
| 2021 |
> |
mpiSimulation_module to DarkSide |
| 2022 |
> |
|
| 2023 |
> |
2004-10-05 14:35 tim |
| 2024 |
> |
|
| 2025 |
> |
* make/: Makefile, Makefile.in: building MPI version;using static |
| 2026 |
> |
library instead of shared library |
| 2027 |
> |
|
| 2028 |
> |
2004-10-05 09:14 tim |
| 2029 |
> |
|
| 2030 |
> |
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
| 2031 |
> |
to filepp |
| 2032 |
> |
|
| 2033 |
> |
2004-10-04 15:56 tim |
| 2034 |
> |
|
| 2035 |
> |
* make/: Makefile, Makefile.in: add make cvslog |
| 2036 |
> |
|
| 2037 |
> |
2004-10-04 11:24 gezelter |
| 2038 |
> |
|
| 2039 |
> |
* make/: Makefile, Makefile.in: more work on the parallel build |
| 2040 |
> |
|
| 2041 |
> |
2004-10-04 11:06 gezelter |
| 2042 |
> |
|
| 2043 |
> |
* make/: Makefile, Makefile.in: changes to backport declare flags |
| 2044 |
> |
|
| 2045 |
> |
2004-10-04 10:27 gezelter |
| 2046 |
> |
|
| 2047 |
> |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
| 2048 |
> |
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
| 2049 |
> |
shapes |
| 2050 |
> |
|
| 2051 |
> |
2004-10-01 23:40 tim |
| 2052 |
> |
|
| 2053 |
> |
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
| 2054 |
> |
|
| 2055 |
> |
2004-10-01 23:22 tim |
| 2056 |
> |
|
| 2057 |
> |
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
| 2058 |
> |
|
| 2059 |
> |
2004-10-01 16:59 tim |
| 2060 |
> |
|
| 2061 |
> |
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
| 2062 |
> |
|
| 2063 |
> |
2004-10-01 16:22 gezelter |
| 2064 |
> |
|
| 2065 |
> |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
| 2066 |
> |
few minor build changes |
| 2067 |
> |
|
| 2068 |
> |
2004-10-01 16:11 tim |
| 2069 |
> |
|
| 2070 |
> |
* scripts/filepp: adding fortran90 make dependency tool |
| 2071 |
> |
|
| 2072 |
> |
2004-09-30 10:41 tim |
| 2073 |
> |
|
| 2074 |
> |
* make/: Makefile, Makefile.in: make clean is smart enough to only |
| 2075 |
> |
remove object files belong to current package. turn off silent |
| 2076 |
> |
mode |
| 2077 |
> |
|
| 2078 |
> |
2004-09-29 16:55 tim |
| 2079 |
> |
|
| 2080 |
> |
* src/: Makefile, UseTheForce/Makefile, |
| 2081 |
> |
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
| 2082 |
> |
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
| 2083 |
> |
brains/Makedepend, brains/Makefile, constraints/Makefile, |
| 2084 |
> |
integrators/Makefile, io/Makefile, math/Makefile, |
| 2085 |
> |
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
| 2086 |
> |
restraints/Makefile, types/Makefile, utils/Makefile, |
| 2087 |
> |
visitors/Makefile: define DEV_ROOT as relative path |
| 2088 |
> |
|
| 2089 |
> |
2004-09-29 16:54 tim |
| 2090 |
> |
|
| 2091 |
> |
* make/: Makefile, Makefile.in: get the relative path by shell |
| 2092 |
> |
script |
| 2093 |
> |
|
| 2094 |
> |
2004-09-29 16:32 tim |
| 2095 |
> |
|
| 2096 |
> |
* make/Makefile: eliminate DEV_ROOT by relative path |
| 2097 |
> |
|
| 2098 |
> |
2004-09-29 13:37 tim |
| 2099 |
> |
|
| 2100 |
> |
* make/Makefile.in: add PackageLibs; fix dependency rule |
| 2101 |
> |
|
| 2102 |
> |
2004-09-29 12:57 gezelter |
| 2103 |
> |
|
| 2104 |
> |
* configure, ac-tools/configure.in: updates |
| 2105 |
> |
|
| 2106 |
> |
2004-09-29 12:56 gezelter |
| 2107 |
> |
|
| 2108 |
> |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
| 2109 |
> |
|
| 2110 |
> |
2004-09-29 12:46 tim |
| 2111 |
> |
|
| 2112 |
> |
* Makefile: If makefile does not exist, print error message |
| 2113 |
> |
|
| 2114 |
> |
2004-09-29 12:12 tim |
| 2115 |
> |
|
| 2116 |
> |
* make/: Make.conf.in, Makefile: fix dependencies rule |
| 2117 |
> |
|
| 2118 |
> |
2004-09-29 10:58 gezelter |
| 2119 |
> |
|
| 2120 |
> |
* Makefile, make/Makefile: still working on build process |
| 2121 |
> |
|
| 2122 |
> |
2004-09-29 10:00 tim |
| 2123 |
> |
|
| 2124 |
> |
* make/Makefile: add print statment to rules |
| 2125 |
> |
|
| 2126 |
> |
2004-09-29 09:59 tim |
| 2127 |
> |
|
| 2128 |
> |
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
| 2129 |
> |
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
| 2130 |
> |
applications/simpleBuilder/Makefile, brains/Makefile, |
| 2131 |
> |
constraints/Makefile, integrators/Makefile, io/Makefile, |
| 2132 |
> |
math/Makefile, minimizers/Makefile, primitives/Makefile, |
| 2133 |
> |
profiling/Makefile, restraints/Makefile, types/Makefile, |
| 2134 |
> |
utils/Makefile, visitors/Makefile: change Makefile to relative path |
| 2135 |
> |
|
| 2136 |
> |
2004-09-28 21:55 tim |
| 2137 |
> |
|
| 2138 |
> |
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
| 2139 |
> |
which cause headache in bulding libutils |
| 2140 |
> |
|
| 2141 |
> |
2004-09-28 18:24 tim |
| 2142 |
> |
|
| 2143 |
> |
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
| 2144 |
> |
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
| 2145 |
> |
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 2146 |
> |
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
| 2147 |
> |
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
| 2148 |
> |
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
| 2149 |
> |
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
| 2150 |
> |
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
| 2151 |
> |
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
| 2152 |
> |
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
| 2153 |
> |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 2154 |
> |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 2155 |
> |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 2156 |
> |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
| 2157 |
> |
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
| 2158 |
> |
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
| 2159 |
> |
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
| 2160 |
> |
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
| 2161 |
> |
change directory structure of application. Every executable file is |
| 2162 |
> |
replaced in seperate directory |
| 2163 |
> |
|
| 2164 |
> |
2004-09-28 17:15 gezelter |
| 2165 |
> |
|
| 2166 |
> |
* lib/dummy: Keep that lib around, please. |
| 2167 |
> |
|
| 2168 |
> |
2004-09-28 17:14 gezelter |
| 2169 |
> |
|
| 2170 |
> |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
| 2171 |
> |
starting a configure version |
| 2172 |
> |
|
| 2173 |
> |
2004-09-28 16:08 tim |
| 2174 |
> |
|
| 2175 |
> |
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
| 2176 |
> |
UseTheForce/DarkSide/Makefile, |
| 2177 |
> |
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 2178 |
> |
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
| 2179 |
> |
brains/Makefile, brains/simulation_module.F90: move fortran files |
| 2180 |
> |
around to solve dependency problem |
| 2181 |
> |
|
| 2182 |
> |
2004-09-28 15:43 tim |
| 2183 |
> |
|
| 2184 |
> |
* Makefile, src/UseTheForce/ForceFields.hpp, |
| 2185 |
> |
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
| 2186 |
> |
src/applications/Makedepend, src/applications/Makefile, |
| 2187 |
> |
src/brains/Makedepend, src/brains/simulation_module.F90, |
| 2188 |
> |
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
| 2189 |
> |
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
| 2190 |
> |
src/utils/Makefile: [no log message] |
| 2191 |
> |
|
| 2192 |
> |
2004-09-28 15:41 tim |
| 2193 |
> |
|
| 2194 |
> |
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
| 2195 |
> |
problem |
| 2196 |
> |
|
| 2197 |
> |
2004-09-28 11:13 tim |
| 2198 |
> |
|
| 2199 |
> |
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
| 2200 |
> |
src/io/Makefile: add yacc and lex rules |
| 2201 |
> |
|
| 2202 |
> |
2004-09-27 15:24 tim |
| 2203 |
> |
|
| 2204 |
> |
* make/Makefile: adding include path to F90Options |
| 2205 |
> |
|
| 2206 |
> |
2004-09-27 15:13 tim |
| 2207 |
> |
|
| 2208 |
> |
* make/Makefile: change suffix from .cc to .cpp |
| 2209 |
> |
|
| 2210 |
> |
2004-09-24 11:27 tim |
| 2211 |
> |
|
| 2212 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 2213 |
> |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 2214 |
> |
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
| 2215 |
> |
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
| 2216 |
> |
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
| 2217 |
> |
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
| 2218 |
> |
UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 2219 |
> |
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 2220 |
> |
UseTheForce/DarkSide/switch_module.F90, |
| 2221 |
> |
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
| 2222 |
> |
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
| 2223 |
> |
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
| 2224 |
> |
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
| 2225 |
> |
applications/MoLocator.cpp, applications/MoLocator.hpp, |
| 2226 |
> |
applications/cmdline.c, applications/nanoBuilder.cpp, |
| 2227 |
> |
applications/oopse.cpp, applications/simpleBuilder.cpp, |
| 2228 |
> |
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
| 2229 |
> |
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 2230 |
> |
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
| 2231 |
> |
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 2232 |
> |
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
| 2233 |
> |
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
| 2234 |
> |
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
| 2235 |
> |
integrators/Integrator.hpp, integrators/NPT.cpp, |
| 2236 |
> |
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
| 2237 |
> |
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
| 2238 |
> |
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
| 2239 |
> |
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
| 2240 |
> |
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
| 2241 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 2242 |
> |
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
| 2243 |
> |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
| 2244 |
> |
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
| 2245 |
> |
math/MatVec3.h, math/randomSPRNG.cpp, |
| 2246 |
> |
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
| 2247 |
> |
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
| 2248 |
> |
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
| 2249 |
> |
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
| 2250 |
> |
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
| 2251 |
> |
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
| 2252 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 2253 |
> |
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
| 2254 |
> |
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
| 2255 |
> |
primitives/RigidBody.hpp, primitives/SRI.hpp, |
| 2256 |
> |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 2257 |
> |
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
| 2258 |
> |
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
| 2259 |
> |
restraints/Restraints.hpp, types/AtomStamp.cpp, |
| 2260 |
> |
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
| 2261 |
> |
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
| 2262 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 2263 |
> |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
| 2264 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 2265 |
> |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 2266 |
> |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 2267 |
> |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
| 2268 |
> |
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
| 2269 |
> |
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
| 2270 |
> |
utils/simError.c, visitors/AtomVisitor.cpp, |
| 2271 |
> |
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
| 2272 |
> |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
| 2273 |
> |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 2274 |
> |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
| 2275 |
> |
visitors/ZconsVisitor.hpp: change the #include in source files |
| 2276 |
> |
|
| 2277 |
> |
2004-09-23 23:16 gezelter |
| 2278 |
> |
|
| 2279 |
> |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 2280 |
> |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 2281 |
> |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 2282 |
> |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 2283 |
> |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 2284 |
> |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 2285 |
> |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 2286 |
> |
src/UseTheForce/fForceField.h, |
| 2287 |
> |
src/UseTheForce/fSwitchingFunction.h, |
| 2288 |
> |
src/UseTheForce/fortranWrapDefines.hpp, |
| 2289 |
> |
src/UseTheForce/fortranWrappers.cpp, |
| 2290 |
> |
src/UseTheForce/fortranWrappers.hpp, |
| 2291 |
> |
src/UseTheForce/mpiComponentPlan.h, |
| 2292 |
> |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 2293 |
> |
src/UseTheForce/mpiSimulation_module.F90, |
| 2294 |
> |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 2295 |
> |
src/UseTheForce/DarkSide/atype_module.F90, |
| 2296 |
> |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 2297 |
> |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 2298 |
> |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 2299 |
> |
src/UseTheForce/DarkSide/calc_eam.F90, |
| 2300 |
> |
src/UseTheForce/DarkSide/calc_gb.F90, |
| 2301 |
> |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 2302 |
> |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 2303 |
> |
src/UseTheForce/DarkSide/force_globals.F90, |
| 2304 |
> |
src/UseTheForce/DarkSide/neighborLists.F90, |
| 2305 |
> |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 2306 |
> |
src/UseTheForce/DarkSide/switch_module.F90, |
| 2307 |
> |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 2308 |
> |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 2309 |
> |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 2310 |
> |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 2311 |
> |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 2312 |
> |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 2313 |
> |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 2314 |
> |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 2315 |
> |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 2316 |
> |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 2317 |
> |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 2318 |
> |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 2319 |
> |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 2320 |
> |
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 2321 |
> |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 2322 |
> |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 2323 |
> |
src/types/MakeStamps.hpp, src/types/Makefile, |
| 2324 |
> |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 2325 |
> |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 2326 |
> |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 2327 |
> |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 2328 |
> |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 2329 |
> |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 2330 |
> |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 2331 |
> |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 2332 |
> |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 2333 |
> |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 2334 |
> |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 2335 |
> |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 2336 |
> |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 2337 |
> |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 2338 |
> |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 2339 |
> |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 2340 |
> |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 2341 |
> |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 2342 |
> |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 2343 |
> |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 2344 |
> |
src/minimizers/OOPSEMinimizer.cpp, |
| 2345 |
> |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 2346 |
> |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 2347 |
> |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 2348 |
> |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 2349 |
> |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 2350 |
> |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 2351 |
> |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 2352 |
> |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 2353 |
> |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 2354 |
> |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 2355 |
> |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 2356 |
> |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 2357 |
> |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 2358 |
> |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 2359 |
> |
src/utils/GenericData.hpp, src/utils/Makefile, |
| 2360 |
> |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 2361 |
> |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 2362 |
> |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 2363 |
> |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 2364 |
> |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 2365 |
> |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 2366 |
> |
src/utils/simError.c, src/utils/simError.h, |
| 2367 |
> |
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 2368 |
> |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 2369 |
> |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 2370 |
> |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 2371 |
> |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 2372 |
> |
src/visitors/RigidBodyVisitor.cpp, |
| 2373 |
> |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 2374 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 2375 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 2376 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 2377 |
> |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 2378 |
> |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 2379 |
> |
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 2380 |
> |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 2381 |
> |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 2382 |
> |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 2383 |
> |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 2384 |
> |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 2385 |
> |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 2386 |
> |
src/applications/LatticeCreator.cpp, |
| 2387 |
> |
src/applications/LatticeCreator.hpp, |
| 2388 |
> |
src/applications/LatticeFactory.cpp, |
| 2389 |
> |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 2390 |
> |
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 2391 |
> |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 2392 |
> |
src/applications/cmdline.c, src/applications/cmdline.h, |
| 2393 |
> |
src/applications/getopt.c, src/applications/getopt1.c, |
| 2394 |
> |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 2395 |
> |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 2396 |
> |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 2397 |
> |
src/applications/simpleBuilder.ggo, |
| 2398 |
> |
src/applications/simpleBuilderCmd.c, |
| 2399 |
> |
src/integrators/AbstractClasses.hpp, |
| 2400 |
> |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 2401 |
> |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 2402 |
> |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 2403 |
> |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 2404 |
> |
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 2405 |
> |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 2406 |
> |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 2407 |
> |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 2408 |
> |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 2409 |
> |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 2410 |
> |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 2411 |
> |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 2412 |
> |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 2413 |
> |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 2414 |
> |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 2415 |
> |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 2416 |
> |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 2417 |
> |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 2418 |
> |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 2419 |
> |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 2420 |
> |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 2421 |
> |
samples/alkane/butane.in, samples/alkane/butane.md, |
| 2422 |
> |
samples/argon/500.in, samples/argon/500.md, |
| 2423 |
> |
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 2424 |
> |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 2425 |
> |
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 2426 |
> |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 2427 |
> |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 2428 |
> |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 2429 |
> |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 2430 |
> |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 2431 |
> |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 2432 |
> |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 2433 |
> |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 2434 |
> |
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 2435 |
> |
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 2436 |
> |
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 2437 |
> |
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 2438 |
> |
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 2439 |
> |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 2440 |
> |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 2441 |
> |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 2442 |
> |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 2443 |
> |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 2444 |
> |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 2445 |
> |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 2446 |
> |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 2447 |
> |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 2448 |
> |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 2449 |
> |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 2450 |
> |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
| 2451 |
> |
|
| 2452 |
> |
2004-09-23 23:16 gezelter |
| 2453 |
> |
|
| 2454 |
> |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 2455 |
> |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 2456 |
> |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 2457 |
> |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 2458 |
> |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 2459 |
> |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 2460 |
> |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 2461 |
> |
src/UseTheForce/fForceField.h, |
| 2462 |
> |
src/UseTheForce/fSwitchingFunction.h, |
| 2463 |
> |
src/UseTheForce/fortranWrapDefines.hpp, |
| 2464 |
> |
src/UseTheForce/fortranWrappers.cpp, |
| 2465 |
> |
src/UseTheForce/fortranWrappers.hpp, |
| 2466 |
> |
src/UseTheForce/mpiComponentPlan.h, |
| 2467 |
> |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 2468 |
> |
src/UseTheForce/mpiSimulation_module.F90, |
| 2469 |
> |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 2470 |
> |
src/UseTheForce/DarkSide/atype_module.F90, |
| 2471 |
> |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 2472 |
> |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 2473 |
> |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 2474 |
> |
src/UseTheForce/DarkSide/calc_eam.F90, |
| 2475 |
> |
src/UseTheForce/DarkSide/calc_gb.F90, |
| 2476 |
> |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 2477 |
> |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 2478 |
> |
src/UseTheForce/DarkSide/force_globals.F90, |
| 2479 |
> |
src/UseTheForce/DarkSide/neighborLists.F90, |
| 2480 |
> |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 2481 |
> |
src/UseTheForce/DarkSide/switch_module.F90, |
| 2482 |
> |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 2483 |
> |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 2484 |
> |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 2485 |
> |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 2486 |
> |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 2487 |
> |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 2488 |
> |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 2489 |
> |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 2490 |
> |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 2491 |
> |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 2492 |
> |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 2493 |
> |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 2494 |
> |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 2495 |
> |
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 2496 |
> |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 2497 |
> |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 2498 |
> |
src/types/MakeStamps.hpp, src/types/Makefile, |
| 2499 |
> |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 2500 |
> |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 2501 |
> |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 2502 |
> |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 2503 |
> |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 2504 |
> |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 2505 |
> |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 2506 |
> |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 2507 |
> |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 2508 |
> |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 2509 |
> |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 2510 |
> |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 2511 |
> |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 2512 |
> |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 2513 |
> |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 2514 |
> |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 2515 |
> |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 2516 |
> |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 2517 |
> |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 2518 |
> |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 2519 |
> |
src/minimizers/OOPSEMinimizer.cpp, |
| 2520 |
> |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 2521 |
> |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 2522 |
> |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 2523 |
> |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 2524 |
> |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 2525 |
> |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 2526 |
> |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 2527 |
> |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 2528 |
> |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 2529 |
> |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 2530 |
> |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 2531 |
> |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 2532 |
> |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 2533 |
> |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 2534 |
> |
src/utils/GenericData.hpp, src/utils/Makefile, |
| 2535 |
> |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 2536 |
> |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 2537 |
> |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 2538 |
> |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 2539 |
> |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 2540 |
> |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 2541 |
> |
src/utils/simError.c, src/utils/simError.h, |
| 2542 |
> |
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 2543 |
> |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 2544 |
> |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 2545 |
> |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 2546 |
> |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 2547 |
> |
src/visitors/RigidBodyVisitor.cpp, |
| 2548 |
> |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 2549 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 2550 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 2551 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 2552 |
> |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 2553 |
> |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 2554 |
> |
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 2555 |
> |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 2556 |
> |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 2557 |
> |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 2558 |
> |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 2559 |
> |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 2560 |
> |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 2561 |
> |
src/applications/LatticeCreator.cpp, |
| 2562 |
> |
src/applications/LatticeCreator.hpp, |
| 2563 |
> |
src/applications/LatticeFactory.cpp, |
| 2564 |
> |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 2565 |
> |
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 2566 |
> |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 2567 |
> |
src/applications/cmdline.c, src/applications/cmdline.h, |
| 2568 |
> |
src/applications/getopt.c, src/applications/getopt1.c, |
| 2569 |
> |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 2570 |
> |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 2571 |
> |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 2572 |
> |
src/applications/simpleBuilder.ggo, |
| 2573 |
> |
src/applications/simpleBuilderCmd.c, |
| 2574 |
> |
src/integrators/AbstractClasses.hpp, |
| 2575 |
> |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 2576 |
> |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 2577 |
> |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 2578 |
> |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 2579 |
> |
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 2580 |
> |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 2581 |
> |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 2582 |
> |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 2583 |
> |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 2584 |
> |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 2585 |
> |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 2586 |
> |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 2587 |
> |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 2588 |
> |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 2589 |
> |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 2590 |
> |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 2591 |
> |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 2592 |
> |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 2593 |
> |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 2594 |
> |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 2595 |
> |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 2596 |
> |
samples/alkane/butane.in, samples/alkane/butane.md, |
| 2597 |
> |
samples/argon/500.in, samples/argon/500.md, |
| 2598 |
> |
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 2599 |
> |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 2600 |
> |
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 2601 |
> |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 2602 |
> |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 2603 |
> |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 2604 |
> |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 2605 |
> |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 2606 |
> |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 2607 |
> |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 2608 |
> |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 2609 |
> |
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 2610 |
> |
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 2611 |
> |
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 2612 |
> |
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 2613 |
> |
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 2614 |
> |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 2615 |
> |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 2616 |
> |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 2617 |
> |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 2618 |
> |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 2619 |
> |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 2620 |
> |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 2621 |
> |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 2622 |
> |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 2623 |
> |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 2624 |
> |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 2625 |
> |
forceFields/Pt.VC.funcfl: Initial revision |
| 2626 |
|
|
