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tim |
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2004-11-24 12:42 tim |
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* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
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brains/DataStorage.hpp, brains/SimCreator.cpp, |
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brains/SimCreator.hpp, integrators/Integrator.hpp, |
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io/ElectrostaticAtomTypesSectionParser.cpp, |
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primitives/DirectionalAtom.cpp: add SetForceManager method to |
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integrator |
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2004-11-23 18:12 tim |
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* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
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integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
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integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
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integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, |
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integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, |
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integrators/NVT.hpp, integrators/Velocitizer.cpp, |
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integrators/VelocityVerletIntegrator.cpp, |
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integrators/VelocityVerletIntegrator.hpp, |
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types/UreyBradleyBendType.hpp: refactory NPT integrator |
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2004-11-23 17:50 chrisfen |
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* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
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Restraints should work in parallel now |
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2004-11-23 17:48 chrisfen |
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* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
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brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
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integrators/Integrator.cpp, integrators/Integrator.hpp, |
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io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, |
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io/RestraintReader.cpp, io/RestraintWriter.cpp, |
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restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
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to restraints |
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2004-11-23 17:47 chrisfen |
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* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
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return to the original on next commit |
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2004-11-23 12:53 tim |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
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UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
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applications/simpleBuilder/simpleBuilder.cpp, |
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io/ChargeAtomTypesSectionParser.cpp, |
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io/DirectionalAtomTypesSectionParser.hpp, |
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io/EAMAtomTypesSectionParser.cpp, |
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io/ElectrostaticAtomTypesSectionParser.cpp, |
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io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
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io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
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utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
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2004-11-23 12:53 tim |
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* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
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ElectrostaticAtomTypesSectionParser.hpp was initially added on |
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branch new_design. |
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2004-11-23 12:53 tim |
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* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
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ElectrostaticAtomTypesSectionParser.cpp was initially added on |
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branch new_design. |
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2004-11-23 01:03 tim |
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* src/: io/EAMAtomTypesSectionParser.cpp, |
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io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
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types/AtomType.hpp, types/DirectionalAtomType.cpp, |
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types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
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2004-11-23 01:03 tim |
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* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
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was initially added on branch new_design. |
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2004-11-23 01:03 tim |
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* src/io/EAMAtomTypesSectionParser.hpp: file |
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EAMAtomTypesSectionParser.hpp was initially added on branch |
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new_design. |
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2004-11-23 01:03 tim |
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* src/io/EAMAtomTypesSectionParser.cpp: file |
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EAMAtomTypesSectionParser.cpp was initially added on branch |
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new_design. |
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2004-11-22 23:35 tim |
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* src/io/TorsionTypesSectionParser.hpp: file |
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TorsionTypesSectionParser.hpp was initially added on branch |
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new_design. |
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2004-11-22 23:35 tim |
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* src/io/BendTypesSectionParser.hpp: file |
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BendTypesSectionParser.hpp was initially added on branch |
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new_design. |
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2004-11-22 23:35 tim |
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* src/io/BondTypesSectionParser.hpp: file |
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BondTypesSectionParser.hpp was initially added on branch |
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new_design. |
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2004-11-22 23:35 tim |
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* src/io/BondTypesSectionParser.cpp: file |
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BondTypesSectionParser.cpp was initially added on branch |
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new_design. |
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2004-11-22 23:35 tim |
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* src/io/TorsionTypesSectionParser.cpp: file |
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TorsionTypesSectionParser.cpp was initially added on branch |
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new_design. |
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2004-11-22 23:35 tim |
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* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
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BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
125 |
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TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add |
126 |
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BondTypesSectionParser, BendTypesSectionParser and |
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TorsionTypeSectionParser |
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129 |
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2004-11-22 23:35 tim |
130 |
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131 |
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* src/io/BendTypesSectionParser.cpp: file |
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BendTypesSectionParser.cpp was initially added on branch |
133 |
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new_design. |
134 |
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135 |
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2004-11-22 18:04 tim |
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* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
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DUFF and EAM |
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140 |
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2004-11-22 18:02 tim |
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* src/io/: DirectionalAtomTypesParser.hpp, |
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DirectionalAtomTypesSectionParser.hpp: adding section parsers |
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145 |
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2004-11-22 18:02 tim |
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147 |
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* src/io/DirectionalAtomTypesSectionParser.hpp: file |
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DirectionalAtomTypesSectionParser.hpp was initially added on branch |
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new_design. |
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151 |
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2004-11-22 15:55 tim |
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153 |
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* src/io/DipoleAtomTypesSectionParser.hpp: file |
154 |
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DipoleAtomTypesSectionParser.hpp was initially added on branch |
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new_design. |
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157 |
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2004-11-22 15:55 tim |
158 |
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159 |
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* src/io/AtomTypesSectionParser.hpp: file |
160 |
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AtomTypesSectionParser.hpp was initially added on branch |
161 |
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new_design. |
162 |
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163 |
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2004-11-22 15:55 tim |
164 |
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165 |
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* src/io/HarmonicBondTypesSectionParser.hpp: file |
166 |
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HarmonicBondTypesSectionParser.hpp was initially added on branch |
167 |
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new_design. |
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169 |
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2004-11-22 15:55 tim |
170 |
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171 |
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* src/io/StickyAtomTypesSectionParser.cpp: file |
172 |
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StickyAtomTypesSectionParser.cpp was initially added on branch |
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new_design. |
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2004-11-22 15:55 tim |
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* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
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LennardJonesAtomTypesSectionParser.hpp was initially added on |
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branch new_design. |
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2004-11-22 15:55 tim |
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* src/io/HarmonicBondTypesSectionParser.cpp: file |
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HarmonicBondTypesSectionParser.cpp was initially added on branch |
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new_design. |
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187 |
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2004-11-22 15:55 tim |
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189 |
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* src/io/DirectionalAtomTypesSectionParser.cpp: file |
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DirectionalAtomTypesSectionParser.cpp was initially added on branch |
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new_design. |
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2004-11-22 15:55 tim |
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* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
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was initially added on branch new_design. |
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198 |
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2004-11-22 15:55 tim |
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200 |
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* src/io/AtomTypesSectionParser.cpp: file |
201 |
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AtomTypesSectionParser.cpp was initially added on branch |
202 |
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new_design. |
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204 |
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2004-11-22 15:55 tim |
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* src/io/ChargeAtomTypesSectionParser.cpp: file |
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ChargeAtomTypesSectionParser.cpp was initially added on branch |
208 |
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new_design. |
209 |
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210 |
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2004-11-22 15:55 tim |
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212 |
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* src/io/DipoleAtomTypesSectionParser.cpp: file |
213 |
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DipoleAtomTypesSectionParser.cpp was initially added on branch |
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new_design. |
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216 |
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2004-11-22 15:55 tim |
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* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
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LennardJonesAtomTypesSectionParser.cpp was initially added on |
220 |
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branch new_design. |
221 |
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222 |
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2004-11-22 15:55 tim |
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* src/io/ChargeAtomTypesSectionParser.hpp: file |
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ChargeAtomTypesSectionParser.hpp was initially added on branch |
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new_design. |
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228 |
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2004-11-22 15:55 tim |
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* src/io/StickyAtomTypesSectionParser.hpp: file |
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StickyAtomTypesSectionParser.hpp was initially added on branch |
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new_design. |
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2004-11-22 15:55 tim |
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* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
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added on branch new_design. |
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239 |
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2004-11-22 15:55 tim |
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241 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
242 |
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brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
243 |
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brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
244 |
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integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
245 |
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io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
246 |
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io/ChargeAtomTypesSectionParser.hpp, |
247 |
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io/DipoleAtomTypesSectionParser.cpp, |
248 |
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io/DipoleAtomTypesSectionParser.hpp, |
249 |
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io/DirectionalAtomTypesParser.hpp, |
250 |
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io/DirectionalAtomTypesSectionParser.cpp, |
251 |
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io/HarmonicBondTypesSectionParser.cpp, |
252 |
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io/HarmonicBondTypesSectionParser.hpp, |
253 |
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io/LennardJonesAtomTypesSectionParser.cpp, |
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io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
255 |
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io/SectionParser.hpp, io/SectionParserManager.cpp, |
256 |
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io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
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io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
258 |
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types/AtomType.hpp, types/DirectionalAtomType.hpp, |
259 |
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utils/GenericData.hpp: adding section parsers |
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2004-11-22 15:55 tim |
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* src/io/DirectionalAtomTypesParser.hpp: file |
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DirectionalAtomTypesParser.hpp was initially added on branch |
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new_design. |
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2004-11-22 15:55 tim |
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269 |
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* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
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was initially added on branch new_design. |
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2004-11-22 15:55 tim |
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* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
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added on branch new_design. |
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2004-11-19 17:12 tim |
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* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
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added on branch new_design. |
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2004-11-19 17:12 tim |
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* src/: brains/SimState.cpp, brains/SimState.hpp, |
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io/InitializeFromFile.cpp, types/FixBondType.hpp, |
286 |
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types/FixedBondType.hpp: remove more useless files |
287 |
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288 |
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2004-11-19 16:47 tim |
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290 |
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* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
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integrators/Integrator.cpp, applications/Makedepend: remove more |
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useless files |
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2004-11-19 16:38 tim |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
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UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
298 |
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integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
299 |
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integrators/NVT.hpp: refactory integrator |
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2004-11-19 16:38 tim |
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* src/integrators/NPTi.hpp: file NPTi.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/NPTf.hpp: file NPTf.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/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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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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2004-11-19 15:37 tim |
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* forceFields/newDUFF.frc: new DUFF forcefield |
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2004-11-19 15:23 tim |
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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, |
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UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
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utils/TypeContainer.hpp: add EAM |
340 |
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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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* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
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error checking |
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2004-11-19 12:56 tim |
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* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
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was initially added on branch new_design. |
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2004-11-19 12:56 tim |
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* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
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was initially added on branch new_design. |
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2004-11-19 12:56 tim |
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* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
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added on branch new_design. |
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2004-11-19 12:56 tim |
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* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
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UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
370 |
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UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, |
371 |
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integrators/IntegratorFactory.cpp, |
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integrators/IntegratorFactory.hpp, integrators/NVE.hpp, |
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integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, |
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utils/StringTokenizer.cpp: DUFF is almost done except error |
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checking |
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2004-11-18 19:11 tim |
378 |
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|
379 |
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* src/UseTheForce/DUFF.cpp: adding DUFF parser |
380 |
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|
381 |
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2004-11-18 18:26 tim |
382 |
|
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|
383 |
|
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* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
384 |
|
|
initially added on branch new_design. |
385 |
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|
386 |
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2004-11-18 18:26 tim |
387 |
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|
388 |
|
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* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
389 |
|
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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 |
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|
400 |
|
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* forceFields/newDUFF.frc: adding new format DUFF force field |
401 |
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|
402 |
|
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2004-11-18 10:57 chrisfen |
403 |
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|
404 |
|
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* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
405 |
|
|
slowed down the force loop |
406 |
|
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|
407 |
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2004-11-18 00:42 tim |
408 |
|
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|
409 |
|
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* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
410 |
|
|
initially added on branch new_design. |
411 |
|
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|
412 |
|
|
2004-11-18 00:42 tim |
413 |
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|
414 |
|
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* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
415 |
|
|
initially added on branch new_design. |
416 |
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|
417 |
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2004-11-18 00:42 tim |
418 |
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|
419 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
420 |
|
|
primitives/Bend.cpp, utils/NumericConstant.cpp, |
421 |
|
|
utils/NumericConstant.hpp: Adding NumericConstant class |
422 |
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|
423 |
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2004-11-17 23:16 tim |
424 |
|
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|
425 |
|
|
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
426 |
|
|
UseTheForce/ForceFields.hpp: remove more junk files |
427 |
|
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|
428 |
|
|
2004-11-17 23:12 tim |
429 |
|
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|
430 |
|
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* 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 |
|
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|
439 |
|
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* src/primitives/BendExtensions.cpp: remove some junk files |
440 |
|
|
|
441 |
|
|
2004-11-17 23:04 tim |
442 |
|
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|
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 |
chrisfen |
1714 |
2004-11-04 21:56 tim |
877 |
tim |
1701 |
|
878 |
chrisfen |
1714 |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
879 |
|
|
primitives/Molecule.hpp: Pain...... |
880 |
tim |
1712 |
|
881 |
chrisfen |
1714 |
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 |
tim |
1712 |
2004-11-04 14:48 tim |
893 |
|
|
|
894 |
|
|
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
895 |
tim |
1701 |
branch new_design. |
896 |
|
|
|
897 |
tim |
1712 |
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 |
chrisfen |
1714 |
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 |
tim |
1712 |
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 |
chrisfen |
1714 |
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 |
tim |
1712 |
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 |
chrisfen |
1714 |
* 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 |
tim |
1712 |
* 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 |
chrisfen |
1714 |
2004-11-02 11:59 tim |
997 |
tim |
1712 |
|
998 |
chrisfen |
1714 |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
999 |
|
|
branch new_design. |
1000 |
tim |
1712 |
|
1001 |
tim |
1701 |
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 |
chrisfen |
1714 |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
1015 |
|
|
functions for dealing with memory issue |
1016 |
tim |
1701 |
|
1017 |
|
|
2004-11-02 10:27 tim |
1018 |
|
|
|
1019 |
chrisfen |
1714 |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
1020 |
|
|
added on branch new_design. |
1021 |
tim |
1701 |
|
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 |
tim |
1681 |
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 |
tim |
1677 |
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 |
tim |
1674 |
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 |
tim |
1677 |
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 |
tim |
1674 |
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 |
tim |
1648 |
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 |
tim |
1644 |
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 |
tim |
1643 |
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 |
tim |
1639 |
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 |
tim |
1630 |
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 |
tim |
1625 |
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 |
tim |
1622 |
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 |
tim |
1616 |
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 |
tim |
1603 |
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 |
tim |
1594 |
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 |
gezelter |
1536 |
2004-10-06 16:22 gezelter |
1983 |
gezelter |
1490 |
|
1984 |
tim |
1594 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
1985 |
|
|
make/Makefile.in: cleaning up build process |
1986 |
gezelter |
1490 |
|
1987 |
tim |
1594 |
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 |
gezelter |
1536 |
2004-10-06 14:51 gezelter |
1998 |
gezelter |
1490 |
|
1999 |
tim |
1594 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
2000 |
|
|
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
2001 |
gezelter |
1490 |
|
2002 |
tim |
1594 |
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 |
gezelter |
1536 |
2004-10-01 16:22 gezelter |
2064 |
gezelter |
1490 |
|
2065 |
tim |
1594 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
2066 |
|
|
few minor build changes |
2067 |
gezelter |
1490 |
|
2068 |
tim |
1594 |
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 |
gezelter |
1536 |
2004-09-29 12:57 gezelter |
2103 |
gezelter |
1490 |
|
2104 |
gezelter |
1536 |
* configure, ac-tools/configure.in: updates |
2105 |
gezelter |
1490 |
|
2106 |
tim |
1594 |
2004-09-29 12:56 gezelter |
2107 |
|
|
|
2108 |
tim |
1779 |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
2109 |
tim |
1594 |
|
2110 |
gezelter |
1536 |
2004-09-29 12:46 tim |
2111 |
gezelter |
1490 |
|
2112 |
gezelter |
1536 |
* Makefile: If makefile does not exist, print error message |
2113 |
gezelter |
1490 |
|
2114 |
tim |
1594 |
2004-09-29 12:12 tim |
2115 |
|
|
|
2116 |
|
|
* make/: Make.conf.in, Makefile: fix dependencies rule |
2117 |
|
|
|
2118 |
gezelter |
1536 |
2004-09-29 10:58 gezelter |
2119 |
gezelter |
1490 |
|
2120 |
tim |
1594 |
* Makefile, make/Makefile: still working on build process |
2121 |
gezelter |
1490 |
|
2122 |
tim |
1594 |
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 |
gezelter |
1536 |
2004-09-28 17:14 gezelter |
2169 |
gezelter |
1490 |
|
2170 |
tim |
1594 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
2171 |
|
|
starting a configure version |
2172 |
gezelter |
1490 |
|
2173 |
tim |
1594 |
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 |
gezelter |
1536 |
2004-09-28 15:43 tim |
2183 |
gezelter |
1490 |
|
2184 |
tim |
1594 |
* 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 |
gezelter |
1490 |
|
2192 |
tim |
1594 |
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 |
gezelter |
1536 |
2004-09-23 23:16 gezelter |
2278 |
gezelter |
1490 |
|
2279 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
2280 |
tim |
1594 |
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 |
tim |
1779 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
2375 |
tim |
1594 |
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 |
gezelter |
1536 |
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 |
tim |
1594 |
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 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
2451 |
gezelter |
1490 |
|
2452 |
gezelter |
1536 |
2004-09-23 23:16 gezelter |
2453 |
gezelter |
1490 |
|
2454 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
2455 |
tim |
1594 |
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 |
tim |
1779 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
2550 |
tim |
1594 |
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 |
gezelter |
1536 |
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 |
tim |
1594 |
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 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Initial revision |
2626 |
gezelter |
1490 |
|