| 1 |
+ |
2004-05-27 10:31 tim |
| 2 |
+ |
|
| 3 |
+ |
* libmdtools/SimInfo.cpp: groupList new bases on global index of |
| 4 |
+ |
atoms |
| 5 |
+ |
|
| 6 |
+ |
2004-05-27 10:21 gezelter |
| 7 |
+ |
|
| 8 |
+ |
* src/: oopse.cpp, oose.cpp: Modified the nifty banner |
| 9 |
+ |
|
| 10 |
+ |
2004-05-27 10:21 gezelter |
| 11 |
+ |
|
| 12 |
+ |
* libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: |
| 13 |
+ |
Fixed off-by-one error in groupStartRow and groupStartCol |
| 14 |
+ |
|
| 15 |
+ |
2004-05-26 19:48 tim |
| 16 |
+ |
|
| 17 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, |
| 18 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
| 19 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 20 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, |
| 21 |
+ |
libmdtools/calc_charge_charge.F90, |
| 22 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
| 23 |
+ |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 24 |
+ |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 25 |
+ |
libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, |
| 26 |
+ |
libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, |
| 27 |
+ |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 28 |
+ |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 29 |
+ |
libmdtools/simulation_module.F90: in the progress of fixing MPI |
| 30 |
+ |
version of cutoff group |
| 31 |
+ |
|
| 32 |
+ |
2004-05-26 11:41 gezelter |
| 33 |
+ |
|
| 34 |
+ |
* libmdtools/do_Forces.F90: Compacted all of the 8 copies of the |
| 35 |
+ |
force loop into one. |
| 36 |
+ |
|
| 37 |
+ |
2004-05-24 17:24 gezelter |
| 38 |
+ |
|
| 39 |
+ |
* libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
| 40 |
+ |
|
| 41 |
+ |
2004-05-24 16:23 chrisfen |
| 42 |
+ |
|
| 43 |
+ |
* libmdtools/Restraints.cpp: Removed unnecessary variables and |
| 44 |
+ |
changed error messages in Restraints.cpp |
| 45 |
+ |
|
| 46 |
+ |
2004-05-24 16:03 gezelter |
| 47 |
+ |
|
| 48 |
+ |
* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
| 49 |
+ |
calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
| 50 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
| 51 |
+ |
for stress / pressure tensor by cutoff group |
| 52 |
+ |
|
| 53 |
+ |
2004-05-22 15:55 chrisfen |
| 54 |
+ |
|
| 55 |
+ |
* libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... |
| 56 |
+ |
Too many arguements in a function call. |
| 57 |
+ |
|
| 58 |
+ |
2004-05-22 13:17 chrisfen |
| 59 |
+ |
|
| 60 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
| 61 |
+ |
useThermInt. |
| 62 |
+ |
|
| 63 |
+ |
2004-05-22 13:16 chrisfen |
| 64 |
+ |
|
| 65 |
+ |
* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 66 |
+ |
ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
| 67 |
+ |
Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
| 68 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
| 69 |
+ |
StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
| 70 |
+ |
code. |
| 71 |
+ |
|
| 72 |
+ |
2004-05-21 10:58 gezelter |
| 73 |
+ |
|
| 74 |
+ |
* libmdtools/: do_Forces.F90, simulation_module.F90: Major changes |
| 75 |
+ |
to skipThisPair for efficiency |
| 76 |
+ |
|
| 77 |
+ |
2004-05-21 09:22 gezelter |
| 78 |
+ |
|
| 79 |
+ |
* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
| 80 |
+ |
forceFields/amber99.vdw, forceFields/charmm27.vdw, |
| 81 |
+ |
forceFields/gaff.vdw, forceFields/oplsaal.vdw, |
| 82 |
+ |
samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes |
| 83 |
+ |
for SHAPES potential |
| 84 |
+ |
|
| 85 |
+ |
2004-05-20 15:27 chrisfen |
| 86 |
+ |
|
| 87 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
| 88 |
+ |
included the bass keywords |
| 89 |
+ |
|
| 90 |
+ |
2004-05-20 15:24 chrisfen |
| 91 |
+ |
|
| 92 |
+ |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
| 93 |
+ |
Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
| 94 |
+ |
Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
| 95 |
+ |
additions... Restraints.cpp and .hpp were included for restraining |
| 96 |
+ |
particles in thermodynamic integration. By including these, |
| 97 |
+ |
changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, |
| 98 |
+ |
StatWriter, and possibly some other files. Two bass keywords were |
| 99 |
+ |
also added for performing thermodynamic integration: a lambda value |
| 100 |
+ |
one and a k power one. |
| 101 |
+ |
|
| 102 |
+ |
2004-05-13 16:08 gezelter |
| 103 |
+ |
|
| 104 |
+ |
* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
| 105 |
+ |
|
| 106 |
+ |
2004-05-12 17:01 tim |
| 107 |
+ |
|
| 108 |
+ |
* samples/: argon/Makefile, argon/argonEM.bass, |
| 109 |
+ |
argon/init_argon.eor, minimizer/argon/Makefile, |
| 110 |
+ |
minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, |
| 111 |
+ |
minimizer/water/Makefile, minimizer/water/Makefile.in, |
| 112 |
+ |
minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, |
| 113 |
+ |
minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, |
| 114 |
+ |
minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add |
| 115 |
+ |
minimizer sample |
| 116 |
+ |
|
| 117 |
+ |
2004-05-12 16:54 gezelter |
| 118 |
+ |
|
| 119 |
+ |
* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
| 120 |
+ |
compilation |
| 121 |
+ |
|
| 122 |
+ |
2004-05-12 15:54 gezelter |
| 123 |
+ |
|
| 124 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
| 125 |
+ |
for compilation under Mac OS X with IBM's xl compilers |
| 126 |
+ |
|
| 127 |
+ |
2004-05-12 15:14 gezelter |
| 128 |
+ |
|
| 129 |
+ |
* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
| 130 |
+ |
|
| 131 |
+ |
2004-05-12 15:14 gezelter |
| 132 |
+ |
|
| 133 |
+ |
* libmdtools/LJFF.cpp: Removed an extraneous write |
| 134 |
+ |
|
| 135 |
+ |
2004-05-12 15:13 gezelter |
| 136 |
+ |
|
| 137 |
+ |
* libBASS/simError.h: Starting to change the error model |
| 138 |
+ |
|
| 139 |
+ |
2004-05-12 14:45 gezelter |
| 140 |
+ |
|
| 141 |
+ |
* utils/Dump2XYZ.cpp: const char* fix |
| 142 |
+ |
|
| 143 |
+ |
2004-05-12 14:44 gezelter |
| 144 |
+ |
|
| 145 |
+ |
* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 146 |
+ |
src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
| 147 |
+ |
write statements |
| 148 |
+ |
|
| 149 |
+ |
2004-05-12 11:38 tim |
| 150 |
+ |
|
| 151 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
| 152 |
+ |
ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 153 |
+ |
SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
| 154 |
+ |
massratio from simState, creat cutoff group forevery atom which |
| 155 |
+ |
does not belong to cutoff group defined at mdl file |
| 156 |
+ |
|
| 157 |
+ |
2004-05-12 10:58 gezelter |
| 158 |
+ |
|
| 159 |
+ |
* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
| 160 |
+ |
CutoffGroup |
| 161 |
+ |
|
| 162 |
+ |
2004-05-12 10:35 gezelter |
| 163 |
+ |
|
| 164 |
+ |
* samples/water/water.mdl: Added the cutoff Groups to the default |
| 165 |
+ |
water.mdl file |
| 166 |
+ |
|
| 167 |
+ |
2004-05-12 10:02 tim |
| 168 |
+ |
|
| 169 |
+ |
* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
| 170 |
+ |
fixed a bug in CutoffGroup::getCOM() |
| 171 |
+ |
|
| 172 |
+ |
2004-05-12 09:29 gezelter |
| 173 |
+ |
|
| 174 |
+ |
* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 175 |
+ |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 176 |
+ |
samples/water/ssd.bass: bug fixes for cutoffGroups |
| 177 |
+ |
|
| 178 |
+ |
2004-05-11 17:28 tim |
| 179 |
+ |
|
| 180 |
+ |
* utils/Vector3.hpp: adding generic Vector3 class |
| 181 |
+ |
|
| 182 |
+ |
2004-05-11 16:44 tim |
| 183 |
+ |
|
| 184 |
+ |
* libmdtools/Integrator.hpp: adding instantiation of |
| 185 |
+ |
Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8 |
| 186 |
+ |
|
| 187 |
+ |
2004-05-11 16:31 gezelter |
| 188 |
+ |
|
| 189 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, |
| 190 |
+ |
calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, |
| 191 |
+ |
calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: |
| 192 |
+ |
Fortran-side changes for group-based cutoffs |
| 193 |
+ |
|
| 194 |
+ |
2004-05-11 16:20 tim |
| 195 |
+ |
|
| 196 |
+ |
* libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp |
| 197 |
+ |
|
| 198 |
+ |
2004-05-11 16:14 tim |
| 199 |
+ |
|
| 200 |
+ |
* libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, |
| 201 |
+ |
SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix |
| 202 |
+ |
anoter one in CutoffGroup which causes seg fault |
| 203 |
+ |
|
| 204 |
+ |
2004-05-11 15:33 tim |
| 205 |
+ |
|
| 206 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
| 207 |
+ |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
| 208 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup |
| 209 |
+ |
into OOPSE |
| 210 |
+ |
|
| 211 |
+ |
2004-05-11 15:07 gezelter |
| 212 |
+ |
|
| 213 |
+ |
* libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup |
| 214 |
+ |
|
| 215 |
+ |
2004-05-11 11:00 gezelter |
| 216 |
+ |
|
| 217 |
+ |
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
| 218 |
+ |
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
| 219 |
+ |
use the simplified cutoff stuff in the BASS library |
| 220 |
+ |
|
| 221 |
+ |
2004-05-10 23:21 gezelter |
| 222 |
+ |
|
| 223 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
| 224 |
+ |
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
| 225 |
+ |
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
| 226 |
+ |
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
| 227 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
| 228 |
+ |
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
| 229 |
+ |
Also restructured the plethora of cutoff radii into one |
| 230 |
+ |
cutoffRadius and one switchingRadius. Also removed the |
| 231 |
+ |
useMolecularCutoffs keyword |
| 232 |
+ |
|
| 233 |
+ |
2004-05-10 15:28 tim |
| 234 |
+ |
|
| 235 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
| 236 |
+ |
DumpWriter |
| 237 |
+ |
|
| 238 |
|
2004-05-07 16:36 gezelter |
| 239 |
|
|
| 240 |
|
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
| 732 |
|
|
| 733 |
|
2004-01-27 14:38 gezelter |
| 734 |
|
|
| 735 |
< |
* samples/argon/argon.bass: Longer run time to test argon |
| 735 |
> |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer |
| 736 |
> |
run time to test argon |
| 737 |
|
|
| 738 |
|
2004-01-27 14:38 gezelter |
| 739 |
|
|
| 950 |
|
2004-01-12 15:37 tim |
| 951 |
|
|
| 952 |
|
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
| 953 |
< |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
| 954 |
< |
master nodes |
| 953 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: |
| 954 |
> |
Dumpwriter only write out the atoms on master nodes |
| 955 |
|
|
| 956 |
|
2004-01-10 04:46 tim |
| 957 |
|
|
| 1002 |
|
2004-01-07 14:26 tim |
| 1003 |
|
|
| 1004 |
|
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
| 1005 |
< |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
| 1006 |
< |
sending message from master node to itself in DumpWriter.cpp and |
| 1007 |
< |
InitializeFromFile.cpp |
| 1005 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass, |
| 1006 |
> |
samples/water/ssd.bass: Fixed a bug of sending message from master |
| 1007 |
> |
node to itself in DumpWriter.cpp and InitializeFromFile.cpp |
| 1008 |
|
|
| 1009 |
|
2004-01-06 14:49 chuckv |
| 1010 |
|
|
| 1310 |
|
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
| 1311 |
|
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
| 1312 |
|
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
| 1313 |
< |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
| 1314 |
< |
file. |
| 1313 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi |
| 1314 |
> |
and eta to the comment line of dump file. |
| 1315 |
|
|
| 1316 |
|
2003-10-28 17:25 mmeineke |
| 1317 |
|
|
| 1732 |
|
samples/Makefile.in, samples/alkane/Makefile, |
| 1733 |
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
| 1734 |
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
| 1735 |
< |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
| 1736 |
< |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
| 1737 |
< |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
| 1738 |
< |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
| 1739 |
< |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
| 1740 |
< |
autoconf / configure method of configuring OOPSE |
| 1735 |
> |
samples/minimizer/argon/Makefile, |
| 1736 |
> |
samples/minimizer/argon/Makefile.in, |
| 1737 |
> |
samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, |
| 1738 |
> |
samples/beadLipid/Makefile.in, samples/lipid/Makefile, |
| 1739 |
> |
samples/lipid/Makefile.in, samples/water/Makefile, |
| 1740 |
> |
samples/water/Makefile.in, src/Makefile, src/Makefile.in, |
| 1741 |
> |
utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, |
| 1742 |
> |
utils/sysbuilder/Makefile.in: Changes to autoconf / configure |
| 1743 |
> |
method of configuring OOPSE |
| 1744 |
|
|
| 1745 |
|
2003-09-04 16:48 mmeineke |
| 1746 |
|
|
| 2329 |
|
2003-07-14 18:06 gezelter |
| 2330 |
|
|
| 2331 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
| 2332 |
< |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
| 2333 |
< |
for samples |
| 2332 |
> |
argon/init_argon.eor, minimizer/argon/argon.bass, |
| 2333 |
> |
minimizer/argon/init_argon.eor, lipid/init_5x5.eor, |
| 2334 |
> |
water/init_ssd.eor: Fixes for samples |
| 2335 |
|
|
| 2336 |
|
2003-07-14 18:06 gezelter |
| 2337 |
|
|
| 3004 |
|
|
| 3005 |
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
| 3006 |
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
| 3007 |
< |
samples/argon/argon.bass: more bug fixes.... |
| 3007 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more |
| 3008 |
> |
bug fixes.... |
| 3009 |
|
|
| 3010 |
|
2003-04-01 11:49 mmeineke |
| 3011 |
|
|
| 3212 |
|
2003-03-26 10:37 chuckv |
| 3213 |
|
|
| 3214 |
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 3215 |
< |
samples/argon/argon.bass: Fixes for Parallel thermalization |
| 3215 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes |
| 3216 |
> |
for Parallel thermalization |
| 3217 |
|
|
| 3218 |
|
2003-03-26 09:55 mmeineke |
| 3219 |
|
|
| 3245 |
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
| 3246 |
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
| 3247 |
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
| 3248 |
< |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
| 3249 |
< |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
| 3250 |
< |
samples |
| 3248 |
> |
lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, |
| 3249 |
> |
minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, |
| 3250 |
> |
minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, |
| 3251 |
> |
water/ssd.bass, water/water.mdl: moved tests to samples |
| 3252 |
|
|
| 3253 |
|
2003-03-24 19:51 gezelter |
| 3254 |
|
|
