| 1 |
+ |
2004-05-26 11:41 gezelter |
| 2 |
+ |
|
| 3 |
+ |
* libmdtools/do_Forces.F90: Compacted all of the 8 copies of the |
| 4 |
+ |
force loop into one. |
| 5 |
+ |
|
| 6 |
+ |
2004-05-24 17:24 gezelter |
| 7 |
+ |
|
| 8 |
+ |
* libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
| 9 |
+ |
|
| 10 |
+ |
2004-05-24 16:23 chrisfen |
| 11 |
+ |
|
| 12 |
+ |
* libmdtools/Restraints.cpp: Removed unnecessary variables and |
| 13 |
+ |
changed error messages in Restraints.cpp |
| 14 |
+ |
|
| 15 |
+ |
2004-05-24 16:03 gezelter |
| 16 |
+ |
|
| 17 |
+ |
* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
| 18 |
+ |
calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
| 19 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
| 20 |
+ |
for stress / pressure tensor by cutoff group |
| 21 |
+ |
|
| 22 |
+ |
2004-05-22 15:55 chrisfen |
| 23 |
+ |
|
| 24 |
+ |
* libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... |
| 25 |
+ |
Too many arguements in a function call. |
| 26 |
+ |
|
| 27 |
+ |
2004-05-22 13:17 chrisfen |
| 28 |
+ |
|
| 29 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
| 30 |
+ |
useThermInt. |
| 31 |
+ |
|
| 32 |
+ |
2004-05-22 13:16 chrisfen |
| 33 |
+ |
|
| 34 |
+ |
* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 35 |
+ |
ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
| 36 |
+ |
Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
| 37 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
| 38 |
+ |
StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
| 39 |
+ |
code. |
| 40 |
+ |
|
| 41 |
+ |
2004-05-21 10:58 gezelter |
| 42 |
+ |
|
| 43 |
+ |
* libmdtools/: do_Forces.F90, simulation_module.F90: Major changes |
| 44 |
+ |
to skipThisPair for efficiency |
| 45 |
+ |
|
| 46 |
+ |
2004-05-21 09:22 gezelter |
| 47 |
+ |
|
| 48 |
+ |
* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
| 49 |
+ |
forceFields/amber99.vdw, forceFields/charmm27.vdw, |
| 50 |
+ |
forceFields/gaff.vdw, forceFields/oplsaal.vdw, |
| 51 |
+ |
samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes |
| 52 |
+ |
for SHAPES potential |
| 53 |
+ |
|
| 54 |
+ |
2004-05-20 15:27 chrisfen |
| 55 |
+ |
|
| 56 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
| 57 |
+ |
included the bass keywords |
| 58 |
+ |
|
| 59 |
+ |
2004-05-20 15:24 chrisfen |
| 60 |
+ |
|
| 61 |
+ |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
| 62 |
+ |
Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
| 63 |
+ |
Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
| 64 |
+ |
additions... Restraints.cpp and .hpp were included for restraining |
| 65 |
+ |
particles in thermodynamic integration. By including these, |
| 66 |
+ |
changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, |
| 67 |
+ |
StatWriter, and possibly some other files. Two bass keywords were |
| 68 |
+ |
also added for performing thermodynamic integration: a lambda value |
| 69 |
+ |
one and a k power one. |
| 70 |
+ |
|
| 71 |
+ |
2004-05-13 16:08 gezelter |
| 72 |
+ |
|
| 73 |
+ |
* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
| 74 |
+ |
|
| 75 |
+ |
2004-05-12 17:01 tim |
| 76 |
+ |
|
| 77 |
+ |
* samples/: argon/Makefile, argon/argonEM.bass, |
| 78 |
+ |
argon/init_argon.eor, minimizer/argon/Makefile, |
| 79 |
+ |
minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, |
| 80 |
+ |
minimizer/water/Makefile, minimizer/water/Makefile.in, |
| 81 |
+ |
minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, |
| 82 |
+ |
minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, |
| 83 |
+ |
minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add |
| 84 |
+ |
minimizer sample |
| 85 |
+ |
|
| 86 |
+ |
2004-05-12 16:54 gezelter |
| 87 |
+ |
|
| 88 |
+ |
* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
| 89 |
+ |
compilation |
| 90 |
+ |
|
| 91 |
+ |
2004-05-12 15:54 gezelter |
| 92 |
+ |
|
| 93 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
| 94 |
+ |
for compilation under Mac OS X with IBM's xl compilers |
| 95 |
+ |
|
| 96 |
+ |
2004-05-12 15:14 gezelter |
| 97 |
+ |
|
| 98 |
+ |
* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
| 99 |
+ |
|
| 100 |
+ |
2004-05-12 15:14 gezelter |
| 101 |
+ |
|
| 102 |
+ |
* libmdtools/LJFF.cpp: Removed an extraneous write |
| 103 |
+ |
|
| 104 |
+ |
2004-05-12 15:13 gezelter |
| 105 |
+ |
|
| 106 |
+ |
* libBASS/simError.h: Starting to change the error model |
| 107 |
+ |
|
| 108 |
+ |
2004-05-12 14:45 gezelter |
| 109 |
+ |
|
| 110 |
+ |
* utils/Dump2XYZ.cpp: const char* fix |
| 111 |
+ |
|
| 112 |
+ |
2004-05-12 14:44 gezelter |
| 113 |
+ |
|
| 114 |
+ |
* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 115 |
+ |
src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
| 116 |
+ |
write statements |
| 117 |
+ |
|
| 118 |
+ |
2004-05-12 11:38 tim |
| 119 |
+ |
|
| 120 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
| 121 |
+ |
ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 122 |
+ |
SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
| 123 |
+ |
massratio from simState, creat cutoff group forevery atom which |
| 124 |
+ |
does not belong to cutoff group defined at mdl file |
| 125 |
+ |
|
| 126 |
+ |
2004-05-12 10:58 gezelter |
| 127 |
+ |
|
| 128 |
+ |
* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
| 129 |
+ |
CutoffGroup |
| 130 |
+ |
|
| 131 |
+ |
2004-05-12 10:35 gezelter |
| 132 |
+ |
|
| 133 |
+ |
* samples/water/water.mdl: Added the cutoff Groups to the default |
| 134 |
+ |
water.mdl file |
| 135 |
+ |
|
| 136 |
+ |
2004-05-12 10:02 tim |
| 137 |
+ |
|
| 138 |
+ |
* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
| 139 |
+ |
fixed a bug in CutoffGroup::getCOM() |
| 140 |
+ |
|
| 141 |
|
2004-05-12 09:29 gezelter |
| 142 |
|
|
| 143 |
|
* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 701 |
|
|
| 702 |
|
2004-01-27 14:38 gezelter |
| 703 |
|
|
| 704 |
< |
* samples/argon/argon.bass: Longer run time to test argon |
| 704 |
> |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer |
| 705 |
> |
run time to test argon |
| 706 |
|
|
| 707 |
|
2004-01-27 14:38 gezelter |
| 708 |
|
|
| 919 |
|
2004-01-12 15:37 tim |
| 920 |
|
|
| 921 |
|
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
| 922 |
< |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
| 923 |
< |
master nodes |
| 922 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: |
| 923 |
> |
Dumpwriter only write out the atoms on master nodes |
| 924 |
|
|
| 925 |
|
2004-01-10 04:46 tim |
| 926 |
|
|
| 971 |
|
2004-01-07 14:26 tim |
| 972 |
|
|
| 973 |
|
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
| 974 |
< |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
| 975 |
< |
sending message from master node to itself in DumpWriter.cpp and |
| 976 |
< |
InitializeFromFile.cpp |
| 974 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass, |
| 975 |
> |
samples/water/ssd.bass: Fixed a bug of sending message from master |
| 976 |
> |
node to itself in DumpWriter.cpp and InitializeFromFile.cpp |
| 977 |
|
|
| 978 |
|
2004-01-06 14:49 chuckv |
| 979 |
|
|
| 1279 |
|
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
| 1280 |
|
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
| 1281 |
|
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
| 1282 |
< |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
| 1283 |
< |
file. |
| 1282 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi |
| 1283 |
> |
and eta to the comment line of dump file. |
| 1284 |
|
|
| 1285 |
|
2003-10-28 17:25 mmeineke |
| 1286 |
|
|
| 1701 |
|
samples/Makefile.in, samples/alkane/Makefile, |
| 1702 |
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
| 1703 |
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
| 1704 |
< |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
| 1705 |
< |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
| 1706 |
< |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
| 1707 |
< |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
| 1708 |
< |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
| 1709 |
< |
autoconf / configure method of configuring OOPSE |
| 1704 |
> |
samples/minimizer/argon/Makefile, |
| 1705 |
> |
samples/minimizer/argon/Makefile.in, |
| 1706 |
> |
samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, |
| 1707 |
> |
samples/beadLipid/Makefile.in, samples/lipid/Makefile, |
| 1708 |
> |
samples/lipid/Makefile.in, samples/water/Makefile, |
| 1709 |
> |
samples/water/Makefile.in, src/Makefile, src/Makefile.in, |
| 1710 |
> |
utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, |
| 1711 |
> |
utils/sysbuilder/Makefile.in: Changes to autoconf / configure |
| 1712 |
> |
method of configuring OOPSE |
| 1713 |
|
|
| 1714 |
|
2003-09-04 16:48 mmeineke |
| 1715 |
|
|
| 2298 |
|
2003-07-14 18:06 gezelter |
| 2299 |
|
|
| 2300 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
| 2301 |
< |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
| 2302 |
< |
for samples |
| 2301 |
> |
argon/init_argon.eor, minimizer/argon/argon.bass, |
| 2302 |
> |
minimizer/argon/init_argon.eor, lipid/init_5x5.eor, |
| 2303 |
> |
water/init_ssd.eor: Fixes for samples |
| 2304 |
|
|
| 2305 |
|
2003-07-14 18:06 gezelter |
| 2306 |
|
|
| 2973 |
|
|
| 2974 |
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
| 2975 |
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
| 2976 |
< |
samples/argon/argon.bass: more bug fixes.... |
| 2976 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more |
| 2977 |
> |
bug fixes.... |
| 2978 |
|
|
| 2979 |
|
2003-04-01 11:49 mmeineke |
| 2980 |
|
|
| 3181 |
|
2003-03-26 10:37 chuckv |
| 3182 |
|
|
| 3183 |
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 3184 |
< |
samples/argon/argon.bass: Fixes for Parallel thermalization |
| 3184 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes |
| 3185 |
> |
for Parallel thermalization |
| 3186 |
|
|
| 3187 |
|
2003-03-26 09:55 mmeineke |
| 3188 |
|
|
| 3214 |
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
| 3215 |
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
| 3216 |
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
| 3217 |
< |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
| 3218 |
< |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
| 3219 |
< |
samples |
| 3217 |
> |
lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, |
| 3218 |
> |
minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, |
| 3219 |
> |
minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, |
| 3220 |
> |
water/ssd.bass, water/water.mdl: moved tests to samples |
| 3221 |
|
|
| 3222 |
|
2003-03-24 19:51 gezelter |
| 3223 |
|
|
