 ../
|
obj/
|
400
(21 years ago)
by mmeineke:
*** empty log message ***
|
|
MPIobj/
|
400
(21 years ago)
by mmeineke:
*** empty log message ***
|
forceFactory.hpp
|
378
(21 years ago)
by mmeineke:
This commit was generated by cvs2svn to compensate for changes in r377,
which included commits to RCS files with non-trunk default branches.
|
|
TorsionExtensions.cpp
|
378
(21 years ago)
by mmeineke:
This commit was generated by cvs2svn to compensate for changes in r377,
which included commits to RCS files with non-trunk default branches.
|
|
vector_class.F90
|
378
(21 years ago)
by mmeineke:
This commit was generated by cvs2svn to compensate for changes in r377,
which included commits to RCS files with non-trunk default branches.
|
|
randomSPRNG.hpp
|
450
(21 years ago)
by mmeineke:
just little things like deleteing unused variables and such.
|
|
StreamTokenizer.cpp
|
593
(21 years ago)
by gezelter:
Starting to worry about all the strtok() calls in our code
|
|
StreamTokenizer.hpp
|
593
(21 years ago)
by gezelter:
Starting to worry about all the strtok() calls in our code
|
|
BondExtensions.cpp
|
597
(21 years ago)
by mmeineke:
found a bug. Unit vectors were not being updated
|
|
status_module.F90
|
648
(21 years ago)
by chuckv:
Finished most code for eam....
|
|
wrappers.F90
|
657
(21 years ago)
by chuckv:
More bug fixes for eam.
|
|
Bend.cpp
|
670
(21 years ago)
by mmeineke:
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
|
|
Bond.cpp
|
670
(21 years ago)
by mmeineke:
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
|
|
Torsion.cpp
|
670
(21 years ago)
by mmeineke:
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
|
|
GhostBend.cpp
|
707
(21 years ago)
by mmeineke:
updated the Changelog.
added some bug fixes for setting the random number generator seed value.
fixed a bug where ghostbend atom b was not being set. ( recent bug from SimState conversion)
|
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config.h.in
|
747
(21 years ago)
by gezelter:
Changes to autoconf / configure method of configuring OOPSE
|
|
fInfo.c
|
747
(21 years ago)
by gezelter:
Changes to autoconf / configure method of configuring OOPSE
|
|
definitions_module.F90
|
747
(21 years ago)
by gezelter:
Changes to autoconf / configure method of configuring OOPSE
|
|
randomSPRNG.cpp
|
829
(20 years ago)
by gezelter:
replace c++ header stuff with more portable c header stuff
Also, mod file fixes and portability changes
Some fortran changes will need to be reversed.
|
|
BendExtensions.cpp
|
829
(20 years ago)
by gezelter:
replace c++ header stuff with more portable c header stuff
Also, mod file fixes and portability changes
Some fortran changes will need to be reversed.
|
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fForceField.h
|
834
(20 years ago)
by gezelter:
Compatibility fixes
|
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fortranWrappers.cpp
|
836
(20 years ago)
by mmeineke:
did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.
|
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fortranWrappers.hpp
|
836
(20 years ago)
by mmeineke:
did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.
|
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NPTi.cpp
|
857
(20 years ago)
by mmeineke:
moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
|
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mdProfile.hpp
|
884
(20 years ago)
by mmeineke:
added some profile functionality
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mdProfile.cpp
|
892
(20 years ago)
by chuckv:
Fixes to profile code.
|
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timing.F90
|
892
(20 years ago)
by chuckv:
Fixes to profile code.
|
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oopseMPI_module.F90
|
940
(20 years ago)
by gezelter:
Some changes for new MPI organization and direct charge-charge interactions
|
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atype_module.F90
|
941
(20 years ago)
by gezelter:
Changes for adding direct charge-charge interactions (with switching function)
|
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mpiForceField.h
|
976
(20 years ago)
by chrisfen:
Corrected spelling in several directories, and stated WATER.cpp
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mpiForceField.c
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976
(20 years ago)
by chrisfen:
Corrected spelling in several directories, and stated WATER.cpp
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AbstractClasses.hpp
|
987
(20 years ago)
by tim:
revision of constraint for Nonlinear Optimization Model
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SimpleBoundCons.hpp
|
1011
(20 years ago)
by tim:
*** empty log message ***
|
|
SimpleBoundCons.cpp
|
1011
(20 years ago)
by tim:
*** empty log message ***
|
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AllIntegrator.hpp
|
1032
(20 years ago)
by tim:
Add one more file into Makefile.in
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MinimizerParameterSet.hpp
|
1064
(20 years ago)
by tim:
Using inherit instead of compose to implement Minimizer
both versions are working
|
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SDMinimizer.cpp
|
1064
(20 years ago)
by tim:
Using inherit instead of compose to implement Minimizer
both versions are working
|
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OOPSEMinimizer.hpp
|
1064
(20 years ago)
by tim:
Using inherit instead of compose to implement Minimizer
both versions are working
|
|
CGFamilyMinimizer.cpp
|
1064
(20 years ago)
by tim:
Using inherit instead of compose to implement Minimizer
both versions are working
|
|
PRCG.cpp
|
1066
(20 years ago)
by tim:
*** empty log message ***
|
|
ZConsWriter.cpp
|
1091
(20 years ago)
by tim:
ZConstraint now can support sequential moving. Refactorying is needed to support SMD in ZConstraint
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ZConsWriter.hpp
|
1091
(20 years ago)
by tim:
ZConstraint now can support sequential moving. Refactorying is needed to support SMD in ZConstraint
|
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DUFF.cpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
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MatVec3.c
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
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SkipList.cpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
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Exclude.hpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
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NPTf.cpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
|
Exclude.cpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
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SkipList.hpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
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SRI.hpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
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EAM_FF.cpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
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NPTxyz.cpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
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SimSetup.hpp
|
1108
(20 years ago)
by tim:
Change DumpWriter and InitFromFile
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mpiSimulation.hpp
|
1108
(20 years ago)
by tim:
Change DumpWriter and InitFromFile
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WATER.cpp
|
1113
(20 years ago)
by tim:
fix whole bunch of bugs :-)
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GenericData.cpp
|
1118
(20 years ago)
by tim:
new implement of quickLate using visitor and composite pattern
|
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ZConsReader.cpp
|
1118
(20 years ago)
by tim:
new implement of quickLate using visitor and composite pattern
|
|
ZconsVisitor.hpp
|
1118
(20 years ago)
by tim:
new implement of quickLate using visitor and composite pattern
|
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StuntDouble.cpp
|
1118
(20 years ago)
by tim:
new implement of quickLate using visitor and composite pattern
|
|
StuntDouble.hpp
|
1118
(20 years ago)
by tim:
new implement of quickLate using visitor and composite pattern
|
|
ZConsReader.hpp
|
1118
(20 years ago)
by tim:
new implement of quickLate using visitor and composite pattern
|
|
BaseVisitor.hpp
|
1119
(20 years ago)
by tim:
Dump2XYZ is almost working except atoms in rigidbody are double counted
|
|
RigidBodyVisitor.cpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
CompositeVisitor.cpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
CompositeVisitor.hpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
GenericData.hpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
AtomVisitor.hpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
DirectionalAtom.hpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
RigidBodyVisitor.hpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
OtherVisitor.hpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
Thermo.hpp
|
1127
(20 years ago)
by tim:
fixed getCOMVel and velocitize at thermo
|
|
NVT.cpp
|
1129
(20 years ago)
by tim:
fixed two bugs in MPI version of InitfromFile and one unmatch MPI command in DumpWriter
|
|
NPT.cpp
|
1129
(20 years ago)
by tim:
fixed two bugs in MPI version of InitfromFile and one unmatch MPI command in DumpWriter
|
|
mpiSimulation.cpp
|
1129
(20 years ago)
by tim:
fixed two bugs in MPI version of InitfromFile and one unmatch MPI command in DumpWriter
|
|
DumpReader.cpp
|
1130
(20 years ago)
by tim:
fixed another bug in InitFromFile. MPI verion of OOPSE is working again
|
|
InitializeFromFile.cpp
|
1131
(20 years ago)
by tim:
change the calculation of pressure tensor
|
|
AtomVisitor.cpp
|
1132
(20 years ago)
by tim:
add reaction field correction to charge-charge interaction
|
|
Thermo.cpp
|
1133
(20 years ago)
by gezelter:
Fixed a bug in calc_charge_charge.F90
|
|
MatVec3.h
|
1139
(20 years ago)
by gezelter:
Adding molecular cutoffs
|
|
ZconsVisitor.cpp
|
1140
(20 years ago)
by tim:
fix a bug in Molecule.cpp which initialize massRatio before creat the array.
fix two bugs in ZconsVisitor
|
|
OtherVisitor.cpp
|
1140
(20 years ago)
by tim:
fix a bug in Molecule.cpp which initialize massRatio before creat the array.
fix two bugs in ZconsVisitor
|
|
ZConstraint.cpp
|
1141
(20 years ago)
by tim:
keep the previous position of cantilever in SMD
|
|
OOPSEMinimizer.cpp
|
1144
(20 years ago)
by tim:
C++ pass groupList to fortran
|
|
fSimulation.h
|
1144
(20 years ago)
by tim:
C++ pass groupList to fortran
|
|
mpiSimulation_module.F90
|
1150
(20 years ago)
by gezelter:
Many changes to get group-based cutoffs to work
|
|
calc_eam.F90
|
1150
(20 years ago)
by gezelter:
Many changes to get group-based cutoffs to work
|
|
neighborLists.F90
|
1150
(20 years ago)
by gezelter:
Many changes to get group-based cutoffs to work
|
|
mpiComponentPlan.h
|
1150
(20 years ago)
by gezelter:
Many changes to get group-based cutoffs to work
|
|
force_globals.F90
|
1150
(20 years ago)
by gezelter:
Many changes to get group-based cutoffs to work
|
|
switch_module.F90
|
1151
(20 years ago)
by gezelter:
New module for fortran group-based switching function
|
|
fSwitchingFunction.h
|
1151
(20 years ago)
by gezelter:
New module for fortran group-based switching function
|
|
DumpWriter.cpp
|
1152
(20 years ago)
by tim:
optimize DumpWriter
|
|
fortranWrapDefines.hpp
|
1154
(20 years ago)
by gezelter:
Fixes to libmdtools to use the simplified cutoff stuff in the BASS library
|
|
Make.dep
|
1158
(20 years ago)
by tim:
fix two bugs in siminfo which cause infinite loop; fix anoter one in CutoffGroup which causes seg fault
|
|
calc_dipole_dipole.F90
|
1160
(20 years ago)
by gezelter:
Fortran-side changes for group-based cutoffs
|
|
calc_LJ_FF.F90
|
1160
(20 years ago)
by gezelter:
Fortran-side changes for group-based cutoffs
|
|
calc_sticky_pair.F90
|
1160
(20 years ago)
by gezelter:
Fortran-side changes for group-based cutoffs
|
|
calc_gb.F90
|
1160
(20 years ago)
by gezelter:
Fortran-side changes for group-based cutoffs
|
|
calc_reaction_field.F90
|
1160
(20 years ago)
by gezelter:
Fortran-side changes for group-based cutoffs
|
|
calc_charge_charge.F90
|
1160
(20 years ago)
by gezelter:
Fortran-side changes for group-based cutoffs
|
|
CutoffGroup.hpp
|
1166
(20 years ago)
by gezelter:
efficiency fixes in CutoffGroup
|
|
Atom.cpp
|
1167
(20 years ago)
by tim:
get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file
|
|
SimInfo.cpp
|
1167
(20 years ago)
by tim:
get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file
|
|
Atom.hpp
|
1167
(20 years ago)
by tim:
get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file
|
|
SimState.cpp
|
1167
(20 years ago)
by tim:
get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file
|
|
SimState.hpp
|
1167
(20 years ago)
by tim:
get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file
|
|
Molecule.cpp
|
1167
(20 years ago)
by tim:
get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file
|
|
Molecule.hpp
|
1167
(20 years ago)
by tim:
get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file
|
|
DirectionalAtom.cpp
|
1167
(20 years ago)
by tim:
get rid of rc and massratio from simState, creat cutoff group forevery atom
which does not belong to
cutoff group defined at mdl file
|
|
notifyCutoffs.F90
|
1169
(20 years ago)
by gezelter:
MPI fixes and removal of extraneous write statements
|
|
LJFF.cpp
|
1172
(20 years ago)
by gezelter:
Removed an extraneous write
|
|
RigidBody.cpp
|
1174
(20 years ago)
by gezelter:
Fixes for compilation under Mac OS X with IBM's xl compilers
|
|
RigidBody.hpp
|
1174
(20 years ago)
by gezelter:
Fixes for compilation under Mac OS X with IBM's xl compilers
|
|
Utility.hpp
|
1175
(20 years ago)
by gezelter:
fixes for MacOS X compilation
|
|
Utility.cpp
|
1175
(20 years ago)
by gezelter:
fixes for MacOS X compilation
|
|
Restraints.hpp
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
Integrator.cpp
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
Integrator.hpp
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
ForceFields.cpp
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
Restraints.cpp
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
Makefile.in
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
SimSetup.cpp
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
StatWriter.cpp
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
ForceFields.hpp
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
SimInfo.hpp
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
ReadWrite.hpp
|
1180
(20 years ago)
by chrisfen:
Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration. By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files. Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.
|
|
simulation_module.F90
|
1183
(20 years ago)
by gezelter:
Major changes to skipThisPair for efficiency
|
|
do_Forces.F90
|
1183
(20 years ago)
by gezelter:
Major changes to skipThisPair for efficiency
|
