 ../
|
obj/
|
400
(21 years ago)
by mmeineke:
*** empty log message ***
|
|
MPIobj/
|
400
(21 years ago)
by mmeineke:
*** empty log message ***
|
wrappers.F90
|
1239
(20 years ago)
by gezelter:
More work on Fortran side of error handler
|
|
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.
|
|
timing.F90
|
892
(20 years ago)
by chuckv:
Fixes to profile code.
|
|
switch_module.F90
|
1151
(20 years ago)
by gezelter:
New module for fortran group-based switching function
|
|
status_module.F90
|
1239
(20 years ago)
by gezelter:
More work on Fortran side of error handler
|
|
simulation_module.F90
|
1217
(20 years ago)
by gezelter:
Bug fix (fixes of skipList and neighbor list under MPI)
|
|
randomSPRNG.hpp
|
450
(21 years ago)
by mmeineke:
just little things like deleteing unused variables and such.
|
|
randomSPRNG.cpp
|
1203
(20 years ago)
by gezelter:
Cutoff group changes under MPI
|
|
oopseMPI_module.F90
|
940
(20 years ago)
by gezelter:
Some changes for new MPI organization and direct charge-charge interactions
|
|
notifyCutoffs.F90
|
1239
(20 years ago)
by gezelter:
More work on Fortran side of error handler
|
|
neighborLists.F90
|
1217
(20 years ago)
by gezelter:
Bug fix (fixes of skipList and neighbor list under MPI)
|
|
mpiSimulation_module.F90
|
1214
(20 years ago)
by gezelter:
Cutoff Groups for MPI
|
|
mpiSimulation.hpp
|
1203
(20 years ago)
by gezelter:
Cutoff group changes under MPI
|
|
mpiSimulation.cpp
|
1217
(20 years ago)
by gezelter:
Bug fix (fixes of skipList and neighbor list under MPI)
|
|
mpiForceField.h
|
976
(20 years ago)
by chrisfen:
Corrected spelling in several directories, and stated WATER.cpp
|
|
mpiForceField.c
|
976
(20 years ago)
by chrisfen:
Corrected spelling in several directories, and stated WATER.cpp
|
|
mpiComponentPlan.h
|
1198
(20 years ago)
by tim:
in the progress of fixing MPI version of cutoff group
|
|
mdProfile.hpp
|
884
(20 years ago)
by mmeineke:
added some profile functionality
|
|
mdProfile.cpp
|
1203
(20 years ago)
by gezelter:
Cutoff group changes under MPI
|
|
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.
|
|
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.
|
|
fortranWrapDefines.hpp
|
1214
(20 years ago)
by gezelter:
Cutoff Groups for MPI
|
|
force_globals.F90
|
1198
(20 years ago)
by tim:
in the progress of fixing MPI version of cutoff group
|
|
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.
|
|
fSwitchingFunction.h
|
1151
(20 years ago)
by gezelter:
New module for fortran group-based switching function
|
|
fSimulation.h
|
1144
(20 years ago)
by tim:
C++ pass groupList to fortran
|
|
fForceField.h
|
834
(20 years ago)
by gezelter:
Compatibility fixes
|
|
do_Forces.F90
|
1217
(20 years ago)
by gezelter:
Bug fix (fixes of skipList and neighbor list under MPI)
|
|
definitions_module.F90
|
747
(20 years ago)
by gezelter:
Changes to autoconf / configure method of configuring OOPSE
|
|
config.h.in
|
1233
(20 years ago)
by gezelter:
Config changes for fortran access to SimError
|
|
calc_sticky_pair.F90
|
1198
(20 years ago)
by tim:
in the progress of fixing MPI version of cutoff group
|
|
calc_reaction_field.F90
|
1198
(20 years ago)
by tim:
in the progress of fixing MPI version of cutoff group
|
|
calc_gb.F90
|
1198
(20 years ago)
by tim:
in the progress of fixing MPI version of cutoff group
|
|
calc_eam.F90
|
1198
(20 years ago)
by tim:
in the progress of fixing MPI version of cutoff group
|
|
calc_dipole_dipole.F90
|
1198
(20 years ago)
by tim:
in the progress of fixing MPI version of cutoff group
|
|
calc_charge_charge.F90
|
1198
(20 years ago)
by tim:
in the progress of fixing MPI version of cutoff group
|
|
calc_LJ_FF.F90
|
1217
(20 years ago)
by gezelter:
Bug fix (fixes of skipList and neighbor list under MPI)
|
|
atype_module.F90
|
941
(20 years ago)
by gezelter:
Changes for adding direct charge-charge interactions (with switching function)
|
|
ZconsVisitor.hpp
|
1118
(20 years ago)
by tim:
new implement of quickLate using visitor and composite pattern
|
|
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
|
|
ZConstraint.cpp
|
1203
(20 years ago)
by gezelter:
Cutoff group changes under MPI
|
|
ZConsWriter.hpp
|
1091
(20 years ago)
by tim:
ZConstraint now can support sequential moving. Refactorying is needed to support SMD in ZConstraint
|
|
ZConsWriter.cpp
|
1203
(20 years ago)
by gezelter:
Cutoff group changes under MPI
|
|
ZConsReader.hpp
|
1118
(20 years ago)
by tim:
new implement of quickLate using visitor and composite pattern
|
|
ZConsReader.cpp
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
WATER.cpp
|
1224
(20 years ago)
by gezelter:
formatting error messages, dependency fixes
|
|
Vector3d.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Vector3d.cpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
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
|
|
TypeInfo.hpp
|
1232
(20 years ago)
by tim:
new implementation of constraint
|
|
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.
|
|
Torsion.cpp
|
670
(20 years ago)
by mmeineke:
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
|
|
Thermo.hpp
|
1127
(20 years ago)
by tim:
fixed getCOMVel and velocitize at thermo
|
|
Thermo.cpp
|
1253
(20 years ago)
by gezelter:
Fixed a bug in NPTf (vScale was declared in the cpp file in addition
to the declaration in Integrator.hpp file)
|
|
StuntDouble.hpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
StuntDouble.cpp
|
1253
(20 years ago)
by gezelter:
Fixed a bug in NPTf (vScale was declared in the cpp file in addition
to the declaration in Integrator.hpp file)
|
|
StreamTokenizer.hpp
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
StreamTokenizer.cpp
|
593
(21 years ago)
by gezelter:
Starting to worry about all the strtok() calls in our code
|
|
StatWriter.cpp
|
1221
(20 years ago)
by chrisfen:
Formatting Changes, removed writeRaw
|
|
SkipList.hpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
|
SkipList.cpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
|
SimpleBoundCons.hpp
|
1011
(20 years ago)
by tim:
*** empty log message ***
|
|
SimpleBoundCons.cpp
|
1011
(20 years ago)
by tim:
*** empty log message ***
|
|
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
|
|
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
|
|
SimSetup.hpp
|
1261
(20 years ago)
by gezelter:
Modified EAM to use forceFieldVariant
|
|
SimSetup.cpp
|
1261
(20 years ago)
by gezelter:
Modified EAM to use forceFieldVariant
|
|
SimInfo.hpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
SimInfo.cpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
ShakeMin.hpp
|
1248
(20 years ago)
by tim:
constraint algorithm for minimization is working
|
|
ShakeMin.cpp
|
1248
(20 years ago)
by tim:
constraint algorithm for minimization is working
|
|
Shake.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Shake.cpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
SRI.hpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
|
SDMinimizer.cpp
|
1064
(20 years ago)
by tim:
Using inherit instead of compose to implement Minimizer
both versions are working
|
|
Roll.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Roll.cpp
|
1255
(20 years ago)
by tim:
Roll in progress
|
|
RigidBodyVisitor.hpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
RigidBodyVisitor.cpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
RigidBody.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
RigidBody.cpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Restraints.hpp
|
1187
(20 years ago)
by chrisfen:
Fixed Thermodynamic integration code.
|
|
Restraints.cpp
|
1221
(20 years ago)
by chrisfen:
Formatting Changes, removed writeRaw
|
|
ReadWrite.hpp
|
1221
(20 years ago)
by chrisfen:
Formatting Changes, removed writeRaw
|
|
Rattle.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Rattle.cpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Quaternion.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Quaternion.cpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
PRCG.cpp
|
1066
(20 years ago)
by tim:
*** empty log message ***
|
|
OtherVisitor.hpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
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
|
|
OOPSEMinimizer.hpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
OOPSEMinimizer.cpp
|
1250
(20 years ago)
by gezelter:
small bugfixes
|
|
NVT.cpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
NPTxyz.cpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
|
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.
|
|
NPTf.cpp
|
1253
(20 years ago)
by gezelter:
Fixed a bug in NPTf (vScale was declared in the cpp file in addition
to the declaration in Integrator.hpp file)
|
|
NPT.cpp
|
1253
(20 years ago)
by gezelter:
Fixed a bug in NPTf (vScale was declared in the cpp file in addition
to the declaration in Integrator.hpp file)
|
|
Molecule.hpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
Molecule.cpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
MinimizerParameterSet.hpp
|
1064
(20 years ago)
by tim:
Using inherit instead of compose to implement Minimizer
both versions are working
|
|
MatVec3.h
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
MatVec3.c
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
Mat3x3d.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Mat3x3d.cpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Makefile.in
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Make.dep
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
LJFF.cpp
|
1224
(20 years ago)
by gezelter:
formatting error messages, dependency fixes
|
|
Integrator.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Integrator.cpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
InitializeFromFile.cpp
|
1203
(20 years ago)
by gezelter:
Cutoff group changes under MPI
|
|
GhostBend.cpp
|
707
(20 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)
|
|
GenericData.hpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
GenericData.cpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
ForceFields.hpp
|
1261
(20 years ago)
by gezelter:
Modified EAM to use forceFieldVariant
|
|
ForceFields.cpp
|
1258
(20 years ago)
by chrisfen:
Fixed a thermodynamic integration issue. Force and torque scaling loops over atoms, not stuntdoubles
|
|
Exclude.hpp
|
1097
(20 years ago)
by gezelter:
Changes for RigidBody dynamics (Somewhat extensive)
|
|
Exclude.cpp
|
1217
(20 years ago)
by gezelter:
Bug fix (fixes of skipList and neighbor list under MPI)
|
|
Euler3.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
Euler3.cpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
EAM_FF.cpp
|
1261
(20 years ago)
by gezelter:
Modified EAM to use forceFieldVariant
|
|
DumpWriter.cpp
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
DumpReader.cpp
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
DirectionalAtom.hpp
|
1187
(20 years ago)
by chrisfen:
Fixed Thermodynamic integration code.
|
|
DirectionalAtom.cpp
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
DUFF.cpp
|
1224
(20 years ago)
by gezelter:
formatting error messages, dependency fixes
|
|
CutoffGroup.hpp
|
1211
(20 years ago)
by tim:
cutoff group in progress
|
|
ConstraintPair.hpp
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
ConstraintManager.hpp
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
ConstraintManager.cpp
|
1234
(20 years ago)
by tim:
new rattle algorithm is working
|
|
ConstraintIterator.hpp
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
ConstraintElement.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
ConstraintElement.cpp
|
1232
(20 years ago)
by tim:
new implementation of constraint
|
|
ConstraintAlgorithm.hpp
|
1254
(20 years ago)
by tim:
1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
these classes use anonymous union and struct to support
double[3], double[3][3] and double[4]
2. adding roll constraint algorithm
|
|
ConstraintAlgorithm.cpp
|
1248
(20 years ago)
by tim:
constraint algorithm for minimization is working
|
|
CompositeVisitor.hpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
CompositeVisitor.cpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
CallbackFunctor.hpp
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
CallbackFunctor.cpp
|
1248
(20 years ago)
by tim:
constraint algorithm for minimization is working
|
|
CGFamilyMinimizer.cpp
|
1064
(20 years ago)
by tim:
Using inherit instead of compose to implement Minimizer
both versions are working
|
|
BondExtensions.cpp
|
597
(21 years ago)
by mmeineke:
found a bug. Unit vectors were not being updated
|
|
Bond.cpp
|
670
(20 years ago)
by mmeineke:
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
|
|
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.
|
|
Bend.cpp
|
670
(20 years ago)
by mmeineke:
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
|
|
BaseVisitor.hpp
|
1119
(20 years ago)
by tim:
Dump2XYZ is almost working except atoms in rigidbody are double counted
|
|
AtomVisitor.hpp
|
1126
(20 years ago)
by tim:
DUMP2XYZ 0.99 version
|
|
AtomVisitor.cpp
|
1252
(20 years ago)
by gezelter:
Fixes from gcc -Wall
|
|
Atom.hpp
|
1187
(20 years ago)
by chrisfen:
Fixed Thermodynamic integration code.
|
|
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
|
|
AllIntegrator.hpp
|
1032
(20 years ago)
by tim:
Add one more file into Makefile.in
|
|
AbstractClasses.hpp
|
987
(20 years ago)
by tim:
revision of constraint for Nonlinear Optimization Model
|
