 ../
|
obj/
|
400
(22 years ago)
by mmeineke:
*** empty log message ***
|
|
MPIobj/
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400
(22 years ago)
by mmeineke:
*** empty log message ***
|
wrappers.F90
|
657
(22 years ago)
by chuckv:
More bug fixes for eam.
|
|
vector_class.F90
|
378
(22 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
(21 years ago)
by chuckv:
Fixes to profile code.
|
|
status_module.F90
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648
(22 years ago)
by chuckv:
Finished most code for eam....
|
|
simulation_module.F90
|
941
(21 years ago)
by gezelter:
Changes for adding direct charge-charge interactions (with switching function)
|
|
randomSPRNG.hpp
|
450
(22 years ago)
by mmeineke:
just little things like deleteing unused variables and such.
|
|
randomSPRNG.cpp
|
829
(22 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.
|
|
oopseMPI_module.F90
|
940
(21 years ago)
by gezelter:
Some changes for new MPI organization and direct charge-charge interactions
|
|
notifyCutoffs.F90
|
945
(21 years ago)
by gezelter:
More work for adding charges
|
|
neighborLists.F90
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872
(21 years ago)
by chrisfen:
Fixed a bug in SimInfo ordering of radii
|
|
mpiSimulation_module.F90
|
883
(21 years ago)
by chuckv:
Added functions for simple profiling in fortran.
|
|
mpiSimulation.hpp
|
836
(22 years ago)
by mmeineke:
did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.
|
|
mpiSimulation.cpp
|
989
(21 years ago)
by gezelter:
More BASS changes to do new rigidBody scheme
a copy of WATER.cpp from this morning
|
|
mpiForceField.h
|
976
(21 years ago)
by chrisfen:
Corrected spelling in several directories, and stated WATER.cpp
|
|
mpiForceField.c
|
976
(21 years ago)
by chrisfen:
Corrected spelling in several directories, and stated WATER.cpp
|
|
mpiComponentPlan.h
|
836
(22 years ago)
by mmeineke:
did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.
|
|
mdProfile.hpp
|
884
(21 years ago)
by mmeineke:
added some profile functionality
|
|
mdProfile.cpp
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892
(21 years ago)
by chuckv:
Fixes to profile code.
|
|
fortranWrappers.hpp
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836
(22 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.cpp
|
836
(22 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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fortranWrapDefines.hpp
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
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force_globals.F90
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648
(22 years ago)
by chuckv:
Finished most code for eam....
|
|
forceFactory.hpp
|
378
(22 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.
|
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fSimulation.h
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941
(21 years ago)
by gezelter:
Changes for adding direct charge-charge interactions (with switching function)
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fInfo.c
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747
(22 years ago)
by gezelter:
Changes to autoconf / configure method of configuring OOPSE
|
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fForceField.h
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834
(22 years ago)
by gezelter:
Compatibility fixes
|
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do_Forces.F90
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
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definitions_module.F90
|
747
(22 years ago)
by gezelter:
Changes to autoconf / configure method of configuring OOPSE
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config.h.in
|
747
(22 years ago)
by gezelter:
Changes to autoconf / configure method of configuring OOPSE
|
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calc_sticky_pair.F90
|
898
(21 years ago)
by chuckv:
Attempting to increase performance by reducing spurious function calls
|
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calc_reaction_field.F90
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
|
calc_gb.F90
|
898
(21 years ago)
by chuckv:
Attempting to increase performance by reducing spurious function calls
|
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calc_eam.F90
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898
(21 years ago)
by chuckv:
Attempting to increase performance by reducing spurious function calls
|
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calc_dipole_dipole.F90
|
945
(21 years ago)
by gezelter:
More work for adding charges
|
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calc_charge_charge.F90
|
945
(21 years ago)
by gezelter:
More work for adding charges
|
|
calc_LJ_FF.F90
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
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atype_module.F90
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941
(21 years ago)
by gezelter:
Changes for adding direct charge-charge interactions (with switching function)
|
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ZConstraint.cpp
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830
(22 years ago)
by gezelter:
fixes for compatibility
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ZConsWriter.hpp
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699
(22 years ago)
by tim:
Tested MPI version of Z-Constraint Method
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ZConsWriter.cpp
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830
(22 years ago)
by gezelter:
fixes for compatibility
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WATER.cpp
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
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TraPPE_ExFF.cpp
|
976
(21 years ago)
by chrisfen:
Corrected spelling in several directories, and stated WATER.cpp
|
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TorsionExtensions.cpp
|
378
(22 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.
|
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Torsion.cpp
|
670
(22 years ago)
by mmeineke:
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
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Thermo.hpp
|
799
(22 years ago)
by mmeineke:
removed entahlpy from the statwriter and thermo.
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Thermo.cpp
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853
(21 years ago)
by mmeineke:
did a merge by hand from the new-templateless branch to the main trunk.
bug Fixes include:
* fixed the switching function from ortho to non-ortho box.
!!!!! THis was responsible for all of the sudden deaths we saw.
* some formating in the string when we write out the extended system state.
* added NPT.cpp to the makefile.in
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StreamTokenizer.hpp
|
593
(22 years ago)
by gezelter:
Starting to worry about all the strtok() calls in our code
|
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StreamTokenizer.cpp
|
593
(22 years ago)
by gezelter:
Starting to worry about all the strtok() calls in our code
|
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StatWriter.cpp
|
829
(22 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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SimState.hpp
|
670
(22 years ago)
by mmeineke:
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
|
|
SimState.cpp
|
829
(22 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.
|
|
SimSetup.hpp
|
823
(22 years ago)
by mmeineke:
added routines for the sysbuilder to work with simSetup
|
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SimSetup.cpp
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
|
SimInfo.hpp
|
941
(21 years ago)
by gezelter:
Changes for adding direct charge-charge interactions (with switching function)
|
|
SimInfo.cpp
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
|
SRI.hpp
|
707
(22 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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ReadWrite.hpp
|
936
(21 years ago)
by tim:
open and close the eor file whenever it is used instead of rewinding it
|
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NVT.cpp
|
855
(21 years ago)
by mmeineke:
added the following parameters to BASS:
* useInitialExtendedSystemState
* orthoBoxTolerance
* useIntiTime => useInitialTime
|
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NPTxyz.cpp
|
857
(21 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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NPTi.cpp
|
857
(21 years ago)
by mmeineke:
moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
|
|
NPTf.cpp
|
857
(21 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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NPT.cpp
|
857
(21 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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NLModel1.cpp
|
1000
(21 years ago)
by tim:
using class Minimizer1D derived from MinimizerBase instead of a functor to do line seach
|
|
NLModel0.cpp
|
1000
(21 years ago)
by tim:
using class Minimizer1D derived from MinimizerBase instead of a functor to do line seach
|
|
NLModel.hpp
|
1000
(21 years ago)
by tim:
using class Minimizer1D derived from MinimizerBase instead of a functor to do line seach
|
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Molecule.hpp
|
658
(22 years ago)
by tim:
Added Z constraint.
|
|
Molecule.cpp
|
829
(22 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.
|
|
MinimizerParameterSet.hpp
|
1002
(21 years ago)
by tim:
Adding GoldenSection and Brent LineSearch Method
|
|
MinimizerBase.hpp
|
1002
(21 years ago)
by tim:
Adding GoldenSection and Brent LineSearch Method
|
|
Minimizer1D.hpp
|
1005
(21 years ago)
by tim:
begin unit test of minimizer
|
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Minimizer1D.cpp
|
1005
(21 years ago)
by tim:
begin unit test of minimizer
|
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Makefile.in
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
|
Make.dep
|
998
(21 years ago)
by gezelter:
member list fixes for rigid bodies
|
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LJFF.cpp
|
976
(21 years ago)
by chrisfen:
Corrected spelling in several directories, and stated WATER.cpp
|
|
Integrator.hpp
|
987
(21 years ago)
by tim:
revision of constraint for Nonlinear Optimization Model
|
|
Integrator.cpp
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
|
InitializeFromFile.cpp
|
911
(21 years ago)
by mmeineke:
refixed the NVT readin XS state bug.
|
|
GhostBend.cpp
|
707
(22 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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GenericData.hpp
|
837
(22 years ago)
by tim:
add chi and eta to the comment line of dump file.
|
|
GenericData.cpp
|
787
(22 years ago)
by mmeineke:
cleaned things with gcc -Wall and g++ -Wall
|
|
Functor.hpp
|
1007
(21 years ago)
by tim:
Functor.hpp pass unit test
|
|
ForceFields.hpp
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
|
ForceFields.cpp
|
892
(21 years ago)
by chuckv:
Fixes to profile code.
|
|
Exclude.hpp
|
435
(22 years ago)
by mmeineke:
fixed a bug where the Excludes were not being created properly
|
|
Exclude.cpp
|
829
(22 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.
|
|
EAM_FF.cpp
|
976
(21 years ago)
by chrisfen:
Corrected spelling in several directories, and stated WATER.cpp
|
|
DumpWriter.cpp
|
1000
(21 years ago)
by tim:
using class Minimizer1D derived from MinimizerBase instead of a functor to do line seach
|
|
DumpReader.cpp
|
847
(22 years ago)
by mmeineke:
added template stuff to the Maikefile template
little changes to some printf format statements
|
|
DirectionalAtom.cpp
|
878
(21 years ago)
by gezelter:
Changes for gradients (to do minimizations)
|
|
DipoleTestFF.cpp
|
829
(22 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.
|
|
DUFF.cpp
|
976
(21 years ago)
by chrisfen:
Corrected spelling in several directories, and stated WATER.cpp
|
|
Constraint.hpp
|
995
(21 years ago)
by tim:
revision of NLModel
|
|
Constraint.cpp
|
987
(21 years ago)
by tim:
revision of constraint for Nonlinear Optimization Model
|
|
ConjugateMinimizer.hpp
|
1002
(21 years ago)
by tim:
Adding GoldenSection and Brent LineSearch Method
|
|
BondExtensions.cpp
|
597
(22 years ago)
by mmeineke:
found a bug. Unit vectors were not being updated
|
|
Bond.cpp
|
670
(22 years ago)
by mmeineke:
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
|
|
BendExtensions.cpp
|
829
(22 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
(22 years ago)
by mmeineke:
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
|
|
Atom.hpp
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
|
Atom.cpp
|
999
(21 years ago)
by chrisfen:
Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...
|
|
AllIntegrator.hpp
|
812
(22 years ago)
by mmeineke:
added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
|
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AbstractClasses.hpp
|
987
(21 years ago)
by tim:
revision of constraint for Nonlinear Optimization Model
|
