Change DumpWriter and InitFromFile
Now molecules can keep track of their own IntegrableObjects (and RigidBodies). Also a bug-fix so that SimInfo can keep track of RigidBodies (which was done incorrectly before).
Added Integrable (will back out momentarily)
Oops. Those were old.
Forgot to add IntegrableObjects
Adding RigidBody code
Changes for RigidBody dynamics
Slightly longer test run
Changes for RigidBody dynamics (Somewhat extensive)
incorporate SMD into ZConstraint,it does not sound a good choice, next commit will seperate SMD and ZConstraint
ZConstraint now can support sequential moving. Refactorying is needed to support SMD in ZConstraint
add LARGEFILE_SOURCE64 macro to support large file
Fix a couple of bugs in zsub
Adding zsub, a program which can be used to replace atom type for zconstraint into OOPSE
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remove the old implement of minimizer from cvs tree
Using inherit instead of compose to implement Minimizer both versions are working
adding function shakeF in order to remove the constraint force along bond direction
single version of energy minimization is working.
started a bug fix on the massive memory overusage by OOPSE
Stripped out the hardwired LJ_rcut
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Single version of energy minimization for argon is working, need to add constraint
Add one more file into Makefile.in
Add some lines into global.cpp to make it work with energy minimization
Fix a bunch of bugs :-) Single version of conjugate gradient with golden search linesearch pass a couple of functions test. Brent's algorithm is still broken
NLModel0, NLModel1 pass uit test
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to avoid cyclic depency, refactory constraint class
Functor.hpp pass unit test
begin unit test of minimizer
Adding GoldenSection and Brent LineSearch Method
using class Minimizer1D derived from MinimizerBase instead of a functor to do line seach
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...
member list fixes for rigid bodies
Adding MinimizerParameterSet class.
Revision of NLModel0 and NLModel1
revision of NLModel
Added point-charge models to water.mdl file, updated ssd.bass to use new SSD name
Fix to new RigidBody stuff
Longer run time to test SSD water in MPI
Longer run time to test gold in MPI
Longer run time to test argon
More BASS changes to do new rigidBody scheme a copy of WATER.cpp from this morning
More BASS changes to do new rigidBody scheme
revision of constraint for Nonlinear Optimization Model
Changes to BASS reader to use Euler angles for orientation instead of unit vectors required changes in MoLocator
Changed orientation lines from unit vectors to euler angles
Convert Eulers in degrees into radians
Changed default orientation in BASS to use Euler angles in the following order: phi, theta, psi Removed the ability to set orientation using a unit vector
Changed default orientation in BASS to use Euler angles in the following order: phi, theta, psi Removed the ability to set orientation using a unit vector
Fix broken atom assignment for rigid bodies
Corrected spelling in several directories, and stated WATER.cpp
constraint class in energy minimization
Adding energy minimization
Energy Minimizer
Made some error messages more user-friendly
Updated the default water to SSD/E
Adding warning if sample time, status time, thermal time and reset time are not divisible by dt
Added a bunch of dummy targets so make won't complain
Fixed old bass file
BASS changes to add RigidBodies required a change in how the MoleculeStamps are used by divideLabor in mpiSimulation.cpp
BASS changes to add RigidBodies and LJrcut
fix a bug in creating eor file
fixed a bug where only MPI jobs could write eor files
fixed an struct mismatch error in the mpi initialization of the AtomStruct
Fixes for Dumps
Changes for altivec
Documented the Spud Toss
changes for charge charge interactions
More work for adding charges
autoconf fixes
fixed a periodic box bug
autoconf compatibility changes for icc8
Changes for adding direct charge-charge interactions (with switching function)
Some changes for new MPI organization and direct charge-charge interactions
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Energy Minimization method
open and close the eor file whenever it is used instead of rewinding it
change the interface of writeFrame
Merge the code of writeFinal and writeDump; Adding sortingIndex into DumpWriter; Fix a bug of writing last frame twice in integrator
fix a bug in copying string
Dumpwriter only write out the atoms on master nodes
tagub is not a bug. Just roll it back fix a bug of copying string to a pointer Still have Seg fault, it looks like a random MPI seg fault in totalview
Fix a bug of declaration of tagub
New DumpWriter (Attempt #4)
A work in progress...
null terminate some strings just in case
refixed the NVT readin XS state bug.
added strncpy to DumpWriter
fixed the restart from NVT exstended state bug
First Stab at fixing DumpWriter
added support for the ignore XS state info flag
Fixed a bug of sending message from master node to itself in DumpWriter.cpp and InitializeFromFile.cpp
performance fixes in the dipole dipole and reaction field code
Making do_Forces a little more sane
Attempting to increase performance by reducing spurious function calls
mangling forces even further
mpich mucking
mangled do_forces...
Added bitmask to do_forces property lookup
Added third-party directory for code not written by us. Also added Mersenne Twister random number generator code. This will eventually replace sprng as the random number generator used by OOPSE.
Fixes to profile code.
More profiling fixes.
Another change for MPI in timing.
Small update to timing in MPI
the profiling commands work now. Will start adding PROFILE ifdefs into the code
added some profiling routines
working on adding GofRtheta and GofRomega additional work on randomBilayer
working on adding GofRtheta and GofRomega
added some profile functionality
Added functions for simple profiling in fortran.
Fixed bug in parallel EAM. rho_row and rho_col were scattered into the same array. Unfortunately, MPI zeros the array between scatters so half of the sum was being lost. Fixed by added a temp array for column scatter, then sum loop over nlocal.
finished gofRtheta and added gofRomega. both need to be debugged and tested.
Changes for gradients (to do minimizations)
removed the randombilayer header
edited the makefile to add randomBilayer to the build. Also move the random bilayer builder from bilayerSys to randomBilayer
backed up the old DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and TB3 in DUFF.frc
added a more verbose error message in SimInfo. Added a more informative error message in InitializeFromFile
begun work on add ing in the GofR,CosTheta
Fixed a bug in SimInfo ordering of radii
added a routine to SimInfo.cpp to inline a min function.
reordered the rcut/ecr/boxSize initialization removed the rcut/ecr shrink and grow algorithm. the simulation will now exit when it runs into rcut or ecr.
Added support for compiling fortran without use of mpich modules. We use mpif.h instead.:
moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
fixed the includes in the Make.dep
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
some work on trying to find the compression bug
added template stuff to the Maikefile template little changes to some printf format statements
added template stuff to the Maikefile template
bug fixes for rList problems
Fixed bug that size(q0) was being queried before q0 was allocated.
fixed a stdlib.h include error in bass.l fixed a little bug in the first time step, regarding the setting of ecr and est in fortran
fixed a stdlib.h include error
som efixes to the way rcut is setup, as well as additional debugging comments.
C++ compatibility for templates
Refixed broken makefile
compatibility fixes
add chi and eta to the comment line of dump file.
did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.
Portability fixes
Compatibility fixes
started trying to understand extern "C" stuff for pointers
fixes for compatibility
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.
replace c++ header stuff with more portable c header stuff Also, mod file fixes and portability changes
mod file fixes and portability stuff
Stuff for MOD support in other compilers
added routines for the sysbuilder to work with simSetup remved the QuickBass routines, and had all parsing go through SimSetup. LatticeBilayer is in complete working order now.
added routines for the sysbuilder to work with simSetup
fixes for configure, sysBuild
put QuickBass, MoLocator, and latticeBuilder into a Builder Library overhauled latticeBilayer into its own program. Removed sysBuild from the Makefile
work on bilayer builder
fixed a merge problem
added eam ForceField files to the init fixed an eam mpi parmeter setup bug added the init file to the makefile
added eam ForceField files to the init fixed an eam mpi parmeter setup bug
added eam ForceField files to the init
added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
added useInitTime to the BASS syntax. * useInitTime = false: sets the origin time to 0.0 regardless of the time stamp in the .init file * default=> useInitTime = true;
added the staticProps directory to the build list for both configure and configure.in fixed a number of bugs in the staticProps code. gofr is now working.
added the staticProps directory to the build list for both configure and configure.in
added the staticProps directory to the build list
Changed DumpReader to use linked lists instead of a vector. Fixed the makefile to build DumpReader.cpp Removed a comment output in Exclude.cpp Modified DumpWriter and Integrator to write an eor file every time a frame is written. This lets the .eor file represent the last written frame of a simulation.
removed the props directory, and moved everything over to staticProps
Contiuned work on staticProps. should be in a position where it will compile and run first runs.
Fixed bug in calc_eam.
added Au init file for eam.
removed entahlpy from the statwriter and thermo.
changed the formating ogf the error statements in simError added a function to get the maxCutoff near completion of the staticProps code. still needs the pair loop, and the loop to allocate and read each frame.
changed the formating ogf the error statements in simError added a function to get the maxCutoff
changed the formating ogf the error statements in simError
finishing up the constructs needed to get this program up and running
changed f90Flags so they are no longer overwritten by the compiler.
added mpif90 mod check back same for conifig.in fixed wrappers to extern "C"
added mpif90 mod check back same for conifig.in
added mpif90 mod check back
fixed a lot of warnings and errors found with SUN's SUNWspro.s1s7
light change in syntax. no signifigant change.
fixed some additional remarks from icc -w3 (extra verbose output)
cleaned things with gcc -Wall and g++ -Wall
fixed a bug in configure
fixes for configure
moved readyCheck in the integrator so that it is called before the first Statistics are written.
Added a bunch of Make.dep files to CVS
Removed NPTfm from Integrator.hpp. Some small syntax cleaning in NPTfm and SimSetup
fix bug in calculating maxCutoff
Converted NPTf to work with the NPT base class. Removed NPTfm and NPTim from cvs
added NPT base class. NPTi is up to date. NPTf is not.
removed mpi++ from the makefile
goofing off to test NPTf and NPTi
fixed bugs in NPTf, found (nearly) conserved quantities for both NPTi and NPTf
fixed a typo in the makefile.
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fixed NPTi to now work with constraints.
fixed ecr grow in SimInfo fixed conserved quantity in NPT (Still some small bug) NPTi appears very stable.
add conserved quantity to statWriter fix bug of vector wrapping at NPTi
added AllCorr. It eill still need some work
Added integrators to Makefile.in
Entered changes for configure into ChangeLog
added more work on getting gofR working.
added the beginings of the GofR pair correlation. added identification of identI in matchI.
updated the ChangeLog added two new NPT integrators, they still need work.
updated the ChangeLog
dependency on config.h
fixed sprng problem
New Makefile for metals sample
Changes to autoconf / configure method of configuring OOPSE
added resetTime to the Global namespace. added ability to reset the integrators in the NVT and NPT family.
added resetTime to the Global namespace.
fix a bug at MPI version of PolicyByMass
Added: check uniqueness of molIndex
added the first functional parts of the PairCorrType Abstract classes.
fix bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we turn on the optimization flag, it causes a seg fault
More fixes for stress tensor parallel bug.
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 molMembershipList use global index instead of local index
set default force substraction policy to PolicyByMass
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added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb. commented out some print statements in Zconstraint hard coding some system init into bilayer.sys
added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb. commented out some print statements in Zconstraint
Use make_sprng_seed() to generate seed and check the seed which is specified by user at least contains 9 digits
changed the Makefiel a litle. Fixed a bug in MPI_DUFF. The atom block type was not being properly constucted in MPI. (The MPI struct had 6 doubles declared versus the actual 11)
changed the Makefiel a litle.
More FreeBSD fixes
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small bug fix on frequency of output dumps.
user can setup seed in bass file now, if he does not specify any value for seed, oopse will take the value of seconds of system time as seed
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)
updated the Changelog. added some bug fixes for setting the random number generator seed value.
updated the Changelog.
bug fixed in ghost bend class
quick makefile fix, in make links. added -f to ln -s.
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reformmating ZConstraint and fixe bug of error msg printing
Fixed sysBuild -bilayer works. Nanobuilder still broke.
Tested MPI version of Z-Constraint Method
Stable ZConstraint with average force substraction strategy
Added some profiling code -DPROFILE.
harmonic potential & z-contraint method
fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.
debugging globals
formatting fixes and new atypes in LJFF
fixed a few references to older stuff...
Added comment line for getgetopt.
Missed del of files before.
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commit makefile
added harmonical potential to z-constraint method
Changed makefile to only build quicklate.
added utils/sysbuilder to be built.
Arranged sysbuilder into a subdirectory. Fixed some of sysbuilder to work with new atom allocation in libmdtools.
added method of moving zconstraint molecules to specified positions
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Added zConstraint into the BASS language syntax.
changed the number of degrees of freedom to account for zConstreints
EAM works...... Neighbor list also works.....
moved frameCount's functionality into DumpReader. also split props into staticProps and dynamicProps. (currently only have staticProps)
fixed a deprcated instance of Atom::setZ and Atom::getZ in ZConstaint.
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
Bug fixes for eam...
stable version of Z-Constraint
add index range checking into ZConstraint
added z-constraint parameters to the globals
Added Z constraint.
More bug fixes for eam.
working on the props code
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Added bass models for metals
Added eam to simSetup and added changecutoffeam.
Changed configure to look for both upper and lower cass .mod files
module use fixes for eam and do_forces.
Finished most code for eam....
added the scan function to the DumpReader. It should now save the start of each frame in a vector.
making some changes to read dump files
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Fixed a current time initialization bug in InitFromFile.
some initial changes to Dumpwriter and friends to accomadate random file access
Initialized currentTime to 0, in case no one sets it.
fixed Initializefrom file to start the simulation from the time specified in the init file.
Started work on a DumpReader
Fixes for SSD/E
Changes for SSD/E
commented out an eam line
fixed spelling issue
added info module
Added massive changes for eam....
More up to date version of EAM_FF
Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.
Made quickLate aware of Hmat. quickLate is now somewhat more intelligent about periodic boundaries and wrapping.
Fixed bug in updating mixing lists
added a quick wipe-and-update script for quick rebuilds on BoB
more fixes for box changes
removed some debugging print statements.
fixed a long lived bug in do_forces. Rrf was not being used in the neighborlist correctly. rcut was conssistently being set lowere than Rrf causing the dipole cutoff region to be to small. Also led to the removal of the taper region to buffer the dipole cutoff.
working on fixing ssd bug
Fixes for the NPT ensembles
cleaned up simSetup
fixed some bugs, Changed entry_plug to info where appropriate
added more command line arguments
Fixing force field line
Fixing pressure tensor
more archaic code fixes
removed old outdated code
fixes to get rid of get_vx and set_vx
removing get_vx
Added NPTfm
Bugfix in NPTim, fixes for NPTfm
Checking in changes for NPTim
Broken SysBuilder
Fixes for samples
Removed some debugging write statements
Fixes for get and set routines in Atom and DirectionalAtom
added get and set routines to Atom and DirectionalAtom
added a nanoSysBuilder that takes different cmd line arguments.
found a bug. Unit vectors were not being updated
Working on NPTim
Switched the bond in the force field back to constrained, to preserve energy
working on som integrator bugs
Starting to worry about all the strtok() calls in our code
Fixed Hmat and some namespace strangeness
Fixed hmat in DumpWriter (MPI) and eor.
fixed some bugs
Added nanoBuilder and a general Lattice builder.
Bunch of 1-d array -> 2-d array stuff
Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.
starting some work for xlate
adding in dan's NPT stuff
Fixes and merging NPTf
Removed Qmass
Fixes for both NPTf and NPTi
Fixes in NPTi migrated into NPTf
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fixed box scaling
NPTi
cleaned up the dependecy scripts in the makefiles
fixed the bugs introduced by switching the periodic box to a matrix
Fortran flexi-BOX
Fixes for flexi-BOX
working on adding the box matrix to everything.
Updated the ChangeLog, and Converted most of the SImInfo to use non-Isotropic boxes. wrapVector needs to be finished.
Changed over the bonds to Harmonic bonds in the DUFF frc file fixed constraints.
Changed over the bonds to Harmonic bonds in the DUFF frc file
Fixes to NVT. Check them!
added Harmonic bod into the DUFF forcefield and BondExtensions.cpp
Doing some work to debug the constraint code.
NPT fix
Most of the integrator and NVT seem to be working now.
NVT additions
slowly converting to new integrator and forcefield names.
finished the basics of the integrator and SimSetup.cpp
doing some work on SimSetup to clean it up / get it to work with the new Integrator.
minor changes in an attempt to fix output times.
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex some work on the integrator. ( incomplete)
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex
added constrainA and constrainB to the Symplectic integrator
currently modifiying Symplectic to become the basic integrator. bilayerSys.cpp altered for building tb3.
currently modifiying Symplectic to become the basic integrator.
added some member variables for position, velocity, etc.
changed how NVT is now derived from Integrator
fixed an a mismatched Ghostbend bug.
all seems to be working
still working on the bilayer code
doing some work to overhaul sysbuild.
optimized the ssd calc loop
Added bead lipid model to the sample directory
finished adding the Tail beads into the Trappe extended force field
added the TailBead atom types to the TraPPe_Ex forceField
fixed up the TraPPE_Ex force field. there were some duplicate entries added a two chain lipid to the lipid.mdl in sample
fixed up the TraPPE_Ex force field. there were some duplicate entries
added the utils subdirectory to the configure script added the CH branching group to the TraPPE_Ex fource field
added the utils subdirectory to the configure script
i quick fix to th distance in the random bilayer builder
added a new test for constraint failure
fixed up sysBuild to where it should now build our systems
almost finished.
bilayerSys and sysBuild both will build now. woot!
finished bilayerSys.cpp sysBuild still need to write the bass file. MoLocator.cpp is currently empty
Added eam force files...
More eam work.
working on the system builder
Fixed ordering on NVT calculation in integrators.
working on a system builder
added Ghost bends to the TraPPE_Ex forceField added sysBuild to the utils Makefile
added Ghost bends to the TraPPE_Ex forceField
Added first mangling of EAM.
fixed a memory bug in Fortran, where molMembershipArray was declared nLocal instead of nGlobal.
Bug fix in progress for NPT
added a globalIndex counter to Molecule
Working on ConstantStress
fixed a n mpi init bug in SimSetup. caused a miscalculation of nLocal.
fixed a bug in symplectic, where presure was only being calculated the first time through.
added pentane to the alkane model file
Added volume and enthalpy to status file
fixes for NPT and NVT
It works (kinda)...
Fixes for NPT / NVT
Moved expand neighborlist to init_FF.
fixes for NVT
fixes for nvt / npt
dt/2 fix in nvt
Fixes for affine transform
Changes to integrate the NVT and NPT ensembles
Fixes for NPT and NVT
fixed a sign error in the radial portion of SSD.
doing some testing in sticky through Symplectic.
Working on NVT
Fixed transpose bug in mpi reduce for tau and virial.
bug fixes
Many fixes to add extended system
Fixed a bug caused by my experimentation
Added ExtendedSystem infrastructure for NPT and NVT calculations
Added targetPressure to BASS
final mods to try a fortran compiler
Bug fixes for simulation module rewrites
bug fixes for compilation
bug fixes to fortran wrappers
Breaking c and fortran, c gets smarter, fortran gets dumber...
fixed a memory read bug in neighborlist
Changes for Extended System
Fixes for ExtendedSystem
Added extended system header
changes for extended system code
renamed nvt to extendedsystem
added some little fixes here and there.
fixed a possible call before initialize bug.
just little things like deleteing unused variables and such.
a few fixes to simError.h also some fixes to Molecule.hpp
a few fixes to simError.h
fixed some small things with simError.h
Starting work on NPT
Added NVT file (very broken for now)
Changed Readme, added some files
dipoles mostly work, but there is a memory leak somewhere.
Fixed a bug where MPI was not getting the proper atomIdents.
more bug fixes....
Fixed DumpWriter to be more robust to errors. also added a little namespace to InitFromFile to wrap it's helper functions in MPI
Fixed bug with pot_local not zeroed.
Fixes in MPI force calc and in Trappe_Ex parsing.
bug fix in DumpWriter.cpp
Bug fixes in read-write routines.
fixed a bug where the Excludes were not being created properly
mpi fixes and debugging mpi read write from file.
fixed long range interactions in Trappe
MPI buggy, fixed mpiRefresh issue.
fixed a bug where excludes were not being initialized
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Fixed a single processor segfault bug.
fixed the compile time bugs, Source builds and links
fixed a few more bugs.
added the Molecule.cpp file
fixed the makefile
fixing some compile time bugs
I have implemeted Molecules everywhere I could remember to. will now attempt to compile.
finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
finished conversion of TraPPE_ExFF to use Molecule
LJ_FF has been converted to the new Molecule model. TraPPE_Ex is currently being updated. SimSetups routines are writtten, but not yet called.
fixes for local->global atom numbering in MPI
little bug fixes here and there.
Fixes to fileio for MPI
bug fixes many bug fixes
Making DumpWriter less dependent on sequence of atoms on the other processors. Node 0 now fires potatoes at other processors to get them to send french fries back.
the skeleton for making the molecules is in place. ForceField needs to be updated next.
fixed a couple of the "static" bugs in Atom and Exclude
still working on the SimSetup routine. also fixed some things in Exclude.hpp
Added Atom.cpp and Exclude.cpp
Fixes in Atom and Exclude list
Make Atom.cpp able to add and delete ranges of atoms
added an Exclude class with static arrays similar to the Atom class
I'm overhauling the molecule class to contain it's own bonds, bends, and torsions. may god have mercy on my soul.
Finished globalIndex.
MPI stuff for passing out molecules
working on load balancing
Fixes for Parallel thermalization
fixed an mpi include bug in THermo.cpp
Fixed bugs with calculation of potential energy and temperature.
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added dummy files to keep the build deirectories from being pruned.
moving tests to samples
moved tests to samples
Tests are becoming samples
Added makefiles in tests directories
electrostatic changes for dipole / RF separation
little bug fixes here and there
added an argon test simulation
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added some test bass files for experimenting with
fixed bug where short range interactions were not being calculated. removed some debug print statements
various write statements for debugging
added links to the makefile in forceFields
Fixed F_MACH_DEP bug
Makefile fixes, directory re-org, autoconf fixes
Added license file
Fixed makefile
Makefile for forceFields
Readme changes
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Makefile fixes for depends
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