Adding iterative looping to get better estimates of friction forces from full-step velocities
MnM interaction now works.
updating configure process
Fixed Langevin Dynamics and DLM
Removed older version of openbabel from our code. We now have a configure check to see if openbabel is installed and then we link to the stuff we need. Conversion to OOPSE's md format is handled by only one application (atom2md), so most of the work went on there. ElementsTable still needs some work to function in parallel.
does ifdef check for computational geometry packages
Fixed some bugs in LDForceManager.cpp
Starting NPT Langevin. Added new force manager files.
SF Lennard-Jones was added for everyones' enjoyment. The behavior is tethered to the electrostaticSummationMethod keyword.
Massive update to do virials (both atomic and cutoff-group) correctly. The rigid body constraint contributions had been missing and this was masked by the use of cutoff groups...
Spherical boundary conditions.
Added velocitizer utility program, added samples of its use to the builder samples.
adding NgammaT integrator
fixes to zang writing
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
MPI thermodynamic integration works now.
testing GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor
Massive changes for GB code with multiple ellipsoid types (a la Cleaver's paper). Also, changes in hydrodynamics code to make HydroProp a somewhat smarter class (rather than just a struct).
fix a bug in parsing HydroProp file
Fixed a bug when spherical boundary conditions were off.
Adding single precision capabilities to c++ side
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Adding spherical boundary conditions to LD integrator
NPrT might work now
Fix a bug in friction calculation for ellipsoid
Verify the correctness of Ellipsoid's hydrodynamics properties
refactor Hydrodynamics module.
LagevinDynamics is working?
LangevinDynamics in progress
Got rid of spurious printing out of timestep
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
OptionSectionParser get compiled
fixed a capitalization problem with NPT integrator initialization
Customized StatWriter is working
rewrite Globals
Removed print statement for angular momentum and inertia tensor from velocitizer.
Removed print statements for remove angular momentum.
Changes to remove angular momentum.
Added method to remove system angular momentum to velocitizer and added method to calculate system angular momentum to siminfo.
dding resetIntegrator
adding resetIntegrator
Fix to print pressure tensor.
adding keyword printPressureTensor
NPrT in progress
NPrT in progress
NPAT is working
fix bug in NPAT and NPrT
adding NPAT and NPrT integrators
xemacs has been drafted to perform our indentation services
minor change to TI output
VelocityVerletIntegrator already deletes and Nullifies restWriter, so Integrator shouldn't do it.
First commit of the new restraints code
info_ in Velocitizer is not initialized which causes a seg fault
remove default parameter from MersenneTwister.hpp which causes all kinds of trouble. Refactory random number generator
replace SPRNG by MTRand
fix compilation problem for g++ 3.4
adding OOPSERandNumGen
adding MersenneTwister random number generator
adding basic_teebuf which can operate on multiple stream simutaneously.
fix a bug in VelocityVerletIntegrator : last frame is written twice
maximum length defaults to the cutoff radius
dynamicProps get built
forget to add eorWriter
(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
fix a bug in loading initial extended system parameters
forget to set maxIterNum_ in NVT
moved Package variable into subdirectory makefiles to speed up the building process
merging new_design branch into OOPSE-2.0
improved restraints
Improvements to restraints
Commented out some write statements
Don't remember what I did
replace old GebericData with new GenericData
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
define DEV_ROOT as relative path
change Makefile to relative path
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change the #include in source files
Import of OOPSE v. 2.0