Fixed a DumpWriter parallel bug.
Compilation and portability fixes
Fixed a bunch of stylistic and performance issues discovered via cppcheck.
Fixed a bunch of cppcheck warnings.
Chasing down bugs in the TIP4P_FQ model.
CLearing out some memory leaks
Attempt to fix memory leak in Multiple hull calls
Fixes for Qhull static build strangeness
Some bugfixes for cell-linked-list-style neighbor lists when the simulation doesn't use periodic boundary conditions. Cleaning up some of the Hull stuff while we're in there.
Bug fixes to get new parallel decomposition methods working without periodic boundary conditions. Updated volume in stats file correctly. LangevinHull fixes for low viscosity values.
Fixed a bunch of bugs in CubicSpline debug sections, ForceMatrix Decomp computing costhetas for non-existent rotation matrices, Hidden accumulator counts, and SMIPD non-coupling
Updated the integrator conserved quantity so that it doesn't trail the other properties
Fixed a widespread typo in the license
Cleaning more cruft and unused variables.
A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
Fixes to mdParser to handle vector assignments, fixes for VelocityVerletIntegrator deleting rnemd_ when it doesn't exist yet.
Adding new RNEMD options and output file format
Code readability updates.
Various fixes required to compile OpenMD with the MS Visual C++ compiler
Added Fluctuating Charge Langevin propagator, and made it the default fixed some errors on the one-center slater coulomb integrals, and some parameters in PhysicalConstants.
Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
Some bugfixes (CholeskyDecomposition), more work on fluctuating charges, migrating stats stuff into frameData
fixed a directional StuntDouble bug
Fixed a strange bug where setting tempSet to false would still require a targetTemp
general bugfixes
Removed a line in Integrator.cpp where the forceMan_ was being initialized too early. Additionally, added a dummy value for rCut_ in ForceManager.cpp::setupCutoffs. JRM
added a forceman to the flucq propagator
Mostly whitespace
Reorganized source directories, added RNEMD and flucQ blocks for options parsing.
Fixed compilation issues
resolved
Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
Bug fixes for heat flux import
Merging Shenyu's RNEMD changes from openmd-1 into the development branch.
Adding fluctuating charges, still a work in progress
Adding the propagators for FlucQ
Adding more support structure for Fluctuating Charges.
Some fixes for DataStorage issues. Removed outdated zangle stuff that has been replaced by the more modern restraints.
Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
Fixes for compilation under LLVM compiler Bug-fix for switching function in Gay-Berne
Some fixes for CMake and single precision builds
updated copyright notices
fixing the build system
cleaning up the development branch a bit, removing cruft, etc.
Merging changes from old branch into development branch
Splitting out ifstrstream into a header and an implementation. This means that much of the code that depends on it can be compiled only once and the parallel I/O is concentrated into a few files. To do this, a number of files that relied on basic_ifstrstream to load the mpi header had to be modified to manage their own headers.
migrating cutoff information from InteractionManager to ForceManager
builds
attempts at c++->fortran linkage. Still busticated.
Creating busticated version of OpenMD
removing cruft (atom numbers, do_pot, do_stress) from many modules and force managers
Adding property set to svn entries
Adding a progress bar, and pAngle staticProps
Cleanup of unit normal code in Triangle.cpp SMIPD now call getUnitNormal instead of getNormal.
Added preliminary code for Alpha Hull calculation using qhull. Added preliminary support to SMIPD to support Alpha Hull. Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. Preliminary changes for shadow hamiltonian integrator. Chages to md files so they will work in openMD.
Parallel bugfix in RestraintForceManager Reverted back to hydrodynamics on triangular plates for SMIPDForceManager Removed thermalLength and thermalConductivity keywords from Globals. Bug tracking in openmdformat (not yet resolved).
Merging changes skipped in working copies of OOPSE into the OpenMD tree, fixing make install
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
Removing CGAL from all code
fixed a bug confusing id with localID, stopped adding NULLS to triangles also.
Re-write of convex hull.
added RNEMD scaling
Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
New hotness
units for thermalConductivity, spelling error fixed
Latest version of SMIPD with gamma set to thermal conductivity
Parallel version of RNEMD
Adding boundary element hydrodynamics to SMIPD.
only create RNEMD object if we need it.
Bug fixes and sanity checks for RNEMD (nBins should be even), check to make sure we aren't selecting inappropriate numbers of integrable Objects
bug fix in DLM, added temperature profiles and uniform bins to RNEMD
Added a getStatus routine to check the temperatures
Bug fix
Debugging, but still unstable
fixed some bugs, added some logic to sort stuntdoubles
Adding options to RNEMD for selecting particular StuntDoubles
Added handlers to Integrator to call RNEMD at the right times. Added initialization to RNEMD to make sure values from the MD file are available.
Adding RNEMD
Different method again for Langevin Dynamics.
Cleaning up some cruft.
Code clean-up. Removed old langevin code.
Stupid getRandomNumber return 4;
Fixed bug in variance.
More attempts to get SMIPD to themostat properly
General bug-fixes and other changes to make particle pots work with the Helfand Energy correlation function
Fixed segfault in because of directional atom in SMIPD.
Fixed Memory Leak in ConvexHull.
More changes to SMIPD. Attempting to find memory leak.
Returned old LD forces to SMIPDForceManager.
Fixed nanovol so it now builds.
Work continues on constant pressure langevin dynamics.
Fixed makefile.
Only build SMIPDynamics and register it if we have qhull
Adding back more missing files.
Added large quantities of code for convex hull and constant pressure langevin dynamics.
Added some logic to print out a special pair distance as a column in the stat file. To use this feature, use taggedAtomPair = "0, 10" and printTaggedPairDistance = "true" in the md file. Then, the distance between integrableObjects 0 and 10 will be computed and printed in the stat file on each statWrite.
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
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