New electrostatic method, starting to do some performance tuning.
Fixed a bunch of stylistic and performance issues discovered via cppcheck.
Fixed a bunch of cppcheck warnings.
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
Fixed a widespread typo in the license
Performance increases for cubic spline. Bug fix for electric field in parallel. Cleaned up globals. Started adding infrastructure for long range corrections.
More cruft removal
More cleaning, removing non-C++ MPI calls
Cleaning more cruft and unused variables.
Deleting unused variables
Fixed a bug in Matrix-Matrix cross product
New electrostatic bug fixes.
MERGE OpenMD trunk changes 1803:1811 into development branch
A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
Merged trunk changes into the development branch
Merging some of the trunk changes back to the development branch, cleaning up a datastorage bug
Massive multipole rewrite
Adding new RNEMD options and output file format
Various fixes required to compile OpenMD with the MS Visual C++ compiler
Some bugfixes (CholeskyDecomposition), more work on fluctuating charges, migrating stats stuff into frameData
Added a double dot tensor contraction.
Fixes for minimization
Forgot the factorials!
Adding fluctuating charges, still a work in progress
Adding some new atom types, fixing a convex hull bug, removing silly stuff from Snapshot
qhull modifications for compilation
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.
Build fixes for qhull 2011, fixes for compilation with PGI.
Completing the Fortran removal project. Fixes for compilation with clang / llvm, debugging, removing code that we'd never used.
changes for cell linked lists
More fortran removal, and trimming out unused code
Fortran removal
compiles, builds and runs, but is very slow
Added MAW to the C++ side, removed a whole bunch more fortran.
Added EAM. Still segfaults but compiles.
Added CubicSpline class to replace our interpolation F90 module
Creating busticated version of OpenMD
Adding property set to svn entries
cleaning up some error messages in ConvexHull
Added back NULL for StuntDoubles not owned by the local processor in parallel.
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.
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
converted some dynamically allocated arrays to std::vectors
Removing CGAL dependence
fixed mapping bug
fixed a bug confusing id with localID, stopped adding NULLS to triangles also.
fixed a iproc bug
Re-write of ConvexHull.
More MPI convex hull bug fixes. noffset corresponds to the correct array indexs. Still mismatch in forces between serial and parallel versions.
Stupid parallel bug fixes. Why was this ever working?
Fixed bug in Polynomial
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
Adding hybrid analytic / companion matrix polynomial root solver adapted from David Eberly's Wild Magic code
Modifications to support RMSD calculations, removing classes we aren't using.
making way for jama versions of these routines
Removing unused tnt classes
Adding boundary element hydrodynamics to SMIPD.
adding jama and tnt libraries for various linear algebra routines
Beginning import of SVD and RMSD code to handle orientational restraints of flexible molecules. Work in progress, doesn't compile yet.
Different method again for Langevin Dynamics.
Added global variable.
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 Memory Leak in ConvexHull.
More changes to SMIPD. Attempting to find memory leak.
Fixed nanovol so it now builds.
Work continues on constant pressure langevin dynamics.
Case typo for Hull.hpp.
Added large quantities of code for convex hull and constant pressure langevin dynamics.
Inversion fixes and amber mostly working
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
Added files to module section of Makefile.
Changes....
A bunch of minor changes to make MPI compilation faster than the double compilation we do now...
Changed some logic in Polynomial, PolynomialTorsionType, and CharmmTorsionType to allow for polynomials to be set via the = operator.
updating configure process
Correcting a few typos
Build fixes for include files.
Fixed nesting bug in USE_CGAL and USE_QHULL.
Initial code for AlphaShape.
New configure
Check CGAL and qhull defines
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Many fixes for Charmm-type torsions.
Added volume calculation for hull.
Changes to Build system.
Pos copied into a malloc array now.
Fixed more bugs and removed more CGAL.
Removed CGAL from makefile.
Removed CGAL from OOPSE and replaced it with qhull.
fixed a configuration error
Added preliminary support for CGAL and computation of convex hull.
fixing bond order parameter code
Bugfixes in BondOrderParameter and SphericalHarmonic
added SphericalHarmonics, fixed a few problems with BondOrderParameter
Added utility function to winger3jm from slatac.
Added support for Winger3jm coefficients.
Adding single precision capabilities to c++ side
Getting fortran side prepped for single precision...
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The off diagnal is not set
refactor Hydrodynamics module.
LagevinDynamics is working?
adding Cholesky Decomposition
LangevinDynamics in progress
Adding Hydrodynamics Module
fixed a problem with cutoff radii being set larger than 1/2 the length of the shortest box dimension. added a few fortran utility routines
fix a bug in converting integer to double
adding transpose into SquareMatrix3; fix a bug in AtomStamp where orientation is not set correctly.
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X
Adding :LegendrePolynomial
made some minor changes to allow compilation with the portland group compilers
OptionSectionParser get compiled
using epsilon instead of 0.0 to avoid divergence in rotation matrix to quaternion transformation
fix a bug in convert rotation matrix to quaternion
added error function
replace c++ style comment in c files
Fixed build issues under ifc7.
Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
xemacs has been drafted to perform our indentation services
fix a bug in converting rotation matrix to quaternion
Fixing a bug in BitSet.cpp
adding base class of Random Number generator
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
Making small modifications to allow for use on MPI machines
adding MersenneTwister random number generator
Adding a modified version of MersenneTwister.hpp
(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
moved Package variable into subdirectory makefiles to speed up the building process
port to SGI platform
merging new_design branch into OOPSE-2.0
still debugging
define name collision
add getArray function to RectMatrix and Vector classes
more work in Snapshot
Snapshot and SnapshotManager in progress
Math library pass the unit test
except diagonalize(), all of functions in math library pass the test
more bugs get fixed at math library
more bugs are fixed in Vector class
implement more test cases
more tests on math library
fix some bugs in Quaternion class
Your basic run of the mill real-valued versions of Y_l^m(\theta, \phi)
Working on getting Shapes into OOPSE
math library in progress
add quaternion class
fix incompatible declaration in jacobi
math library in progress
Matrix in progress, test in isOrthogonal of SquareMatrix is failed by some reasons
adding RectMatrix
refactory vector and matrix classes
Remove some Makefile.in
add Vector3d.hpp and Matrix3x3d.hpp
move mpiSimulation_module to DarkSide
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