Updated the manual
ContactAngle2 now requires specification of the location of the droplet centroid in X&Y axes.
Updated manual, and altered some language in the force field files
Updated some of the root-level text files for 2.3 release
Made messages from md-solvator more useful, and will now exit when solute and solvent boxes are not identical.
Changes to make MSVC happy
Removed an unused variable caught by PGI
Corrected punctuation.
Progress bar now writes 100% when we're done
added a skipToken function to StringTokenizer, and used this to remove some silly warnings on compilation.
One bug fix
Reducing the number of warnings when using g++ to compile.
More edits for gcc warnings
More g++ warning fixes
more g++ warning fixes
Trying to eliminate some g++ warnings
Attempting to reduce g++ warnings
Fixes for warning messages, added flags to help debugging.
Removed inlining, updated papers & copyright
Fixed a force field atom problem
Removed warnings, inlined common calls
Fixed a warning on PGI compilation
Got rid of unused variables and spurious warnings
Removed inaccessible lines
Replaced std::iota with explicit code
Performance improvements, Removed CutoffPolicy
Fixes to HullFinder (and by extension to RNEMD) for getSurfaceArea() call. Adding Multipass Correlation Function (unused right now).
Modified SelectionEvalutator to handle positional information for molecules based on the center of mass.
check for atom names in lower cases for hydrogen bond donors/acceptors
Removed dependence on elements table when figuring out H bond donors & acceptors
Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
Fixed a frequency computation bug in a utility script
Bug fix.
Added Geometric HBond StaticProps module.
Changes for STL libraries that are missing std::to_string
Added UniformGradient to perturbation list.
Fixed some broken comments for use with Doxygen. Made changes to allow topology-based force-field overrides in include files. Fixed a calculation of box quadrupole moments for molecules with point dipoles.
Starting to get ready for 2.3 release. Separating type parsers from io routines. Fixing old samples to use newer syntax.
Removed Eigen stuff that we weren't using
Another md2md fix
Added a check for NumPy in the cmake configuration stage
Modified md2md to deal with pvqj fields that don't have v or j.
Added a vcorr2spectrum script to simplify the task of computing spectra
Added a buffer length to ContactAngle2, starting documentation
Fixed a arcsin sign bug
Updated to semi-working contact angle 2 using density threshold
A scan fix for CA2
First checkin of the second contact angle method for sequentialProps.
Updating UniformGradient to the new parameter structure (two unit vectors and a gradient strength).
Fixed a selection issue in ParticleTimeCorrFunc, other whitespace stuff
Forgot to svn add the files. Additionally, examined the files where changes were committed that I didn't realize were going to be changed. Primary one to examine SimplePreprocessor, bufferSize=8192 instead of 1024... everything else was commented cerr/cout or line spacing issues
Added a surface diffusion analyser to staticProps
Fixed the contact angle calculation.
Adding Contact Angle analyzer.
Fixed a selection non-overlap issue when doing particle correlation functions.
Fixed a closing brace bug
Starting to add support for UniformGradient. Changed Vector3d input type to a more general std::vector<RealType> input. This change alters RNEMD and UniformField inputs.
Only print out lines in TetrahedralityParamZ if there are actually observations in that Z bin
Added Radial and Z-projected velocity autocorrelation functions Started to add SequentialProps program Mucking about with angular restraint potentials
Added 3rd selection option for the 2d g(r) analyzers
Added support for accumulateBoxQuadrupole flag
Took out a spurious debugging line
Fixes for restraints, renaming of UniformField
Fix for dynamically linking with qhull
Oops
Latest
changed the output of Tet_Qxyz to Amira Mesh
Changes to include the volume-resolved tetrahedrality parameter.
SVN fix
AUtorev fix
Added mdShrink utility
Added NPA integrator
Fixed a selection bug for integer tokens Dielectric script now uses both clausius-mossotti and conducting boundaries
Fixed a bug
Added correction factor to dielectric script
Most recent version
Added a script to compute dielectric constants
Fixed a strange non-bonded reporting bug.
Added an unload block
Added Frequency Fluctuation Correlation Function
Bug Fix
Bug fixes for MultipoleSum
Bug Fixes
Updating MultipoleSum to scan the cutoff radii
Added the MultipoleSum
myNVT.hpp and myNVT.cpp are my (Joe) attempts at separating out the chi evolution into evolveChiA and evolveChiB functions as a precursor to implementing a langevin thermostat
fixed a bug in parsing the harmonic torsion type
Torsion changes for 180_trans
Added NitrileFrequencyMap module to staticProps
Added sitePotentials for the Choi et al. potential-frequency maps for nitriles
Added FCCOfR and IcosahedralOfR analyzers to staticProps
added selection offset 2 for pAngle
Discovered an old debugging region in OPLS torsions
Fixed the creation of constraintForces files on simulations which don't have constraints
Fixed an initialization bug in pAngle selection offset branch
Removing vestiges of deprecated MPI:: namespace C++ MPI bindings
removed some code that wasn't reachable
Dates updated
Some small compilation fixes for MSVC
Fixes for ConstraintWriter in parallel, some cppcheck cleanup starting preparation for 2.2 release
Migrated ConstraintWriter calls into Shake
Added the ConstraintWriter
Fixes for compilation with PGI compilers
* Changed the stdDev printouts in RNEMD stats to the 95% confidence intervals * Added the ability to specify non-bonded constraints in a molecule * Added the ability to do selection offsets in the pAngle staticProps module
More error message clarifications, added a few steps to the builders sample
Removed some scary errors that are really supposed to be OPENMD_INFO messages
Revision string moves to its own cpp file that is compiled, and out of a defined string. This will make it a bit easier to migrate to git when the time comes.
Fluctuating charge ewald samples
sign error
Some updates for restraints and fluctuating charges in Ewald
Link ordering issue for FluctuatingChargeForces
Fixed a few MPI issues that were triggered in mpich.
Adding a fluctuating charge forces block
Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
Fixed a bug in g(r,theta) and g(r,omega) that assumed all StuntDoubles were atoms.
Added warmed minimum lattice
More changes for memory management.
Memory reporting fix
Fixing some leaks
Report an error if memory requests are very small
Some potential bug fixes.
Moving these data files out to the manuscript directory
Added some ion test files
Adding SSDQ model to test the electrostatics code
One more compilation warning fix
More silencing of compiler warnings
Removing a few compiler warnings
Forgot a few things in the makefile
Rewrote much of selection module, added a bond correlation function
Fixed a token chewing bug
Added the MorseBondType into the Bond type parser
Updated a builder sample and fixed install of icosahedralBuilder
Updated for 2.1
bumped cmake version
Updated in prep for 2.1 release
fixed a bug in the temperature profile calculation
Have the ShellStatistics use the defined coordinateOrigin from the RNEMD block in the dump file.
Fixed a few bugs in the analysis code for RNEMD.
Quiet down a few warnings in MSVC
Fixed some warning messages and NanoVolume issues.
Fixing the angular momentum printout bug
Angular velocity fix in RNEMD
Some fixes for MSVC compilation
Some MPI include re-ordering to work with the Intel MPI implementation.
Fixed a few bugs and added some sanity checks in the analysis codes.
Fixes for clang 5
Fixed a bug in building the self Hash
Added OH bond time correlation function
Fixed a bug (I think) that was caused by a cross product name collision.
Backed out some region nonsense
fixed a sameRegion initialization issue
region fixes, performance boosts
Backing out fluc-rho and putting back the Electrostatic fluctuating charge with coulomb integrals for atoms within a region.
Fixed a few bugs in EAM and Electrostatic.
FlucRho/EAM initial commit
Forgot the parallel changes in Electrostatics
More ewald fixes, reporting reciprocal potential in stats.
Ewald fixes
debugging Ewald implementation
Fixed a few ewald bugs
Fixed a few DumpWriter / FlucQ bugs. Still working on Ewald, updated Quadrupolar test structures.
Had to move initialization of FluctuatingChargeConstraints into FluctuatingChargePropagator::initialize, I think I did this before, but must not have committed it and then an svn up killed it... The change was made because systems weren't undergoing charge constraints JRM
fixed affineScale to know about molecules that have traversed multiple box lengths.
Added a fieldValues script, updated some text in the README file
Fixed all of the dipolar arrays to match the L&T indexing scheme
Adding Quadrupolar arrays
Added Legendre Correlation function (as a function of Z), working on architecture for Ewald Fixed some bugs in FlucQ
Fixed a quaternion bug, updated the affected lattices.
Fixed some bugs in the flucQ constraints.
Fixed a readme file, attempting to find the minimum energy BCC structure.
modified svn propset info
Used larger samples
Updating samples.
Added infrastructure for region-constrained fluctuating charges.
Fixed self energies for the Taylor_shifted method
Fixed a bend issue for James
fixing Luttinger Tisza stuff for Madan, fixing Inversions and wild Cards for James
Use pre-set satellites if they are already there....
Test to see if we can eliminate a bug in MPI runs involving RNEMD.
Added a satellites keyword to the inversion block.
Test for James
Added self-interaction for shifted multipoles
Added the Z basic arrays
More work on the Luttinger & Tisza structure generator
Fixing a DumpReader bug (I think) for site data on integrable objects that are not RigidBodies.
Speedup tests
Speed!
Fixed Madan's problem with QQ interactions
Some performance improvements
Made RNEMD stats exactly the same as in the RNEMD module.
Fixed a URL
Adding HarmonicInversionType for GROMOS and CHARMM style force fields.
Working on madelung energy module for multipoles
Added initial work on packmol->OpenMD converter, fixed a bug in RNEMDStats
Fixes for RNEMDZ
Cleaning up some import nonsense
Added processFrame to RNEMDr
Bug fix.
Another fix.
Minor bug
Fixes for the slab statistics (and for RNEMD stats)
Preparing for official 2.1 release (clean-up)
MERGE OpenMD development 1783:1878 into trunk
Fixed a DumpWriter parallel bug.
New electrostatic method, starting to do some performance tuning.
Compilation and portability fixes
Fixed a bunch of stylistic and performance issues discovered via cppcheck.
Fixed a bunch of cppcheck warnings.
Fixed a bug when there's no electric field being calculated.
Fixed a minor visitor bug
Bugs in the FQ samples, fixed for Dump2XYZ to print out charges and electric fields
Chasing down bugs in the TIP4P_FQ model.
Fixed a de-allocation problem in Sutton Chen
CLearing out some memory leaks
Attempt to fix memory leak in Multiple hull calls
Fixes for Qhull static build strangeness
Adding spatial statistics analysers.
Added an ellipsoidal shaped lattice
compile bug on missing include file
Adding nanoparticle generators, fixing a Qhull static link bug
Added a Harmonic Torsion Type, fixed some bugs in RNEMD and waterReplacer.
Added a new icosahedralBuilder for single-component Mackay Icosahedron nanoparticles.
Adding a few new statsFileFormat options: COM, COM_VELOCITY, ANGULAR_MOMENTUM
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.
Added utility to recenter a simulation on the center of mass
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
First pass at angular momentum aware version of VSS-RNEMD.
Linux compilation fixes (missing cstdio)
Updated the integrator conserved quantity so that it doesn't trail the other properties
Space typos
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.
Merging changes from trunk branch into development.
Fixed a field non-zeroing bug
Bug fix in Tetrahedrality parameter Z exposed another bug in SimInfo.
Fixed a bug in RigidBody, added a check for fixed vs. fluctuating charge
Only compute fields for electrostatic AtomTypes.
Simplified the Tetrahedrality [Qk(z)] analysis code.
Only compute field for sites not excluded from the pairwise electrostatic contribution. Also, now compute the mean field felt by the sites in a rigid body, and report that as the rigid body's field.
Storage Layout needs to allocate the electricField
Merging trunk changes back to development branch
Added bookeeping to add static electric fields and to zero them out when necessary.
Unified the computation of storageLayout into SimCreator, but that value is stored in SimInfo. We used to compute storageLayout values in two places - now only one.
Build instruction changes
Added Release tag if subversion is not found
Left in cerr print line
Bug fix in Sticky potential, label in stats
Bug fix in Sticky potential, column label in stats
More careful with casts, fixed windows compilation issues
Merging trunk changes 1812:1830 into development branch.
Windows compilation fixes
More cruft removal
Fixed some cruft
More cleaning, removing non-C++ MPI calls
Cleaning more cruft and unused variables.
Deleting unused variables
Fixed some picky warnings from the new Intel compiler.
Fixed a bug
Performance boosts, cleaning up debugging cruft
Fixed a bug in Matrix-Matrix cross product
New electrostatic bug fixes.
Added a selection offset for P2 Order parameters
Fixed a dynamic selection problem.
Updating P2 to handle dynamic selections
Updated selections to be frame-addressable (to support selection correlation function).
Fixed a possible bug in histogram in Time correlation functions
Fixed some torque bugs (I think), added a unit vector for Quadrupolar atoms.
Forgot to merge some important accumulator changes
MERGE OpenMD trunk changes 1803:1811 into development branch
Adding the selection correlation function, fixing a sample directory
Added a version and revision comment line to metadata files
Odd bug for parallel simulations - when single-atom groups are row and column indexed, the self-self interaction was correctly eliminated in the force calculation, but not in the stress tensor calculation.
A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
Added extra copies of the libraries to the linker lines so that the Distance finder can be resolved
Fixed a scripting bug in the samples
Started fixing some samples for OpenMD 2.0 release
Fixed a bug when the bins have no objects in them.
Merging trunk changes back to development branch
Parallel fixes for selection syntax (e.g. DistanceFinder).
Some parallel fixes for "select all" selection scripts. The distance finder selection, e.g. "select within(4.0, Au)", still needs work, however.
Updated manual
Adding stat2thcond back
Merged trunk changes into the development branch
More linux compilation fixes
Updating MPI calls to C++, fixing a DumpWriter bug, cleaning cruft
Windows fixes
Merging some of the trunk changes back to the development branch, cleaning up a datastorage bug
Cleaning up some warning messages on linux
Fixed some compilation warnings on the Linux side of things.
switched to a base accumulator to make the hidden function warnings from the intel compiler go away.
Various Windows compilation fixes
Fixing a compilation issue on Windows
Fixed a bug in ForceManager and a compilation issue for cygwin
Massive multipole rewrite
Commenting out some cerrs in tetrahedrality, PL
Trunk: The changes in this commit are confined to applications/staticProps and for the most part deal with a misspelling of initialize. The one other change took place in StaticProps.cpp and deals with the default treatment of sele2. It had previously been set to 'select all' which seems to go against what would be desired by not specifying it with regard to proper operations of many of the analysis programs ( g of r's especially)
Merging Kelsey's new thiols from development branch into trunk.
Added 6, 8, 10 and 12 length alkane chains to thiols
MERGE OpenMD development branch 1465:1781 into trunk
Updated the manual to include the RNEMD stuff. Fixed a holdover bug in a sample file.
Adding an electric field and the architecture for external perturbations. Fixing a bug in MultipoleAtomTypesSectionParser.
Prevent a memory access bug when dump files aren't configured correctly.
Adding a sample of the shear and scale for argon.
Various fixes for the RNEMD output.
Fixes to mdParser to handle vector assignments, fixes for VelocityVerletIntegrator deleting rnemd_ when it doesn't exist yet.
Tracking down a strange bug report. Fixing some output. Fixing some samples.
Cleaning up RNEMD log, adding XY area to Snapshot
Adding new RNEMD options and output file format
Added the same fix for parallel runs
Fixing a neighborlist bug
Adding some RNEMD interface samples
Code readability updates.
Fixed a bug in the FluctuatingChargeLangevin propagator, updated some samples.
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.
Forgot to add Accumulator.hpp on the last commit.
Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
added a line to CMakeLists for the TetrahedralityParamZ module
Calculates the tetrahedrality parameter as a function of zbins. Abandon all hope ye who enter here.
fixes for fluctuating charges
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
Possibly fixed the rigid body global indexing issue. Reformatted
comments. Started work on the FrameData section of Snapshot.
bugfixes for self interactions (particularly in parallel)
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 double dot tensor contraction.
Added SiteData parsing and writing.
Adding Joseph's FlucQ samples for testing
Fixing some bugs in optimization, fixing status functions so that they dump correctly (although some things are deferred until the Stats is accumulator-based).
fixed an uninitialized option bug, fixed gcc 4.6 compilation problems
fixing some bugs, adding Shake
fixes to minimizer parameters, start of intermediate status output for minimizer.
added a minimizer parsing block
test
Fixes for minimization
new goodness
Adding eigen Cmake stuff
Adding initial import of optimization library
Adding the Flucq constraints and objective function for minimization
Moved the propagators for flucq
added a forceman to the flucq propagator
Mostly whitespace
Fixed fluctuating charge forces
Moved FluctuatingChargeNVT to the flucq directory
Fixed the Slater overlap integral code, added dVdFq to the self interaction.
Units fix for electronic temperature, we also need to initialize dVdFq
Make fluctuating charges also charges.
Reorganized source directories, added RNEMD and flucQ blocks for options parsing.
Fixed compilation issues
resolved
resolved
Use the force directory is no longer used.
Forgot to delete the individual FF classes.
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.
DarkSide isn't needed
Bug fixes for heat flux import
Merging Shenyu's RNEMD changes from openmd-1 into the development branch.
Fixing some bugs
Fixed a few bugs in that last commit
Forgot the factorials!
Adding fluctuating charges, still a work in progress
Updating the build
Adding the propagators for FlucQ
Adding more support structure for Fluctuating Charges.
Added ability to read / write dump files with fluctuating charges and electric fields.
adding communication and parallel support for fluctuating charges and polarizability
Bugfixes (mostly related to particlePot and storageLayout).
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.
Moving silly stuff out of Stats and into Snapshot. Most of it should go into a not-yet-implemented FrameData class.
Adding some new atom types, fixing a convex hull bug, removing silly stuff from Snapshot
Use the static version of the qhull library.
fixed an initialization bug in Dump2XYZ
Fixing some bugs in the CMakeLists file
qhull modifications for compilation
JRM Added additional section parsers to EAM_FF.cpp
Un-did some changes that weren't ready to be committed.
Added files for fcc and pentagonal nanorod builders. Updated runMe in samples/builders to include nanorod builders.
Adding a vector parsing option to the parameter Manager.
Simplifying build process
new variables for vss-rnemd
vss-rnemd
tweaking build process
Updating build process, copyright, and publications.
Doing some work to simplify cmake build process
Fixing a compilation warning for CLANG compiler
Fixed a compilation warning for CLANG compiler
Modified lines for new GayBerneAtomTypes section parser
Fixed a number of force files to use new Gay Berne format
Bug fixes for GB. Now using strength parameter mixing ideas from Wu et al. [J. Chem. Phys. 135, 155104 (2011)]. This helps get the dissimilar particle mixing behavior to be the same whichever order the two particles come in. This does require that the force field file to specify explicitly the values for epsilon in the cross (X), side-by-side (S), and end-to-end (E) configurations.
Bug fixes for GB. Now using strength parameter mixing ideas from Wu et al. [J. Chem. Phys. 135, 155104 (2011)]. This helps get the dissimilar particle mixing behavior to be the same whichever order the two particles come in. This does require that the force field file to specify explicitly the values for epsilon in the cross (X), side-by-side (S), and end-to-end (E) configurations.
Fixes for LLVM compilation Bug fix for Gay Berne potential with switching functions
Fixes for compilation under LLVM compiler Bug-fix for switching function in Gay-Berne
Bug squashes. Pre-existing bug where ppot_row and ppot_col were never zeroed. In non-metallic potentials these arrays should be zero.
Fixed bug with rigidbodies not updating velocities for heat flux calculation.
LJ.cpp has been updated to more correctly deal with nonbonded interactions (i.e. explicit interactions where the species are not necessarily defined to be lennardJones type atoms)
Debugging heat flux calculation for rigid bodies.
More bug fixes....
Bug fixes for v_j not being set correctly and accumulation error.
Changed sign of force in stress tensor J_v calculation.
Added revision to svn for Gianluca.
Fixed naming.
Batch of sample files for testing different configurations of Gay-Berne atoms. Included is a force file and test atom build for running the '.md' files.
Updated version of Gianluca's stat2thcond.
Fixed two bugs in new Gay-Berne module. Torque 2 had a sign error, and there was a subtle mixing bug for dissimilar particles in different orderings.
Fixed alignment issues
Update for energy units conversion.
Adding support for atomic heat flux. Is broken w/ group based cuttoffs. Units need to be corrected and their may be a sign error in Jv.
Adding experimental branch for calculation of the heatflux based on old version of OpenMD. This will need to be ported to the development branch later.
Adding Hess Thermal Conductivity Code for version control.
Some fixes for CMake and single precision builds
Fixed typo in thermo.
Changed the calculation for thermal helfand moment.
updated copyright notices
Modified some of the nonbonded interactions and types
Added a waterReplacer script. A bit rough around the edges, but seems to do the right thing for a slab of ice.
Adding new function to check .eor files.
Minor modifications to set environment variable.
Validation script update with logging.
Adding validation python code.
Adding bits for numerical validation of openmd results.
Added <P4> order parameter to the computation done during director axis and <P2> computation.
First few fixes for explicit interactions.
Replacing most of the C-code with C++ code, and migrating the config.h file into the PROJECT_BINARY_DIR so that we can have multiple builds on the same architecture.
fixed a compile bug for PGI
fixing compilation bugs on gcc-4.4
added an INSTALL file, using svn2cl to get the ChangeLog target
Added "doc" build target.
fixing install permissions
removed a directory
cleaning up build cruft
fixing the build system
update for cmake build and install
OK, we need these directories for the build.
removing build cruft
migrating Doxyfile to a more sensible location, removing old build cruft
removing old build cruft
cleaning up cruft
removing cruft from build system
changing build process
Added support to print Thermal Helfand Moment in the stat file.
fixing a link order problem
fixed cmake build system for single and parallel targets
cleaning up the development branch a bit, removing cruft, etc.
indenting fix
Updated antlr, fixed a clang compilation bug, removed a warning message
cleaning up configure script & readme
cleaning up the configure script
updating gengetopt runs
Merging changes from old branch into development branch
ifstrstream in Cmake
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.
Cmake fixes and updates.
Adding RepulsivePower interaction to development branch.
Adding RepulsivePower interaction to the development branch
Adding Repulsive Power potential
Adding repulsive power potential
qhull fixes
qhull fixes
qhull fixes
Build fixes for qhull 2011, fixes for compilation with PGI.
Added sample files for argon: 1000, 10000, 75000.
Fixing cutoff groups
Added Momentum correlation function, imported changes from Vector from development branch, updated comments in some integrators
Updated scalability of OpenMP threads.
Fixed a parallel bug in computing exclude lists. Added file versioning information in MD files. Still tracking down cutoff group bugs.
fixed an offset bug causing problems in MPI
fixed a particle_pot bug. Still another for metals.
Fixed a clang compilation problem, added the ability to output particle potential in the dump files.
New attempt using Helfand's original papers
First OpenMP version.
Added the EADM.frc forcefield file -JRM
Forgot to svn add the SystemDipoleCorrFunc.hpp/cpp. Should be done adding/committing for now though. -JRM
Forgot to svn add the EADM_FF.cpp/hpp -JRM
This commit should allow EADM simulations to be run on the cluster. Main additions include EADM_FF.hpp/cpp as well as a system dipole correlation option in DynamicProps.
good bye fortran!
Fortran begone!
removed spurious prints, fixed one bug, but there's still a parallel problem
Completing the Fortran removal project. Fixes for compilation with clang / llvm, debugging, removing code that we'd never used.
Updated: Build neighbor list method with frequency counter. Additional parameter to md file.
Updated ordered neighbor list generation.
Debugging mainly
Updated the BlockSnapshotManager to use a specified memory footprint in constructor and not to rely on physmem and residentMem to figure out free memory. DynamicProps is the only program that uses the BlockSnapshotManager, so substantial changes were needed there as well.
Adding initial OpenMP support using new neighbor lists.
Branching from main development branch to OpenMP dev version at dev branch 1593
test
test
Efficiency fix
more bug fixes
Fixing some parallel bugs
fixed one MPI bug, working on another
Fixes
bug fixes
Added a module to compute the length of a nanorod
bug fixes.
Bug squashing
Well, the potential energy values are still garbage, but the LJ sample runs.
bug fixes
Forgot Grid3d
bug fixes (not done yet)
be careful with non-EAM types in density calc
bug fixes
migrating cutoff information from InteractionManager to ForceManager
more parallel fixes
fixed an initialization bug in eam
fixed a cutoff bug (i think) in calc_eam_prepair_rho
Forgot some headers and other files
Added Atypes to new C++ force decomposition.
More fixes
A few more fixes for the missing routines
Added neighbor list check, and migrated skinThickness into ForceDecomposition (and out of the InteractionManager). Removed a spurious inline.
Fixed some busted stuff in buildNeighborList
Updated some bugs so dynamic props builds again. Stress Corr func is still a work in progress.
Added files for stress correlation funcion.
Changed dumpwriter to synchronize file writing to avoid file descriptor issuse on large (>1000 nodes).
Matched default Charges for OH and HO (Hydroxyl) to the values from OPLS paper.
changes for cell linked lists
replaced debugging statements with calls to simError() code reformatting for readability
option binShift enables bin division shifts Lz/2N option output3DTemp enables x,y,z dimensional temperature recording disables angular momentum exchange for swapping algorithm fixed a bug for swapping MPI code
added new variables for RNEMD remove requirement of non-negative targetFlux for RNEMD
Updated antlr, some minor formatting changes
re-added SMIPD as ensemble keyword
Changed DUFF to match new option section format.
Bug fix to traverse the base chains for NON-bonded interactions as well as bonded. This allows one to specify Metal - non-Metal interactions based on base types instead of exact matches.
For efficiency, pointers instead of objects will be passed during main force loop.
More fortran removal, and trimming out unused code
Fortran removal
More changes for parallel
more fortran removal
a few more tweaks We're getting somewhat closer to deleting fortran.
Added a check to make sure value matches data type of parameter
more minor changes to help build
closer to a real force loop
still busted, but much progress
More modifications for paralllel rewrite
bug fix in P2
Adding vector handling capability to P2 order parameter
working on communicators
changes for new parallel architecture
Starting a Parallel architecture
Adding parallel classes...
forgot one method
compiles, builds and runs, but is very slow
Well, it compiles and builds, but still has a bus error at runtime.
getting closer to compiling
One more fortran file that we don't need:
Added MAW to the C++ side, removed a whole bunch more fortran.
fixed gengetopt generated files to fix pAngle bug
Moved switching functions and force options over to the C++ side, and removed them from Fortran.
fixes
Doesn't build yet, but getting much closer...
cleaned up some cruft from the md files, got rid of thiols
Completed SMIPD to Langevin Hull integrator name change
added LangevinHull samples and ReadMe; removed old SMIPD folder
added missing files
added hull token
new hotness
Added NPTsz integrator to the makefile
fixed a bug on torques for MPI jobs involving directional atoms
adding new NPTsz integrator (like NPTxyz, but locks x&y together).
fixed a typo
One more fix for rounding issues on x = 0
fixed a sign bug in the new anint replacement lines.
Fixed some selection token strangeness. (Operators for <, >, ==, !=, etc. should be dynamic)
fixed bug in ObjectCount.cpp
Adding an object count option to staticProps
fixed version
Fixed a few bugs in the configure script (FCFLAGS was being ignored) and print out more useful Doxygen documentation
trying to speed up doForces
removing group-selective cutoff cruft
slight boost by avoiding anint calls in doForces
Replaced anint function in get_interatomic_vector with floor and ceiling functions.
inlined the anint call in doForces.F90
Less busted than it was on last check-in, but still won't completely build.
The C++ side now compiles. Moving on to doForces
Changes to remove more of the low level stuff from the fortran side.
Many changes, and we're not quite done with this phase yet.
Starting migration of Morse to C++
More fixes for cmake.
Fixed case typos in cmake.
Different version of FindOpenBabel that actually works.
fixed a bug where chi value wasn't being set in calcConservedQuantity. I'm not 100% sure we actually need this routine here in NPTxyz (instead of inheriting from NPTf), but if it is here, the variables need to be set...
Somewhat working cmake build system now. Does not yet build a parallel target. Builds all non-mpi programs.
Needed by openbabel macro.
Fixing headers. They are now .hpp files.
Removed .h files. They are .hpp files committed yesterday.
Adding exception and reporting mechanism from ProtoMol to OpenMD.
Adding debugging and tracing tools from protomol to openmd.
Adding some error reporting and debuging code to OpenMD. This code is borrowed from ProtoMol.
Migrating Sutton-Chen from Fortran over to C++
fixed a sign error
Updating configure for qhull with c++
simple fix for calls to getCharge for non-charge atoms (triggered by shifted pot / shifted force computations of self-self interactions with out point charges on topologically connected molecules).
Converting Sticky over to C++
removing cruft
Added GB module to the C++ side, got rid of it on the fortran side.
Fixed a bug in EAM. Seems to work now!
fixed phi mixing
no longer segfaults
Added EAM. Still segfaults but compiles.
busticated EAM
added a gcc4.4 compatibility
fixed some destructor bugs dealing with the TypeContainers
Added CubicSpline class to replace our interpolation F90 module
added visitors
fixing c/fortran bugs
fixing calls
Added nonbonded directory. Compiles, links, runs, but gives incorrect answer.
builds
attempts at c++->fortran linkage. Still busticated.
added nonbonded directory
well, it compiles, but still segfaults
Adding stuff for cmake
Creating busticated version of OpenMD
removing cruft (atom numbers, do_pot, do_stress) from many modules and force managers
fixed revision numbering for released versions
fixed empty revision problem
Added svn revision number to build process, incremented minor version number, corrected a minimizer keyword
changed ORNULL
Fixed a potentially serious bug in GhostBend and GhostTorsion. We were using A instead of A.transpose() where we need lab-frame coordinates of the body-fixed axis.
revision
small changes
more changes to make Dump2XYZ do velocities & forces
Updating visitor architecture to something a bit more modern
Adding 2-D g(r) module to static props
testing
testing
added new CosineBendType
Added tests to make sure requisite position & orientation information are present in dump file.
Aluminum fixes
mostly whitespace issues
fixed Doxygen generating file
Fixed a bug in Torsion (and GhostTorsion) which is triggered by a configuration with colinear atoms. The problem was discovered by Brett Donovan. Thanks, Brett!
Changes to gofrz so you can specify the z length
More changes to gofrz.
Fixed a potential bug. If Ghost atoms have no electroFrame (i.e. if they are DirectionalAtoms, but not dipoles), the GhostBend and GhostTorsions would give nans. We should be using getA instead of getElectroFrame.
Adding property set to svn entries
forgot the output file name
Adding a new correlation function to do slab-segregated g(r) calculations. This computes at g(r) for pairs while requiring the z coordinates of the two sites to be at fixed separations. The data is output in: r, z, g(r,z)
Fixed a bug where any program using selection syntax without qhull would fail. We only do a is fatal now if you try to use hullfinder.
Added a build define to check for libqhull before trying to build hullfinder.
Adding nan/inf detection to DumpWriter, fixing one message
Addad a check for inf and nan to statwriter.
Added EAM line for Art Voter's aluminum potential
Fixed a bug with rigid bodies and stuntdoubles. We now update the SD's before doing the distance find.
Fixed include file in ProgressBar.cpp for getenv.
Added check for SGE to progress bar. If we are running under SGE, we should write to file SGE .o file. Under afs it is doubtful that the file will be flushed anyway making the information pointless.
fixing string bugs in ProgressBar
Print revision number in openmd banner
committing a change
automatic property set
testing automagic
Attempting automatic revision string
updating version number
Fixing gradients for minimization
more on the minimizer Frq -> Freq conversion
Fixed a typo so that we use "Freq" instead of "Frq".
ProgressBar should only print status when it is actually attached to a tty. This should quiet down those background jobs.
ProgressBar compilation fixes for linux
Fixed a typo in EAM, cleaned up EAM and sutton chen a bit
new params
One more
modernizing some parameters
fixed some md-solvator over specificity, and an install bug
Added some missing bend and torsion types
Adding a progress bar, and pAngle staticProps
Adding a hull finder to the selection syntax
cleaning up some error messages in ConvexHull
Added back NULL for StuntDoubles not owned by the local processor in parallel.
fixed a typo
Removed hard-wired atom number, trying out the NULL returns in SimInfo.
Fixed bugs in Restraint, refactored RestReader and RestWriter
updating various dates and version numbers for 1.0.1 release
Fixing the build and install method for samples in Madelung, RNEMD, zeolite, SMIPD
Cleanup of unit normal code in Triangle.cpp SMIPD now call getUnitNormal instead of getNormal.
Install bugs, tweaks of samples
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.
Added missing cstdio include lines for gcc 4.4 compatibility
Fixed a missing cstdio include
fixing atom2md and bringing it up to speed with OpenBabel 2.2.3
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).
more changes to fix build process and divorce ourselves from CVS
Merging changes skipped in working copies of OOPSE into the OpenMD tree, fixing make install
fixing make install process
Testing commits
removing spurious cutoffGroup lines from default water.md sample files
Deleting renamed files
Removing renamed files
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
Fixed bug is Sutton-Chen force calculation in parallel.
Removed remaining MPI from metallic potentials. Bug in MPI calculation of energies in Sutton-Chen.
adding interface
removing MPI responsibilities from the lowest level force routines. This is in preparation for migrating these routines (LJ, electrostatic, eam, suttonchen, gay-berne, sticky) to C++
missing shtool for build
converted some dynamically allocated arrays to std::vectors
pythonification of affineScale, translate in md2md, removed spurious cutoffGroups in waterBoxer. Perhaps we need a python md-file parsing library?
Removing CGAL
Removing CGAL from all code
Removing CGAL dependence
Removing CGAL, cleaning up ac-tools directory
fixed mapping bug
fixed a bug confusing id with localID, stopped adding NULLS to triangles also.
fixed a iproc bug
Re-write of convex hull.
Re-write of ConvexHull.
fixing busted mpi configure
fixing mpi configure
More MPI convex hull bug fixes. noffset corresponds to the correct array indexs. Still mismatch in forces between serial and parallel versions.
fixes for surface atoms that expose multiple hydrogens, updated python set syntax
RNEMD temperature and exchange reporting
added RNEMD scaling
added options for RNEMD
more checks for parallel molIndex stuff
Stupid parallel bug fixes. Why was this ever working?
Bug fixes in the SelectionEvaluator and SelectionCompiler Added print option in Restraints
Adding alternate water models to Amber parameters. The approved model for Amber is still TIP3P, but if you want reasonable water dynamics, you need SPC/E. OOPSE/OpenMD will now give you the choice.
Fixed bug in Polynomial
Added missing restraint file
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
Relaxed structure at low T to be not so high up on the PE wall.
Adding hybrid analytic / companion matrix polynomial root solver adapted from David Eberly's Wild Magic code
New hotness
units for thermalConductivity, spelling error fixed
Latest version of SMIPD with gamma set to thermal conductivity
Adding restraint keywords to Globals
Adding one RNEMD sample
fixed one more bug for charge - non-charge interactions
Single / Double for C++ MPI bindings
Parallel version of RNEMD
Modifications to support RMSD calculations, removing classes we aren't using.
making way for jama versions of these routines
Removing unused tnt classes
Fixing a parallel bug in the self-self interaction.
Hopefully a fix for the skipped charge in parallel
Adding boundary element hydrodynamics to SMIPD.
only create RNEMD object if we need it.
Adding Madelung energy sample directory with explanatory notes
Bug fixes and sanity checks for RNEMD (nBins should be even), check to make sure we aren't selecting inappropriate numbers of integrable Objects
Fixed odd bug in electrostatic for self-term forces with neutral molecules
bug fix in DLM, added temperature profiles and uniform bins to RNEMD
Added a getStatus routine to check the temperatures
fixed a bug in self interactions
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.
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
adding support for RNEMD
Added keywords for RNEMD
Adding samples for SMIPD.
Different method again for Langevin Dynamics.
Cleaning up some cruft.
Code clean-up. Removed old langevin code.
use the viscoConvert in OOPSEConstant
added viscoConvert
Stupid getRandomNumber return 4;
missing energyConvert in kinetic energy
Fixed bug in variance.
Added global variable.
More attempts to get SMIPD to themostat properly
doing zeolite sample
fixed a few bugs in the options, added base atom types
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 a QHULL autoconf bug
Fixed a bug in QHULL autoconf logic
many changes to keep track of particle potentials for both bonded and non-bonded interactions
Fixed Memory Leak in ConvexHull.
More changes to SMIPD. Attempting to find memory leak.
Returned old LD forces to SMIPDForceManager.
A few simple mods to remove gcc compile warnings
Fixed nanovol so it now builds.
Fixes for Inversions for use with Amber
Work continues on constant pressure langevin dynamics.
Fixed makefile.
fixed using autoconf 2.6.2
integrators/Makefile.in needs to be created
integrators/Makefile needs to be created
Only build SMIPDynamics and register it if we have qhull
Fixed MPI bug in opening elements.txt.
Case typo for Hull.hpp.
Adding back more missing files.
Added large quantities of code for convex hull and constant pressure langevin dynamics.
fixed thermo bug
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.
Inversion fixes and amber mostly working
Fixes for Torsions and Inversions, Amber is mostly working now.
Exclude is gone. Replaced by a generic PairList to handle 1-2, 1-3, and 1-4 interactions as well as the exclude list
more changes for 1-2, 1-3, 1-4 interactions plus some initialization-ordering fixes to make gcc -Wall happier.
Added support for scaled 1-2, 1-3 and 1-4 interactions.
fixed a missing F[\rho] error for calculating particle potentials in the many body force fields
fixed a strange compiler structure alignment problem with the intel Mac compiler (structs that cross between C and fortran appear to need 8-byte boundary alignment on this compiler).
fixed a spurious visitor deletion
Many fixes
Just reconfigure and it works!
All your base are belong to us!
All Your Base are belong to us!
fixed some incorrect types
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
Changed parameters for S-S interactions on gold surface.
Changes required for Inversions and Base Atom types. This will break OOPSE badly for a few days or so...
Cleaning up oopseformat and adding inversion terms
Changes to thiol model.
Hopefully md-solvator is done.
Adding the Amber_FF files to OOPSE distribution
Adding infrastructure for Amber force field
Adding infrastructure for Amber force field.
More md-solvator work.
Fixed a number of bugs in slab_density calculation
Md solvator writes out md files now. Index problem.
More progress...
More changes to md-solvator. Still don't know if it works.
More work on python version of md-solvator. Pretty sure mol loop is busted.
*** empty log message ***
Added files to module section of Makefile.
Added files to Module section.
Added TraPPE torsions for thiols.
Adding Trappe torsion types and fixing Opls types
Code work on thiols and TraPPE torsions.
*** empty log message ***
Changes.
Removed accidental print lines.
Added model for thiols.
Fixed typo in LJinteraction types. LJ-metal appears to work now.
Added minimizer sample for metal.
Added parameters for Lennard-Jones Thiol potential.
Fixed a bug in BlockSnapshotManager.
Added back correct form, still not updating frames.
More changes, still broken.
Files for Hefland moment.
Checking in changes for Hefland moment calculations
Committing changes made to AtomVisitor to render xyz2pov scenes
Added repeat box options to make larger systems
Changes....
A bunch of minor changes to make MPI compilation faster than the double compilation we do now...
fixed compile flags on Mac
fixed compile flags for mac
Changing functional form
Adding iterative looping to get better estimates of friction forces from full-step velocities
Added surfaces for Ni and Pd.
Added more surfaces.
Fixed sign error in MnM based on atid's.
Added new samples directory for metal surfaces.
Added samples for metal slabs.
MnM interaction now works.
Changed some logic in Polynomial, PolynomialTorsionType, and CharmmTorsionType to allow for polynomials to be set via the = operator.
Changes to MAW. New form of the potential and cleanup.
Changes to simparalell to remove MPI stuff.
Adding new md2md utility program
fixing configure process
updating configure process
Fixed for MPI.
fixing a configure script error
Correcting a few typos
Adding GofZ.cpp
Adding GofZ.hpp
new visitors for some odd molecules
fixed bug in physmem for 64 bit machines
Nothing important
Fixed Langevin Dynamics and DLM
fixed printing of memory available
added stat2visco
fixed a few correlation functions
Added a few visitors
A few formatting changes to prettify the code
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.
Build fixes for include files.
Changes to do hydrodynamics modeling and to explain a diff file
Fixes for building.
Changes to optimization flags.
Removing Qhull from cvs.
does ifdef check for computational geometry packages
Fixed nesting bug in USE_CGAL and USE_QHULL.
Initial code for AlphaShape.
Define USE_QHULL.
New configure
Check CGAL and qhull defines
Added CGAL and qhull defines
Added CGAL test
*** empty log message ***
Many fixes for Charmm-type torsions.
Added more chamges to nanovol.
Fixed Makefile.in for cgal.
Added new config.h to deal with cgal.
Added configure for CGAL.
*** empty log message ***
*** empty log message ***
Added volume calculation for hull.
Changes to Build system.
Added m4 file for qhull
Fixed some bugs in LDForceManager.cpp
Fixed some temperature and conversion constant bugs in Sphere and Ellipsoid
Added: Action Correlation function (for viscosity), Directional RCorr (for non-spherical bodies) Modified: LCorr (for multiple axes)
Case typo in Vector.hpp
Testing files for NPT Langevin dynamics convex hull calculation.
Added code to compute bond angle distributions.
Updated docs to version 4
added a check for non-initialized MnM_map
Bug fixes for non-declared objects
Changes to MetalnonMetal derivatives.
More bug fixes to Metalnonmetal.
adding MetalNonMetal interactions
Added more Morse and Lennard-Jones part of metal-nonmetal.
Formatting to prettify the code
Just some formatting fixes
removed MWM as an atom type property
removed a stray is_MWM
One more to add.
Install process is incomplete
Install process should add some basic text documents
Install process should install the manual
Adding more missing files from metal-nonmetal interaction.
Added c-fortran interaction map.
More changes to MnM.
more changes to MnM.
More Changes to MnM.
Added metal-non-metal section
Makedepend is regenerated each build. Don't need it in repository
Broken files on install
Bug fix to types.
Changes for Non-Bonded interactions.
Added MnM forcefield.
Changes for MnM forcefield.
Added metal-nonmetal forcefield.
Changes to allow for non-bonded interactions.
Non-bonded interactions added.
Adding support for non-bonded interactions to OOPSE.
Structural change to how spohr atoms will be parsed. Will be more like bonds.
Addition of section parser for Spohr water-metal potential.
Fixed Makefile problems with the samples and added several missing makefiles.
Starting NPT Langevin. Added new force manager files.
Removed nanorodBuilder.
Pos copied into a malloc array now.
Build change.
Fixed more bugs and removed more CGAL.
Removed CGAL from makefile.
Removed nanorod builder from OOPSE.
Addded QuickHull to cvs.
Removed CGAL from OOPSE and replaced it with qhull.
Removed debug message from simcreator.
Removed debug message from simParallel.
Changes to sutton-chen force.
Fixed pot in parallel.
forgot the if (do_stress) condition on the previous commit
fixed a bug where the pressure tensor wouldn't update for atoms in the switching region when # of atoms in a group = 1
Added md file for half of a icosahedron.
SF Lennard-Jones was added for everyones' enjoyment. The behavior is tethered to the electrostaticSummationMethod keyword.
Added Bond Order Parameter as a function of radius.
more changes for atomic virials and Lennard-Jones force switching
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...
Adding a starter file for the secondary prism {1,1,-2,0} face.
adding new ice surface files
forgot a tolerance for simple cubic lattice magic number determination
Fixed conversion bug in self_self, when adding self energy to mypot, energy needs to be converted by pre11.
Fixed a bug in NeighborListNeighbors.
Spherical boundary conditions.
fixed a bug in waterBoxer
Support for printPosOnly in Dump2XYZ.
Added printPosOnly to Dump2XYZ as a userbase(BETH) request.
adding md-solvator
Added the ability of waterBoxer to deal with non-cubical boxes.
Added thetacorr functions to dynamic props.
Added more error reporting to simParallel.
Changes to add thetacorr to dynamic props and fixes to radial rcorr.
Remove snapshotcentroid from makefile.
Removeing snapshot centroid and adding support for COM calculaton from snapshot.
More changes to mdsplit.
Breaking more mdsplit stuff....
Changed how mdsplit gets file names. Full path is now removed from name.
Fixing an implementation problem
BSM has to talk to reader about center of mass properties
Adding the ability to compute Center of Mass properties on reading in a dump file. DumpReader must be told if it needs to do this, however.
Added function to calculate volume based on ellipsoid definded by radius of gyration.
new ideal structures
Added a bunch of bond order parameter test cases.
bug fixing Wigner 3-j import to C++
fixed a configuration error
Code to run radial rcorr.
Added preliminary support for CGAL and computation of convex hull.
Adding support for radial rcorr.
Added interface to change number of neighbors in calculating neighbor list.
fixes for BOP
Fix to makefile.
Histogram bin change.
Added support for nanoparticle density profile.
possible fix for unnormalized BO
user selected dampingAlpha now gets set
returned to half self-term values
Support for OOPSE RealType.
fixes for CGAL
Changes to nanorod builder for new dump format. Changes to configure to test for new version of cgal.
fixes for open babel
more openbabel updates, also changing velocitizer to thermalizer to avoid a filename collision on case-insensitve file systems
Updating OpenBabel to version 2.0.2. These files aren't used anymore
updated OpenBabel to version 2.0.2
Slight changes to oopseformat to allow importing of openbabel's perceived atom types into OOPSE md files
Added velocitizer utility program, added samples of its use to the builder samples.
fixing a wrapVector problem in staticProps, also making Shifted force and electrostatic damping the default behavior
bug fixes for vacancies
Adding samples for builders
bug fixes
bugfixing shapedLattice to have crystal origin at one of the occupied lattice sites
More typos...
Typo in mdSplit.
Fixed printing of OOPSE version at header and trailer.
fixed a few bugs
Changed nanoparticle builder for new dump syntax.
now the -n command works
fixing missing lattice arguments, adding a builder sample
adding builder samples
nearly complete rewrite of randomBuilder
oops with the affineScale
who needs .in files for perl? using env
fixing bugs in randomBuilder
Fixing the builders to prepare for OOPSE-4 release
Added utility to split dump file frames into md files.
forgot to adjust the makefile
added solvator and adjusted waterBoxer
improvements to waterBoxer
fixed a bug in waterBoxer for invalid water names
Starting cleanup for 4.0 release
Cleaned up the code for BondOrderParameter and added a bunch of comments. Fixed a memory leak or ten.
Some efficiency fixes (now computes Wigner 3-j coefficients only once in the constructor).
Mostly done with BondOrderParameter. Only a few performance tweaks remain
fixing bond order parameter code
refined the reaction field dielectric passing
bug fixes (still broken, however)
Following Rein ten Wolde article
more bug fixes
more changes to BOP and SH
fixed the half self term for wolf electrostatics and OOPSE now chooses a cutoff radius dependent alpha for damped electrostatics
Fixed a bug in Wl code in BondOrderParameter
Bugfixes in BondOrderParameter and SphericalHarmonic
added SphericalHarmonics, fixed a few problems with BondOrderParameter
fixed bugs (mostly in BondOrderParameter)
Adding BondOrderParameter to StaticProps
Working on BondOrderParameter
Latest Version
fixed a DumpReader bug, took out extra printing statements in residentMem and BlockSnapshotManager
changing configure script to process the new utilities
added some features to waterBoxer
added the waterBoxer script
added comment info
adding NgammaT integrator
modified affineScale to work with the new OOPSE files
fixed TI MPI bug
fixes to zang writing
converted samples over to the OOPSE-4 file format Fixed an MPI bug in thermodynamic integration
removed extra file in Hydro.cpp
Changing utility programs to use the new file format
fixed some bugs in DumpWriter, eliminated some extra printing of debugging information
Massive changes preparing for release of OOPSE-4: The main difference is that the new MD file format (.md, .dump, .eor) now contains meta-data information along with the configuration information.
change the globals.cpp to make sure we can set targetPressure and surfaceTension to be negative.
fixed an ordering issue in quadrupole-charge interactions
starting change of file formats
Changing atom2mdin into atom2md to reflect new unified file format
fixed a pvf bug
fixed dumpConverter problems
added dumpConverter
removed shapes sample
fixed a spelling bug
added perl interpreter to affineScale script
added perl substitution for affineScale script
added install target for scripts
Adding a directory for scripts Adding affineScale script
fixed a getSigma bug
Added tred to sample water.md files
Added TRED water visitor for Dump2XYZ visualization
Added TRED parameters to forcefield
fixed d / sigma0 confusion
testing commit logger
removed printing of GBN and GBM from previous debugging
Fixed a bug in the fftw part of the configure script.
removed icc from C++ search lines, did some formatting work on GB module, mucked around with a GB example
Adding more changes to orientational bond order parameter.
Added utility function to winger3jm from slatac.
Added the multipole interaction routine. It doesn't work yet, so it's not included in the build.
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
fixed forces and torques for GB
more efficient file reading for thermodynamic integration, and fixed some formatting
Beginnings of a order parameter.
Adding code for bond orientational parameters.
MPI thermodynamic integration works now.
fixed a build problem... GB_12b_ratio no longer exists (replaced with BG_l).
Added support for Winger3jm coefficients.
fixes for mpi thermodynamic integration, close to fully working...
output the principle axis of GB
added mpi compilers, demoted pg compilers after pathscale
reformulated some of the electrostatics
damping now works for charge-quadrupole and dipole-dipole
Fixed a spelling error and a bug in MPI Thermodynamic Integration on file read-in
fixed some typos
testing GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor
Added methods to access GB_mu and GB_nu from the force field options
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).
Add the RippleOP to calculate the orderparameter of the ripples.
Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)
Fix a type promotion problem
replace double with RealType
What?
more changes
more changes for MPICH with profiling libraries required
MPI stuff
fixes for Hydrodynamics
fix a bug in parsing HydroProp file
Fixed a bug when spherical boundary conditions were off.
fixed an initialization bug of Hxy.cpp.
wrapping back to PBC by molecule instead of by individual atom
fixed the bugs of Hxy.cpp.
Last bug showed up in 2 places, fixed the other one.
Fix a bug of printing empty line in DumpWriter
change the order of include path and library path
Adding single precision capabilities to c++ side
Adding single precision capabilities to the fortran side
adding --enable-single to configure script
Getting fortran side prepped for single precision...
electrostatic refinement
zlib fixes
Autoconf fixes for FFTW. Multiple FFTW version support.
*** empty log message ***
Changes to calculate undulation spectrum
adding a gay-berne switch to Dump2XYZ
Adding qpole
finding ifort arguments that won't die under two different versions of the intel fortran compiler
missing makefile was hanging up 'make clean'
Added random builder to cvs.
Change in siminfo used in nanoparticleBuilder.
Added random builder
Added a random builder to oopse.
Using OpenBabel element table to pick vdw radii for hydrodynamics if the LJ sigma can't be found.
Adding spherical boundary conditions to LD integrator
Added EAM atom types to Hydro models
put spline subroutines in the EAM module
Removed sqrt splines and shape stuff (doesn't work, so why was it in there?). Changed some of the water samples to use shifted_force. Probably should set the defaults to use the damped version now that we sped it up.
Electrosplines added...
splined up sticky
Complete rewrite of spline code and everything that uses it.
Many performance improvements
added a cubic spline to switcheroo
Since status.F90 is used by interpolation.F90, the former needs to be listed above the later in the Makefile.
changed the interface a bit
added some logical flags
Wiped the spline with derivatives and corrected a boundary comparision error by eliminating the check. This algorithm REQUIRES known first derivatives at the endpoints.
bug fixes for interpolation module
Heavily modified interpolation module, also moved to "utils"
Added interpolation module.
*** empty log message ***
Added status module to simParallel for error reporting.
NPrT might work now
Fixed memory leak bug where SCList capacity was not reset to zero on destruction.
More testing of nanoparticleBuilder.
Added check to make sure md file exists.
Fixed latticeOrt in shapedlatice and latticebuilder.
Fix the normalization problem in calculating correlation functions
(1) RoughShell Model is working; (20)Adding a new option into Hydro which allows user to generate the beads only
Makefile for nanoparticle builder.
Added nanoparticle builder to makefile
Debugging changes to nanoparticle builder.
back to previous DynamicProps
Adding position correlation function. The command line option for DynamicProps is now changed. --rcorr is for position correlation and --rmsd is for mean square displacement.
update writeBeads method
remove a unknown method
The off diagnal is not set
Throw exception if the file can not be opened for preprocessing
Added shaped lattice.
fix a bug in calculating hydrodynamics tensor when the radius of beads are not the same
Fix a bug in friction calculation for ellipsoid
Verify the correctness of Ellipsoid's hydrodynamics properties
New version of Hydro is working now.
refactor Hydrodynamics module.
Generic Shaped Lattice for oopse. Can overload to get spherical or nanorod.
LagevinDynamics is working?
fixed a const problem
unit conversion for diffusion tensor is wrong
change the epsilon of numeric_limit
correcting the unit in HydrodynamicsModel
using setFrc in RigidBody::calcForcesAndTorques will discard if there are force and torque applied in rigid body itself. use addFrc instead.
Adding RoughShell and BeadModel
adding hydrodynamics module into build system
adding Cholesky Decomposition
LangevinDynamics in progress
Fixed a double/int bug. Surprised no one ever noticed before...
fix bugs in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out product of Rij
Bead Model is working
Adding Hydrodynamics Module
fixed a spelling error
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
Changed Names of class files.
*** empty log message ***
fix a bug in converting integer to double
added DPD molecule type parameters
Fixing a bug which reads the wrong frame of trajectory file during analysis
adding transpose into SquareMatrix3; fix a bug in AtomStamp where orientation is not set correctly.
fixed a bug in rigid bodies that contain directional atoms
Adding visitor for GBlipid atom type
added CXXFLAGS to the LinkOptions to allow compilation with icc9 (skipping the gcc-4 std c++ libraries).
Missing brace caused the last commit not to build
Changes to cutoff radius setting to a more logical procedure - still may change...
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X
Adding :LegendrePolynomial
Changes to nanoparticle builder
Added Makefile for nanoparticle builder.
Cleaning up for 3.0.1 release
Prepping 3.0.1 release
new version number
Updated Documentation
Getting ready for release!
Testing commit
Removed MixingRule from Globals. Handled by forceField now.
Added NPAT to Globals integrators.
*** empty log message ***
testing to make sure GNU make is the make that was used to build OOPSE
changed compiler search order
Changes in Sutton-Chen units
fixed some version info and the copyright date
added some missing checks for header files (particularly zlib.h), used autoheader to help generate config.h.in
added some missing checks for header files (particularly zlib.h)
fixed a dependency problem for the Executable builds
Missing Makefile in this sample directory
Old makefile.in no longer required
All of the OpenBabel stuff needs to be installed
Changed formating.
unifying function name in electrostatics
fix make install problem for metals samples
remove samples/metals from install list.
filepp can not handle multiple line macro, just convert multiple line macro into single line macro.
Made some changes to electrostatics for shifted-potential and shifted-force with mono and multipoles
autoconf modernization and cruft removal
autoconf modernization and cruft-removal
fix some error messages
instead of printing to std::cout, throwing an exception when error is found.
Fixed a spelling error
Changed conversion factor.
Sutton and Chen should be working now.
Fixed SC bug with SIM_uses_SC
fixing RhoZ
Added energy scaling to section parsers.
replace isType<int> with isInteger
remove extra forceFieldOptions from SC_FF
Add force file.
Sutton-Chen no longer segfaults or produces 0 potential, but rather produces Inf for the potential. Progress....
More Sutton-Chen bug fixes.
Long range potential return from fortran is already accumulated, it should not be accumulated again; nGroupTypesCol is not initialized; GroupMaxCutoffCol is not allocated;
In order to compile MPI version, we need to cast const char* to void* for stringstream.str(); Previous Makefile use bjects of single version to make the MPI library;
Sutton-Chen bug fixes. Almost there...
Changes in forcefield.
added files for sutton-chen
More cvs changing.
More moving...
More changes to directory structure.
More Directory changes...
More changing of directory structure
Fixed issue with symbol naming and added call to set force options in SimCreator.
More changes to forcefield options.
Force options passed to fortran.
Force option changes.
changed __FUNCTION__ to __func__ to match C99 standard, and then added an autoconf test to check for __func__ usability. Changed some default compile flags for the Sun architecture
added the STL check
make minor change to build oopse under solaris
the standard library came with SUN compiler does not have a conforming std::use_facet, define a macro to handle it. Adding exception handling to SimCreator.
Removed one parasitic argon atom which was living inside the GB particle. No alien-like ripping out of the stomach was required.
replace grammar for numerical parsing
fixed a cutoff bug
Removing compiler dependencies and replacing them with real autoconf checks
Adding checks for various features used by ANTLR
fix a nasty negative integer parsing problem by refining the grammar
made some minor changes to allow compilation with the portland group compilers
fixed compilation problem for icc7
added missing include
added some checks for pathscale compiler
added copyright
added info printout
added pathscale
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
This should really break things.... Started adding support for ForceOptions to section parsers.
*** empty log message ***
Added forceOptions to section parser
Removed geometric distance mixing from individual modules and now use force options to detemine what the deal is.
Further fixes for compiler issues.
Fixed ifc public-private issue.
Added support for fortran force options.
Fixed a bug in checkTorsion
Changes to SC.
Changes to build twinned crystal
Overloaded interface for dumpwriter.
remove deprecated keywords from samples
Fix parsing error in OptionSectionParser
Adding handler for CLAY force field
Fixed build bug in openbabel.
reformat error message
Adding .frc file for CLAYFF
adding more checking for topology
Spurious semicolon removal
We've made big changes. This isn't 2.0 anymore.
removing deprecated nAtoms and nComponents lines
adding SelectionToken.cpp
Adding FragmentStamp
Errors are no longer thrown with consts (fixes compilation bug on the Mac).
Got rid of spurious printing out of timestep
Got rid of spurious printing out of junk
Change build process for libOOPSE.a so that the libraries aren't unpacked. libOOPSE.a is now made directly from the object files
added check for egrep (grep -E) needed for new build of libOOPSE.a
adding DataHolder
Added Gay-Berne / Argon test case for the cutoff policies
update Makefile
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
Code to calculate rho(Z) to calculate density profiles for water slabs.
added checks for some functions to configure script
Changed file names that conflict w/ oopse file name object files.
compilation bug
parsing by filepp
Cutoff Mixing fixes
compilation issue
Cutoff mixing fixes have been made.
Adding ParamConstraint.cpp
adding openbabel data files
adding support for soft linking
Adding support for soft linking
Adding linking stuff
rename mdinConverter to atom2mdin
fixed a bug
Adding some config checks for OpenBabel codes we are using
Adding some checks for OpenBabel code
Unifying config.h stuff from OOPSE and OpenBabel
Unifying config.h stuff and making sure the OpenBabel codes can find our default (and environment variable) Force Field directories.
adding ForceFieldOptions
OptionSectionParser get compiled
ForceField optional parameters....
adding mdinConverter
adding more readers/writers
adding openbabel
register openbabel readers/writers
included shifted potential self term
just some parameters
adding openbabel
removed unnecessary commented code
cleaned up the charge-charge interactions a bit...
just playing
fixed a bug in the shifted_potential case
just playing around - we need to refresh all the samples sometime soon...
Made preforce calc public in suttonchen.
Sutton-Chen added to SimInfo
Added Sutton-Chen to force loop...
Added sutton-chen to makefile.
Build Fixes for sutton-chen.
Missed makefile for sutton-chen.
Sutton-chen stuff
Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen.
Forgot to add some files
added in a 5th order polynomial switching function option
added in a 5th order polynomial switching function
playing with switching functions again
playing with switching functions
Added force files for Sutton-Chen and Quantum Sutton-Chen
Added a keyword and ability to output forces and torques
Added a keyword for output of forces and torques
Working on shifted_force...
Just testing...
removed a poorly commented section
improvements in shifted-force
mmm... damped shifted force...
More work on SC.
More work on suttonchen.
removed some test code
forgot to add the screening method header
changing how we deal with summation and screening methods
again, changing how we deal with summation and screening methods
debug stuff for rf removed
Added suppport to atypes for MEAM and sutton-chen
removed some testing code...
fixed a capitalization problem with NPT integrator initialization
nothing
still fixing up wolf...
In process of adding sutton-chen forcefield.
changed the default switching radius to 85% of rcut
reaction field looks to be working now - for charges and dipoles alike
reaction field looks to be working now
added a test molecule
added a test atom type
added charge-dipole reaction field - don't know if it works...
streamlined reaction field for dipoles (now a good bit faster) and added reaction field for charges - still need to do charge-dipole RF
minor changes when testing reaction field
reaction field now works for charges
Fix the other branch of force calculation in Torision.cpp
Still had some globals toUpper problems - these changes should fix those...
nothing
fixed an MPI compilation bug in GayBerne
fix an index mismathcing between c and fortran
added samples for the cutoff methods that Yang Zheng has been working on
fixed gb/lj and gb/gb torques and a rotation matrix bug
added a few GB test cases
Fixing GB parameters
Changed the parameters for the Gay-Berne type
merged reaction field with electrostatics.F90
Customized StatWriter is working
using notation from Cleaver paper
bugtracking gb
Another bug fix
fix some namespace issues in Globals
changing GB architecture
Adding samples for gb tests
fix a seg fault when try copy a string to event's err_msg, there are still tons of memory leaking problem in Globals
Change error message in Globals
Constraints for parameters are working now
Adding .md files for GB/LJ tests
Adding some Gay Berne tests
Adding some cutoff tests
Add parts for the GayBerne LJ
Adding Parameter Constraint class
added default restraint spring constants into Globals
rewrite Globals
Fix to forceManager to pass potential array to fortran.
Don't remember what we did
simplifying long range potential array
Testing new cutoff methods
Messing with 2-point water models
Breaky, Breaky: c-fortran interface now expects an array for pot.
More Change goodness for calculation of potential.
More changes to MPI potential calculations.
Breaky Breaky: Add Support for seperating potential contributions.
Free some variables that weren't freed before.
Design change for nanoRod builder --twinned.
Added code for nanoparticle builder to cvs.
Bug fix, undeclared local variable in MPI.
Fixed MPI bug with Row and Column indexing of groupToGtype. We now have two seperate maps groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer that is set to groupToGtypeRow in the single processor version.
fixing up the samples
There is still something wrong with inertia tensor projection
erase output of inertia tensor. There is still something wrong with current implementation.
fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
fixed an annoying mass ratio bug that results in simulation failure with massless particles
maybe some work on wolf
just some random changes when testing
fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame (previous commit is wrong)
fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame
working on wolf
fixed some samples
updated
using epsilon instead of 0.0 to avoid divergence in rotation matrix to quaternion transformation
Rotation matrix multiplication order error
tracking down quaternion bug
Added DIP atom types for 2-point water model
fix a bug in convert rotation matrix to quaternion
Added define for ifc 7 so derfc is external. Other compilers should treat erfc as intrinsic.
Changed erfc to derfc and declared it to be external to fix issure with ifc7. Hopefully this will not cause a problem with other compilers where derfc is an intrinsic function.
MPI fix for SimHasAtype in simulation module. We needed a seperate receive buffer.
Added support for skinThickness keyword to Globals.
fix a typo in DumpReader
fixing up some samples
slowdown fixed - now roughly the same speed as the old version when using dipoles energies are now exactly the same between the old version of OOPSE and this version
turned rf on
Fixed "dum-dum" where we ignore the skin thickness and hardcode listSkin to be 1.0. We now get listskin from skin. This will get fixed to where we can manually set skin thickness.
added error function
Removed print statement for angular momentum and inertia tensor from velocitizer.
Removed print statements for remove angular momentum.
Bug fix: If we are not using LJ (say we are using EAM), we probably shouldn't rebuild the LJ mixing map.
DumpReader using pure c++ io
Fixed a defaultCutoff bug (HEMES!)
libz additions
added check for zlib in configure
adding zlib support for DumpWriter
adding testcase for zipstream
adding zipstream.hpp
fixed up some sample md files
Fixed bugs in reaction field, now it appears as though it really is working...
reaction field seems to work now, still need to do some testing...
Added keywords for compressed dump files.
xlf found a bug that ifc missed...
fixing some summation method issues
fixed a capitalization error
moved a header file around
it builds now, but there are known issues - particularly with reaction field...
some fixes but even more breaking (cutting out the old way to do reaction field)
Working on adding WOLF
Fix a bug in DumpReader in case readFrame is called without calling getNFrames
forgot to add a header
Fixed bug where gtypeMaxCutoff was not initialized after creation. When maxval(gtypeMaxCutoff) was called, the largest random garbage value was returned from the array.
changes to include the coulombicCorrection selector
added in the undamped wolf, in the process of doing the damped wolf
some changes to activate the coulombicCorrection selector
just some testing
Equilibrated the sample
re-added Cl- and Na+
EAM now uses eamlist to lookup eamAtypes instead of assuming a 1-1 correspondence to atypes.
fix to put back calculation of r in do_prepair
fixed a bug in the createMixingMap routine. It should now set doShift correctly
Added nGroupsInRow for mpi build.
Added access to mpi logical variables
bugfix on the grouptype finding algorithm
adding c-side interface to change cutoff Policy
Some bug hunting
Just a longer test
Added allocation for gtypeCutoffmap etc..
initialized atomTypeMaxCutoff(i) to zero
wrote createGtypeCutoffMap
made some changes for implementing the wolf potential
updated getEAMCut
added some probably nonfunctional get*cut routines
Added eamType map to atid map.
fixing some of the problems in the interactionHash and gtypeCutoff routines
added fCutoffPolicy.h
breakage in progress
putting spaceballs back where they belong
Complete rewrite of Lennard Jones module
Breaky Breaky BREAKY breaky breaky
In process of re-write for group based cutoff....
fixes in progress
fix a bug which does not update me_i and me_j correctly
Changed cutoffs... Segfaults nicely now...
fixed ACX_MPI to ignore some text error messages from pathscale compiler
std::bind2nd is in <functional>
replace c++ style comment in c files
Added subroutine to set cuttoff for Interaction map and function in simulation.F90 to determine if a particular atype is present in a simulation.
*** empty log message ***
More breaking and destruction of force code. Does not build at this point...
Breaky breaky!
fixed a bug and ran a simulation
working version of DensityPlot
Changes to remove angular momentum.
Fixed bug in typo in nanorodBuilder.
Added method to remove system angular momentum to velocitizer and added method to calculate system angular momentum to siminfo.
Removed balance from the Darkside (files)
Removed balance from doForces
Updated tap sample
Included a tap dimer for testing purposes
Re-entered the TIP4P-Ew water model. It was apparently wiped earlier this month...
ran make cvslog
adding AtomNameVisitor
dding resetIntegrator
adding resetIntegrator
adding DensityPlot into StaticProps
adding SCDOrderParameter into StaticProps
adding AtomNameVisitor to convert atom name to its base name; wrappingvisitor now wrap back to the center of the mass; adding P2OrderParameter into StaticProps
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
just some tap changes
Modifications to temper the dipolar strength in the first solvation shell for tap
added a tap example for testing purposes
Modifications to tap. Also correcting changes to the previous merge that were not caught
Fixed merge issues between Kyle and Chris so OOPSE will actually build.
help
added gb
Better tap
Couple of changes for TAP water. Need to parametrize.
Fixed build issues under ifc7.
More geometry builder changes.
Changed SHED to TAP
OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it...
Adding support for generic geometry to nanorodbuilder.
More changes to nanoRodBuilder....
*** empty log message ***
Added TIP4P-Ew
Fixed issues with nanoRodBuilder....
Got rid of write statements and am closer to a working shapes
Fixed gcc4 bug...
adding CharClassificationFunctor to fix the locale problem of c++
Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
axed because file causes havoc on Mac (capitalization confusion of filenames)
Working on the shapes parser...
gmake in case people forget
fixed the spacing on the banner. Vanity.
Version string in banner (and version numbers in config.h)
Documentation changes
xemacs has been drafted to perform our indentation services
Jedi mind-trick warning messages have been added to make users ignore CGAL.
fix make install
add Makefile of samples
some samples are not installed correctly
configure now searches for perl to use with filepp
Fixed a bug in RigidBodyStamp section of MoLocator
*** empty log message ***
nanorodbuilder now exit's when libCGAL is not present.
fix one more warning message in make_nodes
Changed interface name for SGI Compiler
oops... bad sample
Change typo in CGAL.
fix some warning messages
added CGAL checks
Added destroy methods for Fortran modules.
Added destroy method to clean up memory
more memory leak are fixed
File not needed for nanoRodBuilder.
fix memory leak in nanorodBuilder and simpleBuilder(forget to delete lattice)
refactory lattice
refactory LatticeFactory and LatticeCreator
refactory LatticeFactory and LatticeCreator
refactory LatticeFactory and LatticeCreator
cleaned up vector_class memory leak fix by deallocating in reverse order of how we allocated. Also migrated MoLocator into utils directory
added lattice directory
added lattice directory, so all of these files are now redundant
cleaned up memory leak fix
added lattice subdirectory
no real changes here, maybe added a space by accident
added quadrupole sample
updating samples
destory atom type in fortran side
Further changes to vector_class destroy function.
Fixed pointer memory leak in vector_class.
Updates to deallocate object in fortran.
minor change to TI output
Changes to delete atypes...
Added code to delete vector.
avoid multiple inherit in basic_ifstrstream
Importing nanoRodBuilder application (may not work yet). ((Doesn't work yet.)) (((May never work....)))
forget to delete prepareVisitor in Dump2XYZ
fixing of the quadrupoles. look! it's divide by 3 like stone says!
fixing of the quadrupoles
change the parameter name in constructors
One more bug fix for GNU make versions < 3.80
Fixed the uc and lc functions for GNU make versions < 3.80
added some stuff to clean out module files during "make clean"
quadrupole interactions should be working with a remaining question of interaction magnitude
messing with samples
oops... messed up a sample
Altered signs to fix charge-dipole interactions
changes during debug of charge-dipole
added Cl- and Na+
reinitialize buffer_stack_ptr in BASS parser
support '+' and '-' in atom type name;clean the code a little bit
fix a bug in converting rotation matrix to quaternion
fixed the wrapping
LipidTranVisitor should do the wrapping
fix a bug in getting the dimension of histogram
avoid building parallel executable for dump2XYZ, simpleBuilder, staticProps and dynamicProps
Corrected changes to the forcefield files
Make sure electrostatic_module provides data for reaction_field
Chris debugging stuff. HE WILL CHANGE THIS BACK, RIGHT?
constant back to correct value
fixed an install-related bug. $(InstallCommand) had been set to $(InstallData)
VelocityVerletIntegrator already deletes and Nullifies restWriter, so Integrator shouldn't do it.
fixed three typos
first run at charge-quadrupole interactions
forgot a couple of makefiles
added some samples
fix a typo in MultipoleAtomTypesSectionParser
pairs inside cutoff group should not be excluded
settled on a unit for quadrupoles
quadrupoles for SSD models
clean up SimInfo; modify the images of SelectionExpression.html
fixed a bug in MPI restraints
adding exclude pairs for rigidbody and cutoff group
fixed a doxygen problem
messing with the split dipole test cases
updated some documentation
LinkedList removal project starts now
using map to replace link list
adding test case of split dipole
Oops... MPI now builds...
adding test case for split dipole
added fortran-side support for split dipoles
fixes to restraints
fixing restraints
minor change
First commit of the new restraints code
adding IndexFinder
fix compilation issue
fix a bug in SectionParser (lineNo is not updated)
adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
change the format of DUFF2
new electrostatic module
added splitDipole and fixed quadrupole stuff
removed #include lines for outdated charge and dipole interfaces
addded a few fun charge-dipole test cases
fixing a strange icc8 bug (we think).
OOPSE_itoa!
Electrostatic Unification Project
Dunno
Using OOPSE_itoa and checking a NULL left over from the LinkedList days
electrostatic unification project fixed an uninitialized variable in Lennard Jones mixing map
electrostatic unification project
making some cool test cases
Added a charge for Chlorine
Fixing a bug in BitSet.cpp
SPRNG eradication project
Cleaning up config.h.in by adding comments
avoid using const char*(hope can fixed the missing atom type problem)
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
Adding unit test for random number generator
fixed a file inclusion problem
fixed compilation problem
replace SPRNG by MTRand
Change the name of test case
adding testcase for random number generator
fix compilation problem for g++ 3.4
adding OOPSERandNumGen
Fixed the damned build problem with the libraries not being removed in make clean and make distclean (at least we think it is fixed).
Making small modifications to allow for use on MPI machines
adding MersenneTwister random number generator
Adding a modified version of MersenneTwister.hpp
selection expression
adding soft potential to LJ Module
adding documentation for selection expression
adding basic_teebuf which can operate on multiple stream simutaneously.
Added ssdrf sample
reactionfield get fixed
Fix a bug in GofRAngle
Fix for compilation on the Sun
fix for compilation on the Sun
fix problem in sun
adding LipidTransVisitor, GofXyz is working now
Corrected filename collision for EAM on Mac OS X
Updated copyright information
corrected filename collision for EAM on operating systems which are not case sensitive (aka Mac OS X)
more bug get fixed
fix a bug in GofXyz
make processHistogram non-abstrct function
*** empty log message ***
finish GofXyz
change the output format of 2D radial distribution function
forget the const correctness for BitSet
The change of interface of BitSet cause a bug in SelectionEvaluation
return residentMem in byte
fix a bug in writing out the value of cosang
using PhysMem - RSSMem to estimate avaliable memory
change the default bin number
change the suffix of output files;fix the problem of counting in staticProps
fix a bug in BlockSnapshotManager
BlockSnapshotManager is using reference counting now
replace std::make_pair by VariablesType::value_type to make Sun Compiler happy
adding typedef to TokenMap, using TokenMapType::value_type instead of std::make_pair to make Sun compiler happy
bug fix in StaticProps
(1) adding #ifdef __RWSTD to make sun compiler happy (2) fix pair density calculation problem when two selections intersect with each other
cast of NULL to satisfy xlc++
*** empty log message ***
bug fix for null termination
bugfixing residentMem
bugfixes for residentMem on LINUX
added residentMem
modifications to estimate memory in use by other processes autoconf fixes ps syntax checking config.h file cleaning
ps niceness
ps strangeness
fix a bug in BlockSnapshotManager.hpp
default length for staticProps is 1/2 smallest length of first frame
fix a bug in VelocityVerletIntegrator : last frame is written twice
begin bug fix
refactory CorrelationFunction
bug fix and start of switch for type of correlation function
fix a bug in calculating bytes per stuntdouble
more fix
fixed a bug in CorrelationFunction
fixed a bug in SimInfo::getCutoff()
adding staticProps and dynamicProps into Makefile.in
maximum length defaults to the cutoff radius
adding Algorithm.hpp
dynamicProps get built
dynamicProps in progress
more work in dynamicProps
adding dynamicProps
adding command line option to DynamicProps
adding command line option for DynamicProps
adding dynamicProps
adding SelectionManager.cpp
adding one more constructor to Snapshot to create customized DataStorage
adding beginSelected, nextSelected method to SelectionManager
adding support for physmem
adding supprot for physmem
adding physmem
more work in StaticProps
change the filenames
adding GofRAngle
remove some useless files
staticProps in progress
adding GofR
add getRigidBodyAt function into Molecule class
update help info
support select internal index selection, for example, select DMPC.3
update help info for Dump2XYZ
selection librarys added
adding Makefile
issue commented out in wildcards
forget to reset the pc which cause reevaluate return NULL
fix a bug in determing the global index for rigidbodies
minor change in Bitset
selection library is working
remove SelectionVisitor
IgnoreVisitor and XYZVisitor now use selection library
adding SelectionManager into SimInfo
dump2Xyz now take advantage of selection library
minor change in BitSet
adding missing implementation
half of the selection utility is working need to debug within keyword and atomproperty keyword
selection library get built
fix BitSet
remove some useless files
adding wildcard class; NameFinder is finished
more work in selection library
selection in progress
selection library in progress, except SelectionEvaluator, other files are compiled
adding boost::any
add SelectionCompiler.cpp
Selection in progress
adding selection library
forget to add eorWriter
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the wrong column of electroframe
fix a bug in SimInfo, use number of cutoff stamp as counter to loop over rigidbody stamp
(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
forget to set dipole for lipid head group
fix a bug in loading initial extended system parameters
forget to set maxIterNum_ in NVT
remove WATER.cpp
sync Makefile
moved Package variable into subdirectory makefiles to speed up the building process
Fixed publication details in banner
added dummy subroutine to avoid empty unit, synchronized this dummy routine between C and fortran
separating modules and C/Fortran interface subroutines
more fixes for gnugetopt
fixing for gnugetopt
using c library to do conversion instead of using iostream due to a bug in libstdc++(GCC 3.2)
no message
fix a bug in global index
remove include Integrator.hpp in Minimizer
compile getopt and getopt1 if we need to
template flags
formatting
fixed a MakeDir / MkDir problem added BinDir target
port to SGI platform
change the order of linking (object file comes first and then follow by user built library)
remove useless debug info
minor fix
missing tab
missing tab
LinearVisitor get fixed
merging new_design branch into OOPSE-2.0
remove some useless force fields
adding new format of EAM force field
rename newDUFF.frc to DUFF2.frc
Fixed Makefile test bug under OSX and possibly other BSD's, replaced test -f *.mod with ls function since BSD test apparently doesn't support wildcards.
adding new EAM force field files
fix another bug in WATER.cpp
fix a bug in WATER.cpp when initializing the new Charge AtomType
*** empty log message ***
merge WATER force field into DUFF
change the force constant of bonds
minor fix in DUFF
minor fix in force field file
minor fix
new ForceField format
replace misuse of using namespace std in header files
fixed a sample
spell check
add PolynomialTestCase
Addint StringTokenizerTestCase
change Makefile
improved restraints - mpi should work fine
improved restraints
oops...
Back to normal... Oh... Restraints should work in parallel now
Improvements to restraints
just some testing changes, I'll return to the original on next commit
new DUFF forcefield
adding new format DUFF force field
Fixed a mixing list bug that slowed down the force loop
working sample
working towards parallel restraints
Commented out some write statements
Got rid of some write statements
Fun with ice
Added the linear visitor
current status of the debugging process
included visitors and minimizer
new changes
time to break SimSetup
added new classes in progress
isLinear and linearAxis are virtual in StuntDouble, but are implemented by DirectionalAtom and RigidBody In StuntDouble, they should return false and "-1" but there should be logic to figure them out in the other two classes
Don't remember what I did
Breaky Breaky
fixed useXXX in the entry_plug so that it only is set if the atoms really are in the simulation
testing force fields
testing shapes
mess up ......
Shapes looks like it's working
these core classes get compiled
more work on Molecule class
still debugging
shapes rcut calculator added
shorter run
rewrite Molecule class.
Remove some deprecated files
More painful reconstruction is coming !!!
More work on StuntDouble, Atom, DirectionalAtom and RigidBody
remove old Vector3d.hpp from application/simpleBuilder
Minor change in next_combination
Done with combination
change documentation of next_combination.hpp
ReplaceWildCard is working
adding replace wildcard function
Minor change
STL next_permutation like next_combination is working
fix of setDipoles
forgot to advance lines in the shapeFile
forgot the orientation line
fixed duplicate declaration foo
uncommented .in line
next_combination in progress
adding next_combination test case
STL Compatible combination sequence generator
bug fixed in GenerateCombination.hpp
a STL next_permutaion like next_combination function.
no message
ReplaceWildCard(recursive version) is working, need refactoring. An iterative version is on the way
ReplaceWildCard in progress
Adding Test Case for ReplaceWildCard
adding ReplaceWildCard.hpp, need test
Adding Generic TupleMatcher, wild char matching is on the way
Adding Generic Tuple3 and Tuple4
bug fix
subclass foo
more char* -> string conversion
char* -> string
Making ShapeType into a ShapeAtomType, fixing some isXXX
define name collision
forcefield refactoring for shapes
adding sample shape directory
DataStorage passes unit test
Changes to help advance shapes
Changes to Shapes force field reader
Snaphot and SnapshotTestCase in progress
add getArray function to RectMatrix and Vector classes
adding GenericFactory Test Case. GenericFactory now can bed used to creat ForcefieldFactory and IntegratorFactory etc.
more classes get reconstructed
GenericFactory pass unit test
Refactoring in progress
more work in Snapshot
Dear god! It runs and conserves energy!
strDUP not strCOPY
fixey fixey the breakey breakey
compiler flags
fixey fixey
Added un-busticated fortran files and c/Fortran interfaces
More on AtomType and DirectionalAtomType
Adding AtomType
Snapshot and SnapshotManager in progress
adding test case for Snapshot and snapshotManager.
Breaky Breaky. Fixey Fixey.
remove some junk files
remove backup of GenericData.hpp
replace old GebericData with new GenericData
Added newLJtype to lj module.
Added interface for fortran lj module.
GenericData and PropertyMap pass unit test.
fixed a fortran name problem
adding generic data test case
Fortran/C++ interface de-obfuscation project appears to be complete! Woo hoo!
Fortran/C++ interface de-obfuscation project continues
Fortran/C++ interface de-obfuscation project (It is a very long story)
Math library pass the unit test
Snapshot and SnapshotManager in design phase
namespace problem prevented linking
fixed include
more fortran name mangling
yet more fortran renaming
Fortran name cleanup continues
fixing some broken fortran stuff
name sanity on the fortran side
*** empty log message ***
except diagonalize(), all of functions in math library pass the test
Added correct prototypes for C-fortran interface functions.
Added correct prototypes for C-fortran interface functions.
more bugs get fixed at math library
Added new files for fortran interface.
regressing
working on shapes for portability
working on shapes
changed around findBegin
more bugs are fixed in Vector class
fix some bugs in RectMatrixTestCase
implement more test cases
more tests on math library
adding more testing units
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
Added ShapeType
adding vector test case
adding generic factory and vector test case
math library in progress
add quaternion class
adding test file
fix a bunch of bugs
change const_cast to statc_const
fix a bug in basic_ifstrstream.hpp
forget to use namespace oopse
Changed optimization flags for XLF and XLC.
adding ifstrstream test case
fix include
fix incompatible declaration in jacobi
adding Makefile
adding test case for ifstrstream
add ifstrstreamTestCase
add checkFilename Option
add SquareMatrixTestCase class
adding basic_ifstrstream
math library in progress
FileReader in progress
Matrix in progress, test in isOrthogonal of SquareMatrix is failed by some reasons
adding PropertyMap class
adding testing unit
adding RectMatrix
refactory vector and matrix classes
Remove some Makefile.in
add Vector3d.hpp and Matrix3x3d.hpp
adding c++ coding style
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
fix a bug in filepp
using filepp to generate dependencies instead of compilers
filepp can be used to generate dependencies for c/c++ now
remove -module from F90Options
adding rules to move fortran 90 module to target directory
fixed makefile.in
remove "use bytes" which causes problem in sgi machine
add Makefile
fix Makefile under water directory
remove argon.dump and argon.eor from Makefile
Remove some Makefile.in
*** empty log message ***
fix make install
adding make install
add Makefile to sample directory
moved the getopt stuff
more build fixes
adding doxygen configuration file
filepp can handle different fortran module case and suffix
Chris doesn't know about the OOPSE-2.0 directory structure yet
Yeah yeah, we'lll get around to it later
cleaning up build process
made the file reading in restraints more intelligent - no longer gives uninformative seg faults
cleaning up
Cleaning up a bit
fix make statistics
adding GNU make functions to combine all of the static libraries to a big library
adding shared library flag
move mpiSimulation_module to DarkSide
building MPI version;using static library instead of shared library
pass __FORTRAN90 instead of __F90 to filepp
add make cvslog
more work on the parallel build
changes to backport declare flags
Started work merging shapes
remove sfmakedepend from cvs tree
add oopse_ as library prefix
fix a space trimming bug in filepp
A few minor build changes
adding fortran90 make dependency tool
make clean is smart enough to only remove object files belong to current package. turn off silent mode
define DEV_ROOT as relative path
get the relative path by shell script
eliminate DEV_ROOT by relative path
add PackageLibs; fix dependency rule
updates
Working on make stuff
If makefile does not exist, print error message
fix dependencies rule
still working on build process
add print statment to rules
change Makefile to relative path
remove StringUtils.c which cause headache in bulding libutils
change directory structure of application. Every executable file is replaced in seperate directory
Keep that lib around, please.
starting a configure version
move fortran files around to solve dependency problem
*** empty log message ***
fix fortran dependency problem
add yacc and lex rules
adding include path to F90Options
change suffix from .cc to .cpp
change the #include in source files
Import of OOPSE v. 2.0
Standard project directories initialized by cvs2svn.