Fixed bug is Sutton-Chen force calculation in parallel.
Removed remaining MPI from metallic potentials. Bug in MPI calculation of energies in Sutton-Chen.
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++
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
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.
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
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
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
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.
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
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
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.
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.
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
All your base are belong to us!
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
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
Hopefully md-solvator is done.
Adding the Amber_FF files to OOPSE distribution
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.
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Added files to module section of Makefile.
Added files to Module section.
Adding Trappe torsion types and fixing Opls types
Code work on thiols and TraPPE torsions.
Removed accidental print lines.
Fixed typo in LJinteraction types. LJ-metal appears to work now.
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...
Changing functional form
Adding iterative looping to get better estimates of friction forces from full-step velocities
Fixed sign error in MnM based on atid's.
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.
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.
Removing Qhull from cvs.
does ifdef check for computational geometry packages
Fixed nesting bug in USE_CGAL and USE_QHULL.
Initial code for AlphaShape.
New configure
Check CGAL and qhull defines
Added CGAL and qhull defines
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Many fixes for Charmm-type torsions.
Added more chamges to nanovol.
Added new config.h to deal with cgal.
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Added volume calculation for hull.
Changes to Build system.
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.
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.
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.
Makedepend is regenerated each build. Don't need it in repository
Broken files on install
Bug fix to types.
Changes for Non-Bonded interactions.
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.
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.
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
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...
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.
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.
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
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
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
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
fixed a spelling bug
Adding a directory for scripts Adding affineScale script
fixed a getSigma bug
Added TRED water visitor for Dump2XYZ visualization
fixed d / sigma0 confusion
testing commit logger
removed printing of GBN and GBM from previous debugging
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
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
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
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
Autoconf fixes for FFTW. Multiple FFTW version support.
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Changes to calculate undulation spectrum
adding a gay-berne switch to Dump2XYZ
Adding qpole
missing makefile was hanging up 'make clean'
Added random builder to cvs.
Change in siminfo used in nanoparticleBuilder.
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.
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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.
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fix a bug in converting integer to double
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
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.
new version number
Removed MixingRule from Globals. Handled by forceField now.
Added NPAT to Globals integrators.
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
Changed formating.
unifying function name in electrostatics
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
fix some error messages
instead of printing to std::cout, throwing an exception when error is found.
Fixed a spelling error
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
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...
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
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.
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 copyright
added info printout
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.
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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.
Fix parsing error in OptionSectionParser
Adding handler for CLAY force field
Fixed build bug in openbabel.
reformat error message
adding more checking for topology
Spurious semicolon removal
We've made big changes. This isn't 2.0 anymore.
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
adding DataHolder
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.
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 support for soft linking
rename mdinConverter to atom2mdin
fixed a bug
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
register openbabel readers/writers
included shifted potential self term
adding openbabel
removed unnecessary commented code
cleaned up the charge-charge interactions a bit...
fixed a bug in the shifted_potential case
Made preforce calc public in suttonchen.
Sutton-Chen added to SimInfo
Added Sutton-Chen to force loop...
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
Added a keyword and ability to output forces and torques
Added a keyword for output of forces and torques
Working on shifted_force...
removed a poorly commented section
improvements in 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 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
Fix the other branch of force calculation in Torision.cpp
Still had some globals toUpper problems - these changes should fix those...
fixed an MPI compilation bug in GayBerne
fix an index mismathcing between c and fortran
fixed gb/lj and gb/gb torques and a rotation matrix bug
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
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
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
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.
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
using epsilon instead of 0.0 to avoid divergence in rotation matrix to quaternion transformation
Rotation matrix multiplication order error
tracking down quaternion bug
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
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
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!)
added check for zlib in configure
adding zlib support for DumpWriter
adding zipstream.hpp
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
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
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...
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
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
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
Couple of changes for TAP water. Need to parametrize.
Fixed build issues under ifc7.
More geometry builder changes.
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....
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...
fixed the spacing on the banner. Vanity.
Version string in banner (and version numbers in config.h)
xemacs has been drafted to perform our indentation services
Fixed a bug in RigidBodyStamp section of MoLocator
nanorodbuilder now exit's when libCGAL is not present.
fix one more warning message in make_nodes
Changed interface name for SGI Compiler
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
no real changes here, maybe added a space by accident
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!
change the parameter name in constructors
added some stuff to clean out module files during "make clean"
quadrupole interactions should be working with a remaining question of interaction magnitude
Altered signs to fix charge-dipole interactions
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
Make sure electrostatic_module provides data for reaction_field
constant back to correct value
VelocityVerletIntegrator already deletes and Nullifies restWriter, so Integrator shouldn't do it.
fixed three typos
first run at charge-quadrupole interactions
added some samples
fix a typo in MultipoleAtomTypesSectionParser
pairs inside cutoff group should not be excluded
settled on a unit for quadrupoles
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
LinkedList removal project starts now
using map to replace link list
Oops... MPI now builds...
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;
new electrostatic module
added splitDipole and fixed quadrupole stuff
removed #include lines for outdated charge and dipole interfaces
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
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
fixed a file inclusion problem
replace SPRNG by MTRand
fix compilation problem for g++ 3.4
adding OOPSERandNumGen
Making small modifications to allow for use on MPI machines
adding MersenneTwister random number generator
Adding a modified version of MersenneTwister.hpp
adding soft potential to LJ Module
adding basic_teebuf which can operate on multiple stream simutaneously.
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
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()
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 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
fix a bug in loading initial extended system parameters
forget to set maxIterNum_ in NVT
remove WATER.cpp
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
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
formatting
port to SGI platform
remove useless debug info
minor fix
LinearVisitor get fixed
merging new_design branch into OOPSE-2.0
fix another bug in WATER.cpp
fix a bug in WATER.cpp when initializing the new Charge AtomType
improved restraints - mpi should work fine
improved restraints
Improvements to restraints
Fixed a mixing list bug that slowed down the force loop
working towards parallel restraints
Commented out some write statements
Got rid of some write statements
Added the linear visitor
current status of the debugging process
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
Shapes looks like it's working
still debugging
shapes rcut calculator added
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
fixed duplicate declaration foo
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
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
more work in Snapshot
Dear god! It runs and conserves energy!
strDUP not strCOPY
fixey fixey the breakey breakey
fixey fixey
Added un-busticated fortran files and c/Fortran interfaces
More on AtomType and DirectionalAtomType
Adding AtomType
Snapshot and SnapshotManager in progress
Breaky Breaky. Fixey Fixey.
remove some junk files
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
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
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
implement more test cases
more tests on math library
fix some bugs in Quaternion class
Your basic run of the mill real-valued versions of Y_l^m(\theta, \phi)
Working on getting Shapes into OOPSE
Added ShapeType
adding generic factory and vector test case
math library in progress
add quaternion class
fix a bunch of bugs
change const_cast to statc_const
fix a bug in basic_ifstrstream.hpp
fix include
fix incompatible declaration in jacobi
add checkFilename Option
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 RectMatrix
refactory vector and matrix classes
Remove some Makefile.in
add Vector3d.hpp and Matrix3x3d.hpp
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
moved the getopt stuff
more build fixes
Chris doesn't know about the OOPSE-2.0 directory structure yet
made the file reading in restraints more intelligent - no longer gives uninformative seg faults
cleaning up
Cleaning up a bit
move mpiSimulation_module to DarkSide
Started work merging shapes
define DEV_ROOT as relative path
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
move fortran files around to solve dependency problem
*** empty log message ***
add yacc and lex rules
change the #include in source files
Import of OOPSE v. 2.0