Inversion fixes and amber mostly working
fixed a spurious visitor deletion
Many fixes
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
Cleaning up oopseformat and adding inversion terms
Hopefully md-solvator is done.
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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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
Added repeat box options to make larger systems
A bunch of minor changes to make MPI compilation faster than the double compilation we do now...
Adding new md2md utility program
Correcting a few typos
Adding GofZ.cpp
Adding GofZ.hpp
added stat2visco
fixed a few correlation functions
Added a few visitors
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.
Changes to do hydrodynamics modeling and to explain a diff file
Fixes for building.
Check CGAL and qhull defines
Many fixes for Charmm-type torsions.
Added more chamges to nanovol.
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Added volume calculation for hull.
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.
Bug fixes for non-declared objects
Removed nanorodBuilder.
Build change.
Fixed more bugs and removed more CGAL.
Removed nanorod builder from OOPSE.
Removed CGAL from OOPSE and replaced it with qhull.
Added Bond Order Parameter as a function of radius.
forgot a tolerance for simple cubic lattice magic number determination
fixed a bug in waterBoxer
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.
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.
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.
bug fixing Wigner 3-j import to C++
Code to run radial rcorr.
Adding support for radial rcorr.
fixes for BOP
Fix to makefile.
Histogram bin change.
Added support for nanoparticle density profile.
possible fix for unnormalized BO
Support for OOPSE RealType.
Changes to nanorod builder for new dump format. Changes to configure to test for new version of cgal.
more openbabel updates, also changing velocitizer to thermalizer to avoid a filename collision on case-insensitve file systems
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
bug fixes (still broken, however)
Following Rein ten Wolde article
more bug fixes
more changes to BOP and SH
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
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
removed extra file in Hydro.cpp
Changing utility programs to use the new file format
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
Adding more changes to orientational bond order parameter.
Beginnings of a order parameter.
Adding code for bond orientational parameters.
MPI thermodynamic integration works now.
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.
Fix a type promotion problem
replace double with RealType
fixes for Hydrodynamics
fixed an initialization bug of Hxy.cpp.
wrapping back to PBC by molecule instead of by individual atom
fixed the bugs of Hxy.cpp.
Adding single precision capabilities to c++ side
Autoconf fixes for FFTW. Multiple FFTW version support.
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Changes to calculate undulation spectrum
adding a gay-berne switch to Dump2XYZ
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
Many performance improvements
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More testing of nanoparticleBuilder.
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.
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
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.
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
Adding RoughShell and BeadModel
adding hydrodynamics module into build system
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
Changed Names of class files.
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Fixing a bug which reads the wrong frame of trajectory file during analysis
Adding visitor for GBlipid atom type
Adding :LegendrePolynomial
Changes to nanoparticle builder
Added Makefile for nanoparticle builder.
Removed MixingRule from Globals. Handled by forceField now.
fixed some version info and the copyright date
instead of printing to std::cout, throwing an exception when error is found.
fixing RhoZ
Changes to build twinned crystal
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.
compilation issue
adding support for soft linking
rename mdinConverter to atom2mdin
adding mdinConverter
nothing
Still had some globals toUpper problems - these changes should fix those...
rewrite Globals
Design change for nanoRod builder --twinned.
Added code for nanoparticle builder to cvs.
std::bind2nd is in <functional>
fixed a bug and ran a simulation
working version of DensityPlot
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.
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.
Couple of changes for TAP water. Need to parametrize.
More geometry builder changes.
Adding support for generic geometry to nanorodbuilder.
More changes to nanoRodBuilder....
Fixed issues with nanoRodBuilder....
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
nanorodbuilder now exit's when libCGAL is not present.
added CGAL checks
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
added lattice directory, so all of these files are now redundant
Changes to delete atypes...
Importing nanoRodBuilder application (may not work yet). ((Doesn't work yet.)) (((May never work....)))
forget to delete prepareVisitor in Dump2XYZ
fix a bug in getting the dimension of histogram
avoid building parallel executable for dump2XYZ, simpleBuilder, staticProps and dynamicProps
fix compilation issue
adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
adding MersenneTwister random number generator
adding basic_teebuf which can operate on multiple stream simutaneously.
Fix a bug in GofRAngle
adding LipidTransVisitor, GofXyz is working now
Updated copyright information
more bug get fixed
fix a bug in GofXyz
make processHistogram non-abstrct function
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finish GofXyz
change the output format of 2D radial distribution function
fix a bug in writing out the value of cosang
change the default bin number
change the suffix of output files;fix the problem of counting in staticProps
BlockSnapshotManager is using reference counting now
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
default length for staticProps is 1/2 smallest length of first frame
begin bug fix
refactory CorrelationFunction
bug fix and start of switch for type of correlation function
more fix
fixed a bug in CorrelationFunction
fixed a bug in SimInfo::getCutoff()
maximum length defaults to the cutoff radius
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
more work in StaticProps
change the filenames
adding GofRAngle
remove some useless files
staticProps in progress
adding GofR
update help info
update help info for Dump2XYZ
remove SelectionVisitor
dump2Xyz now take advantage of selection library
(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
moved Package variable into subdirectory makefiles to speed up the building process
Fixed publication details in banner
formatting
minor fix
merging new_design branch into OOPSE-2.0
Added the linear visitor
remove old Vector3d.hpp from application/simpleBuilder
STL next_permutation like next_combination is working
more build fixes
cleaning up
define DEV_ROOT as relative path
change Makefile to relative path
change directory structure of application. Every executable file is replaced in seperate directory
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change the #include in source files
Import of OOPSE v. 2.0