OpenMD

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...

fixed a sign error

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).

added a gcc4.4 compatibility

added visitors

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.

mostly whitespace issues

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.

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

One more

modernizing some parameters

fixed some md-solvator over specificity, and an install bug

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

Cleanup of unit normal code in Triangle.cpp
SMIPD now call getUnitNormal instead of getNormal.

Added preliminary code for Alpha Hull calculation using qhull.
Added preliminary support to SMIPD to support Alpha Hull.
Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. 
Preliminary changes for shadow hamiltonian integrator.
Chages to md files so they will work in openMD. 

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

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.

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.

*** empty log message ***

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

*** empty log message ***

Many fixes for Charmm-type torsions.

Added more chamges to nanovol.

Added new config.h to deal with cgal.

*** empty log message ***

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.

*** empty log message ***

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.

*** 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

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.

*** 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.

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