Import of OOPSE v. 2.0

ran ispell

better gofr and sofq

quick wording change

Included rhombahedral distortion comments

update figures

new sofk plots

bib changes

minor changes

Added reference

figure updates and whatnot

added a plot

changes

minor changes

Added references

Added figures

Added a figure and started in on the conclusions

Added figures and expanded results and discussion section

started methods section

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Fixed an algorithm error for thermodynamic integration with charges

Initial import of OOPSE sources into cvs tree

removing old copies of sysBuild

remove anonymous struct from Vector3d.hpp

First documentation in OOPSE!

Post-submission clean-up

add zconstraint samples

working version of simpleBuilder

Added two new figures

add function isAtomInRigidBody into MoleculeStamp

simpleBuilder in progress

SimpleBuilder in progress

edits done

refactorize Lattice class

change parameter of calling sprintf

BASS eradication project (part 3)

BASS eradication project (part 1)

Fixing required keyword annoyances

fixed an ifdef problem

warning message for nProcessors > nMolecules

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add init files

rename NVT.bass to argonNVT.bass

add butane.in

fixed typo

minimizer sample changes

remove beadLipid

remove TP4init.in

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remove SPCEInit.in

remove eor file from cvs tree at minimizer/water directory

remove beadLipid

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change names for argon

add init file for ssde

support SSD_E SSD_RF SSD1

remove ^M from ZConsReader.cpp

Made init files more OOPSE like.

added sample directory

Added tip3p_ice to Makefile

Added sample files for bulk metals and a bass file for both voter and FBD formulations of EAM.

Fixed a bug where eor file wasn't being written at the end of the run

cleaning up for export

removing staticProps from cvs tree

using gengetopts --unamed-opts="SHAPEFILE [OUTPUTFILE]"

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change protected method writeCorrs to public

minor fix of format string in quicklate.c

remove some comment lines

Shouldn't have been in CVS

These can be generated via lex and yacc at compile time

changes for gnu getopt and fixed SPRNG configure script

Makefiles don't belong in cvs repository

Makefiles don't belong in repository

tip4p makefile.in added

ssd files sorted added

dimer files added

Initial import of OOPSE-1.0 source tree

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Minor changes

Added the SPC water model

Added TIP4P water sample

Good ssde simulation sample added

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Added C70 sample

added SHAPE force routine

Got rid of the _RB_0 in the shape name

started functions

Setting up shaper to accept a tolerance

Added 2 new samples

Fixed the phi grid range for the final time (hopefully)

Really fixed the phi range problem.  Apparently s2Kit10 has a data in ordering problem

Fixed the pdb files

Added cholesterol

Fixes for visualizer for amira

Shape file output format adjusted

got rid of sample PDB files.  Others will be added later in samples directory

Removed some unnecessary C functions from the SHT code

Spherical harmonic tranformations are fully integrated and working

Adding visualization parts

touch up changes

Now prints out a .xyz file of the reference configuration

roll in progress

Fixed the grid builder rotation problems

Fixed XCode auto-indent to match XEmacs

GridBuilder updates grid vectors

Cleaned up unused variables.  Added findMaxExtent to RigidBody.cpp

bug fix on vdw files

configure isn't really necessary

nicer error message formatting

roll in progress

General fixes for formatting

changing file extensions to be more in line with what's actually
in the file

Modified EAM to use forceFieldVariant, show sample in Au.bass

Added forceFieldVariant global

Fixed a thermodynamic integration issue.  Force and torque scaling loops over atoms, not stuntdoubles

Fixed indexing bug in stamps

1. adding some useful math classes(Mat3x3d, Vector3d, Quaternion, Euler3)
 these classes use anonymous union and struct to support
 double[3], double[3][3] and double[4]
2. adding roll constraint algorithm

Fixes from gcc -Wall

small bugfixes

constraint algorithm for minimization is working

Moved to SHAPES

Migrated vdw files from OOPSE

forcer was a binary

More work on Fortran side of error handler

Unifying the error handlers

forgot to add these

Config changes for fortran access to SimError

fixed a bug which only writes out the first atom of a molecule

Fixed groupOffset bug

Shouldn't have been in CVS

Why is this in CVS?

starting fortran-usable version of simError

Formatting Changes, removed writeRaw

Bug in Makefile.in

Bug fix (fixes of skipList and neighbor list under MPI)

Testing

Fixed bug in useLiquidThermInt routine in ForceFields.cpp

cutoff group in progress

Paving the way for separate solid and liquid thermodynamic integration routines

Fixed a bug in Integrator.cpp where it called writeRaw() when useThermInt = false...

Makefile doesn't belong in CVS

Cutoff group changes under MPI

groupList new bases on global index of atoms

Fixed off-by-one error in groupStartRow and groupStartCol

Compacted all of the 8 copies of the force loop into one.

pressure tensor fixes

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Fixed an error in Restraints.cpp...  Too many arguements in a function call.

Fixed Thermodynamic integration code.

Got PDB reading working, and matching atom types too!

Changes for SHAPES potential

Several additions... Restraints.cpp and .hpp were included for restraining particles in thermodynamic integration.  By including these, changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, StatWriter, and possibly some other files.  Two bass keywords were also added for performing thermodynamic integration: a lambda value one and a k power one.

fixes for skip list

add minimizer sample

Fixes for compilation under Mac OS X with IBM's xl compilers

Removed an extraneous write

const char* fix

added more revisions to the paper

efficiency fixes in CutoffGroup

fixed a bug in CutoffGroup::getCOM()

adding generic Vector3 class

Fortran-side changes for group-based cutoffs

fix two bugs in siminfo which cause infinite loop; fix anoter one in CutoffGroup which causes seg fault

bugfix for cutoffGroup

Fixes to libmdtools to use the simplified cutoff stuff in the BASS library

optimize DumpWriter

Many changes to get group-based cutoffs to work

added more tables

adding to the table

C++ pass groupList to fortran

fix an unmatched c/fortran interface

fix a bug in Molecule.cpp which initialize massRatio before creat the array.
fix two bugs in ZconsVisitor

work on molecular cutoffs

add center of mass of the molecule and massRation into atom class

finished removing the trajectory analysis.

took out the rattle derivation.

added a section concerning the creation of init files.

currently working on a table of key words for the package.

add reaction field correction to charge-charge interaction

fixed another bug in InitFromFile. MPI verion of OOPSE is working again

remove some useless files

DUMP2XYZ 0.99 version

forgot to add this

finished cleaning up the old tex files

fixed a bug in CompositeVisitor which cause the double counting problem

new implement of quickLate using visitor and composite pattern

fix a bug in setting exclude list

updated all equations, and finished all requested revisions

some more updates.

Added the WATER.frc force field

Change DumpWriter and InitFromFile

returned the referencess to the thesis layout, and fixed the equation grammer in the Introduction

Now molecules can keep track of their own IntegrableObjects (and
RigidBodies).  Also a bug-fix so that SimInfo can keep track of
RigidBodies (which was done incorrectly before).

Oops.  Those were old.

Adding RigidBody code

Slightly longer test run

added a makefile

more gcc friendly configure script

added lst styles, and some preliminary fixes to the intro.

final draft submitted to the readers.

added revisions to the Preamble and to the Introduction

added support for files larger than 2 Gb

making progress on the results section

NPTf complete, NPTxyz complete

added gofz code

add LARGEFILE_SOURCE64 macro to support large file

more changes for integrators

Adding zsub, a program which can be used to replace atom type for zconstraint into OOPSE

started work on rmsd

switched params for tcR systems

halfway through revisions in OOPSE

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Using inherit instead of compose to implement Minimizer
both versions are working

debugging the director code

added scd correlations, and director and order parameters for the head groups

finished up the rough draft of tcProps with Scd corr

lmost finished with the readWrite routines

started some cleanup on oopse. added a conclusion, finished the foreword, and found all the undefined citations

started on som io

little changes in the twoChain figure

This commit was generated by cvs2svn to compensate for changes in r1047,
which included commits to RCS files with non-trunk default branches.

added a lipid figure. started converting oopse.tex

 started a bug fix on the massive memory overusage by OOPSE

Stripped out the hardwired LJ_rcut

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added a new euler fig, and fixed some things in the degeneractyy section

Single version of energy minimization for argon is working, need to add constraint

I hate revtex

Add some lines into global.cpp to make it work with energy minimization

Changes in response to JCP reviewer

More corrections and fixing of experimental numbers

Fixed a reference

Fix a bunch of bugs   :-)
Single version of conjugate gradient with golden search linesearch pass a couple of
functions test. Brent's  algorithm is still broken

started work on the complete project. Made a makefile, and added preambles

Further improvements. Discussion of the results in the table was added.

Adjustments made based on reviewer recommendations. These include an expansion
of diffusion data as well as inclusion of a table containing heat capacity,
coordination number, and orientational relaxation information.

NLModel0, NLModel1 pass uit test

added the new figure into the Introduction

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added some equations

Functor.hpp pass unit test

begin unit test of minimizer

added some figures to the Intro. Also lots of equations

finished typing in the intro, and started on the lipid chapter

Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...

Adding MinimizerParameterSet class.

revision of NLModel

Fix to new RigidBody stuff

Longer run time to test gold in MPI

More BASS changes to do new rigidBody scheme
a copy of WATER.cpp from this morning

revision of constraint for Nonlinear Optimization Model

Changed orientation lines from unit vectors to euler angles

Changed default orientation in BASS to use Euler angles in the
following order: phi, theta, psi
Removed the ability to set orientation using a unit vector

Fix broken atom assignment for rigid bodies

a few corrections to the introduction

started adding in equations to the introduction

constraint class in energy minimization

minor corrections to the previous commit

started work on the lipid chapter

Energy Minimizer

Corrected .bib file entries

Made some error messages more user-friendly

Updated the default water to SSD/E

Adjusted the SSD part of the paper...

Fixed old bass file

BASS changes to add RigidBodies and LJrcut