final version

Figure added

Add one more file into Makefile.in

Now enthalpies of formation

Added black and white version's of figures

typed up the lipid section

Ran iSpell

More discussion of the orientational results as well as a description of the
experimental tau_2 calculation.

little changes, added the start of the conclusion.

fixed .bib file problems

added in the RSA paper to the dissertation

little fixes

finished putting equations in Introduction
added an euler rotation scheme picture

to avoid cyclic depency, refactory constraint class

ran spellcheck

added a shifted potential figure

updated the two figures in the introduction

Adding GoldenSection and Brent LineSearch Method

using class  Minimizer1D derived from MinimizerBase instead of a functor to do line seach

member list fixes for rigid bodies

Revision of NLModel0 and NLModel1

Added point-charge models to water.mdl file, updated ssd.bass to use
new SSD name

Longer run time to test SSD water in MPI

Longer run time to test argon

More BASS changes to do new rigidBody scheme

Changes to BASS reader to use Euler angles for orientation instead of
unit vectors required changes in MoLocator

Convert Eulers in degrees into radians

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

added in the last bit about symplectic integrators and the liouville formulation

added changes to the introduction

Corrected spelling in several directories, and stated WATER.cpp

added periodic boundry conditions citation

added changes into the Empirical Energy section

Adding energy minimization

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ran spell check, and fixed some little typos

worked listing schemes into the document

Adding warning if sample time, status time, thermal time and reset time are not divisible by dt

Added a bunch of dummy targets so make won't complain

BASS changes to add RigidBodies required a change in
how the MoleculeStamps are used by divideLabor in mpiSimulation.cpp

added in changes to the Monte carlo andMolecular dynamics section

forgt to add these earlier

fix a bug in creating eor file

fixed an struct mismatch error in the mpi initialization of the AtomStruct

Changes for altivec

changes for charge charge interactions

autoconf fixes

autoconf compatibility changes for icc8

Some changes for new MPI organization and direct charge-charge interactions

Energy Minimization method

open and close the eor file whenever it is used instead of rewinding it

change the interface of writeFrame

More typo fixes.

added new revisions

revision

Dumpwriter only write out the atoms on master nodes

added the cover letters

remove extra files

tagub is not a bug. Just roll it back
fix a bug of copying string to a pointer
Still have Seg fault, it looks like a random MPI seg fault in totalview

rotated the lipid figure

added eam to the Emperical Energy

New DumpWriter (Attempt #4)

added some work on the Introduction chapter

null terminate some strings just in case

added strncpy to DumpWriter

Added rigid body discussion and added to .bib file...

added support for the ignore XS state info  flag

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started adding some changes from before break

Making do_Forces a little more sane

Attempting to increase performance by reducing spurious function calls

mpich mucking

Added bitmask to do_forces property lookup

Fixes to profile code.

Another change for MPI in timing.

the profiling commands work now. Will start adding PROFILE ifdefs into the code

working on adding GofRtheta and GofRomega

additional work on randomBilayer

added some profile functionality

Fixed bug in parallel EAM. rho_row and rho_col were scattered into the same array. Unfortunately, MPI zeros the array between scatters so half of the sum was being lost. Fixed by added a temp array for column scatter, then sum loop over nlocal.

test commit...

Changes for gradients (to do minimizations)

edited the makefile to add randomBilayer to the build. Also move the random bilayer builder from
bilayerSys to randomBilayer

added a more verbose error message in SimInfo. Added a more informative error message in InitializeFromFile

Fixed a bug in SimInfo ordering of radii

Again, more color plots...

Fixes for rotation

Really added color figures.

Added Vectors

Considerable corrections to both text and figures from the previous commit.  Now in the true pre-print form.  This is the updated first draft.

added a routine to SimInfo.cpp to inline a min function.

Added support for compiling fortran without use of mpich modules. We use mpif.h instead.:

Fixed plots by including SSD1 data.  Made several images more condensed and
easier to read.  Begun altering text to match the new focus.

fixed the includes in the Make.dep

some work on trying to find the compression bug

added template stuff to the Maikefile template

Fixed bug that size(q0) was being queried before q0 was allocated.

fixed a stdlib.h include error

C++ compatibility for templates

compatibility fixes

did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.

Compatibility fixes

fixes for compatibility

replace c++ header stuff with more portable c header stuff
Also, mod file fixes and portability changes

Stuff for MOD support in other compilers

added routines for the sysbuilder to work with simSetup

put QuickBass, MoLocator, and latticeBuilder into a Builder Library
overhauled latticeBilayer into its own program. Removed sysBuild from the Makefile

New File

work on bilayer builder

added eam ForceField files to the init

fixed an eam mpi parmeter setup bug

added the init file to the makefile

added eam ForceField files to the init

added useInitTime to the BASS syntax.
   * useInitTime = false: sets the origin time to 0.0 regardless of the time stamp in the .init file
   * default=> useInitTime = true;

added the staticProps directory to the build list
for both configure  and configure.in

Fixed a plot (fullContours.eps had bad labels).

changed format to preprint article

removed the props directory, and moved everything over to staticProps

Fixed bug in calc_eam.

removed entahlpy from the statwriter and thermo.

changed the formating ogf the error statements in simError

added a function to get the maxCutoff

finishing up the constructs needed to get this program up and running

added mpif90 mod check back
same for conifig.in

fixed wrappers to extern "C"

added mpif90 mod check back

light change in syntax. no signifigant change.

cleaned things with gcc -Wall and g++ -Wall

fixes for configure

Added a bunch of Make.dep files to CVS

fix bug in calculating maxCutoff

Added zcons.tex

I must have changed something, but for the life of me I can't recall it...

Added the integrator.tex file with figure. This is the same as the ssdePaper, so it needs to be adjusted for the OOPSE paper. Also updated the oopse.bib file.

goofing off to test NPTf and NPTi

fixed a typo in the makefile.

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fixed ecr grow in SimInfo

fixed conserved quantity in NPT (Still some small bug)

NPTi appears very stable.

SSD portion of paper added (ssd.tex).

add conserved quantity to statWriter
fix bug of vector wrapping at NPTi

Added integrators to Makefile.in

Adjustments to the introduction.  Minor additions to the methods section.

Chris

First CVS commit.  Minor changes in the introduction.  More changes to follow...

Chris

updated the ChangeLog

added two new NPT integrators, they still need work.

a rough draft of the intial simulations

Added parallel section of paper.

fixed sprng problem

Changes to autoconf / configure method of configuring OOPSE

added resetTime to the Global namespace.

This is the paper that got scooped

added zConstraint types to the AtomTypes file.

added my J. Peter Grace fellowship.

added some text to DUFF, changed the preamble from two column to preprint format.

added the first functional parts of the PairCorrType Abstract classes.

fix bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to MPI_DOUBLE,
however, the corret type is MPI_INT. Therefore, when we turn on the
optimization flag, it causes a seg fault

added the disertaion bibliography

This commit was generated by cvs2svn to compensate for changes in r728,
which included commits to RCS files with non-trunk default branches.

set default force substraction policy to PolicyByMass

added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb.

commented out some print statements in Zconstraint

hard coding some system init into bilayer.sys

Use make_sprng_seed() to generate seed and check the seed which is specified by user at least contains 9 digits

changed the Makefiel a litle.

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added the lipid figure, and did some work on DUFF.

overhauled the makefile to build oopse.tex from the infiles rather than mess with includes.
Also renamed header and footer to preamble and bibEnd respectively.
make current has been replaced with currMake to tke a look at a single tex section.

added a currMake script to replace the make current

played a little with the headers in DUFF

user can setup seed in bass file now, if he does not specify any value for
seed, oopse will take the value of seconds of system time as seed

updated the Changelog.

added some bug fixes for setting the random number generator seed value.

bug fixed in ghost bend class

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Fixed sysBuild -bilayer works. Nanobuilder still broke.

started working on DUFF

Stable ZConstraint with average force substraction strategy

Added some profiling code -DPROFILE.

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fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.

formatting fixes and new atypes in LJFF

Added comment line for getgetopt.

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added harmonical potential to z-constraint method

Changed makefile to only build quicklate.

Arranged sysbuilder into a subdirectory. Fixed some of sysbuilder to work with new
atom allocation in libmdtools.

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changed the number of degrees of freedom to account for zConstreints

moved frameCount's functionality into DumpReader. also split props into staticProps and dynamicProps. (currently only have staticProps)

switched SimInfo to use a system configuration from SimState rather than arrays from Atom

added the main equations to the analysis section

edited the header to be a revtex style two column layout.

added a current.tex to allow for looking at your current work, just change the include to the current tex file

also seperated all header info into header.tex so that oopse.tex and current.tex will behave the same.

stable version of Z-Constraint

added z-constraint parameters to the globals

More bug fixes for eam.

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Added eam to simSetup and added changecutoffeam.

rewrote the makefiles a little to install two scripts for rendering

added a '-' to the formating of the pov output file.

also removed pov2anim from the project. It will be replaced with shell scripts

added the scan function to the DumpReader. It should now save the start of each frame in a vector.

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some initial changes to Dumpwriter and friends to accomadate random file access

fixed Initializefrom file to start the simulation from the time specified in the init file.

added DUFF lipid models to the AtomTypes file

Started work on a DumpReader

Changes for SSD/E

fixed spelling issue

Added massive changes for eam....

Fixed a the centering on the Periodic Box. Also corrected the y and z switch in the box vectors

More up to date version of EAM_FF

Started work on Hmat stuff to replace box Lengths

Fixed bug in updating mixing lists

more fixes for box changes

fixed a long lived bug in do_forces. Rrf was not being used in the neighborlist correctly. rcut was conssistently being set lowere than Rrf causing the dipole cutoff region to be to small. Also led to the removal of the taper region to buffer the dipole cutoff.

Fixes for the NPT ensembles

added KMol

added more command line arguments

Fixing  pressure tensor

removed old outdated code

removing get_vx

Bugfix in NPTim, fixes for NPTfm

Broken SysBuilder

Removed some debugging write statements

added get and set routines to Atom and DirectionalAtom

found a bug. Unit vectors were not being updated

Switched the bond in the force field back to constrained, to preserve energy

Starting to worry about all the strtok() calls in our code

Fixed hmat in DumpWriter (MPI) and eor.

Added nanoBuilder and a general Lattice builder.

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starting some work for xlate

This is the dp and read file

Removed Qmass

Fixes in NPTi migrated into NPTf

fixed box scaling

 cleaned up the dependecy scripts in the makefiles

Fortran flexi-BOX

working on adding the box matrix to everything.

Changed over the bonds to Harmonic bonds in the DUFF frc file

fixed constraints.

Fixes to NVT.  Check them!

Doing some work to debug the constraint code.

Most of the integrator and NVT seem to be working now.

slowly converting to new integrator and forcefield names.

 doing some work on SimSetup to clean it up / get it to work with the new Integrator.

Added Teng's parmeters fro the ghost Bend in TraPPE_Ex

some work on the integrator. ( incomplete)

mostly final version

fixed the left alignment bug. Bugger if I know what was causing it.

nothing major just some little changes here and there.

updated the logo a little as well as some of the colors

This commit was generated by cvs2svn to compensate for changes in r544,
which included commits to RCS files with non-trunk default branches.

currently modifiying Symplectic to become the basic integrator.

changed how NVT is now derived from Integrator

all seems to be working

doing some work to overhaul sysbuild.

Added bead lipid model to the sample directory

added the TailBead atom types to the TraPPe_Ex forceField

fixed up the TraPPE_Ex force field. there were some duplicate entries

added the utils subdirectory to the configure script

calculation of the pi

We update the Makefile.

 fleshed out all of the ideas we wanted to see in this interface.

 it is still not yet debugged.

Added binary extensions

This commit was generated by cvs2svn to compensate for changes in r516,
which included commits to RCS files with non-trunk default branches.

Added a quick readme, and Identified myself as the author

killing some files

killing misc . crap that shouldn't be inb the source tree.

added some stuff, and forgot to update. who knows whats different now.

i quick fix to th distance in the random bilayer builder

fixed up sysBuild to where it should now build our systems

bilayerSys and sysBuild both will build now. woot!

Added eam force files...

working on the system builder

 working on a system builder

added Ghost bends to the TraPPE_Ex forceField

fixed a memory bug in Fortran, where molMembershipArray was declared nLocal instead of nGlobal.

 added a globalIndex counter to Molecule

fixed a n mpi init bug in SimSetup. caused a miscalculation of nLocal.

added pentane to the alkane model file

fixes for NPT and NVT

Fixes for NPT / NVT

fixes for NVT

dt/2 fix in nvt

Changes to integrate the NVT and NPT ensembles

fixed a sign error in the radial portion of SSD.

Working on NVT

bug fixes

Fixed a bug caused by my experimentation

Added targetPressure to BASS

Bug fixes for simulation module rewrites

bug fixes to fortran wrappers

fixed a memory read bug in neighborlist

Fixes for ExtendedSystem

Added extended system header

renamed nvt to extendedsystem

fixed a possible call before initialize bug.

a few fixes to simError.h
also some fixes to Molecule.hpp

fixed some small things with simError.h

Added NVT file (very broken for now)

dipoles mostly work, but there is a memory leak somewhere.

more bug fixes....

Fixed bug with pot_local not zeroed.

bug fix in DumpWriter.cpp

fixed a bug where the Excludes were not being created properly

fixed long range interactions in Trappe

fixed a bug where excludes were not being initialized

Fixed a single processor segfault bug.

fixed a few more bugs.

 fixed the makefile

I have implemeted Molecules everywhere I could remember to.
will now attempt to compile.

finished conversion of TraPPE_ExFF to use Molecule

fixes for local->global atom numbering in MPI

Fixes to fileio for MPI

Making DumpWriter less dependent on sequence of atoms on the other
processors.  Node 0 now fires potatoes at other processors to get them
to send french fries back.

fixed a couple of the "static" bugs in  Atom and Exclude

Added Atom.cpp and Exclude.cpp

Make Atom.cpp able to add and delete ranges of atoms

I'm overhauling the molecule class to contain it's own bonds, bends, and torsions.

may god have mercy on my soul.

MPI stuff for passing out molecules

Fixes for Parallel thermalization

Fixed bugs with calculation of potential energy and temperature.

added dummy files to keep the build deirectories from being pruned.

moved tests to samples

Added makefiles in tests directories

little bug fixes here and there

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fixed bug where short range interactions were not being calculated.

removed some debug print statements

added links to the makefile in forceFields

Makefile fixes, directory re-org, autoconf fixes

Fixed makefile

Readme changes

Makefile fixes for depends

Bug fixes in TraPPE.
calc_LJ_FF.F90: Removed print lines.
TraPPE_ExFF.cpp: Fixed so idents are being set.

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Working on the Makefile

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Fixed bugs. Single version now runs w/o segfault. Still a conservation of energy bug.
do_Forces.F90: Fixed pot not being passed to do_pair.
neighborLists.F90: Fixed bugs in checkNeighborLists
atype_module.F90: Fixed bug with allocating atypes on each new_atype call.Now checks to see if atypes is null, then calles initialize(16).
vector_class.F90: Fixed some bugs with how MatchList was being allocated.

compiles and links. And promptly segfaults.

added GB

shed implementation of the Fortran interfaces.

brought force_globals back from the dead to fix circular references