Change NumericConstant
minor fix
io get built, next is integrator
brains get built
new plot and some text alterations
brains get built, io is next
fix Thermo
more get fixed
rename LocalndexManager.hpp to LocalIndexManager.hpp
Section Parsers get compiled
minor fixed
minor fixed
#inlcude statement can not be embedded
add PolynomialTestCase
Polynomial passes unit test
rename QuarticTorsion.hpp to QuarticTorsionType.hpp
add CubicTorsionType and QuarticTorsionType
more file get fixed
add Trim Algorithm for std::string
remove some useless files
more files get fixed
part of io get built
types get built
types get built
rename some files
rename some files
more get built
UseTheForce get built
types and primitives get built
Addint StringTokenizerTestCase
StringTokenizer passes unit test
change Makefile
improved restraints - mpi should work fine
improved restraints
oops...
add SetForceManager method to integrator
refactory NPT integrator
Back to normal... Oh... Restraints should work in parallel now
Improvements to restraints
just some testing changes, I'll return to the original on next commit
add Electrostatic AtomType Section Parser
add EAM AtomType Section Parser
add BondTypesSectionParser, BendTypesSectionParser and TorsionTypeSectionParser
minor change in DUFF and EAM
adding section parsers
adding section parsers
remove more useless files
remove more useless files
refactory integrator
new DUFF forcefield
add EAM
DUFF is almost done except error checking
DUFF is almost done except error checking
adding DUFF parser
adding DUFF parser
adding new format DUFF force field
Fixed a mixing list bug that slowed down the force loop
Adding NumericConstant class
remove more junk files
remove some junk files
refine QudraticBond
add QuadraticBendType.hpp
UreyBradleyBend and GhostBend
more types stuff and Chebyshev Polynomial
add PolynomialBondType, PolynomialBendType, PolynomialTorsionType, HarmonicBendType and CharmmTorsionType. Need to refine the design and add document for them
add PolynomialBondType
Adding Polynomial class
added some new stuff
BondType, BendType and TorsionType
adding DUFF class; adding checking statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
adding ForceFieldFactory and LJFF classes
finish DumpReader, DumpWriter.Next Step is LJFF and integrators
refactory, refactory, refactory
bug fix in hasMoreTokens
adding StringUtils, a c-style strtok like class, need unit test
SimCreator and SimInfo are ready for unit test
MoleculeCreator forget to create CutoffGroups for free atoms
OOPSE = Object-Obfuscated Parallel Simulation Engine
working sample
working towards parallel restraints
Commented out some write statements
Got rid of some write statements
Fun with ice
add Snapshot.cpp, remove useless mpiSimulation
more work on SimInfo
another painful day (1) SimCreator, SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom File will be removed) (3) ForceField (at least LJ) and BondType, BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint
add a configurable StatWriter
mpiSimulation in progress
adding ForceManager
More to break
adding ForceField and TypeContainer classes
Fix Exclude class etc.
Added the linear visitor
current status of the debugging process
This commit was manufactured by cvs2svn to create branch 'new_design'.
included visitors and minimizer
new changes
Pain......
time to break SimSetup
added new classes in progress
adding Stats class
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
testing force fields
testing shapes
Adding SimCreator class(similar as SimSetup)
ForceFiled get compiled. Still a long way to go ......
mess up ......
Adding LocalIndexManager and Migrator. Need unit test
SimModel in progress
Shapes looks like it's working
adding MemoryUtils which provide some functions for dealing with memory issue
adding SimModel(something similar as SimInfo)
Molecule, Atom, DirectionalAtom, RigidBody and StuntDouble classes get compiled
add initial version of Bond, Bend and Torsion.
adding BondType, BendType, TorsionType
break, break and break.....
these core classes get compiled
more work on Molecule class
still debugging
shapes rcut calculator added
shorter run
rewrite Molecule class.
Remove some deprecated files
More painful reconstruction is coming !!!
This commit was manufactured by cvs2svn to create branch 'new_design'.
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
forgot the orientation line
fixed duplicate declaration foo
uncommented .in line
next_combination in progress
adding next_combination test case
STL Compatible combination sequence generator
bug fixed in GenerateCombination.hpp
a STL next_permutaion like next_combination function.
no message
ReplaceWildCard(recursive version) is working, need refactoring. An iterative version is on the way
ReplaceWildCard in progress
Adding Test Case for ReplaceWildCard
adding ReplaceWildCard.hpp, need test
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
adding sample shape directory
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
Refactoring in progress
more work in Snapshot
Dear god! It runs and conserves energy!
strDUP not strCOPY
fixey fixey the breakey breakey
compiler flags
fixey fixey
Added un-busticated fortran files and c/Fortran interfaces
More on AtomType and DirectionalAtomType
Adding AtomType
Snapshot and SnapshotManager in progress
adding test case for Snapshot and snapshotManager.
Breaky Breaky. Fixey Fixey.
remove some junk files
remove backup of GenericData.hpp
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
adding generic data test case
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
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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
fix some bugs in RectMatrixTestCase
implement more test cases
more tests on math library
adding more testing units
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 vector test case
adding generic factory and vector test case
math library in progress
add quaternion class
adding test file
fix a bunch of bugs
change const_cast to statc_const
fix a bug in basic_ifstrstream.hpp
forget to use namespace oopse
Changed optimization flags for XLF and XLC.
adding ifstrstream test case
fix include
fix incompatible declaration in jacobi
adding Makefile
adding test case for ifstrstream
add ifstrstreamTestCase
add checkFilename Option
add SquareMatrixTestCase class
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 testing unit
adding RectMatrix
refactory vector and matrix classes
Remove some Makefile.in
add Vector3d.hpp and Matrix3x3d.hpp
adding c++ coding style
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
fix a bug in filepp
using filepp to generate dependencies instead of compilers
filepp can be used to generate dependencies for c/c++ now
Minor additional rephrasing
remove -module from F90Options
adding rules to move fortran 90 module to target directory
fixed makefile.in
remove "use bytes" which causes problem in sgi machine
add Makefile
fix Makefile under water directory
remove argon.dump and argon.eor from Makefile
Remove some Makefile.in
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fix make install
adding make install
add Makefile to sample directory
fixed some numbers and changed some wording
moved the getopt stuff
more build fixes
adding doxygen configuration file
filepp can handle different fortran module case and suffix
Chris doesn't know about the OOPSE-2.0 directory structure yet
Yeah yeah, we'lll get around to it later
cleaning up build process
made the file reading in restraints more intelligent - no longer gives uninformative seg faults
Made the file reading more intelligent in Restraints. No longer gives uninformative seg faults.
cleaning up
Cleaning up a bit
fix make statistics
adding GNU make functions to combine all of the static libraries to a big library
preparing for better cutoff plots
adding shared library flag
move mpiSimulation_module to DarkSide
building MPI version;using static library instead of shared library
pass __FORTRAN90 instead of __F90 to filepp
add make cvslog
more work on the parallel build
changes to backport declare flags
Started work merging shapes
remove sfmakedepend from cvs tree
add oopse_ as library prefix
fix a space trimming bug in filepp
A few minor build changes
adding fortran90 make dependency tool
make clean is smart enough to only remove object files belong to current package. turn off silent mode
define DEV_ROOT as relative path
get the relative path by shell script
eliminate DEV_ROOT by relative path
add PackageLibs; fix dependency rule
updates
Working on make stuff
If makefile does not exist, print error message
fix dependencies rule
still working on build process
add print statment to rules
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
Keep that lib around, please.
starting a configure version
move fortran files around to solve dependency problem
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fix fortran dependency problem
add yacc and lex rules
adding include path to F90Options
change suffix from .cc to .cpp
change the #include in source files
This commit was manufactured by cvs2svn to create tag 'OOPSE_REWRITE'.
Import of OOPSE v. 2.0
fixed some table wonkiness
ran ispell
fixed grammer in abstract
better gofr and sofq
updated image and a little text change
quick wording change
Fixed a char italic issue
Included rhombahedral distortion comments
another fig update
update figures
changes to last bit
new sofk plots
changes for packet
bib changes
changes
minor changes
fixes in error values
Added reference
Considerable changes to content and references
figure updates and whatnot
changes
added a plot
Added gofrs and refs
changes
changes
minor changes
some changes
Added references
Minor corrections
Added figures
Added an introduction
Added a figure and started in on the conclusions
More results and discussion
Added figures and expanded results and discussion section
updated bib file
started methods section
Thus starts the free energy ice i paper...
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Restraint loop is now more versatile
Fixed an algorithm error for thermodynamic integration with charges
minor fix
This commit was manufactured by cvs2svn to create tag 'public'.
Initial import of OOPSE sources into cvs tree
removed antique code and fixed linking problem
removing old copies of sysBuild
refine Vector3d.hpp
remove anonymous struct from Vector3d.hpp
change butane.md
First documentation in OOPSE!
added zcons directory
Post-submission clean-up
add Makefile.in into zcons
add zconstraint samples
simpleBuilder version 1.0
working version of simpleBuilder
Added Water.frc discussion, improved the integrator section, added references
Added two new figures
simpleBuilder is built but Makefile is broken
add function isAtomInRigidBody into MoleculeStamp
add getForcefiled into simSetup
simpleBuilder in progress
new updates
SimpleBuilder in progress
Added utility functions to grab the mass from the force field.
edits done
add simpleBuilder
refactorize Lattice class
Forgot to add them
change parameter of calling sprintf
BASS eradication project (part 4)
BASS eradication project (part 3)
BASS eradication project (part 2)
BASS eradication project (part 1)
better error messages
Fixing required keyword annoyances
Fixing ifdef lines
fixed an ifdef problem
Install procedure modifications
warning message for nProcessors > nMolecules
modify 5x5.bass
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add init files
add init file
rename NVT.bass to argonNVT.bass
add 5x5.in
add butane.in
changed minimizer keywords
fixed typo
fixed sample makefile
minimizer sample changes
removed beadLipid
remove beadLipid
Added core-shell nanoparticle files.
remove TP4init.in
change init file name for tip4p and tip3p_ice
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change init file name for ssd
remove SPCEInit.in
change names for init file
remove eor file from cvs tree at minimizer/water directory
change init file name in lipid directory
remove beadLipid
remove init_argon.eor
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remove eor file
change names for argon
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add init file for ssde
Fixed bug in calc_eam with mixtures and cutoffs associated with mixture.
support SSD_E SSD_RF SSD1
SSDVisitor support SSD_RF, SSD_E, SSD1 now
remove ^M from ZConsReader.cpp
remove unsupport keyword
Made init files more OOPSE like.
Changed init files to be more OOPSE like...
added sample directory
fixed icc7 incompatibility in linking
Added tip3p_ice to Makefile
Added more metal sample to OOPSE for bulk simulations.
Added sample files for bulk metals and a bass file for both voter and FBD formulations of EAM.
Checked a bug where eor file wasn't being written at the end of the run
Fixed a bug where eor file wasn't being written at the end of the run
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cleaning up for export
removing staticProps from cvs tree
removing staticProps from cvs tree
removing static props from OOPSE-1.0 tree
using gengetopts --unamed-opts="SHAPEFILE [OUTPUTFILE]"
Changes for CGI and for gengetopts --unamed-opt="PDBFILE"
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fixing getopt_long
change protected method writeCorrs to public
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minor fix of format string in quicklate.c
remove zsub from cvs tree
remove some comment lines
remove an extra semicolon from OOPSEMinimizer.hpp
Shouldn't have been in CVS
Fix for thermodynamic integration of rigid bodies
These can be generated via lex and yacc at compile time
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changes for gnu getopt and fixed SPRNG configure script
fixing for machines that don't have lex and yacc
Makefiles don't belong in cvs repository
Makefiles don't belong in repository
Makefiles don't belong in repository
Updated configure for new samples
tip4p makefile.in added
ssde makefile.in added
ssd files sorted added
spce makefile.in added
dimer files added
Cleaned up this file considerably
This commit was manufactured by cvs2svn to create tag 'export'.
Initial import of OOPSE-1.0 source tree
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New web address
Minor changes
Expanded the water.mdl file
Added the SPC water model
quick change in tp4.bass
Added TIP4P water sample
Added SPCE water sample
Good ssde simulation sample added
Fixes for MacOS X with xlc++ and xlf
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Added a bunch of stuff
Added C70 sample
fixed a bug in Mat3x3d.cpp
added SHAPE force routine
fixes
Got rid of the _RB_0 in the shape name
Added a range parameter to the visualizer
started functions
Tolerance input is accepted with the -t flag (default 0.01)
Setting up shaper to accept a tolerance
Recentering of the visualized potentials, adding tolerance option
Added 2 new samples
Coefficients are now multiplied by the normalization factor - no longer do we need normalization in the visualizer
Fixed the phi grid range for the final time (hopefully)
atan2, not atan!
Really fixed the phi range problem. Apparently s2Kit10 has a data in ordering problem
Changed gridbuilder phi range to run from pi/2 to 2pi+pi/2
Fixed the pdb files
New cholesterol.pdb
Added cholesterol
More samples added
Fixes for visualizer for amira
work on visualizer
Shape file output format adjusted
Added a few samples
got rid of sample PDB files. Others will be added later in samples directory
renamed forcer, modified factorial, fixed makefile
Removed some unnecessary C functions from the SHT code
Added more friendly progress comments
Spherical harmonic tranformations are fully integrated and working
Added evaluation stuff
Adding visualization parts
Fixed linking specification issues
touch up changes
Major progress towards inclusion of spherical harmonic transform capability - still having some build issues...
Now prints out a .xyz file of the reference configuration
Fixes to gridbuilder. Now gives proper sigma, s, and epsilon values
roll in progress
a few bug fixes
Fixed the grid builder rotation problems
Now calculates energies and builds the grid files. There are still bugs, but it compiles and runs...
Fixed XCode auto-indent to match XEmacs
Built principle axis determination and molecule rotation into calcRefCoords in RigidBody.cpp
GridBuilder updates grid vectors
Added GridBuilder.cpp and .hpp. Doesn't calculate energies yet...
Cleaned up unused variables. Added findMaxExtent to RigidBody.cpp
Added a bandwidth command-line option
bug fix on vdw files
fixed a subdirs bug
configure isn't really necessary
Major changes for rigidbodies
nicer error message formatting
Fixed dependency bug (we hope)
roll in progress
Sample now does variant
General fixes for formatting
Converted D's to E's in the funcfl files so that C can read them.
changing file extensions to be more in line with what's actually in the file
Added a bunch of files for EAM variants
Modified EAM to use forceFieldVariant, show sample in Au.bass
Modified EAM to use forceFieldVariant
Added forceFieldVariant global
reorg of EAM force fields to have variants
Fixed a thermodynamic integration issue. Force and torque scaling loops over atoms, not stuntdoubles
Removed debugging printf statements
Fixed indexing bug in stamps
Roll in progress
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
Fixed a bug in NPTf (vScale was declared in the cpp file in addition to the declaration in Integrator.hpp file)
Fixes from gcc -Wall
Dan cleaned up the pressure calculation a bit... Got rid of some unnecessary lines of code in Thermo.cpp
small bugfixes
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constraint algorithm for minimization is working
Fixes
Moved to SHAPES
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Migrated vdw files from OOPSE
fixing for a separate existence
forcer was a binary
This commit was manufactured by cvs2svn to create tag 'SHAPES'.
Initial import of SHAPES code
More work on Fortran side of error handler
fixed a typo in autoconf script
Unifying the error handlers
Not used anymore
forgot to add these
new rattle algorithm is working
Config changes for fortran access to SimError
new implementation of constraint
fixed a bug which only writes out the first atom of a molecule
SHAPES go somewhere else
Fixed groupOffset bug
Working on MPI scripting for autoconf
Shouldn't have been in CVS
keep the compilation directories around
Why is this in CVS?
formatting error messages, dependency fixes
starting fortran-usable version of simError
Probably shouldn't be in CVS
Formatting Changes, removed writeRaw
Formatting Changes
Bug in Makefile.in
severity levels in simError
Bug fix (fixes of skipList and neighbor list under MPI)
Bug fix (memory leak)
Testing
Cutoff Groups for MPI
Fixed bug in useLiquidThermInt routine in ForceFields.cpp
Implemented a separate solid and liquid thermodynamic integration routines
cutoff group in progress
Added useLiquidThermInt keyword and changed useThermInt to useSolidThermInt
Paving the way for separate solid and liquid thermodynamic integration routines
bugfix starting
Fixed a bug in Integrator.cpp where it called writeRaw() when useThermInt = false...
Bug fix for SkipList
Makefile doesn't belong in CVS
bugfix in simsetup?
Cutoff group changes under MPI
Fixes for xlc++
groupList new bases on global index of atoms
Modified the nifty banner
Fixed off-by-one error in groupStartRow and groupStartCol
in the progress of fixing MPI version of cutoff group
Compacted all of the 8 copies of the force loop into one.
std::cerr missing
pressure tensor fixes
Removed unnecessary variables and changed error messages in Restraints.cpp
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Fixes for stress / pressure tensor by cutoff group
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Fixed an error in Restraints.cpp... Too many arguements in a function call.
Added Bass keyword useThermInt.
Fixed Thermodynamic integration code.
This commit was manufactured by cvs2svn to create tag 'r1'.
this is the ripple codes
Got PDB reading working, and matching atom types too!
Major changes to skipThisPair for efficiency
Changes for SHAPES potential
Hopefully this commit included the bass keywords
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.
more revisions
fixes for skip list
add some keywords
add minimizer sample
fixes for MacOS X compilation
Fixes for compilation under Mac OS X with IBM's xl compilers
Added a nifty neato banner
Removed an extraneous write
Starting to change the error model
const char* fix
MPI fixes and removal of extraneous write statements
added more revisions to the paper
get rid of rc and massratio from simState, creat cutoff group forevery atom which does not belong to cutoff group defined at mdl file
efficiency fixes in CutoffGroup
Added the cutoff Groups to the default water.mdl file
fixed a bug in CutoffGroup::getCOM()
bug fixes for cutoffGroups
adding generic Vector3 class
adding instantiation of Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8
Fortran-side changes for group-based cutoffs
adding CutoffGroup.hpp
fix two bugs in siminfo which cause infinite loop; fix anoter one in CutoffGroup which causes seg fault
adding cutoffGroup into OOPSE
bugfix for cutoffGroup
starting to rearrange the prose after the intro.
Fixes to libmdtools to use the simplified cutoff stuff in the BASS library
BASS changes for adding CutoffGroups to molecules. Also restructured the plethora of cutoff radii into one cutoffRadius and one switchingRadius. Also removed the useMolecularCutoffs keyword
optimize DumpWriter
New module for fortran group-based switching function
Many changes to get group-based cutoffs to work
added more tables.
added more tables
added in all of the general global keywords. Still need to add the zConstraint and minimizer keywords.
adding to the table
adding a separate file to work on the bass keywords.
C++ pass groupList to fortran
fixed two bugs in calc_charge_charge when using molecular cutoff
fix an unmatched c/fortran interface
keep the previous position of cantilever in SMD
fix a bug in Molecule.cpp which initialize massRatio before creat the array. fix two bugs in ZconsVisitor
Adding molecular cutoffs
work on molecular cutoffs
useMolecularCutoffs added to Globals
add center of mass of the molecule and massRation into atom class
modified the defaults for the system init time and system init state.
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.
Fixed a bug in calc_charge_charge.F90
add reaction field correction to charge-charge interaction
change the calculation of pressure tensor
fixed another bug in InitFromFile. MPI verion of OOPSE is working again
fixed two bugs in MPI version of InitfromFile and one unmatch MPI command in DumpWriter
remove some useless files
fixed getCOMVel and velocitize at thermo
DUMP2XYZ 0.99 version
Fixed a charge bug
forgot to add this
fixed the makefile, and fixed some visuals on the schemes
finished cleaning up the old tex files
Just copied over the changes from the dissertation. Also converted the figures to pdf. All revisions now take place on the oopsePaper.tex file
fixed a bug in CompositeVisitor which cause the double counting problem
Dump2XYZ is almost working except atoms in rigidbody are double counted
new implement of quickLate using visitor and composite pattern
final final copy. really really sent to the printers this time.
fix a bug in setting exclude list
final copies sent to the printer
updated all equations, and finished all requested revisions
fix whole bunch of bugs :-)
some more updates.
revised the diffusion numbers.
Added the WATER.frc force field
fixed for get_potential
Change DumpWriter and InitFromFile
some more minor fixes
returned the referencess to the thesis layout, and fixed the equation grammer in the Introduction
started on some revisions
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).
Added Integrable (will back out momentarily)
Oops. Those were old.
Forgot to add IntegrableObjects
Adding RigidBody code
Changes for RigidBody dynamics
Slightly longer test run
Changes for RigidBody dynamics (Somewhat extensive)
added a makefile
more gcc friendly configure script who knows
more gcc friendly configure script
incorporate SMD into ZConstraint,it does not sound a good choice, next commit will seperate SMD and ZConstraint
added lst styles, and some preliminary fixes to the intro.
ZConstraint now can support sequential moving. Refactorying is needed to support SMD in ZConstraint
final draft submitted to the readers.
final draft submitted to the readers.
added revisions to the Preamble and to the Introduction
semi-final draft
added support for files larger than 2 Gb
who knows?, but it works for the most part
making progress on the results section
added several figures to the lipid paper, changed the ndthesis class around a little. some small fixes in oopse.
NPTf complete, NPTxyz complete
NPTi complete
added gofz code
NPT work in progress
add LARGEFILE_SOURCE64 macro to support large file
More DLM changes
more changes for integrators
Fix a couple of bugs in zsub
Adding zsub, a program which can be used to replace atom type for zconstraint into OOPSE
finished the rmsd coding. hasn't been debugged
started work on rmsd
added citations to the bib, and started on a honking huge section of RATTLE in the oopse chapter.
switched params for tcR systems
Work on integrators
halfway through revisions in OOPSE
worked out the diagonalization bugs in head and whole
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remove the old implement of minimizer from cvs tree
Using inherit instead of compose to implement Minimizer both versions are working
added discussion of multiple image periodic boundry conditions, and added a figure to match the discussion
debugging the director code
cleaned up the references and the tables in the lipid section. also spell checked the thing.
added scd correlations, and director and order parameters for the head groups
made a makefile
finished up the rough draft of tcProps with Scd corr
adding function shakeF in order to remove the constraint force along bond direction
lmost finished with the readWrite routines
finished most of the actual dump scane.
started some cleanup on oopse. added a conclusion, finished the foreword, and found all the undefined citations
added a little bit more to readWrite.c
started on som io
added an introduction to oopse, and started smoothing out the wrinkles.
little changes in the twoChain figure
started work on some parameters and initialization
This commit was generated by cvs2svn to compensate for changes in r1047, which included commits to RCS files with non-trunk default branches.
a bunch of hacks for the twoChain systems
single version of energy minimization is working.
added a lipid figure. started converting oopse.tex
added some OOPSE sections
started a bug fix on the massive memory overusage by OOPSE
added some revisions to the intro
Stripped out the hardwired LJ_rcut
Fixed some typos
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added a degeneracy figure
added a new euler fig, and fixed some things in the degeneractyy section
final version
Single version of energy minimization for argon is working, need to add constraint
Figure added
I hate revtex
Add one more file into Makefile.in
Add some lines into global.cpp to make it work with energy minimization
Now enthalpies of formation
Changes in response to JCP reviewer
Added black and white version's of figures
More corrections and fixing of experimental numbers
typed up the lipid section
Fixed a reference
Ran iSpell
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
More discussion of the orientational results as well as a description of the experimental tau_2 calculation.
started work on the complete project. Made a makefile, and added preambles
little changes, added the start of the conclusion.
Further improvements. Discussion of the results in the table was added.
fixed .bib file problems
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.
added in the RSA paper to the dissertation
NLModel0, NLModel1 pass uit test
little fixes
added the new figure into the Introduction
finished putting equations in Introduction added an euler rotation scheme picture
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to avoid cyclic depency, refactory constraint class
added some equations
ran spellcheck
Functor.hpp pass unit test
added a shifted potential figure
begin unit test of minimizer
updated the two figures in the introduction
added some figures to the Intro. Also lots of equations
Adding GoldenSection and Brent LineSearch Method
finished typing in the intro, and started on the lipid chapter
using class Minimizer1D derived from MinimizerBase instead of a functor to do line seach
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...
member list fixes for rigid bodies
Adding MinimizerParameterSet class.
Revision of NLModel0 and NLModel1
revision of NLModel
Added point-charge models to water.mdl file, updated ssd.bass to use new SSD name
Fix to new RigidBody stuff
Longer run time to test SSD water in MPI
Longer run time to test gold in MPI
Longer run time to test argon
More BASS changes to do new rigidBody scheme a copy of WATER.cpp from this morning
More BASS changes to do new rigidBody scheme
revision of constraint for Nonlinear Optimization Model
Changes to BASS reader to use Euler angles for orientation instead of unit vectors required changes in MoLocator
Changed orientation lines from unit vectors to euler angles
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
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
added in the last bit about symplectic integrators and the liouville formulation
a few corrections to the introduction
added changes to the introduction
started adding in equations to the introduction
Corrected spelling in several directories, and stated WATER.cpp
constraint class in energy minimization
added periodic boundry conditions citation
minor corrections to the previous commit
added changes into the Empirical Energy section
started work on the lipid chapter
Adding energy minimization
Energy Minimizer
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Corrected .bib file entries
ran spell check, and fixed some little typos
Made some error messages more user-friendly
worked listing schemes into the document
Updated the default water to SSD/E
Adding warning if sample time, status time, thermal time and reset time are not divisible by dt
Adjusted the SSD part of the paper...
Added a bunch of dummy targets so make won't complain
Fixed old bass file
BASS changes to add RigidBodies required a change in how the MoleculeStamps are used by divideLabor in mpiSimulation.cpp
BASS changes to add RigidBodies and LJrcut
added in changes to the Monte carlo andMolecular dynamics section
adding the monte carlo section to the intro
forgt to add these earlier
did some work, started on the introduction chapter
fix a bug in creating eor file
fixed a bug where only MPI jobs could write eor files
fixed an struct mismatch error in the mpi initialization of the AtomStruct
Fixes for Dumps
Changes for altivec
Documented the Spud Toss
changes for charge charge interactions
More work for adding charges
autoconf fixes
fixed a periodic box bug
autoconf compatibility changes for icc8
Changes for adding direct charge-charge interactions (with switching function)
Some changes for new MPI organization and direct charge-charge interactions
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Energy Minimization method
fixed some things in the periodic image part
open and close the eor file whenever it is used instead of rewinding it
Made changes to the rigid body stuff...
change the interface of writeFrame
more changes to eam section.
More typo fixes.
Changed section on eam.
added new revisions
Merge the code of writeFinal and writeDump; Adding sortingIndex into DumpWriter; Fix a bug of writing last frame twice in integrator
revision
fix a bug in copying string
Dumpwriter only write out the atoms on master nodes
Updated the rigid body and ssd sections
added the cover letters
removed extra files
remove extra files
Edits for publication
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
Fix a bug of declaration of tagub
rotated the lipid figure added eam to the Emperical Energy
Added daw entry.
New DumpWriter (Attempt #4)
added a lennard jones section to the Emperical Energy section
added some work on the Introduction chapter
A work in progress...
null terminate some strings just in case
refixed the NVT readin XS state bug.
added strncpy to DumpWriter
fixed the restart from NVT exstended state bug
Added rigid body discussion and added to .bib file...
First Stab at fixing DumpWriter
added support for the ignore XS state info flag
Fixed a bug of sending message from master node to itself in DumpWriter.cpp and InitializeFromFile.cpp
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Periodic Boundary Conditions
started adding some changes from before break
performance fixes in the dipole dipole and reaction field code
Making do_Forces a little more sane
reworked the directory structure to reflect the Outline of the paper. All major sections now have their own tex file
Attempting to increase performance by reducing spurious function calls
mangling forces even further
mpich mucking
mangled do_forces...
Added bitmask to do_forces property lookup
Added third-party directory for code not written by us. Also added Mersenne Twister random number generator code. This will eventually replace sprng as the random number generator used by OOPSE.
Fixes to profile code.
More profiling fixes.
Another change for MPI in timing.
Small update to timing in MPI
the profiling commands work now. Will start adding PROFILE ifdefs into the code
added some profiling routines
working on adding GofRtheta and GofRomega additional work on randomBilayer
working on adding GofRtheta and GofRomega
added some profile functionality
Added functions for simple profiling in fortran.
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.
Adding missing figures....
test commit...
finished gofRtheta and added gofRomega. both need to be debugged and tested.
Changes for gradients (to do minimizations)
removed the randombilayer header
edited the makefile to add randomBilayer to the build. Also move the random bilayer builder from bilayerSys to randomBilayer
backed up the old DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and TB3 in DUFF.frc
added a more verbose error message in SimInfo. Added a more informative error message in InitializeFromFile
begun work on add ing in the GofR,CosTheta
Fixed a bug in SimInfo ordering of radii
D'oh, more color plots...
Again, more color plots...
Added color denseSSD plot
Fixes for rotation
Learned to use cvs add and cvs remove...
Really added color figures.
Made color figures!
Added Vectors
Changed ice 0 to ice i.
Considerable corrections to both text and figures from the previous commit. Now in the true pre-print form. This is the updated first draft.
Massive changes to content. Declared as first draft.
added a routine to SimInfo.cpp to inline a min function.
reordered the rcut/ecr/boxSize initialization removed the rcut/ecr shrink and grow algorithm. the simulation will now exit when it runs into rcut or ecr.
Added support for compiling fortran without use of mpich modules. We use mpif.h instead.:
moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
Fixed plots by including SSD1 data. Made several images more condensed and easier to read. Begun altering text to match the new focus.
added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
fixed the includes in the Make.dep
did a merge by hand from the new-templateless branch to the main trunk.
bug Fixes include:
* fixed the switching function from ortho to non-ortho box.
!!!!! THis was responsible for all of the sudden deaths we saw.
* some formating in the string when we write out the extended system state.
* added NPT.cpp to the makefile.in
fixed the "Sudden Death" bug. The box was not switching between orthorhombic and non-orthorhombic wrapping correctly. we added a fabs() to the check.which should fix it.
some work on trying to find the compression bug
begun work on removing templates and most of standard template library from OOPSE.
started work on template removal.
This commit was manufactured by cvs2svn to create branch 'new-templateless'.
added template stuff to the Maikefile template little changes to some printf format statements
added template stuff to the Maikefile template
bug fixes for rList problems
Fixed bug that size(q0) was being queried before q0 was allocated.
fixed a stdlib.h include error in bass.l fixed a little bug in the first time step, regarding the setting of ecr and est in fortran
fixed a stdlib.h include error
som efixes to the way rcut is setup, as well as additional debugging comments.
C++ compatibility for templates
Refixed broken makefile
compatibility fixes
add chi and eta to the comment line of dump file.
did a complete overhaul of how c calls fortran. All function pointers and fortran calls are rigidly typecast now.
Portability fixes
Compatibility fixes
started work on template removal
started trying to understand extern "C" stuff for pointers
This commit was manufactured by cvs2svn to create branch 'no-template- branch'.
fixes for compatibility
replace c++ header stuff with more portable c header stuff Also, mod file fixes and portability changes Some fortran changes will need to be reversed.
replace c++ header stuff with more portable c header stuff Also, mod file fixes and portability changes
mod file fixes and portability stuff
Stuff for MOD support in other compilers
added routines for the sysbuilder to work with simSetup remved the QuickBass routines, and had all parsing go through SimSetup. LatticeBilayer is in complete working order now.
This commit was manufactured by cvs2svn to create branch 'templatesBranch10-28-03'.
added routines for the sysbuilder to work with simSetup
fixes for configure, sysBuild
put QuickBass, MoLocator, and latticeBuilder into a Builder Library overhauled latticeBilayer into its own program. Removed sysBuild from the Makefile
Started work on integrator stuff
New File
Formatting changes to get out of RevTex nonsense
work on bilayer builder
fixed a merge problem
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 fixed an eam mpi parmeter setup bug
added eam ForceField files to the init
added a new NPT integrator, NPTxyz. It scales the x, y, and z direction sepeartely. no box skew allowed.
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 number of bugs in the staticProps code. gofr is now working.
added the staticProps directory to the build list for both configure and configure.in
added the staticProps directory to the build list
Fixed a plot (fullContours.eps had bad labels).
dded my handwritten pages from 10-16-03
changed format to preprint article
Changed DumpReader to use linked lists instead of a vector. Fixed the makefile to build DumpReader.cpp Removed a comment output in Exclude.cpp Modified DumpWriter and Integrator to write an eor file every time a frame is written. This lets the .eor file represent the last written frame of a simulation.
removed the props directory, and moved everything over to staticProps
Contiuned work on staticProps. should be in a position where it will compile and run first runs.
Fixed bug in calc_eam.
added Au init file for eam.
removed entahlpy from the statwriter and thermo.
changed the formating ogf the error statements in simError added a function to get the maxCutoff near completion of the staticProps code. still needs the pair loop, and the loop to allocate and read each frame.
changed the formating ogf the error statements in simError added a function to get the maxCutoff
changed the formating ogf the error statements in simError
finishing up the constructs needed to get this program up and running
changed f90Flags so they are no longer overwritten by the compiler.
added mpif90 mod check back same for conifig.in fixed wrappers to extern "C"
added mpif90 mod check back same for conifig.in
added mpif90 mod check back
fixed a lot of warnings and errors found with SUN's SUNWspro.s1s7
light change in syntax. no signifigant change.
fixed some additional remarks from icc -w3 (extra verbose output)
cleaned things with gcc -Wall and g++ -Wall
fixed a bug in configure
fixes for configure
moved readyCheck in the integrator so that it is called before the first Statistics are written.
Added a bunch of Make.dep files to CVS
Removed NPTfm from Integrator.hpp. Some small syntax cleaning in NPTfm and SimSetup
fix bug in calculating maxCutoff
Converted NPTf to work with the NPT base class. Removed NPTfm and NPTim from cvs
Added zcons.tex
added NPT base class. NPTi is up to date. NPTf is not.
I must have changed something, but for the life of me I can't recall it...
Just added to the make file...
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.
removed mpi++ from the makefile
goofing off to test NPTf and NPTi
fixed bugs in NPTf, found (nearly) conserved quantities for both NPTi and NPTf
fixed a typo in the makefile.
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fixed NPTi to now work with constraints.
fixed ecr grow in SimInfo fixed conserved quantity in NPT (Still some small bug) NPTi appears very stable.
made additions to lipidIntro
SSD portion of paper added (ssd.tex).
added an intro to the lipid part
add conserved quantity to statWriter fix bug of vector wrapping at NPTi
added AllCorr. It eill still need some work
Added integrators to Makefile.in
Entered changes for configure into ChangeLog
Adjustments to the introduction. Minor additions to the methods section. Chris
added more work on getting gofR working.
First CVS commit. Minor changes in the introduction. More changes to follow... Chris
added the beginings of the GofR pair correlation. added identification of identI in matchI.
updated the ChangeLog added two new NPT integrators, they still need work.
updated the ChangeLog
a rough draft of the intial simulations
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Added parallel section of paper.
dependency on config.h
fixed sprng problem
New Makefile for metals sample
Changes to autoconf / configure method of configuring OOPSE
added resetTime to the Global namespace. added ability to reset the integrators in the NVT and NPT family.
added resetTime to the Global namespace.
Removed big file
This is the paper that got scooped
added zConstraint types to the AtomTypes file. added two rendering scripts to to aid in rendering. Note:renderRange does not work.
added zConstraint types to the AtomTypes file.
added a charmm citation to the bib file. finished adding all of the equations into DUFF.
added my J. Peter Grace fellowship.
fix a bug at MPI version of PolicyByMass
added some text to DUFF, changed the preamble from two column to preprint format.
Added: check uniqueness of molIndex
added the first functional parts of the PairCorrType Abstract classes.
put in some writing on initialSimulations
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 got the directory setup to build standalone texts.
added the disertaion bibliography
More fixes for stress tensor parallel bug.
This commit was generated by cvs2svn to compensate for changes in r728, which included commits to RCS files with non-trunk default branches.
Matt Meineke's dissertation Files
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 molMembershipList use global index instead of local index
set default force substraction policy to PolicyByMass
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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
added define statemewnt to Statwriter and Dumpwriter to handle files larger than 2 gb. commented out some print statements in Zconstraint
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. Fixed a bug in MPI_DUFF. The atom block type was not being properly constucted in MPI. (The MPI struct had 6 doubles declared versus the actual 11)
changed the Makefiel a litle.
More FreeBSD fixes
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did some more work on DUFF.
added the lipid figure, and did some work on DUFF.
little changes to finish the port from make current to currMake
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 some work to DUFF
added a currMake script to replace the make current
small bug fix on frequency of output dumps.
played a little with the headers in DUFF
made some changes.
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. fixed a bug where ghostbend atom b was not being set. ( recent bug from SimState conversion)
updated the Changelog. added some bug fixes for setting the random number generator seed value.
updated the Changelog.
bug fixed in ghost bend class
quick makefile fix, in make links. added -f to ln -s.
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reformmating ZConstraint and fixe bug of error msg printing
Fixed sysBuild -bilayer works. Nanobuilder still broke.
Tested MPI version of Z-Constraint Method
started working on DUFF
finished a rough draft of the dynamicProps section. added calculation sheme to the staticProps
Stable ZConstraint with average force substraction strategy
added text to the analysis code.
Added some profiling code -DPROFILE.
harmonic potential & z-contraint method
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trying to debug eqn references
fixed a really annoying bug in Directional Atom, where mu was getting written to pseudorandom memory location.
debugging globals
formatting fixes and new atypes in LJFF
fixed a few references to older stuff...
Added comment line for getgetopt.
Missed del of files before.
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commit makefile
added harmonical potential to z-constraint method
changed how the comment line is handled to allow greater flexibility.
Changed makefile to only build quicklate.
added utils/sysbuilder to be built.
Arranged sysbuilder into a subdirectory. Fixed some of sysbuilder to work with new atom allocation in libmdtools.
added method of moving zconstraint molecules to specified positions
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Added zConstraint into the BASS language syntax.
changed the number of degrees of freedom to account for zConstreints
EAM works...... Neighbor list also works.....
moved frameCount's functionality into DumpReader. also split props into staticProps and dynamicProps. (currently only have staticProps)
fixed a deprcated instance of Atom::setZ and Atom::getZ in ZConstaint.
switched SimInfo to use a system configuration from SimState rather than arrays from Atom
Bug fixes for eam...
added the main equations to the analysis section
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edited the header to be a revtex style two column layout.
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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.
This commit was generated by cvs2svn to compensate for changes in r662, which included commits to RCS files with non-trunk default branches.
The OOPSE paper
stable version of Z-Constraint
add index range checking into ZConstraint
added z-constraint parameters to the globals
Added Z constraint.
More bug fixes for eam.
working on the props code
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Added bass models for metals
Added eam to simSetup and added changecutoffeam.
Changed configure to look for both upper and lower cass .mod files
rewrote the makefiles a little to install two scripts for rendering
module use fixes for eam and do_forces.
added a '-' to the formating of the pov output file. also removed pov2anim from the project. It will be replaced with shell scripts
Finished most code for eam....
added the scan function to the DumpReader. It should now save the start of each frame in a vector.
making some changes to read dump files
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Fixed a current time initialization bug in InitFromFile.
some initial changes to Dumpwriter and friends to accomadate random file access
Initialized currentTime to 0, in case no one sets it.
fixed Initializefrom file to start the simulation from the time specified in the init file.
reoved some binary files
added DUFF lipid models to the AtomTypes file
fixed the AtomType file not found bug.
Started work on a DumpReader
Fixes for SSD/E
Changes for SSD/E
commented out an eam line
fixed spelling issue
added info module
Added massive changes for eam....
final fixes
Fixed a the centering on the Periodic Box. Also corrected the y and z switch in the box vectors
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More up to date version of EAM_FF
Changed how cutoffs were handled from C. Now notifyCutoffs in Fortran notifies those who need the information of any changes to cutoffs.
Started work on Hmat stuff to replace box Lengths
Made quickLate aware of Hmat. quickLate is now somewhat more intelligent about periodic boundaries and wrapping.
Fixed bug in updating mixing lists
added a quick wipe-and-update script for quick rebuilds on BoB
more fixes for box changes
removed some debugging print statements.
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.
working on fixing ssd bug
Fixes for the NPT ensembles
cleaned up simSetup
added KMol
fixed some bugs, Changed entry_plug to info where appropriate
added more command line arguments
Fixing force field line
Fixing pressure tensor
more archaic code fixes
removed old outdated code
fixes to get rid of get_vx and set_vx
removing get_vx
Added NPTfm
Bugfix in NPTim, fixes for NPTfm
Checking in changes for NPTim
Broken SysBuilder
Fixes for samples
Removed some debugging write statements
Fixes for get and set routines in Atom and DirectionalAtom
added get and set routines to Atom and DirectionalAtom
added a nanoSysBuilder that takes different cmd line arguments.
found a bug. Unit vectors were not being updated
Working on NPTim
Switched the bond in the force field back to constrained, to preserve energy
working on som integrator bugs
Starting to worry about all the strtok() calls in our code
Fixed Hmat and some namespace strangeness
Fixed hmat in DumpWriter (MPI) and eor.
fixed some bugs
Added nanoBuilder and a general Lattice builder.
Bunch of 1-d array -> 2-d array stuff
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Bug fixing NPTi and NPTf. there is some error in the caclulation of HmatInverse.
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starting some work for xlate
adding in dan's NPT stuff
This is the dp and read file
Fixes and merging NPTf
Removed Qmass
Fixes for both NPTf and NPTi
Fixes in NPTi migrated into NPTf
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fixed box scaling
NPTi
cleaned up the dependecy scripts in the makefiles
fixed the bugs introduced by switching the periodic box to a matrix
Fortran flexi-BOX
Fixes for flexi-BOX
working on adding the box matrix to everything.
Updated the ChangeLog, and Converted most of the SImInfo to use non-Isotropic boxes. wrapVector needs to be finished.
Changed over the bonds to Harmonic bonds in the DUFF frc file fixed constraints.
Changed over the bonds to Harmonic bonds in the DUFF frc file
Fixes to NVT. Check them!
added Harmonic bod into the DUFF forcefield and BondExtensions.cpp
Doing some work to debug the constraint code.
NPT fix
Most of the integrator and NVT seem to be working now.
NVT additions
slowly converting to new integrator and forcefield names.
finished the basics of the integrator and SimSetup.cpp
doing some work on SimSetup to clean it up / get it to work with the new Integrator.
minor changes in an attempt to fix output times.
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex some work on the integrator. ( incomplete)
Added Teng's parmeters fro the ghost Bend in TraPPE_Ex
mostly final version
First completed rough draft (spell checked even).
fixed the left alignment bug. Bugger if I know what was causing it.
about halfway there.
nothing major just some little changes here and there.
added constrainA and constrainB to the Symplectic integrator
updated the logo a little as well as some of the colors
starting to add in the stuff for the poster.
This commit was generated by cvs2svn to compensate for changes in r544, which included commits to RCS files with non-trunk default branches.
Midwest Theoritcal Conference 2003
currently modifiying Symplectic to become the basic integrator. bilayerSys.cpp altered for building tb3.
currently modifiying Symplectic to become the basic integrator.
added some member variables for position, velocity, etc.
changed how NVT is now derived from Integrator
fixed an a mismatched Ghostbend bug.
all seems to be working
still working on the bilayer code
doing some work to overhaul sysbuild.
This commit was manufactured by cvs2svn to create tag 'bob-5_14_03'.
optimized the ssd calc loop
Added bead lipid model to the sample directory
finished adding the Tail beads into the Trappe extended force field
added the TailBead atom types to the TraPPe_Ex forceField
fixed up the TraPPE_Ex force field. there were some duplicate entries added a two chain lipid to the lipid.mdl in sample
fixed up the TraPPE_Ex force field. there were some duplicate entries
added the utils subdirectory to the configure script added the CH branching group to the TraPPE_Ex fource field
added the utils subdirectory to the configure script
I added the calcPi.c
calculation of the pi
added optimization to the compile
We update the Makefile.
we have succesfully debugged the program. it is ready for use in any application we want.
fleshed out all of the ideas we wanted to see in this interface. it is still not yet debugged.
started some initial rewrite for the template.
Added binary extensions
changed the name of madProps.c to commandLine.c
This commit was generated by cvs2svn to compensate for changes in r516, which included commits to RCS files with non-trunk default branches.
a generic template for parseing command line options.
updated xyz2pov to put out better pov scripts. I'm begining to think pov2anim isn't as useful. not sure if I should up date it, or just leave the rendering steps to shell scripts.
Added a quick readme, and Identified myself as the author
this should be the last of the random crap to toss out.
killing some files
killing misc . crap that shouldn't be inb the source tree. cleanning up the makefiles
killing misc . crap that shouldn't be inb the source tree.
Rearranged the source tree to be easier to distribute. Added autoconf and automatic dependency generation
added some stuff, and forgot to update. who knows whats different now.
added all the files
i quick fix to th distance in the random bilayer builder
added a new test for constraint failure
fixed up sysBuild to where it should now build our systems
almost finished.
bilayerSys and sysBuild both will build now. woot!
finished bilayerSys.cpp sysBuild still need to write the bass file. MoLocator.cpp is currently empty
Added eam force files...
More eam work.
working on the system builder
Fixed ordering on NVT calculation in integrators.
This commit was manufactured by cvs2svn to create tag 'no_segfault-01'.
working on a system builder
added Ghost bends to the TraPPE_Ex forceField added sysBuild to the utils Makefile
added Ghost bends to the TraPPE_Ex forceField
Added first mangling of EAM.
fixed a memory bug in Fortran, where molMembershipArray was declared nLocal instead of nGlobal.
Bug fix in progress for NPT
added a globalIndex counter to Molecule
Working on ConstantStress
fixed a n mpi init bug in SimSetup. caused a miscalculation of nLocal.
fixed a bug in symplectic, where presure was only being calculated the first time through.
added pentane to the alkane model file
Added volume and enthalpy to status file
fixes for NPT and NVT
It works (kinda)...
Fixes for NPT / NVT
Moved expand neighborlist to init_FF.
fixes for NVT
fixes for nvt / npt
dt/2 fix in nvt
Fixes for affine transform
Changes to integrate the NVT and NPT ensembles
Fixes for NPT and NVT
fixed a sign error in the radial portion of SSD.
doing some testing in sticky through Symplectic.
Working on NVT
Fixed transpose bug in mpi reduce for tau and virial.
bug fixes
Many fixes to add extended system
Fixed a bug caused by my experimentation
Added ExtendedSystem infrastructure for NPT and NVT calculations
Added targetPressure to BASS
final mods to try a fortran compiler
Bug fixes for simulation module rewrites
bug fixes for compilation
bug fixes to fortran wrappers
Breaking c and fortran, c gets smarter, fortran gets dumber...
fixed a memory read bug in neighborlist
Changes for Extended System
Fixes for ExtendedSystem
Added the SGI award in 2003, also edited papers and presentations to separate the two.
Added extended system header
changes for extended system code
renamed nvt to extendedsystem
added some little fixes here and there.
fixed a possible call before initialize bug.
just little things like deleteing unused variables and such.
a few fixes to simError.h also some fixes to Molecule.hpp
a few fixes to simError.h
fixed some small things with simError.h
Starting work on NPT
Added NVT file (very broken for now)
Changed Readme, added some files
dipoles mostly work, but there is a memory leak somewhere.
Fixed a bug where MPI was not getting the proper atomIdents.
more bug fixes....
Fixed DumpWriter to be more robust to errors. also added a little namespace to InitFromFile to wrap it's helper functions in MPI
Fixed bug with pot_local not zeroed.
Fixes in MPI force calc and in Trappe_Ex parsing.
bug fix in DumpWriter.cpp
Bug fixes in read-write routines.
fixed a bug where the Excludes were not being created properly
mpi fixes and debugging mpi read write from file.
fixed long range interactions in Trappe
MPI buggy, fixed mpiRefresh issue.
fixed a bug where excludes were not being initialized
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Fixed a single processor segfault bug.
fixed the compile time bugs, Source builds and links
fixed a few more bugs.
added the Molecule.cpp file
fixed the makefile
fixing some compile time bugs
I have implemeted Molecules everywhere I could remember to. will now attempt to compile.
finished updating SimSetup to initialize and use the new MPI division of labour, and Molecule class
finished conversion of TraPPE_ExFF to use Molecule
LJ_FF has been converted to the new Molecule model. TraPPE_Ex is currently being updated. SimSetups routines are writtten, but not yet called.
fixes for local->global atom numbering in MPI
little bug fixes here and there.
Fixes to fileio for MPI
bug fixes many bug fixes
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.
the skeleton for making the molecules is in place. ForceField needs to be updated next.
fixed a couple of the "static" bugs in Atom and Exclude
still working on the SimSetup routine. also fixed some things in Exclude.hpp
Added Atom.cpp and Exclude.cpp
Fixes in Atom and Exclude list
Make Atom.cpp able to add and delete ranges of atoms
added an Exclude class with static arrays similar to the Atom class
I'm overhauling the molecule class to contain it's own bonds, bends, and torsions. may god have mercy on my soul.
Finished globalIndex.
MPI stuff for passing out molecules
working on load balancing
Fixes for Parallel thermalization
fixed an mpi include bug in THermo.cpp
Fixed bugs with calculation of potential energy and temperature.
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added dummy files to keep the build deirectories from being pruned.
moving tests to samples
moved tests to samples
Tests are becoming samples
Added makefiles in tests directories
electrostatic changes for dipole / RF separation
little bug fixes here and there
added an argon test simulation
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added some test bass files for experimenting with
fixed bug where short range interactions were not being calculated. removed some debug print statements
various write statements for debugging
added links to the makefile in forceFields
Fixed F_MACH_DEP bug
Makefile fixes, directory re-org, autoconf fixes
Added license file
Fixed makefile
Makefile for forceFields
Readme changes
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Makefile fixes for depends
This commit was generated by cvs2svn to compensate for changes in r377, which included commits to RCS files with non-trunk default branches.
New OOPSE Tree
Bug fixes in TraPPE. calc_LJ_FF.F90: Removed print lines. TraPPE_ExFF.cpp: Fixed so idents are being set.
more bug fixes...
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fixed a bug in the torsions.
Working on the Makefile
Fixed bugs in atype_module.F90 atype_module.F90:new_atype: status was reused for force field checks, created new variable FFcheckStatus to be result of FF checks.
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fixed some bugs. LJ argon works. Error calling new atype for SSD in TraPPE_Ex.
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.
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compiles and links. And promptly segfaults.
some initial bug fixes
added GB
last little changes before compiling and debuging
shed implementation of the Fortran interfaces.
getNlocal no longer in force_globals
brought force_globals back from the dead to fix circular references
adding more to the interface
bug fixes for new fForceField.h
working on the fortran init ForceField interface.
fortran-side fixes to play nice with C
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merged stable-0_5 into the main trunk
this is an inital attempt to implement the new fortran interfaces
some intial version bookeeping
blah!
This commit was manufactured by cvs2svn to create branch 'stable-0_5'.
This commit was manufactured by cvs2svn to create branch 'stable-05'.
mostly compiles. interface twixt c and fortran is broken. (c needs to be brought up to date with fortran.)
Updated the Makefile to contain all of the new fortran
vector class tests correctly.
deprecated the ssd forcefield in C++
Bug fixes in vector_class.
fixed some bugs in BendStamp from when Ghost Bend was implemented.
last minute changes
Minor alterations to the layout
changed the font
spellchecked it.
A near final product
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Setting up my CV.
made som e revisions to the application.
fixes for the exclude lists
just working on some changes to the application.
initialization routines, bug fixes, exclude lists
Fixed some more compile bugs in do_Forces.F90.
forceGlobals is gone (part3)
Stick a fork in it. It's rare.
bye bye atypeGlobals (part2)
bye bye forceGlobals (part 1)
fixes for major rewrite
Massive rewrite
MPI bug fix
bunch of fixes
Massive sticky rewrite
added the force parameter files into the distribution
Fixed mixing list to work with new atypes using vector class.
rearranging source files
Added allocation of module arrays.
Bug fixes
Fixed bugs, added logical routines
Changes to vector_class and removed all traces of linked list.
Fixed a bug
Did a bunch of match/find routines
Bunch o' stuff, particularly the vector_class.F90 module
finished adding the ghostBend into the TraPPE_Ex force Field
Changed generic lists so they work correctly
Massive rewrite underway. This way be dragons.
Added ghostBend into SimSetup. only need to add awareness to TraPPE_Ex
Changed names of calculation modules for do_Forces.
More changes to code. Hopefully these will commit smoothly.
some cleanup
Removed extra copy of dipole dipole
added the ghost bend bend type.
Added stuff for Dipole/Dipole and ReactionField
GhostBend addition
added fortranWrappers and Forcefield.cpp to the makefile
implemented the new fortran force interface
More code clean-up.
Dan Goes Crazy
dded more static arrays to the Atom class;
Split force loop into subroutines. Moved wrap out of simulation module.
finished conversion of all function wrapping into fortranWrappers.cpp and .hpp respectively
cleaning up all of the function wrapping
Changed code to use one generic force loop. Only one super atype that has all information is now used.
overhauled TraPPE_Ex forcfield in C++
Made changes to lj_FF.cpp to pass stress tensor.
added randomSPRNG.hpp to the package (oops, should have beenthere to begin with.) added ssdFF++.cpp to the makefile
Changed lj_FF to use new neighbor list module.
fixed some changes to the Globals in libBASS Added some files to the Makefile and added ssdFF++.cpp to the C++ side of things
fixed some changes to the Globals in libBASS
OOPSE has been braought up to date with the mdtools devfelopment tree. mdtools should no longer be used. All development should take place in the OOPSE tree.
Added neighbor list module that auto expands...
Added simulation struct...
Changes...
Changes they are a comming....
added changelog and NEws info
incremented the version to 0.6
oose and oopse build and distribute!
oopse compiles and links!
oose builds and links oopse builds but can't find mpich++
libmdCode builds.
added mpi for libmdCode (still working out the kinks)
added some checks for libmpich and got single processor to build in libmdCode
dded some stuff
working on getting this distribution working
added libmdCode and a couple help scripts
libBASS and libmpiBASS are completely self encapsulated.
added mpiBASS.c and .h for the mpi libraries
Successfully added all the source for libBASS
Added SSD atypes.
Initial commit of ssd force module.
Fixed bug with pot energy.
Changed to single version. No change.
Changed to single version.
We have working code today... MPI bug fixes to DumpWriter.
Fixed some bugs, made some more.
MPI is Brooooooken...
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MPI is Broooooken. Saving poor state so I know where to begin with.
fixed a bug in the final eor file.
Changes in mpiBass.
Bug fixes for mpi version of code
Added a generic util code directory and moved Linux_ifc_machdep to it. MPI changes to compile MPI modules.
Force loops seems to work, velocitize never being called....
Add print lines to simBASS and fixed Makefile to link w/ icc.
More bug fixes... Forgot to build sprng
For some unknown reason the Single processor builds. Has not been tested!
final version before the single processor build
added generic atypes
lj_FF.F90 and simulation_module now compile. Logical bug still exists in lj_FF.F90 lj_atypes_list.
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added the fortran function wrapping to the mpiSim class
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added wrapping of fortran to a private function of SimInfo
modified the box vairable on setSimulation to be a length 3 array
Added init function to c++ force module.
More changes to lj_ff. Force loop almost ready.
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added some stuf to implement thefortran interface in LJ_FF
this completes the addition of fvortran function wrapping into the LJ_FF class.
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started some additions to wrap LJ down to fortran. INCOMPLETE!
tarted some additions to wrap LJ down to fortran. INCOMPLETE!
A few more changes to force loop.
starting down the crooked path of the fornographer.
More changes to lj_FF.
just some initial fiddling
removed a ps file that should not be backed up
This commit was generated by cvs2svn to compensate for changes in r226, which included commits to RCS files with non-trunk default branches.
the 1st paper based on our lipidModel
fixed up LJ_FF
fixed up the LJ_FF implementation. It is now the standard for building a force routine.
Finished thermo and randomSPRNG classes.
More codeing on fortran force backend.
Thermo now can use SPRNG or rand48 (if not MPI). Finished up work on randomSPRNG. Still need to fix access to MPISimulation.
Added more code to randomSPRNG classes.
Added classes to handle random number generation.
Changed thermo getKinetic and getPotential for MPI. Added header for SPRNG random number generator class.
Added SPRNG header file.
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+ added lennard-jones force module and corresponding class. + created forceFactory directory.
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finishing work on making DumpWriter parrallel
Added mpi to InitializeFromFile read in.
Added replan of gather-scatter routines for future load balancing.
Finished updating mpiSimulation to work with c++.
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added the pareDumpLine routine to the Initialize from File class
Changed name of mpi_force_module to mpiSimulation to match with C++ code.
Initial mpi io conversion.
finished adding in the code to divide and set up the atoms and such across all of the processors.
fixed typo with #ifdef.
Added mpiComponentPlan.h a dual fortran c header file defining mpi simulation parameters for both c and fortran.
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made some shanges to streamline the setup in SimSetup
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cleaned up the divideLabour interface to use the information about Moleculestamps in the entryPlug.
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added the extraction routines so that the moleculeStamps corresponding to the actual components used in the simulation are now persistent throughout, and accessable through the SimInfo object.
Working on the clean removal of key Molecule stamps from the Hash table. stamps will be moved into a persitient linked list.
Added divideLabor.
First addition of mpiDivideLabor to split mpi simulation among processors.
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added files to divide the molecules among the processes.
Addition of c wrapper header for for fortran module proceedures.
some quick optimizations to the indexing in the storage arrays
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made some finishing changes before begining to work on the io
This will run the single processor version of libmdtools
if the libMPImdtools is working this should be the code to run it.
Initial commit of wrappers for fortran module proceedures.
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The simulation can run successfully on parrallel computers!! Now all that is need is the parrallel io routines, and parrallel forces
initial modifications
added simError.h to the makefile
This commit was generated by cvs2svn to compensate for changes in r179, which included commits to RCS files with non-trunk default branches.
This is the mpi version of simBASS
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overhauled the makefiles to be more elegant with regard to builds.
ie. now the name of the library will change when you select single or mpi
build in the Makefile.inc compilers and flags will also be updated
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Fixed the whole lot to be simError safe, ands compiles. Not yet tested however
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Bass shopuld be simError safe
the BASS event loop has finished converiosn to simError. However, it as yet untested.
continuing to refine the error checking in the BASS processing
MPI Force rewrite in progress...
Initial commit of mpi routines for force decomposition.
First commit of mpi force code.
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working on the conversion of the BASS inititialization to be parrallel safe
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adding simError into the mpiBASS Event loop
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finished updates on the easy simError change overs.
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still working on conversion over to simError
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adding in simError
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finished work on the error handling struct and functions
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started work on a global error handling scheme
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making further modifications to make FOrceField objects mpi aware
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more tinkering with the forcefield event loop
minor revisions
more minor changes to the mpi structs
finished adding in the extra structures needed to pass info through mpi. Still need to add the implementation.
finished adding the static storage arrays to the atom class
Changing internal storage of positions, torqes, forces, velocities, etc. not sure here, still working
Changing internal storage of positions, torqes, forces, velocities, etc.
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adding ForceField mpi awareness adding mpi FOrceField awareness
adding ForceField mpi awareness
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changed mpiInterface.c and .h -> mpiBASS.c and .h for clarity of purpose
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Added lhs of assignments..
Fixed double inclusion of mpiBASSEventType with define in header file.
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Clean up with icc debug flags...
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Include makefile
quick bug fix to bassDiag
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added stamp and template diagnostic features
Added make include.
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changed dirs...
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Initial mpi support
Addition of mpiInterface to code base.
First stab at passing base events to mpi....
begin the pain that is MPI. abandon all hope ye who check out this branch.. P.S. we've added consistent BASS error checking
fixed allot of warnings, and adde the molecule
This commit was manufactured by cvs2svn to create tag 'mpi_start'.
This commit was manufactured by cvs2svn to create branch 'serial-branch'.
starting work on the molecule class starting to add in the molecule class adding in the molecule class
starting work on the molecule class starting to add in the molecule class
starting work on the molecule class
the final copy went out this morning. YAYYYYYYYYY!!!!!!!!!!!!!!!
made some final revisions, and started to add some figures
added a bunch of igures
text is finished YAY!!!
finished the revisions of the first draft now only lacks a complete results section, and a future Directions section
revisions to the first draft halfway complete. completed the introduction.
added command line arguments, and a time smoother
fixed a little seen output bug. (Tarega is not always default)
fixed a cosCorr and GofR flag bug, as well as the GofR scaling bug.
running into some problemsd with the figures.
made some changes to the Makefile, and added the sections I think I should write
did a little more typing
additions to the lipid model
got the water SSD model section "done"
added the ssd figure
added some equations and other misc stuff. needs lots of work.
just writing, not much editing yet
This commit was generated by cvs2svn to compensate for changes in r93, which included commits to RCS files with non-trunk default branches.
my Canidacy paper
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VS: ---------------------------------------------------------------------- added more figures, and fixed the slides. GFave a practice talk 6-16-02 with this.
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fixed somebugs with start frame
added a utility to output what time of each frame
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added the capability to specify a start and end frame for cosCorr and GofR
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spell checked
I think I have most of it the way I like it, just need to change the correlation functions, and the final pictures
fixed some figures almost done with slides
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added figures fixed more of the graphs
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changed some of the figures, and put some more polish on the intro
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flexible atom selection
made a new figure. trying to add it to the slide
fixed the citations. continueing to clean up the slides.
switched in Chuck's magic slide enviroment
added a crapload of crap that may or may norbe neccassary. Time will tell. Also, got footnote references working.
This commit was generated by cvs2svn to compensate for changes in r60, which included commits to RCS files with non-trunk default branches.
A pair of utilities to turn an xyz file into a sequence of povray rendered images.
This commit was generated by cvs2svn to compensate for changes in r58, which included commits to RCS files with non-trunk default branches.
This is the original proposal I gave in 2001
This commit was generated by cvs2svn to compensate for changes in r56, which included commits to RCS files with non-trunk default branches.
This is the RSA paper published in 2001
fixed the Makefile
added all of the pictures. And gave a practice talk based on this version. Now begins the process of cleanup and additions of citations.
getting there. Most everything but the motivation slide has been filled out. Lacks only pictures and Diagrams.
Skeletons of most every slide
made some changes
This commit was generated by cvs2svn to compensate for changes in r49, which included commits to RCS files with non-trunk default branches.
Matt's canidacy presentation
This commit was generated by cvs2svn to compensate for changes in r47, which included commits to RCS files with non-trunk default branches.
little utility for catting together dump files.
added the cos correlation function
got the GofR code working, and slimmed down the memory usage.
finished working on the command line options, and started working on the GofR added the GofR header, and moved the strructure definitions to the madProps.h
finished working on the command line options, and started working on the GofR
made a header directory, and fixed the Makefile to work with it the new header dir
made a header directory, and fixed the Makefile to work with it
took out a reference file
This commit was generated by cvs2svn to compensate for changes in r38, which included commits to RCS files with non-trunk default branches.
A half polished version of props
fixed the ordering on the end of file test
moved the actual routine into a seperate source from the main. This allows the routine to be used in other applications.
This commit was generated by cvs2svn to compensate for changes in r34, which included commits to RCS files with non-trunk default branches.
Counts the number of frames in a dump or xyz
cleaned up the output a little
fixed makeRandom to set up a correct simulation
fixed a bug in getA( double the_A[3][3] );
added the getA( double the_A[3][3] ) routine to the Directional Atom Class, to facilitate easier RotMat aquisition
adding the routines to the proogram `
adding a program to make a lipid configuration with random dispersion of lipids.
fixed some bugs in the Makefile
removed xLate.cpp which was part of a seperate project
fixed a precision error in the calculation of the temperature. Also fixed the order that dump file are written.
removed a misc file
This commit was generated by cvs2svn to compensate for changes in r22, which included commits to RCS files with non-trunk default branches.
tools for analyzing BASS simulation dumps
This commit was generated by cvs2svn to compensate for changes in r20, which included commits to RCS files with non-trunk default branches.
runs a simulation from a BASS file
This commit was generated by cvs2svn to compensate for changes in r18, which included commits to RCS files with non-trunk default branches.
translates BASS dumps to xyz files
This commit was generated by cvs2svn to compensate for changes in r16, which included commits to RCS files with non-trunk default branches.
makes a square lipid configuration
This commit was generated by cvs2svn to compensate for changes in r14, which included commits to RCS files with non-trunk default branches.
makes a square lipid configuration
This commit was generated by cvs2svn to compensate for changes in r12, which included commits to RCS files with non-trunk default branches.
forcefield parameter files for libmdtools
This commit was generated by cvs2svn to compensate for changes in r10, which included commits to RCS files with non-trunk default branches.
everything you need to make libmdtools
nose hoover chains added
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Import Root
initial checkin
initial checkin
Standard project directories initialized by cvs2svn.