changing configure script to process the new utilities
added some features to waterBoxer
added the waterBoxer script
added comment info
adding NgammaT integrator
modified affineScale to work with the new OOPSE files
fixed TI MPI bug
fixes to zang writing
converted samples over to the OOPSE-4 file format Fixed an MPI bug in thermodynamic integration
removed extra file in Hydro.cpp
Changing utility programs to use the new file format
fixed some bugs in DumpWriter, eliminated some extra printing of debugging information
Massive changes preparing for release of OOPSE-4: The main difference is that the new MD file format (.md, .dump, .eor) now contains meta-data information along with the configuration information.
change the globals.cpp to make sure we can set targetPressure and surfaceTension to be negative.
fixed an ordering issue in quadrupole-charge interactions
starting change of file formats
Changing atom2mdin into atom2md to reflect new unified file format
fixed a pvf bug
fixed dumpConverter problems
added dumpConverter
removed shapes sample
fixed a spelling bug
added perl interpreter to affineScale script
added perl substitution for affineScale script
added install target for scripts
Adding a directory for scripts Adding affineScale script
fixed a getSigma bug
Added tred to sample water.md files
Added TRED water visitor for Dump2XYZ visualization
Added TRED parameters to forcefield
fixed d / sigma0 confusion
testing commit logger
removed printing of GBN and GBM from previous debugging
Fixed a bug in the fftw part of the configure script.
removed icc from C++ search lines, did some formatting work on GB module, mucked around with a GB example
Adding more changes to orientational bond order parameter.
Added utility function to winger3jm from slatac.
Added the multipole interaction routine. It doesn't work yet, so it's not included in the build.
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
fixed forces and torques for GB
more efficient file reading for thermodynamic integration, and fixed some formatting
Beginnings of a order parameter.
Adding code for bond orientational parameters.
MPI thermodynamic integration works now.
fixed a build problem... GB_12b_ratio no longer exists (replaced with BG_l).
Added support for Winger3jm coefficients.
fixes for mpi thermodynamic integration, close to fully working...
output the principle axis of GB
added mpi compilers, demoted pg compilers after pathscale
reformulated some of the electrostatics
damping now works for charge-quadrupole and dipole-dipole
Fixed a spelling error and a bug in MPI Thermodynamic Integration on file read-in
fixed some typos
testing GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor
Added methods to access GB_mu and GB_nu from the force field options
Massive changes for GB code with multiple ellipsoid types (a la Cleaver's paper). Also, changes in hydrodynamics code to make HydroProp a somewhat smarter class (rather than just a struct).
Add the RippleOP to calculate the orderparameter of the ripples.
Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)
Fix a type promotion problem
replace double with RealType
What?
more changes
more changes for MPICH with profiling libraries required
MPI stuff
fixes for Hydrodynamics
fix a bug in parsing HydroProp file
Fixed a bug when spherical boundary conditions were off.
fixed an initialization bug of Hxy.cpp.
wrapping back to PBC by molecule instead of by individual atom
fixed the bugs of Hxy.cpp.
Last bug showed up in 2 places, fixed the other one.
Fix a bug of printing empty line in DumpWriter
change the order of include path and library path
Adding single precision capabilities to c++ side
Adding single precision capabilities to the fortran side
adding --enable-single to configure script
Getting fortran side prepped for single precision...
electrostatic refinement
zlib fixes
Autoconf fixes for FFTW. Multiple FFTW version support.
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Changes to calculate undulation spectrum
adding a gay-berne switch to Dump2XYZ
Adding qpole
finding ifort arguments that won't die under two different versions of the intel fortran compiler
missing makefile was hanging up 'make clean'
Added random builder to cvs.
Change in siminfo used in nanoparticleBuilder.
Added random builder
Added a random builder to oopse.
Using OpenBabel element table to pick vdw radii for hydrodynamics if the LJ sigma can't be found.
Adding spherical boundary conditions to LD integrator
Added EAM atom types to Hydro models
put spline subroutines in the EAM module
Removed sqrt splines and shape stuff (doesn't work, so why was it in there?). Changed some of the water samples to use shifted_force. Probably should set the defaults to use the damped version now that we sped it up.
Electrosplines added...
splined up sticky
Complete rewrite of spline code and everything that uses it.
Many performance improvements
added a cubic spline to switcheroo
Since status.F90 is used by interpolation.F90, the former needs to be listed above the later in the Makefile.
changed the interface a bit
added some logical flags
Wiped the spline with derivatives and corrected a boundary comparision error by eliminating the check. This algorithm REQUIRES known first derivatives at the endpoints.
bug fixes for interpolation module
Heavily modified interpolation module, also moved to "utils"
Added interpolation module.
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Added status module to simParallel for error reporting.
NPrT might work now
Fixed memory leak bug where SCList capacity was not reset to zero on destruction.
More testing of nanoparticleBuilder.
Added check to make sure md file exists.
Fixed latticeOrt in shapedlatice and latticebuilder.
Fix the normalization problem in calculating correlation functions
(1) RoughShell Model is working; (20)Adding a new option into Hydro which allows user to generate the beads only
Makefile for nanoparticle builder.
Added nanoparticle builder to makefile
Debugging changes to nanoparticle builder.
back to previous DynamicProps
Adding position correlation function. The command line option for DynamicProps is now changed. --rcorr is for position correlation and --rmsd is for mean square displacement.
update writeBeads method
remove a unknown method
The off diagnal is not set
Throw exception if the file can not be opened for preprocessing
Added shaped lattice.
fix a bug in calculating hydrodynamics tensor when the radius of beads are not the same
Fix a bug in friction calculation for ellipsoid
Verify the correctness of Ellipsoid's hydrodynamics properties
New version of Hydro is working now.
refactor Hydrodynamics module.
Generic Shaped Lattice for oopse. Can overload to get spherical or nanorod.
LagevinDynamics is working?
fixed a const problem
unit conversion for diffusion tensor is wrong
change the epsilon of numeric_limit
correcting the unit in HydrodynamicsModel
using setFrc in RigidBody::calcForcesAndTorques will discard if there are force and torque applied in rigid body itself. use addFrc instead.
Adding RoughShell and BeadModel
adding hydrodynamics module into build system
adding Cholesky Decomposition
LangevinDynamics in progress
Fixed a double/int bug. Surprised no one ever noticed before...
fix bugs in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out product of Rij
Bead Model is working
Adding Hydrodynamics Module
fixed a spelling error
fixed a problem with cutoff radii being set larger than 1/2 the length of the shortest box dimension. added a few fortran utility routines
Changed Names of class files.
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fix a bug in converting integer to double
added DPD molecule type parameters
Fixing a bug which reads the wrong frame of trajectory file during analysis
adding transpose into SquareMatrix3; fix a bug in AtomStamp where orientation is not set correctly.
fixed a bug in rigid bodies that contain directional atoms
Adding visitor for GBlipid atom type
added CXXFLAGS to the LinkOptions to allow compilation with icc9 (skipping the gcc-4 std c++ libraries).
Missing brace caused the last commit not to build
Changes to cutoff radius setting to a more logical procedure - still may change...
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X
Adding :LegendrePolynomial
Changes to nanoparticle builder
Added Makefile for nanoparticle builder.
Cleaning up for 3.0.1 release
Prepping 3.0.1 release
new version number
Updated Documentation
Getting ready for release!
Testing commit
Removed MixingRule from Globals. Handled by forceField now.
Added NPAT to Globals integrators.
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testing to make sure GNU make is the make that was used to build OOPSE
changed compiler search order
Changes in Sutton-Chen units
fixed some version info and the copyright date
added some missing checks for header files (particularly zlib.h), used autoheader to help generate config.h.in
added some missing checks for header files (particularly zlib.h)
fixed a dependency problem for the Executable builds
Missing Makefile in this sample directory
Old makefile.in no longer required
All of the OpenBabel stuff needs to be installed
Changed formating.
unifying function name in electrostatics
fix make install problem for metals samples
remove samples/metals from install list.
filepp can not handle multiple line macro, just convert multiple line macro into single line macro.
Made some changes to electrostatics for shifted-potential and shifted-force with mono and multipoles
autoconf modernization and cruft removal
autoconf modernization and cruft-removal
fix some error messages
instead of printing to std::cout, throwing an exception when error is found.
Fixed a spelling error
Changed conversion factor.
Sutton and Chen should be working now.
Fixed SC bug with SIM_uses_SC
fixing RhoZ
Added energy scaling to section parsers.
replace isType<int> with isInteger
remove extra forceFieldOptions from SC_FF
Add force file.
Sutton-Chen no longer segfaults or produces 0 potential, but rather produces Inf for the potential. Progress....
More Sutton-Chen bug fixes.
Long range potential return from fortran is already accumulated, it should not be accumulated again; nGroupTypesCol is not initialized; GroupMaxCutoffCol is not allocated;
In order to compile MPI version, we need to cast const char* to void* for stringstream.str(); Previous Makefile use bjects of single version to make the MPI library;
Sutton-Chen bug fixes. Almost there...
Changes in forcefield.
added files for sutton-chen
More cvs changing.
More moving...
More changes to directory structure.
More Directory changes...
More changing of directory structure
Fixed issue with symbol naming and added call to set force options in SimCreator.
More changes to forcefield options.
Force options passed to fortran.
Force option changes.
changed __FUNCTION__ to __func__ to match C99 standard, and then added an autoconf test to check for __func__ usability. Changed some default compile flags for the Sun architecture
added the STL check
make minor change to build oopse under solaris
the standard library came with SUN compiler does not have a conforming std::use_facet, define a macro to handle it. Adding exception handling to SimCreator.
Removed one parasitic argon atom which was living inside the GB particle. No alien-like ripping out of the stomach was required.
replace grammar for numerical parsing
fixed a cutoff bug
Removing compiler dependencies and replacing them with real autoconf checks
Adding checks for various features used by ANTLR
fix a nasty negative integer parsing problem by refining the grammar
made some minor changes to allow compilation with the portland group compilers
fixed compilation problem for icc7
added missing include
added some checks for pathscale compiler
added copyright
added info printout
added pathscale
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
This should really break things.... Started adding support for ForceOptions to section parsers.
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Added forceOptions to section parser
Removed geometric distance mixing from individual modules and now use force options to detemine what the deal is.
Further fixes for compiler issues.
Fixed ifc public-private issue.
Added support for fortran force options.
Fixed a bug in checkTorsion
Changes to SC.
Changes to build twinned crystal
Overloaded interface for dumpwriter.
remove deprecated keywords from samples
Fix parsing error in OptionSectionParser
Adding handler for CLAY force field
Fixed build bug in openbabel.
reformat error message
Adding .frc file for CLAYFF
adding more checking for topology
Spurious semicolon removal
We've made big changes. This isn't 2.0 anymore.
removing deprecated nAtoms and nComponents lines
adding SelectionToken.cpp
Adding FragmentStamp
Errors are no longer thrown with consts (fixes compilation bug on the Mac).
Got rid of spurious printing out of timestep
Got rid of spurious printing out of junk
Change build process for libOOPSE.a so that the libraries aren't unpacked. libOOPSE.a is now made directly from the object files
added check for egrep (grep -E) needed for new build of libOOPSE.a
adding DataHolder
Added Gay-Berne / Argon test case for the cutoff policies
update Makefile
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
Code to calculate rho(Z) to calculate density profiles for water slabs.
added checks for some functions to configure script
Changed file names that conflict w/ oopse file name object files.
compilation bug
parsing by filepp
Cutoff Mixing fixes
compilation issue
Cutoff mixing fixes have been made.
Adding ParamConstraint.cpp
adding openbabel data files
adding support for soft linking
Adding support for soft linking
Adding linking stuff
rename mdinConverter to atom2mdin
fixed a bug
Adding some config checks for OpenBabel codes we are using
Adding some checks for OpenBabel code
Unifying config.h stuff from OOPSE and OpenBabel
Unifying config.h stuff and making sure the OpenBabel codes can find our default (and environment variable) Force Field directories.
adding ForceFieldOptions
OptionSectionParser get compiled
ForceField optional parameters....
adding mdinConverter
adding more readers/writers
adding openbabel
register openbabel readers/writers
included shifted potential self term
just some parameters
adding openbabel
removed unnecessary commented code
cleaned up the charge-charge interactions a bit...
just playing
fixed a bug in the shifted_potential case
just playing around - we need to refresh all the samples sometime soon...
Made preforce calc public in suttonchen.
Sutton-Chen added to SimInfo
Added Sutton-Chen to force loop...
Added sutton-chen to makefile.
Build Fixes for sutton-chen.
Missed makefile for sutton-chen.
Sutton-chen stuff
Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen.
Forgot to add some files
added in a 5th order polynomial switching function option
added in a 5th order polynomial switching function
playing with switching functions again
playing with switching functions
Added force files for Sutton-Chen and Quantum Sutton-Chen
Added a keyword and ability to output forces and torques
Added a keyword for output of forces and torques
Working on shifted_force...
Just testing...
removed a poorly commented section
improvements in shifted-force
mmm... damped shifted force...
More work on SC.
More work on suttonchen.
removed some test code
forgot to add the screening method header
changing how we deal with summation and screening methods
again, changing how we deal with summation and screening methods
debug stuff for rf removed
Added suppport to atypes for MEAM and sutton-chen
removed some testing code...
fixed a capitalization problem with NPT integrator initialization
nothing
still fixing up wolf...
In process of adding sutton-chen forcefield.
changed the default switching radius to 85% of rcut
reaction field looks to be working now - for charges and dipoles alike
reaction field looks to be working now
added a test molecule
added a test atom type
added charge-dipole reaction field - don't know if it works...
streamlined reaction field for dipoles (now a good bit faster) and added reaction field for charges - still need to do charge-dipole RF
minor changes when testing reaction field
reaction field now works for charges
Fix the other branch of force calculation in Torision.cpp
Still had some globals toUpper problems - these changes should fix those...
nothing
fixed an MPI compilation bug in GayBerne
fix an index mismathcing between c and fortran
added samples for the cutoff methods that Yang Zheng has been working on
fixed gb/lj and gb/gb torques and a rotation matrix bug
added a few GB test cases
Fixing GB parameters
Changed the parameters for the Gay-Berne type
merged reaction field with electrostatics.F90
Customized StatWriter is working
using notation from Cleaver paper
bugtracking gb
Another bug fix
fix some namespace issues in Globals
changing GB architecture
Adding samples for gb tests
fix a seg fault when try copy a string to event's err_msg, there are still tons of memory leaking problem in Globals
Change error message in Globals
Constraints for parameters are working now
Adding .md files for GB/LJ tests
Adding some Gay Berne tests
Adding some cutoff tests
Add parts for the GayBerne LJ
Adding Parameter Constraint class
added default restraint spring constants into Globals
rewrite Globals
Fix to forceManager to pass potential array to fortran.
Don't remember what we did
simplifying long range potential array
Testing new cutoff methods
Messing with 2-point water models
Breaky, Breaky: c-fortran interface now expects an array for pot.
More Change goodness for calculation of potential.
More changes to MPI potential calculations.
Breaky Breaky: Add Support for seperating potential contributions.
Free some variables that weren't freed before.
Design change for nanoRod builder --twinned.
Added code for nanoparticle builder to cvs.
Bug fix, undeclared local variable in MPI.
Fixed MPI bug with Row and Column indexing of groupToGtype. We now have two seperate maps groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer that is set to groupToGtypeRow in the single processor version.
fixing up the samples
There is still something wrong with inertia tensor projection
erase output of inertia tensor. There is still something wrong with current implementation.
fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
fixed an annoying mass ratio bug that results in simulation failure with massless particles
maybe some work on wolf
just some random changes when testing
fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame (previous commit is wrong)
fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame
working on wolf
fixed some samples
updated
using epsilon instead of 0.0 to avoid divergence in rotation matrix to quaternion transformation
Rotation matrix multiplication order error
tracking down quaternion bug
Added DIP atom types for 2-point water model
fix a bug in convert rotation matrix to quaternion
Added define for ifc 7 so derfc is external. Other compilers should treat erfc as intrinsic.
Changed erfc to derfc and declared it to be external to fix issure with ifc7. Hopefully this will not cause a problem with other compilers where derfc is an intrinsic function.
MPI fix for SimHasAtype in simulation module. We needed a seperate receive buffer.
Added support for skinThickness keyword to Globals.
fix a typo in DumpReader
fixing up some samples
slowdown fixed - now roughly the same speed as the old version when using dipoles energies are now exactly the same between the old version of OOPSE and this version
turned rf on
Fixed "dum-dum" where we ignore the skin thickness and hardcode listSkin to be 1.0. We now get listskin from skin. This will get fixed to where we can manually set skin thickness.
added error function
Removed print statement for angular momentum and inertia tensor from velocitizer.
Removed print statements for remove angular momentum.
Bug fix: If we are not using LJ (say we are using EAM), we probably shouldn't rebuild the LJ mixing map.
DumpReader using pure c++ io
Fixed a defaultCutoff bug (HEMES!)
libz additions
added check for zlib in configure
adding zlib support for DumpWriter
adding testcase for zipstream
adding zipstream.hpp
fixed up some sample md files
Fixed bugs in reaction field, now it appears as though it really is working...
reaction field seems to work now, still need to do some testing...
Added keywords for compressed dump files.
xlf found a bug that ifc missed...
fixing some summation method issues
fixed a capitalization error
moved a header file around
it builds now, but there are known issues - particularly with reaction field...
some fixes but even more breaking (cutting out the old way to do reaction field)
Working on adding WOLF
Fix a bug in DumpReader in case readFrame is called without calling getNFrames
forgot to add a header
Fixed bug where gtypeMaxCutoff was not initialized after creation. When maxval(gtypeMaxCutoff) was called, the largest random garbage value was returned from the array.
changes to include the coulombicCorrection selector
added in the undamped wolf, in the process of doing the damped wolf
some changes to activate the coulombicCorrection selector
just some testing
Equilibrated the sample
re-added Cl- and Na+
EAM now uses eamlist to lookup eamAtypes instead of assuming a 1-1 correspondence to atypes.
fix to put back calculation of r in do_prepair
fixed a bug in the createMixingMap routine. It should now set doShift correctly
Added nGroupsInRow for mpi build.
Added access to mpi logical variables
bugfix on the grouptype finding algorithm
adding c-side interface to change cutoff Policy
Some bug hunting
Just a longer test
Added allocation for gtypeCutoffmap etc..
initialized atomTypeMaxCutoff(i) to zero
wrote createGtypeCutoffMap
made some changes for implementing the wolf potential
updated getEAMCut
added some probably nonfunctional get*cut routines
Added eamType map to atid map.
fixing some of the problems in the interactionHash and gtypeCutoff routines
added fCutoffPolicy.h
breakage in progress
putting spaceballs back where they belong
Complete rewrite of Lennard Jones module
Breaky Breaky BREAKY breaky breaky
In process of re-write for group based cutoff....
fixes in progress
fix a bug which does not update me_i and me_j correctly
Changed cutoffs... Segfaults nicely now...
fixed ACX_MPI to ignore some text error messages from pathscale compiler
std::bind2nd is in <functional>
replace c++ style comment in c files
Added subroutine to set cuttoff for Interaction map and function in simulation.F90 to determine if a particular atype is present in a simulation.
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More breaking and destruction of force code. Does not build at this point...
Breaky breaky!
fixed a bug and ran a simulation
working version of DensityPlot
Changes to remove angular momentum.
Fixed bug in typo in nanorodBuilder.
Added method to remove system angular momentum to velocitizer and added method to calculate system angular momentum to siminfo.
Removed balance from the Darkside (files)
Removed balance from doForces
Updated tap sample
Included a tap dimer for testing purposes
Re-entered the TIP4P-Ew water model. It was apparently wiped earlier this month...
ran make cvslog
adding AtomNameVisitor
dding resetIntegrator
adding resetIntegrator
adding DensityPlot into StaticProps
adding SCDOrderParameter into StaticProps
adding AtomNameVisitor to convert atom name to its base name; wrappingvisitor now wrap back to the center of the mass; adding P2OrderParameter into StaticProps
Fix to print pressure tensor.
adding keyword printPressureTensor
NPrT in progress
NPrT in progress
NPAT is working
fix bug in NPAT and NPrT
adding NPAT and NPrT integrators
just some tap changes
Modifications to temper the dipolar strength in the first solvation shell for tap
added a tap example for testing purposes
Modifications to tap. Also correcting changes to the previous merge that were not caught
Fixed merge issues between Kyle and Chris so OOPSE will actually build.
help
added gb
Better tap
Couple of changes for TAP water. Need to parametrize.
Fixed build issues under ifc7.
More geometry builder changes.
Changed SHED to TAP
OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it...
Adding support for generic geometry to nanorodbuilder.
More changes to nanoRodBuilder....
*** empty log message ***
Added TIP4P-Ew
Fixed issues with nanoRodBuilder....
Got rid of write statements and am closer to a working shapes
Fixed gcc4 bug...
adding CharClassificationFunctor to fix the locale problem of c++
Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
axed because file causes havoc on Mac (capitalization confusion of filenames)
Working on the shapes parser...
gmake in case people forget
fixed the spacing on the banner. Vanity.
Version string in banner (and version numbers in config.h)
Documentation changes
xemacs has been drafted to perform our indentation services
Jedi mind-trick warning messages have been added to make users ignore CGAL.
fix make install
add Makefile of samples
some samples are not installed correctly
configure now searches for perl to use with filepp
Fixed a bug in RigidBodyStamp section of MoLocator
*** empty log message ***
nanorodbuilder now exit's when libCGAL is not present.
fix one more warning message in make_nodes
Changed interface name for SGI Compiler
oops... bad sample
Change typo in CGAL.
fix some warning messages
added CGAL checks
Added destroy methods for Fortran modules.
Added destroy method to clean up memory
more memory leak are fixed
File not needed for nanoRodBuilder.
fix memory leak in nanorodBuilder and simpleBuilder(forget to delete lattice)
refactory lattice
refactory LatticeFactory and LatticeCreator
refactory LatticeFactory and LatticeCreator
refactory LatticeFactory and LatticeCreator
cleaned up vector_class memory leak fix by deallocating in reverse order of how we allocated. Also migrated MoLocator into utils directory
added lattice directory
added lattice directory, so all of these files are now redundant
cleaned up memory leak fix
added lattice subdirectory
no real changes here, maybe added a space by accident
added quadrupole sample
updating samples
destory atom type in fortran side
Further changes to vector_class destroy function.
Fixed pointer memory leak in vector_class.
Updates to deallocate object in fortran.
minor change to TI output
Changes to delete atypes...
Added code to delete vector.
avoid multiple inherit in basic_ifstrstream
Importing nanoRodBuilder application (may not work yet). ((Doesn't work yet.)) (((May never work....)))
forget to delete prepareVisitor in Dump2XYZ
fixing of the quadrupoles. look! it's divide by 3 like stone says!
fixing of the quadrupoles
change the parameter name in constructors
One more bug fix for GNU make versions < 3.80
Fixed the uc and lc functions for GNU make versions < 3.80
added some stuff to clean out module files during "make clean"
quadrupole interactions should be working with a remaining question of interaction magnitude
messing with samples
oops... messed up a sample
Altered signs to fix charge-dipole interactions
changes during debug of charge-dipole
added Cl- and Na+
reinitialize buffer_stack_ptr in BASS parser
support '+' and '-' in atom type name;clean the code a little bit
fix a bug in converting rotation matrix to quaternion
fixed the wrapping
LipidTranVisitor should do the wrapping
fix a bug in getting the dimension of histogram
avoid building parallel executable for dump2XYZ, simpleBuilder, staticProps and dynamicProps
Corrected changes to the forcefield files
Make sure electrostatic_module provides data for reaction_field
Chris debugging stuff. HE WILL CHANGE THIS BACK, RIGHT?
constant back to correct value
fixed an install-related bug. $(InstallCommand) had been set to $(InstallData)
VelocityVerletIntegrator already deletes and Nullifies restWriter, so Integrator shouldn't do it.
fixed three typos
first run at charge-quadrupole interactions
forgot a couple of makefiles
added some samples
fix a typo in MultipoleAtomTypesSectionParser
pairs inside cutoff group should not be excluded
settled on a unit for quadrupoles
quadrupoles for SSD models
clean up SimInfo; modify the images of SelectionExpression.html
fixed a bug in MPI restraints
adding exclude pairs for rigidbody and cutoff group
fixed a doxygen problem
messing with the split dipole test cases
updated some documentation
LinkedList removal project starts now
using map to replace link list
adding test case of split dipole
Oops... MPI now builds...
adding test case for split dipole
added fortran-side support for split dipoles
fixes to restraints
fixing restraints
minor change
First commit of the new restraints code
adding IndexFinder
fix compilation issue
fix a bug in SectionParser (lineNo is not updated)
adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
change the format of DUFF2
new electrostatic module
added splitDipole and fixed quadrupole stuff
removed #include lines for outdated charge and dipole interfaces
addded a few fun charge-dipole test cases
fixing a strange icc8 bug (we think).
OOPSE_itoa!
Electrostatic Unification Project
Dunno
Using OOPSE_itoa and checking a NULL left over from the LinkedList days
electrostatic unification project fixed an uninitialized variable in Lennard Jones mixing map
electrostatic unification project
making some cool test cases
Added a charge for Chlorine
Fixing a bug in BitSet.cpp
SPRNG eradication project
Cleaning up config.h.in by adding comments
avoid using const char*(hope can fixed the missing atom type problem)
adding base class of Random Number generator
info_ in Velocitizer is not initialized which causes a seg fault
remove default parameter from MersenneTwister.hpp which causes all kinds of trouble. Refactory random number generator
Adding unit test for random number generator
fixed a file inclusion problem
fixed compilation problem
replace SPRNG by MTRand
Change the name of test case
adding testcase for random number generator
fix compilation problem for g++ 3.4
adding OOPSERandNumGen
Fixed the damned build problem with the libraries not being removed in make clean and make distclean (at least we think it is fixed).
Making small modifications to allow for use on MPI machines
adding MersenneTwister random number generator
Adding a modified version of MersenneTwister.hpp
selection expression
adding soft potential to LJ Module
adding documentation for selection expression
adding basic_teebuf which can operate on multiple stream simutaneously.
Added ssdrf sample
reactionfield get fixed
Fix a bug in GofRAngle
Fix for compilation on the Sun
fix for compilation on the Sun
fix problem in sun
adding LipidTransVisitor, GofXyz is working now
Corrected filename collision for EAM on Mac OS X
Updated copyright information
corrected filename collision for EAM on operating systems which are not case sensitive (aka Mac OS X)
more bug get fixed
fix a bug in GofXyz
make processHistogram non-abstrct function
*** empty log message ***
finish GofXyz
change the output format of 2D radial distribution function
forget the const correctness for BitSet
The change of interface of BitSet cause a bug in SelectionEvaluation
return residentMem in byte
fix a bug in writing out the value of cosang
using PhysMem - RSSMem to estimate avaliable memory
change the default bin number
change the suffix of output files;fix the problem of counting in staticProps
fix a bug in BlockSnapshotManager
BlockSnapshotManager is using reference counting now
replace std::make_pair by VariablesType::value_type to make Sun Compiler happy
adding typedef to TokenMap, using TokenMapType::value_type instead of std::make_pair to make Sun compiler happy
bug fix in StaticProps
(1) adding #ifdef __RWSTD to make sun compiler happy (2) fix pair density calculation problem when two selections intersect with each other
cast of NULL to satisfy xlc++
*** empty log message ***
bug fix for null termination
bugfixing residentMem
bugfixes for residentMem on LINUX
added residentMem
modifications to estimate memory in use by other processes autoconf fixes ps syntax checking config.h file cleaning
ps niceness
ps strangeness
fix a bug in BlockSnapshotManager.hpp
default length for staticProps is 1/2 smallest length of first frame
fix a bug in VelocityVerletIntegrator : last frame is written twice
begin bug fix
refactory CorrelationFunction
bug fix and start of switch for type of correlation function
fix a bug in calculating bytes per stuntdouble
more fix
fixed a bug in CorrelationFunction
fixed a bug in SimInfo::getCutoff()
adding staticProps and dynamicProps into Makefile.in
maximum length defaults to the cutoff radius
adding Algorithm.hpp
dynamicProps get built
dynamicProps in progress
more work in dynamicProps
adding dynamicProps
adding command line option to DynamicProps
adding command line option for DynamicProps
adding dynamicProps
adding SelectionManager.cpp
adding one more constructor to Snapshot to create customized DataStorage
adding beginSelected, nextSelected method to SelectionManager
adding support for physmem
adding supprot for physmem
adding physmem
more work in StaticProps
change the filenames
adding GofRAngle
remove some useless files
staticProps in progress
adding GofR
add getRigidBodyAt function into Molecule class
update help info
support select internal index selection, for example, select DMPC.3
update help info for Dump2XYZ
selection librarys added
adding Makefile
issue commented out in wildcards
forget to reset the pc which cause reevaluate return NULL
fix a bug in determing the global index for rigidbodies
minor change in Bitset
selection library is working
remove SelectionVisitor
IgnoreVisitor and XYZVisitor now use selection library
adding SelectionManager into SimInfo
dump2Xyz now take advantage of selection library
minor change in BitSet
adding missing implementation
half of the selection utility is working need to debug within keyword and atomproperty keyword
selection library get built
fix BitSet
remove some useless files
adding wildcard class; NameFinder is finished
more work in selection library
selection in progress
selection library in progress, except SelectionEvaluator, other files are compiled
adding boost::any
add SelectionCompiler.cpp
Selection in progress
adding selection library
forget to add eorWriter
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the wrong column of electroframe
fix a bug in SimInfo, use number of cutoff stamp as counter to loop over rigidbody stamp
(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
forget to set dipole for lipid head group
fix a bug in loading initial extended system parameters
forget to set maxIterNum_ in NVT
remove WATER.cpp
sync Makefile
moved Package variable into subdirectory makefiles to speed up the building process
Fixed publication details in banner
added dummy subroutine to avoid empty unit, synchronized this dummy routine between C and fortran
separating modules and C/Fortran interface subroutines
more fixes for gnugetopt
fixing for gnugetopt
using c library to do conversion instead of using iostream due to a bug in libstdc++(GCC 3.2)
no message
fix a bug in global index
remove include Integrator.hpp in Minimizer
compile getopt and getopt1 if we need to
template flags
formatting
fixed a MakeDir / MkDir problem added BinDir target
port to SGI platform
change the order of linking (object file comes first and then follow by user built library)
remove useless debug info
minor fix
missing tab
missing tab
LinearVisitor get fixed
merging new_design branch into OOPSE-2.0
remove some useless force fields
adding new format of EAM force field
rename newDUFF.frc to DUFF2.frc
Fixed Makefile test bug under OSX and possibly other BSD's, replaced test -f *.mod with ls function since BSD test apparently doesn't support wildcards.
adding new EAM force field files
fix another bug in WATER.cpp
fix a bug in WATER.cpp when initializing the new Charge AtomType
*** empty log message ***
merge WATER force field into DUFF
change the force constant of bonds
minor fix in DUFF
minor fix in force field file
minor fix
new ForceField format
replace misuse of using namespace std in header files
fixed a sample
spell check
add PolynomialTestCase
Addint StringTokenizerTestCase
change Makefile
improved restraints - mpi should work fine
improved restraints
oops...
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
new DUFF forcefield
adding new format DUFF force field
Fixed a mixing list bug that slowed down the force loop
working sample
working towards parallel restraints
Commented out some write statements
Got rid of some write statements
Fun with ice
Added the linear visitor
current status of the debugging process
included visitors and minimizer
new changes
time to break SimSetup
added new classes in progress
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
mess up ......
Shapes looks like it's working
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 !!!
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
*** empty log message ***
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
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
*** empty log message ***
fix make install
adding make install
add Makefile to sample directory
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
cleaning up
Cleaning up a bit
fix make statistics
adding GNU make functions to combine all of the static libraries to a big library
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
*** empty log message ***
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
Import of OOPSE v. 2.0
Standard project directories initialized by cvs2svn.