units for thermalConductivity, spelling error fixed
added viscoConvert
General bug-fixes and other changes to make particle pots work with the Helfand Energy correlation function
A few simple mods to remove gcc compile warnings
Fixes for Inversions for use with Amber
Fixed MPI bug in opening elements.txt.
Added large quantities of code for convex hull and constant pressure langevin dynamics.
Added some logic to print out a special pair distance as a column in the stat file. To use this feature, use taggedAtomPair = "0, 10" and printTaggedPairDistance = "true" in the md file. Then, the distance between integrableObjects 0 and 10 will be computed and printed in the stat file on each statWrite.
Inversion fixes and amber mostly working
Many fixes
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
Adding infrastructure for Amber force field.
A bunch of minor changes to make MPI compilation faster than the double compilation we do now...
updating configure process
Fixed for MPI.
fixed bug in physmem for 64 bit machines
Removed older version of openbabel from our code. We now have a configure check to see if openbabel is installed and then we link to the stuff we need. Conversion to OOPSE's md format is handled by only one application (atom2md), so most of the work went on there. ElementsTable still needs some work to function in parallel.
fixing bugs in randomBuilder
fixed a DumpReader bug, took out extra printing statements in residentMem and BlockSnapshotManager
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.
testing GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor
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).
Adding single precision capabilities to c++ side
Adding single precision capabilities to the fortran side
Getting fortran side prepped for single precision...
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Complete rewrite of spline code and everything that uses it.
Many performance improvements
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"
refactor Hydrodynamics module.
change the epsilon of numeric_limit
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X
autoconf modernization and cruft removal
instead of printing to std::cout, throwing an exception when error is found.
replace isType<int> with isInteger
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.
fixed compilation problem for icc7
added missing include
adding more checking for topology
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
compilation bug
OptionSectionParser get compiled
ForceField optional parameters....
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.
Breaky breaky!
adding SCDOrderParameter into StaticProps
NPrT in progress
Fixed build issues under ifc7.
Fixed gcc4 bug...
adding CharClassificationFunctor to fix the locale problem of c++
xemacs has been drafted to perform our indentation services
Fixed a bug in RigidBodyStamp section of MoLocator
more memory leak are fixed
cleaned up vector_class memory leak fix by deallocating in reverse order of how we allocated. Also migrated MoLocator into utils directory
Further changes to vector_class destroy function.
Fixed pointer memory leak in vector_class.
Added code to delete vector.
added some stuff to clean out module files during "make clean"
OOPSE_itoa!
Fixing a bug in BitSet.cpp
fix compilation problem for g++ 3.4
fix for compilation on the Sun
fix problem in sun
forget the const correctness for BitSet
return residentMem in byte
change the suffix of output files;fix the problem of counting in staticProps
(1) adding #ifdef __RWSTD to make sun compiler happy (2) fix pair density calculation problem when two selections intersect with each other
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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
adding Algorithm.hpp
dynamicProps get built
adding physmem
issue commented out in wildcards
minor change in Bitset
minor change in BitSet
fix BitSet
adding wildcard class; NameFinder is finished
adding boost::any
Selection in progress
adding selection library
moved Package variable into subdirectory makefiles to speed up the building process
fixing for gnugetopt
using c library to do conversion instead of using iostream due to a bug in libstdc++(GCC 3.2)
compile getopt and getopt1 if we need to
port to SGI platform
merging new_design branch into OOPSE-2.0
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
Adding Generic TupleMatcher, wild char matching is on the way
Adding Generic Tuple3 and Tuple4
adding GenericFactory Test Case. GenericFactory now can bed used to creat ForcefieldFactory and IntegratorFactory etc.
more classes get reconstructed
GenericFactory pass unit test
remove some junk files
replace old GebericData with new GenericData
GenericData and PropertyMap pass unit test.
namespace problem prevented linking
more fortran name mangling
working on shapes for portability
changed around findBegin
more tests on math library
fix some bugs in Quaternion class
Working on getting Shapes into OOPSE
adding generic factory and vector test case
adding PropertyMap class
moved the getopt stuff
define DEV_ROOT as relative path
change Makefile to relative path
remove StringUtils.c which cause headache in bulding libutils
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change the #include in source files
Import of OOPSE v. 2.0