cleaning up the development branch a bit, removing cruft, etc.
Merging changes from old branch into development branch
removed spurious prints, fixed one bug, but there's still a parallel problem
Completing the Fortran removal project. Fixes for compilation with clang / llvm, debugging, removing code that we'd never used.
Creating busticated version of OpenMD
Adding 2-D g(r) module to static props
Changes to gofrz so you can specify the z length
More changes to gofrz.
Adding property set to svn entries
forgot the output file name
Adding a new correlation function to do slab-segregated g(r) calculations. This computes at g(r) for pairs while requiring the z coordinates of the two sites to be at fixed separations. The data is output in: r, z, g(r,z)
Adding a progress bar, and pAngle staticProps
Cleanup of unit normal code in Triangle.cpp SMIPD now call getUnitNormal instead of getNormal.
Added preliminary code for Alpha Hull calculation using qhull. Added preliminary support to SMIPD to support Alpha Hull. Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. Preliminary changes for shadow hamiltonian integrator. Chages to md files so they will work in openMD.
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
Removing CGAL
Returned old LD forces to SMIPDForceManager.
Fixed nanovol so it now builds.
Added large quantities of code for convex hull and constant pressure langevin dynamics.
Many fixes
Fixed a number of bugs in slab_density calculation
Correcting a few typos
Adding GofZ.cpp
Adding GofZ.hpp
fixed a few correlation functions
Fixes for building.
Check CGAL and qhull defines
Many fixes for Charmm-type torsions.
Added more chamges to nanovol.
Added volume calculation for hull.
Case typo in Vector.hpp
Testing files for NPT Langevin dynamics convex hull calculation.
Added code to compute bond angle distributions.
Build change.
Fixed more bugs and removed more CGAL.
Removed CGAL from OOPSE and replaced it with qhull.
Added Bond Order Parameter as a function of radius.
bug fixing Wigner 3-j import to C++
fixes for BOP
Fix to makefile.
Histogram bin change.
Added support for nanoparticle density profile.
possible fix for unnormalized BO
fixing a wrapVector problem in staticProps, also making Shifted force and electrostatic damping the default behavior
Cleaned up the code for BondOrderParameter and added a bunch of comments. Fixed a memory leak or ten.
Some efficiency fixes (now computes Wigner 3-j coefficients only once in the constructor).
Mostly done with BondOrderParameter. Only a few performance tweaks remain
fixing bond order parameter code
bug fixes (still broken, however)
Following Rein ten Wolde article
more bug fixes
more changes to BOP and SH
Fixed a bug in Wl code in BondOrderParameter
Bugfixes in BondOrderParameter and SphericalHarmonic
added SphericalHarmonics, fixed a few problems with BondOrderParameter
fixed bugs (mostly in BondOrderParameter)
Adding BondOrderParameter to StaticProps
Working on BondOrderParameter
Latest Version
Changing utility programs to use the new file format
Adding more changes to orientational bond order parameter.
Beginnings of a order parameter.
Adding code for bond orientational parameters.
Add the RippleOP to calculate the orderparameter of the ripples.
fixed an initialization bug of Hxy.cpp.
fixed the bugs of Hxy.cpp.
Adding single precision capabilities to c++ side
Autoconf fixes for FFTW. Multiple FFTW version support.
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Changes to calculate undulation spectrum
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Fixed a double/int bug. Surprised no one ever noticed before...
instead of printing to std::cout, throwing an exception when error is found.
fixing RhoZ
Code to calculate rho(Z) to calculate density profiles for water slabs.
std::bind2nd is in <functional>
fixed a bug and ran a simulation
working version of DensityPlot
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
xemacs has been drafted to perform our indentation services
fix a bug in getting the dimension of histogram
avoid building parallel executable for dump2XYZ, simpleBuilder, staticProps and dynamicProps
Fix a bug in GofRAngle
adding LipidTransVisitor, GofXyz is working now
more bug get fixed
fix a bug in GofXyz
make processHistogram non-abstrct function
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finish GofXyz
change the output format of 2D radial distribution function
fix a bug in writing out the value of cosang
change the default bin number
change the suffix of output files;fix the problem of counting in staticProps
BlockSnapshotManager is using reference counting now
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
default length for staticProps is 1/2 smallest length of first frame
fixed a bug in SimInfo::getCutoff()
maximum length defaults to the cutoff radius
adding dynamicProps
more work in StaticProps
change the filenames
adding GofRAngle
remove some useless files
staticProps in progress
adding GofR