The Programs:

• simulation codes:
  • gcmc.x --- serial program to do Grand Canonical Monte Carlo simulations. (Can also, trivially, handle Canonical Monte Carlo.) This now works for N-component mixtures.
  • gemc.x --- serial program to do both traditional and constant-pressure (for binary mixtures) Gibbs Ensmble Monte Carlo simulations.
  • pgcmc.x --- parallel implementation of Grand Canonical Monte Carlo program. This program requires a working implementation of the SPRNG parallel random number generator. It has essentially the same functionality as the serial GCMC program, and is implemented using a domain-decomposition approach.
  • md.x --- serial program to do molecular dynamics simulations using one of several integration algorithms, including constant-T and constant-T,P simulations.
  • pmd.x --- parallel implementation of molecular dynamics program, with essentially the same functionality. This is accomplished via a domain-decomposition approach, and has been tested on as many as 217 processors.

• analysis codes:
  • xhist --- performs local density and mole-fraction histogramming. Has optional "interface removal" code as well.
  • vlica --- Vapor/Liquid interface analysis code; experimental.
  • counter --- counts the size and number of clusters of a single species in a configuration file.
  • grid_dvdr --- obtains the cumulative volume curve used in geometrical measurements of pore size distribution.
  • mdstats.x --- reads in a set of configurations, optionally performs short molecular dynamics runs on each of them, and calculates several statisical averages. Mostly obsolete, and currently not functional.
  • rdf_sample --- caculates radial distribution functions by statistical sampling, rather than the full N*(N-1) loop.
  • rdf_imsamp --- as rdf_sample, but also includes first periodic images in the calculation.
  • stereo --- performs a number of stereological calculations on a pore system configuration file. Not wholly functional at this time.

• visualization codes:
  • toxyz --- converts a formatted configuration file into a .xyz file, primarily for use with the xmol or rasmol programs.
  • toxyz_2 --- converts a two-box formatted configuration file into a single .xyz file.
  • animate --- reads a series of configurations from an unformatted dump-file, and outputs concatenated .xyz molecular configuration files; for use with the xmol program, primarily.
  • fillet --- takes a big configuration file and "fillets" it into 16 slab-sections, which are laid out in a plane. Useful for looking at porous matrices.
  • topov --- the most sophisticated viz program here; this generates one or many scene files for rendering with POV-RAY; it can optionally perform many manipulations on a porous substrate, and can color atoms by their instantaneous potential energies. For some graphics done with this program and POV-RAY, see my CPG visualizations page.

• utility programs:
  • ic.x --- generates starting configurations for one, two and three-dimensionally periodic simulation cells.
  • ic_gemc.x --- generates starting configurations for one, two and three-dimensionally periodic "two-box" systems for use in GEMC calculations.
  • boxrep --- creates a big 3D simulation cell by periodic replication of a smaller one.
  • carve_config --- performs geometric particle removal from a simulation cell.
  • merge_configs --- merges two simulation cells, removing overlapping particles.
  • move_species --- another configuration editor; adds/deletes atoms of specified type, and converts between fluid and wall atoms.
  • nxtrim --- randomly removes particles and changes species until a specified density and mole fraction are achieved.
  • shave --- finds uncoordinated particles and "shaves" them off. Used in preparation of model pore systems.

Obsolete Programs. A number of other programs were developed for my work on liquid-liquid mixtures and phase-separation in very long cylindrical pores. Because these programs were very specialized and difficult to use, they have not been included in this distribution. Nearly all of their capability has been included in the present codes, or could be added with minor modifications.

• xesgmc.x --- histogram-biased Semi-Grand Monte Carlo serial program, used in confined liquid-liquid studies. Since I did this work considerably better histogram methods were developed that did not rely on biasing functions, which should be used in future work; this would only require trivial modification of the gcmc.x code plus some post-run analysis programs. (See Panagiotopoulos' group pages and papers for more info.)
• p-xesgmc.x --- parallel version of xesgmc.x that ran independent simulations on each processor and averaged all the data. Later versions could run different umbrella-biasing functions on each processor as well. This approach was dropped because it failed for large systems, which was the whole point of using it in the first place.