This directory contains initial setup files for a replica exchange
molecular dynamics run that couples replica exchange (parallel
tempering) with hybrid MC/MD. The programs will cycle between MD
simulations run in parallel at several temperatures, and a Monte Carlo
phase. The Monte Carlo attempts to swap temperatures between different
runs.  The setup here is optimal for a private computer cluster where
it is allowed to submit multiple short independent jobs, but it can
easily be modified to run on a supercomputer cluster efficiently
utilizing many nodes.

The directory B-ready contains an initial example setup ready to run.
Specifically, one needs a collection of "run" directories, e.g. run0,
run1, ..., each of which contains the standard input files for a VASP
MD run. It must also contain a file Trun with the initial temperature
at which the run will occur, and Vrun with the initial volume
appropriate for that temperature (this version allows for volume
expansion).

To perform a run in B-ready, first carry out a single cycle of
MD with a command such as
for r in run* ; do cd $r ; qsub ../pbs_remd1 ; cd - ; done
This will serve as a test of your configuration and will produce files
named "output" containing the standard outputs of the VASP runs that
are needed to proceed.  After this, a single step of replica exchange
may be performed via the command "./remd1.py".  The queuing option
"./remd1.py -q" will submit the pbs_remcmd1 jobs.  It is convenient to
run a while loop to periodically execute "remd1.py -q" so as to
continue cycling automatically (see while.cmd).

The directory B-done contains a complete worked example of replica
exchange for a 107-atom boron system.  See diagnostic files Tvst.pdf,
Fvst.pdf, FatTvst.pdf and Fhist.pdf.

REMD scripts in order of calling -
1. pbs_remd1 is a PBS job script (as used at CMU)
2. md1.sh performs a single MD run
3. vasp.cmd contains the command line to run VASP (here as implemented at CMU)
4. mcmdrename copies MD run files and appends cycle number Nrun
5. while.cmd is an example looping script to automatically continue the process
6. clean-run will remove many run files leaving the system ready to start fresh
7. disentangle will reconstruct sequences of configurations with common temperatures

If you use these programs for published research, please cite the
papers:
1. M. Widom, P. Ganesh, S. Kazimirov, D. Louca and M. Mihalkovic, "First-principles
simulation of supercooled liquid alloys", J. Phys.: Condens. Matter 20 (2008) 114114
http://euler.phys.cmu.edu/widom/pubs/PDF/JPhysCondMat20_2008_p114114.pdf
2. P. Ganesh and M. Widom, "Liquid-liquid transition in supercooled silicon determined by first-principles simulation", Phys. Rev. Lett. 102 (2009) 075701
http://euler.phys.cmu.edu/widom/pubs/PDF/PhysRevLett_102_075701.pdf