This directory contains initial setup files for a replica exchange
Monte Carlo/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 swaps of atomic species
within the run at a given temperature, and then 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 MoNbTaW-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.

To perform a run in MoNbTaW-ready, first carry out a single step of
MCMD with a command such as
for r in run* ; do cd $r ; qsub ../pbs_remcmd1 ; 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 "./remcmd1.py".  The queuing option
"./remcmd1.py -q" will submit the pbs_remcmd1 jobs.  It is convenient
to run a while loop to periodically execute "remcmd1.py -q" so as to
continue cycling automatically (see while.cmd).

The directory MoNbTaW-done contains a complete worked example of
hybrid MC/MD with replica exchange for a small 16-atom system.  See
diagnostic files Tvst.pdf, Fvst.pdf, FatTvst.pdf and Fhist.pdf.

MCMD scripts in order of calling -
1. pbs_remcmd1 is a PBS job script (as used at CMU)
2. mcmd1.sh performs an MD run then calls mc.py once
3. mc.py executes a Monte Carlo swap
4. vasp.cmd contains the command line to run VASP (here as implemented at CMU)
5. mcmdrename copies MD run files and appends cycle number Nrun
6. stats is a utility program to report species swap acceptance rates
7. while.cmd is an example looping script to automatically continue the process
8. clean-run will remove many run files leaving the system ready to start fresh
9. 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. M. Widom, W.P. Huhn, S. Maiti and W. Steurer, "Hybrid Monte
Carlo/molecular dynamics simulation of a refractory metal high entropy
alloy", Met. Mat. Trans A 45 (2013) 196-200 (http://arxiv.org/abs/1304.7800)

I thank Chris Woodward and Jim Lill for useful discussions and
inspiring this public code distribution. This current version works at
fixed volume (i.e. neglects thermal expansion). An alternate version
including thermal expansion will be released in the future.