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PM-Dreamer: Genetic Programming for Functional Optimization of Force Fields

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PM-Dreamer: Genetic Programming for Functional Optimization of Force Fields

Copyright (2009) Sandia Corporation.  Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software.  This software is distributed under
the GNU General Public License.

----------------------------------------------------------------------


#############################################################################
# 1. Directory Contents
#############################################################################

./bin     Location of executables
./data    Sample data for Lennard-Jones and Stillinger-Weber Targets
./doc     Documentation for executables
./libs    External libraries required for GP_Force
./obj     Location of object files
./src     Location of source files
./param   Various GP parameter files for symbolic regression


#############################################################################
# 2. Installation from $ROOT_DIR
#############################################################################

# ------- GSL
/tmp> tar -zxvf $ROOT_DIR/libs/gsl-1.9.tar.gz
/tmp> cd gsl-1.9
/tmp> ./configure
/tmp> make
/tmp> su -c "make install"
# ------- Beagle
/tmp> tar -zxvf $ROOT_DIR/libs/beagle-3.0.3.tar.gz
/tmp> cd beagle-3.0.3
/tmp/beagle-3.0.3> ./configure --enable-optimization CPPFLAGS=-DNDEBUG CXXFLAGS='-march=i686 -ffast-math -O3'
/tmp/beagle-3.0.3> make
/tmp/beagle-3.0.3> su -c "make install"
/tmp/beagle-3.0.3> cd ..
# ------- Beagle Visualizer
/tmp> tar -zxvf $ROOT_DIR/visualizer-0.2.1.tar.gz
/tmp> cd visualizer-0.2.1/
/tmp/visualizer-0.2.1> ./configure
/tmp/visualizer-0.2.1> make
/tmp/visualizer-0.2.1> su -c "make install"
# ------- GP_Force
# GP_Force can be run in serial or in parallel. This can
# be altered by editing the file $ROOT_DIR/src/Makefile.vars
# to choose the appropriate compilation parameters.
cd $ROOT_DIR/src/pm_dreamer
make

#############################################################################
# 3. Local Installation from $ROOT_DIR to $HOME_DIR
#############################################################################

For a local installation (in home) follow the steps above, but configure with:

/tmp> mkdir $HOME_DIR/gsl-lib
/tmp> mkdir $HOME_DIR/beagle-lib

# for GSL

/tmp> ./configure --prefix=$HOME_DIR/gsl-lib

# for Beagle

/tmp> ./configure --enable-optimization CPPFLAGS=-DNDEBUG CXXFLAGS='-march=i686 -ffast-math -O3' --prefix=$HOME_DIR/beagle-lib

#############################################################################
# 4. PM-Dreamer
#############################################################################

This program will perform genetic programming optimization of functional
forms for force-fields.

TWO-BODY EXAMPLE: 4*(x^-12-x^-6)

cd /tmp
$ROOT_DIR/bin/pm_dreamer $ROOT_DIR/data/lj3.pair $ROOT_DIR/param/pair-generational.conf -s CORR

or

mpirun -np 2 $ROOT_DIR/bin/pm_dreamer $ROOT_DIR/data/lj3.pair $ROOT_DIR/param/pair-generational.conf -s CORR

THREE-BODY EXAMPLE: f=sum(4.32*r^2+2.36)+sum(-1.51*(r1*r2+a)+.045)

$ROOT_DIR/bin/pm_dreamer $ROOT_DIR/data/madeup.twothree $ROOT_DIR/param/three-generational.conf -s CORR -t twothree

or

mpirun -np 2 $ROOT_DIR/bin/pm_dreamer $ROOT_DIR/data/madeup.twothree $ROOT_DIR/param/three-generational.conf -s CORR -t twothree


Documentation of parameters is in the doc/ directory.


#############################################################################
# 5. vis_gp
#############################################################################

This is a script for visualizing results from PM-Dreamer on a UNIX-like
system. It requires that the ImageMagick 'convert' be in the
current path. It takes a single argument
which is the directory for the visualization output files. Upon successful
completion, an html browser can be used to visualize the results. It must be
run in the directory containing PM-Dreamer .log and .obm files.

cd /tmp
$ROOT_DIR/bin/pm_dreamer $ROOT_DIR/data/lj3.pair $ROOT_DIR/param/pair-generational.conf -s CORR
$ROOT_DIR/bin/vis_gp ./vis_dir
firefox ./vis_dir/index.html &


#############################################################################
# 6. get_fitness
#############################################################################

This is a script for extracting the best fitness from a log file or
set of log files:

$ROOT_DIR/bin/get_fitness *.log

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