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PM-Dreamer: Genetic Programming for Functional Optimization of Force Fields
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sandialabs/pm-dreamer
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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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