forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4679 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
8b9c8ed7a9
commit
4df5a5dee0
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@ -20,7 +20,8 @@ createatoms generate lattices of atoms within a geometry
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data2xmovie convert a data file to a snapshot that xmovie can viz
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eam_database one tool to generate EAM alloy potential files
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eam_generate 2nd tool to generate EAM alloy potential files
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eff scripts for working with the EFF (electron force field)
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eff scripts for working with the eFF (electron force field)
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ipp input pre-processor Perl tool for creating input scripts
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lmp2arc convert LAMMPS output to Accelrys Insight format
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lmp2cfg convert LAMMPS output to CFG files for AtomEye viz
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lmp2traj convert LAMMPS output to contour, density profiles
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@ -11,5 +11,8 @@ The tool is authored by Xiaowang Zhou (Sandia) who can be contacted at
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xzhou at sandia.gov for questions.
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Sample build of program:
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gfortran createAtoms.f which produces a.out
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This tool can be used in conjunction with the ipp tool for creating
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its input commands. See tools/ipp/README.txt for an example.
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@ -0,0 +1,29 @@
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Ipp is a Perl script for facilitating the creation of a complicated
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file (say, a lammps input file or tools/createatoms input file) using
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a template file.
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ipp was created and is maintained by Reese Jones (Sandia), rjones at
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sandia.gov.
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Example 1:
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If one has a template for a long lammps input file called
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"template_lammps.input" where a few parameters need to be changed. One
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can define these parameters in a short file called
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"fill_parameters_lammps.input" and execute "ipp -p
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fill_parameters_lammps.input template_lammps.input >
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lammps.input". The file "lammps.input" file will be the final lammps
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input file.
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Example 2:
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If one has a template for a long createAtoms input file called
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"template_createAtoms.input" that creates double elpasolite
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crystals. One wants to change the lattice constants and tilting angle
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of the octahedrons. One can define these parameters in a short file
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called "fill_parameters_createAtoms.input" and execute "ipp -p
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fill_parameters_createAtoms.input template_createAtoms.input >
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createAtoms.input". The "createAtoms.input" file will be the final
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createAtoms input file. If one has an excetable for createAtoms called
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"create", one can simply execute "create<createAtoms.input" to create
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the crystal that LAMMPS can read.
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@ -0,0 +1,15 @@
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amass1= 132.899994
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amass2= 22.9899998
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amass3= 138.899994
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amass4= 126.900002
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amass5= 1.
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ielement1= 55
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ielement2= 11
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ielement3= 57
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ielement4= 53
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ielement5= 1
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n1=3
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n2=3
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n3=3
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a=11.0
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theta=10.0
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@ -0,0 +1,3 @@
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Tmid=300
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Tbnd=300
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NPTave=10000
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@ -0,0 +1,290 @@
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#!/usr/bin/perl
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# ipp: a preprocessor script
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# author : Reese Jones rjones@sandia.gov (based on dprepro [Sandia])
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# to do :
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# priority (overide file defaults e.g. a=1 pfile a=2 -> a=2)
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# also order precedence: a=10 -p p.file b=12
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# nested if/else/endif blocks
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# Regular expressions for numeric fields
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$e = "-?(?:\\d+\\.?\\d*|\\.\\d+)[eEdD](?:\\+|-)?\\d+"; # exponential notation
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$f = "-?\\d+\\.\\d*|-?\\.\\d+"; # floating point
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$i = "-?\\d+"; # integer
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$ui = "\\d+"; # unsigned integer
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$n = "$e|$f|$i"; # numeric field
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# Read command line arguments
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while (scalar(@ARGV)) {
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$arg = shift(@ARGV);
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if ($arg =~ /-p/) { $parameter_file = shift(@ARGV);
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parse_parameter_file($parameter_file);
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}
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elsif ($arg =~ /-o/) { $new_file = shift(@ARGV); }
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elsif ($arg =~ /=/) { ($tag,$value) = split(/=/,$arg);
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$values_p1{$tag} = $value;
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}
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else { $template_file = $arg; }
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}
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# Check for correct command line arguments
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if( ! defined($template_file) ) {
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print STDERR "Usage: ipp <-p parameters_file> <name=value> template_file <-o new_file>\n";
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print STDERR " note: \"value\" must be numeric (not a character string)\n";
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print STDERR " parameter file format : name = value\n";
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print STDERR " or : value name\n";
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print STDERR " template file example: modulus is {10.0*name +3.2}\n";
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exit(-1);
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}
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# output
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$output_fh = \*STDOUT;
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if( defined($new_file) ) {
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open(NEW,">$new_file");
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$output_fh = \*NEW;
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}
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output($template_file,$output_fh);
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if( defined($new_file) ) { close(NEW); }
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# debug : print key--> value
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#foreach $key (sort keys %values_p1) {
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# print "# $key ---> ",$values_p1{$key},"\n";
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#}
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###########################################################################
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# parse parameter file
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###########################################################################
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# Read parameters file, extract tags and corresponding values in either aprepro
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# "{ tag = value }" format or standard "value tag" format, and store the
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# tag/value pairs in %values_p1.
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# NOTE : compound expressions are not currently allowed.
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sub parse_parameter_file {
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my $pfile = shift(@_);
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# (1) parse numerical values
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open (PARAMETERS, "<$pfile") || die "Can't open parameters file: $pfile: $!";
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while (<PARAMETERS>) { # read each line of file, one at a time
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# extract tag/value fields allowing multiple matches per line in either format
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foreach $field (m/(?:$n)\s+\w+|\s*\w+\s*=\s*(?:$n)\s*/go) {
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# extract tag/value pair from each field NOTE () are memory
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if ( ( ($value, $tag) = ($field =~ m/^($n)\s+(\w+)$/o) ) || # Standard
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( ($tag, $value) = ($field =~ m/^\s*(\w+)\s*=\s*($n)\s*$/o))){# Apr
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$value =~ s/[dD]/e/o; # convert any F77 dbl prec exponents
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$values_p1{$tag} = $value; # store in hash
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}
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}
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}
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close (PARAMETERS);
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# (2) parse string values in dbl quotes
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open (PARAMETERS, "<$pfile") || die "Can't open parameters file: $pfile: $!";
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while (<PARAMETERS>) { # read each line of file, one at a time
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# extract tag/value fields allowing multiple matches per line in either format
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#if ( m/=/ && m/\"/ ){
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if ( ($tag, $value) = ($_ =~ m/^\s*(\w+)\s*=\s*\"(.*)\"\s*$/o)){
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$values_p1{$tag} = $value; # store in hash
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}
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}
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close (PARAMETERS);
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}
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#################################################################
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# Process template simulation file and create new simulation file
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#################################################################
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# Read each line of template_file, find the {} fields, process any
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# assignments or expressions, and substitute the corresponding values.
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# Print each line with substitution to new_file. The parameters
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# file assignments (%values_p1 = precedence 1) take precedence over any
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# duplicate template file assignments (%values_p2 = precedence 2) in
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# order to allow the flexibility to define defaults in the template
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# file which can then be overridden by a particular parameters file.
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sub output{
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my $tfile = shift (@_);
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# Open the template simulation file for input.
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open (TEMPLATE, "<$tfile") || die "Can't open template file $tfile: $!";
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# Open the new simulation file for output.
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#$print_to_file = 0;
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#if (defined($new_file)) {
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#open (NEW, ">$new_file") || die "Can't create instance file $new_file: $!";
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#$print_to_file = 1;
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#}
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$print_to_file = 1;
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$fh = shift (@_);
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$print = 1; # print line flag
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while (<TEMPLATE>) {
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# Extract each {} match from this line
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foreach $field (m/\{\s*(.+?)\s*\}/go) { # ".+?" provides a minimal match
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# Case 1: test for simple tag match "{tag}"
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if ($field =~ m/^\w+$/o) {
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if ( defined ( $value = $values_p1{$field} ) ||
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defined ( $value = $values_p2{$field} ) ) { # or exists $values{$tag}
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s/\{\s*$field\s*\}/$value/;
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}
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}
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# Case 2: test for assignment "{tag = field}"
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elsif ( ($tag, $assign) = ($field =~ m/^(\w+)\s*=\s*(.+?)$/o) ) {
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# Case 2a: assignment of numerical value
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# ($n = exponential notation $e, floating point $f, or integer $i)
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if ($assign =~ m/^($n)$/o) {
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$assign =~ s/[dD]/e/o; # convert F77 dbl prec exponents
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$values_p2{$tag} = $assign; # store in priority 2 hash
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s/\{\s*$tag\s*=\s*.+?\s*\}/$assign/; # replace assignment with value
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}
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# Case 2b: assignment of expression. Evaluate $assign by replacing any
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# known tags with their values and then eval the remaining expression.
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else {
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foreach $exptag ($assign =~ m/\b(\w*[a-zA-Z_]+\w*)\b/go) {
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if ( defined ( $value = $values_p1{$exptag} ) ||
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defined ( $value = $values_p2{$exptag} ) ) {
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$assign =~ s/$exptag/$value/;
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}
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}
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$value = eval $assign;
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if ($@) { die "Eval error: $@"; }
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$values_p2{$tag} = $value; # store in priority 2 hash
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s/\{\s*$tag\s*=\s*.+?\s*\}/$value/; # replace assignment with value
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}
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}
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# Case 3: assume general expression in all remaining $field matches.
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# Evaluate $field by replacing any known tags with their values and
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# then eval the remaining expression.
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else {
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foreach $tag ($field =~ m/\b(\w*[a-zA-Z_]+\w*)\b/go) {
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if ( defined ( $value = $values_p1{$tag} ) ||
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defined ( $value = $values_p2{$tag} ) ) {
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$field =~ s/$tag/$value/;
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}
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}
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s/\{\s*.+?\s*\}/eval $field/e;
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if ($@) { die "Eval error: $@"; }
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}
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}
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# if/else blocks
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if ($_ =~ /#if/) {
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$line = $_; chomp($line); $line =~ s/^\s+//; $line =~ s/\s+$//;
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@items = split(/\s+/,$line);
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if (eval($items[1])) {;}
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else { $print = 0;}
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}
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elsif ($_ =~ /#else/) {
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if ($print) {$print = 0;} else {$print = 1;}
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}
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elsif ($_ =~ /#endif/) {
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$print = 1;
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}
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else {
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# output the processed line
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if ($print) { print $fh $_; }
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}
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}
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close (TEMPLATE);
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if ($print_to_file ) { close (NEW); }
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}
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###########################################################################
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# math operators
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###########################################################################
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# Intrinsic numeric operators include +,-,*,/,**,%,<<,>>,sqrt(),abs(),
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# sin(),cos(),atan2(),exp(),log(),int(),hex(),oct(),rand(),srand().
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# Augment these with others (adapted/extended from bprepro by Bob Walton).
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# NOTE: convert from degs to rads by pi/180 = (pi/4)/45 = atan2(1,1)/45
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# convert from rads to degs by 180/pi = 45/atan2(1,1)
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# additional logarithmic functions
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sub log10 { log($_[0])/log(10) }
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# additional trigonometric functions with radian input
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sub tan { sin($_[0])/cos($_[0]) }
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sub cot { cos($_[0])/sin($_[0]) }
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sub csc { 1/sin($_[0]) }
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sub sec { 1/cos($_[0]) }
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# trigonometric functions with degree input
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sub sind { sin($_[0]*atan2(1,1)/45) }
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sub cosd { cos($_[0]*atan2(1,1)/45) }
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sub tand { tan($_[0]*atan2(1,1)/45) }
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sub cotd { cot($_[0]*atan2(1,1)/45) }
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sub cscd { 1/sin($_[0]*atan2(1,1)/45) }
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sub secd { 1/cos($_[0]*atan2(1,1)/45) }
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# inverse trigonometric functions returning radians
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sub asin {
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if (abs($_[0]) > 1) { die "input out of range in asin()\n"; }
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atan2($_[0],sqrt(1-$_[0]**2));
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}
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sub acos {
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if (abs($_[0]) > 1) { die "input out of range in acos()\n"; }
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atan2(sqrt(1-$_[0]**2),$_[0]);
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}
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sub atan { atan2($_[0],1) }
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# inverse trigonometric functions returning degrees
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sub asind { asin($_[0])*45/atan2(1,1) }
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sub acosd { acos($_[0])*45/atan2(1,1) }
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sub atand { atan2($_[0],1)*45/atan2(1,1) }
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sub atan2d { atan2($_[0],$_[1])*45/atan2(1,1) }
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# hyperbolic functions
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sub sinh { (exp($_[0]) - exp(-$_[0]))/2 }
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sub cosh { (exp($_[0]) + exp(-$_[0]))/2 }
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sub tanh { sinh($_[0])/cosh($_[0]) }
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sub coth {
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if ($_[0] == 0) { die "input out of range in coth()\n"; }
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cosh($_[0])/sinh($_[0]);
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}
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sub csch {
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if ($_[0] == 0) { die "input out of range in csch()\n"; }
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1/sinh($_[0]);
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}
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sub sech { 1/cosh($_[0]) }
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# inverse hyperbolic functions
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sub asinh { log($_[0] + sqrt($_[0]**2 + 1)) }
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sub acosh {
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if ($_[0] < 1) { die "input out of range in acosh()\n"; }
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log($_[0] + sqrt($_[0]**2 - 1));
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}
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sub atanh {
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if (abs($_[0]) >= 1) { die "input out of range in atanh()\n"; }
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log((1+$_[0])/(1-$_[0]))/2;
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}
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@ -0,0 +1,213 @@
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&maincard
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ntypes=4
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perub={n1*a-0.5},{n2*a-0.5},{n3*a/cos(3.14159265/180.0*theta)-0.5}
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perlb=-0.5,-0.5,-0.5
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ilatseed=0
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amass={amass1},{amass2},{amass3},{amass4},{amass5}
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ielement={ielement1},{ielement2},{ielement3},{ielement4},{ielement5}
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&end
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&latcard
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lattype='sc'
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alat={a},{a},{a/cos(3.14159265/180.0*theta)}
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xrot=1.0 0.0 0.0
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yrot=0.0 1.0 0.0
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zrot=0.0,0.0,1.0
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xbound=-0.5,{n1*a-0.5}
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ybound=-0.5,{n2*a-0.5}
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zbound=-0.5,{n3*a/cos(3.14159265/180.0*theta)-0.5}
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periodicity=1.0,1.0,1.0
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strain=0.0,0.0,0.0
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delx=0.0,0.0,0.0
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&end
|
||||
&subcard
|
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rcell=0.250000,0.250000,0.250000
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ccell=1.0,0.0,0.0,0.0,0.0
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&end
|
||||
&subcard
|
||||
rcell=0.000000,0.000000,0.000000
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ccell=0.0,1.0,0.0,0.0,0.0
|
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&end
|
||||
&subcard
|
||||
rcell=0.250000,{0.5*tan(3.14159265/180.0*theta)},0.000000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell={1.0-0.5*tan(3.14159265/180.0*theta)},0.250000,0.000000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.000000,0.000000,0.250000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.750000,0.250000,0.250000
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||||
ccell=1.0,0.0,0.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.500000,0.000000,0.000000
|
||||
ccell=0.0,0.0,1.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.750000,{1.0-0.5*tan(3.14159265/180.0*theta)},0.000000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell={0.5+0.5*tan(3.14159265/180.0*theta)},0.250000,0.000000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.500000,0.000000,0.250000
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||||
ccell=0.0,0.0,0.0,1.0,0.0
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&end
|
||||
&subcard
|
||||
rcell=0.750000,0.750000,0.250000
|
||||
ccell=1.0,0.0,0.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.500000,0.500000,0.000000
|
||||
ccell=0.0,1.0,0.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.750000,{0.5+0.5*tan(3.14159265/180.0*theta)},0.000000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell={0.5-0.5*tan(3.14159265/180.0*theta)},0.750000,0.000000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
|
||||
&subcard
|
||||
rcell=0.500000,0.500000,0.250000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.250000,0.750000,0.250000
|
||||
ccell=1.0,0.0,0.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.000000,0.500000,0.000000
|
||||
ccell=0.0,0.0,1.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.250000,{0.5-0.5*tan(3.14159265/180.0*theta)},0.000000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell={0.5*tan(3.14159265/180.0*theta)},0.750000,0.000000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.000000,0.500000,0.250000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.250000,0.250000,0.750000
|
||||
ccell=1.0,0.0,0.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.000000,0.000000,0.500000
|
||||
ccell=0.0,0.0,1.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.250000,{0.5*tan(3.14159265/180.0*theta)},0.500000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell={1.0-0.5*tan(3.14159265/180.0*theta)},0.250000,0.500000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.000000,0.000000,0.750000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.750000,0.250000,0.750000
|
||||
ccell=1.0,0.0,0.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.500000,0.000000,0.500000
|
||||
ccell=0.0,1.0,0.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.750000,{1.0-0.5*tan(3.14159265/180.0*theta)},0.500000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell={0.5+0.5*tan(3.14159265/180.0*theta)},0.250000,0.500000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.500000,0.000000,0.750000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.750000,0.750000,0.750000
|
||||
ccell=1.0,0.0,0.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.500000,0.500000,0.500000
|
||||
ccell=0.0,0.0,1.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.750000,{0.5+0.5*tan(3.14159265/180.0*theta)},0.500000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell={0.5-0.5*tan(3.14159265/180.0*theta)},0.750000,0.500000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.500000,0.500000,0.750000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.250000,0.750000,0.750000
|
||||
ccell=1.0,0.0,0.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.000000,0.500000,0.500000
|
||||
ccell=0.0,1.0,0.0,0.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.250000,{0.5-0.5*tan(3.14159265/180.0*theta)},0.500000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell={0.5*tan(3.14159265/180.0*theta)},0.750000,0.500000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
rcell=0.000000,0.500000,0.750000
|
||||
ccell=0.0,0.0,0.0,1.0,0.0
|
||||
&end
|
||||
&subcard
|
||||
&end
|
||||
|
||||
&defcard
|
||||
&end
|
||||
|
||||
&latcard
|
||||
&end
|
||||
|
||||
&hitcard
|
||||
&end
|
||||
|
||||
&disturbcard
|
||||
dismax=0.0
|
||||
strain=0.0,0.0,0.0
|
||||
&end
|
||||
|
||||
&shiftcard
|
||||
mode=0
|
||||
&end
|
||||
|
||||
&velcard
|
||||
&end
|
||||
|
||||
&filecard
|
||||
dynamo="none"
|
||||
paradyn="none"
|
||||
lammps="r0.lmp"
|
||||
xyz="none"
|
||||
&end
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
log relax.log
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice diamond 4.511
|
||||
read_data rout
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * /ascldap/users/xzhou/2010/GaN/files/GaN1.sw Ga N Ga N Ga N
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
variable xlen equal lx
|
||||
variable ylen equal ly
|
||||
variable zlen equal lz
|
||||
variable temper equal temp
|
||||
variable Etot equal etotal
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix temp all temp/rescale 1 {(Tmid+Tbnd)/2} {(Tmid+Tbnd)/2} 0.0 1.0
|
||||
fix int all nph xyz 0.0 0.0 0.1
|
||||
fix ave all ave/time 1 {NPTave} {2*NPTave} v_xlen v_ylen v_zlen v_temper v_Etot file avelen
|
||||
|
||||
run {2*NPTave}
|
||||
Loading…
Reference in New Issue