HackaMol-X-Calculator

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examples/dftb3/PrepXyzACS.pl  view on Meta::CPAN

# DMR: old school perl script that downloads a yaml and prints out some xyz
# files
use Modern::Perl;
use YAML::XS qw(Dump LoadFile);
use Path::Tiny;
use File::chdir;

my $yaml = "ct300296k_si_001.txt";
my $webyaml =
  "http://pubs.acs.org/doi/suppl/10.1021/ct300296k/suppl_file/$yaml";

system("wget $webyaml") unless ( -e $yaml );
my $data   = LoadFile($yaml);

examples/dftb3/dftb3.pl  view on Meta::CPAN

#
# with BJ-damping,
# Stefan Grimme, Stephan Ehrlich and Lars Goerigk
# J. Comput. Chem. 32, 1456 (2011); DOI:10.1002/jcc.21759
#
# wget http://www.thch.uni-bonn.de/tc/downloads/DFT-D3/data/dftd3.tgz
#
# cd into directory and install with fortran compiler  (e.g. gfortran or intel's ifort)
# may have to edit make file to use whichever compiler you have

use Modern::Perl;
use HackaMol;
use HackaMol::X::Calculator;
use Path::Tiny;

my $hack = HackaMol->new( data => "examples/xyzs", );

my $i = 0;

my $scratch = path('tmp');

examples/dftb3/dftb3_in.pl  view on Meta::CPAN

#!/usr/bin/env perl
# DMR May 27, 2014
#
#   perl examples/dftd3_in.pl
#
# generate input.. for dftb3, input is an xyz file with atom symbols (not numbers)
#
# See examples/dftd3.pl for full script that writes input,
# runs program, and processes output.

use Modern::Perl;
use HackaMol;
use HackaMol::X::Calculator;
use Path::Tiny;

my $hack = HackaMol->new( data => "examples/xyzs", );

foreach my $xyz ( grep {!/^symbol_/} $hack->data->children(qr/\.xyz$/) ) {

    my $mol = $hack->read_file_mol($xyz);
    my $sym_xyz = 'symbol_' . $xyz->basename;

examples/dftb3/dftb3_out.pl  view on Meta::CPAN

#!/usr/bin/env perl
# DMR May 27, 2014
#
#   perl examples/dftd3_out.pl
#
# process the output
#
# See examples/dftd3.pl for full script that writes input,
# runs program, and processes output.

use Modern::Perl;
use HackaMol;
use HackaMol::X::Calculator;
use Path::Tiny;

my $hack = HackaMol->new( data => "examples/xyzs", );

foreach my $out ( $hack->data->children(qr/symbol_.+\.out$/) ) {

    my $Calc = HackaMol::X::Calculator->new(
        scratch => $hack->data,

examples/dftb3/dftb3_run.pl  view on Meta::CPAN

#!/usr/bin/env perl
# DMR May 27, 2014
#
#   perl examples/dftd3_run.pl
#
# run the program, generate output
#
# See examples/dftd3.pl for full script that writes input,
# runs program, and processes output.
use Modern::Perl;
use HackaMol;
use HackaMol::X::Calculator;
use Path::Tiny;

my $hack = HackaMol->new( data => "examples/xyzs", );

foreach my $xyz ( $hack->data->children(qr/symbol_.+\.xyz$/) ) {

    my $in  = $xyz->basename ;  
    my $out = $in =~ s/\.xyz/\.out/r; 

examples/g09/g09_in_ss-scan.pl  view on Meta::CPAN

#!/usr/bin/env perl
# Demian Riccardi, June 3, 2014
#
# This example takes an xyz/pdb file of a molecule with a disulfide 
# (or modified disulfide R-S-Hg-S-R), rotates the R-S...S-R from 0 
# to 180 in steps of 10, and  generates Gaussian 09 inputs for the 
# B3PW91/[SDD/]6-31+G** level of theory.
#
use Modern::Perl;
use HackaMol;
use HackaMol::X::Calculator;
use lib 'basis_sets';
use YAML::XS;
use Path::Tiny;

##############################################################################
#         load in the molecule and initialize charge and multiplicity        #
##############################################################################
my $bldr = new HackaMol;

examples/g09/g09_in_ss-set.pl  view on Meta::CPAN

#!/usr/bin/env perl
# Demian Riccardi, June 3, 2014
#
# This example takes an xyz/pdb file of a molecule with a disulfide 
# (or modified disulfide R-S-Hg-S-R), rotates the R-S...S-R to a  
# set angle passed at command line, and  generates Gaussian 09 inputs 
# for the B3PW91/[SDD/]6-31+G** level of theory.
# 
use Modern::Perl;
use HackaMol;
use HackaMol::X::Calculator;
use lib 'basis_sets';
use YAML::XS;
use Path::Tiny;

###############################################################################
#          load in the molecule and initialize charge and multiplicity        #
###############################################################################
my $bldr = new HackaMol;

examples/g09/g09_out_pdb.pl  view on Meta::CPAN

#!/usr/bin/env perl
# DMR April 30, 2014
#
#   perl examples/g09_pdb.pl ~/some/path
#
# pull coordinates (all) and charges from Gaussian output (path submitted
# on commandline)
# write out pdbs in tmp directory with charges in the bfactor column..
#

use Modern::Perl;
use HackaMol;
use HackaMol::X::Calculator;
use Math::Vector::Real;
use Path::Tiny;
use File::chdir;

my $path = shift || die "pass path to gaussian outputs";

my $hack = HackaMol->new( data => $path, );

examples/g09/g09_out_scfdone.pl  view on Meta::CPAN

# and print in kcal/mol.
#
# The regex in output_map will return the last match. This is relevant
#   for optimizations that will print an energy for each step. As
#   an exercise, create a new script, based on this one, that takes
#   output files from optimization runs (~/some/path/*_opt.out) and
#   calculates the energy difference between the initial structure and
#   the final structure.
#

use Modern::Perl;
use HackaMol;
use HackaMol::X::Calculator;
use Path::Tiny;

my $path = shift || die "pass path to gaussian outputs";

my $hack = HackaMol->new( data => $path, );

foreach my $out ( $hack->data->children(qr/opt\.out$/) ) {

examples/g09/g09_out_xyz.pl  view on Meta::CPAN

#!/usr/bin/env perl
# DMR April 30, 2014
#
#   perl examples/g09_xyz.pl ~/some/path
#
# pull coordinates (all) from Gaussian output (path submitted
# on commandline)
# write out xyzs in tmp directory
#

use Modern::Perl;
use HackaMol;
use HackaMol::X::Calculator;
use Math::Vector::Real;
use Path::Tiny;
use File::chdir;

my $path = shift || die "pass path to gaussian outputs";

my $hack = HackaMol->new( data => $path, );

lib/HackaMol/X/Calculator.pm  view on Meta::CPAN

=head1 NAME

HackaMol::X::Calculator - Abstract calculator class for HackaMol

=head1 VERSION

version 0.012

=head1 SYNOPSIS

   use Modern::Perl;
   use HackaMol;
   use HackaMol::X::Calculator;
   use Path::Tiny;
   
   my $path = shift || die "pass path to gaussian outputs";
   
   my $hack = HackaMol->new( data => $path, );
   
   foreach my $out ( $hack->data->children(qr/\.out$/) ) {