NAME

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

VERSION

version 0.012

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

       my $Calc = HackaMol::X::Calculator->new(
           out_fn  => $out,
           map_out => \&output_map,
       );
   
       my $energy = $Calc->map_output(627.51);
   
       printf( "%-40s: %10.6f\n", $Calc->out_fn->basename, $energy );
   
   }
   
   #  our function to map molec info from output
   
   sub output_map {
       my $calc = shift;
       my $conv = shift;
       my $re   = qr/-\d+.\d+/;
       my @energys = $calc->out_fn->slurp =~ m/SCF Done:.*(${re})/g;
       return ( $energys[-1] * $conv );
   }

DESCRIPTION

The HackaMol::X::Calculator extension generalizes molecular calculations using external programs. The Calculator class consumes the HackaMol::X::Roles::ExtensionRole role, which manage the running of executables... perhaps on files; perhaps in directories. This extension is intended to provide a simple example of interfaces with external programs. This is a barebones use of the ExtensionRole that is intended to be flexible. See the examples and testing directory for use of the map_in and map_out functions inside and outside of the map_input and map_output functions. Extensions with more rigid and encapsulated APIs can evolve from this starting point. In the synopsis, a Gaussian output is processed for the SCF Done value (a classic scripting of problem computational chemists). See the examples and tests to learn how the calculator can be used to:

  1. generate inputs 
  2. run programs
  3. process outputs

via interactions with HackaMol objects.

ATTRIBUTES

scratch

If scratch is set, the object will build that directory if needed. See HackaMol::PathRole for more information about the scratch attribute.

SEE ALSO

• HackaMol

• HackaMol::X::Roles::Extension

• HackaMol::PathRole

• Path::Tiny

EXTENDS

• Moose::Object

CONSUMES

• HackaMol::Roles::ExeRole

• HackaMol::Roles::ExeRole

• HackaMol::Roles::PathRole

• HackaMol::X::Roles::ExtensionRole

AUTHOR

Demian Riccardi <demianriccardi@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2015 by Demian Riccardi.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.