File Coverage

blib/lib/HackaMol/Roles/QmMolRole.pm

Criterion	Covered	Total	%
statement	6	6	100.0
branch			n/a
condition			n/a
subroutine	2	2	100.0
pod			n/a
total	8	8	100.0

line	stmt	sub	time	code
1				package HackaMol::Roles::QmMolRole;
2				$HackaMol::Roles::QmMolRole::VERSION = '0.051';
3				#ABSTRACT: provides attributes needed for quantum chemistry calculations
4				# this will need updating as needs arise
5	12	12	6293	use Moose::Role;
	12		32
	12		95
6
7				with 'HackaMol::Roles::QmAtomRole';
8
9				has 'multiplicity', is => 'rw', isa => 'Int', lazy => 1, default => 1;
10
11				my @tscl = qw(
12				score
13				energy
14				Etot Eelec Enuc
15				qm_dipole_moment ionization_energy gradient_norm
16				Hform
17				U H G S
18				S_t
19				S_r
20				S_v
21				Etot_mp2
22				Etot_ccsdt
23				Ecds
24				);
25
26				has "$_" => (
27				traits => ['Array'],
28				is => 'ro',
29				isa => 'ArrayRef[Num]',
30				default => sub { [] },
31				handles => {
32				"push_$_" => 'push',
33				"get_$_" => 'get',
34				"all_$_" => 'elements',
35				"clear_$_" => 'clear',
36				"count_$_" => 'count',
37				},
38				lazy => 1,
39				) foreach @tscl;
40
41				has "$_" => (
42				traits => ['Array'],
43				is => 'ro',
44				isa => 'ArrayRef[Math::Vector::Real]',
45				default => sub { [] },
46				handles => {
47				"push_$_" => 'push',
48				"get_$_" => 'get',
49				"all_$_" => 'elements',
50				"clear_$_" => 'clear',
51				"count_$_" => 'count',
52				},
53				lazy => 1,
54				) for qw(qm_dipole frequencies eigvec alpha beta);
55
56	12	12	64282	no Moose::Role;
	12		27
	12		66
57
58				1;
59
60				__END__
61
62				=pod
63
64				=head1 NAME
65
66				HackaMol::Roles::QmMolRole - provides attributes needed for quantum chemistry calculations
67
68				=head1 VERSION
69
70				version 0.051
71
72				=head1 SYNOPSIS
73
74				# instance of class that consumes the QmMolRole.
75
76				$obj->multiplicity(1);
77				my @energies = $mol->all_Etot;
78
79				=head1 DESCRIPTION
80
81				QmMolRole provides attributes that will be useful for setting up interfaces to
82				quantum chemistry packages. This role consumes the QmAtomRole so there is some
83				overlap for basis_geom, basis, and ecp. For interfaces, the Molecule should
84				take precedence over the atom; i.e. if a Molecule has a basis of 6-31G*, that
85				should be used for all atoms regardless of the basis set that they may have.
86				All attributes are 'rw' and lazy, so they will not contaminate the namespace
87				unless called upon. QmMolRole has 'basis_atoms' that should be generated from the
88				binned unique atoms in a molecule. basis_atoms are just instances of the
89				HackaMol::Atom class with all the basis sets and effective core potentials loaded,
90				either as simple strings supported by the package or the full descriptions
91				pulled from the EMSL basis set exchange as a single Str.
92				https://bse.pnl.gov/bse/portal
93
94				A dream is to interface with EMSL library directly. Attributes below are
95				described without much detail; they will contain information mapped from
96				calculations and are not exhaustive. This role will probably evolve as
97				interfaces are added.
98
99				=head1 ATTRIBUTES
100
101				=head2 multiplicity
102
103				isa Int that is lazy and rw
104
105				=head2 Etot Eelec Enuc
106
107				each isa ArrayRef[Num] that is lazy with public ARRAY traits: push_$_ get_$_
108				all_$_ clear_$_ count_$_
109
110				=head2 qm_dipole_moment ionization_energy gradient_norm Hform
111
112				each isa ArrayRef[Num] that is lazy with public ARRAY traits: push_$_ get_$_
113				all_$_ clear_$_ count_$_
114
115				=head2 U H G S S_t S_r S_v
116
117				each isa ArrayRef[Num] that is lazy with public ARRAY traits: push_$_ get_$_
118				all_$_ clear_$_ count_$_
119
120				=head2 Etot_mp2 Etot_ccsdt Ecds
121
122				each isa ArrayRef[Num] that is lazy with public ARRAY traits: push_$_ get_$_
123				all_$_ clear_$_ count_$_
124
125				=head2 qm_dipole frequencies eigvec alpha beta
126
127				each isa ArrayRef[Math::Vector::Real] that is lazy with public ARRAY traits: push_$_ get_$_
128				all_$_ clear_$_ count_$_
129
130				=head1 SEE ALSO
131
132				=over 4
133
134				=item *
135
136				L<HackaMol::Molecule>
137
138				=item *
139
140				L<EMSL \| https://bse.pnl.gov/bse/portal>
141
142				=back
143
144				=head1 CONSUMES
145
146				=over 4
147
148				=item * L<HackaMol::Roles::QmAtomRole>
149
150				=back
151
152				=head1 AUTHOR
153
154				Demian Riccardi <demianriccardi@gmail.com>
155
156				=head1 COPYRIGHT AND LICENSE
157
158				This software is copyright (c) 2017 by Demian Riccardi.
159
160				This is free software; you can redistribute it and/or modify it under
161				the same terms as the Perl 5 programming language system itself.
162
163				=cut