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				$HackaMol::Roles::QmMolRole::VERSION = '0.053';
2				#ABSTRACT: provides attributes needed for quantum chemistry calculations
3				# this will need updating as needs arise
4				use Moose::Role;
5	12	12	5943
	12		26
	12		89
6				with 'HackaMol::Roles::QmAtomRole';
7
8				has 'multiplicity', is => 'rw', isa => 'Int', lazy => 1, default => 1;
9
10				my @tscl = qw(
11				score
12				energy
13				Etot Eelec Enuc
14				qm_dipole_moment ionization_energy gradient_norm
15				Hform
16				U H G S
17				S_t
18				S_r
19				S_v
20				Etot_mp2
21				Etot_ccsdt
22				Ecds
23				);
24
25				has "$_" => (
26				traits => ['Array'],
27				is => 'ro',
28				isa => 'ArrayRef[Num]',
29				default => sub { [] },
30				handles => {
31				"push_$_" => 'push',
32				"get_$_" => 'get',
33				"all_$_" => 'elements',
34				"clear_$_" => 'clear',
35				"count_$_" => 'count',
36				},
37				lazy => 1,
38				) foreach @tscl;
39
40				has "$_" => (
41				traits => ['Array'],
42				is => 'ro',
43				isa => 'ArrayRef[Math::Vector::Real]',
44				default => sub { [] },
45				handles => {
46				"push_$_" => 'push',
47				"get_$_" => 'get',
48				"all_$_" => 'elements',
49				"clear_$_" => 'clear',
50				"count_$_" => 'count',
51				},
52				lazy => 1,
53				) for qw(qm_dipole frequencies eigvec alpha beta);
54
55				no Moose::Role;
56	12	12	54327
	12		70
	12		61
57				1;
58
59
60				=pod
61
62				=head1 NAME
63
64				HackaMol::Roles::QmMolRole - provides attributes needed for quantum chemistry calculations
65
66				=head1 VERSION
67
68				version 0.053
69
70				=head1 SYNOPSIS
71
72				# instance of class that consumes the QmMolRole.
73
74				$obj->multiplicity(1);
75				my @energies = $mol->all_Etot;
76
77				=head1 DESCRIPTION
78
79				QmMolRole provides attributes that will be useful for setting up interfaces to
80				quantum chemistry packages. This role consumes the QmAtomRole so there is some
81				overlap for basis_geom, basis, and ecp. For interfaces, the Molecule should
82				take precedence over the atom; i.e. if a Molecule has a basis of 6-31G*, that
83				should be used for all atoms regardless of the basis set that they may have.
84				All attributes are 'rw' and lazy, so they will not contaminate the namespace
85				unless called upon. QmMolRole has 'basis_atoms' that should be generated from the
86				binned unique atoms in a molecule. basis_atoms are just instances of the
87				HackaMol::Atom class with all the basis sets and effective core potentials loaded,
88				either as simple strings supported by the package or the full descriptions
89				pulled from the EMSL basis set exchange as a single Str.
90				https://bse.pnl.gov/bse/portal
91
92				A dream is to interface with EMSL library directly. Attributes below are
93				described without much detail; they will contain information mapped from
94				calculations and are not exhaustive. This role will probably evolve as
95				interfaces are added.
96
97				=head1 ATTRIBUTES
98
99				=head2 multiplicity
100
101				isa Int that is lazy and rw
102
103				=head2 Etot Eelec Enuc
104
105				each isa ArrayRef[Num] that is lazy with public ARRAY traits: push_$_ get_$_
106				all_$_ clear_$_ count_$_
107
108				=head2 qm_dipole_moment ionization_energy gradient_norm Hform
109
110				each isa ArrayRef[Num] that is lazy with public ARRAY traits: push_$_ get_$_
111				all_$_ clear_$_ count_$_
112
113				=head2 U H G S S_t S_r S_v
114
115				each isa ArrayRef[Num] that is lazy with public ARRAY traits: push_$_ get_$_
116				all_$_ clear_$_ count_$_
117
118				=head2 Etot_mp2 Etot_ccsdt Ecds
119
120				each isa ArrayRef[Num] that is lazy with public ARRAY traits: push_$_ get_$_
121				all_$_ clear_$_ count_$_
122
123				=head2 qm_dipole frequencies eigvec alpha beta
124
125				each isa ArrayRef[Math::Vector::Real] that is lazy with public ARRAY traits: push_$_ get_$_
126				all_$_ clear_$_ count_$_
127
128				=head1 SEE ALSO
129
130				=over 4
131
132				=item *
133
134				L<HackaMol::Molecule>
135
136				=item *
137
138				L<EMSL \| https://bse.pnl.gov/bse/portal>
139
140				=back
141
142				=head1 CONSUMES
143
144				=over 4
145
146				=item * L<HackaMol::Roles::QmAtomRole>
147
148				=back
149
150				=head1 AUTHOR
151
152				Demian Riccardi <demianriccardi@gmail.com>
153
154				=head1 COPYRIGHT AND LICENSE
155
156				This software is copyright (c) 2017 by Demian Riccardi.
157
158				This is free software; you can redistribute it and/or modify it under
159				the same terms as the Perl 5 programming language system itself.
160
161				=cut