bse 0.1.4

Basis Set Exchange (BSE) library in Rust for quantum chemistry applications.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190

use assert_json_diff::assert_json_include;
use bse::prelude::*;
use rstest::rstest;
use std::fs::{read_to_string, write as write_from_string};

#[cfg(test)]
mod test {
    use super::*;

    #[rstest]
    #[case("naive"                 , "cc-pVTZ"    , ["elements = '1, 6-O'"         ,                                ].join("\n"))]
    #[case("naive"                 , "def2-TZVPD" , ["elements = '1-3, 49-51'"     ,                                ].join("\n"))]
    #[case("remove_free_primitives", "cc-pVTZ"    , ["elements = '1, 6-O'"         , "remove_free_primitives = true"].join("\n"))]
    #[case("remove_free_primitives", "def2-TZVPD" , ["elements = '1-3, 49-51'"     , "remove_free_primitives = true"].join("\n"))]
    #[case("make_general"          , "aug-cc-pVTZ", ["elements = '1, 6-O'"         , "make_general = true"          ].join("\n"))]
    #[case("optimize_general"      , "aug-cc-pVTZ", ["elements = '1, 6-O'"         , "optimize_general = true"      ].join("\n"))]
    #[case("uncontract_segmented"  , "aug-cc-pVTZ", ["elements = '1, 6-O'"         , "uncontract_segmented = true"  ].join("\n"))]
    #[case("uncontract_general"    , "aug-cc-pVTZ", ["elements = '1, 6-O'"         , "uncontract_general = true"    ].join("\n"))]
    #[case("uncontract_spdf"       , "6-31G"      , ["elements = '1, 6-O'"         , "uncontract_spdf = true"       ].join("\n"))]
    #[case("augment_diffuse"       , "cc-pVTZ"    , ["elements = '1, 6-O'"         , "augment_diffuse = 2"          ].join("\n"))]
    #[case("augment_steep"         , "cc-pVTZ"    , ["elements = '1, 6-O'"         , "augment_steep = 2"            ].join("\n"))]
    #[case("get_aux"               , "def2-SVP"   , ["elements = '1,6,15,25,59,86'", "get_aux = 1"                  ].join("\n"))]
    #[case("get_aux"               , "cc-pVTZ"    , ["elements = '1,6,15,25'"      , "get_aux = 1"                  ].join("\n"))]
    #[case("get_abs"               , "def2-SVP"   , ["elements = '1,6,15,25,59,86'", "get_aux = 2"                  ].join("\n"))]
    #[case("get_abs"               , "cc-pVTZ"    , ["elements = '1,6,15,25'"      , "get_aux = 2"                  ].join("\n"))]
    fn test_get_basis(#[case] scene: &str, #[case] basis: &str, #[case] args: String) {
        let manifest_dir = env!("CARGO_MANIFEST_DIR");
        let ref_file = format!("{manifest_dir}/tests/python_ref/get_basis_json/{basis}-{scene}.json");
        let write_file = format!("{manifest_dir}/tests/tmp.json");

        let args = toml::from_str::<BseGetBasisArgs>(&args).unwrap();
        let basis = get_basis(basis, args);

        let basis_str = serde_json::to_string_pretty(&basis).unwrap();
        let basis_json = serde_json::from_str::<serde_json::Value>(&basis_str).unwrap();
        write_from_string(&write_file, &basis_str).unwrap();

        let ref_str = read_to_string(ref_file).unwrap();
        let ref_json = serde_json::from_str::<serde_json::Value>(&ref_str).unwrap();
        assert_json_include!(actual: basis_json, expected: ref_json);
    }

    #[rstest]
    #[case("nwchem"        , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("nwchem"        , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("nwchem"        , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("gaussian94"    , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("gaussian94"    , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("gaussian94"    , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("gaussian94lib" , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("gaussian94lib" , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("gaussian94lib" , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("psi4"          , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("psi4"          , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("psi4"          , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("molcas"        , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("molcas"        , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("molcas"        , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("qchem"         , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("qchem"         , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("qchem"         , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("gamess_us"     , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("gamess_us"     , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("gamess_us"     , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("orca"          , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("orca"          , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("orca"          , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("dalton"        , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("dalton"        , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("dalton"        , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("cp2k"          , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("cp2k"          , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("cp2k"          , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("pqs"           , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("pqs"           , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("pqs"           , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("demon2k"       , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("demon2k"       , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("demon2k"       , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("turbomole"     , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("turbomole"     , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("turbomole"     , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("gamess_uk"     , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("gamess_uk"     , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("gamess_uk"     , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("molpro"        , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("molpro"        , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("molpro"        , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("cfour"         , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("cfour"         , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("cfour"         , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("acesii"        , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("acesii"        , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("acesii"        , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("bdf"           , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("bdf"           , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("bdf"           , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("jaguar"        , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("jaguar"        , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("jaguar"        , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("crystal"       , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("crystal"       , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("veloxchem"     , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("molcas_library", "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("molcas_library", "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("molcas_library", "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("libmol"        , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("libmol"        , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("libmol"        , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("bsedebug"      , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("bsedebug"      , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("bsedebug"      , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("ricdwrap"      , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("ricdwrap"      , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("ricdwrap"      , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    fn test_get_formatted_basis(#[case] fmt: &str, #[case] basis: &str, #[case] args: String) {
        let manifest_dir = env!("CARGO_MANIFEST_DIR");
        let ref_file = format!("{manifest_dir}/tests/python_ref/get_basis_fmt/{basis}-{fmt}.txt");
        let write_file = format!("{manifest_dir}/tests/tmp.txt");

        let mut args = toml::from_str::<BseGetBasisArgs>(&args).unwrap();
        args.header = false;
        let basis_str = get_formatted_basis(basis, fmt, args);
        write_from_string(&write_file, &basis_str).unwrap();

        let ref_str = read_to_string(ref_file).unwrap();

        use similar::{ChangeTag, TextDiff};
        let diff = TextDiff::from_lines(&basis_str, &ref_str);
        for change in diff.iter_all_changes() {
            let sign = match change.tag() {
                ChangeTag::Delete => "-",
                ChangeTag::Insert => "+",
                ChangeTag::Equal => " ",
            };
            print!("{sign}{change}");
        }

        assert_eq!(basis_str, ref_str);
    }

    #[rstest]
    #[case("fhiaims"       , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[should_panic(expected = "does not support all function types")]
    #[case("fhiaims"       , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[should_panic(expected = "does not support all function types")]
    #[case("fhiaims"       , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    fn test_get_formatted_basis_fhiaims(#[case] fmt: &str, #[case] basis: &str, #[case] args: String) {
        // fhi-aims format suffers from pythons's indent
        let manifest_dir = env!("CARGO_MANIFEST_DIR");
        let ref_file = format!("{manifest_dir}/tests/python_ref/get_basis_fmt/{basis}-{fmt}.txt");
        let write_file = format!("{manifest_dir}/tests/tmp.txt");

        let mut args = toml::from_str::<BseGetBasisArgs>(&args).unwrap();
        args.header = false;
        let basis_str = get_formatted_basis(basis, fmt, args);
        write_from_string(&write_file, &basis_str).unwrap();

        let ref_str = read_to_string(ref_file).unwrap();

        use itertools::Itertools;
        let basis_str = basis_str.split('\n').map(|line| line.trim()).collect_vec().join("\n");
        let ref_str = ref_str.split('\n').map(|line| line.trim()).collect_vec().join("\n");

        assert_eq!(basis_str, ref_str);
    }

    #[rstest]
    #[case("qcschema"      , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("qcschema"      , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("qcschema"      , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    #[case("bsejson"       , "cc-pVTZ"   , ["elements = '1, 6-O'"    ].join("\n"))]
    #[case("bsejson"       , "def2-ECP"  , ["elements = '49-51'"     ].join("\n"))]
    #[case("bsejson"       , "def2-TZVPD", ["elements = '1-3, 49-51'"].join("\n"))]
    fn test_get_formatted_json(#[case] fmt: &str, #[case] basis: &str, #[case] args: String) {
        let manifest_dir = env!("CARGO_MANIFEST_DIR");
        let ref_file = format!("{manifest_dir}/tests/python_ref/get_basis_fmt/{basis}-{fmt}.txt");
        let write_file = format!("{manifest_dir}/tests/tmp.txt");

        let mut args = toml::from_str::<BseGetBasisArgs>(&args).unwrap();
        args.header = false;
        let basis_str = get_formatted_basis(basis, fmt, args);
        write_from_string(&write_file, &basis_str).unwrap();

        let ref_str = read_to_string(ref_file).unwrap();
        let basis_json = serde_json::from_str::<serde_json::Value>(&basis_str).unwrap();
        let ref_json = serde_json::from_str::<serde_json::Value>(&ref_str).unwrap();
        assert_json_include!(actual: basis_json, expected: ref_json);
    }
}