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
use crate::molecule_io::Molecule;
use crate::geom_io;
use crate::basis_io;
use crate::scf_io::SCF;
use rest_tensors::{MatrixFull};
use rest_libcint::CINTR2CDATA;
use rest_libcint::CintType;
use std::borrow::BorrowMut;
use std::collections::HashMap;
use rayon::iter::{IntoParallelRefIterator, IndexedParallelIterator, ParallelIterator, IntoParallelRefMutIterator};
use std::fs::{self, File};
use std::io::prelude::*;
use std::io::LineWriter;
pub fn gen_header(mol: &Molecule) -> String{
let mut header = "[Molden Format]\n".to_owned();
header += "[Title]\n";
header += "Molden file created by REST.\n";
header += "\n[Atoms] AU\n";
let geometry = &mol.geom;
let atom_mass_charge = geom_io::get_mass_charge(&geometry.elem).clone();
geometry.elem.iter().zip(1..(geometry.elem.len()+1)).zip(geometry.position.iter_columns_full()).zip(atom_mass_charge.iter())
.for_each(|(((elem,index),position),(mass,charge))|{
header += elem;
header += " ";
header += &index.to_string();
header += " ";
let charge_u = *charge as usize;
header += &charge_u.to_string();
position.iter().for_each(|x|{
header += " ";
header += &x.to_string();
});
header += "\n";
});
header += "[GTO]\n";
let num_atom = mol.geom.elem.len();
mol.basis4elem.iter().zip(1..(num_atom+1)).for_each(|(bas,index)|{
header += " ";
header += &index.to_string();
header += " 0\n";
let mut ele_shells =bas.electron_shells.clone();
ele_shells.iter_mut().for_each(|ao_ele|{
let mut tmp_ang = ao_ele.angular_momentum[0];
let mut tmp_coefficients: Vec<Vec<f64>> = vec![];
for coe_vec in ao_ele.coefficients.iter() {
let mut tmp_coefficients_column: Vec<f64> = vec![];
coe_vec.iter().enumerate().for_each(|(ix,x)| {
let tmp_value = CINTR2CDATA::gto_norm(tmp_ang as std::os::raw::c_int,
ao_ele.exponents[ix]);
tmp_coefficients_column.push(*x/tmp_value);
});
tmp_coefficients.push(tmp_coefficients_column);
};
ao_ele.coefficients = tmp_coefficients.clone();
ao_ele.coefficients.iter().for_each(|co|{
header += " ";
header += &match_angular_momentum(ao_ele.angular_momentum[0]);
header += " ";
header += &ao_ele.exponents.len().to_string();
header += " 1.00\n";
co.iter().zip(ao_ele.exponents.iter()).for_each(|(c,alpha)|{
header += " ";
header += &alpha.to_string();
header += " ";
header += &c.to_string();
header += "\n";
});
})
});
});
header += "\n[5D]\n[9G]\n";
header
}
pub fn gen_mo_info(scf_data: &SCF) -> String {
let mut mo_info = "[MO]\n".to_owned();
let energy = &scf_data.eigenvalues[0];
let coeff = &scf_data.eigenvectors[0];
let occup = &scf_data.occupation[0];
coeff.iter_columns_full().zip(energy.iter().zip(occup.iter())).for_each(|(mo_co,(eig,occ))|{
mo_info += " Sym= 1a\n Ene= ";
mo_info += &eig.to_string();
mo_info += "\n Spin= Alpha\n Occup= ";
mo_info += &occ.to_string();
mo_info += "\n";
let num_ao = mo_co.len();
mo_co.iter().zip(1..(num_ao+1)).for_each(|(ao_co,index)|{
mo_info += " ";
mo_info += &index.to_string();
mo_info += " ";
mo_info += &ao_co.to_string();
mo_info += "\n";
});
});
mo_info
}
pub fn gen_molden(scf_data: &SCF) -> String {
let mol = &scf_data.mol;
let mut text = gen_header(&mol);
text += &gen_mo_info(scf_data);
let mut path = "src/post_scf_analysis/generated_file/".to_owned();
path += &mol.geom.name;
path += ".molden";
let file = File::create(path);
let mut file = LineWriter::new(file.unwrap());
file.write_all(&text.into_bytes());
"Molden successfull built.".to_owned()
}
pub fn match_angular_momentum(angular_momentum: i32) -> String{
let i = HashMap::from([
(0, "s".to_owned()),
(1, "p".to_owned()),
(2, "d".to_owned()),
(3, "f".to_owned()),
(4, "g".to_owned()),
]);
i.get(&angular_momentum).unwrap().clone()
}