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
|
/* Ergo, version 3.8, a program for linear scaling electronic structure
* calculations.
* Copyright (C) 2019 Elias Rudberg, Emanuel H. Rubensson, Pawel Salek,
* and Anastasia Kruchinina.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
* Primary academic reference:
* Ergo: An open-source program for linear-scaling electronic structure
* calculations,
* Elias Rudberg, Emanuel H. Rubensson, Pawel Salek, and Anastasia
* Kruchinina,
* SoftwareX 7, 107 (2018),
* <http://dx.doi.org/10.1016/j.softx.2018.03.005>
*
* For further information about Ergo, see <http://www.ergoscf.org>.
*/
/** @file atom_labels.cc
@brief Provides a way to map atom labels to their charges. The
main procedure provided by this file is
get_charge_int_from_atom_label().
@author: Elias Rudberg <em>responsible</em>
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <string>
#include "atom_labels.h"
#define kMaxNoOfAtomTypes 200
static void setupLabelList(std::string labelList []) {
int i;
for(i = 0; i < kMaxNoOfAtomTypes; i++)
labelList[i] = "";
labelList[1] = "H";
labelList[2] = "He";
labelList[3] = "Li";
labelList[4] = "Be";
labelList[5] = "B";
labelList[6] = "C";
labelList[7] = "N";
labelList[8] = "O";
labelList[9] = "F";
labelList[10] = "Ne";
labelList[11] = "Na";
labelList[12] = "Mg";
labelList[13] = "Al";
labelList[14] = "Si";
labelList[15] = "P";
labelList[16] = "S";
labelList[17] = "Cl";
labelList[18] = "Ar";
labelList[19] = "K";
labelList[20] = "Ca";
labelList[21] = "Sc";
labelList[22] = "Ti";
labelList[23] = "V";
labelList[24] = "Cr";
labelList[25] = "Mn";
labelList[26] = "Fe";
labelList[27] = "Co";
labelList[28] = "Ni";
labelList[29] = "Cu";
labelList[30] = "Zn";
labelList[31] = "Ga";
labelList[32] = "Ge";
labelList[33] = "As";
labelList[34] = "Se";
labelList[35] = "Br";
labelList[36] = "Kr";
labelList[37] = "Rb";
labelList[38] = "Sr";
labelList[39] = "Y";
labelList[40] = "Zr";
labelList[41] = "Nb";
labelList[42] = "Mo";
labelList[43] = "Tc";
labelList[44] = "Ru";
labelList[45] = "Rh";
labelList[46] = "Pd";
labelList[47] = "Ag";
labelList[48] = "Cd";
labelList[49] = "In";
labelList[50] = "Sn";
labelList[51] = "Sb";
labelList[52] = "Te";
labelList[53] = "I";
labelList[54] = "Xe";
}
int get_charge_int_from_atom_label(const char* atomLabel)
{
std::string labelList[kMaxNoOfAtomTypes];
int i;
if(atomLabel == NULL)
return -1;
if(atomLabel[0] == '\0')
return -1;
/* handle all-digit atomLabels */
for(i=0; atomLabel[i] && isdigit(atomLabel[i]); i++)
;
if( atomLabel[i] == '\0') /* all digit atom label */
return atoi(atomLabel);
setupLabelList(labelList);
for(i = 1; i < kMaxNoOfAtomTypes; i++)
{
if(strcasecmp(atomLabel, labelList[i].c_str()) == 0)
return i;
}
return -1;
}
int get_atom_label_from_charge_int(int charge, char* atomLabelString, size_t bufferSize)
{
std::string labelList[kMaxNoOfAtomTypes];
memset(atomLabelString, 0, bufferSize);
if(charge <= 0 || charge >= kMaxNoOfAtomTypes)
return -1;
setupLabelList(labelList);
if(labelList[charge].length() >= bufferSize)
return -1;
strcpy(atomLabelString, labelList[charge].c_str());
return 0;
}
|
