1 |
/* |
2 |
* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
3 |
* |
4 |
* Contact: oopse@oopse.org |
5 |
* |
6 |
* This program is free software; you can redistribute it and/or |
7 |
* modify it under the terms of the GNU Lesser General Public License |
8 |
* as published by the Free Software Foundation; either version 2.1 |
9 |
* of the License, or (at your option) any later version. |
10 |
* All we ask is that proper credit is given for our work, which includes |
11 |
* - but is not limited to - adding the above copyright notice to the beginning |
12 |
* of your source code files, and to any copyright notice that you may distribute |
13 |
* with programs based on this work. |
14 |
* |
15 |
* This program is distributed in the hope that it will be useful, |
16 |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
17 |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
18 |
* GNU Lesser General Public License for more details. |
19 |
* |
20 |
* You should have received a copy of the GNU Lesser General Public License |
21 |
* along with this program; if not, write to the Free Software |
22 |
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
23 |
* |
24 |
*/ |
25 |
|
26 |
#include "UseTheForce/EAM.hpp" |
27 |
|
28 |
namespace oopse { |
29 |
|
30 |
//definition of createEAM |
31 |
ForceField* createEAM() { |
32 |
return new EAM(); |
33 |
} |
34 |
|
35 |
//register createDUFF to ForceFieldFactory |
36 |
ForceFieldFactory::getInstance()->registerForceField("EAM", createDUFF); |
37 |
|
38 |
void EAM::parse(const std::string& filename) { |
39 |
ifstrstream* ffStream; |
40 |
ffStream = openForceFiledFile(filename); |
41 |
const int bufferSize = 65535; |
42 |
char buffer[bufferSize]; |
43 |
std::string line; |
44 |
|
45 |
int status; |
46 |
int ident = 1; //fortran's index begins from 1 |
47 |
int lineNo = 0; |
48 |
|
49 |
while(ffStream.getline(buffer, bufferSize)){ |
50 |
++lineNo; |
51 |
line = trimSpaces(buffer); |
52 |
|
53 |
if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) { |
54 |
continue; |
55 |
} else { |
56 |
AtomType* atomType; |
57 |
std::string atomTypeName; |
58 |
double mass; |
59 |
StringTokenizer tokenizer(line); |
60 |
|
61 |
if (tokenizer.countTokens() >= 3) { |
62 |
atomTypeName = tokenizer.nextToken(); |
63 |
mass = tokenizer.nextTokenAsDouble(); |
64 |
std::string potentialParamFile = tokenizer.nextToken(); |
65 |
|
66 |
atomType = new AtomType(); |
67 |
atomType->setName(atomTypeName); |
68 |
atomType->setMass(mass); |
69 |
|
70 |
atomType->setIdent(ident); |
71 |
atomType->setEAM(); |
72 |
atomType->complete(); |
73 |
|
74 |
parseEAMParamFile(potentialParamFile); |
75 |
|
76 |
//add atom type to AtomTypeContainer |
77 |
addAtomType(atomTypeName, atomType); |
78 |
++ident; |
79 |
|
80 |
|
81 |
} else { |
82 |
sprintf( painCave.errMsg, |
83 |
"Not enough tokens when parsing Lennard-Jones Force Field : %s\n" |
84 |
"in line %d : %s\n", |
85 |
filename.c_str(), lineNo, line); |
86 |
painCave.severity = OOPSE_ERROR; |
87 |
painCave.isFatal = 1; |
88 |
simError(); |
89 |
} |
90 |
|
91 |
} |
92 |
|
93 |
} |
94 |
|
95 |
delete ffStream; |
96 |
|
97 |
} |
98 |
|
99 |
void EAM::parseEAMParamFile(const std::string& potentialParamFile) { |
100 |
|
101 |
ifstrstream* ppfStream; |
102 |
ppfStream = openForceFiledFile(potentialParamFile); |
103 |
const int bufferSize = 65535; |
104 |
char buffer[bufferSize]; |
105 |
std::string line; |
106 |
|
107 |
//skip first line |
108 |
ppfStream->getline(buffer, bufferSize); |
109 |
|
110 |
|
111 |
//The Second line contains atomic number, atomic mass, a lattice constant and lattic type |
112 |
int ident; |
113 |
double mass; |
114 |
double latticeConstant; |
115 |
std::string lattic; |
116 |
if (ppfStream->getline(buffer, bufferSize)) { |
117 |
StringTokenizer tokenizer1(buffer); |
118 |
ident = tokenizer1.nextTokenAsInt(); |
119 |
|
120 |
if (tokenizer1.countTokens() >= 4) { |
121 |
ident = tokenizer1.nextTokenAsInt(); |
122 |
mass = tokenizer1.nextTokenAsDouble(); |
123 |
latticeConstant = tokenizer1.nextTokenAsDouble(); |
124 |
lattice = tokenizer1.nextToken(); |
125 |
}else { |
126 |
std::cerr << "Not enought tokens" << std::endl; |
127 |
} |
128 |
} else { |
129 |
|
130 |
} |
131 |
|
132 |
// The third line is nrho, drho, nr, dr and rcut |
133 |
int nrho; |
134 |
double drho; |
135 |
int nr; |
136 |
double dr; |
137 |
double rcut; |
138 |
|
139 |
if (ppfStream->getline(buffer, bufferSize)) { |
140 |
StringTokenizer tokenizer2(buffer); |
141 |
|
142 |
if (tokenizer2.countTokens() >= 5){ |
143 |
nrho = tokenizer2.nextTokenAsInt(); |
144 |
drho = tokenizer2.nextTokenAsDouble(); |
145 |
nr = tokenizer2.nextTokenAsInt(); |
146 |
dr = tokenizer2.nextTokenAsDouble(); |
147 |
rcut = tokenizer2.nextTokenAsDouble(); |
148 |
}else { |
149 |
std::cerr << "Not enought tokens" << std::endl; |
150 |
} |
151 |
} else { |
152 |
|
153 |
} |
154 |
|
155 |
std::vector<double> rvals; |
156 |
std::vector<double> rhovals; |
157 |
std::vector<double> Frhovals; |
158 |
|
159 |
parseEAMArray(ppfStream, rvals, nr); |
160 |
parseEAMArray(ppfStream, rhovals, nr); |
161 |
parseEAMArray(ppfStream, Frhovals, nrho); |
162 |
|
163 |
int status; |
164 |
newEAMtype(&latticeConstant, &nrho, &drho, &nr, &dr, &rcut, |
165 |
&rvals[0], &rhovals[0], &Frhovals[0], &ident, &status ); |
166 |
|
167 |
if (status == 0) { |
168 |
|
169 |
} |
170 |
|
171 |
} |
172 |
|
173 |
void EAM::parseEAMArray(ifstrstream* ppfStream, std::vector<double>& array, int num) { |
174 |
|
175 |
const int dataPerLine = 5; |
176 |
if (num % dataPerLine != 0) { |
177 |
|
178 |
} |
179 |
|
180 |
const int bufferSize = 65535; |
181 |
char buffer[bufferSize]; |
182 |
std::string line; |
183 |
int readLines = num/dataPerLine; |
184 |
int lineCount = 0; |
185 |
while(ffStream.getline(buffer, bufferSize) && lineCount < num){ |
186 |
|
187 |
StringTokenizer tokenizer(buffer); |
188 |
if (tokenizer.countTokens() >= 5) { |
189 |
array.push_back(tokenizer.nextTokenAsDouble)); |
190 |
} else { |
191 |
|
192 |
} |
193 |
++lineCount; |
194 |
} |
195 |
|
196 |
if (lineCount < num) { |
197 |
|
198 |
} |
199 |
|
200 |
} |
201 |
|
202 |
} //end namespace oopse |