| 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 "io/EAMAtomTypesSectionParser.hpp" |
| 27 |
#include "types/AtomType.hpp" |
| 28 |
|
| 29 |
namespace oopse { |
| 30 |
|
| 31 |
EAMAtomTypesSectionParser::EAMAtomTypesSectionParser() { |
| 32 |
setSectionName("EAMAtomTypes"); |
| 33 |
} |
| 34 |
|
| 35 |
void EAMAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){ |
| 36 |
AtomType* atomType; |
| 37 |
std::string atomTypeName; |
| 38 |
double mass; |
| 39 |
StringTokenizer tokenizer(line); |
| 40 |
|
| 41 |
if (tokenizer.countTokens() >= 2) { |
| 42 |
atomTypeName = tokenizer.nextToken(); |
| 43 |
std::string potentialParamFile = tokenizer.nextToken(); |
| 44 |
|
| 45 |
AtomType* atomType = ff.getAtomType(atomTypeName); |
| 46 |
if (atomType != NULL) { |
| 47 |
atomType->setEAM(); |
| 48 |
parseEAMParamFile(atomType, potentialParamFile, atomType->getIdent()); |
| 49 |
} else { |
| 50 |
|
| 51 |
} |
| 52 |
|
| 53 |
} else { |
| 54 |
sprintf( painCave.errMsg, |
| 55 |
"Not enough tokens when parsing EAM Force Field : %s\n" |
| 56 |
"in line %d : %s\n", |
| 57 |
filename.c_str(), lineNo, line); |
| 58 |
painCave.severity = OOPSE_ERROR; |
| 59 |
painCave.isFatal = 1; |
| 60 |
simError(); |
| 61 |
} |
| 62 |
|
| 63 |
|
| 64 |
} |
| 65 |
|
| 66 |
void EAMAtomTypesSectionParser::parseEAMParamFile(AtomType* atomType, |
| 67 |
const std::string& potentialParamFile, int ident) { |
| 68 |
|
| 69 |
ifstrstream* ppfStream; |
| 70 |
ppfStream = openForceFieldFile(potentialParamFile); |
| 71 |
const int bufferSize = 65535; |
| 72 |
char buffer[bufferSize]; |
| 73 |
std::string line; |
| 74 |
|
| 75 |
//skip first line |
| 76 |
ppfStream->getline(buffer, bufferSize); |
| 77 |
|
| 78 |
|
| 79 |
//The Second line contains atomic number, atomic mass, a lattice constant and lattic type |
| 80 |
int junk; |
| 81 |
double mass; |
| 82 |
double latticeConstant; |
| 83 |
std::string lattice; |
| 84 |
if (ppfStream->getline(buffer, bufferSize)) { |
| 85 |
StringTokenizer tokenizer1(buffer); |
| 86 |
ident = tokenizer1.nextTokenAsInt(); |
| 87 |
|
| 88 |
if (tokenizer1.countTokens() >= 4) { |
| 89 |
junk = tokenizer1.nextTokenAsInt(); |
| 90 |
mass = tokenizer1.nextTokenAsDouble(); |
| 91 |
latticeConstant = tokenizer1.nextTokenAsDouble(); |
| 92 |
lattice = tokenizer1.nextToken(); |
| 93 |
}else { |
| 94 |
std::cerr << "Not enought tokens" << std::endl; |
| 95 |
} |
| 96 |
} else { |
| 97 |
|
| 98 |
} |
| 99 |
|
| 100 |
// The third line is nrho, drho, nr, dr and rcut |
| 101 |
EAMParam eamParam; |
| 102 |
eamParam.latticeConstant = latticeConstant; |
| 103 |
|
| 104 |
if (ppfStream->getline(buffer, bufferSize)) { |
| 105 |
StringTokenizer tokenizer2(buffer); |
| 106 |
|
| 107 |
if (tokenizer2.countTokens() >= 5){ |
| 108 |
eamParam.nrho = tokenizer2.nextTokenAsInt(); |
| 109 |
eamParam.drho = tokenizer2.nextTokenAsDouble(); |
| 110 |
eamParam.nr = tokenizer2.nextTokenAsInt(); |
| 111 |
eamParam.dr = tokenizer2.nextTokenAsDouble(); |
| 112 |
eamParam.rcut = tokenizer2.nextTokenAsDouble(); |
| 113 |
}else { |
| 114 |
std::cerr << "Not enought tokens" << std::endl; |
| 115 |
} |
| 116 |
} else { |
| 117 |
|
| 118 |
} |
| 119 |
|
| 120 |
parseEAMArray(ppfStream, eamParam.rvals, eamParam.nr); |
| 121 |
parseEAMArray(ppfStream, eamParam.rhovals, eamParam.nr); |
| 122 |
parseEAMArray(ppfStream, eamParam.Frhovals, eamParam.nrho); |
| 123 |
|
| 124 |
atomType->addProperty(EAMParamGenericData("EAM", eamParam)); |
| 125 |
} |
| 126 |
|
| 127 |
void EAMAtomTypesSectionParser::parseEAMArray(ifstrstream* ppfStream, |
| 128 |
std::vector<double>& array, int num) { |
| 129 |
|
| 130 |
const int dataPerLine = 5; |
| 131 |
if (num % dataPerLine != 0) { |
| 132 |
|
| 133 |
} |
| 134 |
|
| 135 |
const int bufferSize = 65535; |
| 136 |
char buffer[bufferSize]; |
| 137 |
std::string line; |
| 138 |
int readLines = num/dataPerLine; |
| 139 |
int lineCount = 0; |
| 140 |
while(ffStream.getline(buffer, bufferSize) && lineCount < num){ |
| 141 |
|
| 142 |
StringTokenizer tokenizer(buffer); |
| 143 |
if (tokenizer.countTokens() >= dataPerLine) { |
| 144 |
for (int i = 0; i < dataPerLine; ++i) { |
| 145 |
array.push_back(tokenizer.nextTokenAsDouble())); |
| 146 |
} |
| 147 |
} else { |
| 148 |
|
| 149 |
} |
| 150 |
++lineCount; |
| 151 |
} |
| 152 |
|
| 153 |
if (lineCount < num) { |
| 154 |
|
| 155 |
} |
| 156 |
|
| 157 |
} |
| 158 |
|
| 159 |
|
| 160 |
} //end namespace oopse |
| 161 |
|
