| 1 |
< |
#include <cstdlib> |
| 2 |
< |
#include <cstdio> |
| 3 |
< |
#include <cstring> |
| 4 |
< |
#include <cmath> |
| 5 |
< |
#include <iostream> |
| 6 |
< |
#include <string> |
| 7 |
< |
#include <map> |
| 8 |
< |
#include <fstream> |
| 9 |
< |
|
| 10 |
< |
#include "io/Globals.hpp" |
| 11 |
< |
#include "brains/SimInfo.hpp" |
| 12 |
< |
#include "brains/SimSetup.hpp" |
| 13 |
< |
#include "applications/simpleBuilder/simpleBuilderCmd.h" |
| 14 |
< |
#include "utils/StringUtils.hpp" |
| 15 |
< |
#include "applications/simpleBuilder/LatticeFactory.hpp" |
| 16 |
< |
#include "math/Vector3.hpp" |
| 17 |
< |
#include "applications/simpleBuilder/MoLocator.hpp" |
| 18 |
< |
#include "applications/simpleBuilder/Lattice.hpp" |
| 19 |
< |
|
| 20 |
< |
using namespace std; |
| 21 |
< |
|
| 22 |
< |
void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol); |
| 23 |
< |
double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF); |
| 24 |
< |
|
| 25 |
< |
int main( int argc, char* argv[]){ |
| 26 |
< |
|
| 27 |
< |
gengetopt_args_info args_info; |
| 28 |
< |
string latticeType; |
| 29 |
< |
string inputFileName; |
| 30 |
< |
string outPrefix; |
| 31 |
< |
string outMdFileName; |
| 32 |
< |
string outInitFileName; |
| 33 |
< |
SimInfo* oldInfo; |
| 34 |
< |
SimSetup* oldSimSetup; |
| 35 |
< |
BaseLattice* simpleLat; |
| 36 |
< |
int numMol; |
| 37 |
< |
double latticeConstant; |
| 38 |
< |
vector<double> lc; |
| 39 |
< |
double mass; |
| 40 |
< |
const double rhoConvertConst = 1.661; |
| 41 |
< |
double density; |
| 42 |
< |
int nx, ny, nz; |
| 43 |
< |
double Hmat[3][3]; |
| 44 |
< |
MoLocator *locator; |
| 45 |
< |
vector<Vector3d> latticePos; |
| 46 |
< |
vector<Vector3d> latticeOrt; |
| 47 |
< |
int numMolPerCell; |
| 48 |
< |
int curMolIndex; |
| 49 |
< |
DumpWriter* writer; |
| 50 |
< |
|
| 51 |
< |
// parse command line arguments |
| 52 |
< |
if (cmdline_parser (argc, argv, &args_info) != 0) |
| 53 |
< |
exit(1) ; |
| 54 |
< |
|
| 55 |
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density = args_info.density_arg; |
| 56 |
< |
|
| 57 |
< |
//get lattice type |
| 58 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
| 59 |
< |
if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){ |
| 60 |
< |
cerr << latticeType << " is an invalid lattice type" << endl; |
| 61 |
< |
cerr << LatticeFactory::getInstance()->toString() << endl; |
| 62 |
< |
exit(1); |
| 63 |
< |
} |
| 64 |
< |
|
| 65 |
< |
//get the number of unit cell |
| 66 |
< |
nx = args_info.nx_arg; |
| 67 |
< |
if(nx <= 0){ |
| 68 |
< |
cerr << "The number of unit cell in h direction must be greater than 0" << endl; |
| 69 |
< |
exit(1); |
| 70 |
< |
} |
| 71 |
< |
|
| 72 |
< |
ny = args_info.ny_arg; |
| 73 |
< |
if(ny <= 0){ |
| 74 |
< |
cerr << "The number of unit cell in l direction must be greater than 0" << endl; |
| 75 |
< |
exit(1); |
| 76 |
< |
} |
| 77 |
< |
|
| 78 |
< |
nz = args_info.nz_arg; |
| 79 |
< |
if(nz <= 0){ |
| 80 |
< |
cerr << "The number of unit cell in k direction must be greater than 0" << endl; |
| 81 |
< |
exit(1); |
| 82 |
< |
} |
| 83 |
< |
|
| 84 |
< |
//get input file name |
| 85 |
< |
if (args_info.inputs_num) |
| 86 |
< |
inputFileName = args_info.inputs[0]; |
| 87 |
< |
else { |
| 88 |
< |
cerr <<"You must specify a input file name.\n" << endl; |
| 89 |
< |
cmdline_parser_print_help(); |
| 90 |
< |
exit(1); |
| 91 |
< |
} |
| 92 |
< |
|
| 93 |
< |
|
| 94 |
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//parse md file and set up the system |
| 95 |
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oldInfo = new SimInfo; |
| 96 |
< |
if(oldInfo == NULL){ |
| 97 |
< |
cerr << "error in creating SimInfo" << endl; |
| 98 |
< |
exit(1); |
| 99 |
< |
} |
| 100 |
< |
|
| 101 |
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oldSimSetup = new SimSetup(); |
| 102 |
< |
if(oldSimSetup == NULL){ |
| 103 |
< |
cerr << "error in creating SimSetup" << endl; |
| 104 |
< |
exit(1); |
| 105 |
< |
} |
| 106 |
< |
|
| 107 |
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oldSimSetup->suspendInit(); |
| 108 |
< |
oldSimSetup->setSimInfo(oldInfo ); |
| 109 |
< |
oldSimSetup->parseFile(&inputFileName[0] ); |
| 110 |
< |
oldSimSetup->createSim(); |
| 111 |
< |
|
| 112 |
< |
if(oldInfo->nComponents >=2){ |
| 113 |
< |
cerr << "can not build the system with more than two components" << endl; |
| 114 |
< |
exit(1); |
| 115 |
< |
} |
| 116 |
< |
|
| 117 |
< |
//get mass of molecule. |
| 118 |
< |
//Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass |
| 119 |
< |
mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
| 120 |
< |
|
| 121 |
< |
//creat lattice |
| 122 |
< |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 123 |
< |
if(simpleLat == NULL){ |
| 124 |
< |
cerr << "Error in creating lattice" << endl; |
| 125 |
< |
exit(1); |
| 126 |
< |
} |
| 127 |
< |
|
| 128 |
< |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
| 129 |
< |
|
| 130 |
< |
//calculate lattice constant (in Angstrom) |
| 131 |
< |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass /density, 1.0/3.0); |
| 132 |
< |
|
| 133 |
< |
//set lattice constant |
| 134 |
< |
lc.push_back(latticeConstant); |
| 135 |
< |
simpleLat->setLatticeConstant(lc); |
| 136 |
< |
|
| 137 |
< |
//calculate the total number of molecules |
| 138 |
< |
numMol = nx * ny * nz * numMolPerCell; |
| 139 |
< |
|
| 140 |
< |
if (oldInfo->n_mol != numMol){ |
| 141 |
< |
|
| 142 |
< |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
| 143 |
< |
outMdFileName = outPrefix + ".md"; |
| 144 |
< |
|
| 145 |
< |
//creat new .md file on fly which corrects the number of molecule |
| 146 |
< |
createMdFile(inputFileName, outMdFileName, numMol); |
| 147 |
< |
cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl; |
| 148 |
< |
cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl; |
| 149 |
< |
exit(1); |
| 150 |
< |
} |
| 151 |
< |
|
| 152 |
< |
//determine the output file names |
| 153 |
< |
if (args_info.output_given) |
| 154 |
< |
outInitFileName = args_info.output_arg; |
| 155 |
< |
else |
| 156 |
< |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
| 157 |
< |
|
| 158 |
< |
|
| 159 |
< |
//allocat memory for storing pos, vel and etc |
| 160 |
< |
oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms); |
| 161 |
< |
for (int i = 0; i < oldInfo->n_atoms; i++) |
| 162 |
< |
oldInfo->atoms[i]->setCoords(); |
| 163 |
< |
|
| 164 |
< |
//creat Molocator |
| 165 |
< |
locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
| 166 |
< |
|
| 167 |
< |
//fill Hmat |
| 168 |
< |
Hmat[0][0] = nx * latticeConstant; |
| 169 |
< |
Hmat[0][1] = 0.0; |
| 170 |
< |
Hmat[0][2] = 0.0; |
| 171 |
< |
|
| 172 |
< |
Hmat[1][0] = 0.0; |
| 173 |
< |
Hmat[1][1] = ny * latticeConstant; |
| 174 |
< |
Hmat[1][2] = 0.0; |
| 175 |
< |
|
| 176 |
< |
Hmat[2][0] = 0.0; |
| 177 |
< |
Hmat[2][1] = 0.0; |
| 178 |
< |
Hmat[2][2] = nz * latticeConstant ; |
| 179 |
< |
|
| 180 |
< |
//set Hmat |
| 181 |
< |
oldInfo->setBoxM(Hmat); |
| 182 |
< |
|
| 183 |
< |
//place the molecules |
| 184 |
< |
|
| 185 |
< |
curMolIndex = 0; |
| 186 |
< |
|
| 187 |
< |
//get the orientation of the cell sites |
| 188 |
< |
//for the same type of molecule in same lattice, it will not change |
| 189 |
< |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 190 |
< |
|
| 191 |
< |
for(int i =0; i < nx; i++){ |
| 192 |
< |
for(int j=0; j < ny; j++){ |
| 193 |
< |
for(int k = 0; k < nz; k++){ |
| 194 |
< |
|
| 195 |
< |
//get the position of the cell sites |
| 196 |
< |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 197 |
< |
|
| 198 |
< |
for(int l = 0; l < numMolPerCell; l++) |
| 199 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++])); |
| 200 |
< |
} |
| 201 |
< |
} |
| 202 |
< |
} |
| 203 |
< |
|
| 204 |
< |
//create dumpwriter and write out the coordinates |
| 205 |
< |
oldInfo->finalName = outInitFileName; |
| 206 |
< |
writer = new DumpWriter( oldInfo ); |
| 207 |
< |
if(writer == NULL){ |
| 208 |
< |
cerr << "error in creating DumpWriter" << endl; |
| 209 |
< |
exit(1); |
| 210 |
< |
} |
| 211 |
< |
writer->writeFinal(0); |
| 212 |
< |
cout << "new initial configuration file: " << outInitFileName <<" is generated." << endl; |
| 213 |
< |
//delete objects |
| 214 |
< |
|
| 215 |
< |
//delete oldInfo and oldSimSetup |
| 216 |
< |
if(oldInfo != NULL) |
| 217 |
< |
delete oldInfo; |
| 218 |
< |
|
| 219 |
< |
if(oldSimSetup != NULL) |
| 220 |
< |
delete oldSimSetup; |
| 221 |
< |
|
| 222 |
< |
if (writer != NULL) |
| 223 |
< |
delete writer; |
| 224 |
< |
return 0; |
| 225 |
< |
} |
| 226 |
< |
|
| 227 |
< |
void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol){ |
| 228 |
< |
ifstream oldMdFile; |
| 229 |
< |
ofstream newMdFile; |
| 230 |
< |
const int MAXLEN = 65535; |
| 231 |
< |
char buffer[MAXLEN]; |
| 232 |
< |
|
| 233 |
< |
//create new .md file based on old .md file |
| 234 |
< |
oldMdFile.open(oldMdFileName.c_str()); |
| 235 |
< |
newMdFile.open(newMdFileName.c_str()); |
| 236 |
< |
|
| 237 |
< |
oldMdFile.getline(buffer, MAXLEN); |
| 238 |
< |
while(!oldMdFile.eof()){ |
| 239 |
< |
|
| 240 |
< |
//correct molecule number |
| 241 |
< |
if(strstr(buffer, "nMol") !=NULL){ |
| 242 |
< |
sprintf(buffer, "\t\tnMol = %d;", numMol); |
| 243 |
< |
newMdFile << buffer << endl; |
| 244 |
< |
} |
| 245 |
< |
else |
| 246 |
< |
newMdFile << buffer << endl; |
| 247 |
< |
|
| 248 |
< |
oldMdFile.getline(buffer, MAXLEN); |
| 249 |
< |
} |
| 250 |
< |
|
| 251 |
< |
oldMdFile.close(); |
| 252 |
< |
newMdFile.close(); |
| 253 |
< |
|
| 254 |
< |
} |
| 255 |
< |
|
| 256 |
< |
double getMolMass(MoleculeStamp* molStamp, ForceFields* myFF){ |
| 257 |
< |
int nAtoms; |
| 258 |
< |
AtomStamp* currAtomStamp; |
| 259 |
< |
double totMass; |
| 260 |
< |
|
| 261 |
< |
totMass = 0; |
| 262 |
< |
nAtoms = molStamp->getNAtoms(); |
| 263 |
< |
|
| 264 |
< |
for(size_t i=0; i<nAtoms; i++){ |
| 265 |
< |
currAtomStamp = molStamp->getAtom(i); |
| 266 |
< |
totMass += myFF->getAtomTypeMass(currAtomStamp->getType()); |
| 267 |
< |
} |
| 268 |
< |
|
| 269 |
< |
return totMass; |
| 270 |
< |
} |
| 1 |
> |
#include <cstdlib> |
| 2 |
> |
#include <cstdio> |
| 3 |
> |
#include <cstring> |
| 4 |
> |
#include <cmath> |
| 5 |
> |
#include <iostream> |
| 6 |
> |
#include <string> |
| 7 |
> |
#include <map> |
| 8 |
> |
#include <fstream> |
| 9 |
> |
|
| 10 |
> |
#include "io/Globals.hpp" |
| 11 |
> |
#include "brains/SimInfo.hpp" |
| 12 |
> |
#include "brains/SimSetup.hpp" |
| 13 |
> |
#include "applications/simpleBuilder/simpleBuilderCmd.h" |
| 14 |
> |
#include "utils/StringUtils.hpp" |
| 15 |
> |
#include "applications/simpleBuilder/LatticeFactory.hpp" |
| 16 |
> |
#include "math/Vector3.hpp" |
| 17 |
> |
#include "applications/simpleBuilder/MoLocator.hpp" |
| 18 |
> |
#include "applications/simpleBuilder/Lattice.hpp" |
| 19 |
> |
|
| 20 |
> |
using namespace std; |
| 21 |
> |
|
| 22 |
> |
void createMdFile(const string&oldMdFileName, const string&newMdFileName, |
| 23 |
> |
int numMol); |
| 24 |
> |
double getMolMass(MoleculeStamp * molStamp, ForceFields * myFF); |
| 25 |
> |
|
| 26 |
> |
int main(int argc, char *argv []) { |
| 27 |
> |
gengetopt_args_info args_info; |
| 28 |
> |
string latticeType; |
| 29 |
> |
string inputFileName; |
| 30 |
> |
string outPrefix; |
| 31 |
> |
string outMdFileName; |
| 32 |
> |
string outInitFileName; |
| 33 |
> |
SimInfo *oldInfo; |
| 34 |
> |
SimSetup *oldSimSetup; |
| 35 |
> |
BaseLattice *simpleLat; |
| 36 |
> |
int numMol; |
| 37 |
> |
double latticeConstant; |
| 38 |
> |
vector < double > lc; |
| 39 |
> |
double mass; |
| 40 |
> |
const double rhoConvertConst = 1.661; |
| 41 |
> |
double density; |
| 42 |
> |
int nx, |
| 43 |
> |
ny, |
| 44 |
> |
nz; |
| 45 |
> |
double Hmat[3][3]; |
| 46 |
> |
MoLocator *locator; |
| 47 |
> |
vector < Vector3d > latticePos; |
| 48 |
> |
vector < Vector3d > latticeOrt; |
| 49 |
> |
int numMolPerCell; |
| 50 |
> |
int curMolIndex; |
| 51 |
> |
DumpWriter *writer; |
| 52 |
> |
|
| 53 |
> |
// parse command line arguments |
| 54 |
> |
if (cmdline_parser(argc, argv, &args_info) != 0) |
| 55 |
> |
exit(1); |
| 56 |
> |
|
| 57 |
> |
density = args_info.density_arg; |
| 58 |
> |
|
| 59 |
> |
//get lattice type |
| 60 |
> |
latticeType = UpperCase(args_info.latticetype_arg); |
| 61 |
> |
|
| 62 |
> |
if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) { |
| 63 |
> |
cerr << latticeType << " is an invalid lattice type" << endl; |
| 64 |
> |
cerr << LatticeFactory::getInstance()->toString() << endl; |
| 65 |
> |
exit(1); |
| 66 |
> |
} |
| 67 |
> |
|
| 68 |
> |
//get the number of unit cell |
| 69 |
> |
nx = args_info.nx_arg; |
| 70 |
> |
|
| 71 |
> |
if (nx <= 0) { |
| 72 |
> |
cerr << "The number of unit cell in h direction must be greater than 0" |
| 73 |
> |
<< endl; |
| 74 |
> |
exit(1); |
| 75 |
> |
} |
| 76 |
> |
|
| 77 |
> |
ny = args_info.ny_arg; |
| 78 |
> |
|
| 79 |
> |
if (ny <= 0) { |
| 80 |
> |
cerr << "The number of unit cell in l direction must be greater than 0" |
| 81 |
> |
<< endl; |
| 82 |
> |
exit(1); |
| 83 |
> |
} |
| 84 |
> |
|
| 85 |
> |
nz = args_info.nz_arg; |
| 86 |
> |
|
| 87 |
> |
if (nz <= 0) { |
| 88 |
> |
cerr << "The number of unit cell in k direction must be greater than 0" |
| 89 |
> |
<< endl; |
| 90 |
> |
exit(1); |
| 91 |
> |
} |
| 92 |
> |
|
| 93 |
> |
//get input file name |
| 94 |
> |
if (args_info.inputs_num) |
| 95 |
> |
inputFileName = args_info.inputs[0]; |
| 96 |
> |
else { |
| 97 |
> |
cerr << "You must specify a input file name.\n" << endl; |
| 98 |
> |
cmdline_parser_print_help(); |
| 99 |
> |
exit(1); |
| 100 |
> |
} |
| 101 |
> |
|
| 102 |
> |
//parse md file and set up the system |
| 103 |
> |
oldInfo = new SimInfo; |
| 104 |
> |
|
| 105 |
> |
if (oldInfo == NULL) { |
| 106 |
> |
cerr << "error in creating SimInfo" << endl; |
| 107 |
> |
exit(1); |
| 108 |
> |
} |
| 109 |
> |
|
| 110 |
> |
oldSimSetup = new SimSetup(); |
| 111 |
> |
|
| 112 |
> |
if (oldSimSetup == NULL) { |
| 113 |
> |
cerr << "error in creating SimSetup" << endl; |
| 114 |
> |
exit(1); |
| 115 |
> |
} |
| 116 |
> |
|
| 117 |
> |
oldSimSetup->suspendInit(); |
| 118 |
> |
oldSimSetup->setSimInfo(oldInfo); |
| 119 |
> |
oldSimSetup->parseFile(&inputFileName[0]); |
| 120 |
> |
oldSimSetup->createSim(); |
| 121 |
> |
|
| 122 |
> |
if (oldInfo->nComponents >= 2) { |
| 123 |
> |
cerr << "can not build the system with more than two components" |
| 124 |
> |
<< endl; |
| 125 |
> |
exit(1); |
| 126 |
> |
} |
| 127 |
> |
|
| 128 |
> |
//get mass of molecule. |
| 129 |
> |
//Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass |
| 130 |
> |
mass = getMolMass(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
| 131 |
> |
|
| 132 |
> |
//creat lattice |
| 133 |
> |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 134 |
> |
|
| 135 |
> |
if (simpleLat == NULL) { |
| 136 |
> |
cerr << "Error in creating lattice" << endl; |
| 137 |
> |
exit(1); |
| 138 |
> |
} |
| 139 |
> |
|
| 140 |
> |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
| 141 |
> |
|
| 142 |
> |
//calculate lattice constant (in Angstrom) |
| 143 |
> |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
| 144 |
> |
1.0 / 3.0); |
| 145 |
> |
|
| 146 |
> |
//set lattice constant |
| 147 |
> |
lc.push_back(latticeConstant); |
| 148 |
> |
simpleLat->setLatticeConstant(lc); |
| 149 |
> |
|
| 150 |
> |
//calculate the total number of molecules |
| 151 |
> |
numMol = nx * ny * nz * numMolPerCell; |
| 152 |
> |
|
| 153 |
> |
if (oldInfo->n_mol != numMol) { |
| 154 |
> |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
| 155 |
> |
outMdFileName = outPrefix + ".md"; |
| 156 |
> |
|
| 157 |
> |
//creat new .md file on fly which corrects the number of molecule |
| 158 |
> |
createMdFile(inputFileName, outMdFileName, numMol); |
| 159 |
> |
cerr |
| 160 |
> |
<< "SimpleBuilder Error: the number of molecule and the density are not matched" |
| 161 |
> |
<< endl; |
| 162 |
> |
cerr << "A new .md file: " << outMdFileName |
| 163 |
> |
<< " is generated, use it to rerun the simpleBuilder" << endl; |
| 164 |
> |
exit(1); |
| 165 |
> |
} |
| 166 |
> |
|
| 167 |
> |
//determine the output file names |
| 168 |
> |
if (args_info.output_given) |
| 169 |
> |
outInitFileName = args_info.output_arg; |
| 170 |
> |
else |
| 171 |
> |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
| 172 |
> |
|
| 173 |
> |
//allocat memory for storing pos, vel and etc |
| 174 |
> |
oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms); |
| 175 |
> |
|
| 176 |
> |
for(int i = 0; i < oldInfo->n_atoms; i++) |
| 177 |
> |
oldInfo->atoms[i]->setCoords(); |
| 178 |
> |
|
| 179 |
> |
//creat Molocator |
| 180 |
> |
locator = new MoLocator(oldInfo->compStamps[0], |
| 181 |
> |
oldSimSetup->getForceField()); |
| 182 |
> |
|
| 183 |
> |
//fill Hmat |
| 184 |
> |
Hmat[0][0] = nx * latticeConstant; |
| 185 |
> |
Hmat[0][1] = 0.0; |
| 186 |
> |
Hmat[0][2] = 0.0; |
| 187 |
> |
|
| 188 |
> |
Hmat[1][0] = 0.0; |
| 189 |
> |
Hmat[1][1] = ny * latticeConstant; |
| 190 |
> |
Hmat[1][2] = 0.0; |
| 191 |
> |
|
| 192 |
> |
Hmat[2][0] = 0.0; |
| 193 |
> |
Hmat[2][1] = 0.0; |
| 194 |
> |
Hmat[2][2] = nz * latticeConstant; |
| 195 |
> |
|
| 196 |
> |
//set Hmat |
| 197 |
> |
oldInfo->setBoxM(Hmat); |
| 198 |
> |
|
| 199 |
> |
//place the molecules |
| 200 |
> |
|
| 201 |
> |
curMolIndex = 0; |
| 202 |
> |
|
| 203 |
> |
//get the orientation of the cell sites |
| 204 |
> |
//for the same type of molecule in same lattice, it will not change |
| 205 |
> |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 206 |
> |
|
| 207 |
> |
for(int i = 0; i < nx; i++) { |
| 208 |
> |
for(int j = 0; j < ny; j++) { |
| 209 |
> |
for(int k = 0; k < nz; k++) { |
| 210 |
> |
|
| 211 |
> |
//get the position of the cell sites |
| 212 |
> |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 213 |
> |
|
| 214 |
> |
for(int l = 0; l < numMolPerCell; l++) |
| 215 |
> |
locator->placeMol(latticePos[l], latticeOrt[l], |
| 216 |
> |
&(oldInfo->molecules[curMolIndex++])); |
| 217 |
> |
} |
| 218 |
> |
} |
| 219 |
> |
} |
| 220 |
> |
|
| 221 |
> |
//create dumpwriter and write out the coordinates |
| 222 |
> |
oldInfo->finalName = outInitFileName; |
| 223 |
> |
writer = new DumpWriter(oldInfo); |
| 224 |
> |
|
| 225 |
> |
if (writer == NULL) { |
| 226 |
> |
cerr << "error in creating DumpWriter" << endl; |
| 227 |
> |
exit(1); |
| 228 |
> |
} |
| 229 |
> |
|
| 230 |
> |
writer->writeFinal(0); |
| 231 |
> |
cout << "new initial configuration file: " << outInitFileName |
| 232 |
> |
<< " is generated." << endl; |
| 233 |
> |
|
| 234 |
> |
//delete objects |
| 235 |
> |
|
| 236 |
> |
//delete oldInfo and oldSimSetup |
| 237 |
> |
if (oldInfo != NULL) |
| 238 |
> |
delete oldInfo; |
| 239 |
> |
|
| 240 |
> |
if (oldSimSetup != NULL) |
| 241 |
> |
delete oldSimSetup; |
| 242 |
> |
|
| 243 |
> |
if (writer != NULL) |
| 244 |
> |
delete writer; |
| 245 |
> |
|
| 246 |
> |
return 0; |
| 247 |
> |
} |
| 248 |
> |
|
| 249 |
> |
void createMdFile(const string&oldMdFileName, const string&newMdFileName, |
| 250 |
> |
int numMol) { |
| 251 |
> |
ifstream oldMdFile; |
| 252 |
> |
ofstream newMdFile; |
| 253 |
> |
const int MAXLEN = 65535; |
| 254 |
> |
char buffer[MAXLEN]; |
| 255 |
> |
|
| 256 |
> |
//create new .md file based on old .md file |
| 257 |
> |
oldMdFile.open(oldMdFileName.c_str()); |
| 258 |
> |
newMdFile.open(newMdFileName.c_str()); |
| 259 |
> |
|
| 260 |
> |
oldMdFile.getline(buffer, MAXLEN); |
| 261 |
> |
|
| 262 |
> |
while (!oldMdFile.eof()) { |
| 263 |
> |
|
| 264 |
> |
//correct molecule number |
| 265 |
> |
if (strstr(buffer, "nMol") != NULL) { |
| 266 |
> |
sprintf(buffer, "\t\tnMol = %d;", numMol); |
| 267 |
> |
newMdFile << buffer << endl; |
| 268 |
> |
} else |
| 269 |
> |
newMdFile << buffer << endl; |
| 270 |
> |
|
| 271 |
> |
oldMdFile.getline(buffer, MAXLEN); |
| 272 |
> |
} |
| 273 |
> |
|
| 274 |
> |
oldMdFile.close(); |
| 275 |
> |
newMdFile.close(); |
| 276 |
> |
} |
| 277 |
> |
|
| 278 |
> |
double getMolMass(MoleculeStamp *molStamp, ForceFields *myFF) { |
| 279 |
> |
int nAtoms; |
| 280 |
> |
AtomStamp *currAtomStamp; |
| 281 |
> |
double totMass; |
| 282 |
> |
|
| 283 |
> |
totMass = 0; |
| 284 |
> |
nAtoms = molStamp->getNAtoms(); |
| 285 |
> |
|
| 286 |
> |
for(size_t i = 0; i < nAtoms; i++) { |
| 287 |
> |
currAtomStamp = molStamp->getAtom(i); |
| 288 |
> |
totMass += myFF->getAtomTypeMass(currAtomStamp->getType()); |
| 289 |
> |
} |
| 290 |
> |
|
| 291 |
> |
return totMass; |
| 292 |
> |
} |
