| 42 |
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* |
| 43 |
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* Created by Charles F. Vardeman II on 10 Apr 2006. |
| 44 |
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* @author Charles F. Vardeman II |
| 45 |
< |
* @version $Id: randomBuilder.cpp,v 1.2 2006-05-17 21:51:42 tim Exp $ |
| 45 |
> |
* @version $Id: randomBuilder.cpp,v 1.6 2006-10-10 18:34:12 gezelter Exp $ |
| 46 |
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* |
| 47 |
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*/ |
| 48 |
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|
| 73 |
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|
| 74 |
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void createMdFile(const std::string&oldMdFileName, |
| 75 |
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const std::string&newMdFileName, |
| 76 |
< |
int components,int* numMol); |
| 76 |
> |
std::vector<int> nMol); |
| 77 |
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|
| 78 |
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int main(int argc, char *argv []) { |
| 79 |
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|
| 80 |
< |
//register force fields |
| 80 |
> |
// register force fields |
| 81 |
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registerForceFields(); |
| 82 |
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registerLattice(); |
| 83 |
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|
| 84 |
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gengetopt_args_info args_info; |
| 85 |
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std::string latticeType; |
| 86 |
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std::string inputFileName; |
| 87 |
< |
std::string outPrefix; |
| 88 |
< |
std::string outMdFileName; |
| 89 |
< |
std::string outInitFileName; |
| 87 |
> |
std::string outputFileName; |
| 88 |
|
Lattice *simpleLat; |
| 91 |
– |
int* numMol; |
| 89 |
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RealType latticeConstant; |
| 90 |
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std::vector<RealType> lc; |
| 94 |
– |
RealType mass; |
| 91 |
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const RealType rhoConvertConst = 1.661; |
| 92 |
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RealType density; |
| 93 |
< |
int nx, |
| 98 |
< |
ny, |
| 99 |
< |
nz; |
| 93 |
> |
int nx, ny, nz; |
| 94 |
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Mat3x3d hmat; |
| 95 |
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MoLocator *locator; |
| 96 |
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std::vector<Vector3d> latticePos; |
| 97 |
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std::vector<Vector3d> latticeOrt; |
| 98 |
< |
int numMolPerCell; |
| 105 |
< |
int curMolIndex; |
| 98 |
> |
int nMolPerCell; |
| 99 |
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DumpWriter *writer; |
| 100 |
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|
| 101 |
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// parse command line arguments |
| 105 |
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density = args_info.density_arg; |
| 106 |
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|
| 107 |
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//get lattice type |
| 108 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
| 108 |
> |
latticeType = "FCC"; |
| 109 |
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|
| 110 |
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 111 |
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|
| 115 |
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painCave.isFatal = 1; |
| 116 |
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simError(); |
| 117 |
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} |
| 118 |
+ |
nMolPerCell = simpleLat->getNumSitesPerCell(); |
| 119 |
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|
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< |
//get the number of unit cell |
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> |
//get the number of unit cells in each direction: |
| 121 |
> |
|
| 122 |
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nx = args_info.nx_arg; |
| 123 |
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|
| 124 |
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if (nx <= 0) { |
| 125 |
< |
std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl; |
| 126 |
< |
exit(1); |
| 125 |
> |
sprintf(painCave.errMsg, "The number of unit cells in the x direction " |
| 126 |
> |
"must be greater than 0."); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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} |
| 130 |
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ny = args_info.ny_arg; |
| 132 |
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|
| 133 |
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if (ny <= 0) { |
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< |
std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl; |
| 135 |
< |
exit(1); |
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> |
sprintf(painCave.errMsg, "The number of unit cells in the y direction " |
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> |
"must be greater than 0."); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
| 138 |
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} |
| 139 |
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| 140 |
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nz = args_info.nz_arg; |
| 141 |
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|
| 142 |
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if (nz <= 0) { |
| 143 |
< |
std::cerr << "The number of unit cell in k direction must be greater than 0" << std::endl; |
| 144 |
< |
exit(1); |
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> |
sprintf(painCave.errMsg, "The number of unit cells in the z direction " |
| 144 |
> |
"must be greater than 0."); |
| 145 |
> |
painCave.isFatal = 1; |
| 146 |
> |
simError(); |
| 147 |
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} |
| 148 |
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|
| 149 |
+ |
int nSites = nMolPerCell * nx * ny * nz; |
| 150 |
+ |
|
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//get input file name |
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if (args_info.inputs_num) |
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inputFileName = args_info.inputs[0]; |
| 154 |
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else { |
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< |
std::cerr << "You must specify a input file name.\n" << std::endl; |
| 156 |
< |
cmdline_parser_print_help(); |
| 157 |
< |
exit(1); |
| 155 |
> |
sprintf(painCave.errMsg, "No input .md file name was specified " |
| 156 |
> |
"on the command line"); |
| 157 |
> |
painCave.isFatal = 1; |
| 158 |
> |
simError(); |
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} |
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|
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//parse md file and set up the system |
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+ |
|
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SimCreator oldCreator; |
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SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
| 165 |
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Globals* simParams = oldInfo->getSimParams(); |
| 166 |
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|
| 167 |
< |
int nComponents =simParams->getNComponents(); |
| 163 |
< |
if (oldInfo->getNMoleculeStamp()>= 2) { |
| 164 |
< |
std::cerr << "can not build the system with more than two components" |
| 165 |
< |
<< std::endl; |
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< |
exit(1); |
| 167 |
< |
} |
| 167 |
> |
// Calculate lattice constant (in Angstroms) |
| 168 |
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|
| 169 |
< |
//get mass of molecule. |
| 169 |
> |
std::vector<Component*> components = simParams->getComponents(); |
| 170 |
> |
std::vector<RealType> molFractions; |
| 171 |
> |
std::vector<RealType> molecularMasses; |
| 172 |
> |
std::vector<int> nMol; |
| 173 |
> |
int nComponents = components.size(); |
| 174 |
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|
| 175 |
< |
mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
| 175 |
> |
if (nComponents == 1) { |
| 176 |
> |
molFractions.push_back(1.0); |
| 177 |
> |
} else { |
| 178 |
> |
if (args_info.molFraction_given == nComponents) { |
| 179 |
> |
for (int i = 0; i < nComponents; i++) { |
| 180 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
| 181 |
> |
} |
| 182 |
> |
} else if (args_info.molFraction_given == nComponents-1) { |
| 183 |
> |
RealType remainingFraction = 1.0; |
| 184 |
> |
for (int i = 0; i < nComponents-1; i++) { |
| 185 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
| 186 |
> |
remainingFraction -= molFractions[i]; |
| 187 |
> |
} |
| 188 |
> |
molFractions.push_back(remainingFraction); |
| 189 |
> |
} else { |
| 190 |
> |
sprintf(painCave.errMsg, "randomBuilder can't figure out molFractions " |
| 191 |
> |
"for all of the components in the <MetaData> block."); |
| 192 |
> |
painCave.isFatal = 1; |
| 193 |
> |
simError(); |
| 194 |
> |
} |
| 195 |
> |
} |
| 196 |
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|
| 197 |
< |
//creat lattice |
| 198 |
< |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 197 |
> |
// do some sanity checking: |
| 198 |
> |
|
| 199 |
> |
RealType totalFraction = 0.0; |
| 200 |
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|
| 201 |
< |
if (simpleLat == NULL) { |
| 202 |
< |
std::cerr << "Error in creating lattice" << std::endl; |
| 203 |
< |
exit(1); |
| 201 |
> |
for (int i = 0; i < nComponents; i++) { |
| 202 |
> |
if (molFractions.at(i) < 0.0) { |
| 203 |
> |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 204 |
> |
" less than zero!"); |
| 205 |
> |
painCave.isFatal = 1; |
| 206 |
> |
simError(); |
| 207 |
> |
} |
| 208 |
> |
if (molFractions.at(i) > 1.0) { |
| 209 |
> |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 210 |
> |
" greater than one!"); |
| 211 |
> |
painCave.isFatal = 1; |
| 212 |
> |
simError(); |
| 213 |
> |
} |
| 214 |
> |
totalFraction += molFractions.at(i); |
| 215 |
|
} |
| 216 |
+ |
if (abs(totalFraction - 1.0) > 1e-6) { |
| 217 |
+ |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
| 218 |
+ |
painCave.isFatal = 1; |
| 219 |
+ |
simError(); |
| 220 |
+ |
} |
| 221 |
|
|
| 222 |
< |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
| 222 |
> |
int remaining = nSites; |
| 223 |
> |
for (int i=0; i < nComponents-1; i++) { |
| 224 |
> |
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
| 225 |
> |
remaining -= nMol.at(i); |
| 226 |
> |
} |
| 227 |
> |
nMol.push_back(remaining); |
| 228 |
|
|
| 229 |
< |
//calculate lattice constant (in Angstrom) |
| 184 |
< |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
| 185 |
< |
(RealType)(1.0 / 3.0)); |
| 229 |
> |
// recompute actual mol fractions and perform final sanity check: |
| 230 |
|
|
| 231 |
< |
//set lattice constant |
| 231 |
> |
int totalMolecules = 0; |
| 232 |
> |
RealType totalMass = 0.0; |
| 233 |
> |
for (int i=0; i < nComponents; i++) { |
| 234 |
> |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
| 235 |
> |
totalMolecules += nMol.at(i); |
| 236 |
> |
molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i), |
| 237 |
> |
oldInfo->getForceField())); |
| 238 |
> |
totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i); |
| 239 |
> |
} |
| 240 |
> |
RealType avgMass = totalMass / (RealType) totalMolecules; |
| 241 |
> |
|
| 242 |
> |
if (totalMolecules != nSites) { |
| 243 |
> |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
| 244 |
> |
"to the number of lattice sites!"); |
| 245 |
> |
painCave.isFatal = 1; |
| 246 |
> |
simError(); |
| 247 |
> |
} |
| 248 |
> |
|
| 249 |
> |
latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density, |
| 250 |
> |
(RealType)(1.0 / 3.0)); |
| 251 |
> |
|
| 252 |
> |
// Set the lattice constant |
| 253 |
> |
|
| 254 |
|
lc.push_back(latticeConstant); |
| 255 |
|
simpleLat->setLatticeConstant(lc); |
| 256 |
+ |
|
| 257 |
+ |
// Calculate the lattice sites and fill the lattice vector. |
| 258 |
|
|
| 259 |
< |
//calculate the total number of molecules |
| 192 |
< |
int totMol = nx * ny * nz * numMolPerCell; |
| 259 |
> |
// Get the standard orientations of the cell sites |
| 260 |
|
|
| 261 |
< |
// Calculate the lattice sites and fill lattice vector. |
| 262 |
< |
vector<Vector3d> latticeSites; |
| 261 |
> |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 262 |
> |
|
| 263 |
> |
vector<Vector3d> sites; |
| 264 |
> |
vector<Vector3d> orientations; |
| 265 |
|
|
| 266 |
|
for(int i = 0; i < nx; i++) { |
| 267 |
|
for(int j = 0; j < ny; j++) { |
| 268 |
|
for(int k = 0; k < nz; k++) { |
| 269 |
|
|
| 270 |
< |
//get the position of the cell sites |
| 270 |
> |
// Get the position of the cell sites |
| 271 |
> |
|
| 272 |
|
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 273 |
|
|
| 274 |
< |
for(int l = 0; l < numMolPerCell; l++) { |
| 275 |
< |
latticeSites.push_back(latticePos[l]); |
| 274 |
> |
for(int l = 0; l < nMolPerCell; l++) { |
| 275 |
> |
sites.push_back(latticePos[l]); |
| 276 |
> |
orientations.push_back(latticeOrt[l]); |
| 277 |
|
} |
| 278 |
|
} |
| 279 |
|
} |
| 280 |
|
} |
| 210 |
– |
|
| 211 |
– |
int numSites = latticeSites.size(); |
| 212 |
– |
|
| 213 |
– |
numMol = new int[nComponents]; |
| 214 |
– |
if (nComponents != args_info.molFraction_given && nComponents != 1){ |
| 215 |
– |
std::cerr << "Number of components does not equal molFraction occurances." << std::endl; |
| 216 |
– |
exit(1); |
| 217 |
– |
} |
| 218 |
– |
int totComponents = 0; |
| 219 |
– |
for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */ |
| 220 |
– |
numMol[i] = int((RealType)numSites * args_info.molFraction_arg[i]); |
| 221 |
– |
std::cout<<numMol[i]<<std::endl; |
| 222 |
– |
totComponents += numMol[i]; |
| 223 |
– |
} |
| 224 |
– |
numMol[nComponents-1] = numSites - totComponents; |
| 281 |
|
|
| 282 |
+ |
outputFileName = args_info.output_arg; |
| 283 |
|
|
| 284 |
< |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
| 228 |
< |
outMdFileName = outPrefix + ".md"; |
| 284 |
> |
// create a new .md file on the fly which corrects the number of molecules |
| 285 |
|
|
| 286 |
< |
//creat new .md file on fly which corrects the number of molecule |
| 231 |
< |
createMdFile(inputFileName, outMdFileName, nComponents,numMol); |
| 286 |
> |
createMdFile(inputFileName, outputFileName, nMol); |
| 287 |
|
|
| 288 |
+ |
if (oldInfo != NULL) |
| 289 |
+ |
delete oldInfo; |
| 290 |
|
|
| 291 |
+ |
// We need to read in the new SimInfo object, then Parse the |
| 292 |
+ |
// md file and set up the system |
| 293 |
|
|
| 294 |
< |
//determine the output file names |
| 295 |
< |
if (args_info.output_given){ |
| 237 |
< |
outInitFileName = args_info.output_arg; |
| 238 |
< |
}else{ |
| 239 |
< |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
| 240 |
< |
} |
| 294 |
> |
SimCreator newCreator; |
| 295 |
> |
SimInfo* newInfo = newCreator.createSim(outputFileName, false); |
| 296 |
|
|
| 297 |
< |
//fill Hmat |
| 298 |
< |
hmat(0, 0)= nx * latticeConstant; |
| 297 |
> |
// fill Hmat |
| 298 |
> |
|
| 299 |
> |
hmat(0, 0) = nx * latticeConstant; |
| 300 |
|
hmat(0, 1) = 0.0; |
| 301 |
|
hmat(0, 2) = 0.0; |
| 302 |
|
|
| 308 |
|
hmat(2, 1) = 0.0; |
| 309 |
|
hmat(2, 2) = nz * latticeConstant; |
| 310 |
|
|
| 311 |
< |
//set Hmat |
| 256 |
< |
oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 311 |
> |
// Set Hmat |
| 312 |
|
|
| 313 |
< |
//place the molecules |
| 313 |
> |
newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 314 |
|
|
| 315 |
< |
curMolIndex = 0; |
| 315 |
> |
// place the molecules |
| 316 |
|
|
| 317 |
< |
//get the orientation of the cell sites |
| 263 |
< |
//for the same type of molecule in same lattice, it will not change |
| 264 |
< |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 317 |
> |
// Randomize a vector of ints: |
| 318 |
|
|
| 319 |
< |
|
| 320 |
< |
/* Randomize position vector */ |
| 321 |
< |
std::random_shuffle(latticeSites.begin(), latticeSites.end()); |
| 319 |
> |
vector<int> ids; |
| 320 |
> |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
| 321 |
> |
std::random_shuffle(ids.begin(), ids.end()); |
| 322 |
|
|
| 270 |
– |
|
| 271 |
– |
if (oldInfo != NULL) |
| 272 |
– |
delete oldInfo; |
| 273 |
– |
|
| 274 |
– |
|
| 275 |
– |
// We need to read in new siminfo object. |
| 276 |
– |
//parse md file and set up the system |
| 277 |
– |
//SimCreator NewCreator; |
| 278 |
– |
SimCreator newCreator; |
| 279 |
– |
SimInfo* NewInfo = newCreator.createSim(outMdFileName, false); |
| 280 |
– |
|
| 281 |
– |
/* create Molocators */ |
| 282 |
– |
locator = new MoLocator(NewInfo->getMoleculeStamp(0), NewInfo->getForceField()); |
| 283 |
– |
|
| 284 |
– |
|
| 285 |
– |
|
| 323 |
|
Molecule* mol; |
| 287 |
– |
SimInfo::MoleculeIterator mi; |
| 288 |
– |
mol = NewInfo->beginMolecule(mi); |
| 324 |
|
int l = 0; |
| 325 |
< |
for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
| 326 |
< |
locator->placeMol(latticeSites[l], latticeOrt[l], mol); |
| 327 |
< |
l++; |
| 325 |
> |
for (int i = 0; i < nComponents; i++){ |
| 326 |
> |
locator = new MoLocator(newInfo->getMoleculeStamp(i), |
| 327 |
> |
newInfo->getForceField()); |
| 328 |
> |
for (int n = 0; n < nMol.at(i); n++) { |
| 329 |
> |
mol = newInfo->getMoleculeByGlobalIndex(l); |
| 330 |
> |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
| 331 |
> |
l++; |
| 332 |
> |
} |
| 333 |
|
} |
| 334 |
+ |
|
| 335 |
+ |
// Create DumpWriter and write out the coordinates |
| 336 |
|
|
| 337 |
+ |
writer = new DumpWriter(newInfo, outputFileName); |
| 338 |
|
|
| 296 |
– |
|
| 297 |
– |
//create dumpwriter and write out the coordinates |
| 298 |
– |
oldInfo->setFinalConfigFileName(outInitFileName); |
| 299 |
– |
writer = new DumpWriter(oldInfo); |
| 300 |
– |
|
| 339 |
|
if (writer == NULL) { |
| 340 |
< |
std::cerr << "error in creating DumpWriter" << std::endl; |
| 341 |
< |
exit(1); |
| 340 |
> |
sprintf(painCave.errMsg, "error in creating DumpWriter"); |
| 341 |
> |
painCave.isFatal = 1; |
| 342 |
> |
simError(); |
| 343 |
|
} |
| 344 |
|
|
| 345 |
|
writer->writeDump(); |
| 307 |
– |
std::cout << "new initial configuration file: " << outInitFileName |
| 308 |
– |
<< " is generated." << std::endl; |
| 346 |
|
|
| 347 |
< |
//delete objects |
| 347 |
> |
// deleting the writer will put the closing at the end of the dump file. |
| 348 |
|
|
| 349 |
< |
//delete oldInfo and oldSimSetup |
| 313 |
< |
if (oldInfo != NULL) |
| 314 |
< |
delete oldInfo; |
| 349 |
> |
delete writer; |
| 350 |
|
|
| 351 |
< |
if (writer != NULL) |
| 352 |
< |
delete writer; |
| 353 |
< |
|
| 354 |
< |
delete simpleLat; |
| 320 |
< |
|
| 351 |
> |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 352 |
> |
"generated.\n", outputFileName.c_str()); |
| 353 |
> |
painCave.isFatal = 0; |
| 354 |
> |
simError(); |
| 355 |
|
return 0; |
| 356 |
|
} |
| 357 |
|
|
| 358 |
< |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
| 359 |
< |
int components,int* numMol) { |
| 358 |
> |
void createMdFile(const std::string&oldMdFileName, |
| 359 |
> |
const std::string&newMdFileName, |
| 360 |
> |
std::vector<int> nMol) { |
| 361 |
|
ifstream oldMdFile; |
| 362 |
|
ofstream newMdFile; |
| 363 |
|
const int MAXLEN = 65535; |
| 364 |
|
char buffer[MAXLEN]; |
| 365 |
|
|
| 366 |
|
//create new .md file based on old .md file |
| 367 |
+ |
|
| 368 |
|
oldMdFile.open(oldMdFileName.c_str()); |
| 369 |
|
newMdFile.open(newMdFileName.c_str()); |
| 370 |
|
|
| 375 |
|
|
| 376 |
|
//correct molecule number |
| 377 |
|
if (strstr(buffer, "nMol") != NULL) { |
| 378 |
< |
if(i<components){ |
| 379 |
< |
sprintf(buffer, "\tnMol = %i;", numMol[i]); |
| 378 |
> |
if(i<nMol.size()){ |
| 379 |
> |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
| 380 |
|
newMdFile << buffer << std::endl; |
| 381 |
|
i++; |
| 382 |
|
} |
