| 67 |
|
using namespace oopse; |
| 68 |
|
void createMdFile(const std::string&oldMdFileName, |
| 69 |
|
const std::string&newMdFileName, |
| 70 |
< |
int components,int* numMol); |
| 70 |
> |
std::vector<int> numMol); |
| 71 |
|
|
| 72 |
|
int main(int argc, char *argv []) { |
| 73 |
|
|
| 78 |
|
gengetopt_args_info args_info; |
| 79 |
|
std::string latticeType; |
| 80 |
|
std::string inputFileName; |
| 81 |
< |
std::string outPrefix; |
| 82 |
< |
std::string outMdFileName; |
| 83 |
< |
std::string outInitFileName; |
| 81 |
> |
std::string outputFileName; |
| 82 |
|
|
| 85 |
– |
|
| 86 |
– |
|
| 87 |
– |
Lattice *simpleLat; |
| 83 |
|
MoLocator* locator; |
| 89 |
– |
int* numMol; |
| 84 |
|
int nComponents; |
| 85 |
|
double latticeConstant; |
| 86 |
|
std::vector<double> lc; |
| 87 |
< |
double mass; |
| 94 |
< |
const double rhoConvertConst = 1.661; |
| 95 |
< |
double density; |
| 87 |
> |
|
| 88 |
|
double particleRadius; |
| 97 |
– |
|
| 98 |
– |
|
| 89 |
|
|
| 90 |
|
Mat3x3d hmat; |
| 91 |
|
std::vector<Vector3d> latticePos; |
| 92 |
|
std::vector<Vector3d> latticeOrt; |
| 93 |
< |
int numMolPerCell; |
| 104 |
< |
int nShells; /* Number of shells in nanoparticle*/ |
| 105 |
< |
int numSites; |
| 106 |
< |
|
| 93 |
> |
|
| 94 |
|
DumpWriter *writer; |
| 95 |
|
|
| 96 |
|
// Parse Command Line Arguments |
| 97 |
|
if (cmdline_parser(argc, argv, &args_info) != 0) |
| 98 |
|
exit(1); |
| 99 |
< |
|
| 113 |
< |
|
| 114 |
< |
|
| 99 |
> |
|
| 100 |
|
/* get lattice type */ |
| 101 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
| 102 |
< |
|
| 101 |
> |
latticeType = "FCC"; |
| 102 |
> |
|
| 103 |
|
/* get input file name */ |
| 104 |
|
if (args_info.inputs_num) |
| 105 |
|
inputFileName = args_info.inputs[0]; |
| 106 |
|
else { |
| 107 |
< |
std::cerr << "You must specify a input file name.\n" << std::endl; |
| 107 |
> |
sprintf(painCave.errMsg, "No input .md file name was specified" |
| 108 |
> |
"on the command line"); |
| 109 |
> |
painCave.isFatal = 1; |
| 110 |
|
cmdline_parser_print_help(); |
| 111 |
< |
exit(1); |
| 111 |
> |
simError(); |
| 112 |
|
} |
| 113 |
|
|
| 114 |
|
/* parse md file and set up the system */ |
| 115 |
|
SimCreator oldCreator; |
| 116 |
|
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
| 117 |
|
|
| 131 |
– |
|
| 132 |
– |
/*calculate lattice constant (in Angstrom) |
| 133 |
– |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
| 134 |
– |
1.0 / 3.0);*/ |
| 135 |
– |
|
| 118 |
|
latticeConstant = args_info.latticeCnst_arg; |
| 119 |
|
particleRadius = args_info.radius_arg; |
| 120 |
|
Globals* simParams = oldInfo->getSimParams(); |
| 121 |
|
|
| 140 |
– |
/* Find out how many different components in this simualtion */ |
| 141 |
– |
nComponents =simParams->getNComponents(); |
| 142 |
– |
|
| 143 |
– |
/*determine the output file names*/ |
| 144 |
– |
if (args_info.output_given){ |
| 145 |
– |
outInitFileName = args_info.output_arg; |
| 146 |
– |
}else{ |
| 147 |
– |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
| 148 |
– |
} |
| 149 |
– |
|
| 150 |
– |
std::cout <<"Before build shaped lattice. "<<std::endl; |
| 151 |
– |
|
| 152 |
– |
/* create Molocators */ |
| 153 |
– |
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
| 154 |
– |
|
| 122 |
|
/* Create nanoparticle */ |
| 123 |
< |
shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius); |
| 123 |
> |
shapedLatticeSpherical nanoParticle(latticeConstant, latticeType, |
| 124 |
> |
particleRadius); |
| 125 |
|
|
| 158 |
– |
std::cout <<"Before build getPoints. "<<std::endl; |
| 126 |
|
/* Build a lattice and get lattice points for this lattice constant */ |
| 127 |
< |
vector<Vector3d> nanoParticleSites = nanoParticle.getPoints(); |
| 128 |
< |
|
| 127 |
> |
vector<Vector3d> sites = nanoParticle.getSites(); |
| 128 |
> |
vector<Vector3d> orientations = nanoParticle.getOrientations(); |
| 129 |
> |
|
| 130 |
> |
std::cout <<"nSites: " << sites.size() << std::endl; |
| 131 |
> |
|
| 132 |
|
/* Get number of lattice sites */ |
| 133 |
< |
numSites = nanoParticleSites.size(); |
| 134 |
< |
|
| 135 |
< |
//std::cout <<"numSites are %d "<<numSites<<std::endl; |
| 136 |
< |
// std::cout <<"nComponents are %d "<<nComponents<<std::endl; |
| 137 |
< |
numMol = new int[nComponents]; |
| 138 |
< |
|
| 133 |
> |
int nSites = sites.size(); |
| 134 |
> |
|
| 135 |
> |
std::vector<Component*> components = simParams->getComponents(); |
| 136 |
> |
std::vector<RealType> molFractions; |
| 137 |
> |
std::vector<RealType> shellRadii; |
| 138 |
> |
std::vector<RealType> molecularMasses; |
| 139 |
> |
std::vector<int> nMol; |
| 140 |
> |
std::map<int, int> componentFromSite; |
| 141 |
> |
nComponents = components.size(); |
| 142 |
> |
|
| 143 |
> |
if (args_info.molFraction_given && args_info.ShellRadius_given) { |
| 144 |
> |
sprintf(painCave.errMsg, "Specify either molFraction or ShellRadius " |
| 145 |
> |
"arguments, but not both!"); |
| 146 |
> |
painCave.isFatal = 1; |
| 147 |
> |
simError(); |
| 148 |
> |
} |
| 149 |
|
|
| 150 |
< |
/* Random particle is the default case*/ |
| 151 |
< |
if (!args_info.ShellRadius_given){ |
| 152 |
< |
std::cout << "Creating a random nanoparticle" << std::endl; |
| 153 |
< |
/* Check to see if we have enough components */ |
| 154 |
< |
if (nComponents != args_info.molFraction_given && nComponents != 1){ |
| 155 |
< |
std::cerr << "Number of components does not equal molFraction occurances." << std::endl; |
| 156 |
< |
exit(1); |
| 150 |
> |
if (nComponents == 1) { |
| 151 |
> |
molFractions.push_back(1.0); |
| 152 |
> |
shellRadii.push_back(particleRadius); |
| 153 |
> |
} else if (args_info.molFraction_given) { |
| 154 |
> |
if ((int)args_info.molFraction_given == nComponents) { |
| 155 |
> |
for (int i = 0; i < nComponents; i++) { |
| 156 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
| 157 |
> |
} |
| 158 |
> |
} else if ((int)args_info.molFraction_given == nComponents-1) { |
| 159 |
> |
RealType remainingFraction = 1.0; |
| 160 |
> |
for (int i = 0; i < nComponents-1; i++) { |
| 161 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
| 162 |
> |
remainingFraction -= molFractions[i]; |
| 163 |
> |
} |
| 164 |
> |
molFractions.push_back(remainingFraction); |
| 165 |
> |
} else { |
| 166 |
> |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions " |
| 167 |
> |
"for all of the components in the <MetaData> block."); |
| 168 |
> |
painCave.isFatal = 1; |
| 169 |
> |
simError(); |
| 170 |
|
} |
| 171 |
< |
/* Build the mole fractions and number of molecules of each type */ |
| 172 |
< |
int totComponents = 0; |
| 173 |
< |
for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */ |
| 174 |
< |
numMol[i] = int((double)numSites * args_info.molFraction_arg[i]); |
| 175 |
< |
std::cout<<numMol[i]<<std::endl; |
| 176 |
< |
totComponents += numMol[i]; |
| 171 |
> |
} else if ((int)args_info.ShellRadius_given) { |
| 172 |
> |
if ((int)args_info.ShellRadius_given == nComponents) { |
| 173 |
> |
for (int i = 0; i < nComponents; i++) { |
| 174 |
> |
shellRadii.push_back(args_info.ShellRadius_arg[i]); |
| 175 |
> |
} |
| 176 |
> |
} else if ((int)args_info.ShellRadius_given == nComponents-1) { |
| 177 |
> |
for (int i = 0; i < nComponents-1; i++) { |
| 178 |
> |
shellRadii.push_back(args_info.ShellRadius_arg[i]); |
| 179 |
> |
} |
| 180 |
> |
shellRadii.push_back(particleRadius); |
| 181 |
> |
} else { |
| 182 |
> |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the shell radii " |
| 183 |
> |
"for all of the components in the <MetaData> block."); |
| 184 |
> |
painCave.isFatal = 1; |
| 185 |
> |
simError(); |
| 186 |
|
} |
| 187 |
< |
numMol[nComponents-1] = numSites - totComponents; |
| 188 |
< |
|
| 189 |
< |
/* do the iPod thing, Shuffle da vector */ |
| 190 |
< |
std::random_shuffle(nanoParticleSites.begin(), nanoParticleSites.end()); |
| 191 |
< |
} else{ /*Handle core-shell with multiple components.*/ |
| 192 |
< |
std::cout << "Creating a core-shell nanoparticle." << std::endl; |
| 191 |
< |
if (nComponents != args_info.ShellRadius_given + 1){ |
| 192 |
< |
std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl; |
| 193 |
< |
exit(1); |
| 194 |
< |
} |
| 187 |
> |
} else { |
| 188 |
> |
sprintf(painCave.errMsg, "You have a multi-component <MetaData> block, but have not " |
| 189 |
> |
"specified either molFraction or ShellRadius arguments."); |
| 190 |
> |
painCave.isFatal = 1; |
| 191 |
> |
simError(); |
| 192 |
> |
} |
| 193 |
|
|
| 194 |
+ |
if (args_info.molFraction_given) { |
| 195 |
+ |
RealType totalFraction = 0.0; |
| 196 |
+ |
|
| 197 |
+ |
/* Do some simple sanity checking*/ |
| 198 |
+ |
|
| 199 |
+ |
for (int i = 0; i < nComponents; i++) { |
| 200 |
+ |
if (molFractions.at(i) < 0.0) { |
| 201 |
+ |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 202 |
+ |
" less than zero!"); |
| 203 |
+ |
painCave.isFatal = 1; |
| 204 |
+ |
simError(); |
| 205 |
+ |
} |
| 206 |
+ |
if (molFractions.at(i) > 1.0) { |
| 207 |
+ |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 208 |
+ |
" greater than one!"); |
| 209 |
+ |
painCave.isFatal = 1; |
| 210 |
+ |
simError(); |
| 211 |
+ |
} |
| 212 |
+ |
totalFraction += molFractions.at(i); |
| 213 |
+ |
} |
| 214 |
+ |
if (abs(totalFraction - 1.0) > 1e-6) { |
| 215 |
+ |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
| 216 |
+ |
painCave.isFatal = 1; |
| 217 |
+ |
simError(); |
| 218 |
+ |
} |
| 219 |
+ |
|
| 220 |
+ |
int remaining = nSites; |
| 221 |
+ |
for (int i=0; i < nComponents-1; i++) { |
| 222 |
+ |
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
| 223 |
+ |
remaining -= nMol.at(i); |
| 224 |
+ |
} |
| 225 |
+ |
nMol.push_back(remaining); |
| 226 |
+ |
|
| 227 |
+ |
// recompute actual mol fractions and perform final sanity check: |
| 228 |
+ |
|
| 229 |
+ |
int totalMolecules = 0; |
| 230 |
+ |
for (int i=0; i < nComponents; i++) { |
| 231 |
+ |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
| 232 |
+ |
totalMolecules += nMol.at(i); |
| 233 |
+ |
} |
| 234 |
+ |
|
| 235 |
+ |
if (totalMolecules != nSites) { |
| 236 |
+ |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
| 237 |
+ |
"to the number of lattice sites!"); |
| 238 |
+ |
painCave.isFatal = 1; |
| 239 |
+ |
simError(); |
| 240 |
+ |
} |
| 241 |
+ |
} else { |
| 242 |
+ |
|
| 243 |
+ |
for (int i = 0; i < shellRadii.size(); i++) { |
| 244 |
+ |
if (shellRadii.at(i) > particleRadius + 1e-6 ) { |
| 245 |
+ |
sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius."); |
| 246 |
+ |
painCave.isFatal = 1; |
| 247 |
+ |
simError(); |
| 248 |
+ |
} |
| 249 |
+ |
if (shellRadii.at(i) <= 0.0 ) { |
| 250 |
+ |
sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!"); |
| 251 |
+ |
painCave.isFatal = 1; |
| 252 |
+ |
simError(); |
| 253 |
+ |
} |
| 254 |
+ |
} |
| 255 |
|
} |
| 256 |
+ |
|
| 257 |
+ |
vector<int> ids; |
| 258 |
+ |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
| 259 |
+ |
/* Random particle is the default case*/ |
| 260 |
+ |
if ((int)args_info.molFraction_given){ |
| 261 |
+ |
sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle."); |
| 262 |
+ |
painCave.isFatal = 0; |
| 263 |
+ |
simError(); |
| 264 |
+ |
std::random_shuffle(ids.begin(), ids.end()); |
| 265 |
+ |
} else{ |
| 266 |
+ |
sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle."); |
| 267 |
+ |
painCave.isFatal = 0; |
| 268 |
+ |
simError(); |
| 269 |
|
|
| 270 |
+ |
Vector3d myLoc; |
| 271 |
+ |
RealType myR; |
| 272 |
+ |
RealType smallestSoFar; |
| 273 |
+ |
int myComponent = -1; |
| 274 |
+ |
nMol.clear(); |
| 275 |
+ |
nMol.resize(nComponents); |
| 276 |
+ |
|
| 277 |
+ |
for (int i = 0; i < sites.size(); i++) { |
| 278 |
+ |
myLoc = sites[i]; |
| 279 |
+ |
myR = myLoc.length(); |
| 280 |
+ |
smallestSoFar = particleRadius; |
| 281 |
+ |
|
| 282 |
+ |
for (int j = 0; j < nComponents; j++) { |
| 283 |
+ |
if (myR <= shellRadii[j]) { |
| 284 |
+ |
if (shellRadii[j] <= smallestSoFar) { |
| 285 |
+ |
smallestSoFar = shellRadii[j]; |
| 286 |
+ |
myComponent = j; |
| 287 |
+ |
} |
| 288 |
+ |
} |
| 289 |
+ |
} |
| 290 |
+ |
componentFromSite[i] = myComponent; |
| 291 |
+ |
nMol[myComponent]++; |
| 292 |
+ |
} |
| 293 |
+ |
} |
| 294 |
|
|
| 295 |
< |
//get the orientation of the cell sites |
| 296 |
< |
//for the same type of molecule in same lattice, it will not change |
| 201 |
< |
latticeOrt = nanoParticle.getPointsOrt(); |
| 202 |
< |
std::cout<<"Orientational vector Size: "<< std::endl; |
| 203 |
< |
std::cout<<latticeOrt.size()<< std::endl; |
| 295 |
> |
outputFileName = args_info.output_arg; |
| 296 |
> |
|
| 297 |
|
|
| 205 |
– |
|
| 206 |
– |
|
| 207 |
– |
// needed for writing out new md file. |
| 208 |
– |
|
| 209 |
– |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
| 210 |
– |
outMdFileName = outPrefix + ".md"; |
| 211 |
– |
|
| 298 |
|
//creat new .md file on fly which corrects the number of molecule |
| 299 |
< |
createMdFile(inputFileName, outMdFileName, nComponents,numMol); |
| 299 |
> |
createMdFile(inputFileName, outputFileName, nMol); |
| 300 |
|
|
| 301 |
|
if (oldInfo != NULL) |
| 302 |
|
delete oldInfo; |
| 303 |
|
|
| 218 |
– |
|
| 219 |
– |
// We need to read in new siminfo object. |
| 220 |
– |
//parse md file and set up the system |
| 221 |
– |
//SimCreator NewCreator; |
| 304 |
|
SimCreator newCreator; |
| 305 |
< |
SimInfo* NewInfo = newCreator.createSim(outMdFileName, false); |
| 306 |
< |
|
| 225 |
< |
|
| 305 |
> |
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
| 306 |
> |
|
| 307 |
|
// Place molecules |
| 308 |
|
Molecule* mol; |
| 309 |
|
SimInfo::MoleculeIterator mi; |
| 310 |
|
mol = NewInfo->beginMolecule(mi); |
| 311 |
|
int l = 0; |
| 312 |
< |
for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
| 313 |
< |
locator->placeMol(nanoParticleSites[l], latticeOrt[l], mol); |
| 314 |
< |
l++; |
| 315 |
< |
} |
| 316 |
< |
|
| 312 |
> |
|
| 313 |
> |
for (int i = 0; i < nComponents; i++){ |
| 314 |
> |
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
| 315 |
> |
NewInfo->getForceField()); |
| 316 |
> |
|
| 317 |
> |
if (args_info.ShellRadius_given) { |
| 318 |
> |
for (int n = 0; n < sites.size(); n++) { |
| 319 |
> |
if (componentFromSite[n] == i) { |
| 320 |
> |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 321 |
> |
locator->placeMol(sites[n], orientations[n], mol); |
| 322 |
> |
l++; |
| 323 |
> |
} |
| 324 |
> |
} |
| 325 |
> |
} else { |
| 326 |
> |
for (int n = 0; n < nMol.at(i); n++) { |
| 327 |
> |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 328 |
> |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
| 329 |
> |
l++; |
| 330 |
> |
} |
| 331 |
> |
} |
| 332 |
> |
} |
| 333 |
|
|
| 334 |
|
//fill Hmat |
| 335 |
< |
hmat(0, 0)= latticeConstant; |
| 335 |
> |
hmat(0, 0)= 10.0*particleRadius; |
| 336 |
|
hmat(0, 1) = 0.0; |
| 337 |
|
hmat(0, 2) = 0.0; |
| 338 |
|
|
| 339 |
|
hmat(1, 0) = 0.0; |
| 340 |
< |
hmat(1, 1) = latticeConstant; |
| 340 |
> |
hmat(1, 1) = 10.0*particleRadius; |
| 341 |
|
hmat(1, 2) = 0.0; |
| 342 |
|
|
| 343 |
|
hmat(2, 0) = 0.0; |
| 344 |
|
hmat(2, 1) = 0.0; |
| 345 |
< |
hmat(2, 2) = latticeConstant; |
| 345 |
> |
hmat(2, 2) = 10.0*particleRadius; |
| 346 |
|
|
| 347 |
|
//set Hmat |
| 348 |
|
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 349 |
|
|
| 350 |
|
|
| 351 |
|
//create dumpwriter and write out the coordinates |
| 352 |
< |
NewInfo->setFinalConfigFileName(outInitFileName); |
| 256 |
< |
writer = new DumpWriter(NewInfo); |
| 352 |
> |
writer = new DumpWriter(NewInfo, outputFileName); |
| 353 |
|
|
| 354 |
|
if (writer == NULL) { |
| 355 |
< |
std::cerr << "error in creating DumpWriter" << std::endl; |
| 356 |
< |
exit(1); |
| 355 |
> |
sprintf(painCave.errMsg, "Error in creating dumpwrite object "); |
| 356 |
> |
painCave.isFatal = 1; |
| 357 |
> |
simError(); |
| 358 |
|
} |
| 359 |
|
|
| 360 |
|
writer->writeDump(); |
| 361 |
< |
std::cout << "new initial configuration file: " << outInitFileName |
| 362 |
< |
<< " is generated." << std::endl; |
| 363 |
< |
|
| 364 |
< |
//delete objects |
| 365 |
< |
|
| 366 |
< |
//delete oldInfo and oldSimSetup |
| 367 |
< |
|
| 368 |
< |
if (NewInfo != NULL) |
| 369 |
< |
delete NewInfo; |
| 370 |
< |
|
| 274 |
< |
if (writer != NULL) |
| 275 |
< |
delete writer; |
| 276 |
< |
cmdline_parser_free(&args_info); |
| 361 |
> |
|
| 362 |
> |
// deleting the writer will put the closing at the end of the dump file |
| 363 |
> |
|
| 364 |
> |
delete writer; |
| 365 |
> |
|
| 366 |
> |
// cleanup a by calling sim error..... |
| 367 |
> |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 368 |
> |
"generated.\n", outputFileName.c_str()); |
| 369 |
> |
painCave.isFatal = 0; |
| 370 |
> |
simError(); |
| 371 |
|
return 0; |
| 372 |
|
} |
| 373 |
|
|
| 374 |
< |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
| 375 |
< |
int components,int* numMol) { |
| 374 |
> |
void createMdFile(const std::string&oldMdFileName, |
| 375 |
> |
const std::string&newMdFileName, |
| 376 |
> |
std::vector<int> nMol) { |
| 377 |
|
ifstream oldMdFile; |
| 378 |
|
ofstream newMdFile; |
| 379 |
|
const int MAXLEN = 65535; |
| 390 |
|
|
| 391 |
|
//correct molecule number |
| 392 |
|
if (strstr(buffer, "nMol") != NULL) { |
| 393 |
< |
if(i<components){ |
| 394 |
< |
sprintf(buffer, "\tnMol = %i;", numMol[i]); |
| 393 |
> |
if(i<nMol.size()){ |
| 394 |
> |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
| 395 |
|
newMdFile << buffer << std::endl; |
| 396 |
|
i++; |
| 397 |
|
} |
