| 5 |
|
* redistribute this software in source and binary code form, provided |
| 6 |
|
* that the following conditions are met: |
| 7 |
|
* |
| 8 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 9 |
< |
* publication of scientific results based in part on use of the |
| 10 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 11 |
< |
* the article in which the program was described (Matthew |
| 12 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 13 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 14 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 15 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 16 |
< |
* |
| 17 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 8 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 9 |
|
* notice, this list of conditions and the following disclaimer. |
| 10 |
|
* |
| 11 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 11 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 12 |
|
* notice, this list of conditions and the following disclaimer in the |
| 13 |
|
* documentation and/or other materials provided with the |
| 14 |
|
* distribution. |
| 28 |
|
* University of Notre Dame has been advised of the possibility of |
| 29 |
|
* such damages. |
| 30 |
|
* |
| 31 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 32 |
+ |
* research, please cite the appropriate papers when you publish your |
| 33 |
+ |
* work. Good starting points are: |
| 34 |
+ |
* |
| 35 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 37 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 39 |
+ |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 40 |
|
* |
| 41 |
|
* randomBuilder.cpp |
| 42 |
|
* |
| 43 |
|
* Created by Charles F. Vardeman II on 10 Apr 2006. |
| 44 |
|
* @author Charles F. Vardeman II |
| 45 |
< |
* @version $Id: randomBuilder.cpp,v 1.4 2006-10-10 02:44:13 gezelter Exp $ |
| 45 |
> |
* @version $Id$ |
| 46 |
|
* |
| 47 |
|
*/ |
| 48 |
|
|
| 69 |
|
#include "utils/StringUtils.hpp" |
| 70 |
|
|
| 71 |
|
using namespace std; |
| 72 |
< |
using namespace oopse; |
| 72 |
> |
using namespace OpenMD; |
| 73 |
|
|
| 74 |
|
void createMdFile(const std::string&oldMdFileName, |
| 75 |
|
const std::string&newMdFileName, |
| 76 |
< |
int components, int* numMol); |
| 76 |
> |
std::vector<int> nMol); |
| 77 |
|
|
| 78 |
|
int main(int argc, char *argv []) { |
| 79 |
|
|
| 80 |
– |
// register force fields |
| 81 |
– |
registerForceFields(); |
| 80 |
|
registerLattice(); |
| 81 |
|
|
| 82 |
|
gengetopt_args_info args_info; |
| 84 |
|
std::string inputFileName; |
| 85 |
|
std::string outputFileName; |
| 86 |
|
Lattice *simpleLat; |
| 89 |
– |
int* numMol; |
| 87 |
|
RealType latticeConstant; |
| 88 |
|
std::vector<RealType> lc; |
| 92 |
– |
RealType mass; |
| 89 |
|
const RealType rhoConvertConst = 1.661; |
| 90 |
|
RealType density; |
| 91 |
|
int nx, ny, nz; |
| 93 |
|
MoLocator *locator; |
| 94 |
|
std::vector<Vector3d> latticePos; |
| 95 |
|
std::vector<Vector3d> latticeOrt; |
| 96 |
< |
int numMolPerCell; |
| 101 |
< |
int curMolIndex; |
| 96 |
> |
int nMolPerCell; |
| 97 |
|
DumpWriter *writer; |
| 98 |
|
|
| 99 |
|
// parse command line arguments |
| 103 |
|
density = args_info.density_arg; |
| 104 |
|
|
| 105 |
|
//get lattice type |
| 106 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
| 106 |
> |
latticeType = "FCC"; |
| 107 |
|
|
| 108 |
|
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 109 |
|
|
| 113 |
|
painCave.isFatal = 1; |
| 114 |
|
simError(); |
| 115 |
|
} |
| 116 |
+ |
nMolPerCell = simpleLat->getNumSitesPerCell(); |
| 117 |
|
|
| 118 |
|
//get the number of unit cells in each direction: |
| 119 |
|
|
| 144 |
|
simError(); |
| 145 |
|
} |
| 146 |
|
|
| 147 |
+ |
int nSites = nMolPerCell * nx * ny * nz; |
| 148 |
+ |
|
| 149 |
|
//get input file name |
| 150 |
|
if (args_info.inputs_num) |
| 151 |
|
inputFileName = args_info.inputs[0]; |
| 162 |
|
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
| 163 |
|
Globals* simParams = oldInfo->getSimParams(); |
| 164 |
|
|
| 165 |
< |
int nComponents =simParams->getNComponents(); |
| 168 |
< |
if (oldInfo->getNMoleculeStamp() > 2) { |
| 169 |
< |
sprintf(painCave.errMsg, "randomBuilder can't yet build a system with " |
| 170 |
< |
"more than two components."); |
| 171 |
< |
painCave.isFatal = 1; |
| 172 |
< |
simError(); |
| 173 |
< |
} |
| 165 |
> |
// Calculate lattice constant (in Angstroms) |
| 166 |
|
|
| 167 |
< |
//get mass of molecule. |
| 167 |
> |
std::vector<Component*> components = simParams->getComponents(); |
| 168 |
> |
std::vector<RealType> molFractions; |
| 169 |
> |
std::vector<RealType> molecularMasses; |
| 170 |
> |
std::vector<int> nMol; |
| 171 |
> |
int nComponents = components.size(); |
| 172 |
|
|
| 173 |
< |
mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
| 173 |
> |
if (nComponents == 1) { |
| 174 |
> |
molFractions.push_back(1.0); |
| 175 |
> |
} else { |
| 176 |
> |
if (args_info.molFraction_given == nComponents) { |
| 177 |
> |
for (int i = 0; i < nComponents; i++) { |
| 178 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
| 179 |
> |
} |
| 180 |
> |
} else if (args_info.molFraction_given == nComponents-1) { |
| 181 |
> |
RealType remainingFraction = 1.0; |
| 182 |
> |
for (int i = 0; i < nComponents-1; i++) { |
| 183 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
| 184 |
> |
remainingFraction -= molFractions[i]; |
| 185 |
> |
} |
| 186 |
> |
molFractions.push_back(remainingFraction); |
| 187 |
> |
} else { |
| 188 |
> |
sprintf(painCave.errMsg, "randomBuilder can't figure out molFractions " |
| 189 |
> |
"for all of the components in the <MetaData> block."); |
| 190 |
> |
painCave.isFatal = 1; |
| 191 |
> |
simError(); |
| 192 |
> |
} |
| 193 |
> |
} |
| 194 |
|
|
| 195 |
< |
// Create the lattice |
| 195 |
> |
// do some sanity checking: |
| 196 |
> |
|
| 197 |
> |
RealType totalFraction = 0.0; |
| 198 |
|
|
| 199 |
< |
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
| 200 |
< |
|
| 201 |
< |
if (simpleLat == NULL) { |
| 202 |
< |
sprintf(painCave.errMsg, "Error in creating lattice."); |
| 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 |
< |
numMolPerCell = simpleLat->getNumSitesPerCell(); |
| 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 |
< |
// Calculate lattice constant (in Angstroms) |
| 227 |
> |
// recompute actual mol fractions and perform final sanity check: |
| 228 |
|
|
| 229 |
< |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
| 230 |
< |
(RealType)(1.0 / 3.0)); |
| 229 |
> |
int totalMolecules = 0; |
| 230 |
> |
RealType totalMass = 0.0; |
| 231 |
> |
for (int i=0; i < nComponents; i++) { |
| 232 |
> |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
| 233 |
> |
totalMolecules += nMol.at(i); |
| 234 |
> |
molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i), |
| 235 |
> |
oldInfo->getForceField())); |
| 236 |
> |
totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i); |
| 237 |
> |
} |
| 238 |
> |
RealType avgMass = totalMass / (RealType) totalMolecules; |
| 239 |
|
|
| 240 |
+ |
if (totalMolecules != nSites) { |
| 241 |
+ |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
| 242 |
+ |
"to the number of lattice sites!"); |
| 243 |
+ |
painCave.isFatal = 1; |
| 244 |
+ |
simError(); |
| 245 |
+ |
} |
| 246 |
+ |
|
| 247 |
+ |
latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density, |
| 248 |
+ |
(RealType)(1.0 / 3.0)); |
| 249 |
+ |
|
| 250 |
|
// Set the lattice constant |
| 251 |
< |
|
| 251 |
> |
|
| 252 |
|
lc.push_back(latticeConstant); |
| 253 |
|
simpleLat->setLatticeConstant(lc); |
| 254 |
< |
|
| 201 |
< |
// Calculate the total number of molecules |
| 202 |
< |
|
| 203 |
< |
int totMol = nx * ny * nz * numMolPerCell; |
| 204 |
< |
|
| 254 |
> |
|
| 255 |
|
// Calculate the lattice sites and fill the lattice vector. |
| 256 |
|
|
| 257 |
|
// Get the standard orientations of the cell sites |
| 269 |
|
|
| 270 |
|
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 271 |
|
|
| 272 |
< |
for(int l = 0; l < numMolPerCell; l++) { |
| 272 |
> |
for(int l = 0; l < nMolPerCell; l++) { |
| 273 |
|
sites.push_back(latticePos[l]); |
| 274 |
|
orientations.push_back(latticeOrt[l]); |
| 275 |
|
} |
| 276 |
|
} |
| 277 |
|
} |
| 278 |
|
} |
| 229 |
– |
|
| 230 |
– |
int numSites = sites.size(); |
| 231 |
– |
|
| 232 |
– |
numMol = new int[nComponents]; |
| 233 |
– |
if (nComponents != args_info.molFraction_given && nComponents != 1){ |
| 234 |
– |
sprintf(painCave.errMsg, "There needs to be the same number of " |
| 235 |
– |
"molFraction arguments as there are components in the " |
| 236 |
– |
"<MetaData> block."); |
| 237 |
– |
painCave.isFatal = 1; |
| 238 |
– |
simError(); |
| 239 |
– |
} |
| 240 |
– |
int totComponents = 0; |
| 241 |
– |
for (int i = 0;i<nComponents-1;i++){ |
| 242 |
– |
numMol[i] = int((RealType)numSites * args_info.molFraction_arg[i]); |
| 243 |
– |
std::cout<<numMol[i]<<std::endl; |
| 244 |
– |
totComponents += numMol[i]; |
| 245 |
– |
} |
| 246 |
– |
numMol[nComponents-1] = numSites - totComponents; |
| 279 |
|
|
| 280 |
|
outputFileName = args_info.output_arg; |
| 281 |
|
|
| 282 |
|
// create a new .md file on the fly which corrects the number of molecules |
| 283 |
|
|
| 284 |
< |
createMdFile(inputFileName, outputFileName, nComponents, numMol); |
| 284 |
> |
createMdFile(inputFileName, outputFileName, nMol); |
| 285 |
|
|
| 286 |
|
if (oldInfo != NULL) |
| 287 |
|
delete oldInfo; |
| 312 |
|
|
| 313 |
|
// place the molecules |
| 314 |
|
|
| 283 |
– |
curMolIndex = 0; |
| 284 |
– |
|
| 315 |
|
// Randomize a vector of ints: |
| 316 |
|
|
| 317 |
|
vector<int> ids; |
| 318 |
< |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
| 318 |
> |
for (unsigned int i = 0; i < sites.size(); i++) ids.push_back(i); |
| 319 |
|
std::random_shuffle(ids.begin(), ids.end()); |
| 320 |
|
|
| 321 |
|
Molecule* mol; |
| 323 |
|
for (int i = 0; i < nComponents; i++){ |
| 324 |
|
locator = new MoLocator(newInfo->getMoleculeStamp(i), |
| 325 |
|
newInfo->getForceField()); |
| 326 |
< |
for (int n = 0; n < numMol[i]; n++) { |
| 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++; |
| 346 |
|
|
| 347 |
|
delete writer; |
| 348 |
|
|
| 349 |
< |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 350 |
< |
"generated.", outputFileName.c_str()); |
| 349 |
> |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 350 |
> |
"generated.\n", outputFileName.c_str()); |
| 351 |
|
painCave.isFatal = 0; |
| 352 |
|
simError(); |
| 353 |
|
return 0; |
| 355 |
|
|
| 356 |
|
void createMdFile(const std::string&oldMdFileName, |
| 357 |
|
const std::string&newMdFileName, |
| 358 |
< |
int components, int* numMol) { |
| 358 |
> |
std::vector<int> nMol) { |
| 359 |
|
ifstream oldMdFile; |
| 360 |
|
ofstream newMdFile; |
| 361 |
|
const int MAXLEN = 65535; |
| 368 |
|
|
| 369 |
|
oldMdFile.getline(buffer, MAXLEN); |
| 370 |
|
|
| 371 |
< |
int i = 0; |
| 371 |
> |
unsigned int i = 0; |
| 372 |
|
while (!oldMdFile.eof()) { |
| 373 |
|
|
| 374 |
|
//correct molecule number |
| 375 |
|
if (strstr(buffer, "nMol") != NULL) { |
| 376 |
< |
if(i<components){ |
| 377 |
< |
sprintf(buffer, "\tnMol = %i;", numMol[i]); |
| 376 |
> |
if (i<nMol.size()){ |
| 377 |
> |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
| 378 |
|
newMdFile << buffer << std::endl; |
| 379 |
|
i++; |
| 380 |
|
} |
| 386 |
|
|
| 387 |
|
oldMdFile.close(); |
| 388 |
|
newMdFile.close(); |
| 389 |
+ |
|
| 390 |
+ |
if (i != nMol.size()) { |
| 391 |
+ |
sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n" |
| 392 |
+ |
"\tstatements in component blocks. Make sure that all\n" |
| 393 |
+ |
"\tcomponents in the template file have nMol=1"); |
| 394 |
+ |
painCave.isFatal = 1; |
| 395 |
+ |
simError(); |
| 396 |
+ |
} |
| 397 |
+ |
|
| 398 |
|
} |
| 399 |
|
|
