| 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, 234107 (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 |
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* |
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|
* Created by Charles F. Vardeman II on 10 Apr 2006. |
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* @author Charles F. Vardeman II |
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< |
* @version $Id: randomBuilder.cpp,v 1.6 2006-10-10 18:34:12 gezelter Exp $ |
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> |
* @version $Id$ |
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* |
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*/ |
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|
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#include "utils/StringUtils.hpp" |
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|
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using namespace std; |
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using namespace oopse; |
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> |
using namespace OpenMD; |
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|
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void createMdFile(const std::string&oldMdFileName, |
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const std::string&newMdFileName, |
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|
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int main(int argc, char *argv []) { |
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|
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– |
// register force fields |
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– |
registerForceFields(); |
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registerLattice(); |
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|
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gengetopt_args_info args_info; |
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std::vector<RealType> molFractions; |
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std::vector<RealType> molecularMasses; |
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std::vector<int> nMol; |
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int nComponents = components.size(); |
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|
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> |
std::size_t nComponents = components.size(); |
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> |
|
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if (nComponents == 1) { |
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molFractions.push_back(1.0); |
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} else { |
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if (args_info.molFraction_given == nComponents) { |
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< |
for (int i = 0; i < nComponents; i++) { |
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> |
for (std::size_t i = 0; i < nComponents; i++) { |
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molFractions.push_back(args_info.molFraction_arg[i]); |
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} |
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} else if (args_info.molFraction_given == nComponents-1) { |
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RealType remainingFraction = 1.0; |
| 182 |
< |
for (int i = 0; i < nComponents-1; i++) { |
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> |
for (std::size_t i = 0; i < nComponents-1; i++) { |
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|
molFractions.push_back(args_info.molFraction_arg[i]); |
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remainingFraction -= molFractions[i]; |
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} |
| 196 |
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|
| 197 |
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RealType totalFraction = 0.0; |
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|
| 199 |
< |
for (int i = 0; i < nComponents; i++) { |
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> |
for (std::size_t i = 0; i < nComponents; i++) { |
| 200 |
|
if (molFractions.at(i) < 0.0) { |
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|
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 202 |
|
" less than zero!"); |
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|
} |
| 219 |
|
|
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int remaining = nSites; |
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< |
for (int i=0; i < nComponents-1; i++) { |
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> |
for (std::size_t i=0; i < nComponents-1; i++) { |
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|
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
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remaining -= nMol.at(i); |
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|
} |
| 228 |
|
|
| 229 |
|
int totalMolecules = 0; |
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|
RealType totalMass = 0.0; |
| 231 |
< |
for (int i=0; i < nComponents; i++) { |
| 231 |
> |
for (std::size_t i=0; i < nComponents; i++) { |
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|
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
| 233 |
|
totalMolecules += nMol.at(i); |
| 234 |
< |
molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i), |
| 235 |
< |
oldInfo->getForceField())); |
| 234 |
> |
molecularMasses.push_back(MoLocator::getMolMass(oldInfo->getMoleculeStamp(i), |
| 235 |
> |
oldInfo->getForceField())); |
| 236 |
|
totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i); |
| 237 |
|
} |
| 238 |
|
RealType avgMass = totalMass / (RealType) totalMolecules; |
| 283 |
|
|
| 284 |
|
createMdFile(inputFileName, outputFileName, nMol); |
| 285 |
|
|
| 286 |
< |
if (oldInfo != NULL) |
| 289 |
< |
delete oldInfo; |
| 286 |
> |
delete oldInfo; |
| 287 |
|
|
| 288 |
|
// We need to read in the new SimInfo object, then Parse the |
| 289 |
|
// md file and set up the system |
| 314 |
|
// Randomize a vector of ints: |
| 315 |
|
|
| 316 |
|
vector<int> ids; |
| 317 |
< |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
| 317 |
> |
for (std::size_t i = 0; i < sites.size(); i++) ids.push_back(i); |
| 318 |
|
std::random_shuffle(ids.begin(), ids.end()); |
| 319 |
|
|
| 320 |
|
Molecule* mol; |
| 321 |
|
int l = 0; |
| 322 |
< |
for (int i = 0; i < nComponents; i++){ |
| 322 |
> |
for (std::size_t i = 0; i < nComponents; i++){ |
| 323 |
|
locator = new MoLocator(newInfo->getMoleculeStamp(i), |
| 324 |
|
newInfo->getForceField()); |
| 325 |
|
for (int n = 0; n < nMol.at(i); n++) { |
| 345 |
|
|
| 346 |
|
delete writer; |
| 347 |
|
|
| 348 |
< |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 348 |
> |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 349 |
|
"generated.\n", outputFileName.c_str()); |
| 350 |
|
painCave.isFatal = 0; |
| 351 |
+ |
painCave.severity = OPENMD_INFO; |
| 352 |
|
simError(); |
| 353 |
|
return 0; |
| 354 |
|
} |
| 368 |
|
|
| 369 |
|
oldMdFile.getline(buffer, MAXLEN); |
| 370 |
|
|
| 371 |
< |
int i = 0; |
| 371 |
> |
std::size_t i = 0; |
| 372 |
|
while (!oldMdFile.eof()) { |
| 373 |
|
|
| 374 |
|
//correct molecule number |
| 375 |
|
if (strstr(buffer, "nMol") != NULL) { |
| 376 |
< |
if(i<nMol.size()){ |
| 376 |
> |
if (i<nMol.size()){ |
| 377 |
|
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
| 378 |
|
newMdFile << buffer << std::endl; |
| 379 |
|
i++; |
| 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 |
|
|
