5 |
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* 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 |
|
* |
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+ |
* 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 |
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* |
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|
* randomBuilder.cpp |
42 |
|
* |
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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 1.4 2006-10-10 02:44:13 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; |
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; |
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|
Lattice *simpleLat; |
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– |
int* numMol; |
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|
RealType latticeConstant; |
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|
std::vector<RealType> lc; |
92 |
– |
RealType mass; |
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|
const RealType rhoConvertConst = 1.661; |
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|
RealType density; |
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int nx, ny, nz; |
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MoLocator *locator; |
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std::vector<Vector3d> latticePos; |
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|
std::vector<Vector3d> latticeOrt; |
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< |
int numMolPerCell; |
101 |
< |
int curMolIndex; |
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> |
int nMolPerCell; |
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|
DumpWriter *writer; |
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|
|
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// parse command line arguments |
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density = args_info.density_arg; |
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|
|
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//get lattice type |
106 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
106 |
> |
latticeType = "FCC"; |
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|
|
108 |
|
simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
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|
|
113 |
|
painCave.isFatal = 1; |
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|
simError(); |
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|
} |
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+ |
nMolPerCell = simpleLat->getNumSitesPerCell(); |
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|
|
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//get the number of unit cells in each direction: |
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|
|
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|
simError(); |
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|
} |
146 |
|
|
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+ |
int nSites = nMolPerCell * nx * ny * nz; |
148 |
+ |
|
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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]; |
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|
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
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|
Globals* simParams = oldInfo->getSimParams(); |
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|
|
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."); |
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< |
painCave.isFatal = 1; |
172 |
< |
simError(); |
173 |
< |
} |
165 |
> |
// Calculate lattice constant (in Angstroms) |
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|
|
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< |
//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; |
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> |
int nComponents = components.size(); |
172 |
|
|
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< |
mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
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> |
if (nComponents == 1) { |
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> |
molFractions.push_back(1.0); |
175 |
> |
} else { |
176 |
> |
if (args_info.molFraction_given == nComponents) { |
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> |
for (int i = 0; i < nComponents; i++) { |
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> |
molFractions.push_back(args_info.molFraction_arg[i]); |
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> |
} |
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(MoLocator::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) |
255 |
< |
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 |
311 |
|
|
312 |
|
// place the molecules |
313 |
|
|
283 |
– |
curMolIndex = 0; |
284 |
– |
|
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 (unsigned int i = 0; i < sites.size(); i++) ids.push_back(i); |
318 |
|
std::random_shuffle(ids.begin(), ids.end()); |
319 |
|
|
320 |
|
Molecule* mol; |
322 |
|
for (int i = 0; i < nComponents; i++){ |
323 |
|
locator = new MoLocator(newInfo->getMoleculeStamp(i), |
324 |
|
newInfo->getForceField()); |
325 |
< |
for (int n = 0; n < numMol[i]; n++) { |
325 |
> |
for (int n = 0; n < nMol.at(i); n++) { |
326 |
|
mol = newInfo->getMoleculeByGlobalIndex(l); |
327 |
|
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
328 |
|
l++; |
345 |
|
|
346 |
|
delete writer; |
347 |
|
|
348 |
< |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
349 |
< |
"generated.", outputFileName.c_str()); |
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 |
|
} |
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 |
|
|