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 1.1 2006-04-25 22:59:27 chuckv 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 |
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Lattice *simpleLat; |
89 |
< |
int* numMol; |
90 |
< |
double latticeConstant; |
91 |
< |
std::vector<double> lc; |
92 |
< |
double mass; |
93 |
< |
const double rhoConvertConst = 1.661; |
96 |
< |
double density; |
97 |
< |
int nx, |
98 |
< |
ny, |
99 |
< |
nz; |
89 |
> |
RealType latticeConstant; |
90 |
> |
std::vector<RealType> lc; |
91 |
> |
const RealType rhoConvertConst = 1.661; |
92 |
> |
RealType density; |
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 |
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nMolPerCell = simpleLat->getNumSitesPerCell(); |
119 |
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|
120 |
< |
//get the number of unit cell |
120 |
> |
//get the number of unit cells in each direction: |
121 |
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|
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; |
128 |
> |
simError(); |
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} |
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|
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ny = args_info.ny_arg; |
132 |
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|
133 |
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if (ny <= 0) { |
134 |
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std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl; |
135 |
< |
exit(1); |
134 |
> |
sprintf(painCave.errMsg, "The number of unit cells in the y direction " |
135 |
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"must be greater than 0."); |
136 |
> |
painCave.isFatal = 1; |
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simError(); |
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} |
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|
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nz = args_info.nz_arg; |
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|
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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 |
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exit(1); |
143 |
> |
sprintf(painCave.errMsg, "The number of unit cells in the z direction " |
144 |
> |
"must be greater than 0."); |
145 |
> |
painCave.isFatal = 1; |
146 |
> |
simError(); |
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} |
148 |
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|
149 |
+ |
int nSites = nMolPerCell * nx * ny * nz; |
150 |
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|
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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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else { |
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std::cerr << "You must specify a input file name.\n" << std::endl; |
156 |
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cmdline_parser_print_help(); |
157 |
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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); |
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Globals* simParams = oldInfo->getSimParams(); |
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|
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int nComponents =simParams->getNComponents(); |
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if (oldInfo->getNMoleculeStamp()>= 2) { |
164 |
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std::cerr << "can not build the system with more than two components" |
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<< std::endl; |
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exit(1); |
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} |
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// Calculate lattice constant (in Angstroms) |
168 |
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|
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< |
//get mass of molecule. |
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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(); |
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|
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< |
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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|
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< |
//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 |
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|
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 |
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|
229 |
< |
//calculate lattice constant (in Angstrom) |
184 |
< |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
185 |
< |
1.0 / 3.0); |
229 |
> |
// recompute actual mol fractions and perform final sanity check: |
230 |
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|
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((double)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 |
|
} |