80 |
|
std::string inputFileName; |
81 |
|
std::string outputFileName; |
82 |
|
|
83 |
– |
Lattice *simpleLat; |
83 |
|
MoLocator* locator; |
85 |
– |
int* numMol; |
84 |
|
int nComponents; |
85 |
|
double latticeConstant; |
86 |
|
std::vector<double> lc; |
89 |
– |
double mass; |
90 |
– |
const double rhoConvertConst = 1.661; |
91 |
– |
double density; |
92 |
– |
double particleRadius; |
87 |
|
|
88 |
+ |
RealType particleRadius; |
89 |
+ |
|
90 |
|
Mat3x3d hmat; |
91 |
|
std::vector<Vector3d> latticePos; |
92 |
|
std::vector<Vector3d> latticeOrt; |
97 |
– |
int numMolPerCell; |
98 |
– |
int nShells; /* Number of shells in nanoparticle*/ |
93 |
|
|
94 |
|
DumpWriter *writer; |
95 |
|
|
104 |
|
if (args_info.inputs_num) |
105 |
|
inputFileName = args_info.inputs[0]; |
106 |
|
else { |
107 |
< |
sprintf(painCave.errMsg, "No input .md file name was specified" |
108 |
< |
"on the command line"); |
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 |
|
simError(); |
115 |
|
SimCreator oldCreator; |
116 |
|
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
117 |
|
|
118 |
< |
latticeConstant = args_info.latticeCnst_arg; |
118 |
> |
latticeConstant = args_info.latticeConstant_arg; |
119 |
|
particleRadius = args_info.radius_arg; |
120 |
|
Globals* simParams = oldInfo->getSimParams(); |
121 |
|
|
126 |
|
/* Build a lattice and get lattice points for this lattice constant */ |
127 |
|
vector<Vector3d> sites = nanoParticle.getSites(); |
128 |
|
vector<Vector3d> orientations = nanoParticle.getOrientations(); |
129 |
+ |
std::vector<int> vacancyTargets; |
130 |
+ |
vector<bool> isVacancy; |
131 |
+ |
|
132 |
+ |
Vector3d myLoc; |
133 |
+ |
RealType myR; |
134 |
+ |
|
135 |
+ |
for (int i = 0; i < sites.size(); i++) |
136 |
+ |
isVacancy.push_back(false); |
137 |
|
|
138 |
< |
std::cout <<"nSites: " << sites.size() << std::endl; |
138 |
> |
if (args_info.vacancyPercent_given) { |
139 |
> |
if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) { |
140 |
> |
sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value."); |
141 |
> |
painCave.isFatal = 1; |
142 |
> |
simError(); |
143 |
> |
} else { |
144 |
> |
RealType vF = args_info.vacancyPercent_arg / 100.0; |
145 |
> |
RealType vIR; |
146 |
> |
RealType vOR; |
147 |
> |
if (args_info.vacancyInnerRadius_given) { |
148 |
> |
vIR = args_info.vacancyInnerRadius_arg; |
149 |
> |
} else { |
150 |
> |
vIR = 0.0; |
151 |
> |
} |
152 |
> |
if (args_info.vacancyOuterRadius_given) { |
153 |
> |
vOR = args_info.vacancyOuterRadius_arg; |
154 |
> |
} else { |
155 |
> |
vOR = particleRadius; |
156 |
> |
} |
157 |
> |
if (vIR >= 0.0 && vOR <= particleRadius && vOR >= vIR) { |
158 |
> |
|
159 |
> |
for (int i = 0; i < sites.size(); i++) { |
160 |
> |
myLoc = sites[i]; |
161 |
> |
myR = myLoc.length(); |
162 |
> |
if (myR >= vIR && myR <= vOR) { |
163 |
> |
vacancyTargets.push_back(i); |
164 |
> |
} |
165 |
> |
} |
166 |
> |
std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end()); |
167 |
> |
|
168 |
> |
int nTargets = vacancyTargets.size(); |
169 |
> |
vacancyTargets.resize((int)(vF * nTargets)); |
170 |
> |
|
171 |
> |
|
172 |
> |
sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n" |
173 |
> |
"\tsites between %lf and %lf.", vacancyTargets.size(), |
174 |
> |
vIR, vOR); |
175 |
> |
painCave.isFatal = 0; |
176 |
> |
simError(); |
177 |
|
|
178 |
+ |
isVacancy.clear(); |
179 |
+ |
for (int i = 0; i < sites.size(); i++) { |
180 |
+ |
bool vac = false; |
181 |
+ |
for (int j = 0; j < vacancyTargets.size(); j++) { |
182 |
+ |
if (i == vacancyTargets[j]) vac = true; |
183 |
+ |
} |
184 |
+ |
isVacancy.push_back(vac); |
185 |
+ |
} |
186 |
+ |
|
187 |
+ |
} else { |
188 |
+ |
sprintf(painCave.errMsg, "Something is strange about the vacancy\n" |
189 |
+ |
"\tinner or outer radii. Check their values."); |
190 |
+ |
painCave.isFatal = 1; |
191 |
+ |
simError(); |
192 |
+ |
} |
193 |
+ |
} |
194 |
+ |
} |
195 |
+ |
|
196 |
|
/* Get number of lattice sites */ |
197 |
< |
int nSites = sites.size(); |
197 |
> |
int nSites = sites.size() - vacancyTargets.size(); |
198 |
|
|
199 |
|
std::vector<Component*> components = simParams->getComponents(); |
200 |
|
std::vector<RealType> molFractions; |
201 |
+ |
std::vector<RealType> shellRadii; |
202 |
|
std::vector<RealType> molecularMasses; |
203 |
|
std::vector<int> nMol; |
204 |
+ |
std::map<int, int> componentFromSite; |
205 |
|
nComponents = components.size(); |
206 |
|
|
207 |
< |
if (nComponents == 1) { |
207 |
> |
if (args_info.molFraction_given && args_info.shellRadius_given) { |
208 |
> |
sprintf(painCave.errMsg, "Specify either molFraction or shellRadius " |
209 |
> |
"arguments, but not both!"); |
210 |
> |
painCave.isFatal = 1; |
211 |
> |
simError(); |
212 |
> |
} |
213 |
> |
|
214 |
> |
if (nComponents == 1) { |
215 |
|
molFractions.push_back(1.0); |
216 |
< |
} else { |
217 |
< |
if (args_info.molFraction_given == nComponents) { |
218 |
< |
for (int i = 0; i < nComponents; i++) { |
219 |
< |
molFractions.push_back(args_info.molFraction_arg[i]); |
220 |
< |
} |
221 |
< |
} else if (args_info.molFraction_given == nComponents-1) { |
222 |
< |
RealType remainingFraction = 1.0; |
223 |
< |
for (int i = 0; i < nComponents-1; i++) { |
224 |
< |
molFractions.push_back(args_info.molFraction_arg[i]); |
225 |
< |
remainingFraction -= molFractions[i]; |
226 |
< |
} |
227 |
< |
molFractions.push_back(remainingFraction); |
228 |
< |
} else { |
229 |
< |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions " |
230 |
< |
"for all of the components in the <MetaData> block."); |
231 |
< |
painCave.isFatal = 1; |
165 |
< |
simError(); |
166 |
< |
} |
167 |
< |
} |
168 |
< |
|
169 |
< |
RealType totalFraction = 0.0; |
170 |
< |
|
171 |
< |
/* Do some simple sanity checking*/ |
172 |
< |
|
173 |
< |
for (int i = 0; i < nComponents; i++) { |
174 |
< |
if (molFractions.at(i) < 0.0) { |
175 |
< |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
176 |
< |
" less than zero!"); |
216 |
> |
shellRadii.push_back(particleRadius); |
217 |
> |
} else if (args_info.molFraction_given) { |
218 |
> |
if ((int)args_info.molFraction_given == nComponents) { |
219 |
> |
for (int i = 0; i < nComponents; i++) { |
220 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
221 |
> |
} |
222 |
> |
} else if ((int)args_info.molFraction_given == nComponents-1) { |
223 |
> |
RealType remainingFraction = 1.0; |
224 |
> |
for (int i = 0; i < nComponents-1; i++) { |
225 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
226 |
> |
remainingFraction -= molFractions[i]; |
227 |
> |
} |
228 |
> |
molFractions.push_back(remainingFraction); |
229 |
> |
} else { |
230 |
> |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions " |
231 |
> |
"for all of the components in the <MetaData> block."); |
232 |
|
painCave.isFatal = 1; |
233 |
|
simError(); |
234 |
|
} |
235 |
< |
if (molFractions.at(i) > 1.0) { |
236 |
< |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
237 |
< |
" greater than one!"); |
235 |
> |
} else if ((int)args_info.shellRadius_given) { |
236 |
> |
if ((int)args_info.shellRadius_given == nComponents) { |
237 |
> |
for (int i = 0; i < nComponents; i++) { |
238 |
> |
shellRadii.push_back(args_info.shellRadius_arg[i]); |
239 |
> |
} |
240 |
> |
} else if ((int)args_info.shellRadius_given == nComponents-1) { |
241 |
> |
for (int i = 0; i < nComponents-1; i++) { |
242 |
> |
shellRadii.push_back(args_info.shellRadius_arg[i]); |
243 |
> |
} |
244 |
> |
shellRadii.push_back(particleRadius); |
245 |
> |
} else { |
246 |
> |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the\n" |
247 |
> |
"\tshell radii for all of the components in the <MetaData> block."); |
248 |
|
painCave.isFatal = 1; |
249 |
|
simError(); |
250 |
|
} |
251 |
< |
totalFraction += molFractions.at(i); |
252 |
< |
} |
253 |
< |
if (abs(totalFraction - 1.0) > 1e-6) { |
189 |
< |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
251 |
> |
} else { |
252 |
> |
sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n" |
253 |
> |
"\tbut have not specified either molFraction or shellRadius arguments."); |
254 |
|
painCave.isFatal = 1; |
255 |
|
simError(); |
256 |
|
} |
257 |
< |
|
258 |
< |
int remaining = nSites; |
259 |
< |
for (int i=0; i < nComponents-1; i++) { |
260 |
< |
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
261 |
< |
remaining -= nMol.at(i); |
262 |
< |
} |
263 |
< |
nMol.push_back(remaining); |
257 |
> |
|
258 |
> |
if (args_info.molFraction_given) { |
259 |
> |
RealType totalFraction = 0.0; |
260 |
> |
|
261 |
> |
/* Do some simple sanity checking*/ |
262 |
> |
|
263 |
> |
for (int i = 0; i < nComponents; i++) { |
264 |
> |
if (molFractions.at(i) < 0.0) { |
265 |
> |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
266 |
> |
" less than zero!"); |
267 |
> |
painCave.isFatal = 1; |
268 |
> |
simError(); |
269 |
> |
} |
270 |
> |
if (molFractions.at(i) > 1.0) { |
271 |
> |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
272 |
> |
" greater than one!"); |
273 |
> |
painCave.isFatal = 1; |
274 |
> |
simError(); |
275 |
> |
} |
276 |
> |
totalFraction += molFractions.at(i); |
277 |
> |
} |
278 |
> |
if (abs(totalFraction - 1.0) > 1e-6) { |
279 |
> |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
280 |
> |
painCave.isFatal = 1; |
281 |
> |
simError(); |
282 |
> |
} |
283 |
> |
|
284 |
> |
int remaining = nSites; |
285 |
> |
for (int i=0; i < nComponents-1; i++) { |
286 |
> |
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
287 |
> |
remaining -= nMol.at(i); |
288 |
> |
} |
289 |
> |
nMol.push_back(remaining); |
290 |
> |
|
291 |
> |
// recompute actual mol fractions and perform final sanity check: |
292 |
> |
|
293 |
> |
int totalMolecules = 0; |
294 |
> |
for (int i=0; i < nComponents; i++) { |
295 |
> |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
296 |
> |
totalMolecules += nMol.at(i); |
297 |
> |
} |
298 |
> |
|
299 |
> |
if (totalMolecules != nSites) { |
300 |
> |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
301 |
> |
"to the number of lattice sites!"); |
302 |
> |
painCave.isFatal = 1; |
303 |
> |
simError(); |
304 |
> |
} |
305 |
> |
} else { |
306 |
|
|
307 |
< |
|
308 |
< |
|
309 |
< |
// recompute actual mol fractions and perform final sanity check: |
310 |
< |
|
311 |
< |
int totalMolecules = 0; |
312 |
< |
RealType totalMass = 0.0; |
313 |
< |
for (int i=0; i < nComponents; i++) { |
314 |
< |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
315 |
< |
totalMolecules += nMol.at(i); |
316 |
< |
molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i), |
317 |
< |
oldInfo->getForceField())); |
318 |
< |
totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i); |
307 |
> |
for (int i = 0; i < shellRadii.size(); i++) { |
308 |
> |
if (shellRadii.at(i) > particleRadius + 1e-6 ) { |
309 |
> |
sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius."); |
310 |
> |
painCave.isFatal = 1; |
311 |
> |
simError(); |
312 |
> |
} |
313 |
> |
if (shellRadii.at(i) <= 0.0 ) { |
314 |
> |
sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!"); |
315 |
> |
painCave.isFatal = 1; |
316 |
> |
simError(); |
317 |
> |
} |
318 |
> |
} |
319 |
|
} |
214 |
– |
RealType avgMass = totalMass / (RealType) totalMolecules; |
320 |
|
|
321 |
< |
if (totalMolecules != nSites) { |
322 |
< |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
323 |
< |
"to the number of lattice sites!"); |
324 |
< |
painCave.isFatal = 1; |
321 |
> |
vector<int> ids; |
322 |
> |
if ((int)args_info.molFraction_given){ |
323 |
> |
sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle."); |
324 |
> |
painCave.isFatal = 0; |
325 |
|
simError(); |
326 |
< |
} |
327 |
< |
|
328 |
< |
vector<int> ids; |
329 |
< |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
330 |
< |
/* Random particle is the default case*/ |
226 |
< |
if (!args_info.ShellRadius_given){ |
227 |
< |
/* do the iPod thing, Shuffle da vector */ |
326 |
> |
/* Random particle is the default case*/ |
327 |
> |
|
328 |
> |
for (int i = 0; i < sites.size(); i++) |
329 |
> |
if (!isVacancy[i]) ids.push_back(i); |
330 |
> |
|
331 |
|
std::random_shuffle(ids.begin(), ids.end()); |
229 |
– |
} else{ /*Handle core-shell with multiple components.*/ |
230 |
– |
std::cout << "Creating a core-shell nanoparticle." << std::endl; |
231 |
– |
if (nComponents != args_info.ShellRadius_given + 1){ |
232 |
– |
sprintf(painCave.errMsg, "Number of .md components " |
233 |
– |
"does not match the number of shell radius specifications"); |
234 |
– |
painCave.isFatal = 1; |
235 |
– |
simError(); |
236 |
– |
} |
332 |
|
|
333 |
< |
} |
333 |
> |
} else{ |
334 |
> |
sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle."); |
335 |
> |
painCave.isFatal = 0; |
336 |
> |
simError(); |
337 |
|
|
338 |
+ |
RealType smallestSoFar; |
339 |
+ |
int myComponent = -1; |
340 |
+ |
nMol.clear(); |
341 |
+ |
nMol.resize(nComponents); |
342 |
+ |
|
343 |
+ |
for (int i = 0; i < sites.size(); i++) { |
344 |
+ |
myLoc = sites[i]; |
345 |
+ |
myR = myLoc.length(); |
346 |
+ |
smallestSoFar = particleRadius; |
347 |
+ |
if (!isVacancy[i]) { |
348 |
+ |
for (int j = 0; j < nComponents; j++) { |
349 |
+ |
if (myR <= shellRadii[j]) { |
350 |
+ |
if (shellRadii[j] <= smallestSoFar) { |
351 |
+ |
smallestSoFar = shellRadii[j]; |
352 |
+ |
myComponent = j; |
353 |
+ |
} |
354 |
+ |
} |
355 |
+ |
} |
356 |
+ |
componentFromSite[i] = myComponent; |
357 |
+ |
nMol[myComponent]++; |
358 |
+ |
} |
359 |
+ |
} |
360 |
+ |
} |
361 |
|
|
241 |
– |
|
242 |
– |
|
362 |
|
outputFileName = args_info.output_arg; |
363 |
< |
|
364 |
< |
|
246 |
< |
//creat new .md file on fly which corrects the number of molecule |
363 |
> |
|
364 |
> |
//creat new .md file on fly which corrects the number of molecule |
365 |
|
createMdFile(inputFileName, outputFileName, nMol); |
366 |
|
|
367 |
|
if (oldInfo != NULL) |
368 |
|
delete oldInfo; |
369 |
|
|
252 |
– |
|
253 |
– |
// We need to read in new siminfo object. |
254 |
– |
//parse md file and set up the system |
255 |
– |
//SimCreator NewCreator; |
370 |
|
SimCreator newCreator; |
371 |
|
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
372 |
< |
|
259 |
< |
|
372 |
> |
|
373 |
|
// Place molecules |
374 |
|
Molecule* mol; |
375 |
|
SimInfo::MoleculeIterator mi; |
376 |
|
mol = NewInfo->beginMolecule(mi); |
377 |
+ |
|
378 |
|
int l = 0; |
379 |
+ |
int whichSite = 0; |
380 |
|
|
381 |
|
for (int i = 0; i < nComponents; i++){ |
382 |
|
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
383 |
|
NewInfo->getForceField()); |
384 |
< |
for (int n = 0; n < nMol.at(i); n++) { |
385 |
< |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
386 |
< |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
387 |
< |
l++; |
384 |
> |
|
385 |
> |
if (!args_info.molFraction_given) { |
386 |
> |
for (int n = 0; n < sites.size(); n++) { |
387 |
> |
if (!isVacancy[n]) { |
388 |
> |
if (componentFromSite[n] == i) { |
389 |
> |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
390 |
> |
locator->placeMol(sites[n], orientations[n], mol); |
391 |
> |
l++; |
392 |
> |
} |
393 |
> |
} |
394 |
> |
} |
395 |
> |
} else { |
396 |
> |
for (int n = 0; n < nMol.at(i); n++) { |
397 |
> |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
398 |
> |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
399 |
> |
l++; |
400 |
> |
} |
401 |
|
} |
402 |
|
} |
403 |
|
|
276 |
– |
|
277 |
– |
|
404 |
|
//fill Hmat |
405 |
< |
hmat(0, 0)= 2.0*particleRadius; |
405 |
> |
hmat(0, 0)= 10.0*particleRadius; |
406 |
|
hmat(0, 1) = 0.0; |
407 |
|
hmat(0, 2) = 0.0; |
408 |
|
|
409 |
|
hmat(1, 0) = 0.0; |
410 |
< |
hmat(1, 1) = 2.0*particleRadius; |
410 |
> |
hmat(1, 1) = 10.0*particleRadius; |
411 |
|
hmat(1, 2) = 0.0; |
412 |
|
|
413 |
|
hmat(2, 0) = 0.0; |
414 |
|
hmat(2, 1) = 0.0; |
415 |
< |
hmat(2, 2) = 2.0*particleRadius; |
415 |
> |
hmat(2, 2) = 10.0*particleRadius; |
416 |
|
|
417 |
|
//set Hmat |
418 |
|
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
422 |
|
writer = new DumpWriter(NewInfo, outputFileName); |
423 |
|
|
424 |
|
if (writer == NULL) { |
425 |
< |
sprintf(painCave.errMsg, "Error in creating dumpwrite object "); |
426 |
< |
painCave.isFatal = 1; |
427 |
< |
simError(); |
425 |
> |
sprintf(painCave.errMsg, "Error in creating dumpwriter object "); |
426 |
> |
painCave.isFatal = 1; |
427 |
> |
simError(); |
428 |
|
} |
429 |
|
|
430 |
|
writer->writeDump(); |
441 |
|
return 0; |
442 |
|
} |
443 |
|
|
444 |
< |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
444 |
> |
void createMdFile(const std::string&oldMdFileName, |
445 |
> |
const std::string&newMdFileName, |
446 |
|
std::vector<int> nMol) { |
447 |
|
ifstream oldMdFile; |
448 |
|
ofstream newMdFile; |
452 |
|
//create new .md file based on old .md file |
453 |
|
oldMdFile.open(oldMdFileName.c_str()); |
454 |
|
newMdFile.open(newMdFileName.c_str()); |
328 |
– |
|
455 |
|
oldMdFile.getline(buffer, MAXLEN); |
456 |
< |
|
456 |
> |
|
457 |
|
int i = 0; |
458 |
|
while (!oldMdFile.eof()) { |
459 |
< |
|
459 |
> |
|
460 |
|
//correct molecule number |
461 |
|
if (strstr(buffer, "nMol") != NULL) { |
462 |
|
if(i<nMol.size()){ |
463 |
< |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
463 |
> |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
464 |
|
newMdFile << buffer << std::endl; |
465 |
|
i++; |
466 |
|
} |
472 |
|
|
473 |
|
oldMdFile.close(); |
474 |
|
newMdFile.close(); |
475 |
+ |
|
476 |
+ |
if (i != nMol.size()) { |
477 |
+ |
sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n" |
478 |
+ |
"\tstatements in component blocks. Make sure that all\n" |
479 |
+ |
"\tcomponents in the template file have nMol=1"); |
480 |
+ |
painCave.isFatal = 1; |
481 |
+ |
simError(); |
482 |
+ |
} |
483 |
+ |
|
484 |
|
} |
485 |
|
|