85 |
|
double latticeConstant; |
86 |
|
std::vector<double> lc; |
87 |
|
|
88 |
< |
double particleRadius; |
88 |
> |
RealType particleRadius; |
89 |
|
|
90 |
|
Mat3x3d hmat; |
91 |
|
std::vector<Vector3d> latticePos; |
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" |
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(); |
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; |
204 |
|
std::map<int, int> componentFromSite; |
205 |
|
nComponents = components.size(); |
206 |
|
|
207 |
< |
if (args_info.molFraction_given && args_info.ShellRadius_given) { |
208 |
< |
sprintf(painCave.errMsg, "Specify either molFraction or ShellRadius " |
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(); |
232 |
|
painCave.isFatal = 1; |
233 |
|
simError(); |
234 |
|
} |
235 |
< |
} else if ((int)args_info.ShellRadius_given) { |
236 |
< |
if ((int)args_info.ShellRadius_given == nComponents) { |
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]); |
238 |
> |
shellRadii.push_back(args_info.shellRadius_arg[i]); |
239 |
|
} |
240 |
< |
} else if ((int)args_info.ShellRadius_given == nComponents-1) { |
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]); |
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 shell radii " |
247 |
< |
"for all of the components in the <MetaData> block."); |
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 |
|
} else { |
252 |
< |
sprintf(painCave.errMsg, "You have a multi-component <MetaData> block, but have not " |
253 |
< |
"specified either molFraction or ShellRadius arguments."); |
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 |
|
} |
317 |
|
} |
318 |
|
} |
319 |
|
} |
320 |
< |
|
321 |
< |
vector<int> ids; |
258 |
< |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
259 |
< |
/* Random particle is the default case*/ |
320 |
> |
|
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 |
+ |
/* 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()); |
332 |
+ |
|
333 |
|
} else{ |
334 |
|
sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle."); |
335 |
|
painCave.isFatal = 0; |
336 |
|
simError(); |
337 |
|
|
270 |
– |
Vector3d myLoc; |
271 |
– |
RealType myR; |
338 |
|
RealType smallestSoFar; |
339 |
|
int myComponent = -1; |
340 |
|
nMol.clear(); |
343 |
|
for (int i = 0; i < sites.size(); i++) { |
344 |
|
myLoc = sites[i]; |
345 |
|
myR = myLoc.length(); |
346 |
< |
smallestSoFar = particleRadius; |
347 |
< |
|
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; |
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 |
< |
componentFromSite[i] = myComponent; |
360 |
< |
nMol[myComponent]++; |
292 |
< |
} |
293 |
< |
} |
359 |
> |
} |
360 |
> |
} |
361 |
|
|
362 |
|
outputFileName = args_info.output_arg; |
363 |
< |
|
297 |
< |
|
363 |
> |
|
364 |
|
//creat new .md file on fly which corrects the number of molecule |
365 |
|
createMdFile(inputFileName, outputFileName, nMol); |
366 |
|
|
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 |
< |
|
385 |
< |
if (args_info.ShellRadius_given) { |
384 |
> |
|
385 |
> |
if (!args_info.molFraction_given) { |
386 |
|
for (int n = 0; n < sites.size(); n++) { |
387 |
< |
if (componentFromSite[n] == i) { |
388 |
< |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
389 |
< |
locator->placeMol(sites[n], orientations[n], mol); |
390 |
< |
l++; |
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 { |
399 |
|
l++; |
400 |
|
} |
401 |
|
} |
402 |
< |
} |
402 |
> |
} |
403 |
|
|
404 |
|
//fill Hmat |
405 |
|
hmat(0, 0)= 10.0*particleRadius; |
422 |
|
writer = new DumpWriter(NewInfo, outputFileName); |
423 |
|
|
424 |
|
if (writer == NULL) { |
425 |
< |
sprintf(painCave.errMsg, "Error in creating dumpwrite object "); |
425 |
> |
sprintf(painCave.errMsg, "Error in creating dumpwriter object "); |
426 |
|
painCave.isFatal = 1; |
427 |
|
simError(); |
428 |
|
} |
452 |
|
//create new .md file based on old .md file |
453 |
|
oldMdFile.open(oldMdFileName.c_str()); |
454 |
|
newMdFile.open(newMdFileName.c_str()); |
385 |
– |
|
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 |
|
|