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; |
87 |
< |
double mass; |
90 |
< |
const double rhoConvertConst = 1.661; |
91 |
< |
double density; |
87 |
> |
|
88 |
|
double 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(); |
134 |
|
|
135 |
|
std::vector<Component*> components = simParams->getComponents(); |
136 |
|
std::vector<RealType> molFractions; |
137 |
+ |
std::vector<RealType> shellRadii; |
138 |
|
std::vector<RealType> molecularMasses; |
139 |
|
std::vector<int> nMol; |
140 |
+ |
std::map<int, int> componentFromSite; |
141 |
|
nComponents = components.size(); |
142 |
|
|
143 |
< |
if (nComponents == 1) { |
143 |
> |
if (args_info.molFraction_given && args_info.ShellRadius_given) { |
144 |
> |
sprintf(painCave.errMsg, "Specify either molFraction or ShellRadius " |
145 |
> |
"arguments, but not both!"); |
146 |
> |
painCave.isFatal = 1; |
147 |
> |
simError(); |
148 |
> |
} |
149 |
> |
|
150 |
> |
if (nComponents == 1) { |
151 |
|
molFractions.push_back(1.0); |
152 |
< |
} else { |
153 |
< |
if (args_info.molFraction_given == nComponents) { |
154 |
< |
for (int i = 0; i < nComponents; i++) { |
155 |
< |
molFractions.push_back(args_info.molFraction_arg[i]); |
156 |
< |
} |
157 |
< |
} else if (args_info.molFraction_given == nComponents-1) { |
158 |
< |
RealType remainingFraction = 1.0; |
159 |
< |
for (int i = 0; i < nComponents-1; i++) { |
160 |
< |
molFractions.push_back(args_info.molFraction_arg[i]); |
161 |
< |
remainingFraction -= molFractions[i]; |
162 |
< |
} |
163 |
< |
molFractions.push_back(remainingFraction); |
164 |
< |
} else { |
165 |
< |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions " |
166 |
< |
"for all of the components in the <MetaData> block."); |
167 |
< |
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!"); |
152 |
> |
shellRadii.push_back(particleRadius); |
153 |
> |
} else if (args_info.molFraction_given) { |
154 |
> |
if ((int)args_info.molFraction_given == nComponents) { |
155 |
> |
for (int i = 0; i < nComponents; i++) { |
156 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
157 |
> |
} |
158 |
> |
} else if ((int)args_info.molFraction_given == nComponents-1) { |
159 |
> |
RealType remainingFraction = 1.0; |
160 |
> |
for (int i = 0; i < nComponents-1; i++) { |
161 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
162 |
> |
remainingFraction -= molFractions[i]; |
163 |
> |
} |
164 |
> |
molFractions.push_back(remainingFraction); |
165 |
> |
} else { |
166 |
> |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions " |
167 |
> |
"for all of the components in the <MetaData> block."); |
168 |
|
painCave.isFatal = 1; |
169 |
|
simError(); |
170 |
|
} |
171 |
< |
if (molFractions.at(i) > 1.0) { |
172 |
< |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
173 |
< |
" greater than one!"); |
171 |
> |
} else if ((int)args_info.ShellRadius_given) { |
172 |
> |
if ((int)args_info.ShellRadius_given == nComponents) { |
173 |
> |
for (int i = 0; i < nComponents; i++) { |
174 |
> |
shellRadii.push_back(args_info.ShellRadius_arg[i]); |
175 |
> |
} |
176 |
> |
} else if ((int)args_info.ShellRadius_given == nComponents-1) { |
177 |
> |
for (int i = 0; i < nComponents-1; i++) { |
178 |
> |
shellRadii.push_back(args_info.ShellRadius_arg[i]); |
179 |
> |
} |
180 |
> |
shellRadii.push_back(particleRadius); |
181 |
> |
} else { |
182 |
> |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out the shell radii " |
183 |
> |
"for all of the components in the <MetaData> block."); |
184 |
|
painCave.isFatal = 1; |
185 |
|
simError(); |
186 |
|
} |
187 |
< |
totalFraction += molFractions.at(i); |
188 |
< |
} |
189 |
< |
if (abs(totalFraction - 1.0) > 1e-6) { |
189 |
< |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
187 |
> |
} else { |
188 |
> |
sprintf(painCave.errMsg, "You have a multi-component <MetaData> block, but have not " |
189 |
> |
"specified either molFraction or ShellRadius arguments."); |
190 |
|
painCave.isFatal = 1; |
191 |
|
simError(); |
192 |
|
} |
193 |
< |
|
194 |
< |
int remaining = nSites; |
195 |
< |
for (int i=0; i < nComponents-1; i++) { |
196 |
< |
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
197 |
< |
remaining -= nMol.at(i); |
198 |
< |
} |
199 |
< |
nMol.push_back(remaining); |
200 |
< |
|
201 |
< |
|
202 |
< |
|
203 |
< |
// recompute actual mol fractions and perform final sanity check: |
204 |
< |
|
205 |
< |
int totalMolecules = 0; |
206 |
< |
RealType totalMass = 0.0; |
207 |
< |
for (int i=0; i < nComponents; i++) { |
208 |
< |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
209 |
< |
totalMolecules += nMol.at(i); |
210 |
< |
molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i), |
211 |
< |
oldInfo->getForceField())); |
212 |
< |
totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i); |
213 |
< |
} |
214 |
< |
RealType avgMass = totalMass / (RealType) totalMolecules; |
215 |
< |
|
216 |
< |
if (totalMolecules != nSites) { |
217 |
< |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
218 |
< |
"to the number of lattice sites!"); |
219 |
< |
painCave.isFatal = 1; |
220 |
< |
simError(); |
221 |
< |
} |
222 |
< |
|
223 |
< |
vector<int> ids; |
224 |
< |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
225 |
< |
/* Random particle is the default case*/ |
226 |
< |
if (!args_info.ShellRadius_given){ |
227 |
< |
/* do the iPod thing, Shuffle da vector */ |
228 |
< |
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"); |
193 |
> |
|
194 |
> |
if (args_info.molFraction_given) { |
195 |
> |
RealType totalFraction = 0.0; |
196 |
> |
|
197 |
> |
/* Do some simple sanity checking*/ |
198 |
> |
|
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 |
< |
} |
218 |
> |
} |
219 |
|
|
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 |
+ |
// recompute actual mol fractions and perform final sanity check: |
228 |
+ |
|
229 |
+ |
int totalMolecules = 0; |
230 |
+ |
for (int i=0; i < nComponents; i++) { |
231 |
+ |
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
232 |
+ |
totalMolecules += nMol.at(i); |
233 |
+ |
} |
234 |
+ |
|
235 |
+ |
if (totalMolecules != nSites) { |
236 |
+ |
sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
237 |
+ |
"to the number of lattice sites!"); |
238 |
+ |
painCave.isFatal = 1; |
239 |
+ |
simError(); |
240 |
+ |
} |
241 |
+ |
} else { |
242 |
+ |
|
243 |
+ |
for (int i = 0; i < shellRadii.size(); i++) { |
244 |
+ |
if (shellRadii.at(i) > particleRadius + 1e-6 ) { |
245 |
+ |
sprintf(painCave.errMsg, "One of the shellRadius values exceeds the particle Radius."); |
246 |
+ |
painCave.isFatal = 1; |
247 |
+ |
simError(); |
248 |
+ |
} |
249 |
+ |
if (shellRadii.at(i) <= 0.0 ) { |
250 |
+ |
sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!"); |
251 |
+ |
painCave.isFatal = 1; |
252 |
+ |
simError(); |
253 |
+ |
} |
254 |
+ |
} |
255 |
|
} |
256 |
+ |
|
257 |
+ |
vector<int> ids; |
258 |
+ |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
259 |
+ |
/* Random particle is the default case*/ |
260 |
+ |
if ((int)args_info.molFraction_given){ |
261 |
+ |
sprintf(painCave.errMsg, "Creating a randomized spherical nanoparticle."); |
262 |
+ |
painCave.isFatal = 0; |
263 |
+ |
simError(); |
264 |
+ |
std::random_shuffle(ids.begin(), ids.end()); |
265 |
+ |
} else{ |
266 |
+ |
sprintf(painCave.errMsg, "Creating a core-shell spherical nanoparticle."); |
267 |
+ |
painCave.isFatal = 0; |
268 |
+ |
simError(); |
269 |
|
|
270 |
+ |
Vector3d myLoc; |
271 |
+ |
RealType myR; |
272 |
+ |
RealType smallestSoFar; |
273 |
+ |
int myComponent = -1; |
274 |
+ |
nMol.clear(); |
275 |
+ |
nMol.resize(nComponents); |
276 |
+ |
|
277 |
+ |
for (int i = 0; i < sites.size(); i++) { |
278 |
+ |
myLoc = sites[i]; |
279 |
+ |
myR = myLoc.length(); |
280 |
+ |
smallestSoFar = particleRadius; |
281 |
+ |
|
282 |
+ |
for (int j = 0; j < nComponents; j++) { |
283 |
+ |
if (myR <= shellRadii[j]) { |
284 |
+ |
if (shellRadii[j] <= smallestSoFar) { |
285 |
+ |
smallestSoFar = shellRadii[j]; |
286 |
+ |
myComponent = j; |
287 |
+ |
} |
288 |
+ |
} |
289 |
+ |
} |
290 |
+ |
componentFromSite[i] = myComponent; |
291 |
+ |
nMol[myComponent]++; |
292 |
+ |
} |
293 |
+ |
} |
294 |
|
|
241 |
– |
|
242 |
– |
|
295 |
|
outputFileName = args_info.output_arg; |
296 |
|
|
297 |
|
|
298 |
< |
//creat new .md file on fly which corrects the number of molecule |
298 |
> |
//creat new .md file on fly which corrects the number of molecule |
299 |
|
createMdFile(inputFileName, outputFileName, nMol); |
300 |
|
|
301 |
|
if (oldInfo != NULL) |
302 |
|
delete oldInfo; |
303 |
|
|
252 |
– |
|
253 |
– |
// We need to read in new siminfo object. |
254 |
– |
//parse md file and set up the system |
255 |
– |
//SimCreator NewCreator; |
304 |
|
SimCreator newCreator; |
305 |
|
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
306 |
< |
|
259 |
< |
|
306 |
> |
|
307 |
|
// Place molecules |
308 |
|
Molecule* mol; |
309 |
|
SimInfo::MoleculeIterator mi; |
313 |
|
for (int i = 0; i < nComponents; i++){ |
314 |
|
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
315 |
|
NewInfo->getForceField()); |
316 |
< |
for (int n = 0; n < nMol.at(i); n++) { |
317 |
< |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
318 |
< |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
319 |
< |
l++; |
316 |
> |
|
317 |
> |
if (args_info.ShellRadius_given) { |
318 |
> |
for (int n = 0; n < sites.size(); n++) { |
319 |
> |
if (componentFromSite[n] == i) { |
320 |
> |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
321 |
> |
locator->placeMol(sites[n], orientations[n], mol); |
322 |
> |
l++; |
323 |
> |
} |
324 |
> |
} |
325 |
> |
} else { |
326 |
> |
for (int n = 0; n < nMol.at(i); n++) { |
327 |
> |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
328 |
> |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
329 |
> |
l++; |
330 |
> |
} |
331 |
|
} |
332 |
< |
} |
332 |
> |
} |
333 |
|
|
276 |
– |
|
277 |
– |
|
334 |
|
//fill Hmat |
335 |
< |
hmat(0, 0)= 2.0*particleRadius; |
335 |
> |
hmat(0, 0)= 10.0*particleRadius; |
336 |
|
hmat(0, 1) = 0.0; |
337 |
|
hmat(0, 2) = 0.0; |
338 |
|
|
339 |
|
hmat(1, 0) = 0.0; |
340 |
< |
hmat(1, 1) = 2.0*particleRadius; |
340 |
> |
hmat(1, 1) = 10.0*particleRadius; |
341 |
|
hmat(1, 2) = 0.0; |
342 |
|
|
343 |
|
hmat(2, 0) = 0.0; |
344 |
|
hmat(2, 1) = 0.0; |
345 |
< |
hmat(2, 2) = 2.0*particleRadius; |
345 |
> |
hmat(2, 2) = 10.0*particleRadius; |
346 |
|
|
347 |
|
//set Hmat |
348 |
|
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
353 |
|
|
354 |
|
if (writer == NULL) { |
355 |
|
sprintf(painCave.errMsg, "Error in creating dumpwrite object "); |
356 |
< |
painCave.isFatal = 1; |
357 |
< |
simError(); |
356 |
> |
painCave.isFatal = 1; |
357 |
> |
simError(); |
358 |
|
} |
359 |
|
|
360 |
|
writer->writeDump(); |
371 |
|
return 0; |
372 |
|
} |
373 |
|
|
374 |
< |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
374 |
> |
void createMdFile(const std::string&oldMdFileName, |
375 |
> |
const std::string&newMdFileName, |
376 |
|
std::vector<int> nMol) { |
377 |
|
ifstream oldMdFile; |
378 |
|
ofstream newMdFile; |