67 |
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using namespace oopse; |
68 |
|
void createMdFile(const std::string&oldMdFileName, |
69 |
|
const std::string&newMdFileName, |
70 |
< |
int components,int* numMol); |
70 |
> |
std::vector<int> numMol); |
71 |
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|
72 |
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int main(int argc, char *argv []) { |
73 |
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|
78 |
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gengetopt_args_info args_info; |
79 |
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std::string latticeType; |
80 |
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std::string inputFileName; |
81 |
< |
std::string outPrefix; |
82 |
< |
std::string outMdFileName; |
83 |
< |
std::string outInitFileName; |
81 |
> |
std::string outputFileName; |
82 |
|
|
85 |
– |
|
86 |
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|
87 |
– |
Lattice *simpleLat; |
83 |
|
MoLocator* locator; |
89 |
– |
int* numMol; |
84 |
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int nComponents; |
85 |
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double latticeConstant; |
86 |
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std::vector<double> lc; |
87 |
< |
double mass; |
94 |
< |
const double rhoConvertConst = 1.661; |
95 |
< |
double density; |
87 |
> |
|
88 |
|
double particleRadius; |
97 |
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|
98 |
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|
89 |
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|
90 |
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Mat3x3d hmat; |
91 |
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std::vector<Vector3d> latticePos; |
92 |
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std::vector<Vector3d> latticeOrt; |
93 |
< |
int numMolPerCell; |
104 |
< |
int nShells; /* Number of shells in nanoparticle*/ |
105 |
< |
int numSites; |
106 |
< |
|
93 |
> |
|
94 |
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DumpWriter *writer; |
95 |
|
|
96 |
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// Parse Command Line Arguments |
97 |
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if (cmdline_parser(argc, argv, &args_info) != 0) |
98 |
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exit(1); |
99 |
< |
|
113 |
< |
|
114 |
< |
|
99 |
> |
|
100 |
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/* get lattice type */ |
101 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
102 |
< |
|
101 |
> |
latticeType = "FCC"; |
102 |
> |
|
103 |
|
/* get input file name */ |
104 |
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if (args_info.inputs_num) |
105 |
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inputFileName = args_info.inputs[0]; |
106 |
|
else { |
107 |
< |
std::cerr << "You must specify a input file name.\n" << std::endl; |
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 |
< |
exit(1); |
111 |
> |
simError(); |
112 |
|
} |
113 |
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|
114 |
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/* parse md file and set up the system */ |
115 |
|
SimCreator oldCreator; |
116 |
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SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
117 |
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|
131 |
– |
|
132 |
– |
/*calculate lattice constant (in Angstrom) |
133 |
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latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
134 |
– |
1.0 / 3.0);*/ |
135 |
– |
|
118 |
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latticeConstant = args_info.latticeCnst_arg; |
119 |
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particleRadius = args_info.radius_arg; |
120 |
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Globals* simParams = oldInfo->getSimParams(); |
121 |
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|
140 |
– |
/* Find out how many different components in this simualtion */ |
141 |
– |
nComponents =simParams->getNComponents(); |
142 |
– |
|
143 |
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/*determine the output file names*/ |
144 |
– |
if (args_info.output_given){ |
145 |
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outInitFileName = args_info.output_arg; |
146 |
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}else{ |
147 |
– |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
148 |
– |
} |
149 |
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|
150 |
– |
std::cout <<"Before build shaped lattice. "<<std::endl; |
151 |
– |
|
152 |
– |
/* create Molocators */ |
153 |
– |
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
154 |
– |
|
122 |
|
/* Create nanoparticle */ |
123 |
< |
shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius); |
123 |
> |
shapedLatticeSpherical nanoParticle(latticeConstant, latticeType, |
124 |
> |
particleRadius); |
125 |
|
|
158 |
– |
std::cout <<"Before build getPoints. "<<std::endl; |
126 |
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/* Build a lattice and get lattice points for this lattice constant */ |
127 |
< |
vector<Vector3d> nanoParticleSites = nanoParticle.getPoints(); |
128 |
< |
|
127 |
> |
vector<Vector3d> sites = nanoParticle.getSites(); |
128 |
> |
vector<Vector3d> orientations = nanoParticle.getOrientations(); |
129 |
> |
|
130 |
> |
std::cout <<"nSites: " << sites.size() << std::endl; |
131 |
> |
|
132 |
|
/* Get number of lattice sites */ |
133 |
< |
numSites = nanoParticleSites.size(); |
134 |
< |
|
135 |
< |
//std::cout <<"numSites are %d "<<numSites<<std::endl; |
136 |
< |
// std::cout <<"nComponents are %d "<<nComponents<<std::endl; |
137 |
< |
numMol = new int[nComponents]; |
138 |
< |
|
133 |
> |
int nSites = sites.size(); |
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 (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 |
< |
/* Random particle is the default case*/ |
151 |
< |
if (!args_info.ShellRadius_given){ |
152 |
< |
std::cout << "Creating a random nanoparticle" << std::endl; |
153 |
< |
/* Check to see if we have enough components */ |
154 |
< |
if (nComponents != args_info.molFraction_given && nComponents != 1){ |
155 |
< |
std::cerr << "Number of components does not equal molFraction occurances." << std::endl; |
156 |
< |
exit(1); |
150 |
> |
if (nComponents == 1) { |
151 |
> |
molFractions.push_back(1.0); |
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 |
< |
/* Build the mole fractions and number of molecules of each type */ |
172 |
< |
int totComponents = 0; |
173 |
< |
for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */ |
174 |
< |
numMol[i] = int((double)numSites * args_info.molFraction_arg[i]); |
175 |
< |
std::cout<<numMol[i]<<std::endl; |
176 |
< |
totComponents += numMol[i]; |
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 |
< |
numMol[nComponents-1] = numSites - totComponents; |
188 |
< |
|
189 |
< |
/* do the iPod thing, Shuffle da vector */ |
190 |
< |
std::random_shuffle(nanoParticleSites.begin(), nanoParticleSites.end()); |
191 |
< |
} else{ /*Handle core-shell with multiple components.*/ |
192 |
< |
std::cout << "Creating a core-shell nanoparticle." << std::endl; |
191 |
< |
if (nComponents != args_info.ShellRadius_given + 1){ |
192 |
< |
std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl; |
193 |
< |
exit(1); |
194 |
< |
} |
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 |
+ |
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 |
+ |
} |
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 |
|
|
295 |
< |
//get the orientation of the cell sites |
296 |
< |
//for the same type of molecule in same lattice, it will not change |
201 |
< |
latticeOrt = nanoParticle.getPointsOrt(); |
202 |
< |
std::cout<<"Orientational vector Size: "<< std::endl; |
203 |
< |
std::cout<<latticeOrt.size()<< std::endl; |
295 |
> |
outputFileName = args_info.output_arg; |
296 |
> |
|
297 |
|
|
205 |
– |
|
206 |
– |
|
207 |
– |
// needed for writing out new md file. |
208 |
– |
|
209 |
– |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
210 |
– |
outMdFileName = outPrefix + ".md"; |
211 |
– |
|
298 |
|
//creat new .md file on fly which corrects the number of molecule |
299 |
< |
createMdFile(inputFileName, outMdFileName, nComponents,numMol); |
299 |
> |
createMdFile(inputFileName, outputFileName, nMol); |
300 |
|
|
301 |
|
if (oldInfo != NULL) |
302 |
|
delete oldInfo; |
303 |
|
|
218 |
– |
|
219 |
– |
// We need to read in new siminfo object. |
220 |
– |
//parse md file and set up the system |
221 |
– |
//SimCreator NewCreator; |
304 |
|
SimCreator newCreator; |
305 |
< |
SimInfo* NewInfo = newCreator.createSim(outMdFileName, false); |
306 |
< |
|
225 |
< |
|
305 |
> |
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
306 |
> |
|
307 |
|
// Place molecules |
308 |
|
Molecule* mol; |
309 |
|
SimInfo::MoleculeIterator mi; |
310 |
|
mol = NewInfo->beginMolecule(mi); |
311 |
|
int l = 0; |
231 |
– |
for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
232 |
– |
locator->placeMol(nanoParticleSites[l], latticeOrt[l], mol); |
233 |
– |
l++; |
234 |
– |
} |
235 |
– |
|
312 |
|
|
313 |
+ |
for (int i = 0; i < nComponents; i++){ |
314 |
+ |
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
315 |
+ |
NewInfo->getForceField()); |
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 |
+ |
} |
333 |
|
|
334 |
|
//fill Hmat |
335 |
< |
hmat(0, 0)= latticeConstant; |
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) = latticeConstant; |
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) = latticeConstant; |
345 |
> |
hmat(2, 2) = 10.0*particleRadius; |
346 |
|
|
347 |
|
//set Hmat |
348 |
|
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
349 |
|
|
350 |
|
|
351 |
|
//create dumpwriter and write out the coordinates |
352 |
< |
NewInfo->setFinalConfigFileName(outInitFileName); |
258 |
< |
writer = new DumpWriter(NewInfo); |
352 |
> |
writer = new DumpWriter(NewInfo, outputFileName); |
353 |
|
|
354 |
|
if (writer == NULL) { |
355 |
< |
std::cerr << "error in creating DumpWriter" << std::endl; |
356 |
< |
exit(1); |
355 |
> |
sprintf(painCave.errMsg, "Error in creating dumpwrite object "); |
356 |
> |
painCave.isFatal = 1; |
357 |
> |
simError(); |
358 |
|
} |
359 |
|
|
360 |
|
writer->writeDump(); |
361 |
< |
std::cout << "new initial configuration file: " << outInitFileName |
362 |
< |
<< " is generated." << std::endl; |
363 |
< |
|
364 |
< |
//delete objects |
365 |
< |
|
366 |
< |
//delete oldInfo and oldSimSetup |
367 |
< |
|
368 |
< |
if (NewInfo != NULL) |
369 |
< |
delete NewInfo; |
370 |
< |
|
276 |
< |
if (writer != NULL) |
277 |
< |
delete writer; |
278 |
< |
cmdline_parser_free(&args_info); |
361 |
> |
|
362 |
> |
// deleting the writer will put the closing at the end of the dump file |
363 |
> |
|
364 |
> |
delete writer; |
365 |
> |
|
366 |
> |
// cleanup a by calling sim error..... |
367 |
> |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
368 |
> |
"generated.\n", outputFileName.c_str()); |
369 |
> |
painCave.isFatal = 0; |
370 |
> |
simError(); |
371 |
|
return 0; |
372 |
|
} |
373 |
|
|
374 |
< |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
375 |
< |
int components,int* numMol) { |
374 |
> |
void createMdFile(const std::string&oldMdFileName, |
375 |
> |
const std::string&newMdFileName, |
376 |
> |
std::vector<int> nMol) { |
377 |
|
ifstream oldMdFile; |
378 |
|
ofstream newMdFile; |
379 |
|
const int MAXLEN = 65535; |
390 |
|
|
391 |
|
//correct molecule number |
392 |
|
if (strstr(buffer, "nMol") != NULL) { |
393 |
< |
if(i<components){ |
394 |
< |
sprintf(buffer, "\tnMol = %i;", numMol[i]); |
393 |
> |
if(i<nMol.size()){ |
394 |
> |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
395 |
|
newMdFile << buffer << std::endl; |
396 |
|
i++; |
397 |
|
} |