67 |
|
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 |
|
|
72 |
|
int main(int argc, char *argv []) { |
73 |
|
|
78 |
|
gengetopt_args_info args_info; |
79 |
|
std::string latticeType; |
80 |
|
std::string inputFileName; |
81 |
< |
std::string outPrefix; |
82 |
< |
std::string outMdFileName; |
83 |
< |
std::string outInitFileName; |
81 |
> |
std::string outputFileName; |
82 |
|
|
85 |
– |
|
86 |
– |
|
83 |
|
Lattice *simpleLat; |
84 |
|
MoLocator* locator; |
85 |
|
int* numMol; |
86 |
|
int nComponents; |
87 |
|
double latticeConstant; |
88 |
|
std::vector<double> lc; |
89 |
< |
double mass; |
89 |
> |
double mass; |
90 |
|
const double rhoConvertConst = 1.661; |
91 |
|
double density; |
92 |
|
double particleRadius; |
97 |
– |
|
98 |
– |
|
93 |
|
|
94 |
|
Mat3x3d hmat; |
95 |
|
std::vector<Vector3d> latticePos; |
96 |
|
std::vector<Vector3d> latticeOrt; |
97 |
|
int numMolPerCell; |
98 |
|
int nShells; /* Number of shells in nanoparticle*/ |
99 |
< |
int numSites; |
106 |
< |
|
99 |
> |
|
100 |
|
DumpWriter *writer; |
101 |
|
|
102 |
|
// Parse Command Line Arguments |
103 |
|
if (cmdline_parser(argc, argv, &args_info) != 0) |
104 |
|
exit(1); |
105 |
< |
|
113 |
< |
|
114 |
< |
|
105 |
> |
|
106 |
|
/* get lattice type */ |
107 |
< |
latticeType = UpperCase(args_info.latticetype_arg); |
108 |
< |
|
107 |
> |
latticeType = "FCC"; |
108 |
> |
|
109 |
|
/* get input file name */ |
110 |
|
if (args_info.inputs_num) |
111 |
|
inputFileName = args_info.inputs[0]; |
112 |
|
else { |
113 |
< |
std::cerr << "You must specify a input file name.\n" << std::endl; |
113 |
> |
sprintf(painCave.errMsg, "No input .md file name was specified" |
114 |
> |
"on the command line"); |
115 |
> |
painCave.isFatal = 1; |
116 |
|
cmdline_parser_print_help(); |
117 |
< |
exit(1); |
117 |
> |
simError(); |
118 |
|
} |
119 |
|
|
120 |
|
/* parse md file and set up the system */ |
121 |
|
SimCreator oldCreator; |
122 |
|
SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
123 |
|
|
131 |
– |
|
132 |
– |
/*calculate lattice constant (in Angstrom) |
133 |
– |
latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
134 |
– |
1.0 / 3.0);*/ |
135 |
– |
|
124 |
|
latticeConstant = args_info.latticeCnst_arg; |
125 |
|
particleRadius = args_info.radius_arg; |
126 |
|
Globals* simParams = oldInfo->getSimParams(); |
127 |
|
|
140 |
– |
/* Find out how many different components in this simualtion */ |
141 |
– |
nComponents =simParams->getNComponents(); |
142 |
– |
|
143 |
– |
/*determine the output file names*/ |
144 |
– |
if (args_info.output_given){ |
145 |
– |
outInitFileName = args_info.output_arg; |
146 |
– |
}else{ |
147 |
– |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
148 |
– |
} |
149 |
– |
|
150 |
– |
std::cout <<"Before build shaped lattice. "<<std::endl; |
151 |
– |
|
152 |
– |
/* create Molocators */ |
153 |
– |
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
154 |
– |
|
128 |
|
/* Create nanoparticle */ |
129 |
< |
shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius); |
129 |
> |
shapedLatticeSpherical nanoParticle(latticeConstant, latticeType, |
130 |
> |
particleRadius); |
131 |
|
|
158 |
– |
std::cout <<"Before build getPoints. "<<std::endl; |
132 |
|
/* Build a lattice and get lattice points for this lattice constant */ |
133 |
< |
vector<Vector3d> nanoParticleSites = nanoParticle.getPoints(); |
134 |
< |
|
133 |
> |
vector<Vector3d> sites = nanoParticle.getSites(); |
134 |
> |
vector<Vector3d> orientations = nanoParticle.getOrientations(); |
135 |
> |
|
136 |
> |
std::cout <<"nSites: " << sites.size() << std::endl; |
137 |
> |
|
138 |
|
/* Get number of lattice sites */ |
139 |
< |
numSites = nanoParticleSites.size(); |
139 |
> |
int nSites = sites.size(); |
140 |
> |
|
141 |
> |
std::vector<Component*> components = simParams->getComponents(); |
142 |
> |
std::vector<RealType> molFractions; |
143 |
> |
std::vector<RealType> molecularMasses; |
144 |
> |
std::vector<int> nMol; |
145 |
> |
nComponents = components.size(); |
146 |
> |
|
147 |
> |
if (nComponents == 1) { |
148 |
> |
molFractions.push_back(1.0); |
149 |
> |
} else { |
150 |
> |
if (args_info.molFraction_given == nComponents) { |
151 |
> |
for (int i = 0; i < nComponents; i++) { |
152 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
153 |
> |
} |
154 |
> |
} else if (args_info.molFraction_given == nComponents-1) { |
155 |
> |
RealType remainingFraction = 1.0; |
156 |
> |
for (int i = 0; i < nComponents-1; i++) { |
157 |
> |
molFractions.push_back(args_info.molFraction_arg[i]); |
158 |
> |
remainingFraction -= molFractions[i]; |
159 |
> |
} |
160 |
> |
molFractions.push_back(remainingFraction); |
161 |
> |
} else { |
162 |
> |
sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions " |
163 |
> |
"for all of the components in the <MetaData> block."); |
164 |
> |
painCave.isFatal = 1; |
165 |
> |
simError(); |
166 |
> |
} |
167 |
> |
} |
168 |
|
|
169 |
< |
//std::cout <<"numSites are %d "<<numSites<<std::endl; |
166 |
< |
// std::cout <<"nComponents are %d "<<nComponents<<std::endl; |
167 |
< |
numMol = new int[nComponents]; |
169 |
> |
RealType totalFraction = 0.0; |
170 |
|
|
171 |
< |
|
172 |
< |
/* Random particle is the default case*/ |
173 |
< |
if (!args_info.ShellRadius_given){ |
174 |
< |
std::cout << "Creating a random nanoparticle" << std::endl; |
175 |
< |
/* Check to see if we have enough components */ |
176 |
< |
if (nComponents != args_info.molFraction_given && nComponents != 1){ |
177 |
< |
std::cerr << "Number of components does not equal molFraction occurances." << std::endl; |
178 |
< |
exit(1); |
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!"); |
177 |
> |
painCave.isFatal = 1; |
178 |
> |
simError(); |
179 |
|
} |
180 |
< |
/* Build the mole fractions and number of molecules of each type */ |
181 |
< |
int totComponents = 0; |
182 |
< |
for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */ |
183 |
< |
numMol[i] = int((double)numSites * args_info.molFraction_arg[i]); |
184 |
< |
std::cout<<numMol[i]<<std::endl; |
183 |
< |
totComponents += numMol[i]; |
180 |
> |
if (molFractions.at(i) > 1.0) { |
181 |
> |
sprintf(painCave.errMsg, "One of the requested molFractions was" |
182 |
> |
" greater than one!"); |
183 |
> |
painCave.isFatal = 1; |
184 |
> |
simError(); |
185 |
|
} |
186 |
< |
numMol[nComponents-1] = numSites - totComponents; |
187 |
< |
|
188 |
< |
/* do the iPod thing, Shuffle da vector */ |
189 |
< |
std::random_shuffle(nanoParticleSites.begin(), nanoParticleSites.end()); |
186 |
> |
totalFraction += molFractions.at(i); |
187 |
> |
} |
188 |
> |
if (abs(totalFraction - 1.0) > 1e-6) { |
189 |
> |
sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
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 |
< |
std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl; |
233 |
< |
exit(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 |
|
} |
237 |
|
|
238 |
|
} |
239 |
|
|
198 |
– |
|
199 |
– |
//get the orientation of the cell sites |
200 |
– |
//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; |
204 |
– |
|
240 |
|
|
206 |
– |
|
207 |
– |
// needed for writing out new md file. |
241 |
|
|
209 |
– |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
210 |
– |
outMdFileName = outPrefix + ".md"; |
242 |
|
|
243 |
< |
//creat new .md file on fly which corrects the number of molecule |
244 |
< |
createMdFile(inputFileName, outMdFileName, nComponents,numMol); |
243 |
> |
outputFileName = args_info.output_arg; |
244 |
> |
|
245 |
|
|
246 |
+ |
//creat new .md file on fly which corrects the number of molecule |
247 |
+ |
createMdFile(inputFileName, outputFileName, nMol); |
248 |
+ |
|
249 |
|
if (oldInfo != NULL) |
250 |
|
delete oldInfo; |
251 |
|
|
253 |
|
// We need to read in new siminfo object. |
254 |
|
//parse md file and set up the system |
255 |
|
//SimCreator NewCreator; |
256 |
< |
SimCreator newCreator; |
257 |
< |
SimInfo* NewInfo = newCreator.createSim(outMdFileName, false); |
256 |
> |
SimCreator newCreator; |
257 |
> |
SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
258 |
|
|
259 |
|
|
260 |
|
// Place molecules |
261 |
|
Molecule* mol; |
262 |
|
SimInfo::MoleculeIterator mi; |
263 |
|
mol = NewInfo->beginMolecule(mi); |
264 |
< |
int l = 0; |
265 |
< |
for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
266 |
< |
locator->placeMol(nanoParticleSites[l], latticeOrt[l], mol); |
267 |
< |
l++; |
264 |
> |
int l = 0; |
265 |
> |
|
266 |
> |
for (int i = 0; i < nComponents; i++){ |
267 |
> |
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
268 |
> |
NewInfo->getForceField()); |
269 |
> |
for (int n = 0; n < nMol.at(i); n++) { |
270 |
> |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
271 |
> |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
272 |
> |
l++; |
273 |
> |
} |
274 |
|
} |
275 |
< |
|
275 |
> |
|
276 |
|
|
237 |
– |
|
277 |
|
|
278 |
|
//fill Hmat |
279 |
< |
hmat(0, 0)= latticeConstant; |
279 |
> |
hmat(0, 0)= 2.0*particleRadius; |
280 |
|
hmat(0, 1) = 0.0; |
281 |
|
hmat(0, 2) = 0.0; |
282 |
|
|
283 |
|
hmat(1, 0) = 0.0; |
284 |
< |
hmat(1, 1) = latticeConstant; |
284 |
> |
hmat(1, 1) = 2.0*particleRadius; |
285 |
|
hmat(1, 2) = 0.0; |
286 |
|
|
287 |
|
hmat(2, 0) = 0.0; |
288 |
|
hmat(2, 1) = 0.0; |
289 |
< |
hmat(2, 2) = latticeConstant; |
289 |
> |
hmat(2, 2) = 2.0*particleRadius; |
290 |
|
|
291 |
|
//set Hmat |
292 |
|
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
293 |
|
|
294 |
|
|
295 |
|
//create dumpwriter and write out the coordinates |
296 |
< |
NewInfo->setFinalConfigFileName(outInitFileName); |
258 |
< |
writer = new DumpWriter(NewInfo); |
296 |
> |
writer = new DumpWriter(NewInfo, outputFileName); |
297 |
|
|
298 |
|
if (writer == NULL) { |
299 |
< |
std::cerr << "error in creating DumpWriter" << std::endl; |
300 |
< |
exit(1); |
299 |
> |
sprintf(painCave.errMsg, "Error in creating dumpwrite object "); |
300 |
> |
painCave.isFatal = 1; |
301 |
> |
simError(); |
302 |
|
} |
303 |
|
|
304 |
|
writer->writeDump(); |
305 |
< |
std::cout << "new initial configuration file: " << outInitFileName |
306 |
< |
<< " is generated." << std::endl; |
307 |
< |
|
308 |
< |
//delete objects |
309 |
< |
|
310 |
< |
//delete oldInfo and oldSimSetup |
311 |
< |
|
312 |
< |
if (NewInfo != NULL) |
313 |
< |
delete NewInfo; |
314 |
< |
|
276 |
< |
if (writer != NULL) |
277 |
< |
delete writer; |
278 |
< |
cmdline_parser_free(&args_info); |
305 |
> |
|
306 |
> |
// deleting the writer will put the closing at the end of the dump file |
307 |
> |
|
308 |
> |
delete writer; |
309 |
> |
|
310 |
> |
// cleanup a by calling sim error..... |
311 |
> |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
312 |
> |
"generated.\n", outputFileName.c_str()); |
313 |
> |
painCave.isFatal = 0; |
314 |
> |
simError(); |
315 |
|
return 0; |
316 |
|
} |
317 |
|
|
318 |
|
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
319 |
< |
int components,int* numMol) { |
319 |
> |
std::vector<int> nMol) { |
320 |
|
ifstream oldMdFile; |
321 |
|
ofstream newMdFile; |
322 |
|
const int MAXLEN = 65535; |
333 |
|
|
334 |
|
//correct molecule number |
335 |
|
if (strstr(buffer, "nMol") != NULL) { |
336 |
< |
if(i<components){ |
337 |
< |
sprintf(buffer, "\tnMol = %i;", numMol[i]); |
338 |
< |
newMdFile << buffer << std::endl; |
339 |
< |
i++; |
340 |
< |
} |
336 |
> |
if(i<nMol.size()){ |
337 |
> |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
338 |
> |
newMdFile << buffer << std::endl; |
339 |
> |
i++; |
340 |
> |
} |
341 |
|
} else |
342 |
|
newMdFile << buffer << std::endl; |
343 |
|
|