29 |
|
string inputFileName; |
30 |
|
string outPrefix; |
31 |
|
string outMdFileName; |
32 |
– |
string outInitFileName; |
32 |
|
SimInfo* oldInfo; |
34 |
– |
SimInfo* newInfo; |
33 |
|
SimSetup* oldSimSetup; |
36 |
– |
SimSetup* newSimSetup; |
34 |
|
BaseLattice* simpleLat; |
35 |
|
int numMol; |
36 |
|
double latticeConstant; |
113 |
|
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
114 |
|
|
115 |
|
outMdFileName = outPrefix + ".md"; |
119 |
– |
outInitFileName = outPrefix + ".in"; |
116 |
|
|
117 |
|
//parse md file and set up the system |
118 |
|
oldInfo = new SimInfo; |
126 |
|
cerr << "error in creating SimSetup" << endl; |
127 |
|
exit(1); |
128 |
|
} |
129 |
< |
|
129 |
> |
|
130 |
> |
oldSimSetup->suspendInit(); |
131 |
|
oldSimSetup->setSimInfo(oldInfo ); |
132 |
|
oldSimSetup->parseFile(&inputFileName[0] ); |
133 |
|
oldSimSetup->createSim(); |
134 |
+ |
|
135 |
|
if(oldInfo->nComponents >=2){ |
136 |
|
cerr << "can not build the system with more than two components" << endl; |
137 |
|
exit(1); |
138 |
|
} |
141 |
– |
|
139 |
|
|
140 |
|
//get mass of molecule. |
141 |
|
//Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass |
158 |
|
simpleLat->setLatticeConstant(lc); |
159 |
|
|
160 |
|
//calculate the total number of molecules |
161 |
< |
numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell; |
165 |
< |
|
166 |
< |
//creat new .md file on fly |
167 |
< |
createMdFile(inputFileName, outMdFileName, numMol); |
161 |
> |
numMol = nx * ny * nz * numMolPerCell; |
162 |
|
|
163 |
< |
//parse new .md file and set up the system |
164 |
< |
newInfo = new SimInfo; |
165 |
< |
if(newInfo == NULL){ |
166 |
< |
cerr << "error in creating SimInfo" << endl; |
167 |
< |
exit(1); |
163 |
> |
if (oldInfo->n_mol != numMol){ |
164 |
> |
//creat new .md file on fly which corrects the number of molecule |
165 |
> |
createMdFile(inputFileName, outMdFileName, numMol); |
166 |
> |
cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl; |
167 |
> |
cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl; |
168 |
> |
exit(1); |
169 |
|
} |
175 |
– |
|
176 |
– |
newSimSetup = new SimSetup(); |
177 |
– |
if(newSimSetup == NULL){ |
178 |
– |
cerr << "error in creating SimSetup" << endl; |
179 |
– |
exit(1); |
180 |
– |
} |
181 |
– |
|
182 |
– |
newSimSetup->setSimInfo(newInfo ); |
183 |
– |
newSimSetup->parseFile(&outMdFileName[0] ); |
184 |
– |
newSimSetup->createSim(); |
170 |
|
|
171 |
|
//allocat memory for storing pos, vel and etc |
172 |
< |
newInfo->getConfiguration()->createArrays(newInfo->n_atoms); |
173 |
< |
for (int i = 0; i < newInfo->n_atoms; i++) |
174 |
< |
newInfo->atoms[i]->setCoords(); |
172 |
> |
oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms); |
173 |
> |
for (int i = 0; i < oldInfo->n_atoms; i++) |
174 |
> |
oldInfo->atoms[i]->setCoords(); |
175 |
|
|
176 |
|
//creat Molocator |
177 |
< |
locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField()); |
177 |
> |
locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField()); |
178 |
|
|
179 |
|
//fill Hmat |
180 |
|
Hmat[0][0] = nx * latticeConstant; |
181 |
|
Hmat[0][1] = 0.0; |
182 |
|
Hmat[0][2] = 0.0; |
183 |
|
|
184 |
< |
Hmat[1][0] = ny * latticeConstant; |
185 |
< |
Hmat[1][1] = 0.0; |
184 |
> |
Hmat[1][0] = 0.0; |
185 |
> |
Hmat[1][1] = ny * latticeConstant; |
186 |
|
Hmat[1][2] = 0.0; |
187 |
|
|
188 |
< |
Hmat[2][0] = nz * latticeConstant; |
188 |
> |
Hmat[2][0] = 0.0; |
189 |
|
Hmat[2][1] = 0.0; |
190 |
< |
Hmat[2][2] = 0.0; |
190 |
> |
Hmat[2][2] = nz * latticeConstant ; |
191 |
|
|
192 |
|
//set Hmat |
193 |
< |
newInfo->setBoxM(Hmat); |
193 |
> |
oldInfo->setBoxM(Hmat); |
194 |
|
|
195 |
|
//place the molecules |
196 |
|
|
208 |
|
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
209 |
|
|
210 |
|
for(int l = 0; l < numMolPerCell; l++) |
211 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], &(newInfo->molecules[curMolIndex++])); |
211 |
> |
locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++])); |
212 |
|
} |
213 |
|
} |
214 |
|
} |
215 |
|
|
216 |
|
//create dumpwriter and write out the coordinates |
217 |
< |
writer = new DumpWriter( newInfo ); |
217 |
> |
writer = new DumpWriter( oldInfo ); |
218 |
|
if(writer == NULL){ |
219 |
|
cerr << "error in creating DumpWriter" << endl; |
220 |
|
exit(1); |
222 |
|
writer->writeFinal(0); |
223 |
|
|
224 |
|
//delete objects |
225 |
< |
if(!oldInfo) |
225 |
> |
|
226 |
> |
//delete oldInfo and oldSimSetup |
227 |
> |
if(oldInfo != NULL) |
228 |
|
delete oldInfo; |
229 |
|
|
230 |
< |
if(!oldSimSetup) |
231 |
< |
delete oldSimSetup; |
245 |
< |
|
246 |
< |
if(!newInfo) |
247 |
< |
delete newInfo; |
230 |
> |
if(oldSimSetup != NULL) |
231 |
> |
delete oldSimSetup; |
232 |
|
|
249 |
– |
if(!newSimSetup) |
250 |
– |
delete newSimSetup; |
251 |
– |
|
233 |
|
if (writer != NULL) |
234 |
|
delete writer; |
235 |
|
return 0; |
240 |
|
ofstream newMdFile; |
241 |
|
const int MAXLEN = 65535; |
242 |
|
char buffer[MAXLEN]; |
262 |
– |
string line; |
243 |
|
|
244 |
|
//create new .md file based on old .md file |
245 |
|
oldMdFile.open(oldMdFileName.c_str()); |
248 |
|
oldMdFile.getline(buffer, MAXLEN); |
249 |
|
while(!oldMdFile.eof()){ |
250 |
|
|
251 |
< |
if(line.find("nMol") < line.size()){ |
252 |
< |
|
251 |
> |
//correct molecule number |
252 |
> |
if(strstr(buffer, "nMol") !=NULL){ |
253 |
|
sprintf(buffer, "\t\tnMol = %d;", numMol); |
254 |
|
newMdFile << buffer << endl; |
255 |
|
} |