32 |
|
*/ |
33 |
|
|
34 |
|
#include "brains/SimCreator.hpp" |
35 |
+ |
|
36 |
|
namespace oopse { |
37 |
|
|
38 |
< |
void SimSetup::parseFile(char* mdfile, MakeStamps* stamps, Globals* globals){ |
38 |
> |
void SimSetup::parseFile(const std::string& mdFileName, MakeStamps *stamps, Globals *globals) { |
39 |
> |
|
40 |
|
#ifdef IS_MPI |
41 |
< |
if (worldRank == 0){ |
41 |
> |
|
42 |
> |
if (worldRank == 0) { |
43 |
|
#endif // is_mpi |
44 |
|
|
45 |
+ |
globals->initalize(); |
46 |
+ |
set_interface_stamps(stamps, globals); |
47 |
|
|
43 |
– |
globals->initalize(); |
44 |
– |
set_interface_stamps(stamps, globals); |
45 |
– |
|
48 |
|
#ifdef IS_MPI |
49 |
< |
mpiEventInit(); |
49 |
> |
|
50 |
> |
mpiEventInit(); |
51 |
> |
|
52 |
|
#endif |
53 |
|
|
54 |
< |
yacc_BASS(mdfile); |
54 |
> |
yacc_BASS(mdFileName.c_str()); |
55 |
|
|
56 |
|
#ifdef IS_MPI |
57 |
< |
throwMPIEvent(NULL); |
58 |
< |
} |
59 |
< |
else{ |
60 |
< |
set_interface_stamps(stamps, globals); |
61 |
< |
mpiEventInit(); |
62 |
< |
MPIcheckPoint(); |
63 |
< |
mpiEventLoop(); |
64 |
< |
} |
57 |
> |
|
58 |
> |
throwMPIEvent(NULL); |
59 |
> |
} else { |
60 |
> |
set_interface_stamps(stamps, globals); |
61 |
> |
mpiEventInit(); |
62 |
> |
MPIcheckPoint(); |
63 |
> |
mpiEventLoop(); |
64 |
> |
} |
65 |
> |
|
66 |
|
#endif |
67 |
|
|
68 |
|
} |
69 |
|
|
70 |
+ |
SimInfo* SimCreator::createSim(const std::string & mdFileName) { |
71 |
|
|
72 |
< |
SimInfo* SimCreator::createSim(const std::string& mdfile) { |
67 |
< |
MakeStamps* stamps = new MakeStamps(); |
72 |
> |
mdFileName_ = mdFileName; |
73 |
|
|
74 |
< |
Globals* globals = new Globals(); |
74 |
> |
MakeStamps * stamps = new MakeStamps(); |
75 |
|
|
76 |
+ |
Globals * globals = new Globals(); |
77 |
+ |
|
78 |
|
//parse meta-data file |
79 |
< |
parseFile(mdfile, stamps, globals); |
79 |
> |
parseFile(mdFileName_, stamps, globals); |
80 |
|
|
81 |
|
//create the force field |
82 |
< |
ForceFiled* ff = ForceFieldFactory::getInstance()->createObject(globals->getForceField()); |
83 |
< |
|
82 |
> |
ForceFiled * ff = ForceFieldFactory::getInstance()->createObject( |
83 |
> |
globals->getForceField()); |
84 |
> |
|
85 |
> |
if (ff == NULL) { |
86 |
> |
sprintf(painCave.errMsg, "ForceFiled Factory can not create %s force field\n", |
87 |
> |
globals->getForceField()); |
88 |
> |
painCave.isFatal = 1; |
89 |
> |
simError(); |
90 |
> |
} |
91 |
> |
|
92 |
> |
//extract the molecule stamps |
93 |
> |
std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs; |
94 |
> |
compList(stamps, globals, moleculeStampPairs); |
95 |
> |
|
96 |
|
//create SimInfo |
97 |
< |
SimInfo* info = new SimInfo(); |
79 |
< |
info->setGlobals(globals); |
80 |
< |
info->setForceField(ff); |
97 |
> |
SimInfo * info = new SimInfo(moleculeStampPairs, ff, globals); |
98 |
|
|
99 |
< |
//extract the molecule stamps and add them into SimInfo |
83 |
< |
compList(stamps, info); |
84 |
< |
|
85 |
< |
//gather parameters (SimCreator only retrieves the parameters which will be used to create |
86 |
< |
// the simulation) |
99 |
> |
//gather parameters (SimCreator only retrieves part of the parameters) |
100 |
|
gatherParameters(info); |
101 |
< |
|
101 |
> |
|
102 |
|
//divide the molecules and determine the global index of molecules |
103 |
< |
|
103 |
> |
divideMolecules(info); |
104 |
> |
|
105 |
|
//create the molecules |
106 |
|
createMolecules(info); |
107 |
|
|
108 |
|
//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the |
109 |
|
//global index will never change again). Local indices of atoms and rigidbodies are already set by |
110 |
< |
//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
110 |
> |
//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
111 |
|
setGlobalIndices(info); |
112 |
< |
|
112 |
> |
|
113 |
|
//allocate memory for DataStorage(circular reference, need to break it) |
114 |
< |
info->setSnapshotManager(new SimSnapshotManager(info); |
101 |
< |
|
102 |
< |
//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
103 |
< |
//eta, chi for NPT integrator) |
104 |
< |
DumpReader reader(info->getInitFilename()); |
105 |
< |
int nframes = reader->getNframes(); |
114 |
> |
info->setSnapshotManager(new SimSnapshotManager(info)); |
115 |
|
|
116 |
< |
if (nframes > 0) { |
117 |
< |
reader.readFrame(info, nframes - 1); |
109 |
< |
} else { |
110 |
< |
//invalid initial coordinate file |
111 |
< |
|
112 |
< |
} |
116 |
> |
//initialize fortran -- setup the cutoff |
117 |
> |
initFortran(info); |
118 |
|
|
119 |
< |
|
120 |
< |
//initialize fortran |
121 |
< |
|
119 |
> |
//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
120 |
> |
//eta, chi for NPT integrator) |
121 |
> |
loadCoordinates(info); |
122 |
|
return info; |
123 |
< |
} |
123 |
> |
} |
124 |
|
|
125 |
< |
void SimCreator::gatherParameters(SimInfo* info) { |
121 |
< |
//model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled())); |
122 |
< |
//model->addProperty(new DoubleGenericData("dt"), globals->getDt()); |
125 |
> |
void SimCreator::gatherParameters(SimInfo *info) { |
126 |
|
|
127 |
|
//setup seed for random number generator |
128 |
|
int seedValue; |
129 |
< |
Globals* globals = info->getGlobals(); |
130 |
< |
|
131 |
< |
if (globals->haveSeed()){ |
129 |
> |
Globals * globals = info->getGlobals(); |
130 |
> |
|
131 |
> |
if (globals->haveSeed()) { |
132 |
|
seedValue = globals->getSeed(); |
133 |
|
|
134 |
< |
if(seedValue / 1000000000 == 0){ |
134 |
> |
if (seedValue / 1000000000 == 0) { |
135 |
|
sprintf(painCave.errMsg, |
136 |
< |
"Seed for sprng library should contain at least 9 digits\n" |
137 |
< |
"OOPSE will generate a seed for user\n"); |
136 |
> |
"Seed for sprng library should contain at least 9 digits\n" |
137 |
> |
"OOPSE will generate a seed for user\n"); |
138 |
> |
|
139 |
|
painCave.isFatal = 0; |
140 |
|
simError(); |
141 |
|
|
142 |
< |
//using seed generated by system instead of invalid seed set by user |
142 |
> |
//using seed generated by system instead of invalid seed set by user |
143 |
> |
|
144 |
|
#ifndef IS_MPI |
145 |
+ |
|
146 |
|
seedValue = make_sprng_seed(); |
147 |
< |
#else |
148 |
< |
if (worldRank == 0){ |
147 |
> |
|
148 |
> |
#else |
149 |
> |
|
150 |
> |
if (worldRank == 0) { |
151 |
|
seedValue = make_sprng_seed(); |
152 |
|
} |
153 |
< |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
154 |
< |
#endif |
153 |
> |
|
154 |
> |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
155 |
> |
|
156 |
> |
#endif |
157 |
> |
|
158 |
|
} //end if (seedValue /1000000000 == 0) |
159 |
< |
} else{ |
160 |
< |
|
159 |
> |
} else { |
160 |
> |
|
161 |
|
#ifndef IS_MPI |
162 |
+ |
|
163 |
|
seedValue = make_sprng_seed(); |
164 |
< |
#else |
165 |
< |
if (worldRank == 0){ |
164 |
> |
|
165 |
> |
#else |
166 |
> |
|
167 |
> |
if (worldRank == 0) { |
168 |
|
seedValue = make_sprng_seed(); |
169 |
|
} |
170 |
< |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
170 |
> |
|
171 |
> |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
172 |
> |
|
173 |
|
#endif |
174 |
< |
}//end of globals->haveSeed() |
174 |
> |
|
175 |
> |
} //end of globals->haveSeed() |
176 |
> |
|
177 |
|
info->setSeed(seedValue); |
178 |
|
|
179 |
< |
// |
179 |
> |
|
180 |
> |
//figure out the ouput file names |
181 |
|
std::string prefix; |
182 |
+ |
|
183 |
|
#ifdef IS_MPI |
184 |
< |
if (worldRank == 0){ |
184 |
> |
|
185 |
> |
if (worldRank == 0) { |
186 |
|
#endif // is_mpi |
187 |
< |
|
188 |
< |
if(globals->haveFinalConfig()) { |
189 |
< |
prefix = getPrefix(globals->getFinalConfig()); |
187 |
> |
|
188 |
> |
if (globals->haveFinalConfig()) { |
189 |
> |
prefix = StringUtils::getPrefix(globals->getFinalConfig()); |
190 |
|
} else { |
191 |
< |
prefix = getPrefix(mdfile_); |
191 |
> |
prefix = StringUtils::getPrefix(mdfile_); |
192 |
|
} |
193 |
< |
|
194 |
< |
info->setFinalConfFileName(prefix + ".eor"); |
193 |
> |
|
194 |
> |
info->setFinalConfigFileName(prefix + ".eor"); |
195 |
|
info->setDumpFileName(prefix + ".dump"); |
196 |
|
info->setStatFileName(prefix + ".stat"); |
197 |
|
|
198 |
|
#ifdef IS_MPI |
199 |
+ |
|
200 |
|
} |
179 |
– |
#endif |
201 |
|
|
202 |
+ |
#endif |
203 |
|
|
182 |
– |
|
204 |
|
} |
205 |
|
|
206 |
|
#ifdef IS_MPI |
186 |
– |
void SimCreator::divideMolecules(SimInfo* info){ |
187 |
– |
int nComponents; |
188 |
– |
MoleculeStamp ** compStamps; |
189 |
– |
randomSPRNG * myRandom; |
190 |
– |
int * componentsNmol; |
191 |
– |
int * AtomsPerProc; |
207 |
|
|
208 |
+ |
void SimCreator::divideMolecules(SimInfo *info) { |
209 |
|
double numerator; |
210 |
|
double denominator; |
211 |
|
double precast; |
215 |
|
int old_atoms; |
216 |
|
int add_atoms; |
217 |
|
int new_atoms; |
202 |
– |
|
218 |
|
int nTarget; |
204 |
– |
int molIndex; |
205 |
– |
int atomIndex; |
219 |
|
int done; |
220 |
|
int i; |
221 |
|
int j; |
222 |
|
int loops; |
223 |
|
int which_proc; |
224 |
< |
int nmol_global, |
225 |
< |
nmol_local; |
226 |
< |
int natoms_global, |
224 |
> |
int nProcessors; |
225 |
> |
int nGlobalMols; |
226 |
> |
std::vector < int > atomsPerProc; |
227 |
> |
randomSPRNG myRandom(info->getSeed()); |
228 |
> |
int * molToProcMap = info->getMolToProcMapPointer(); |
229 |
|
|
230 |
< |
int baseSeed = info->getSeed(); |
231 |
< |
CutoffGroupStamp * cg; |
230 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
231 |
> |
nGlobalMols = info->getNGlobalMolecules(); |
232 |
|
|
233 |
< |
nComponents = info->nComponents; |
219 |
< |
compStamps = info->compStamps; |
220 |
< |
componentsNmol = info->componentsNmol; |
221 |
< |
AtomsPerProc = new int[parallelData->nProcessors]; |
222 |
< |
|
223 |
< |
parallelData->nMolGlobal = info->n_mol; |
224 |
< |
|
225 |
< |
if (parallelData->nProcessors > parallelData->nMolGlobal) { |
233 |
> |
if (nProcessors > nGlobalMols) { |
234 |
|
sprintf(painCave.errMsg, |
235 |
|
"nProcessors (%d) > nMol (%d)\n" |
236 |
|
"\tThe number of processors is larger than\n" |
237 |
|
"\tthe number of molecules. This will not result in a \n" |
238 |
|
"\tusable division of atoms for force decomposition.\n" |
239 |
|
"\tEither try a smaller number of processors, or run the\n" |
240 |
< |
"\tsingle-processor version of OOPSE.\n", |
233 |
< |
parallelData->nProcessors, |
234 |
< |
parallelData->nMolGlobal); |
240 |
> |
"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
241 |
|
|
242 |
|
painCave.isFatal = 1; |
243 |
|
simError(); |
244 |
|
} |
245 |
|
|
246 |
< |
myRandom = new randomSPRNG(baseSeed); |
246 |
> |
a = 3.0 * nGlobalMols / info->getNGlobalAtoms(); |
247 |
|
|
248 |
< |
a = 3.0 * parallelData->nMolGlobal / parallelData->nAtomsGlobal; |
248 |
> |
//initialize atomsPerProc |
249 |
> |
atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
250 |
|
|
251 |
< |
// Initialize things that we'll send out later: |
245 |
< |
for( i = 0; i < parallelData->nProcessors; i++ ) { |
246 |
< |
AtomsPerProc[i] = 0; |
247 |
< |
} |
248 |
< |
|
249 |
< |
for( i = 0; i < parallelData->nMolGlobal; i++ ) { |
251 |
> |
for(i = 0; i < nGlobalMols; i++) { |
252 |
|
// default to an error condition: |
253 |
< |
MolToProcMap[i] = -1; |
253 |
> |
molToProcMap[i] = -1; |
254 |
|
} |
255 |
|
|
256 |
< |
if (parallelData->myNode == 0) { |
257 |
< |
numerator = info->n_atoms; |
258 |
< |
denominator = parallelData->nProcessors; |
256 |
> |
if (worldRank == 0) { |
257 |
> |
numerator = info->getNGlobalAtoms(); |
258 |
> |
denominator = nProcessors; |
259 |
|
precast = numerator / denominator; |
260 |
|
nTarget = (int)(precast + 0.5); |
261 |
|
|
262 |
< |
// Build the array of molecule component types first |
261 |
< |
molIndex = 0; |
262 |
< |
|
263 |
< |
for( i = 0; i < nComponents; i++ ) { |
264 |
< |
for( j = 0; j < componentsNmol[i]; j++ ) { |
265 |
< |
molIndex++; |
266 |
< |
} |
267 |
< |
} |
268 |
< |
|
269 |
< |
for( i = 0; i < molIndex; i++ ) { |
262 |
> |
for(i = 0; i < nGlobalMols; i++) { |
263 |
|
done = 0; |
264 |
|
loops = 0; |
265 |
|
|
268 |
|
|
269 |
|
// Pick a processor at random |
270 |
|
|
271 |
< |
which_proc |
271 |
> |
which_proc = (int) (myRandom.getRandom() * nProcessors); |
272 |
|
|
273 |
< |
= (int) (myRandom->getRandom() * parallelData->nProcessors); |
273 |
> |
//get the molecule stamp first |
274 |
> |
int stampId = info->getMoleculeStampId(i); |
275 |
> |
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
276 |
|
|
277 |
< |
// How many atoms does this processor have? |
278 |
< |
|
279 |
< |
old_atoms = AtomsPerProc[which_proc]; |
285 |
< |
add_atoms = compStamps[MolComponentType[i]]->getNAtoms(); |
277 |
> |
// How many atoms does this processor have so far? |
278 |
> |
old_atoms = atomsPerProc[which_proc]; |
279 |
> |
add_atoms = moleculeStamp->getNAtoms(); |
280 |
|
new_atoms = old_atoms + add_atoms; |
281 |
|
|
282 |
|
// If we've been through this loop too many times, we need |
284 |
|
// and be done with it. |
285 |
|
|
286 |
|
if (loops > 100) { |
287 |
< |
sprintf( |
288 |
< |
painCave.errMsg, |
289 |
< |
"I've tried 100 times to assign molecule %d to a " |
290 |
< |
" processor, but can't find a good spot.\n" |
291 |
< |
"I'm assigning it at random to processor %d.\n", |
298 |
< |
i, |
299 |
< |
which_proc); |
287 |
> |
sprintf(painCave.errMsg, |
288 |
> |
"I've tried 100 times to assign molecule %d to a " |
289 |
> |
" processor, but can't find a good spot.\n" |
290 |
> |
"I'm assigning it at random to processor %d.\n", |
291 |
> |
i, which_proc); |
292 |
|
|
293 |
|
painCave.isFatal = 0; |
294 |
|
simError(); |
295 |
|
|
296 |
< |
MolToProcMap[i] = which_proc; |
297 |
< |
AtomsPerProc[which_proc] += add_atoms; |
296 |
> |
molToProcMap[i] = which_proc; |
297 |
> |
atomsPerProc[which_proc] += add_atoms; |
298 |
|
|
299 |
|
done = 1; |
300 |
|
continue; |
304 |
|
// it above nTarget, then go ahead and do it: |
305 |
|
|
306 |
|
if (new_atoms <= nTarget) { |
307 |
< |
MolToProcMap[i] = which_proc; |
308 |
< |
AtomsPerProc[which_proc] += add_atoms; |
307 |
> |
molToProcMap[i] = which_proc; |
308 |
> |
atomsPerProc[which_proc] += add_atoms; |
309 |
|
|
310 |
|
done = 1; |
311 |
|
continue; |
320 |
|
// where a = penalty / (average atoms per molecule) |
321 |
|
|
322 |
|
x = (double)(new_atoms - nTarget); |
323 |
< |
y = myRandom->getRandom(); |
323 |
> |
y = myRandom.getRandom(); |
324 |
|
|
325 |
|
if (y < exp(- a * x)) { |
326 |
< |
MolToProcMap[i] = which_proc; |
327 |
< |
AtomsPerProc[which_proc] += add_atoms; |
326 |
> |
molToProcMap[i] = which_proc; |
327 |
> |
atomsPerProc[which_proc] += add_atoms; |
328 |
|
|
329 |
|
done = 1; |
330 |
|
continue; |
331 |
< |
} else { continue; } |
331 |
> |
} else { |
332 |
> |
continue; |
333 |
> |
} |
334 |
|
} |
335 |
|
} |
336 |
|
|
337 |
|
// Spray out this nonsense to all other processors: |
338 |
|
|
339 |
< |
MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, MPI_INT, 0, |
346 |
< |
MPI_COMM_WORLD); |
339 |
> |
MPI_Bcast(molToProcMap, nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
340 |
|
} else { |
341 |
|
|
342 |
< |
// Listen to your marching orders from processor 0: |
342 |
> |
// Listen to your marching orders from processor 0: |
343 |
|
|
344 |
< |
MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, MPI_INT, 0, |
352 |
< |
MPI_COMM_WORLD); } |
353 |
< |
|
354 |
< |
// Let's all check for sanity: |
355 |
< |
|
356 |
< |
nmol_local = 0; |
357 |
< |
|
358 |
< |
for( i = 0; i < parallelData->nMolGlobal; i++ ) { |
359 |
< |
if (MolToProcMap[i] == parallelData->myNode) { |
360 |
< |
nmol_local++; |
361 |
< |
} |
344 |
> |
MPI_Bcast(molToProcMap, nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
345 |
|
} |
346 |
|
|
364 |
– |
MPI_Allreduce(&nmol_local, &nmol_global, 1, MPI_INT, MPI_SUM, |
365 |
– |
MPI_COMM_WORLD); |
366 |
– |
|
367 |
– |
if (nmol_global != info->n_mol) { |
368 |
– |
sprintf(painCave.errMsg, |
369 |
– |
"The sum of all nmol_local, %d, did not equal the " |
370 |
– |
"total number of molecules, %d.\n", |
371 |
– |
nmol_global, |
372 |
– |
info->n_mol); |
373 |
– |
|
374 |
– |
painCave.isFatal = 1; |
375 |
– |
simError(); |
376 |
– |
} |
377 |
– |
|
347 |
|
sprintf(checkPointMsg, |
348 |
|
"Successfully divided the molecules among the processors.\n"); |
349 |
|
MPIcheckPoint(); |
381 |
– |
|
350 |
|
} |
351 |
+ |
|
352 |
|
#endif |
353 |
|
|
354 |
< |
Molecule* SimCreator::createMolecules(SimInfo* info) { |
354 |
> |
void SimCreator::createMolecules(SimInfo *info) { |
355 |
|
MoleculeCreator molCreator; |
356 |
|
int stampId; |
357 |
|
|
358 |
< |
|
390 |
< |
for (int i = 0; i < info->getNGlobalMolecules(); i++){ |
391 |
< |
if (info->getMolToProc(i) == worldRank){ |
358 |
> |
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
359 |
|
|
360 |
+ |
#ifdef IS_MPI |
361 |
+ |
|
362 |
+ |
if (info->getMolToProc(i) == worldRank) { |
363 |
+ |
#endif |
364 |
+ |
|
365 |
|
stampId = info->getMoleculeStampId(i); |
366 |
< |
Molecule* mol = molCreator.createMolecule(info->getForceField(), |
367 |
< |
info->getMoleculeStamp(stampId), stampId, i); |
368 |
< |
|
366 |
> |
Molecule * mol = molCreator.createMolecule(info->getForceField(), |
367 |
> |
info->getMoleculeStamp(stampId), stampId, i); |
368 |
> |
|
369 |
|
info->addMolecule(mol); |
370 |
+ |
|
371 |
+ |
#ifdef IS_MPI |
372 |
+ |
|
373 |
|
} |
374 |
< |
} |
375 |
< |
|
374 |
> |
|
375 |
> |
#endif |
376 |
> |
|
377 |
> |
} //end for(int i=0) |
378 |
|
} |
379 |
|
|
380 |
< |
void SimSetup::compList(MakeStamps* stamps,SimInfo* info) { |
380 |
> |
void SimSetup::compList(MakeStamps *stamps, Globals* globals, |
381 |
> |
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
382 |
|
int i; |
383 |
< |
char* id; |
384 |
< |
MoleculeStamp* currentStamp; |
385 |
< |
Component* the_components = info->getGlobals()->getComponents(); |
386 |
< |
int n_components = info->getGlobals()->getNComponents(); |
383 |
> |
char * id; |
384 |
> |
MoleculeStamp * currentStamp; |
385 |
> |
Component * the_components = globals->getComponents(); |
386 |
> |
int n_components = globals->getNComponents(); |
387 |
|
|
388 |
< |
if (!globals->haveNMol()){ |
388 |
> |
if (!globals->haveNMol()) { |
389 |
|
// we don't have the total number of molecules, so we assume it is |
390 |
|
// given in each component |
391 |
|
|
392 |
< |
for (i = 0; i < n_components; i++){ |
393 |
< |
if (!the_components[i]->haveNMol()){ |
392 |
> |
for(i = 0; i < n_components; i++) { |
393 |
> |
if (!the_components[i]->haveNMol()) { |
394 |
|
// we have a problem |
395 |
|
sprintf(painCave.errMsg, |
396 |
< |
"SimSetup Error. No global NMol or component NMol given.\n" |
397 |
< |
"\tCannot calculate the number of atoms.\n"); |
396 |
> |
"SimSetup Error. No global NMol or component NMol given.\n" |
397 |
> |
"\tCannot calculate the number of atoms.\n"); |
398 |
> |
|
399 |
|
painCave.isFatal = 1; |
400 |
|
simError(); |
401 |
|
} |
402 |
|
|
403 |
|
id = the_components[i]->getType(); |
404 |
|
currentStamp = stamps->extractMolStamp(id); |
405 |
< |
if (currentStamp == NULL){ |
405 |
> |
|
406 |
> |
if (currentStamp == NULL) { |
407 |
|
sprintf(painCave.errMsg, |
408 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
409 |
< |
"list of declared molecules\n", |
410 |
< |
id); |
408 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
409 |
> |
"list of declared molecules\n", id); |
410 |
> |
|
411 |
|
painCave.isFatal = 1; |
412 |
|
simError(); |
413 |
< |
} |
413 |
> |
} |
414 |
|
|
415 |
< |
info->addMoleculeStamp(currentStamp, the_components[i]->getNMol); |
416 |
< |
|
415 |
> |
moleculeStampPairs.push_back( |
416 |
> |
make_pair(currentStamp, the_components[i]->getNMol)); |
417 |
|
} //end for (i = 0; i < n_components; i++) |
418 |
< |
|
419 |
< |
} else{ |
420 |
< |
sprintf(painCave.errMsg, |
421 |
< |
"SimSetup error.\n" |
422 |
< |
"\tSorry, the ability to specify total" |
423 |
< |
" nMols and then give molfractions in the components\n" |
424 |
< |
"\tis not currently supported." |
445 |
< |
" Please give nMol in the components.\n"); |
418 |
> |
} else { |
419 |
> |
sprintf(painCave.errMsg, "SimSetup error.\n" |
420 |
> |
"\tSorry, the ability to specify total" |
421 |
> |
" nMols and then give molfractions in the components\n" |
422 |
> |
"\tis not currently supported." |
423 |
> |
" Please give nMol in the components.\n"); |
424 |
> |
|
425 |
|
painCave.isFatal = 1; |
426 |
|
simError(); |
427 |
|
} |
428 |
< |
|
428 |
> |
|
429 |
|
#ifdef IS_MPI |
430 |
< |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
431 |
< |
MPIcheckPoint(); |
430 |
> |
|
431 |
> |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
432 |
> |
MPIcheckPoint(); |
433 |
> |
|
434 |
|
#endif // is_mpi |
435 |
+ |
|
436 |
|
} |
437 |
|
|
438 |
< |
void SimCreator::setGlobalIndices(SimInfo* info) { |
438 |
> |
void SimCreator::setGlobalIndex(SimInfo *info) { |
439 |
|
typename SimInfo::MoleculeIterator mi; |
440 |
|
typename Molecule::AtomIterator ai; |
441 |
|
typename Molecule::RigidBodyIterator ri; |
442 |
|
typename Molecule::CutoffGroupIterator ci; |
443 |
< |
Molecule* mol; |
444 |
< |
Atom* atom; |
445 |
< |
RigidBody* rb; |
446 |
< |
CutoffGroup* cg; |
443 |
> |
Molecule * mol; |
444 |
> |
Atom * atom; |
445 |
> |
RigidBody * rb; |
446 |
> |
CutoffGroup * cg; |
447 |
|
int beginAtomIndex; |
448 |
|
int beginRigidBodyIndex; |
449 |
|
int beginCutoffGroupIndex; |
450 |
|
|
451 |
< |
#ifdef IS_MPI |
451 |
> |
#ifndef IS_MPI |
452 |
> |
|
453 |
|
beginAtomIndex = 0; |
454 |
|
beginRigidBodyIndex = 0; |
455 |
|
beginCutoffGroupIndex = 0; |
456 |
+ |
|
457 |
|
#else |
458 |
+ |
|
459 |
|
int nproc; |
460 |
|
int myNode; |
461 |
|
|
462 |
|
myNode = worldRank; |
463 |
|
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
479 |
– |
|
480 |
– |
std::vector<int> tmpAtomsInProc(nproc, 0); |
481 |
– |
std::vector<int> tmpRigidBodiesInProc(nproc, 0); |
482 |
– |
std::vector<int> tmpCutoffGroupsInProc(nproc, 0); |
483 |
– |
std::vector<int> NumAtomsInProc(nproc, 0); |
484 |
– |
std::vector<int> NumRigidBodiesInProc(nproc, 0); |
485 |
– |
std::vector<int> NumCutoffGroupsInProc(nproc, 0); |
464 |
|
|
465 |
< |
tmpAtomInProc[myNode] = info->getNAtoms(); |
466 |
< |
tmpRigidBodiesInProc[myNode] = info->getNRigidBodiess(); |
467 |
< |
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroupss(); |
468 |
< |
|
465 |
> |
std::vector < int > tmpAtomsInProc(nproc, 0); |
466 |
> |
std::vector < int > tmpRigidBodiesInProc(nproc, 0); |
467 |
> |
std::vector < int > tmpCutoffGroupsInProc(nproc, 0); |
468 |
> |
std::vector < int > NumAtomsInProc(nproc, 0); |
469 |
> |
std::vector < int > NumRigidBodiesInProc(nproc, 0); |
470 |
> |
std::vector < int > NumCutoffGroupsInProc(nproc, 0); |
471 |
> |
|
472 |
> |
tmpAtomsInProc[myNode] = info->getNAtoms(); |
473 |
> |
tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); |
474 |
> |
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); |
475 |
> |
|
476 |
|
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
477 |
< |
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
478 |
< |
MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
479 |
< |
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
477 |
> |
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, |
478 |
> |
MPI_SUM, MPI_COMM_WORLD); |
479 |
> |
MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, |
480 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
481 |
> |
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, |
482 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
483 |
|
|
484 |
|
beginAtomIndex = 0; |
485 |
|
beginRigidBodyIndex = 0; |
486 |
|
beginCutoffGroupIndex = 0; |
487 |
|
|
488 |
< |
for (int i = 0; i < nproc; i++) { |
488 |
> |
for(int i = 0; i < nproc; i++) { |
489 |
|
beginAtomIndex += NumAtomsInProc[i]; |
490 |
|
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
491 |
< |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
491 |
> |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
492 |
|
} |
493 |
< |
|
493 |
> |
|
494 |
|
#endif |
507 |
– |
|
508 |
– |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
495 |
|
|
496 |
+ |
for(mol = info->beginMolecule(mi); mol != NULL; |
497 |
+ |
mol = info->nextMolecule(mi)) { |
498 |
+ |
|
499 |
|
//local index(index in DataStorge) of atom is important |
500 |
< |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
500 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
501 |
|
atom->setGlobalIndex(beginAtomIndex++); |
502 |
|
} |
503 |
|
|
504 |
< |
for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) { |
504 |
> |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
505 |
> |
rb = mol->nextRigidBody(ri)) { |
506 |
|
rb->setGlobalIndex(beginRigidBodyIndex++); |
507 |
|
} |
508 |
< |
|
508 |
> |
|
509 |
|
//local index of cutoff group is trivial, it only depends on the order of travesing |
510 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
510 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
511 |
> |
cg = mol->nextCutoffGroup(ci)) { |
512 |
|
cg->setGlobalIndex(beginCutoffGroupIndex++); |
513 |
< |
} |
513 |
> |
} |
514 |
> |
} |
515 |
> |
|
516 |
> |
//fill globalGroupMembership |
517 |
> |
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
518 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
519 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
520 |
> |
|
521 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
522 |
> |
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
523 |
> |
} |
524 |
> |
|
525 |
> |
} |
526 |
> |
} |
527 |
> |
|
528 |
> |
#ifdef IS_MPI |
529 |
> |
// Since the globalGroupMembership has been zero filled and we've only |
530 |
> |
// poked values into the atoms we know, we can do an Allreduce |
531 |
> |
// to get the full globalGroupMembership array (We think). |
532 |
> |
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
533 |
> |
// docs said we could. |
534 |
> |
|
535 |
> |
MPI_Allreduce(&globalGroupMembership[0], |
536 |
> |
info->getGlobalGroupMembershipPointer(), |
537 |
> |
info->getNGlobalAtoms(), |
538 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
539 |
> |
#else |
540 |
> |
std::copy(globalGroupMembership.begin(), globalGroupMembership.end(), |
541 |
> |
info->getGlobalGroupMembershipPointer()); |
542 |
> |
#endif |
543 |
> |
|
544 |
> |
//fill molMembership |
545 |
> |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
546 |
> |
|
547 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
548 |
> |
|
549 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
550 |
> |
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
551 |
> |
} |
552 |
> |
|
553 |
> |
#ifdef IS_MPI |
554 |
> |
MPI_Allreduce(&globalMolMembership[0], |
555 |
> |
info->getGlobalMolMembershipPointer(), |
556 |
> |
info->getNGlobalAtoms(), |
557 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
558 |
> |
#else |
559 |
> |
std::copy(globalMolMembership.begin(), globalMolMembership.end(), |
560 |
> |
info->getGlobalMolMembershipPointer()); |
561 |
> |
#endif |
562 |
> |
|
563 |
> |
} |
564 |
> |
|
565 |
> |
void SimCreator::loadCoordinates(SimInfo* info) { |
566 |
> |
Globals* globals; |
567 |
> |
globals = info->getGlobals(); |
568 |
> |
|
569 |
> |
if (!globals->haveInitialConfig()) { |
570 |
> |
sprintf(painCave.errMsg, |
571 |
> |
"Cannot intialize a simulation without an initial configuration file.\n"); |
572 |
> |
painCave.isFatal = 1;; |
573 |
> |
simError(); |
574 |
> |
} |
575 |
|
|
576 |
+ |
DumpReader reader(globals->getInitialConfig()); |
577 |
+ |
int nframes = reader->getNframes(); |
578 |
+ |
|
579 |
+ |
if (nframes > 0) { |
580 |
+ |
reader.readFrame(info, nframes - 1); |
581 |
+ |
} else { |
582 |
+ |
//invalid initial coordinate file |
583 |
+ |
sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
584 |
+ |
globals->getInitialConfig()); |
585 |
+ |
painCave.isFatal = 1; |
586 |
+ |
simError(); |
587 |
|
} |
588 |
+ |
|
589 |
|
} |
590 |
|
|
591 |
|
} //end namespace oopse |