22 |
|
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
23 |
|
* |
24 |
|
*/ |
25 |
– |
|
26 |
– |
/** |
27 |
– |
* @file SimCreator.cpp |
28 |
– |
* @author tlin |
29 |
– |
* @date 11/03/2004 |
30 |
– |
* @time 13:51am |
31 |
– |
* @version 1.0 |
32 |
– |
*/ |
25 |
|
|
26 |
< |
#include "brains/SimCreator.hpp" |
26 |
> |
/** |
27 |
> |
* @file SimCreator.cpp |
28 |
> |
* @author tlin |
29 |
> |
* @date 11/03/2004 |
30 |
> |
* @time 13:51am |
31 |
> |
* @version 1.0 |
32 |
> |
*/ |
33 |
> |
|
34 |
> |
#include "brains/SimCreator.hpp" |
35 |
|
namespace oopse { |
36 |
|
|
37 |
|
void SimSetup::parseFile(char* mdfile, MakeStamps* stamps, Globals* globals){ |
63 |
|
} |
64 |
|
|
65 |
|
|
66 |
< |
SimModel* SimCreator::createSim(const std::string& mdfile) { |
67 |
< |
MakeStamps* stamps; |
66 |
> |
SimInfo* SimCreator::createSim(const std::string& mdfile) { |
67 |
> |
MakeStamps* stamps = new MakeStamps(); |
68 |
|
|
69 |
|
Globals* globals = new Globals(); |
70 |
|
|
72 |
|
parseFile(mdfile, stamps, globals); |
73 |
|
|
74 |
|
//create the force field |
75 |
< |
ForceFiled* ff = ForceFiledFactory::getInstance()->createForceField(globals->getForceField()); |
75 |
> |
ForceFiled* ff = ForceFieldFactory::getInstance()->createObject(globals->getForceField()); |
76 |
|
|
77 |
< |
//create SimModel |
78 |
< |
model = new SimInfo(); |
77 |
> |
//create SimInfo |
78 |
> |
SimInfo* info = new SimInfo(); |
79 |
> |
info->setGlobals(globals); |
80 |
> |
info->setForceField(ff); |
81 |
> |
|
82 |
> |
//extract the molecule stamps and add them into SimInfo |
83 |
> |
compList(stamps, info); |
84 |
|
|
85 |
< |
//gather parameters |
86 |
< |
gatherParameters(model); |
85 |
> |
//gather parameters (SimCreator only retrieves the parameters which will be used to create |
86 |
> |
// the simulation) |
87 |
> |
gatherParameters(info); |
88 |
|
|
83 |
– |
|
84 |
– |
|
89 |
|
//divide the molecules and determine the global index of molecules |
90 |
< |
|
90 |
> |
|
91 |
|
//create the molecules |
92 |
+ |
createMolecules(info); |
93 |
|
|
94 |
< |
//create atoms, bonds, bend, torsions, rigidbodies |
95 |
< |
|
94 |
> |
//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the |
95 |
> |
//global index will never change again). Local indices of atoms and rigidbodies are already set by |
96 |
> |
//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
97 |
> |
setGlobalIndices(info); |
98 |
> |
|
99 |
|
//allocate memory for DataStorage(circular reference, need to break it) |
100 |
< |
model->setSnapshotManager(new SimSnapshotManager(model); |
100 |
> |
info->setSnapshotManager(new SimSnapshotManager(info); |
101 |
|
|
102 |
< |
//load initial coordinates |
103 |
< |
DumpReader reader(); |
104 |
< |
reader.readFrame(model); |
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(); |
106 |
> |
|
107 |
> |
if (nframes > 0) { |
108 |
> |
reader.readFrame(info, nframes - 1); |
109 |
> |
} else { |
110 |
> |
//invalid initial coordinate file |
111 |
> |
|
112 |
> |
} |
113 |
> |
|
114 |
|
|
115 |
|
//initialize fortran |
116 |
< |
return model; |
116 |
> |
|
117 |
> |
return info; |
118 |
|
} |
119 |
|
|
120 |
< |
void SimCreator::gatherParameters(SimModel* model) { |
121 |
< |
model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled())); |
122 |
< |
model->addProperty(new DoubleGenericData("dt"), globals->getDt()); |
120 |
> |
void SimCreator::gatherParameters(SimInfo* info) { |
121 |
> |
//model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled())); |
122 |
> |
//model->addProperty(new DoubleGenericData("dt"), globals->getDt()); |
123 |
> |
|
124 |
> |
//setup seed for random number generator |
125 |
> |
int seedValue; |
126 |
> |
Globals* globals = info->getGlobals(); |
127 |
> |
|
128 |
> |
if (globals->haveSeed()){ |
129 |
> |
seedValue = globals->getSeed(); |
130 |
> |
|
131 |
> |
if(seedValue / 1000000000 == 0){ |
132 |
> |
sprintf(painCave.errMsg, |
133 |
> |
"Seed for sprng library should contain at least 9 digits\n" |
134 |
> |
"OOPSE will generate a seed for user\n"); |
135 |
> |
painCave.isFatal = 0; |
136 |
> |
simError(); |
137 |
> |
|
138 |
> |
//using seed generated by system instead of invalid seed set by user |
139 |
> |
#ifndef IS_MPI |
140 |
> |
seedValue = make_sprng_seed(); |
141 |
> |
#else |
142 |
> |
if (worldRank == 0){ |
143 |
> |
seedValue = make_sprng_seed(); |
144 |
> |
} |
145 |
> |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
146 |
> |
#endif |
147 |
> |
} //end if (seedValue /1000000000 == 0) |
148 |
> |
} else{ |
149 |
> |
|
150 |
> |
#ifndef IS_MPI |
151 |
> |
seedValue = make_sprng_seed(); |
152 |
> |
#else |
153 |
> |
if (worldRank == 0){ |
154 |
> |
seedValue = make_sprng_seed(); |
155 |
> |
} |
156 |
> |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
157 |
> |
#endif |
158 |
> |
}//end of globals->haveSeed() |
159 |
> |
info->setSeed(seedValue); |
160 |
> |
|
161 |
> |
// |
162 |
> |
std::string prefix; |
163 |
> |
#ifdef IS_MPI |
164 |
> |
if (worldRank == 0){ |
165 |
> |
#endif // is_mpi |
166 |
> |
|
167 |
> |
if(globals->haveFinalConfig()) { |
168 |
> |
prefix = getPrefix(globals->getFinalConfig()); |
169 |
> |
} else { |
170 |
> |
prefix = getPrefix(mdfile_); |
171 |
> |
} |
172 |
> |
|
173 |
> |
info->setFinalConfFileName(prefix + ".eor"); |
174 |
> |
info->setDumpFileName(prefix + ".dump"); |
175 |
> |
info->setStatFileName(prefix + ".stat"); |
176 |
> |
|
177 |
> |
#ifdef IS_MPI |
178 |
> |
} |
179 |
> |
#endif |
180 |
> |
|
181 |
> |
|
182 |
> |
|
183 |
|
} |
184 |
|
|
185 |
|
#ifdef IS_MPI |
186 |
< |
void SimCreator::mpiMolDivide() { |
186 |
> |
void SimCreator::divideMolecules(SimInfo* info){ |
187 |
> |
int nComponents; |
188 |
> |
MoleculeStamp ** compStamps; |
189 |
> |
randomSPRNG * myRandom; |
190 |
> |
int * componentsNmol; |
191 |
> |
int * AtomsPerProc; |
192 |
|
|
193 |
+ |
double numerator; |
194 |
+ |
double denominator; |
195 |
+ |
double precast; |
196 |
+ |
double x; |
197 |
+ |
double y; |
198 |
+ |
double a; |
199 |
+ |
int old_atoms; |
200 |
+ |
int add_atoms; |
201 |
+ |
int new_atoms; |
202 |
|
|
203 |
+ |
int nTarget; |
204 |
+ |
int molIndex; |
205 |
+ |
int atomIndex; |
206 |
+ |
int done; |
207 |
+ |
int i; |
208 |
+ |
int j; |
209 |
+ |
int loops; |
210 |
+ |
int which_proc; |
211 |
+ |
int nmol_global, |
212 |
+ |
nmol_local; |
213 |
+ |
int natoms_global, |
214 |
+ |
|
215 |
+ |
int baseSeed = info->getSeed(); |
216 |
+ |
CutoffGroupStamp * cg; |
217 |
+ |
|
218 |
+ |
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) { |
226 |
+ |
sprintf(painCave.errMsg, |
227 |
+ |
"nProcessors (%d) > nMol (%d)\n" |
228 |
+ |
"\tThe number of processors is larger than\n" |
229 |
+ |
"\tthe number of molecules. This will not result in a \n" |
230 |
+ |
"\tusable division of atoms for force decomposition.\n" |
231 |
+ |
"\tEither try a smaller number of processors, or run the\n" |
232 |
+ |
"\tsingle-processor version of OOPSE.\n", |
233 |
+ |
parallelData->nProcessors, |
234 |
+ |
parallelData->nMolGlobal); |
235 |
+ |
|
236 |
+ |
painCave.isFatal = 1; |
237 |
+ |
simError(); |
238 |
+ |
} |
239 |
+ |
|
240 |
+ |
myRandom = new randomSPRNG(baseSeed); |
241 |
+ |
|
242 |
+ |
a = 3.0 * parallelData->nMolGlobal / parallelData->nAtomsGlobal; |
243 |
+ |
|
244 |
+ |
// 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++ ) { |
250 |
+ |
// default to an error condition: |
251 |
+ |
MolToProcMap[i] = -1; |
252 |
+ |
} |
253 |
+ |
|
254 |
+ |
if (parallelData->myNode == 0) { |
255 |
+ |
numerator = info->n_atoms; |
256 |
+ |
denominator = parallelData->nProcessors; |
257 |
+ |
precast = numerator / denominator; |
258 |
+ |
nTarget = (int)(precast + 0.5); |
259 |
+ |
|
260 |
+ |
// 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++ ) { |
270 |
+ |
done = 0; |
271 |
+ |
loops = 0; |
272 |
+ |
|
273 |
+ |
while (!done) { |
274 |
+ |
loops++; |
275 |
+ |
|
276 |
+ |
// Pick a processor at random |
277 |
+ |
|
278 |
+ |
which_proc |
279 |
+ |
|
280 |
+ |
= (int) (myRandom->getRandom() * parallelData->nProcessors); |
281 |
+ |
|
282 |
+ |
// How many atoms does this processor have? |
283 |
+ |
|
284 |
+ |
old_atoms = AtomsPerProc[which_proc]; |
285 |
+ |
add_atoms = compStamps[MolComponentType[i]]->getNAtoms(); |
286 |
+ |
new_atoms = old_atoms + add_atoms; |
287 |
+ |
|
288 |
+ |
// If we've been through this loop too many times, we need |
289 |
+ |
// to just give up and assign the molecule to this processor |
290 |
+ |
// and be done with it. |
291 |
+ |
|
292 |
+ |
if (loops > 100) { |
293 |
+ |
sprintf( |
294 |
+ |
painCave.errMsg, |
295 |
+ |
"I've tried 100 times to assign molecule %d to a " |
296 |
+ |
" processor, but can't find a good spot.\n" |
297 |
+ |
"I'm assigning it at random to processor %d.\n", |
298 |
+ |
i, |
299 |
+ |
which_proc); |
300 |
+ |
|
301 |
+ |
painCave.isFatal = 0; |
302 |
+ |
simError(); |
303 |
+ |
|
304 |
+ |
MolToProcMap[i] = which_proc; |
305 |
+ |
AtomsPerProc[which_proc] += add_atoms; |
306 |
+ |
|
307 |
+ |
done = 1; |
308 |
+ |
continue; |
309 |
+ |
} |
310 |
+ |
|
311 |
+ |
// If we can add this molecule to this processor without sending |
312 |
+ |
// it above nTarget, then go ahead and do it: |
313 |
+ |
|
314 |
+ |
if (new_atoms <= nTarget) { |
315 |
+ |
MolToProcMap[i] = which_proc; |
316 |
+ |
AtomsPerProc[which_proc] += add_atoms; |
317 |
+ |
|
318 |
+ |
done = 1; |
319 |
+ |
continue; |
320 |
+ |
} |
321 |
+ |
|
322 |
+ |
// The only situation left is when new_atoms > nTarget. We |
323 |
+ |
// want to accept this with some probability that dies off the |
324 |
+ |
// farther we are from nTarget |
325 |
+ |
|
326 |
+ |
// roughly: x = new_atoms - nTarget |
327 |
+ |
// Pacc(x) = exp(- a * x) |
328 |
+ |
// where a = penalty / (average atoms per molecule) |
329 |
+ |
|
330 |
+ |
x = (double)(new_atoms - nTarget); |
331 |
+ |
y = myRandom->getRandom(); |
332 |
+ |
|
333 |
+ |
if (y < exp(- a * x)) { |
334 |
+ |
MolToProcMap[i] = which_proc; |
335 |
+ |
AtomsPerProc[which_proc] += add_atoms; |
336 |
+ |
|
337 |
+ |
done = 1; |
338 |
+ |
continue; |
339 |
+ |
} else { continue; } |
340 |
+ |
} |
341 |
+ |
} |
342 |
+ |
|
343 |
+ |
// Spray out this nonsense to all other processors: |
344 |
+ |
|
345 |
+ |
MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, MPI_INT, 0, |
346 |
+ |
MPI_COMM_WORLD); |
347 |
+ |
} else { |
348 |
+ |
|
349 |
+ |
// Listen to your marching orders from processor 0: |
350 |
+ |
|
351 |
+ |
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 |
+ |
} |
362 |
+ |
} |
363 |
+ |
|
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 |
+ |
|
378 |
+ |
sprintf(checkPointMsg, |
379 |
+ |
"Successfully divided the molecules among the processors.\n"); |
380 |
+ |
MPIcheckPoint(); |
381 |
+ |
|
382 |
|
} |
383 |
+ |
#endif |
384 |
|
|
385 |
+ |
Molecule* SimCreator::createMolecules(SimInfo* info) { |
386 |
+ |
MoleculeCreator molCreator; |
387 |
+ |
int stampId; |
388 |
+ |
|
389 |
+ |
|
390 |
+ |
for (int i = 0; i < info->getNGlobalMolecules(); i++){ |
391 |
+ |
if (info->getMolToProc(i) == worldRank){ |
392 |
+ |
|
393 |
+ |
stampId = info->getMoleculeStampId(i); |
394 |
+ |
Molecule* mol = molCreator.createMolecule(info->getForceField(), |
395 |
+ |
info->getMoleculeStamp(stampId), stampId, i); |
396 |
+ |
|
397 |
+ |
info->addMolecule(mol); |
398 |
+ |
} |
399 |
+ |
} |
400 |
+ |
|
401 |
+ |
} |
402 |
+ |
|
403 |
+ |
void SimSetup::compList(MakeStamps* stamps,SimInfo* info) { |
404 |
+ |
int i; |
405 |
+ |
char* id; |
406 |
+ |
MoleculeStamp* currentStamp; |
407 |
+ |
Component* the_components = info->getGlobals()->getComponents(); |
408 |
+ |
int n_components = info->getGlobals()->getNComponents(); |
409 |
+ |
|
410 |
+ |
if (!globals->haveNMol()){ |
411 |
+ |
// we don't have the total number of molecules, so we assume it is |
412 |
+ |
// given in each component |
413 |
+ |
|
414 |
+ |
for (i = 0; i < n_components; i++){ |
415 |
+ |
if (!the_components[i]->haveNMol()){ |
416 |
+ |
// we have a problem |
417 |
+ |
sprintf(painCave.errMsg, |
418 |
+ |
"SimSetup Error. No global NMol or component NMol given.\n" |
419 |
+ |
"\tCannot calculate the number of atoms.\n"); |
420 |
+ |
painCave.isFatal = 1; |
421 |
+ |
simError(); |
422 |
+ |
} |
423 |
+ |
|
424 |
+ |
id = the_components[i]->getType(); |
425 |
+ |
currentStamp = stamps->extractMolStamp(id); |
426 |
+ |
if (currentStamp == NULL){ |
427 |
+ |
sprintf(painCave.errMsg, |
428 |
+ |
"SimSetup error: Component \"%s\" was not found in the " |
429 |
+ |
"list of declared molecules\n", |
430 |
+ |
id); |
431 |
+ |
painCave.isFatal = 1; |
432 |
+ |
simError(); |
433 |
+ |
} |
434 |
+ |
|
435 |
+ |
info->addMoleculeStamp(currentStamp, the_components[i]->getNMol); |
436 |
+ |
|
437 |
+ |
} //end for (i = 0; i < n_components; i++) |
438 |
+ |
|
439 |
+ |
} else{ |
440 |
+ |
sprintf(painCave.errMsg, |
441 |
+ |
"SimSetup error.\n" |
442 |
+ |
"\tSorry, the ability to specify total" |
443 |
+ |
" nMols and then give molfractions in the components\n" |
444 |
+ |
"\tis not currently supported." |
445 |
+ |
" Please give nMol in the components.\n"); |
446 |
+ |
painCave.isFatal = 1; |
447 |
+ |
simError(); |
448 |
+ |
} |
449 |
+ |
|
450 |
+ |
#ifdef IS_MPI |
451 |
+ |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
452 |
+ |
MPIcheckPoint(); |
453 |
+ |
#endif // is_mpi |
454 |
+ |
} |
455 |
+ |
|
456 |
+ |
void SimCreator::setGlobalIndices(SimInfo* info) { |
457 |
+ |
typename SimInfo::MoleculeIterator mi; |
458 |
+ |
typename Molecule::AtomIterator ai; |
459 |
+ |
typename Molecule::RigidBodyIterator ri; |
460 |
+ |
typename Molecule::CutoffGroupIterator ci; |
461 |
+ |
Molecule* mol; |
462 |
+ |
Atom* atom; |
463 |
+ |
RigidBody* rb; |
464 |
+ |
CutoffGroup* cg; |
465 |
+ |
int beginAtomIndex; |
466 |
+ |
int beginRigidBodyIndex; |
467 |
+ |
int beginCutoffGroupIndex; |
468 |
+ |
|
469 |
+ |
#ifdef IS_MPI |
470 |
+ |
beginAtomIndex = 0; |
471 |
+ |
beginRigidBodyIndex = 0; |
472 |
+ |
beginCutoffGroupIndex = 0; |
473 |
+ |
#else |
474 |
+ |
int nproc; |
475 |
+ |
int myNode; |
476 |
+ |
|
477 |
+ |
myNode = worldRank; |
478 |
+ |
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); |
486 |
+ |
|
487 |
+ |
tmpAtomInProc[myNode] = info->getNAtoms(); |
488 |
+ |
tmpRigidBodiesInProc[myNode] = info->getNRigidBodiess(); |
489 |
+ |
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroupss(); |
490 |
+ |
|
491 |
+ |
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
492 |
+ |
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
493 |
+ |
MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
494 |
+ |
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
495 |
+ |
|
496 |
+ |
beginAtomIndex = 0; |
497 |
+ |
beginRigidBodyIndex = 0; |
498 |
+ |
beginCutoffGroupIndex = 0; |
499 |
+ |
|
500 |
+ |
for (int i = 0; i < nproc; i++) { |
501 |
+ |
beginAtomIndex += NumAtomsInProc[i]; |
502 |
+ |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
503 |
+ |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
504 |
+ |
} |
505 |
+ |
|
506 |
|
#endif |
507 |
+ |
|
508 |
+ |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
509 |
+ |
|
510 |
+ |
//local index(index in DataStorge) of atom is important |
511 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
512 |
+ |
atom->setGlobalIndex(beginAtomIndex++); |
513 |
+ |
} |
514 |
+ |
|
515 |
+ |
for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) { |
516 |
+ |
rb->setGlobalIndex(beginRigidBodyIndex++); |
517 |
+ |
} |
518 |
+ |
|
519 |
+ |
//local index of cutoff group is trivial, it only depends on the order of travesing |
520 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
521 |
+ |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
522 |
+ |
} |
523 |
+ |
|
524 |
+ |
} |
525 |
+ |
} |
526 |
+ |
|
527 |
|
} //end namespace oopse |