[ViewVC] Diff of: group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1093 by tim, Wed Mar 17 14:22:59 2004 UTC vs.
Revision 1154 by gezelter, Tue May 11 16:00:22 2004 UTC

#	Line 9 \| Line 9
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13		//#include "ConjugateMinimizer.hpp"
14		#include "OOPSEMinimizer.hpp"
15
#	Line 146 \| Line 147 \| void SimSetup::createSim(void){
147		// make the output filenames
148
149		makeOutNames();
149	–
150	–	if (globals->haveMinimizer())
151	–	// make minimizer
152	–	makeMinimizer();
153	–	else
154	–	// make the integrator
155	–	makeIntegrator();
150
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
#	Line 161 \| Line 155 \| void SimSetup::createSim(void){
155		// initialize the Fortran
156
157		initFortran();
158	+
159	+	if (globals->haveMinimizer())
160	+	// make minimizer
161	+	makeMinimizer();
162	+	else
163	+	// make the integrator
164	+	makeIntegrator();
165	+
166		}
167
168
169		void SimSetup::makeMolecules(void){
170	<	int k;
171	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175		molInit molInfo;
176		DirectionalAtom* dAtom;
177	+	RigidBody* myRB;
178	+	StuntDouble* mySD;
179		LinkedAssign* extras;
180		LinkedAssign* current_extra;
181		AtomStamp* currentAtom;
182		BondStamp* currentBond;
183		BendStamp* currentBend;
184		TorsionStamp* currentTorsion;
185	+	RigidBodyStamp* currentRigidBody;
186
187		bond_pair* theBonds;
188		bend_set* theBends;
189		torsion_set* theTorsions;
190
191	+	set<int> skipList;
192	+
193	+	double phi, theta, psi;
194	+	char* molName;
195	+	char rbName[100];
196	+
197		//init the forceField paramters
198
199		the_ff->readParams();
200
187	–
201		// init the atoms
202
203	<	double phi, theta, psi;
191	<	double sux, suy, suz;
192	<	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
193	<	double ux, uy, uz, u, uSqr;
203	>	int nMembers, nNew, rb1, rb2;
204
205		for (k = 0; k < nInfo; k++){
206		the_ff->setSimInfo(&(info[k]));
207
208		atomOffset = 0;
209	<	excludeOffset = 0;
209	>
210		for (i = 0; i < info[k].n_mol; i++){
211		stampID = info[k].molecules[i].getStampID();
212	+	molName = comp_stamps[stampID]->getID();
213
214		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216		molInfo.nBends = comp_stamps[stampID]->getNBends();
217		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
219	<
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219	>
220		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
210	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
211	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
212	–	molInfo.myBends = new Bend * [molInfo.nBends];
213	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
221
222	+	if (molInfo.nBonds > 0)
223	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	+	else
225	+	molInfo.myBonds = NULL;
226	+
227	+	if (molInfo.nBends > 0)
228	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	+	else
230	+	molInfo.myBends = NULL;
231	+
232	+	if (molInfo.nTorsions > 0)
233	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	+	else
235	+	molInfo.myTorsions = NULL;
236	+
237		theBonds = new bond_pair[molInfo.nBonds];
238		theBends = new bend_set[molInfo.nBends];
239		theTorsions = new torsion_set[molInfo.nTorsions];
240	<
240	>
241		// make the Atoms
242
243		for (j = 0; j < molInfo.nAtoms; j++){
244		currentAtom = comp_stamps[stampID]->getAtom(j);
245	+
246		if (currentAtom->haveOrientation()){
247		dAtom = new DirectionalAtom((j + atomOffset),
248		info[k].getConfiguration());
#	Line 233 \| Line 256 \| void SimSetup::makeMolecules(void){
256		phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257		theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258		psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259	+
260	+	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261
262	<	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
263	<	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
239	<	Axz = sin(theta) * sin(psi);
240	<
241	<	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
242	<	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
243	<	Ayz = sin(theta) * cos(psi);
244	<
245	<	Azx = sin(phi) * sin(theta);
246	<	Azy = -cos(phi) * sin(theta);
247	<	Azz = cos(theta);
262	>	}
263	>	else{
264
265	<	sux = 0.0;
250	<	suy = 0.0;
251	<	suz = 1.0;
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266
253	–	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
254	–	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
255	–	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
256	–
257	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
258	–
259	–	u = sqrt(uSqr);
260	–	ux = ux / u;
261	–	uy = uy / u;
262	–	uz = uz / u;
263	–
264	–	dAtom->setSUx(ux);
265	–	dAtom->setSUy(uy);
266	–	dAtom->setSUz(uz);
267		}
268	–	else{
269	–	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
270	–	info[k].getConfiguration());
271	–	}
272	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
268
269	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
270		#ifdef IS_MPI
271
272	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273
274		#endif // is_mpi
275		}
#	Line 284 \| Line 280 \| void SimSetup::makeMolecules(void){
280		theBonds[j].a = currentBond->getA() + atomOffset;
281		theBonds[j].b = currentBond->getB() + atomOffset;
282
283	<	exI = theBonds[j].a;
284	<	exJ = theBonds[j].b;
283	>	tempI = theBonds[j].a;
284	>	tempJ = theBonds[j].b;
285
290	–	// exclude_I must always be the smaller of the pair
291	–	if (exI > exJ){
292	–	tempEx = exI;
293	–	exI = exJ;
294	–	exJ = tempEx;
295	–	}
286		#ifdef IS_MPI
287	<	tempEx = exI;
288	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
289	<	tempEx = exJ;
290	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293
294	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
303	<	#else // isn't MPI
304	<
305	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
306	<	#endif //is_mpi
294	>	info[k].excludes->addPair(exI, exJ);
295		}
308	–	excludeOffset += molInfo.nBonds;
296
297		//make the bends
298		for (j = 0; j < molInfo.nBends; j++){
#	Line 355 \| Line 342 \| void SimSetup::makeMolecules(void){
342		}
343		}
344
345	<	if (!theBends[j].isGhost){
346	<	exI = theBends[j].a;
347	<	exJ = theBends[j].c;
348	<	}
349	<	else{
363	<	exI = theBends[j].a;
364	<	exJ = theBends[j].b;
365	<	}
366	<
367	<	// exclude_I must always be the smaller of the pair
368	<	if (exI > exJ){
369	<	tempEx = exI;
370	<	exI = exJ;
371	<	exJ = tempEx;
372	<	}
345	>	if (theBends[j].isGhost) {
346	>
347	>	tempI = theBends[j].a;
348	>	tempJ = theBends[j].b;
349	>
350		#ifdef IS_MPI
351	<	tempEx = exI;
352	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
353	<	tempEx = exJ;
354	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
360	<	#else // isn't MPI
361	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
362	<	#endif //is_mpi
359	>	} else {
360	>
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379		}
384	–	excludeOffset += molInfo.nBends;
380
381		for (j = 0; j < molInfo.nTorsions; j++){
382		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 390 \| Line 385 \| void SimSetup::makeMolecules(void){
385		theTorsions[j].c = currentTorsion->getC() + atomOffset;
386		theTorsions[j].d = currentTorsion->getD() + atomOffset;
387
388	<	exI = theTorsions[j].a;
389	<	exJ = theTorsions[j].d;
388	>	tempI = theTorsions[j].a;
389	>	tempJ = theTorsions[j].b;
390	>	tempK = theTorsions[j].c;
391	>	tempL = theTorsions[j].d;
392
396	–	// exclude_I must always be the smaller of the pair
397	–	if (exI > exJ){
398	–	tempEx = exI;
399	–	exI = exJ;
400	–	exJ = tempEx;
401	–	}
393		#ifdef IS_MPI
394	<	tempEx = exI;
395	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
396	<	tempEx = exJ;
397	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403	>	#endif
404
405	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
406	<	#else // isn't MPI
407	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
408	<	#endif //is_mpi
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411		}
413	–	excludeOffset += molInfo.nTorsions;
412
413	+
414	+	molInfo.myRigidBodies.clear();
415	+
416	+	for (j = 0; j < molInfo.nRigidBodies; j++){
417
418	<	// send the arrays off to the forceField for init.
418	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	>	nMembers = currentRigidBody->getNMembers();
420
421	+	// Create the Rigid Body:
422	+
423	+	myRB = new RigidBody();
424	+
425	+	sprintf(rbName,"%s_RB_%d", molName, j);
426	+	myRB->setType(rbName);
427	+
428	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
429	+
430	+	// molI is atom numbering inside this molecule
431	+	molI = currentRigidBody->getMember(rb1);
432	+
433	+	// tempI is atom numbering on local processor
434	+	tempI = molI + atomOffset;
435	+
436	+	// currentAtom is the AtomStamp (which we need for
437	+	// rigid body reference positions)
438	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
439	+
440	+	// When we add to the rigid body, add the atom itself and
441	+	// the stamp info:
442	+
443	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	+
445	+	// Add this atom to the Skip List for the integrators
446	+	#ifdef IS_MPI
447	+	slI = info[k].atoms[tempI]->getGlobalIndex();
448	+	#else
449	+	slI = tempI;
450	+	#endif
451	+	skipList.insert(slI);
452	+
453	+	}
454	+
455	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	+
458	+	tempI = currentRigidBody->getMember(rb1);
459	+	tempJ = currentRigidBody->getMember(rb2);
460	+
461	+	// Some explanation is required here.
462	+	// Fortran indexing starts at 1, while c indexing starts at 0
463	+	// Also, in parallel computations, the GlobalIndex is
464	+	// used for the exclude list:
465	+
466	+	#ifdef IS_MPI
467	+	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	+	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	+	#else
470	+	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	+	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	+	#endif
473	+
474	+	info[k].excludes->addPair(exI, exJ);
475	+
476	+	}
477	+	}
478	+
479	+	molInfo.myRigidBodies.push_back(myRB);
480	+	info[k].rigidBodies.push_back(myRB);
481	+	}
482	+
483	+
484	+	// After this is all set up, scan through the atoms to
485	+	// see if they can be added to the integrableObjects:
486	+
487	+	molInfo.myIntegrableObjects.clear();
488	+
489	+
490	+	for (j = 0; j < molInfo.nAtoms; j++){
491	+
492	+	#ifdef IS_MPI
493	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	+	#else
495	+	slJ = j+atomOffset;
496	+	#endif
497	+
498	+	// if they aren't on the skip list, then they can be integrated
499	+
500	+	if (skipList.find(slJ) == skipList.end()) {
501	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	+	info[k].integrableObjects.push_back(mySD);
503	+	molInfo.myIntegrableObjects.push_back(mySD);
504	+	}
505	+	}
506	+
507	+	// all rigid bodies are integrated:
508	+
509	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	+	info[k].integrableObjects.push_back(mySD);
512	+	molInfo.myIntegrableObjects.push_back(mySD);
513	+	}
514	+
515	+
516	+	// send the arrays off to the forceField for init.
517	+
518		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522		theTorsions);
523
424	–
524		info[k].molecules[i].initialize(molInfo);
525
526
#	Line 429 \| Line 528 \| void SimSetup::makeMolecules(void){
528		delete[] theBonds;
529		delete[] theBends;
530		delete[] theTorsions;
531	<	}
531	>	}
532		}
533
534		#ifdef IS_MPI
#	Line 439 \| Line 538 \| void SimSetup::makeMolecules(void){
538
539		// clean up the forcefield
540
541	<	the_ff->calcRcut();
541	>	if (!globals->haveRcut()){
542	>
543	>	the_ff->calcRcut();
544	>
545	>	} else {
546	>
547	>	the_ff->setRcut( globals->getRcut() );
548	>	}
549	>
550		the_ff->cleanMe();
551		}
552
#	Line 727 \| Line 834 \| void SimSetup::gatherInfo(void){
834		}
835
836		//check whether sample time, status time, thermal time and reset time are divisble by dt
837	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
837	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
838		sprintf(painCave.errMsg,
839		"Sample time is not divisible by dt.\n"
840		"\tThis will result in samples that are not uniformly\n"
#	Line 737 \| Line 844 \| void SimSetup::gatherInfo(void){
844		simError();
845		}
846
847	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
847	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848		sprintf(painCave.errMsg,
849		"Status time is not divisible by dt.\n"
850		"\tThis will result in status reports that are not uniformly\n"
#	Line 773 \| Line 880 \| void SimSetup::gatherInfo(void){
880		if (globals->haveSampleTime()){
881		info[i].sampleTime = globals->getSampleTime();
882		info[i].statusTime = info[i].sampleTime;
776	–	info[i].thermalTime = info[i].sampleTime;
883		}
884		else{
885		info[i].sampleTime = globals->getRunTime();
886		info[i].statusTime = info[i].sampleTime;
781	–	info[i].thermalTime = info[i].sampleTime;
887		}
888
889		if (globals->haveStatusTime()){
#	Line 787 \| Line 892 \| void SimSetup::gatherInfo(void){
892
893		if (globals->haveThermalTime()){
894		info[i].thermalTime = globals->getThermalTime();
895	+	} else {
896	+	info[i].thermalTime = globals->getRunTime();
897		}
898
899		info[i].resetIntegrator = 0;
#	Line 857 \| Line 964 \| void SimSetup::finalInfoCheck(void){
964		void SimSetup::finalInfoCheck(void){
965		int index;
966		int usesDipoles;
967	+	int usesCharges;
968		int i;
969
970		for (i = 0; i < nInfo; i++){
#	Line 868 \| Line 976 \| void SimSetup::finalInfoCheck(void){
976		usesDipoles = (info[i].atoms[index])->hasDipole();
977		index++;
978		}
979	<
979	>	index = 0;
980	>	usesCharges = 0;
981	>	while ((index < info[i].n_atoms) && !usesCharges){
982	>	usesCharges= (info[i].atoms[index])->hasCharge();
983	>	index++;
984	>	}
985		#ifdef IS_MPI
986		int myUse = usesDipoles;
987		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
988		#endif //is_mpi
989
990	<	double theEcr, theEst;
990	>	double theRcut, theRsw;
991
992		if (globals->getUseRF()){
993		info[i].useReactionField = 1;
994
995	<	if (!globals->haveECR()){
995	>	if (!globals->haveRcut()){
996		sprintf(painCave.errMsg,
997	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
997	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
998		"\tOOPSE will use a default value of 15.0 angstroms"
999	<	"\tfor the electrostaticCutoffRadius.\n");
999	>	"\tfor the cutoffRadius.\n");
1000		painCave.isFatal = 0;
1001		simError();
1002	<	theEcr = 15.0;
1002	>	theRcut = 15.0;
1003		}
1004		else{
1005	<	theEcr = globals->getECR();
1005	>	theRcut = globals->getRcut();
1006		}
1007
1008	<	if (!globals->haveEST()){
1008	>	if (!globals->haveRsw()){
1009		sprintf(painCave.errMsg,
1010	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1010	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1011		"\tOOPSE will use a default value of\n"
1012	<	"\t0.05 * electrostaticCutoffRadius\n"
900	<	"\tfor the electrostaticSkinThickness\n");
1012	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1013		painCave.isFatal = 0;
1014		simError();
1015	<	theEst = 0.05 * theEcr;
1015	>	theRsw = 0.95 * theRcut;
1016		}
1017		else{
1018	<	theEst = globals->getEST();
1018	>	theRsw = globals->getRsw();
1019		}
1020
1021	<	info[i].setDefaultEcr(theEcr, theEst);
1021	>	info[i].setDefaultRcut(theRcut, theRsw);
1022
1023		if (!globals->haveDielectric()){
1024		sprintf(painCave.errMsg,
#	Line 919 \| Line 1031 \| void SimSetup::finalInfoCheck(void){
1031		info[i].dielectric = globals->getDielectric();
1032		}
1033		else{
1034	<	if (usesDipoles){
1035	<	if (!globals->haveECR()){
1034	>	if (usesDipoles \|\| usesCharges){
1035	>
1036	>	if (!globals->haveRcut()){
1037		sprintf(painCave.errMsg,
1038	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1038	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1039		"\tOOPSE will use a default value of 15.0 angstroms"
1040	<	"\tfor the electrostaticCutoffRadius.\n");
1041	<	painCave.isFatal = 0;
1042	<	simError();
1043	<	theEcr = 15.0;
1044	<	}
1040	>	"\tfor the cutoffRadius.\n");
1041	>	painCave.isFatal = 0;
1042	>	simError();
1043	>	theRcut = 15.0;
1044	>	}
1045		else{
1046	<	theEcr = globals->getECR();
1046	>	theRcut = globals->getRcut();
1047		}
1048	<
1049	<	if (!globals->haveEST()){
1048	>
1049	>	if (!globals->haveRsw()){
1050		sprintf(painCave.errMsg,
1051	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1051	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1052		"\tOOPSE will use a default value of\n"
1053	<	"\t0.05 * electrostaticCutoffRadius\n"
941	<	"\tfor the electrostaticSkinThickness\n");
1053	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1054		painCave.isFatal = 0;
1055		simError();
1056	<	theEst = 0.05 * theEcr;
1056	>	theRsw = 0.95 * theRcut;
1057		}
1058		else{
1059	<	theEst = globals->getEST();
1059	>	theRsw = globals->getRsw();
1060		}
1061	+
1062	+	info[i].setDefaultRcut(theRcut, theRsw);
1063
950	–	info[i].setDefaultEcr(theEcr, theEst);
1064		}
1065		}
1066		}
#	Line 1221 \| Line 1334 \| void SimSetup::calcSysValues(void){
1334		tot_bonds = 0;
1335		tot_bends = 0;
1336		tot_torsions = 0;
1337	+	tot_rigid = 0;
1338		for (i = 0; i < n_components; i++){
1339		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1340		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1341		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1342		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1343	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1344		}
1345	<
1345	>
1346		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1347		molMembershipArray = new int[tot_atoms];
1348
#	Line 1249 \| Line 1364 \| void SimSetup::mpiMolDivide(void){
1364		int i, j, k;
1365		int localMol, allMol;
1366		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1367	+	int local_rigid;
1368	+	vector<int> globalMolIndex;
1369
1370		mpiSim = new mpiSimulation(info);
1371
1372	<	globalIndex = mpiSim->divideLabor();
1372	>	mpiSim->divideLabor();
1373	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1374	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1375
1376		// set up the local variables
1377
#	Line 1265 \| Line 1384 \| void SimSetup::mpiMolDivide(void){
1384		local_bonds = 0;
1385		local_bends = 0;
1386		local_torsions = 0;
1387	<	globalAtomIndex = 0;
1387	>	local_rigid = 0;
1388	>	globalAtomCounter = 0;
1389
1270	–
1390		for (i = 0; i < n_components; i++){
1391		for (j = 0; j < components_nmol[i]; j++){
1392		if (mol2proc[allMol] == worldRank){
#	Line 1275 \| Line 1394 \| void SimSetup::mpiMolDivide(void){
1394		local_bonds += comp_stamps[i]->getNBonds();
1395		local_bends += comp_stamps[i]->getNBends();
1396		local_torsions += comp_stamps[i]->getNTorsions();
1397	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1398		localMol++;
1399		}
1400		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1401	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1402	<	globalAtomIndex++;
1401	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1402	>	globalAtomCounter++;
1403		}
1404
1405		allMol++;
#	Line 1288 \| Line 1408 \| void SimSetup::mpiMolDivide(void){
1408		local_SRI = local_bonds + local_bends + local_torsions;
1409
1410		info[0].n_atoms = mpiSim->getMyNlocal();
1411	+
1412
1413		if (local_atoms != info[0].n_atoms){
1414		sprintf(painCave.errMsg,
#	Line 1320 \| Line 1441 \| void SimSetup::makeSysArrays(void){
1441
1442		Atom** the_atoms;
1443		Molecule* the_molecules;
1323	–	Exclude** the_excludes;
1444
1325	–
1445		for (l = 0; l < nInfo; l++){
1446		// create the atom and short range interaction arrays
1447
#	Line 1348 \| Line 1467 \| void SimSetup::makeSysArrays(void){
1467		#else // is_mpi
1468
1469		molIndex = 0;
1470	<	globalAtomIndex = 0;
1470	>	globalAtomCounter = 0;
1471		for (i = 0; i < n_components; i++){
1472		for (j = 0; j < components_nmol[i]; j++){
1473		the_molecules[molIndex].setStampID(i);
1474		the_molecules[molIndex].setMyIndex(molIndex);
1475		the_molecules[molIndex].setGlobalIndex(molIndex);
1476		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1477	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1478	<	globalAtomIndex++;
1477	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1478	>	globalAtomCounter++;
1479		}
1480		molIndex++;
1481		}
#	Line 1365 \| Line 1484 \| void SimSetup::makeSysArrays(void){
1484
1485		#endif // is_mpi
1486
1487	<
1488	<	if (info[l].n_SRI){
1489	<	Exclude::createArray(info[l].n_SRI);
1371	<	the_excludes = new Exclude * [info[l].n_SRI];
1372	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1373	<	the_excludes[ex] = new Exclude(ex);
1374	<	}
1375	<	info[l].globalExcludes = new int;
1376	<	info[l].n_exclude = info[l].n_SRI;
1377	<	}
1378	<	else{
1379	<	Exclude::createArray(1);
1380	<	the_excludes = new Exclude * ;
1381	<	the_excludes[0] = new Exclude(0);
1382	<	the_excludes[0]->setPair(0, 0);
1383	<	info[l].globalExcludes = new int;
1384	<	info[l].globalExcludes[0] = 0;
1385	<	info[l].n_exclude = 0;
1386	<	}
1387	<
1487	>	info[l].globalExcludes = new int;
1488	>	info[l].globalExcludes[0] = 0;
1489	>
1490		// set the arrays into the SimInfo object
1491
1492		info[l].atoms = the_atoms;
1493		info[l].molecules = the_molecules;
1494		info[l].nGlobalExcludes = 0;
1393	–	info[l].excludes = the_excludes;
1495
1496		the_ff->setSimInfo(info);
1497		}

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 1093 by tim, Wed Mar 17 14:22:59 2004 UTC vs. Revision 1154 by gezelter, Tue May 11 16:00:22 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1093 by tim, Wed Mar 17 14:22:59 2004 UTC vs.
Revision 1154 by gezelter, Tue May 11 16:00:22 2004 UTC