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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 984 by gezelter, Mon Jan 26 21:52:56 2004 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 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
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 24 \| Line 27
27		#define NPTxyz_ENS 4
28
29
30	<	#define FF_DUFF 0
31	<	#define FF_LJ 1
32	<	#define FF_EAM 2
30	>	#define FF_DUFF 0
31	>	#define FF_LJ 1
32	>	#define FF_EAM 2
33	>	#define FF_H2O 3
34
35		using namespace std;
36
#	Line 143 \| Line 147 \| void SimSetup::createSim(void){
147		// make the output filenames
148
149		makeOutNames();
150	<
147	<	// make the integrator
148	<
149	<	makeIntegrator();
150	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 155 \| 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	<
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>
189		bond_pair* theBonds;
190		bend_set* theBends;
191		torsion_set* theTorsions;
192
193	+	set<int> skipList;
194	+
195	+	double phi, theta, psi;
196	+	char* molName;
197	+	char rbName[100];
198	+
199		//init the forceField paramters
200
201		the_ff->readParams();
202
181	–
203		// init the atoms
204
205	<	double phi, theta, psi;
185	<	double sux, suy, suz;
186	<	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
187	<	double ux, uy, uz, u, uSqr;
205	>	int nMembers, nNew, rb1, rb2;
206
207		for (k = 0; k < nInfo; k++){
208		the_ff->setSimInfo(&(info[k]));
209
210		atomOffset = 0;
211	<	excludeOffset = 0;
211	>
212		for (i = 0; i < info[k].n_mol; i++){
213		stampID = info[k].molecules[i].getStampID();
214	+	molName = comp_stamps[stampID]->getID();
215
216		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
217		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
218		molInfo.nBends = comp_stamps[stampID]->getNBends();
219		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
221	<
220	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221	>	molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222	>
223		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
204	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
205	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
206	–	molInfo.myBends = new Bend * [molInfo.nBends];
207	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
224
225	+	if (molInfo.nBonds > 0)
226	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227	+	else
228	+	molInfo.myBonds = NULL;
229	+
230	+	if (molInfo.nBends > 0)
231	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
232	+	else
233	+	molInfo.myBends = NULL;
234	+
235	+	if (molInfo.nTorsions > 0)
236	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237	+	else
238	+	molInfo.myTorsions = NULL;
239	+
240		theBonds = new bond_pair[molInfo.nBonds];
241		theBends = new bend_set[molInfo.nBends];
242		theTorsions = new torsion_set[molInfo.nTorsions];
243	<
243	>
244		// make the Atoms
245
246		for (j = 0; j < molInfo.nAtoms; j++){
247		currentAtom = comp_stamps[stampID]->getAtom(j);
248	+
249		if (currentAtom->haveOrientation()){
250		dAtom = new DirectionalAtom((j + atomOffset),
251		info[k].getConfiguration());
#	Line 227 \| Line 259 \| void SimSetup::makeMolecules(void){
259		phi = currentAtom->getEulerPhi() * M_PI / 180.0;
260		theta = currentAtom->getEulerTheta() * M_PI / 180.0;
261		psi = currentAtom->getEulerPsi()* M_PI / 180.0;
230	–
231	–	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
232	–	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
233	–	Axz = sin(theta) * sin(psi);
234	–
235	–	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
236	–	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
237	–	Ayz = sin(theta) * cos(psi);
238	–
239	–	Azx = sin(phi) * sin(theta);
240	–	Azy = -cos(phi) * sin(theta);
241	–	Azz = cos(theta);
262
263	<	sux = 0.0;
264	<	suy = 0.0;
265	<	suz = 1.0;
263	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
264	>
265	>	}
266	>	else{
267
268	<	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
248	<	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
249	<	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
268	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
269
251	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
252	–
253	–	u = sqrt(uSqr);
254	–	ux = ux / u;
255	–	uy = uy / u;
256	–	uz = uz / u;
257	–
258	–	dAtom->setSUx(ux);
259	–	dAtom->setSUy(uy);
260	–	dAtom->setSUz(uz);
270		}
262	–	else{
263	–	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
264	–	info[k].getConfiguration());
265	–	}
266	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
271
272	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
273		#ifdef IS_MPI
274
275	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
276
277		#endif // is_mpi
278		}
#	Line 278 \| Line 283 \| void SimSetup::makeMolecules(void){
283		theBonds[j].a = currentBond->getA() + atomOffset;
284		theBonds[j].b = currentBond->getB() + atomOffset;
285
286	<	exI = theBonds[j].a;
287	<	exJ = theBonds[j].b;
286	>	tempI = theBonds[j].a;
287	>	tempJ = theBonds[j].b;
288
284	–	// exclude_I must always be the smaller of the pair
285	–	if (exI > exJ){
286	–	tempEx = exI;
287	–	exI = exJ;
288	–	exJ = tempEx;
289	–	}
289		#ifdef IS_MPI
290	<	tempEx = exI;
291	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
292	<	tempEx = exJ;
293	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
290	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
291	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
292	>	#else
293	>	exI = tempI + 1;
294	>	exJ = tempJ + 1;
295	>	#endif
296
297	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
297	<	#else // isn't MPI
298	<
299	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
300	<	#endif //is_mpi
297	>	info[k].excludes->addPair(exI, exJ);
298		}
302	–	excludeOffset += molInfo.nBonds;
299
300		//make the bends
301		for (j = 0; j < molInfo.nBends; j++){
#	Line 349 \| Line 345 \| void SimSetup::makeMolecules(void){
345		}
346		}
347
348	<	if (!theBends[j].isGhost){
349	<	exI = theBends[j].a;
350	<	exJ = theBends[j].c;
351	<	}
352	<	else{
357	<	exI = theBends[j].a;
358	<	exJ = theBends[j].b;
359	<	}
360	<
361	<	// exclude_I must always be the smaller of the pair
362	<	if (exI > exJ){
363	<	tempEx = exI;
364	<	exI = exJ;
365	<	exJ = tempEx;
366	<	}
348	>	if (theBends[j].isGhost) {
349	>
350	>	tempI = theBends[j].a;
351	>	tempJ = theBends[j].b;
352	>
353		#ifdef IS_MPI
354	<	tempEx = exI;
355	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
356	<	tempEx = exJ;
357	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
354	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
355	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
356	>	#else
357	>	exI = tempI + 1;
358	>	exJ = tempJ + 1;
359	>	#endif
360	>	info[k].excludes->addPair(exI, exJ);
361
362	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
363	<	#else // isn't MPI
364	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
365	<	#endif //is_mpi
362	>	} else {
363	>
364	>	tempI = theBends[j].a;
365	>	tempJ = theBends[j].b;
366	>	tempK = theBends[j].c;
367	>
368	>	#ifdef IS_MPI
369	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
370	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
371	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
372	>	#else
373	>	exI = tempI + 1;
374	>	exJ = tempJ + 1;
375	>	exK = tempK + 1;
376	>	#endif
377	>
378	>	info[k].excludes->addPair(exI, exK);
379	>	info[k].excludes->addPair(exI, exJ);
380	>	info[k].excludes->addPair(exJ, exK);
381	>	}
382		}
378	–	excludeOffset += molInfo.nBends;
383
384		for (j = 0; j < molInfo.nTorsions; j++){
385		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 384 \| Line 388 \| void SimSetup::makeMolecules(void){
388		theTorsions[j].c = currentTorsion->getC() + atomOffset;
389		theTorsions[j].d = currentTorsion->getD() + atomOffset;
390
391	<	exI = theTorsions[j].a;
392	<	exJ = theTorsions[j].d;
391	>	tempI = theTorsions[j].a;
392	>	tempJ = theTorsions[j].b;
393	>	tempK = theTorsions[j].c;
394	>	tempL = theTorsions[j].d;
395
396	<	// exclude_I must always be the smaller of the pair
397	<	if (exI > exJ){
398	<	tempEx = exI;
399	<	exI = exJ;
400	<	exJ = tempEx;
396	>	#ifdef IS_MPI
397	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
398	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
399	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
400	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
401	>	#else
402	>	exI = tempI + 1;
403	>	exJ = tempJ + 1;
404	>	exK = tempK + 1;
405	>	exL = tempL + 1;
406	>	#endif
407	>
408	>	info[k].excludes->addPair(exI, exJ);
409	>	info[k].excludes->addPair(exI, exK);
410	>	info[k].excludes->addPair(exI, exL);
411	>	info[k].excludes->addPair(exJ, exK);
412	>	info[k].excludes->addPair(exJ, exL);
413	>	info[k].excludes->addPair(exK, exL);
414	>	}
415	>
416	>
417	>	molInfo.myRigidBodies.clear();
418	>
419	>	for (j = 0; j < molInfo.nRigidBodies; j++){
420	>
421	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422	>	nMembers = currentRigidBody->getNMembers();
423	>
424	>	// Create the Rigid Body:
425	>
426	>	myRB = new RigidBody();
427	>
428	>	sprintf(rbName,"%s_RB_%d", molName, j);
429	>	myRB->setType(rbName);
430	>
431	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
432	>
433	>	// molI is atom numbering inside this molecule
434	>	molI = currentRigidBody->getMember(rb1);
435	>
436	>	// tempI is atom numbering on local processor
437	>	tempI = molI + atomOffset;
438	>
439	>	// currentAtom is the AtomStamp (which we need for
440	>	// rigid body reference positions)
441	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
442	>
443	>	// When we add to the rigid body, add the atom itself and
444	>	// the stamp info:
445	>
446	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
447	>
448	>	// Add this atom to the Skip List for the integrators
449	>	#ifdef IS_MPI
450	>	slI = info[k].atoms[tempI]->getGlobalIndex();
451	>	#else
452	>	slI = tempI;
453	>	#endif
454	>	skipList.insert(slI);
455	>
456		}
457	+
458	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
459	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
460	+
461	+	tempI = currentRigidBody->getMember(rb1);
462	+	tempJ = currentRigidBody->getMember(rb2);
463	+
464	+	// Some explanation is required here.
465	+	// Fortran indexing starts at 1, while c indexing starts at 0
466	+	// Also, in parallel computations, the GlobalIndex is
467	+	// used for the exclude list:
468	+
469		#ifdef IS_MPI
470	<	tempEx = exI;
471	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
472	<	tempEx = exJ;
473	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
470	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472	>	#else
473	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475	>	#endif
476	>
477	>	info[k].excludes->addPair(exI, exJ);
478	>
479	>	}
480	>	}
481
482	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
483	<	#else // isn't MPI
404	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
405	<	#endif //is_mpi
482	>	molInfo.myRigidBodies.push_back(myRB);
483	>	info[k].rigidBodies.push_back(myRB);
484		}
485	<	excludeOffset += molInfo.nTorsions;
485	>
486
487	+	//creat cutoff group for molecule
488	+	molInfo.myCutoffGroups.clear();
489	+	for (j = 0; j < molInfo.nCutoffGroups; j++){
490
491	<	// send the arrays off to the forceField for init.
491	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492	>	nMembers = currentCutoffGroup->getNMembers();
493
494	+	myCutoffGroup = new CutoffGroup();
495	+
496	+	for (int cg = 0; cg < nMembers; cg++) {
497	+
498	+	// molI is atom numbering inside this molecule
499	+	molI = currentCutoffGroup->getMember(cg);
500	+
501	+	// tempI is atom numbering on local processor
502	+	tempI = molI + atomOffset;
503	+
504	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
505	+	}
506	+
507	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
508	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509	+
510	+
511	+
512	+	// After this is all set up, scan through the atoms to
513	+	// see if they can be added to the integrableObjects:
514	+
515	+	molInfo.myIntegrableObjects.clear();
516	+
517	+
518	+	for (j = 0; j < molInfo.nAtoms; j++){
519	+
520	+	#ifdef IS_MPI
521	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
522	+	#else
523	+	slJ = j+atomOffset;
524	+	#endif
525	+
526	+	// if they aren't on the skip list, then they can be integrated
527	+
528	+	if (skipList.find(slJ) == skipList.end()) {
529	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
530	+	info[k].integrableObjects.push_back(mySD);
531	+	molInfo.myIntegrableObjects.push_back(mySD);
532	+	}
533	+	}
534	+
535	+	// all rigid bodies are integrated:
536	+
537	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
538	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
539	+	info[k].integrableObjects.push_back(mySD);
540	+	molInfo.myIntegrableObjects.push_back(mySD);
541	+	}
542	+
543	+
544	+	// send the arrays off to the forceField for init.
545	+
546		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
547		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
548		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
549		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
550		theTorsions);
551
418	–
552		info[k].molecules[i].initialize(molInfo);
553
554
#	Line 423 \| Line 556 \| void SimSetup::makeMolecules(void){
556		delete[] theBonds;
557		delete[] theBends;
558		delete[] theTorsions;
559	<	}
559	>	}
560		}
561
562		#ifdef IS_MPI
#	Line 433 \| Line 566 \| void SimSetup::makeMolecules(void){
566
567		// clean up the forcefield
568
569	<	the_ff->calcRcut();
569	>	if (!globals->haveRcut()){
570	>
571	>	the_ff->calcRcut();
572	>
573	>	} else {
574	>
575	>	the_ff->setRcut( globals->getRcut() );
576	>	}
577	>
578		the_ff->cleanMe();
579		}
580
#	Line 635 \| Line 776 \| void SimSetup::gatherInfo(void){
776		else if (!strcasecmp(force_field, "EAM")){
777		ffCase = FF_EAM;
778		}
779	+	else if (!strcasecmp(force_field, "WATER")){
780	+	ffCase = FF_H2O;
781	+	}
782		else{
783		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
784		force_field);
#	Line 718 \| Line 862 \| void SimSetup::gatherInfo(void){
862		}
863
864		//check whether sample time, status time, thermal time and reset time are divisble by dt
865	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
865	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
866		sprintf(painCave.errMsg,
867		"Sample time is not divisible by dt.\n"
868		"\tThis will result in samples that are not uniformly\n"
#	Line 728 \| Line 872 \| void SimSetup::gatherInfo(void){
872		simError();
873		}
874
875	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
876		sprintf(painCave.errMsg,
877		"Status time is not divisible by dt.\n"
878		"\tThis will result in status reports that are not uniformly\n"
#	Line 764 \| Line 908 \| void SimSetup::gatherInfo(void){
908		if (globals->haveSampleTime()){
909		info[i].sampleTime = globals->getSampleTime();
910		info[i].statusTime = info[i].sampleTime;
767	–	info[i].thermalTime = info[i].sampleTime;
911		}
912		else{
913		info[i].sampleTime = globals->getRunTime();
914		info[i].statusTime = info[i].sampleTime;
772	–	info[i].thermalTime = info[i].sampleTime;
915		}
916
917		if (globals->haveStatusTime()){
#	Line 778 \| Line 920 \| void SimSetup::gatherInfo(void){
920
921		if (globals->haveThermalTime()){
922		info[i].thermalTime = globals->getThermalTime();
923	+	} else {
924	+	info[i].thermalTime = globals->getRunTime();
925		}
926
927		info[i].resetIntegrator = 0;
#	Line 837 \| Line 981 \| void SimSetup::gatherInfo(void){
981		for (int i = 0; i < nInfo; i++){
982		info[i].setSeed(seedValue);
983		}
984	<
984	>
985		#ifdef IS_MPI
986	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
986	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
987		MPIcheckPoint();
988		#endif // is_mpi
989		}
#	Line 848 \| Line 992 \| void SimSetup::finalInfoCheck(void){
992		void SimSetup::finalInfoCheck(void){
993		int index;
994		int usesDipoles;
995	+	int usesCharges;
996		int i;
997
998		for (i = 0; i < nInfo; i++){
#	Line 859 \| Line 1004 \| void SimSetup::finalInfoCheck(void){
1004		usesDipoles = (info[i].atoms[index])->hasDipole();
1005		index++;
1006		}
1007	<
1007	>	index = 0;
1008	>	usesCharges = 0;
1009	>	while ((index < info[i].n_atoms) && !usesCharges){
1010	>	usesCharges= (info[i].atoms[index])->hasCharge();
1011	>	index++;
1012	>	}
1013		#ifdef IS_MPI
1014		int myUse = usesDipoles;
1015		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1016		#endif //is_mpi
1017
1018	<	double theEcr, theEst;
1018	>	double theRcut, theRsw;
1019
1020		if (globals->getUseRF()){
1021		info[i].useReactionField = 1;
1022
1023	<	if (!globals->haveECR()){
1023	>	if (!globals->haveRcut()){
1024		sprintf(painCave.errMsg,
1025	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1025	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1026		"\tOOPSE will use a default value of 15.0 angstroms"
1027	<	"\tfor the electrostaticCutoffRadius.\n");
1027	>	"\tfor the cutoffRadius.\n");
1028		painCave.isFatal = 0;
1029		simError();
1030	<	theEcr = 15.0;
1030	>	theRcut = 15.0;
1031		}
1032		else{
1033	<	theEcr = globals->getECR();
1033	>	theRcut = globals->getRcut();
1034		}
1035
1036	<	if (!globals->haveEST()){
1037	<	sprintf(painCave.errMsg,
1038	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1036	>	if (!globals->haveRsw()){
1037	>	sprintf(painCave.errMsg,
1038	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1039		"\tOOPSE will use a default value of\n"
1040	<	"\t0.05 * electrostaticCutoffRadius\n"
891	<	"\tfor the electrostaticSkinThickness\n");
1040	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1041		painCave.isFatal = 0;
1042		simError();
1043	<	theEst = 0.05 * theEcr;
1043	>	theRsw = 0.95 * theRcut;
1044		}
1045		else{
1046	<	theEst = globals->getEST();
1046	>	theRsw = globals->getRsw();
1047		}
1048
1049	<	info[i].setDefaultEcr(theEcr, theEst);
1049	>	info[i].setDefaultRcut(theRcut, theRsw);
1050
1051		if (!globals->haveDielectric()){
1052		sprintf(painCave.errMsg,
#	Line 910 \| Line 1059 \| void SimSetup::finalInfoCheck(void){
1059		info[i].dielectric = globals->getDielectric();
1060		}
1061		else{
1062	<	if (usesDipoles){
1063	<	if (!globals->haveECR()){
1062	>	if (usesDipoles \|\| usesCharges){
1063	>
1064	>	if (!globals->haveRcut()){
1065		sprintf(painCave.errMsg,
1066	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1066	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1067		"\tOOPSE will use a default value of 15.0 angstroms"
1068	<	"\tfor the electrostaticCutoffRadius.\n");
1069	<	painCave.isFatal = 0;
1070	<	simError();
1071	<	theEcr = 15.0;
1072	<	}
1068	>	"\tfor the cutoffRadius.\n");
1069	>	painCave.isFatal = 0;
1070	>	simError();
1071	>	theRcut = 15.0;
1072	>	}
1073		else{
1074	<	theEcr = globals->getECR();
1074	>	theRcut = globals->getRcut();
1075		}
1076	<
1077	<	if (!globals->haveEST()){
1078	<	sprintf(painCave.errMsg,
1079	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1076	>
1077	>	if (!globals->haveRsw()){
1078	>	sprintf(painCave.errMsg,
1079	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1080		"\tOOPSE will use a default value of\n"
1081	<	"\t0.05 * electrostaticCutoffRadius\n"
932	<	"\tfor the electrostaticSkinThickness\n");
1081	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1082		painCave.isFatal = 0;
1083		simError();
1084	<	theEst = 0.05 * theEcr;
1084	>	theRsw = 0.95 * theRcut;
1085		}
1086		else{
1087	<	theEst = globals->getEST();
1087	>	theRsw = globals->getRsw();
1088		}
1089	+
1090	+	info[i].setDefaultRcut(theRcut, theRsw);
1091
941	–	info[i].setDefaultEcr(theEcr, theEst);
1092		}
1093		}
1094		}
#	Line 1136 \| Line 1286 \| void SimSetup::createFF(void){
1286		the_ff = new EAM_FF();
1287		break;
1288
1289	+	case FF_H2O:
1290	+	the_ff = new WATER();
1291	+	break;
1292	+
1293		default:
1294		sprintf(painCave.errMsg,
1295		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1156 \| Line 1310 \| void SimSetup::compList(void){
1310		LinkedMolStamp* headStamp = new LinkedMolStamp();
1311		LinkedMolStamp* currentStamp = NULL;
1312		comp_stamps = new MoleculeStamp * [n_components];
1313	+	bool haveCutoffGroups;
1314
1315	+	haveCutoffGroups = false;
1316	+
1317		// make an array of molecule stamps that match the components used.
1318		// also extract the used stamps out into a separate linked list
1319
#	Line 1191 \| Line 1348 \| void SimSetup::compList(void){
1348		headStamp->add(currentStamp);
1349		comp_stamps[i] = headStamp->match(id);
1350		}
1351	+
1352	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1353	+	haveCutoffGroups = true;
1354		}
1355	+
1356	+	for (i = 0; i < nInfo; i++)
1357	+	info[i].haveCutoffGroups = haveCutoffGroups;
1358
1359		#ifdef IS_MPI
1360		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1208 \| Line 1371 \| void SimSetup::calcSysValues(void){
1371		tot_bonds = 0;
1372		tot_bends = 0;
1373		tot_torsions = 0;
1374	+	tot_rigid = 0;
1375		for (i = 0; i < n_components; i++){
1376		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1377		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1378		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1379		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1380	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1381		}
1382	<
1382	>
1383		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1384		molMembershipArray = new int[tot_atoms];
1385
#	Line 1236 \| Line 1401 \| void SimSetup::mpiMolDivide(void){
1401		int i, j, k;
1402		int localMol, allMol;
1403		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1404	+	int local_rigid;
1405	+	vector<int> globalMolIndex;
1406
1407		mpiSim = new mpiSimulation(info);
1408
1409	<	globalIndex = mpiSim->divideLabor();
1409	>	mpiSim->divideLabor();
1410	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1411	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1412
1413		// set up the local variables
1414
#	Line 1252 \| Line 1421 \| void SimSetup::mpiMolDivide(void){
1421		local_bonds = 0;
1422		local_bends = 0;
1423		local_torsions = 0;
1424	<	globalAtomIndex = 0;
1424	>	local_rigid = 0;
1425	>	globalAtomCounter = 0;
1426
1257	–
1427		for (i = 0; i < n_components; i++){
1428		for (j = 0; j < components_nmol[i]; j++){
1429		if (mol2proc[allMol] == worldRank){
#	Line 1262 \| Line 1431 \| void SimSetup::mpiMolDivide(void){
1431		local_bonds += comp_stamps[i]->getNBonds();
1432		local_bends += comp_stamps[i]->getNBends();
1433		local_torsions += comp_stamps[i]->getNTorsions();
1434	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1435		localMol++;
1436		}
1437		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1438	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1439	<	globalAtomIndex++;
1438	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1439	>	globalAtomCounter++;
1440		}
1441
1442		allMol++;
#	Line 1275 \| Line 1445 \| void SimSetup::mpiMolDivide(void){
1445		local_SRI = local_bonds + local_bends + local_torsions;
1446
1447		info[0].n_atoms = mpiSim->getMyNlocal();
1448	+
1449
1450		if (local_atoms != info[0].n_atoms){
1451		sprintf(painCave.errMsg,
#	Line 1307 \| Line 1478 \| void SimSetup::makeSysArrays(void){
1478
1479		Atom** the_atoms;
1480		Molecule* the_molecules;
1310	–	Exclude** the_excludes;
1481
1312	–
1482		for (l = 0; l < nInfo; l++){
1483		// create the atom and short range interaction arrays
1484
#	Line 1335 \| Line 1504 \| void SimSetup::makeSysArrays(void){
1504		#else // is_mpi
1505
1506		molIndex = 0;
1507	<	globalAtomIndex = 0;
1507	>	globalAtomCounter = 0;
1508		for (i = 0; i < n_components; i++){
1509		for (j = 0; j < components_nmol[i]; j++){
1510		the_molecules[molIndex].setStampID(i);
1511		the_molecules[molIndex].setMyIndex(molIndex);
1512		the_molecules[molIndex].setGlobalIndex(molIndex);
1513		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1514	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1515	<	globalAtomIndex++;
1514	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1515	>	globalAtomCounter++;
1516		}
1517		molIndex++;
1518		}
#	Line 1352 \| Line 1521 \| void SimSetup::makeSysArrays(void){
1521
1522		#endif // is_mpi
1523
1524	<
1525	<	if (info[l].n_SRI){
1526	<	Exclude::createArray(info[l].n_SRI);
1358	<	the_excludes = new Exclude * [info[l].n_SRI];
1359	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1360	<	the_excludes[ex] = new Exclude(ex);
1361	<	}
1362	<	info[l].globalExcludes = new int;
1363	<	info[l].n_exclude = info[l].n_SRI;
1364	<	}
1365	<	else{
1366	<	Exclude::createArray(1);
1367	<	the_excludes = new Exclude * ;
1368	<	the_excludes[0] = new Exclude(0);
1369	<	the_excludes[0]->setPair(0, 0);
1370	<	info[l].globalExcludes = new int;
1371	<	info[l].globalExcludes[0] = 0;
1372	<	info[l].n_exclude = 0;
1373	<	}
1374	<
1524	>	info[l].globalExcludes = new int;
1525	>	info[l].globalExcludes[0] = 0;
1526	>
1527		// set the arrays into the SimInfo object
1528
1529		info[l].atoms = the_atoms;
1530		info[l].molecules = the_molecules;
1531		info[l].nGlobalExcludes = 0;
1532	<	info[l].excludes = the_excludes;
1381	<
1532	>
1533		the_ff->setSimInfo(info);
1534		}
1535		}
#	Line 1650 \| Line 1801 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1801		}
1802
1803		theInfo.addProperty(zconsForcePolicy);
1804	+
1805	+	//set zcons gap
1806	+	DoubleData* zconsGap = new DoubleData();
1807	+	zconsGap->setID(ZCONSGAP_ID);
1808	+
1809	+	if (globals->haveZConsGap()){
1810	+	zconsGap->setData(globals->getZconsGap());
1811	+	theInfo.addProperty(zconsGap);
1812	+	}
1813
1814	+	//set zcons fixtime
1815	+	DoubleData* zconsFixtime = new DoubleData();
1816	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1817	+
1818	+	if (globals->haveZConsFixTime()){
1819	+	zconsFixtime->setData(globals->getZconsFixtime());
1820	+	theInfo.addProperty(zconsFixtime);
1821	+	}
1822	+
1823	+	//set zconsUsingSMD
1824	+	IntData* zconsUsingSMD = new IntData();
1825	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1826	+
1827	+	if (globals->haveZConsUsingSMD()){
1828	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1829	+	theInfo.addProperty(zconsUsingSMD);
1830	+	}
1831	+
1832		//Determine the name of ouput file and add it into SimInfo's property list
1833		//Be careful, do not use inFileName, since it is a pointer which
1834		//point to a string at master node, and slave nodes do not contain that string
#	Line 1680 \| Line 1858 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1858		tempParaItem.zPos = zconStamp[i]->getZpos();
1859		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1860		tempParaItem.kRatio = zconStamp[i]->getKratio();
1861	<
1861	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1862	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1863		zconsParaData->addItem(tempParaItem);
1864		}
1865
#	Line 1698 \| Line 1877 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1877		//push data into siminfo, therefore, we can retrieve later
1878		theInfo.addProperty(zconsParaData);
1879		}
1880	+
1881	+	void SimSetup::makeMinimizer(){
1882	+
1883	+	OOPSEMinimizer* myOOPSEMinimizer;
1884	+	MinimizerParameterSet* param;
1885	+	char minimizerName[100];
1886	+
1887	+	for (int i = 0; i < nInfo; i++){
1888	+
1889	+	//prepare parameter set for minimizer
1890	+	param = new MinimizerParameterSet();
1891	+	param->setDefaultParameter();
1892	+
1893	+	if (globals->haveMinimizer()){
1894	+	param->setFTol(globals->getMinFTol());
1895	+	}
1896	+
1897	+	if (globals->haveMinGTol()){
1898	+	param->setGTol(globals->getMinGTol());
1899	+	}
1900	+
1901	+	if (globals->haveMinMaxIter()){
1902	+	param->setMaxIteration(globals->getMinMaxIter());
1903	+	}
1904	+
1905	+	if (globals->haveMinWriteFrq()){
1906	+	param->setMaxIteration(globals->getMinMaxIter());
1907	+	}
1908	+
1909	+	if (globals->haveMinWriteFrq()){
1910	+	param->setWriteFrq(globals->getMinWriteFrq());
1911	+	}
1912	+
1913	+	if (globals->haveMinStepSize()){
1914	+	param->setStepSize(globals->getMinStepSize());
1915	+	}
1916	+
1917	+	if (globals->haveMinLSMaxIter()){
1918	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1919	+	}
1920	+
1921	+	if (globals->haveMinLSTol()){
1922	+	param->setLineSearchTol(globals->getMinLSTol());
1923	+	}
1924	+
1925	+	strcpy(minimizerName, globals->getMinimizer());
1926	+
1927	+	if (!strcasecmp(minimizerName, "CG")){
1928	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1929	+	}
1930	+	else if (!strcasecmp(minimizerName, "SD")){
1931	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1932	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1933	+	}
1934	+	else{
1935	+	sprintf(painCave.errMsg,
1936	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1937	+	painCave.isFatal = 0;
1938	+	simError();
1939	+
1940	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1941	+	}
1942	+	info[i].the_integrator = myOOPSEMinimizer;
1943	+
1944	+	//store the minimizer into simInfo
1945	+	info[i].the_minimizer = myOOPSEMinimizer;
1946	+	info[i].has_minimizer = true;
1947	+	}
1948	+
1949	+	}

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 984 by gezelter, Mon Jan 26 21:52:56 2004 UTC vs. Revision 1157 by tim, Tue May 11 20:33:41 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 984 by gezelter, Mon Jan 26 21:52:56 2004 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 2004 UTC