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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 999 by chrisfen, Fri Jan 30 15:01:09 2004 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 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 27 \| Line 30
30		#define FF_DUFF 0
31		#define FF_LJ 1
32		#define FF_EAM 2
33	<	#define FF_H2O 3
33	>	#define FF_H2O 3
34
35		using namespace std;
36
#	Line 144 \| Line 147 \| void SimSetup::createSim(void){
147		// make the output filenames
148
149		makeOutNames();
150	<
148	<	// make the integrator
149	<
150	<	makeIntegrator();
151	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 156 \| 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	+	CutoffGroupStamp* currentCutoffGroup;
187	+	CutoffGroup* myCutoffGroup;
188	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	+	set<int> cutoffAtomSet; //atoms belong to cutoffgroup defined at mdl file
190
191		bond_pair* theBonds;
192		bend_set* theBends;
193		torsion_set* theTorsions;
194
195	+	set<int> skipList;
196	+
197	+	double phi, theta, psi;
198	+	char* molName;
199	+	char rbName[100];
200	+
201		//init the forceField paramters
202
203		the_ff->readParams();
204
182	–
205		// init the atoms
206
207	<	double phi, theta, psi;
186	<	double sux, suy, suz;
187	<	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
188	<	double ux, uy, uz, u, uSqr;
207	>	int nMembers, nNew, rb1, rb2;
208
209		for (k = 0; k < nInfo; k++){
210		the_ff->setSimInfo(&(info[k]));
211
212		atomOffset = 0;
213	<	excludeOffset = 0;
213	>
214		for (i = 0; i < info[k].n_mol; i++){
215		stampID = info[k].molecules[i].getStampID();
216	+	molName = comp_stamps[stampID]->getID();
217
218		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220		molInfo.nBends = comp_stamps[stampID]->getNBends();
221		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	+
226		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
205	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
206	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
207	–	molInfo.myBends = new Bend * [molInfo.nBends];
208	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
227
228	+	if (molInfo.nBonds > 0)
229	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	+	else
231	+	molInfo.myBonds = NULL;
232	+
233	+	if (molInfo.nBends > 0)
234	+	molInfo.myBends = new Bend*[molInfo.nBends];
235	+	else
236	+	molInfo.myBends = NULL;
237	+
238	+	if (molInfo.nTorsions > 0)
239	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	+	else
241	+	molInfo.myTorsions = NULL;
242	+
243		theBonds = new bond_pair[molInfo.nBonds];
244		theBends = new bend_set[molInfo.nBends];
245		theTorsions = new torsion_set[molInfo.nTorsions];
246	<
246	>
247		// make the Atoms
248
249		for (j = 0; j < molInfo.nAtoms; j++){
250		currentAtom = comp_stamps[stampID]->getAtom(j);
251	+
252		if (currentAtom->haveOrientation()){
253		dAtom = new DirectionalAtom((j + atomOffset),
254		info[k].getConfiguration());
#	Line 228 \| Line 262 \| void SimSetup::makeMolecules(void){
262		phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263		theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264		psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265	+
266	+	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267
268	<	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
269	<	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
234	<	Axz = sin(theta) * sin(psi);
235	<
236	<	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
237	<	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
238	<	Ayz = sin(theta) * cos(psi);
239	<
240	<	Azx = sin(phi) * sin(theta);
241	<	Azy = -cos(phi) * sin(theta);
242	<	Azz = cos(theta);
268	>	}
269	>	else{
270
271	<	sux = 0.0;
245	<	suy = 0.0;
246	<	suz = 1.0;
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272
248	–	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
249	–	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
250	–	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
251	–
252	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
253	–
254	–	u = sqrt(uSqr);
255	–	ux = ux / u;
256	–	uy = uy / u;
257	–	uz = uz / u;
258	–
259	–	dAtom->setSUx(ux);
260	–	dAtom->setSUy(uy);
261	–	dAtom->setSUz(uz);
273		}
263	–	else{
264	–	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
265	–	info[k].getConfiguration());
266	–	}
267	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
274
275	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277
278	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
280		#endif // is_mpi
281		}
#	Line 279 \| Line 286 \| void SimSetup::makeMolecules(void){
286		theBonds[j].a = currentBond->getA() + atomOffset;
287		theBonds[j].b = currentBond->getB() + atomOffset;
288
289	<	exI = theBonds[j].a;
290	<	exJ = theBonds[j].b;
289	>	tempI = theBonds[j].a;
290	>	tempJ = theBonds[j].b;
291
285	–	// exclude_I must always be the smaller of the pair
286	–	if (exI > exJ){
287	–	tempEx = exI;
288	–	exI = exJ;
289	–	exJ = tempEx;
290	–	}
292		#ifdef IS_MPI
293	<	tempEx = exI;
294	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
295	<	tempEx = exJ;
296	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
298	<	#else // isn't MPI
299	<
300	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
301	<	#endif //is_mpi
300	>	info[k].excludes->addPair(exI, exJ);
301		}
303	–	excludeOffset += molInfo.nBonds;
302
303		//make the bends
304		for (j = 0; j < molInfo.nBends; j++){
#	Line 350 \| Line 348 \| void SimSetup::makeMolecules(void){
348		}
349		}
350
351	<	if (!theBends[j].isGhost){
352	<	exI = theBends[j].a;
353	<	exJ = theBends[j].c;
354	<	}
355	<	else{
358	<	exI = theBends[j].a;
359	<	exJ = theBends[j].b;
360	<	}
361	<
362	<	// exclude_I must always be the smaller of the pair
363	<	if (exI > exJ){
364	<	tempEx = exI;
365	<	exI = exJ;
366	<	exJ = tempEx;
367	<	}
351	>	if (theBends[j].isGhost) {
352	>
353	>	tempI = theBends[j].a;
354	>	tempJ = theBends[j].b;
355	>
356		#ifdef IS_MPI
357	<	tempEx = exI;
358	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
359	<	tempEx = exJ;
360	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
366	<	#else // isn't MPI
367	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
368	<	#endif //is_mpi
365	>	} else {
366	>
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
379	–	excludeOffset += molInfo.nBends;
386
387		for (j = 0; j < molInfo.nTorsions; j++){
388		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 385 \| Line 391 \| void SimSetup::makeMolecules(void){
391		theTorsions[j].c = currentTorsion->getC() + atomOffset;
392		theTorsions[j].d = currentTorsion->getD() + atomOffset;
393
394	<	exI = theTorsions[j].a;
395	<	exJ = theTorsions[j].d;
394	>	tempI = theTorsions[j].a;
395	>	tempJ = theTorsions[j].b;
396	>	tempK = theTorsions[j].c;
397	>	tempL = theTorsions[j].d;
398
399	<	// exclude_I must always be the smaller of the pair
400	<	if (exI > exJ){
401	<	tempEx = exI;
402	<	exI = exJ;
403	<	exJ = tempEx;
399	>	#ifdef IS_MPI
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410	>
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418	>
419	>
420	>	molInfo.myRigidBodies.clear();
421	>
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423	>
424	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	>	nMembers = currentRigidBody->getNMembers();
426	>
427	>	// Create the Rigid Body:
428	>
429	>	myRB = new RigidBody();
430	>
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435	>
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438	>
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441	>
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445	>
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448	>
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452	>	#ifdef IS_MPI
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459		}
460	+
461	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	+
464	+	tempI = currentRigidBody->getMember(rb1);
465	+	tempJ = currentRigidBody->getMember(rb2);
466	+
467	+	// Some explanation is required here.
468	+	// Fortran indexing starts at 1, while c indexing starts at 0
469	+	// Also, in parallel computations, the GlobalIndex is
470	+	// used for the exclude list:
471	+
472		#ifdef IS_MPI
473	<	tempEx = exI;
474	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
475	<	tempEx = exJ;
476	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484
485	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
486	<	#else // isn't MPI
405	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
406	<	#endif //is_mpi
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487		}
488	<	excludeOffset += molInfo.nTorsions;
488	>
489
490	+	//create cutoff group for molecule
491
492	<	// send the arrays off to the forceField for init.
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496	>
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499	>
500	>	myCutoffGroup = new CutoffGroup();
501	>
502	>	for (int cg = 0; cg < nMembers; cg++) {
503	>
504	>	// molI is atom numbering inside this molecule
505	>	molI = currentCutoffGroup->getMember(cg);
506	>
507	>	// tempI is atom numbering on local processor
508	>	tempI = molI + atomOffset;
509	>
510	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	>
512	>	cutoffAtomSet.insert(tempI);
513	>	}
514	>
515	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	>
518	>	//creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file
519	>
520	>	for(j = 0; j < molInfo.nAtoms; j++){
521	>
522	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	>	myCutoffGroup = new CutoffGroup();
524	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	>	}
527	>
528	>	}
529	>
530	>
531	>
532	>
533	>	// After this is all set up, scan through the atoms to
534	>	// see if they can be added to the integrableObjects:
535	>
536	>	molInfo.myIntegrableObjects.clear();
537	>
538	>
539	>	for (j = 0; j < molInfo.nAtoms; j++){
540	>
541	>	#ifdef IS_MPI
542	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	>	#else
544	>	slJ = j+atomOffset;
545	>	#endif
546	>
547	>	// if they aren't on the skip list, then they can be integrated
548	>
549	>	if (skipList.find(slJ) == skipList.end()) {
550	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	>	info[k].integrableObjects.push_back(mySD);
552	>	molInfo.myIntegrableObjects.push_back(mySD);
553	>	}
554	>	}
555	>
556	>	// all rigid bodies are integrated:
557
558	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	+	info[k].integrableObjects.push_back(mySD);
561	+	molInfo.myIntegrableObjects.push_back(mySD);
562	+	}
563	+
564	+
565	+	// send the arrays off to the forceField for init.
566	+
567		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571		theTorsions);
572
419	–
573		info[k].molecules[i].initialize(molInfo);
574
575
#	Line 424 \| Line 577 \| void SimSetup::makeMolecules(void){
577		delete[] theBonds;
578		delete[] theBends;
579		delete[] theTorsions;
580	<	}
580	>	}
581		}
582
583		#ifdef IS_MPI
#	Line 432 \| Line 585 \| void SimSetup::makeMolecules(void){
585		MPIcheckPoint();
586		#endif // is_mpi
587
435	–	// clean up the forcefield
436	–
437	–	the_ff->calcRcut();
438	–	the_ff->cleanMe();
588		}
589
590		void SimSetup::initFromBass(void){
#	Line 722 \| Line 871 \| void SimSetup::gatherInfo(void){
871		}
872
873		//check whether sample time, status time, thermal time and reset time are divisble by dt
874	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
874	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875		sprintf(painCave.errMsg,
876		"Sample time is not divisible by dt.\n"
877		"\tThis will result in samples that are not uniformly\n"
#	Line 732 \| Line 881 \| void SimSetup::gatherInfo(void){
881		simError();
882		}
883
884	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
884	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885		sprintf(painCave.errMsg,
886		"Status time is not divisible by dt.\n"
887		"\tThis will result in status reports that are not uniformly\n"
#	Line 768 \| Line 917 \| void SimSetup::gatherInfo(void){
917		if (globals->haveSampleTime()){
918		info[i].sampleTime = globals->getSampleTime();
919		info[i].statusTime = info[i].sampleTime;
771	–	info[i].thermalTime = info[i].sampleTime;
920		}
921		else{
922		info[i].sampleTime = globals->getRunTime();
923		info[i].statusTime = info[i].sampleTime;
776	–	info[i].thermalTime = info[i].sampleTime;
924		}
925
926		if (globals->haveStatusTime()){
#	Line 782 \| Line 929 \| void SimSetup::gatherInfo(void){
929
930		if (globals->haveThermalTime()){
931		info[i].thermalTime = globals->getThermalTime();
932	+	} else {
933	+	info[i].thermalTime = globals->getRunTime();
934		}
935
936		info[i].resetIntegrator = 0;
#	Line 799 \| Line 948 \| void SimSetup::gatherInfo(void){
948
949		info[i].useInitXSstate = globals->getUseInitXSstate();
950		info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951	<
951	>
952	>	// check for thermodynamic integration
953	>	if (globals->getUseThermInt()) {
954	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
955	>	info[i].useThermInt = globals->getUseThermInt();
956	>	info[i].thermIntLambda = globals->getThermIntLambda();
957	>	info[i].thermIntK = globals->getThermIntK();
958	>
959	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
960	>	info[i].restraint = myRestraint;
961	>	}
962	>	else {
963	>	sprintf(painCave.errMsg,
964	>	"SimSetup Error:\n"
965	>	"\tKeyword useThermInt was set to 'true' but\n"
966	>	"\tthermodynamicIntegrationLambda (and/or\n"
967	>	"\tthermodynamicIntegrationK) was not specified.\n"
968	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
969	>	painCave.isFatal = 1;
970	>	simError();
971	>	}
972	>	}
973	>	else if(globals->haveThermIntLambda() \|\| globals->haveThermIntK()){
974	>	sprintf(painCave.errMsg,
975	>	"SimSetup Warning: If you want to use Thermodynamic\n"
976	>	"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
977	>	"\tThe useThermInt keyword is 'false' by default, so your\n"
978	>	"\tlambda and/or k values are being ignored.\n");
979	>	painCave.isFatal = 0;
980	>	simError();
981	>	}
982		}
983
984		//setup seed for random number generator
#	Line 841 \| Line 1020 \| void SimSetup::gatherInfo(void){
1020		for (int i = 0; i < nInfo; i++){
1021		info[i].setSeed(seedValue);
1022		}
1023	<
1023	>
1024		#ifdef IS_MPI
1025		strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1026		MPIcheckPoint();
#	Line 852 \| Line 1031 \| void SimSetup::finalInfoCheck(void){
1031		void SimSetup::finalInfoCheck(void){
1032		int index;
1033		int usesDipoles;
1034	+	int usesCharges;
1035		int i;
1036
1037		for (i = 0; i < nInfo; i++){
#	Line 863 \| Line 1043 \| void SimSetup::finalInfoCheck(void){
1043		usesDipoles = (info[i].atoms[index])->hasDipole();
1044		index++;
1045		}
1046	<
1046	>	index = 0;
1047	>	usesCharges = 0;
1048	>	while ((index < info[i].n_atoms) && !usesCharges){
1049	>	usesCharges= (info[i].atoms[index])->hasCharge();
1050	>	index++;
1051	>	}
1052		#ifdef IS_MPI
1053		int myUse = usesDipoles;
1054		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1055		#endif //is_mpi
1056
1057	<	double theEcr, theEst;
1057	>	double theRcut, theRsw;
1058
1059	+	if (globals->haveRcut()) {
1060	+	theRcut = globals->getRcut();
1061	+
1062	+	if (globals->haveRsw())
1063	+	theRsw = globals->getRsw();
1064	+	else
1065	+	theRsw = theRcut;
1066	+
1067	+	info[i].setDefaultRcut(theRcut, theRsw);
1068	+
1069	+	} else {
1070	+
1071	+	the_ff->calcRcut();
1072	+	theRcut = info[i].getRcut();
1073	+
1074	+	if (globals->haveRsw())
1075	+	theRsw = globals->getRsw();
1076	+	else
1077	+	theRsw = theRcut;
1078	+
1079	+	info[i].setDefaultRcut(theRcut, theRsw);
1080	+	}
1081	+
1082		if (globals->getUseRF()){
1083		info[i].useReactionField = 1;
1084	<
1085	<	if (!globals->haveECR()){
1084	>
1085	>	if (!globals->haveRcut()){
1086		sprintf(painCave.errMsg,
1087	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1087	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1088		"\tOOPSE will use a default value of 15.0 angstroms"
1089	<	"\tfor the electrostaticCutoffRadius.\n");
1089	>	"\tfor the cutoffRadius.\n");
1090		painCave.isFatal = 0;
1091		simError();
1092	<	theEcr = 15.0;
1092	>	theRcut = 15.0;
1093		}
1094		else{
1095	<	theEcr = globals->getECR();
1095	>	theRcut = globals->getRcut();
1096		}
1097
1098	<	if (!globals->haveEST()){
1098	>	if (!globals->haveRsw()){
1099		sprintf(painCave.errMsg,
1100	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1100	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1101		"\tOOPSE will use a default value of\n"
1102	<	"\t0.05 * electrostaticCutoffRadius\n"
895	<	"\tfor the electrostaticSkinThickness\n");
1102	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1103		painCave.isFatal = 0;
1104		simError();
1105	<	theEst = 0.05 * theEcr;
1105	>	theRsw = 0.95 * theRcut;
1106		}
1107		else{
1108	<	theEst = globals->getEST();
1108	>	theRsw = globals->getRsw();
1109		}
1110
1111	<	info[i].setDefaultEcr(theEcr, theEst);
1111	>	info[i].setDefaultRcut(theRcut, theRsw);
1112
1113		if (!globals->haveDielectric()){
1114		sprintf(painCave.errMsg,
#	Line 914 \| Line 1121 \| void SimSetup::finalInfoCheck(void){
1121		info[i].dielectric = globals->getDielectric();
1122		}
1123		else{
1124	<	if (usesDipoles){
1125	<	if (!globals->haveECR()){
1124	>	if (usesDipoles \|\| usesCharges){
1125	>
1126	>	if (!globals->haveRcut()){
1127		sprintf(painCave.errMsg,
1128	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1128	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1129		"\tOOPSE will use a default value of 15.0 angstroms"
1130	<	"\tfor the electrostaticCutoffRadius.\n");
1131	<	painCave.isFatal = 0;
1132	<	simError();
1133	<	theEcr = 15.0;
1134	<	}
1130	>	"\tfor the cutoffRadius.\n");
1131	>	painCave.isFatal = 0;
1132	>	simError();
1133	>	theRcut = 15.0;
1134	>	}
1135		else{
1136	<	theEcr = globals->getECR();
1136	>	theRcut = globals->getRcut();
1137		}
1138	<
1139	<	if (!globals->haveEST()){
1138	>
1139	>	if (!globals->haveRsw()){
1140		sprintf(painCave.errMsg,
1141	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1141	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1142		"\tOOPSE will use a default value of\n"
1143	<	"\t0.05 * electrostaticCutoffRadius\n"
936	<	"\tfor the electrostaticSkinThickness\n");
1143	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1144		painCave.isFatal = 0;
1145		simError();
1146	<	theEst = 0.05 * theEcr;
1146	>	theRsw = 0.95 * theRcut;
1147		}
1148		else{
1149	<	theEst = globals->getEST();
1149	>	theRsw = globals->getRsw();
1150		}
1151	+
1152	+	info[i].setDefaultRcut(theRcut, theRsw);
1153
945	–	info[i].setDefaultEcr(theEcr, theEst);
1154		}
1155		}
1156		}
#	Line 950 \| Line 1158 \| void SimSetup::finalInfoCheck(void){
1158		strcpy(checkPointMsg, "post processing checks out");
1159		MPIcheckPoint();
1160		#endif // is_mpi
1161	+
1162	+	// clean up the forcefield
1163	+	the_ff->cleanMe();
1164		}
1165
1166		void SimSetup::initSystemCoords(void){
#	Line 1080 \| Line 1291 \| void SimSetup::makeOutNames(void){
1291		}
1292		}
1293
1294	+	strcpy(info[k].rawPotName, inFileName);
1295	+	nameLength = strlen(info[k].rawPotName);
1296	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1297	+	if (!strcmp(endTest, ".bass")){
1298	+	strcpy(endTest, ".raw");
1299	+	}
1300	+	else if (!strcmp(endTest, ".BASS")){
1301	+	strcpy(endTest, ".raw");
1302	+	}
1303	+	else{
1304	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1305	+	if (!strcmp(endTest, ".bss")){
1306	+	strcpy(endTest, ".raw");
1307	+	}
1308	+	else if (!strcmp(endTest, ".mdl")){
1309	+	strcpy(endTest, ".raw");
1310	+	}
1311	+	else{
1312	+	strcat(info[k].rawPotName, ".raw");
1313	+	}
1314	+	}
1315	+
1316		#ifdef IS_MPI
1317
1318		}
#	Line 1164 \| Line 1397 \| void SimSetup::compList(void){
1397		LinkedMolStamp* headStamp = new LinkedMolStamp();
1398		LinkedMolStamp* currentStamp = NULL;
1399		comp_stamps = new MoleculeStamp * [n_components];
1400	+	bool haveCutoffGroups;
1401
1402	+	haveCutoffGroups = false;
1403	+
1404		// make an array of molecule stamps that match the components used.
1405		// also extract the used stamps out into a separate linked list
1406
#	Line 1199 \| Line 1435 \| void SimSetup::compList(void){
1435		headStamp->add(currentStamp);
1436		comp_stamps[i] = headStamp->match(id);
1437		}
1438	+
1439	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1440	+	haveCutoffGroups = true;
1441		}
1442	+
1443	+	for (i = 0; i < nInfo; i++)
1444	+	info[i].haveCutoffGroups = haveCutoffGroups;
1445
1446		#ifdef IS_MPI
1447		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1216 \| Line 1458 \| void SimSetup::calcSysValues(void){
1458		tot_bonds = 0;
1459		tot_bends = 0;
1460		tot_torsions = 0;
1461	+	tot_rigid = 0;
1462		for (i = 0; i < n_components; i++){
1463		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1464		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1465		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1466		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1467	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1468		}
1469	<
1469	>
1470		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1471		molMembershipArray = new int[tot_atoms];
1472
#	Line 1244 \| Line 1488 \| void SimSetup::mpiMolDivide(void){
1488		int i, j, k;
1489		int localMol, allMol;
1490		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1491	+	int local_rigid;
1492	+	vector<int> globalMolIndex;
1493
1494		mpiSim = new mpiSimulation(info);
1495
1496	<	globalIndex = mpiSim->divideLabor();
1496	>	mpiSim->divideLabor();
1497	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1498	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1499
1500		// set up the local variables
1501
#	Line 1260 \| Line 1508 \| void SimSetup::mpiMolDivide(void){
1508		local_bonds = 0;
1509		local_bends = 0;
1510		local_torsions = 0;
1511	<	globalAtomIndex = 0;
1511	>	local_rigid = 0;
1512	>	globalAtomCounter = 0;
1513
1265	–
1514		for (i = 0; i < n_components; i++){
1515		for (j = 0; j < components_nmol[i]; j++){
1516		if (mol2proc[allMol] == worldRank){
#	Line 1270 \| Line 1518 \| void SimSetup::mpiMolDivide(void){
1518		local_bonds += comp_stamps[i]->getNBonds();
1519		local_bends += comp_stamps[i]->getNBends();
1520		local_torsions += comp_stamps[i]->getNTorsions();
1521	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1522		localMol++;
1523		}
1524		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1525	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1526	<	globalAtomIndex++;
1525	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1526	>	globalAtomCounter++;
1527		}
1528
1529		allMol++;
#	Line 1283 \| Line 1532 \| void SimSetup::mpiMolDivide(void){
1532		local_SRI = local_bonds + local_bends + local_torsions;
1533
1534		info[0].n_atoms = mpiSim->getMyNlocal();
1535	+
1536
1537		if (local_atoms != info[0].n_atoms){
1538		sprintf(painCave.errMsg,
#	Line 1315 \| Line 1565 \| void SimSetup::makeSysArrays(void){
1565
1566		Atom** the_atoms;
1567		Molecule* the_molecules;
1318	–	Exclude** the_excludes;
1568
1320	–
1569		for (l = 0; l < nInfo; l++){
1570		// create the atom and short range interaction arrays
1571
#	Line 1343 \| Line 1591 \| void SimSetup::makeSysArrays(void){
1591		#else // is_mpi
1592
1593		molIndex = 0;
1594	<	globalAtomIndex = 0;
1594	>	globalAtomCounter = 0;
1595		for (i = 0; i < n_components; i++){
1596		for (j = 0; j < components_nmol[i]; j++){
1597		the_molecules[molIndex].setStampID(i);
1598		the_molecules[molIndex].setMyIndex(molIndex);
1599		the_molecules[molIndex].setGlobalIndex(molIndex);
1600		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1601	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1602	<	globalAtomIndex++;
1601	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1602	>	globalAtomCounter++;
1603		}
1604		molIndex++;
1605		}
#	Line 1360 \| Line 1608 \| void SimSetup::makeSysArrays(void){
1608
1609		#endif // is_mpi
1610
1611	<
1612	<	if (info[l].n_SRI){
1613	<	Exclude::createArray(info[l].n_SRI);
1366	<	the_excludes = new Exclude * [info[l].n_SRI];
1367	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1368	<	the_excludes[ex] = new Exclude(ex);
1369	<	}
1370	<	info[l].globalExcludes = new int;
1371	<	info[l].n_exclude = info[l].n_SRI;
1372	<	}
1373	<	else{
1374	<	Exclude::createArray(1);
1375	<	the_excludes = new Exclude * ;
1376	<	the_excludes[0] = new Exclude(0);
1377	<	the_excludes[0]->setPair(0, 0);
1378	<	info[l].globalExcludes = new int;
1379	<	info[l].globalExcludes[0] = 0;
1380	<	info[l].n_exclude = 0;
1381	<	}
1382	<
1611	>	info[l].globalExcludes = new int;
1612	>	info[l].globalExcludes[0] = 0;
1613	>
1614		// set the arrays into the SimInfo object
1615
1616		info[l].atoms = the_atoms;
1617		info[l].molecules = the_molecules;
1618		info[l].nGlobalExcludes = 0;
1619	<	info[l].excludes = the_excludes;
1389	<
1619	>
1620		the_ff->setSimInfo(info);
1621		}
1622		}
#	Line 1658 \| Line 1888 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1888		}
1889
1890		theInfo.addProperty(zconsForcePolicy);
1891	+
1892	+	//set zcons gap
1893	+	DoubleData* zconsGap = new DoubleData();
1894	+	zconsGap->setID(ZCONSGAP_ID);
1895	+
1896	+	if (globals->haveZConsGap()){
1897	+	zconsGap->setData(globals->getZconsGap());
1898	+	theInfo.addProperty(zconsGap);
1899	+	}
1900
1901	+	//set zcons fixtime
1902	+	DoubleData* zconsFixtime = new DoubleData();
1903	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1904	+
1905	+	if (globals->haveZConsFixTime()){
1906	+	zconsFixtime->setData(globals->getZconsFixtime());
1907	+	theInfo.addProperty(zconsFixtime);
1908	+	}
1909	+
1910	+	//set zconsUsingSMD
1911	+	IntData* zconsUsingSMD = new IntData();
1912	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1913	+
1914	+	if (globals->haveZConsUsingSMD()){
1915	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1916	+	theInfo.addProperty(zconsUsingSMD);
1917	+	}
1918	+
1919		//Determine the name of ouput file and add it into SimInfo's property list
1920		//Be careful, do not use inFileName, since it is a pointer which
1921		//point to a string at master node, and slave nodes do not contain that string
#	Line 1688 \| Line 1945 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1945		tempParaItem.zPos = zconStamp[i]->getZpos();
1946		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1947		tempParaItem.kRatio = zconStamp[i]->getKratio();
1948	<
1948	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1949	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1950		zconsParaData->addItem(tempParaItem);
1951		}
1952
#	Line 1706 \| Line 1964 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1964		//push data into siminfo, therefore, we can retrieve later
1965		theInfo.addProperty(zconsParaData);
1966		}
1967	+
1968	+	void SimSetup::makeMinimizer(){
1969	+
1970	+	OOPSEMinimizer* myOOPSEMinimizer;
1971	+	MinimizerParameterSet* param;
1972	+	char minimizerName[100];
1973	+
1974	+	for (int i = 0; i < nInfo; i++){
1975	+
1976	+	//prepare parameter set for minimizer
1977	+	param = new MinimizerParameterSet();
1978	+	param->setDefaultParameter();
1979	+
1980	+	if (globals->haveMinimizer()){
1981	+	param->setFTol(globals->getMinFTol());
1982	+	}
1983	+
1984	+	if (globals->haveMinGTol()){
1985	+	param->setGTol(globals->getMinGTol());
1986	+	}
1987	+
1988	+	if (globals->haveMinMaxIter()){
1989	+	param->setMaxIteration(globals->getMinMaxIter());
1990	+	}
1991	+
1992	+	if (globals->haveMinWriteFrq()){
1993	+	param->setMaxIteration(globals->getMinMaxIter());
1994	+	}
1995	+
1996	+	if (globals->haveMinWriteFrq()){
1997	+	param->setWriteFrq(globals->getMinWriteFrq());
1998	+	}
1999	+
2000	+	if (globals->haveMinStepSize()){
2001	+	param->setStepSize(globals->getMinStepSize());
2002	+	}
2003	+
2004	+	if (globals->haveMinLSMaxIter()){
2005	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2006	+	}
2007	+
2008	+	if (globals->haveMinLSTol()){
2009	+	param->setLineSearchTol(globals->getMinLSTol());
2010	+	}
2011	+
2012	+	strcpy(minimizerName, globals->getMinimizer());
2013	+
2014	+	if (!strcasecmp(minimizerName, "CG")){
2015	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2016	+	}
2017	+	else if (!strcasecmp(minimizerName, "SD")){
2018	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2019	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2020	+	}
2021	+	else{
2022	+	sprintf(painCave.errMsg,
2023	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2024	+	painCave.isFatal = 0;
2025	+	simError();
2026	+
2027	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2028	+	}
2029	+	info[i].the_integrator = myOOPSEMinimizer;
2030	+
2031	+	//store the minimizer into simInfo
2032	+	info[i].the_minimizer = myOOPSEMinimizer;
2033	+	info[i].has_minimizer = true;
2034	+	}
2035	+
2036	+	}

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 999 by chrisfen, Fri Jan 30 15:01:09 2004 UTC vs. Revision 1187 by chrisfen, Sat May 22 18:16:18 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 999 by chrisfen, Fri Jan 30 15:01:09 2004 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 2004 UTC