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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 841 by mmeineke, Wed Oct 29 17:55:28 2003 UTC vs.
Revision 1229 by gezelter, Thu Jun 3 20:02:25 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 "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
#	Line 24 | Line 28
28		#define NPTxyz_ENS     4
29
30
31	<	#define FF_DUFF 0
32	<	#define FF_LJ   1
33	<	#define FF_EAM  2
31	>	#define FF_DUFF  0
32	>	#define FF_LJ    1
33	>	#define FF_EAM   2
34	>	#define FF_H2O   3
35
36		using namespace std;
37
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63
64		initSuspend = false;
#	Line 103 | Line 132 | void SimSetup::createSim(void){
132
133		sysObjectsCreation();
134
135	+	// check on the post processing info
136	+
137	+	finalInfoCheck();
138	+
139		// initialize the system coordinates
140
141		if ( !initSuspend ){
#	Line 112 | Line 145 | void SimSetup::createSim(void){
145		info[0].currentTime = 0.0;
146		}
147
115	–	// check on the post processing info
116	–
117	–	finalInfoCheck();
118	–
148		// make the output filenames
149
150		makeOutNames();
151	<
123	<	// make the integrator
124	<
125	<	makeIntegrator();
126	<
151	>
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
154		#endif
#	Line 131 | Line 156 | void SimSetup::createSim(void){
156		// initialize the Fortran
157
158		initFortran();
159	+
160	+	if (globals->haveMinimizer())
161	+	// make minimizer
162	+	makeMinimizer();
163	+	else
164	+	// make the integrator
165	+	makeIntegrator();
166	+
167		}
168
169
170		void SimSetup::makeMolecules(void){
171	<	int k;
172	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI, globalID;
175	>	int stampID, atomOffset, rbOffset, groupOffset;
176		molInit molInfo;
177		DirectionalAtom* dAtom;
178	+	RigidBody* myRB;
179	+	StuntDouble* mySD;
180		LinkedAssign* extras;
181		LinkedAssign* current_extra;
182		AtomStamp* currentAtom;
183		BondStamp* currentBond;
184		BendStamp* currentBend;
185		TorsionStamp* currentTorsion;
186	+	RigidBodyStamp* currentRigidBody;
187	+	CutoffGroupStamp* currentCutoffGroup;
188	+	CutoffGroup* myCutoffGroup;
189	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
190	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
191
192		bond_pair* theBonds;
193		bend_set* theBends;
194		torsion_set* theTorsions;
195
196	+	set<int> skipList;
197
198	+	double phi, theta, psi;
199	+	char* molName;
200	+	char rbName[100];
201	+
202	+	//ConstraintPair* consPair; //constraint pair
203	+	//ConstraintElement* consElement1;  //first element of constraint pair
204	+	//ConstraintElement* consElement2;  //second element of constraint pair
205	+	//int whichRigidBody;
206	+	//int consAtomIndex;  //index of constraint atom in rigid body's atom array
207	+	//vector<pair<int, int> > jointAtoms;
208		//init the forceField paramters
209
210		the_ff->readParams();
211
158	–
212		// init the atoms
213
214	<	double ux, uy, uz, u, uSqr;
214	>	int nMembers, nNew, rb1, rb2;
215
216		for (k = 0; k < nInfo; k++){
217		the_ff->setSimInfo(&(info[k]));
218
219	+	#ifdef IS_MPI
220	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
221	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
222	+	info[k].globalGroupMembership[i] = 0;
223	+	#else
224	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
225	+	for (i = 0; i < info[k].n_atoms; i++)
226	+	info[k].globalGroupMembership[i] = 0;
227	+	#endif
228	+
229		atomOffset = 0;
230	<	excludeOffset = 0;
230	>	groupOffset = 0;
231	>
232		for (i = 0; i < info[k].n_mol; i++){
233		stampID = info[k].molecules[i].getStampID();
234	+	molName = comp_stamps[stampID]->getID();
235
236		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
237		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
238		molInfo.nBends = comp_stamps[stampID]->getNBends();
239		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
240	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
240	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
241
242	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
243	+
244		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	–	molInfo.myBends = new Bend * [molInfo.nBends];
181	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
245
246	+	if (molInfo.nBonds > 0)
247	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
248	+	else
249	+	molInfo.myBonds = NULL;
250	+
251	+	if (molInfo.nBends > 0)
252	+	molInfo.myBends = new Bend*[molInfo.nBends];
253	+	else
254	+	molInfo.myBends = NULL;
255	+
256	+	if (molInfo.nTorsions > 0)
257	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
258	+	else
259	+	molInfo.myTorsions = NULL;
260	+
261		theBonds = new bond_pair[molInfo.nBonds];
262		theBends = new bend_set[molInfo.nBends];
263		theTorsions = new torsion_set[molInfo.nTorsions];
264	<
264	>
265		// make the Atoms
266
267		for (j = 0; j < molInfo.nAtoms; j++){
268		currentAtom = comp_stamps[stampID]->getAtom(j);
269	+
270		if (currentAtom->haveOrientation()){
271		dAtom = new DirectionalAtom((j + atomOffset),
272		info[k].getConfiguration());
273		info[k].n_oriented++;
274		molInfo.myAtoms[j] = dAtom;
275
276	<	ux = currentAtom->getOrntX();
277	<	uy = currentAtom->getOrntY();
278	<	uz = currentAtom->getOrntZ();
276	>	// Directional Atoms have standard unit vectors which are oriented
277	>	// in space using the three Euler angles.  We assume the standard
278	>	// unit vector was originally along the z axis below.
279
280	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
280	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
281	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
282	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
283
284	<	u = sqrt(uSqr);
285	<	ux = ux / u;
205	<	uy = uy / u;
206	<	uz = uz / u;
207	<
208	<	dAtom->setSUx(ux);
209	<	dAtom->setSUy(uy);
210	<	dAtom->setSUz(uz);
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286		}
287		else{
213	–	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	–	info[k].getConfiguration());
215	–	}
216	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
288
289	<	#ifdef IS_MPI
289	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
290
291	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
291	>	}
292
293	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
294	+	#ifdef IS_MPI
295	+	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
296		#endif // is_mpi
297		}
298
#	Line 228 | Line 302 | void SimSetup::makeMolecules(void){
302		theBonds[j].a = currentBond->getA() + atomOffset;
303		theBonds[j].b = currentBond->getB() + atomOffset;
304
305	<	exI = theBonds[j].a;
306	<	exJ = theBonds[j].b;
305	>	tempI = theBonds[j].a;
306	>	tempJ = theBonds[j].b;
307
234	–	// exclude_I must always be the smaller of the pair
235	–	if (exI > exJ){
236	–	tempEx = exI;
237	–	exI = exJ;
238	–	exJ = tempEx;
239	–	}
308		#ifdef IS_MPI
309	<	tempEx = exI;
310	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
311	<	tempEx = exJ;
312	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
309	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
310	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
311	>	#else
312	>	exI = tempI + 1;
313	>	exJ = tempJ + 1;
314	>	#endif
315
316	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	<	#else  // isn't MPI
248	<
249	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	<	#endif  //is_mpi
316	>	info[k].excludes->addPair(exI, exJ);
317		}
252	–	excludeOffset += molInfo.nBonds;
318
319		//make the bends
320		for (j = 0; j < molInfo.nBends; j++){
#	Line 299 | Line 364 | void SimSetup::makeMolecules(void){
364		}
365		}
366
367	<	if (!theBends[j].isGhost){
368	<	exI = theBends[j].a;
369	<	exJ = theBends[j].c;
370	<	}
371	<	else{
307	<	exI = theBends[j].a;
308	<	exJ = theBends[j].b;
309	<	}
310	<
311	<	// exclude_I must always be the smaller of the pair
312	<	if (exI > exJ){
313	<	tempEx = exI;
314	<	exI = exJ;
315	<	exJ = tempEx;
316	<	}
367	>	if (theBends[j].isGhost) {
368	>
369	>	tempI = theBends[j].a;
370	>	tempJ = theBends[j].b;
371	>
372		#ifdef IS_MPI
373	<	tempEx = exI;
374	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	<	tempEx = exJ;
376	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
374	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	#endif
379	>	info[k].excludes->addPair(exI, exJ);
380
381	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
382	<	#else  // isn't MPI
383	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
384	<	#endif  //is_mpi
381	>	} else {
382	>
383	>	tempI = theBends[j].a;
384	>	tempJ = theBends[j].b;
385	>	tempK = theBends[j].c;
386	>
387	>	#ifdef IS_MPI
388	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
389	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
390	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
391	>	#else
392	>	exI = tempI + 1;
393	>	exJ = tempJ + 1;
394	>	exK = tempK + 1;
395	>	#endif
396	>
397	>	info[k].excludes->addPair(exI, exK);
398	>	info[k].excludes->addPair(exI, exJ);
399	>	info[k].excludes->addPair(exJ, exK);
400	>	}
401		}
328	–	excludeOffset += molInfo.nBends;
402
403		for (j = 0; j < molInfo.nTorsions; j++){
404		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 334 | Line 407 | void SimSetup::makeMolecules(void){
407		theTorsions[j].c = currentTorsion->getC() + atomOffset;
408		theTorsions[j].d = currentTorsion->getD() + atomOffset;
409
410	<	exI = theTorsions[j].a;
411	<	exJ = theTorsions[j].d;
410	>	tempI = theTorsions[j].a;
411	>	tempJ = theTorsions[j].b;
412	>	tempK = theTorsions[j].c;
413	>	tempL = theTorsions[j].d;
414
340	–	// exclude_I must always be the smaller of the pair
341	–	if (exI > exJ){
342	–	tempEx = exI;
343	–	exI = exJ;
344	–	exJ = tempEx;
345	–	}
415		#ifdef IS_MPI
416	<	tempEx = exI;
417	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
418	<	tempEx = exJ;
419	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
416	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
417	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
418	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
419	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
420	>	#else
421	>	exI = tempI + 1;
422	>	exJ = tempJ + 1;
423	>	exK = tempK + 1;
424	>	exL = tempL + 1;
425	>	#endif
426
427	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
428	<	#else  // isn't MPI
429	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
430	<	#endif  //is_mpi
431	<	}
432	<	excludeOffset += molInfo.nTorsions;
427	>	info[k].excludes->addPair(exI, exJ);
428	>	info[k].excludes->addPair(exI, exK);
429	>	info[k].excludes->addPair(exI, exL);
430	>	info[k].excludes->addPair(exJ, exK);
431	>	info[k].excludes->addPair(exJ, exL);
432	>	info[k].excludes->addPair(exK, exL);
433	>	}
434
435	+
436	+	molInfo.myRigidBodies.clear();
437	+
438	+	for (j = 0; j < molInfo.nRigidBodies; j++){
439
440	<	// send the arrays off to the forceField for init.
440	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
441	>	nMembers = currentRigidBody->getNMembers();
442	>
443	>	// Create the Rigid Body:
444	>
445	>	myRB = new RigidBody();
446	>
447	>	sprintf(rbName,"%s_RB_%d", molName, j);
448	>	myRB->setType(rbName);
449	>
450	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
451	>
452	>	// molI is atom numbering inside this molecule
453	>	molI = currentRigidBody->getMember(rb1);
454	>
455	>	// tempI is atom numbering on local processor
456	>	tempI = molI + atomOffset;
457	>
458	>	// currentAtom is the AtomStamp (which we need for
459	>	// rigid body reference positions)
460	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
461	>
462	>	// When we add to the rigid body, add the atom itself and
463	>	// the stamp info:
464	>
465	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
466	>
467	>	// Add this atom to the Skip List for the integrators
468	>	#ifdef IS_MPI
469	>	slI = info[k].atoms[tempI]->getGlobalIndex();
470	>	#else
471	>	slI = tempI;
472	>	#endif
473	>	skipList.insert(slI);
474	>
475	>	}
476	>
477	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
478	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
479	>
480	>	tempI = currentRigidBody->getMember(rb1);
481	>	tempJ = currentRigidBody->getMember(rb2);
482	>
483	>	// Some explanation is required here.
484	>	// Fortran indexing starts at 1, while c indexing starts at 0
485	>	// Also, in parallel computations, the GlobalIndex is
486	>	// used for the exclude list:
487	>
488	>	#ifdef IS_MPI
489	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
490	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
491	>	#else
492	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
493	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
494	>	#endif
495	>
496	>	info[k].excludes->addPair(exI, exJ);
497	>
498	>	}
499	>	}
500	>
501	>	molInfo.myRigidBodies.push_back(myRB);
502	>	info[k].rigidBodies.push_back(myRB);
503	>	}
504	>
505	>
506	>	//create cutoff group for molecule
507	>
508	>	cutoffAtomSet.clear();
509	>	molInfo.myCutoffGroups.clear();
510	>
511	>	for (j = 0; j < nCutoffGroups; j++){
512	>
513	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
514	>	nMembers = currentCutoffGroup->getNMembers();
515	>
516	>	myCutoffGroup = new CutoffGroup();
517	>
518	>	#ifdef IS_MPI
519	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
520	>	#else
521	>	myCutoffGroup->setGlobalIndex(groupOffset);
522	>	#endif
523	>
524	>	for (int cg = 0; cg < nMembers; cg++) {
525	>
526	>	// molI is atom numbering inside this molecule
527	>	molI = currentCutoffGroup->getMember(cg);
528	>
529	>	// tempI is atom numbering on local processor
530	>	tempI = molI + atomOffset;
531	>
532	>	#ifdef IS_MPI
533	>	globalID = info[k].atoms[tempI]->getGlobalIndex();
534	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
535	>	#else
536	>	globalID = info[k].atoms[tempI]->getIndex();
537	>	info[k].globalGroupMembership[globalID] = groupOffset;
538	>	#endif
539	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
540	>	cutoffAtomSet.insert(tempI);
541	>	}
542	>
543	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
544	>	groupOffset++;
545	>
546	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
547	>
548	>
549	>	// create a cutoff group for every atom in current molecule which
550	>	// does not belong to cutoffgroup defined at mdl file
551	>
552	>	for(j = 0; j < molInfo.nAtoms; j++){
553	>
554	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
555	>	myCutoffGroup = new CutoffGroup();
556	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
557	>
558	>	#ifdef IS_MPI
559	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
560	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
561	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
562	>	#else
563	>	myCutoffGroup->setGlobalIndex(groupOffset);
564	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
565	>	info[k].globalGroupMembership[globalID] = groupOffset;
566	>	#endif
567	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
568	>	groupOffset++;
569	>	}
570	>	}
571	>
572	>	// After this is all set up, scan through the atoms to
573	>	// see if they can be added to the integrableObjects:
574	>
575	>	molInfo.myIntegrableObjects.clear();
576	>
577	>
578	>	for (j = 0; j < molInfo.nAtoms; j++){
579	>
580	>	#ifdef IS_MPI
581	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
582	>	#else
583	>	slJ = j+atomOffset;
584	>	#endif
585	>
586	>	// if they aren't on the skip list, then they can be integrated
587	>
588	>	if (skipList.find(slJ) == skipList.end()) {
589	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
590	>	info[k].integrableObjects.push_back(mySD);
591	>	molInfo.myIntegrableObjects.push_back(mySD);
592	>	}
593	>	}
594	>
595	>	// all rigid bodies are integrated:
596	>
597	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
598	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
599	>	info[k].integrableObjects.push_back(mySD);
600	>	molInfo.myIntegrableObjects.push_back(mySD);
601	>	}
602	>
603	>
604	>	/*
605	>
606	>	//creat ConstraintPair.
607	>	molInfo.myConstraintPair.clear();
608	>
609	>	for (j = 0; j < molInfo.nBonds; j++){
610	>
611	>	//if both atoms are in the same rigid body, just skip it
612	>	currentBond = comp_stamps[stampID]->getBond(j);
613	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
614	>
615	>	tempI = currentBond->getA() + atomOffset;
616	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
617	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
618	>	else
619	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
620	>
621	>	tempJ =  currentBond->getB() + atomOffset;
622	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
623	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
624	>	else
625	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
626	>
627	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
628	>	molInfo.myConstraintPairs.push_back(consPair);
629	>	}
630	>	}
631	>
632	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
633	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
634	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
635	>
636	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
637	>
638	>	for(size_t m = 0; m < jointAtoms.size(); m++){
639	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
640	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
641
642	+	consPair = new JointConstraintPair(consElement1, consElement2);
643	+	molInfo.myConstraintPairs.push_back(consPair);
644	+	}
645	+
646	+	}
647	+	}
648	+
649	+	*/
650	+	// send the arrays off to the forceField for init.
651	+
652		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
653		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
654		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
655		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
656		theTorsions);
657
368	–
658		info[k].molecules[i].initialize(molInfo);
659	<
660	<
659	>
660	>
661		atomOffset += molInfo.nAtoms;
662		delete[] theBonds;
663		delete[] theBends;
664		delete[] theTorsions;
665		}
666	+
667	+
668	+
669	+	#ifdef IS_MPI
670	+	// Since the globalGroupMembership has been zero filled and we've only
671	+	// poked values into the atoms we know, we can do an Allreduce
672	+	// to get the full globalGroupMembership array (We think).
673	+	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
674	+	// docs said we could.
675	+
676	+	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
677	+
678	+	MPI_Allreduce(info[k].globalGroupMembership,
679	+	ggMjunk,
680	+	mpiSim->getNAtomsGlobal(),
681	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
682	+
683	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
684	+	info[k].globalGroupMembership[i] = ggMjunk[i];
685	+
686	+	delete[] ggMjunk;
687	+
688	+	#endif
689	+
690	+
691	+
692		}
693
694		#ifdef IS_MPI
#	Line 381 | Line 696 | void SimSetup::makeMolecules(void){
696		MPIcheckPoint();
697		#endif // is_mpi
698
384	–	// clean up the forcefield
385	–
386	–	the_ff->calcRcut();
387	–	the_ff->cleanMe();
699		}
700
701		void SimSetup::initFromBass(void){
#	Line 585 | Line 896 | void SimSetup::gatherInfo(void){
896		else if (!strcasecmp(force_field, "EAM")){
897		ffCase = FF_EAM;
898		}
899	+	else if (!strcasecmp(force_field, "WATER")){
900	+	ffCase = FF_H2O;
901	+	}
902		else{
903		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
904		force_field);
#	Line 613 | Line 927 | void SimSetup::gatherInfo(void){
927		}
928		else{
929		sprintf(painCave.errMsg,
930	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
931	<	"reverting to NVE for this simulation.\n",
930	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
931	>	"\treverting to NVE for this simulation.\n",
932		ensemble);
933		painCave.isFatal = 0;
934		simError();
#	Line 646 | Line 960 | void SimSetup::gatherInfo(void){
960		if (!the_components[i]->haveNMol()){
961		// we have a problem
962		sprintf(painCave.errMsg,
963	<	"SimSetup Error. No global NMol or component NMol"
964	<	" given. Cannot calculate the number of atoms.\n");
963	>	"SimSetup Error. No global NMol or component NMol given.\n"
964	>	"\tCannot calculate the number of atoms.\n");
965		painCave.isFatal = 1;
966		simError();
967		}
#	Line 667 | Line 981 | void SimSetup::gatherInfo(void){
981		simError();
982		}
983
984	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
985	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
986	+	sprintf(painCave.errMsg,
987	+	"Sample time is not divisible by dt.\n"
988	+	"\tThis will result in samples that are not uniformly\n"
989	+	"\tdistributed in time.  If this is a problem, change\n"
990	+	"\tyour sampleTime variable.\n");
991	+	painCave.isFatal = 0;
992	+	simError();
993	+	}
994	+
995	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
996	+	sprintf(painCave.errMsg,
997	+	"Status time is not divisible by dt.\n"
998	+	"\tThis will result in status reports that are not uniformly\n"
999	+	"\tdistributed in time.  If this is a problem, change \n"
1000	+	"\tyour statusTime variable.\n");
1001	+	painCave.isFatal = 0;
1002	+	simError();
1003	+	}
1004	+
1005	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1006	+	sprintf(painCave.errMsg,
1007	+	"Thermal time is not divisible by dt.\n"
1008	+	"\tThis will result in thermalizations that are not uniformly\n"
1009	+	"\tdistributed in time.  If this is a problem, change \n"
1010	+	"\tyour thermalTime variable.\n");
1011	+	painCave.isFatal = 0;
1012	+	simError();
1013	+	}
1014	+
1015	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1016	+	sprintf(painCave.errMsg,
1017	+	"Reset time is not divisible by dt.\n"
1018	+	"\tThis will result in integrator resets that are not uniformly\n"
1019	+	"\tdistributed in time.  If this is a problem, change\n"
1020	+	"\tyour resetTime variable.\n");
1021	+	painCave.isFatal = 0;
1022	+	simError();
1023	+	}
1024	+
1025		// set the status, sample, and thermal kick times
1026
1027		for (i = 0; i < nInfo; i++){
1028		if (globals->haveSampleTime()){
1029		info[i].sampleTime = globals->getSampleTime();
1030		info[i].statusTime = info[i].sampleTime;
676	–	info[i].thermalTime = info[i].sampleTime;
1031		}
1032		else{
1033		info[i].sampleTime = globals->getRunTime();
1034		info[i].statusTime = info[i].sampleTime;
681	–	info[i].thermalTime = info[i].sampleTime;
1035		}
1036
1037		if (globals->haveStatusTime()){
#	Line 687 | Line 1040 | void SimSetup::gatherInfo(void){
1040
1041		if (globals->haveThermalTime()){
1042		info[i].thermalTime = globals->getThermalTime();
1043	+	} else {
1044	+	info[i].thermalTime = globals->getRunTime();
1045		}
1046
1047		info[i].resetIntegrator = 0;
#	Line 699 | Line 1054 | void SimSetup::gatherInfo(void){
1054
1055		if (globals->haveTempSet())
1056		info[i].setTemp = globals->getTempSet();
1057	<
1057	>
1058	>	// check for the extended State init
1059	>
1060	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1061	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1062	>
1063	>	// check for thermodynamic integration
1064	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1065	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1066	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1067	>	info[i].thermIntLambda = globals->getThermIntLambda();
1068	>	info[i].thermIntK = globals->getThermIntK();
1069	>
1070	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1071	>	info[i].restraint = myRestraint;
1072	>	}
1073	>	else {
1074	>	sprintf(painCave.errMsg,
1075	>	"SimSetup Error:\n"
1076	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1077	>	"\tthermodynamicIntegrationLambda (and/or\n"
1078	>	"\tthermodynamicIntegrationK) was not specified.\n"
1079	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1080	>	painCave.isFatal = 1;
1081	>	simError();
1082	>	}
1083	>	}
1084	>	else if(globals->getUseLiquidThermInt()) {
1085	>	if (globals->getUseSolidThermInt()) {
1086	>	sprintf( painCave.errMsg,
1087	>	"SimSetup Warning: It appears that you have both solid and\n"
1088	>	"\tliquid thermodynamic integration activated in your .bass\n"
1089	>	"\tfile. To avoid confusion, specify only one technique in\n"
1090	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1091	>	"\twill be assumed for the current simulation. If this is not\n"
1092	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1093	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1094	>	painCave.isFatal = 0;
1095	>	simError();
1096	>	}
1097	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1098	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1099	>	info[i].thermIntLambda = globals->getThermIntLambda();
1100	>	info[i].thermIntK = globals->getThermIntK();
1101	>	}
1102	>	else {
1103	>	sprintf(painCave.errMsg,
1104	>	"SimSetup Error:\n"
1105	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1106	>	"\tthermodynamicIntegrationLambda (and/or\n"
1107	>	"\tthermodynamicIntegrationK) was not specified.\n"
1108	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1109	>	painCave.isFatal = 1;
1110	>	simError();
1111	>	}
1112	>	}
1113	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1116	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1117	>	"\t'true' in your .bass file.  These keywords are set to\n"
1118	>	"\t'false' by default, so your lambda and/or k values are\n"
1119	>	"\tbeing ignored.\n");
1120	>	painCave.isFatal = 0;
1121	>	simError();
1122	>	}
1123		}
1124
1125		//setup seed for random number generator
#	Line 741 | Line 1161 | void SimSetup::gatherInfo(void){
1161		for (int i = 0; i < nInfo; i++){
1162		info[i].setSeed(seedValue);
1163		}
1164	<
1164	>
1165		#ifdef IS_MPI
1166	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1166	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1167		MPIcheckPoint();
1168		#endif // is_mpi
1169		}
#	Line 752 | Line 1172 | void SimSetup::finalInfoCheck(void){
1172		void SimSetup::finalInfoCheck(void){
1173		int index;
1174		int usesDipoles;
1175	+	int usesCharges;
1176		int i;
1177
1178		for (i = 0; i < nInfo; i++){
#	Line 763 | Line 1184 | void SimSetup::finalInfoCheck(void){
1184		usesDipoles = (info[i].atoms[index])->hasDipole();
1185		index++;
1186		}
1187	<
1187	>	index = 0;
1188	>	usesCharges = 0;
1189	>	while ((index < info[i].n_atoms) && !usesCharges){
1190	>	usesCharges= (info[i].atoms[index])->hasCharge();
1191	>	index++;
1192	>	}
1193		#ifdef IS_MPI
1194		int myUse = usesDipoles;
1195		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1196		#endif //is_mpi
1197
1198	<	double theEcr, theEst;
1198	>	double theRcut, theRsw;
1199
1200	+	if (globals->haveRcut()) {
1201	+	theRcut = globals->getRcut();
1202	+
1203	+	if (globals->haveRsw())
1204	+	theRsw = globals->getRsw();
1205	+	else
1206	+	theRsw = theRcut;
1207	+
1208	+	info[i].setDefaultRcut(theRcut, theRsw);
1209	+
1210	+	} else {
1211	+
1212	+	the_ff->calcRcut();
1213	+	theRcut = info[i].getRcut();
1214	+
1215	+	if (globals->haveRsw())
1216	+	theRsw = globals->getRsw();
1217	+	else
1218	+	theRsw = theRcut;
1219	+
1220	+	info[i].setDefaultRcut(theRcut, theRsw);
1221	+	}
1222	+
1223		if (globals->getUseRF()){
1224		info[i].useReactionField = 1;
1225	<
1226	<	if (!globals->haveECR()){
1225	>
1226	>	if (!globals->haveRcut()){
1227		sprintf(painCave.errMsg,
1228	<	"SimSetup Warning: using default value of 1/2 the smallest "
1229	<	"box length for the electrostaticCutoffRadius.\n"
1230	<	"I hope you have a very fast processor!\n");
1228	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1229	>	"\tOOPSE will use a default value of 15.0 angstroms"
1230	>	"\tfor the cutoffRadius.\n");
1231		painCave.isFatal = 0;
1232		simError();
1233	<	double smallest;
785	<	smallest = info[i].boxL[0];
786	<	if (info[i].boxL[1] <= smallest)
787	<	smallest = info[i].boxL[1];
788	<	if (info[i].boxL[2] <= smallest)
789	<	smallest = info[i].boxL[2];
790	<	theEcr = 0.5 * smallest;
1233	>	theRcut = 15.0;
1234		}
1235		else{
1236	<	theEcr = globals->getECR();
1236	>	theRcut = globals->getRcut();
1237		}
1238
1239	<	if (!globals->haveEST()){
1239	>	if (!globals->haveRsw()){
1240		sprintf(painCave.errMsg,
1241	<	"SimSetup Warning: using default value of 0.05 * the "
1242	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1241	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1242	>	"\tOOPSE will use a default value of\n"
1243	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1244		painCave.isFatal = 0;
1245		simError();
1246	<	theEst = 0.05 * theEcr;
1246	>	theRsw = 0.95 * theRcut;
1247		}
1248		else{
1249	<	theEst = globals->getEST();
1249	>	theRsw = globals->getRsw();
1250		}
1251
1252	<	info[i].setDefaultEcr(theEcr, theEst);
1252	>	info[i].setDefaultRcut(theRcut, theRsw);
1253
1254		if (!globals->haveDielectric()){
1255		sprintf(painCave.errMsg,
1256	<	"SimSetup Error: You are trying to use Reaction Field without"
1257	<	"setting a dielectric constant!\n");
1256	>	"SimSetup Error: No Dielectric constant was set.\n"
1257	>	"\tYou are trying to use Reaction Field without"
1258	>	"\tsetting a dielectric constant!\n");
1259		painCave.isFatal = 1;
1260		simError();
1261		}
1262		info[i].dielectric = globals->getDielectric();
1263		}
1264		else{
1265	<	if (usesDipoles){
1266	<	if (!globals->haveECR()){
1265	>	if (usesDipoles || usesCharges){
1266	>
1267	>	if (!globals->haveRcut()){
1268		sprintf(painCave.errMsg,
1269	<	"SimSetup Warning: using default value of 1/2 the smallest "
1270	<	"box length for the electrostaticCutoffRadius.\n"
1271	<	"I hope you have a very fast processor!\n");
1269	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1270	>	"\tOOPSE will use a default value of 15.0 angstroms"
1271	>	"\tfor the cutoffRadius.\n");
1272		painCave.isFatal = 0;
1273		simError();
1274	<	double smallest;
1275	<	smallest = info[i].boxL[0];
830	<	if (info[i].boxL[1] <= smallest)
831	<	smallest = info[i].boxL[1];
832	<	if (info[i].boxL[2] <= smallest)
833	<	smallest = info[i].boxL[2];
834	<	theEcr = 0.5 * smallest;
835	<	}
1274	>	theRcut = 15.0;
1275	>	}
1276		else{
1277	<	theEcr = globals->getECR();
1277	>	theRcut = globals->getRcut();
1278		}
1279	<
1280	<	if (!globals->haveEST()){
1279	>
1280	>	if (!globals->haveRsw()){
1281		sprintf(painCave.errMsg,
1282	<	"SimSetup Warning: using default value of 0.05 * the "
1283	<	"electrostaticCutoffRadius for the "
1284	<	"electrostaticSkinThickness\n");
1282	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1283	>	"\tOOPSE will use a default value of\n"
1284	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1285		painCave.isFatal = 0;
1286		simError();
1287	<	theEst = 0.05 * theEcr;
1287	>	theRsw = 0.95 * theRcut;
1288		}
1289		else{
1290	<	theEst = globals->getEST();
1290	>	theRsw = globals->getRsw();
1291		}
1292	<
1293	<	info[i].setDefaultEcr(theEcr, theEst);
1292	>
1293	>	info[i].setDefaultRcut(theRcut, theRsw);
1294	>
1295		}
1296		}
1297		}
857	–
1298		#ifdef IS_MPI
1299		strcpy(checkPointMsg, "post processing checks out");
1300		MPIcheckPoint();
1301		#endif // is_mpi
862	–	}
1302
1303	+	// clean up the forcefield
1304	+	the_ff->cleanMe();
1305	+	}
1306	+
1307		void SimSetup::initSystemCoords(void){
1308		int i;
1309
#	Line 888 | Line 1331 | void SimSetup::initSystemCoords(void){
1331		delete fileInit;
1332		}
1333		else{
1334	<	#ifdef IS_MPI
892	<
1334	>
1335		// no init from bass
1336	<
1336	>
1337		sprintf(painCave.errMsg,
1338	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1338	>	"Cannot intialize a simulation without an initial configuration file.\n");
1339		painCave.isFatal = 1;;
1340		simError();
1341	<
900	<	#else
901	<
902	<	initFromBass();
903	<
904	<
905	<	#endif
1341	>
1342		}
1343
1344		#ifdef IS_MPI
#	Line 996 | Line 1432 | void SimSetup::makeOutNames(void){
1432		}
1433		}
1434
1435	+	strcpy(info[k].rawPotName, inFileName);
1436	+	nameLength = strlen(info[k].rawPotName);
1437	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1438	+	if (!strcmp(endTest, ".bass")){
1439	+	strcpy(endTest, ".raw");
1440	+	}
1441	+	else if (!strcmp(endTest, ".BASS")){
1442	+	strcpy(endTest, ".raw");
1443	+	}
1444	+	else{
1445	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1446	+	if (!strcmp(endTest, ".bss")){
1447	+	strcpy(endTest, ".raw");
1448	+	}
1449	+	else if (!strcmp(endTest, ".mdl")){
1450	+	strcpy(endTest, ".raw");
1451	+	}
1452	+	else{
1453	+	strcat(info[k].rawPotName, ".raw");
1454	+	}
1455	+	}
1456	+
1457		#ifdef IS_MPI
1458
1459		}
#	Line 1056 | Line 1514 | void SimSetup::createFF(void){
1514		the_ff = new EAM_FF();
1515		break;
1516
1517	+	case FF_H2O:
1518	+	the_ff = new WATER();
1519	+	break;
1520	+
1521		default:
1522		sprintf(painCave.errMsg,
1523		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1076 | Line 1538 | void SimSetup::compList(void){
1538		LinkedMolStamp* headStamp = new LinkedMolStamp();
1539		LinkedMolStamp* currentStamp = NULL;
1540		comp_stamps = new MoleculeStamp * [n_components];
1541	+	bool haveCutoffGroups;
1542
1543	+	haveCutoffGroups = false;
1544	+
1545		// make an array of molecule stamps that match the components used.
1546		// also extract the used stamps out into a separate linked list
1547
#	Line 1111 | Line 1576 | void SimSetup::compList(void){
1576		headStamp->add(currentStamp);
1577		comp_stamps[i] = headStamp->match(id);
1578		}
1579	+
1580	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1581	+	haveCutoffGroups = true;
1582		}
1583	+
1584	+	for (i = 0; i < nInfo; i++)
1585	+	info[i].haveCutoffGroups = haveCutoffGroups;
1586
1587		#ifdef IS_MPI
1588		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1120 | Line 1591 | void SimSetup::calcSysValues(void){
1591		}
1592
1593		void SimSetup::calcSysValues(void){
1594	<	int i;
1594	>	int i, j;
1595	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1596
1597		int* molMembershipArray;
1598	+	CutoffGroupStamp* cg;
1599
1600		tot_atoms = 0;
1601		tot_bonds = 0;
1602		tot_bends = 0;
1603		tot_torsions = 0;
1604	+	tot_rigid = 0;
1605	+	tot_groups = 0;
1606		for (i = 0; i < n_components; i++){
1607		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1608		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1609		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1610		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1611	<	}
1611	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1612
1613	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1614	+	atomsingroups = 0;
1615	+	for (j=0; j < ncutgroups; j++) {
1616	+	cg = comp_stamps[i]->getCutoffGroup(j);
1617	+	atomsingroups += cg->getNMembers();
1618	+	}
1619	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1620	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1621	+	}
1622	+
1623		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1624		molMembershipArray = new int[tot_atoms];
1625
#	Line 1145 | Line 1630 | void SimSetup::calcSysValues(void){
1630		info[i].n_torsions = tot_torsions;
1631		info[i].n_SRI = tot_SRI;
1632		info[i].n_mol = tot_nmol;
1633	<
1633	>	info[i].ngroup = tot_groups;
1634		info[i].molMembershipArray = molMembershipArray;
1635		}
1636		}
#	Line 1156 | Line 1641 | void SimSetup::mpiMolDivide(void){
1641		int i, j, k;
1642		int localMol, allMol;
1643		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1644	+	int local_rigid, local_groups;
1645	+	vector<int> globalMolIndex;
1646	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1647	+	CutoffGroupStamp* cg;
1648
1649		mpiSim = new mpiSimulation(info);
1650
1651	<	globalIndex = mpiSim->divideLabor();
1651	>	mpiSim->divideLabor();
1652	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1653	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1654	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1655
1656		// set up the local variables
1657
#	Line 1172 | Line 1664 | void SimSetup::mpiMolDivide(void){
1664		local_bonds = 0;
1665		local_bends = 0;
1666		local_torsions = 0;
1667	<	globalAtomIndex = 0;
1667	>	local_rigid = 0;
1668	>	local_groups = 0;
1669	>	globalAtomCounter = 0;
1670
1177	–
1671		for (i = 0; i < n_components; i++){
1672		for (j = 0; j < components_nmol[i]; j++){
1673		if (mol2proc[allMol] == worldRank){
#	Line 1182 | Line 1675 | void SimSetup::mpiMolDivide(void){
1675		local_bonds += comp_stamps[i]->getNBonds();
1676		local_bends += comp_stamps[i]->getNBends();
1677		local_torsions += comp_stamps[i]->getNTorsions();
1678	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1679	+
1680	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1681	+	atomsingroups = 0;
1682	+	for (k=0; k < ncutgroups; k++) {
1683	+	cg = comp_stamps[i]->getCutoffGroup(k);
1684	+	atomsingroups += cg->getNMembers();
1685	+	}
1686	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1687	+	ncutgroups;
1688	+	local_groups += ngroupsinstamp;
1689	+
1690		localMol++;
1691		}
1692		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1693	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1694	<	globalAtomIndex++;
1693	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1694	>	globalAtomCounter++;
1695		}
1696
1697		allMol++;
#	Line 1194 | Line 1699 | void SimSetup::mpiMolDivide(void){
1699		}
1700		local_SRI = local_bonds + local_bends + local_torsions;
1701
1702	<	info[0].n_atoms = mpiSim->getMyNlocal();
1703	<
1702	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1703	>
1704		if (local_atoms != info[0].n_atoms){
1705		sprintf(painCave.errMsg,
1706	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1707	<	" localAtom (%d) are not equal.\n",
1706	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1707	>	"\tlocalAtom (%d) are not equal.\n",
1708		info[0].n_atoms, local_atoms);
1709		painCave.isFatal = 1;
1710		simError();
1711		}
1712
1713	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1714	+	if (local_groups != info[0].ngroup){
1715	+	sprintf(painCave.errMsg,
1716	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1717	+	"\tlocalGroups (%d) are not equal.\n",
1718	+	info[0].ngroup, local_groups);
1719	+	painCave.isFatal = 1;
1720	+	simError();
1721	+	}
1722	+
1723		info[0].n_bonds = local_bonds;
1724		info[0].n_bends = local_bends;
1725		info[0].n_torsions = local_torsions;
#	Line 1227 | Line 1742 | void SimSetup::makeSysArrays(void){
1742
1743		Atom** the_atoms;
1744		Molecule* the_molecules;
1230	–	Exclude** the_excludes;
1745
1232	–
1746		for (l = 0; l < nInfo; l++){
1747		// create the atom and short range interaction arrays
1748
#	Line 1243 | Line 1756 | void SimSetup::makeSysArrays(void){
1756
1757
1758		molIndex = 0;
1759	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1759	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1760		if (mol2proc[i] == worldRank){
1761		the_molecules[molIndex].setStampID(molCompType[i]);
1762		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1255 | Line 1768 | void SimSetup::makeSysArrays(void){
1768		#else // is_mpi
1769
1770		molIndex = 0;
1771	<	globalAtomIndex = 0;
1771	>	globalAtomCounter = 0;
1772		for (i = 0; i < n_components; i++){
1773		for (j = 0; j < components_nmol[i]; j++){
1774		the_molecules[molIndex].setStampID(i);
1775		the_molecules[molIndex].setMyIndex(molIndex);
1776		the_molecules[molIndex].setGlobalIndex(molIndex);
1777		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1778	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1779	<	globalAtomIndex++;
1778	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1779	>	globalAtomCounter++;
1780		}
1781		molIndex++;
1782		}
#	Line 1272 | Line 1785 | void SimSetup::makeSysArrays(void){
1785
1786		#endif // is_mpi
1787
1788	<
1789	<	if (info[l].n_SRI){
1790	<	Exclude::createArray(info[l].n_SRI);
1278	<	the_excludes = new Exclude * [info[l].n_SRI];
1279	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1280	<	the_excludes[ex] = new Exclude(ex);
1281	<	}
1282	<	info[l].globalExcludes = new int;
1283	<	info[l].n_exclude = info[l].n_SRI;
1284	<	}
1285	<	else{
1286	<	Exclude::createArray(1);
1287	<	the_excludes = new Exclude * ;
1288	<	the_excludes[0] = new Exclude(0);
1289	<	the_excludes[0]->setPair(0, 0);
1290	<	info[l].globalExcludes = new int;
1291	<	info[l].globalExcludes[0] = 0;
1292	<	info[l].n_exclude = 0;
1293	<	}
1294	<
1788	>	info[l].globalExcludes = new int;
1789	>	info[l].globalExcludes[0] = 0;
1790	>
1791		// set the arrays into the SimInfo object
1792
1793		info[l].atoms = the_atoms;
1794		info[l].molecules = the_molecules;
1795		info[l].nGlobalExcludes = 0;
1796	<	info[l].excludes = the_excludes;
1301	<
1796	>
1797		the_ff->setSimInfo(info);
1798		}
1799		}
#	Line 1341 | Line 1836 | void SimSetup::makeIntegrator(void){
1836		else{
1837		sprintf(painCave.errMsg,
1838		"SimSetup error: If you use the NVT\n"
1839	<	"    ensemble, you must set tauThermostat.\n");
1839	>	"\tensemble, you must set tauThermostat.\n");
1840		painCave.isFatal = 1;
1841		simError();
1842		}
#	Line 1364 | Line 1859 | void SimSetup::makeIntegrator(void){
1859		else{
1860		sprintf(painCave.errMsg,
1861		"SimSetup error: If you use a constant pressure\n"
1862	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1862	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1863		painCave.isFatal = 1;
1864		simError();
1865		}
#	Line 1374 | Line 1869 | void SimSetup::makeIntegrator(void){
1869		else{
1870		sprintf(painCave.errMsg,
1871		"SimSetup error: If you use an NPT\n"
1872	<	"    ensemble, you must set tauThermostat.\n");
1872	>	"\tensemble, you must set tauThermostat.\n");
1873		painCave.isFatal = 1;
1874		simError();
1875		}
#	Line 1384 | Line 1879 | void SimSetup::makeIntegrator(void){
1879		else{
1880		sprintf(painCave.errMsg,
1881		"SimSetup error: If you use an NPT\n"
1882	<	"    ensemble, you must set tauBarostat.\n");
1882	>	"\tensemble, you must set tauBarostat.\n");
1883		painCave.isFatal = 1;
1884		simError();
1885		}
#	Line 1407 | Line 1902 | void SimSetup::makeIntegrator(void){
1902		else{
1903		sprintf(painCave.errMsg,
1904		"SimSetup error: If you use a constant pressure\n"
1905	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1905	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1906		painCave.isFatal = 1;
1907		simError();
1908		}
1909
1910		if (globals->haveTauThermostat())
1911		myNPTf->setTauThermostat(globals->getTauThermostat());
1912	+
1913		else{
1914		sprintf(painCave.errMsg,
1915		"SimSetup error: If you use an NPT\n"
1916	<	"    ensemble, you must set tauThermostat.\n");
1916	>	"\tensemble, you must set tauThermostat.\n");
1917		painCave.isFatal = 1;
1918		simError();
1919		}
1920
1921		if (globals->haveTauBarostat())
1922		myNPTf->setTauBarostat(globals->getTauBarostat());
1923	+
1924		else{
1925		sprintf(painCave.errMsg,
1926		"SimSetup error: If you use an NPT\n"
1927	<	"    ensemble, you must set tauBarostat.\n");
1927	>	"\tensemble, you must set tauBarostat.\n");
1928		painCave.isFatal = 1;
1929		simError();
1930		}
#	Line 1450 | Line 1947 | void SimSetup::makeIntegrator(void){
1947		else{
1948		sprintf(painCave.errMsg,
1949		"SimSetup error: If you use a constant pressure\n"
1950	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1950	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1951		painCave.isFatal = 1;
1952		simError();
1953		}
#	Line 1460 | Line 1957 | void SimSetup::makeIntegrator(void){
1957		else{
1958		sprintf(painCave.errMsg,
1959		"SimSetup error: If you use an NPT\n"
1960	<	"    ensemble, you must set tauThermostat.\n");
1960	>	"\tensemble, you must set tauThermostat.\n");
1961		painCave.isFatal = 1;
1962		simError();
1963		}
#	Line 1470 | Line 1967 | void SimSetup::makeIntegrator(void){
1967		else{
1968		sprintf(painCave.errMsg,
1969		"SimSetup error: If you use an NPT\n"
1970	<	"    ensemble, you must set tauBarostat.\n");
1970	>	"\tensemble, you must set tauBarostat.\n");
1971		painCave.isFatal = 1;
1972		simError();
1973		}
#	Line 1523 | Line 2020 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2020		}
2021		else{
2022		sprintf(painCave.errMsg,
2023	<	"ZConstraint error: If you use an ZConstraint\n"
2024	<	" , you must set sample time.\n");
2023	>	"ZConstraint error: If you use a ZConstraint,\n"
2024	>	"\tyou must set zconsTime.\n");
2025		painCave.isFatal = 1;
2026		simError();
2027		}
#	Line 1539 | Line 2036 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2036		else{
2037		double defaultZConsTol = 0.01;
2038		sprintf(painCave.errMsg,
2039	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
2040	<	" , default value %f is used.\n",
2039	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2040	>	"\tOOPSE will use a default value of %f.\n"
2041	>	"\tTo set the tolerance, use the zconsTol variable.\n",
2042		defaultZConsTol);
2043		painCave.isFatal = 0;
2044		simError();
#	Line 1558 | Line 2056 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2056		}
2057		else{
2058		sprintf(painCave.errMsg,
2059	<	"ZConstraint Warning: User does not set force Subtraction policy, "
2060	<	"PolicyByMass is used\n");
2059	>	"ZConstraint Warning: No force subtraction policy was set.\n"
2060	>	"\tOOPSE will use PolicyByMass.\n"
2061	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2062		painCave.isFatal = 0;
2063		simError();
2064		zconsForcePolicy->setData("BYMASS");
#	Line 1567 | Line 2066 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2066
2067		theInfo.addProperty(zconsForcePolicy);
2068
2069	+	//set zcons gap
2070	+	DoubleData* zconsGap = new DoubleData();
2071	+	zconsGap->setID(ZCONSGAP_ID);
2072	+
2073	+	if (globals->haveZConsGap()){
2074	+	zconsGap->setData(globals->getZconsGap());
2075	+	theInfo.addProperty(zconsGap);
2076	+	}
2077	+
2078	+	//set zcons fixtime
2079	+	DoubleData* zconsFixtime = new DoubleData();
2080	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2081	+
2082	+	if (globals->haveZConsFixTime()){
2083	+	zconsFixtime->setData(globals->getZconsFixtime());
2084	+	theInfo.addProperty(zconsFixtime);
2085	+	}
2086	+
2087	+	//set zconsUsingSMD
2088	+	IntData* zconsUsingSMD = new IntData();
2089	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2090	+
2091	+	if (globals->haveZConsUsingSMD()){
2092	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2093	+	theInfo.addProperty(zconsUsingSMD);
2094	+	}
2095	+
2096		//Determine the name of ouput file and add it into SimInfo's property list
2097		//Be careful, do not use inFileName, since it is a pointer which
2098		//point to a string at master node, and slave nodes do not contain that string
#	Line 1596 | Line 2122 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2122		tempParaItem.zPos = zconStamp[i]->getZpos();
2123		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2124		tempParaItem.kRatio = zconStamp[i]->getKratio();
2125	<
2125	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2126	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2127		zconsParaData->addItem(tempParaItem);
2128		}
2129
2130		//check the uniqueness of index
2131		if(!zconsParaData->isIndexUnique()){
2132		sprintf(painCave.errMsg,
2133	<	"ZConstraint Error: molIndex is not unique\n");
2133	>	"ZConstraint Error: molIndex is not unique!\n");
2134		painCave.isFatal = 1;
2135		simError();
2136		}
#	Line 1613 | Line 2140 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2140
2141		//push data into siminfo, therefore, we can retrieve later
2142		theInfo.addProperty(zconsParaData);
2143	+	}
2144	+
2145	+	void SimSetup::makeMinimizer(){
2146	+
2147	+	OOPSEMinimizer* myOOPSEMinimizer;
2148	+	MinimizerParameterSet* param;
2149	+	char minimizerName[100];
2150	+
2151	+	for (int i = 0; i < nInfo; i++){
2152	+
2153	+	//prepare parameter set for minimizer
2154	+	param = new MinimizerParameterSet();
2155	+	param->setDefaultParameter();
2156	+
2157	+	if (globals->haveMinimizer()){
2158	+	param->setFTol(globals->getMinFTol());
2159	+	}
2160	+
2161	+	if (globals->haveMinGTol()){
2162	+	param->setGTol(globals->getMinGTol());
2163	+	}
2164	+
2165	+	if (globals->haveMinMaxIter()){
2166	+	param->setMaxIteration(globals->getMinMaxIter());
2167	+	}
2168	+
2169	+	if (globals->haveMinWriteFrq()){
2170	+	param->setMaxIteration(globals->getMinMaxIter());
2171	+	}
2172	+
2173	+	if (globals->haveMinWriteFrq()){
2174	+	param->setWriteFrq(globals->getMinWriteFrq());
2175	+	}
2176	+
2177	+	if (globals->haveMinStepSize()){
2178	+	param->setStepSize(globals->getMinStepSize());
2179	+	}
2180	+
2181	+	if (globals->haveMinLSMaxIter()){
2182	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2183	+	}
2184	+
2185	+	if (globals->haveMinLSTol()){
2186	+	param->setLineSearchTol(globals->getMinLSTol());
2187	+	}
2188	+
2189	+	strcpy(minimizerName, globals->getMinimizer());
2190	+
2191	+	if (!strcasecmp(minimizerName, "CG")){
2192	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2193	+	}
2194	+	else if (!strcasecmp(minimizerName, "SD")){
2195	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2196	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2197	+	}
2198	+	else{
2199	+	sprintf(painCave.errMsg,
2200	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2201	+	painCave.isFatal = 0;
2202	+	simError();
2203	+
2204	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2205	+	}
2206	+	info[i].the_integrator = myOOPSEMinimizer;
2207	+
2208	+	//store the minimizer into simInfo
2209	+	info[i].the_minimizer = myOOPSEMinimizer;
2210	+	info[i].has_minimizer = true;
2211	+	}
2212	+
2213		}

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