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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 814 by mmeineke, Thu Oct 23 19:57:25 2003 UTC vs.
Revision 1330 by gezelter, Fri Jul 16 16:29:44 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6		#include <sprng.h>
7		#include "SimSetup.hpp"
#	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	+	#include "ConstraintManager.hpp"
17
18		#ifdef IS_MPI
19		#include "mpiBASS.h"
#	Line 24 | Line 29
29		#define NPTxyz_ENS     4
30
31
32	<	#define FF_DUFF 0
33	<	#define FF_LJ   1
34	<	#define FF_EAM  2
32	>	#define FF_DUFF  0
33	>	#define FF_LJ    1
34	>	#define FF_EAM   2
35	>	#define FF_H2O   3
36
37		using namespace std;
38
39	+	/**
40	+	* Check whether dividend is divisble by divisor or not
41	+	*/
42	+	bool isDivisible(double dividend, double divisor){
43	+	double tolerance = 0.000001;
44	+	double quotient;
45	+	double diff;
46	+	int intQuotient;
47	+
48	+	quotient = dividend / divisor;
49	+
50	+	if (quotient < 0)
51	+	quotient = -quotient;
52	+
53	+	intQuotient = int (quotient + tolerance);
54	+
55	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
56	+
57	+	if (diff <= tolerance)
58	+	return true;
59	+	else
60	+	return false;
61	+	}
62	+
63		SimSetup::SimSetup(){
64	+
65	+	initSuspend = false;
66		isInfoArray = 0;
67		nInfo = 1;
68
#	Line 53 | Line 85 | void SimSetup::setSimInfo(SimInfo* the_info, int theNi
85		info = the_info;
86		nInfo = theNinfo;
87		isInfoArray = 1;
88	+	initSuspend = true;
89		}
90
91
#	Line 106 | Line 139 | void SimSetup::createSim(void){
139
140		// initialize the system coordinates
141
142	<	if (!isInfoArray){
142	>	if ( !initSuspend ){
143		initSystemCoords();
144
145		if( !(globals->getUseInitTime()) )
#	Line 116 | Line 149 | void SimSetup::createSim(void){
149		// make the output filenames
150
151		makeOutNames();
152	<
120	<	// make the integrator
121	<
122	<	makeIntegrator();
123	<
152	>
153		#ifdef IS_MPI
154		mpiSim->mpiRefresh();
155		#endif
#	Line 128 | Line 157 | void SimSetup::createSim(void){
157		// initialize the Fortran
158
159		initFortran();
160	+
161	+	//creat constraint manager
162	+	for(int i = 0; i < nInfo; i++)
163	+	info[i].consMan = new ConstraintManager(&info[i]);
164	+
165	+	if (globals->haveMinimizer())
166	+	// make minimizer
167	+	makeMinimizer();
168	+	else
169	+	// make the integrator
170	+	makeIntegrator();
171	+
172		}
173
174
175		void SimSetup::makeMolecules(void){
176	<	int k;
177	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
176	>	int i, j, k;
177	>	int exI, exJ, exK, exL, slI, slJ;
178	>	int tempI, tempJ, tempK, tempL;
179	>	int molI, globalID;
180	>	int stampID, atomOffset, rbOffset, groupOffset;
181		molInit molInfo;
182		DirectionalAtom* dAtom;
183	+	RigidBody* myRB;
184	+	StuntDouble* mySD;
185		LinkedAssign* extras;
186		LinkedAssign* current_extra;
187		AtomStamp* currentAtom;
188		BondStamp* currentBond;
189		BendStamp* currentBend;
190		TorsionStamp* currentTorsion;
191	+	RigidBodyStamp* currentRigidBody;
192	+	CutoffGroupStamp* currentCutoffGroup;
193	+	CutoffGroup* myCutoffGroup;
194	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
195	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
196
197		bond_pair* theBonds;
198		bend_set* theBends;
199		torsion_set* theTorsions;
200
201	+	set<int> skipList;
202
203	+	double phi, theta, psi;
204	+	char* molName;
205	+	char rbName[100];
206	+
207	+	ConstraintPair* consPair; //constraint pair
208	+	ConstraintElement* consElement1;  //first element of constraint pair
209	+	ConstraintElement* consElement2;  //second element of constraint pair
210	+	int whichRigidBody;
211	+	int consAtomIndex;  //index of constraint atom in rigid body's atom array
212	+	vector<pair<int, int> > jointAtoms;
213	+	double bondLength2;
214		//init the forceField paramters
215
216		the_ff->readParams();
217
155	–
218		// init the atoms
219
220	<	double ux, uy, uz, u, uSqr;
220	>	int nMembers, nNew, rb1, rb2;
221
222		for (k = 0; k < nInfo; k++){
223		the_ff->setSimInfo(&(info[k]));
224
225	+	#ifdef IS_MPI
226	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
227	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
228	+	info[k].globalGroupMembership[i] = 0;
229	+	#else
230	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
231	+	for (i = 0; i < info[k].n_atoms; i++)
232	+	info[k].globalGroupMembership[i] = 0;
233	+	#endif
234	+
235		atomOffset = 0;
236	<	excludeOffset = 0;
236	>	groupOffset = 0;
237	>
238		for (i = 0; i < info[k].n_mol; i++){
239		stampID = info[k].molecules[i].getStampID();
240	+	molName = comp_stamps[stampID]->getID();
241
242		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
243		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
244		molInfo.nBends = comp_stamps[stampID]->getNBends();
245		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
246	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
246	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
247
248	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
249	+
250		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
175	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
176	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
177	–	molInfo.myBends = new Bend * [molInfo.nBends];
178	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
251
252	+	if (molInfo.nBonds > 0)
253	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
254	+	else
255	+	molInfo.myBonds = NULL;
256	+
257	+	if (molInfo.nBends > 0)
258	+	molInfo.myBends = new Bend*[molInfo.nBends];
259	+	else
260	+	molInfo.myBends = NULL;
261	+
262	+	if (molInfo.nTorsions > 0)
263	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
264	+	else
265	+	molInfo.myTorsions = NULL;
266	+
267		theBonds = new bond_pair[molInfo.nBonds];
268		theBends = new bend_set[molInfo.nBends];
269		theTorsions = new torsion_set[molInfo.nTorsions];
270	<
270	>
271		// make the Atoms
272
273		for (j = 0; j < molInfo.nAtoms; j++){
274		currentAtom = comp_stamps[stampID]->getAtom(j);
275	+
276		if (currentAtom->haveOrientation()){
277		dAtom = new DirectionalAtom((j + atomOffset),
278		info[k].getConfiguration());
279		info[k].n_oriented++;
280		molInfo.myAtoms[j] = dAtom;
281
282	<	ux = currentAtom->getOrntX();
283	<	uy = currentAtom->getOrntY();
284	<	uz = currentAtom->getOrntZ();
282	>	// Directional Atoms have standard unit vectors which are oriented
283	>	// in space using the three Euler angles.  We assume the standard
284	>	// unit vector was originally along the z axis below.
285
286	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
286	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
287	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
288	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
289
290	<	u = sqrt(uSqr);
291	<	ux = ux / u;
202	<	uy = uy / u;
203	<	uz = uz / u;
204	<
205	<	dAtom->setSUx(ux);
206	<	dAtom->setSUy(uy);
207	<	dAtom->setSUz(uz);
290	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
291	>
292		}
293		else{
294	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
295	<	info[k].getConfiguration());
294	>
295	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
296	>
297		}
213	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
298
299	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
300		#ifdef IS_MPI
301	<
217	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
218	<
301	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
302		#endif // is_mpi
303		}
304
#	Line 225 | Line 308 | void SimSetup::makeMolecules(void){
308		theBonds[j].a = currentBond->getA() + atomOffset;
309		theBonds[j].b = currentBond->getB() + atomOffset;
310
311	<	exI = theBonds[j].a;
312	<	exJ = theBonds[j].b;
311	>	tempI = theBonds[j].a;
312	>	tempJ = theBonds[j].b;
313
231	–	// exclude_I must always be the smaller of the pair
232	–	if (exI > exJ){
233	–	tempEx = exI;
234	–	exI = exJ;
235	–	exJ = tempEx;
236	–	}
314		#ifdef IS_MPI
315	<	tempEx = exI;
316	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
317	<	tempEx = exJ;
318	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
315	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
316	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
317	>	#else
318	>	exI = tempI + 1;
319	>	exJ = tempJ + 1;
320	>	#endif
321
322	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
244	<	#else  // isn't MPI
245	<
246	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
247	<	#endif  //is_mpi
322	>	info[k].excludes->addPair(exI, exJ);
323		}
249	–	excludeOffset += molInfo.nBonds;
324
325		//make the bends
326		for (j = 0; j < molInfo.nBends; j++){
#	Line 296 | Line 370 | void SimSetup::makeMolecules(void){
370		}
371		}
372
373	<	if (!theBends[j].isGhost){
374	<	exI = theBends[j].a;
375	<	exJ = theBends[j].c;
376	<	}
377	<	else{
304	<	exI = theBends[j].a;
305	<	exJ = theBends[j].b;
306	<	}
307	<
308	<	// exclude_I must always be the smaller of the pair
309	<	if (exI > exJ){
310	<	tempEx = exI;
311	<	exI = exJ;
312	<	exJ = tempEx;
313	<	}
373	>	if (theBends[j].isGhost) {
374	>
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>
378		#ifdef IS_MPI
379	<	tempEx = exI;
380	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
381	<	tempEx = exJ;
382	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
379	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
380	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
381	>	#else
382	>	exI = tempI + 1;
383	>	exJ = tempJ + 1;
384	>	#endif
385	>	info[k].excludes->addPair(exI, exJ);
386
387	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
388	<	#else  // isn't MPI
389	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
390	<	#endif  //is_mpi
387	>	} else {
388	>
389	>	tempI = theBends[j].a;
390	>	tempJ = theBends[j].b;
391	>	tempK = theBends[j].c;
392	>
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	#else
398	>	exI = tempI + 1;
399	>	exJ = tempJ + 1;
400	>	exK = tempK + 1;
401	>	#endif
402	>
403	>	info[k].excludes->addPair(exI, exK);
404	>	info[k].excludes->addPair(exI, exJ);
405	>	info[k].excludes->addPair(exJ, exK);
406	>	}
407		}
325	–	excludeOffset += molInfo.nBends;
408
409		for (j = 0; j < molInfo.nTorsions; j++){
410		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 331 | Line 413 | void SimSetup::makeMolecules(void){
413		theTorsions[j].c = currentTorsion->getC() + atomOffset;
414		theTorsions[j].d = currentTorsion->getD() + atomOffset;
415
416	<	exI = theTorsions[j].a;
417	<	exJ = theTorsions[j].d;
416	>	tempI = theTorsions[j].a;
417	>	tempJ = theTorsions[j].b;
418	>	tempK = theTorsions[j].c;
419	>	tempL = theTorsions[j].d;
420
337	–	// exclude_I must always be the smaller of the pair
338	–	if (exI > exJ){
339	–	tempEx = exI;
340	–	exI = exJ;
341	–	exJ = tempEx;
342	–	}
421		#ifdef IS_MPI
422	<	tempEx = exI;
423	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
424	<	tempEx = exJ;
425	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
422	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
423	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
424	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
425	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
426	>	#else
427	>	exI = tempI + 1;
428	>	exJ = tempJ + 1;
429	>	exK = tempK + 1;
430	>	exL = tempL + 1;
431	>	#endif
432
433	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
434	<	#else  // isn't MPI
435	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
436	<	#endif  //is_mpi
433	>	info[k].excludes->addPair(exI, exJ);
434	>	info[k].excludes->addPair(exI, exK);
435	>	info[k].excludes->addPair(exI, exL);
436	>	info[k].excludes->addPair(exJ, exK);
437	>	info[k].excludes->addPair(exJ, exL);
438	>	info[k].excludes->addPair(exK, exL);
439		}
354	–	excludeOffset += molInfo.nTorsions;
440
441	+
442	+	molInfo.myRigidBodies.clear();
443	+
444	+	for (j = 0; j < molInfo.nRigidBodies; j++){
445
446	<	// send the arrays off to the forceField for init.
446	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
447	>	nMembers = currentRigidBody->getNMembers();
448
449	+	// Create the Rigid Body:
450	+
451	+	myRB = new RigidBody();
452	+
453	+	sprintf(rbName,"%s_RB_%d", molName, j);
454	+	myRB->setType(rbName);
455	+
456	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
457	+
458	+	// molI is atom numbering inside this molecule
459	+	molI = currentRigidBody->getMember(rb1);
460	+
461	+	// tempI is atom numbering on local processor
462	+	tempI = molI + atomOffset;
463	+
464	+	// currentAtom is the AtomStamp (which we need for
465	+	// rigid body reference positions)
466	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
467	+
468	+	// When we add to the rigid body, add the atom itself and
469	+	// the stamp info:
470	+
471	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
472	+
473	+	// Add this atom to the Skip List for the integrators
474	+	#ifdef IS_MPI
475	+	slI = info[k].atoms[tempI]->getGlobalIndex();
476	+	#else
477	+	slI = tempI;
478	+	#endif
479	+	skipList.insert(slI);
480	+
481	+	}
482	+
483	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
484	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
485	+
486	+	tempI = currentRigidBody->getMember(rb1);
487	+	tempJ = currentRigidBody->getMember(rb2);
488	+
489	+	// Some explanation is required here.
490	+	// Fortran indexing starts at 1, while c indexing starts at 0
491	+	// Also, in parallel computations, the GlobalIndex is
492	+	// used for the exclude list:
493	+
494	+	#ifdef IS_MPI
495	+	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
496	+	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
497	+	#else
498	+	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
499	+	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
500	+	#endif
501	+
502	+	info[k].excludes->addPair(exI, exJ);
503	+
504	+	}
505	+	}
506	+
507	+	molInfo.myRigidBodies.push_back(myRB);
508	+	info[k].rigidBodies.push_back(myRB);
509	+	}
510	+
511	+
512	+	//create cutoff group for molecule
513	+
514	+	cutoffAtomSet.clear();
515	+	molInfo.myCutoffGroups.clear();
516	+
517	+	for (j = 0; j < nCutoffGroups; j++){
518	+
519	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
520	+	nMembers = currentCutoffGroup->getNMembers();
521	+
522	+	myCutoffGroup = new CutoffGroup();
523	+
524	+	#ifdef IS_MPI
525	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
526	+	#else
527	+	myCutoffGroup->setGlobalIndex(groupOffset);
528	+	#endif
529	+
530	+	for (int cg = 0; cg < nMembers; cg++) {
531	+
532	+	// molI is atom numbering inside this molecule
533	+	molI = currentCutoffGroup->getMember(cg);
534	+
535	+	// tempI is atom numbering on local processor
536	+	tempI = molI + atomOffset;
537	+
538	+	#ifdef IS_MPI
539	+	globalID = info[k].atoms[tempI]->getGlobalIndex();
540	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
541	+	#else
542	+	globalID = info[k].atoms[tempI]->getIndex();
543	+	info[k].globalGroupMembership[globalID] = groupOffset;
544	+	#endif
545	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
546	+	cutoffAtomSet.insert(tempI);
547	+	}
548	+
549	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
550	+	groupOffset++;
551	+
552	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
553	+
554	+
555	+	// create a cutoff group for every atom in current molecule which
556	+	// does not belong to cutoffgroup defined at mdl file
557	+
558	+	for(j = 0; j < molInfo.nAtoms; j++){
559	+
560	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
561	+	myCutoffGroup = new CutoffGroup();
562	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
563	+
564	+	#ifdef IS_MPI
565	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
566	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
567	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
568	+	#else
569	+	myCutoffGroup->setGlobalIndex(groupOffset);
570	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
571	+	info[k].globalGroupMembership[globalID] = groupOffset;
572	+	#endif
573	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
574	+	groupOffset++;
575	+	}
576	+	}
577	+
578	+	// After this is all set up, scan through the atoms to
579	+	// see if they can be added to the integrableObjects:
580	+
581	+	molInfo.myIntegrableObjects.clear();
582	+
583	+
584	+	for (j = 0; j < molInfo.nAtoms; j++){
585	+
586	+	#ifdef IS_MPI
587	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
588	+	#else
589	+	slJ = j+atomOffset;
590	+	#endif
591	+
592	+	// if they aren't on the skip list, then they can be integrated
593	+
594	+	if (skipList.find(slJ) == skipList.end()) {
595	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
596	+	info[k].integrableObjects.push_back(mySD);
597	+	molInfo.myIntegrableObjects.push_back(mySD);
598	+	}
599	+	}
600	+
601	+	// all rigid bodies are integrated:
602	+
603	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
604	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
605	+	info[k].integrableObjects.push_back(mySD);
606	+	molInfo.myIntegrableObjects.push_back(mySD);
607	+	}
608	+
609	+	// send the arrays off to the forceField for init.
610	+
611		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
612		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
613		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
#	Line 363 | Line 615 | void SimSetup::makeMolecules(void){
615		theTorsions);
616
617
618	<	info[k].molecules[i].initialize(molInfo);
618	>	//creat ConstraintPair.
619	>	molInfo.myConstraintPairs.clear();
620	>
621	>	for (j = 0; j < molInfo.nBonds; j++){
622
623	+	//if bond is constrained bond, add it into constraint pair
624	+	if(molInfo.myBonds[j]->is_constrained()){
625
626	+	//if both atoms are in the same rigid body, just skip it
627	+	currentBond = comp_stamps[stampID]->getBond(j);
628	+
629	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
630	+
631	+	tempI = currentBond->getA() + atomOffset;
632	+	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
633	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
634	+	else
635	+	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
636	+
637	+	tempJ =  currentBond->getB() + atomOffset;
638	+	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
639	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
640	+	else
641	+	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
642	+
643	+	bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();
644	+	consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
645	+
646	+	molInfo.myConstraintPairs.push_back(consPair);
647	+	}
648	+	}//end if(molInfo.myBonds[j]->is_constrained())
649	+	}
650	+
651	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair
652	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
653	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
654	+
655	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
656	+
657	+	for(size_t m = 0; m < jointAtoms.size(); m++){
658	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
659	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
660	+
661	+	consPair = new JointConstraintPair(consElement1, consElement2);
662	+	molInfo.myConstraintPairs.push_back(consPair);
663	+	}
664	+
665	+	}
666	+	}
667	+
668	+
669	+	info[k].molecules[i].initialize(molInfo);
670	+
671	+
672		atomOffset += molInfo.nAtoms;
673		delete[] theBonds;
674		delete[] theBends;
675		delete[] theTorsions;
676		}
677	+
678	+
679	+
680	+	#ifdef IS_MPI
681	+	// Since the globalGroupMembership has been zero filled and we've only
682	+	// poked values into the atoms we know, we can do an Allreduce
683	+	// to get the full globalGroupMembership array (We think).
684	+	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
685	+	// docs said we could.
686	+
687	+	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
688	+
689	+	MPI_Allreduce(info[k].globalGroupMembership,
690	+	ggMjunk,
691	+	mpiSim->getNAtomsGlobal(),
692	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
693	+
694	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
695	+	info[k].globalGroupMembership[i] = ggMjunk[i];
696	+
697	+	delete[] ggMjunk;
698	+
699	+	#endif
700	+
701	+
702	+
703		}
704
705		#ifdef IS_MPI
#	Line 378 | Line 707 | void SimSetup::makeMolecules(void){
707		MPIcheckPoint();
708		#endif // is_mpi
709
381	–	// clean up the forcefield
382	–
383	–	the_ff->calcRcut();
384	–	the_ff->cleanMe();
710		}
711
712		void SimSetup::initFromBass(void){
#	Line 582 | Line 907 | void SimSetup::gatherInfo(void){
907		else if (!strcasecmp(force_field, "EAM")){
908		ffCase = FF_EAM;
909		}
910	+	else if (!strcasecmp(force_field, "WATER")){
911	+	ffCase = FF_H2O;
912	+	}
913		else{
914		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
915		force_field);
916		painCave.isFatal = 1;
917		simError();
918		}
919	<
920	<	// get the ensemble
919	>	if (globals->haveForceFieldVariant()) {
920	>	strcpy(forcefield_variant, globals->getForceFieldVariant());
921	>	has_forcefield_variant = 1;
922	>	}
923	>
924	>	// get the ensemble
925
926		strcpy(ensemble, globals->getEnsemble());
927
#	Line 610 | Line 942 | void SimSetup::gatherInfo(void){
942		}
943		else{
944		sprintf(painCave.errMsg,
945	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
946	<	"reverting to NVE for this simulation.\n",
945	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
946	>	"\treverting to NVE for this simulation.\n",
947		ensemble);
948		painCave.isFatal = 0;
949		simError();
#	Line 643 | Line 975 | void SimSetup::gatherInfo(void){
975		if (!the_components[i]->haveNMol()){
976		// we have a problem
977		sprintf(painCave.errMsg,
978	<	"SimSetup Error. No global NMol or component NMol"
979	<	" given. Cannot calculate the number of atoms.\n");
978	>	"SimSetup Error. No global NMol or component NMol given.\n"
979	>	"\tCannot calculate the number of atoms.\n");
980		painCave.isFatal = 1;
981		simError();
982		}
#	Line 664 | Line 996 | void SimSetup::gatherInfo(void){
996		simError();
997		}
998
999	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
1000	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1001	+	sprintf(painCave.errMsg,
1002	+	"Sample time is not divisible by dt.\n"
1003	+	"\tThis will result in samples that are not uniformly\n"
1004	+	"\tdistributed in time.  If this is a problem, change\n"
1005	+	"\tyour sampleTime variable.\n");
1006	+	painCave.isFatal = 0;
1007	+	simError();
1008	+	}
1009	+
1010	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1011	+	sprintf(painCave.errMsg,
1012	+	"Status time is not divisible by dt.\n"
1013	+	"\tThis will result in status reports that are not uniformly\n"
1014	+	"\tdistributed in time.  If this is a problem, change \n"
1015	+	"\tyour statusTime variable.\n");
1016	+	painCave.isFatal = 0;
1017	+	simError();
1018	+	}
1019	+
1020	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1021	+	sprintf(painCave.errMsg,
1022	+	"Thermal time is not divisible by dt.\n"
1023	+	"\tThis will result in thermalizations that are not uniformly\n"
1024	+	"\tdistributed in time.  If this is a problem, change \n"
1025	+	"\tyour thermalTime variable.\n");
1026	+	painCave.isFatal = 0;
1027	+	simError();
1028	+	}
1029	+
1030	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1031	+	sprintf(painCave.errMsg,
1032	+	"Reset time is not divisible by dt.\n"
1033	+	"\tThis will result in integrator resets that are not uniformly\n"
1034	+	"\tdistributed in time.  If this is a problem, change\n"
1035	+	"\tyour resetTime variable.\n");
1036	+	painCave.isFatal = 0;
1037	+	simError();
1038	+	}
1039	+
1040		// set the status, sample, and thermal kick times
1041
1042		for (i = 0; i < nInfo; i++){
1043		if (globals->haveSampleTime()){
1044		info[i].sampleTime = globals->getSampleTime();
1045		info[i].statusTime = info[i].sampleTime;
673	–	info[i].thermalTime = info[i].sampleTime;
1046		}
1047		else{
1048		info[i].sampleTime = globals->getRunTime();
1049		info[i].statusTime = info[i].sampleTime;
678	–	info[i].thermalTime = info[i].sampleTime;
1050		}
1051
1052		if (globals->haveStatusTime()){
#	Line 684 | Line 1055 | void SimSetup::gatherInfo(void){
1055
1056		if (globals->haveThermalTime()){
1057		info[i].thermalTime = globals->getThermalTime();
1058	+	} else {
1059	+	info[i].thermalTime = globals->getRunTime();
1060		}
1061
1062		info[i].resetIntegrator = 0;
#	Line 693 | Line 1066 | void SimSetup::gatherInfo(void){
1066		}
1067
1068		// check for the temperature set flag
1069	<
1069	>
1070		if (globals->haveTempSet())
1071		info[i].setTemp = globals->getTempSet();
1072
1073	<	// get some of the tricky things that may still be in the globals
1073	>	// check for the extended State init
1074
1075	<	double boxVector[3];
1076	<	if (globals->haveBox()){
704	<	boxVector[0] = globals->getBox();
705	<	boxVector[1] = globals->getBox();
706	<	boxVector[2] = globals->getBox();
1075	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1076	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1077
1078	<	info[i].setBox(boxVector);
1078	>	// check for thermodynamic integration
1079	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1080	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1081	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1082	>	info[i].thermIntLambda = globals->getThermIntLambda();
1083	>	info[i].thermIntK = globals->getThermIntK();
1084	>
1085	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1086	>	info[i].restraint = myRestraint;
1087	>	}
1088	>	else {
1089	>	sprintf(painCave.errMsg,
1090	>	"SimSetup Error:\n"
1091	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1092	>	"\tthermodynamicIntegrationLambda (and/or\n"
1093	>	"\tthermodynamicIntegrationK) was not specified.\n"
1094	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1095	>	painCave.isFatal = 1;
1096	>	simError();
1097	>	}
1098		}
1099	<	else if (globals->haveDensity()){
1100	<	double vol;
1101	<	vol = (double) tot_nmol / globals->getDensity();
1102	<	boxVector[0] = pow(vol, (1.0 / 3.0));
1103	<	boxVector[1] = boxVector[0];
1104	<	boxVector[2] = boxVector[0];
1105	<
1106	<	info[i].setBox(boxVector);
1107	<	}
1108	<	else{
1109	<	if (!globals->haveBoxX()){
1110	<	sprintf(painCave.errMsg,
722	<	"SimSetup error, no periodic BoxX size given.\n");
723	<	painCave.isFatal = 1;
724	<	simError();
1099	>	else if(globals->getUseLiquidThermInt()) {
1100	>	if (globals->getUseSolidThermInt()) {
1101	>	sprintf( painCave.errMsg,
1102	>	"SimSetup Warning: It appears that you have both solid and\n"
1103	>	"\tliquid thermodynamic integration activated in your .bass\n"
1104	>	"\tfile. To avoid confusion, specify only one technique in\n"
1105	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1106	>	"\twill be assumed for the current simulation. If this is not\n"
1107	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1108	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1109	>	painCave.isFatal = 0;
1110	>	simError();
1111		}
1112	<	boxVector[0] = globals->getBoxX();
1113	<
1114	<	if (!globals->haveBoxY()){
1115	<	sprintf(painCave.errMsg,
730	<	"SimSetup error, no periodic BoxY size given.\n");
731	<	painCave.isFatal = 1;
732	<	simError();
1112	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1113	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1114	>	info[i].thermIntLambda = globals->getThermIntLambda();
1115	>	info[i].thermIntK = globals->getThermIntK();
1116		}
1117	<	boxVector[1] = globals->getBoxY();
1118	<
1119	<	if (!globals->haveBoxZ()){
1120	<	sprintf(painCave.errMsg,
1121	<	"SimSetup error, no periodic BoxZ size given.\n");
1122	<	painCave.isFatal = 1;
1123	<	simError();
1117	>	else {
1118	>	sprintf(painCave.errMsg,
1119	>	"SimSetup Error:\n"
1120	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1121	>	"\tthermodynamicIntegrationLambda (and/or\n"
1122	>	"\tthermodynamicIntegrationK) was not specified.\n"
1123	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1124	>	painCave.isFatal = 1;
1125	>	simError();
1126		}
742	–	boxVector[2] = globals->getBoxZ();
743	–
744	–	info[i].setBox(boxVector);
1127		}
1128	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1129	+	sprintf(painCave.errMsg,
1130	+	"SimSetup Warning: If you want to use Thermodynamic\n"
1131	+	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1132	+	"\t'true' in your .bass file.  These keywords are set to\n"
1133	+	"\t'false' by default, so your lambda and/or k values are\n"
1134	+	"\tbeing ignored.\n");
1135	+	painCave.isFatal = 0;
1136	+	simError();
1137	+	}
1138		}
1139	<
1139	>
1140		//setup seed for random number generator
1141		int seedValue;
1142
#	Line 784 | Line 1176 | void SimSetup::gatherInfo(void){
1176		for (int i = 0; i < nInfo; i++){
1177		info[i].setSeed(seedValue);
1178		}
1179	<
1179	>
1180		#ifdef IS_MPI
1181	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1181	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1182		MPIcheckPoint();
1183		#endif // is_mpi
1184		}
#	Line 795 | Line 1187 | void SimSetup::finalInfoCheck(void){
1187		void SimSetup::finalInfoCheck(void){
1188		int index;
1189		int usesDipoles;
1190	+	int usesCharges;
1191		int i;
1192
1193		for (i = 0; i < nInfo; i++){
#	Line 806 | Line 1199 | void SimSetup::finalInfoCheck(void){
1199		usesDipoles = (info[i].atoms[index])->hasDipole();
1200		index++;
1201		}
1202	<
1202	>	index = 0;
1203	>	usesCharges = 0;
1204	>	while ((index < info[i].n_atoms) && !usesCharges){
1205	>	usesCharges= (info[i].atoms[index])->hasCharge();
1206	>	index++;
1207	>	}
1208		#ifdef IS_MPI
1209		int myUse = usesDipoles;
1210		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1211		#endif //is_mpi
1212
1213	<	double theEcr, theEst;
1213	>	double theRcut, theRsw;
1214
1215	<	if (globals->getUseRF()){
1216	<	info[i].useReactionField = 1;
1215	>	if (globals->haveRcut()) {
1216	>	theRcut = globals->getRcut();
1217
1218	<	if (!globals->haveECR()){
1218	>	if (globals->haveRsw())
1219	>	theRsw = globals->getRsw();
1220	>	else
1221	>	theRsw = theRcut;
1222	>
1223	>	info[i].setDefaultRcut(theRcut, theRsw);
1224	>
1225	>	} else {
1226	>
1227	>	the_ff->calcRcut();
1228	>	theRcut = info[i].getRcut();
1229	>
1230	>	if (globals->haveRsw())
1231	>	theRsw = globals->getRsw();
1232	>	else
1233	>	theRsw = theRcut;
1234	>
1235	>	info[i].setDefaultRcut(theRcut, theRsw);
1236	>	}
1237	>
1238	>	if (globals->getUseRF()){
1239	>	info[i].useReactionField = 1;
1240	>
1241	>	if (!globals->haveRcut()){
1242		sprintf(painCave.errMsg,
1243	<	"SimSetup Warning: using default value of 1/2 the smallest "
1244	<	"box length for the electrostaticCutoffRadius.\n"
1245	<	"I hope you have a very fast processor!\n");
1243	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1244	>	"\tOOPSE will use a default value of 15.0 angstroms"
1245	>	"\tfor the cutoffRadius.\n");
1246		painCave.isFatal = 0;
1247		simError();
1248	<	double smallest;
828	<	smallest = info[i].boxL[0];
829	<	if (info[i].boxL[1] <= smallest)
830	<	smallest = info[i].boxL[1];
831	<	if (info[i].boxL[2] <= smallest)
832	<	smallest = info[i].boxL[2];
833	<	theEcr = 0.5 * smallest;
1248	>	theRcut = 15.0;
1249		}
1250		else{
1251	<	theEcr = globals->getECR();
1251	>	theRcut = globals->getRcut();
1252		}
1253
1254	<	if (!globals->haveEST()){
1254	>	if (!globals->haveRsw()){
1255		sprintf(painCave.errMsg,
1256	<	"SimSetup Warning: using default value of 0.05 * the "
1257	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1256	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1257	>	"\tOOPSE will use a default value of\n"
1258	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1259		painCave.isFatal = 0;
1260		simError();
1261	<	theEst = 0.05 * theEcr;
1261	>	theRsw = 0.95 * theRcut;
1262		}
1263		else{
1264	<	theEst = globals->getEST();
1264	>	theRsw = globals->getRsw();
1265		}
1266
1267	<	info[i].setEcr(theEcr, theEst);
1267	>	info[i].setDefaultRcut(theRcut, theRsw);
1268
1269		if (!globals->haveDielectric()){
1270		sprintf(painCave.errMsg,
1271	<	"SimSetup Error: You are trying to use Reaction Field without"
1272	<	"setting a dielectric constant!\n");
1271	>	"SimSetup Error: No Dielectric constant was set.\n"
1272	>	"\tYou are trying to use Reaction Field without"
1273	>	"\tsetting a dielectric constant!\n");
1274		painCave.isFatal = 1;
1275		simError();
1276		}
1277		info[i].dielectric = globals->getDielectric();
1278		}
1279		else{
1280	<	if (usesDipoles){
1281	<	if (!globals->haveECR()){
1280	>	if (usesDipoles || usesCharges){
1281	>
1282	>	if (!globals->haveRcut()){
1283		sprintf(painCave.errMsg,
1284	<	"SimSetup Warning: using default value of 1/2 the smallest "
1285	<	"box length for the electrostaticCutoffRadius.\n"
1286	<	"I hope you have a very fast processor!\n");
1284	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1285	>	"\tOOPSE will use a default value of 15.0 angstroms"
1286	>	"\tfor the cutoffRadius.\n");
1287		painCave.isFatal = 0;
1288		simError();
1289	<	double smallest;
1290	<	smallest = info[i].boxL[0];
873	<	if (info[i].boxL[1] <= smallest)
874	<	smallest = info[i].boxL[1];
875	<	if (info[i].boxL[2] <= smallest)
876	<	smallest = info[i].boxL[2];
877	<	theEcr = 0.5 * smallest;
878	<	}
1289	>	theRcut = 15.0;
1290	>	}
1291		else{
1292	<	theEcr = globals->getECR();
1292	>	theRcut = globals->getRcut();
1293		}
1294	<
1295	<	if (!globals->haveEST()){
1294	>
1295	>	if (!globals->haveRsw()){
1296		sprintf(painCave.errMsg,
1297	<	"SimSetup Warning: using default value of 0.05 * the "
1298	<	"electrostaticCutoffRadius for the "
1299	<	"electrostaticSkinThickness\n");
1297	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1298	>	"\tOOPSE will use a default value of\n"
1299	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1300		painCave.isFatal = 0;
1301		simError();
1302	<	theEst = 0.05 * theEcr;
1302	>	theRsw = 0.95 * theRcut;
1303		}
1304		else{
1305	<	theEst = globals->getEST();
1305	>	theRsw = globals->getRsw();
1306		}
1307	<
1308	<	info[i].setEcr(theEcr, theEst);
1307	>
1308	>	info[i].setDefaultRcut(theRcut, theRsw);
1309	>
1310		}
1311		}
1312		}
900	–
1313		#ifdef IS_MPI
1314		strcpy(checkPointMsg, "post processing checks out");
1315		MPIcheckPoint();
1316		#endif // is_mpi
905	–	}
1317
1318	+	// clean up the forcefield
1319	+	the_ff->cleanMe();
1320	+	}
1321	+
1322		void SimSetup::initSystemCoords(void){
1323		int i;
1324
#	Line 931 | Line 1346 | void SimSetup::initSystemCoords(void){
1346		delete fileInit;
1347		}
1348		else{
1349	<	#ifdef IS_MPI
935	<
1349	>
1350		// no init from bass
1351	<
1351	>
1352		sprintf(painCave.errMsg,
1353	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1353	>	"Cannot intialize a simulation without an initial configuration file.\n");
1354		painCave.isFatal = 1;;
1355		simError();
1356	<
943	<	#else
944	<
945	<	initFromBass();
946	<
947	<
948	<	#endif
1356	>
1357		}
1358
1359		#ifdef IS_MPI
#	Line 1039 | Line 1447 | void SimSetup::makeOutNames(void){
1447		}
1448		}
1449
1450	+	strcpy(info[k].rawPotName, inFileName);
1451	+	nameLength = strlen(info[k].rawPotName);
1452	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1453	+	if (!strcmp(endTest, ".bass")){
1454	+	strcpy(endTest, ".raw");
1455	+	}
1456	+	else if (!strcmp(endTest, ".BASS")){
1457	+	strcpy(endTest, ".raw");
1458	+	}
1459	+	else{
1460	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1461	+	if (!strcmp(endTest, ".bss")){
1462	+	strcpy(endTest, ".raw");
1463	+	}
1464	+	else if (!strcmp(endTest, ".mdl")){
1465	+	strcpy(endTest, ".raw");
1466	+	}
1467	+	else{
1468	+	strcat(info[k].rawPotName, ".raw");
1469	+	}
1470	+	}
1471	+
1472		#ifdef IS_MPI
1473
1474		}
#	Line 1088 | Line 1518 | void SimSetup::createFF(void){
1518		void SimSetup::createFF(void){
1519		switch (ffCase){
1520		case FF_DUFF:
1521	<	the_ff = new DUFF();
1521	>	the_ff = new DUFF();
1522		break;
1523
1524		case FF_LJ:
#	Line 1096 | Line 1526 | void SimSetup::createFF(void){
1526		break;
1527
1528		case FF_EAM:
1529	<	the_ff = new EAM_FF();
1529	>	if (has_forcefield_variant)
1530	>	the_ff = new EAM_FF(forcefield_variant);
1531	>	else
1532	>	the_ff = new EAM_FF();
1533		break;
1534
1535	+	case FF_H2O:
1536	+	the_ff = new WATER();
1537	+	break;
1538	+
1539		default:
1540		sprintf(painCave.errMsg,
1541		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1106 | Line 1543 | void SimSetup::createFF(void){
1543		simError();
1544		}
1545
1546	+
1547		#ifdef IS_MPI
1548		strcpy(checkPointMsg, "ForceField creation successful");
1549		MPIcheckPoint();
#	Line 1119 | Line 1557 | void SimSetup::compList(void){
1557		LinkedMolStamp* headStamp = new LinkedMolStamp();
1558		LinkedMolStamp* currentStamp = NULL;
1559		comp_stamps = new MoleculeStamp * [n_components];
1560	+	bool haveCutoffGroups;
1561
1562	+	haveCutoffGroups = false;
1563	+
1564		// make an array of molecule stamps that match the components used.
1565		// also extract the used stamps out into a separate linked list
1566
#	Line 1154 | Line 1595 | void SimSetup::compList(void){
1595		headStamp->add(currentStamp);
1596		comp_stamps[i] = headStamp->match(id);
1597		}
1598	+
1599	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1600	+	haveCutoffGroups = true;
1601		}
1602	+
1603	+	for (i = 0; i < nInfo; i++)
1604	+	info[i].haveCutoffGroups = haveCutoffGroups;
1605
1606		#ifdef IS_MPI
1607		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1163 | Line 1610 | void SimSetup::calcSysValues(void){
1610		}
1611
1612		void SimSetup::calcSysValues(void){
1613	<	int i;
1613	>	int i, j;
1614	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1615
1616		int* molMembershipArray;
1617	+	CutoffGroupStamp* cg;
1618
1619		tot_atoms = 0;
1620		tot_bonds = 0;
1621		tot_bends = 0;
1622		tot_torsions = 0;
1623	+	tot_rigid = 0;
1624	+	tot_groups = 0;
1625		for (i = 0; i < n_components; i++){
1626		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1627		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1628		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1629		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1630	<	}
1630	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1631
1632	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1633	+	atomsingroups = 0;
1634	+	for (j=0; j < ncutgroups; j++) {
1635	+	cg = comp_stamps[i]->getCutoffGroup(j);
1636	+	atomsingroups += cg->getNMembers();
1637	+	}
1638	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1639	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1640	+	}
1641	+
1642		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1643		molMembershipArray = new int[tot_atoms];
1644
#	Line 1188 | Line 1649 | void SimSetup::calcSysValues(void){
1649		info[i].n_torsions = tot_torsions;
1650		info[i].n_SRI = tot_SRI;
1651		info[i].n_mol = tot_nmol;
1652	<
1652	>	info[i].ngroup = tot_groups;
1653		info[i].molMembershipArray = molMembershipArray;
1654		}
1655		}
#	Line 1199 | Line 1660 | void SimSetup::mpiMolDivide(void){
1660		int i, j, k;
1661		int localMol, allMol;
1662		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1663	+	int local_rigid, local_groups;
1664	+	vector<int> globalMolIndex;
1665	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1666	+	CutoffGroupStamp* cg;
1667
1668		mpiSim = new mpiSimulation(info);
1669
1670	<	globalIndex = mpiSim->divideLabor();
1670	>	mpiSim->divideLabor();
1671	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1672	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1673	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1674
1675		// set up the local variables
1676
#	Line 1215 | Line 1683 | void SimSetup::mpiMolDivide(void){
1683		local_bonds = 0;
1684		local_bends = 0;
1685		local_torsions = 0;
1686	<	globalAtomIndex = 0;
1686	>	local_rigid = 0;
1687	>	local_groups = 0;
1688	>	globalAtomCounter = 0;
1689
1220	–
1690		for (i = 0; i < n_components; i++){
1691		for (j = 0; j < components_nmol[i]; j++){
1692		if (mol2proc[allMol] == worldRank){
#	Line 1225 | Line 1694 | void SimSetup::mpiMolDivide(void){
1694		local_bonds += comp_stamps[i]->getNBonds();
1695		local_bends += comp_stamps[i]->getNBends();
1696		local_torsions += comp_stamps[i]->getNTorsions();
1697	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1698	+
1699	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1700	+	atomsingroups = 0;
1701	+	for (k=0; k < ncutgroups; k++) {
1702	+	cg = comp_stamps[i]->getCutoffGroup(k);
1703	+	atomsingroups += cg->getNMembers();
1704	+	}
1705	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1706	+	ncutgroups;
1707	+	local_groups += ngroupsinstamp;
1708	+
1709		localMol++;
1710		}
1711		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1712	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1713	<	globalAtomIndex++;
1712	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1713	>	globalAtomCounter++;
1714		}
1715
1716		allMol++;
#	Line 1237 | Line 1718 | void SimSetup::mpiMolDivide(void){
1718		}
1719		local_SRI = local_bonds + local_bends + local_torsions;
1720
1721	<	info[0].n_atoms = mpiSim->getMyNlocal();
1722	<
1721	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1722	>
1723		if (local_atoms != info[0].n_atoms){
1724		sprintf(painCave.errMsg,
1725	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1726	<	" localAtom (%d) are not equal.\n",
1725	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1726	>	"\tlocalAtom (%d) are not equal.\n",
1727		info[0].n_atoms, local_atoms);
1728		painCave.isFatal = 1;
1729		simError();
1730		}
1731
1732	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1733	+	if (local_groups != info[0].ngroup){
1734	+	sprintf(painCave.errMsg,
1735	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1736	+	"\tlocalGroups (%d) are not equal.\n",
1737	+	info[0].ngroup, local_groups);
1738	+	painCave.isFatal = 1;
1739	+	simError();
1740	+	}
1741	+
1742		info[0].n_bonds = local_bonds;
1743		info[0].n_bends = local_bends;
1744		info[0].n_torsions = local_torsions;
#	Line 1270 | Line 1761 | void SimSetup::makeSysArrays(void){
1761
1762		Atom** the_atoms;
1763		Molecule* the_molecules;
1273	–	Exclude** the_excludes;
1764
1275	–
1765		for (l = 0; l < nInfo; l++){
1766		// create the atom and short range interaction arrays
1767
#	Line 1286 | Line 1775 | void SimSetup::makeSysArrays(void){
1775
1776
1777		molIndex = 0;
1778	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1778	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1779		if (mol2proc[i] == worldRank){
1780		the_molecules[molIndex].setStampID(molCompType[i]);
1781		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1298 | Line 1787 | void SimSetup::makeSysArrays(void){
1787		#else // is_mpi
1788
1789		molIndex = 0;
1790	<	globalAtomIndex = 0;
1790	>	globalAtomCounter = 0;
1791		for (i = 0; i < n_components; i++){
1792		for (j = 0; j < components_nmol[i]; j++){
1793		the_molecules[molIndex].setStampID(i);
1794		the_molecules[molIndex].setMyIndex(molIndex);
1795		the_molecules[molIndex].setGlobalIndex(molIndex);
1796		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1797	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1798	<	globalAtomIndex++;
1797	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1798	>	globalAtomCounter++;
1799		}
1800		molIndex++;
1801		}
#	Line 1315 | Line 1804 | void SimSetup::makeSysArrays(void){
1804
1805		#endif // is_mpi
1806
1807	<
1808	<	if (info[l].n_SRI){
1809	<	Exclude::createArray(info[l].n_SRI);
1321	<	the_excludes = new Exclude * [info[l].n_SRI];
1322	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1323	<	the_excludes[ex] = new Exclude(ex);
1324	<	}
1325	<	info[l].globalExcludes = new int;
1326	<	info[l].n_exclude = info[l].n_SRI;
1327	<	}
1328	<	else{
1329	<	Exclude::createArray(1);
1330	<	the_excludes = new Exclude * ;
1331	<	the_excludes[0] = new Exclude(0);
1332	<	the_excludes[0]->setPair(0, 0);
1333	<	info[l].globalExcludes = new int;
1334	<	info[l].globalExcludes[0] = 0;
1335	<	info[l].n_exclude = 0;
1336	<	}
1337	<
1807	>	info[l].globalExcludes = new int;
1808	>	info[l].globalExcludes[0] = 0;
1809	>
1810		// set the arrays into the SimInfo object
1811
1812		info[l].atoms = the_atoms;
1813		info[l].molecules = the_molecules;
1814		info[l].nGlobalExcludes = 0;
1815	<	info[l].excludes = the_excludes;
1344	<
1815	>
1816		the_ff->setSimInfo(info);
1817		}
1818		}
#	Line 1349 | Line 1820 | void SimSetup::makeIntegrator(void){
1820		void SimSetup::makeIntegrator(void){
1821		int k;
1822
1823	<	NVE<RealIntegrator>* myNVE = NULL;
1824	<	NVT<RealIntegrator>* myNVT = NULL;
1825	<	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1826	<	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1827	<	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1823	>	NVE<Integrator<BaseIntegrator> >* myNVE = NULL;
1824	>	NVT<Integrator<BaseIntegrator> >* myNVT = NULL;
1825	>	NPTi<NPT<Integrator<BaseIntegrator> > >* myNPTi = NULL;
1826	>	NPTf<NPT<Integrator<BaseIntegrator> > >* myNPTf = NULL;
1827	>	NPTxyz<NPT<Integrator<BaseIntegrator> > >* myNPTxyz = NULL;
1828
1829		for (k = 0; k < nInfo; k++){
1830		switch (ensembleCase){
#	Line 1384 | Line 1855 | void SimSetup::makeIntegrator(void){
1855		else{
1856		sprintf(painCave.errMsg,
1857		"SimSetup error: If you use the NVT\n"
1858	<	"    ensemble, you must set tauThermostat.\n");
1858	>	"\tensemble, you must set tauThermostat.\n");
1859		painCave.isFatal = 1;
1860		simError();
1861		}
#	Line 1407 | Line 1878 | void SimSetup::makeIntegrator(void){
1878		else{
1879		sprintf(painCave.errMsg,
1880		"SimSetup error: If you use a constant pressure\n"
1881	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1881	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1882		painCave.isFatal = 1;
1883		simError();
1884		}
#	Line 1417 | Line 1888 | void SimSetup::makeIntegrator(void){
1888		else{
1889		sprintf(painCave.errMsg,
1890		"SimSetup error: If you use an NPT\n"
1891	<	"    ensemble, you must set tauThermostat.\n");
1891	>	"\tensemble, you must set tauThermostat.\n");
1892		painCave.isFatal = 1;
1893		simError();
1894		}
#	Line 1427 | Line 1898 | void SimSetup::makeIntegrator(void){
1898		else{
1899		sprintf(painCave.errMsg,
1900		"SimSetup error: If you use an NPT\n"
1901	<	"    ensemble, you must set tauBarostat.\n");
1901	>	"\tensemble, you must set tauBarostat.\n");
1902		painCave.isFatal = 1;
1903		simError();
1904		}
#	Line 1450 | Line 1921 | void SimSetup::makeIntegrator(void){
1921		else{
1922		sprintf(painCave.errMsg,
1923		"SimSetup error: If you use a constant pressure\n"
1924	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1924	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1925		painCave.isFatal = 1;
1926		simError();
1927		}
1928
1929		if (globals->haveTauThermostat())
1930		myNPTf->setTauThermostat(globals->getTauThermostat());
1931	+
1932		else{
1933		sprintf(painCave.errMsg,
1934		"SimSetup error: If you use an NPT\n"
1935	<	"    ensemble, you must set tauThermostat.\n");
1935	>	"\tensemble, you must set tauThermostat.\n");
1936		painCave.isFatal = 1;
1937		simError();
1938		}
1939
1940		if (globals->haveTauBarostat())
1941		myNPTf->setTauBarostat(globals->getTauBarostat());
1942	+
1943		else{
1944		sprintf(painCave.errMsg,
1945		"SimSetup error: If you use an NPT\n"
1946	<	"    ensemble, you must set tauBarostat.\n");
1946	>	"\tensemble, you must set tauBarostat.\n");
1947		painCave.isFatal = 1;
1948		simError();
1949		}
#	Line 1493 | Line 1966 | void SimSetup::makeIntegrator(void){
1966		else{
1967		sprintf(painCave.errMsg,
1968		"SimSetup error: If you use a constant pressure\n"
1969	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1969	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1970		painCave.isFatal = 1;
1971		simError();
1972		}
#	Line 1503 | Line 1976 | void SimSetup::makeIntegrator(void){
1976		else{
1977		sprintf(painCave.errMsg,
1978		"SimSetup error: If you use an NPT\n"
1979	<	"    ensemble, you must set tauThermostat.\n");
1979	>	"\tensemble, you must set tauThermostat.\n");
1980		painCave.isFatal = 1;
1981		simError();
1982		}
#	Line 1513 | Line 1986 | void SimSetup::makeIntegrator(void){
1986		else{
1987		sprintf(painCave.errMsg,
1988		"SimSetup error: If you use an NPT\n"
1989	<	"    ensemble, you must set tauBarostat.\n");
1989	>	"\tensemble, you must set tauBarostat.\n");
1990		painCave.isFatal = 1;
1991		simError();
1992		}
#	Line 1566 | Line 2039 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2039		}
2040		else{
2041		sprintf(painCave.errMsg,
2042	<	"ZConstraint error: If you use an ZConstraint\n"
2043	<	" , you must set sample time.\n");
2042	>	"ZConstraint error: If you use a ZConstraint,\n"
2043	>	"\tyou must set zconsTime.\n");
2044		painCave.isFatal = 1;
2045		simError();
2046		}
#	Line 1582 | Line 2055 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2055		else{
2056		double defaultZConsTol = 0.01;
2057		sprintf(painCave.errMsg,
2058	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
2059	<	" , default value %f is used.\n",
2058	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2059	>	"\tOOPSE will use a default value of %f.\n"
2060	>	"\tTo set the tolerance, use the zconsTol variable.\n",
2061		defaultZConsTol);
2062		painCave.isFatal = 0;
2063		simError();
#	Line 1601 | Line 2075 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2075		}
2076		else{
2077		sprintf(painCave.errMsg,
2078	<	"ZConstraint Warning: User does not set force Subtraction policy, "
2079	<	"PolicyByMass is used\n");
2078	>	"ZConstraint Warning: No force subtraction policy was set.\n"
2079	>	"\tOOPSE will use PolicyByMass.\n"
2080	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2081		painCave.isFatal = 0;
2082		simError();
2083		zconsForcePolicy->setData("BYMASS");
#	Line 1610 | Line 2085 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2085
2086		theInfo.addProperty(zconsForcePolicy);
2087
2088	+	//set zcons gap
2089	+	DoubleData* zconsGap = new DoubleData();
2090	+	zconsGap->setID(ZCONSGAP_ID);
2091	+
2092	+	if (globals->haveZConsGap()){
2093	+	zconsGap->setData(globals->getZconsGap());
2094	+	theInfo.addProperty(zconsGap);
2095	+	}
2096	+
2097	+	//set zcons fixtime
2098	+	DoubleData* zconsFixtime = new DoubleData();
2099	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2100	+
2101	+	if (globals->haveZConsFixTime()){
2102	+	zconsFixtime->setData(globals->getZconsFixtime());
2103	+	theInfo.addProperty(zconsFixtime);
2104	+	}
2105	+
2106	+	//set zconsUsingSMD
2107	+	IntData* zconsUsingSMD = new IntData();
2108	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2109	+
2110	+	if (globals->haveZConsUsingSMD()){
2111	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2112	+	theInfo.addProperty(zconsUsingSMD);
2113	+	}
2114	+
2115		//Determine the name of ouput file and add it into SimInfo's property list
2116		//Be careful, do not use inFileName, since it is a pointer which
2117		//point to a string at master node, and slave nodes do not contain that string
#	Line 1639 | Line 2141 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2141		tempParaItem.zPos = zconStamp[i]->getZpos();
2142		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2143		tempParaItem.kRatio = zconStamp[i]->getKratio();
2144	<
2144	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2145	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2146		zconsParaData->addItem(tempParaItem);
2147		}
2148
2149		//check the uniqueness of index
2150		if(!zconsParaData->isIndexUnique()){
2151		sprintf(painCave.errMsg,
2152	<	"ZConstraint Error: molIndex is not unique\n");
2152	>	"ZConstraint Error: molIndex is not unique!\n");
2153		painCave.isFatal = 1;
2154		simError();
2155		}
#	Line 1656 | Line 2159 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2159
2160		//push data into siminfo, therefore, we can retrieve later
2161		theInfo.addProperty(zconsParaData);
2162	+	}
2163	+
2164	+	void SimSetup::makeMinimizer(){
2165	+
2166	+	OOPSEMinimizer* myOOPSEMinimizer;
2167	+	MinimizerParameterSet* param;
2168	+	char minimizerName[100];
2169	+
2170	+	for (int i = 0; i < nInfo; i++){
2171	+
2172	+	//prepare parameter set for minimizer
2173	+	param = new MinimizerParameterSet();
2174	+	param->setDefaultParameter();
2175	+
2176	+	if (globals->haveMinimizer()){
2177	+	param->setFTol(globals->getMinFTol());
2178	+	}
2179	+
2180	+	if (globals->haveMinGTol()){
2181	+	param->setGTol(globals->getMinGTol());
2182	+	}
2183	+
2184	+	if (globals->haveMinMaxIter()){
2185	+	param->setMaxIteration(globals->getMinMaxIter());
2186	+	}
2187	+
2188	+	if (globals->haveMinWriteFrq()){
2189	+	param->setMaxIteration(globals->getMinMaxIter());
2190	+	}
2191	+
2192	+	if (globals->haveMinWriteFrq()){
2193	+	param->setWriteFrq(globals->getMinWriteFrq());
2194	+	}
2195	+
2196	+	if (globals->haveMinStepSize()){
2197	+	param->setStepSize(globals->getMinStepSize());
2198	+	}
2199	+
2200	+	if (globals->haveMinLSMaxIter()){
2201	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2202	+	}
2203	+
2204	+	if (globals->haveMinLSTol()){
2205	+	param->setLineSearchTol(globals->getMinLSTol());
2206	+	}
2207	+
2208	+	strcpy(minimizerName, globals->getMinimizer());
2209	+
2210	+	if (!strcasecmp(minimizerName, "CG")){
2211	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2212	+	}
2213	+	else if (!strcasecmp(minimizerName, "SD")){
2214	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2215	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2216	+	}
2217	+	else{
2218	+	sprintf(painCave.errMsg,
2219	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2220	+	painCave.isFatal = 0;
2221	+	simError();
2222	+
2223	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2224	+	}
2225	+	info[i].the_integrator = myOOPSEMinimizer;
2226	+
2227	+	//store the minimizer into simInfo
2228	+	info[i].the_minimizer = myOOPSEMinimizer;
2229	+	info[i].has_minimizer = true;
2230	+	}
2231	+
2232		}

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