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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 780 by mmeineke, Mon Sep 22 21:23:25 2003 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 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	–
7		#include "SimSetup.hpp"
8		#include "ReadWrite.hpp"
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 22 | Line 25
25		#define NVT_ENS        1
26		#define NPTi_ENS       2
27		#define NPTf_ENS       3
28	+	#define NPTxyz_ENS     4
29
26	–	#define FF_DUFF 0
27	–	#define FF_LJ   1
28	–	#define FF_EAM  2
30
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;
65		isInfoArray = 0;
66		nInfo = 1;
67
#	Line 52 | Line 84 | void SimSetup::setSimInfo(SimInfo* the_info, int theNi
84		info = the_info;
85		nInfo = theNinfo;
86		isInfoArray = 1;
87	+	initSuspend = true;
88		}
89
90
#	Line 90 | Line 123 | void SimSetup::createSim(void){
123		#endif // is_mpi
124
125		void SimSetup::createSim(void){
93	–	int i, j, k, globalAtomIndex;
126
127		// gather all of the information from the Bass file
128
#	Line 106 | Line 138 | void SimSetup::createSim(void){
138
139		// initialize the system coordinates
140
141	<	if (!isInfoArray){
141	>	if ( !initSuspend ){
142		initSystemCoords();
143	+
144	+	if( !(globals->getUseInitTime()) )
145	+	info[0].currentTime = 0.0;
146		}
147
148		// make the output filenames
149
150		makeOutNames();
151	<
117	<	// make the integrator
118	<
119	<	makeIntegrator();
120	<
151	>
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
154		#endif
#	Line 125 | 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, l;
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;
175	>	int stampID, atomOffset, rbOffset;
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
152	–
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		atomOffset = 0;
220	<	excludeOffset = 0;
220	>	groupOffset = 0;
221	>
222		for (i = 0; i < info[k].n_mol; i++){
223		stampID = info[k].molecules[i].getStampID();
224	+	molName = comp_stamps[stampID]->getID();
225
226		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
227		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
228		molInfo.nBends = comp_stamps[stampID]->getNBends();
229		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
230	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
230	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
231
232	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
233	+
234		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
172	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
173	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
174	–	molInfo.myBends = new Bend * [molInfo.nBends];
175	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
235
236	+	if (molInfo.nBonds > 0)
237	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
238	+	else
239	+	molInfo.myBonds = NULL;
240	+
241	+	if (molInfo.nBends > 0)
242	+	molInfo.myBends = new Bend*[molInfo.nBends];
243	+	else
244	+	molInfo.myBends = NULL;
245	+
246	+	if (molInfo.nTorsions > 0)
247	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
248	+	else
249	+	molInfo.myTorsions = NULL;
250	+
251		theBonds = new bond_pair[molInfo.nBonds];
252		theBends = new bend_set[molInfo.nBends];
253		theTorsions = new torsion_set[molInfo.nTorsions];
254	<
254	>
255		// make the Atoms
256
257		for (j = 0; j < molInfo.nAtoms; j++){
258		currentAtom = comp_stamps[stampID]->getAtom(j);
259	+
260		if (currentAtom->haveOrientation()){
261		dAtom = new DirectionalAtom((j + atomOffset),
262		info[k].getConfiguration());
263		info[k].n_oriented++;
264		molInfo.myAtoms[j] = dAtom;
265
266	<	ux = currentAtom->getOrntX();
267	<	uy = currentAtom->getOrntY();
268	<	uz = currentAtom->getOrntZ();
266	>	// Directional Atoms have standard unit vectors which are oriented
267	>	// in space using the three Euler angles.  We assume the standard
268	>	// unit vector was originally along the z axis below.
269
270	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
270	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
271	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
272	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
273
274	<	u = sqrt(uSqr);
275	<	ux = ux / u;
199	<	uy = uy / u;
200	<	uz = uz / u;
201	<
202	<	dAtom->setSUx(ux);
203	<	dAtom->setSUy(uy);
204	<	dAtom->setSUz(uz);
274	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
275	>
276		}
277		else{
278	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
279	<	info[k].getConfiguration());
278	>
279	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
280	>
281		}
210	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
282
283	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
284		#ifdef IS_MPI
285
286	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
286	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
287
288		#endif // is_mpi
289		}
#	Line 222 | Line 294 | void SimSetup::makeMolecules(void){
294		theBonds[j].a = currentBond->getA() + atomOffset;
295		theBonds[j].b = currentBond->getB() + atomOffset;
296
297	<	exI = theBonds[j].a;
298	<	exJ = theBonds[j].b;
297	>	tempI = theBonds[j].a;
298	>	tempJ = theBonds[j].b;
299
228	–	// exclude_I must always be the smaller of the pair
229	–	if (exI > exJ){
230	–	tempEx = exI;
231	–	exI = exJ;
232	–	exJ = tempEx;
233	–	}
300		#ifdef IS_MPI
301	<	tempEx = exI;
302	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
303	<	tempEx = exJ;
304	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
301	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
302	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
303	>	#else
304	>	exI = tempI + 1;
305	>	exJ = tempJ + 1;
306	>	#endif
307
308	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
241	<	#else  // isn't MPI
242	<
243	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
244	<	#endif  //is_mpi
308	>	info[k].excludes->addPair(exI, exJ);
309		}
246	–	excludeOffset += molInfo.nBonds;
310
311		//make the bends
312		for (j = 0; j < molInfo.nBends; j++){
#	Line 293 | Line 356 | void SimSetup::makeMolecules(void){
356		}
357		}
358
359	<	if (!theBends[j].isGhost){
360	<	exI = theBends[j].a;
361	<	exJ = theBends[j].c;
362	<	}
363	<	else{
301	<	exI = theBends[j].a;
302	<	exJ = theBends[j].b;
303	<	}
304	<
305	<	// exclude_I must always be the smaller of the pair
306	<	if (exI > exJ){
307	<	tempEx = exI;
308	<	exI = exJ;
309	<	exJ = tempEx;
310	<	}
359	>	if (theBends[j].isGhost) {
360	>
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>
364		#ifdef IS_MPI
365	<	tempEx = exI;
366	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	<	tempEx = exJ;
368	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
366	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
367	>	#else
368	>	exI = tempI + 1;
369	>	exJ = tempJ + 1;
370	>	#endif
371	>	info[k].excludes->addPair(exI, exJ);
372
373	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
374	<	#else  // isn't MPI
375	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
376	<	#endif  //is_mpi
373	>	} else {
374	>
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>	tempK = theBends[j].c;
378	>
379	>	#ifdef IS_MPI
380	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
381	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
382	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
383	>	#else
384	>	exI = tempI + 1;
385	>	exJ = tempJ + 1;
386	>	exK = tempK + 1;
387	>	#endif
388	>
389	>	info[k].excludes->addPair(exI, exK);
390	>	info[k].excludes->addPair(exI, exJ);
391	>	info[k].excludes->addPair(exJ, exK);
392	>	}
393		}
322	–	excludeOffset += molInfo.nBends;
394
395		for (j = 0; j < molInfo.nTorsions; j++){
396		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 328 | Line 399 | void SimSetup::makeMolecules(void){
399		theTorsions[j].c = currentTorsion->getC() + atomOffset;
400		theTorsions[j].d = currentTorsion->getD() + atomOffset;
401
402	<	exI = theTorsions[j].a;
403	<	exJ = theTorsions[j].d;
402	>	tempI = theTorsions[j].a;
403	>	tempJ = theTorsions[j].b;
404	>	tempK = theTorsions[j].c;
405	>	tempL = theTorsions[j].d;
406
334	–	// exclude_I must always be the smaller of the pair
335	–	if (exI > exJ){
336	–	tempEx = exI;
337	–	exI = exJ;
338	–	exJ = tempEx;
339	–	}
407		#ifdef IS_MPI
408	<	tempEx = exI;
409	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
410	<	tempEx = exJ;
411	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
408	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
409	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
410	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
411	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
412	>	#else
413	>	exI = tempI + 1;
414	>	exJ = tempJ + 1;
415	>	exK = tempK + 1;
416	>	exL = tempL + 1;
417	>	#endif
418
419	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
420	<	#else  // isn't MPI
421	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
422	<	#endif  //is_mpi
419	>	info[k].excludes->addPair(exI, exJ);
420	>	info[k].excludes->addPair(exI, exK);
421	>	info[k].excludes->addPair(exI, exL);
422	>	info[k].excludes->addPair(exJ, exK);
423	>	info[k].excludes->addPair(exJ, exL);
424	>	info[k].excludes->addPair(exK, exL);
425		}
351	–	excludeOffset += molInfo.nTorsions;
426
427	+
428	+	molInfo.myRigidBodies.clear();
429	+
430	+	for (j = 0; j < molInfo.nRigidBodies; j++){
431
432	<	// send the arrays off to the forceField for init.
432	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
433	>	nMembers = currentRigidBody->getNMembers();
434
435	+	// Create the Rigid Body:
436	+
437	+	myRB = new RigidBody();
438	+
439	+	sprintf(rbName,"%s_RB_%d", molName, j);
440	+	myRB->setType(rbName);
441	+
442	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
443	+
444	+	// molI is atom numbering inside this molecule
445	+	molI = currentRigidBody->getMember(rb1);
446	+
447	+	// tempI is atom numbering on local processor
448	+	tempI = molI + atomOffset;
449	+
450	+	// currentAtom is the AtomStamp (which we need for
451	+	// rigid body reference positions)
452	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
453	+
454	+	// When we add to the rigid body, add the atom itself and
455	+	// the stamp info:
456	+
457	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
458	+
459	+	// Add this atom to the Skip List for the integrators
460	+	#ifdef IS_MPI
461	+	slI = info[k].atoms[tempI]->getGlobalIndex();
462	+	#else
463	+	slI = tempI;
464	+	#endif
465	+	skipList.insert(slI);
466	+
467	+	}
468	+
469	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
470	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
471	+
472	+	tempI = currentRigidBody->getMember(rb1);
473	+	tempJ = currentRigidBody->getMember(rb2);
474	+
475	+	// Some explanation is required here.
476	+	// Fortran indexing starts at 1, while c indexing starts at 0
477	+	// Also, in parallel computations, the GlobalIndex is
478	+	// used for the exclude list:
479	+
480	+	#ifdef IS_MPI
481	+	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
482	+	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
483	+	#else
484	+	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
485	+	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
486	+	#endif
487	+
488	+	info[k].excludes->addPair(exI, exJ);
489	+
490	+	}
491	+	}
492	+
493	+	molInfo.myRigidBodies.push_back(myRB);
494	+	info[k].rigidBodies.push_back(myRB);
495	+	}
496	+
497	+
498	+	//create cutoff group for molecule
499	+
500	+	cutoffAtomSet.clear();
501	+	molInfo.myCutoffGroups.clear();
502	+
503	+	for (j = 0; j < nCutoffGroups; j++){
504	+
505	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
506	+	nMembers = currentCutoffGroup->getNMembers();
507	+
508	+	myCutoffGroup = new CutoffGroup();
509	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
510	+
511	+	for (int cg = 0; cg < nMembers; cg++) {
512	+
513	+	// molI is atom numbering inside this molecule
514	+	molI = currentCutoffGroup->getMember(cg);
515	+
516	+	// tempI is atom numbering on local processor
517	+	tempI = molI + atomOffset;
518	+
519	+	#ifdef IS_MPI
520	+	globalID = info[k].atoms[tempI]->getGlobalIndex()
521	+	#else
522	+	globalID = info[k].atoms[tempI]->getIndex();
523	+	#endif
524	+
525	+	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
526	+
527	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
528	+
529	+	cutoffAtomSet.insert(tempI);
530	+	}
531	+
532	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
533	+	groupOffset++;
534	+
535	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
536	+
537	+	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
538	+
539	+	for(j = 0; j < molInfo.nAtoms; j++){
540	+
541	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
542	+	myCutoffGroup = new CutoffGroup();
543	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
544	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
545	+	#ifdef IS_MPI
546	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex()
547	+	#else
548	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
549	+	#endif
550	+	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
551	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
552	+	groupOffset++;
553	+	}
554	+
555	+	}
556	+
557	+	// After this is all set up, scan through the atoms to
558	+	// see if they can be added to the integrableObjects:
559	+
560	+	molInfo.myIntegrableObjects.clear();
561	+
562	+
563	+	for (j = 0; j < molInfo.nAtoms; j++){
564	+
565	+	#ifdef IS_MPI
566	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
567	+	#else
568	+	slJ = j+atomOffset;
569	+	#endif
570	+
571	+	// if they aren't on the skip list, then they can be integrated
572	+
573	+	if (skipList.find(slJ) == skipList.end()) {
574	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
575	+	info[k].integrableObjects.push_back(mySD);
576	+	molInfo.myIntegrableObjects.push_back(mySD);
577	+	}
578	+	}
579	+
580	+	// all rigid bodies are integrated:
581	+
582	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
583	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
584	+	info[k].integrableObjects.push_back(mySD);
585	+	molInfo.myIntegrableObjects.push_back(mySD);
586	+	}
587	+
588	+
589	+	/*
590	+
591	+	//creat ConstraintPair.
592	+	molInfo.myConstraintPair.clear();
593	+
594	+	for (j = 0; j < molInfo.nBonds; j++){
595	+
596	+	//if both atoms are in the same rigid body, just skip it
597	+	currentBond = comp_stamps[stampID]->getBond(j);
598	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
599	+
600	+	tempI = currentBond->getA() + atomOffset;
601	+	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
602	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
603	+	else
604	+	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
605	+
606	+	tempJ =  currentBond->getB() + atomOffset;
607	+	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
608	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
609	+	else
610	+	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
611	+
612	+	consPair = new DistanceConstraintPair(consElement1, consElement2);
613	+	molInfo.myConstraintPairs.push_back(consPair);
614	+	}
615	+	}
616	+
617	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
618	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
619	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
620	+
621	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
622	+
623	+	for(size_t m = 0; m < jointAtoms.size(); m++){
624	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
625	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
626	+
627	+	consPair = new JointConstraintPair(consElement1, consElement2);
628	+	molInfo.myConstraintPairs.push_back(consPair);
629	+	}
630	+
631	+	}
632	+	}
633	+
634	+	*/
635	+	// send the arrays off to the forceField for init.
636	+
637		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
638		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
639		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
640		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
641		theTorsions);
642
362	–
643		info[k].molecules[i].initialize(molInfo);
644
645
#	Line 367 | Line 647 | void SimSetup::makeMolecules(void){
647		delete[] theBonds;
648		delete[] theBends;
649		delete[] theTorsions;
650	<	}
650	>	}
651		}
652
653		#ifdef IS_MPI
#	Line 375 | Line 655 | void SimSetup::makeMolecules(void){
655		MPIcheckPoint();
656		#endif // is_mpi
657
378	–	// clean up the forcefield
379	–
380	–	the_ff->calcRcut();
381	–	the_ff->cleanMe();
658		}
659
660		void SimSetup::initFromBass(void){
#	Line 551 | Line 827 | void SimSetup::gatherInfo(void){
827
828
829		void SimSetup::gatherInfo(void){
830	<	int i, j, k;
830	>	int i;
831
832		ensembleCase = -1;
833		ffCase = -1;
#	Line 579 | Line 855 | void SimSetup::gatherInfo(void){
855		else if (!strcasecmp(force_field, "EAM")){
856		ffCase = FF_EAM;
857		}
858	+	else if (!strcasecmp(force_field, "WATER")){
859	+	ffCase = FF_H2O;
860	+	}
861		else{
862		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
863		force_field);
#	Line 601 | Line 880 | void SimSetup::gatherInfo(void){
880		}
881		else if (!strcasecmp(ensemble, "NPTf")){
882		ensembleCase = NPTf_ENS;
883	+	}
884	+	else if (!strcasecmp(ensemble, "NPTxyz")){
885	+	ensembleCase = NPTxyz_ENS;
886		}
887		else{
888		sprintf(painCave.errMsg,
889	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
890	<	"reverting to NVE for this simulation.\n",
889	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
890	>	"\treverting to NVE for this simulation.\n",
891		ensemble);
892		painCave.isFatal = 0;
893		simError();
#	Line 637 | Line 919 | void SimSetup::gatherInfo(void){
919		if (!the_components[i]->haveNMol()){
920		// we have a problem
921		sprintf(painCave.errMsg,
922	<	"SimSetup Error. No global NMol or component NMol"
923	<	" given. Cannot calculate the number of atoms.\n");
922	>	"SimSetup Error. No global NMol or component NMol given.\n"
923	>	"\tCannot calculate the number of atoms.\n");
924		painCave.isFatal = 1;
925		simError();
926		}
#	Line 656 | Line 938 | void SimSetup::gatherInfo(void){
938		" Please give nMol in the components.\n");
939		painCave.isFatal = 1;
940		simError();
941	+	}
942	+
943	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
944	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
945	+	sprintf(painCave.errMsg,
946	+	"Sample time is not divisible by dt.\n"
947	+	"\tThis will result in samples that are not uniformly\n"
948	+	"\tdistributed in time.  If this is a problem, change\n"
949	+	"\tyour sampleTime variable.\n");
950	+	painCave.isFatal = 0;
951	+	simError();
952		}
953
954	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
955	+	sprintf(painCave.errMsg,
956	+	"Status time is not divisible by dt.\n"
957	+	"\tThis will result in status reports that are not uniformly\n"
958	+	"\tdistributed in time.  If this is a problem, change \n"
959	+	"\tyour statusTime variable.\n");
960	+	painCave.isFatal = 0;
961	+	simError();
962	+	}
963	+
964	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
965	+	sprintf(painCave.errMsg,
966	+	"Thermal time is not divisible by dt.\n"
967	+	"\tThis will result in thermalizations that are not uniformly\n"
968	+	"\tdistributed in time.  If this is a problem, change \n"
969	+	"\tyour thermalTime variable.\n");
970	+	painCave.isFatal = 0;
971	+	simError();
972	+	}
973	+
974	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
975	+	sprintf(painCave.errMsg,
976	+	"Reset time is not divisible by dt.\n"
977	+	"\tThis will result in integrator resets that are not uniformly\n"
978	+	"\tdistributed in time.  If this is a problem, change\n"
979	+	"\tyour resetTime variable.\n");
980	+	painCave.isFatal = 0;
981	+	simError();
982	+	}
983	+
984		// set the status, sample, and thermal kick times
985
986		for (i = 0; i < nInfo; i++){
987		if (globals->haveSampleTime()){
988		info[i].sampleTime = globals->getSampleTime();
989		info[i].statusTime = info[i].sampleTime;
667	–	info[i].thermalTime = info[i].sampleTime;
990		}
991		else{
992		info[i].sampleTime = globals->getRunTime();
993		info[i].statusTime = info[i].sampleTime;
672	–	info[i].thermalTime = info[i].sampleTime;
994		}
995
996		if (globals->haveStatusTime()){
#	Line 678 | Line 999 | void SimSetup::gatherInfo(void){
999
1000		if (globals->haveThermalTime()){
1001		info[i].thermalTime = globals->getThermalTime();
1002	+	} else {
1003	+	info[i].thermalTime = globals->getRunTime();
1004		}
1005
1006		info[i].resetIntegrator = 0;
#	Line 687 | Line 1010 | void SimSetup::gatherInfo(void){
1010		}
1011
1012		// check for the temperature set flag
1013	<
1013	>
1014		if (globals->haveTempSet())
1015		info[i].setTemp = globals->getTempSet();
1016
1017	<	// get some of the tricky things that may still be in the globals
1017	>	// check for the extended State init
1018
1019	<	double boxVector[3];
1020	<	if (globals->haveBox()){
698	<	boxVector[0] = globals->getBox();
699	<	boxVector[1] = globals->getBox();
700	<	boxVector[2] = globals->getBox();
1019	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1020	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1021
1022	<	info[i].setBox(boxVector);
1023	<	}
1024	<	else if (globals->haveDensity()){
1025	<	double vol;
1026	<	vol = (double) tot_nmol / globals->getDensity();
1027	<	boxVector[0] = pow(vol, (1.0 / 3.0));
1028	<	boxVector[1] = boxVector[0];
1029	<	boxVector[2] = boxVector[0];
1030	<
711	<	info[i].setBox(boxVector);
712	<	}
713	<	else{
714	<	if (!globals->haveBoxX()){
715	<	sprintf(painCave.errMsg,
716	<	"SimSetup error, no periodic BoxX size given.\n");
717	<	painCave.isFatal = 1;
718	<	simError();
719	<	}
720	<	boxVector[0] = globals->getBoxX();
721	<
722	<	if (!globals->haveBoxY()){
723	<	sprintf(painCave.errMsg,
724	<	"SimSetup error, no periodic BoxY size given.\n");
725	<	painCave.isFatal = 1;
726	<	simError();
1022	>	// check for thermodynamic integration
1023	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1024	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1025	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1026	>	info[i].thermIntLambda = globals->getThermIntLambda();
1027	>	info[i].thermIntK = globals->getThermIntK();
1028	>
1029	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1030	>	info[i].restraint = myRestraint;
1031		}
1032	<	boxVector[1] = globals->getBoxY();
1033	<
1034	<	if (!globals->haveBoxZ()){
1035	<	sprintf(painCave.errMsg,
1036	<	"SimSetup error, no periodic BoxZ size given.\n");
1037	<	painCave.isFatal = 1;
1038	<	simError();
1032	>	else {
1033	>	sprintf(painCave.errMsg,
1034	>	"SimSetup Error:\n"
1035	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1036	>	"\tthermodynamicIntegrationLambda (and/or\n"
1037	>	"\tthermodynamicIntegrationK) was not specified.\n"
1038	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1039	>	painCave.isFatal = 1;
1040	>	simError();
1041		}
736	–	boxVector[2] = globals->getBoxZ();
737	–
738	–	info[i].setBox(boxVector);
1042		}
1043	+	else if(globals->getUseLiquidThermInt()) {
1044	+	if (globals->getUseSolidThermInt()) {
1045	+	sprintf( painCave.errMsg,
1046	+	"SimSetup Warning: It appears that you have both solid and\n"
1047	+	"\tliquid thermodynamic integration activated in your .bass\n"
1048	+	"\tfile. To avoid confusion, specify only one technique in\n"
1049	+	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1050	+	"\twill be assumed for the current simulation. If this is not\n"
1051	+	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1052	+	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1053	+	painCave.isFatal = 0;
1054	+	simError();
1055	+	}
1056	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1057	+	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1058	+	info[i].thermIntLambda = globals->getThermIntLambda();
1059	+	info[i].thermIntK = globals->getThermIntK();
1060	+	}
1061	+	else {
1062	+	sprintf(painCave.errMsg,
1063	+	"SimSetup Error:\n"
1064	+	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1065	+	"\tthermodynamicIntegrationLambda (and/or\n"
1066	+	"\tthermodynamicIntegrationK) was not specified.\n"
1067	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1068	+	painCave.isFatal = 1;
1069	+	simError();
1070	+	}
1071	+	}
1072	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1073	+	sprintf(painCave.errMsg,
1074	+	"SimSetup Warning: If you want to use Thermodynamic\n"
1075	+	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1076	+	"\t'true' in your .bass file.  These keywords are set to\n"
1077	+	"\t'false' by default, so your lambda and/or k values are\n"
1078	+	"\tbeing ignored.\n");
1079	+	painCave.isFatal = 0;
1080	+	simError();
1081	+	}
1082		}
1083	<
1083	>
1084		//setup seed for random number generator
1085		int seedValue;
1086
#	Line 778 | Line 1120 | void SimSetup::gatherInfo(void){
1120		for (int i = 0; i < nInfo; i++){
1121		info[i].setSeed(seedValue);
1122		}
1123	<
1123	>
1124		#ifdef IS_MPI
1125	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1125	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1126		MPIcheckPoint();
1127		#endif // is_mpi
1128		}
#	Line 789 | Line 1131 | void SimSetup::finalInfoCheck(void){
1131		void SimSetup::finalInfoCheck(void){
1132		int index;
1133		int usesDipoles;
1134	+	int usesCharges;
1135		int i;
1136
1137		for (i = 0; i < nInfo; i++){
#	Line 800 | Line 1143 | void SimSetup::finalInfoCheck(void){
1143		usesDipoles = (info[i].atoms[index])->hasDipole();
1144		index++;
1145		}
1146	<
1146	>	index = 0;
1147	>	usesCharges = 0;
1148	>	while ((index < info[i].n_atoms) && !usesCharges){
1149	>	usesCharges= (info[i].atoms[index])->hasCharge();
1150	>	index++;
1151	>	}
1152		#ifdef IS_MPI
1153		int myUse = usesDipoles;
1154		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1155		#endif //is_mpi
1156
1157	<	double theEcr, theEst;
1157	>	double theRcut, theRsw;
1158
1159	+	if (globals->haveRcut()) {
1160	+	theRcut = globals->getRcut();
1161	+
1162	+	if (globals->haveRsw())
1163	+	theRsw = globals->getRsw();
1164	+	else
1165	+	theRsw = theRcut;
1166	+
1167	+	info[i].setDefaultRcut(theRcut, theRsw);
1168	+
1169	+	} else {
1170	+
1171	+	the_ff->calcRcut();
1172	+	theRcut = info[i].getRcut();
1173	+
1174	+	if (globals->haveRsw())
1175	+	theRsw = globals->getRsw();
1176	+	else
1177	+	theRsw = theRcut;
1178	+
1179	+	info[i].setDefaultRcut(theRcut, theRsw);
1180	+	}
1181	+
1182		if (globals->getUseRF()){
1183		info[i].useReactionField = 1;
1184	<
1185	<	if (!globals->haveECR()){
1184	>
1185	>	if (!globals->haveRcut()){
1186		sprintf(painCave.errMsg,
1187	<	"SimSetup Warning: using default value of 1/2 the smallest "
1188	<	"box length for the electrostaticCutoffRadius.\n"
1189	<	"I hope you have a very fast processor!\n");
1187	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1188	>	"\tOOPSE will use a default value of 15.0 angstroms"
1189	>	"\tfor the cutoffRadius.\n");
1190		painCave.isFatal = 0;
1191		simError();
1192	<	double smallest;
822	<	smallest = info[i].boxL[0];
823	<	if (info[i].boxL[1] <= smallest)
824	<	smallest = info[i].boxL[1];
825	<	if (info[i].boxL[2] <= smallest)
826	<	smallest = info[i].boxL[2];
827	<	theEcr = 0.5 * smallest;
1192	>	theRcut = 15.0;
1193		}
1194		else{
1195	<	theEcr = globals->getECR();
1195	>	theRcut = globals->getRcut();
1196		}
1197
1198	<	if (!globals->haveEST()){
1198	>	if (!globals->haveRsw()){
1199		sprintf(painCave.errMsg,
1200	<	"SimSetup Warning: using default value of 0.05 * the "
1201	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1200	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1201	>	"\tOOPSE will use a default value of\n"
1202	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1203		painCave.isFatal = 0;
1204		simError();
1205	<	theEst = 0.05 * theEcr;
1205	>	theRsw = 0.95 * theRcut;
1206		}
1207		else{
1208	<	theEst = globals->getEST();
1208	>	theRsw = globals->getRsw();
1209		}
1210
1211	<	info[i].setEcr(theEcr, theEst);
1211	>	info[i].setDefaultRcut(theRcut, theRsw);
1212
1213		if (!globals->haveDielectric()){
1214		sprintf(painCave.errMsg,
1215	<	"SimSetup Error: You are trying to use Reaction Field without"
1216	<	"setting a dielectric constant!\n");
1215	>	"SimSetup Error: No Dielectric constant was set.\n"
1216	>	"\tYou are trying to use Reaction Field without"
1217	>	"\tsetting a dielectric constant!\n");
1218		painCave.isFatal = 1;
1219		simError();
1220		}
1221		info[i].dielectric = globals->getDielectric();
1222		}
1223		else{
1224	<	if (usesDipoles){
1225	<	if (!globals->haveECR()){
1224	>	if (usesDipoles || usesCharges){
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;
1234	<	smallest = info[i].boxL[0];
867	<	if (info[i].boxL[1] <= smallest)
868	<	smallest = info[i].boxL[1];
869	<	if (info[i].boxL[2] <= smallest)
870	<	smallest = info[i].boxL[2];
871	<	theEcr = 0.5 * smallest;
872	<	}
1233	>	theRcut = 15.0;
1234	>	}
1235		else{
1236	<	theEcr = globals->getECR();
1236	>	theRcut = globals->getRcut();
1237		}
1238	<
1239	<	if (!globals->haveEST()){
1238	>
1239	>	if (!globals->haveRsw()){
1240		sprintf(painCave.errMsg,
1241	<	"SimSetup Warning: using default value of 0.05 * the "
1242	<	"electrostaticCutoffRadius for the "
1243	<	"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].setEcr(theEcr, theEst);
1251	>
1252	>	info[i].setDefaultRcut(theRcut, theRsw);
1253	>
1254		}
1255		}
1256		}
894	–
1257		#ifdef IS_MPI
1258		strcpy(checkPointMsg, "post processing checks out");
1259		MPIcheckPoint();
1260		#endif // is_mpi
899	–	}
1261
1262	+	// clean up the forcefield
1263	+	the_ff->cleanMe();
1264	+	}
1265	+
1266		void SimSetup::initSystemCoords(void){
1267		int i;
1268
#	Line 914 | Line 1279 | void SimSetup::initSystemCoords(void){
1279		if (worldRank == 0){
1280		#endif //is_mpi
1281		inName = globals->getInitialConfig();
917	–	double* tempDouble = new double[1000000];
1282		fileInit = new InitializeFromFile(inName);
1283		#ifdef IS_MPI
1284		}
#	Line 926 | Line 1290 | void SimSetup::initSystemCoords(void){
1290		delete fileInit;
1291		}
1292		else{
1293	<	#ifdef IS_MPI
930	<
1293	>
1294		// no init from bass
1295	<
1295	>
1296		sprintf(painCave.errMsg,
1297	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1298	<	painCave.isFatal;
1297	>	"Cannot intialize a simulation without an initial configuration file.\n");
1298	>	painCave.isFatal = 1;;
1299		simError();
1300	<
938	<	#else
939	<
940	<	initFromBass();
941	<
942	<
943	<	#endif
1300	>
1301		}
1302
1303		#ifdef IS_MPI
#	Line 1031 | Line 1388 | void SimSetup::makeOutNames(void){
1388		}
1389		else{
1390		strcat(info[k].statusName, ".stat");
1391	+	}
1392	+	}
1393	+
1394	+	strcpy(info[k].rawPotName, inFileName);
1395	+	nameLength = strlen(info[k].rawPotName);
1396	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1397	+	if (!strcmp(endTest, ".bass")){
1398	+	strcpy(endTest, ".raw");
1399	+	}
1400	+	else if (!strcmp(endTest, ".BASS")){
1401	+	strcpy(endTest, ".raw");
1402	+	}
1403	+	else{
1404	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1405	+	if (!strcmp(endTest, ".bss")){
1406	+	strcpy(endTest, ".raw");
1407		}
1408	+	else if (!strcmp(endTest, ".mdl")){
1409	+	strcpy(endTest, ".raw");
1410	+	}
1411	+	else{
1412	+	strcat(info[k].rawPotName, ".raw");
1413	+	}
1414		}
1415
1416		#ifdef IS_MPI
#	Line 1094 | Line 1473 | void SimSetup::createFF(void){
1473		the_ff = new EAM_FF();
1474		break;
1475
1476	+	case FF_H2O:
1477	+	the_ff = new WATER();
1478	+	break;
1479	+
1480		default:
1481		sprintf(painCave.errMsg,
1482		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1114 | Line 1497 | void SimSetup::compList(void){
1497		LinkedMolStamp* headStamp = new LinkedMolStamp();
1498		LinkedMolStamp* currentStamp = NULL;
1499		comp_stamps = new MoleculeStamp * [n_components];
1500	+	bool haveCutoffGroups;
1501
1502	+	haveCutoffGroups = false;
1503	+
1504		// make an array of molecule stamps that match the components used.
1505		// also extract the used stamps out into a separate linked list
1506
#	Line 1149 | Line 1535 | void SimSetup::compList(void){
1535		headStamp->add(currentStamp);
1536		comp_stamps[i] = headStamp->match(id);
1537		}
1538	+
1539	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1540	+	haveCutoffGroups = true;
1541		}
1542	+
1543	+	for (i = 0; i < nInfo; i++)
1544	+	info[i].haveCutoffGroups = haveCutoffGroups;
1545
1546		#ifdef IS_MPI
1547		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1158 | Line 1550 | void SimSetup::calcSysValues(void){
1550		}
1551
1552		void SimSetup::calcSysValues(void){
1553	<	int i, j, k;
1553	>	int i, j;
1554	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1555
1556		int* molMembershipArray;
1557	+	CutoffGroupStamp* cg;
1558
1559		tot_atoms = 0;
1560		tot_bonds = 0;
1561		tot_bends = 0;
1562		tot_torsions = 0;
1563	+	tot_rigid = 0;
1564	+	tot_groups = 0;
1565		for (i = 0; i < n_components; i++){
1566		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1567		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1568		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1569		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1570	<	}
1570	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1571
1572	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1573	+	atomsingroups = 0;
1574	+	for (j=0; j < ncutgroups; j++) {
1575	+	cg = comp_stamps[i]->getCutoffGroup(j);
1576	+	atomsingroups += cg->getNMembers();
1577	+	}
1578	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1579	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1580	+	}
1581	+
1582		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1583		molMembershipArray = new int[tot_atoms];
1584
#	Line 1183 | Line 1589 | void SimSetup::calcSysValues(void){
1589		info[i].n_torsions = tot_torsions;
1590		info[i].n_SRI = tot_SRI;
1591		info[i].n_mol = tot_nmol;
1592	<
1592	>	info[i].ngroup = tot_groups;
1593		info[i].molMembershipArray = molMembershipArray;
1594		}
1595		}
#	Line 1194 | Line 1600 | void SimSetup::mpiMolDivide(void){
1600		int i, j, k;
1601		int localMol, allMol;
1602		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1603	+	int local_rigid, local_groups;
1604	+	vector<int> globalMolIndex;
1605	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1606	+	CutoffGroupStamp* cg;
1607
1608		mpiSim = new mpiSimulation(info);
1609
1610	<	globalIndex = mpiSim->divideLabor();
1610	>	mpiSim->divideLabor();
1611	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1612	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1613
1614		// set up the local variables
1615
#	Line 1210 | Line 1622 | void SimSetup::mpiMolDivide(void){
1622		local_bonds = 0;
1623		local_bends = 0;
1624		local_torsions = 0;
1625	<	globalAtomIndex = 0;
1626	<
1625	>	local_rigid = 0;
1626	>	local_groups = 0;
1627	>	globalAtomCounter = 0;
1628
1629		for (i = 0; i < n_components; i++){
1630		for (j = 0; j < components_nmol[i]; j++){
#	Line 1220 | Line 1633 | void SimSetup::mpiMolDivide(void){
1633		local_bonds += comp_stamps[i]->getNBonds();
1634		local_bends += comp_stamps[i]->getNBends();
1635		local_torsions += comp_stamps[i]->getNTorsions();
1636	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1637	+
1638	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1639	+	atomsingroups = 0;
1640	+	for (k=0; k < ncutgroups; k++) {
1641	+	cg = comp_stamps[i]->getCutoffGroup(k);
1642	+	atomsingroups += cg->getNMembers();
1643	+	}
1644	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1645	+	ncutgroups;
1646	+	local_groups += ngroupsinstamp;
1647	+
1648		localMol++;
1649		}
1650		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1651	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1652	<	globalAtomIndex++;
1651	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1652	>	globalAtomCounter++;
1653		}
1654
1655		allMol++;
#	Line 1232 | Line 1657 | void SimSetup::mpiMolDivide(void){
1657		}
1658		local_SRI = local_bonds + local_bends + local_torsions;
1659
1660	<	info[0].n_atoms = mpiSim->getMyNlocal();
1661	<
1660	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1661	>
1662		if (local_atoms != info[0].n_atoms){
1663		sprintf(painCave.errMsg,
1664	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1665	<	" localAtom (%d) are not equal.\n",
1664	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1665	>	"\tlocalAtom (%d) are not equal.\n",
1666		info[0].n_atoms, local_atoms);
1667		painCave.isFatal = 1;
1668		simError();
1669		}
1670
1671	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1672	+	if (local_groups != info[0].ngroup){
1673	+	sprintf(painCave.errMsg,
1674	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1675	+	"\tlocalGroups (%d) are not equal.\n",
1676	+	info[0].ngroup, local_groups);
1677	+	painCave.isFatal = 1;
1678	+	simError();
1679	+	}
1680	+
1681		info[0].n_bonds = local_bonds;
1682		info[0].n_bends = local_bends;
1683		info[0].n_torsions = local_torsions;
#	Line 1257 | Line 1692 | void SimSetup::makeSysArrays(void){
1692
1693
1694		void SimSetup::makeSysArrays(void){
1695	<	int i, j, k, l;
1695	>
1696	>	#ifndef IS_MPI
1697	>	int k, j;
1698	>	#endif // is_mpi
1699	>	int i, l;
1700
1701		Atom** the_atoms;
1702		Molecule* the_molecules;
1264	–	Exclude** the_excludes;
1703
1266	–
1704		for (l = 0; l < nInfo; l++){
1705		// create the atom and short range interaction arrays
1706
#	Line 1277 | Line 1714 | void SimSetup::makeSysArrays(void){
1714
1715
1716		molIndex = 0;
1717	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1717	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1718		if (mol2proc[i] == worldRank){
1719		the_molecules[molIndex].setStampID(molCompType[i]);
1720		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1289 | Line 1726 | void SimSetup::makeSysArrays(void){
1726		#else // is_mpi
1727
1728		molIndex = 0;
1729	<	globalAtomIndex = 0;
1729	>	globalAtomCounter = 0;
1730		for (i = 0; i < n_components; i++){
1731		for (j = 0; j < components_nmol[i]; j++){
1732		the_molecules[molIndex].setStampID(i);
1733		the_molecules[molIndex].setMyIndex(molIndex);
1734		the_molecules[molIndex].setGlobalIndex(molIndex);
1735		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1736	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1737	<	globalAtomIndex++;
1736	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1737	>	globalAtomCounter++;
1738		}
1739		molIndex++;
1740		}
#	Line 1306 | Line 1743 | void SimSetup::makeSysArrays(void){
1743
1744		#endif // is_mpi
1745
1746	<
1747	<	if (info[l].n_SRI){
1748	<	Exclude::createArray(info[l].n_SRI);
1312	<	the_excludes = new Exclude * [info[l].n_SRI];
1313	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1314	<	the_excludes[ex] = new Exclude(ex);
1315	<	}
1316	<	info[l].globalExcludes = new int;
1317	<	info[l].n_exclude = info[l].n_SRI;
1318	<	}
1319	<	else{
1320	<	Exclude::createArray(1);
1321	<	the_excludes = new Exclude * ;
1322	<	the_excludes[0] = new Exclude(0);
1323	<	the_excludes[0]->setPair(0, 0);
1324	<	info[l].globalExcludes = new int;
1325	<	info[l].globalExcludes[0] = 0;
1326	<	info[l].n_exclude = 0;
1327	<	}
1328	<
1746	>	info[l].globalExcludes = new int;
1747	>	info[l].globalExcludes[0] = 0;
1748	>
1749		// set the arrays into the SimInfo object
1750
1751		info[l].atoms = the_atoms;
1752		info[l].molecules = the_molecules;
1753		info[l].nGlobalExcludes = 0;
1754	<	info[l].excludes = the_excludes;
1335	<
1754	>
1755		the_ff->setSimInfo(info);
1756		}
1757		}
#	Line 1340 | Line 1759 | void SimSetup::makeIntegrator(void){
1759		void SimSetup::makeIntegrator(void){
1760		int k;
1761
1762	+	NVE<RealIntegrator>* myNVE = NULL;
1763		NVT<RealIntegrator>* myNVT = NULL;
1764		NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1765		NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1766	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1767
1768		for (k = 0; k < nInfo; k++){
1769		switch (ensembleCase){
1770		case NVE_ENS:
1771		if (globals->haveZconstraints()){
1772		setupZConstraint(info[k]);
1773	<	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1773	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1774		}
1775	<	else
1776	<	new NVE<RealIntegrator>(&(info[k]), the_ff);
1775	>	else{
1776	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1777	>	}
1778	>
1779	>	info->the_integrator = myNVE;
1780		break;
1781
1782		case NVT_ENS:
#	Line 1370 | Line 1794 | void SimSetup::makeIntegrator(void){
1794		else{
1795		sprintf(painCave.errMsg,
1796		"SimSetup error: If you use the NVT\n"
1797	<	"    ensemble, you must set tauThermostat.\n");
1797	>	"\tensemble, you must set tauThermostat.\n");
1798		painCave.isFatal = 1;
1799		simError();
1800		}
1801	+
1802	+	info->the_integrator = myNVT;
1803		break;
1804
1805		case NPTi_ENS:
#	Line 1391 | Line 1817 | void SimSetup::makeIntegrator(void){
1817		else{
1818		sprintf(painCave.errMsg,
1819		"SimSetup error: If you use a constant pressure\n"
1820	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1820	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1821		painCave.isFatal = 1;
1822		simError();
1823		}
#	Line 1401 | Line 1827 | void SimSetup::makeIntegrator(void){
1827		else{
1828		sprintf(painCave.errMsg,
1829		"SimSetup error: If you use an NPT\n"
1830	<	"    ensemble, you must set tauThermostat.\n");
1830	>	"\tensemble, you must set tauThermostat.\n");
1831		painCave.isFatal = 1;
1832		simError();
1833		}
#	Line 1411 | Line 1837 | void SimSetup::makeIntegrator(void){
1837		else{
1838		sprintf(painCave.errMsg,
1839		"SimSetup error: If you use an NPT\n"
1840	<	"    ensemble, you must set tauBarostat.\n");
1840	>	"\tensemble, you must set tauBarostat.\n");
1841		painCave.isFatal = 1;
1842		simError();
1843		}
1844	+
1845	+	info->the_integrator = myNPTi;
1846		break;
1847
1848		case NPTf_ENS:
#	Line 1432 | Line 1860 | void SimSetup::makeIntegrator(void){
1860		else{
1861		sprintf(painCave.errMsg,
1862		"SimSetup error: If you use a constant pressure\n"
1863	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1863	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1864		painCave.isFatal = 1;
1865		simError();
1866		}
1867
1868		if (globals->haveTauThermostat())
1869		myNPTf->setTauThermostat(globals->getTauThermostat());
1870	+
1871		else{
1872		sprintf(painCave.errMsg,
1873		"SimSetup error: If you use an NPT\n"
1874	<	"    ensemble, you must set tauThermostat.\n");
1874	>	"\tensemble, you must set tauThermostat.\n");
1875		painCave.isFatal = 1;
1876		simError();
1877		}
1878
1879		if (globals->haveTauBarostat())
1880		myNPTf->setTauBarostat(globals->getTauBarostat());
1881	+
1882		else{
1883		sprintf(painCave.errMsg,
1884		"SimSetup error: If you use an NPT\n"
1885	<	"    ensemble, you must set tauBarostat.\n");
1885	>	"\tensemble, you must set tauBarostat.\n");
1886		painCave.isFatal = 1;
1887		simError();
1888		}
1889	+
1890	+	info->the_integrator = myNPTf;
1891		break;
1892
1893	+	case NPTxyz_ENS:
1894	+	if (globals->haveZconstraints()){
1895	+	setupZConstraint(info[k]);
1896	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1897	+	}
1898	+	else
1899	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1900	+
1901	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1902	+
1903	+	if (globals->haveTargetPressure())
1904	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1905	+	else{
1906	+	sprintf(painCave.errMsg,
1907	+	"SimSetup error: If you use a constant pressure\n"
1908	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1909	+	painCave.isFatal = 1;
1910	+	simError();
1911	+	}
1912	+
1913	+	if (globals->haveTauThermostat())
1914	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1915	+	else{
1916	+	sprintf(painCave.errMsg,
1917	+	"SimSetup error: If you use an NPT\n"
1918	+	"\tensemble, you must set tauThermostat.\n");
1919	+	painCave.isFatal = 1;
1920	+	simError();
1921	+	}
1922	+
1923	+	if (globals->haveTauBarostat())
1924	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1925	+	else{
1926	+	sprintf(painCave.errMsg,
1927	+	"SimSetup error: If you use an NPT\n"
1928	+	"\tensemble, you must set tauBarostat.\n");
1929	+	painCave.isFatal = 1;
1930	+	simError();
1931	+	}
1932	+
1933	+	info->the_integrator = myNPTxyz;
1934	+	break;
1935	+
1936		default:
1937		sprintf(painCave.errMsg,
1938		"SimSetup Error. Unrecognized ensemble in case statement.\n");
#	Line 1503 | Line 1978 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1978		}
1979		else{
1980		sprintf(painCave.errMsg,
1981	<	"ZConstraint error: If you use an ZConstraint\n"
1982	<	" , you must set sample time.\n");
1981	>	"ZConstraint error: If you use a ZConstraint,\n"
1982	>	"\tyou must set zconsTime.\n");
1983		painCave.isFatal = 1;
1984		simError();
1985		}
#	Line 1519 | Line 1994 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1994		else{
1995		double defaultZConsTol = 0.01;
1996		sprintf(painCave.errMsg,
1997	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1998	<	" , default value %f is used.\n",
1997	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1998	>	"\tOOPSE will use a default value of %f.\n"
1999	>	"\tTo set the tolerance, use the zconsTol variable.\n",
2000		defaultZConsTol);
2001		painCave.isFatal = 0;
2002		simError();
#	Line 1538 | Line 2014 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2014		}
2015		else{
2016		sprintf(painCave.errMsg,
2017	<	"ZConstraint Warning: User does not set force Subtraction policy, "
2018	<	"PolicyByMass is used\n");
2017	>	"ZConstraint Warning: No force subtraction policy was set.\n"
2018	>	"\tOOPSE will use PolicyByMass.\n"
2019	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2020		painCave.isFatal = 0;
2021		simError();
2022		zconsForcePolicy->setData("BYMASS");
#	Line 1547 | Line 2024 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2024
2025		theInfo.addProperty(zconsForcePolicy);
2026
2027	+	//set zcons gap
2028	+	DoubleData* zconsGap = new DoubleData();
2029	+	zconsGap->setID(ZCONSGAP_ID);
2030	+
2031	+	if (globals->haveZConsGap()){
2032	+	zconsGap->setData(globals->getZconsGap());
2033	+	theInfo.addProperty(zconsGap);
2034	+	}
2035	+
2036	+	//set zcons fixtime
2037	+	DoubleData* zconsFixtime = new DoubleData();
2038	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2039	+
2040	+	if (globals->haveZConsFixTime()){
2041	+	zconsFixtime->setData(globals->getZconsFixtime());
2042	+	theInfo.addProperty(zconsFixtime);
2043	+	}
2044	+
2045	+	//set zconsUsingSMD
2046	+	IntData* zconsUsingSMD = new IntData();
2047	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2048	+
2049	+	if (globals->haveZConsUsingSMD()){
2050	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2051	+	theInfo.addProperty(zconsUsingSMD);
2052	+	}
2053	+
2054		//Determine the name of ouput file and add it into SimInfo's property list
2055		//Be careful, do not use inFileName, since it is a pointer which
2056		//point to a string at master node, and slave nodes do not contain that string
#	Line 1576 | Line 2080 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2080		tempParaItem.zPos = zconStamp[i]->getZpos();
2081		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2082		tempParaItem.kRatio = zconStamp[i]->getKratio();
2083	<
2083	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2084	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2085		zconsParaData->addItem(tempParaItem);
2086		}
2087
2088		//check the uniqueness of index
2089		if(!zconsParaData->isIndexUnique()){
2090		sprintf(painCave.errMsg,
2091	<	"ZConstraint Error: molIndex is not unique\n");
2091	>	"ZConstraint Error: molIndex is not unique!\n");
2092		painCave.isFatal = 1;
2093		simError();
2094		}
#	Line 1594 | Line 2099 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2099		//push data into siminfo, therefore, we can retrieve later
2100		theInfo.addProperty(zconsParaData);
2101		}
2102	+
2103	+	void SimSetup::makeMinimizer(){
2104	+
2105	+	OOPSEMinimizer* myOOPSEMinimizer;
2106	+	MinimizerParameterSet* param;
2107	+	char minimizerName[100];
2108	+
2109	+	for (int i = 0; i < nInfo; i++){
2110	+
2111	+	//prepare parameter set for minimizer
2112	+	param = new MinimizerParameterSet();
2113	+	param->setDefaultParameter();
2114	+
2115	+	if (globals->haveMinimizer()){
2116	+	param->setFTol(globals->getMinFTol());
2117	+	}
2118	+
2119	+	if (globals->haveMinGTol()){
2120	+	param->setGTol(globals->getMinGTol());
2121	+	}
2122	+
2123	+	if (globals->haveMinMaxIter()){
2124	+	param->setMaxIteration(globals->getMinMaxIter());
2125	+	}
2126	+
2127	+	if (globals->haveMinWriteFrq()){
2128	+	param->setMaxIteration(globals->getMinMaxIter());
2129	+	}
2130	+
2131	+	if (globals->haveMinWriteFrq()){
2132	+	param->setWriteFrq(globals->getMinWriteFrq());
2133	+	}
2134	+
2135	+	if (globals->haveMinStepSize()){
2136	+	param->setStepSize(globals->getMinStepSize());
2137	+	}
2138	+
2139	+	if (globals->haveMinLSMaxIter()){
2140	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2141	+	}
2142	+
2143	+	if (globals->haveMinLSTol()){
2144	+	param->setLineSearchTol(globals->getMinLSTol());
2145	+	}
2146	+
2147	+	strcpy(minimizerName, globals->getMinimizer());
2148	+
2149	+	if (!strcasecmp(minimizerName, "CG")){
2150	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2151	+	}
2152	+	else if (!strcasecmp(minimizerName, "SD")){
2153	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2154	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2155	+	}
2156	+	else{
2157	+	sprintf(painCave.errMsg,
2158	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2159	+	painCave.isFatal = 0;
2160	+	simError();
2161	+
2162	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2163	+	}
2164	+	info[i].the_integrator = myOOPSEMinimizer;
2165	+
2166	+	//store the minimizer into simInfo
2167	+	info[i].the_minimizer = myOOPSEMinimizer;
2168	+	info[i].has_minimizer = true;
2169	+	}
2170	+
2171	+	}

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