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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC vs.
Revision 1204 by gezelter, Thu May 27 19:26:42 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 "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 22 | Line 24
24		#define NVT_ENS        1
25		#define NPTi_ENS       2
26		#define NPTf_ENS       3
27	+	#define NPTxyz_ENS     4
28
26	–	#define FF_DUFF 0
27	–	#define FF_LJ   1
28	–	#define FF_EAM  2
29
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34	+
35		using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64		isInfoArray = 0;
65		nInfo = 1;
66
#	Line 52 | Line 83 | void SimSetup::setSimInfo(SimInfo* the_info, int theNi
83		info = the_info;
84		nInfo = theNinfo;
85		isInfoArray = 1;
86	+	initSuspend = true;
87		}
88
89
#	Line 105 | Line 137 | void SimSetup::createSim(void){
137
138		// initialize the system coordinates
139
140	<	if (!isInfoArray){
140	>	if ( !initSuspend ){
141		initSystemCoords();
142	+
143	+	if( !(globals->getUseInitTime()) )
144	+	info[0].currentTime = 0.0;
145		}
146
147		// make the output filenames
148
149		makeOutNames();
150	<
116	<	// make the integrator
117	<
118	<	makeIntegrator();
119	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 124 | Line 155 | void SimSetup::createSim(void){
155		// initialize the Fortran
156
157		initFortran();
158	+
159	+	if (globals->haveMinimizer())
160	+	// make minimizer
161	+	makeMinimizer();
162	+	else
163	+	// make the integrator
164	+	makeIntegrator();
165	+
166		}
167
168
169		void SimSetup::makeMolecules(void){
170	<	int k;
171	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175		molInit molInfo;
176		DirectionalAtom* dAtom;
177	+	RigidBody* myRB;
178	+	StuntDouble* mySD;
179		LinkedAssign* extras;
180		LinkedAssign* current_extra;
181		AtomStamp* currentAtom;
182		BondStamp* currentBond;
183		BendStamp* currentBend;
184		TorsionStamp* currentTorsion;
185	+	RigidBodyStamp* currentRigidBody;
186	+	CutoffGroupStamp* currentCutoffGroup;
187	+	CutoffGroup* myCutoffGroup;
188	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191		bond_pair* theBonds;
192		bend_set* theBends;
193		torsion_set* theTorsions;
194
195	+	set<int> skipList;
196
197	+	double phi, theta, psi;
198	+	char* molName;
199	+	char rbName[100];
200	+
201		//init the forceField paramters
202
203		the_ff->readParams();
204
151	–
205		// init the atoms
206
207	<	double ux, uy, uz, u, uSqr;
207	>	int nMembers, nNew, rb1, rb2;
208
209		for (k = 0; k < nInfo; k++){
210		the_ff->setSimInfo(&(info[k]));
211
212		atomOffset = 0;
213	<	excludeOffset = 0;
213	>
214		for (i = 0; i < info[k].n_mol; i++){
215		stampID = info[k].molecules[i].getStampID();
216	+	molName = comp_stamps[stampID]->getID();
217
218		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220		molInfo.nBends = comp_stamps[stampID]->getNBends();
221		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	+
226		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
171	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
172	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
173	–	molInfo.myBends = new Bend * [molInfo.nBends];
174	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
227
228	+	if (molInfo.nBonds > 0)
229	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	+	else
231	+	molInfo.myBonds = NULL;
232	+
233	+	if (molInfo.nBends > 0)
234	+	molInfo.myBends = new Bend*[molInfo.nBends];
235	+	else
236	+	molInfo.myBends = NULL;
237	+
238	+	if (molInfo.nTorsions > 0)
239	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	+	else
241	+	molInfo.myTorsions = NULL;
242	+
243		theBonds = new bond_pair[molInfo.nBonds];
244		theBends = new bend_set[molInfo.nBends];
245		theTorsions = new torsion_set[molInfo.nTorsions];
246	<
246	>
247		// make the Atoms
248
249		for (j = 0; j < molInfo.nAtoms; j++){
250		currentAtom = comp_stamps[stampID]->getAtom(j);
251	+
252		if (currentAtom->haveOrientation()){
253		dAtom = new DirectionalAtom((j + atomOffset),
254		info[k].getConfiguration());
255		info[k].n_oriented++;
256		molInfo.myAtoms[j] = dAtom;
257
258	<	ux = currentAtom->getOrntX();
259	<	uy = currentAtom->getOrntY();
260	<	uz = currentAtom->getOrntZ();
258	>	// Directional Atoms have standard unit vectors which are oriented
259	>	// in space using the three Euler angles.  We assume the standard
260	>	// unit vector was originally along the z axis below.
261
262	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265
266	<	u = sqrt(uSqr);
267	<	ux = ux / u;
198	<	uy = uy / u;
199	<	uz = uz / u;
200	<
201	<	dAtom->setSUx(ux);
202	<	dAtom->setSUy(uy);
203	<	dAtom->setSUz(uz);
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268		}
269		else{
270	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
271	<	info[k].getConfiguration());
270	>
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272	>
273		}
209	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
274
275	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277
278	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
280		#endif // is_mpi
281		}
#	Line 221 | Line 286 | void SimSetup::makeMolecules(void){
286		theBonds[j].a = currentBond->getA() + atomOffset;
287		theBonds[j].b = currentBond->getB() + atomOffset;
288
289	<	exI = theBonds[j].a;
290	<	exJ = theBonds[j].b;
289	>	tempI = theBonds[j].a;
290	>	tempJ = theBonds[j].b;
291
227	–	// exclude_I must always be the smaller of the pair
228	–	if (exI > exJ){
229	–	tempEx = exI;
230	–	exI = exJ;
231	–	exJ = tempEx;
232	–	}
292		#ifdef IS_MPI
293	<	tempEx = exI;
294	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
295	<	tempEx = exJ;
296	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
240	<	#else  // isn't MPI
241	<
242	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
243	<	#endif  //is_mpi
300	>	info[k].excludes->addPair(exI, exJ);
301		}
245	–	excludeOffset += molInfo.nBonds;
302
303		//make the bends
304		for (j = 0; j < molInfo.nBends; j++){
#	Line 292 | Line 348 | void SimSetup::makeMolecules(void){
348		}
349		}
350
351	<	if (!theBends[j].isGhost){
352	<	exI = theBends[j].a;
353	<	exJ = theBends[j].c;
354	<	}
355	<	else{
300	<	exI = theBends[j].a;
301	<	exJ = theBends[j].b;
302	<	}
303	<
304	<	// exclude_I must always be the smaller of the pair
305	<	if (exI > exJ){
306	<	tempEx = exI;
307	<	exI = exJ;
308	<	exJ = tempEx;
309	<	}
351	>	if (theBends[j].isGhost) {
352	>
353	>	tempI = theBends[j].a;
354	>	tempJ = theBends[j].b;
355	>
356		#ifdef IS_MPI
357	<	tempEx = exI;
358	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
359	<	tempEx = exJ;
360	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
366	<	#else  // isn't MPI
367	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
368	<	#endif  //is_mpi
365	>	} else {
366	>
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
321	–	excludeOffset += molInfo.nBends;
386
387		for (j = 0; j < molInfo.nTorsions; j++){
388		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 327 | Line 391 | void SimSetup::makeMolecules(void){
391		theTorsions[j].c = currentTorsion->getC() + atomOffset;
392		theTorsions[j].d = currentTorsion->getD() + atomOffset;
393
394	<	exI = theTorsions[j].a;
395	<	exJ = theTorsions[j].d;
394	>	tempI = theTorsions[j].a;
395	>	tempJ = theTorsions[j].b;
396	>	tempK = theTorsions[j].c;
397	>	tempL = theTorsions[j].d;
398
333	–	// exclude_I must always be the smaller of the pair
334	–	if (exI > exJ){
335	–	tempEx = exI;
336	–	exI = exJ;
337	–	exJ = tempEx;
338	–	}
399		#ifdef IS_MPI
400	<	tempEx = exI;
401	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
402	<	tempEx = exJ;
403	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410
411	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
412	<	#else  // isn't MPI
413	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
414	<	#endif  //is_mpi
415	<	}
416	<	excludeOffset += molInfo.nTorsions;
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418
419	+
420	+	molInfo.myRigidBodies.clear();
421	+
422	+	for (j = 0; j < molInfo.nRigidBodies; j++){
423
424	<	// send the arrays off to the forceField for init.
424	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	>	nMembers = currentRigidBody->getNMembers();
426	>
427	>	// Create the Rigid Body:
428	>
429	>	myRB = new RigidBody();
430	>
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435	>
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438	>
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441	>
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445	>
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448	>
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452	>	#ifdef IS_MPI
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484	>
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487	>	}
488	>
489	>
490	>	//create cutoff group for molecule
491	>
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496	>
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499	>
500	>	myCutoffGroup = new CutoffGroup();
501	>
502	>	for (int cg = 0; cg < nMembers; cg++) {
503	>
504	>	// molI is atom numbering inside this molecule
505	>	molI = currentCutoffGroup->getMember(cg);
506	>
507	>	// tempI is atom numbering on local processor
508	>	tempI = molI + atomOffset;
509	>
510	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	>
512	>	cutoffAtomSet.insert(tempI);
513	>	}
514	>
515	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	>
518	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519	>
520	>	for(j = 0; j < molInfo.nAtoms; j++){
521	>
522	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	>	myCutoffGroup = new CutoffGroup();
524	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	>	}
527	>
528	>	}
529	>
530	>
531	>
532	>
533	>	// After this is all set up, scan through the atoms to
534	>	// see if they can be added to the integrableObjects:
535	>
536	>	molInfo.myIntegrableObjects.clear();
537	>
538	>
539	>	for (j = 0; j < molInfo.nAtoms; j++){
540	>
541	>	#ifdef IS_MPI
542	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	>	#else
544	>	slJ = j+atomOffset;
545	>	#endif
546	>
547	>	// if they aren't on the skip list, then they can be integrated
548	>
549	>	if (skipList.find(slJ) == skipList.end()) {
550	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	>	info[k].integrableObjects.push_back(mySD);
552	>	molInfo.myIntegrableObjects.push_back(mySD);
553	>	}
554	>	}
555
556	+	// all rigid bodies are integrated:
557	+
558	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	+	info[k].integrableObjects.push_back(mySD);
561	+	molInfo.myIntegrableObjects.push_back(mySD);
562	+	}
563	+
564	+
565	+	// send the arrays off to the forceField for init.
566	+
567		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571		theTorsions);
572
361	–
573		info[k].molecules[i].initialize(molInfo);
574
575
#	Line 366 | Line 577 | void SimSetup::makeMolecules(void){
577		delete[] theBonds;
578		delete[] theBends;
579		delete[] theTorsions;
580	<	}
580	>	}
581		}
582
583		#ifdef IS_MPI
#	Line 374 | Line 585 | void SimSetup::makeMolecules(void){
585		MPIcheckPoint();
586		#endif // is_mpi
587
377	–	// clean up the forcefield
378	–
379	–	the_ff->calcRcut();
380	–	the_ff->cleanMe();
588		}
589
590		void SimSetup::initFromBass(void){
#	Line 578 | Line 785 | void SimSetup::gatherInfo(void){
785		else if (!strcasecmp(force_field, "EAM")){
786		ffCase = FF_EAM;
787		}
788	+	else if (!strcasecmp(force_field, "WATER")){
789	+	ffCase = FF_H2O;
790	+	}
791		else{
792		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793		force_field);
#	Line 601 | Line 811 | void SimSetup::gatherInfo(void){
811		else if (!strcasecmp(ensemble, "NPTf")){
812		ensembleCase = NPTf_ENS;
813		}
814	+	else if (!strcasecmp(ensemble, "NPTxyz")){
815	+	ensembleCase = NPTxyz_ENS;
816	+	}
817		else{
818		sprintf(painCave.errMsg,
819	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
820	<	"reverting to NVE for this simulation.\n",
819	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	>	"\treverting to NVE for this simulation.\n",
821		ensemble);
822		painCave.isFatal = 0;
823		simError();
#	Line 636 | Line 849 | void SimSetup::gatherInfo(void){
849		if (!the_components[i]->haveNMol()){
850		// we have a problem
851		sprintf(painCave.errMsg,
852	<	"SimSetup Error. No global NMol or component NMol"
853	<	" given. Cannot calculate the number of atoms.\n");
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854		painCave.isFatal = 1;
855		simError();
856		}
#	Line 656 | Line 869 | void SimSetup::gatherInfo(void){
869		painCave.isFatal = 1;
870		simError();
871		}
872	+
873	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	+	sprintf(painCave.errMsg,
876	+	"Sample time is not divisible by dt.\n"
877	+	"\tThis will result in samples that are not uniformly\n"
878	+	"\tdistributed in time.  If this is a problem, change\n"
879	+	"\tyour sampleTime variable.\n");
880	+	painCave.isFatal = 0;
881	+	simError();
882	+	}
883	+
884	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	+	sprintf(painCave.errMsg,
886	+	"Status time is not divisible by dt.\n"
887	+	"\tThis will result in status reports that are not uniformly\n"
888	+	"\tdistributed in time.  If this is a problem, change \n"
889	+	"\tyour statusTime variable.\n");
890	+	painCave.isFatal = 0;
891	+	simError();
892	+	}
893	+
894	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	+	sprintf(painCave.errMsg,
896	+	"Thermal time is not divisible by dt.\n"
897	+	"\tThis will result in thermalizations that are not uniformly\n"
898	+	"\tdistributed in time.  If this is a problem, change \n"
899	+	"\tyour thermalTime variable.\n");
900	+	painCave.isFatal = 0;
901	+	simError();
902	+	}
903
904	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	+	sprintf(painCave.errMsg,
906	+	"Reset time is not divisible by dt.\n"
907	+	"\tThis will result in integrator resets that are not uniformly\n"
908	+	"\tdistributed in time.  If this is a problem, change\n"
909	+	"\tyour resetTime variable.\n");
910	+	painCave.isFatal = 0;
911	+	simError();
912	+	}
913	+
914		// set the status, sample, and thermal kick times
915
916		for (i = 0; i < nInfo; i++){
917		if (globals->haveSampleTime()){
918		info[i].sampleTime = globals->getSampleTime();
919		info[i].statusTime = info[i].sampleTime;
666	–	info[i].thermalTime = info[i].sampleTime;
920		}
921		else{
922		info[i].sampleTime = globals->getRunTime();
923		info[i].statusTime = info[i].sampleTime;
671	–	info[i].thermalTime = info[i].sampleTime;
924		}
925
926		if (globals->haveStatusTime()){
#	Line 677 | Line 929 | void SimSetup::gatherInfo(void){
929
930		if (globals->haveThermalTime()){
931		info[i].thermalTime = globals->getThermalTime();
932	+	} else {
933	+	info[i].thermalTime = globals->getRunTime();
934		}
935
936		info[i].resetIntegrator = 0;
#	Line 686 | Line 940 | void SimSetup::gatherInfo(void){
940		}
941
942		// check for the temperature set flag
943	<
943	>
944		if (globals->haveTempSet())
945		info[i].setTemp = globals->getTempSet();
946
947	<	// get some of the tricky things that may still be in the globals
947	>	// check for the extended State init
948
949	<	double boxVector[3];
950	<	if (globals->haveBox()){
697	<	boxVector[0] = globals->getBox();
698	<	boxVector[1] = globals->getBox();
699	<	boxVector[2] = globals->getBox();
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951
952	<	info[i].setBox(boxVector);
953	<	}
954	<	else if (globals->haveDensity()){
955	<	double vol;
956	<	vol = (double) tot_nmol / globals->getDensity();
957	<	boxVector[0] = pow(vol, (1.0 / 3.0));
958	<	boxVector[1] = boxVector[0];
959	<	boxVector[2] = boxVector[0];
960	<
710	<	info[i].setBox(boxVector);
711	<	}
712	<	else{
713	<	if (!globals->haveBoxX()){
714	<	sprintf(painCave.errMsg,
715	<	"SimSetup error, no periodic BoxX size given.\n");
716	<	painCave.isFatal = 1;
717	<	simError();
952	>	// check for thermodynamic integration
953	>	if (globals->getUseThermInt()) {
954	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
955	>	info[i].useThermInt = globals->getUseThermInt();
956	>	info[i].thermIntLambda = globals->getThermIntLambda();
957	>	info[i].thermIntK = globals->getThermIntK();
958	>
959	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
960	>	info[i].restraint = myRestraint;
961		}
962	<	boxVector[0] = globals->getBoxX();
963	<
964	<	if (!globals->haveBoxY()){
965	<	sprintf(painCave.errMsg,
966	<	"SimSetup error, no periodic BoxY size given.\n");
967	<	painCave.isFatal = 1;
968	<	simError();
962	>	else {
963	>	sprintf(painCave.errMsg,
964	>	"SimSetup Error:\n"
965	>	"\tKeyword useThermInt was set to 'true' but\n"
966	>	"\tthermodynamicIntegrationLambda (and/or\n"
967	>	"\tthermodynamicIntegrationK) was not specified.\n"
968	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
969	>	painCave.isFatal = 1;
970	>	simError();
971		}
727	–	boxVector[1] = globals->getBoxY();
728	–
729	–	if (!globals->haveBoxZ()){
730	–	sprintf(painCave.errMsg,
731	–	"SimSetup error, no periodic BoxZ size given.\n");
732	–	painCave.isFatal = 1;
733	–	simError();
734	–	}
735	–	boxVector[2] = globals->getBoxZ();
736	–
737	–	info[i].setBox(boxVector);
972		}
973	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
974	+	sprintf(painCave.errMsg,
975	+	"SimSetup Warning: If you want to use Thermodynamic\n"
976	+	"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
977	+	"\tThe useThermInt keyword is 'false' by default, so your\n"
978	+	"\tlambda and/or k values are being ignored.\n");
979	+	painCave.isFatal = 0;
980	+	simError();
981	+	}
982		}
983	<
983	>
984		//setup seed for random number generator
985		int seedValue;
986
#	Line 777 | Line 1020 | void SimSetup::gatherInfo(void){
1020		for (int i = 0; i < nInfo; i++){
1021		info[i].setSeed(seedValue);
1022		}
1023	<
1023	>
1024		#ifdef IS_MPI
1025	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1025	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1026		MPIcheckPoint();
1027		#endif // is_mpi
1028		}
#	Line 788 | Line 1031 | void SimSetup::finalInfoCheck(void){
1031		void SimSetup::finalInfoCheck(void){
1032		int index;
1033		int usesDipoles;
1034	+	int usesCharges;
1035		int i;
1036
1037		for (i = 0; i < nInfo; i++){
#	Line 799 | Line 1043 | void SimSetup::finalInfoCheck(void){
1043		usesDipoles = (info[i].atoms[index])->hasDipole();
1044		index++;
1045		}
1046	<
1046	>	index = 0;
1047	>	usesCharges = 0;
1048	>	while ((index < info[i].n_atoms) && !usesCharges){
1049	>	usesCharges= (info[i].atoms[index])->hasCharge();
1050	>	index++;
1051	>	}
1052		#ifdef IS_MPI
1053		int myUse = usesDipoles;
1054		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1055		#endif //is_mpi
1056
1057	<	double theEcr, theEst;
1057	>	double theRcut, theRsw;
1058
1059	+	if (globals->haveRcut()) {
1060	+	theRcut = globals->getRcut();
1061	+
1062	+	if (globals->haveRsw())
1063	+	theRsw = globals->getRsw();
1064	+	else
1065	+	theRsw = theRcut;
1066	+
1067	+	info[i].setDefaultRcut(theRcut, theRsw);
1068	+
1069	+	} else {
1070	+
1071	+	the_ff->calcRcut();
1072	+	theRcut = info[i].getRcut();
1073	+
1074	+	if (globals->haveRsw())
1075	+	theRsw = globals->getRsw();
1076	+	else
1077	+	theRsw = theRcut;
1078	+
1079	+	info[i].setDefaultRcut(theRcut, theRsw);
1080	+	}
1081	+
1082		if (globals->getUseRF()){
1083		info[i].useReactionField = 1;
1084	<
1085	<	if (!globals->haveECR()){
1084	>
1085	>	if (!globals->haveRcut()){
1086		sprintf(painCave.errMsg,
1087	<	"SimSetup Warning: using default value of 1/2 the smallest "
1088	<	"box length for the electrostaticCutoffRadius.\n"
1089	<	"I hope you have a very fast processor!\n");
1087	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1088	>	"\tOOPSE will use a default value of 15.0 angstroms"
1089	>	"\tfor the cutoffRadius.\n");
1090		painCave.isFatal = 0;
1091		simError();
1092	<	double smallest;
821	<	smallest = info[i].boxL[0];
822	<	if (info[i].boxL[1] <= smallest)
823	<	smallest = info[i].boxL[1];
824	<	if (info[i].boxL[2] <= smallest)
825	<	smallest = info[i].boxL[2];
826	<	theEcr = 0.5 * smallest;
1092	>	theRcut = 15.0;
1093		}
1094		else{
1095	<	theEcr = globals->getECR();
1095	>	theRcut = globals->getRcut();
1096		}
1097
1098	<	if (!globals->haveEST()){
1098	>	if (!globals->haveRsw()){
1099		sprintf(painCave.errMsg,
1100	<	"SimSetup Warning: using default value of 0.05 * the "
1101	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1100	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1101	>	"\tOOPSE will use a default value of\n"
1102	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1103		painCave.isFatal = 0;
1104		simError();
1105	<	theEst = 0.05 * theEcr;
1105	>	theRsw = 0.95 * theRcut;
1106		}
1107		else{
1108	<	theEst = globals->getEST();
1108	>	theRsw = globals->getRsw();
1109		}
1110
1111	<	info[i].setEcr(theEcr, theEst);
1111	>	info[i].setDefaultRcut(theRcut, theRsw);
1112
1113		if (!globals->haveDielectric()){
1114		sprintf(painCave.errMsg,
1115	<	"SimSetup Error: You are trying to use Reaction Field without"
1116	<	"setting a dielectric constant!\n");
1115	>	"SimSetup Error: No Dielectric constant was set.\n"
1116	>	"\tYou are trying to use Reaction Field without"
1117	>	"\tsetting a dielectric constant!\n");
1118		painCave.isFatal = 1;
1119		simError();
1120		}
1121		info[i].dielectric = globals->getDielectric();
1122		}
1123		else{
1124	<	if (usesDipoles){
1125	<	if (!globals->haveECR()){
1124	>	if (usesDipoles || usesCharges){
1125	>
1126	>	if (!globals->haveRcut()){
1127		sprintf(painCave.errMsg,
1128	<	"SimSetup Warning: using default value of 1/2 the smallest "
1129	<	"box length for the electrostaticCutoffRadius.\n"
1130	<	"I hope you have a very fast processor!\n");
1128	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1129	>	"\tOOPSE will use a default value of 15.0 angstroms"
1130	>	"\tfor the cutoffRadius.\n");
1131		painCave.isFatal = 0;
1132		simError();
1133	<	double smallest;
1134	<	smallest = info[i].boxL[0];
866	<	if (info[i].boxL[1] <= smallest)
867	<	smallest = info[i].boxL[1];
868	<	if (info[i].boxL[2] <= smallest)
869	<	smallest = info[i].boxL[2];
870	<	theEcr = 0.5 * smallest;
871	<	}
1133	>	theRcut = 15.0;
1134	>	}
1135		else{
1136	<	theEcr = globals->getECR();
1136	>	theRcut = globals->getRcut();
1137		}
1138	<
1139	<	if (!globals->haveEST()){
1138	>
1139	>	if (!globals->haveRsw()){
1140		sprintf(painCave.errMsg,
1141	<	"SimSetup Warning: using default value of 0.05 * the "
1142	<	"electrostaticCutoffRadius for the "
1143	<	"electrostaticSkinThickness\n");
1141	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1142	>	"\tOOPSE will use a default value of\n"
1143	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1144		painCave.isFatal = 0;
1145		simError();
1146	<	theEst = 0.05 * theEcr;
1146	>	theRsw = 0.95 * theRcut;
1147		}
1148		else{
1149	<	theEst = globals->getEST();
1149	>	theRsw = globals->getRsw();
1150		}
1151	<
1152	<	info[i].setEcr(theEcr, theEst);
1151	>
1152	>	info[i].setDefaultRcut(theRcut, theRsw);
1153	>
1154		}
1155		}
1156		}
893	–
1157		#ifdef IS_MPI
1158		strcpy(checkPointMsg, "post processing checks out");
1159		MPIcheckPoint();
1160		#endif // is_mpi
898	–	}
1161
1162	+	// clean up the forcefield
1163	+	the_ff->cleanMe();
1164	+	}
1165	+
1166		void SimSetup::initSystemCoords(void){
1167		int i;
1168
#	Line 924 | Line 1190 | void SimSetup::initSystemCoords(void){
1190		delete fileInit;
1191		}
1192		else{
1193	<	#ifdef IS_MPI
928	<
1193	>
1194		// no init from bass
1195	<
1195	>
1196		sprintf(painCave.errMsg,
1197	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1197	>	"Cannot intialize a simulation without an initial configuration file.\n");
1198		painCave.isFatal = 1;;
1199		simError();
1200	<
936	<	#else
937	<
938	<	initFromBass();
939	<
940	<
941	<	#endif
1200	>
1201		}
1202
1203		#ifdef IS_MPI
#	Line 1032 | Line 1291 | void SimSetup::makeOutNames(void){
1291		}
1292		}
1293
1294	+	strcpy(info[k].rawPotName, inFileName);
1295	+	nameLength = strlen(info[k].rawPotName);
1296	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1297	+	if (!strcmp(endTest, ".bass")){
1298	+	strcpy(endTest, ".raw");
1299	+	}
1300	+	else if (!strcmp(endTest, ".BASS")){
1301	+	strcpy(endTest, ".raw");
1302	+	}
1303	+	else{
1304	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1305	+	if (!strcmp(endTest, ".bss")){
1306	+	strcpy(endTest, ".raw");
1307	+	}
1308	+	else if (!strcmp(endTest, ".mdl")){
1309	+	strcpy(endTest, ".raw");
1310	+	}
1311	+	else{
1312	+	strcat(info[k].rawPotName, ".raw");
1313	+	}
1314	+	}
1315	+
1316		#ifdef IS_MPI
1317
1318		}
#	Line 1092 | Line 1373 | void SimSetup::createFF(void){
1373		the_ff = new EAM_FF();
1374		break;
1375
1376	+	case FF_H2O:
1377	+	the_ff = new WATER();
1378	+	break;
1379	+
1380		default:
1381		sprintf(painCave.errMsg,
1382		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1112 | Line 1397 | void SimSetup::compList(void){
1397		LinkedMolStamp* headStamp = new LinkedMolStamp();
1398		LinkedMolStamp* currentStamp = NULL;
1399		comp_stamps = new MoleculeStamp * [n_components];
1400	+	bool haveCutoffGroups;
1401
1402	+	haveCutoffGroups = false;
1403	+
1404		// make an array of molecule stamps that match the components used.
1405		// also extract the used stamps out into a separate linked list
1406
#	Line 1147 | Line 1435 | void SimSetup::compList(void){
1435		headStamp->add(currentStamp);
1436		comp_stamps[i] = headStamp->match(id);
1437		}
1438	+
1439	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1440	+	haveCutoffGroups = true;
1441		}
1442	+
1443	+	for (i = 0; i < nInfo; i++)
1444	+	info[i].haveCutoffGroups = haveCutoffGroups;
1445
1446		#ifdef IS_MPI
1447		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1156 | Line 1450 | void SimSetup::calcSysValues(void){
1450		}
1451
1452		void SimSetup::calcSysValues(void){
1453	<	int i;
1453	>	int i, j;
1454	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1455
1456		int* molMembershipArray;
1457	+	CutoffGroupStamp* cg;
1458
1459		tot_atoms = 0;
1460		tot_bonds = 0;
1461		tot_bends = 0;
1462		tot_torsions = 0;
1463	+	tot_rigid = 0;
1464	+	tot_groups = 0;
1465		for (i = 0; i < n_components; i++){
1466		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1467		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1468		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1469		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1470	<	}
1470	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1471
1472	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1473	+	atomsingroups = 0;
1474	+	for (j=0; j < ncutgroups; j++) {
1475	+	cg = comp_stamps[i]->getCutoffGroup(j);
1476	+	atomsingroups += cg->getNMembers();
1477	+	}
1478	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1479	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1480	+	}
1481	+
1482		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1483		molMembershipArray = new int[tot_atoms];
1484
#	Line 1181 | Line 1489 | void SimSetup::calcSysValues(void){
1489		info[i].n_torsions = tot_torsions;
1490		info[i].n_SRI = tot_SRI;
1491		info[i].n_mol = tot_nmol;
1492	<
1492	>	info[i].ngroup = tot_groups;
1493		info[i].molMembershipArray = molMembershipArray;
1494		}
1495		}
#	Line 1192 | Line 1500 | void SimSetup::mpiMolDivide(void){
1500		int i, j, k;
1501		int localMol, allMol;
1502		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1503	+	int local_rigid, local_groups;
1504	+	vector<int> globalMolIndex;
1505	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1506	+	CutoffGroupStamp* cg;
1507
1508		mpiSim = new mpiSimulation(info);
1509
1510	<	globalIndex = mpiSim->divideLabor();
1510	>	mpiSim->divideLabor();
1511	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1512	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1513
1514		// set up the local variables
1515
#	Line 1208 | Line 1522 | void SimSetup::mpiMolDivide(void){
1522		local_bonds = 0;
1523		local_bends = 0;
1524		local_torsions = 0;
1525	<	globalAtomIndex = 0;
1525	>	local_rigid = 0;
1526	>	local_groups = 0;
1527	>	globalAtomCounter = 0;
1528
1213	–
1529		for (i = 0; i < n_components; i++){
1530		for (j = 0; j < components_nmol[i]; j++){
1531		if (mol2proc[allMol] == worldRank){
#	Line 1218 | Line 1533 | void SimSetup::mpiMolDivide(void){
1533		local_bonds += comp_stamps[i]->getNBonds();
1534		local_bends += comp_stamps[i]->getNBends();
1535		local_torsions += comp_stamps[i]->getNTorsions();
1536	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1537	+
1538	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1539	+	atomsingroups = 0;
1540	+	for (k=0; k < ncutgroups; k++) {
1541	+	cg = comp_stamps[i]->getCutoffGroup(k);
1542	+	atomsingroups += cg->getNMembers();
1543	+	}
1544	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1545	+	ncutgroups;
1546	+	local_groups += ngroupsinstamp;
1547	+
1548		localMol++;
1549		}
1550		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1551	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1552	<	globalAtomIndex++;
1551	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1552	>	globalAtomCounter++;
1553		}
1554
1555		allMol++;
#	Line 1230 | Line 1557 | void SimSetup::mpiMolDivide(void){
1557		}
1558		local_SRI = local_bonds + local_bends + local_torsions;
1559
1560	<	info[0].n_atoms = mpiSim->getMyNlocal();
1561	<
1560	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1561	>
1562		if (local_atoms != info[0].n_atoms){
1563		sprintf(painCave.errMsg,
1564	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1565	<	" localAtom (%d) are not equal.\n",
1564	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1565	>	"\tlocalAtom (%d) are not equal.\n",
1566		info[0].n_atoms, local_atoms);
1567		painCave.isFatal = 1;
1568		simError();
1569		}
1570
1571	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1572	+	if (local_groups != info[0].ngroup){
1573	+	sprintf(painCave.errMsg,
1574	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1575	+	"\tlocalGroups (%d) are not equal.\n",
1576	+	info[0].ngroup, local_groups);
1577	+	painCave.isFatal = 1;
1578	+	simError();
1579	+	}
1580	+
1581		info[0].n_bonds = local_bonds;
1582		info[0].n_bends = local_bends;
1583		info[0].n_torsions = local_torsions;
#	Line 1263 | Line 1600 | void SimSetup::makeSysArrays(void){
1600
1601		Atom** the_atoms;
1602		Molecule* the_molecules;
1266	–	Exclude** the_excludes;
1603
1268	–
1604		for (l = 0; l < nInfo; l++){
1605		// create the atom and short range interaction arrays
1606
#	Line 1279 | Line 1614 | void SimSetup::makeSysArrays(void){
1614
1615
1616		molIndex = 0;
1617	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1617	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1618		if (mol2proc[i] == worldRank){
1619		the_molecules[molIndex].setStampID(molCompType[i]);
1620		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1291 | Line 1626 | void SimSetup::makeSysArrays(void){
1626		#else // is_mpi
1627
1628		molIndex = 0;
1629	<	globalAtomIndex = 0;
1629	>	globalAtomCounter = 0;
1630		for (i = 0; i < n_components; i++){
1631		for (j = 0; j < components_nmol[i]; j++){
1632		the_molecules[molIndex].setStampID(i);
1633		the_molecules[molIndex].setMyIndex(molIndex);
1634		the_molecules[molIndex].setGlobalIndex(molIndex);
1635		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1636	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1637	<	globalAtomIndex++;
1636	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1637	>	globalAtomCounter++;
1638		}
1639		molIndex++;
1640		}
#	Line 1308 | Line 1643 | void SimSetup::makeSysArrays(void){
1643
1644		#endif // is_mpi
1645
1646	<
1647	<	if (info[l].n_SRI){
1648	<	Exclude::createArray(info[l].n_SRI);
1314	<	the_excludes = new Exclude * [info[l].n_SRI];
1315	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	<	the_excludes[ex] = new Exclude(ex);
1317	<	}
1318	<	info[l].globalExcludes = new int;
1319	<	info[l].n_exclude = info[l].n_SRI;
1320	<	}
1321	<	else{
1322	<	Exclude::createArray(1);
1323	<	the_excludes = new Exclude * ;
1324	<	the_excludes[0] = new Exclude(0);
1325	<	the_excludes[0]->setPair(0, 0);
1326	<	info[l].globalExcludes = new int;
1327	<	info[l].globalExcludes[0] = 0;
1328	<	info[l].n_exclude = 0;
1329	<	}
1330	<
1646	>	info[l].globalExcludes = new int;
1647	>	info[l].globalExcludes[0] = 0;
1648	>
1649		// set the arrays into the SimInfo object
1650
1651		info[l].atoms = the_atoms;
1652		info[l].molecules = the_molecules;
1653		info[l].nGlobalExcludes = 0;
1654	<	info[l].excludes = the_excludes;
1337	<
1654	>
1655		the_ff->setSimInfo(info);
1656		}
1657		}
#	Line 1346 | Line 1663 | void SimSetup::makeIntegrator(void){
1663		NVT<RealIntegrator>* myNVT = NULL;
1664		NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1665		NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1666	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1667
1668		for (k = 0; k < nInfo; k++){
1669		switch (ensembleCase){
#	Line 1376 | Line 1694 | void SimSetup::makeIntegrator(void){
1694		else{
1695		sprintf(painCave.errMsg,
1696		"SimSetup error: If you use the NVT\n"
1697	<	"    ensemble, you must set tauThermostat.\n");
1697	>	"\tensemble, you must set tauThermostat.\n");
1698		painCave.isFatal = 1;
1699		simError();
1700		}
#	Line 1399 | Line 1717 | void SimSetup::makeIntegrator(void){
1717		else{
1718		sprintf(painCave.errMsg,
1719		"SimSetup error: If you use a constant pressure\n"
1720	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1720	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1721		painCave.isFatal = 1;
1722		simError();
1723		}
#	Line 1409 | Line 1727 | void SimSetup::makeIntegrator(void){
1727		else{
1728		sprintf(painCave.errMsg,
1729		"SimSetup error: If you use an NPT\n"
1730	<	"    ensemble, you must set tauThermostat.\n");
1730	>	"\tensemble, you must set tauThermostat.\n");
1731		painCave.isFatal = 1;
1732		simError();
1733		}
#	Line 1419 | Line 1737 | void SimSetup::makeIntegrator(void){
1737		else{
1738		sprintf(painCave.errMsg,
1739		"SimSetup error: If you use an NPT\n"
1740	<	"    ensemble, you must set tauBarostat.\n");
1740	>	"\tensemble, you must set tauBarostat.\n");
1741		painCave.isFatal = 1;
1742		simError();
1743		}
#	Line 1442 | Line 1760 | void SimSetup::makeIntegrator(void){
1760		else{
1761		sprintf(painCave.errMsg,
1762		"SimSetup error: If you use a constant pressure\n"
1763	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1763	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1764		painCave.isFatal = 1;
1765		simError();
1766		}
1767
1768		if (globals->haveTauThermostat())
1769		myNPTf->setTauThermostat(globals->getTauThermostat());
1770	+
1771		else{
1772		sprintf(painCave.errMsg,
1773		"SimSetup error: If you use an NPT\n"
1774	<	"    ensemble, you must set tauThermostat.\n");
1774	>	"\tensemble, you must set tauThermostat.\n");
1775		painCave.isFatal = 1;
1776		simError();
1777		}
1778
1779		if (globals->haveTauBarostat())
1780		myNPTf->setTauBarostat(globals->getTauBarostat());
1781	+
1782		else{
1783		sprintf(painCave.errMsg,
1784		"SimSetup error: If you use an NPT\n"
1785	<	"    ensemble, you must set tauBarostat.\n");
1785	>	"\tensemble, you must set tauBarostat.\n");
1786		painCave.isFatal = 1;
1787		simError();
1788		}
1789
1790		info->the_integrator = myNPTf;
1791	+	break;
1792	+
1793	+	case NPTxyz_ENS:
1794	+	if (globals->haveZconstraints()){
1795	+	setupZConstraint(info[k]);
1796	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1797	+	}
1798	+	else
1799	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1800	+
1801	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1802	+
1803	+	if (globals->haveTargetPressure())
1804	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1805	+	else{
1806	+	sprintf(painCave.errMsg,
1807	+	"SimSetup error: If you use a constant pressure\n"
1808	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1809	+	painCave.isFatal = 1;
1810	+	simError();
1811	+	}
1812	+
1813	+	if (globals->haveTauThermostat())
1814	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1815	+	else{
1816	+	sprintf(painCave.errMsg,
1817	+	"SimSetup error: If you use an NPT\n"
1818	+	"\tensemble, you must set tauThermostat.\n");
1819	+	painCave.isFatal = 1;
1820	+	simError();
1821	+	}
1822	+
1823	+	if (globals->haveTauBarostat())
1824	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1825	+	else{
1826	+	sprintf(painCave.errMsg,
1827	+	"SimSetup error: If you use an NPT\n"
1828	+	"\tensemble, you must set tauBarostat.\n");
1829	+	painCave.isFatal = 1;
1830	+	simError();
1831	+	}
1832	+
1833	+	info->the_integrator = myNPTxyz;
1834		break;
1835
1836		default:
#	Line 1515 | Line 1878 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1878		}
1879		else{
1880		sprintf(painCave.errMsg,
1881	<	"ZConstraint error: If you use an ZConstraint\n"
1882	<	" , you must set sample time.\n");
1881	>	"ZConstraint error: If you use a ZConstraint,\n"
1882	>	"\tyou must set zconsTime.\n");
1883		painCave.isFatal = 1;
1884		simError();
1885		}
#	Line 1531 | Line 1894 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1894		else{
1895		double defaultZConsTol = 0.01;
1896		sprintf(painCave.errMsg,
1897	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1898	<	" , default value %f is used.\n",
1897	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1898	>	"\tOOPSE will use a default value of %f.\n"
1899	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1900		defaultZConsTol);
1901		painCave.isFatal = 0;
1902		simError();
#	Line 1550 | Line 1914 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1914		}
1915		else{
1916		sprintf(painCave.errMsg,
1917	<	"ZConstraint Warning: User does not set force Subtraction policy, "
1918	<	"PolicyByMass is used\n");
1917	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1918	>	"\tOOPSE will use PolicyByMass.\n"
1919	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1920		painCave.isFatal = 0;
1921		simError();
1922		zconsForcePolicy->setData("BYMASS");
#	Line 1559 | Line 1924 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1924
1925		theInfo.addProperty(zconsForcePolicy);
1926
1927	+	//set zcons gap
1928	+	DoubleData* zconsGap = new DoubleData();
1929	+	zconsGap->setID(ZCONSGAP_ID);
1930	+
1931	+	if (globals->haveZConsGap()){
1932	+	zconsGap->setData(globals->getZconsGap());
1933	+	theInfo.addProperty(zconsGap);
1934	+	}
1935	+
1936	+	//set zcons fixtime
1937	+	DoubleData* zconsFixtime = new DoubleData();
1938	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1939	+
1940	+	if (globals->haveZConsFixTime()){
1941	+	zconsFixtime->setData(globals->getZconsFixtime());
1942	+	theInfo.addProperty(zconsFixtime);
1943	+	}
1944	+
1945	+	//set zconsUsingSMD
1946	+	IntData* zconsUsingSMD = new IntData();
1947	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1948	+
1949	+	if (globals->haveZConsUsingSMD()){
1950	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1951	+	theInfo.addProperty(zconsUsingSMD);
1952	+	}
1953	+
1954		//Determine the name of ouput file and add it into SimInfo's property list
1955		//Be careful, do not use inFileName, since it is a pointer which
1956		//point to a string at master node, and slave nodes do not contain that string
#	Line 1588 | Line 1980 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1980		tempParaItem.zPos = zconStamp[i]->getZpos();
1981		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1982		tempParaItem.kRatio = zconStamp[i]->getKratio();
1983	<
1983	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1984	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1985		zconsParaData->addItem(tempParaItem);
1986		}
1987
1988		//check the uniqueness of index
1989		if(!zconsParaData->isIndexUnique()){
1990		sprintf(painCave.errMsg,
1991	<	"ZConstraint Error: molIndex is not unique\n");
1991	>	"ZConstraint Error: molIndex is not unique!\n");
1992		painCave.isFatal = 1;
1993		simError();
1994		}
#	Line 1606 | Line 1999 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1999		//push data into siminfo, therefore, we can retrieve later
2000		theInfo.addProperty(zconsParaData);
2001		}
2002	+
2003	+	void SimSetup::makeMinimizer(){
2004	+
2005	+	OOPSEMinimizer* myOOPSEMinimizer;
2006	+	MinimizerParameterSet* param;
2007	+	char minimizerName[100];
2008	+
2009	+	for (int i = 0; i < nInfo; i++){
2010	+
2011	+	//prepare parameter set for minimizer
2012	+	param = new MinimizerParameterSet();
2013	+	param->setDefaultParameter();
2014	+
2015	+	if (globals->haveMinimizer()){
2016	+	param->setFTol(globals->getMinFTol());
2017	+	}
2018	+
2019	+	if (globals->haveMinGTol()){
2020	+	param->setGTol(globals->getMinGTol());
2021	+	}
2022	+
2023	+	if (globals->haveMinMaxIter()){
2024	+	param->setMaxIteration(globals->getMinMaxIter());
2025	+	}
2026	+
2027	+	if (globals->haveMinWriteFrq()){
2028	+	param->setMaxIteration(globals->getMinMaxIter());
2029	+	}
2030	+
2031	+	if (globals->haveMinWriteFrq()){
2032	+	param->setWriteFrq(globals->getMinWriteFrq());
2033	+	}
2034	+
2035	+	if (globals->haveMinStepSize()){
2036	+	param->setStepSize(globals->getMinStepSize());
2037	+	}
2038	+
2039	+	if (globals->haveMinLSMaxIter()){
2040	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2041	+	}
2042	+
2043	+	if (globals->haveMinLSTol()){
2044	+	param->setLineSearchTol(globals->getMinLSTol());
2045	+	}
2046	+
2047	+	strcpy(minimizerName, globals->getMinimizer());
2048	+
2049	+	if (!strcasecmp(minimizerName, "CG")){
2050	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2051	+	}
2052	+	else if (!strcasecmp(minimizerName, "SD")){
2053	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2054	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2055	+	}
2056	+	else{
2057	+	sprintf(painCave.errMsg,
2058	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2059	+	painCave.isFatal = 0;
2060	+	simError();
2061	+
2062	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2063	+	}
2064	+	info[i].the_integrator = myOOPSEMinimizer;
2065	+
2066	+	//store the minimizer into simInfo
2067	+	info[i].the_minimizer = myOOPSEMinimizer;
2068	+	info[i].has_minimizer = true;
2069	+	}
2070	+
2071	+	}

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