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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 1163 by gezelter, Wed May 12 14:30:12 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 90 | Line 122 | void SimSetup::createSim(void){
122		#endif // is_mpi
123
124		void SimSetup::createSim(void){
93	–	int i, j, k, globalAtomIndex;
125
126		// gather all of the information from the Bass file
127
#	Line 106 | 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	<
117	<	// make the integrator
118	<
119	<	makeIntegrator();
120	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 125 | 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, l;
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	<
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>
189		bond_pair* theBonds;
190		bend_set* theBends;
191		torsion_set* theTorsions;
192
193	+	set<int> skipList;
194
195	+	double phi, theta, psi;
196	+	char* molName;
197	+	char rbName[100];
198	+
199		//init the forceField paramters
200
201		the_ff->readParams();
202
152	–
203		// init the atoms
204
205	<	double ux, uy, uz, u, uSqr;
205	>	int nMembers, nNew, rb1, rb2;
206
207		for (k = 0; k < nInfo; k++){
208		the_ff->setSimInfo(&(info[k]));
209
210		atomOffset = 0;
211	<	excludeOffset = 0;
211	>
212		for (i = 0; i < info[k].n_mol; i++){
213		stampID = info[k].molecules[i].getStampID();
214	+	molName = comp_stamps[stampID]->getID();
215
216		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
217		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
218		molInfo.nBends = comp_stamps[stampID]->getNBends();
219		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
221	<
220	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221	>	molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222	>
223		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];
224
225	+	if (molInfo.nBonds > 0)
226	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227	+	else
228	+	molInfo.myBonds = NULL;
229	+
230	+	if (molInfo.nBends > 0)
231	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
232	+	else
233	+	molInfo.myBends = NULL;
234	+
235	+	if (molInfo.nTorsions > 0)
236	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237	+	else
238	+	molInfo.myTorsions = NULL;
239	+
240		theBonds = new bond_pair[molInfo.nBonds];
241		theBends = new bend_set[molInfo.nBends];
242		theTorsions = new torsion_set[molInfo.nTorsions];
243	<
243	>
244		// make the Atoms
245
246		for (j = 0; j < molInfo.nAtoms; j++){
247		currentAtom = comp_stamps[stampID]->getAtom(j);
248	+
249		if (currentAtom->haveOrientation()){
250		dAtom = new DirectionalAtom((j + atomOffset),
251		info[k].getConfiguration());
252		info[k].n_oriented++;
253		molInfo.myAtoms[j] = dAtom;
254
255	<	ux = currentAtom->getOrntX();
256	<	uy = currentAtom->getOrntY();
257	<	uz = currentAtom->getOrntZ();
255	>	// Directional Atoms have standard unit vectors which are oriented
256	>	// in space using the three Euler angles.  We assume the standard
257	>	// unit vector was originally along the z axis below.
258
259	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
259	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
260	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
261	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
262
263	<	u = sqrt(uSqr);
264	<	ux = ux / u;
199	<	uy = uy / u;
200	<	uz = uz / u;
201	<
202	<	dAtom->setSUx(ux);
203	<	dAtom->setSUy(uy);
204	<	dAtom->setSUz(uz);
263	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
264	>
265		}
266		else{
267	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
268	<	info[k].getConfiguration());
267	>
268	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
269	>
270		}
210	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
271
272	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
273		#ifdef IS_MPI
274
275	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
276
277		#endif // is_mpi
278		}
#	Line 222 | Line 283 | void SimSetup::makeMolecules(void){
283		theBonds[j].a = currentBond->getA() + atomOffset;
284		theBonds[j].b = currentBond->getB() + atomOffset;
285
286	<	exI = theBonds[j].a;
287	<	exJ = theBonds[j].b;
286	>	tempI = theBonds[j].a;
287	>	tempJ = theBonds[j].b;
288
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	–	}
289		#ifdef IS_MPI
290	<	tempEx = exI;
291	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
292	<	tempEx = exJ;
293	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
290	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
291	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
292	>	#else
293	>	exI = tempI + 1;
294	>	exJ = tempJ + 1;
295	>	#endif
296
297	<	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
297	>	info[k].excludes->addPair(exI, exJ);
298		}
246	–	excludeOffset += molInfo.nBonds;
299
300		//make the bends
301		for (j = 0; j < molInfo.nBends; j++){
#	Line 293 | Line 345 | void SimSetup::makeMolecules(void){
345		}
346		}
347
348	<	if (!theBends[j].isGhost){
349	<	exI = theBends[j].a;
350	<	exJ = theBends[j].c;
351	<	}
352	<	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	<	}
348	>	if (theBends[j].isGhost) {
349	>
350	>	tempI = theBends[j].a;
351	>	tempJ = theBends[j].b;
352	>
353		#ifdef IS_MPI
354	<	tempEx = exI;
355	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
356	<	tempEx = exJ;
357	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
354	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
355	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
356	>	#else
357	>	exI = tempI + 1;
358	>	exJ = tempJ + 1;
359	>	#endif
360	>	info[k].excludes->addPair(exI, exJ);
361
362	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
363	<	#else  // isn't MPI
364	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
365	<	#endif  //is_mpi
362	>	} else {
363	>
364	>	tempI = theBends[j].a;
365	>	tempJ = theBends[j].b;
366	>	tempK = theBends[j].c;
367	>
368	>	#ifdef IS_MPI
369	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
370	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
371	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
372	>	#else
373	>	exI = tempI + 1;
374	>	exJ = tempJ + 1;
375	>	exK = tempK + 1;
376	>	#endif
377	>
378	>	info[k].excludes->addPair(exI, exK);
379	>	info[k].excludes->addPair(exI, exJ);
380	>	info[k].excludes->addPair(exJ, exK);
381	>	}
382		}
322	–	excludeOffset += molInfo.nBends;
383
384		for (j = 0; j < molInfo.nTorsions; j++){
385		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 328 | Line 388 | void SimSetup::makeMolecules(void){
388		theTorsions[j].c = currentTorsion->getC() + atomOffset;
389		theTorsions[j].d = currentTorsion->getD() + atomOffset;
390
391	<	exI = theTorsions[j].a;
392	<	exJ = theTorsions[j].d;
391	>	tempI = theTorsions[j].a;
392	>	tempJ = theTorsions[j].b;
393	>	tempK = theTorsions[j].c;
394	>	tempL = theTorsions[j].d;
395
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	–	}
396		#ifdef IS_MPI
397	<	tempEx = exI;
398	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
399	<	tempEx = exJ;
400	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
397	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
398	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
399	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
400	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
401	>	#else
402	>	exI = tempI + 1;
403	>	exJ = tempJ + 1;
404	>	exK = tempK + 1;
405	>	exL = tempL + 1;
406	>	#endif
407
408	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
409	<	#else  // isn't MPI
410	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
411	<	#endif  //is_mpi
408	>	info[k].excludes->addPair(exI, exJ);
409	>	info[k].excludes->addPair(exI, exK);
410	>	info[k].excludes->addPair(exI, exL);
411	>	info[k].excludes->addPair(exJ, exK);
412	>	info[k].excludes->addPair(exJ, exL);
413	>	info[k].excludes->addPair(exK, exL);
414		}
351	–	excludeOffset += molInfo.nTorsions;
415
416	+
417	+	molInfo.myRigidBodies.clear();
418	+
419	+	for (j = 0; j < molInfo.nRigidBodies; j++){
420
421	<	// send the arrays off to the forceField for init.
421	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422	>	nMembers = currentRigidBody->getNMembers();
423
424	+	// Create the Rigid Body:
425	+
426	+	myRB = new RigidBody();
427	+
428	+	sprintf(rbName,"%s_RB_%d", molName, j);
429	+	myRB->setType(rbName);
430	+
431	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
432	+
433	+	// molI is atom numbering inside this molecule
434	+	molI = currentRigidBody->getMember(rb1);
435	+
436	+	// tempI is atom numbering on local processor
437	+	tempI = molI + atomOffset;
438	+
439	+	// currentAtom is the AtomStamp (which we need for
440	+	// rigid body reference positions)
441	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
442	+
443	+	// When we add to the rigid body, add the atom itself and
444	+	// the stamp info:
445	+
446	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
447	+
448	+	// Add this atom to the Skip List for the integrators
449	+	#ifdef IS_MPI
450	+	slI = info[k].atoms[tempI]->getGlobalIndex();
451	+	#else
452	+	slI = tempI;
453	+	#endif
454	+	skipList.insert(slI);
455	+
456	+	}
457	+
458	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
459	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
460	+
461	+	tempI = currentRigidBody->getMember(rb1);
462	+	tempJ = currentRigidBody->getMember(rb2);
463	+
464	+	// Some explanation is required here.
465	+	// Fortran indexing starts at 1, while c indexing starts at 0
466	+	// Also, in parallel computations, the GlobalIndex is
467	+	// used for the exclude list:
468	+
469	+	#ifdef IS_MPI
470	+	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471	+	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472	+	#else
473	+	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474	+	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475	+	#endif
476	+
477	+	info[k].excludes->addPair(exI, exJ);
478	+
479	+	}
480	+	}
481	+
482	+	molInfo.myRigidBodies.push_back(myRB);
483	+	info[k].rigidBodies.push_back(myRB);
484	+	}
485	+
486	+
487	+	//create cutoff group for molecule
488	+	molInfo.myCutoffGroups.clear();
489	+	for (j = 0; j < molInfo.nCutoffGroups; j++){
490	+
491	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492	+	nMembers = currentCutoffGroup->getNMembers();
493	+
494	+	myCutoffGroup = new CutoffGroup();
495	+
496	+	for (int cg = 0; cg < nMembers; cg++) {
497	+
498	+	// molI is atom numbering inside this molecule
499	+	molI = currentCutoffGroup->getMember(cg);
500	+
501	+	// tempI is atom numbering on local processor
502	+	tempI = molI + atomOffset;
503	+
504	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
505	+	}
506	+
507	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
508	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509	+
510	+
511	+
512	+	// After this is all set up, scan through the atoms to
513	+	// see if they can be added to the integrableObjects:
514	+
515	+	molInfo.myIntegrableObjects.clear();
516	+
517	+
518	+	for (j = 0; j < molInfo.nAtoms; j++){
519	+
520	+	#ifdef IS_MPI
521	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
522	+	#else
523	+	slJ = j+atomOffset;
524	+	#endif
525	+
526	+	// if they aren't on the skip list, then they can be integrated
527	+
528	+	if (skipList.find(slJ) == skipList.end()) {
529	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
530	+	info[k].integrableObjects.push_back(mySD);
531	+	molInfo.myIntegrableObjects.push_back(mySD);
532	+	}
533	+	}
534	+
535	+	// all rigid bodies are integrated:
536	+
537	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
538	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
539	+	info[k].integrableObjects.push_back(mySD);
540	+	molInfo.myIntegrableObjects.push_back(mySD);
541	+	}
542	+
543	+
544	+	// send the arrays off to the forceField for init.
545	+
546		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
547		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
548		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
549		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
550		theTorsions);
551
362	–
552		info[k].molecules[i].initialize(molInfo);
553
554
#	Line 367 | Line 556 | void SimSetup::makeMolecules(void){
556		delete[] theBonds;
557		delete[] theBends;
558		delete[] theTorsions;
559	<	}
559	>	}
560		}
561
562		#ifdef IS_MPI
#	Line 375 | Line 564 | void SimSetup::makeMolecules(void){
564		MPIcheckPoint();
565		#endif // is_mpi
566
378	–	// clean up the forcefield
379	–
380	–	the_ff->calcRcut();
381	–	the_ff->cleanMe();
567		}
568
569		void SimSetup::initFromBass(void){
#	Line 551 | Line 736 | void SimSetup::gatherInfo(void){
736
737
738		void SimSetup::gatherInfo(void){
739	<	int i, j, k;
739	>	int i;
740
741		ensembleCase = -1;
742		ffCase = -1;
#	Line 579 | Line 764 | void SimSetup::gatherInfo(void){
764		else if (!strcasecmp(force_field, "EAM")){
765		ffCase = FF_EAM;
766		}
767	+	else if (!strcasecmp(force_field, "WATER")){
768	+	ffCase = FF_H2O;
769	+	}
770		else{
771		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
772		force_field);
#	Line 602 | Line 790 | void SimSetup::gatherInfo(void){
790		else if (!strcasecmp(ensemble, "NPTf")){
791		ensembleCase = NPTf_ENS;
792		}
793	+	else if (!strcasecmp(ensemble, "NPTxyz")){
794	+	ensembleCase = NPTxyz_ENS;
795	+	}
796		else{
797		sprintf(painCave.errMsg,
798	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
799	<	"reverting to NVE for this simulation.\n",
798	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
799	>	"\treverting to NVE for this simulation.\n",
800		ensemble);
801		painCave.isFatal = 0;
802		simError();
#	Line 637 | Line 828 | void SimSetup::gatherInfo(void){
828		if (!the_components[i]->haveNMol()){
829		// we have a problem
830		sprintf(painCave.errMsg,
831	<	"SimSetup Error. No global NMol or component NMol"
832	<	" given. Cannot calculate the number of atoms.\n");
831	>	"SimSetup Error. No global NMol or component NMol given.\n"
832	>	"\tCannot calculate the number of atoms.\n");
833		painCave.isFatal = 1;
834		simError();
835		}
#	Line 656 | Line 847 | void SimSetup::gatherInfo(void){
847		" Please give nMol in the components.\n");
848		painCave.isFatal = 1;
849		simError();
850	+	}
851	+
852	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
853	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
854	+	sprintf(painCave.errMsg,
855	+	"Sample time is not divisible by dt.\n"
856	+	"\tThis will result in samples that are not uniformly\n"
857	+	"\tdistributed in time.  If this is a problem, change\n"
858	+	"\tyour sampleTime variable.\n");
859	+	painCave.isFatal = 0;
860	+	simError();
861		}
862
863	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
864	+	sprintf(painCave.errMsg,
865	+	"Status time is not divisible by dt.\n"
866	+	"\tThis will result in status reports that are not uniformly\n"
867	+	"\tdistributed in time.  If this is a problem, change \n"
868	+	"\tyour statusTime variable.\n");
869	+	painCave.isFatal = 0;
870	+	simError();
871	+	}
872	+
873	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
874	+	sprintf(painCave.errMsg,
875	+	"Thermal time is not divisible by dt.\n"
876	+	"\tThis will result in thermalizations that are not uniformly\n"
877	+	"\tdistributed in time.  If this is a problem, change \n"
878	+	"\tyour thermalTime variable.\n");
879	+	painCave.isFatal = 0;
880	+	simError();
881	+	}
882	+
883	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
884	+	sprintf(painCave.errMsg,
885	+	"Reset time is not divisible by dt.\n"
886	+	"\tThis will result in integrator resets that are not uniformly\n"
887	+	"\tdistributed in time.  If this is a problem, change\n"
888	+	"\tyour resetTime variable.\n");
889	+	painCave.isFatal = 0;
890	+	simError();
891	+	}
892	+
893		// set the status, sample, and thermal kick times
894
895		for (i = 0; i < nInfo; i++){
896		if (globals->haveSampleTime()){
897		info[i].sampleTime = globals->getSampleTime();
898		info[i].statusTime = info[i].sampleTime;
667	–	info[i].thermalTime = info[i].sampleTime;
899		}
900		else{
901		info[i].sampleTime = globals->getRunTime();
902		info[i].statusTime = info[i].sampleTime;
672	–	info[i].thermalTime = info[i].sampleTime;
903		}
904
905		if (globals->haveStatusTime()){
#	Line 678 | Line 908 | void SimSetup::gatherInfo(void){
908
909		if (globals->haveThermalTime()){
910		info[i].thermalTime = globals->getThermalTime();
911	+	} else {
912	+	info[i].thermalTime = globals->getRunTime();
913		}
914
915		info[i].resetIntegrator = 0;
#	Line 687 | Line 919 | void SimSetup::gatherInfo(void){
919		}
920
921		// check for the temperature set flag
922	<
922	>
923		if (globals->haveTempSet())
924		info[i].setTemp = globals->getTempSet();
925
926	<	// get some of the tricky things that may still be in the globals
926	>	// check for the extended State init
927
928	<	double boxVector[3];
929	<	if (globals->haveBox()){
930	<	boxVector[0] = globals->getBox();
699	<	boxVector[1] = globals->getBox();
700	<	boxVector[2] = globals->getBox();
701	<
702	<	info[i].setBox(boxVector);
703	<	}
704	<	else if (globals->haveDensity()){
705	<	double vol;
706	<	vol = (double) tot_nmol / globals->getDensity();
707	<	boxVector[0] = pow(vol, (1.0 / 3.0));
708	<	boxVector[1] = boxVector[0];
709	<	boxVector[2] = boxVector[0];
710	<
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();
727	<	}
728	<	boxVector[1] = globals->getBoxY();
729	<
730	<	if (!globals->haveBoxZ()){
731	<	sprintf(painCave.errMsg,
732	<	"SimSetup error, no periodic BoxZ size given.\n");
733	<	painCave.isFatal = 1;
734	<	simError();
735	<	}
736	<	boxVector[2] = globals->getBoxZ();
737	<
738	<	info[i].setBox(boxVector);
739	<	}
928	>	info[i].useInitXSstate = globals->getUseInitXSstate();
929	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
930	>
931		}
932	<
932	>
933		//setup seed for random number generator
934		int seedValue;
935
#	Line 778 | Line 969 | void SimSetup::gatherInfo(void){
969		for (int i = 0; i < nInfo; i++){
970		info[i].setSeed(seedValue);
971		}
972	<
972	>
973		#ifdef IS_MPI
974	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
974	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
975		MPIcheckPoint();
976		#endif // is_mpi
977		}
#	Line 789 | Line 980 | void SimSetup::finalInfoCheck(void){
980		void SimSetup::finalInfoCheck(void){
981		int index;
982		int usesDipoles;
983	+	int usesCharges;
984		int i;
985
986		for (i = 0; i < nInfo; i++){
#	Line 800 | Line 992 | void SimSetup::finalInfoCheck(void){
992		usesDipoles = (info[i].atoms[index])->hasDipole();
993		index++;
994		}
995	<
995	>	index = 0;
996	>	usesCharges = 0;
997	>	while ((index < info[i].n_atoms) && !usesCharges){
998	>	usesCharges= (info[i].atoms[index])->hasCharge();
999	>	index++;
1000	>	}
1001		#ifdef IS_MPI
1002		int myUse = usesDipoles;
1003		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1004		#endif //is_mpi
1005
1006	<	double theEcr, theEst;
1006	>	double theRcut, theRsw;
1007
1008	+	if (globals->haveRcut()) {
1009	+	theRcut = globals->getRcut();
1010	+
1011	+	if (globals->haveRsw())
1012	+	theRsw = globals->getRsw();
1013	+	else
1014	+	theRsw = theRcut;
1015	+
1016	+	info[i].setDefaultRcut(theRcut, theRsw);
1017	+
1018	+	} else {
1019	+
1020	+	the_ff->calcRcut();
1021	+	theRcut = info[i].getRcut();
1022	+
1023	+	if (globals->haveRsw())
1024	+	theRsw = globals->getRsw();
1025	+	else
1026	+	theRsw = theRcut;
1027	+
1028	+	info[i].setDefaultRcut(theRcut, theRsw);
1029	+	}
1030	+
1031		if (globals->getUseRF()){
1032		info[i].useReactionField = 1;
1033	<
1034	<	if (!globals->haveECR()){
1033	>
1034	>	if (!globals->haveRcut()){
1035		sprintf(painCave.errMsg,
1036	<	"SimSetup Warning: using default value of 1/2 the smallest "
1037	<	"box length for the electrostaticCutoffRadius.\n"
1038	<	"I hope you have a very fast processor!\n");
1036	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1037	>	"\tOOPSE will use a default value of 15.0 angstroms"
1038	>	"\tfor the cutoffRadius.\n");
1039		painCave.isFatal = 0;
1040		simError();
1041	<	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;
1041	>	theRcut = 15.0;
1042		}
1043		else{
1044	<	theEcr = globals->getECR();
1044	>	theRcut = globals->getRcut();
1045		}
1046
1047	<	if (!globals->haveEST()){
1047	>	if (!globals->haveRsw()){
1048		sprintf(painCave.errMsg,
1049	<	"SimSetup Warning: using default value of 0.05 * the "
1050	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1049	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1050	>	"\tOOPSE will use a default value of\n"
1051	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1052		painCave.isFatal = 0;
1053		simError();
1054	<	theEst = 0.05 * theEcr;
1054	>	theRsw = 0.95 * theRcut;
1055		}
1056		else{
1057	<	theEst = globals->getEST();
1057	>	theRsw = globals->getRsw();
1058		}
1059
1060	<	info[i].setEcr(theEcr, theEst);
1060	>	info[i].setDefaultRcut(theRcut, theRsw);
1061
1062		if (!globals->haveDielectric()){
1063		sprintf(painCave.errMsg,
1064	<	"SimSetup Error: You are trying to use Reaction Field without"
1065	<	"setting a dielectric constant!\n");
1064	>	"SimSetup Error: No Dielectric constant was set.\n"
1065	>	"\tYou are trying to use Reaction Field without"
1066	>	"\tsetting a dielectric constant!\n");
1067		painCave.isFatal = 1;
1068		simError();
1069		}
1070		info[i].dielectric = globals->getDielectric();
1071		}
1072		else{
1073	<	if (usesDipoles){
858	<	if (!globals->haveECR()){
859	<	sprintf(painCave.errMsg,
860	<	"SimSetup Warning: using default value of 1/2 the smallest "
861	<	"box length for the electrostaticCutoffRadius.\n"
862	<	"I hope you have a very fast processor!\n");
863	<	painCave.isFatal = 0;
864	<	simError();
865	<	double smallest;
866	<	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	<	}
873	<	else{
874	<	theEcr = globals->getECR();
875	<	}
1073	>	if (usesDipoles || usesCharges){
1074
1075	<	if (!globals->haveEST()){
1075	>	if (!globals->haveRcut()){
1076		sprintf(painCave.errMsg,
1077	<	"SimSetup Warning: using default value of 0.05 * the "
1078	<	"electrostaticCutoffRadius for the "
1079	<	"electrostaticSkinThickness\n");
1077	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1078	>	"\tOOPSE will use a default value of 15.0 angstroms"
1079	>	"\tfor the cutoffRadius.\n");
1080		painCave.isFatal = 0;
1081		simError();
1082	<	theEst = 0.05 * theEcr;
1082	>	theRcut = 15.0;
1083	>	}
1084	>	else{
1085	>	theRcut = globals->getRcut();
1086		}
1087	+
1088	+	if (!globals->haveRsw()){
1089	+	sprintf(painCave.errMsg,
1090	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1091	+	"\tOOPSE will use a default value of\n"
1092	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1093	+	painCave.isFatal = 0;
1094	+	simError();
1095	+	theRsw = 0.95 * theRcut;
1096	+	}
1097		else{
1098	<	theEst = globals->getEST();
1098	>	theRsw = globals->getRsw();
1099		}
1100	<
1101	<	info[i].setEcr(theEcr, theEst);
1100	>
1101	>	info[i].setDefaultRcut(theRcut, theRsw);
1102	>
1103		}
1104		}
1105		}
894	–
1106		#ifdef IS_MPI
1107		strcpy(checkPointMsg, "post processing checks out");
1108		MPIcheckPoint();
1109		#endif // is_mpi
899	–	}
1110
1111	+	// clean up the forcefield
1112	+	the_ff->cleanMe();
1113	+	}
1114	+
1115		void SimSetup::initSystemCoords(void){
1116		int i;
1117
#	Line 914 | Line 1128 | void SimSetup::initSystemCoords(void){
1128		if (worldRank == 0){
1129		#endif //is_mpi
1130		inName = globals->getInitialConfig();
917	–	double* tempDouble = new double[1000000];
1131		fileInit = new InitializeFromFile(inName);
1132		#ifdef IS_MPI
1133		}
#	Line 926 | Line 1139 | void SimSetup::initSystemCoords(void){
1139		delete fileInit;
1140		}
1141		else{
1142	<	#ifdef IS_MPI
930	<
1142	>
1143		// no init from bass
1144	<
1144	>
1145		sprintf(painCave.errMsg,
1146	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1147	<	painCave.isFatal;
1146	>	"Cannot intialize a simulation without an initial configuration file.\n");
1147	>	painCave.isFatal = 1;;
1148		simError();
1149	<
938	<	#else
939	<
940	<	initFromBass();
941	<
942	<
943	<	#endif
1149	>
1150		}
1151
1152		#ifdef IS_MPI
#	Line 1094 | Line 1300 | void SimSetup::createFF(void){
1300		the_ff = new EAM_FF();
1301		break;
1302
1303	+	case FF_H2O:
1304	+	the_ff = new WATER();
1305	+	break;
1306	+
1307		default:
1308		sprintf(painCave.errMsg,
1309		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1114 | Line 1324 | void SimSetup::compList(void){
1324		LinkedMolStamp* headStamp = new LinkedMolStamp();
1325		LinkedMolStamp* currentStamp = NULL;
1326		comp_stamps = new MoleculeStamp * [n_components];
1327	+	bool haveCutoffGroups;
1328
1329	+	haveCutoffGroups = false;
1330	+
1331		// make an array of molecule stamps that match the components used.
1332		// also extract the used stamps out into a separate linked list
1333
#	Line 1149 | Line 1362 | void SimSetup::compList(void){
1362		headStamp->add(currentStamp);
1363		comp_stamps[i] = headStamp->match(id);
1364		}
1365	+
1366	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1367	+	haveCutoffGroups = true;
1368		}
1369	+
1370	+	for (i = 0; i < nInfo; i++)
1371	+	info[i].haveCutoffGroups = haveCutoffGroups;
1372
1373		#ifdef IS_MPI
1374		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1158 | Line 1377 | void SimSetup::calcSysValues(void){
1377		}
1378
1379		void SimSetup::calcSysValues(void){
1380	<	int i, j, k;
1380	>	int i;
1381
1382		int* molMembershipArray;
1383
#	Line 1166 | Line 1385 | void SimSetup::calcSysValues(void){
1385		tot_bonds = 0;
1386		tot_bends = 0;
1387		tot_torsions = 0;
1388	+	tot_rigid = 0;
1389		for (i = 0; i < n_components; i++){
1390		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1391		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1392		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1393		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1394	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1395		}
1396	<
1396	>
1397		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1398		molMembershipArray = new int[tot_atoms];
1399
#	Line 1194 | Line 1415 | void SimSetup::mpiMolDivide(void){
1415		int i, j, k;
1416		int localMol, allMol;
1417		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1418	+	int local_rigid;
1419	+	vector<int> globalMolIndex;
1420
1421		mpiSim = new mpiSimulation(info);
1422
1423	<	globalIndex = mpiSim->divideLabor();
1423	>	mpiSim->divideLabor();
1424	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1425	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1426
1427		// set up the local variables
1428
#	Line 1210 | Line 1435 | void SimSetup::mpiMolDivide(void){
1435		local_bonds = 0;
1436		local_bends = 0;
1437		local_torsions = 0;
1438	<	globalAtomIndex = 0;
1438	>	local_rigid = 0;
1439	>	globalAtomCounter = 0;
1440
1215	–
1441		for (i = 0; i < n_components; i++){
1442		for (j = 0; j < components_nmol[i]; j++){
1443		if (mol2proc[allMol] == worldRank){
#	Line 1220 | Line 1445 | void SimSetup::mpiMolDivide(void){
1445		local_bonds += comp_stamps[i]->getNBonds();
1446		local_bends += comp_stamps[i]->getNBends();
1447		local_torsions += comp_stamps[i]->getNTorsions();
1448	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1449		localMol++;
1450		}
1451		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1452	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1453	<	globalAtomIndex++;
1452	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1453	>	globalAtomCounter++;
1454		}
1455
1456		allMol++;
#	Line 1233 | Line 1459 | void SimSetup::mpiMolDivide(void){
1459		local_SRI = local_bonds + local_bends + local_torsions;
1460
1461		info[0].n_atoms = mpiSim->getMyNlocal();
1462	+
1463
1464		if (local_atoms != info[0].n_atoms){
1465		sprintf(painCave.errMsg,
1466	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1467	<	" localAtom (%d) are not equal.\n",
1466	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1467	>	"\tlocalAtom (%d) are not equal.\n",
1468		info[0].n_atoms, local_atoms);
1469		painCave.isFatal = 1;
1470		simError();
#	Line 1257 | Line 1484 | void SimSetup::makeSysArrays(void){
1484
1485
1486		void SimSetup::makeSysArrays(void){
1487	<	int i, j, k, l;
1487	>
1488	>	#ifndef IS_MPI
1489	>	int k, j;
1490	>	#endif // is_mpi
1491	>	int i, l;
1492
1493		Atom** the_atoms;
1494		Molecule* the_molecules;
1264	–	Exclude** the_excludes;
1495
1266	–
1496		for (l = 0; l < nInfo; l++){
1497		// create the atom and short range interaction arrays
1498
#	Line 1289 | Line 1518 | void SimSetup::makeSysArrays(void){
1518		#else // is_mpi
1519
1520		molIndex = 0;
1521	<	globalAtomIndex = 0;
1521	>	globalAtomCounter = 0;
1522		for (i = 0; i < n_components; i++){
1523		for (j = 0; j < components_nmol[i]; j++){
1524		the_molecules[molIndex].setStampID(i);
1525		the_molecules[molIndex].setMyIndex(molIndex);
1526		the_molecules[molIndex].setGlobalIndex(molIndex);
1527		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1528	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1529	<	globalAtomIndex++;
1528	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1529	>	globalAtomCounter++;
1530		}
1531		molIndex++;
1532		}
#	Line 1306 | Line 1535 | void SimSetup::makeSysArrays(void){
1535
1536		#endif // is_mpi
1537
1538	<
1539	<	if (info[l].n_SRI){
1540	<	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	<
1538	>	info[l].globalExcludes = new int;
1539	>	info[l].globalExcludes[0] = 0;
1540	>
1541		// set the arrays into the SimInfo object
1542
1543		info[l].atoms = the_atoms;
1544		info[l].molecules = the_molecules;
1545		info[l].nGlobalExcludes = 0;
1546	<	info[l].excludes = the_excludes;
1335	<
1546	>
1547		the_ff->setSimInfo(info);
1548		}
1549		}
#	Line 1340 | Line 1551 | void SimSetup::makeIntegrator(void){
1551		void SimSetup::makeIntegrator(void){
1552		int k;
1553
1554	+	NVE<RealIntegrator>* myNVE = NULL;
1555		NVT<RealIntegrator>* myNVT = NULL;
1556		NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1557		NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1558	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1559
1560		for (k = 0; k < nInfo; k++){
1561		switch (ensembleCase){
1562		case NVE_ENS:
1563		if (globals->haveZconstraints()){
1564		setupZConstraint(info[k]);
1565	<	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1565	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1566		}
1567	<	else
1568	<	new NVE<RealIntegrator>(&(info[k]), the_ff);
1567	>	else{
1568	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1569	>	}
1570	>
1571	>	info->the_integrator = myNVE;
1572		break;
1573
1574		case NVT_ENS:
#	Line 1370 | Line 1586 | void SimSetup::makeIntegrator(void){
1586		else{
1587		sprintf(painCave.errMsg,
1588		"SimSetup error: If you use the NVT\n"
1589	<	"    ensemble, you must set tauThermostat.\n");
1589	>	"\tensemble, you must set tauThermostat.\n");
1590		painCave.isFatal = 1;
1591		simError();
1592		}
1593	+
1594	+	info->the_integrator = myNVT;
1595		break;
1596
1597		case NPTi_ENS:
#	Line 1391 | Line 1609 | void SimSetup::makeIntegrator(void){
1609		else{
1610		sprintf(painCave.errMsg,
1611		"SimSetup error: If you use a constant pressure\n"
1612	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1612	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1613		painCave.isFatal = 1;
1614		simError();
1615		}
#	Line 1401 | Line 1619 | void SimSetup::makeIntegrator(void){
1619		else{
1620		sprintf(painCave.errMsg,
1621		"SimSetup error: If you use an NPT\n"
1622	<	"    ensemble, you must set tauThermostat.\n");
1622	>	"\tensemble, you must set tauThermostat.\n");
1623		painCave.isFatal = 1;
1624		simError();
1625		}
#	Line 1411 | Line 1629 | void SimSetup::makeIntegrator(void){
1629		else{
1630		sprintf(painCave.errMsg,
1631		"SimSetup error: If you use an NPT\n"
1632	<	"    ensemble, you must set tauBarostat.\n");
1632	>	"\tensemble, you must set tauBarostat.\n");
1633		painCave.isFatal = 1;
1634		simError();
1635		}
1636	+
1637	+	info->the_integrator = myNPTi;
1638		break;
1639
1640		case NPTf_ENS:
#	Line 1432 | Line 1652 | void SimSetup::makeIntegrator(void){
1652		else{
1653		sprintf(painCave.errMsg,
1654		"SimSetup error: If you use a constant pressure\n"
1655	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1655	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1656		painCave.isFatal = 1;
1657		simError();
1658		}
1659
1660		if (globals->haveTauThermostat())
1661		myNPTf->setTauThermostat(globals->getTauThermostat());
1662	+
1663		else{
1664		sprintf(painCave.errMsg,
1665		"SimSetup error: If you use an NPT\n"
1666	<	"    ensemble, you must set tauThermostat.\n");
1666	>	"\tensemble, you must set tauThermostat.\n");
1667		painCave.isFatal = 1;
1668		simError();
1669		}
1670
1671		if (globals->haveTauBarostat())
1672		myNPTf->setTauBarostat(globals->getTauBarostat());
1673	+
1674		else{
1675		sprintf(painCave.errMsg,
1676		"SimSetup error: If you use an NPT\n"
1677	<	"    ensemble, you must set tauBarostat.\n");
1677	>	"\tensemble, you must set tauBarostat.\n");
1678		painCave.isFatal = 1;
1679		simError();
1680		}
1681	+
1682	+	info->the_integrator = myNPTf;
1683		break;
1684
1685	+	case NPTxyz_ENS:
1686	+	if (globals->haveZconstraints()){
1687	+	setupZConstraint(info[k]);
1688	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1689	+	}
1690	+	else
1691	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1692	+
1693	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1694	+
1695	+	if (globals->haveTargetPressure())
1696	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1697	+	else{
1698	+	sprintf(painCave.errMsg,
1699	+	"SimSetup error: If you use a constant pressure\n"
1700	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1701	+	painCave.isFatal = 1;
1702	+	simError();
1703	+	}
1704	+
1705	+	if (globals->haveTauThermostat())
1706	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1707	+	else{
1708	+	sprintf(painCave.errMsg,
1709	+	"SimSetup error: If you use an NPT\n"
1710	+	"\tensemble, you must set tauThermostat.\n");
1711	+	painCave.isFatal = 1;
1712	+	simError();
1713	+	}
1714	+
1715	+	if (globals->haveTauBarostat())
1716	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1717	+	else{
1718	+	sprintf(painCave.errMsg,
1719	+	"SimSetup error: If you use an NPT\n"
1720	+	"\tensemble, you must set tauBarostat.\n");
1721	+	painCave.isFatal = 1;
1722	+	simError();
1723	+	}
1724	+
1725	+	info->the_integrator = myNPTxyz;
1726	+	break;
1727	+
1728		default:
1729		sprintf(painCave.errMsg,
1730		"SimSetup Error. Unrecognized ensemble in case statement.\n");
#	Line 1503 | Line 1770 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1770		}
1771		else{
1772		sprintf(painCave.errMsg,
1773	<	"ZConstraint error: If you use an ZConstraint\n"
1774	<	" , you must set sample time.\n");
1773	>	"ZConstraint error: If you use a ZConstraint,\n"
1774	>	"\tyou must set zconsTime.\n");
1775		painCave.isFatal = 1;
1776		simError();
1777		}
#	Line 1519 | Line 1786 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1786		else{
1787		double defaultZConsTol = 0.01;
1788		sprintf(painCave.errMsg,
1789	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1790	<	" , default value %f is used.\n",
1789	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1790	>	"\tOOPSE will use a default value of %f.\n"
1791	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1792		defaultZConsTol);
1793		painCave.isFatal = 0;
1794		simError();
#	Line 1538 | Line 1806 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1806		}
1807		else{
1808		sprintf(painCave.errMsg,
1809	<	"ZConstraint Warning: User does not set force Subtraction policy, "
1810	<	"PolicyByMass is used\n");
1809	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1810	>	"\tOOPSE will use PolicyByMass.\n"
1811	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1812		painCave.isFatal = 0;
1813		simError();
1814		zconsForcePolicy->setData("BYMASS");
#	Line 1547 | Line 1816 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1816
1817		theInfo.addProperty(zconsForcePolicy);
1818
1819	+	//set zcons gap
1820	+	DoubleData* zconsGap = new DoubleData();
1821	+	zconsGap->setID(ZCONSGAP_ID);
1822	+
1823	+	if (globals->haveZConsGap()){
1824	+	zconsGap->setData(globals->getZconsGap());
1825	+	theInfo.addProperty(zconsGap);
1826	+	}
1827	+
1828	+	//set zcons fixtime
1829	+	DoubleData* zconsFixtime = new DoubleData();
1830	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1831	+
1832	+	if (globals->haveZConsFixTime()){
1833	+	zconsFixtime->setData(globals->getZconsFixtime());
1834	+	theInfo.addProperty(zconsFixtime);
1835	+	}
1836	+
1837	+	//set zconsUsingSMD
1838	+	IntData* zconsUsingSMD = new IntData();
1839	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1840	+
1841	+	if (globals->haveZConsUsingSMD()){
1842	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1843	+	theInfo.addProperty(zconsUsingSMD);
1844	+	}
1845	+
1846		//Determine the name of ouput file and add it into SimInfo's property list
1847		//Be careful, do not use inFileName, since it is a pointer which
1848		//point to a string at master node, and slave nodes do not contain that string
#	Line 1576 | Line 1872 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1872		tempParaItem.zPos = zconStamp[i]->getZpos();
1873		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1874		tempParaItem.kRatio = zconStamp[i]->getKratio();
1875	<
1875	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1876	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1877		zconsParaData->addItem(tempParaItem);
1878		}
1879
1880		//check the uniqueness of index
1881		if(!zconsParaData->isIndexUnique()){
1882		sprintf(painCave.errMsg,
1883	<	"ZConstraint Error: molIndex is not unique\n");
1883	>	"ZConstraint Error: molIndex is not unique!\n");
1884		painCave.isFatal = 1;
1885		simError();
1886		}
#	Line 1594 | Line 1891 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1891		//push data into siminfo, therefore, we can retrieve later
1892		theInfo.addProperty(zconsParaData);
1893		}
1894	+
1895	+	void SimSetup::makeMinimizer(){
1896	+
1897	+	OOPSEMinimizer* myOOPSEMinimizer;
1898	+	MinimizerParameterSet* param;
1899	+	char minimizerName[100];
1900	+
1901	+	for (int i = 0; i < nInfo; i++){
1902	+
1903	+	//prepare parameter set for minimizer
1904	+	param = new MinimizerParameterSet();
1905	+	param->setDefaultParameter();
1906	+
1907	+	if (globals->haveMinimizer()){
1908	+	param->setFTol(globals->getMinFTol());
1909	+	}
1910	+
1911	+	if (globals->haveMinGTol()){
1912	+	param->setGTol(globals->getMinGTol());
1913	+	}
1914	+
1915	+	if (globals->haveMinMaxIter()){
1916	+	param->setMaxIteration(globals->getMinMaxIter());
1917	+	}
1918	+
1919	+	if (globals->haveMinWriteFrq()){
1920	+	param->setMaxIteration(globals->getMinMaxIter());
1921	+	}
1922	+
1923	+	if (globals->haveMinWriteFrq()){
1924	+	param->setWriteFrq(globals->getMinWriteFrq());
1925	+	}
1926	+
1927	+	if (globals->haveMinStepSize()){
1928	+	param->setStepSize(globals->getMinStepSize());
1929	+	}
1930	+
1931	+	if (globals->haveMinLSMaxIter()){
1932	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1933	+	}
1934	+
1935	+	if (globals->haveMinLSTol()){
1936	+	param->setLineSearchTol(globals->getMinLSTol());
1937	+	}
1938	+
1939	+	strcpy(minimizerName, globals->getMinimizer());
1940	+
1941	+	if (!strcasecmp(minimizerName, "CG")){
1942	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1943	+	}
1944	+	else if (!strcasecmp(minimizerName, "SD")){
1945	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1946	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1947	+	}
1948	+	else{
1949	+	sprintf(painCave.errMsg,
1950	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1951	+	painCave.isFatal = 0;
1952	+	simError();
1953	+
1954	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1955	+	}
1956	+	info[i].the_integrator = myOOPSEMinimizer;
1957	+
1958	+	//store the minimizer into simInfo
1959	+	info[i].the_minimizer = myOOPSEMinimizer;
1960	+	info[i].has_minimizer = true;
1961	+	}
1962	+
1963	+	}

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