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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 746 by mmeineke, Thu Sep 4 21:48:35 2003 UTC vs.
Revision 1113 by tim, Thu Apr 15 16:18:26 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 NPTim_ENS      4
26	<	#define NPTfm_ENS      5
27	>	#define NPTxyz_ENS     4
28
28	–	#define FF_DUFF 0
29	–	#define FF_LJ   1
30	–	#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 54 | 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 92 | Line 122 | void SimSetup::createSim(void){
122		#endif // is_mpi
123
124		void SimSetup::createSim(void){
95	–	int i, j, k, globalAtomIndex;
125
126		// gather all of the information from the Bass file
127
#	Line 108 | 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	<
119	<	// make the integrator
120	<
121	<	makeIntegrator();
122	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 127 | 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	+	RigidBodyStamp* currentRigidBody;
186
187		bond_pair* theBonds;
188		bend_set* theBends;
189		torsion_set* theTorsions;
190
191	+	set<int> skipList;
192
193	+	double phi, theta, psi;
194	+	char* molName;
195	+	char rbName[100];
196	+
197		//init the forceField paramters
198
199		the_ff->readParams();
200
154	–
201		// init the atoms
202
203	<	double ux, uy, uz, u, uSqr;
203	>	int nMembers, nNew, rb1, rb2;
204
205		for (k = 0; k < nInfo; k++){
206		the_ff->setSimInfo(&(info[k]));
207
208		atomOffset = 0;
209	<	excludeOffset = 0;
209	>
210		for (i = 0; i < info[k].n_mol; i++){
211		stampID = info[k].molecules[i].getStampID();
212	+	molName = comp_stamps[stampID]->getID();
213
214		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216		molInfo.nBends = comp_stamps[stampID]->getNBends();
217		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
219	<
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219	>
220		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
174	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
175	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
176	–	molInfo.myBends = new Bend * [molInfo.nBends];
177	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
221
222	+	if (molInfo.nBonds > 0)
223	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	+	else
225	+	molInfo.myBonds = NULL;
226	+
227	+	if (molInfo.nBends > 0)
228	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	+	else
230	+	molInfo.myBends = NULL;
231	+
232	+	if (molInfo.nTorsions > 0)
233	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	+	else
235	+	molInfo.myTorsions = NULL;
236	+
237		theBonds = new bond_pair[molInfo.nBonds];
238		theBends = new bend_set[molInfo.nBends];
239		theTorsions = new torsion_set[molInfo.nTorsions];
240	<
240	>
241		// make the Atoms
242
243		for (j = 0; j < molInfo.nAtoms; j++){
244		currentAtom = comp_stamps[stampID]->getAtom(j);
245	+
246		if (currentAtom->haveOrientation()){
247		dAtom = new DirectionalAtom((j + atomOffset),
248		info[k].getConfiguration());
249		info[k].n_oriented++;
250		molInfo.myAtoms[j] = dAtom;
251
252	<	ux = currentAtom->getOrntX();
253	<	uy = currentAtom->getOrntY();
254	<	uz = currentAtom->getOrntZ();
252	>	// Directional Atoms have standard unit vectors which are oriented
253	>	// in space using the three Euler angles.  We assume the standard
254	>	// unit vector was originally along the z axis below.
255
256	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259
260	<	u = sqrt(uSqr);
261	<	ux = ux / u;
201	<	uy = uy / u;
202	<	uz = uz / u;
203	<
204	<	dAtom->setSUx(ux);
205	<	dAtom->setSUy(uy);
206	<	dAtom->setSUz(uz);
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262		}
263		else{
264	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
265	<	info[k].getConfiguration());
264	>
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266	>
267		}
212	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
268
269	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
270		#ifdef IS_MPI
271
272	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273
274		#endif // is_mpi
275		}
#	Line 224 | Line 280 | void SimSetup::makeMolecules(void){
280		theBonds[j].a = currentBond->getA() + atomOffset;
281		theBonds[j].b = currentBond->getB() + atomOffset;
282
283	<	exI = theBonds[j].a;
284	<	exJ = theBonds[j].b;
283	>	tempI = theBonds[j].a;
284	>	tempJ = theBonds[j].b;
285
230	–	// exclude_I must always be the smaller of the pair
231	–	if (exI > exJ){
232	–	tempEx = exI;
233	–	exI = exJ;
234	–	exJ = tempEx;
235	–	}
286		#ifdef IS_MPI
287	<	tempEx = exI;
288	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
289	<	tempEx = exJ;
290	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293
294	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243	<	#else  // isn't MPI
244	<
245	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246	<	#endif  //is_mpi
294	>	info[k].excludes->addPair(exI, exJ);
295		}
248	–	excludeOffset += molInfo.nBonds;
296
297		//make the bends
298		for (j = 0; j < molInfo.nBends; j++){
#	Line 295 | Line 342 | void SimSetup::makeMolecules(void){
342		}
343		}
344
345	<	if (!theBends[j].isGhost){
346	<	exI = theBends[j].a;
347	<	exJ = theBends[j].c;
348	<	}
349	<	else{
303	<	exI = theBends[j].a;
304	<	exJ = theBends[j].b;
305	<	}
306	<
307	<	// exclude_I must always be the smaller of the pair
308	<	if (exI > exJ){
309	<	tempEx = exI;
310	<	exI = exJ;
311	<	exJ = tempEx;
312	<	}
345	>	if (theBends[j].isGhost) {
346	>
347	>	tempI = theBends[j].a;
348	>	tempJ = theBends[j].b;
349	>
350		#ifdef IS_MPI
351	<	tempEx = exI;
352	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
353	<	tempEx = exJ;
354	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
360	<	#else  // isn't MPI
361	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
362	<	#endif  //is_mpi
359	>	} else {
360	>
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379		}
324	–	excludeOffset += molInfo.nBends;
380
381		for (j = 0; j < molInfo.nTorsions; j++){
382		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 330 | Line 385 | void SimSetup::makeMolecules(void){
385		theTorsions[j].c = currentTorsion->getC() + atomOffset;
386		theTorsions[j].d = currentTorsion->getD() + atomOffset;
387
388	<	exI = theTorsions[j].a;
389	<	exJ = theTorsions[j].d;
388	>	tempI = theTorsions[j].a;
389	>	tempJ = theTorsions[j].b;
390	>	tempK = theTorsions[j].c;
391	>	tempL = theTorsions[j].d;
392
393	<	// exclude_I must always be the smaller of the pair
394	<	if (exI > exJ){
395	<	tempEx = exI;
396	<	exI = exJ;
397	<	exJ = tempEx;
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403	>	#endif
404	>
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411	>	}
412	>
413	>
414	>	molInfo.myRigidBodies.clear();
415	>
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417	>
418	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	>	nMembers = currentRigidBody->getNMembers();
420	>
421	>	// Create the Rigid Body:
422	>
423	>	myRB = new RigidBody();
424	>
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429	>
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432	>
433	>	// tempI is atom numbering on local processor
434	>	tempI = molI + atomOffset;
435	>
436	>	// currentAtom is the AtomStamp (which we need for
437	>	// rigid body reference positions)
438	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
439	>
440	>	// When we add to the rigid body, add the atom itself and
441	>	// the stamp info:
442	>
443	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	>
445	>	// Add this atom to the Skip List for the integrators
446	>	#ifdef IS_MPI
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453		}
454	+
455	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	+
458	+	tempI = currentRigidBody->getMember(rb1);
459	+	tempJ = currentRigidBody->getMember(rb2);
460	+
461	+	// Some explanation is required here.
462	+	// Fortran indexing starts at 1, while c indexing starts at 0
463	+	// Also, in parallel computations, the GlobalIndex is
464	+	// used for the exclude list:
465	+
466		#ifdef IS_MPI
467	<	tempEx = exI;
468	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
469	<	tempEx = exJ;
470	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
467	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = tempI + 1;
471	>	exJ = tempJ + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478
479	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
480	<	#else  // isn't MPI
350	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
351	<	#endif  //is_mpi
479	>	molInfo.myRigidBodies.push_back(myRB);
480	>	info[k].rigidBodies.push_back(myRB);
481		}
482	<	excludeOffset += molInfo.nTorsions;
482	>
483
484	+	// After this is all set up, scan through the atoms to
485	+	// see if they can be added to the integrableObjects:
486
487	<	// send the arrays off to the forceField for init.
487	>	molInfo.myIntegrableObjects.clear();
488	>
489
490	+	for (j = 0; j < molInfo.nAtoms; j++){
491	+
492	+	#ifdef IS_MPI
493	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	+	#else
495	+	slJ = j+atomOffset;
496	+	#endif
497	+
498	+	// if they aren't on the skip list, then they can be integrated
499	+
500	+	if (skipList.find(slJ) == skipList.end()) {
501	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	+	info[k].integrableObjects.push_back(mySD);
503	+	molInfo.myIntegrableObjects.push_back(mySD);
504	+	}
505	+	}
506	+
507	+	// all rigid bodies are integrated:
508	+
509	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	+	info[k].integrableObjects.push_back(mySD);
512	+	molInfo.myIntegrableObjects.push_back(mySD);
513	+	}
514	+
515	+
516	+	// send the arrays off to the forceField for init.
517	+
518		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522		theTorsions);
523
364	–
524		info[k].molecules[i].initialize(molInfo);
525
526
#	Line 369 | Line 528 | void SimSetup::makeMolecules(void){
528		delete[] theBonds;
529		delete[] theBends;
530		delete[] theTorsions;
531	<	}
531	>	}
532		}
533
534		#ifdef IS_MPI
#	Line 379 | Line 538 | void SimSetup::makeMolecules(void){
538
539		// clean up the forcefield
540
541	<	the_ff->calcRcut();
541	>	if (!globals->haveLJrcut()){
542	>
543	>	the_ff->calcRcut();
544	>
545	>	} else {
546	>
547	>	the_ff->setRcut( globals->getLJrcut() );
548	>	}
549	>
550		the_ff->cleanMe();
551		}
552
#	Line 553 | Line 720 | void SimSetup::gatherInfo(void){
720
721
722		void SimSetup::gatherInfo(void){
723	<	int i, j, k;
723	>	int i;
724
725		ensembleCase = -1;
726		ffCase = -1;
#	Line 581 | Line 748 | void SimSetup::gatherInfo(void){
748		else if (!strcasecmp(force_field, "EAM")){
749		ffCase = FF_EAM;
750		}
751	+	else if (!strcasecmp(force_field, "WATER")){
752	+	ffCase = FF_H2O;
753	+	}
754		else{
755		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756		force_field);
#	Line 604 | Line 774 | void SimSetup::gatherInfo(void){
774		else if (!strcasecmp(ensemble, "NPTf")){
775		ensembleCase = NPTf_ENS;
776		}
777	<	else if (!strcasecmp(ensemble, "NPTim")){
778	<	ensembleCase = NPTim_ENS;
777	>	else if (!strcasecmp(ensemble, "NPTxyz")){
778	>	ensembleCase = NPTxyz_ENS;
779		}
610	–	else if (!strcasecmp(ensemble, "NPTfm")){
611	–	ensembleCase = NPTfm_ENS;
612	–	}
780		else{
781		sprintf(painCave.errMsg,
782	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
783	<	"reverting to NVE for this simulation.\n",
782	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	>	"\treverting to NVE for this simulation.\n",
784		ensemble);
785		painCave.isFatal = 0;
786		simError();
#	Line 645 | Line 812 | void SimSetup::gatherInfo(void){
812		if (!the_components[i]->haveNMol()){
813		// we have a problem
814		sprintf(painCave.errMsg,
815	<	"SimSetup Error. No global NMol or component NMol"
816	<	" given. Cannot calculate the number of atoms.\n");
815	>	"SimSetup Error. No global NMol or component NMol given.\n"
816	>	"\tCannot calculate the number of atoms.\n");
817		painCave.isFatal = 1;
818		simError();
819		}
#	Line 666 | Line 833 | void SimSetup::gatherInfo(void){
833		simError();
834		}
835
836	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
838	+	sprintf(painCave.errMsg,
839	+	"Sample time is not divisible by dt.\n"
840	+	"\tThis will result in samples that are not uniformly\n"
841	+	"\tdistributed in time.  If this is a problem, change\n"
842	+	"\tyour sampleTime variable.\n");
843	+	painCave.isFatal = 0;
844	+	simError();
845	+	}
846	+
847	+	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
848	+	sprintf(painCave.errMsg,
849	+	"Status time is not divisible by dt.\n"
850	+	"\tThis will result in status reports that are not uniformly\n"
851	+	"\tdistributed in time.  If this is a problem, change \n"
852	+	"\tyour statusTime variable.\n");
853	+	painCave.isFatal = 0;
854	+	simError();
855	+	}
856	+
857	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	+	sprintf(painCave.errMsg,
859	+	"Thermal time is not divisible by dt.\n"
860	+	"\tThis will result in thermalizations that are not uniformly\n"
861	+	"\tdistributed in time.  If this is a problem, change \n"
862	+	"\tyour thermalTime variable.\n");
863	+	painCave.isFatal = 0;
864	+	simError();
865	+	}
866	+
867	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	+	sprintf(painCave.errMsg,
869	+	"Reset time is not divisible by dt.\n"
870	+	"\tThis will result in integrator resets that are not uniformly\n"
871	+	"\tdistributed in time.  If this is a problem, change\n"
872	+	"\tyour resetTime variable.\n");
873	+	painCave.isFatal = 0;
874	+	simError();
875	+	}
876	+
877		// set the status, sample, and thermal kick times
878
879		for (i = 0; i < nInfo; i++){
#	Line 695 | Line 903 | void SimSetup::gatherInfo(void){
903		}
904
905		// check for the temperature set flag
906	<
906	>
907		if (globals->haveTempSet())
908		info[i].setTemp = globals->getTempSet();
909
910	<	// get some of the tricky things that may still be in the globals
910	>	// check for the extended State init
911
912	<	double boxVector[3];
913	<	if (globals->haveBox()){
914	<	boxVector[0] = globals->getBox();
707	<	boxVector[1] = globals->getBox();
708	<	boxVector[2] = globals->getBox();
709	<
710	<	info[i].setBox(boxVector);
711	<	}
712	<	else if (globals->haveDensity()){
713	<	double vol;
714	<	vol = (double) tot_nmol / globals->getDensity();
715	<	boxVector[0] = pow(vol, (1.0 / 3.0));
716	<	boxVector[1] = boxVector[0];
717	<	boxVector[2] = boxVector[0];
718	<
719	<	info[i].setBox(boxVector);
720	<	}
721	<	else{
722	<	if (!globals->haveBoxX()){
723	<	sprintf(painCave.errMsg,
724	<	"SimSetup error, no periodic BoxX size given.\n");
725	<	painCave.isFatal = 1;
726	<	simError();
727	<	}
728	<	boxVector[0] = globals->getBoxX();
729	<
730	<	if (!globals->haveBoxY()){
731	<	sprintf(painCave.errMsg,
732	<	"SimSetup error, no periodic BoxY size given.\n");
733	<	painCave.isFatal = 1;
734	<	simError();
735	<	}
736	<	boxVector[1] = globals->getBoxY();
737	<
738	<	if (!globals->haveBoxZ()){
739	<	sprintf(painCave.errMsg,
740	<	"SimSetup error, no periodic BoxZ size given.\n");
741	<	painCave.isFatal = 1;
742	<	simError();
743	<	}
744	<	boxVector[2] = globals->getBoxZ();
745	<
746	<	info[i].setBox(boxVector);
747	<	}
912	>	info[i].useInitXSstate = globals->getUseInitXSstate();
913	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914	>
915		}
916	<
916	>
917		//setup seed for random number generator
918		int seedValue;
919
#	Line 786 | Line 953 | void SimSetup::gatherInfo(void){
953		for (int i = 0; i < nInfo; i++){
954		info[i].setSeed(seedValue);
955		}
956	<
956	>
957		#ifdef IS_MPI
958	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
958	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
959		MPIcheckPoint();
960		#endif // is_mpi
961		}
#	Line 797 | Line 964 | void SimSetup::finalInfoCheck(void){
964		void SimSetup::finalInfoCheck(void){
965		int index;
966		int usesDipoles;
967	+	int usesCharges;
968		int i;
969
970		for (i = 0; i < nInfo; i++){
#	Line 808 | Line 976 | void SimSetup::finalInfoCheck(void){
976		usesDipoles = (info[i].atoms[index])->hasDipole();
977		index++;
978		}
979	<
979	>	index = 0;
980	>	usesCharges = 0;
981	>	while ((index < info[i].n_atoms) && !usesCharges){
982	>	usesCharges= (info[i].atoms[index])->hasCharge();
983	>	index++;
984	>	}
985		#ifdef IS_MPI
986		int myUse = usesDipoles;
987		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
#	Line 821 | Line 994 | void SimSetup::finalInfoCheck(void){
994
995		if (!globals->haveECR()){
996		sprintf(painCave.errMsg,
997	<	"SimSetup Warning: using default value of 1/2 the smallest "
998	<	"box length for the electrostaticCutoffRadius.\n"
999	<	"I hope you have a very fast processor!\n");
997	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
998	>	"\tOOPSE will use a default value of 15.0 angstroms"
999	>	"\tfor the electrostaticCutoffRadius.\n");
1000		painCave.isFatal = 0;
1001		simError();
1002	<	double smallest;
830	<	smallest = info[i].boxL[0];
831	<	if (info[i].boxL[1] <= smallest)
832	<	smallest = info[i].boxL[1];
833	<	if (info[i].boxL[2] <= smallest)
834	<	smallest = info[i].boxL[2];
835	<	theEcr = 0.5 * smallest;
1002	>	theEcr = 15.0;
1003		}
1004		else{
1005		theEcr = globals->getECR();
#	Line 840 | Line 1007 | void SimSetup::finalInfoCheck(void){
1007
1008		if (!globals->haveEST()){
1009		sprintf(painCave.errMsg,
1010	<	"SimSetup Warning: using default value of 0.05 * the "
1011	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1010	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1011	>	"\tOOPSE will use a default value of\n"
1012	>	"\t0.05 * electrostaticCutoffRadius\n"
1013	>	"\tfor the electrostaticSkinThickness\n");
1014		painCave.isFatal = 0;
1015		simError();
1016		theEst = 0.05 * theEcr;
#	Line 850 | Line 1019 | void SimSetup::finalInfoCheck(void){
1019		theEst = globals->getEST();
1020		}
1021
1022	<	info[i].setEcr(theEcr, theEst);
1022	>	info[i].setDefaultEcr(theEcr, theEst);
1023
1024		if (!globals->haveDielectric()){
1025		sprintf(painCave.errMsg,
1026	<	"SimSetup Error: You are trying to use Reaction Field without"
1027	<	"setting a dielectric constant!\n");
1026	>	"SimSetup Error: No Dielectric constant was set.\n"
1027	>	"\tYou are trying to use Reaction Field without"
1028	>	"\tsetting a dielectric constant!\n");
1029		painCave.isFatal = 1;
1030		simError();
1031		}
1032		info[i].dielectric = globals->getDielectric();
1033		}
1034		else{
1035	<	if (usesDipoles){
1035	>	if (usesDipoles || usesCharges){
1036		if (!globals->haveECR()){
1037		sprintf(painCave.errMsg,
1038	<	"SimSetup Warning: using default value of 1/2 the smallest "
1039	<	"box length for the electrostaticCutoffRadius.\n"
1040	<	"I hope you have a very fast processor!\n");
1041	<	painCave.isFatal = 0;
1042	<	simError();
1043	<	double smallest;
874	<	smallest = info[i].boxL[0];
875	<	if (info[i].boxL[1] <= smallest)
876	<	smallest = info[i].boxL[1];
877	<	if (info[i].boxL[2] <= smallest)
878	<	smallest = info[i].boxL[2];
879	<	theEcr = 0.5 * smallest;
1038	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1039	>	"\tOOPSE will use a default value of 15.0 angstroms"
1040	>	"\tfor the electrostaticCutoffRadius.\n");
1041	>	painCave.isFatal = 0;
1042	>	simError();
1043	>	theEcr = 15.0;
1044		}
1045		else{
1046		theEcr = globals->getECR();
1047		}
1048	<
1048	>
1049		if (!globals->haveEST()){
1050		sprintf(painCave.errMsg,
1051	<	"SimSetup Warning: using default value of 0.05 * the "
1052	<	"electrostaticCutoffRadius for the "
1053	<	"electrostaticSkinThickness\n");
1051	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1052	>	"\tOOPSE will use a default value of\n"
1053	>	"\t0.05 * electrostaticCutoffRadius\n"
1054	>	"\tfor the electrostaticSkinThickness\n");
1055		painCave.isFatal = 0;
1056		simError();
1057		theEst = 0.05 * theEcr;
#	Line 894 | Line 1059 | void SimSetup::finalInfoCheck(void){
1059		else{
1060		theEst = globals->getEST();
1061		}
1062	<
1063	<	info[i].setEcr(theEcr, theEst);
1062	>
1063	>	info[i].setDefaultEcr(theEcr, theEst);
1064		}
1065		}
1066		}
902	–
1067		#ifdef IS_MPI
1068		strcpy(checkPointMsg, "post processing checks out");
1069		MPIcheckPoint();
1070		#endif // is_mpi
1071		}
1072	<
1072	>
1073		void SimSetup::initSystemCoords(void){
1074		int i;
1075
#	Line 922 | Line 1086 | void SimSetup::initSystemCoords(void){
1086		if (worldRank == 0){
1087		#endif //is_mpi
1088		inName = globals->getInitialConfig();
925	–	double* tempDouble = new double[1000000];
1089		fileInit = new InitializeFromFile(inName);
1090		#ifdef IS_MPI
1091		}
#	Line 934 | Line 1097 | void SimSetup::initSystemCoords(void){
1097		delete fileInit;
1098		}
1099		else{
1100	<	#ifdef IS_MPI
938	<
1100	>
1101		// no init from bass
1102	<
1102	>
1103		sprintf(painCave.errMsg,
1104	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1105	<	painCave.isFatal;
1104	>	"Cannot intialize a simulation without an initial configuration file.\n");
1105	>	painCave.isFatal = 1;;
1106		simError();
1107	<
946	<	#else
947	<
948	<	initFromBass();
949	<
950	<
951	<	#endif
1107	>
1108		}
1109
1110		#ifdef IS_MPI
#	Line 1102 | Line 1258 | void SimSetup::createFF(void){
1258		the_ff = new EAM_FF();
1259		break;
1260
1261	+	case FF_H2O:
1262	+	the_ff = new WATER();
1263	+	break;
1264	+
1265		default:
1266		sprintf(painCave.errMsg,
1267		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1166 | Line 1326 | void SimSetup::calcSysValues(void){
1326		}
1327
1328		void SimSetup::calcSysValues(void){
1329	<	int i, j, k;
1329	>	int i;
1330
1331		int* molMembershipArray;
1332
#	Line 1174 | Line 1334 | void SimSetup::calcSysValues(void){
1334		tot_bonds = 0;
1335		tot_bends = 0;
1336		tot_torsions = 0;
1337	+	tot_rigid = 0;
1338		for (i = 0; i < n_components; i++){
1339		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1340		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1341		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1342		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1343	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1344		}
1345	<
1345	>
1346		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1347		molMembershipArray = new int[tot_atoms];
1348
#	Line 1202 | Line 1364 | void SimSetup::mpiMolDivide(void){
1364		int i, j, k;
1365		int localMol, allMol;
1366		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1367	+	int local_rigid;
1368	+	vector<int> globalAtomIndex;
1369	+	vector<int> globalMolIndex;
1370
1371		mpiSim = new mpiSimulation(info);
1372
1373	<	globalIndex = mpiSim->divideLabor();
1373	>	mpiSim->divideLabor();
1374	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1375	>	globalMolIndex = mpiSim->getGlobalMolIndex();
1376
1377		// set up the local variables
1378
#	Line 1218 | Line 1385 | void SimSetup::mpiMolDivide(void){
1385		local_bonds = 0;
1386		local_bends = 0;
1387		local_torsions = 0;
1388	<	globalAtomIndex = 0;
1388	>	local_rigid = 0;
1389	>	globalAtomCounter = 0;
1390
1223	–
1391		for (i = 0; i < n_components; i++){
1392		for (j = 0; j < components_nmol[i]; j++){
1393		if (mol2proc[allMol] == worldRank){
#	Line 1228 | Line 1395 | void SimSetup::mpiMolDivide(void){
1395		local_bonds += comp_stamps[i]->getNBonds();
1396		local_bends += comp_stamps[i]->getNBends();
1397		local_torsions += comp_stamps[i]->getNTorsions();
1398	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1399		localMol++;
1400		}
1401		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1402	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1403	<	globalAtomIndex++;
1402	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1403	>	globalAtomCounter++;
1404		}
1405
1406		allMol++;
#	Line 1241 | Line 1409 | void SimSetup::mpiMolDivide(void){
1409		local_SRI = local_bonds + local_bends + local_torsions;
1410
1411		info[0].n_atoms = mpiSim->getMyNlocal();
1412	+
1413
1414		if (local_atoms != info[0].n_atoms){
1415		sprintf(painCave.errMsg,
1416	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1417	<	" localAtom (%d) are not equal.\n",
1416	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1417	>	"\tlocalAtom (%d) are not equal.\n",
1418		info[0].n_atoms, local_atoms);
1419		painCave.isFatal = 1;
1420		simError();
#	Line 1265 | Line 1434 | void SimSetup::makeSysArrays(void){
1434
1435
1436		void SimSetup::makeSysArrays(void){
1437	<	int i, j, k, l;
1437	>
1438	>	#ifndef IS_MPI
1439	>	int k, j;
1440	>	#endif // is_mpi
1441	>	int i, l;
1442
1443		Atom** the_atoms;
1444		Molecule* the_molecules;
1272	–	Exclude** the_excludes;
1445
1274	–
1446		for (l = 0; l < nInfo; l++){
1447		// create the atom and short range interaction arrays
1448
#	Line 1297 | Line 1468 | void SimSetup::makeSysArrays(void){
1468		#else // is_mpi
1469
1470		molIndex = 0;
1471	<	globalAtomIndex = 0;
1471	>	globalAtomCounter = 0;
1472		for (i = 0; i < n_components; i++){
1473		for (j = 0; j < components_nmol[i]; j++){
1474		the_molecules[molIndex].setStampID(i);
1475		the_molecules[molIndex].setMyIndex(molIndex);
1476		the_molecules[molIndex].setGlobalIndex(molIndex);
1477		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1478	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1479	<	globalAtomIndex++;
1478	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1479	>	globalAtomCounter++;
1480		}
1481		molIndex++;
1482		}
#	Line 1314 | Line 1485 | void SimSetup::makeSysArrays(void){
1485
1486		#endif // is_mpi
1487
1488	<
1489	<	if (info[l].n_SRI){
1490	<	Exclude::createArray(info[l].n_SRI);
1320	<	the_excludes = new Exclude * [info[l].n_SRI];
1321	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1322	<	the_excludes[ex] = new Exclude(ex);
1323	<	}
1324	<	info[l].globalExcludes = new int;
1325	<	info[l].n_exclude = info[l].n_SRI;
1326	<	}
1327	<	else{
1328	<	Exclude::createArray(1);
1329	<	the_excludes = new Exclude * ;
1330	<	the_excludes[0] = new Exclude(0);
1331	<	the_excludes[0]->setPair(0, 0);
1332	<	info[l].globalExcludes = new int;
1333	<	info[l].globalExcludes[0] = 0;
1334	<	info[l].n_exclude = 0;
1335	<	}
1336	<
1488	>	info[l].globalExcludes = new int;
1489	>	info[l].globalExcludes[0] = 0;
1490	>
1491		// set the arrays into the SimInfo object
1492
1493		info[l].atoms = the_atoms;
1494		info[l].molecules = the_molecules;
1495		info[l].nGlobalExcludes = 0;
1342	–	info[l].excludes = the_excludes;
1496
1497		the_ff->setSimInfo(info);
1498		}
#	Line 1348 | Line 1501 | void SimSetup::makeIntegrator(void){
1501		void SimSetup::makeIntegrator(void){
1502		int k;
1503
1504	+	NVE<RealIntegrator>* myNVE = NULL;
1505		NVT<RealIntegrator>* myNVT = NULL;
1506	<	NPTi<RealIntegrator>* myNPTi = NULL;
1507	<	NPTf<RealIntegrator>* myNPTf = NULL;
1508	<	NPTim<RealIntegrator>* myNPTim = NULL;
1355	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1506	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1507	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1508	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1509
1510		for (k = 0; k < nInfo; k++){
1511		switch (ensembleCase){
1512		case NVE_ENS:
1513		if (globals->haveZconstraints()){
1514		setupZConstraint(info[k]);
1515	<	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1515	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1516		}
1517	<	else
1518	<	new NVE<RealIntegrator>(&(info[k]), the_ff);
1517	>	else{
1518	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1519	>	}
1520	>
1521	>	info->the_integrator = myNVE;
1522		break;
1523
1524		case NVT_ENS:
#	Line 1380 | Line 1536 | void SimSetup::makeIntegrator(void){
1536		else{
1537		sprintf(painCave.errMsg,
1538		"SimSetup error: If you use the NVT\n"
1539	<	"    ensemble, you must set tauThermostat.\n");
1539	>	"\tensemble, you must set tauThermostat.\n");
1540		painCave.isFatal = 1;
1541		simError();
1542		}
1543	+
1544	+	info->the_integrator = myNVT;
1545		break;
1546
1547		case NPTi_ENS:
1548		if (globals->haveZconstraints()){
1549		setupZConstraint(info[k]);
1550	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1550	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1551		}
1552		else
1553	<	myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1553	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1554
1555		myNPTi->setTargetTemp(globals->getTargetTemp());
1556
#	Line 1401 | Line 1559 | void SimSetup::makeIntegrator(void){
1559		else{
1560		sprintf(painCave.errMsg,
1561		"SimSetup error: If you use a constant pressure\n"
1562	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1562	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1563		painCave.isFatal = 1;
1564		simError();
1565		}
#	Line 1411 | Line 1569 | void SimSetup::makeIntegrator(void){
1569		else{
1570		sprintf(painCave.errMsg,
1571		"SimSetup error: If you use an NPT\n"
1572	<	"    ensemble, you must set tauThermostat.\n");
1572	>	"\tensemble, you must set tauThermostat.\n");
1573		painCave.isFatal = 1;
1574		simError();
1575		}
#	Line 1421 | Line 1579 | void SimSetup::makeIntegrator(void){
1579		else{
1580		sprintf(painCave.errMsg,
1581		"SimSetup error: If you use an NPT\n"
1582	<	"    ensemble, you must set tauBarostat.\n");
1582	>	"\tensemble, you must set tauBarostat.\n");
1583		painCave.isFatal = 1;
1584		simError();
1585		}
1586	+
1587	+	info->the_integrator = myNPTi;
1588		break;
1589
1590		case NPTf_ENS:
1591		if (globals->haveZconstraints()){
1592		setupZConstraint(info[k]);
1593	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1593	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1594		}
1595		else
1596	<	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1596	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1597
1598		myNPTf->setTargetTemp(globals->getTargetTemp());
1599
#	Line 1442 | Line 1602 | void SimSetup::makeIntegrator(void){
1602		else{
1603		sprintf(painCave.errMsg,
1604		"SimSetup error: If you use a constant pressure\n"
1605	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1605	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1606		painCave.isFatal = 1;
1607		simError();
1608		}
1609
1610		if (globals->haveTauThermostat())
1611		myNPTf->setTauThermostat(globals->getTauThermostat());
1612	+
1613		else{
1614		sprintf(painCave.errMsg,
1615		"SimSetup error: If you use an NPT\n"
1616	<	"    ensemble, you must set tauThermostat.\n");
1616	>	"\tensemble, you must set tauThermostat.\n");
1617		painCave.isFatal = 1;
1618		simError();
1619		}
1620
1621		if (globals->haveTauBarostat())
1622		myNPTf->setTauBarostat(globals->getTauBarostat());
1462	–	else{
1463	–	sprintf(painCave.errMsg,
1464	–	"SimSetup error: If you use an NPT\n"
1465	–	"    ensemble, you must set tauBarostat.\n");
1466	–	painCave.isFatal = 1;
1467	–	simError();
1468	–	}
1469	–	break;
1623
1471	–	case NPTim_ENS:
1472	–	if (globals->haveZconstraints()){
1473	–	setupZConstraint(info[k]);
1474	–	myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1475	–	}
1476	–	else
1477	–	myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1478	–
1479	–	myNPTim->setTargetTemp(globals->getTargetTemp());
1480	–
1481	–	if (globals->haveTargetPressure())
1482	–	myNPTim->setTargetPressure(globals->getTargetPressure());
1624		else{
1625		sprintf(painCave.errMsg,
1485	–	"SimSetup error: If you use a constant pressure\n"
1486	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1487	–	painCave.isFatal = 1;
1488	–	simError();
1489	–	}
1490	–
1491	–	if (globals->haveTauThermostat())
1492	–	myNPTim->setTauThermostat(globals->getTauThermostat());
1493	–	else{
1494	–	sprintf(painCave.errMsg,
1626		"SimSetup error: If you use an NPT\n"
1627	<	"    ensemble, you must set tauThermostat.\n");
1627	>	"\tensemble, you must set tauBarostat.\n");
1628		painCave.isFatal = 1;
1629		simError();
1630		}
1631
1632	<	if (globals->haveTauBarostat())
1502	<	myNPTim->setTauBarostat(globals->getTauBarostat());
1503	<	else{
1504	<	sprintf(painCave.errMsg,
1505	<	"SimSetup error: If you use an NPT\n"
1506	<	"    ensemble, you must set tauBarostat.\n");
1507	<	painCave.isFatal = 1;
1508	<	simError();
1509	<	}
1632	>	info->the_integrator = myNPTf;
1633		break;
1634
1635	<	case NPTfm_ENS:
1635	>	case NPTxyz_ENS:
1636		if (globals->haveZconstraints()){
1637		setupZConstraint(info[k]);
1638	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1638	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1639		}
1640		else
1641	<	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1641	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1642
1643	<	myNPTfm->setTargetTemp(globals->getTargetTemp());
1643	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1644
1645		if (globals->haveTargetPressure())
1646	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1646	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1647		else{
1648		sprintf(painCave.errMsg,
1649		"SimSetup error: If you use a constant pressure\n"
1650	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1650	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1651		painCave.isFatal = 1;
1652		simError();
1653	<	}
1653	>	}
1654
1655		if (globals->haveTauThermostat())
1656	<	myNPTfm->setTauThermostat(globals->getTauThermostat());
1656	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1657		else{
1658		sprintf(painCave.errMsg,
1659		"SimSetup error: If you use an NPT\n"
1660	<	"    ensemble, you must set tauThermostat.\n");
1660	>	"\tensemble, you must set tauThermostat.\n");
1661		painCave.isFatal = 1;
1662		simError();
1663		}
1664
1665		if (globals->haveTauBarostat())
1666	<	myNPTfm->setTauBarostat(globals->getTauBarostat());
1666	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1667		else{
1668		sprintf(painCave.errMsg,
1669		"SimSetup error: If you use an NPT\n"
1670	<	"    ensemble, you must set tauBarostat.\n");
1670	>	"\tensemble, you must set tauBarostat.\n");
1671		painCave.isFatal = 1;
1672		simError();
1673		}
1674	+
1675	+	info->the_integrator = myNPTxyz;
1676		break;
1677
1678		default:
#	Line 1595 | Line 1720 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1720		}
1721		else{
1722		sprintf(painCave.errMsg,
1723	<	"ZConstraint error: If you use an ZConstraint\n"
1724	<	" , you must set sample time.\n");
1723	>	"ZConstraint error: If you use a ZConstraint,\n"
1724	>	"\tyou must set zconsTime.\n");
1725		painCave.isFatal = 1;
1726		simError();
1727		}
#	Line 1611 | Line 1736 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1736		else{
1737		double defaultZConsTol = 0.01;
1738		sprintf(painCave.errMsg,
1739	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1740	<	" , default value %f is used.\n",
1739	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1740	>	"\tOOPSE will use a default value of %f.\n"
1741	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1742		defaultZConsTol);
1743		painCave.isFatal = 0;
1744		simError();
#	Line 1630 | Line 1756 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1756		}
1757		else{
1758		sprintf(painCave.errMsg,
1759	<	"ZConstraint Warning: User does not set force Subtraction policy, "
1760	<	"PolicyByMass is used\n");
1759	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1760	>	"\tOOPSE will use PolicyByMass.\n"
1761	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1762		painCave.isFatal = 0;
1763		simError();
1764		zconsForcePolicy->setData("BYMASS");
#	Line 1639 | Line 1766 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1766
1767		theInfo.addProperty(zconsForcePolicy);
1768
1769	+	//set zcons gap
1770	+	DoubleData* zconsGap = new DoubleData();
1771	+	zconsGap->setID(ZCONSGAP_ID);
1772	+
1773	+	if (globals->haveZConsGap()){
1774	+	zconsGap->setData(globals->getZconsGap());
1775	+	theInfo.addProperty(zconsGap);
1776	+	}
1777	+
1778	+	//set zcons fixtime
1779	+	DoubleData* zconsFixtime = new DoubleData();
1780	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1781	+
1782	+	if (globals->haveZConsFixTime()){
1783	+	zconsFixtime->setData(globals->getZconsFixtime());
1784	+	theInfo.addProperty(zconsFixtime);
1785	+	}
1786	+
1787	+	//set zconsUsingSMD
1788	+	IntData* zconsUsingSMD = new IntData();
1789	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1790	+
1791	+	if (globals->haveZConsUsingSMD()){
1792	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1793	+	theInfo.addProperty(zconsUsingSMD);
1794	+	}
1795	+
1796		//Determine the name of ouput file and add it into SimInfo's property list
1797		//Be careful, do not use inFileName, since it is a pointer which
1798		//point to a string at master node, and slave nodes do not contain that string
#	Line 1668 | Line 1822 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1822		tempParaItem.zPos = zconStamp[i]->getZpos();
1823		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1824		tempParaItem.kRatio = zconStamp[i]->getKratio();
1825	<
1825	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1826	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1827		zconsParaData->addItem(tempParaItem);
1828		}
1829
1830		//check the uniqueness of index
1831		if(!zconsParaData->isIndexUnique()){
1832		sprintf(painCave.errMsg,
1833	<	"ZConstraint Error: molIndex is not unique\n");
1833	>	"ZConstraint Error: molIndex is not unique!\n");
1834		painCave.isFatal = 1;
1835		simError();
1836		}
#	Line 1686 | Line 1841 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1841		//push data into siminfo, therefore, we can retrieve later
1842		theInfo.addProperty(zconsParaData);
1843		}
1844	+
1845	+	void SimSetup::makeMinimizer(){
1846	+
1847	+	OOPSEMinimizer* myOOPSEMinimizer;
1848	+	MinimizerParameterSet* param;
1849	+	char minimizerName[100];
1850	+
1851	+	for (int i = 0; i < nInfo; i++){
1852	+
1853	+	//prepare parameter set for minimizer
1854	+	param = new MinimizerParameterSet();
1855	+	param->setDefaultParameter();
1856	+
1857	+	if (globals->haveMinimizer()){
1858	+	param->setFTol(globals->getMinFTol());
1859	+	}
1860	+
1861	+	if (globals->haveMinGTol()){
1862	+	param->setGTol(globals->getMinGTol());
1863	+	}
1864	+
1865	+	if (globals->haveMinMaxIter()){
1866	+	param->setMaxIteration(globals->getMinMaxIter());
1867	+	}
1868	+
1869	+	if (globals->haveMinWriteFrq()){
1870	+	param->setMaxIteration(globals->getMinMaxIter());
1871	+	}
1872	+
1873	+	if (globals->haveMinWriteFrq()){
1874	+	param->setWriteFrq(globals->getMinWriteFrq());
1875	+	}
1876	+
1877	+	if (globals->haveMinStepSize()){
1878	+	param->setStepSize(globals->getMinStepSize());
1879	+	}
1880	+
1881	+	if (globals->haveMinLSMaxIter()){
1882	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1883	+	}
1884	+
1885	+	if (globals->haveMinLSTol()){
1886	+	param->setLineSearchTol(globals->getMinLSTol());
1887	+	}
1888	+
1889	+	strcpy(minimizerName, globals->getMinimizer());
1890	+
1891	+	if (!strcasecmp(minimizerName, "CG")){
1892	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1893	+	}
1894	+	else if (!strcasecmp(minimizerName, "SD")){
1895	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1896	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1897	+	}
1898	+	else{
1899	+	sprintf(painCave.errMsg,
1900	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1901	+	painCave.isFatal = 0;
1902	+	simError();
1903	+
1904	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1905	+	}
1906	+	info[i].the_integrator = myOOPSEMinimizer;
1907	+
1908	+	//store the minimizer into simInfo
1909	+	info[i].the_minimizer = myOOPSEMinimizer;
1910	+	info[i].has_minimizer = true;
1911	+	}
1912	+
1913	+	}

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