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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 733 by tim, Wed Aug 27 19:23:29 2003 UTC vs.
Revision 1139 by gezelter, Wed Apr 28 22:06:29 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;
390	<
391	<	// exclude_I must always be the smaller of the pair
392	<	if (exI > exJ){
393	<	tempEx = exI;
394	<	exI = exJ;
395	<	exJ = tempEx;
388	>	tempI = theTorsions[j].a;
389	>	tempJ = theTorsions[j].b;
390	>	tempK = theTorsions[j].c;
391	>	tempL = theTorsions[j].d;
392	>
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	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 = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 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 664 | Line 831 | void SimSetup::gatherInfo(void){
831		" Please give nMol in the components.\n");
832		painCave.isFatal = 1;
833		simError();
834	+	}
835	+
836	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	+	if (globals->haveSampleTime() && !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->getStatusTime(), 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++){
880		if (globals->haveSampleTime()){
881		info[i].sampleTime = globals->getSampleTime();
882		info[i].statusTime = info[i].sampleTime;
675	–	info[i].thermalTime = info[i].sampleTime;
883		}
884		else{
885		info[i].sampleTime = globals->getRunTime();
886		info[i].statusTime = info[i].sampleTime;
680	–	info[i].thermalTime = info[i].sampleTime;
887		}
888
889		if (globals->haveStatusTime()){
#	Line 686 | Line 892 | void SimSetup::gatherInfo(void){
892
893		if (globals->haveThermalTime()){
894		info[i].thermalTime = globals->getThermalTime();
895	+	} else {
896	+	info[i].thermalTime = globals->getRunTime();
897		}
898
899	<	// check for the temperature set flag
899	>	info[i].resetIntegrator = 0;
900	>	if( globals->haveResetTime() ){
901	>	info[i].resetTime = globals->getResetTime();
902	>	info[i].resetIntegrator = 1;
903	>	}
904
905	+	// check for the temperature set flag
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();
701	<	boxVector[1] = globals->getBox();
702	<	boxVector[2] = globals->getBox();
912	>	info[i].useInitXSstate = globals->getUseInitXSstate();
913	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914	>	info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs();
915
916	<	info[i].setBox(boxVector);
705	<	}
706	<	else if (globals->haveDensity()){
707	<	double vol;
708	<	vol = (double) tot_nmol / globals->getDensity();
709	<	boxVector[0] = pow(vol, (1.0 / 3.0));
710	<	boxVector[1] = boxVector[0];
711	<	boxVector[2] = boxVector[0];
712	<
713	<	info[i].setBox(boxVector);
714	<	}
715	<	else{
716	<	if (!globals->haveBoxX()){
717	<	sprintf(painCave.errMsg,
718	<	"SimSetup error, no periodic BoxX size given.\n");
719	<	painCave.isFatal = 1;
720	<	simError();
721	<	}
722	<	boxVector[0] = globals->getBoxX();
723	<
724	<	if (!globals->haveBoxY()){
725	<	sprintf(painCave.errMsg,
726	<	"SimSetup error, no periodic BoxY size given.\n");
727	<	painCave.isFatal = 1;
728	<	simError();
729	<	}
730	<	boxVector[1] = globals->getBoxY();
731	<
732	<	if (!globals->haveBoxZ()){
733	<	sprintf(painCave.errMsg,
734	<	"SimSetup error, no periodic BoxZ size given.\n");
735	<	painCave.isFatal = 1;
736	<	simError();
737	<	}
738	<	boxVector[2] = globals->getBoxZ();
739	<
740	<	info[i].setBox(boxVector);
741	<	}
916	>
917		}
918	<
918	>
919		//setup seed for random number generator
920		int seedValue;
921
#	Line 780 | Line 955 | void SimSetup::gatherInfo(void){
955		for (int i = 0; i < nInfo; i++){
956		info[i].setSeed(seedValue);
957		}
958	<
958	>
959		#ifdef IS_MPI
960	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
960	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
961		MPIcheckPoint();
962		#endif // is_mpi
963		}
#	Line 791 | Line 966 | void SimSetup::finalInfoCheck(void){
966		void SimSetup::finalInfoCheck(void){
967		int index;
968		int usesDipoles;
969	+	int usesCharges;
970		int i;
971
972		for (i = 0; i < nInfo; i++){
#	Line 802 | Line 978 | void SimSetup::finalInfoCheck(void){
978		usesDipoles = (info[i].atoms[index])->hasDipole();
979		index++;
980		}
981	<
981	>	index = 0;
982	>	usesCharges = 0;
983	>	while ((index < info[i].n_atoms) && !usesCharges){
984	>	usesCharges= (info[i].atoms[index])->hasCharge();
985	>	index++;
986	>	}
987		#ifdef IS_MPI
988		int myUse = usesDipoles;
989		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
#	Line 815 | Line 996 | void SimSetup::finalInfoCheck(void){
996
997		if (!globals->haveECR()){
998		sprintf(painCave.errMsg,
999	<	"SimSetup Warning: using default value of 1/2 the smallest "
1000	<	"box length for the electrostaticCutoffRadius.\n"
1001	<	"I hope you have a very fast processor!\n");
999	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1000	>	"\tOOPSE will use a default value of 15.0 angstroms"
1001	>	"\tfor the electrostaticCutoffRadius.\n");
1002		painCave.isFatal = 0;
1003		simError();
1004	<	double smallest;
824	<	smallest = info[i].boxL[0];
825	<	if (info[i].boxL[1] <= smallest)
826	<	smallest = info[i].boxL[1];
827	<	if (info[i].boxL[2] <= smallest)
828	<	smallest = info[i].boxL[2];
829	<	theEcr = 0.5 * smallest;
1004	>	theEcr = 15.0;
1005		}
1006		else{
1007		theEcr = globals->getECR();
#	Line 834 | Line 1009 | void SimSetup::finalInfoCheck(void){
1009
1010		if (!globals->haveEST()){
1011		sprintf(painCave.errMsg,
1012	<	"SimSetup Warning: using default value of 0.05 * the "
1013	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1012	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1013	>	"\tOOPSE will use a default value of\n"
1014	>	"\t0.05 * electrostaticCutoffRadius\n"
1015	>	"\tfor the electrostaticSkinThickness\n");
1016		painCave.isFatal = 0;
1017		simError();
1018		theEst = 0.05 * theEcr;
#	Line 844 | Line 1021 | void SimSetup::finalInfoCheck(void){
1021		theEst = globals->getEST();
1022		}
1023
1024	<	info[i].setEcr(theEcr, theEst);
1024	>	info[i].setDefaultEcr(theEcr, theEst);
1025
1026		if (!globals->haveDielectric()){
1027		sprintf(painCave.errMsg,
1028	<	"SimSetup Error: You are trying to use Reaction Field without"
1029	<	"setting a dielectric constant!\n");
1028	>	"SimSetup Error: No Dielectric constant was set.\n"
1029	>	"\tYou are trying to use Reaction Field without"
1030	>	"\tsetting a dielectric constant!\n");
1031		painCave.isFatal = 1;
1032		simError();
1033		}
1034		info[i].dielectric = globals->getDielectric();
1035		}
1036		else{
1037	<	if (usesDipoles){
1037	>	if (usesDipoles || usesCharges){
1038		if (!globals->haveECR()){
1039		sprintf(painCave.errMsg,
1040	<	"SimSetup Warning: using default value of 1/2 the smallest "
1041	<	"box length for the electrostaticCutoffRadius.\n"
1042	<	"I hope you have a very fast processor!\n");
1043	<	painCave.isFatal = 0;
1044	<	simError();
1045	<	double smallest;
868	<	smallest = info[i].boxL[0];
869	<	if (info[i].boxL[1] <= smallest)
870	<	smallest = info[i].boxL[1];
871	<	if (info[i].boxL[2] <= smallest)
872	<	smallest = info[i].boxL[2];
873	<	theEcr = 0.5 * smallest;
1040	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1041	>	"\tOOPSE will use a default value of 15.0 angstroms"
1042	>	"\tfor the electrostaticCutoffRadius.\n");
1043	>	painCave.isFatal = 0;
1044	>	simError();
1045	>	theEcr = 15.0;
1046		}
1047		else{
1048		theEcr = globals->getECR();
1049		}
1050	<
1050	>
1051		if (!globals->haveEST()){
1052		sprintf(painCave.errMsg,
1053	<	"SimSetup Warning: using default value of 0.05 * the "
1054	<	"electrostaticCutoffRadius for the "
1055	<	"electrostaticSkinThickness\n");
1053	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1054	>	"\tOOPSE will use a default value of\n"
1055	>	"\t0.05 * electrostaticCutoffRadius\n"
1056	>	"\tfor the electrostaticSkinThickness\n");
1057		painCave.isFatal = 0;
1058		simError();
1059		theEst = 0.05 * theEcr;
#	Line 888 | Line 1061 | void SimSetup::finalInfoCheck(void){
1061		else{
1062		theEst = globals->getEST();
1063		}
1064	<
1065	<	info[i].setEcr(theEcr, theEst);
1064	>
1065	>	info[i].setDefaultEcr(theEcr, theEst);
1066		}
1067		}
1068		}
896	–
1069		#ifdef IS_MPI
1070		strcpy(checkPointMsg, "post processing checks out");
1071		MPIcheckPoint();
1072		#endif // is_mpi
1073		}
1074	<
1074	>
1075		void SimSetup::initSystemCoords(void){
1076		int i;
1077
#	Line 916 | Line 1088 | void SimSetup::initSystemCoords(void){
1088		if (worldRank == 0){
1089		#endif //is_mpi
1090		inName = globals->getInitialConfig();
919	–	double* tempDouble = new double[1000000];
1091		fileInit = new InitializeFromFile(inName);
1092		#ifdef IS_MPI
1093		}
#	Line 928 | Line 1099 | void SimSetup::initSystemCoords(void){
1099		delete fileInit;
1100		}
1101		else{
1102	<	#ifdef IS_MPI
932	<
1102	>
1103		// no init from bass
1104	<
1104	>
1105		sprintf(painCave.errMsg,
1106	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1107	<	painCave.isFatal;
1106	>	"Cannot intialize a simulation without an initial configuration file.\n");
1107	>	painCave.isFatal = 1;;
1108		simError();
1109	<
940	<	#else
941	<
942	<	initFromBass();
943	<
944	<
945	<	#endif
1109	>
1110		}
1111
1112		#ifdef IS_MPI
#	Line 1096 | Line 1260 | void SimSetup::createFF(void){
1260		the_ff = new EAM_FF();
1261		break;
1262
1263	+	case FF_H2O:
1264	+	the_ff = new WATER();
1265	+	break;
1266	+
1267		default:
1268		sprintf(painCave.errMsg,
1269		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1160 | Line 1328 | void SimSetup::calcSysValues(void){
1328		}
1329
1330		void SimSetup::calcSysValues(void){
1331	<	int i, j, k;
1331	>	int i;
1332
1333		int* molMembershipArray;
1334
#	Line 1168 | Line 1336 | void SimSetup::calcSysValues(void){
1336		tot_bonds = 0;
1337		tot_bends = 0;
1338		tot_torsions = 0;
1339	+	tot_rigid = 0;
1340		for (i = 0; i < n_components; i++){
1341		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1342		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1343		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1344		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1345	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1346		}
1347	<
1347	>
1348		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1349		molMembershipArray = new int[tot_atoms];
1350
#	Line 1196 | Line 1366 | void SimSetup::mpiMolDivide(void){
1366		int i, j, k;
1367		int localMol, allMol;
1368		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1369	+	int local_rigid;
1370	+	vector<int> globalMolIndex;
1371
1372		mpiSim = new mpiSimulation(info);
1373
1374	<	globalIndex = mpiSim->divideLabor();
1374	>	mpiSim->divideLabor();
1375	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1376	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1377
1378		// set up the local variables
1379
#	Line 1212 | Line 1386 | void SimSetup::mpiMolDivide(void){
1386		local_bonds = 0;
1387		local_bends = 0;
1388		local_torsions = 0;
1389	<	globalAtomIndex = 0;
1389	>	local_rigid = 0;
1390	>	globalAtomCounter = 0;
1391
1217	–
1392		for (i = 0; i < n_components; i++){
1393		for (j = 0; j < components_nmol[i]; j++){
1394		if (mol2proc[allMol] == worldRank){
#	Line 1222 | Line 1396 | void SimSetup::mpiMolDivide(void){
1396		local_bonds += comp_stamps[i]->getNBonds();
1397		local_bends += comp_stamps[i]->getNBends();
1398		local_torsions += comp_stamps[i]->getNTorsions();
1399	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1400		localMol++;
1401		}
1402		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1403	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1404	<	globalAtomIndex++;
1403	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1404	>	globalAtomCounter++;
1405		}
1406
1407		allMol++;
#	Line 1235 | Line 1410 | void SimSetup::mpiMolDivide(void){
1410		local_SRI = local_bonds + local_bends + local_torsions;
1411
1412		info[0].n_atoms = mpiSim->getMyNlocal();
1413	+
1414
1415		if (local_atoms != info[0].n_atoms){
1416		sprintf(painCave.errMsg,
1417	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1418	<	" localAtom (%d) are not equal.\n",
1417	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1418	>	"\tlocalAtom (%d) are not equal.\n",
1419		info[0].n_atoms, local_atoms);
1420		painCave.isFatal = 1;
1421		simError();
#	Line 1259 | Line 1435 | void SimSetup::makeSysArrays(void){
1435
1436
1437		void SimSetup::makeSysArrays(void){
1438	<	int i, j, k, l;
1438	>
1439	>	#ifndef IS_MPI
1440	>	int k, j;
1441	>	#endif // is_mpi
1442	>	int i, l;
1443
1444		Atom** the_atoms;
1445		Molecule* the_molecules;
1266	–	Exclude** the_excludes;
1446
1268	–
1447		for (l = 0; l < nInfo; l++){
1448		// create the atom and short range interaction arrays
1449
#	Line 1291 | Line 1469 | void SimSetup::makeSysArrays(void){
1469		#else // is_mpi
1470
1471		molIndex = 0;
1472	<	globalAtomIndex = 0;
1472	>	globalAtomCounter = 0;
1473		for (i = 0; i < n_components; i++){
1474		for (j = 0; j < components_nmol[i]; j++){
1475		the_molecules[molIndex].setStampID(i);
1476		the_molecules[molIndex].setMyIndex(molIndex);
1477		the_molecules[molIndex].setGlobalIndex(molIndex);
1478		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1479	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1480	<	globalAtomIndex++;
1479	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1480	>	globalAtomCounter++;
1481		}
1482		molIndex++;
1483		}
#	Line 1308 | Line 1486 | void SimSetup::makeSysArrays(void){
1486
1487		#endif // is_mpi
1488
1489	<
1490	<	if (info[l].n_SRI){
1491	<	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	<
1489	>	info[l].globalExcludes = new int;
1490	>	info[l].globalExcludes[0] = 0;
1491	>
1492		// set the arrays into the SimInfo object
1493
1494		info[l].atoms = the_atoms;
1495		info[l].molecules = the_molecules;
1496		info[l].nGlobalExcludes = 0;
1336	–	info[l].excludes = the_excludes;
1497
1498		the_ff->setSimInfo(info);
1499		}
#	Line 1342 | Line 1502 | void SimSetup::makeIntegrator(void){
1502		void SimSetup::makeIntegrator(void){
1503		int k;
1504
1505	+	NVE<RealIntegrator>* myNVE = NULL;
1506		NVT<RealIntegrator>* myNVT = NULL;
1507	<	NPTi<RealIntegrator>* myNPTi = NULL;
1508	<	NPTf<RealIntegrator>* myNPTf = NULL;
1509	<	NPTim<RealIntegrator>* myNPTim = NULL;
1349	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1507	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1508	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1509	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1510
1511		for (k = 0; k < nInfo; k++){
1512		switch (ensembleCase){
1513		case NVE_ENS:
1514		if (globals->haveZconstraints()){
1515		setupZConstraint(info[k]);
1516	<	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1516	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1517		}
1518	<	else
1519	<	new NVE<RealIntegrator>(&(info[k]), the_ff);
1518	>	else{
1519	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1520	>	}
1521	>
1522	>	info->the_integrator = myNVE;
1523		break;
1524
1525		case NVT_ENS:
#	Line 1374 | Line 1537 | void SimSetup::makeIntegrator(void){
1537		else{
1538		sprintf(painCave.errMsg,
1539		"SimSetup error: If you use the NVT\n"
1540	<	"    ensemble, you must set tauThermostat.\n");
1540	>	"\tensemble, you must set tauThermostat.\n");
1541		painCave.isFatal = 1;
1542		simError();
1543		}
1544	+
1545	+	info->the_integrator = myNVT;
1546		break;
1547
1548		case NPTi_ENS:
1549		if (globals->haveZconstraints()){
1550		setupZConstraint(info[k]);
1551	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1551	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1552		}
1553		else
1554	<	myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1554	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1555
1556		myNPTi->setTargetTemp(globals->getTargetTemp());
1557
#	Line 1395 | Line 1560 | void SimSetup::makeIntegrator(void){
1560		else{
1561		sprintf(painCave.errMsg,
1562		"SimSetup error: If you use a constant pressure\n"
1563	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1563	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1564		painCave.isFatal = 1;
1565		simError();
1566		}
#	Line 1405 | Line 1570 | void SimSetup::makeIntegrator(void){
1570		else{
1571		sprintf(painCave.errMsg,
1572		"SimSetup error: If you use an NPT\n"
1573	<	"    ensemble, you must set tauThermostat.\n");
1573	>	"\tensemble, you must set tauThermostat.\n");
1574		painCave.isFatal = 1;
1575		simError();
1576		}
#	Line 1415 | Line 1580 | void SimSetup::makeIntegrator(void){
1580		else{
1581		sprintf(painCave.errMsg,
1582		"SimSetup error: If you use an NPT\n"
1583	<	"    ensemble, you must set tauBarostat.\n");
1583	>	"\tensemble, you must set tauBarostat.\n");
1584		painCave.isFatal = 1;
1585		simError();
1586		}
1587	+
1588	+	info->the_integrator = myNPTi;
1589		break;
1590
1591		case NPTf_ENS:
1592		if (globals->haveZconstraints()){
1593		setupZConstraint(info[k]);
1594	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1594	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1595		}
1596		else
1597	<	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1597	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1598
1599		myNPTf->setTargetTemp(globals->getTargetTemp());
1600
#	Line 1436 | Line 1603 | void SimSetup::makeIntegrator(void){
1603		else{
1604		sprintf(painCave.errMsg,
1605		"SimSetup error: If you use a constant pressure\n"
1606	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1606	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1607		painCave.isFatal = 1;
1608		simError();
1609		}
1610
1611		if (globals->haveTauThermostat())
1612		myNPTf->setTauThermostat(globals->getTauThermostat());
1613	+
1614		else{
1615		sprintf(painCave.errMsg,
1616		"SimSetup error: If you use an NPT\n"
1617	<	"    ensemble, you must set tauThermostat.\n");
1617	>	"\tensemble, you must set tauThermostat.\n");
1618		painCave.isFatal = 1;
1619		simError();
1620		}
1621
1622		if (globals->haveTauBarostat())
1623		myNPTf->setTauBarostat(globals->getTauBarostat());
1456	–	else{
1457	–	sprintf(painCave.errMsg,
1458	–	"SimSetup error: If you use an NPT\n"
1459	–	"    ensemble, you must set tauBarostat.\n");
1460	–	painCave.isFatal = 1;
1461	–	simError();
1462	–	}
1463	–	break;
1624
1465	–	case NPTim_ENS:
1466	–	if (globals->haveZconstraints()){
1467	–	setupZConstraint(info[k]);
1468	–	myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1469	–	}
1470	–	else
1471	–	myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1472	–
1473	–	myNPTim->setTargetTemp(globals->getTargetTemp());
1474	–
1475	–	if (globals->haveTargetPressure())
1476	–	myNPTim->setTargetPressure(globals->getTargetPressure());
1625		else{
1626		sprintf(painCave.errMsg,
1479	–	"SimSetup error: If you use a constant pressure\n"
1480	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1481	–	painCave.isFatal = 1;
1482	–	simError();
1483	–	}
1484	–
1485	–	if (globals->haveTauThermostat())
1486	–	myNPTim->setTauThermostat(globals->getTauThermostat());
1487	–	else{
1488	–	sprintf(painCave.errMsg,
1627		"SimSetup error: If you use an NPT\n"
1628	<	"    ensemble, you must set tauThermostat.\n");
1628	>	"\tensemble, you must set tauBarostat.\n");
1629		painCave.isFatal = 1;
1630		simError();
1631		}
1632
1633	<	if (globals->haveTauBarostat())
1496	<	myNPTim->setTauBarostat(globals->getTauBarostat());
1497	<	else{
1498	<	sprintf(painCave.errMsg,
1499	<	"SimSetup error: If you use an NPT\n"
1500	<	"    ensemble, you must set tauBarostat.\n");
1501	<	painCave.isFatal = 1;
1502	<	simError();
1503	<	}
1633	>	info->the_integrator = myNPTf;
1634		break;
1635
1636	<	case NPTfm_ENS:
1636	>	case NPTxyz_ENS:
1637		if (globals->haveZconstraints()){
1638		setupZConstraint(info[k]);
1639	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1639	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1640		}
1641		else
1642	<	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1642	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1643
1644	<	myNPTfm->setTargetTemp(globals->getTargetTemp());
1644	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1645
1646		if (globals->haveTargetPressure())
1647	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1647	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1648		else{
1649		sprintf(painCave.errMsg,
1650		"SimSetup error: If you use a constant pressure\n"
1651	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1651	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1652		painCave.isFatal = 1;
1653		simError();
1654	<	}
1654	>	}
1655
1656		if (globals->haveTauThermostat())
1657	<	myNPTfm->setTauThermostat(globals->getTauThermostat());
1657	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1658		else{
1659		sprintf(painCave.errMsg,
1660		"SimSetup error: If you use an NPT\n"
1661	<	"    ensemble, you must set tauThermostat.\n");
1661	>	"\tensemble, you must set tauThermostat.\n");
1662		painCave.isFatal = 1;
1663		simError();
1664		}
1665
1666		if (globals->haveTauBarostat())
1667	<	myNPTfm->setTauBarostat(globals->getTauBarostat());
1667	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1668		else{
1669		sprintf(painCave.errMsg,
1670		"SimSetup error: If you use an NPT\n"
1671	<	"    ensemble, you must set tauBarostat.\n");
1671	>	"\tensemble, you must set tauBarostat.\n");
1672		painCave.isFatal = 1;
1673		simError();
1674		}
1675	+
1676	+	info->the_integrator = myNPTxyz;
1677		break;
1678
1679		default:
#	Line 1589 | Line 1721 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1721		}
1722		else{
1723		sprintf(painCave.errMsg,
1724	<	"ZConstraint error: If you use an ZConstraint\n"
1725	<	" , you must set sample time.\n");
1724	>	"ZConstraint error: If you use a ZConstraint,\n"
1725	>	"\tyou must set zconsTime.\n");
1726		painCave.isFatal = 1;
1727		simError();
1728		}
#	Line 1605 | Line 1737 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1737		else{
1738		double defaultZConsTol = 0.01;
1739		sprintf(painCave.errMsg,
1740	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1741	<	" , default value %f is used.\n",
1740	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1741	>	"\tOOPSE will use a default value of %f.\n"
1742	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1743		defaultZConsTol);
1744		painCave.isFatal = 0;
1745		simError();
#	Line 1615 | Line 1748 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1748		}
1749		theInfo.addProperty(zconsTol);
1750
1751	<	//set Force Substraction Policy
1751	>	//set Force Subtraction Policy
1752		StringData* zconsForcePolicy = new StringData();
1753		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1754
#	Line 1624 | Line 1757 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1757		}
1758		else{
1759		sprintf(painCave.errMsg,
1760	<	"ZConstraint Warning: User does not set force substraction policy, "
1761	<	"average force substraction policy is used\n");
1760	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1761	>	"\tOOPSE will use PolicyByMass.\n"
1762	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1763		painCave.isFatal = 0;
1764		simError();
1765	<	zconsForcePolicy->setData("BYNUMBER");
1765	>	zconsForcePolicy->setData("BYMASS");
1766		}
1767
1768		theInfo.addProperty(zconsForcePolicy);
1769	+
1770	+	//set zcons gap
1771	+	DoubleData* zconsGap = new DoubleData();
1772	+	zconsGap->setID(ZCONSGAP_ID);
1773
1774	+	if (globals->haveZConsGap()){
1775	+	zconsGap->setData(globals->getZconsGap());
1776	+	theInfo.addProperty(zconsGap);
1777	+	}
1778	+
1779	+	//set zcons fixtime
1780	+	DoubleData* zconsFixtime = new DoubleData();
1781	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1782	+
1783	+	if (globals->haveZConsFixTime()){
1784	+	zconsFixtime->setData(globals->getZconsFixtime());
1785	+	theInfo.addProperty(zconsFixtime);
1786	+	}
1787	+
1788	+	//set zconsUsingSMD
1789	+	IntData* zconsUsingSMD = new IntData();
1790	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1791	+
1792	+	if (globals->haveZConsUsingSMD()){
1793	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1794	+	theInfo.addProperty(zconsUsingSMD);
1795	+	}
1796	+
1797		//Determine the name of ouput file and add it into SimInfo's property list
1798		//Be careful, do not use inFileName, since it is a pointer which
1799		//point to a string at master node, and slave nodes do not contain that string
#	Line 1662 | Line 1823 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1823		tempParaItem.zPos = zconStamp[i]->getZpos();
1824		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1825		tempParaItem.kRatio = zconStamp[i]->getKratio();
1826	<
1826	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1827	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1828		zconsParaData->addItem(tempParaItem);
1829		}
1830
1831	+	//check the uniqueness of index
1832	+	if(!zconsParaData->isIndexUnique()){
1833	+	sprintf(painCave.errMsg,
1834	+	"ZConstraint Error: molIndex is not unique!\n");
1835	+	painCave.isFatal = 1;
1836	+	simError();
1837	+	}
1838	+
1839		//sort the parameters by index of molecules
1840		zconsParaData->sortByIndex();
1841	<
1841	>
1842		//push data into siminfo, therefore, we can retrieve later
1843		theInfo.addProperty(zconsParaData);
1844		}
1845	+
1846	+	void SimSetup::makeMinimizer(){
1847	+
1848	+	OOPSEMinimizer* myOOPSEMinimizer;
1849	+	MinimizerParameterSet* param;
1850	+	char minimizerName[100];
1851	+
1852	+	for (int i = 0; i < nInfo; i++){
1853	+
1854	+	//prepare parameter set for minimizer
1855	+	param = new MinimizerParameterSet();
1856	+	param->setDefaultParameter();
1857	+
1858	+	if (globals->haveMinimizer()){
1859	+	param->setFTol(globals->getMinFTol());
1860	+	}
1861	+
1862	+	if (globals->haveMinGTol()){
1863	+	param->setGTol(globals->getMinGTol());
1864	+	}
1865	+
1866	+	if (globals->haveMinMaxIter()){
1867	+	param->setMaxIteration(globals->getMinMaxIter());
1868	+	}
1869	+
1870	+	if (globals->haveMinWriteFrq()){
1871	+	param->setMaxIteration(globals->getMinMaxIter());
1872	+	}
1873	+
1874	+	if (globals->haveMinWriteFrq()){
1875	+	param->setWriteFrq(globals->getMinWriteFrq());
1876	+	}
1877	+
1878	+	if (globals->haveMinStepSize()){
1879	+	param->setStepSize(globals->getMinStepSize());
1880	+	}
1881	+
1882	+	if (globals->haveMinLSMaxIter()){
1883	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1884	+	}
1885	+
1886	+	if (globals->haveMinLSTol()){
1887	+	param->setLineSearchTol(globals->getMinLSTol());
1888	+	}
1889	+
1890	+	strcpy(minimizerName, globals->getMinimizer());
1891	+
1892	+	if (!strcasecmp(minimizerName, "CG")){
1893	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1894	+	}
1895	+	else if (!strcasecmp(minimizerName, "SD")){
1896	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1897	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1898	+	}
1899	+	else{
1900	+	sprintf(painCave.errMsg,
1901	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1902	+	painCave.isFatal = 0;
1903	+	simError();
1904	+
1905	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1906	+	}
1907	+	info[i].the_integrator = myOOPSEMinimizer;
1908	+
1909	+	//store the minimizer into simInfo
1910	+	info[i].the_minimizer = myOOPSEMinimizer;
1911	+	info[i].has_minimizer = true;
1912	+	}
1913	+
1914	+	}

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