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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 736 by tim, Thu Aug 28 21:09:47 2003 UTC vs.
Revision 1180 by chrisfen, Thu May 20 20:24:07 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	+	CutoffGroupStamp* currentCutoffGroup;
187	+	CutoffGroup* myCutoffGroup;
188	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191		bond_pair* theBonds;
192		bend_set* theBends;
193		torsion_set* theTorsions;
194
195	+	set<int> skipList;
196
197	+	double phi, theta, psi;
198	+	char* molName;
199	+	char rbName[100];
200	+
201		//init the forceField paramters
202
203		the_ff->readParams();
204
154	–
205		// init the atoms
206
207	<	double ux, uy, uz, u, uSqr;
207	>	int nMembers, nNew, rb1, rb2;
208
209		for (k = 0; k < nInfo; k++){
210		the_ff->setSimInfo(&(info[k]));
211
212		atomOffset = 0;
213	<	excludeOffset = 0;
213	>
214		for (i = 0; i < info[k].n_mol; i++){
215		stampID = info[k].molecules[i].getStampID();
216	+	molName = comp_stamps[stampID]->getID();
217
218		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220		molInfo.nBends = comp_stamps[stampID]->getNBends();
221		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	+
226		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
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];
227
228	+	if (molInfo.nBonds > 0)
229	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	+	else
231	+	molInfo.myBonds = NULL;
232	+
233	+	if (molInfo.nBends > 0)
234	+	molInfo.myBends = new Bend*[molInfo.nBends];
235	+	else
236	+	molInfo.myBends = NULL;
237	+
238	+	if (molInfo.nTorsions > 0)
239	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	+	else
241	+	molInfo.myTorsions = NULL;
242	+
243		theBonds = new bond_pair[molInfo.nBonds];
244		theBends = new bend_set[molInfo.nBends];
245		theTorsions = new torsion_set[molInfo.nTorsions];
246	<
246	>
247		// make the Atoms
248
249		for (j = 0; j < molInfo.nAtoms; j++){
250		currentAtom = comp_stamps[stampID]->getAtom(j);
251	+
252		if (currentAtom->haveOrientation()){
253		dAtom = new DirectionalAtom((j + atomOffset),
254		info[k].getConfiguration());
255		info[k].n_oriented++;
256		molInfo.myAtoms[j] = dAtom;
257
258	<	ux = currentAtom->getOrntX();
259	<	uy = currentAtom->getOrntY();
260	<	uz = currentAtom->getOrntZ();
258	>	// Directional Atoms have standard unit vectors which are oriented
259	>	// in space using the three Euler angles.  We assume the standard
260	>	// unit vector was originally along the z axis below.
261
262	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265
266	<	u = sqrt(uSqr);
267	<	ux = ux / u;
201	<	uy = uy / u;
202	<	uz = uz / u;
203	<
204	<	dAtom->setSUx(ux);
205	<	dAtom->setSUy(uy);
206	<	dAtom->setSUz(uz);
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268		}
269		else{
270	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
271	<	info[k].getConfiguration());
270	>
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272	>
273		}
212	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
274
275	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277
278	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
280		#endif // is_mpi
281		}
#	Line 224 | Line 286 | void SimSetup::makeMolecules(void){
286		theBonds[j].a = currentBond->getA() + atomOffset;
287		theBonds[j].b = currentBond->getB() + atomOffset;
288
289	<	exI = theBonds[j].a;
290	<	exJ = theBonds[j].b;
289	>	tempI = theBonds[j].a;
290	>	tempJ = theBonds[j].b;
291
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	–	}
292		#ifdef IS_MPI
293	<	tempEx = exI;
294	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
295	<	tempEx = exJ;
296	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243	<	#else  // isn't MPI
244	<
245	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246	<	#endif  //is_mpi
300	>	info[k].excludes->addPair(exI, exJ);
301		}
248	–	excludeOffset += molInfo.nBonds;
302
303		//make the bends
304		for (j = 0; j < molInfo.nBends; j++){
#	Line 295 | Line 348 | void SimSetup::makeMolecules(void){
348		}
349		}
350
351	<	if (!theBends[j].isGhost){
352	<	exI = theBends[j].a;
353	<	exJ = theBends[j].c;
354	<	}
355	<	else{
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	<	}
351	>	if (theBends[j].isGhost) {
352	>
353	>	tempI = theBends[j].a;
354	>	tempJ = theBends[j].b;
355	>
356		#ifdef IS_MPI
357	<	tempEx = exI;
358	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
359	<	tempEx = exJ;
360	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
366	<	#else  // isn't MPI
367	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
368	<	#endif  //is_mpi
365	>	} else {
366	>
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
324	–	excludeOffset += molInfo.nBends;
386
387		for (j = 0; j < molInfo.nTorsions; j++){
388		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 330 | Line 391 | void SimSetup::makeMolecules(void){
391		theTorsions[j].c = currentTorsion->getC() + atomOffset;
392		theTorsions[j].d = currentTorsion->getD() + atomOffset;
393
394	<	exI = theTorsions[j].a;
395	<	exJ = theTorsions[j].d;
394	>	tempI = theTorsions[j].a;
395	>	tempJ = theTorsions[j].b;
396	>	tempK = theTorsions[j].c;
397	>	tempL = theTorsions[j].d;
398
336	–	// exclude_I must always be the smaller of the pair
337	–	if (exI > exJ){
338	–	tempEx = exI;
339	–	exI = exJ;
340	–	exJ = tempEx;
341	–	}
399		#ifdef IS_MPI
400	<	tempEx = exI;
401	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
402	<	tempEx = exJ;
403	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410
411	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
412	<	#else  // isn't MPI
413	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
414	<	#endif  //is_mpi
415	<	}
416	<	excludeOffset += molInfo.nTorsions;
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418
419	+
420	+	molInfo.myRigidBodies.clear();
421	+
422	+	for (j = 0; j < molInfo.nRigidBodies; j++){
423
424	<	// send the arrays off to the forceField for init.
424	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	>	nMembers = currentRigidBody->getNMembers();
426	>
427	>	// Create the Rigid Body:
428	>
429	>	myRB = new RigidBody();
430	>
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435	>
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438	>
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441	>
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445	>
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448	>
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452	>	#ifdef IS_MPI
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484	>
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487	>	}
488	>
489	>
490	>	//create cutoff group for molecule
491	>
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496	>
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499	>
500	>	myCutoffGroup = new CutoffGroup();
501	>
502	>	for (int cg = 0; cg < nMembers; cg++) {
503	>
504	>	// molI is atom numbering inside this molecule
505	>	molI = currentCutoffGroup->getMember(cg);
506	>
507	>	// tempI is atom numbering on local processor
508	>	tempI = molI + atomOffset;
509	>
510	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	>
512	>	cutoffAtomSet.insert(tempI);
513	>	}
514	>
515	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	>
518	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519	>
520	>	for(j = 0; j < molInfo.nAtoms; j++){
521	>
522	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	>	myCutoffGroup = new CutoffGroup();
524	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	>	}
527	>
528	>	}
529	>
530	>
531	>
532	>
533	>	// After this is all set up, scan through the atoms to
534	>	// see if they can be added to the integrableObjects:
535	>
536	>	molInfo.myIntegrableObjects.clear();
537	>
538	>
539	>	for (j = 0; j < molInfo.nAtoms; j++){
540	>
541	>	#ifdef IS_MPI
542	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	>	#else
544	>	slJ = j+atomOffset;
545	>	#endif
546	>
547	>	// if they aren't on the skip list, then they can be integrated
548	>
549	>	if (skipList.find(slJ) == skipList.end()) {
550	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	>	info[k].integrableObjects.push_back(mySD);
552	>	molInfo.myIntegrableObjects.push_back(mySD);
553	>	}
554	>	}
555
556	+	// all rigid bodies are integrated:
557	+
558	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	+	info[k].integrableObjects.push_back(mySD);
561	+	molInfo.myIntegrableObjects.push_back(mySD);
562	+	}
563	+
564	+
565	+	// send the arrays off to the forceField for init.
566	+
567		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571		theTorsions);
572
364	–
573		info[k].molecules[i].initialize(molInfo);
574
575
#	Line 369 | Line 577 | void SimSetup::makeMolecules(void){
577		delete[] theBonds;
578		delete[] theBends;
579		delete[] theTorsions;
580	<	}
580	>	}
581		}
582
583		#ifdef IS_MPI
#	Line 377 | Line 585 | void SimSetup::makeMolecules(void){
585		MPIcheckPoint();
586		#endif // is_mpi
587
380	–	// clean up the forcefield
381	–
382	–	the_ff->calcRcut();
383	–	the_ff->cleanMe();
588		}
589
590		void SimSetup::initFromBass(void){
#	Line 553 | Line 757 | void SimSetup::gatherInfo(void){
757
758
759		void SimSetup::gatherInfo(void){
760	<	int i, j, k;
760	>	int i;
761
762		ensembleCase = -1;
763		ffCase = -1;
#	Line 581 | Line 785 | void SimSetup::gatherInfo(void){
785		else if (!strcasecmp(force_field, "EAM")){
786		ffCase = FF_EAM;
787		}
788	+	else if (!strcasecmp(force_field, "WATER")){
789	+	ffCase = FF_H2O;
790	+	}
791		else{
792		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793		force_field);
#	Line 604 | Line 811 | void SimSetup::gatherInfo(void){
811		else if (!strcasecmp(ensemble, "NPTf")){
812		ensembleCase = NPTf_ENS;
813		}
814	<	else if (!strcasecmp(ensemble, "NPTim")){
815	<	ensembleCase = NPTim_ENS;
609	<	}
610	<	else if (!strcasecmp(ensemble, "NPTfm")){
611	<	ensembleCase = NPTfm_ENS;
814	>	else if (!strcasecmp(ensemble, "NPTxyz")){
815	>	ensembleCase = NPTxyz_ENS;
816		}
817		else{
818		sprintf(painCave.errMsg,
819	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
820	<	"reverting to NVE for this simulation.\n",
819	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	>	"\treverting to NVE for this simulation.\n",
821		ensemble);
822		painCave.isFatal = 0;
823		simError();
#	Line 645 | Line 849 | void SimSetup::gatherInfo(void){
849		if (!the_components[i]->haveNMol()){
850		// we have a problem
851		sprintf(painCave.errMsg,
852	<	"SimSetup Error. No global NMol or component NMol"
853	<	" given. Cannot calculate the number of atoms.\n");
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854		painCave.isFatal = 1;
855		simError();
856		}
#	Line 666 | Line 870 | void SimSetup::gatherInfo(void){
870		simError();
871		}
872
873	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	+	sprintf(painCave.errMsg,
876	+	"Sample time is not divisible by dt.\n"
877	+	"\tThis will result in samples that are not uniformly\n"
878	+	"\tdistributed in time.  If this is a problem, change\n"
879	+	"\tyour sampleTime variable.\n");
880	+	painCave.isFatal = 0;
881	+	simError();
882	+	}
883	+
884	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	+	sprintf(painCave.errMsg,
886	+	"Status time is not divisible by dt.\n"
887	+	"\tThis will result in status reports that are not uniformly\n"
888	+	"\tdistributed in time.  If this is a problem, change \n"
889	+	"\tyour statusTime variable.\n");
890	+	painCave.isFatal = 0;
891	+	simError();
892	+	}
893	+
894	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	+	sprintf(painCave.errMsg,
896	+	"Thermal time is not divisible by dt.\n"
897	+	"\tThis will result in thermalizations that are not uniformly\n"
898	+	"\tdistributed in time.  If this is a problem, change \n"
899	+	"\tyour thermalTime variable.\n");
900	+	painCave.isFatal = 0;
901	+	simError();
902	+	}
903	+
904	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	+	sprintf(painCave.errMsg,
906	+	"Reset time is not divisible by dt.\n"
907	+	"\tThis will result in integrator resets that are not uniformly\n"
908	+	"\tdistributed in time.  If this is a problem, change\n"
909	+	"\tyour resetTime variable.\n");
910	+	painCave.isFatal = 0;
911	+	simError();
912	+	}
913	+
914		// set the status, sample, and thermal kick times
915
916		for (i = 0; i < nInfo; i++){
917		if (globals->haveSampleTime()){
918		info[i].sampleTime = globals->getSampleTime();
919		info[i].statusTime = info[i].sampleTime;
675	–	info[i].thermalTime = info[i].sampleTime;
920		}
921		else{
922		info[i].sampleTime = globals->getRunTime();
923		info[i].statusTime = info[i].sampleTime;
680	–	info[i].thermalTime = info[i].sampleTime;
924		}
925
926		if (globals->haveStatusTime()){
#	Line 686 | Line 929 | void SimSetup::gatherInfo(void){
929
930		if (globals->haveThermalTime()){
931		info[i].thermalTime = globals->getThermalTime();
932	+	} else {
933	+	info[i].thermalTime = globals->getRunTime();
934		}
935
936	<	// check for the temperature set flag
936	>	info[i].resetIntegrator = 0;
937	>	if( globals->haveResetTime() ){
938	>	info[i].resetTime = globals->getResetTime();
939	>	info[i].resetIntegrator = 1;
940	>	}
941
942	+	// check for the temperature set flag
943	+
944		if (globals->haveTempSet())
945		info[i].setTemp = globals->getTempSet();
946
947	<	// get some of the tricky things that may still be in the globals
947	>	// check for the extended State init
948
949	<	double boxVector[3];
950	<	if (globals->haveBox()){
700	<	boxVector[0] = globals->getBox();
701	<	boxVector[1] = globals->getBox();
702	<	boxVector[2] = globals->getBox();
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951
952	<	info[i].setBox(boxVector);
953	<	}
954	<	else if (globals->haveDensity()){
955	<	double vol;
956	<	vol = (double) tot_nmol / globals->getDensity();
957	<	boxVector[0] = pow(vol, (1.0 / 3.0));
958	<	boxVector[1] = boxVector[0];
959	<	boxVector[2] = boxVector[0];
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);
952	>	// check for thermodynamic integration
953	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
954	>	info[i].thermIntLambda = globals->getThermIntLambda();
955	>	info[i].thermIntK = globals->getThermIntK();
956	>	info[i].useThermInt = 1;
957	>
958	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
959	>	info[i].restraint = myRestraint;
960		}
961		}
962	<
962	>
963		//setup seed for random number generator
964		int seedValue;
965
#	Line 780 | Line 999 | void SimSetup::gatherInfo(void){
999		for (int i = 0; i < nInfo; i++){
1000		info[i].setSeed(seedValue);
1001		}
1002	<
1002	>
1003		#ifdef IS_MPI
1004	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1004	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1005		MPIcheckPoint();
1006		#endif // is_mpi
1007		}
#	Line 791 | Line 1010 | void SimSetup::finalInfoCheck(void){
1010		void SimSetup::finalInfoCheck(void){
1011		int index;
1012		int usesDipoles;
1013	+	int usesCharges;
1014		int i;
1015
1016		for (i = 0; i < nInfo; i++){
#	Line 802 | Line 1022 | void SimSetup::finalInfoCheck(void){
1022		usesDipoles = (info[i].atoms[index])->hasDipole();
1023		index++;
1024		}
1025	<
1025	>	index = 0;
1026	>	usesCharges = 0;
1027	>	while ((index < info[i].n_atoms) && !usesCharges){
1028	>	usesCharges= (info[i].atoms[index])->hasCharge();
1029	>	index++;
1030	>	}
1031		#ifdef IS_MPI
1032		int myUse = usesDipoles;
1033		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1034		#endif //is_mpi
1035
1036	<	double theEcr, theEst;
1036	>	double theRcut, theRsw;
1037
1038	+	if (globals->haveRcut()) {
1039	+	theRcut = globals->getRcut();
1040	+
1041	+	if (globals->haveRsw())
1042	+	theRsw = globals->getRsw();
1043	+	else
1044	+	theRsw = theRcut;
1045	+
1046	+	info[i].setDefaultRcut(theRcut, theRsw);
1047	+
1048	+	} else {
1049	+
1050	+	the_ff->calcRcut();
1051	+	theRcut = info[i].getRcut();
1052	+
1053	+	if (globals->haveRsw())
1054	+	theRsw = globals->getRsw();
1055	+	else
1056	+	theRsw = theRcut;
1057	+
1058	+	info[i].setDefaultRcut(theRcut, theRsw);
1059	+	}
1060	+
1061		if (globals->getUseRF()){
1062		info[i].useReactionField = 1;
1063	<
1064	<	if (!globals->haveECR()){
1063	>
1064	>	if (!globals->haveRcut()){
1065		sprintf(painCave.errMsg,
1066	<	"SimSetup Warning: using default value of 1/2 the smallest "
1067	<	"box length for the electrostaticCutoffRadius.\n"
1068	<	"I hope you have a very fast processor!\n");
1066	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1067	>	"\tOOPSE will use a default value of 15.0 angstroms"
1068	>	"\tfor the cutoffRadius.\n");
1069		painCave.isFatal = 0;
1070		simError();
1071	<	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;
1071	>	theRcut = 15.0;
1072		}
1073		else{
1074	<	theEcr = globals->getECR();
1074	>	theRcut = globals->getRcut();
1075		}
1076
1077	<	if (!globals->haveEST()){
1077	>	if (!globals->haveRsw()){
1078		sprintf(painCave.errMsg,
1079	<	"SimSetup Warning: using default value of 0.05 * the "
1080	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1079	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1080	>	"\tOOPSE will use a default value of\n"
1081	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1082		painCave.isFatal = 0;
1083		simError();
1084	<	theEst = 0.05 * theEcr;
1084	>	theRsw = 0.95 * theRcut;
1085		}
1086		else{
1087	<	theEst = globals->getEST();
1087	>	theRsw = globals->getRsw();
1088		}
1089
1090	<	info[i].setEcr(theEcr, theEst);
1090	>	info[i].setDefaultRcut(theRcut, theRsw);
1091
1092		if (!globals->haveDielectric()){
1093		sprintf(painCave.errMsg,
1094	<	"SimSetup Error: You are trying to use Reaction Field without"
1095	<	"setting a dielectric constant!\n");
1094	>	"SimSetup Error: No Dielectric constant was set.\n"
1095	>	"\tYou are trying to use Reaction Field without"
1096	>	"\tsetting a dielectric constant!\n");
1097		painCave.isFatal = 1;
1098		simError();
1099		}
1100		info[i].dielectric = globals->getDielectric();
1101		}
1102		else{
1103	<	if (usesDipoles){
1104	<	if (!globals->haveECR()){
1103	>	if (usesDipoles || usesCharges){
1104	>
1105	>	if (!globals->haveRcut()){
1106		sprintf(painCave.errMsg,
1107	<	"SimSetup Warning: using default value of 1/2 the smallest "
1108	<	"box length for the electrostaticCutoffRadius.\n"
1109	<	"I hope you have a very fast processor!\n");
1107	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1108	>	"\tOOPSE will use a default value of 15.0 angstroms"
1109	>	"\tfor the cutoffRadius.\n");
1110		painCave.isFatal = 0;
1111		simError();
1112	<	double smallest;
1113	<	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;
874	<	}
1112	>	theRcut = 15.0;
1113	>	}
1114		else{
1115	<	theEcr = globals->getECR();
1115	>	theRcut = globals->getRcut();
1116		}
1117	<
1118	<	if (!globals->haveEST()){
1117	>
1118	>	if (!globals->haveRsw()){
1119		sprintf(painCave.errMsg,
1120	<	"SimSetup Warning: using default value of 0.05 * the "
1121	<	"electrostaticCutoffRadius for the "
1122	<	"electrostaticSkinThickness\n");
1123	<	painCave.isFatal = 0;
1124	<	simError();
1125	<	theEst = 0.05 * theEcr;
1120	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1121	>	"\tOOPSE will use a default value of\n"
1122	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1123	>	painCave.isFatal = 0;
1124	>	simError();
1125	>	theRsw = 0.95 * theRcut;
1126		}
1127		else{
1128	<	theEst = globals->getEST();
1128	>	theRsw = globals->getRsw();
1129		}
1130	<
1131	<	info[i].setEcr(theEcr, theEst);
1130	>
1131	>	info[i].setDefaultRcut(theRcut, theRsw);
1132	>
1133		}
1134		}
1135		}
896	–
1136		#ifdef IS_MPI
1137		strcpy(checkPointMsg, "post processing checks out");
1138		MPIcheckPoint();
1139		#endif // is_mpi
901	–	}
1140
1141	+	// clean up the forcefield
1142	+	the_ff->cleanMe();
1143	+	}
1144	+
1145		void SimSetup::initSystemCoords(void){
1146		int i;
1147
#	Line 916 | Line 1158 | void SimSetup::initSystemCoords(void){
1158		if (worldRank == 0){
1159		#endif //is_mpi
1160		inName = globals->getInitialConfig();
919	–	double* tempDouble = new double[1000000];
1161		fileInit = new InitializeFromFile(inName);
1162		#ifdef IS_MPI
1163		}
#	Line 928 | Line 1169 | void SimSetup::initSystemCoords(void){
1169		delete fileInit;
1170		}
1171		else{
1172	<	#ifdef IS_MPI
932	<
1172	>
1173		// no init from bass
1174	<
1174	>
1175		sprintf(painCave.errMsg,
1176	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1177	<	painCave.isFatal;
1176	>	"Cannot intialize a simulation without an initial configuration file.\n");
1177	>	painCave.isFatal = 1;;
1178		simError();
1179	<
940	<	#else
941	<
942	<	initFromBass();
943	<
944	<
945	<	#endif
1179	>
1180		}
1181
1182		#ifdef IS_MPI
#	Line 1036 | Line 1270 | void SimSetup::makeOutNames(void){
1270		}
1271		}
1272
1273	+	strcpy(info[k].rawPotName, inFileName);
1274	+	nameLength = strlen(info[k].rawPotName);
1275	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1276	+	if (!strcmp(endTest, ".bass")){
1277	+	strcpy(endTest, ".raw");
1278	+	}
1279	+	else if (!strcmp(endTest, ".BASS")){
1280	+	strcpy(endTest, ".raw");
1281	+	}
1282	+	else{
1283	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1284	+	if (!strcmp(endTest, ".bss")){
1285	+	strcpy(endTest, ".raw");
1286	+	}
1287	+	else if (!strcmp(endTest, ".mdl")){
1288	+	strcpy(endTest, ".raw");
1289	+	}
1290	+	else{
1291	+	strcat(info[k].rawPotName, ".raw");
1292	+	}
1293	+	}
1294	+
1295		#ifdef IS_MPI
1296
1297		}
#	Line 1096 | Line 1352 | void SimSetup::createFF(void){
1352		the_ff = new EAM_FF();
1353		break;
1354
1355	+	case FF_H2O:
1356	+	the_ff = new WATER();
1357	+	break;
1358	+
1359		default:
1360		sprintf(painCave.errMsg,
1361		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1116 | Line 1376 | void SimSetup::compList(void){
1376		LinkedMolStamp* headStamp = new LinkedMolStamp();
1377		LinkedMolStamp* currentStamp = NULL;
1378		comp_stamps = new MoleculeStamp * [n_components];
1379	+	bool haveCutoffGroups;
1380
1381	+	haveCutoffGroups = false;
1382	+
1383		// make an array of molecule stamps that match the components used.
1384		// also extract the used stamps out into a separate linked list
1385
#	Line 1151 | Line 1414 | void SimSetup::compList(void){
1414		headStamp->add(currentStamp);
1415		comp_stamps[i] = headStamp->match(id);
1416		}
1417	+
1418	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1419	+	haveCutoffGroups = true;
1420		}
1421	+
1422	+	for (i = 0; i < nInfo; i++)
1423	+	info[i].haveCutoffGroups = haveCutoffGroups;
1424
1425		#ifdef IS_MPI
1426		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1160 | Line 1429 | void SimSetup::calcSysValues(void){
1429		}
1430
1431		void SimSetup::calcSysValues(void){
1432	<	int i, j, k;
1432	>	int i;
1433
1434		int* molMembershipArray;
1435
#	Line 1168 | Line 1437 | void SimSetup::calcSysValues(void){
1437		tot_bonds = 0;
1438		tot_bends = 0;
1439		tot_torsions = 0;
1440	+	tot_rigid = 0;
1441		for (i = 0; i < n_components; i++){
1442		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1443		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1444		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1445		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1446	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1447		}
1448	<
1448	>
1449		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1450		molMembershipArray = new int[tot_atoms];
1451
#	Line 1196 | Line 1467 | void SimSetup::mpiMolDivide(void){
1467		int i, j, k;
1468		int localMol, allMol;
1469		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1470	+	int local_rigid;
1471	+	vector<int> globalMolIndex;
1472
1473		mpiSim = new mpiSimulation(info);
1474
1475	<	globalIndex = mpiSim->divideLabor();
1475	>	mpiSim->divideLabor();
1476	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1477	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1478
1479		// set up the local variables
1480
#	Line 1212 | Line 1487 | void SimSetup::mpiMolDivide(void){
1487		local_bonds = 0;
1488		local_bends = 0;
1489		local_torsions = 0;
1490	<	globalAtomIndex = 0;
1490	>	local_rigid = 0;
1491	>	globalAtomCounter = 0;
1492
1217	–
1493		for (i = 0; i < n_components; i++){
1494		for (j = 0; j < components_nmol[i]; j++){
1495		if (mol2proc[allMol] == worldRank){
#	Line 1222 | Line 1497 | void SimSetup::mpiMolDivide(void){
1497		local_bonds += comp_stamps[i]->getNBonds();
1498		local_bends += comp_stamps[i]->getNBends();
1499		local_torsions += comp_stamps[i]->getNTorsions();
1500	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1501		localMol++;
1502		}
1503		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1504	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1505	<	globalAtomIndex++;
1504	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1505	>	globalAtomCounter++;
1506		}
1507
1508		allMol++;
#	Line 1235 | Line 1511 | void SimSetup::mpiMolDivide(void){
1511		local_SRI = local_bonds + local_bends + local_torsions;
1512
1513		info[0].n_atoms = mpiSim->getMyNlocal();
1514	+
1515
1516		if (local_atoms != info[0].n_atoms){
1517		sprintf(painCave.errMsg,
1518	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1519	<	" localAtom (%d) are not equal.\n",
1518	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1519	>	"\tlocalAtom (%d) are not equal.\n",
1520		info[0].n_atoms, local_atoms);
1521		painCave.isFatal = 1;
1522		simError();
#	Line 1259 | Line 1536 | void SimSetup::makeSysArrays(void){
1536
1537
1538		void SimSetup::makeSysArrays(void){
1539	<	int i, j, k, l;
1539	>
1540	>	#ifndef IS_MPI
1541	>	int k, j;
1542	>	#endif // is_mpi
1543	>	int i, l;
1544
1545		Atom** the_atoms;
1546		Molecule* the_molecules;
1266	–	Exclude** the_excludes;
1547
1268	–
1548		for (l = 0; l < nInfo; l++){
1549		// create the atom and short range interaction arrays
1550
#	Line 1291 | Line 1570 | void SimSetup::makeSysArrays(void){
1570		#else // is_mpi
1571
1572		molIndex = 0;
1573	<	globalAtomIndex = 0;
1573	>	globalAtomCounter = 0;
1574		for (i = 0; i < n_components; i++){
1575		for (j = 0; j < components_nmol[i]; j++){
1576		the_molecules[molIndex].setStampID(i);
1577		the_molecules[molIndex].setMyIndex(molIndex);
1578		the_molecules[molIndex].setGlobalIndex(molIndex);
1579		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1580	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1581	<	globalAtomIndex++;
1580	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1581	>	globalAtomCounter++;
1582		}
1583		molIndex++;
1584		}
#	Line 1308 | Line 1587 | void SimSetup::makeSysArrays(void){
1587
1588		#endif // is_mpi
1589
1590	<
1591	<	if (info[l].n_SRI){
1592	<	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	<
1590	>	info[l].globalExcludes = new int;
1591	>	info[l].globalExcludes[0] = 0;
1592	>
1593		// set the arrays into the SimInfo object
1594
1595		info[l].atoms = the_atoms;
1596		info[l].molecules = the_molecules;
1597		info[l].nGlobalExcludes = 0;
1598	<	info[l].excludes = the_excludes;
1337	<
1598	>
1599		the_ff->setSimInfo(info);
1600		}
1601		}
#	Line 1342 | Line 1603 | void SimSetup::makeIntegrator(void){
1603		void SimSetup::makeIntegrator(void){
1604		int k;
1605
1606	+	NVE<RealIntegrator>* myNVE = NULL;
1607		NVT<RealIntegrator>* myNVT = NULL;
1608	<	NPTi<RealIntegrator>* myNPTi = NULL;
1609	<	NPTf<RealIntegrator>* myNPTf = NULL;
1610	<	NPTim<RealIntegrator>* myNPTim = NULL;
1349	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1608	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1609	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1610	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1611
1612		for (k = 0; k < nInfo; k++){
1613		switch (ensembleCase){
1614		case NVE_ENS:
1615		if (globals->haveZconstraints()){
1616		setupZConstraint(info[k]);
1617	<	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1617	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1618		}
1619	<	else
1620	<	new NVE<RealIntegrator>(&(info[k]), the_ff);
1619	>	else{
1620	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1621	>	}
1622	>
1623	>	info->the_integrator = myNVE;
1624		break;
1625
1626		case NVT_ENS:
#	Line 1374 | Line 1638 | void SimSetup::makeIntegrator(void){
1638		else{
1639		sprintf(painCave.errMsg,
1640		"SimSetup error: If you use the NVT\n"
1641	<	"    ensemble, you must set tauThermostat.\n");
1641	>	"\tensemble, you must set tauThermostat.\n");
1642		painCave.isFatal = 1;
1643		simError();
1644		}
1645	+
1646	+	info->the_integrator = myNVT;
1647		break;
1648
1649		case NPTi_ENS:
1650		if (globals->haveZconstraints()){
1651		setupZConstraint(info[k]);
1652	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1652	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1653		}
1654		else
1655	<	myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1655	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1656
1657		myNPTi->setTargetTemp(globals->getTargetTemp());
1658
#	Line 1395 | Line 1661 | void SimSetup::makeIntegrator(void){
1661		else{
1662		sprintf(painCave.errMsg,
1663		"SimSetup error: If you use a constant pressure\n"
1664	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1664	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1665		painCave.isFatal = 1;
1666		simError();
1667		}
#	Line 1405 | Line 1671 | void SimSetup::makeIntegrator(void){
1671		else{
1672		sprintf(painCave.errMsg,
1673		"SimSetup error: If you use an NPT\n"
1674	<	"    ensemble, you must set tauThermostat.\n");
1674	>	"\tensemble, you must set tauThermostat.\n");
1675		painCave.isFatal = 1;
1676		simError();
1677		}
#	Line 1415 | Line 1681 | void SimSetup::makeIntegrator(void){
1681		else{
1682		sprintf(painCave.errMsg,
1683		"SimSetup error: If you use an NPT\n"
1684	<	"    ensemble, you must set tauBarostat.\n");
1684	>	"\tensemble, you must set tauBarostat.\n");
1685		painCave.isFatal = 1;
1686		simError();
1687		}
1688	+
1689	+	info->the_integrator = myNPTi;
1690		break;
1691
1692		case NPTf_ENS:
1693		if (globals->haveZconstraints()){
1694		setupZConstraint(info[k]);
1695	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1695	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1696		}
1697		else
1698	<	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1698	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1699
1700		myNPTf->setTargetTemp(globals->getTargetTemp());
1701
#	Line 1436 | Line 1704 | void SimSetup::makeIntegrator(void){
1704		else{
1705		sprintf(painCave.errMsg,
1706		"SimSetup error: If you use a constant pressure\n"
1707	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1707	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1708		painCave.isFatal = 1;
1709		simError();
1710		}
1711
1712		if (globals->haveTauThermostat())
1713		myNPTf->setTauThermostat(globals->getTauThermostat());
1714	+
1715		else{
1716		sprintf(painCave.errMsg,
1717		"SimSetup error: If you use an NPT\n"
1718	<	"    ensemble, you must set tauThermostat.\n");
1718	>	"\tensemble, you must set tauThermostat.\n");
1719		painCave.isFatal = 1;
1720		simError();
1721		}
1722
1723		if (globals->haveTauBarostat())
1724		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;
1725
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());
1726		else{
1727		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,
1728		"SimSetup error: If you use an NPT\n"
1729	<	"    ensemble, you must set tauThermostat.\n");
1729	>	"\tensemble, you must set tauBarostat.\n");
1730		painCave.isFatal = 1;
1731		simError();
1732		}
1733
1734	<	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	<	}
1734	>	info->the_integrator = myNPTf;
1735		break;
1736
1737	<	case NPTfm_ENS:
1737	>	case NPTxyz_ENS:
1738		if (globals->haveZconstraints()){
1739		setupZConstraint(info[k]);
1740	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1740	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1741		}
1742		else
1743	<	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1743	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1744
1745	<	myNPTfm->setTargetTemp(globals->getTargetTemp());
1745	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1746
1747		if (globals->haveTargetPressure())
1748	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1748	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1749		else{
1750		sprintf(painCave.errMsg,
1751		"SimSetup error: If you use a constant pressure\n"
1752	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1752	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1753		painCave.isFatal = 1;
1754		simError();
1755	<	}
1755	>	}
1756
1757		if (globals->haveTauThermostat())
1758	<	myNPTfm->setTauThermostat(globals->getTauThermostat());
1758	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1759		else{
1760		sprintf(painCave.errMsg,
1761		"SimSetup error: If you use an NPT\n"
1762	<	"    ensemble, you must set tauThermostat.\n");
1762	>	"\tensemble, you must set tauThermostat.\n");
1763		painCave.isFatal = 1;
1764		simError();
1765		}
1766
1767		if (globals->haveTauBarostat())
1768	<	myNPTfm->setTauBarostat(globals->getTauBarostat());
1768	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1769		else{
1770		sprintf(painCave.errMsg,
1771		"SimSetup error: If you use an NPT\n"
1772	<	"    ensemble, you must set tauBarostat.\n");
1772	>	"\tensemble, you must set tauBarostat.\n");
1773		painCave.isFatal = 1;
1774		simError();
1775		}
1776	+
1777	+	info->the_integrator = myNPTxyz;
1778		break;
1779
1780		default:
#	Line 1589 | Line 1822 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1822		}
1823		else{
1824		sprintf(painCave.errMsg,
1825	<	"ZConstraint error: If you use an ZConstraint\n"
1826	<	" , you must set sample time.\n");
1825	>	"ZConstraint error: If you use a ZConstraint,\n"
1826	>	"\tyou must set zconsTime.\n");
1827		painCave.isFatal = 1;
1828		simError();
1829		}
#	Line 1605 | Line 1838 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1838		else{
1839		double defaultZConsTol = 0.01;
1840		sprintf(painCave.errMsg,
1841	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1842	<	" , default value %f is used.\n",
1841	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1842	>	"\tOOPSE will use a default value of %f.\n"
1843	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1844		defaultZConsTol);
1845		painCave.isFatal = 0;
1846		simError();
#	Line 1615 | Line 1849 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1849		}
1850		theInfo.addProperty(zconsTol);
1851
1852	<	//set Force Substraction Policy
1852	>	//set Force Subtraction Policy
1853		StringData* zconsForcePolicy = new StringData();
1854		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1855
#	Line 1624 | Line 1858 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1858		}
1859		else{
1860		sprintf(painCave.errMsg,
1861	<	"ZConstraint Warning: User does not set force substraction policy, "
1862	<	"PolicyByMass is used\n");
1861	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1862	>	"\tOOPSE will use PolicyByMass.\n"
1863	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1864		painCave.isFatal = 0;
1865		simError();
1866		zconsForcePolicy->setData("BYMASS");
#	Line 1633 | Line 1868 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1868
1869		theInfo.addProperty(zconsForcePolicy);
1870
1871	+	//set zcons gap
1872	+	DoubleData* zconsGap = new DoubleData();
1873	+	zconsGap->setID(ZCONSGAP_ID);
1874	+
1875	+	if (globals->haveZConsGap()){
1876	+	zconsGap->setData(globals->getZconsGap());
1877	+	theInfo.addProperty(zconsGap);
1878	+	}
1879	+
1880	+	//set zcons fixtime
1881	+	DoubleData* zconsFixtime = new DoubleData();
1882	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1883	+
1884	+	if (globals->haveZConsFixTime()){
1885	+	zconsFixtime->setData(globals->getZconsFixtime());
1886	+	theInfo.addProperty(zconsFixtime);
1887	+	}
1888	+
1889	+	//set zconsUsingSMD
1890	+	IntData* zconsUsingSMD = new IntData();
1891	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1892	+
1893	+	if (globals->haveZConsUsingSMD()){
1894	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1895	+	theInfo.addProperty(zconsUsingSMD);
1896	+	}
1897	+
1898		//Determine the name of ouput file and add it into SimInfo's property list
1899		//Be careful, do not use inFileName, since it is a pointer which
1900		//point to a string at master node, and slave nodes do not contain that string
#	Line 1662 | Line 1924 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1924		tempParaItem.zPos = zconStamp[i]->getZpos();
1925		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1926		tempParaItem.kRatio = zconStamp[i]->getKratio();
1927	<
1927	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1928	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1929		zconsParaData->addItem(tempParaItem);
1930		}
1931
1932		//check the uniqueness of index
1933		if(!zconsParaData->isIndexUnique()){
1934		sprintf(painCave.errMsg,
1935	<	"ZConstraint Error: molIndex is not unique\n");
1935	>	"ZConstraint Error: molIndex is not unique!\n");
1936		painCave.isFatal = 1;
1937		simError();
1938		}
#	Line 1680 | Line 1943 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1943		//push data into siminfo, therefore, we can retrieve later
1944		theInfo.addProperty(zconsParaData);
1945		}
1946	+
1947	+	void SimSetup::makeMinimizer(){
1948	+
1949	+	OOPSEMinimizer* myOOPSEMinimizer;
1950	+	MinimizerParameterSet* param;
1951	+	char minimizerName[100];
1952	+
1953	+	for (int i = 0; i < nInfo; i++){
1954	+
1955	+	//prepare parameter set for minimizer
1956	+	param = new MinimizerParameterSet();
1957	+	param->setDefaultParameter();
1958	+
1959	+	if (globals->haveMinimizer()){
1960	+	param->setFTol(globals->getMinFTol());
1961	+	}
1962	+
1963	+	if (globals->haveMinGTol()){
1964	+	param->setGTol(globals->getMinGTol());
1965	+	}
1966	+
1967	+	if (globals->haveMinMaxIter()){
1968	+	param->setMaxIteration(globals->getMinMaxIter());
1969	+	}
1970	+
1971	+	if (globals->haveMinWriteFrq()){
1972	+	param->setMaxIteration(globals->getMinMaxIter());
1973	+	}
1974	+
1975	+	if (globals->haveMinWriteFrq()){
1976	+	param->setWriteFrq(globals->getMinWriteFrq());
1977	+	}
1978	+
1979	+	if (globals->haveMinStepSize()){
1980	+	param->setStepSize(globals->getMinStepSize());
1981	+	}
1982	+
1983	+	if (globals->haveMinLSMaxIter()){
1984	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1985	+	}
1986	+
1987	+	if (globals->haveMinLSTol()){
1988	+	param->setLineSearchTol(globals->getMinLSTol());
1989	+	}
1990	+
1991	+	strcpy(minimizerName, globals->getMinimizer());
1992	+
1993	+	if (!strcasecmp(minimizerName, "CG")){
1994	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1995	+	}
1996	+	else if (!strcasecmp(minimizerName, "SD")){
1997	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1998	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1999	+	}
2000	+	else{
2001	+	sprintf(painCave.errMsg,
2002	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2003	+	painCave.isFatal = 0;
2004	+	simError();
2005	+
2006	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2007	+	}
2008	+	info[i].the_integrator = myOOPSEMinimizer;
2009	+
2010	+	//store the minimizer into simInfo
2011	+	info[i].the_minimizer = myOOPSEMinimizer;
2012	+	info[i].has_minimizer = true;
2013	+	}
2014	+
2015	+	}

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