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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 738 by tim, Tue Sep 2 14:30:12 2003 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 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	<
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>
189		bond_pair* theBonds;
190		bend_set* theBends;
191		torsion_set* theTorsions;
192
193	+	set<int> skipList;
194
195	+	double phi, theta, psi;
196	+	char* molName;
197	+	char rbName[100];
198	+
199		//init the forceField paramters
200
201		the_ff->readParams();
202
154	–
203		// init the atoms
204
205	<	double ux, uy, uz, u, uSqr;
205	>	int nMembers, nNew, rb1, rb2;
206
207		for (k = 0; k < nInfo; k++){
208		the_ff->setSimInfo(&(info[k]));
209
210		atomOffset = 0;
211	<	excludeOffset = 0;
211	>
212		for (i = 0; i < info[k].n_mol; i++){
213		stampID = info[k].molecules[i].getStampID();
214	+	molName = comp_stamps[stampID]->getID();
215
216		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
217		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
218		molInfo.nBends = comp_stamps[stampID]->getNBends();
219		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
221	<
220	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221	>	molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222	>
223		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
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];
224
225	+	if (molInfo.nBonds > 0)
226	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227	+	else
228	+	molInfo.myBonds = NULL;
229	+
230	+	if (molInfo.nBends > 0)
231	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
232	+	else
233	+	molInfo.myBends = NULL;
234	+
235	+	if (molInfo.nTorsions > 0)
236	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237	+	else
238	+	molInfo.myTorsions = NULL;
239	+
240		theBonds = new bond_pair[molInfo.nBonds];
241		theBends = new bend_set[molInfo.nBends];
242		theTorsions = new torsion_set[molInfo.nTorsions];
243	<
243	>
244		// make the Atoms
245
246		for (j = 0; j < molInfo.nAtoms; j++){
247		currentAtom = comp_stamps[stampID]->getAtom(j);
248	+
249		if (currentAtom->haveOrientation()){
250		dAtom = new DirectionalAtom((j + atomOffset),
251		info[k].getConfiguration());
252		info[k].n_oriented++;
253		molInfo.myAtoms[j] = dAtom;
254
255	<	ux = currentAtom->getOrntX();
256	<	uy = currentAtom->getOrntY();
257	<	uz = currentAtom->getOrntZ();
255	>	// Directional Atoms have standard unit vectors which are oriented
256	>	// in space using the three Euler angles.  We assume the standard
257	>	// unit vector was originally along the z axis below.
258
259	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
259	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
260	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
261	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
262
263	<	u = sqrt(uSqr);
264	<	ux = ux / u;
201	<	uy = uy / u;
202	<	uz = uz / u;
203	<
204	<	dAtom->setSUx(ux);
205	<	dAtom->setSUy(uy);
206	<	dAtom->setSUz(uz);
263	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
264	>
265		}
266		else{
267	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
268	<	info[k].getConfiguration());
267	>
268	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
269	>
270		}
212	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
271
272	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
273		#ifdef IS_MPI
274
275	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
276
277		#endif // is_mpi
278		}
#	Line 224 | Line 283 | void SimSetup::makeMolecules(void){
283		theBonds[j].a = currentBond->getA() + atomOffset;
284		theBonds[j].b = currentBond->getB() + atomOffset;
285
286	<	exI = theBonds[j].a;
287	<	exJ = theBonds[j].b;
286	>	tempI = theBonds[j].a;
287	>	tempJ = theBonds[j].b;
288
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	–	}
289		#ifdef IS_MPI
290	<	tempEx = exI;
291	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
292	<	tempEx = exJ;
293	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
290	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
291	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
292	>	#else
293	>	exI = tempI + 1;
294	>	exJ = tempJ + 1;
295	>	#endif
296
297	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243	<	#else  // isn't MPI
244	<
245	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246	<	#endif  //is_mpi
297	>	info[k].excludes->addPair(exI, exJ);
298		}
248	–	excludeOffset += molInfo.nBonds;
299
300		//make the bends
301		for (j = 0; j < molInfo.nBends; j++){
#	Line 295 | Line 345 | void SimSetup::makeMolecules(void){
345		}
346		}
347
348	<	if (!theBends[j].isGhost){
349	<	exI = theBends[j].a;
350	<	exJ = theBends[j].c;
351	<	}
352	<	else{
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	<	}
348	>	if (theBends[j].isGhost) {
349	>
350	>	tempI = theBends[j].a;
351	>	tempJ = theBends[j].b;
352	>
353		#ifdef IS_MPI
354	<	tempEx = exI;
355	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
356	<	tempEx = exJ;
357	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
354	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
355	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
356	>	#else
357	>	exI = tempI + 1;
358	>	exJ = tempJ + 1;
359	>	#endif
360	>	info[k].excludes->addPair(exI, exJ);
361
362	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
363	<	#else  // isn't MPI
364	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
365	<	#endif  //is_mpi
362	>	} else {
363	>
364	>	tempI = theBends[j].a;
365	>	tempJ = theBends[j].b;
366	>	tempK = theBends[j].c;
367	>
368	>	#ifdef IS_MPI
369	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
370	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
371	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
372	>	#else
373	>	exI = tempI + 1;
374	>	exJ = tempJ + 1;
375	>	exK = tempK + 1;
376	>	#endif
377	>
378	>	info[k].excludes->addPair(exI, exK);
379	>	info[k].excludes->addPair(exI, exJ);
380	>	info[k].excludes->addPair(exJ, exK);
381	>	}
382		}
324	–	excludeOffset += molInfo.nBends;
383
384		for (j = 0; j < molInfo.nTorsions; j++){
385		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 330 | Line 388 | void SimSetup::makeMolecules(void){
388		theTorsions[j].c = currentTorsion->getC() + atomOffset;
389		theTorsions[j].d = currentTorsion->getD() + atomOffset;
390
391	<	exI = theTorsions[j].a;
392	<	exJ = theTorsions[j].d;
393	<
394	<	// exclude_I must always be the smaller of the pair
337	<	if (exI > exJ){
338	<	tempEx = exI;
339	<	exI = exJ;
340	<	exJ = tempEx;
341	<	}
342	<	#ifdef IS_MPI
343	<	tempEx = exI;
344	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	<	tempEx = exJ;
346	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	<
348	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
349	<	#else  // isn't MPI
350	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
351	<	#endif  //is_mpi
352	<	}
353	<	excludeOffset += molInfo.nTorsions;
391	>	tempI = theTorsions[j].a;
392	>	tempJ = theTorsions[j].b;
393	>	tempK = theTorsions[j].c;
394	>	tempL = theTorsions[j].d;
395
396	+	#ifdef IS_MPI
397	+	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
398	+	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
399	+	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
400	+	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
401	+	#else
402	+	exI = tempI + 1;
403	+	exJ = tempJ + 1;
404	+	exK = tempK + 1;
405	+	exL = tempL + 1;
406	+	#endif
407
408	<	// send the arrays off to the forceField for init.
408	>	info[k].excludes->addPair(exI, exJ);
409	>	info[k].excludes->addPair(exI, exK);
410	>	info[k].excludes->addPair(exI, exL);
411	>	info[k].excludes->addPair(exJ, exK);
412	>	info[k].excludes->addPair(exJ, exL);
413	>	info[k].excludes->addPair(exK, exL);
414	>	}
415	>
416	>
417	>	molInfo.myRigidBodies.clear();
418	>
419	>	for (j = 0; j < molInfo.nRigidBodies; j++){
420	>
421	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422	>	nMembers = currentRigidBody->getNMembers();
423	>
424	>	// Create the Rigid Body:
425	>
426	>	myRB = new RigidBody();
427	>
428	>	sprintf(rbName,"%s_RB_%d", molName, j);
429	>	myRB->setType(rbName);
430	>
431	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
432	>
433	>	// molI is atom numbering inside this molecule
434	>	molI = currentRigidBody->getMember(rb1);
435	>
436	>	// tempI is atom numbering on local processor
437	>	tempI = molI + atomOffset;
438	>
439	>	// currentAtom is the AtomStamp (which we need for
440	>	// rigid body reference positions)
441	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
442	>
443	>	// When we add to the rigid body, add the atom itself and
444	>	// the stamp info:
445	>
446	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
447	>
448	>	// Add this atom to the Skip List for the integrators
449	>	#ifdef IS_MPI
450	>	slI = info[k].atoms[tempI]->getGlobalIndex();
451	>	#else
452	>	slI = tempI;
453	>	#endif
454	>	skipList.insert(slI);
455	>
456	>	}
457	>
458	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
459	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
460	>
461	>	tempI = currentRigidBody->getMember(rb1);
462	>	tempJ = currentRigidBody->getMember(rb2);
463	>
464	>	// Some explanation is required here.
465	>	// Fortran indexing starts at 1, while c indexing starts at 0
466	>	// Also, in parallel computations, the GlobalIndex is
467	>	// used for the exclude list:
468	>
469	>	#ifdef IS_MPI
470	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472	>	#else
473	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475	>	#endif
476	>
477	>	info[k].excludes->addPair(exI, exJ);
478	>
479	>	}
480	>	}
481	>
482	>	molInfo.myRigidBodies.push_back(myRB);
483	>	info[k].rigidBodies.push_back(myRB);
484	>	}
485	>
486	>
487	>	//creat cutoff group for molecule
488	>	molInfo.myCutoffGroups.clear();
489	>	for (j = 0; j < molInfo.nCutoffGroups; j++){
490	>
491	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492	>	nMembers = currentCutoffGroup->getNMembers();
493	>
494	>	myCutoffGroup = new CutoffGroup();
495	>
496	>	for (int cg = 0; cg < nMembers; cg++) {
497	>
498	>	// molI is atom numbering inside this molecule
499	>	molI = currentCutoffGroup->getMember(cg);
500	>
501	>	// tempI is atom numbering on local processor
502	>	tempI = molI + atomOffset;
503	>
504	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
505	>	}
506	>
507	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
508	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509	>
510	>
511	>
512	>	// After this is all set up, scan through the atoms to
513	>	// see if they can be added to the integrableObjects:
514	>
515	>	molInfo.myIntegrableObjects.clear();
516	>
517	>
518	>	for (j = 0; j < molInfo.nAtoms; j++){
519
520	+	#ifdef IS_MPI
521	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
522	+	#else
523	+	slJ = j+atomOffset;
524	+	#endif
525	+
526	+	// if they aren't on the skip list, then they can be integrated
527	+
528	+	if (skipList.find(slJ) == skipList.end()) {
529	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
530	+	info[k].integrableObjects.push_back(mySD);
531	+	molInfo.myIntegrableObjects.push_back(mySD);
532	+	}
533	+	}
534	+
535	+	// all rigid bodies are integrated:
536	+
537	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
538	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
539	+	info[k].integrableObjects.push_back(mySD);
540	+	molInfo.myIntegrableObjects.push_back(mySD);
541	+	}
542	+
543	+
544	+	// send the arrays off to the forceField for init.
545	+
546		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
547		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
548		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
549		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
550		theTorsions);
551
364	–
552		info[k].molecules[i].initialize(molInfo);
553
554
#	Line 369 | Line 556 | void SimSetup::makeMolecules(void){
556		delete[] theBonds;
557		delete[] theBends;
558		delete[] theTorsions;
559	<	}
559	>	}
560		}
561
562		#ifdef IS_MPI
#	Line 379 | Line 566 | void SimSetup::makeMolecules(void){
566
567		// clean up the forcefield
568
569	<	the_ff->calcRcut();
569	>	if (!globals->haveRcut()){
570	>
571	>	the_ff->calcRcut();
572	>
573	>	} else {
574	>
575	>	the_ff->setRcut( globals->getRcut() );
576	>	}
577	>
578		the_ff->cleanMe();
579		}
580
#	Line 553 | Line 748 | void SimSetup::gatherInfo(void){
748
749
750		void SimSetup::gatherInfo(void){
751	<	int i, j, k;
751	>	int i;
752
753		ensembleCase = -1;
754		ffCase = -1;
#	Line 581 | Line 776 | void SimSetup::gatherInfo(void){
776		else if (!strcasecmp(force_field, "EAM")){
777		ffCase = FF_EAM;
778		}
779	+	else if (!strcasecmp(force_field, "WATER")){
780	+	ffCase = FF_H2O;
781	+	}
782		else{
783		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
784		force_field);
#	Line 604 | Line 802 | void SimSetup::gatherInfo(void){
802		else if (!strcasecmp(ensemble, "NPTf")){
803		ensembleCase = NPTf_ENS;
804		}
805	<	else if (!strcasecmp(ensemble, "NPTim")){
806	<	ensembleCase = NPTim_ENS;
805	>	else if (!strcasecmp(ensemble, "NPTxyz")){
806	>	ensembleCase = NPTxyz_ENS;
807		}
610	–	else if (!strcasecmp(ensemble, "NPTfm")){
611	–	ensembleCase = NPTfm_ENS;
612	–	}
808		else{
809		sprintf(painCave.errMsg,
810	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
811	<	"reverting to NVE for this simulation.\n",
810	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
811	>	"\treverting to NVE for this simulation.\n",
812		ensemble);
813		painCave.isFatal = 0;
814		simError();
#	Line 645 | Line 840 | void SimSetup::gatherInfo(void){
840		if (!the_components[i]->haveNMol()){
841		// we have a problem
842		sprintf(painCave.errMsg,
843	<	"SimSetup Error. No global NMol or component NMol"
844	<	" given. Cannot calculate the number of atoms.\n");
843	>	"SimSetup Error. No global NMol or component NMol given.\n"
844	>	"\tCannot calculate the number of atoms.\n");
845		painCave.isFatal = 1;
846		simError();
847		}
#	Line 664 | Line 859 | void SimSetup::gatherInfo(void){
859		" Please give nMol in the components.\n");
860		painCave.isFatal = 1;
861		simError();
862	+	}
863	+
864	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
865	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
866	+	sprintf(painCave.errMsg,
867	+	"Sample time is not divisible by dt.\n"
868	+	"\tThis will result in samples that are not uniformly\n"
869	+	"\tdistributed in time.  If this is a problem, change\n"
870	+	"\tyour sampleTime variable.\n");
871	+	painCave.isFatal = 0;
872	+	simError();
873		}
874
875	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
876	+	sprintf(painCave.errMsg,
877	+	"Status time is not divisible by dt.\n"
878	+	"\tThis will result in status reports that are not uniformly\n"
879	+	"\tdistributed in time.  If this is a problem, change \n"
880	+	"\tyour statusTime variable.\n");
881	+	painCave.isFatal = 0;
882	+	simError();
883	+	}
884	+
885	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
886	+	sprintf(painCave.errMsg,
887	+	"Thermal time is not divisible by dt.\n"
888	+	"\tThis will result in thermalizations that are not uniformly\n"
889	+	"\tdistributed in time.  If this is a problem, change \n"
890	+	"\tyour thermalTime variable.\n");
891	+	painCave.isFatal = 0;
892	+	simError();
893	+	}
894	+
895	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
896	+	sprintf(painCave.errMsg,
897	+	"Reset time is not divisible by dt.\n"
898	+	"\tThis will result in integrator resets that are not uniformly\n"
899	+	"\tdistributed in time.  If this is a problem, change\n"
900	+	"\tyour resetTime variable.\n");
901	+	painCave.isFatal = 0;
902	+	simError();
903	+	}
904	+
905		// set the status, sample, and thermal kick times
906
907		for (i = 0; i < nInfo; i++){
908		if (globals->haveSampleTime()){
909		info[i].sampleTime = globals->getSampleTime();
910		info[i].statusTime = info[i].sampleTime;
675	–	info[i].thermalTime = info[i].sampleTime;
911		}
912		else{
913		info[i].sampleTime = globals->getRunTime();
914		info[i].statusTime = info[i].sampleTime;
680	–	info[i].thermalTime = info[i].sampleTime;
915		}
916
917		if (globals->haveStatusTime()){
#	Line 686 | Line 920 | void SimSetup::gatherInfo(void){
920
921		if (globals->haveThermalTime()){
922		info[i].thermalTime = globals->getThermalTime();
923	+	} else {
924	+	info[i].thermalTime = globals->getRunTime();
925		}
926
927	<	// check for the temperature set flag
927	>	info[i].resetIntegrator = 0;
928	>	if( globals->haveResetTime() ){
929	>	info[i].resetTime = globals->getResetTime();
930	>	info[i].resetIntegrator = 1;
931	>	}
932
933	+	// check for the temperature set flag
934	+
935		if (globals->haveTempSet())
936		info[i].setTemp = globals->getTempSet();
937
938	<	// get some of the tricky things that may still be in the globals
938	>	// check for the extended State init
939
940	<	double boxVector[3];
941	<	if (globals->haveBox()){
942	<	boxVector[0] = globals->getBox();
701	<	boxVector[1] = globals->getBox();
702	<	boxVector[2] = globals->getBox();
703	<
704	<	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	<	}
940	>	info[i].useInitXSstate = globals->getUseInitXSstate();
941	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
942	>
943		}
944	<
944	>
945		//setup seed for random number generator
946		int seedValue;
947
#	Line 780 | Line 981 | void SimSetup::gatherInfo(void){
981		for (int i = 0; i < nInfo; i++){
982		info[i].setSeed(seedValue);
983		}
984	<
984	>
985		#ifdef IS_MPI
986	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
986	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
987		MPIcheckPoint();
988		#endif // is_mpi
989		}
#	Line 791 | Line 992 | void SimSetup::finalInfoCheck(void){
992		void SimSetup::finalInfoCheck(void){
993		int index;
994		int usesDipoles;
995	+	int usesCharges;
996		int i;
997
998		for (i = 0; i < nInfo; i++){
#	Line 802 | Line 1004 | void SimSetup::finalInfoCheck(void){
1004		usesDipoles = (info[i].atoms[index])->hasDipole();
1005		index++;
1006		}
1007	<
1007	>	index = 0;
1008	>	usesCharges = 0;
1009	>	while ((index < info[i].n_atoms) && !usesCharges){
1010	>	usesCharges= (info[i].atoms[index])->hasCharge();
1011	>	index++;
1012	>	}
1013		#ifdef IS_MPI
1014		int myUse = usesDipoles;
1015		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1016		#endif //is_mpi
1017
1018	<	double theEcr, theEst;
1018	>	double theRcut, theRsw;
1019
1020		if (globals->getUseRF()){
1021		info[i].useReactionField = 1;
1022
1023	<	if (!globals->haveECR()){
1023	>	if (!globals->haveRcut()){
1024		sprintf(painCave.errMsg,
1025	<	"SimSetup Warning: using default value of 1/2 the smallest "
1026	<	"box length for the electrostaticCutoffRadius.\n"
1027	<	"I hope you have a very fast processor!\n");
1025	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1026	>	"\tOOPSE will use a default value of 15.0 angstroms"
1027	>	"\tfor the cutoffRadius.\n");
1028		painCave.isFatal = 0;
1029		simError();
1030	<	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;
1030	>	theRcut = 15.0;
1031		}
1032		else{
1033	<	theEcr = globals->getECR();
1033	>	theRcut = globals->getRcut();
1034		}
1035
1036	<	if (!globals->haveEST()){
1036	>	if (!globals->haveRsw()){
1037		sprintf(painCave.errMsg,
1038	<	"SimSetup Warning: using default value of 0.05 * the "
1039	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1038	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1039	>	"\tOOPSE will use a default value of\n"
1040	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1041		painCave.isFatal = 0;
1042		simError();
1043	<	theEst = 0.05 * theEcr;
1043	>	theRsw = 0.95 * theRcut;
1044		}
1045		else{
1046	<	theEst = globals->getEST();
1046	>	theRsw = globals->getRsw();
1047		}
1048
1049	<	info[i].setEcr(theEcr, theEst);
1049	>	info[i].setDefaultRcut(theRcut, theRsw);
1050
1051		if (!globals->haveDielectric()){
1052		sprintf(painCave.errMsg,
1053	<	"SimSetup Error: You are trying to use Reaction Field without"
1054	<	"setting a dielectric constant!\n");
1053	>	"SimSetup Error: No Dielectric constant was set.\n"
1054	>	"\tYou are trying to use Reaction Field without"
1055	>	"\tsetting a dielectric constant!\n");
1056		painCave.isFatal = 1;
1057		simError();
1058		}
1059		info[i].dielectric = globals->getDielectric();
1060		}
1061		else{
1062	<	if (usesDipoles){
1063	<	if (!globals->haveECR()){
1062	>	if (usesDipoles || usesCharges){
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;
1072	<	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	<	}
1071	>	theRcut = 15.0;
1072	>	}
1073		else{
1074	<	theEcr = globals->getECR();
1074	>	theRcut = globals->getRcut();
1075		}
1076	<
1077	<	if (!globals->haveEST()){
1076	>
1077	>	if (!globals->haveRsw()){
1078		sprintf(painCave.errMsg,
1079	<	"SimSetup Warning: using default value of 0.05 * the "
1080	<	"electrostaticCutoffRadius for the "
1081	<	"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);
1089	>
1090	>	info[i].setDefaultRcut(theRcut, theRsw);
1091	>
1092		}
1093		}
1094		}
896	–
1095		#ifdef IS_MPI
1096		strcpy(checkPointMsg, "post processing checks out");
1097		MPIcheckPoint();
1098		#endif // is_mpi
1099		}
1100	<
1100	>
1101		void SimSetup::initSystemCoords(void){
1102		int i;
1103
#	Line 916 | Line 1114 | void SimSetup::initSystemCoords(void){
1114		if (worldRank == 0){
1115		#endif //is_mpi
1116		inName = globals->getInitialConfig();
919	–	double* tempDouble = new double[1000000];
1117		fileInit = new InitializeFromFile(inName);
1118		#ifdef IS_MPI
1119		}
#	Line 928 | Line 1125 | void SimSetup::initSystemCoords(void){
1125		delete fileInit;
1126		}
1127		else{
1128	<	#ifdef IS_MPI
932	<
1128	>
1129		// no init from bass
1130	<
1130	>
1131		sprintf(painCave.errMsg,
1132	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1133	<	painCave.isFatal;
1132	>	"Cannot intialize a simulation without an initial configuration file.\n");
1133	>	painCave.isFatal = 1;;
1134		simError();
1135	<
940	<	#else
941	<
942	<	initFromBass();
943	<
944	<
945	<	#endif
1135	>
1136		}
1137
1138		#ifdef IS_MPI
#	Line 1096 | Line 1286 | void SimSetup::createFF(void){
1286		the_ff = new EAM_FF();
1287		break;
1288
1289	+	case FF_H2O:
1290	+	the_ff = new WATER();
1291	+	break;
1292	+
1293		default:
1294		sprintf(painCave.errMsg,
1295		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1116 | Line 1310 | void SimSetup::compList(void){
1310		LinkedMolStamp* headStamp = new LinkedMolStamp();
1311		LinkedMolStamp* currentStamp = NULL;
1312		comp_stamps = new MoleculeStamp * [n_components];
1313	+	bool haveCutoffGroups;
1314
1315	+	haveCutoffGroups = false;
1316	+
1317		// make an array of molecule stamps that match the components used.
1318		// also extract the used stamps out into a separate linked list
1319
#	Line 1151 | Line 1348 | void SimSetup::compList(void){
1348		headStamp->add(currentStamp);
1349		comp_stamps[i] = headStamp->match(id);
1350		}
1351	+
1352	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1353	+	haveCutoffGroups = true;
1354		}
1355	+
1356	+	for (i = 0; i < nInfo; i++)
1357	+	info[i].haveCutoffGroups = haveCutoffGroups;
1358
1359		#ifdef IS_MPI
1360		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1160 | Line 1363 | void SimSetup::calcSysValues(void){
1363		}
1364
1365		void SimSetup::calcSysValues(void){
1366	<	int i, j, k;
1366	>	int i;
1367
1368		int* molMembershipArray;
1369
#	Line 1168 | Line 1371 | void SimSetup::calcSysValues(void){
1371		tot_bonds = 0;
1372		tot_bends = 0;
1373		tot_torsions = 0;
1374	+	tot_rigid = 0;
1375		for (i = 0; i < n_components; i++){
1376		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1377		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1378		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1379		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1380	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1381		}
1382	<
1382	>
1383		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1384		molMembershipArray = new int[tot_atoms];
1385
#	Line 1196 | Line 1401 | void SimSetup::mpiMolDivide(void){
1401		int i, j, k;
1402		int localMol, allMol;
1403		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1404	+	int local_rigid;
1405	+	vector<int> globalMolIndex;
1406
1407		mpiSim = new mpiSimulation(info);
1408
1409	<	globalIndex = mpiSim->divideLabor();
1409	>	mpiSim->divideLabor();
1410	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1411	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1412
1413		// set up the local variables
1414
#	Line 1212 | Line 1421 | void SimSetup::mpiMolDivide(void){
1421		local_bonds = 0;
1422		local_bends = 0;
1423		local_torsions = 0;
1424	<	globalAtomIndex = 0;
1424	>	local_rigid = 0;
1425	>	globalAtomCounter = 0;
1426
1217	–
1427		for (i = 0; i < n_components; i++){
1428		for (j = 0; j < components_nmol[i]; j++){
1429		if (mol2proc[allMol] == worldRank){
#	Line 1222 | Line 1431 | void SimSetup::mpiMolDivide(void){
1431		local_bonds += comp_stamps[i]->getNBonds();
1432		local_bends += comp_stamps[i]->getNBends();
1433		local_torsions += comp_stamps[i]->getNTorsions();
1434	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1435		localMol++;
1436		}
1437		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1438	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1439	<	globalAtomIndex++;
1438	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1439	>	globalAtomCounter++;
1440		}
1441
1442		allMol++;
#	Line 1235 | Line 1445 | void SimSetup::mpiMolDivide(void){
1445		local_SRI = local_bonds + local_bends + local_torsions;
1446
1447		info[0].n_atoms = mpiSim->getMyNlocal();
1448	+
1449
1450		if (local_atoms != info[0].n_atoms){
1451		sprintf(painCave.errMsg,
1452	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1453	<	" localAtom (%d) are not equal.\n",
1452	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1453	>	"\tlocalAtom (%d) are not equal.\n",
1454		info[0].n_atoms, local_atoms);
1455		painCave.isFatal = 1;
1456		simError();
#	Line 1259 | Line 1470 | void SimSetup::makeSysArrays(void){
1470
1471
1472		void SimSetup::makeSysArrays(void){
1473	<	int i, j, k, l;
1473	>
1474	>	#ifndef IS_MPI
1475	>	int k, j;
1476	>	#endif // is_mpi
1477	>	int i, l;
1478
1479		Atom** the_atoms;
1480		Molecule* the_molecules;
1266	–	Exclude** the_excludes;
1481
1268	–
1482		for (l = 0; l < nInfo; l++){
1483		// create the atom and short range interaction arrays
1484
#	Line 1291 | Line 1504 | void SimSetup::makeSysArrays(void){
1504		#else // is_mpi
1505
1506		molIndex = 0;
1507	<	globalAtomIndex = 0;
1507	>	globalAtomCounter = 0;
1508		for (i = 0; i < n_components; i++){
1509		for (j = 0; j < components_nmol[i]; j++){
1510		the_molecules[molIndex].setStampID(i);
1511		the_molecules[molIndex].setMyIndex(molIndex);
1512		the_molecules[molIndex].setGlobalIndex(molIndex);
1513		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1514	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1515	<	globalAtomIndex++;
1514	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1515	>	globalAtomCounter++;
1516		}
1517		molIndex++;
1518		}
#	Line 1308 | Line 1521 | void SimSetup::makeSysArrays(void){
1521
1522		#endif // is_mpi
1523
1524	<
1525	<	if (info[l].n_SRI){
1526	<	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	<
1524	>	info[l].globalExcludes = new int;
1525	>	info[l].globalExcludes[0] = 0;
1526	>
1527		// set the arrays into the SimInfo object
1528
1529		info[l].atoms = the_atoms;
1530		info[l].molecules = the_molecules;
1531		info[l].nGlobalExcludes = 0;
1532	<	info[l].excludes = the_excludes;
1337	<
1532	>
1533		the_ff->setSimInfo(info);
1534		}
1535		}
#	Line 1342 | Line 1537 | void SimSetup::makeIntegrator(void){
1537		void SimSetup::makeIntegrator(void){
1538		int k;
1539
1540	+	NVE<RealIntegrator>* myNVE = NULL;
1541		NVT<RealIntegrator>* myNVT = NULL;
1542	<	NPTi<RealIntegrator>* myNPTi = NULL;
1543	<	NPTf<RealIntegrator>* myNPTf = NULL;
1544	<	NPTim<RealIntegrator>* myNPTim = NULL;
1349	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1542	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1543	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1544	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1545
1546		for (k = 0; k < nInfo; k++){
1547		switch (ensembleCase){
1548		case NVE_ENS:
1549		if (globals->haveZconstraints()){
1550		setupZConstraint(info[k]);
1551	<	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1551	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1552		}
1553	<	else
1554	<	new NVE<RealIntegrator>(&(info[k]), the_ff);
1553	>	else{
1554	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1555	>	}
1556	>
1557	>	info->the_integrator = myNVE;
1558		break;
1559
1560		case NVT_ENS:
#	Line 1374 | Line 1572 | void SimSetup::makeIntegrator(void){
1572		else{
1573		sprintf(painCave.errMsg,
1574		"SimSetup error: If you use the NVT\n"
1575	<	"    ensemble, you must set tauThermostat.\n");
1575	>	"\tensemble, you must set tauThermostat.\n");
1576		painCave.isFatal = 1;
1577		simError();
1578		}
1579	+
1580	+	info->the_integrator = myNVT;
1581		break;
1582
1583		case NPTi_ENS:
1584		if (globals->haveZconstraints()){
1585		setupZConstraint(info[k]);
1586	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1586	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1587		}
1588		else
1589	<	myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1589	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1590
1591		myNPTi->setTargetTemp(globals->getTargetTemp());
1592
#	Line 1395 | Line 1595 | void SimSetup::makeIntegrator(void){
1595		else{
1596		sprintf(painCave.errMsg,
1597		"SimSetup error: If you use a constant pressure\n"
1598	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1598	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1599		painCave.isFatal = 1;
1600		simError();
1601		}
#	Line 1405 | Line 1605 | void SimSetup::makeIntegrator(void){
1605		else{
1606		sprintf(painCave.errMsg,
1607		"SimSetup error: If you use an NPT\n"
1608	<	"    ensemble, you must set tauThermostat.\n");
1608	>	"\tensemble, you must set tauThermostat.\n");
1609		painCave.isFatal = 1;
1610		simError();
1611		}
#	Line 1415 | Line 1615 | void SimSetup::makeIntegrator(void){
1615		else{
1616		sprintf(painCave.errMsg,
1617		"SimSetup error: If you use an NPT\n"
1618	<	"    ensemble, you must set tauBarostat.\n");
1618	>	"\tensemble, you must set tauBarostat.\n");
1619		painCave.isFatal = 1;
1620		simError();
1621		}
1622	+
1623	+	info->the_integrator = myNPTi;
1624		break;
1625
1626		case NPTf_ENS:
1627		if (globals->haveZconstraints()){
1628		setupZConstraint(info[k]);
1629	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1629	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1630		}
1631		else
1632	<	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1632	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1633
1634		myNPTf->setTargetTemp(globals->getTargetTemp());
1635
#	Line 1436 | Line 1638 | void SimSetup::makeIntegrator(void){
1638		else{
1639		sprintf(painCave.errMsg,
1640		"SimSetup error: If you use a constant pressure\n"
1641	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1641	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1642		painCave.isFatal = 1;
1643		simError();
1644		}
1645
1646		if (globals->haveTauThermostat())
1647		myNPTf->setTauThermostat(globals->getTauThermostat());
1648	+
1649		else{
1650		sprintf(painCave.errMsg,
1651		"SimSetup error: If you use an NPT\n"
1652	<	"    ensemble, you must set tauThermostat.\n");
1652	>	"\tensemble, you must set tauThermostat.\n");
1653		painCave.isFatal = 1;
1654		simError();
1655		}
1656
1657		if (globals->haveTauBarostat())
1658		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;
1659
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());
1660		else{
1661		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,
1662		"SimSetup error: If you use an NPT\n"
1663	<	"    ensemble, you must set tauThermostat.\n");
1663	>	"\tensemble, you must set tauBarostat.\n");
1664		painCave.isFatal = 1;
1665		simError();
1666		}
1667
1668	<	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	<	}
1668	>	info->the_integrator = myNPTf;
1669		break;
1670
1671	<	case NPTfm_ENS:
1671	>	case NPTxyz_ENS:
1672		if (globals->haveZconstraints()){
1673		setupZConstraint(info[k]);
1674	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1674	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1675		}
1676		else
1677	<	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1677	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1678
1679	<	myNPTfm->setTargetTemp(globals->getTargetTemp());
1679	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1680
1681		if (globals->haveTargetPressure())
1682	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1682	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1683		else{
1684		sprintf(painCave.errMsg,
1685		"SimSetup error: If you use a constant pressure\n"
1686	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1686	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1687		painCave.isFatal = 1;
1688		simError();
1689	<	}
1689	>	}
1690
1691		if (globals->haveTauThermostat())
1692	<	myNPTfm->setTauThermostat(globals->getTauThermostat());
1692	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1693		else{
1694		sprintf(painCave.errMsg,
1695		"SimSetup error: If you use an NPT\n"
1696	<	"    ensemble, you must set tauThermostat.\n");
1696	>	"\tensemble, you must set tauThermostat.\n");
1697		painCave.isFatal = 1;
1698		simError();
1699		}
1700
1701		if (globals->haveTauBarostat())
1702	<	myNPTfm->setTauBarostat(globals->getTauBarostat());
1702	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1703		else{
1704		sprintf(painCave.errMsg,
1705		"SimSetup error: If you use an NPT\n"
1706	<	"    ensemble, you must set tauBarostat.\n");
1706	>	"\tensemble, you must set tauBarostat.\n");
1707		painCave.isFatal = 1;
1708		simError();
1709		}
1710	+
1711	+	info->the_integrator = myNPTxyz;
1712		break;
1713
1714		default:
#	Line 1589 | Line 1756 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1756		}
1757		else{
1758		sprintf(painCave.errMsg,
1759	<	"ZConstraint error: If you use an ZConstraint\n"
1760	<	" , you must set sample time.\n");
1759	>	"ZConstraint error: If you use a ZConstraint,\n"
1760	>	"\tyou must set zconsTime.\n");
1761		painCave.isFatal = 1;
1762		simError();
1763		}
#	Line 1605 | Line 1772 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1772		else{
1773		double defaultZConsTol = 0.01;
1774		sprintf(painCave.errMsg,
1775	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1776	<	" , default value %f is used.\n",
1775	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1776	>	"\tOOPSE will use a default value of %f.\n"
1777	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1778		defaultZConsTol);
1779		painCave.isFatal = 0;
1780		simError();
#	Line 1624 | Line 1792 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1792		}
1793		else{
1794		sprintf(painCave.errMsg,
1795	<	"ZConstraint Warning: User does not set force Subtraction policy, "
1796	<	"PolicyByMass is used\n");
1795	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1796	>	"\tOOPSE will use PolicyByMass.\n"
1797	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1798		painCave.isFatal = 0;
1799		simError();
1800		zconsForcePolicy->setData("BYMASS");
#	Line 1633 | Line 1802 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1802
1803		theInfo.addProperty(zconsForcePolicy);
1804
1805	+	//set zcons gap
1806	+	DoubleData* zconsGap = new DoubleData();
1807	+	zconsGap->setID(ZCONSGAP_ID);
1808	+
1809	+	if (globals->haveZConsGap()){
1810	+	zconsGap->setData(globals->getZconsGap());
1811	+	theInfo.addProperty(zconsGap);
1812	+	}
1813	+
1814	+	//set zcons fixtime
1815	+	DoubleData* zconsFixtime = new DoubleData();
1816	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1817	+
1818	+	if (globals->haveZConsFixTime()){
1819	+	zconsFixtime->setData(globals->getZconsFixtime());
1820	+	theInfo.addProperty(zconsFixtime);
1821	+	}
1822	+
1823	+	//set zconsUsingSMD
1824	+	IntData* zconsUsingSMD = new IntData();
1825	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1826	+
1827	+	if (globals->haveZConsUsingSMD()){
1828	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1829	+	theInfo.addProperty(zconsUsingSMD);
1830	+	}
1831	+
1832		//Determine the name of ouput file and add it into SimInfo's property list
1833		//Be careful, do not use inFileName, since it is a pointer which
1834		//point to a string at master node, and slave nodes do not contain that string
#	Line 1662 | Line 1858 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1858		tempParaItem.zPos = zconStamp[i]->getZpos();
1859		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1860		tempParaItem.kRatio = zconStamp[i]->getKratio();
1861	<
1861	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1862	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1863		zconsParaData->addItem(tempParaItem);
1864		}
1865
1866		//check the uniqueness of index
1867		if(!zconsParaData->isIndexUnique()){
1868		sprintf(painCave.errMsg,
1869	<	"ZConstraint Error: molIndex is not unique\n");
1869	>	"ZConstraint Error: molIndex is not unique!\n");
1870		painCave.isFatal = 1;
1871		simError();
1872		}
#	Line 1680 | Line 1877 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1877		//push data into siminfo, therefore, we can retrieve later
1878		theInfo.addProperty(zconsParaData);
1879		}
1880	+
1881	+	void SimSetup::makeMinimizer(){
1882	+
1883	+	OOPSEMinimizer* myOOPSEMinimizer;
1884	+	MinimizerParameterSet* param;
1885	+	char minimizerName[100];
1886	+
1887	+	for (int i = 0; i < nInfo; i++){
1888	+
1889	+	//prepare parameter set for minimizer
1890	+	param = new MinimizerParameterSet();
1891	+	param->setDefaultParameter();
1892	+
1893	+	if (globals->haveMinimizer()){
1894	+	param->setFTol(globals->getMinFTol());
1895	+	}
1896	+
1897	+	if (globals->haveMinGTol()){
1898	+	param->setGTol(globals->getMinGTol());
1899	+	}
1900	+
1901	+	if (globals->haveMinMaxIter()){
1902	+	param->setMaxIteration(globals->getMinMaxIter());
1903	+	}
1904	+
1905	+	if (globals->haveMinWriteFrq()){
1906	+	param->setMaxIteration(globals->getMinMaxIter());
1907	+	}
1908	+
1909	+	if (globals->haveMinWriteFrq()){
1910	+	param->setWriteFrq(globals->getMinWriteFrq());
1911	+	}
1912	+
1913	+	if (globals->haveMinStepSize()){
1914	+	param->setStepSize(globals->getMinStepSize());
1915	+	}
1916	+
1917	+	if (globals->haveMinLSMaxIter()){
1918	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1919	+	}
1920	+
1921	+	if (globals->haveMinLSTol()){
1922	+	param->setLineSearchTol(globals->getMinLSTol());
1923	+	}
1924	+
1925	+	strcpy(minimizerName, globals->getMinimizer());
1926	+
1927	+	if (!strcasecmp(minimizerName, "CG")){
1928	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1929	+	}
1930	+	else if (!strcasecmp(minimizerName, "SD")){
1931	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1932	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1933	+	}
1934	+	else{
1935	+	sprintf(painCave.errMsg,
1936	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1937	+	painCave.isFatal = 0;
1938	+	simError();
1939	+
1940	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1941	+	}
1942	+	info[i].the_integrator = myOOPSEMinimizer;
1943	+
1944	+	//store the minimizer into simInfo
1945	+	info[i].the_minimizer = myOOPSEMinimizer;
1946	+	info[i].has_minimizer = true;
1947	+	}
1948	+
1949	+	}

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