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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 733 by tim, Wed Aug 27 19:23:29 2003 UTC vs.
Revision 1211 by tim, Tue Jun 1 15:57:30 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 "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
#	Line 22 | Line 25
25		#define NVT_ENS        1
26		#define NPTi_ENS       2
27		#define NPTf_ENS       3
28	<	#define NPTim_ENS      4
26	<	#define NPTfm_ENS      5
28	>	#define NPTxyz_ENS     4
29
28	–	#define FF_DUFF 0
29	–	#define FF_LJ   1
30	–	#define FF_EAM  2
30
31	+	#define FF_DUFF  0
32	+	#define FF_LJ    1
33	+	#define FF_EAM   2
34	+	#define FF_H2O   3
35	+
36		using namespace std;
37
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63	+
64	+	initSuspend = false;
65		isInfoArray = 0;
66		nInfo = 1;
67
#	Line 54 | Line 84 | void SimSetup::setSimInfo(SimInfo* the_info, int theNi
84		info = the_info;
85		nInfo = theNinfo;
86		isInfoArray = 1;
87	+	initSuspend = true;
88		}
89
90
#	Line 92 | Line 123 | void SimSetup::createSim(void){
123		#endif // is_mpi
124
125		void SimSetup::createSim(void){
95	–	int i, j, k, globalAtomIndex;
126
127		// gather all of the information from the Bass file
128
#	Line 108 | Line 138 | void SimSetup::createSim(void){
138
139		// initialize the system coordinates
140
141	<	if (!isInfoArray){
141	>	if ( !initSuspend ){
142		initSystemCoords();
143	+
144	+	if( !(globals->getUseInitTime()) )
145	+	info[0].currentTime = 0.0;
146		}
147
148		// make the output filenames
149
150		makeOutNames();
151	<
119	<	// make the integrator
120	<
121	<	makeIntegrator();
122	<
151	>
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
154		#endif
#	Line 127 | Line 156 | void SimSetup::createSim(void){
156		// initialize the Fortran
157
158		initFortran();
159	+
160	+	if (globals->haveMinimizer())
161	+	// make minimizer
162	+	makeMinimizer();
163	+	else
164	+	// make the integrator
165	+	makeIntegrator();
166	+
167		}
168
169
170		void SimSetup::makeMolecules(void){
171	<	int k, l;
172	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI;
175	>	int stampID, atomOffset, rbOffset;
176		molInit molInfo;
177		DirectionalAtom* dAtom;
178	+	RigidBody* myRB;
179	+	StuntDouble* mySD;
180		LinkedAssign* extras;
181		LinkedAssign* current_extra;
182		AtomStamp* currentAtom;
183		BondStamp* currentBond;
184		BendStamp* currentBend;
185		TorsionStamp* currentTorsion;
186	+	RigidBodyStamp* currentRigidBody;
187	+	CutoffGroupStamp* currentCutoffGroup;
188	+	CutoffGroup* myCutoffGroup;
189	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
190	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
191
192		bond_pair* theBonds;
193		bend_set* theBends;
194		torsion_set* theTorsions;
195
196	+	set<int> skipList;
197	+
198	+	double phi, theta, psi;
199	+	char* molName;
200	+	char rbName[100];
201
202	+	//ConstraintPair* consPair; //constraint pair
203	+	//ConstraintElement* consElement1;  //first element of constraint pair
204	+	//ConstraintElement* consElement2;  //second element of constraint pair
205	+	//int whichRigidBody;
206	+	//int consAtomIndex;  //index of constraint atom in rigid body's atom array
207	+	//vector<pair<int, int> > jointAtoms;
208		//init the forceField paramters
209
210		the_ff->readParams();
211
154	–
212		// init the atoms
213
214	<	double ux, uy, uz, u, uSqr;
214	>	int nMembers, nNew, rb1, rb2;
215
216		for (k = 0; k < nInfo; k++){
217		the_ff->setSimInfo(&(info[k]));
218
219		atomOffset = 0;
220	<	excludeOffset = 0;
220	>	groupOffset = 0;
221	>
222		for (i = 0; i < info[k].n_mol; i++){
223		stampID = info[k].molecules[i].getStampID();
224	+	molName = comp_stamps[stampID]->getID();
225
226		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
227		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
228		molInfo.nBends = comp_stamps[stampID]->getNBends();
229		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
230	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
230	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
231
232	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
233	+
234		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];
235
236	+	if (molInfo.nBonds > 0)
237	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
238	+	else
239	+	molInfo.myBonds = NULL;
240	+
241	+	if (molInfo.nBends > 0)
242	+	molInfo.myBends = new Bend*[molInfo.nBends];
243	+	else
244	+	molInfo.myBends = NULL;
245	+
246	+	if (molInfo.nTorsions > 0)
247	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
248	+	else
249	+	molInfo.myTorsions = NULL;
250	+
251		theBonds = new bond_pair[molInfo.nBonds];
252		theBends = new bend_set[molInfo.nBends];
253		theTorsions = new torsion_set[molInfo.nTorsions];
254	<
254	>
255		// make the Atoms
256
257		for (j = 0; j < molInfo.nAtoms; j++){
258		currentAtom = comp_stamps[stampID]->getAtom(j);
259	+
260		if (currentAtom->haveOrientation()){
261		dAtom = new DirectionalAtom((j + atomOffset),
262		info[k].getConfiguration());
263		info[k].n_oriented++;
264		molInfo.myAtoms[j] = dAtom;
265
266	<	ux = currentAtom->getOrntX();
267	<	uy = currentAtom->getOrntY();
268	<	uz = currentAtom->getOrntZ();
266	>	// Directional Atoms have standard unit vectors which are oriented
267	>	// in space using the three Euler angles.  We assume the standard
268	>	// unit vector was originally along the z axis below.
269
270	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
270	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
271	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
272	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
273
274	<	u = sqrt(uSqr);
275	<	ux = ux / u;
201	<	uy = uy / u;
202	<	uz = uz / u;
203	<
204	<	dAtom->setSUx(ux);
205	<	dAtom->setSUy(uy);
206	<	dAtom->setSUz(uz);
274	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
275	>
276		}
277		else{
278	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
279	<	info[k].getConfiguration());
278	>
279	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
280	>
281		}
212	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
282
283	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
284		#ifdef IS_MPI
285
286	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
286	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
287
288		#endif // is_mpi
289		}
#	Line 224 | Line 294 | void SimSetup::makeMolecules(void){
294		theBonds[j].a = currentBond->getA() + atomOffset;
295		theBonds[j].b = currentBond->getB() + atomOffset;
296
297	<	exI = theBonds[j].a;
298	<	exJ = theBonds[j].b;
297	>	tempI = theBonds[j].a;
298	>	tempJ = theBonds[j].b;
299
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	–	}
300		#ifdef IS_MPI
301	<	tempEx = exI;
302	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
303	<	tempEx = exJ;
304	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
301	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
302	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
303	>	#else
304	>	exI = tempI + 1;
305	>	exJ = tempJ + 1;
306	>	#endif
307
308	<	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
308	>	info[k].excludes->addPair(exI, exJ);
309		}
248	–	excludeOffset += molInfo.nBonds;
310
311		//make the bends
312		for (j = 0; j < molInfo.nBends; j++){
#	Line 295 | Line 356 | void SimSetup::makeMolecules(void){
356		}
357		}
358
359	<	if (!theBends[j].isGhost){
360	<	exI = theBends[j].a;
361	<	exJ = theBends[j].c;
362	<	}
363	<	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	<	}
359	>	if (theBends[j].isGhost) {
360	>
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>
364		#ifdef IS_MPI
365	<	tempEx = exI;
366	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	<	tempEx = exJ;
368	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
366	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
367	>	#else
368	>	exI = tempI + 1;
369	>	exJ = tempJ + 1;
370	>	#endif
371	>	info[k].excludes->addPair(exI, exJ);
372
373	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
374	<	#else  // isn't MPI
375	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
376	<	#endif  //is_mpi
373	>	} else {
374	>
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>	tempK = theBends[j].c;
378	>
379	>	#ifdef IS_MPI
380	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
381	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
382	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
383	>	#else
384	>	exI = tempI + 1;
385	>	exJ = tempJ + 1;
386	>	exK = tempK + 1;
387	>	#endif
388	>
389	>	info[k].excludes->addPair(exI, exK);
390	>	info[k].excludes->addPair(exI, exJ);
391	>	info[k].excludes->addPair(exJ, exK);
392	>	}
393		}
324	–	excludeOffset += molInfo.nBends;
394
395		for (j = 0; j < molInfo.nTorsions; j++){
396		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 330 | Line 399 | void SimSetup::makeMolecules(void){
399		theTorsions[j].c = currentTorsion->getC() + atomOffset;
400		theTorsions[j].d = currentTorsion->getD() + atomOffset;
401
402	<	exI = theTorsions[j].a;
403	<	exJ = theTorsions[j].d;
402	>	tempI = theTorsions[j].a;
403	>	tempJ = theTorsions[j].b;
404	>	tempK = theTorsions[j].c;
405	>	tempL = theTorsions[j].d;
406
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	–	}
407		#ifdef IS_MPI
408	<	tempEx = exI;
409	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
410	<	tempEx = exJ;
411	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
408	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
409	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
410	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
411	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
412	>	#else
413	>	exI = tempI + 1;
414	>	exJ = tempJ + 1;
415	>	exK = tempK + 1;
416	>	exL = tempL + 1;
417	>	#endif
418
419	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
420	<	#else  // isn't MPI
421	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
422	<	#endif  //is_mpi
419	>	info[k].excludes->addPair(exI, exJ);
420	>	info[k].excludes->addPair(exI, exK);
421	>	info[k].excludes->addPair(exI, exL);
422	>	info[k].excludes->addPair(exJ, exK);
423	>	info[k].excludes->addPair(exJ, exL);
424	>	info[k].excludes->addPair(exK, exL);
425		}
353	–	excludeOffset += molInfo.nTorsions;
426
427	+
428	+	molInfo.myRigidBodies.clear();
429	+
430	+	for (j = 0; j < molInfo.nRigidBodies; j++){
431
432	<	// send the arrays off to the forceField for init.
432	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
433	>	nMembers = currentRigidBody->getNMembers();
434
435	+	// Create the Rigid Body:
436	+
437	+	myRB = new RigidBody();
438	+
439	+	sprintf(rbName,"%s_RB_%d", molName, j);
440	+	myRB->setType(rbName);
441	+
442	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
443	+
444	+	// molI is atom numbering inside this molecule
445	+	molI = currentRigidBody->getMember(rb1);
446	+
447	+	// tempI is atom numbering on local processor
448	+	tempI = molI + atomOffset;
449	+
450	+	// currentAtom is the AtomStamp (which we need for
451	+	// rigid body reference positions)
452	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
453	+
454	+	// When we add to the rigid body, add the atom itself and
455	+	// the stamp info:
456	+
457	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
458	+
459	+	// Add this atom to the Skip List for the integrators
460	+	#ifdef IS_MPI
461	+	slI = info[k].atoms[tempI]->getGlobalIndex();
462	+	#else
463	+	slI = tempI;
464	+	#endif
465	+	skipList.insert(slI);
466	+
467	+	}
468	+
469	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
470	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
471	+
472	+	tempI = currentRigidBody->getMember(rb1);
473	+	tempJ = currentRigidBody->getMember(rb2);
474	+
475	+	// Some explanation is required here.
476	+	// Fortran indexing starts at 1, while c indexing starts at 0
477	+	// Also, in parallel computations, the GlobalIndex is
478	+	// used for the exclude list:
479	+
480	+	#ifdef IS_MPI
481	+	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
482	+	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
483	+	#else
484	+	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
485	+	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
486	+	#endif
487	+
488	+	info[k].excludes->addPair(exI, exJ);
489	+
490	+	}
491	+	}
492	+
493	+	molInfo.myRigidBodies.push_back(myRB);
494	+	info[k].rigidBodies.push_back(myRB);
495	+	}
496	+
497	+
498	+	//create cutoff group for molecule
499	+
500	+	cutoffAtomSet.clear();
501	+	molInfo.myCutoffGroups.clear();
502	+
503	+	for (j = 0; j < nCutoffGroups; j++){
504	+
505	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
506	+	nMembers = currentCutoffGroup->getNMembers();
507	+
508	+	myCutoffGroup = new CutoffGroup();
509	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
510	+
511	+	for (int cg = 0; cg < nMembers; cg++) {
512	+
513	+	// molI is atom numbering inside this molecule
514	+	molI = currentCutoffGroup->getMember(cg);
515	+
516	+	// tempI is atom numbering on local processor
517	+	tempI = molI + atomOffset;
518	+
519	+	#ifdef IS_MPI
520	+	globalID = info[k].atoms[tempI]->getGlobalIndex()
521	+	#else
522	+	globalID = info[k].atoms[tempI]->getIndex();
523	+	#endif
524	+
525	+	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
526	+
527	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
528	+
529	+	cutoffAtomSet.insert(tempI);
530	+	}
531	+
532	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
533	+	groupOffset++;
534	+
535	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
536	+
537	+	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
538	+
539	+	for(j = 0; j < molInfo.nAtoms; j++){
540	+
541	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
542	+	myCutoffGroup = new CutoffGroup();
543	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
544	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
545	+	#ifdef IS_MPI
546	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex()
547	+	#else
548	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
549	+	#endif
550	+	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
551	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
552	+	groupOffset++;
553	+	}
554	+
555	+	}
556	+
557	+	// After this is all set up, scan through the atoms to
558	+	// see if they can be added to the integrableObjects:
559	+
560	+	molInfo.myIntegrableObjects.clear();
561	+
562	+
563	+	for (j = 0; j < molInfo.nAtoms; j++){
564	+
565	+	#ifdef IS_MPI
566	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
567	+	#else
568	+	slJ = j+atomOffset;
569	+	#endif
570	+
571	+	// if they aren't on the skip list, then they can be integrated
572	+
573	+	if (skipList.find(slJ) == skipList.end()) {
574	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
575	+	info[k].integrableObjects.push_back(mySD);
576	+	molInfo.myIntegrableObjects.push_back(mySD);
577	+	}
578	+	}
579	+
580	+	// all rigid bodies are integrated:
581	+
582	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
583	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
584	+	info[k].integrableObjects.push_back(mySD);
585	+	molInfo.myIntegrableObjects.push_back(mySD);
586	+	}
587	+
588	+
589	+	/*
590	+
591	+	//creat ConstraintPair.
592	+	molInfo.myConstraintPair.clear();
593	+
594	+	for (j = 0; j < molInfo.nBonds; j++){
595	+
596	+	//if both atoms are in the same rigid body, just skip it
597	+	currentBond = comp_stamps[stampID]->getBond(j);
598	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
599	+
600	+	tempI = currentBond->getA() + atomOffset;
601	+	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
602	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
603	+	else
604	+	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
605	+
606	+	tempJ =  currentBond->getB() + atomOffset;
607	+	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
608	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
609	+	else
610	+	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
611	+
612	+	consPair = new DistanceConstraintPair(consElement1, consElement2);
613	+	molInfo.myConstraintPairs.push_back(consPair);
614	+	}
615	+	}
616	+
617	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
618	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
619	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
620	+
621	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
622	+
623	+	for(size_t m = 0; m < jointAtoms.size(); m++){
624	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
625	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
626	+
627	+	consPair = new JointConstraintPair(consElement1, consElement2);
628	+	molInfo.myConstraintPairs.push_back(consPair);
629	+	}
630	+
631	+	}
632	+	}
633	+
634	+	*/
635	+	// send the arrays off to the forceField for init.
636	+
637		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
638		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
639		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
640		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
641		theTorsions);
642
364	–
643		info[k].molecules[i].initialize(molInfo);
644
645
#	Line 369 | Line 647 | void SimSetup::makeMolecules(void){
647		delete[] theBonds;
648		delete[] theBends;
649		delete[] theTorsions;
650	<	}
650	>	}
651		}
652
653		#ifdef IS_MPI
#	Line 377 | Line 655 | void SimSetup::makeMolecules(void){
655		MPIcheckPoint();
656		#endif // is_mpi
657
380	–	// clean up the forcefield
381	–
382	–	the_ff->calcRcut();
383	–	the_ff->cleanMe();
658		}
659
660		void SimSetup::initFromBass(void){
#	Line 553 | Line 827 | void SimSetup::gatherInfo(void){
827
828
829		void SimSetup::gatherInfo(void){
830	<	int i, j, k;
830	>	int i;
831
832		ensembleCase = -1;
833		ffCase = -1;
#	Line 581 | Line 855 | void SimSetup::gatherInfo(void){
855		else if (!strcasecmp(force_field, "EAM")){
856		ffCase = FF_EAM;
857		}
858	+	else if (!strcasecmp(force_field, "WATER")){
859	+	ffCase = FF_H2O;
860	+	}
861		else{
862		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
863		force_field);
#	Line 604 | Line 881 | void SimSetup::gatherInfo(void){
881		else if (!strcasecmp(ensemble, "NPTf")){
882		ensembleCase = NPTf_ENS;
883		}
884	<	else if (!strcasecmp(ensemble, "NPTim")){
885	<	ensembleCase = NPTim_ENS;
884	>	else if (!strcasecmp(ensemble, "NPTxyz")){
885	>	ensembleCase = NPTxyz_ENS;
886		}
610	–	else if (!strcasecmp(ensemble, "NPTfm")){
611	–	ensembleCase = NPTfm_ENS;
612	–	}
887		else{
888		sprintf(painCave.errMsg,
889	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
890	<	"reverting to NVE for this simulation.\n",
889	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
890	>	"\treverting to NVE for this simulation.\n",
891		ensemble);
892		painCave.isFatal = 0;
893		simError();
#	Line 645 | Line 919 | void SimSetup::gatherInfo(void){
919		if (!the_components[i]->haveNMol()){
920		// we have a problem
921		sprintf(painCave.errMsg,
922	<	"SimSetup Error. No global NMol or component NMol"
923	<	" given. Cannot calculate the number of atoms.\n");
922	>	"SimSetup Error. No global NMol or component NMol given.\n"
923	>	"\tCannot calculate the number of atoms.\n");
924		painCave.isFatal = 1;
925		simError();
926		}
#	Line 664 | Line 938 | void SimSetup::gatherInfo(void){
938		" Please give nMol in the components.\n");
939		painCave.isFatal = 1;
940		simError();
941	+	}
942	+
943	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
944	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
945	+	sprintf(painCave.errMsg,
946	+	"Sample time is not divisible by dt.\n"
947	+	"\tThis will result in samples that are not uniformly\n"
948	+	"\tdistributed in time.  If this is a problem, change\n"
949	+	"\tyour sampleTime variable.\n");
950	+	painCave.isFatal = 0;
951	+	simError();
952	+	}
953	+
954	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
955	+	sprintf(painCave.errMsg,
956	+	"Status time is not divisible by dt.\n"
957	+	"\tThis will result in status reports that are not uniformly\n"
958	+	"\tdistributed in time.  If this is a problem, change \n"
959	+	"\tyour statusTime variable.\n");
960	+	painCave.isFatal = 0;
961	+	simError();
962		}
963
964	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
965	+	sprintf(painCave.errMsg,
966	+	"Thermal time is not divisible by dt.\n"
967	+	"\tThis will result in thermalizations that are not uniformly\n"
968	+	"\tdistributed in time.  If this is a problem, change \n"
969	+	"\tyour thermalTime variable.\n");
970	+	painCave.isFatal = 0;
971	+	simError();
972	+	}
973	+
974	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
975	+	sprintf(painCave.errMsg,
976	+	"Reset time is not divisible by dt.\n"
977	+	"\tThis will result in integrator resets that are not uniformly\n"
978	+	"\tdistributed in time.  If this is a problem, change\n"
979	+	"\tyour resetTime variable.\n");
980	+	painCave.isFatal = 0;
981	+	simError();
982	+	}
983	+
984		// set the status, sample, and thermal kick times
985
986		for (i = 0; i < nInfo; i++){
987		if (globals->haveSampleTime()){
988		info[i].sampleTime = globals->getSampleTime();
989		info[i].statusTime = info[i].sampleTime;
675	–	info[i].thermalTime = info[i].sampleTime;
990		}
991		else{
992		info[i].sampleTime = globals->getRunTime();
993		info[i].statusTime = info[i].sampleTime;
680	–	info[i].thermalTime = info[i].sampleTime;
994		}
995
996		if (globals->haveStatusTime()){
#	Line 686 | Line 999 | void SimSetup::gatherInfo(void){
999
1000		if (globals->haveThermalTime()){
1001		info[i].thermalTime = globals->getThermalTime();
1002	+	} else {
1003	+	info[i].thermalTime = globals->getRunTime();
1004		}
1005
1006	<	// check for the temperature set flag
1006	>	info[i].resetIntegrator = 0;
1007	>	if( globals->haveResetTime() ){
1008	>	info[i].resetTime = globals->getResetTime();
1009	>	info[i].resetIntegrator = 1;
1010	>	}
1011
1012	+	// check for the temperature set flag
1013	+
1014		if (globals->haveTempSet())
1015		info[i].setTemp = globals->getTempSet();
1016
1017	<	// get some of the tricky things that may still be in the globals
1017	>	// check for the extended State init
1018
1019	<	double boxVector[3];
1020	<	if (globals->haveBox()){
700	<	boxVector[0] = globals->getBox();
701	<	boxVector[1] = globals->getBox();
702	<	boxVector[2] = globals->getBox();
1019	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1020	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1021
1022	<	info[i].setBox(boxVector);
1023	<	}
1024	<	else if (globals->haveDensity()){
1025	<	double vol;
1026	<	vol = (double) tot_nmol / globals->getDensity();
1027	<	boxVector[0] = pow(vol, (1.0 / 3.0));
1028	<	boxVector[1] = boxVector[0];
1029	<	boxVector[2] = boxVector[0];
1030	<
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();
1022	>	// check for thermodynamic integration
1023	>	if (globals->getUseThermInt()) {
1024	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1025	>	info[i].useThermInt = globals->getUseThermInt();
1026	>	info[i].thermIntLambda = globals->getThermIntLambda();
1027	>	info[i].thermIntK = globals->getThermIntK();
1028	>
1029	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1030	>	info[i].restraint = myRestraint;
1031		}
1032	<	boxVector[1] = globals->getBoxY();
1033	<
1034	<	if (!globals->haveBoxZ()){
1035	<	sprintf(painCave.errMsg,
1036	<	"SimSetup error, no periodic BoxZ size given.\n");
1037	<	painCave.isFatal = 1;
1038	<	simError();
1032	>	else {
1033	>	sprintf(painCave.errMsg,
1034	>	"SimSetup Error:\n"
1035	>	"\tKeyword useThermInt was set to 'true' but\n"
1036	>	"\tthermodynamicIntegrationLambda (and/or\n"
1037	>	"\tthermodynamicIntegrationK) was not specified.\n"
1038	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1039	>	painCave.isFatal = 1;
1040	>	simError();
1041		}
738	–	boxVector[2] = globals->getBoxZ();
739	–
740	–	info[i].setBox(boxVector);
1042		}
1043	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1044	+	sprintf(painCave.errMsg,
1045	+	"SimSetup Warning: If you want to use Thermodynamic\n"
1046	+	"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
1047	+	"\tThe useThermInt keyword is 'false' by default, so your\n"
1048	+	"\tlambda and/or k values are being ignored.\n");
1049	+	painCave.isFatal = 0;
1050	+	simError();
1051	+	}
1052		}
1053	<
1053	>
1054		//setup seed for random number generator
1055		int seedValue;
1056
#	Line 780 | Line 1090 | void SimSetup::gatherInfo(void){
1090		for (int i = 0; i < nInfo; i++){
1091		info[i].setSeed(seedValue);
1092		}
1093	<
1093	>
1094		#ifdef IS_MPI
1095	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1095	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1096		MPIcheckPoint();
1097		#endif // is_mpi
1098		}
#	Line 791 | Line 1101 | void SimSetup::finalInfoCheck(void){
1101		void SimSetup::finalInfoCheck(void){
1102		int index;
1103		int usesDipoles;
1104	+	int usesCharges;
1105		int i;
1106
1107		for (i = 0; i < nInfo; i++){
#	Line 802 | Line 1113 | void SimSetup::finalInfoCheck(void){
1113		usesDipoles = (info[i].atoms[index])->hasDipole();
1114		index++;
1115		}
1116	<
1116	>	index = 0;
1117	>	usesCharges = 0;
1118	>	while ((index < info[i].n_atoms) && !usesCharges){
1119	>	usesCharges= (info[i].atoms[index])->hasCharge();
1120	>	index++;
1121	>	}
1122		#ifdef IS_MPI
1123		int myUse = usesDipoles;
1124		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1125		#endif //is_mpi
1126
1127	<	double theEcr, theEst;
1127	>	double theRcut, theRsw;
1128
1129	+	if (globals->haveRcut()) {
1130	+	theRcut = globals->getRcut();
1131	+
1132	+	if (globals->haveRsw())
1133	+	theRsw = globals->getRsw();
1134	+	else
1135	+	theRsw = theRcut;
1136	+
1137	+	info[i].setDefaultRcut(theRcut, theRsw);
1138	+
1139	+	} else {
1140	+
1141	+	the_ff->calcRcut();
1142	+	theRcut = info[i].getRcut();
1143	+
1144	+	if (globals->haveRsw())
1145	+	theRsw = globals->getRsw();
1146	+	else
1147	+	theRsw = theRcut;
1148	+
1149	+	info[i].setDefaultRcut(theRcut, theRsw);
1150	+	}
1151	+
1152		if (globals->getUseRF()){
1153		info[i].useReactionField = 1;
1154	<
1155	<	if (!globals->haveECR()){
1154	>
1155	>	if (!globals->haveRcut()){
1156		sprintf(painCave.errMsg,
1157	<	"SimSetup Warning: using default value of 1/2 the smallest "
1158	<	"box length for the electrostaticCutoffRadius.\n"
1159	<	"I hope you have a very fast processor!\n");
1157	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1158	>	"\tOOPSE will use a default value of 15.0 angstroms"
1159	>	"\tfor the cutoffRadius.\n");
1160		painCave.isFatal = 0;
1161		simError();
1162	<	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;
1162	>	theRcut = 15.0;
1163		}
1164		else{
1165	<	theEcr = globals->getECR();
1165	>	theRcut = globals->getRcut();
1166		}
1167
1168	<	if (!globals->haveEST()){
1168	>	if (!globals->haveRsw()){
1169		sprintf(painCave.errMsg,
1170	<	"SimSetup Warning: using default value of 0.05 * the "
1171	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1170	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1171	>	"\tOOPSE will use a default value of\n"
1172	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1173		painCave.isFatal = 0;
1174		simError();
1175	<	theEst = 0.05 * theEcr;
1175	>	theRsw = 0.95 * theRcut;
1176		}
1177		else{
1178	<	theEst = globals->getEST();
1178	>	theRsw = globals->getRsw();
1179		}
1180
1181	<	info[i].setEcr(theEcr, theEst);
1181	>	info[i].setDefaultRcut(theRcut, theRsw);
1182
1183		if (!globals->haveDielectric()){
1184		sprintf(painCave.errMsg,
1185	<	"SimSetup Error: You are trying to use Reaction Field without"
1186	<	"setting a dielectric constant!\n");
1185	>	"SimSetup Error: No Dielectric constant was set.\n"
1186	>	"\tYou are trying to use Reaction Field without"
1187	>	"\tsetting a dielectric constant!\n");
1188		painCave.isFatal = 1;
1189		simError();
1190		}
1191		info[i].dielectric = globals->getDielectric();
1192		}
1193		else{
1194	<	if (usesDipoles){
1195	<	if (!globals->haveECR()){
1194	>	if (usesDipoles || usesCharges){
1195	>
1196	>	if (!globals->haveRcut()){
1197		sprintf(painCave.errMsg,
1198	<	"SimSetup Warning: using default value of 1/2 the smallest "
1199	<	"box length for the electrostaticCutoffRadius.\n"
1200	<	"I hope you have a very fast processor!\n");
1198	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1199	>	"\tOOPSE will use a default value of 15.0 angstroms"
1200	>	"\tfor the cutoffRadius.\n");
1201		painCave.isFatal = 0;
1202		simError();
1203	<	double smallest;
1204	<	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	<	}
1203	>	theRcut = 15.0;
1204	>	}
1205		else{
1206	<	theEcr = globals->getECR();
1206	>	theRcut = globals->getRcut();
1207		}
1208	<
1209	<	if (!globals->haveEST()){
1208	>
1209	>	if (!globals->haveRsw()){
1210		sprintf(painCave.errMsg,
1211	<	"SimSetup Warning: using default value of 0.05 * the "
1212	<	"electrostaticCutoffRadius for the "
1213	<	"electrostaticSkinThickness\n");
1211	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1212	>	"\tOOPSE will use a default value of\n"
1213	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1214		painCave.isFatal = 0;
1215		simError();
1216	<	theEst = 0.05 * theEcr;
1216	>	theRsw = 0.95 * theRcut;
1217		}
1218		else{
1219	<	theEst = globals->getEST();
1219	>	theRsw = globals->getRsw();
1220		}
1221	<
1222	<	info[i].setEcr(theEcr, theEst);
1221	>
1222	>	info[i].setDefaultRcut(theRcut, theRsw);
1223	>
1224		}
1225		}
1226		}
896	–
1227		#ifdef IS_MPI
1228		strcpy(checkPointMsg, "post processing checks out");
1229		MPIcheckPoint();
1230		#endif // is_mpi
901	–	}
1231
1232	+	// clean up the forcefield
1233	+	the_ff->cleanMe();
1234	+	}
1235	+
1236		void SimSetup::initSystemCoords(void){
1237		int i;
1238
#	Line 916 | Line 1249 | void SimSetup::initSystemCoords(void){
1249		if (worldRank == 0){
1250		#endif //is_mpi
1251		inName = globals->getInitialConfig();
919	–	double* tempDouble = new double[1000000];
1252		fileInit = new InitializeFromFile(inName);
1253		#ifdef IS_MPI
1254		}
#	Line 928 | Line 1260 | void SimSetup::initSystemCoords(void){
1260		delete fileInit;
1261		}
1262		else{
1263	<	#ifdef IS_MPI
932	<
1263	>
1264		// no init from bass
1265	<
1265	>
1266		sprintf(painCave.errMsg,
1267	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1268	<	painCave.isFatal;
1267	>	"Cannot intialize a simulation without an initial configuration file.\n");
1268	>	painCave.isFatal = 1;;
1269		simError();
1270	<
940	<	#else
941	<
942	<	initFromBass();
943	<
944	<
945	<	#endif
1270	>
1271		}
1272
1273		#ifdef IS_MPI
#	Line 1033 | Line 1358 | void SimSetup::makeOutNames(void){
1358		}
1359		else{
1360		strcat(info[k].statusName, ".stat");
1361	+	}
1362	+	}
1363	+
1364	+	strcpy(info[k].rawPotName, inFileName);
1365	+	nameLength = strlen(info[k].rawPotName);
1366	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1367	+	if (!strcmp(endTest, ".bass")){
1368	+	strcpy(endTest, ".raw");
1369	+	}
1370	+	else if (!strcmp(endTest, ".BASS")){
1371	+	strcpy(endTest, ".raw");
1372	+	}
1373	+	else{
1374	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1375	+	if (!strcmp(endTest, ".bss")){
1376	+	strcpy(endTest, ".raw");
1377		}
1378	+	else if (!strcmp(endTest, ".mdl")){
1379	+	strcpy(endTest, ".raw");
1380	+	}
1381	+	else{
1382	+	strcat(info[k].rawPotName, ".raw");
1383	+	}
1384		}
1385
1386		#ifdef IS_MPI
#	Line 1096 | Line 1443 | void SimSetup::createFF(void){
1443		the_ff = new EAM_FF();
1444		break;
1445
1446	+	case FF_H2O:
1447	+	the_ff = new WATER();
1448	+	break;
1449	+
1450		default:
1451		sprintf(painCave.errMsg,
1452		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1116 | Line 1467 | void SimSetup::compList(void){
1467		LinkedMolStamp* headStamp = new LinkedMolStamp();
1468		LinkedMolStamp* currentStamp = NULL;
1469		comp_stamps = new MoleculeStamp * [n_components];
1470	+	bool haveCutoffGroups;
1471
1472	+	haveCutoffGroups = false;
1473	+
1474		// make an array of molecule stamps that match the components used.
1475		// also extract the used stamps out into a separate linked list
1476
#	Line 1151 | Line 1505 | void SimSetup::compList(void){
1505		headStamp->add(currentStamp);
1506		comp_stamps[i] = headStamp->match(id);
1507		}
1508	+
1509	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1510	+	haveCutoffGroups = true;
1511		}
1512	+
1513	+	for (i = 0; i < nInfo; i++)
1514	+	info[i].haveCutoffGroups = haveCutoffGroups;
1515
1516		#ifdef IS_MPI
1517		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1160 | Line 1520 | void SimSetup::calcSysValues(void){
1520		}
1521
1522		void SimSetup::calcSysValues(void){
1523	<	int i, j, k;
1523	>	int i, j;
1524	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1525
1526		int* molMembershipArray;
1527	+	CutoffGroupStamp* cg;
1528
1529		tot_atoms = 0;
1530		tot_bonds = 0;
1531		tot_bends = 0;
1532		tot_torsions = 0;
1533	+	tot_rigid = 0;
1534	+	tot_groups = 0;
1535		for (i = 0; i < n_components; i++){
1536		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1537		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1538		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1539		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1540	<	}
1540	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1541
1542	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1543	+	atomsingroups = 0;
1544	+	for (j=0; j < ncutgroups; j++) {
1545	+	cg = comp_stamps[i]->getCutoffGroup(j);
1546	+	atomsingroups += cg->getNMembers();
1547	+	}
1548	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1549	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1550	+	}
1551	+
1552		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1553		molMembershipArray = new int[tot_atoms];
1554
#	Line 1185 | Line 1559 | void SimSetup::calcSysValues(void){
1559		info[i].n_torsions = tot_torsions;
1560		info[i].n_SRI = tot_SRI;
1561		info[i].n_mol = tot_nmol;
1562	<
1562	>	info[i].ngroup = tot_groups;
1563		info[i].molMembershipArray = molMembershipArray;
1564		}
1565		}
#	Line 1196 | Line 1570 | void SimSetup::mpiMolDivide(void){
1570		int i, j, k;
1571		int localMol, allMol;
1572		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1573	+	int local_rigid, local_groups;
1574	+	vector<int> globalMolIndex;
1575	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1576	+	CutoffGroupStamp* cg;
1577
1578		mpiSim = new mpiSimulation(info);
1579
1580	<	globalIndex = mpiSim->divideLabor();
1580	>	mpiSim->divideLabor();
1581	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1582	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1583
1584		// set up the local variables
1585
#	Line 1212 | Line 1592 | void SimSetup::mpiMolDivide(void){
1592		local_bonds = 0;
1593		local_bends = 0;
1594		local_torsions = 0;
1595	<	globalAtomIndex = 0;
1595	>	local_rigid = 0;
1596	>	local_groups = 0;
1597	>	globalAtomCounter = 0;
1598
1217	–
1599		for (i = 0; i < n_components; i++){
1600		for (j = 0; j < components_nmol[i]; j++){
1601		if (mol2proc[allMol] == worldRank){
#	Line 1222 | Line 1603 | void SimSetup::mpiMolDivide(void){
1603		local_bonds += comp_stamps[i]->getNBonds();
1604		local_bends += comp_stamps[i]->getNBends();
1605		local_torsions += comp_stamps[i]->getNTorsions();
1606	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1607	+
1608	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1609	+	atomsingroups = 0;
1610	+	for (k=0; k < ncutgroups; k++) {
1611	+	cg = comp_stamps[i]->getCutoffGroup(k);
1612	+	atomsingroups += cg->getNMembers();
1613	+	}
1614	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1615	+	ncutgroups;
1616	+	local_groups += ngroupsinstamp;
1617	+
1618		localMol++;
1619		}
1620		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1621	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1622	<	globalAtomIndex++;
1621	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1622	>	globalAtomCounter++;
1623		}
1624
1625		allMol++;
#	Line 1234 | Line 1627 | void SimSetup::mpiMolDivide(void){
1627		}
1628		local_SRI = local_bonds + local_bends + local_torsions;
1629
1630	<	info[0].n_atoms = mpiSim->getMyNlocal();
1631	<
1630	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1631	>
1632		if (local_atoms != info[0].n_atoms){
1633		sprintf(painCave.errMsg,
1634	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1635	<	" localAtom (%d) are not equal.\n",
1634	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1635	>	"\tlocalAtom (%d) are not equal.\n",
1636		info[0].n_atoms, local_atoms);
1637		painCave.isFatal = 1;
1638		simError();
1639		}
1640
1641	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1642	+	if (local_groups != info[0].ngroup){
1643	+	sprintf(painCave.errMsg,
1644	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1645	+	"\tlocalGroups (%d) are not equal.\n",
1646	+	info[0].ngroup, local_groups);
1647	+	painCave.isFatal = 1;
1648	+	simError();
1649	+	}
1650	+
1651		info[0].n_bonds = local_bonds;
1652		info[0].n_bends = local_bends;
1653		info[0].n_torsions = local_torsions;
#	Line 1259 | Line 1662 | void SimSetup::makeSysArrays(void){
1662
1663
1664		void SimSetup::makeSysArrays(void){
1665	<	int i, j, k, l;
1665	>
1666	>	#ifndef IS_MPI
1667	>	int k, j;
1668	>	#endif // is_mpi
1669	>	int i, l;
1670
1671		Atom** the_atoms;
1672		Molecule* the_molecules;
1266	–	Exclude** the_excludes;
1673
1268	–
1674		for (l = 0; l < nInfo; l++){
1675		// create the atom and short range interaction arrays
1676
#	Line 1279 | Line 1684 | void SimSetup::makeSysArrays(void){
1684
1685
1686		molIndex = 0;
1687	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1687	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1688		if (mol2proc[i] == worldRank){
1689		the_molecules[molIndex].setStampID(molCompType[i]);
1690		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1291 | Line 1696 | void SimSetup::makeSysArrays(void){
1696		#else // is_mpi
1697
1698		molIndex = 0;
1699	<	globalAtomIndex = 0;
1699	>	globalAtomCounter = 0;
1700		for (i = 0; i < n_components; i++){
1701		for (j = 0; j < components_nmol[i]; j++){
1702		the_molecules[molIndex].setStampID(i);
1703		the_molecules[molIndex].setMyIndex(molIndex);
1704		the_molecules[molIndex].setGlobalIndex(molIndex);
1705		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1706	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1707	<	globalAtomIndex++;
1706	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1707	>	globalAtomCounter++;
1708		}
1709		molIndex++;
1710		}
#	Line 1308 | Line 1713 | void SimSetup::makeSysArrays(void){
1713
1714		#endif // is_mpi
1715
1716	<
1717	<	if (info[l].n_SRI){
1718	<	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	<
1716	>	info[l].globalExcludes = new int;
1717	>	info[l].globalExcludes[0] = 0;
1718	>
1719		// set the arrays into the SimInfo object
1720
1721		info[l].atoms = the_atoms;
1722		info[l].molecules = the_molecules;
1723		info[l].nGlobalExcludes = 0;
1724	<	info[l].excludes = the_excludes;
1337	<
1724	>
1725		the_ff->setSimInfo(info);
1726		}
1727		}
#	Line 1342 | Line 1729 | void SimSetup::makeIntegrator(void){
1729		void SimSetup::makeIntegrator(void){
1730		int k;
1731
1732	+	NVE<RealIntegrator>* myNVE = NULL;
1733		NVT<RealIntegrator>* myNVT = NULL;
1734	<	NPTi<RealIntegrator>* myNPTi = NULL;
1735	<	NPTf<RealIntegrator>* myNPTf = NULL;
1736	<	NPTim<RealIntegrator>* myNPTim = NULL;
1349	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1734	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1735	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1736	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1737
1738		for (k = 0; k < nInfo; k++){
1739		switch (ensembleCase){
1740		case NVE_ENS:
1741		if (globals->haveZconstraints()){
1742		setupZConstraint(info[k]);
1743	<	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1743	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1744		}
1745	<	else
1746	<	new NVE<RealIntegrator>(&(info[k]), the_ff);
1745	>	else{
1746	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1747	>	}
1748	>
1749	>	info->the_integrator = myNVE;
1750		break;
1751
1752		case NVT_ENS:
#	Line 1374 | Line 1764 | void SimSetup::makeIntegrator(void){
1764		else{
1765		sprintf(painCave.errMsg,
1766		"SimSetup error: If you use the NVT\n"
1767	<	"    ensemble, you must set tauThermostat.\n");
1767	>	"\tensemble, you must set tauThermostat.\n");
1768		painCave.isFatal = 1;
1769		simError();
1770		}
1771	+
1772	+	info->the_integrator = myNVT;
1773		break;
1774
1775		case NPTi_ENS:
1776		if (globals->haveZconstraints()){
1777		setupZConstraint(info[k]);
1778	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1778	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1779		}
1780		else
1781	<	myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1781	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1782
1783		myNPTi->setTargetTemp(globals->getTargetTemp());
1784
#	Line 1395 | Line 1787 | void SimSetup::makeIntegrator(void){
1787		else{
1788		sprintf(painCave.errMsg,
1789		"SimSetup error: If you use a constant pressure\n"
1790	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1790	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1791		painCave.isFatal = 1;
1792		simError();
1793		}
#	Line 1405 | Line 1797 | void SimSetup::makeIntegrator(void){
1797		else{
1798		sprintf(painCave.errMsg,
1799		"SimSetup error: If you use an NPT\n"
1800	<	"    ensemble, you must set tauThermostat.\n");
1800	>	"\tensemble, you must set tauThermostat.\n");
1801		painCave.isFatal = 1;
1802		simError();
1803		}
#	Line 1415 | Line 1807 | void SimSetup::makeIntegrator(void){
1807		else{
1808		sprintf(painCave.errMsg,
1809		"SimSetup error: If you use an NPT\n"
1810	<	"    ensemble, you must set tauBarostat.\n");
1810	>	"\tensemble, you must set tauBarostat.\n");
1811		painCave.isFatal = 1;
1812		simError();
1813		}
1814	+
1815	+	info->the_integrator = myNPTi;
1816		break;
1817
1818		case NPTf_ENS:
1819		if (globals->haveZconstraints()){
1820		setupZConstraint(info[k]);
1821	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1821	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1822		}
1823		else
1824	<	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1824	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1825
1826		myNPTf->setTargetTemp(globals->getTargetTemp());
1827
#	Line 1436 | Line 1830 | void SimSetup::makeIntegrator(void){
1830		else{
1831		sprintf(painCave.errMsg,
1832		"SimSetup error: If you use a constant pressure\n"
1833	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1833	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1834		painCave.isFatal = 1;
1835		simError();
1836		}
1837
1838		if (globals->haveTauThermostat())
1839		myNPTf->setTauThermostat(globals->getTauThermostat());
1840	+
1841		else{
1842		sprintf(painCave.errMsg,
1843		"SimSetup error: If you use an NPT\n"
1844	<	"    ensemble, you must set tauThermostat.\n");
1844	>	"\tensemble, you must set tauThermostat.\n");
1845		painCave.isFatal = 1;
1846		simError();
1847		}
1848
1849		if (globals->haveTauBarostat())
1850		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;
1851
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());
1852		else{
1853		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,
1854		"SimSetup error: If you use an NPT\n"
1855	<	"    ensemble, you must set tauThermostat.\n");
1855	>	"\tensemble, you must set tauBarostat.\n");
1856		painCave.isFatal = 1;
1857		simError();
1858		}
1859
1860	<	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	<	}
1860	>	info->the_integrator = myNPTf;
1861		break;
1862
1863	<	case NPTfm_ENS:
1863	>	case NPTxyz_ENS:
1864		if (globals->haveZconstraints()){
1865		setupZConstraint(info[k]);
1866	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1866	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1867		}
1868		else
1869	<	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1869	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1870
1871	<	myNPTfm->setTargetTemp(globals->getTargetTemp());
1871	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1872
1873		if (globals->haveTargetPressure())
1874	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1874	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1875		else{
1876		sprintf(painCave.errMsg,
1877		"SimSetup error: If you use a constant pressure\n"
1878	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1878	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1879		painCave.isFatal = 1;
1880		simError();
1881	<	}
1881	>	}
1882
1883		if (globals->haveTauThermostat())
1884	<	myNPTfm->setTauThermostat(globals->getTauThermostat());
1884	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1885		else{
1886		sprintf(painCave.errMsg,
1887		"SimSetup error: If you use an NPT\n"
1888	<	"    ensemble, you must set tauThermostat.\n");
1888	>	"\tensemble, you must set tauThermostat.\n");
1889		painCave.isFatal = 1;
1890		simError();
1891		}
1892
1893		if (globals->haveTauBarostat())
1894	<	myNPTfm->setTauBarostat(globals->getTauBarostat());
1894	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1895		else{
1896		sprintf(painCave.errMsg,
1897		"SimSetup error: If you use an NPT\n"
1898	<	"    ensemble, you must set tauBarostat.\n");
1898	>	"\tensemble, you must set tauBarostat.\n");
1899		painCave.isFatal = 1;
1900		simError();
1901		}
1902	+
1903	+	info->the_integrator = myNPTxyz;
1904		break;
1905
1906		default:
#	Line 1589 | Line 1948 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1948		}
1949		else{
1950		sprintf(painCave.errMsg,
1951	<	"ZConstraint error: If you use an ZConstraint\n"
1952	<	" , you must set sample time.\n");
1951	>	"ZConstraint error: If you use a ZConstraint,\n"
1952	>	"\tyou must set zconsTime.\n");
1953		painCave.isFatal = 1;
1954		simError();
1955		}
#	Line 1605 | Line 1964 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1964		else{
1965		double defaultZConsTol = 0.01;
1966		sprintf(painCave.errMsg,
1967	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1968	<	" , default value %f is used.\n",
1967	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1968	>	"\tOOPSE will use a default value of %f.\n"
1969	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1970		defaultZConsTol);
1971		painCave.isFatal = 0;
1972		simError();
#	Line 1615 | Line 1975 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1975		}
1976		theInfo.addProperty(zconsTol);
1977
1978	<	//set Force Substraction Policy
1978	>	//set Force Subtraction Policy
1979		StringData* zconsForcePolicy = new StringData();
1980		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1981
#	Line 1624 | Line 1984 | void SimSetup::setupZConstraint(SimInfo& theInfo){
1984		}
1985		else{
1986		sprintf(painCave.errMsg,
1987	<	"ZConstraint Warning: User does not set force substraction policy, "
1988	<	"average force substraction policy is used\n");
1987	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1988	>	"\tOOPSE will use PolicyByMass.\n"
1989	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1990		painCave.isFatal = 0;
1991		simError();
1992	<	zconsForcePolicy->setData("BYNUMBER");
1992	>	zconsForcePolicy->setData("BYMASS");
1993		}
1994
1995		theInfo.addProperty(zconsForcePolicy);
1996
1997	+	//set zcons gap
1998	+	DoubleData* zconsGap = new DoubleData();
1999	+	zconsGap->setID(ZCONSGAP_ID);
2000	+
2001	+	if (globals->haveZConsGap()){
2002	+	zconsGap->setData(globals->getZconsGap());
2003	+	theInfo.addProperty(zconsGap);
2004	+	}
2005	+
2006	+	//set zcons fixtime
2007	+	DoubleData* zconsFixtime = new DoubleData();
2008	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2009	+
2010	+	if (globals->haveZConsFixTime()){
2011	+	zconsFixtime->setData(globals->getZconsFixtime());
2012	+	theInfo.addProperty(zconsFixtime);
2013	+	}
2014	+
2015	+	//set zconsUsingSMD
2016	+	IntData* zconsUsingSMD = new IntData();
2017	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2018	+
2019	+	if (globals->haveZConsUsingSMD()){
2020	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2021	+	theInfo.addProperty(zconsUsingSMD);
2022	+	}
2023	+
2024		//Determine the name of ouput file and add it into SimInfo's property list
2025		//Be careful, do not use inFileName, since it is a pointer which
2026		//point to a string at master node, and slave nodes do not contain that string
#	Line 1662 | Line 2050 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2050		tempParaItem.zPos = zconStamp[i]->getZpos();
2051		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2052		tempParaItem.kRatio = zconStamp[i]->getKratio();
2053	<
2053	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2054	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2055		zconsParaData->addItem(tempParaItem);
2056		}
2057
2058	+	//check the uniqueness of index
2059	+	if(!zconsParaData->isIndexUnique()){
2060	+	sprintf(painCave.errMsg,
2061	+	"ZConstraint Error: molIndex is not unique!\n");
2062	+	painCave.isFatal = 1;
2063	+	simError();
2064	+	}
2065	+
2066		//sort the parameters by index of molecules
2067		zconsParaData->sortByIndex();
2068	<
2068	>
2069		//push data into siminfo, therefore, we can retrieve later
2070		theInfo.addProperty(zconsParaData);
2071		}
2072	+
2073	+	void SimSetup::makeMinimizer(){
2074	+
2075	+	OOPSEMinimizer* myOOPSEMinimizer;
2076	+	MinimizerParameterSet* param;
2077	+	char minimizerName[100];
2078	+
2079	+	for (int i = 0; i < nInfo; i++){
2080	+
2081	+	//prepare parameter set for minimizer
2082	+	param = new MinimizerParameterSet();
2083	+	param->setDefaultParameter();
2084	+
2085	+	if (globals->haveMinimizer()){
2086	+	param->setFTol(globals->getMinFTol());
2087	+	}
2088	+
2089	+	if (globals->haveMinGTol()){
2090	+	param->setGTol(globals->getMinGTol());
2091	+	}
2092	+
2093	+	if (globals->haveMinMaxIter()){
2094	+	param->setMaxIteration(globals->getMinMaxIter());
2095	+	}
2096	+
2097	+	if (globals->haveMinWriteFrq()){
2098	+	param->setMaxIteration(globals->getMinMaxIter());
2099	+	}
2100	+
2101	+	if (globals->haveMinWriteFrq()){
2102	+	param->setWriteFrq(globals->getMinWriteFrq());
2103	+	}
2104	+
2105	+	if (globals->haveMinStepSize()){
2106	+	param->setStepSize(globals->getMinStepSize());
2107	+	}
2108	+
2109	+	if (globals->haveMinLSMaxIter()){
2110	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2111	+	}
2112	+
2113	+	if (globals->haveMinLSTol()){
2114	+	param->setLineSearchTol(globals->getMinLSTol());
2115	+	}
2116	+
2117	+	strcpy(minimizerName, globals->getMinimizer());
2118	+
2119	+	if (!strcasecmp(minimizerName, "CG")){
2120	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2121	+	}
2122	+	else if (!strcasecmp(minimizerName, "SD")){
2123	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2124	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2125	+	}
2126	+	else{
2127	+	sprintf(painCave.errMsg,
2128	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2129	+	painCave.isFatal = 0;
2130	+	simError();
2131	+
2132	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2133	+	}
2134	+	info[i].the_integrator = myOOPSEMinimizer;
2135	+
2136	+	//store the minimizer into simInfo
2137	+	info[i].the_minimizer = myOOPSEMinimizer;
2138	+	info[i].has_minimizer = true;
2139	+	}
2140	+
2141	+	}

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