[ViewVC] Diff of: group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC vs.
Revision 1174 by gezelter, Wed May 12 20:54:10 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 25 \| Line 27
27		#define NPTxyz_ENS 4
28
29
30	<	#define FF_DUFF 0
31	<	#define FF_LJ 1
32	<	#define FF_EAM 2
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 107 \| 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()) )
#	Line 117 \| Line 147 \| void SimSetup::createSim(void){
147		// make the output filenames
148
149		makeOutNames();
150	<
121	<	// make the integrator
122	<
123	<	makeIntegrator();
124	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 129 \| 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;
171	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175		molInit molInfo;
176		DirectionalAtom* dAtom;
177	+	RigidBody* myRB;
178	+	StuntDouble* mySD;
179		LinkedAssign* extras;
180		LinkedAssign* current_extra;
181		AtomStamp* currentAtom;
182		BondStamp* currentBond;
183		BendStamp* currentBend;
184		TorsionStamp* currentTorsion;
185	+	RigidBodyStamp* currentRigidBody;
186	+	CutoffGroupStamp* currentCutoffGroup;
187	+	CutoffGroup* myCutoffGroup;
188	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	+	set<int> cutoffAtomSet; //atoms belong to cutoffgroup defined at mdl file
190
191		bond_pair* theBonds;
192		bend_set* theBends;
193		torsion_set* theTorsions;
194
195	+	set<int> skipList;
196
197	+	double phi, theta, psi;
198	+	char* molName;
199	+	char rbName[100];
200	+
201		//init the forceField paramters
202
203		the_ff->readParams();
204
156	–
205		// init the atoms
206
207	<	double ux, uy, uz, u, uSqr;
207	>	int nMembers, nNew, rb1, rb2;
208
209		for (k = 0; k < nInfo; k++){
210		the_ff->setSimInfo(&(info[k]));
211
212		atomOffset = 0;
213	<	excludeOffset = 0;
213	>
214		for (i = 0; i < info[k].n_mol; i++){
215		stampID = info[k].molecules[i].getStampID();
216	+	molName = comp_stamps[stampID]->getID();
217
218		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220		molInfo.nBends = comp_stamps[stampID]->getNBends();
221		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	+
226		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
176	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
177	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
178	–	molInfo.myBends = new Bend * [molInfo.nBends];
179	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
227
228	+	if (molInfo.nBonds > 0)
229	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	+	else
231	+	molInfo.myBonds = NULL;
232	+
233	+	if (molInfo.nBends > 0)
234	+	molInfo.myBends = new Bend*[molInfo.nBends];
235	+	else
236	+	molInfo.myBends = NULL;
237	+
238	+	if (molInfo.nTorsions > 0)
239	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	+	else
241	+	molInfo.myTorsions = NULL;
242	+
243		theBonds = new bond_pair[molInfo.nBonds];
244		theBends = new bend_set[molInfo.nBends];
245		theTorsions = new torsion_set[molInfo.nTorsions];
246	<
246	>
247		// make the Atoms
248
249		for (j = 0; j < molInfo.nAtoms; j++){
250		currentAtom = comp_stamps[stampID]->getAtom(j);
251	+
252		if (currentAtom->haveOrientation()){
253		dAtom = new DirectionalAtom((j + atomOffset),
254		info[k].getConfiguration());
255		info[k].n_oriented++;
256		molInfo.myAtoms[j] = dAtom;
257
258	<	ux = currentAtom->getOrntX();
259	<	uy = currentAtom->getOrntY();
260	<	uz = currentAtom->getOrntZ();
258	>	// Directional Atoms have standard unit vectors which are oriented
259	>	// in space using the three Euler angles. We assume the standard
260	>	// unit vector was originally along the z axis below.
261
262	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265
266	<	u = sqrt(uSqr);
267	<	ux = ux / u;
203	<	uy = uy / u;
204	<	uz = uz / u;
205	<
206	<	dAtom->setSUx(ux);
207	<	dAtom->setSUy(uy);
208	<	dAtom->setSUz(uz);
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268		}
269		else{
270	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
271	<	info[k].getConfiguration());
270	>
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272	>
273		}
214	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
274
275	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277
278	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
280		#endif // is_mpi
281		}
#	Line 226 \| Line 286 \| void SimSetup::makeMolecules(void){
286		theBonds[j].a = currentBond->getA() + atomOffset;
287		theBonds[j].b = currentBond->getB() + atomOffset;
288
289	<	exI = theBonds[j].a;
290	<	exJ = theBonds[j].b;
289	>	tempI = theBonds[j].a;
290	>	tempJ = theBonds[j].b;
291
232	–	// exclude_I must always be the smaller of the pair
233	–	if (exI > exJ){
234	–	tempEx = exI;
235	–	exI = exJ;
236	–	exJ = tempEx;
237	–	}
292		#ifdef IS_MPI
293	<	tempEx = exI;
294	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
295	<	tempEx = exJ;
296	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
245	<	#else // isn't MPI
246	<
247	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
248	<	#endif //is_mpi
300	>	info[k].excludes->addPair(exI, exJ);
301		}
250	–	excludeOffset += molInfo.nBonds;
302
303		//make the bends
304		for (j = 0; j < molInfo.nBends; j++){
#	Line 297 \| Line 348 \| void SimSetup::makeMolecules(void){
348		}
349		}
350
351	<	if (!theBends[j].isGhost){
352	<	exI = theBends[j].a;
353	<	exJ = theBends[j].c;
354	<	}
355	<	else{
305	<	exI = theBends[j].a;
306	<	exJ = theBends[j].b;
307	<	}
308	<
309	<	// exclude_I must always be the smaller of the pair
310	<	if (exI > exJ){
311	<	tempEx = exI;
312	<	exI = exJ;
313	<	exJ = tempEx;
314	<	}
351	>	if (theBends[j].isGhost) {
352	>
353	>	tempI = theBends[j].a;
354	>	tempJ = theBends[j].b;
355	>
356		#ifdef IS_MPI
357	<	tempEx = exI;
358	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
359	<	tempEx = exJ;
360	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
366	<	#else // isn't MPI
367	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
368	<	#endif //is_mpi
365	>	} else {
366	>
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
326	–	excludeOffset += molInfo.nBends;
386
387		for (j = 0; j < molInfo.nTorsions; j++){
388		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 332 \| Line 391 \| void SimSetup::makeMolecules(void){
391		theTorsions[j].c = currentTorsion->getC() + atomOffset;
392		theTorsions[j].d = currentTorsion->getD() + atomOffset;
393
394	<	exI = theTorsions[j].a;
395	<	exJ = theTorsions[j].d;
396	<
397	<	// exclude_I must always be the smaller of the pair
398	<	if (exI > exJ){
399	<	tempEx = exI;
400	<	exI = exJ;
401	<	exJ = tempEx;
394	>	tempI = theTorsions[j].a;
395	>	tempJ = theTorsions[j].b;
396	>	tempK = theTorsions[j].c;
397	>	tempL = theTorsions[j].d;
398	>
399	>	#ifdef IS_MPI
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410	>
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418	>
419	>
420	>	molInfo.myRigidBodies.clear();
421	>
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423	>
424	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	>	nMembers = currentRigidBody->getNMembers();
426	>
427	>	// Create the Rigid Body:
428	>
429	>	myRB = new RigidBody();
430	>
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435	>
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438	>
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441	>
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445	>
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448	>
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452	>	#ifdef IS_MPI
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459		}
460	+
461	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	+
464	+	tempI = currentRigidBody->getMember(rb1);
465	+	tempJ = currentRigidBody->getMember(rb2);
466	+
467	+	// Some explanation is required here.
468	+	// Fortran indexing starts at 1, while c indexing starts at 0
469	+	// Also, in parallel computations, the GlobalIndex is
470	+	// used for the exclude list:
471	+
472		#ifdef IS_MPI
473	<	tempEx = exI;
474	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
475	<	tempEx = exJ;
476	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484
485	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
486	<	#else // isn't MPI
352	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
353	<	#endif //is_mpi
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487		}
488	<	excludeOffset += molInfo.nTorsions;
488	>
489
490	+	//create cutoff group for molecule
491
492	<	// send the arrays off to the forceField for init.
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496	>
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499	>
500	>	myCutoffGroup = new CutoffGroup();
501	>
502	>	for (int cg = 0; cg < nMembers; cg++) {
503
504	+	// molI is atom numbering inside this molecule
505	+	molI = currentCutoffGroup->getMember(cg);
506	+
507	+	// tempI is atom numbering on local processor
508	+	tempI = molI + atomOffset;
509	+
510	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	+
512	+	cutoffAtomSet.insert(tempI);
513	+	}
514	+
515	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	+
518	+	//creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file
519	+
520	+	for(j = 0; j < molInfo.nAtoms; j++){
521	+
522	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	+	myCutoffGroup = new CutoffGroup();
524	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	+	}
527	+
528	+	}
529	+
530	+
531	+
532	+
533	+	// After this is all set up, scan through the atoms to
534	+	// see if they can be added to the integrableObjects:
535	+
536	+	molInfo.myIntegrableObjects.clear();
537	+
538	+
539	+	for (j = 0; j < molInfo.nAtoms; j++){
540	+
541	+	#ifdef IS_MPI
542	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	+	#else
544	+	slJ = j+atomOffset;
545	+	#endif
546	+
547	+	// if they aren't on the skip list, then they can be integrated
548	+
549	+	if (skipList.find(slJ) == skipList.end()) {
550	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	+	info[k].integrableObjects.push_back(mySD);
552	+	molInfo.myIntegrableObjects.push_back(mySD);
553	+	}
554	+	}
555	+
556	+	// all rigid bodies are integrated:
557	+
558	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	+	info[k].integrableObjects.push_back(mySD);
561	+	molInfo.myIntegrableObjects.push_back(mySD);
562	+	}
563	+
564	+
565	+	// send the arrays off to the forceField for init.
566	+
567		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571		theTorsions);
572
366	–
573		info[k].molecules[i].initialize(molInfo);
574
575
#	Line 371 \| Line 577 \| void SimSetup::makeMolecules(void){
577		delete[] theBonds;
578		delete[] theBends;
579		delete[] theTorsions;
580	<	}
580	>	}
581		}
582
583		#ifdef IS_MPI
#	Line 379 \| Line 585 \| void SimSetup::makeMolecules(void){
585		MPIcheckPoint();
586		#endif // is_mpi
587
382	–	// clean up the forcefield
383	–
384	–	the_ff->calcRcut();
385	–	the_ff->cleanMe();
588		}
589
590		void SimSetup::initFromBass(void){
#	Line 583 \| Line 785 \| void SimSetup::gatherInfo(void){
785		else if (!strcasecmp(force_field, "EAM")){
786		ffCase = FF_EAM;
787		}
788	+	else if (!strcasecmp(force_field, "WATER")){
789	+	ffCase = FF_H2O;
790	+	}
791		else{
792		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793		force_field);
#	Line 611 \| Line 816 \| void SimSetup::gatherInfo(void){
816		}
817		else{
818		sprintf(painCave.errMsg,
819	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
820	<	"reverting to NVE for this simulation.\n",
819	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	>	"\treverting to NVE for this simulation.\n",
821		ensemble);
822		painCave.isFatal = 0;
823		simError();
#	Line 644 \| Line 849 \| void SimSetup::gatherInfo(void){
849		if (!the_components[i]->haveNMol()){
850		// we have a problem
851		sprintf(painCave.errMsg,
852	<	"SimSetup Error. No global NMol or component NMol"
853	<	" given. Cannot calculate the number of atoms.\n");
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854		painCave.isFatal = 1;
855		simError();
856		}
#	Line 663 \| Line 868 \| void SimSetup::gatherInfo(void){
868		" Please give nMol in the components.\n");
869		painCave.isFatal = 1;
870		simError();
871	+	}
872	+
873	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	+	sprintf(painCave.errMsg,
876	+	"Sample time is not divisible by dt.\n"
877	+	"\tThis will result in samples that are not uniformly\n"
878	+	"\tdistributed in time. If this is a problem, change\n"
879	+	"\tyour sampleTime variable.\n");
880	+	painCave.isFatal = 0;
881	+	simError();
882		}
883	+
884	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	+	sprintf(painCave.errMsg,
886	+	"Status time is not divisible by dt.\n"
887	+	"\tThis will result in status reports that are not uniformly\n"
888	+	"\tdistributed in time. If this is a problem, change \n"
889	+	"\tyour statusTime variable.\n");
890	+	painCave.isFatal = 0;
891	+	simError();
892	+	}
893	+
894	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	+	sprintf(painCave.errMsg,
896	+	"Thermal time is not divisible by dt.\n"
897	+	"\tThis will result in thermalizations that are not uniformly\n"
898	+	"\tdistributed in time. If this is a problem, change \n"
899	+	"\tyour thermalTime variable.\n");
900	+	painCave.isFatal = 0;
901	+	simError();
902	+	}
903
904	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	+	sprintf(painCave.errMsg,
906	+	"Reset time is not divisible by dt.\n"
907	+	"\tThis will result in integrator resets that are not uniformly\n"
908	+	"\tdistributed in time. If this is a problem, change\n"
909	+	"\tyour resetTime variable.\n");
910	+	painCave.isFatal = 0;
911	+	simError();
912	+	}
913	+
914		// set the status, sample, and thermal kick times
915
916		for (i = 0; i < nInfo; i++){
917		if (globals->haveSampleTime()){
918		info[i].sampleTime = globals->getSampleTime();
919		info[i].statusTime = info[i].sampleTime;
674	–	info[i].thermalTime = info[i].sampleTime;
920		}
921		else{
922		info[i].sampleTime = globals->getRunTime();
923		info[i].statusTime = info[i].sampleTime;
679	–	info[i].thermalTime = info[i].sampleTime;
924		}
925
926		if (globals->haveStatusTime()){
#	Line 685 \| Line 929 \| void SimSetup::gatherInfo(void){
929
930		if (globals->haveThermalTime()){
931		info[i].thermalTime = globals->getThermalTime();
932	+	} else {
933	+	info[i].thermalTime = globals->getRunTime();
934		}
935
936		info[i].resetIntegrator = 0;
#	Line 694 \| Line 940 \| void SimSetup::gatherInfo(void){
940		}
941
942		// check for the temperature set flag
943	<
943	>
944		if (globals->haveTempSet())
945		info[i].setTemp = globals->getTempSet();
946
947	<	// get some of the tricky things that may still be in the globals
947	>	// check for the extended State init
948
949	<	double boxVector[3];
950	<	if (globals->haveBox()){
951	<	boxVector[0] = globals->getBox();
706	<	boxVector[1] = globals->getBox();
707	<	boxVector[2] = globals->getBox();
708	<
709	<	info[i].setBox(boxVector);
710	<	}
711	<	else if (globals->haveDensity()){
712	<	double vol;
713	<	vol = (double) tot_nmol / globals->getDensity();
714	<	boxVector[0] = pow(vol, (1.0 / 3.0));
715	<	boxVector[1] = boxVector[0];
716	<	boxVector[2] = boxVector[0];
717	<
718	<	info[i].setBox(boxVector);
719	<	}
720	<	else{
721	<	if (!globals->haveBoxX()){
722	<	sprintf(painCave.errMsg,
723	<	"SimSetup error, no periodic BoxX size given.\n");
724	<	painCave.isFatal = 1;
725	<	simError();
726	<	}
727	<	boxVector[0] = globals->getBoxX();
728	<
729	<	if (!globals->haveBoxY()){
730	<	sprintf(painCave.errMsg,
731	<	"SimSetup error, no periodic BoxY size given.\n");
732	<	painCave.isFatal = 1;
733	<	simError();
734	<	}
735	<	boxVector[1] = globals->getBoxY();
736	<
737	<	if (!globals->haveBoxZ()){
738	<	sprintf(painCave.errMsg,
739	<	"SimSetup error, no periodic BoxZ size given.\n");
740	<	painCave.isFatal = 1;
741	<	simError();
742	<	}
743	<	boxVector[2] = globals->getBoxZ();
744	<
745	<	info[i].setBox(boxVector);
746	<	}
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951	>
952		}
953	<
953	>
954		//setup seed for random number generator
955		int seedValue;
956
#	Line 785 \| Line 990 \| void SimSetup::gatherInfo(void){
990		for (int i = 0; i < nInfo; i++){
991		info[i].setSeed(seedValue);
992		}
993	<
993	>
994		#ifdef IS_MPI
995	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
995	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
996		MPIcheckPoint();
997		#endif // is_mpi
998		}
#	Line 796 \| Line 1001 \| void SimSetup::finalInfoCheck(void){
1001		void SimSetup::finalInfoCheck(void){
1002		int index;
1003		int usesDipoles;
1004	+	int usesCharges;
1005		int i;
1006
1007		for (i = 0; i < nInfo; i++){
#	Line 807 \| Line 1013 \| void SimSetup::finalInfoCheck(void){
1013		usesDipoles = (info[i].atoms[index])->hasDipole();
1014		index++;
1015		}
1016	<
1016	>	index = 0;
1017	>	usesCharges = 0;
1018	>	while ((index < info[i].n_atoms) && !usesCharges){
1019	>	usesCharges= (info[i].atoms[index])->hasCharge();
1020	>	index++;
1021	>	}
1022		#ifdef IS_MPI
1023		int myUse = usesDipoles;
1024		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1025		#endif //is_mpi
1026
1027	<	double theEcr, theEst;
1027	>	double theRcut, theRsw;
1028
1029	+	if (globals->haveRcut()) {
1030	+	theRcut = globals->getRcut();
1031	+
1032	+	if (globals->haveRsw())
1033	+	theRsw = globals->getRsw();
1034	+	else
1035	+	theRsw = theRcut;
1036	+
1037	+	info[i].setDefaultRcut(theRcut, theRsw);
1038	+
1039	+	} else {
1040	+
1041	+	the_ff->calcRcut();
1042	+	theRcut = info[i].getRcut();
1043	+
1044	+	if (globals->haveRsw())
1045	+	theRsw = globals->getRsw();
1046	+	else
1047	+	theRsw = theRcut;
1048	+
1049	+	info[i].setDefaultRcut(theRcut, theRsw);
1050	+	}
1051	+
1052		if (globals->getUseRF()){
1053		info[i].useReactionField = 1;
1054	<
1055	<	if (!globals->haveECR()){
1054	>
1055	>	if (!globals->haveRcut()){
1056		sprintf(painCave.errMsg,
1057	<	"SimSetup Warning: using default value of 1/2 the smallest "
1058	<	"box length for the electrostaticCutoffRadius.\n"
1059	<	"I hope you have a very fast processor!\n");
1057	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1058	>	"\tOOPSE will use a default value of 15.0 angstroms"
1059	>	"\tfor the cutoffRadius.\n");
1060		painCave.isFatal = 0;
1061		simError();
1062	<	double smallest;
829	<	smallest = info[i].boxL[0];
830	<	if (info[i].boxL[1] <= smallest)
831	<	smallest = info[i].boxL[1];
832	<	if (info[i].boxL[2] <= smallest)
833	<	smallest = info[i].boxL[2];
834	<	theEcr = 0.5 * smallest;
1062	>	theRcut = 15.0;
1063		}
1064		else{
1065	<	theEcr = globals->getECR();
1065	>	theRcut = globals->getRcut();
1066		}
1067
1068	<	if (!globals->haveEST()){
1068	>	if (!globals->haveRsw()){
1069		sprintf(painCave.errMsg,
1070	<	"SimSetup Warning: using default value of 0.05 * the "
1071	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1070	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1071	>	"\tOOPSE will use a default value of\n"
1072	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1073		painCave.isFatal = 0;
1074		simError();
1075	<	theEst = 0.05 * theEcr;
1075	>	theRsw = 0.95 * theRcut;
1076		}
1077		else{
1078	<	theEst = globals->getEST();
1078	>	theRsw = globals->getRsw();
1079		}
1080
1081	<	info[i].setEcr(theEcr, theEst);
1081	>	info[i].setDefaultRcut(theRcut, theRsw);
1082
1083		if (!globals->haveDielectric()){
1084		sprintf(painCave.errMsg,
1085	<	"SimSetup Error: You are trying to use Reaction Field without"
1086	<	"setting a dielectric constant!\n");
1085	>	"SimSetup Error: No Dielectric constant was set.\n"
1086	>	"\tYou are trying to use Reaction Field without"
1087	>	"\tsetting a dielectric constant!\n");
1088		painCave.isFatal = 1;
1089		simError();
1090		}
1091		info[i].dielectric = globals->getDielectric();
1092		}
1093		else{
1094	<	if (usesDipoles){
1095	<	if (!globals->haveECR()){
1094	>	if (usesDipoles \|\| usesCharges){
1095	>
1096	>	if (!globals->haveRcut()){
1097		sprintf(painCave.errMsg,
1098	<	"SimSetup Warning: using default value of 1/2 the smallest "
1099	<	"box length for the electrostaticCutoffRadius.\n"
1100	<	"I hope you have a very fast processor!\n");
1098	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1099	>	"\tOOPSE will use a default value of 15.0 angstroms"
1100	>	"\tfor the cutoffRadius.\n");
1101		painCave.isFatal = 0;
1102		simError();
1103	<	double smallest;
1104	<	smallest = info[i].boxL[0];
874	<	if (info[i].boxL[1] <= smallest)
875	<	smallest = info[i].boxL[1];
876	<	if (info[i].boxL[2] <= smallest)
877	<	smallest = info[i].boxL[2];
878	<	theEcr = 0.5 * smallest;
879	<	}
1103	>	theRcut = 15.0;
1104	>	}
1105		else{
1106	<	theEcr = globals->getECR();
1106	>	theRcut = globals->getRcut();
1107		}
1108	<
1109	<	if (!globals->haveEST()){
1108	>
1109	>	if (!globals->haveRsw()){
1110		sprintf(painCave.errMsg,
1111	<	"SimSetup Warning: using default value of 0.05 * the "
1112	<	"electrostaticCutoffRadius for the "
1113	<	"electrostaticSkinThickness\n");
1111	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1112	>	"\tOOPSE will use a default value of\n"
1113	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1114		painCave.isFatal = 0;
1115		simError();
1116	<	theEst = 0.05 * theEcr;
1116	>	theRsw = 0.95 * theRcut;
1117		}
1118		else{
1119	<	theEst = globals->getEST();
1119	>	theRsw = globals->getRsw();
1120		}
1121	<
1122	<	info[i].setEcr(theEcr, theEst);
1121	>
1122	>	info[i].setDefaultRcut(theRcut, theRsw);
1123	>
1124		}
1125		}
1126		}
901	–
1127		#ifdef IS_MPI
1128		strcpy(checkPointMsg, "post processing checks out");
1129		MPIcheckPoint();
1130		#endif // is_mpi
906	–	}
1131
1132	+	// clean up the forcefield
1133	+	the_ff->cleanMe();
1134	+	}
1135	+
1136		void SimSetup::initSystemCoords(void){
1137		int i;
1138
#	Line 932 \| Line 1160 \| void SimSetup::initSystemCoords(void){
1160		delete fileInit;
1161		}
1162		else{
1163	<	#ifdef IS_MPI
936	<
1163	>
1164		// no init from bass
1165	<
1165	>
1166		sprintf(painCave.errMsg,
1167	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1167	>	"Cannot intialize a simulation without an initial configuration file.\n");
1168		painCave.isFatal = 1;;
1169		simError();
1170	<
944	<	#else
945	<
946	<	initFromBass();
947	<
948	<
949	<	#endif
1170	>
1171		}
1172
1173		#ifdef IS_MPI
#	Line 1098 \| Line 1319 \| void SimSetup::createFF(void){
1319
1320		case FF_EAM:
1321		the_ff = new EAM_FF();
1322	+	break;
1323	+
1324	+	case FF_H2O:
1325	+	the_ff = new WATER();
1326		break;
1327
1328		default:
#	Line 1120 \| Line 1345 \| void SimSetup::compList(void){
1345		LinkedMolStamp* headStamp = new LinkedMolStamp();
1346		LinkedMolStamp* currentStamp = NULL;
1347		comp_stamps = new MoleculeStamp * [n_components];
1348	+	bool haveCutoffGroups;
1349
1350	+	haveCutoffGroups = false;
1351	+
1352		// make an array of molecule stamps that match the components used.
1353		// also extract the used stamps out into a separate linked list
1354
#	Line 1155 \| Line 1383 \| void SimSetup::compList(void){
1383		headStamp->add(currentStamp);
1384		comp_stamps[i] = headStamp->match(id);
1385		}
1386	+
1387	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1388	+	haveCutoffGroups = true;
1389		}
1390	+
1391	+	for (i = 0; i < nInfo; i++)
1392	+	info[i].haveCutoffGroups = haveCutoffGroups;
1393
1394		#ifdef IS_MPI
1395		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1172 \| Line 1406 \| void SimSetup::calcSysValues(void){
1406		tot_bonds = 0;
1407		tot_bends = 0;
1408		tot_torsions = 0;
1409	+	tot_rigid = 0;
1410		for (i = 0; i < n_components; i++){
1411		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1412		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1413		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1414		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1415	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1416		}
1417	<
1417	>
1418		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1419		molMembershipArray = new int[tot_atoms];
1420
#	Line 1200 \| Line 1436 \| void SimSetup::mpiMolDivide(void){
1436		int i, j, k;
1437		int localMol, allMol;
1438		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1439	+	int local_rigid;
1440	+	vector<int> globalMolIndex;
1441
1442		mpiSim = new mpiSimulation(info);
1443
1444	<	globalIndex = mpiSim->divideLabor();
1444	>	mpiSim->divideLabor();
1445	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1446	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1447
1448		// set up the local variables
1449
#	Line 1216 \| Line 1456 \| void SimSetup::mpiMolDivide(void){
1456		local_bonds = 0;
1457		local_bends = 0;
1458		local_torsions = 0;
1459	<	globalAtomIndex = 0;
1459	>	local_rigid = 0;
1460	>	globalAtomCounter = 0;
1461
1221	–
1462		for (i = 0; i < n_components; i++){
1463		for (j = 0; j < components_nmol[i]; j++){
1464		if (mol2proc[allMol] == worldRank){
#	Line 1226 \| Line 1466 \| void SimSetup::mpiMolDivide(void){
1466		local_bonds += comp_stamps[i]->getNBonds();
1467		local_bends += comp_stamps[i]->getNBends();
1468		local_torsions += comp_stamps[i]->getNTorsions();
1469	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1470		localMol++;
1471		}
1472		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1473	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1474	<	globalAtomIndex++;
1473	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1474	>	globalAtomCounter++;
1475		}
1476
1477		allMol++;
#	Line 1239 \| Line 1480 \| void SimSetup::mpiMolDivide(void){
1480		local_SRI = local_bonds + local_bends + local_torsions;
1481
1482		info[0].n_atoms = mpiSim->getMyNlocal();
1483	+
1484
1485		if (local_atoms != info[0].n_atoms){
1486		sprintf(painCave.errMsg,
1487	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1488	<	" localAtom (%d) are not equal.\n",
1487	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1488	>	"\tlocalAtom (%d) are not equal.\n",
1489		info[0].n_atoms, local_atoms);
1490		painCave.isFatal = 1;
1491		simError();
#	Line 1271 \| Line 1513 \| void SimSetup::makeSysArrays(void){
1513
1514		Atom** the_atoms;
1515		Molecule* the_molecules;
1274	–	Exclude** the_excludes;
1516
1276	–
1517		for (l = 0; l < nInfo; l++){
1518		// create the atom and short range interaction arrays
1519
#	Line 1299 \| Line 1539 \| void SimSetup::makeSysArrays(void){
1539		#else // is_mpi
1540
1541		molIndex = 0;
1542	<	globalAtomIndex = 0;
1542	>	globalAtomCounter = 0;
1543		for (i = 0; i < n_components; i++){
1544		for (j = 0; j < components_nmol[i]; j++){
1545		the_molecules[molIndex].setStampID(i);
1546		the_molecules[molIndex].setMyIndex(molIndex);
1547		the_molecules[molIndex].setGlobalIndex(molIndex);
1548		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1549	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1550	<	globalAtomIndex++;
1549	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1550	>	globalAtomCounter++;
1551		}
1552		molIndex++;
1553		}
#	Line 1316 \| Line 1556 \| void SimSetup::makeSysArrays(void){
1556
1557		#endif // is_mpi
1558
1559	<
1560	<	if (info[l].n_SRI){
1561	<	Exclude::createArray(info[l].n_SRI);
1322	<	the_excludes = new Exclude * [info[l].n_SRI];
1323	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1324	<	the_excludes[ex] = new Exclude(ex);
1325	<	}
1326	<	info[l].globalExcludes = new int;
1327	<	info[l].n_exclude = info[l].n_SRI;
1328	<	}
1329	<	else{
1330	<	Exclude::createArray(1);
1331	<	the_excludes = new Exclude * ;
1332	<	the_excludes[0] = new Exclude(0);
1333	<	the_excludes[0]->setPair(0, 0);
1334	<	info[l].globalExcludes = new int;
1335	<	info[l].globalExcludes[0] = 0;
1336	<	info[l].n_exclude = 0;
1337	<	}
1338	<
1559	>	info[l].globalExcludes = new int;
1560	>	info[l].globalExcludes[0] = 0;
1561	>
1562		// set the arrays into the SimInfo object
1563
1564		info[l].atoms = the_atoms;
1565		info[l].molecules = the_molecules;
1566		info[l].nGlobalExcludes = 0;
1567	<	info[l].excludes = the_excludes;
1345	<
1567	>
1568		the_ff->setSimInfo(info);
1569		}
1570		}
#	Line 1385 \| Line 1607 \| void SimSetup::makeIntegrator(void){
1607		else{
1608		sprintf(painCave.errMsg,
1609		"SimSetup error: If you use the NVT\n"
1610	<	" ensemble, you must set tauThermostat.\n");
1610	>	"\tensemble, you must set tauThermostat.\n");
1611		painCave.isFatal = 1;
1612		simError();
1613		}
#	Line 1408 \| Line 1630 \| void SimSetup::makeIntegrator(void){
1630		else{
1631		sprintf(painCave.errMsg,
1632		"SimSetup error: If you use a constant pressure\n"
1633	<	" ensemble, you must set targetPressure in the BASS file.\n");
1633	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1634		painCave.isFatal = 1;
1635		simError();
1636		}
#	Line 1418 \| Line 1640 \| void SimSetup::makeIntegrator(void){
1640		else{
1641		sprintf(painCave.errMsg,
1642		"SimSetup error: If you use an NPT\n"
1643	<	" ensemble, you must set tauThermostat.\n");
1643	>	"\tensemble, you must set tauThermostat.\n");
1644		painCave.isFatal = 1;
1645		simError();
1646		}
#	Line 1428 \| Line 1650 \| void SimSetup::makeIntegrator(void){
1650		else{
1651		sprintf(painCave.errMsg,
1652		"SimSetup error: If you use an NPT\n"
1653	<	" ensemble, you must set tauBarostat.\n");
1653	>	"\tensemble, you must set tauBarostat.\n");
1654		painCave.isFatal = 1;
1655		simError();
1656		}
#	Line 1451 \| Line 1673 \| void SimSetup::makeIntegrator(void){
1673		else{
1674		sprintf(painCave.errMsg,
1675		"SimSetup error: If you use a constant pressure\n"
1676	<	" ensemble, you must set targetPressure in the BASS file.\n");
1676	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1677		painCave.isFatal = 1;
1678		simError();
1679		}
1680
1681		if (globals->haveTauThermostat())
1682		myNPTf->setTauThermostat(globals->getTauThermostat());
1683	+
1684		else{
1685		sprintf(painCave.errMsg,
1686		"SimSetup error: If you use an NPT\n"
1687	<	" ensemble, you must set tauThermostat.\n");
1687	>	"\tensemble, you must set tauThermostat.\n");
1688		painCave.isFatal = 1;
1689		simError();
1690		}
1691
1692		if (globals->haveTauBarostat())
1693		myNPTf->setTauBarostat(globals->getTauBarostat());
1694	+
1695		else{
1696		sprintf(painCave.errMsg,
1697		"SimSetup error: If you use an NPT\n"
1698	<	" ensemble, you must set tauBarostat.\n");
1698	>	"\tensemble, you must set tauBarostat.\n");
1699		painCave.isFatal = 1;
1700		simError();
1701		}
#	Line 1494 \| Line 1718 \| void SimSetup::makeIntegrator(void){
1718		else{
1719		sprintf(painCave.errMsg,
1720		"SimSetup error: If you use a constant pressure\n"
1721	<	" ensemble, you must set targetPressure in the BASS file.\n");
1721	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1722		painCave.isFatal = 1;
1723		simError();
1724		}
#	Line 1504 \| Line 1728 \| void SimSetup::makeIntegrator(void){
1728		else{
1729		sprintf(painCave.errMsg,
1730		"SimSetup error: If you use an NPT\n"
1731	<	" ensemble, you must set tauThermostat.\n");
1731	>	"\tensemble, you must set tauThermostat.\n");
1732		painCave.isFatal = 1;
1733		simError();
1734		}
#	Line 1514 \| Line 1738 \| void SimSetup::makeIntegrator(void){
1738		else{
1739		sprintf(painCave.errMsg,
1740		"SimSetup error: If you use an NPT\n"
1741	<	" ensemble, you must set tauBarostat.\n");
1741	>	"\tensemble, you must set tauBarostat.\n");
1742		painCave.isFatal = 1;
1743		simError();
1744		}
#	Line 1567 \| Line 1791 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1791		}
1792		else{
1793		sprintf(painCave.errMsg,
1794	<	"ZConstraint error: If you use an ZConstraint\n"
1795	<	" , you must set sample time.\n");
1794	>	"ZConstraint error: If you use a ZConstraint,\n"
1795	>	"\tyou must set zconsTime.\n");
1796		painCave.isFatal = 1;
1797		simError();
1798		}
#	Line 1583 \| Line 1807 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1807		else{
1808		double defaultZConsTol = 0.01;
1809		sprintf(painCave.errMsg,
1810	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1811	<	" , default value %f is used.\n",
1810	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1811	>	"\tOOPSE will use a default value of %f.\n"
1812	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1813		defaultZConsTol);
1814		painCave.isFatal = 0;
1815		simError();
#	Line 1602 \| Line 1827 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1827		}
1828		else{
1829		sprintf(painCave.errMsg,
1830	<	"ZConstraint Warning: User does not set force Subtraction policy, "
1831	<	"PolicyByMass is used\n");
1830	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1831	>	"\tOOPSE will use PolicyByMass.\n"
1832	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1833		painCave.isFatal = 0;
1834		simError();
1835		zconsForcePolicy->setData("BYMASS");
#	Line 1611 \| Line 1837 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1837
1838		theInfo.addProperty(zconsForcePolicy);
1839
1840	+	//set zcons gap
1841	+	DoubleData* zconsGap = new DoubleData();
1842	+	zconsGap->setID(ZCONSGAP_ID);
1843	+
1844	+	if (globals->haveZConsGap()){
1845	+	zconsGap->setData(globals->getZconsGap());
1846	+	theInfo.addProperty(zconsGap);
1847	+	}
1848	+
1849	+	//set zcons fixtime
1850	+	DoubleData* zconsFixtime = new DoubleData();
1851	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1852	+
1853	+	if (globals->haveZConsFixTime()){
1854	+	zconsFixtime->setData(globals->getZconsFixtime());
1855	+	theInfo.addProperty(zconsFixtime);
1856	+	}
1857	+
1858	+	//set zconsUsingSMD
1859	+	IntData* zconsUsingSMD = new IntData();
1860	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1861	+
1862	+	if (globals->haveZConsUsingSMD()){
1863	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1864	+	theInfo.addProperty(zconsUsingSMD);
1865	+	}
1866	+
1867		//Determine the name of ouput file and add it into SimInfo's property list
1868		//Be careful, do not use inFileName, since it is a pointer which
1869		//point to a string at master node, and slave nodes do not contain that string
#	Line 1640 \| Line 1893 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1893		tempParaItem.zPos = zconStamp[i]->getZpos();
1894		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1895		tempParaItem.kRatio = zconStamp[i]->getKratio();
1896	<
1896	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1897	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1898		zconsParaData->addItem(tempParaItem);
1899		}
1900
1901		//check the uniqueness of index
1902		if(!zconsParaData->isIndexUnique()){
1903		sprintf(painCave.errMsg,
1904	<	"ZConstraint Error: molIndex is not unique\n");
1904	>	"ZConstraint Error: molIndex is not unique!\n");
1905		painCave.isFatal = 1;
1906		simError();
1907		}
#	Line 1658 \| Line 1912 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1912		//push data into siminfo, therefore, we can retrieve later
1913		theInfo.addProperty(zconsParaData);
1914		}
1915	+
1916	+	void SimSetup::makeMinimizer(){
1917	+
1918	+	OOPSEMinimizer* myOOPSEMinimizer;
1919	+	MinimizerParameterSet* param;
1920	+	char minimizerName[100];
1921	+
1922	+	for (int i = 0; i < nInfo; i++){
1923	+
1924	+	//prepare parameter set for minimizer
1925	+	param = new MinimizerParameterSet();
1926	+	param->setDefaultParameter();
1927	+
1928	+	if (globals->haveMinimizer()){
1929	+	param->setFTol(globals->getMinFTol());
1930	+	}
1931	+
1932	+	if (globals->haveMinGTol()){
1933	+	param->setGTol(globals->getMinGTol());
1934	+	}
1935	+
1936	+	if (globals->haveMinMaxIter()){
1937	+	param->setMaxIteration(globals->getMinMaxIter());
1938	+	}
1939	+
1940	+	if (globals->haveMinWriteFrq()){
1941	+	param->setMaxIteration(globals->getMinMaxIter());
1942	+	}
1943	+
1944	+	if (globals->haveMinWriteFrq()){
1945	+	param->setWriteFrq(globals->getMinWriteFrq());
1946	+	}
1947	+
1948	+	if (globals->haveMinStepSize()){
1949	+	param->setStepSize(globals->getMinStepSize());
1950	+	}
1951	+
1952	+	if (globals->haveMinLSMaxIter()){
1953	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1954	+	}
1955	+
1956	+	if (globals->haveMinLSTol()){
1957	+	param->setLineSearchTol(globals->getMinLSTol());
1958	+	}
1959	+
1960	+	strcpy(minimizerName, globals->getMinimizer());
1961	+
1962	+	if (!strcasecmp(minimizerName, "CG")){
1963	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1964	+	}
1965	+	else if (!strcasecmp(minimizerName, "SD")){
1966	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1967	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1968	+	}
1969	+	else{
1970	+	sprintf(painCave.errMsg,
1971	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1972	+	painCave.isFatal = 0;
1973	+	simError();
1974	+
1975	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1976	+	}
1977	+	info[i].the_integrator = myOOPSEMinimizer;
1978	+
1979	+	//store the minimizer into simInfo
1980	+	info[i].the_minimizer = myOOPSEMinimizer;
1981	+	info[i].has_minimizer = true;
1982	+	}
1983	+
1984	+	}

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC vs. Revision 1174 by gezelter, Wed May 12 20:54:10 2004 UTC

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC vs.
Revision 1174 by gezelter, Wed May 12 20:54:10 2004 UTC