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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 859 by mmeineke, Mon Nov 10 21:50:36 2003 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 2004 UTC

#	Line 9 \| Line 9
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 24 \| 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;
#	Line 119 \| Line 147 \| void SimSetup::createSim(void){
147		// make the output filenames
148
149		makeOutNames();
150	<
123	<	// make the integrator
124	<
125	<	makeIntegrator();
126	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 131 \| 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
187		bond_pair* theBonds;
188		bend_set* theBends;
189		torsion_set* theTorsions;
190
191	+	set<int> skipList;
192
193	+	double phi, theta, psi;
194	+	char* molName;
195	+	char rbName[100];
196	+
197		//init the forceField paramters
198
199		the_ff->readParams();
200
158	–
201		// init the atoms
202
203	<	double ux, uy, uz, u, uSqr;
203	>	int nMembers, nNew, rb1, rb2;
204
205		for (k = 0; k < nInfo; k++){
206		the_ff->setSimInfo(&(info[k]));
207
208		atomOffset = 0;
209	<	excludeOffset = 0;
209	>
210		for (i = 0; i < info[k].n_mol; i++){
211		stampID = info[k].molecules[i].getStampID();
212	+	molName = comp_stamps[stampID]->getID();
213
214		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216		molInfo.nBends = comp_stamps[stampID]->getNBends();
217		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
219	<
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219	>
220		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	–	molInfo.myBends = new Bend * [molInfo.nBends];
181	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
221
222	+	if (molInfo.nBonds > 0)
223	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	+	else
225	+	molInfo.myBonds = NULL;
226	+
227	+	if (molInfo.nBends > 0)
228	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	+	else
230	+	molInfo.myBends = NULL;
231	+
232	+	if (molInfo.nTorsions > 0)
233	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	+	else
235	+	molInfo.myTorsions = NULL;
236	+
237		theBonds = new bond_pair[molInfo.nBonds];
238		theBends = new bend_set[molInfo.nBends];
239		theTorsions = new torsion_set[molInfo.nTorsions];
240	<
240	>
241		// make the Atoms
242
243		for (j = 0; j < molInfo.nAtoms; j++){
244		currentAtom = comp_stamps[stampID]->getAtom(j);
245	+
246		if (currentAtom->haveOrientation()){
247		dAtom = new DirectionalAtom((j + atomOffset),
248		info[k].getConfiguration());
249		info[k].n_oriented++;
250		molInfo.myAtoms[j] = dAtom;
251
252	<	ux = currentAtom->getOrntX();
253	<	uy = currentAtom->getOrntY();
254	<	uz = currentAtom->getOrntZ();
252	>	// Directional Atoms have standard unit vectors which are oriented
253	>	// in space using the three Euler angles. We assume the standard
254	>	// unit vector was originally along the z axis below.
255
256	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259
260	<	u = sqrt(uSqr);
261	<	ux = ux / u;
205	<	uy = uy / u;
206	<	uz = uz / u;
207	<
208	<	dAtom->setSUx(ux);
209	<	dAtom->setSUy(uy);
210	<	dAtom->setSUz(uz);
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262		}
263		else{
264	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
265	<	info[k].getConfiguration());
264	>
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266	>
267		}
216	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
268
269	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
270		#ifdef IS_MPI
271
272	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273
274		#endif // is_mpi
275		}
#	Line 228 \| Line 280 \| void SimSetup::makeMolecules(void){
280		theBonds[j].a = currentBond->getA() + atomOffset;
281		theBonds[j].b = currentBond->getB() + atomOffset;
282
283	<	exI = theBonds[j].a;
284	<	exJ = theBonds[j].b;
283	>	tempI = theBonds[j].a;
284	>	tempJ = theBonds[j].b;
285
234	–	// exclude_I must always be the smaller of the pair
235	–	if (exI > exJ){
236	–	tempEx = exI;
237	–	exI = exJ;
238	–	exJ = tempEx;
239	–	}
286		#ifdef IS_MPI
287	<	tempEx = exI;
288	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
289	<	tempEx = exJ;
290	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293
294	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	<	#else // isn't MPI
248	<
249	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	<	#endif //is_mpi
294	>	info[k].excludes->addPair(exI, exJ);
295		}
252	–	excludeOffset += molInfo.nBonds;
296
297		//make the bends
298		for (j = 0; j < molInfo.nBends; j++){
#	Line 299 \| Line 342 \| void SimSetup::makeMolecules(void){
342		}
343		}
344
345	<	if (!theBends[j].isGhost){
346	<	exI = theBends[j].a;
347	<	exJ = theBends[j].c;
348	<	}
349	<	else{
350	<	exI = theBends[j].a;
351	<	exJ = theBends[j].b;
352	<	}
345	>	if (theBends[j].isGhost) {
346	>
347	>	tempI = theBends[j].a;
348	>	tempJ = theBends[j].b;
349	>
350	>	#ifdef IS_MPI
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	<	// exclude_I must always be the smaller of the pair
312	<	if (exI > exJ){
313	<	tempEx = exI;
314	<	exI = exJ;
315	<	exJ = tempEx;
316	<	}
317	<	#ifdef IS_MPI
318	<	tempEx = exI;
319	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	<	tempEx = exJ;
321	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
359	>	} else {
360
361	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
362	<	#else // isn't MPI
363	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
364	<	#endif //is_mpi
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379		}
328	–	excludeOffset += molInfo.nBends;
380
381		for (j = 0; j < molInfo.nTorsions; j++){
382		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 334 \| Line 385 \| void SimSetup::makeMolecules(void){
385		theTorsions[j].c = currentTorsion->getC() + atomOffset;
386		theTorsions[j].d = currentTorsion->getD() + atomOffset;
387
388	<	exI = theTorsions[j].a;
389	<	exJ = theTorsions[j].d;
388	>	tempI = theTorsions[j].a;
389	>	tempJ = theTorsions[j].b;
390	>	tempK = theTorsions[j].c;
391	>	tempL = theTorsions[j].d;
392
393	<	// exclude_I must always be the smaller of the pair
394	<	if (exI > exJ){
395	<	tempEx = exI;
396	<	exI = exJ;
397	<	exJ = tempEx;
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403	>	#endif
404	>
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411	>	}
412	>
413	>
414	>	molInfo.myRigidBodies.clear();
415	>
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417	>
418	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	>	nMembers = currentRigidBody->getNMembers();
420	>
421	>	// Create the Rigid Body:
422	>
423	>	myRB = new RigidBody();
424	>
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429	>
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432	>
433	>	// tempI is atom numbering on local processor
434	>	tempI = molI + atomOffset;
435	>
436	>	// currentAtom is the AtomStamp (which we need for
437	>	// rigid body reference positions)
438	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
439	>
440	>	// When we add to the rigid body, add the atom itself and
441	>	// the stamp info:
442	>
443	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	>
445	>	// Add this atom to the Skip List for the integrators
446	>	#ifdef IS_MPI
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453		}
454	+
455	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	+
458	+	tempI = currentRigidBody->getMember(rb1);
459	+	tempJ = currentRigidBody->getMember(rb2);
460	+
461	+	// Some explanation is required here.
462	+	// Fortran indexing starts at 1, while c indexing starts at 0
463	+	// Also, in parallel computations, the GlobalIndex is
464	+	// used for the exclude list:
465	+
466		#ifdef IS_MPI
467	<	tempEx = exI;
468	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
469	<	tempEx = exJ;
470	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478
479	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
480	<	#else // isn't MPI
354	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355	<	#endif //is_mpi
479	>	molInfo.myRigidBodies.push_back(myRB);
480	>	info[k].rigidBodies.push_back(myRB);
481		}
482	<	excludeOffset += molInfo.nTorsions;
482	>
483
484	+	// After this is all set up, scan through the atoms to
485	+	// see if they can be added to the integrableObjects:
486
487	<	// send the arrays off to the forceField for init.
487	>	molInfo.myIntegrableObjects.clear();
488	>
489
490	+	for (j = 0; j < molInfo.nAtoms; j++){
491	+
492	+	#ifdef IS_MPI
493	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	+	#else
495	+	slJ = j+atomOffset;
496	+	#endif
497	+
498	+	// if they aren't on the skip list, then they can be integrated
499	+
500	+	if (skipList.find(slJ) == skipList.end()) {
501	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	+	info[k].integrableObjects.push_back(mySD);
503	+	molInfo.myIntegrableObjects.push_back(mySD);
504	+	}
505	+	}
506	+
507	+	// all rigid bodies are integrated:
508	+
509	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	+	info[k].integrableObjects.push_back(mySD);
512	+	molInfo.myIntegrableObjects.push_back(mySD);
513	+	}
514	+
515	+
516	+	// send the arrays off to the forceField for init.
517	+
518		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522		theTorsions);
523
368	–
524		info[k].molecules[i].initialize(molInfo);
525
526
#	Line 373 \| Line 528 \| void SimSetup::makeMolecules(void){
528		delete[] theBonds;
529		delete[] theBends;
530		delete[] theTorsions;
531	<	}
531	>	}
532		}
533
534		#ifdef IS_MPI
#	Line 383 \| Line 538 \| void SimSetup::makeMolecules(void){
538
539		// clean up the forcefield
540
541	<	the_ff->calcRcut();
541	>	if (!globals->haveLJrcut()){
542	>
543	>	the_ff->calcRcut();
544	>
545	>	} else {
546	>
547	>	the_ff->setRcut( globals->getLJrcut() );
548	>	}
549	>
550		the_ff->cleanMe();
551		}
552
#	Line 585 \| Line 748 \| void SimSetup::gatherInfo(void){
748		else if (!strcasecmp(force_field, "EAM")){
749		ffCase = FF_EAM;
750		}
751	+	else if (!strcasecmp(force_field, "WATER")){
752	+	ffCase = FF_H2O;
753	+	}
754		else{
755		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756		force_field);
#	Line 613 \| Line 779 \| void SimSetup::gatherInfo(void){
779		}
780		else{
781		sprintf(painCave.errMsg,
782	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
783	<	"reverting to NVE for this simulation.\n",
782	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	>	"\treverting to NVE for this simulation.\n",
784		ensemble);
785		painCave.isFatal = 0;
786		simError();
#	Line 646 \| Line 812 \| void SimSetup::gatherInfo(void){
812		if (!the_components[i]->haveNMol()){
813		// we have a problem
814		sprintf(painCave.errMsg,
815	<	"SimSetup Error. No global NMol or component NMol"
816	<	" given. Cannot calculate the number of atoms.\n");
815	>	"SimSetup Error. No global NMol or component NMol given.\n"
816	>	"\tCannot calculate the number of atoms.\n");
817		painCave.isFatal = 1;
818		simError();
819		}
#	Line 666 \| Line 832 \| void SimSetup::gatherInfo(void){
832		painCave.isFatal = 1;
833		simError();
834		}
835	+
836	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
838	+	sprintf(painCave.errMsg,
839	+	"Sample time is not divisible by dt.\n"
840	+	"\tThis will result in samples that are not uniformly\n"
841	+	"\tdistributed in time. If this is a problem, change\n"
842	+	"\tyour sampleTime variable.\n");
843	+	painCave.isFatal = 0;
844	+	simError();
845	+	}
846	+
847	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848	+	sprintf(painCave.errMsg,
849	+	"Status time is not divisible by dt.\n"
850	+	"\tThis will result in status reports that are not uniformly\n"
851	+	"\tdistributed in time. If this is a problem, change \n"
852	+	"\tyour statusTime variable.\n");
853	+	painCave.isFatal = 0;
854	+	simError();
855	+	}
856	+
857	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	+	sprintf(painCave.errMsg,
859	+	"Thermal time is not divisible by dt.\n"
860	+	"\tThis will result in thermalizations that are not uniformly\n"
861	+	"\tdistributed in time. If this is a problem, change \n"
862	+	"\tyour thermalTime variable.\n");
863	+	painCave.isFatal = 0;
864	+	simError();
865	+	}
866	+
867	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	+	sprintf(painCave.errMsg,
869	+	"Reset time is not divisible by dt.\n"
870	+	"\tThis will result in integrator resets that are not uniformly\n"
871	+	"\tdistributed in time. If this is a problem, change\n"
872	+	"\tyour resetTime variable.\n");
873	+	painCave.isFatal = 0;
874	+	simError();
875	+	}
876
877		// set the status, sample, and thermal kick times
878
#	Line 673 \| Line 880 \| void SimSetup::gatherInfo(void){
880		if (globals->haveSampleTime()){
881		info[i].sampleTime = globals->getSampleTime();
882		info[i].statusTime = info[i].sampleTime;
676	–	info[i].thermalTime = info[i].sampleTime;
883		}
884		else{
885		info[i].sampleTime = globals->getRunTime();
886		info[i].statusTime = info[i].sampleTime;
681	–	info[i].thermalTime = info[i].sampleTime;
887		}
888
889		if (globals->haveStatusTime()){
#	Line 687 \| Line 892 \| void SimSetup::gatherInfo(void){
892
893		if (globals->haveThermalTime()){
894		info[i].thermalTime = globals->getThermalTime();
895	+	} else {
896	+	info[i].thermalTime = globals->getRunTime();
897		}
898
899		info[i].resetIntegrator = 0;
#	Line 746 \| Line 953 \| void SimSetup::gatherInfo(void){
953		for (int i = 0; i < nInfo; i++){
954		info[i].setSeed(seedValue);
955		}
956	<
956	>
957		#ifdef IS_MPI
958	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
958	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
959		MPIcheckPoint();
960		#endif // is_mpi
961		}
#	Line 757 \| Line 964 \| void SimSetup::finalInfoCheck(void){
964		void SimSetup::finalInfoCheck(void){
965		int index;
966		int usesDipoles;
967	+	int usesCharges;
968		int i;
969
970		for (i = 0; i < nInfo; i++){
#	Line 768 \| Line 976 \| void SimSetup::finalInfoCheck(void){
976		usesDipoles = (info[i].atoms[index])->hasDipole();
977		index++;
978		}
979	<
979	>	index = 0;
980	>	usesCharges = 0;
981	>	while ((index < info[i].n_atoms) && !usesCharges){
982	>	usesCharges= (info[i].atoms[index])->hasCharge();
983	>	index++;
984	>	}
985		#ifdef IS_MPI
986		int myUse = usesDipoles;
987		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
#	Line 781 \| Line 994 \| void SimSetup::finalInfoCheck(void){
994
995		if (!globals->haveECR()){
996		sprintf(painCave.errMsg,
997	<	"SimSetup Warning: using default value of 15.0 angstroms"
998	<	"box length for the electrostaticCutoffRadius.\n");
997	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
998	>	"\tOOPSE will use a default value of 15.0 angstroms"
999	>	"\tfor the electrostaticCutoffRadius.\n");
1000		painCave.isFatal = 0;
1001		simError();
1002		theEcr = 15.0;
#	Line 793 \| Line 1007 \| void SimSetup::finalInfoCheck(void){
1007
1008		if (!globals->haveEST()){
1009		sprintf(painCave.errMsg,
1010	<	"SimSetup Warning: using default value of 0.05 * the "
1011	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1010	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1011	>	"\tOOPSE will use a default value of\n"
1012	>	"\t0.05 * electrostaticCutoffRadius\n"
1013	>	"\tfor the electrostaticSkinThickness\n");
1014		painCave.isFatal = 0;
1015		simError();
1016		theEst = 0.05 * theEcr;
#	Line 807 \| Line 1023 \| void SimSetup::finalInfoCheck(void){
1023
1024		if (!globals->haveDielectric()){
1025		sprintf(painCave.errMsg,
1026	<	"SimSetup Error: You are trying to use Reaction Field without"
1027	<	"setting a dielectric constant!\n");
1026	>	"SimSetup Error: No Dielectric constant was set.\n"
1027	>	"\tYou are trying to use Reaction Field without"
1028	>	"\tsetting a dielectric constant!\n");
1029		painCave.isFatal = 1;
1030		simError();
1031		}
1032		info[i].dielectric = globals->getDielectric();
1033		}
1034		else{
1035	<	if (usesDipoles){
1035	>	if (usesDipoles \|\| usesCharges){
1036		if (!globals->haveECR()){
1037		sprintf(painCave.errMsg,
1038	<	"SimSetup Warning: using default value of 15.0 angstroms"
1039	<	"box length for the electrostaticCutoffRadius.\n");
1038	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1039	>	"\tOOPSE will use a default value of 15.0 angstroms"
1040	>	"\tfor the electrostaticCutoffRadius.\n");
1041		painCave.isFatal = 0;
1042		simError();
1043		theEcr = 15.0;
#	Line 830 \| Line 1048 \| void SimSetup::finalInfoCheck(void){
1048
1049		if (!globals->haveEST()){
1050		sprintf(painCave.errMsg,
1051	<	"SimSetup Warning: using default value of 0.05 * the "
1052	<	"electrostaticCutoffRadius for the "
1053	<	"electrostaticSkinThickness\n");
1051	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1052	>	"\tOOPSE will use a default value of\n"
1053	>	"\t0.05 * electrostaticCutoffRadius\n"
1054	>	"\tfor the electrostaticSkinThickness\n");
1055		painCave.isFatal = 0;
1056		simError();
1057		theEst = 0.05 * theEcr;
#	Line 1037 \| Line 1256 \| void SimSetup::createFF(void){
1256
1257		case FF_EAM:
1258		the_ff = new EAM_FF();
1259	+	break;
1260	+
1261	+	case FF_H2O:
1262	+	the_ff = new WATER();
1263		break;
1264
1265		default:
#	Line 1111 \| Line 1334 \| void SimSetup::calcSysValues(void){
1334		tot_bonds = 0;
1335		tot_bends = 0;
1336		tot_torsions = 0;
1337	+	tot_rigid = 0;
1338		for (i = 0; i < n_components; i++){
1339		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1340		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1341		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1342		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1343	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1344		}
1345	<
1345	>
1346		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1347		molMembershipArray = new int[tot_atoms];
1348
#	Line 1139 \| Line 1364 \| void SimSetup::mpiMolDivide(void){
1364		int i, j, k;
1365		int localMol, allMol;
1366		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1367	+	int local_rigid;
1368	+	vector<int> globalMolIndex;
1369
1370		mpiSim = new mpiSimulation(info);
1371
1372	<	globalIndex = mpiSim->divideLabor();
1372	>	mpiSim->divideLabor();
1373	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1374	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1375
1376		// set up the local variables
1377
#	Line 1155 \| Line 1384 \| void SimSetup::mpiMolDivide(void){
1384		local_bonds = 0;
1385		local_bends = 0;
1386		local_torsions = 0;
1387	<	globalAtomIndex = 0;
1387	>	local_rigid = 0;
1388	>	globalAtomCounter = 0;
1389
1160	–
1390		for (i = 0; i < n_components; i++){
1391		for (j = 0; j < components_nmol[i]; j++){
1392		if (mol2proc[allMol] == worldRank){
#	Line 1165 \| Line 1394 \| void SimSetup::mpiMolDivide(void){
1394		local_bonds += comp_stamps[i]->getNBonds();
1395		local_bends += comp_stamps[i]->getNBends();
1396		local_torsions += comp_stamps[i]->getNTorsions();
1397	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1398		localMol++;
1399		}
1400		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1401	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1402	<	globalAtomIndex++;
1401	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1402	>	globalAtomCounter++;
1403		}
1404
1405		allMol++;
#	Line 1178 \| Line 1408 \| void SimSetup::mpiMolDivide(void){
1408		local_SRI = local_bonds + local_bends + local_torsions;
1409
1410		info[0].n_atoms = mpiSim->getMyNlocal();
1411	+
1412
1413		if (local_atoms != info[0].n_atoms){
1414		sprintf(painCave.errMsg,
1415	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1416	<	" localAtom (%d) are not equal.\n",
1415	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1416	>	"\tlocalAtom (%d) are not equal.\n",
1417		info[0].n_atoms, local_atoms);
1418		painCave.isFatal = 1;
1419		simError();
#	Line 1210 \| Line 1441 \| void SimSetup::makeSysArrays(void){
1441
1442		Atom** the_atoms;
1443		Molecule* the_molecules;
1213	–	Exclude** the_excludes;
1444
1215	–
1445		for (l = 0; l < nInfo; l++){
1446		// create the atom and short range interaction arrays
1447
#	Line 1238 \| Line 1467 \| void SimSetup::makeSysArrays(void){
1467		#else // is_mpi
1468
1469		molIndex = 0;
1470	<	globalAtomIndex = 0;
1470	>	globalAtomCounter = 0;
1471		for (i = 0; i < n_components; i++){
1472		for (j = 0; j < components_nmol[i]; j++){
1473		the_molecules[molIndex].setStampID(i);
1474		the_molecules[molIndex].setMyIndex(molIndex);
1475		the_molecules[molIndex].setGlobalIndex(molIndex);
1476		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1477	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1478	<	globalAtomIndex++;
1477	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1478	>	globalAtomCounter++;
1479		}
1480		molIndex++;
1481		}
#	Line 1255 \| Line 1484 \| void SimSetup::makeSysArrays(void){
1484
1485		#endif // is_mpi
1486
1487	<
1488	<	if (info[l].n_SRI){
1489	<	Exclude::createArray(info[l].n_SRI);
1261	<	the_excludes = new Exclude * [info[l].n_SRI];
1262	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1263	<	the_excludes[ex] = new Exclude(ex);
1264	<	}
1265	<	info[l].globalExcludes = new int;
1266	<	info[l].n_exclude = info[l].n_SRI;
1267	<	}
1268	<	else{
1269	<	Exclude::createArray(1);
1270	<	the_excludes = new Exclude * ;
1271	<	the_excludes[0] = new Exclude(0);
1272	<	the_excludes[0]->setPair(0, 0);
1273	<	info[l].globalExcludes = new int;
1274	<	info[l].globalExcludes[0] = 0;
1275	<	info[l].n_exclude = 0;
1276	<	}
1277	<
1487	>	info[l].globalExcludes = new int;
1488	>	info[l].globalExcludes[0] = 0;
1489	>
1490		// set the arrays into the SimInfo object
1491
1492		info[l].atoms = the_atoms;
1493		info[l].molecules = the_molecules;
1494		info[l].nGlobalExcludes = 0;
1283	–	info[l].excludes = the_excludes;
1495
1496		the_ff->setSimInfo(info);
1497		}
#	Line 1324 \| Line 1535 \| void SimSetup::makeIntegrator(void){
1535		else{
1536		sprintf(painCave.errMsg,
1537		"SimSetup error: If you use the NVT\n"
1538	<	" ensemble, you must set tauThermostat.\n");
1538	>	"\tensemble, you must set tauThermostat.\n");
1539		painCave.isFatal = 1;
1540		simError();
1541		}
#	Line 1347 \| Line 1558 \| void SimSetup::makeIntegrator(void){
1558		else{
1559		sprintf(painCave.errMsg,
1560		"SimSetup error: If you use a constant pressure\n"
1561	<	" ensemble, you must set targetPressure in the BASS file.\n");
1561	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1562		painCave.isFatal = 1;
1563		simError();
1564		}
#	Line 1357 \| Line 1568 \| void SimSetup::makeIntegrator(void){
1568		else{
1569		sprintf(painCave.errMsg,
1570		"SimSetup error: If you use an NPT\n"
1571	<	" ensemble, you must set tauThermostat.\n");
1571	>	"\tensemble, you must set tauThermostat.\n");
1572		painCave.isFatal = 1;
1573		simError();
1574		}
#	Line 1367 \| Line 1578 \| void SimSetup::makeIntegrator(void){
1578		else{
1579		sprintf(painCave.errMsg,
1580		"SimSetup error: If you use an NPT\n"
1581	<	" ensemble, you must set tauBarostat.\n");
1581	>	"\tensemble, you must set tauBarostat.\n");
1582		painCave.isFatal = 1;
1583		simError();
1584		}
#	Line 1390 \| Line 1601 \| void SimSetup::makeIntegrator(void){
1601		else{
1602		sprintf(painCave.errMsg,
1603		"SimSetup error: If you use a constant pressure\n"
1604	<	" ensemble, you must set targetPressure in the BASS file.\n");
1604	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1605		painCave.isFatal = 1;
1606		simError();
1607		}
#	Line 1401 \| Line 1612 \| void SimSetup::makeIntegrator(void){
1612		else{
1613		sprintf(painCave.errMsg,
1614		"SimSetup error: If you use an NPT\n"
1615	<	" ensemble, you must set tauThermostat.\n");
1615	>	"\tensemble, you must set tauThermostat.\n");
1616		painCave.isFatal = 1;
1617		simError();
1618		}
#	Line 1412 \| Line 1623 \| void SimSetup::makeIntegrator(void){
1623		else{
1624		sprintf(painCave.errMsg,
1625		"SimSetup error: If you use an NPT\n"
1626	<	" ensemble, you must set tauBarostat.\n");
1626	>	"\tensemble, you must set tauBarostat.\n");
1627		painCave.isFatal = 1;
1628		simError();
1629		}
#	Line 1435 \| Line 1646 \| void SimSetup::makeIntegrator(void){
1646		else{
1647		sprintf(painCave.errMsg,
1648		"SimSetup error: If you use a constant pressure\n"
1649	<	" ensemble, you must set targetPressure in the BASS file.\n");
1649	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1650		painCave.isFatal = 1;
1651		simError();
1652		}
#	Line 1445 \| Line 1656 \| void SimSetup::makeIntegrator(void){
1656		else{
1657		sprintf(painCave.errMsg,
1658		"SimSetup error: If you use an NPT\n"
1659	<	" ensemble, you must set tauThermostat.\n");
1659	>	"\tensemble, you must set tauThermostat.\n");
1660		painCave.isFatal = 1;
1661		simError();
1662		}
#	Line 1455 \| Line 1666 \| void SimSetup::makeIntegrator(void){
1666		else{
1667		sprintf(painCave.errMsg,
1668		"SimSetup error: If you use an NPT\n"
1669	<	" ensemble, you must set tauBarostat.\n");
1669	>	"\tensemble, you must set tauBarostat.\n");
1670		painCave.isFatal = 1;
1671		simError();
1672		}
#	Line 1508 \| Line 1719 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1719		}
1720		else{
1721		sprintf(painCave.errMsg,
1722	<	"ZConstraint error: If you use an ZConstraint\n"
1723	<	" , you must set sample time.\n");
1722	>	"ZConstraint error: If you use a ZConstraint,\n"
1723	>	"\tyou must set zconsTime.\n");
1724		painCave.isFatal = 1;
1725		simError();
1726		}
#	Line 1524 \| Line 1735 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1735		else{
1736		double defaultZConsTol = 0.01;
1737		sprintf(painCave.errMsg,
1738	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1739	<	" , default value %f is used.\n",
1738	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1739	>	"\tOOPSE will use a default value of %f.\n"
1740	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1741		defaultZConsTol);
1742		painCave.isFatal = 0;
1743		simError();
#	Line 1543 \| Line 1755 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1755		}
1756		else{
1757		sprintf(painCave.errMsg,
1758	<	"ZConstraint Warning: User does not set force Subtraction policy, "
1759	<	"PolicyByMass is used\n");
1758	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1759	>	"\tOOPSE will use PolicyByMass.\n"
1760	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1761		painCave.isFatal = 0;
1762		simError();
1763		zconsForcePolicy->setData("BYMASS");
1764		}
1765
1766		theInfo.addProperty(zconsForcePolicy);
1767	+
1768	+	//set zcons gap
1769	+	DoubleData* zconsGap = new DoubleData();
1770	+	zconsGap->setID(ZCONSGAP_ID);
1771	+
1772	+	if (globals->haveZConsGap()){
1773	+	zconsGap->setData(globals->getZconsGap());
1774	+	theInfo.addProperty(zconsGap);
1775	+	}
1776	+
1777	+	//set zcons fixtime
1778	+	DoubleData* zconsFixtime = new DoubleData();
1779	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1780	+
1781	+	if (globals->haveZConsFixTime()){
1782	+	zconsFixtime->setData(globals->getZconsFixtime());
1783	+	theInfo.addProperty(zconsFixtime);
1784	+	}
1785	+
1786	+	//set zconsUsingSMD
1787	+	IntData* zconsUsingSMD = new IntData();
1788	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1789
1790	+	if (globals->haveZConsUsingSMD()){
1791	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1792	+	theInfo.addProperty(zconsUsingSMD);
1793	+	}
1794	+
1795		//Determine the name of ouput file and add it into SimInfo's property list
1796		//Be careful, do not use inFileName, since it is a pointer which
1797		//point to a string at master node, and slave nodes do not contain that string
#	Line 1581 \| Line 1821 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1821		tempParaItem.zPos = zconStamp[i]->getZpos();
1822		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1823		tempParaItem.kRatio = zconStamp[i]->getKratio();
1824	<
1824	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1825	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1826		zconsParaData->addItem(tempParaItem);
1827		}
1828
1829		//check the uniqueness of index
1830		if(!zconsParaData->isIndexUnique()){
1831		sprintf(painCave.errMsg,
1832	<	"ZConstraint Error: molIndex is not unique\n");
1832	>	"ZConstraint Error: molIndex is not unique!\n");
1833		painCave.isFatal = 1;
1834		simError();
1835		}
#	Line 1599 \| Line 1840 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1840		//push data into siminfo, therefore, we can retrieve later
1841		theInfo.addProperty(zconsParaData);
1842		}
1843	+
1844	+	void SimSetup::makeMinimizer(){
1845	+
1846	+	OOPSEMinimizer* myOOPSEMinimizer;
1847	+	MinimizerParameterSet* param;
1848	+	char minimizerName[100];
1849	+
1850	+	for (int i = 0; i < nInfo; i++){
1851	+
1852	+	//prepare parameter set for minimizer
1853	+	param = new MinimizerParameterSet();
1854	+	param->setDefaultParameter();
1855	+
1856	+	if (globals->haveMinimizer()){
1857	+	param->setFTol(globals->getMinFTol());
1858	+	}
1859	+
1860	+	if (globals->haveMinGTol()){
1861	+	param->setGTol(globals->getMinGTol());
1862	+	}
1863	+
1864	+	if (globals->haveMinMaxIter()){
1865	+	param->setMaxIteration(globals->getMinMaxIter());
1866	+	}
1867	+
1868	+	if (globals->haveMinWriteFrq()){
1869	+	param->setMaxIteration(globals->getMinMaxIter());
1870	+	}
1871	+
1872	+	if (globals->haveMinWriteFrq()){
1873	+	param->setWriteFrq(globals->getMinWriteFrq());
1874	+	}
1875	+
1876	+	if (globals->haveMinStepSize()){
1877	+	param->setStepSize(globals->getMinStepSize());
1878	+	}
1879	+
1880	+	if (globals->haveMinLSMaxIter()){
1881	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1882	+	}
1883	+
1884	+	if (globals->haveMinLSTol()){
1885	+	param->setLineSearchTol(globals->getMinLSTol());
1886	+	}
1887	+
1888	+	strcpy(minimizerName, globals->getMinimizer());
1889	+
1890	+	if (!strcasecmp(minimizerName, "CG")){
1891	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1892	+	}
1893	+	else if (!strcasecmp(minimizerName, "SD")){
1894	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1895	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1896	+	}
1897	+	else{
1898	+	sprintf(painCave.errMsg,
1899	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1900	+	painCave.isFatal = 0;
1901	+	simError();
1902	+
1903	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1904	+	}
1905	+	info[i].the_integrator = myOOPSEMinimizer;
1906	+
1907	+	//store the minimizer into simInfo
1908	+	info[i].the_minimizer = myOOPSEMinimizer;
1909	+	info[i].has_minimizer = true;
1910	+	}
1911	+
1912	+	}

Diff Legend

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 859 by mmeineke, Mon Nov 10 21:50:36 2003 UTC vs. Revision 1129 by tim, Thu Apr 22 03:29:30 2004 UTC

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 859 by mmeineke, Mon Nov 10 21:50:36 2003 UTC vs.
Revision 1129 by tim, Thu Apr 22 03:29:30 2004 UTC