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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 845 by gezelter, Thu Oct 30 18:59:20 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 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 103 \| Line 131 \| void SimSetup::createSim(void){
131
132		sysObjectsCreation();
133
134	+	// check on the post processing info
135	+
136	+	finalInfoCheck();
137	+
138		// initialize the system coordinates
139
140		if ( !initSuspend ){
#	Line 112 \| Line 144 \| void SimSetup::createSim(void){
144		info[0].currentTime = 0.0;
145		}
146
115	–	// check on the post processing info
116	–
117	–	finalInfoCheck();
118	–
147		// make the output filenames
148
149		makeOutNames();
150
151	<	// make the integrator
152	<
153	<	makeIntegrator();
154	<
151	>	if (globals->haveMinimizer())
152	>	// make minimizer
153	>	makeMinimizer();
154	>	else
155	>	// make the integrator
156	>	makeIntegrator();
157	>
158		#ifdef IS_MPI
159		mpiSim->mpiRefresh();
160		#endif
#	Line 135 \| Line 166 \| void SimSetup::makeMolecules(void){
166
167
168		void SimSetup::makeMolecules(void){
169	<	int k;
170	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
169	>	int i, j, k;
170	>	int exI, exJ, exK, exL, slI, slJ;
171	>	int tempI, tempJ, tempK, tempL;
172	>	int molI;
173	>	int stampID, atomOffset, rbOffset;
174		molInit molInfo;
175		DirectionalAtom* dAtom;
176	+	RigidBody* myRB;
177	+	StuntDouble* mySD;
178		LinkedAssign* extras;
179		LinkedAssign* current_extra;
180		AtomStamp* currentAtom;
181		BondStamp* currentBond;
182		BendStamp* currentBend;
183		TorsionStamp* currentTorsion;
184	+	RigidBodyStamp* currentRigidBody;
185
186		bond_pair* theBonds;
187		bend_set* theBends;
188		torsion_set* theTorsions;
189
190	+	set<int> skipList;
191
192	+	double phi, theta, psi;
193	+	char* molName;
194	+	char rbName[100];
195	+
196		//init the forceField paramters
197
198		the_ff->readParams();
199
158	–
200		// init the atoms
201
202	<	double ux, uy, uz, u, uSqr;
202	>	int nMembers, nNew, rb1, rb2;
203
204		for (k = 0; k < nInfo; k++){
205		the_ff->setSimInfo(&(info[k]));
206
207		atomOffset = 0;
208	<	excludeOffset = 0;
208	>
209		for (i = 0; i < info[k].n_mol; i++){
210		stampID = info[k].molecules[i].getStampID();
211	+	molName = comp_stamps[stampID]->getID();
212
213		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
214		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
215		molInfo.nBends = comp_stamps[stampID]->getNBends();
216		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
217	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
218	<
217	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
218	>
219		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];
220
221	+	if (molInfo.nBonds > 0)
222	+	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
223	+	else
224	+	molInfo.myBonds = NULL;
225	+
226	+	if (molInfo.nBends > 0)
227	+	molInfo.myBends = new (Bend *) [molInfo.nBends];
228	+	else
229	+	molInfo.myBends = NULL;
230	+
231	+	if (molInfo.nTorsions > 0)
232	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
233	+	else
234	+	molInfo.myTorsions = NULL;
235	+
236		theBonds = new bond_pair[molInfo.nBonds];
237		theBends = new bend_set[molInfo.nBends];
238		theTorsions = new torsion_set[molInfo.nTorsions];
239	<
239	>
240		// make the Atoms
241
242		for (j = 0; j < molInfo.nAtoms; j++){
243		currentAtom = comp_stamps[stampID]->getAtom(j);
244	+
245		if (currentAtom->haveOrientation()){
246		dAtom = new DirectionalAtom((j + atomOffset),
247		info[k].getConfiguration());
248		info[k].n_oriented++;
249		molInfo.myAtoms[j] = dAtom;
250
251	<	ux = currentAtom->getOrntX();
252	<	uy = currentAtom->getOrntY();
253	<	uz = currentAtom->getOrntZ();
251	>	// Directional Atoms have standard unit vectors which are oriented
252	>	// in space using the three Euler angles. We assume the standard
253	>	// unit vector was originally along the z axis below.
254
255	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
255	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
256	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
257	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
258
259	<	u = sqrt(uSqr);
260	<	ux = ux / u;
205	<	uy = uy / u;
206	<	uz = uz / u;
207	<
208	<	dAtom->setSUx(ux);
209	<	dAtom->setSUy(uy);
210	<	dAtom->setSUz(uz);
259	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
260	>
261		}
262		else{
263	<	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
264	<	info[k].getConfiguration());
263	>
264	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
265		}
266	+
267		molInfo.myAtoms[j]->setType(currentAtom->getType());
268
269		#ifdef IS_MPI
270
271	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
271	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
272
273		#endif // is_mpi
274		}
#	Line 228 \| Line 279 \| void SimSetup::makeMolecules(void){
279		theBonds[j].a = currentBond->getA() + atomOffset;
280		theBonds[j].b = currentBond->getB() + atomOffset;
281
282	<	exI = theBonds[j].a;
283	<	exJ = theBonds[j].b;
282	>	tempI = theBonds[j].a;
283	>	tempJ = theBonds[j].b;
284
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	–	}
285		#ifdef IS_MPI
286	<	tempEx = exI;
287	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
288	<	tempEx = exJ;
289	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
286	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
287	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
288	>	#else
289	>	exI = tempI + 1;
290	>	exJ = tempJ + 1;
291	>	#endif
292
293	<	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
293	>	info[k].excludes->addPair(exI, exJ);
294		}
252	–	excludeOffset += molInfo.nBonds;
295
296		//make the bends
297		for (j = 0; j < molInfo.nBends; j++){
#	Line 299 \| Line 341 \| void SimSetup::makeMolecules(void){
341		}
342		}
343
344	<	if (!theBends[j].isGhost){
345	<	exI = theBends[j].a;
346	<	exJ = theBends[j].c;
347	<	}
348	<	else{
307	<	exI = theBends[j].a;
308	<	exJ = theBends[j].b;
309	<	}
310	<
311	<	// exclude_I must always be the smaller of the pair
312	<	if (exI > exJ){
313	<	tempEx = exI;
314	<	exI = exJ;
315	<	exJ = tempEx;
316	<	}
344	>	if (theBends[j].isGhost) {
345	>
346	>	tempI = theBends[j].a;
347	>	tempJ = theBends[j].b;
348	>
349		#ifdef IS_MPI
350	<	tempEx = exI;
351	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
352	<	tempEx = exJ;
353	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
350	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
351	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
352	>	#else
353	>	exI = tempI + 1;
354	>	exJ = tempJ + 1;
355	>	#endif
356	>	info[k].excludes->addPair(exI, exJ);
357
358	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
359	<	#else // isn't MPI
360	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
361	<	#endif //is_mpi
358	>	} else {
359	>
360	>	tempI = theBends[j].a;
361	>	tempJ = theBends[j].b;
362	>	tempK = theBends[j].c;
363	>
364	>	#ifdef IS_MPI
365	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
366	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
367	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
368	>	#else
369	>	exI = tempI + 1;
370	>	exJ = tempJ + 1;
371	>	exK = tempK + 1;
372	>	#endif
373	>
374	>	info[k].excludes->addPair(exI, exK);
375	>	info[k].excludes->addPair(exI, exJ);
376	>	info[k].excludes->addPair(exJ, exK);
377	>	}
378		}
328	–	excludeOffset += molInfo.nBends;
379
380		for (j = 0; j < molInfo.nTorsions; j++){
381		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 334 \| Line 384 \| void SimSetup::makeMolecules(void){
384		theTorsions[j].c = currentTorsion->getC() + atomOffset;
385		theTorsions[j].d = currentTorsion->getD() + atomOffset;
386
387	<	exI = theTorsions[j].a;
388	<	exJ = theTorsions[j].d;
387	>	tempI = theTorsions[j].a;
388	>	tempJ = theTorsions[j].b;
389	>	tempK = theTorsions[j].c;
390	>	tempL = theTorsions[j].d;
391
392	<	// exclude_I must always be the smaller of the pair
393	<	if (exI > exJ){
394	<	tempEx = exI;
395	<	exI = exJ;
396	<	exJ = tempEx;
392	>	#ifdef IS_MPI
393	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
394	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
395	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
396	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
397	>	#else
398	>	exI = tempI + 1;
399	>	exJ = tempJ + 1;
400	>	exK = tempK + 1;
401	>	exL = tempL + 1;
402	>	#endif
403	>
404	>	info[k].excludes->addPair(exI, exJ);
405	>	info[k].excludes->addPair(exI, exK);
406	>	info[k].excludes->addPair(exI, exL);
407	>	info[k].excludes->addPair(exJ, exK);
408	>	info[k].excludes->addPair(exJ, exL);
409	>	info[k].excludes->addPair(exK, exL);
410	>	}
411	>
412	>	for (j = 0; j < molInfo.nRigidBodies; j++){
413	>
414	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
415	>	nMembers = currentRigidBody->getNMembers();
416	>
417	>	// Create the Rigid Body:
418	>
419	>	myRB = new RigidBody();
420	>
421	>	sprintf(rbName,"%s_RB_%s", molName, j);
422	>	myRB->setType(rbName);
423	>
424	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
425	>
426	>	// molI is atom numbering inside this molecule
427	>	molI = currentRigidBody->getMember(rb1);
428	>
429	>	// tempI is atom numbering on local processor
430	>	tempI = molI + atomOffset;
431	>
432	>	// currentAtom is the AtomStamp (which we need for
433	>	// rigid body reference positions)
434	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
435	>
436	>	// When we add to the rigid body, add the atom itself and
437	>	// the stamp info:
438	>
439	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
440	>
441	>	// Add this atom to the Skip List for the integrators
442	>	#ifdef IS_MPI
443	>	slI = info[k].atoms[tempI]->getGlobalIndex();
444	>	#else
445	>	slI = tempI;
446	>	#endif
447	>	skipList.insert(slI);
448	>
449		}
450	+
451	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
452	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
453	+
454	+	tempI = currentRigidBody->getMember(rb1);
455	+	tempJ = currentRigidBody->getMember(rb2);
456	+
457	+	// Some explanation is required here.
458	+	// Fortran indexing starts at 1, while c indexing starts at 0
459	+	// Also, in parallel computations, the GlobalIndex is
460	+	// used for the exclude list:
461	+
462		#ifdef IS_MPI
463	<	tempEx = exI;
464	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
465	<	tempEx = exJ;
466	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
463	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
464	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
465	>	#else
466	>	exI = tempI + 1;
467	>	exJ = tempJ + 1;
468	>	#endif
469	>
470	>	info[k].excludes->addPair(exI, exJ);
471	>
472	>	}
473	>	}
474
475	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
476	<	#else // isn't MPI
354	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355	<	#endif //is_mpi
475	>	molInfo.myRigidBodies.push_back(myRB);
476	>	info[k].rigidBodies.push_back(myRB);
477		}
478	<	excludeOffset += molInfo.nTorsions;
478	>
479
480	+	// After this is all set up, scan through the atoms to
481	+	// see if they can be added to the integrableObjects:
482
483	<	// send the arrays off to the forceField for init.
483	>	for (j = 0; j < molInfo.nAtoms; j++){
484
485	+	#ifdef IS_MPI
486	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
487	+	#else
488	+	slJ = j+atomOffset;
489	+	#endif
490	+
491	+	// if they aren't on the skip list, then they can be integrated
492	+
493	+	if (skipList.find(slJ) == skipList.end()) {
494	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
495	+	info[k].integrableObjects.push_back(mySD);
496	+	molInfo.myIntegrableObjects.push_back(mySD);
497	+	}
498	+	}
499	+
500	+	// all rigid bodies are integrated:
501	+
502	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
503	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
504	+	info[k].integrableObjects.push_back(mySD);
505	+	molInfo.myIntegrableObjects.push_back(mySD);
506	+	}
507	+
508	+
509	+	// send the arrays off to the forceField for init.
510	+
511		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
512		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
513		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
514		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
515		theTorsions);
516
368	–
517		info[k].molecules[i].initialize(molInfo);
518
519
#	Line 373 \| Line 521 \| void SimSetup::makeMolecules(void){
521		delete[] theBonds;
522		delete[] theBends;
523		delete[] theTorsions;
524	<	}
524	>	}
525		}
526
527		#ifdef IS_MPI
#	Line 383 \| Line 531 \| void SimSetup::makeMolecules(void){
531
532		// clean up the forcefield
533
534	<	the_ff->calcRcut();
534	>	if (!globals->haveLJrcut()){
535	>
536	>	the_ff->calcRcut();
537	>
538	>	} else {
539	>
540	>	the_ff->setRcut( globals->getLJrcut() );
541	>	}
542	>
543		the_ff->cleanMe();
544		}
545
#	Line 584 \| Line 740 \| void SimSetup::gatherInfo(void){
740		}
741		else if (!strcasecmp(force_field, "EAM")){
742		ffCase = FF_EAM;
743	+	}
744	+	else if (!strcasecmp(force_field, "WATER")){
745	+	ffCase = FF_H2O;
746		}
747		else{
748		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
#	Line 613 \| Line 772 \| void SimSetup::gatherInfo(void){
772		}
773		else{
774		sprintf(painCave.errMsg,
775	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
776	<	"reverting to NVE for this simulation.\n",
775	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
776	>	"\treverting to NVE for this simulation.\n",
777		ensemble);
778		painCave.isFatal = 0;
779		simError();
#	Line 646 \| Line 805 \| void SimSetup::gatherInfo(void){
805		if (!the_components[i]->haveNMol()){
806		// we have a problem
807		sprintf(painCave.errMsg,
808	<	"SimSetup Error. No global NMol or component NMol"
809	<	" given. Cannot calculate the number of atoms.\n");
808	>	"SimSetup Error. No global NMol or component NMol given.\n"
809	>	"\tCannot calculate the number of atoms.\n");
810		painCave.isFatal = 1;
811		simError();
812		}
#	Line 665 \| Line 824 \| void SimSetup::gatherInfo(void){
824		" Please give nMol in the components.\n");
825		painCave.isFatal = 1;
826		simError();
827	+	}
828	+
829	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
830	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
831	+	sprintf(painCave.errMsg,
832	+	"Sample time is not divisible by dt.\n"
833	+	"\tThis will result in samples that are not uniformly\n"
834	+	"\tdistributed in time. If this is a problem, change\n"
835	+	"\tyour sampleTime variable.\n");
836	+	painCave.isFatal = 0;
837	+	simError();
838		}
839
840	+	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
841	+	sprintf(painCave.errMsg,
842	+	"Status time is not divisible by dt.\n"
843	+	"\tThis will result in status reports that are not uniformly\n"
844	+	"\tdistributed in time. If this is a problem, change \n"
845	+	"\tyour statusTime variable.\n");
846	+	painCave.isFatal = 0;
847	+	simError();
848	+	}
849	+
850	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
851	+	sprintf(painCave.errMsg,
852	+	"Thermal time is not divisible by dt.\n"
853	+	"\tThis will result in thermalizations that are not uniformly\n"
854	+	"\tdistributed in time. If this is a problem, change \n"
855	+	"\tyour thermalTime variable.\n");
856	+	painCave.isFatal = 0;
857	+	simError();
858	+	}
859	+
860	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
861	+	sprintf(painCave.errMsg,
862	+	"Reset time is not divisible by dt.\n"
863	+	"\tThis will result in integrator resets that are not uniformly\n"
864	+	"\tdistributed in time. If this is a problem, change\n"
865	+	"\tyour resetTime variable.\n");
866	+	painCave.isFatal = 0;
867	+	simError();
868	+	}
869	+
870		// set the status, sample, and thermal kick times
871
872		for (i = 0; i < nInfo; i++){
#	Line 699 \| Line 899 \| void SimSetup::gatherInfo(void){
899
900		if (globals->haveTempSet())
901		info[i].setTemp = globals->getTempSet();
902	+
903	+	// check for the extended State init
904	+
905	+	info[i].useInitXSstate = globals->getUseInitXSstate();
906	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
907
908		}
909
#	Line 741 \| Line 946 \| void SimSetup::gatherInfo(void){
946		for (int i = 0; i < nInfo; i++){
947		info[i].setSeed(seedValue);
948		}
949	<
949	>
950		#ifdef IS_MPI
951	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
951	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
952		MPIcheckPoint();
953		#endif // is_mpi
954		}
#	Line 776 \| Line 981 \| void SimSetup::finalInfoCheck(void){
981
982		if (!globals->haveECR()){
983		sprintf(painCave.errMsg,
984	<	"SimSetup Warning: using default value of 1/2 the smallest "
985	<	"box length for the electrostaticCutoffRadius.\n"
986	<	"I hope you have a very fast processor!\n");
984	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
985	>	"\tOOPSE will use a default value of 15.0 angstroms"
986	>	"\tfor the electrostaticCutoffRadius.\n");
987		painCave.isFatal = 0;
988		simError();
989	<	double smallest;
785	<	smallest = info[i].boxL[0];
786	<	if (info[i].boxL[1] <= smallest)
787	<	smallest = info[i].boxL[1];
788	<	if (info[i].boxL[2] <= smallest)
789	<	smallest = info[i].boxL[2];
790	<	theEcr = 0.5 * smallest;
989	>	theEcr = 15.0;
990		}
991		else{
992		theEcr = globals->getECR();
#	Line 795 \| Line 994 \| void SimSetup::finalInfoCheck(void){
994
995		if (!globals->haveEST()){
996		sprintf(painCave.errMsg,
997	<	"SimSetup Warning: using default value of 0.05 * the "
998	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
997	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
998	>	"\tOOPSE will use a default value of\n"
999	>	"\t0.05 * electrostaticCutoffRadius\n"
1000	>	"\tfor the electrostaticSkinThickness\n");
1001		painCave.isFatal = 0;
1002		simError();
1003		theEst = 0.05 * theEcr;
#	Line 809 \| Line 1010 \| void SimSetup::finalInfoCheck(void){
1010
1011		if (!globals->haveDielectric()){
1012		sprintf(painCave.errMsg,
1013	<	"SimSetup Error: You are trying to use Reaction Field without"
1014	<	"setting a dielectric constant!\n");
1013	>	"SimSetup Error: No Dielectric constant was set.\n"
1014	>	"\tYou are trying to use Reaction Field without"
1015	>	"\tsetting a dielectric constant!\n");
1016		painCave.isFatal = 1;
1017		simError();
1018		}
#	Line 820 \| Line 1022 \| void SimSetup::finalInfoCheck(void){
1022		if (usesDipoles){
1023		if (!globals->haveECR()){
1024		sprintf(painCave.errMsg,
1025	<	"SimSetup Warning: using default value of 1/2 the smallest "
1026	<	"box length for the electrostaticCutoffRadius.\n"
1027	<	"I hope you have a very fast processor!\n");
1028	<	painCave.isFatal = 0;
1029	<	simError();
1030	<	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;
1025	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1026	>	"\tOOPSE will use a default value of 15.0 angstroms"
1027	>	"\tfor the electrostaticCutoffRadius.\n");
1028	>	painCave.isFatal = 0;
1029	>	simError();
1030	>	theEcr = 15.0;
1031		}
1032		else{
1033		theEcr = globals->getECR();
1034		}
1035	<
1035	>
1036		if (!globals->haveEST()){
1037		sprintf(painCave.errMsg,
1038	<	"SimSetup Warning: using default value of 0.05 * the "
1039	<	"electrostaticCutoffRadius for the "
1040	<	"electrostaticSkinThickness\n");
1038	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1039	>	"\tOOPSE will use a default value of\n"
1040	>	"\t0.05 * electrostaticCutoffRadius\n"
1041	>	"\tfor the electrostaticSkinThickness\n");
1042		painCave.isFatal = 0;
1043		simError();
1044		theEst = 0.05 * theEcr;
#	Line 849 \| Line 1046 \| void SimSetup::finalInfoCheck(void){
1046		else{
1047		theEst = globals->getEST();
1048		}
1049	<
1049	>
1050		info[i].setDefaultEcr(theEcr, theEst);
1051		}
1052		}
856	–	info[i].checkCutOffs();
1053		}
858	–
1054		#ifdef IS_MPI
1055		strcpy(checkPointMsg, "post processing checks out");
1056		MPIcheckPoint();
1057		#endif // is_mpi
1058		}
1059	<
1059	>
1060		void SimSetup::initSystemCoords(void){
1061		int i;
1062
#	Line 889 \| Line 1084 \| void SimSetup::initSystemCoords(void){
1084		delete fileInit;
1085		}
1086		else{
1087	<	#ifdef IS_MPI
893	<
1087	>
1088		// no init from bass
1089	<
1089	>
1090		sprintf(painCave.errMsg,
1091	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1091	>	"Cannot intialize a simulation without an initial configuration file.\n");
1092		painCave.isFatal = 1;;
1093		simError();
1094	<
901	<	#else
902	<
903	<	initFromBass();
904	<
905	<
906	<	#endif
1094	>
1095		}
1096
1097		#ifdef IS_MPI
#	Line 1057 \| Line 1245 \| void SimSetup::createFF(void){
1245		the_ff = new EAM_FF();
1246		break;
1247
1248	+	case FF_H2O:
1249	+	the_ff = new WATER();
1250	+	break;
1251	+
1252		default:
1253		sprintf(painCave.errMsg,
1254		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1129 \| Line 1321 \| void SimSetup::calcSysValues(void){
1321		tot_bonds = 0;
1322		tot_bends = 0;
1323		tot_torsions = 0;
1324	+	tot_rigid = 0;
1325		for (i = 0; i < n_components; i++){
1326		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1327		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1328		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1329		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1330	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1331		}
1332	<
1332	>
1333		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1334		molMembershipArray = new int[tot_atoms];
1335
#	Line 1157 \| Line 1351 \| void SimSetup::mpiMolDivide(void){
1351		int i, j, k;
1352		int localMol, allMol;
1353		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1354	+	int local_rigid;
1355	+	vector<int> globalAtomIndex;
1356	+	vector<int> globalMolIndex;
1357
1358		mpiSim = new mpiSimulation(info);
1359
1360	<	globalIndex = mpiSim->divideLabor();
1360	>	mpiSim->divideLabor();
1361	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1362	>	globalMolIndex = mpiSim->getGlobalMolIndex();
1363
1364		// set up the local variables
1365
#	Line 1173 \| Line 1372 \| void SimSetup::mpiMolDivide(void){
1372		local_bonds = 0;
1373		local_bends = 0;
1374		local_torsions = 0;
1375	<	globalAtomIndex = 0;
1375	>	local_rigid = 0;
1376	>	globalAtomCounter = 0;
1377
1178	–
1378		for (i = 0; i < n_components; i++){
1379		for (j = 0; j < components_nmol[i]; j++){
1380		if (mol2proc[allMol] == worldRank){
#	Line 1183 \| Line 1382 \| void SimSetup::mpiMolDivide(void){
1382		local_bonds += comp_stamps[i]->getNBonds();
1383		local_bends += comp_stamps[i]->getNBends();
1384		local_torsions += comp_stamps[i]->getNTorsions();
1385	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1386		localMol++;
1387		}
1388		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1389	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1390	<	globalAtomIndex++;
1389	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1390	>	globalAtomCounter++;
1391		}
1392
1393		allMol++;
#	Line 1196 \| Line 1396 \| void SimSetup::mpiMolDivide(void){
1396		local_SRI = local_bonds + local_bends + local_torsions;
1397
1398		info[0].n_atoms = mpiSim->getMyNlocal();
1399	+
1400
1401		if (local_atoms != info[0].n_atoms){
1402		sprintf(painCave.errMsg,
1403	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1404	<	" localAtom (%d) are not equal.\n",
1403	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1404	>	"\tlocalAtom (%d) are not equal.\n",
1405		info[0].n_atoms, local_atoms);
1406		painCave.isFatal = 1;
1407		simError();
#	Line 1228 \| Line 1429 \| void SimSetup::makeSysArrays(void){
1429
1430		Atom** the_atoms;
1431		Molecule* the_molecules;
1231	–	Exclude** the_excludes;
1432
1233	–
1433		for (l = 0; l < nInfo; l++){
1434		// create the atom and short range interaction arrays
1435
#	Line 1256 \| Line 1455 \| void SimSetup::makeSysArrays(void){
1455		#else // is_mpi
1456
1457		molIndex = 0;
1458	<	globalAtomIndex = 0;
1458	>	globalAtomCounter = 0;
1459		for (i = 0; i < n_components; i++){
1460		for (j = 0; j < components_nmol[i]; j++){
1461		the_molecules[molIndex].setStampID(i);
1462		the_molecules[molIndex].setMyIndex(molIndex);
1463		the_molecules[molIndex].setGlobalIndex(molIndex);
1464		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1465	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1466	<	globalAtomIndex++;
1465	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1466	>	globalAtomCounter++;
1467		}
1468		molIndex++;
1469		}
#	Line 1273 \| Line 1472 \| void SimSetup::makeSysArrays(void){
1472
1473		#endif // is_mpi
1474
1475	<
1476	<	if (info[l].n_SRI){
1477	<	Exclude::createArray(info[l].n_SRI);
1279	<	the_excludes = new Exclude * [info[l].n_SRI];
1280	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1281	<	the_excludes[ex] = new Exclude(ex);
1282	<	}
1283	<	info[l].globalExcludes = new int;
1284	<	info[l].n_exclude = info[l].n_SRI;
1285	<	}
1286	<	else{
1287	<	Exclude::createArray(1);
1288	<	the_excludes = new Exclude * ;
1289	<	the_excludes[0] = new Exclude(0);
1290	<	the_excludes[0]->setPair(0, 0);
1291	<	info[l].globalExcludes = new int;
1292	<	info[l].globalExcludes[0] = 0;
1293	<	info[l].n_exclude = 0;
1294	<	}
1295	<
1475	>	info[l].globalExcludes = new int;
1476	>	info[l].globalExcludes[0] = 0;
1477	>
1478		// set the arrays into the SimInfo object
1479
1480		info[l].atoms = the_atoms;
1481		info[l].molecules = the_molecules;
1482		info[l].nGlobalExcludes = 0;
1301	–	info[l].excludes = the_excludes;
1483
1484		the_ff->setSimInfo(info);
1485		}
#	Line 1342 \| Line 1523 \| void SimSetup::makeIntegrator(void){
1523		else{
1524		sprintf(painCave.errMsg,
1525		"SimSetup error: If you use the NVT\n"
1526	<	" ensemble, you must set tauThermostat.\n");
1526	>	"\tensemble, you must set tauThermostat.\n");
1527		painCave.isFatal = 1;
1528		simError();
1529		}
#	Line 1365 \| Line 1546 \| void SimSetup::makeIntegrator(void){
1546		else{
1547		sprintf(painCave.errMsg,
1548		"SimSetup error: If you use a constant pressure\n"
1549	<	" ensemble, you must set targetPressure in the BASS file.\n");
1549	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1550		painCave.isFatal = 1;
1551		simError();
1552		}
#	Line 1375 \| Line 1556 \| void SimSetup::makeIntegrator(void){
1556		else{
1557		sprintf(painCave.errMsg,
1558		"SimSetup error: If you use an NPT\n"
1559	<	" ensemble, you must set tauThermostat.\n");
1559	>	"\tensemble, you must set tauThermostat.\n");
1560		painCave.isFatal = 1;
1561		simError();
1562		}
#	Line 1385 \| Line 1566 \| void SimSetup::makeIntegrator(void){
1566		else{
1567		sprintf(painCave.errMsg,
1568		"SimSetup error: If you use an NPT\n"
1569	<	" ensemble, you must set tauBarostat.\n");
1569	>	"\tensemble, you must set tauBarostat.\n");
1570		painCave.isFatal = 1;
1571		simError();
1572		}
#	Line 1408 \| Line 1589 \| void SimSetup::makeIntegrator(void){
1589		else{
1590		sprintf(painCave.errMsg,
1591		"SimSetup error: If you use a constant pressure\n"
1592	<	" ensemble, you must set targetPressure in the BASS file.\n");
1592	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1593		painCave.isFatal = 1;
1594		simError();
1595		}
#	Line 1419 \| Line 1600 \| void SimSetup::makeIntegrator(void){
1600		else{
1601		sprintf(painCave.errMsg,
1602		"SimSetup error: If you use an NPT\n"
1603	<	" ensemble, you must set tauThermostat.\n");
1603	>	"\tensemble, you must set tauThermostat.\n");
1604		painCave.isFatal = 1;
1605		simError();
1606		}
#	Line 1430 \| Line 1611 \| void SimSetup::makeIntegrator(void){
1611		else{
1612		sprintf(painCave.errMsg,
1613		"SimSetup error: If you use an NPT\n"
1614	<	" ensemble, you must set tauBarostat.\n");
1614	>	"\tensemble, you must set tauBarostat.\n");
1615		painCave.isFatal = 1;
1616		simError();
1617		}
#	Line 1453 \| Line 1634 \| void SimSetup::makeIntegrator(void){
1634		else{
1635		sprintf(painCave.errMsg,
1636		"SimSetup error: If you use a constant pressure\n"
1637	<	" ensemble, you must set targetPressure in the BASS file.\n");
1637	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1638		painCave.isFatal = 1;
1639		simError();
1640		}
#	Line 1463 \| Line 1644 \| void SimSetup::makeIntegrator(void){
1644		else{
1645		sprintf(painCave.errMsg,
1646		"SimSetup error: If you use an NPT\n"
1647	<	" ensemble, you must set tauThermostat.\n");
1647	>	"\tensemble, you must set tauThermostat.\n");
1648		painCave.isFatal = 1;
1649		simError();
1650		}
#	Line 1473 \| Line 1654 \| void SimSetup::makeIntegrator(void){
1654		else{
1655		sprintf(painCave.errMsg,
1656		"SimSetup error: If you use an NPT\n"
1657	<	" ensemble, you must set tauBarostat.\n");
1657	>	"\tensemble, you must set tauBarostat.\n");
1658		painCave.isFatal = 1;
1659		simError();
1660		}
#	Line 1526 \| Line 1707 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1707		}
1708		else{
1709		sprintf(painCave.errMsg,
1710	<	"ZConstraint error: If you use an ZConstraint\n"
1711	<	" , you must set sample time.\n");
1710	>	"ZConstraint error: If you use a ZConstraint,\n"
1711	>	"\tyou must set zconsTime.\n");
1712		painCave.isFatal = 1;
1713		simError();
1714		}
#	Line 1542 \| Line 1723 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1723		else{
1724		double defaultZConsTol = 0.01;
1725		sprintf(painCave.errMsg,
1726	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1727	<	" , default value %f is used.\n",
1726	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1727	>	"\tOOPSE will use a default value of %f.\n"
1728	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1729		defaultZConsTol);
1730		painCave.isFatal = 0;
1731		simError();
#	Line 1561 \| Line 1743 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1743		}
1744		else{
1745		sprintf(painCave.errMsg,
1746	<	"ZConstraint Warning: User does not set force Subtraction policy, "
1747	<	"PolicyByMass is used\n");
1746	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1747	>	"\tOOPSE will use PolicyByMass.\n"
1748	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1749		painCave.isFatal = 0;
1750		simError();
1751		zconsForcePolicy->setData("BYMASS");
#	Line 1570 \| Line 1753 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1753
1754		theInfo.addProperty(zconsForcePolicy);
1755
1756	+	//set zcons gap
1757	+	DoubleData* zconsGap = new DoubleData();
1758	+	zconsGap->setID(ZCONSGAP_ID);
1759	+
1760	+	if (globals->haveZConsGap()){
1761	+	zconsGap->setData(globals->getZconsGap());
1762	+	theInfo.addProperty(zconsGap);
1763	+	}
1764	+
1765	+	//set zcons fixtime
1766	+	DoubleData* zconsFixtime = new DoubleData();
1767	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1768	+
1769	+	if (globals->haveZConsFixTime()){
1770	+	zconsFixtime->setData(globals->getZconsFixtime());
1771	+	theInfo.addProperty(zconsFixtime);
1772	+	}
1773	+
1774	+	//set zconsUsingSMD
1775	+	IntData* zconsUsingSMD = new IntData();
1776	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1777	+
1778	+	if (globals->haveZConsUsingSMD()){
1779	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1780	+	theInfo.addProperty(zconsUsingSMD);
1781	+	}
1782	+
1783		//Determine the name of ouput file and add it into SimInfo's property list
1784		//Be careful, do not use inFileName, since it is a pointer which
1785		//point to a string at master node, and slave nodes do not contain that string
#	Line 1599 \| Line 1809 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1809		tempParaItem.zPos = zconStamp[i]->getZpos();
1810		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1811		tempParaItem.kRatio = zconStamp[i]->getKratio();
1812	<
1812	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1813	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1814		zconsParaData->addItem(tempParaItem);
1815		}
1816
1817		//check the uniqueness of index
1818		if(!zconsParaData->isIndexUnique()){
1819		sprintf(painCave.errMsg,
1820	<	"ZConstraint Error: molIndex is not unique\n");
1820	>	"ZConstraint Error: molIndex is not unique!\n");
1821		painCave.isFatal = 1;
1822		simError();
1823		}
#	Line 1617 \| Line 1828 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1828		//push data into siminfo, therefore, we can retrieve later
1829		theInfo.addProperty(zconsParaData);
1830		}
1831	+
1832	+	void SimSetup::makeMinimizer(){
1833	+
1834	+	OOPSEMinimizer* myOOPSEMinimizer;
1835	+	MinimizerParameterSet* param;
1836	+	char minimizerName[100];
1837	+
1838	+	for (int i = 0; i < nInfo; i++){
1839	+
1840	+	//prepare parameter set for minimizer
1841	+	param = new MinimizerParameterSet();
1842	+	param->setDefaultParameter();
1843	+
1844	+	if (globals->haveMinimizer()){
1845	+	param->setFTol(globals->getMinFTol());
1846	+	}
1847	+
1848	+	if (globals->haveMinGTol()){
1849	+	param->setGTol(globals->getMinGTol());
1850	+	}
1851	+
1852	+	if (globals->haveMinMaxIter()){
1853	+	param->setMaxIteration(globals->getMinMaxIter());
1854	+	}
1855	+
1856	+	if (globals->haveMinWriteFrq()){
1857	+	param->setMaxIteration(globals->getMinMaxIter());
1858	+	}
1859	+
1860	+	if (globals->haveMinWriteFrq()){
1861	+	param->setWriteFrq(globals->getMinWriteFrq());
1862	+	}
1863	+
1864	+	if (globals->haveMinStepSize()){
1865	+	param->setStepSize(globals->getMinStepSize());
1866	+	}
1867	+
1868	+	if (globals->haveMinLSMaxIter()){
1869	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1870	+	}
1871	+
1872	+	if (globals->haveMinLSTol()){
1873	+	param->setLineSearchTol(globals->getMinLSTol());
1874	+	}
1875	+
1876	+	strcpy(minimizerName, globals->getMinimizer());
1877	+
1878	+	if (!strcasecmp(minimizerName, "CG")){
1879	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1880	+	}
1881	+	else if (!strcasecmp(minimizerName, "SD")){
1882	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1883	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1884	+	}
1885	+	else{
1886	+	sprintf(painCave.errMsg,
1887	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1888	+	painCave.isFatal = 0;
1889	+	simError();
1890	+
1891	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1892	+	}
1893	+	info[i].the_integrator = myOOPSEMinimizer;
1894	+
1895	+	//store the minimizer into simInfo
1896	+	info[i].the_minimizer = myOOPSEMinimizer;
1897	+	info[i].has_minimizer = true;
1898	+	}
1899	+
1900	+	}

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 845 by gezelter, Thu Oct 30 18:59:20 2003 UTC vs. Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 845 by gezelter, Thu Oct 30 18:59:20 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC