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root/OpenMD/trunk/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC vs.
Revision 1558 by gezelter, Wed May 11 16:32:48 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 74 | Line 74
74		#include "UseTheForce/DarkSide/simParallel_interface.h"
75		#endif
76
77	<	namespace oopse {
77	>	namespace OpenMD {
78		std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79		std::map<int, std::set<int> >::iterator i = container.find(index);
80		std::set<int> result;
#	Line 90 | Line 90 | namespace oopse {
90		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
94	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96	<	useAtomicVirial_(true) {
93	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
94	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
95	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
96	>	calcBoxDipole_(false), useAtomicVirial_(true) {
97
98	+
99		MoleculeStamp* molStamp;
100		int nMolWithSameStamp;
101		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
#	Line 102 | Line 103 | namespace oopse {
103		CutoffGroupStamp* cgStamp;
104		RigidBodyStamp* rbStamp;
105		int nRigidAtoms = 0;
106	+
107		std::vector<Component*> components = simParams->getComponents();
108
109		for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
#	Line 156 | Line 158 | namespace oopse {
158		+ nGlobalRigidBodies_;
159
160		nGlobalMols_ = molStampIds_.size();
159	–
160	–	#ifdef IS_MPI
161		molToProcMap_.resize(nGlobalMols_);
162	–	#endif
163	–
162		}
163
164		SimInfo::~SimInfo() {
#	Line 198 | Line 196 | namespace oopse {
196		nBonds_ += mol->getNBonds();
197		nBends_ += mol->getNBends();
198		nTorsions_ += mol->getNTorsions();
199	+	nInversions_ += mol->getNInversions();
200		nRigidBodies_ += mol->getNRigidBodies();
201		nIntegrableObjects_ += mol->getNIntegrableObjects();
202		nCutoffGroups_ += mol->getNCutoffGroups();
203		nConstraints_ += mol->getNConstraintPairs();
204
205	<	addExcludePairs(mol);
206	<
205	>	addInteractionPairs(mol);
206	>
207		return true;
208		} else {
209		return false;
#	Line 223 | Line 222 | namespace oopse {
222		nBonds_ -= mol->getNBonds();
223		nBends_ -= mol->getNBends();
224		nTorsions_ -= mol->getNTorsions();
225	+	nInversions_ -= mol->getNInversions();
226		nRigidBodies_ -= mol->getNRigidBodies();
227		nIntegrableObjects_ -= mol->getNIntegrableObjects();
228		nCutoffGroups_ -= mol->getNCutoffGroups();
229		nConstraints_ -= mol->getNConstraintPairs();
230
231	<	removeExcludePairs(mol);
231	>	removeInteractionPairs(mol);
232		molecules_.erase(mol->getGlobalIndex());
233
234		delete mol;
#	Line 354 | Line 354 | namespace oopse {
354
355		}
356
357	<	void SimInfo::addExcludePairs(Molecule* mol) {
357	>	void SimInfo::addInteractionPairs(Molecule* mol) {
358	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
359		std::vector<Bond*>::iterator bondIter;
360		std::vector<Bend*>::iterator bendIter;
361		std::vector<Torsion*>::iterator torsionIter;
362	+	std::vector<Inversion*>::iterator inversionIter;
363		Bond* bond;
364		Bend* bend;
365		Torsion* torsion;
366	+	Inversion* inversion;
367		int a;
368		int b;
369		int c;
370		int d;
371
372	<	std::map<int, std::set<int> > atomGroups;
372	>	// atomGroups can be used to add special interaction maps between
373	>	// groups of atoms that are in two separate rigid bodies.
374	>	// However, most site-site interactions between two rigid bodies
375	>	// are probably not special, just the ones between the physically
376	>	// bonded atoms.  Interactions *within* a single rigid body should
377	>	// always be excluded.  These are done at the bottom of this
378	>	// function.
379
380	+	std::map<int, std::set<int> > atomGroups;
381		Molecule::RigidBodyIterator rbIter;
382		RigidBody* rb;
383		Molecule::IntegrableObjectIterator ii;
384		StuntDouble* integrableObject;
385
386	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
387	<	integrableObject = mol->nextIntegrableObject(ii)) {
388	<
386	>	for (integrableObject = mol->beginIntegrableObject(ii);
387	>	integrableObject != NULL;
388	>	integrableObject = mol->nextIntegrableObject(ii)) {
389	>
390		if (integrableObject->isRigidBody()) {
391	<	rb = static_cast<RigidBody*>(integrableObject);
392	<	std::vector<Atom*> atoms = rb->getAtoms();
393	<	std::set<int> rigidAtoms;
394	<	for (int i = 0; i < atoms.size(); ++i) {
395	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
396	<	}
397	<	for (int i = 0; i < atoms.size(); ++i) {
398	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399	<	}
391	>	rb = static_cast<RigidBody*>(integrableObject);
392	>	std::vector<Atom*> atoms = rb->getAtoms();
393	>	std::set<int> rigidAtoms;
394	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
396	>	}
397	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399	>	}
400		} else {
401		std::set<int> oneAtomSet;
402		oneAtomSet.insert(integrableObject->getGlobalIndex());
403		atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
404		}
405		}
406	+
407	+	for (bond= mol->beginBond(bondIter); bond != NULL;
408	+	bond = mol->nextBond(bondIter)) {
409
396	–
397	–
398	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
410		a = bond->getAtomA()->getGlobalIndex();
411	<	b = bond->getAtomB()->getGlobalIndex();
412	<	exclude_.addPair(a, b);
411	>	b = bond->getAtomB()->getGlobalIndex();
412	>
413	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	>	oneTwoInteractions_.addPair(a, b);
415	>	} else {
416	>	excludedInteractions_.addPair(a, b);
417	>	}
418		}
419
420	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
420	>	for (bend= mol->beginBend(bendIter); bend != NULL;
421	>	bend = mol->nextBend(bendIter)) {
422	>
423		a = bend->getAtomA()->getGlobalIndex();
424		b = bend->getAtomB()->getGlobalIndex();
425		c = bend->getAtomC()->getGlobalIndex();
408	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
409	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
410	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
411	–
412	–	exclude_.addPairs(rigidSetA, rigidSetB);
413	–	exclude_.addPairs(rigidSetA, rigidSetC);
414	–	exclude_.addPairs(rigidSetB, rigidSetC);
426
427	<	//exclude_.addPair(a, b);
428	<	//exclude_.addPair(a, c);
429	<	//exclude_.addPair(b, c);
427	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	>	oneTwoInteractions_.addPair(a, b);
429	>	oneTwoInteractions_.addPair(b, c);
430	>	} else {
431	>	excludedInteractions_.addPair(a, b);
432	>	excludedInteractions_.addPair(b, c);
433	>	}
434	>
435	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
436	>	oneThreeInteractions_.addPair(a, c);
437	>	} else {
438	>	excludedInteractions_.addPair(a, c);
439	>	}
440		}
441
442	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
442	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
443	>	torsion = mol->nextTorsion(torsionIter)) {
444	>
445		a = torsion->getAtomA()->getGlobalIndex();
446		b = torsion->getAtomB()->getGlobalIndex();
447		c = torsion->getAtomC()->getGlobalIndex();
448	<	d = torsion->getAtomD()->getGlobalIndex();
426	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
427	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
428	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
429	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
448	>	d = torsion->getAtomD()->getGlobalIndex();
449
450	<	exclude_.addPairs(rigidSetA, rigidSetB);
451	<	exclude_.addPairs(rigidSetA, rigidSetC);
452	<	exclude_.addPairs(rigidSetA, rigidSetD);
453	<	exclude_.addPairs(rigidSetB, rigidSetC);
454	<	exclude_.addPairs(rigidSetB, rigidSetD);
455	<	exclude_.addPairs(rigidSetC, rigidSetD);
450	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
451	>	oneTwoInteractions_.addPair(a, b);
452	>	oneTwoInteractions_.addPair(b, c);
453	>	oneTwoInteractions_.addPair(c, d);
454	>	} else {
455	>	excludedInteractions_.addPair(a, b);
456	>	excludedInteractions_.addPair(b, c);
457	>	excludedInteractions_.addPair(c, d);
458	>	}
459
460	<	/*
461	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
462	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
463	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
464	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
465	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
466	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
467	<
468	<
469	<	exclude_.addPair(a, b);
470	<	exclude_.addPair(a, c);
471	<	exclude_.addPair(a, d);
472	<	exclude_.addPair(b, c);
451	<	exclude_.addPair(b, d);
452	<	exclude_.addPair(c, d);
453	<	*/
460	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
461	>	oneThreeInteractions_.addPair(a, c);
462	>	oneThreeInteractions_.addPair(b, d);
463	>	} else {
464	>	excludedInteractions_.addPair(a, c);
465	>	excludedInteractions_.addPair(b, d);
466	>	}
467	>
468	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
469	>	oneFourInteractions_.addPair(a, d);
470	>	} else {
471	>	excludedInteractions_.addPair(a, d);
472	>	}
473		}
474
475	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
475	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
476	>	inversion = mol->nextInversion(inversionIter)) {
477	>
478	>	a = inversion->getAtomA()->getGlobalIndex();
479	>	b = inversion->getAtomB()->getGlobalIndex();
480	>	c = inversion->getAtomC()->getGlobalIndex();
481	>	d = inversion->getAtomD()->getGlobalIndex();
482	>
483	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
484	>	oneTwoInteractions_.addPair(a, b);
485	>	oneTwoInteractions_.addPair(a, c);
486	>	oneTwoInteractions_.addPair(a, d);
487	>	} else {
488	>	excludedInteractions_.addPair(a, b);
489	>	excludedInteractions_.addPair(a, c);
490	>	excludedInteractions_.addPair(a, d);
491	>	}
492	>
493	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
494	>	oneThreeInteractions_.addPair(b, c);
495	>	oneThreeInteractions_.addPair(b, d);
496	>	oneThreeInteractions_.addPair(c, d);
497	>	} else {
498	>	excludedInteractions_.addPair(b, c);
499	>	excludedInteractions_.addPair(b, d);
500	>	excludedInteractions_.addPair(c, d);
501	>	}
502	>	}
503	>
504	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
505	>	rb = mol->nextRigidBody(rbIter)) {
506		std::vector<Atom*> atoms = rb->getAtoms();
507	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
508	<	for (int j = i + 1; j < atoms.size(); ++j) {
507	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
508	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
509		a = atoms[i]->getGlobalIndex();
510		b = atoms[j]->getGlobalIndex();
511	<	exclude_.addPair(a, b);
511	>	excludedInteractions_.addPair(a, b);
512		}
513		}
514		}
515
516		}
517
518	<	void SimInfo::removeExcludePairs(Molecule* mol) {
518	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
519	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
520		std::vector<Bond*>::iterator bondIter;
521		std::vector<Bend*>::iterator bendIter;
522		std::vector<Torsion*>::iterator torsionIter;
523	+	std::vector<Inversion*>::iterator inversionIter;
524		Bond* bond;
525		Bend* bend;
526		Torsion* torsion;
527	+	Inversion* inversion;
528		int a;
529		int b;
530		int c;
531		int d;
532
533		std::map<int, std::set<int> > atomGroups;
482	–
534		Molecule::RigidBodyIterator rbIter;
535		RigidBody* rb;
536		Molecule::IntegrableObjectIterator ii;
537		StuntDouble* integrableObject;
538
539	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
540	<	integrableObject = mol->nextIntegrableObject(ii)) {
541	<
539	>	for (integrableObject = mol->beginIntegrableObject(ii);
540	>	integrableObject != NULL;
541	>	integrableObject = mol->nextIntegrableObject(ii)) {
542	>
543		if (integrableObject->isRigidBody()) {
544	<	rb = static_cast<RigidBody*>(integrableObject);
545	<	std::vector<Atom*> atoms = rb->getAtoms();
546	<	std::set<int> rigidAtoms;
547	<	for (int i = 0; i < atoms.size(); ++i) {
548	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
549	<	}
550	<	for (int i = 0; i < atoms.size(); ++i) {
551	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552	<	}
544	>	rb = static_cast<RigidBody*>(integrableObject);
545	>	std::vector<Atom*> atoms = rb->getAtoms();
546	>	std::set<int> rigidAtoms;
547	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
549	>	}
550	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552	>	}
553		} else {
554		std::set<int> oneAtomSet;
555		oneAtomSet.insert(integrableObject->getGlobalIndex());
#	Line 505 | Line 557 | namespace oopse {
557		}
558		}
559
560	<
561	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
560	>	for (bond= mol->beginBond(bondIter); bond != NULL;
561	>	bond = mol->nextBond(bondIter)) {
562	>
563		a = bond->getAtomA()->getGlobalIndex();
564	<	b = bond->getAtomB()->getGlobalIndex();
565	<	exclude_.removePair(a, b);
564	>	b = bond->getAtomB()->getGlobalIndex();
565	>
566	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	>	oneTwoInteractions_.removePair(a, b);
568	>	} else {
569	>	excludedInteractions_.removePair(a, b);
570	>	}
571		}
572
573	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
573	>	for (bend= mol->beginBend(bendIter); bend != NULL;
574	>	bend = mol->nextBend(bendIter)) {
575	>
576		a = bend->getAtomA()->getGlobalIndex();
577		b = bend->getAtomB()->getGlobalIndex();
578		c = bend->getAtomC()->getGlobalIndex();
519	–
520	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
521	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
522	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
523	–
524	–	exclude_.removePairs(rigidSetA, rigidSetB);
525	–	exclude_.removePairs(rigidSetA, rigidSetC);
526	–	exclude_.removePairs(rigidSetB, rigidSetC);
579
580	<	//exclude_.removePair(a, b);
581	<	//exclude_.removePair(a, c);
582	<	//exclude_.removePair(b, c);
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	oneTwoInteractions_.removePair(b, c);
583	>	} else {
584	>	excludedInteractions_.removePair(a, b);
585	>	excludedInteractions_.removePair(b, c);
586	>	}
587	>
588	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
589	>	oneThreeInteractions_.removePair(a, c);
590	>	} else {
591	>	excludedInteractions_.removePair(a, c);
592	>	}
593		}
594
595	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
595	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
596	>	torsion = mol->nextTorsion(torsionIter)) {
597	>
598		a = torsion->getAtomA()->getGlobalIndex();
599		b = torsion->getAtomB()->getGlobalIndex();
600		c = torsion->getAtomC()->getGlobalIndex();
601	<	d = torsion->getAtomD()->getGlobalIndex();
601	>	d = torsion->getAtomD()->getGlobalIndex();
602	>
603	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
604	>	oneTwoInteractions_.removePair(a, b);
605	>	oneTwoInteractions_.removePair(b, c);
606	>	oneTwoInteractions_.removePair(c, d);
607	>	} else {
608	>	excludedInteractions_.removePair(a, b);
609	>	excludedInteractions_.removePair(b, c);
610	>	excludedInteractions_.removePair(c, d);
611	>	}
612
613	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
614	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
615	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
616	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
613	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
614	>	oneThreeInteractions_.removePair(a, c);
615	>	oneThreeInteractions_.removePair(b, d);
616	>	} else {
617	>	excludedInteractions_.removePair(a, c);
618	>	excludedInteractions_.removePair(b, d);
619	>	}
620
621	<	exclude_.removePairs(rigidSetA, rigidSetB);
622	<	exclude_.removePairs(rigidSetA, rigidSetC);
623	<	exclude_.removePairs(rigidSetA, rigidSetD);
624	<	exclude_.removePairs(rigidSetB, rigidSetC);
625	<	exclude_.removePairs(rigidSetB, rigidSetD);
626	<	exclude_.removePairs(rigidSetC, rigidSetD);
621	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
622	>	oneFourInteractions_.removePair(a, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, d);
625	>	}
626	>	}
627
628	<	/*
629	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
553	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
554	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
555	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
556	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
557	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
628	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
629	>	inversion = mol->nextInversion(inversionIter)) {
630
631	<
632	<	exclude_.removePair(a, b);
633	<	exclude_.removePair(a, c);
634	<	exclude_.removePair(a, d);
563	<	exclude_.removePair(b, c);
564	<	exclude_.removePair(b, d);
565	<	exclude_.removePair(c, d);
566	<	*/
567	<	}
631	>	a = inversion->getAtomA()->getGlobalIndex();
632	>	b = inversion->getAtomB()->getGlobalIndex();
633	>	c = inversion->getAtomC()->getGlobalIndex();
634	>	d = inversion->getAtomD()->getGlobalIndex();
635
636	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
636	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
637	>	oneTwoInteractions_.removePair(a, b);
638	>	oneTwoInteractions_.removePair(a, c);
639	>	oneTwoInteractions_.removePair(a, d);
640	>	} else {
641	>	excludedInteractions_.removePair(a, b);
642	>	excludedInteractions_.removePair(a, c);
643	>	excludedInteractions_.removePair(a, d);
644	>	}
645	>
646	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
647	>	oneThreeInteractions_.removePair(b, c);
648	>	oneThreeInteractions_.removePair(b, d);
649	>	oneThreeInteractions_.removePair(c, d);
650	>	} else {
651	>	excludedInteractions_.removePair(b, c);
652	>	excludedInteractions_.removePair(b, d);
653	>	excludedInteractions_.removePair(c, d);
654	>	}
655	>	}
656	>
657	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
658	>	rb = mol->nextRigidBody(rbIter)) {
659		std::vector<Atom*> atoms = rb->getAtoms();
660	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
661	<	for (int j = i + 1; j < atoms.size(); ++j) {
660	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
661	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
662		a = atoms[i]->getGlobalIndex();
663		b = atoms[j]->getGlobalIndex();
664	<	exclude_.removePair(a, b);
664	>	excludedInteractions_.removePair(a, b);
665		}
666		}
667		}
668	<
668	>
669		}
670	<
671	<
670	>
671	>
672		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
673		int curStampId;
674	<
674	>
675		//index from 0
676		curStampId = moleculeStamps_.size();
677
#	Line 674 | Line 763 | namespace oopse {
763		useRF = 0;
764		useSF = 0;
765		useSP = 0;
766	+	useBoxDipole = 0;
767
768
769		if (simParams_->haveElectrostaticSummationMethod()) {
#	Line 798 | Line 888 | namespace oopse {
888
889		void SimInfo::setupFortranSim() {
890		int isError;
891	<	int nExclude;
891	>	int nExclude, nOneTwo, nOneThree, nOneFour;
892		std::vector<int> fortranGlobalGroupMembership;
893
804	–	nExclude = exclude_.getSize();
894		isError = 0;
895
896		//globalGroupMembership_ is filled by SimCreator
#	Line 833 | Line 922 | namespace oopse {
922		else
923		mfact.push_back( 1.0 );
924		}
836	–
925		}
926		}
927
#	Line 857 | Line 945 | namespace oopse {
945		}
946
947		//setup fortran simulation
860	–	int nGlobalExcludes = 0;
861	–	int* globalExcludes = NULL;
862	–	int* excludeList = exclude_.getExcludeList();
863	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
864	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
865	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
948
949	<	if( isError ){
949	>	nExclude = excludedInteractions_.getSize();
950	>	nOneTwo = oneTwoInteractions_.getSize();
951	>	nOneThree = oneThreeInteractions_.getSize();
952	>	nOneFour = oneFourInteractions_.getSize();
953
954	+	int* excludeList = excludedInteractions_.getPairList();
955	+	int* oneTwoList = oneTwoInteractions_.getPairList();
956	+	int* oneThreeList = oneThreeInteractions_.getPairList();
957	+	int* oneFourList = oneFourInteractions_.getPairList();
958	+
959	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
960	+	&nExclude, excludeList,
961	+	&nOneTwo, oneTwoList,
962	+	&nOneThree, oneThreeList,
963	+	&nOneFour, oneFourList,
964	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965	+	&fortranGlobalGroupMembership[0], &isError);
966	+
967	+	if( isError ){
968	+
969		sprintf( painCave.errMsg,
970		"There was an error setting the simulation information in fortran.\n" );
971		painCave.isFatal = 1;
972	<	painCave.severity = OOPSE_ERROR;
972	>	painCave.severity = OPENMD_ERROR;
973		simError();
974		}
975	<
976	<	#ifdef IS_MPI
975	>
976	>
977		sprintf( checkPointMsg,
978		"succesfully sent the simulation information to fortran.\n");
979	<	MPIcheckPoint();
980	<	#endif // is_mpi
981	<
979	>
980	>	errorCheckPoint();
981	>
982		// Setup number of neighbors in neighbor list if present
983		if (simParams_->haveNeighborListNeighbors()) {
984		int nlistNeighbors = simParams_->getNeighborListNeighbors();
#	Line 889 | Line 989 | namespace oopse {
989		}
990
991
892	–	#ifdef IS_MPI
992		void SimInfo::setupFortranParallel() {
993	<
993	>	#ifdef IS_MPI
994		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
995		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
996		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 941 | Line 1040 | namespace oopse {
1040		}
1041
1042		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1043	<	MPIcheckPoint();
1043	>	errorCheckPoint();
1044
1045	<
1045	>	#endif
1046		}
1047
949	–	#endif
950	–
1048		void SimInfo::setupCutoff() {
1049
1050		ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
#	Line 956 | Line 1053 | namespace oopse {
1053		int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054
1055		// Set LJ shifting bools to false
1056	<	ljsp_ = false;
1057	<	ljsf_ = false;
1056	>	ljsp_ = 0;
1057	>	ljsf_ = 0;
1058
1059		std::string myPolicy;
1060		if (forceFieldOptions_.haveCutoffPolicy()){
#	Line 1008 | Line 1105 | namespace oopse {
1105		rsw_ = 0.85 * rcut_;
1106		sprintf(painCave.errMsg,
1107		"SimCreator Warning: No value was set for the switchingRadius.\n"
1108	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1108	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1109		"\tswitchingRadius = %f. for this simulation\n", rsw_);
1110		painCave.isFatal = 0;
1111		simError();
#	Line 1016 | Line 1113 | namespace oopse {
1113		rsw_ = rcut_;
1114		sprintf(painCave.errMsg,
1115		"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1116	>	"\tOpenMD will use the same value as the cutoffRadius.\n"
1117		"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118		painCave.isFatal = 0;
1119		simError();
#	Line 1028 | Line 1125 | namespace oopse {
1125		toUpper(myMethod);
1126
1127		if (myMethod == "SHIFTED_POTENTIAL") {
1128	<	ljsp_ = true;
1128	>	ljsp_ = 1;
1129		} else if (myMethod == "SHIFTED_FORCE") {
1130	<	ljsf_ = true;
1130	>	ljsf_ = 1;
1131		}
1132		}
1133	+
1134		notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1135
1136		} else {
#	Line 1041 | Line 1139 | namespace oopse {
1139		if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1140		sprintf(painCave.errMsg,
1141		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1142	<	"\tOOPSE will use a default value of 15.0 angstroms"
1142	>	"\tOpenMD will use a default value of 15.0 angstroms"
1143		"\tfor the cutoffRadius.\n");
1144		painCave.isFatal = 0;
1145		simError();
#	Line 1054 | Line 1152 | namespace oopse {
1152		// For the time being, we're tethering the LJ shifted behavior to the
1153		// electrostaticSummationMethod keyword options
1154		if (myMethod == "SHIFTED_POTENTIAL") {
1155	<	ljsp_ = true;
1155	>	ljsp_ = 1;
1156		} else if (myMethod == "SHIFTED_FORCE") {
1157	<	ljsf_ = true;
1157	>	ljsf_ = 1;
1158		}
1159		if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1160		if (simParams_->haveSwitchingRadius()){
#	Line 1075 | Line 1173 | namespace oopse {
1173		} else {
1174		sprintf(painCave.errMsg,
1175		"SimCreator Warning: No value was set for switchingRadius.\n"
1176	<	"\tOOPSE will use a default value of\n"
1176	>	"\tOpenMD will use a default value of\n"
1177		"\t0.85 * cutoffRadius for the switchingRadius\n");
1178		painCave.isFatal = 0;
1179		simError();
#	Line 1536 | Line 1634 | namespace oopse {
1634		return sdByGlobalIndex_.at(index);
1635		}
1636		*/
1637	<	}//end namespace oopse
1637	>	}//end namespace OpenMD
1638

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC vs.
Revision 1558 by gezelter, Wed May 11 16:32:48 2011 UTC

#	Line 0 | Line 1
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