[ViewVC] Diff of: OpenMD/branches/development/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC

#	Line 53 \| Line 53
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	+	#include "primitives/StuntDouble.hpp"
57		#include "UseTheForce/fCutoffPolicy.h"
58		#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59		#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61		#include "UseTheForce/doForces_interface.h"
62	+	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63		#include "UseTheForce/DarkSide/electrostatic_interface.h"
64		#include "UseTheForce/DarkSide/switcheroo_interface.h"
65		#include "utils/MemoryUtils.hpp"
#	Line 66 \| Line 68
68		#include "io/ForceFieldOptions.hpp"
69		#include "UseTheForce/ForceField.hpp"
70
71	+
72		#ifdef IS_MPI
73		#include "UseTheForce/mpiComponentPlan.h"
74		#include "UseTheForce/DarkSide/simParallel_interface.h"
#	Line 87 \| 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) {
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 98 \| 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 152 \| Line 158 \| namespace oopse {
158		+ nGlobalRigidBodies_;
159
160		nGlobalMols_ = molStampIds_.size();
155	–
156	–	#ifdef IS_MPI
161		molToProcMap_.resize(nGlobalMols_);
158	–	#endif
159	–
162		}
163
164		SimInfo::~SimInfo() {
#	Line 194 \| 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 219 \| 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 350 \| 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
392	–
393	–
394	–	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();
404	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407	–
408	–	exclude_.addPairs(rigidSetA, rigidSetB);
409	–	exclude_.addPairs(rigidSetA, rigidSetC);
410	–	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();
422	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	<	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);
447	<	exclude_.addPair(b, d);
448	<	exclude_.addPair(c, d);
449	<	*/
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;
478	–
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 501 \| 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();
515	–
516	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	–
520	–	exclude_.removePairs(rigidSetA, rigidSetB);
521	–	exclude_.removePairs(rigidSetA, rigidSetC);
522	–	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);
546	<
547	<	/*
548	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
621	>	if (options_.havevdw14scale() \|\| options_.haveelectrostatic14scale()) {
622	>	oneFourInteractions_.removePair(a, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, d);
625	>	}
626	>	}
627
628	<
629	<	exclude_.removePair(a, b);
630	<	exclude_.removePair(a, c);
631	<	exclude_.removePair(a, d);
632	<	exclude_.removePair(b, c);
633	<	exclude_.removePair(b, d);
634	<	exclude_.removePair(c, d);
635	<	*/
628	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
629	>	inversion = mol->nextInversion(inversionIter)) {
630	>
631	>	a = inversion->getAtomA()->getGlobalIndex();
632	>	b = inversion->getAtomB()->getGlobalIndex();
633	>	c = inversion->getAtomC()->getGlobalIndex();
634	>	d = inversion->getAtomD()->getGlobalIndex();
635	>
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; rb = mol->nextRigidBody(rbIter)) {
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 600 \| Line 693 \| namespace oopse {
693		/** @deprecate */
694		int isError = 0;
695
696	+	setupCutoff();
697	+
698		setupElectrostaticSummationMethod( isError );
699		setupSwitchingFunction();
700	+	setupAccumulateBoxDipole();
701
702		if(isError){
703		sprintf( painCave.errMsg,
#	Line 609 \| Line 705 \| namespace oopse {
705		painCave.isFatal = 1;
706		simError();
707		}
612	–
613	–
614	–	setupCutoff();
708
709		calcNdf();
710		calcNdfRaw();
#	Line 661 \| Line 754 \| namespace oopse {
754		int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755		int useRF;
756		int useSF;
757	+	int useSP;
758	+	int useBoxDipole;
759	+
760		std::string myMethod;
761
762		// set the useRF logical
763		useRF = 0;
764		useSF = 0;
765	+	useSP = 0;
766
767
768		if (simParams_->haveElectrostaticSummationMethod()) {
769		std::string myMethod = simParams_->getElectrostaticSummationMethod();
770		toUpper(myMethod);
771	<	if (myMethod == "REACTION_FIELD") {
772	<	useRF=1;
773	<	} else {
774	<	if (myMethod == "SHIFTED_FORCE") {
775	<	useSF = 1;
776	<	}
771	>	if (myMethod == "REACTION_FIELD"){
772	>	useRF = 1;
773	>	} else if (myMethod == "SHIFTED_FORCE"){
774	>	useSF = 1;
775	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
776	>	useSP = 1;
777		}
778		}
779	+
780	+	if (simParams_->haveAccumulateBoxDipole())
781	+	if (simParams_->getAccumulateBoxDipole())
782	+	useBoxDipole = 1;
783
784	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
785	+
786		//loop over all of the atom types
787		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
788		useLennardJones \|= (*i)->isLennardJones();
#	Line 749 \| Line 852 \| namespace oopse {
852		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853
854		temp = useSF;
855	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
855	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856
857	+	temp = useSP;
858	+	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	+
860	+	temp = useBoxDipole;
861	+	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	+
863	+	temp = useAtomicVirial_;
864	+	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865	+
866		#endif
867
868		fInfo_.SIM_uses_PBC = usePBC;
#	Line 768 \| Line 880 \| namespace oopse {
880		fInfo_.SIM_uses_FLARB = useFLARB;
881		fInfo_.SIM_uses_RF = useRF;
882		fInfo_.SIM_uses_SF = useSF;
883	<
884	<	if( myMethod == "REACTION_FIELD") {
885	<
774	<	if (simParams_->haveDielectric()) {
775	<	fInfo_.dielect = simParams_->getDielectric();
776	<	} else {
777	<	sprintf(painCave.errMsg,
778	<	"SimSetup Error: No Dielectric constant was set.\n"
779	<	"\tYou are trying to use Reaction Field without"
780	<	"\tsetting a dielectric constant!\n");
781	<	painCave.isFatal = 1;
782	<	simError();
783	<	}
784	<	}
785	<
883	>	fInfo_.SIM_uses_SP = useSP;
884	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
885	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
886		}
887
888		void SimInfo::setupFortranSim() {
889		int isError;
890	<	int nExclude;
890	>	int nExclude, nOneTwo, nOneThree, nOneFour;
891		std::vector<int> fortranGlobalGroupMembership;
892
793	–	nExclude = exclude_.getSize();
893		isError = 0;
894
895		//globalGroupMembership_ is filled by SimCreator
#	Line 822 \| Line 921 \| namespace oopse {
921		else
922		mfact.push_back( 1.0 );
923		}
825	–
924		}
925		}
926
#	Line 846 \| Line 944 \| namespace oopse {
944		}
945
946		//setup fortran simulation
849	–	int nGlobalExcludes = 0;
850	–	int* globalExcludes = NULL;
851	–	int* excludeList = exclude_.getExcludeList();
852	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
853	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
854	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
947
948	<	if( isError ){
948	>	nExclude = excludedInteractions_.getSize();
949	>	nOneTwo = oneTwoInteractions_.getSize();
950	>	nOneThree = oneThreeInteractions_.getSize();
951	>	nOneFour = oneFourInteractions_.getSize();
952
953	+	std::cerr << "excludedInteractions contains: " << excludedInteractions_.getSize() << " pairs \n";
954	+	std::cerr << "oneTwoInteractions contains: " << oneTwoInteractions_.getSize() << " pairs \n";
955	+	std::cerr << "oneThreeInteractions contains: " << oneThreeInteractions_.getSize() << " pairs \n";
956	+	std::cerr << "oneFourInteractions contains: " << oneFourInteractions_.getSize() << " pairs \n";
957	+
958	+	int* excludeList = excludedInteractions_.getPairList();
959	+	int* oneTwoList = oneTwoInteractions_.getPairList();
960	+	int* oneThreeList = oneThreeInteractions_.getPairList();
961	+	int* oneFourList = oneFourInteractions_.getPairList();
962	+
963	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
964	+	&nExclude, excludeList,
965	+	&nOneTwo, oneTwoList,
966	+	&nOneThree, oneThreeList,
967	+	&nOneFour, oneFourList,
968	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
969	+	&fortranGlobalGroupMembership[0], &isError);
970	+
971	+	if( isError ){
972	+
973		sprintf( painCave.errMsg,
974		"There was an error setting the simulation information in fortran.\n" );
975		painCave.isFatal = 1;
976		painCave.severity = OOPSE_ERROR;
977		simError();
978		}
979	<
980	<	#ifdef IS_MPI
979	>
980	>
981		sprintf( checkPointMsg,
982		"succesfully sent the simulation information to fortran.\n");
983	<	MPIcheckPoint();
984	<	#endif // is_mpi
983	>
984	>	errorCheckPoint();
985	>
986	>	// Setup number of neighbors in neighbor list if present
987	>	if (simParams_->haveNeighborListNeighbors()) {
988	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
989	>	setNeighbors(&nlistNeighbors);
990	>	}
991	>
992	>
993		}
994
995
873	–	#ifdef IS_MPI
996		void SimInfo::setupFortranParallel() {
997	<
997	>	#ifdef IS_MPI
998		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
999		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1000		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 922 \| Line 1044 \| namespace oopse {
1044		}
1045
1046		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1047	<	MPIcheckPoint();
1047	>	errorCheckPoint();
1048
1049	<
1049	>	#endif
1050		}
1051
930	–	#endif
931	–
1052		void SimInfo::setupCutoff() {
1053
1054		ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
#	Line 936 \| Line 1056 \| namespace oopse {
1056		// Check the cutoff policy
1057		int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1058
1059	+	// Set LJ shifting bools to false
1060	+	ljsp_ = false;
1061	+	ljsf_ = false;
1062	+
1063		std::string myPolicy;
1064		if (forceFieldOptions_.haveCutoffPolicy()){
1065		myPolicy = forceFieldOptions_.getCutoffPolicy();
#	Line 999 \| Line 1123 \| namespace oopse {
1123		simError();
1124		}
1125		}
1126	+
1127	+	if (simParams_->haveElectrostaticSummationMethod()) {
1128	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1129	+	toUpper(myMethod);
1130	+
1131	+	if (myMethod == "SHIFTED_POTENTIAL") {
1132	+	ljsp_ = true;
1133	+	} else if (myMethod == "SHIFTED_FORCE") {
1134	+	ljsf_ = true;
1135	+	}
1136	+	}
1137	+	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1138
1003	–	notifyFortranCutoffs(&rcut_, &rsw_);
1004	–
1139		} else {
1140
1141		// For electrostatic atoms, we'll assume a large safe value:
#	Line 1017 \| Line 1151 \| namespace oopse {
1151		if (simParams_->haveElectrostaticSummationMethod()) {
1152		std::string myMethod = simParams_->getElectrostaticSummationMethod();
1153		toUpper(myMethod);
1154	<	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1154	>
1155	>	// For the time being, we're tethering the LJ shifted behavior to the
1156	>	// electrostaticSummationMethod keyword options
1157	>	if (myMethod == "SHIFTED_POTENTIAL") {
1158	>	ljsp_ = true;
1159	>	} else if (myMethod == "SHIFTED_FORCE") {
1160	>	ljsf_ = true;
1161	>	}
1162	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1163		if (simParams_->haveSwitchingRadius()){
1164		sprintf(painCave.errMsg,
1165		"SimInfo Warning: A value was set for the switchingRadius\n"
#	Line 1040 \| Line 1182 \| namespace oopse {
1182		simError();
1183		rsw_ = 0.85 * rcut_;
1184		}
1185	<	notifyFortranCutoffs(&rcut_, &rsw_);
1185	>
1186	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1187	>
1188		} else {
1189		// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1190		// We'll punt and let fortran figure out the cutoffs later.
#	Line 1058 \| Line 1202 \| namespace oopse {
1202		int sm = UNDAMPED;
1203		RealType alphaVal;
1204		RealType dielectric;
1205	<
1205	>
1206		errorOut = isError;
1063	–	alphaVal = simParams_->getDampingAlpha();
1064	–	dielectric = simParams_->getDielectric();
1207
1208		if (simParams_->haveElectrostaticSummationMethod()) {
1209		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 1078 \| Line 1220 \| namespace oopse {
1220		if (myMethod == "SHIFTED_FORCE") {
1221		esm = SHIFTED_FORCE;
1222		} else {
1223	<	if (myMethod == "REACTION_FIELD") {
1223	>	if (myMethod == "REACTION_FIELD") {
1224		esm = REACTION_FIELD;
1225	+	dielectric = simParams_->getDielectric();
1226	+	if (!simParams_->haveDielectric()) {
1227	+	// throw warning
1228	+	sprintf( painCave.errMsg,
1229	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1230	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1231	+	painCave.isFatal = 0;
1232	+	simError();
1233	+	}
1234		} else {
1235		// throw error
1236		sprintf( painCave.errMsg,
#	Line 1106 \| Line 1257 \| namespace oopse {
1257		if (myScreen == "DAMPED") {
1258		sm = DAMPED;
1259		if (!simParams_->haveDampingAlpha()) {
1260	<	//throw error
1260	>	// first set a cutoff dependent alpha value
1261	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1262	>	alphaVal = 0.5125 - rcut_* 0.025;
1263	>	// for values rcut > 20.5, alpha is zero
1264	>	if (alphaVal < 0) alphaVal = 0;
1265	>
1266	>	// throw warning
1267		sprintf( painCave.errMsg,
1268		"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1269	<	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1269	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1270		painCave.isFatal = 0;
1271		simError();
1272	+	} else {
1273	+	alphaVal = simParams_->getDampingAlpha();
1274		}
1275	+
1276		} else {
1277		// throw error
1278		sprintf( painCave.errMsg,
#	Line 1158 \| Line 1318 \| namespace oopse {
1318
1319		// send switching function notification to switcheroo
1320		setFunctionType(&ft);
1321	+
1322	+	}
1323	+
1324	+	void SimInfo::setupAccumulateBoxDipole() {
1325	+
1326	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1327	+	if ( simParams_->haveAccumulateBoxDipole() )
1328	+	if ( simParams_->getAccumulateBoxDipole() ) {
1329	+	setAccumulateBoxDipole();
1330	+	calcBoxDipole_ = true;
1331	+	}
1332
1333		}
1334
#	Line 1410 \| Line 1581 \| namespace oopse {
1581		return angularMomentum;
1582		}
1583
1584	<
1584	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1585	>	return IOIndexToIntegrableObject.at(index);
1586	>	}
1587	>
1588	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1589	>	IOIndexToIntegrableObject= v;
1590	>	}
1591	>
1592	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1593	>	based on the radius of gyration V=4/3PiR_1R_2R_3
1594	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1595	>	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1596	>	*/
1597	>	void SimInfo::getGyrationalVolume(RealType &volume){
1598	>	Mat3x3d intTensor;
1599	>	RealType det;
1600	>	Vector3d dummyAngMom;
1601	>	RealType sysconstants;
1602	>	RealType geomCnst;
1603	>
1604	>	geomCnst = 3.0/2.0;
1605	>	/* Get the inertial tensor and angular momentum for free*/
1606	>	getInertiaTensor(intTensor,dummyAngMom);
1607	>
1608	>	det = intTensor.determinant();
1609	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1610	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1611	>	return;
1612	>	}
1613	>
1614	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1615	>	Mat3x3d intTensor;
1616	>	Vector3d dummyAngMom;
1617	>	RealType sysconstants;
1618	>	RealType geomCnst;
1619	>
1620	>	geomCnst = 3.0/2.0;
1621	>	/* Get the inertial tensor and angular momentum for free*/
1622	>	getInertiaTensor(intTensor,dummyAngMom);
1623	>
1624	>	detI = intTensor.determinant();
1625	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1626	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1627	>	return;
1628	>	}
1629	>	/*
1630	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1631	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1632	>	sdByGlobalIndex_ = v;
1633	>	}
1634	>
1635	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1636	>	//assert(index < nAtoms_ + nRigidBodies_);
1637	>	return sdByGlobalIndex_.at(index);
1638	>	}
1639	>	*/
1640		}//end namespace oopse
1641

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs. Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC