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root/OpenMD/branches/development/src/brains/SimInfo.cpp

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 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 55 | Line 55
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"
58		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60		#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
61		#include "UseTheForce/DarkSide/switcheroo_interface.h"
62		#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
#	Line 74 | Line 71
71		#include "UseTheForce/DarkSide/simParallel_interface.h"
72		#endif
73
74	<	namespace oopse {
74	>	namespace OpenMD {
75		std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76		std::map<int, std::set<int> >::iterator i = container.find(index);
77		std::set<int> result;
#	Line 90 | Line 87 | namespace oopse {
87		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
91	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
92	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
93	<	useAtomicVirial_(true) {
90	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
91	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
92	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
93	>	calcBoxDipole_(false), useAtomicVirial_(true) {
94	>
95
96		MoleculeStamp* molStamp;
97		int nMolWithSameStamp;
#	Line 102 | Line 100 | namespace oopse {
100		CutoffGroupStamp* cgStamp;
101		RigidBodyStamp* rbStamp;
102		int nRigidAtoms = 0;
103	+
104		std::vector<Component*> components = simParams->getComponents();
105
106		for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
#	Line 156 | Line 155 | namespace oopse {
155		+ nGlobalRigidBodies_;
156
157		nGlobalMols_ = molStampIds_.size();
159	–
160	–	#ifdef IS_MPI
158		molToProcMap_.resize(nGlobalMols_);
162	–	#endif
163	–
159		}
160
161		SimInfo::~SimInfo() {
#	Line 198 | Line 193 | namespace oopse {
193		nBonds_ += mol->getNBonds();
194		nBends_ += mol->getNBends();
195		nTorsions_ += mol->getNTorsions();
196	+	nInversions_ += mol->getNInversions();
197		nRigidBodies_ += mol->getNRigidBodies();
198		nIntegrableObjects_ += mol->getNIntegrableObjects();
199		nCutoffGroups_ += mol->getNCutoffGroups();
200		nConstraints_ += mol->getNConstraintPairs();
201
202	<	addExcludePairs(mol);
203	<
202	>	addInteractionPairs(mol);
203	>
204		return true;
205		} else {
206		return false;
#	Line 223 | Line 219 | namespace oopse {
219		nBonds_ -= mol->getNBonds();
220		nBends_ -= mol->getNBends();
221		nTorsions_ -= mol->getNTorsions();
222	+	nInversions_ -= mol->getNInversions();
223		nRigidBodies_ -= mol->getNRigidBodies();
224		nIntegrableObjects_ -= mol->getNIntegrableObjects();
225		nCutoffGroups_ -= mol->getNCutoffGroups();
226		nConstraints_ -= mol->getNConstraintPairs();
227
228	<	removeExcludePairs(mol);
228	>	removeInteractionPairs(mol);
229		molecules_.erase(mol->getGlobalIndex());
230
231		delete mol;
#	Line 354 | Line 351 | namespace oopse {
351
352		}
353
354	<	void SimInfo::addExcludePairs(Molecule* mol) {
354	>	void SimInfo::addInteractionPairs(Molecule* mol) {
355	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
356		std::vector<Bond*>::iterator bondIter;
357		std::vector<Bend*>::iterator bendIter;
358		std::vector<Torsion*>::iterator torsionIter;
359	+	std::vector<Inversion*>::iterator inversionIter;
360		Bond* bond;
361		Bend* bend;
362		Torsion* torsion;
363	+	Inversion* inversion;
364		int a;
365		int b;
366		int c;
367		int d;
368
369	<	std::map<int, std::set<int> > atomGroups;
369	>	// atomGroups can be used to add special interaction maps between
370	>	// groups of atoms that are in two separate rigid bodies.
371	>	// However, most site-site interactions between two rigid bodies
372	>	// are probably not special, just the ones between the physically
373	>	// bonded atoms.  Interactions *within* a single rigid body should
374	>	// always be excluded.  These are done at the bottom of this
375	>	// function.
376
377	+	std::map<int, std::set<int> > atomGroups;
378		Molecule::RigidBodyIterator rbIter;
379		RigidBody* rb;
380		Molecule::IntegrableObjectIterator ii;
381		StuntDouble* integrableObject;
382
383	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
384	<	integrableObject = mol->nextIntegrableObject(ii)) {
385	<
383	>	for (integrableObject = mol->beginIntegrableObject(ii);
384	>	integrableObject != NULL;
385	>	integrableObject = mol->nextIntegrableObject(ii)) {
386	>
387		if (integrableObject->isRigidBody()) {
388	<	rb = static_cast<RigidBody*>(integrableObject);
389	<	std::vector<Atom*> atoms = rb->getAtoms();
390	<	std::set<int> rigidAtoms;
391	<	for (int i = 0; i < atoms.size(); ++i) {
392	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
393	<	}
394	<	for (int i = 0; i < atoms.size(); ++i) {
395	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
396	<	}
388	>	rb = static_cast<RigidBody*>(integrableObject);
389	>	std::vector<Atom*> atoms = rb->getAtoms();
390	>	std::set<int> rigidAtoms;
391	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
392	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
393	>	}
394	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
396	>	}
397		} else {
398		std::set<int> oneAtomSet;
399		oneAtomSet.insert(integrableObject->getGlobalIndex());
400		atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
401		}
402		}
403	+
404	+	for (bond= mol->beginBond(bondIter); bond != NULL;
405	+	bond = mol->nextBond(bondIter)) {
406
396	–
397	–
398	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
407		a = bond->getAtomA()->getGlobalIndex();
408	<	b = bond->getAtomB()->getGlobalIndex();
409	<	exclude_.addPair(a, b);
408	>	b = bond->getAtomB()->getGlobalIndex();
409	>
410	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
411	>	oneTwoInteractions_.addPair(a, b);
412	>	} else {
413	>	excludedInteractions_.addPair(a, b);
414	>	}
415		}
416
417	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
417	>	for (bend= mol->beginBend(bendIter); bend != NULL;
418	>	bend = mol->nextBend(bendIter)) {
419	>
420		a = bend->getAtomA()->getGlobalIndex();
421		b = bend->getAtomB()->getGlobalIndex();
422		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);
423
424	<	//exclude_.addPair(a, b);
425	<	//exclude_.addPair(a, c);
426	<	//exclude_.addPair(b, c);
424	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
425	>	oneTwoInteractions_.addPair(a, b);
426	>	oneTwoInteractions_.addPair(b, c);
427	>	} else {
428	>	excludedInteractions_.addPair(a, b);
429	>	excludedInteractions_.addPair(b, c);
430	>	}
431	>
432	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	>	oneThreeInteractions_.addPair(a, c);
434	>	} else {
435	>	excludedInteractions_.addPair(a, c);
436	>	}
437		}
438
439	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
439	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
440	>	torsion = mol->nextTorsion(torsionIter)) {
441	>
442		a = torsion->getAtomA()->getGlobalIndex();
443		b = torsion->getAtomB()->getGlobalIndex();
444		c = torsion->getAtomC()->getGlobalIndex();
445	<	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);
445	>	d = torsion->getAtomD()->getGlobalIndex();
446
447	<	exclude_.addPairs(rigidSetA, rigidSetB);
448	<	exclude_.addPairs(rigidSetA, rigidSetC);
449	<	exclude_.addPairs(rigidSetA, rigidSetD);
450	<	exclude_.addPairs(rigidSetB, rigidSetC);
451	<	exclude_.addPairs(rigidSetB, rigidSetD);
452	<	exclude_.addPairs(rigidSetC, rigidSetD);
447	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
448	>	oneTwoInteractions_.addPair(a, b);
449	>	oneTwoInteractions_.addPair(b, c);
450	>	oneTwoInteractions_.addPair(c, d);
451	>	} else {
452	>	excludedInteractions_.addPair(a, b);
453	>	excludedInteractions_.addPair(b, c);
454	>	excludedInteractions_.addPair(c, d);
455	>	}
456
457	<	/*
458	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
459	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
460	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
461	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
462	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
463	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
464	<
465	<
466	<	exclude_.addPair(a, b);
467	<	exclude_.addPair(a, c);
468	<	exclude_.addPair(a, d);
469	<	exclude_.addPair(b, c);
451	<	exclude_.addPair(b, d);
452	<	exclude_.addPair(c, d);
453	<	*/
457	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
458	>	oneThreeInteractions_.addPair(a, c);
459	>	oneThreeInteractions_.addPair(b, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, c);
462	>	excludedInteractions_.addPair(b, d);
463	>	}
464	>
465	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
466	>	oneFourInteractions_.addPair(a, d);
467	>	} else {
468	>	excludedInteractions_.addPair(a, d);
469	>	}
470		}
471
472	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
472	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
473	>	inversion = mol->nextInversion(inversionIter)) {
474	>
475	>	a = inversion->getAtomA()->getGlobalIndex();
476	>	b = inversion->getAtomB()->getGlobalIndex();
477	>	c = inversion->getAtomC()->getGlobalIndex();
478	>	d = inversion->getAtomD()->getGlobalIndex();
479	>
480	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
481	>	oneTwoInteractions_.addPair(a, b);
482	>	oneTwoInteractions_.addPair(a, c);
483	>	oneTwoInteractions_.addPair(a, d);
484	>	} else {
485	>	excludedInteractions_.addPair(a, b);
486	>	excludedInteractions_.addPair(a, c);
487	>	excludedInteractions_.addPair(a, d);
488	>	}
489	>
490	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
491	>	oneThreeInteractions_.addPair(b, c);
492	>	oneThreeInteractions_.addPair(b, d);
493	>	oneThreeInteractions_.addPair(c, d);
494	>	} else {
495	>	excludedInteractions_.addPair(b, c);
496	>	excludedInteractions_.addPair(b, d);
497	>	excludedInteractions_.addPair(c, d);
498	>	}
499	>	}
500	>
501	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
502	>	rb = mol->nextRigidBody(rbIter)) {
503		std::vector<Atom*> atoms = rb->getAtoms();
504	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
505	<	for (int j = i + 1; j < atoms.size(); ++j) {
504	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
505	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
506		a = atoms[i]->getGlobalIndex();
507		b = atoms[j]->getGlobalIndex();
508	<	exclude_.addPair(a, b);
508	>	excludedInteractions_.addPair(a, b);
509		}
510		}
511		}
512
513		}
514
515	<	void SimInfo::removeExcludePairs(Molecule* mol) {
515	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
516	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
517		std::vector<Bond*>::iterator bondIter;
518		std::vector<Bend*>::iterator bendIter;
519		std::vector<Torsion*>::iterator torsionIter;
520	+	std::vector<Inversion*>::iterator inversionIter;
521		Bond* bond;
522		Bend* bend;
523		Torsion* torsion;
524	+	Inversion* inversion;
525		int a;
526		int b;
527		int c;
528		int d;
529
530		std::map<int, std::set<int> > atomGroups;
482	–
531		Molecule::RigidBodyIterator rbIter;
532		RigidBody* rb;
533		Molecule::IntegrableObjectIterator ii;
534		StuntDouble* integrableObject;
535
536	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
537	<	integrableObject = mol->nextIntegrableObject(ii)) {
538	<
536	>	for (integrableObject = mol->beginIntegrableObject(ii);
537	>	integrableObject != NULL;
538	>	integrableObject = mol->nextIntegrableObject(ii)) {
539	>
540		if (integrableObject->isRigidBody()) {
541	<	rb = static_cast<RigidBody*>(integrableObject);
542	<	std::vector<Atom*> atoms = rb->getAtoms();
543	<	std::set<int> rigidAtoms;
544	<	for (int i = 0; i < atoms.size(); ++i) {
545	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
546	<	}
547	<	for (int i = 0; i < atoms.size(); ++i) {
548	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
549	<	}
541	>	rb = static_cast<RigidBody*>(integrableObject);
542	>	std::vector<Atom*> atoms = rb->getAtoms();
543	>	std::set<int> rigidAtoms;
544	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
545	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
546	>	}
547	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
549	>	}
550		} else {
551		std::set<int> oneAtomSet;
552		oneAtomSet.insert(integrableObject->getGlobalIndex());
#	Line 505 | Line 554 | namespace oopse {
554		}
555		}
556
557	<
558	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
557	>	for (bond= mol->beginBond(bondIter); bond != NULL;
558	>	bond = mol->nextBond(bondIter)) {
559	>
560		a = bond->getAtomA()->getGlobalIndex();
561	<	b = bond->getAtomB()->getGlobalIndex();
562	<	exclude_.removePair(a, b);
561	>	b = bond->getAtomB()->getGlobalIndex();
562	>
563	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
564	>	oneTwoInteractions_.removePair(a, b);
565	>	} else {
566	>	excludedInteractions_.removePair(a, b);
567	>	}
568		}
569
570	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
570	>	for (bend= mol->beginBend(bendIter); bend != NULL;
571	>	bend = mol->nextBend(bendIter)) {
572	>
573		a = bend->getAtomA()->getGlobalIndex();
574		b = bend->getAtomB()->getGlobalIndex();
575		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);
576
577	<	//exclude_.removePair(a, b);
578	<	//exclude_.removePair(a, c);
579	<	//exclude_.removePair(b, c);
577	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
578	>	oneTwoInteractions_.removePair(a, b);
579	>	oneTwoInteractions_.removePair(b, c);
580	>	} else {
581	>	excludedInteractions_.removePair(a, b);
582	>	excludedInteractions_.removePair(b, c);
583	>	}
584	>
585	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	>	oneThreeInteractions_.removePair(a, c);
587	>	} else {
588	>	excludedInteractions_.removePair(a, c);
589	>	}
590		}
591
592	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
592	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
593	>	torsion = mol->nextTorsion(torsionIter)) {
594	>
595		a = torsion->getAtomA()->getGlobalIndex();
596		b = torsion->getAtomB()->getGlobalIndex();
597		c = torsion->getAtomC()->getGlobalIndex();
598	<	d = torsion->getAtomD()->getGlobalIndex();
598	>	d = torsion->getAtomD()->getGlobalIndex();
599	>
600	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
601	>	oneTwoInteractions_.removePair(a, b);
602	>	oneTwoInteractions_.removePair(b, c);
603	>	oneTwoInteractions_.removePair(c, d);
604	>	} else {
605	>	excludedInteractions_.removePair(a, b);
606	>	excludedInteractions_.removePair(b, c);
607	>	excludedInteractions_.removePair(c, d);
608	>	}
609
610	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
611	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
612	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
613	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
610	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
611	>	oneThreeInteractions_.removePair(a, c);
612	>	oneThreeInteractions_.removePair(b, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(b, d);
616	>	}
617
618	<	exclude_.removePairs(rigidSetA, rigidSetB);
619	<	exclude_.removePairs(rigidSetA, rigidSetC);
620	<	exclude_.removePairs(rigidSetA, rigidSetD);
621	<	exclude_.removePairs(rigidSetB, rigidSetC);
622	<	exclude_.removePairs(rigidSetB, rigidSetD);
623	<	exclude_.removePairs(rigidSetC, rigidSetD);
618	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
619	>	oneFourInteractions_.removePair(a, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, d);
622	>	}
623	>	}
624
625	<	/*
626	<	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());
625	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
626	>	inversion = mol->nextInversion(inversionIter)) {
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	>	a = inversion->getAtomA()->getGlobalIndex();
629	>	b = inversion->getAtomB()->getGlobalIndex();
630	>	c = inversion->getAtomC()->getGlobalIndex();
631	>	d = inversion->getAtomD()->getGlobalIndex();
632	>
633	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
634	>	oneTwoInteractions_.removePair(a, b);
635	>	oneTwoInteractions_.removePair(a, c);
636	>	oneTwoInteractions_.removePair(a, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, b);
639	>	excludedInteractions_.removePair(a, c);
640	>	excludedInteractions_.removePair(a, d);
641	>	}
642	>
643	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
644	>	oneThreeInteractions_.removePair(b, c);
645	>	oneThreeInteractions_.removePair(b, d);
646	>	oneThreeInteractions_.removePair(c, d);
647	>	} else {
648	>	excludedInteractions_.removePair(b, c);
649	>	excludedInteractions_.removePair(b, d);
650	>	excludedInteractions_.removePair(c, d);
651	>	}
652		}
653
654	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
654	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
655	>	rb = mol->nextRigidBody(rbIter)) {
656		std::vector<Atom*> atoms = rb->getAtoms();
657	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
658	<	for (int j = i + 1; j < atoms.size(); ++j) {
657	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
658	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
659		a = atoms[i]->getGlobalIndex();
660		b = atoms[j]->getGlobalIndex();
661	<	exclude_.removePair(a, b);
661	>	excludedInteractions_.removePair(a, b);
662		}
663		}
664		}
665	<
665	>
666		}
667	<
668	<
667	>
668	>
669		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
670		int curStampId;
671	<
671	>
672		//index from 0
673		curStampId = moleculeStamps_.size();
674
#	Line 674 | Line 760 | namespace oopse {
760		useRF = 0;
761		useSF = 0;
762		useSP = 0;
763	+	useBoxDipole = 0;
764
678	–
765		if (simParams_->haveElectrostaticSummationMethod()) {
766		std::string myMethod = simParams_->getElectrostaticSummationMethod();
767		toUpper(myMethod);
#	Line 775 | Line 861 | namespace oopse {
861		MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862
863		#endif
778	–
864		fInfo_.SIM_uses_PBC = usePBC;
865		fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
866		fInfo_.SIM_uses_LennardJones = useLennardJones;
#	Line 798 | Line 883 | namespace oopse {
883
884		void SimInfo::setupFortranSim() {
885		int isError;
886	<	int nExclude;
886	>	int nExclude, nOneTwo, nOneThree, nOneFour;
887		std::vector<int> fortranGlobalGroupMembership;
888
804	–	nExclude = exclude_.getSize();
889		isError = 0;
890
891		//globalGroupMembership_ is filled by SimCreator
#	Line 833 | Line 917 | namespace oopse {
917		else
918		mfact.push_back( 1.0 );
919		}
836	–
920		}
921		}
922
#	Line 857 | Line 940 | namespace oopse {
940		}
941
942		//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);
943
944	<	if( isError ){
944	>	nExclude = excludedInteractions_.getSize();
945	>	nOneTwo = oneTwoInteractions_.getSize();
946	>	nOneThree = oneThreeInteractions_.getSize();
947	>	nOneFour = oneFourInteractions_.getSize();
948
949	+	int* excludeList = excludedInteractions_.getPairList();
950	+	int* oneTwoList = oneTwoInteractions_.getPairList();
951	+	int* oneThreeList = oneThreeInteractions_.getPairList();
952	+	int* oneFourList = oneFourInteractions_.getPairList();
953	+
954	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
955	+	&nExclude, excludeList,
956	+	&nOneTwo, oneTwoList,
957	+	&nOneThree, oneThreeList,
958	+	&nOneFour, oneFourList,
959	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
960	+	&fortranGlobalGroupMembership[0], &isError);
961	+
962	+	if( isError ){
963	+
964		sprintf( painCave.errMsg,
965		"There was an error setting the simulation information in fortran.\n" );
966		painCave.isFatal = 1;
967	<	painCave.severity = OOPSE_ERROR;
967	>	painCave.severity = OPENMD_ERROR;
968		simError();
969		}
970	<
971	<	#ifdef IS_MPI
970	>
971	>
972		sprintf( checkPointMsg,
973		"succesfully sent the simulation information to fortran.\n");
974	<	MPIcheckPoint();
975	<	#endif // is_mpi
976	<
974	>
975	>	errorCheckPoint();
976	>
977		// Setup number of neighbors in neighbor list if present
978		if (simParams_->haveNeighborListNeighbors()) {
979		int nlistNeighbors = simParams_->getNeighborListNeighbors();
#	Line 889 | Line 984 | namespace oopse {
984		}
985
986
892	–	#ifdef IS_MPI
987		void SimInfo::setupFortranParallel() {
988	<
988	>	#ifdef IS_MPI
989		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
990		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
991		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 941 | Line 1035 | namespace oopse {
1035		}
1036
1037		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1038	<	MPIcheckPoint();
945	<
1038	>	errorCheckPoint();
1039
1040	+	#endif
1041		}
1042
949	–	#endif
950	–
1043		void SimInfo::setupCutoff() {
1044
1045		ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
#	Line 956 | Line 1048 | namespace oopse {
1048		int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1049
1050		// Set LJ shifting bools to false
1051	<	ljsp_ = false;
1052	<	ljsf_ = false;
1051	>	ljsp_ = 0;
1052	>	ljsf_ = 0;
1053
1054		std::string myPolicy;
1055		if (forceFieldOptions_.haveCutoffPolicy()){
#	Line 1008 | Line 1100 | namespace oopse {
1100		rsw_ = 0.85 * rcut_;
1101		sprintf(painCave.errMsg,
1102		"SimCreator Warning: No value was set for the switchingRadius.\n"
1103	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1103	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1104		"\tswitchingRadius = %f. for this simulation\n", rsw_);
1105		painCave.isFatal = 0;
1106		simError();
#	Line 1016 | Line 1108 | namespace oopse {
1108		rsw_ = rcut_;
1109		sprintf(painCave.errMsg,
1110		"SimCreator Warning: No value was set for the switchingRadius.\n"
1111	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1111	>	"\tOpenMD will use the same value as the cutoffRadius.\n"
1112		"\tswitchingRadius = %f. for this simulation\n", rsw_);
1113		painCave.isFatal = 0;
1114		simError();
#	Line 1028 | Line 1120 | namespace oopse {
1120		toUpper(myMethod);
1121
1122		if (myMethod == "SHIFTED_POTENTIAL") {
1123	<	ljsp_ = true;
1123	>	ljsp_ = 1;
1124		} else if (myMethod == "SHIFTED_FORCE") {
1125	<	ljsf_ = true;
1125	>	ljsf_ = 1;
1126		}
1127		}
1128	+
1129		notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1130
1131		} else {
#	Line 1041 | Line 1134 | namespace oopse {
1134		if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1135		sprintf(painCave.errMsg,
1136		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1137	<	"\tOOPSE will use a default value of 15.0 angstroms"
1137	>	"\tOpenMD will use a default value of 15.0 angstroms"
1138		"\tfor the cutoffRadius.\n");
1139		painCave.isFatal = 0;
1140		simError();
#	Line 1050 | Line 1143 | namespace oopse {
1143		if (simParams_->haveElectrostaticSummationMethod()) {
1144		std::string myMethod = simParams_->getElectrostaticSummationMethod();
1145		toUpper(myMethod);
1146	<
1147	<	// For the time being, we're tethering the LJ shifted behavior to the
1148	<	// electrostaticSummationMethod keyword options
1146	>
1147	>	// For the time being, we're tethering the LJ shifted behavior to the
1148	>	// electrostaticSummationMethod keyword options
1149		if (myMethod == "SHIFTED_POTENTIAL") {
1150	<	ljsp_ = true;
1150	>	ljsp_ = 1;
1151		} else if (myMethod == "SHIFTED_FORCE") {
1152	<	ljsf_ = true;
1152	>	ljsf_ = 1;
1153		}
1154		if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1155		if (simParams_->haveSwitchingRadius()){
#	Line 1075 | Line 1168 | namespace oopse {
1168		} else {
1169		sprintf(painCave.errMsg,
1170		"SimCreator Warning: No value was set for switchingRadius.\n"
1171	<	"\tOOPSE will use a default value of\n"
1171	>	"\tOpenMD will use a default value of\n"
1172		"\t0.85 * cutoffRadius for the switchingRadius\n");
1173		painCave.isFatal = 0;
1174		simError();
1175		rsw_ = 0.85 * rcut_;
1176		}
1177
1178	+	Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1179		notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1180
1181		} else {
#	Line 1097 | Line 1191 | namespace oopse {
1191		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1192
1193		int errorOut;
1194	<	int esm =  NONE;
1195	<	int sm = UNDAMPED;
1194	>	ElectrostaticSummationMethod esm = NONE;
1195	>	ElectrostaticScreeningMethod sm = UNDAMPED;
1196		RealType alphaVal;
1197		RealType dielectric;
1198
#	Line 1185 | Line 1279 | namespace oopse {
1279		}
1280		}
1281
1282	<	// let's pass some summation method variables to fortran
1283	<	setElectrostaticSummationMethod( &esm );
1284	<	setFortranElectrostaticMethod( &esm );
1285	<	setScreeningMethod( &sm );
1286	<	setDampingAlpha( &alphaVal );
1193	<	setReactionFieldDielectric( &dielectric );
1282	>
1283	>	Electrostatic::setElectrostaticSummationMethod( esm );
1284	>	Electrostatic::setElectrostaticScreeningMethod( sm );
1285	>	Electrostatic::setDampingAlpha( alphaVal );
1286	>	Electrostatic::setReactionFieldDielectric( dielectric );
1287		initFortranFF( &errorOut );
1288		}
1289
#	Line 1377 | Line 1470 | namespace oopse {
1470
1471
1472		[  Ixx -Ixy  -Ixz ]
1473	<	J =| -Iyx  Iyy  -Iyz |
1473	>	J =| -Iyx  Iyy  -Iyz |
1474		[ -Izx -Iyz   Izz ]
1475		*/
1476
#	Line 1536 | Line 1629 | namespace oopse {
1629		return sdByGlobalIndex_.at(index);
1630		}
1631		*/
1632	<	}//end namespace oopse
1632	>	}//end namespace OpenMD
1633

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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