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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1503 by gezelter, Sat Oct 2 19:54:41 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/electrostatic_interface.h"
60	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61		#include "UseTheForce/DarkSide/switcheroo_interface.h"
62		#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
#	Line 67 | Line 65
65		#include "io/ForceFieldOptions.hpp"
66		#include "UseTheForce/ForceField.hpp"
67
68	+
69		#ifdef IS_MPI
70		#include "UseTheForce/mpiComponentPlan.h"
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 88 | 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) {
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;
98		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
#	Line 99 | 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 153 | Line 155 | namespace oopse {
155		+ nGlobalRigidBodies_;
156
157		nGlobalMols_ = molStampIds_.size();
156	–
157	–	#ifdef IS_MPI
158		molToProcMap_.resize(nGlobalMols_);
159	–	#endif
160	–
159		}
160
161		SimInfo::~SimInfo() {
#	Line 195 | 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 220 | 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 351 | 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
393	–
394	–
395	–	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();
405	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
406	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
407	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
408	–
409	–	exclude_.addPairs(rigidSetA, rigidSetB);
410	–	exclude_.addPairs(rigidSetA, rigidSetC);
411	–	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();
423	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
424	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
425	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
426	<	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);
448	<	exclude_.addPair(b, d);
449	<	exclude_.addPair(c, d);
450	<	*/
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;
479	–
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 502 | 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();
516	–
517	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
518	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
519	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
520	–
521	–	exclude_.removePairs(rigidSetA, rigidSetB);
522	–	exclude_.removePairs(rigidSetA, rigidSetC);
523	–	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());
550	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
551	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
552	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
553	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
554	<	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);
560	<	exclude_.removePair(b, c);
561	<	exclude_.removePair(b, d);
562	<	exclude_.removePair(c, d);
563	<	*/
564	<	}
628	>	a = inversion->getAtomA()->getGlobalIndex();
629	>	b = inversion->getAtomB()->getGlobalIndex();
630	>	c = inversion->getAtomC()->getGlobalIndex();
631	>	d = inversion->getAtomD()->getGlobalIndex();
632
633	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
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;
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 664 | Line 753 | namespace oopse {
753		int useSF;
754		int useSP;
755		int useBoxDipole;
756	+
757		std::string myMethod;
758
759		// set the useRF logical
760		useRF = 0;
761		useSF = 0;
762	+	useSP = 0;
763	+	useBoxDipole = 0;
764
765
766		if (simParams_->haveElectrostaticSummationMethod()) {
767		std::string myMethod = simParams_->getElectrostaticSummationMethod();
768		toUpper(myMethod);
769		if (myMethod == "REACTION_FIELD"){
770	<	useRF=1;
770	>	useRF = 1;
771		} else if (myMethod == "SHIFTED_FORCE"){
772		useSF = 1;
773		} else if (myMethod == "SHIFTED_POTENTIAL"){
#	Line 687 | Line 779 | namespace oopse {
779		if (simParams_->getAccumulateBoxDipole())
780		useBoxDipole = 1;
781
782	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
783	+
784		//loop over all of the atom types
785		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
786		useLennardJones |= (*i)->isLennardJones();
#	Line 764 | Line 858 | namespace oopse {
858		temp = useBoxDipole;
859		MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860
861	+	temp = useAtomicVirial_;
862	+	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	+
864		#endif
865
866		fInfo_.SIM_uses_PBC = usePBC;
#	Line 783 | Line 880 | namespace oopse {
880		fInfo_.SIM_uses_SF = useSF;
881		fInfo_.SIM_uses_SP = useSP;
882		fInfo_.SIM_uses_BoxDipole = useBoxDipole;
883	+	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
884		}
885
886		void SimInfo::setupFortranSim() {
887		int isError;
888	<	int nExclude;
888	>	int nExclude, nOneTwo, nOneThree, nOneFour;
889		std::vector<int> fortranGlobalGroupMembership;
890
793	–	nExclude = exclude_.getSize();
891		isError = 0;
892
893		//globalGroupMembership_ is filled by SimCreator
#	Line 822 | Line 919 | namespace oopse {
919		else
920		mfact.push_back( 1.0 );
921		}
825	–
922		}
923		}
924
#	Line 846 | Line 942 | namespace oopse {
942		}
943
944		//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);
945
946	<	if( isError ){
946	>	nExclude = excludedInteractions_.getSize();
947	>	nOneTwo = oneTwoInteractions_.getSize();
948	>	nOneThree = oneThreeInteractions_.getSize();
949	>	nOneFour = oneFourInteractions_.getSize();
950
951	+	int* excludeList = excludedInteractions_.getPairList();
952	+	int* oneTwoList = oneTwoInteractions_.getPairList();
953	+	int* oneThreeList = oneThreeInteractions_.getPairList();
954	+	int* oneFourList = oneFourInteractions_.getPairList();
955	+
956	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
957	+	&nExclude, excludeList,
958	+	&nOneTwo, oneTwoList,
959	+	&nOneThree, oneThreeList,
960	+	&nOneFour, oneFourList,
961	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
962	+	&fortranGlobalGroupMembership[0], &isError);
963	+
964	+	if( isError ){
965	+
966		sprintf( painCave.errMsg,
967		"There was an error setting the simulation information in fortran.\n" );
968		painCave.isFatal = 1;
969	<	painCave.severity = OOPSE_ERROR;
969	>	painCave.severity = OPENMD_ERROR;
970		simError();
971		}
972	<
973	<	#ifdef IS_MPI
972	>
973	>
974		sprintf( checkPointMsg,
975		"succesfully sent the simulation information to fortran.\n");
976	<	MPIcheckPoint();
977	<	#endif // is_mpi
976	>
977	>	errorCheckPoint();
978	>
979	>	// Setup number of neighbors in neighbor list if present
980	>	if (simParams_->haveNeighborListNeighbors()) {
981	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
982	>	setNeighbors(&nlistNeighbors);
983	>	}
984	>
985	>
986		}
987
988
873	–	#ifdef IS_MPI
989		void SimInfo::setupFortranParallel() {
990	<
990	>	#ifdef IS_MPI
991		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
992		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
993		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 922 | Line 1037 | namespace oopse {
1037		}
1038
1039		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1040	<	MPIcheckPoint();
1040	>	errorCheckPoint();
1041
1042	<
1042	>	#endif
1043		}
1044
930	–	#endif
931	–
1045		void SimInfo::setupCutoff() {
1046
1047		ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
#	Line 936 | Line 1049 | namespace oopse {
1049		// Check the cutoff policy
1050		int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1051
1052	+	// Set LJ shifting bools to false
1053	+	ljsp_ = 0;
1054	+	ljsf_ = 0;
1055	+
1056		std::string myPolicy;
1057		if (forceFieldOptions_.haveCutoffPolicy()){
1058		myPolicy = forceFieldOptions_.getCutoffPolicy();
#	Line 985 | Line 1102 | namespace oopse {
1102		rsw_ = 0.85 * rcut_;
1103		sprintf(painCave.errMsg,
1104		"SimCreator Warning: No value was set for the switchingRadius.\n"
1105	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1105	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1106		"\tswitchingRadius = %f. for this simulation\n", rsw_);
1107		painCave.isFatal = 0;
1108		simError();
#	Line 993 | Line 1110 | namespace oopse {
1110		rsw_ = rcut_;
1111		sprintf(painCave.errMsg,
1112		"SimCreator Warning: No value was set for the switchingRadius.\n"
1113	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1113	>	"\tOpenMD will use the same value as the cutoffRadius.\n"
1114		"\tswitchingRadius = %f. for this simulation\n", rsw_);
1115		painCave.isFatal = 0;
1116		simError();
1117		}
1118		}
1119	+
1120	+	if (simParams_->haveElectrostaticSummationMethod()) {
1121	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1122	+	toUpper(myMethod);
1123	+
1124	+	if (myMethod == "SHIFTED_POTENTIAL") {
1125	+	ljsp_ = 1;
1126	+	} else if (myMethod == "SHIFTED_FORCE") {
1127	+	ljsf_ = 1;
1128	+	}
1129	+	}
1130	+
1131	+	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1132
1003	–	notifyFortranCutoffs(&rcut_, &rsw_);
1004	–
1133		} else {
1134
1135		// For electrostatic atoms, we'll assume a large safe value:
1136		if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1137		sprintf(painCave.errMsg,
1138		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1139	<	"\tOOPSE will use a default value of 15.0 angstroms"
1139	>	"\tOpenMD will use a default value of 15.0 angstroms"
1140		"\tfor the cutoffRadius.\n");
1141		painCave.isFatal = 0;
1142		simError();
#	Line 1017 | Line 1145 | namespace oopse {
1145		if (simParams_->haveElectrostaticSummationMethod()) {
1146		std::string myMethod = simParams_->getElectrostaticSummationMethod();
1147		toUpper(myMethod);
1148	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1148	>
1149	>	// For the time being, we're tethering the LJ shifted behavior to the
1150	>	// electrostaticSummationMethod keyword options
1151	>	if (myMethod == "SHIFTED_POTENTIAL") {
1152	>	ljsp_ = 1;
1153	>	} else if (myMethod == "SHIFTED_FORCE") {
1154	>	ljsf_ = 1;
1155	>	}
1156	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1157		if (simParams_->haveSwitchingRadius()){
1158		sprintf(painCave.errMsg,
1159		"SimInfo Warning: A value was set for the switchingRadius\n"
#	Line 1034 | Line 1170 | namespace oopse {
1170		} else {
1171		sprintf(painCave.errMsg,
1172		"SimCreator Warning: No value was set for switchingRadius.\n"
1173	<	"\tOOPSE will use a default value of\n"
1173	>	"\tOpenMD will use a default value of\n"
1174		"\t0.85 * cutoffRadius for the switchingRadius\n");
1175		painCave.isFatal = 0;
1176		simError();
1177		rsw_ = 0.85 * rcut_;
1178		}
1179	<	notifyFortranCutoffs(&rcut_, &rsw_);
1179	>
1180	>	Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1181	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1182	>
1183		} else {
1184		// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1185		// We'll punt and let fortran figure out the cutoffs later.
#	Line 1054 | Line 1193 | namespace oopse {
1193		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1194
1195		int errorOut;
1196	<	int esm =  NONE;
1197	<	int sm = UNDAMPED;
1196	>	ElectrostaticSummationMethod esm = NONE;
1197	>	ElectrostaticScreeningMethod sm = UNDAMPED;
1198		RealType alphaVal;
1199		RealType dielectric;
1200
#	Line 1125 | Line 1264 | namespace oopse {
1264		"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1265		painCave.isFatal = 0;
1266		simError();
1267	+	} else {
1268	+	alphaVal = simParams_->getDampingAlpha();
1269		}
1270	+
1271		} else {
1272		// throw error
1273		sprintf( painCave.errMsg,
#	Line 1139 | Line 1281 | namespace oopse {
1281		}
1282		}
1283
1284	<	// let's pass some summation method variables to fortran
1285	<	setElectrostaticSummationMethod( &esm );
1286	<	setFortranElectrostaticMethod( &esm );
1287	<	setScreeningMethod( &sm );
1288	<	setDampingAlpha( &alphaVal );
1147	<	setReactionFieldDielectric( &dielectric );
1284	>
1285	>	Electrostatic::setElectrostaticSummationMethod( esm );
1286	>	Electrostatic::setElectrostaticScreeningMethod( sm );
1287	>	Electrostatic::setDampingAlpha( alphaVal );
1288	>	Electrostatic::setReactionFieldDielectric( dielectric );
1289		initFortranFF( &errorOut );
1290		}
1291
#	Line 1440 | Line 1581 | namespace oopse {
1581
1582		void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1583		IOIndexToIntegrableObject= v;
1584	+	}
1585	+
1586	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1587	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1588	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1589	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1590	+	*/
1591	+	void SimInfo::getGyrationalVolume(RealType &volume){
1592	+	Mat3x3d intTensor;
1593	+	RealType det;
1594	+	Vector3d dummyAngMom;
1595	+	RealType sysconstants;
1596	+	RealType geomCnst;
1597	+
1598	+	geomCnst = 3.0/2.0;
1599	+	/* Get the inertial tensor and angular momentum for free*/
1600	+	getInertiaTensor(intTensor,dummyAngMom);
1601	+
1602	+	det = intTensor.determinant();
1603	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1604	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1605	+	return;
1606		}
1607
1608	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1609	+	Mat3x3d intTensor;
1610	+	Vector3d dummyAngMom;
1611	+	RealType sysconstants;
1612	+	RealType geomCnst;
1613	+
1614	+	geomCnst = 3.0/2.0;
1615	+	/* Get the inertial tensor and angular momentum for free*/
1616	+	getInertiaTensor(intTensor,dummyAngMom);
1617	+
1618	+	detI = intTensor.determinant();
1619	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1620	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1621	+	return;
1622	+	}
1623		/*
1624		void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1625		assert( v.size() == nAtoms_ + nRigidBodies_);
#	Line 1453 | Line 1631 | namespace oopse {
1631		return sdByGlobalIndex_.at(index);
1632		}
1633		*/
1634	<	}//end namespace oopse
1634	>	}//end namespace OpenMD
1635

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC

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