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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 878 by chrisfen, Wed Feb 1 20:54:46 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 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"
57	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	–	#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 66 | 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 84 | Line 84 | namespace oopse {
84
85		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86		forceField_(ff), simParams_(simParams),
87	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
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) {
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 98 | 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 152 | Line 155 | namespace oopse {
155		+ nGlobalRigidBodies_;
156
157		nGlobalMols_ = molStampIds_.size();
155	–
156	–	#ifdef IS_MPI
158		molToProcMap_.resize(nGlobalMols_);
158	–	#endif
159	–
159		}
160
161		SimInfo::~SimInfo() {
#	Line 194 | 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 219 | 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 290 | Line 291 | namespace oopse {
291
292		}
293
294	+	int SimInfo::getFdf() {
295	+	#ifdef IS_MPI
296	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297	+	#else
298	+	fdf_ = fdf_local;
299	+	#endif
300	+	return fdf_;
301	+	}
302	+
303		void SimInfo::calcNdfRaw() {
304		int ndfRaw_local;
305
#	Line 341 | 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
407	<
407	>	a = bond->getAtomA()->getGlobalIndex();
408	>	b = bond->getAtomB()->getGlobalIndex();
409
410	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
411	<	a = bond->getAtomA()->getGlobalIndex();
412	<	b = bond->getAtomB()->getGlobalIndex();
413	<	exclude_.addPair(a, b);
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();
395	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
396	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
397	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
398	–
399	–	exclude_.addPairs(rigidSetA, rigidSetB);
400	–	exclude_.addPairs(rigidSetA, rigidSetC);
401	–	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();
413	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
414	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
415	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
416	<	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);
438	<	exclude_.addPair(b, d);
439	<	exclude_.addPair(c, d);
440	<	*/
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;
469	–
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 492 | 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();
506	–
507	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
508	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
509	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
510	–
511	–	exclude_.removePairs(rigidSetA, rigidSetB);
512	–	exclude_.removePairs(rigidSetA, rigidSetC);
513	–	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());
540	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
541	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
542	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
543	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
544	<	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);
550	<	exclude_.removePair(b, c);
551	<	exclude_.removePair(b, d);
552	<	exclude_.removePair(c, d);
553	<	*/
554	<	}
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 591 | Line 690 | namespace oopse {
690		/** @deprecate */
691		int isError = 0;
692
693	+	setupCutoff();
694	+
695		setupElectrostaticSummationMethod( isError );
696		setupSwitchingFunction();
697	+	setupAccumulateBoxDipole();
698
699		if(isError){
700		sprintf( painCave.errMsg,
#	Line 600 | Line 702 | namespace oopse {
702		painCave.isFatal = 1;
703		simError();
704		}
603	–
604	–
605	–	setupCutoff();
705
706		calcNdf();
707		calcNdfRaw();
#	Line 652 | Line 751 | namespace oopse {
751		int usePBC = simParams_->getUsePeriodicBoundaryConditions();
752		int useRF;
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;
771	<	} else {
772	<	if (myMethod == "SHIFTED_FORCE") {
773	<	useSF = 1;
774	<	}
769	>	if (myMethod == "REACTION_FIELD"){
770	>	useRF = 1;
771	>	} else if (myMethod == "SHIFTED_FORCE"){
772	>	useSF = 1;
773	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
774	>	useSP = 1;
775		}
776		}
777	+
778	+	if (simParams_->haveAccumulateBoxDipole())
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 740 | Line 850 | namespace oopse {
850		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851
852		temp = useSF;
853	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854
855	+	temp = useSP;
856	+	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	+
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 759 | Line 878 | namespace oopse {
878		fInfo_.SIM_uses_FLARB = useFLARB;
879		fInfo_.SIM_uses_RF = useRF;
880		fInfo_.SIM_uses_SF = useSF;
881	<
882	<	if( myMethod == "REACTION_FIELD") {
883	<
765	<	if (simParams_->haveDielectric()) {
766	<	fInfo_.dielect = simParams_->getDielectric();
767	<	} else {
768	<	sprintf(painCave.errMsg,
769	<	"SimSetup Error: No Dielectric constant was set.\n"
770	<	"\tYou are trying to use Reaction Field without"
771	<	"\tsetting a dielectric constant!\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
775	<	}
776	<
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
784	–	nExclude = exclude_.getSize();
891		isError = 0;
892
893		//globalGroupMembership_ is filled by SimCreator
#	Line 790 | Line 896 | namespace oopse {
896		}
897
898		//calculate mass ratio of cutoff group
899	<	std::vector<double> mfact;
899	>	std::vector<RealType> mfact;
900		SimInfo::MoleculeIterator mi;
901		Molecule* mol;
902		Molecule::CutoffGroupIterator ci;
903		CutoffGroup* cg;
904		Molecule::AtomIterator ai;
905		Atom* atom;
906	<	double totalMass;
906	>	RealType totalMass;
907
908		//to avoid memory reallocation, reserve enough space for mfact
909		mfact.reserve(getNCutoffGroups());
#	Line 813 | Line 919 | namespace oopse {
919		else
920		mfact.push_back( 1.0 );
921		}
816	–
922		}
923		}
924
#	Line 837 | Line 942 | namespace oopse {
942		}
943
944		//setup fortran simulation
840	–	int nGlobalExcludes = 0;
841	–	int* globalExcludes = NULL;
842	–	int* excludeList = exclude_.getExcludeList();
843	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
844	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
845	–	&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
864	–	#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 913 | Line 1037 | namespace oopse {
1037		}
1038
1039		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1040	<	MPIcheckPoint();
1040	>	errorCheckPoint();
1041
1042	<
1042	>	#endif
1043		}
1044
921	–	#endif
922	–
1045		void SimInfo::setupCutoff() {
1046
1047		ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
#	Line 927 | 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 957 | Line 1083 | namespace oopse {
1083		notifyFortranCutoffPolicy(&cp);
1084
1085		// Check the Skin Thickness for neighborlists
1086	<	double skin;
1086	>	RealType skin;
1087		if (simParams_->haveSkinThickness()) {
1088		skin = simParams_->getSkinThickness();
1089		notifyFortranSkinThickness(&skin);
#	Line 976 | 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\% of the cutoffRadius"
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 984 | 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	<	notifyFortranCutoffs(&rcut_, &rsw_);
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
1133		} else {
1134
#	Line 998 | Line 1136 | namespace oopse {
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 1007 | 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 1024 | 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 1044 | Line 1193 | namespace oopse {
1193		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1194
1195		int errorOut;
1196	<	int esm =  NONE;
1197	<	int sm = UNDAMPED;
1198	<	double alphaVal;
1199	<	double dielectric;
1200	<
1196	>	ElectrostaticSummationMethod esm = NONE;
1197	>	ElectrostaticScreeningMethod sm = UNDAMPED;
1198	>	RealType alphaVal;
1199	>	RealType dielectric;
1200	>
1201		errorOut = isError;
1053	–	alphaVal = simParams_->getDampingAlpha();
1054	–	dielectric = simParams_->getDielectric();
1202
1203		if (simParams_->haveElectrostaticSummationMethod()) {
1204		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 1068 | Line 1215 | namespace oopse {
1215		if (myMethod == "SHIFTED_FORCE") {
1216		esm = SHIFTED_FORCE;
1217		} else {
1218	<	if (myMethod == "REACTION_FIELD") {
1218	>	if (myMethod == "REACTION_FIELD") {
1219		esm = REACTION_FIELD;
1220	+	dielectric = simParams_->getDielectric();
1221	+	if (!simParams_->haveDielectric()) {
1222	+	// throw warning
1223	+	sprintf( painCave.errMsg,
1224	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1225	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1226	+	painCave.isFatal = 0;
1227	+	simError();
1228	+	}
1229		} else {
1230		// throw error
1231		sprintf( painCave.errMsg,
#	Line 1096 | Line 1252 | namespace oopse {
1252		if (myScreen == "DAMPED") {
1253		sm = DAMPED;
1254		if (!simParams_->haveDampingAlpha()) {
1255	<	//throw error
1255	>	// first set a cutoff dependent alpha value
1256	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1257	>	alphaVal = 0.5125 - rcut_* 0.025;
1258	>	// for values rcut > 20.5, alpha is zero
1259	>	if (alphaVal < 0) alphaVal = 0;
1260	>
1261	>	// throw warning
1262		sprintf( painCave.errMsg,
1263		"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1264	<	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
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 1116 | 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 );
1124	<	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 1151 | Line 1315 | namespace oopse {
1315
1316		}
1317
1318	+	void SimInfo::setupAccumulateBoxDipole() {
1319	+
1320	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1321	+	if ( simParams_->haveAccumulateBoxDipole() )
1322	+	if ( simParams_->getAccumulateBoxDipole() ) {
1323	+	setAccumulateBoxDipole();
1324	+	calcBoxDipole_ = true;
1325	+	}
1326	+
1327	+	}
1328	+
1329		void SimInfo::addProperty(GenericData* genData) {
1330		properties_.addProperty(genData);
1331		}
#	Line 1207 | Line 1382 | namespace oopse {
1382		Molecule* mol;
1383
1384		Vector3d comVel(0.0);
1385	<	double totalMass = 0.0;
1385	>	RealType totalMass = 0.0;
1386
1387
1388		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1389	<	double mass = mol->getMass();
1389	>	RealType mass = mol->getMass();
1390		totalMass += mass;
1391		comVel += mass * mol->getComVel();
1392		}
1393
1394		#ifdef IS_MPI
1395	<	double tmpMass = totalMass;
1395	>	RealType tmpMass = totalMass;
1396		Vector3d tmpComVel(comVel);
1397	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1398	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1397	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399		#endif
1400
1401		comVel /= totalMass;
#	Line 1233 | Line 1408 | namespace oopse {
1408		Molecule* mol;
1409
1410		Vector3d com(0.0);
1411	<	double totalMass = 0.0;
1411	>	RealType totalMass = 0.0;
1412
1413		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1414	<	double mass = mol->getMass();
1414	>	RealType mass = mol->getMass();
1415		totalMass += mass;
1416		com += mass * mol->getCom();
1417		}
1418
1419		#ifdef IS_MPI
1420	<	double tmpMass = totalMass;
1420	>	RealType tmpMass = totalMass;
1421		Vector3d tmpCom(com);
1422	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1423	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1422	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1423	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1424		#endif
1425
1426		com /= totalMass;
#	Line 1269 | Line 1444 | namespace oopse {
1444		Molecule* mol;
1445
1446
1447	<	double totalMass = 0.0;
1447	>	RealType totalMass = 0.0;
1448
1449
1450		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1451	<	double mass = mol->getMass();
1451	>	RealType mass = mol->getMass();
1452		totalMass += mass;
1453		com += mass * mol->getCom();
1454		comVel += mass * mol->getComVel();
1455		}
1456
1457		#ifdef IS_MPI
1458	<	double tmpMass = totalMass;
1458	>	RealType tmpMass = totalMass;
1459		Vector3d tmpCom(com);
1460		Vector3d tmpComVel(comVel);
1461	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1462	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1463	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1461	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1462	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1463	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1464		#endif
1465
1466		com /= totalMass;
#	Line 1304 | Line 1479 | namespace oopse {
1479		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1480
1481
1482	<	double xx = 0.0;
1483	<	double yy = 0.0;
1484	<	double zz = 0.0;
1485	<	double xy = 0.0;
1486	<	double xz = 0.0;
1487	<	double yz = 0.0;
1482	>	RealType xx = 0.0;
1483	>	RealType yy = 0.0;
1484	>	RealType zz = 0.0;
1485	>	RealType xy = 0.0;
1486	>	RealType xz = 0.0;
1487	>	RealType yz = 0.0;
1488		Vector3d com(0.0);
1489		Vector3d comVel(0.0);
1490
#	Line 1321 | Line 1496 | namespace oopse {
1496		Vector3d thisq(0.0);
1497		Vector3d thisv(0.0);
1498
1499	<	double thisMass = 0.0;
1499	>	RealType thisMass = 0.0;
1500
1501
1502
#	Line 1359 | Line 1534 | namespace oopse {
1534		#ifdef IS_MPI
1535		Mat3x3d tmpI(inertiaTensor);
1536		Vector3d tmpAngMom;
1537	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1538	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1537	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1538	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1539		#endif
1540
1541		return;
#	Line 1381 | Line 1556 | namespace oopse {
1556		Vector3d thisr(0.0);
1557		Vector3d thisp(0.0);
1558
1559	<	double thisMass;
1559	>	RealType thisMass;
1560
1561		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1562		thisMass = mol->getMass();
#	Line 1394 | Line 1569 | namespace oopse {
1569
1570		#ifdef IS_MPI
1571		Vector3d tmpAngMom;
1572	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1572	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1573		#endif
1574
1575		return angularMomentum;
1576		}
1577
1578	<
1579	<	}//end namespace oopse
1578	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1579	>	return IOIndexToIntegrableObject.at(index);
1580	>	}
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_);
1626	+	sdByGlobalIndex_ = v;
1627	+	}
1628	+
1629	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1630	+	//assert(index < nAtoms_ + nRigidBodies_);
1631	+	return sdByGlobalIndex_.at(index);
1632	+	}
1633	+	*/
1634	+	}//end namespace OpenMD
1635	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 878 by chrisfen, Wed Feb 1 20:54:46 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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