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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 764 by gezelter, Mon Nov 21 22:59:21 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 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"
58		#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59		#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61		#include "UseTheForce/doForces_interface.h"
62	+	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63		#include "UseTheForce/DarkSide/electrostatic_interface.h"
64		#include "UseTheForce/DarkSide/switcheroo_interface.h"
65		#include "utils/MemoryUtils.hpp"
66		#include "utils/simError.h"
67		#include "selection/SelectionManager.hpp"
68	+	#include "io/ForceFieldOptions.hpp"
69	+	#include "UseTheForce/ForceField.hpp"
70
71	+
72		#ifdef IS_MPI
73		#include "UseTheForce/mpiComponentPlan.h"
74		#include "UseTheForce/DarkSide/simParallel_interface.h"
75		#endif
76
77	<	namespace oopse {
77	>	namespace OpenMD {
78		std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79		std::map<int, std::set<int> >::iterator i = container.find(index);
80		std::set<int> result;
#	Line 80 | Line 85 | namespace oopse {
85		return result;
86		}
87
88	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
89	<	ForceField* ff, Globals* simParams) :
90	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
86	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89	>	forceField_(ff), simParams_(simParams),
90	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
94	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95	<	sman_(NULL), fortranInitialized_(false) {
93	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
94	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
95	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
96	>	calcBoxDipole_(false), useAtomicVirial_(true) {
97
98	<
94	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
98	>
99		MoleculeStamp* molStamp;
100		int nMolWithSameStamp;
101		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
#	Line 99 | Line 103 | namespace oopse {
103		CutoffGroupStamp* cgStamp;
104		RigidBodyStamp* rbStamp;
105		int nRigidAtoms = 0;
106	<
107	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
108	<	molStamp = i->first;
109	<	nMolWithSameStamp = i->second;
106	>
107	>	std::vector<Component*> components = simParams->getComponents();
108	>
109	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
110	>	molStamp = (*i)->getMoleculeStamp();
111	>	nMolWithSameStamp = (*i)->getNMol();
112
113		addMoleculeStamp(molStamp, nMolWithSameStamp);
114
115		//calculate atoms in molecules
116		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
117
112	–
118		//calculate atoms in cutoff groups
119		int nAtomsInGroups = 0;
120		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121
122		for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	<	cgStamp = molStamp->getCutoffGroup(j);
123	>	cgStamp = molStamp->getCutoffGroupStamp(j);
124		nAtomsInGroups += cgStamp->getNMembers();
125		}
126
#	Line 128 | Line 133 | namespace oopse {
133		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134
135		for (int j=0; j < nRigidBodiesInStamp; j++) {
136	<	rbStamp = molStamp->getRigidBody(j);
136	>	rbStamp = molStamp->getRigidBodyStamp(j);
137		nAtomsInRigidBodies += rbStamp->getNMembers();
138		}
139
#	Line 153 | Line 158 | namespace oopse {
158		+ nGlobalRigidBodies_;
159
160		nGlobalMols_ = molStampIds_.size();
156	–
157	–	#ifdef IS_MPI
161		molToProcMap_.resize(nGlobalMols_);
159	–	#endif
160	–
162		}
163
164		SimInfo::~SimInfo() {
#	Line 167 | Line 168 | namespace oopse {
168		}
169		molecules_.clear();
170
170	–	delete stamps_;
171		delete sman_;
172		delete simParams_;
173		delete forceField_;
#	Line 196 | Line 196 | namespace oopse {
196		nBonds_ += mol->getNBonds();
197		nBends_ += mol->getNBends();
198		nTorsions_ += mol->getNTorsions();
199	+	nInversions_ += mol->getNInversions();
200		nRigidBodies_ += mol->getNRigidBodies();
201		nIntegrableObjects_ += mol->getNIntegrableObjects();
202		nCutoffGroups_ += mol->getNCutoffGroups();
203		nConstraints_ += mol->getNConstraintPairs();
204
205	<	addExcludePairs(mol);
206	<
205	>	addInteractionPairs(mol);
206	>
207		return true;
208		} else {
209		return false;
#	Line 221 | Line 222 | namespace oopse {
222		nBonds_ -= mol->getNBonds();
223		nBends_ -= mol->getNBends();
224		nTorsions_ -= mol->getNTorsions();
225	+	nInversions_ -= mol->getNInversions();
226		nRigidBodies_ -= mol->getNRigidBodies();
227		nIntegrableObjects_ -= mol->getNIntegrableObjects();
228		nCutoffGroups_ -= mol->getNCutoffGroups();
229		nConstraints_ -= mol->getNConstraintPairs();
230
231	<	removeExcludePairs(mol);
231	>	removeInteractionPairs(mol);
232		molecules_.erase(mol->getGlobalIndex());
233
234		delete mol;
#	Line 274 | Line 276 | namespace oopse {
276		}
277		}
278
279	<	}//end for (integrableObject)
280	<	}// end for (mol)
279	>	}
280	>	}
281
282		// n_constraints is local, so subtract them on each processor
283		ndf_local -= nConstraints_;
#	Line 292 | Line 294 | namespace oopse {
294
295		}
296
297	+	int SimInfo::getFdf() {
298	+	#ifdef IS_MPI
299	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300	+	#else
301	+	fdf_ = fdf_local;
302	+	#endif
303	+	return fdf_;
304	+	}
305	+
306		void SimInfo::calcNdfRaw() {
307		int ndfRaw_local;
308
#	Line 343 | Line 354 | namespace oopse {
354
355		}
356
357	<	void SimInfo::addExcludePairs(Molecule* mol) {
357	>	void SimInfo::addInteractionPairs(Molecule* mol) {
358	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
359		std::vector<Bond*>::iterator bondIter;
360		std::vector<Bend*>::iterator bendIter;
361		std::vector<Torsion*>::iterator torsionIter;
362	+	std::vector<Inversion*>::iterator inversionIter;
363		Bond* bond;
364		Bend* bend;
365		Torsion* torsion;
366	+	Inversion* inversion;
367		int a;
368		int b;
369		int c;
370		int d;
371
372	<	std::map<int, std::set<int> > atomGroups;
372	>	// atomGroups can be used to add special interaction maps between
373	>	// groups of atoms that are in two separate rigid bodies.
374	>	// However, most site-site interactions between two rigid bodies
375	>	// are probably not special, just the ones between the physically
376	>	// bonded atoms.  Interactions *within* a single rigid body should
377	>	// always be excluded.  These are done at the bottom of this
378	>	// function.
379
380	+	std::map<int, std::set<int> > atomGroups;
381		Molecule::RigidBodyIterator rbIter;
382		RigidBody* rb;
383		Molecule::IntegrableObjectIterator ii;
384		StuntDouble* integrableObject;
385
386	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
387	<	integrableObject = mol->nextIntegrableObject(ii)) {
388	<
386	>	for (integrableObject = mol->beginIntegrableObject(ii);
387	>	integrableObject != NULL;
388	>	integrableObject = mol->nextIntegrableObject(ii)) {
389	>
390		if (integrableObject->isRigidBody()) {
391	<	rb = static_cast<RigidBody*>(integrableObject);
392	<	std::vector<Atom*> atoms = rb->getAtoms();
393	<	std::set<int> rigidAtoms;
394	<	for (int i = 0; i < atoms.size(); ++i) {
395	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
396	<	}
397	<	for (int i = 0; i < atoms.size(); ++i) {
398	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399	<	}
391	>	rb = static_cast<RigidBody*>(integrableObject);
392	>	std::vector<Atom*> atoms = rb->getAtoms();
393	>	std::set<int> rigidAtoms;
394	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
396	>	}
397	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399	>	}
400		} else {
401		std::set<int> oneAtomSet;
402		oneAtomSet.insert(integrableObject->getGlobalIndex());
403		atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
404		}
405		}
406	+
407	+	for (bond= mol->beginBond(bondIter); bond != NULL;
408	+	bond = mol->nextBond(bondIter)) {
409
385	–
386	–
387	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
410		a = bond->getAtomA()->getGlobalIndex();
411	<	b = bond->getAtomB()->getGlobalIndex();
412	<	exclude_.addPair(a, b);
411	>	b = bond->getAtomB()->getGlobalIndex();
412	>
413	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	>	oneTwoInteractions_.addPair(a, b);
415	>	} else {
416	>	excludedInteractions_.addPair(a, b);
417	>	}
418		}
419
420	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
420	>	for (bend= mol->beginBend(bendIter); bend != NULL;
421	>	bend = mol->nextBend(bendIter)) {
422	>
423		a = bend->getAtomA()->getGlobalIndex();
424		b = bend->getAtomB()->getGlobalIndex();
425		c = bend->getAtomC()->getGlobalIndex();
397	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
398	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
399	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
400	–
401	–	exclude_.addPairs(rigidSetA, rigidSetB);
402	–	exclude_.addPairs(rigidSetA, rigidSetC);
403	–	exclude_.addPairs(rigidSetB, rigidSetC);
426
427	<	//exclude_.addPair(a, b);
428	<	//exclude_.addPair(a, c);
429	<	//exclude_.addPair(b, c);
427	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	>	oneTwoInteractions_.addPair(a, b);
429	>	oneTwoInteractions_.addPair(b, c);
430	>	} else {
431	>	excludedInteractions_.addPair(a, b);
432	>	excludedInteractions_.addPair(b, c);
433	>	}
434	>
435	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
436	>	oneThreeInteractions_.addPair(a, c);
437	>	} else {
438	>	excludedInteractions_.addPair(a, c);
439	>	}
440		}
441
442	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
442	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
443	>	torsion = mol->nextTorsion(torsionIter)) {
444	>
445		a = torsion->getAtomA()->getGlobalIndex();
446		b = torsion->getAtomB()->getGlobalIndex();
447		c = torsion->getAtomC()->getGlobalIndex();
448	<	d = torsion->getAtomD()->getGlobalIndex();
415	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
416	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
417	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
418	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
448	>	d = torsion->getAtomD()->getGlobalIndex();
449
450	<	exclude_.addPairs(rigidSetA, rigidSetB);
451	<	exclude_.addPairs(rigidSetA, rigidSetC);
452	<	exclude_.addPairs(rigidSetA, rigidSetD);
453	<	exclude_.addPairs(rigidSetB, rigidSetC);
454	<	exclude_.addPairs(rigidSetB, rigidSetD);
455	<	exclude_.addPairs(rigidSetC, rigidSetD);
450	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
451	>	oneTwoInteractions_.addPair(a, b);
452	>	oneTwoInteractions_.addPair(b, c);
453	>	oneTwoInteractions_.addPair(c, d);
454	>	} else {
455	>	excludedInteractions_.addPair(a, b);
456	>	excludedInteractions_.addPair(b, c);
457	>	excludedInteractions_.addPair(c, d);
458	>	}
459
460	<	/*
461	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
462	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
463	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
464	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
465	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
466	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
467	<
468	<
469	<	exclude_.addPair(a, b);
470	<	exclude_.addPair(a, c);
471	<	exclude_.addPair(a, d);
472	<	exclude_.addPair(b, c);
440	<	exclude_.addPair(b, d);
441	<	exclude_.addPair(c, d);
442	<	*/
460	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
461	>	oneThreeInteractions_.addPair(a, c);
462	>	oneThreeInteractions_.addPair(b, d);
463	>	} else {
464	>	excludedInteractions_.addPair(a, c);
465	>	excludedInteractions_.addPair(b, d);
466	>	}
467	>
468	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
469	>	oneFourInteractions_.addPair(a, d);
470	>	} else {
471	>	excludedInteractions_.addPair(a, d);
472	>	}
473		}
474
475	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
475	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
476	>	inversion = mol->nextInversion(inversionIter)) {
477	>
478	>	a = inversion->getAtomA()->getGlobalIndex();
479	>	b = inversion->getAtomB()->getGlobalIndex();
480	>	c = inversion->getAtomC()->getGlobalIndex();
481	>	d = inversion->getAtomD()->getGlobalIndex();
482	>
483	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
484	>	oneTwoInteractions_.addPair(a, b);
485	>	oneTwoInteractions_.addPair(a, c);
486	>	oneTwoInteractions_.addPair(a, d);
487	>	} else {
488	>	excludedInteractions_.addPair(a, b);
489	>	excludedInteractions_.addPair(a, c);
490	>	excludedInteractions_.addPair(a, d);
491	>	}
492	>
493	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
494	>	oneThreeInteractions_.addPair(b, c);
495	>	oneThreeInteractions_.addPair(b, d);
496	>	oneThreeInteractions_.addPair(c, d);
497	>	} else {
498	>	excludedInteractions_.addPair(b, c);
499	>	excludedInteractions_.addPair(b, d);
500	>	excludedInteractions_.addPair(c, d);
501	>	}
502	>	}
503	>
504	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
505	>	rb = mol->nextRigidBody(rbIter)) {
506		std::vector<Atom*> atoms = rb->getAtoms();
507	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
508	<	for (int j = i + 1; j < atoms.size(); ++j) {
507	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
508	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
509		a = atoms[i]->getGlobalIndex();
510		b = atoms[j]->getGlobalIndex();
511	<	exclude_.addPair(a, b);
511	>	excludedInteractions_.addPair(a, b);
512		}
513		}
514		}
515
516		}
517
518	<	void SimInfo::removeExcludePairs(Molecule* mol) {
518	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
519	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
520		std::vector<Bond*>::iterator bondIter;
521		std::vector<Bend*>::iterator bendIter;
522		std::vector<Torsion*>::iterator torsionIter;
523	+	std::vector<Inversion*>::iterator inversionIter;
524		Bond* bond;
525		Bend* bend;
526		Torsion* torsion;
527	+	Inversion* inversion;
528		int a;
529		int b;
530		int c;
531		int d;
532
533		std::map<int, std::set<int> > atomGroups;
471	–
534		Molecule::RigidBodyIterator rbIter;
535		RigidBody* rb;
536		Molecule::IntegrableObjectIterator ii;
537		StuntDouble* integrableObject;
538
539	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
540	<	integrableObject = mol->nextIntegrableObject(ii)) {
541	<
539	>	for (integrableObject = mol->beginIntegrableObject(ii);
540	>	integrableObject != NULL;
541	>	integrableObject = mol->nextIntegrableObject(ii)) {
542	>
543		if (integrableObject->isRigidBody()) {
544	<	rb = static_cast<RigidBody*>(integrableObject);
545	<	std::vector<Atom*> atoms = rb->getAtoms();
546	<	std::set<int> rigidAtoms;
547	<	for (int i = 0; i < atoms.size(); ++i) {
548	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
549	<	}
550	<	for (int i = 0; i < atoms.size(); ++i) {
551	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552	<	}
544	>	rb = static_cast<RigidBody*>(integrableObject);
545	>	std::vector<Atom*> atoms = rb->getAtoms();
546	>	std::set<int> rigidAtoms;
547	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
549	>	}
550	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552	>	}
553		} else {
554		std::set<int> oneAtomSet;
555		oneAtomSet.insert(integrableObject->getGlobalIndex());
#	Line 494 | Line 557 | namespace oopse {
557		}
558		}
559
560	<
561	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
560	>	for (bond= mol->beginBond(bondIter); bond != NULL;
561	>	bond = mol->nextBond(bondIter)) {
562	>
563		a = bond->getAtomA()->getGlobalIndex();
564	<	b = bond->getAtomB()->getGlobalIndex();
565	<	exclude_.removePair(a, b);
564	>	b = bond->getAtomB()->getGlobalIndex();
565	>
566	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	>	oneTwoInteractions_.removePair(a, b);
568	>	} else {
569	>	excludedInteractions_.removePair(a, b);
570	>	}
571		}
572
573	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
573	>	for (bend= mol->beginBend(bendIter); bend != NULL;
574	>	bend = mol->nextBend(bendIter)) {
575	>
576		a = bend->getAtomA()->getGlobalIndex();
577		b = bend->getAtomB()->getGlobalIndex();
578		c = bend->getAtomC()->getGlobalIndex();
508	–
509	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
510	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
511	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
512	–
513	–	exclude_.removePairs(rigidSetA, rigidSetB);
514	–	exclude_.removePairs(rigidSetA, rigidSetC);
515	–	exclude_.removePairs(rigidSetB, rigidSetC);
579
580	<	//exclude_.removePair(a, b);
581	<	//exclude_.removePair(a, c);
582	<	//exclude_.removePair(b, c);
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	oneTwoInteractions_.removePair(b, c);
583	>	} else {
584	>	excludedInteractions_.removePair(a, b);
585	>	excludedInteractions_.removePair(b, c);
586	>	}
587	>
588	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
589	>	oneThreeInteractions_.removePair(a, c);
590	>	} else {
591	>	excludedInteractions_.removePair(a, c);
592	>	}
593		}
594
595	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
595	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
596	>	torsion = mol->nextTorsion(torsionIter)) {
597	>
598		a = torsion->getAtomA()->getGlobalIndex();
599		b = torsion->getAtomB()->getGlobalIndex();
600		c = torsion->getAtomC()->getGlobalIndex();
601	<	d = torsion->getAtomD()->getGlobalIndex();
601	>	d = torsion->getAtomD()->getGlobalIndex();
602	>
603	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
604	>	oneTwoInteractions_.removePair(a, b);
605	>	oneTwoInteractions_.removePair(b, c);
606	>	oneTwoInteractions_.removePair(c, d);
607	>	} else {
608	>	excludedInteractions_.removePair(a, b);
609	>	excludedInteractions_.removePair(b, c);
610	>	excludedInteractions_.removePair(c, d);
611	>	}
612
613	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
614	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
615	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
616	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
613	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
614	>	oneThreeInteractions_.removePair(a, c);
615	>	oneThreeInteractions_.removePair(b, d);
616	>	} else {
617	>	excludedInteractions_.removePair(a, c);
618	>	excludedInteractions_.removePair(b, d);
619	>	}
620
621	<	exclude_.removePairs(rigidSetA, rigidSetB);
622	<	exclude_.removePairs(rigidSetA, rigidSetC);
623	<	exclude_.removePairs(rigidSetA, rigidSetD);
624	<	exclude_.removePairs(rigidSetB, rigidSetC);
625	<	exclude_.removePairs(rigidSetB, rigidSetD);
626	<	exclude_.removePairs(rigidSetC, rigidSetD);
621	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
622	>	oneFourInteractions_.removePair(a, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, d);
625	>	}
626	>	}
627
628	<	/*
629	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
542	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
543	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
544	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
545	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
546	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
628	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
629	>	inversion = mol->nextInversion(inversionIter)) {
630
631	<
632	<	exclude_.removePair(a, b);
633	<	exclude_.removePair(a, c);
634	<	exclude_.removePair(a, d);
552	<	exclude_.removePair(b, c);
553	<	exclude_.removePair(b, d);
554	<	exclude_.removePair(c, d);
555	<	*/
556	<	}
631	>	a = inversion->getAtomA()->getGlobalIndex();
632	>	b = inversion->getAtomB()->getGlobalIndex();
633	>	c = inversion->getAtomC()->getGlobalIndex();
634	>	d = inversion->getAtomD()->getGlobalIndex();
635
636	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
636	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
637	>	oneTwoInteractions_.removePair(a, b);
638	>	oneTwoInteractions_.removePair(a, c);
639	>	oneTwoInteractions_.removePair(a, d);
640	>	} else {
641	>	excludedInteractions_.removePair(a, b);
642	>	excludedInteractions_.removePair(a, c);
643	>	excludedInteractions_.removePair(a, d);
644	>	}
645	>
646	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
647	>	oneThreeInteractions_.removePair(b, c);
648	>	oneThreeInteractions_.removePair(b, d);
649	>	oneThreeInteractions_.removePair(c, d);
650	>	} else {
651	>	excludedInteractions_.removePair(b, c);
652	>	excludedInteractions_.removePair(b, d);
653	>	excludedInteractions_.removePair(c, d);
654	>	}
655	>	}
656	>
657	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
658	>	rb = mol->nextRigidBody(rbIter)) {
659		std::vector<Atom*> atoms = rb->getAtoms();
660	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
661	<	for (int j = i + 1; j < atoms.size(); ++j) {
660	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
661	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
662		a = atoms[i]->getGlobalIndex();
663		b = atoms[j]->getGlobalIndex();
664	<	exclude_.removePair(a, b);
664	>	excludedInteractions_.removePair(a, b);
665		}
666		}
667		}
668	<
668	>
669		}
670	<
671	<
670	>
671	>
672		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
673		int curStampId;
674	<
674	>
675		//index from 0
676		curStampId = moleculeStamps_.size();
677
#	Line 593 | Line 693 | namespace oopse {
693		/** @deprecate */
694		int isError = 0;
695
696	+	setupCutoff();
697	+
698		setupElectrostaticSummationMethod( isError );
699		setupSwitchingFunction();
700	+	setupAccumulateBoxDipole();
701
702		if(isError){
703		sprintf( painCave.errMsg,
#	Line 602 | Line 705 | namespace oopse {
705		painCave.isFatal = 1;
706		simError();
707		}
605	–
606	–
607	–	setupCutoff();
708
709		calcNdf();
710		calcNdfRaw();
#	Line 654 | Line 754 | namespace oopse {
754		int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755		int useRF;
756		int useSF;
757	+	int useSP;
758	+	int useBoxDipole;
759	+
760		std::string myMethod;
761
762		// set the useRF logical
763		useRF = 0;
764		useSF = 0;
765	+	useSP = 0;
766	+	useBoxDipole = 0;
767
768
769		if (simParams_->haveElectrostaticSummationMethod()) {
770		std::string myMethod = simParams_->getElectrostaticSummationMethod();
771		toUpper(myMethod);
772	<	if (myMethod == "REACTION_FIELD") {
773	<	useRF=1;
774	<	} else {
775	<	if (myMethod == "SHIFTED_FORCE") {
776	<	useSF = 1;
777	<	}
772	>	if (myMethod == "REACTION_FIELD"){
773	>	useRF = 1;
774	>	} else if (myMethod == "SHIFTED_FORCE"){
775	>	useSF = 1;
776	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
777	>	useSP = 1;
778		}
779		}
780	+
781	+	if (simParams_->haveAccumulateBoxDipole())
782	+	if (simParams_->getAccumulateBoxDipole())
783	+	useBoxDipole = 1;
784
785	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
786	+
787		//loop over all of the atom types
788		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
789		useLennardJones |= (*i)->isLennardJones();
#	Line 742 | Line 853 | namespace oopse {
853		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854
855		temp = useSF;
856	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857
858	+	temp = useSP;
859	+	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	+
861	+	temp = useBoxDipole;
862	+	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	+
864	+	temp = useAtomicVirial_;
865	+	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	+
867		#endif
868
869		fInfo_.SIM_uses_PBC = usePBC;
#	Line 761 | Line 881 | namespace oopse {
881		fInfo_.SIM_uses_FLARB = useFLARB;
882		fInfo_.SIM_uses_RF = useRF;
883		fInfo_.SIM_uses_SF = useSF;
884	<
885	<	if( myMethod == "REACTION_FIELD") {
886	<
767	<	if (simParams_->haveDielectric()) {
768	<	fInfo_.dielect = simParams_->getDielectric();
769	<	} else {
770	<	sprintf(painCave.errMsg,
771	<	"SimSetup Error: No Dielectric constant was set.\n"
772	<	"\tYou are trying to use Reaction Field without"
773	<	"\tsetting a dielectric constant!\n");
774	<	painCave.isFatal = 1;
775	<	simError();
776	<	}
777	<	}
778	<
884	>	fInfo_.SIM_uses_SP = useSP;
885	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
886	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
887		}
888
889		void SimInfo::setupFortranSim() {
890		int isError;
891	<	int nExclude;
891	>	int nExclude, nOneTwo, nOneThree, nOneFour;
892		std::vector<int> fortranGlobalGroupMembership;
893
786	–	nExclude = exclude_.getSize();
894		isError = 0;
895
896		//globalGroupMembership_ is filled by SimCreator
#	Line 792 | Line 899 | namespace oopse {
899		}
900
901		//calculate mass ratio of cutoff group
902	<	std::vector<double> mfact;
902	>	std::vector<RealType> mfact;
903		SimInfo::MoleculeIterator mi;
904		Molecule* mol;
905		Molecule::CutoffGroupIterator ci;
906		CutoffGroup* cg;
907		Molecule::AtomIterator ai;
908		Atom* atom;
909	<	double totalMass;
909	>	RealType totalMass;
910
911		//to avoid memory reallocation, reserve enough space for mfact
912		mfact.reserve(getNCutoffGroups());
#	Line 815 | Line 922 | namespace oopse {
922		else
923		mfact.push_back( 1.0 );
924		}
818	–
925		}
926		}
927
#	Line 839 | Line 945 | namespace oopse {
945		}
946
947		//setup fortran simulation
842	–	int nGlobalExcludes = 0;
843	–	int* globalExcludes = NULL;
844	–	int* excludeList = exclude_.getExcludeList();
845	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
846	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
847	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
948
949	<	if( isError ){
949	>	nExclude = excludedInteractions_.getSize();
950	>	nOneTwo = oneTwoInteractions_.getSize();
951	>	nOneThree = oneThreeInteractions_.getSize();
952	>	nOneFour = oneFourInteractions_.getSize();
953
954	+	int* excludeList = excludedInteractions_.getPairList();
955	+	int* oneTwoList = oneTwoInteractions_.getPairList();
956	+	int* oneThreeList = oneThreeInteractions_.getPairList();
957	+	int* oneFourList = oneFourInteractions_.getPairList();
958	+
959	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
960	+	&nExclude, excludeList,
961	+	&nOneTwo, oneTwoList,
962	+	&nOneThree, oneThreeList,
963	+	&nOneFour, oneFourList,
964	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965	+	&fortranGlobalGroupMembership[0], &isError);
966	+
967	+	if( isError ){
968	+
969		sprintf( painCave.errMsg,
970		"There was an error setting the simulation information in fortran.\n" );
971		painCave.isFatal = 1;
972	<	painCave.severity = OOPSE_ERROR;
972	>	painCave.severity = OPENMD_ERROR;
973		simError();
974		}
975	<
976	<	#ifdef IS_MPI
975	>
976	>
977		sprintf( checkPointMsg,
978		"succesfully sent the simulation information to fortran.\n");
979	<	MPIcheckPoint();
980	<	#endif // is_mpi
979	>
980	>	errorCheckPoint();
981	>
982	>	// Setup number of neighbors in neighbor list if present
983	>	if (simParams_->haveNeighborListNeighbors()) {
984	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
985	>	setNeighbors(&nlistNeighbors);
986	>	}
987	>
988	>
989		}
990
991
866	–	#ifdef IS_MPI
992		void SimInfo::setupFortranParallel() {
993	<
993	>	#ifdef IS_MPI
994		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
995		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
996		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 915 | Line 1040 | namespace oopse {
1040		}
1041
1042		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1043	<	MPIcheckPoint();
1043	>	errorCheckPoint();
1044
1045	<
1045	>	#endif
1046		}
1047
923	–	#endif
924	–
1048		void SimInfo::setupCutoff() {
1049
1050	+	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1051	+
1052		// Check the cutoff policy
1053	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
1054	<	if (simParams_->haveCutoffPolicy()) {
1055	<	std::string myPolicy = simParams_->getCutoffPolicy();
1053	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054	>
1055	>	// Set LJ shifting bools to false
1056	>	ljsp_ = 0;
1057	>	ljsf_ = 0;
1058	>
1059	>	std::string myPolicy;
1060	>	if (forceFieldOptions_.haveCutoffPolicy()){
1061	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1062	>	}else if (simParams_->haveCutoffPolicy()) {
1063	>	myPolicy = simParams_->getCutoffPolicy();
1064	>	}
1065	>
1066	>	if (!myPolicy.empty()){
1067		toUpper(myPolicy);
1068		if (myPolicy == "MIX") {
1069		cp = MIX_CUTOFF_POLICY;
#	Line 950 | Line 1086 | namespace oopse {
1086		notifyFortranCutoffPolicy(&cp);
1087
1088		// Check the Skin Thickness for neighborlists
1089	<	double skin;
1089	>	RealType skin;
1090		if (simParams_->haveSkinThickness()) {
1091		skin = simParams_->getSkinThickness();
1092		notifyFortranSkinThickness(&skin);
#	Line 962 | Line 1098 | namespace oopse {
1098		if (simParams_->haveSwitchingRadius()) {
1099		rsw_  = simParams_->getSwitchingRadius();
1100		} else {
1101	<	rsw_ = rcut_;
1101	>	if (fInfo_.SIM_uses_Charges |
1102	>	fInfo_.SIM_uses_Dipoles |
1103	>	fInfo_.SIM_uses_RF) {
1104	>
1105	>	rsw_ = 0.85 * rcut_;
1106	>	sprintf(painCave.errMsg,
1107	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1108	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1109	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1110	>	painCave.isFatal = 0;
1111	>	simError();
1112	>	} else {
1113	>	rsw_ = rcut_;
1114	>	sprintf(painCave.errMsg,
1115	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	>	"\tOpenMD will use the same value as the cutoffRadius.\n"
1117	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118	>	painCave.isFatal = 0;
1119	>	simError();
1120	>	}
1121		}
1122	<	notifyFortranCutoffs(&rcut_, &rsw_);
1122	>
1123	>	if (simParams_->haveElectrostaticSummationMethod()) {
1124	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1125	>	toUpper(myMethod);
1126	>
1127	>	if (myMethod == "SHIFTED_POTENTIAL") {
1128	>	ljsp_ = 1;
1129	>	} else if (myMethod == "SHIFTED_FORCE") {
1130	>	ljsf_ = 1;
1131	>	}
1132	>	}
1133	>
1134	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1135
1136		} else {
1137
#	Line 972 | Line 1139 | namespace oopse {
1139		if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1140		sprintf(painCave.errMsg,
1141		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1142	<	"\tOOPSE will use a default value of 15.0 angstroms"
1142	>	"\tOpenMD will use a default value of 15.0 angstroms"
1143		"\tfor the cutoffRadius.\n");
1144		painCave.isFatal = 0;
1145		simError();
#	Line 981 | Line 1148 | namespace oopse {
1148		if (simParams_->haveElectrostaticSummationMethod()) {
1149		std::string myMethod = simParams_->getElectrostaticSummationMethod();
1150		toUpper(myMethod);
1151	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1151	>
1152	>	// For the time being, we're tethering the LJ shifted behavior to the
1153	>	// electrostaticSummationMethod keyword options
1154	>	if (myMethod == "SHIFTED_POTENTIAL") {
1155	>	ljsp_ = 1;
1156	>	} else if (myMethod == "SHIFTED_FORCE") {
1157	>	ljsf_ = 1;
1158	>	}
1159	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1160		if (simParams_->haveSwitchingRadius()){
1161		sprintf(painCave.errMsg,
1162		"SimInfo Warning: A value was set for the switchingRadius\n"
#	Line 998 | Line 1173 | namespace oopse {
1173		} else {
1174		sprintf(painCave.errMsg,
1175		"SimCreator Warning: No value was set for switchingRadius.\n"
1176	<	"\tOOPSE will use a default value of\n"
1176	>	"\tOpenMD will use a default value of\n"
1177		"\t0.85 * cutoffRadius for the switchingRadius\n");
1178		painCave.isFatal = 0;
1179		simError();
1180		rsw_ = 0.85 * rcut_;
1181		}
1182	<	notifyFortranCutoffs(&rcut_, &rsw_);
1182	>
1183	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1184	>
1185		} else {
1186		// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1187		// We'll punt and let fortran figure out the cutoffs later.
#	Line 1020 | Line 1197 | namespace oopse {
1197		int errorOut;
1198		int esm =  NONE;
1199		int sm = UNDAMPED;
1200	<	double alphaVal;
1201	<	double dielectric;
1202	<
1200	>	RealType alphaVal;
1201	>	RealType dielectric;
1202	>
1203		errorOut = isError;
1027	–	alphaVal = simParams_->getDampingAlpha();
1028	–	dielectric = simParams_->getDielectric();
1204
1205		if (simParams_->haveElectrostaticSummationMethod()) {
1206		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 1042 | Line 1217 | namespace oopse {
1217		if (myMethod == "SHIFTED_FORCE") {
1218		esm = SHIFTED_FORCE;
1219		} else {
1220	<	if (myMethod == "REACTION_FIELD") {
1220	>	if (myMethod == "REACTION_FIELD") {
1221		esm = REACTION_FIELD;
1222	+	dielectric = simParams_->getDielectric();
1223	+	if (!simParams_->haveDielectric()) {
1224	+	// throw warning
1225	+	sprintf( painCave.errMsg,
1226	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1227	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1228	+	painCave.isFatal = 0;
1229	+	simError();
1230	+	}
1231		} else {
1232		// throw error
1233		sprintf( painCave.errMsg,
#	Line 1070 | Line 1254 | namespace oopse {
1254		if (myScreen == "DAMPED") {
1255		sm = DAMPED;
1256		if (!simParams_->haveDampingAlpha()) {
1257	<	//throw error
1257	>	// first set a cutoff dependent alpha value
1258	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1259	>	alphaVal = 0.5125 - rcut_* 0.025;
1260	>	// for values rcut > 20.5, alpha is zero
1261	>	if (alphaVal < 0) alphaVal = 0;
1262	>
1263	>	// throw warning
1264		sprintf( painCave.errMsg,
1265		"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1266	<	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1266	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1267		painCave.isFatal = 0;
1268		simError();
1269	+	} else {
1270	+	alphaVal = simParams_->getDampingAlpha();
1271		}
1272	+
1273		} else {
1274		// throw error
1275		sprintf( painCave.errMsg,
#	Line 1092 | Line 1285 | namespace oopse {
1285
1286		// let's pass some summation method variables to fortran
1287		setElectrostaticSummationMethod( &esm );
1288	<	notifyFortranElectrostaticMethod( &esm );
1288	>	setFortranElectrostaticMethod( &esm );
1289		setScreeningMethod( &sm );
1290		setDampingAlpha( &alphaVal );
1291		setReactionFieldDielectric( &dielectric );
#	Line 1125 | Line 1318 | namespace oopse {
1318
1319		}
1320
1321	+	void SimInfo::setupAccumulateBoxDipole() {
1322	+
1323	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1324	+	if ( simParams_->haveAccumulateBoxDipole() )
1325	+	if ( simParams_->getAccumulateBoxDipole() ) {
1326	+	setAccumulateBoxDipole();
1327	+	calcBoxDipole_ = true;
1328	+	}
1329	+
1330	+	}
1331	+
1332		void SimInfo::addProperty(GenericData* genData) {
1333		properties_.addProperty(genData);
1334		}
#	Line 1181 | Line 1385 | namespace oopse {
1385		Molecule* mol;
1386
1387		Vector3d comVel(0.0);
1388	<	double totalMass = 0.0;
1388	>	RealType totalMass = 0.0;
1389
1390
1391		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1392	<	double mass = mol->getMass();
1392	>	RealType mass = mol->getMass();
1393		totalMass += mass;
1394		comVel += mass * mol->getComVel();
1395		}
1396
1397		#ifdef IS_MPI
1398	<	double tmpMass = totalMass;
1398	>	RealType tmpMass = totalMass;
1399		Vector3d tmpComVel(comVel);
1400	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1401	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1400	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1401	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1402		#endif
1403
1404		comVel /= totalMass;
#	Line 1207 | Line 1411 | namespace oopse {
1411		Molecule* mol;
1412
1413		Vector3d com(0.0);
1414	<	double totalMass = 0.0;
1414	>	RealType totalMass = 0.0;
1415
1416		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1417	<	double mass = mol->getMass();
1417	>	RealType mass = mol->getMass();
1418		totalMass += mass;
1419		com += mass * mol->getCom();
1420		}
1421
1422		#ifdef IS_MPI
1423	<	double tmpMass = totalMass;
1423	>	RealType tmpMass = totalMass;
1424		Vector3d tmpCom(com);
1425	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1426	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1425	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1426	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1427		#endif
1428
1429		com /= totalMass;
#	Line 1243 | Line 1447 | namespace oopse {
1447		Molecule* mol;
1448
1449
1450	<	double totalMass = 0.0;
1450	>	RealType totalMass = 0.0;
1451
1452
1453		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1454	<	double mass = mol->getMass();
1454	>	RealType mass = mol->getMass();
1455		totalMass += mass;
1456		com += mass * mol->getCom();
1457		comVel += mass * mol->getComVel();
1458		}
1459
1460		#ifdef IS_MPI
1461	<	double tmpMass = totalMass;
1461	>	RealType tmpMass = totalMass;
1462		Vector3d tmpCom(com);
1463		Vector3d tmpComVel(comVel);
1464	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1465	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1466	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1464	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1465	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1466	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1467		#endif
1468
1469		com /= totalMass;
#	Line 1278 | Line 1482 | namespace oopse {
1482		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1483
1484
1485	<	double xx = 0.0;
1486	<	double yy = 0.0;
1487	<	double zz = 0.0;
1488	<	double xy = 0.0;
1489	<	double xz = 0.0;
1490	<	double yz = 0.0;
1485	>	RealType xx = 0.0;
1486	>	RealType yy = 0.0;
1487	>	RealType zz = 0.0;
1488	>	RealType xy = 0.0;
1489	>	RealType xz = 0.0;
1490	>	RealType yz = 0.0;
1491		Vector3d com(0.0);
1492		Vector3d comVel(0.0);
1493
#	Line 1295 | Line 1499 | namespace oopse {
1499		Vector3d thisq(0.0);
1500		Vector3d thisv(0.0);
1501
1502	<	double thisMass = 0.0;
1502	>	RealType thisMass = 0.0;
1503
1504
1505
#	Line 1333 | Line 1537 | namespace oopse {
1537		#ifdef IS_MPI
1538		Mat3x3d tmpI(inertiaTensor);
1539		Vector3d tmpAngMom;
1540	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1541	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1540	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1541	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1542		#endif
1543
1544		return;
#	Line 1355 | Line 1559 | namespace oopse {
1559		Vector3d thisr(0.0);
1560		Vector3d thisp(0.0);
1561
1562	<	double thisMass;
1562	>	RealType thisMass;
1563
1564		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1565		thisMass = mol->getMass();
#	Line 1368 | Line 1572 | namespace oopse {
1572
1573		#ifdef IS_MPI
1574		Vector3d tmpAngMom;
1575	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1575	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1576		#endif
1577
1578		return angularMomentum;
1579		}
1580
1581	<
1582	<	}//end namespace oopse
1581	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1582	>	return IOIndexToIntegrableObject.at(index);
1583	>	}
1584	>
1585	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1586	>	IOIndexToIntegrableObject= v;
1587	>	}
1588
1589	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1590	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1591	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1592	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1593	+	*/
1594	+	void SimInfo::getGyrationalVolume(RealType &volume){
1595	+	Mat3x3d intTensor;
1596	+	RealType det;
1597	+	Vector3d dummyAngMom;
1598	+	RealType sysconstants;
1599	+	RealType geomCnst;
1600	+
1601	+	geomCnst = 3.0/2.0;
1602	+	/* Get the inertial tensor and angular momentum for free*/
1603	+	getInertiaTensor(intTensor,dummyAngMom);
1604	+
1605	+	det = intTensor.determinant();
1606	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1607	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1608	+	return;
1609	+	}
1610	+
1611	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1612	+	Mat3x3d intTensor;
1613	+	Vector3d dummyAngMom;
1614	+	RealType sysconstants;
1615	+	RealType geomCnst;
1616	+
1617	+	geomCnst = 3.0/2.0;
1618	+	/* Get the inertial tensor and angular momentum for free*/
1619	+	getInertiaTensor(intTensor,dummyAngMom);
1620	+
1621	+	detI = intTensor.determinant();
1622	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1623	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1624	+	return;
1625	+	}
1626	+	/*
1627	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1628	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1629	+	sdByGlobalIndex_ = v;
1630	+	}
1631	+
1632	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1633	+	//assert(index < nAtoms_ + nRigidBodies_);
1634	+	return sdByGlobalIndex_.at(index);
1635	+	}
1636	+	*/
1637	+	}//end namespace OpenMD
1638	+

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 764 by gezelter, Mon Nov 21 22:59:21 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

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