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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
Revision 1386 by gezelter, Fri Oct 23 18:41:09 2009 UTC

#	Line 48 | Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
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/notifyCutoffs_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 {
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;
81	+	if (i != container.end()) {
82	+	result = i->second;
83	+	}
84
85	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
86	<	ForceField* ff, Globals* simParams) :
87	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
88	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
85	>	return result;
86	>	}
87	>
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	<
81	<	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
102	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
102	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
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
99	–
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
127		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128	+
129		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130
131		//calculate atoms in rigid bodies
#	Line 114 | 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 123 | Line 142 | namespace oopse {
142
143		}
144
145	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
146	<	//therefore the total number of cutoff groups in the system is equal to
147	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
148	<	//file plus the number of cutoff groups defined in meta-data file
145	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
146	>	//group therefore the total number of cutoff groups in the system is
147	>	//equal to the total number of atoms minus number of atoms belong to
148	>	//cutoff group defined in meta-data file plus the number of cutoff
149	>	//groups defined in meta-data file
150		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
151
152	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
153	<	//therefore the total number of  integrable objects in the system is equal to
154	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
155	<	//file plus the number of  rigid bodies defined in meta-data file
156	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
157	<
152	>	//every free atom (atom does not belong to rigid bodies) is an
153	>	//integrable object therefore the total number of integrable objects
154	>	//in the system is equal to the total number of atoms minus number of
155	>	//atoms belong to rigid body defined in meta-data file plus the number
156	>	//of rigid bodies defined in meta-data file
157	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
158	>	+ nGlobalRigidBodies_;
159	>
160		nGlobalMols_ = molStampIds_.size();
139	–
140	–	#ifdef IS_MPI
161		molToProcMap_.resize(nGlobalMols_);
142	–	#endif
143	–
162		}
163
164		SimInfo::~SimInfo() {
#	Line 150 | Line 168 | namespace oopse {
168		}
169		molecules_.clear();
170
153	–	delete stamps_;
171		delete sman_;
172		delete simParams_;
173		delete forceField_;
#	Line 179 | 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 204 | 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 257 | 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 275 | 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 326 | 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	+	// 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 (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
387	<	a = bond->getAtomA()->getGlobalIndex();
388	<	b = bond->getAtomB()->getGlobalIndex();
389	<	exclude_.addPair(a, b);
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 < 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	>
410	>	a = bond->getAtomA()->getGlobalIndex();
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();
426	+
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	<	exclude_.addPair(a, b);
436	<	exclude_.addPair(a, c);
437	<	exclude_.addPair(b, c);
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();
448	>	d = torsion->getAtomD()->getGlobalIndex();
449
450	<	exclude_.addPair(a, b);
451	<	exclude_.addPair(a, c);
452	<	exclude_.addPair(a, d);
453	<	exclude_.addPair(b, c);
454	<	exclude_.addPair(b, d);
455	<	exclude_.addPair(c, d);
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	>	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	<	Molecule::RigidBodyIterator rbIter;
476	<	RigidBody* rb;
477	<	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	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
534	<	a = bond->getAtomA()->getGlobalIndex();
535	<	b = bond->getAtomB()->getGlobalIndex();
536	<	exclude_.removePair(a, b);
532	>
533	>	std::map<int, std::set<int> > atomGroups;
534	>	Molecule::RigidBodyIterator rbIter;
535	>	RigidBody* rb;
536	>	Molecule::IntegrableObjectIterator ii;
537	>	StuntDouble* integrableObject;
538	>
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 < 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());
556	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
557	>	}
558	>	}
559	>
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	>
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();
579	+
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	<	exclude_.removePair(a, b);
589	<	exclude_.removePair(a, c);
590	<	exclude_.removePair(b, c);
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	<	exclude_.removePair(a, b);
614	<	exclude_.removePair(a, c);
615	<	exclude_.removePair(a, d);
616	<	exclude_.removePair(b, c);
617	<	exclude_.removePair(b, d);
618	<	exclude_.removePair(c, d);
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	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
622	>	oneFourInteractions_.removePair(a, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, d);
625	>	}
626		}
627
628	<	Molecule::RigidBodyIterator rbIter;
629	<	RigidBody* rb;
630	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
628	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
629	>	inversion = mol->nextInversion(inversionIter)) {
630	>
631	>	a = inversion->getAtomA()->getGlobalIndex();
632	>	b = inversion->getAtomB()->getGlobalIndex();
633	>	c = inversion->getAtomC()->getGlobalIndex();
634	>	d = inversion->getAtomD()->getGlobalIndex();
635	>
636	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
637	>	oneTwoInteractions_.removePair(a, b);
638	>	oneTwoInteractions_.removePair(a, c);
639	>	oneTwoInteractions_.removePair(a, d);
640	>	} else {
641	>	excludedInteractions_.removePair(a, b);
642	>	excludedInteractions_.removePair(a, c);
643	>	excludedInteractions_.removePair(a, d);
644	>	}
645	>
646	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
647	>	oneThreeInteractions_.removePair(b, c);
648	>	oneThreeInteractions_.removePair(b, d);
649	>	oneThreeInteractions_.removePair(c, d);
650	>	} else {
651	>	excludedInteractions_.removePair(b, c);
652	>	excludedInteractions_.removePair(b, d);
653	>	excludedInteractions_.removePair(c, d);
654	>	}
655	>	}
656	>
657	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
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 465 | 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 473 | Line 705 | namespace oopse {
705		painCave.isFatal = 1;
706		simError();
707		}
476	–
477	–
478	–	setupCutoff();
708
709		calcNdf();
710		calcNdfRaw();
#	Line 510 | Line 739 | namespace oopse {
739		int useLennardJones = 0;
740		int useElectrostatic = 0;
741		int useEAM = 0;
742	+	int useSC = 0;
743		int useCharge = 0;
744		int useDirectional = 0;
745		int useDipole = 0;
#	Line 521 | Line 751 | namespace oopse {
751		int useDirectionalAtom = 0;
752		int useElectrostatics = 0;
753		//usePBC and useRF are from simParams
754	<	int usePBC = simParams_->getPBC();
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 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();
790		useElectrostatic |= (*i)->isElectrostatic();
791		useEAM |= (*i)->isEAM();
792	+	useSC |= (*i)->isSC();
793		useCharge |= (*i)->isCharge();
794		useDirectional |= (*i)->isDirectional();
795		useDipole |= (*i)->isDipole();
#	Line 578 | Line 840 | namespace oopse {
840		temp = useEAM;
841		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842
843	+	temp = useSC;
844	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845	+
846		temp = useShape;
847		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
848
849		temp = useFLARB;
850		MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851
852	+	temp = useRF;
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);
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 596 | Line 876 | namespace oopse {
876		fInfo_.SIM_uses_StickyPower = useStickyPower;
877		fInfo_.SIM_uses_GayBerne = useGayBerne;
878		fInfo_.SIM_uses_EAM = useEAM;
879	+	fInfo_.SIM_uses_SC = useSC;
880		fInfo_.SIM_uses_Shapes = useShape;
881		fInfo_.SIM_uses_FLARB = useFLARB;
882	<
883	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
884	<
885	<	if (simParams_->haveDielectric()) {
886	<	fInfo_.dielect = simParams_->getDielectric();
606	<	} else {
607	<	sprintf(painCave.errMsg,
608	<	"SimSetup Error: No Dielectric constant was set.\n"
609	<	"\tYou are trying to use Reaction Field without"
610	<	"\tsetting a dielectric constant!\n");
611	<	painCave.isFatal = 1;
612	<	simError();
613	<	}
614	<
615	<	} else {
616	<	fInfo_.dielect = 0.0;
617	<	}
618	<
882	>	fInfo_.SIM_uses_RF = useRF;
883	>	fInfo_.SIM_uses_SF = useSF;
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
626	–	nExclude = exclude_.getSize();
894		isError = 0;
895
896		//globalGroupMembership_ is filled by SimCreator
#	Line 632 | 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 649 | Line 916 | namespace oopse {
916
917		totalMass = cg->getMass();
918		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
919	<	mfact.push_back(atom->getMass()/totalMass);
919	>	// Check for massless groups - set mfact to 1 if true
920	>	if (totalMass != 0)
921	>	mfact.push_back(atom->getMass()/totalMass);
922	>	else
923	>	mfact.push_back( 1.0 );
924		}
654	–
925		}
926		}
927
#	Line 675 | Line 945 | namespace oopse {
945		}
946
947		//setup fortran simulation
678	–	int nGlobalExcludes = 0;
679	–	int* globalExcludes = NULL;
680	–	int* excludeList = exclude_.getExcludeList();
681	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
682	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
683	–	&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;
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
702	–	#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 751 | Line 1040 | namespace oopse {
1040		}
1041
1042		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1043	<	MPIcheckPoint();
1043	>	errorCheckPoint();
1044
756	–
757	–	}
758	–
1045		#endif
760	–
761	–	double SimInfo::calcMaxCutoffRadius() {
762	–
763	–
764	–	std::set<AtomType*> atomTypes;
765	–	std::set<AtomType*>::iterator i;
766	–	std::vector<double> cutoffRadius;
767	–
768	–	//get the unique atom types
769	–	atomTypes = getUniqueAtomTypes();
770	–
771	–	//query the max cutoff radius among these atom types
772	–	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
773	–	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
774	–	}
775	–
776	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
777	–	#ifdef IS_MPI
778	–	//pick the max cutoff radius among the processors
779	–	#endif
780	–
781	–	return maxCutoffRadius;
1046		}
1047
1048	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
1048	>	void SimInfo::setupCutoff() {
1049
1050	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
787	<
788	<	if (!simParams_->haveRcut()){
789	<	sprintf(painCave.errMsg,
790	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
791	<	"\tOOPSE will use a default value of 15.0 angstroms"
792	<	"\tfor the cutoffRadius.\n");
793	<	painCave.isFatal = 0;
794	<	simError();
795	<	rcut = 15.0;
796	<	} else{
797	<	rcut = simParams_->getRcut();
798	<	}
1050	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1051
1052	<	if (!simParams_->haveRsw()){
1053	<	sprintf(painCave.errMsg,
802	<	"SimCreator Warning: No value was set for switchingRadius.\n"
803	<	"\tOOPSE will use a default value of\n"
804	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
805	<	painCave.isFatal = 0;
806	<	simError();
807	<	rsw = 0.95 * rcut;
808	<	} else{
809	<	rsw = simParams_->getRsw();
810	<	}
1052	>	// Check the cutoff policy
1053	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054
1055	<	} else {
1056	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1057	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
815	<
816	<	if (simParams_->haveRcut()) {
817	<	rcut = simParams_->getRcut();
818	<	} else {
819	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
820	<	rcut = calcMaxCutoffRadius();
821	<	}
1055	>	// Set LJ shifting bools to false
1056	>	ljsp_ = 0;
1057	>	ljsf_ = 0;
1058
1059	<	if (simParams_->haveRsw()) {
1060	<	rsw  = simParams_->getRsw();
1061	<	} else {
1062	<	rsw = rcut;
1063	<	}
828	<
1059	>	std::string myPolicy;
1060	>	if (forceFieldOptions_.haveCutoffPolicy()){
1061	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1062	>	}else if (simParams_->haveCutoffPolicy()) {
1063	>	myPolicy = simParams_->getCutoffPolicy();
1064		}
830	–	}
1065
1066	<	void SimInfo::setupCutoff() {
1067	<	getCutoff(rcut_, rsw_);
834	<	double rnblist = rcut_ + 1; // skin of neighbor list
835	<
836	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
837	<
838	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
839	<	if (simParams_->haveCutoffPolicy()) {
840	<	std::string myPolicy = simParams_->getCutoffPolicy();
1066	>	if (!myPolicy.empty()){
1067	>	toUpper(myPolicy);
1068		if (myPolicy == "MIX") {
1069		cp = MIX_CUTOFF_POLICY;
1070		} else {
#	Line 855 | Line 1082 | namespace oopse {
1082		}
1083		}
1084		}
1085	+	}
1086	+	notifyFortranCutoffPolicy(&cp);
1087	+
1088	+	// Check the Skin Thickness for neighborlists
1089	+	RealType skin;
1090	+	if (simParams_->haveSkinThickness()) {
1091	+	skin = simParams_->getSkinThickness();
1092	+	notifyFortranSkinThickness(&skin);
1093	+	}
1094	+
1095	+	// Check if the cutoff was set explicitly:
1096	+	if (simParams_->haveCutoffRadius()) {
1097	+	rcut_ = simParams_->getCutoffRadius();
1098	+	if (simParams_->haveSwitchingRadius()) {
1099	+	rsw_  = simParams_->getSwitchingRadius();
1100	+	} else {
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	+	"\tOOPSE 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	+	"\tOOPSE 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	+
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	+
1138	+	// For electrostatic atoms, we'll assume a large safe value:
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"
1143	+	"\tfor the cutoffRadius.\n");
1144	+	painCave.isFatal = 0;
1145	+	simError();
1146	+	rcut_ = 15.0;
1147	+
1148	+	if (simParams_->haveElectrostaticSummationMethod()) {
1149	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1150	+	toUpper(myMethod);
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"
1163	+	"\teven though the electrostaticSummationMethod was\n"
1164	+	"\tset to %s\n", myMethod.c_str());
1165	+	painCave.isFatal = 1;
1166	+	simError();
1167	+	}
1168	+	}
1169	+	}
1170	+
1171	+	if (simParams_->haveSwitchingRadius()){
1172	+	rsw_ = simParams_->getSwitchingRadius();
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"
1177	+	"\t0.85 * cutoffRadius for the switchingRadius\n");
1178	+	painCave.isFatal = 0;
1179	+	simError();
1180	+	rsw_ = 0.85 * rcut_;
1181	+	}
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.
1188	+
1189	+	notifyFortranYouAreOnYourOwn();
1190	+
1191	+	}
1192		}
859	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1193		}
1194
1195		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1196
1197		int errorOut;
1198		int esm =  NONE;
1199	<	double alphaVal;
1200	<
1199	>	int sm = UNDAMPED;
1200	>	RealType alphaVal;
1201	>	RealType dielectric;
1202	>
1203		errorOut = isError;
1204
1205		if (simParams_->haveElectrostaticSummationMethod()) {
1206		std::string myMethod = simParams_->getElectrostaticSummationMethod();
1207	+	toUpper(myMethod);
1208		if (myMethod == "NONE") {
1209		esm = NONE;
1210		} else {
1211	<	if (myMethod == "UNDAMPED_WOLF") {
1212	<	esm = UNDAMPED_WOLF;
1211	>	if (myMethod == "SWITCHING_FUNCTION") {
1212	>	esm = SWITCHING_FUNCTION;
1213		} else {
1214	<	if (myMethod == "DAMPED_WOLF") {
1215	<	esm = DAMPED_WOLF;
1216	<	if (!simParams_->haveDampingAlpha()) {
1217	<	//throw error
1218	<	sprintf( painCave.errMsg,
883	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", simParams_->getDampingAlpha());
884	<	painCave.isFatal = 0;
885	<	simError();
886	<	}
887	<	alphaVal = simParams_->getDampingAlpha();
888	<	} else {
889	<	if (myMethod == "REACTION_FIELD") {
890	<	esm = REACTION_FIELD;
1214	>	if (myMethod == "SHIFTED_POTENTIAL") {
1215	>	esm = SHIFTED_POTENTIAL;
1216	>	} else {
1217	>	if (myMethod == "SHIFTED_FORCE") {
1218	>	esm = SHIFTED_FORCE;
1219		} else {
1220	<	// throw error
1221	<	sprintf( painCave.errMsg,
1222	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
1223	<	painCave.isFatal = 1;
1224	<	simError();
1225	<	}
1226	<	}
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,
1234	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1235	>	"\t(Input file specified %s .)\n"
1236	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1237	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1238	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1239	>	painCave.isFatal = 1;
1240	>	simError();
1241	>	}
1242	>	}
1243	>	}
1244		}
1245		}
1246		}
1247	<	initFortranFF( &esm, &alphaVal, &errorOut );
1247	>
1248	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1249	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1250	>	toUpper(myScreen);
1251	>	if (myScreen == "UNDAMPED") {
1252	>	sm = UNDAMPED;
1253	>	} else {
1254	>	if (myScreen == "DAMPED") {
1255	>	sm = DAMPED;
1256	>	if (!simParams_->haveDampingAlpha()) {
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 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,
1276	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1277	>	"\t(Input file specified %s .)\n"
1278	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1279	>	"or \"damped\".\n", myScreen.c_str() );
1280	>	painCave.isFatal = 1;
1281	>	simError();
1282	>	}
1283	>	}
1284	>	}
1285	>
1286	>	// let's pass some summation method variables to fortran
1287	>	setElectrostaticSummationMethod( &esm );
1288	>	setFortranElectrostaticMethod( &esm );
1289	>	setScreeningMethod( &sm );
1290	>	setDampingAlpha( &alphaVal );
1291	>	setReactionFieldDielectric( &dielectric );
1292	>	initFortranFF( &errorOut );
1293		}
1294
1295	+	void SimInfo::setupSwitchingFunction() {
1296	+	int ft = CUBIC;
1297	+
1298	+	if (simParams_->haveSwitchingFunctionType()) {
1299	+	std::string funcType = simParams_->getSwitchingFunctionType();
1300	+	toUpper(funcType);
1301	+	if (funcType == "CUBIC") {
1302	+	ft = CUBIC;
1303	+	} else {
1304	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1305	+	ft = FIFTH_ORDER_POLY;
1306	+	} else {
1307	+	// throw error
1308	+	sprintf( painCave.errMsg,
1309	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1310	+	painCave.isFatal = 1;
1311	+	simError();
1312	+	}
1313	+	}
1314	+	}
1315	+
1316	+	// send switching function notification to switcheroo
1317	+	setFunctionType(&ft);
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 958 | 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 984 | 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 1020 | 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 1055 | 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 1072 | 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 1110 | 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 1132 | 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 1145 | 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	<
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 oopse
1638

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