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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 629 by chuckv, Mon Sep 26 15:58:17 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 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"
58	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
61	<	#include "UseTheForce/notifyCutoffs_interface.h"
60	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
62		#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
64		#include "selection/SelectionManager.hpp"
65	+	#include "io/ForceFieldOptions.hpp"
66	+	#include "UseTheForce/ForceField.hpp"
67
68	+
69		#ifdef IS_MPI
70		#include "UseTheForce/mpiComponentPlan.h"
71		#include "UseTheForce/DarkSide/simParallel_interface.h"
72		#endif
73
74	<	namespace oopse {
74	>	namespace OpenMD {
75	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	>	std::map<int, std::set<int> >::iterator i = container.find(index);
77	>	std::set<int> result;
78	>	if (i != container.end()) {
79	>	result = i->second;
80	>	}
81
82	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
83	<	ForceField* ff, Globals* simParams) :
84	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
85	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82	>	return result;
83	>	}
84	>
85	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86	>	forceField_(ff), simParams_(simParams),
87	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
91	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
92	<	sman_(NULL), fortranInitialized_(false) {
90	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
91	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
92	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
93	>	calcBoxDipole_(false), useAtomicVirial_(true) {
94
95	<
82	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
95	>
96		MoleculeStamp* molStamp;
97		int nMolWithSameStamp;
98		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
99	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
99	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
100		CutoffGroupStamp* cgStamp;
101		RigidBodyStamp* rbStamp;
102		int nRigidAtoms = 0;
103	<
104	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
105	<	molStamp = i->first;
106	<	nMolWithSameStamp = i->second;
103	>
104	>	std::vector<Component*> components = simParams->getComponents();
105	>
106	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
107	>	molStamp = (*i)->getMoleculeStamp();
108	>	nMolWithSameStamp = (*i)->getNMol();
109
110		addMoleculeStamp(molStamp, nMolWithSameStamp);
111
112		//calculate atoms in molecules
113		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114
100	–
115		//calculate atoms in cutoff groups
116		int nAtomsInGroups = 0;
117		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118
119		for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroup(j);
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121		nAtomsInGroups += cgStamp->getNMembers();
122		}
123
124		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	+
126		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127
128		//calculate atoms in rigid bodies
#	Line 115 | Line 130 | namespace oopse {
130		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131
132		for (int j=0; j < nRigidBodiesInStamp; j++) {
133	<	rbStamp = molStamp->getRigidBody(j);
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134		nAtomsInRigidBodies += rbStamp->getNMembers();
135		}
136
#	Line 124 | Line 139 | namespace oopse {
139
140		}
141
142	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
143	<	//therefore the total number of cutoff groups in the system is equal to
144	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
145	<	//file plus the number of cutoff groups defined in meta-data file
142	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	>	//group therefore the total number of cutoff groups in the system is
144	>	//equal to the total number of atoms minus number of atoms belong to
145	>	//cutoff group defined in meta-data file plus the number of cutoff
146	>	//groups defined in meta-data file
147		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148
149	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
150	<	//therefore the total number of  integrable objects in the system is equal to
151	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
152	<	//file plus the number of  rigid bodies defined in meta-data file
153	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
154	<
149	>	//every free atom (atom does not belong to rigid bodies) is an
150	>	//integrable object therefore the total number of integrable objects
151	>	//in the system is equal to the total number of atoms minus number of
152	>	//atoms belong to rigid body defined in meta-data file plus the number
153	>	//of rigid bodies defined in meta-data file
154	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	>	+ nGlobalRigidBodies_;
156	>
157		nGlobalMols_ = molStampIds_.size();
140	–
141	–	#ifdef IS_MPI
158		molToProcMap_.resize(nGlobalMols_);
143	–	#endif
144	–
159		}
160
161		SimInfo::~SimInfo() {
#	Line 151 | Line 165 | namespace oopse {
165		}
166		molecules_.clear();
167
154	–	delete stamps_;
168		delete sman_;
169		delete simParams_;
170		delete forceField_;
#	Line 180 | Line 193 | namespace oopse {
193		nBonds_ += mol->getNBonds();
194		nBends_ += mol->getNBends();
195		nTorsions_ += mol->getNTorsions();
196	+	nInversions_ += mol->getNInversions();
197		nRigidBodies_ += mol->getNRigidBodies();
198		nIntegrableObjects_ += mol->getNIntegrableObjects();
199		nCutoffGroups_ += mol->getNCutoffGroups();
200		nConstraints_ += mol->getNConstraintPairs();
201
202	<	addExcludePairs(mol);
203	<
202	>	addInteractionPairs(mol);
203	>
204		return true;
205		} else {
206		return false;
#	Line 205 | Line 219 | namespace oopse {
219		nBonds_ -= mol->getNBonds();
220		nBends_ -= mol->getNBends();
221		nTorsions_ -= mol->getNTorsions();
222	+	nInversions_ -= mol->getNInversions();
223		nRigidBodies_ -= mol->getNRigidBodies();
224		nIntegrableObjects_ -= mol->getNIntegrableObjects();
225		nCutoffGroups_ -= mol->getNCutoffGroups();
226		nConstraints_ -= mol->getNConstraintPairs();
227
228	<	removeExcludePairs(mol);
228	>	removeInteractionPairs(mol);
229		molecules_.erase(mol->getGlobalIndex());
230
231		delete mol;
#	Line 258 | Line 273 | namespace oopse {
273		}
274		}
275
276	<	}//end for (integrableObject)
277	<	}// end for (mol)
276	>	}
277	>	}
278
279		// n_constraints is local, so subtract them on each processor
280		ndf_local -= nConstraints_;
#	Line 276 | Line 291 | namespace oopse {
291
292		}
293
294	+	int SimInfo::getFdf() {
295	+	#ifdef IS_MPI
296	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297	+	#else
298	+	fdf_ = fdf_local;
299	+	#endif
300	+	return fdf_;
301	+	}
302	+
303		void SimInfo::calcNdfRaw() {
304		int ndfRaw_local;
305
#	Line 327 | Line 351 | namespace oopse {
351
352		}
353
354	<	void SimInfo::addExcludePairs(Molecule* mol) {
354	>	void SimInfo::addInteractionPairs(Molecule* mol) {
355	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
356		std::vector<Bond*>::iterator bondIter;
357		std::vector<Bend*>::iterator bendIter;
358		std::vector<Torsion*>::iterator torsionIter;
359	+	std::vector<Inversion*>::iterator inversionIter;
360		Bond* bond;
361		Bend* bend;
362		Torsion* torsion;
363	+	Inversion* inversion;
364		int a;
365		int b;
366		int c;
367		int d;
368	<
369	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
370	<	a = bond->getAtomA()->getGlobalIndex();
371	<	b = bond->getAtomB()->getGlobalIndex();
372	<	exclude_.addPair(a, b);
368	>
369	>	// atomGroups can be used to add special interaction maps between
370	>	// groups of atoms that are in two separate rigid bodies.
371	>	// However, most site-site interactions between two rigid bodies
372	>	// are probably not special, just the ones between the physically
373	>	// bonded atoms.  Interactions *within* a single rigid body should
374	>	// always be excluded.  These are done at the bottom of this
375	>	// function.
376	>
377	>	std::map<int, std::set<int> > atomGroups;
378	>	Molecule::RigidBodyIterator rbIter;
379	>	RigidBody* rb;
380	>	Molecule::IntegrableObjectIterator ii;
381	>	StuntDouble* integrableObject;
382	>
383	>	for (integrableObject = mol->beginIntegrableObject(ii);
384	>	integrableObject != NULL;
385	>	integrableObject = mol->nextIntegrableObject(ii)) {
386	>
387	>	if (integrableObject->isRigidBody()) {
388	>	rb = static_cast<RigidBody*>(integrableObject);
389	>	std::vector<Atom*> atoms = rb->getAtoms();
390	>	std::set<int> rigidAtoms;
391	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
392	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
393	>	}
394	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
396	>	}
397	>	} else {
398	>	std::set<int> oneAtomSet;
399	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
400	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
401	>	}
402	>	}
403	>
404	>	for (bond= mol->beginBond(bondIter); bond != NULL;
405	>	bond = mol->nextBond(bondIter)) {
406	>
407	>	a = bond->getAtomA()->getGlobalIndex();
408	>	b = bond->getAtomB()->getGlobalIndex();
409	>
410	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
411	>	oneTwoInteractions_.addPair(a, b);
412	>	} else {
413	>	excludedInteractions_.addPair(a, b);
414	>	}
415		}
416
417	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
417	>	for (bend= mol->beginBend(bendIter); bend != NULL;
418	>	bend = mol->nextBend(bendIter)) {
419	>
420		a = bend->getAtomA()->getGlobalIndex();
421		b = bend->getAtomB()->getGlobalIndex();
422		c = bend->getAtomC()->getGlobalIndex();
423	+
424	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
425	+	oneTwoInteractions_.addPair(a, b);
426	+	oneTwoInteractions_.addPair(b, c);
427	+	} else {
428	+	excludedInteractions_.addPair(a, b);
429	+	excludedInteractions_.addPair(b, c);
430	+	}
431
432	<	exclude_.addPair(a, b);
433	<	exclude_.addPair(a, c);
434	<	exclude_.addPair(b, c);
432	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	>	oneThreeInteractions_.addPair(a, c);
434	>	} else {
435	>	excludedInteractions_.addPair(a, c);
436	>	}
437		}
438
439	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
439	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
440	>	torsion = mol->nextTorsion(torsionIter)) {
441	>
442		a = torsion->getAtomA()->getGlobalIndex();
443		b = torsion->getAtomB()->getGlobalIndex();
444		c = torsion->getAtomC()->getGlobalIndex();
445	<	d = torsion->getAtomD()->getGlobalIndex();
445	>	d = torsion->getAtomD()->getGlobalIndex();
446
447	<	exclude_.addPair(a, b);
448	<	exclude_.addPair(a, c);
449	<	exclude_.addPair(a, d);
450	<	exclude_.addPair(b, c);
451	<	exclude_.addPair(b, d);
452	<	exclude_.addPair(c, d);
447	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
448	>	oneTwoInteractions_.addPair(a, b);
449	>	oneTwoInteractions_.addPair(b, c);
450	>	oneTwoInteractions_.addPair(c, d);
451	>	} else {
452	>	excludedInteractions_.addPair(a, b);
453	>	excludedInteractions_.addPair(b, c);
454	>	excludedInteractions_.addPair(c, d);
455	>	}
456	>
457	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
458	>	oneThreeInteractions_.addPair(a, c);
459	>	oneThreeInteractions_.addPair(b, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, c);
462	>	excludedInteractions_.addPair(b, d);
463	>	}
464	>
465	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
466	>	oneFourInteractions_.addPair(a, d);
467	>	} else {
468	>	excludedInteractions_.addPair(a, d);
469	>	}
470		}
471
472	<	Molecule::RigidBodyIterator rbIter;
473	<	RigidBody* rb;
474	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
472	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
473	>	inversion = mol->nextInversion(inversionIter)) {
474	>
475	>	a = inversion->getAtomA()->getGlobalIndex();
476	>	b = inversion->getAtomB()->getGlobalIndex();
477	>	c = inversion->getAtomC()->getGlobalIndex();
478	>	d = inversion->getAtomD()->getGlobalIndex();
479	>
480	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
481	>	oneTwoInteractions_.addPair(a, b);
482	>	oneTwoInteractions_.addPair(a, c);
483	>	oneTwoInteractions_.addPair(a, d);
484	>	} else {
485	>	excludedInteractions_.addPair(a, b);
486	>	excludedInteractions_.addPair(a, c);
487	>	excludedInteractions_.addPair(a, d);
488	>	}
489	>
490	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
491	>	oneThreeInteractions_.addPair(b, c);
492	>	oneThreeInteractions_.addPair(b, d);
493	>	oneThreeInteractions_.addPair(c, d);
494	>	} else {
495	>	excludedInteractions_.addPair(b, c);
496	>	excludedInteractions_.addPair(b, d);
497	>	excludedInteractions_.addPair(c, d);
498	>	}
499	>	}
500	>
501	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
502	>	rb = mol->nextRigidBody(rbIter)) {
503		std::vector<Atom*> atoms = rb->getAtoms();
504	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
505	<	for (int j = i + 1; j < atoms.size(); ++j) {
504	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
505	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
506		a = atoms[i]->getGlobalIndex();
507		b = atoms[j]->getGlobalIndex();
508	<	exclude_.addPair(a, b);
508	>	excludedInteractions_.addPair(a, b);
509		}
510		}
511		}
512
513		}
514
515	<	void SimInfo::removeExcludePairs(Molecule* mol) {
515	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
516	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
517		std::vector<Bond*>::iterator bondIter;
518		std::vector<Bend*>::iterator bendIter;
519		std::vector<Torsion*>::iterator torsionIter;
520	+	std::vector<Inversion*>::iterator inversionIter;
521		Bond* bond;
522		Bend* bend;
523		Torsion* torsion;
524	+	Inversion* inversion;
525		int a;
526		int b;
527		int c;
528		int d;
529	+
530	+	std::map<int, std::set<int> > atomGroups;
531	+	Molecule::RigidBodyIterator rbIter;
532	+	RigidBody* rb;
533	+	Molecule::IntegrableObjectIterator ii;
534	+	StuntDouble* integrableObject;
535
536	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
536	>	for (integrableObject = mol->beginIntegrableObject(ii);
537	>	integrableObject != NULL;
538	>	integrableObject = mol->nextIntegrableObject(ii)) {
539	>
540	>	if (integrableObject->isRigidBody()) {
541	>	rb = static_cast<RigidBody*>(integrableObject);
542	>	std::vector<Atom*> atoms = rb->getAtoms();
543	>	std::set<int> rigidAtoms;
544	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
545	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
546	>	}
547	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
549	>	}
550	>	} else {
551	>	std::set<int> oneAtomSet;
552	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
553	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
554	>	}
555	>	}
556	>
557	>	for (bond= mol->beginBond(bondIter); bond != NULL;
558	>	bond = mol->nextBond(bondIter)) {
559	>
560		a = bond->getAtomA()->getGlobalIndex();
561	<	b = bond->getAtomB()->getGlobalIndex();
562	<	exclude_.removePair(a, b);
561	>	b = bond->getAtomB()->getGlobalIndex();
562	>
563	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
564	>	oneTwoInteractions_.removePair(a, b);
565	>	} else {
566	>	excludedInteractions_.removePair(a, b);
567	>	}
568		}
569
570	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
570	>	for (bend= mol->beginBend(bendIter); bend != NULL;
571	>	bend = mol->nextBend(bendIter)) {
572	>
573		a = bend->getAtomA()->getGlobalIndex();
574		b = bend->getAtomB()->getGlobalIndex();
575		c = bend->getAtomC()->getGlobalIndex();
576	+
577	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
578	+	oneTwoInteractions_.removePair(a, b);
579	+	oneTwoInteractions_.removePair(b, c);
580	+	} else {
581	+	excludedInteractions_.removePair(a, b);
582	+	excludedInteractions_.removePair(b, c);
583	+	}
584
585	<	exclude_.removePair(a, b);
586	<	exclude_.removePair(a, c);
587	<	exclude_.removePair(b, c);
585	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	>	oneThreeInteractions_.removePair(a, c);
587	>	} else {
588	>	excludedInteractions_.removePair(a, c);
589	>	}
590		}
591
592	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
592	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
593	>	torsion = mol->nextTorsion(torsionIter)) {
594	>
595		a = torsion->getAtomA()->getGlobalIndex();
596		b = torsion->getAtomB()->getGlobalIndex();
597		c = torsion->getAtomC()->getGlobalIndex();
598	<	d = torsion->getAtomD()->getGlobalIndex();
598	>	d = torsion->getAtomD()->getGlobalIndex();
599	>
600	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
601	>	oneTwoInteractions_.removePair(a, b);
602	>	oneTwoInteractions_.removePair(b, c);
603	>	oneTwoInteractions_.removePair(c, d);
604	>	} else {
605	>	excludedInteractions_.removePair(a, b);
606	>	excludedInteractions_.removePair(b, c);
607	>	excludedInteractions_.removePair(c, d);
608	>	}
609
610	<	exclude_.removePair(a, b);
611	<	exclude_.removePair(a, c);
612	<	exclude_.removePair(a, d);
613	<	exclude_.removePair(b, c);
614	<	exclude_.removePair(b, d);
615	<	exclude_.removePair(c, d);
610	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
611	>	oneThreeInteractions_.removePair(a, c);
612	>	oneThreeInteractions_.removePair(b, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(b, d);
616	>	}
617	>
618	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
619	>	oneFourInteractions_.removePair(a, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, d);
622	>	}
623		}
624
625	<	Molecule::RigidBodyIterator rbIter;
626	<	RigidBody* rb;
627	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
625	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
626	>	inversion = mol->nextInversion(inversionIter)) {
627	>
628	>	a = inversion->getAtomA()->getGlobalIndex();
629	>	b = inversion->getAtomB()->getGlobalIndex();
630	>	c = inversion->getAtomC()->getGlobalIndex();
631	>	d = inversion->getAtomD()->getGlobalIndex();
632	>
633	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
634	>	oneTwoInteractions_.removePair(a, b);
635	>	oneTwoInteractions_.removePair(a, c);
636	>	oneTwoInteractions_.removePair(a, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, b);
639	>	excludedInteractions_.removePair(a, c);
640	>	excludedInteractions_.removePair(a, d);
641	>	}
642	>
643	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
644	>	oneThreeInteractions_.removePair(b, c);
645	>	oneThreeInteractions_.removePair(b, d);
646	>	oneThreeInteractions_.removePair(c, d);
647	>	} else {
648	>	excludedInteractions_.removePair(b, c);
649	>	excludedInteractions_.removePair(b, d);
650	>	excludedInteractions_.removePair(c, d);
651	>	}
652	>	}
653	>
654	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
655	>	rb = mol->nextRigidBody(rbIter)) {
656		std::vector<Atom*> atoms = rb->getAtoms();
657	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
658	<	for (int j = i + 1; j < atoms.size(); ++j) {
657	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
658	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
659		a = atoms[i]->getGlobalIndex();
660		b = atoms[j]->getGlobalIndex();
661	<	exclude_.removePair(a, b);
661	>	excludedInteractions_.removePair(a, b);
662		}
663		}
664		}
665	<
665	>
666		}
667	<
668	<
667	>
668	>
669		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
670		int curStampId;
671	<
671	>
672		//index from 0
673		curStampId = moleculeStamps_.size();
674
#	Line 466 | Line 690 | namespace oopse {
690		/** @deprecate */
691		int isError = 0;
692
693	+	setupCutoff();
694	+
695		setupElectrostaticSummationMethod( isError );
696	+	setupSwitchingFunction();
697	+	setupAccumulateBoxDipole();
698
699		if(isError){
700		sprintf( painCave.errMsg,
#	Line 474 | Line 702 | namespace oopse {
702		painCave.isFatal = 1;
703		simError();
704		}
477	–
478	–
479	–	setupCutoff();
705
706		calcNdf();
707		calcNdfRaw();
#	Line 511 | Line 736 | namespace oopse {
736		int useLennardJones = 0;
737		int useElectrostatic = 0;
738		int useEAM = 0;
739	+	int useSC = 0;
740		int useCharge = 0;
741		int useDirectional = 0;
742		int useDipole = 0;
#	Line 522 | Line 748 | namespace oopse {
748		int useDirectionalAtom = 0;
749		int useElectrostatics = 0;
750		//usePBC and useRF are from simParams
751	<	int usePBC = simParams_->getPBC();
751	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
752		int useRF;
753	+	int useSF;
754	+	int useSP;
755	+	int useBoxDipole;
756
757	+	std::string myMethod;
758	+
759		// set the useRF logical
760	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
761	<	if (myMethod == "REACTION_FIELD")
762	<	useRF = 1;
763	<	else
533	<	useRF = 0;
760	>	useRF = 0;
761	>	useSF = 0;
762	>	useSP = 0;
763	>	useBoxDipole = 0;
764
765	+	if (simParams_->haveElectrostaticSummationMethod()) {
766	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
767	+	toUpper(myMethod);
768	+	if (myMethod == "REACTION_FIELD"){
769	+	useRF = 1;
770	+	} else if (myMethod == "SHIFTED_FORCE"){
771	+	useSF = 1;
772	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
773	+	useSP = 1;
774	+	}
775	+	}
776	+
777	+	if (simParams_->haveAccumulateBoxDipole())
778	+	if (simParams_->getAccumulateBoxDipole())
779	+	useBoxDipole = 1;
780	+
781	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
782	+
783		//loop over all of the atom types
784		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785		useLennardJones |= (*i)->isLennardJones();
786		useElectrostatic |= (*i)->isElectrostatic();
787		useEAM |= (*i)->isEAM();
788	+	useSC |= (*i)->isSC();
789		useCharge |= (*i)->isCharge();
790		useDirectional |= (*i)->isDirectional();
791		useDipole |= (*i)->isDipole();
#	Line 587 | Line 836 | namespace oopse {
836		temp = useEAM;
837		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838
839	+	temp = useSC;
840	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841	+
842		temp = useShape;
843		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844
#	Line 596 | Line 848 | namespace oopse {
848		temp = useRF;
849		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850
851	<	#endif
851	>	temp = useSF;
852	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853
854	+	temp = useSP;
855	+	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	+
857	+	temp = useBoxDipole;
858	+	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	+
860	+	temp = useAtomicVirial_;
861	+	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	+
863	+	#endif
864		fInfo_.SIM_uses_PBC = usePBC;
865		fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
866		fInfo_.SIM_uses_LennardJones = useLennardJones;
#	Line 608 | Line 871 | namespace oopse {
871		fInfo_.SIM_uses_StickyPower = useStickyPower;
872		fInfo_.SIM_uses_GayBerne = useGayBerne;
873		fInfo_.SIM_uses_EAM = useEAM;
874	+	fInfo_.SIM_uses_SC = useSC;
875		fInfo_.SIM_uses_Shapes = useShape;
876		fInfo_.SIM_uses_FLARB = useFLARB;
877		fInfo_.SIM_uses_RF = useRF;
878	<
879	<	if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") {
880	<
881	<	if (simParams_->haveDielectric()) {
618	<	fInfo_.dielect = simParams_->getDielectric();
619	<	} else {
620	<	sprintf(painCave.errMsg,
621	<	"SimSetup Error: No Dielectric constant was set.\n"
622	<	"\tYou are trying to use Reaction Field without"
623	<	"\tsetting a dielectric constant!\n");
624	<	painCave.isFatal = 1;
625	<	simError();
626	<	}
627	<
628	<	} else {
629	<	fInfo_.dielect = 0.0;
630	<	}
631	<
878	>	fInfo_.SIM_uses_SF = useSF;
879	>	fInfo_.SIM_uses_SP = useSP;
880	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
881	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
882		}
883
884		void SimInfo::setupFortranSim() {
885		int isError;
886	<	int nExclude;
886	>	int nExclude, nOneTwo, nOneThree, nOneFour;
887		std::vector<int> fortranGlobalGroupMembership;
888
639	–	nExclude = exclude_.getSize();
889		isError = 0;
890
891		//globalGroupMembership_ is filled by SimCreator
#	Line 645 | Line 894 | namespace oopse {
894		}
895
896		//calculate mass ratio of cutoff group
897	<	std::vector<double> mfact;
897	>	std::vector<RealType> mfact;
898		SimInfo::MoleculeIterator mi;
899		Molecule* mol;
900		Molecule::CutoffGroupIterator ci;
901		CutoffGroup* cg;
902		Molecule::AtomIterator ai;
903		Atom* atom;
904	<	double totalMass;
904	>	RealType totalMass;
905
906		//to avoid memory reallocation, reserve enough space for mfact
907		mfact.reserve(getNCutoffGroups());
#	Line 662 | Line 911 | namespace oopse {
911
912		totalMass = cg->getMass();
913		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
914	<	mfact.push_back(atom->getMass()/totalMass);
914	>	// Check for massless groups - set mfact to 1 if true
915	>	if (totalMass != 0)
916	>	mfact.push_back(atom->getMass()/totalMass);
917	>	else
918	>	mfact.push_back( 1.0 );
919		}
667	–
920		}
921		}
922
#	Line 688 | Line 940 | namespace oopse {
940		}
941
942		//setup fortran simulation
691	–	int nGlobalExcludes = 0;
692	–	int* globalExcludes = NULL;
693	–	int* excludeList = exclude_.getExcludeList();
694	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
695	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
696	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
943
944	<	if( isError ){
944	>	nExclude = excludedInteractions_.getSize();
945	>	nOneTwo = oneTwoInteractions_.getSize();
946	>	nOneThree = oneThreeInteractions_.getSize();
947	>	nOneFour = oneFourInteractions_.getSize();
948	>
949	>	int* excludeList = excludedInteractions_.getPairList();
950	>	int* oneTwoList = oneTwoInteractions_.getPairList();
951	>	int* oneThreeList = oneThreeInteractions_.getPairList();
952	>	int* oneFourList = oneFourInteractions_.getPairList();
953
954	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
955	+	&nExclude, excludeList,
956	+	&nOneTwo, oneTwoList,
957	+	&nOneThree, oneThreeList,
958	+	&nOneFour, oneFourList,
959	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
960	+	&fortranGlobalGroupMembership[0], &isError);
961	+
962	+	if( isError ){
963	+
964		sprintf( painCave.errMsg,
965		"There was an error setting the simulation information in fortran.\n" );
966		painCave.isFatal = 1;
967	<	painCave.severity = OOPSE_ERROR;
967	>	painCave.severity = OPENMD_ERROR;
968		simError();
969		}
970	<
971	<	#ifdef IS_MPI
970	>
971	>
972		sprintf( checkPointMsg,
973		"succesfully sent the simulation information to fortran.\n");
974	<	MPIcheckPoint();
975	<	#endif // is_mpi
974	>
975	>	errorCheckPoint();
976	>
977	>	// Setup number of neighbors in neighbor list if present
978	>	if (simParams_->haveNeighborListNeighbors()) {
979	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
980	>	setNeighbors(&nlistNeighbors);
981	>	}
982	>
983	>
984		}
985
986
715	–	#ifdef IS_MPI
987		void SimInfo::setupFortranParallel() {
988	<
988	>	#ifdef IS_MPI
989		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
990		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
991		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 764 | Line 1035 | namespace oopse {
1035		}
1036
1037		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1038	<	MPIcheckPoint();
1038	>	errorCheckPoint();
1039
769	–
770	–	}
771	–
1040		#endif
773	–
774	–	double SimInfo::calcMaxCutoffRadius() {
775	–
776	–
777	–	std::set<AtomType*> atomTypes;
778	–	std::set<AtomType*>::iterator i;
779	–	std::vector<double> cutoffRadius;
780	–
781	–	//get the unique atom types
782	–	atomTypes = getUniqueAtomTypes();
783	–
784	–	//query the max cutoff radius among these atom types
785	–	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
786	–	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
787	–	}
788	–
789	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
790	–	#ifdef IS_MPI
791	–	//pick the max cutoff radius among the processors
792	–	#endif
793	–
794	–	return maxCutoffRadius;
1041		}
1042
1043	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
1043	>	void SimInfo::setupCutoff() {
1044
1045	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
800	<
801	<	if (!simParams_->haveRcut()){
802	<	sprintf(painCave.errMsg,
803	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
804	<	"\tOOPSE will use a default value of 15.0 angstroms"
805	<	"\tfor the cutoffRadius.\n");
806	<	painCave.isFatal = 0;
807	<	simError();
808	<	rcut = 15.0;
809	<	} else{
810	<	rcut = simParams_->getRcut();
811	<	}
1045	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1046
1047	<	if (!simParams_->haveRsw()){
1048	<	sprintf(painCave.errMsg,
815	<	"SimCreator Warning: No value was set for switchingRadius.\n"
816	<	"\tOOPSE will use a default value of\n"
817	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	rsw = 0.95 * rcut;
821	<	} else{
822	<	rsw = simParams_->getRsw();
823	<	}
1047	>	// Check the cutoff policy
1048	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1049
1050	<	} else {
1051	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1052	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
828	<
829	<	if (simParams_->haveRcut()) {
830	<	rcut = simParams_->getRcut();
831	<	} else {
832	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
833	<	rcut = calcMaxCutoffRadius();
834	<	}
1050	>	// Set LJ shifting bools to false
1051	>	ljsp_ = 0;
1052	>	ljsf_ = 0;
1053
1054	<	if (simParams_->haveRsw()) {
1055	<	rsw  = simParams_->getRsw();
1056	<	} else {
1057	<	rsw = rcut;
1058	<	}
841	<
1054	>	std::string myPolicy;
1055	>	if (forceFieldOptions_.haveCutoffPolicy()){
1056	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1057	>	}else if (simParams_->haveCutoffPolicy()) {
1058	>	myPolicy = simParams_->getCutoffPolicy();
1059		}
843	–	}
1060
1061	<	void SimInfo::setupCutoff() {
1062	<	getCutoff(rcut_, rsw_);
847	<	double rnblist = rcut_ + 1; // skin of neighbor list
848	<
849	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
850	<
851	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
852	<	if (simParams_->haveCutoffPolicy()) {
853	<	std::string myPolicy = simParams_->getCutoffPolicy();
1061	>	if (!myPolicy.empty()){
1062	>	toUpper(myPolicy);
1063		if (myPolicy == "MIX") {
1064		cp = MIX_CUTOFF_POLICY;
1065		} else {
#	Line 868 | Line 1077 | namespace oopse {
1077		}
1078		}
1079		}
1080	<	}
1080	>	}
1081	>	notifyFortranCutoffPolicy(&cp);
1082
1083	<
1083	>	// Check the Skin Thickness for neighborlists
1084	>	RealType skin;
1085		if (simParams_->haveSkinThickness()) {
1086	<	double skinThickness = simParams_->getSkinThickness();
1087	<	}
1086	>	skin = simParams_->getSkinThickness();
1087	>	notifyFortranSkinThickness(&skin);
1088	>	}
1089	>
1090	>	// Check if the cutoff was set explicitly:
1091	>	if (simParams_->haveCutoffRadius()) {
1092	>	rcut_ = simParams_->getCutoffRadius();
1093	>	if (simParams_->haveSwitchingRadius()) {
1094	>	rsw_  = simParams_->getSwitchingRadius();
1095	>	} else {
1096	>	if (fInfo_.SIM_uses_Charges |
1097	>	fInfo_.SIM_uses_Dipoles |
1098	>	fInfo_.SIM_uses_RF) {
1099	>
1100	>	rsw_ = 0.85 * rcut_;
1101	>	sprintf(painCave.errMsg,
1102	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1103	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1104	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1105	>	painCave.isFatal = 0;
1106	>	simError();
1107	>	} else {
1108	>	rsw_ = rcut_;
1109	>	sprintf(painCave.errMsg,
1110	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1111	>	"\tOpenMD will use the same value as the cutoffRadius.\n"
1112	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1113	>	painCave.isFatal = 0;
1114	>	simError();
1115	>	}
1116	>	}
1117
1118	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1119	<	// also send cutoff notification to electrostatics
1120	<	setElectrostaticCutoffRadius(&rcut_);
1118	>	if (simParams_->haveElectrostaticSummationMethod()) {
1119	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1120	>	toUpper(myMethod);
1121	>
1122	>	if (myMethod == "SHIFTED_POTENTIAL") {
1123	>	ljsp_ = 1;
1124	>	} else if (myMethod == "SHIFTED_FORCE") {
1125	>	ljsf_ = 1;
1126	>	}
1127	>	}
1128	>
1129	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1130	>
1131	>	} else {
1132	>
1133	>	// For electrostatic atoms, we'll assume a large safe value:
1134	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1135	>	sprintf(painCave.errMsg,
1136	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1137	>	"\tOpenMD will use a default value of 15.0 angstroms"
1138	>	"\tfor the cutoffRadius.\n");
1139	>	painCave.isFatal = 0;
1140	>	simError();
1141	>	rcut_ = 15.0;
1142	>
1143	>	if (simParams_->haveElectrostaticSummationMethod()) {
1144	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1145	>	toUpper(myMethod);
1146	>
1147	>	// For the time being, we're tethering the LJ shifted behavior to the
1148	>	// electrostaticSummationMethod keyword options
1149	>	if (myMethod == "SHIFTED_POTENTIAL") {
1150	>	ljsp_ = 1;
1151	>	} else if (myMethod == "SHIFTED_FORCE") {
1152	>	ljsf_ = 1;
1153	>	}
1154	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1155	>	if (simParams_->haveSwitchingRadius()){
1156	>	sprintf(painCave.errMsg,
1157	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1158	>	"\teven though the electrostaticSummationMethod was\n"
1159	>	"\tset to %s\n", myMethod.c_str());
1160	>	painCave.isFatal = 1;
1161	>	simError();
1162	>	}
1163	>	}
1164	>	}
1165	>
1166	>	if (simParams_->haveSwitchingRadius()){
1167	>	rsw_ = simParams_->getSwitchingRadius();
1168	>	} else {
1169	>	sprintf(painCave.errMsg,
1170	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1171	>	"\tOpenMD will use a default value of\n"
1172	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1173	>	painCave.isFatal = 0;
1174	>	simError();
1175	>	rsw_ = 0.85 * rcut_;
1176	>	}
1177	>
1178	>	Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1179	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1180	>
1181	>	} else {
1182	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1183	>	// We'll punt and let fortran figure out the cutoffs later.
1184	>
1185	>	notifyFortranYouAreOnYourOwn();
1186	>
1187	>	}
1188	>	}
1189		}
1190
1191		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1192
1193		int errorOut;
1194	<	int esm =  NONE;
1195	<	double alphaVal;
1196	<	double dielectric;
1197	<
1194	>	ElectrostaticSummationMethod esm = NONE;
1195	>	ElectrostaticScreeningMethod sm = UNDAMPED;
1196	>	RealType alphaVal;
1197	>	RealType dielectric;
1198	>
1199		errorOut = isError;
891	–	alphaVal = simParams_->getDampingAlpha();
892	–	dielectric = simParams_->getDielectric();
1200
1201		if (simParams_->haveElectrostaticSummationMethod()) {
1202		std::string myMethod = simParams_->getElectrostaticSummationMethod();
1203	+	toUpper(myMethod);
1204		if (myMethod == "NONE") {
1205		esm = NONE;
1206		} else {
1207	<	if (myMethod == "UNDAMPED_WOLF") {
1208	<	esm = UNDAMPED_WOLF;
1207	>	if (myMethod == "SWITCHING_FUNCTION") {
1208	>	esm = SWITCHING_FUNCTION;
1209		} else {
1210	<	if (myMethod == "DAMPED_WOLF") {
1211	<	esm = DAMPED_WOLF;
1212	<	if (!simParams_->haveDampingAlpha()) {
1213	<	//throw error
1214	<	sprintf( painCave.errMsg,
907	<	"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.", alphaVal);
908	<	painCave.isFatal = 0;
909	<	simError();
910	<	}
911	<	} else {
912	<	if (myMethod == "REACTION_FIELD") {
913	<	esm = REACTION_FIELD;
1210	>	if (myMethod == "SHIFTED_POTENTIAL") {
1211	>	esm = SHIFTED_POTENTIAL;
1212	>	} else {
1213	>	if (myMethod == "SHIFTED_FORCE") {
1214	>	esm = SHIFTED_FORCE;
1215		} else {
1216	<	// throw error
1217	<	sprintf( painCave.errMsg,
1218	<	"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() );
1219	<	painCave.isFatal = 1;
1220	<	simError();
1221	<	}
1222	<	}
1216	>	if (myMethod == "REACTION_FIELD") {
1217	>	esm = REACTION_FIELD;
1218	>	dielectric = simParams_->getDielectric();
1219	>	if (!simParams_->haveDielectric()) {
1220	>	// throw warning
1221	>	sprintf( painCave.errMsg,
1222	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1223	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1224	>	painCave.isFatal = 0;
1225	>	simError();
1226	>	}
1227	>	} else {
1228	>	// throw error
1229	>	sprintf( painCave.errMsg,
1230	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1231	>	"\t(Input file specified %s .)\n"
1232	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1233	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1234	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1235	>	painCave.isFatal = 1;
1236	>	simError();
1237	>	}
1238	>	}
1239	>	}
1240		}
1241		}
1242		}
1243	<	// let's pass some summation method variables to fortran
1244	<	setElectrostaticSummationMethod( &esm );
1245	<	setDampedWolfAlpha( &alphaVal );
1246	<	setReactionFieldDielectric( &dielectric );
1247	<	initFortranFF( &esm, &errorOut );
1243	>
1244	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1245	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1246	>	toUpper(myScreen);
1247	>	if (myScreen == "UNDAMPED") {
1248	>	sm = UNDAMPED;
1249	>	} else {
1250	>	if (myScreen == "DAMPED") {
1251	>	sm = DAMPED;
1252	>	if (!simParams_->haveDampingAlpha()) {
1253	>	// first set a cutoff dependent alpha value
1254	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1255	>	alphaVal = 0.5125 - rcut_* 0.025;
1256	>	// for values rcut > 20.5, alpha is zero
1257	>	if (alphaVal < 0) alphaVal = 0;
1258	>
1259	>	// throw warning
1260	>	sprintf( painCave.errMsg,
1261	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1262	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1263	>	painCave.isFatal = 0;
1264	>	simError();
1265	>	} else {
1266	>	alphaVal = simParams_->getDampingAlpha();
1267	>	}
1268	>
1269	>	} else {
1270	>	// throw error
1271	>	sprintf( painCave.errMsg,
1272	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1273	>	"\t(Input file specified %s .)\n"
1274	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1275	>	"or \"damped\".\n", myScreen.c_str() );
1276	>	painCave.isFatal = 1;
1277	>	simError();
1278	>	}
1279	>	}
1280	>	}
1281	>
1282	>
1283	>	Electrostatic::setElectrostaticSummationMethod( esm );
1284	>	Electrostatic::setElectrostaticScreeningMethod( sm );
1285	>	Electrostatic::setDampingAlpha( alphaVal );
1286	>	Electrostatic::setReactionFieldDielectric( dielectric );
1287	>	initFortranFF( &errorOut );
1288	>	}
1289	>
1290	>	void SimInfo::setupSwitchingFunction() {
1291	>	int ft = CUBIC;
1292	>
1293	>	if (simParams_->haveSwitchingFunctionType()) {
1294	>	std::string funcType = simParams_->getSwitchingFunctionType();
1295	>	toUpper(funcType);
1296	>	if (funcType == "CUBIC") {
1297	>	ft = CUBIC;
1298	>	} else {
1299	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1300	>	ft = FIFTH_ORDER_POLY;
1301	>	} else {
1302	>	// throw error
1303	>	sprintf( painCave.errMsg,
1304	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1305	>	painCave.isFatal = 1;
1306	>	simError();
1307	>	}
1308	>	}
1309	>	}
1310	>
1311	>	// send switching function notification to switcheroo
1312	>	setFunctionType(&ft);
1313	>
1314	>	}
1315	>
1316	>	void SimInfo::setupAccumulateBoxDipole() {
1317	>
1318	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1319	>	if ( simParams_->haveAccumulateBoxDipole() )
1320	>	if ( simParams_->getAccumulateBoxDipole() ) {
1321	>	setAccumulateBoxDipole();
1322	>	calcBoxDipole_ = true;
1323	>	}
1324	>
1325		}
1326
1327		void SimInfo::addProperty(GenericData* genData) {
#	Line 985 | Line 1380 | namespace oopse {
1380		Molecule* mol;
1381
1382		Vector3d comVel(0.0);
1383	<	double totalMass = 0.0;
1383	>	RealType totalMass = 0.0;
1384
1385
1386		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1387	<	double mass = mol->getMass();
1387	>	RealType mass = mol->getMass();
1388		totalMass += mass;
1389		comVel += mass * mol->getComVel();
1390		}
1391
1392		#ifdef IS_MPI
1393	<	double tmpMass = totalMass;
1393	>	RealType tmpMass = totalMass;
1394		Vector3d tmpComVel(comVel);
1395	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1396	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1395	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1396	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1397		#endif
1398
1399		comVel /= totalMass;
#	Line 1011 | Line 1406 | namespace oopse {
1406		Molecule* mol;
1407
1408		Vector3d com(0.0);
1409	<	double totalMass = 0.0;
1409	>	RealType totalMass = 0.0;
1410
1411		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1412	<	double mass = mol->getMass();
1412	>	RealType mass = mol->getMass();
1413		totalMass += mass;
1414		com += mass * mol->getCom();
1415		}
1416
1417		#ifdef IS_MPI
1418	<	double tmpMass = totalMass;
1418	>	RealType tmpMass = totalMass;
1419		Vector3d tmpCom(com);
1420	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1421	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1420	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1421	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1422		#endif
1423
1424		com /= totalMass;
#	Line 1047 | Line 1442 | namespace oopse {
1442		Molecule* mol;
1443
1444
1445	<	double totalMass = 0.0;
1445	>	RealType totalMass = 0.0;
1446
1447
1448		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1449	<	double mass = mol->getMass();
1449	>	RealType mass = mol->getMass();
1450		totalMass += mass;
1451		com += mass * mol->getCom();
1452		comVel += mass * mol->getComVel();
1453		}
1454
1455		#ifdef IS_MPI
1456	<	double tmpMass = totalMass;
1456	>	RealType tmpMass = totalMass;
1457		Vector3d tmpCom(com);
1458		Vector3d tmpComVel(comVel);
1459	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1460	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1461	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1459	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1460	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1461	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1462		#endif
1463
1464		com /= totalMass;
#	Line 1075 | Line 1470 | namespace oopse {
1470
1471
1472		[  Ixx -Ixy  -Ixz ]
1473	<	J =| -Iyx  Iyy  -Iyz |
1473	>	J =| -Iyx  Iyy  -Iyz |
1474		[ -Izx -Iyz   Izz ]
1475		*/
1476
1477		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1478
1479
1480	<	double xx = 0.0;
1481	<	double yy = 0.0;
1482	<	double zz = 0.0;
1483	<	double xy = 0.0;
1484	<	double xz = 0.0;
1485	<	double yz = 0.0;
1480	>	RealType xx = 0.0;
1481	>	RealType yy = 0.0;
1482	>	RealType zz = 0.0;
1483	>	RealType xy = 0.0;
1484	>	RealType xz = 0.0;
1485	>	RealType yz = 0.0;
1486		Vector3d com(0.0);
1487		Vector3d comVel(0.0);
1488
#	Line 1099 | Line 1494 | namespace oopse {
1494		Vector3d thisq(0.0);
1495		Vector3d thisv(0.0);
1496
1497	<	double thisMass = 0.0;
1497	>	RealType thisMass = 0.0;
1498
1499
1500
#	Line 1137 | Line 1532 | namespace oopse {
1532		#ifdef IS_MPI
1533		Mat3x3d tmpI(inertiaTensor);
1534		Vector3d tmpAngMom;
1535	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1536	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1535	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1536	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1537		#endif
1538
1539		return;
#	Line 1159 | Line 1554 | namespace oopse {
1554		Vector3d thisr(0.0);
1555		Vector3d thisp(0.0);
1556
1557	<	double thisMass;
1557	>	RealType thisMass;
1558
1559		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1560		thisMass = mol->getMass();
#	Line 1172 | Line 1567 | namespace oopse {
1567
1568		#ifdef IS_MPI
1569		Vector3d tmpAngMom;
1570	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1570	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1571		#endif
1572
1573		return angularMomentum;
1574		}
1575
1576	<
1577	<	}//end namespace oopse
1576	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1577	>	return IOIndexToIntegrableObject.at(index);
1578	>	}
1579	>
1580	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1581	>	IOIndexToIntegrableObject= v;
1582	>	}
1583
1584	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1585	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1586	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1587	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1588	+	*/
1589	+	void SimInfo::getGyrationalVolume(RealType &volume){
1590	+	Mat3x3d intTensor;
1591	+	RealType det;
1592	+	Vector3d dummyAngMom;
1593	+	RealType sysconstants;
1594	+	RealType geomCnst;
1595	+
1596	+	geomCnst = 3.0/2.0;
1597	+	/* Get the inertial tensor and angular momentum for free*/
1598	+	getInertiaTensor(intTensor,dummyAngMom);
1599	+
1600	+	det = intTensor.determinant();
1601	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1602	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1603	+	return;
1604	+	}
1605	+
1606	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1607	+	Mat3x3d intTensor;
1608	+	Vector3d dummyAngMom;
1609	+	RealType sysconstants;
1610	+	RealType geomCnst;
1611	+
1612	+	geomCnst = 3.0/2.0;
1613	+	/* Get the inertial tensor and angular momentum for free*/
1614	+	getInertiaTensor(intTensor,dummyAngMom);
1615	+
1616	+	detI = intTensor.determinant();
1617	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1618	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1619	+	return;
1620	+	}
1621	+	/*
1622	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1623	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1624	+	sdByGlobalIndex_ = v;
1625	+	}
1626	+
1627	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1628	+	//assert(index < nAtoms_ + nRigidBodies_);
1629	+	return sdByGlobalIndex_.at(index);
1630	+	}
1631	+	*/
1632	+	}//end namespace OpenMD
1633	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 629 by chuckv, Mon Sep 26 15:58:17 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC

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