ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/src/brains/SimInfo.cpp (file contents), Revision 598 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 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/fCoulombicCorrection.h"
58	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60	<	#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	<
81	<	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
99	–
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 114 | 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 123 | 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();
139	–
140	–	#ifdef IS_MPI
158		molToProcMap_.resize(nGlobalMols_);
142	–	#endif
143	–
159		}
160
161		SimInfo::~SimInfo() {
#	Line 150 | Line 165 | namespace oopse {
165		}
166		molecules_.clear();
167
153	–	delete stamps_;
168		delete sman_;
169		delete simParams_;
170		delete forceField_;
#	Line 179 | 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 204 | 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 257 | 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 275 | 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 326 | 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 465 | Line 690 | namespace oopse {
690		/** @deprecate */
691		int isError = 0;
692
693	<	setupCoulombicCorrection( isError );
693	>	setupCutoff();
694	>
695	>	setupElectrostaticSummationMethod( isError );
696	>	setupSwitchingFunction();
697	>	setupAccumulateBoxDipole();
698
699		if(isError){
700		sprintf( painCave.errMsg,
#	Line 473 | Line 702 | namespace oopse {
702		painCave.isFatal = 1;
703		simError();
704		}
476	–
477	–
478	–	setupCutoff();
705
706		calcNdf();
707		calcNdfRaw();
#	Line 510 | 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 521 | Line 748 | namespace oopse {
748		int useDirectionalAtom = 0;
749		int useElectrostatics = 0;
750		//usePBC and useRF are from simParams
751	<	int usePBC = simParams_->getPBC();
752	<	int useRF = simParams_->getUseRF();
751	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
752	>	int useRF;
753	>	int useSF;
754	>	int useSP;
755	>	int useBoxDipole;
756
757	+	std::string myMethod;
758	+
759	+	// set the useRF logical
760	+	useRF = 0;
761	+	useSF = 0;
762	+	useSP = 0;
763	+	useBoxDipole = 0;
764	+
765	+
766	+	if (simParams_->haveElectrostaticSummationMethod()) {
767	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
768	+	toUpper(myMethod);
769	+	if (myMethod == "REACTION_FIELD"){
770	+	useRF = 1;
771	+	} else if (myMethod == "SHIFTED_FORCE"){
772	+	useSF = 1;
773	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
774	+	useSP = 1;
775	+	}
776	+	}
777	+
778	+	if (simParams_->haveAccumulateBoxDipole())
779	+	if (simParams_->getAccumulateBoxDipole())
780	+	useBoxDipole = 1;
781	+
782	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
783	+
784		//loop over all of the atom types
785		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
786		useLennardJones |= (*i)->isLennardJones();
787		useElectrostatic |= (*i)->isElectrostatic();
788		useEAM |= (*i)->isEAM();
789	+	useSC |= (*i)->isSC();
790		useCharge |= (*i)->isCharge();
791		useDirectional |= (*i)->isDirectional();
792		useDipole |= (*i)->isDipole();
#	Line 579 | Line 837 | namespace oopse {
837		temp = useEAM;
838		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839
840	+	temp = useSC;
841	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842	+
843		temp = useShape;
844		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845
#	Line 588 | Line 849 | namespace oopse {
849		temp = useRF;
850		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851
852	<	temp = useUW;
853	<	MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	temp = useSF;
853	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	>
855	>	temp = useSP;
856	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857
858	<	temp = useDW;
859	<	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	<
858	>	temp = useBoxDipole;
859	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>
861	>	temp = useAtomicVirial_;
862	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	>
864		#endif
865
866		fInfo_.SIM_uses_PBC = usePBC;
#	Line 606 | Line 873 | namespace oopse {
873		fInfo_.SIM_uses_StickyPower = useStickyPower;
874		fInfo_.SIM_uses_GayBerne = useGayBerne;
875		fInfo_.SIM_uses_EAM = useEAM;
876	+	fInfo_.SIM_uses_SC = useSC;
877		fInfo_.SIM_uses_Shapes = useShape;
878		fInfo_.SIM_uses_FLARB = useFLARB;
879		fInfo_.SIM_uses_RF = useRF;
880	<
881	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
882	<
883	<	if (simParams_->haveDielectric()) {
616	<	fInfo_.dielect = simParams_->getDielectric();
617	<	} else {
618	<	sprintf(painCave.errMsg,
619	<	"SimSetup Error: No Dielectric constant was set.\n"
620	<	"\tYou are trying to use Reaction Field without"
621	<	"\tsetting a dielectric constant!\n");
622	<	painCave.isFatal = 1;
623	<	simError();
624	<	}
625	<
626	<	} else {
627	<	fInfo_.dielect = 0.0;
628	<	}
629	<
880	>	fInfo_.SIM_uses_SF = useSF;
881	>	fInfo_.SIM_uses_SP = useSP;
882	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
883	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
884		}
885
886		void SimInfo::setupFortranSim() {
887		int isError;
888	<	int nExclude;
888	>	int nExclude, nOneTwo, nOneThree, nOneFour;
889		std::vector<int> fortranGlobalGroupMembership;
890
637	–	nExclude = exclude_.getSize();
891		isError = 0;
892
893		//globalGroupMembership_ is filled by SimCreator
#	Line 643 | Line 896 | namespace oopse {
896		}
897
898		//calculate mass ratio of cutoff group
899	<	std::vector<double> mfact;
899	>	std::vector<RealType> mfact;
900		SimInfo::MoleculeIterator mi;
901		Molecule* mol;
902		Molecule::CutoffGroupIterator ci;
903		CutoffGroup* cg;
904		Molecule::AtomIterator ai;
905		Atom* atom;
906	<	double totalMass;
906	>	RealType totalMass;
907
908		//to avoid memory reallocation, reserve enough space for mfact
909		mfact.reserve(getNCutoffGroups());
#	Line 660 | Line 913 | namespace oopse {
913
914		totalMass = cg->getMass();
915		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
916	<	mfact.push_back(atom->getMass()/totalMass);
916	>	// Check for massless groups - set mfact to 1 if true
917	>	if (totalMass != 0)
918	>	mfact.push_back(atom->getMass()/totalMass);
919	>	else
920	>	mfact.push_back( 1.0 );
921		}
665	–
922		}
923		}
924
#	Line 686 | Line 942 | namespace oopse {
942		}
943
944		//setup fortran simulation
689	–	int nGlobalExcludes = 0;
690	–	int* globalExcludes = NULL;
691	–	int* excludeList = exclude_.getExcludeList();
692	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
693	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
694	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
945
946	<	if( isError ){
946	>	nExclude = excludedInteractions_.getSize();
947	>	nOneTwo = oneTwoInteractions_.getSize();
948	>	nOneThree = oneThreeInteractions_.getSize();
949	>	nOneFour = oneFourInteractions_.getSize();
950	>
951	>	int* excludeList = excludedInteractions_.getPairList();
952	>	int* oneTwoList = oneTwoInteractions_.getPairList();
953	>	int* oneThreeList = oneThreeInteractions_.getPairList();
954	>	int* oneFourList = oneFourInteractions_.getPairList();
955
956	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
957	+	&nExclude, excludeList,
958	+	&nOneTwo, oneTwoList,
959	+	&nOneThree, oneThreeList,
960	+	&nOneFour, oneFourList,
961	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
962	+	&fortranGlobalGroupMembership[0], &isError);
963	+
964	+	if( isError ){
965	+
966		sprintf( painCave.errMsg,
967		"There was an error setting the simulation information in fortran.\n" );
968		painCave.isFatal = 1;
969	<	painCave.severity = OOPSE_ERROR;
969	>	painCave.severity = OPENMD_ERROR;
970		simError();
971		}
972	<
973	<	#ifdef IS_MPI
972	>
973	>
974		sprintf( checkPointMsg,
975		"succesfully sent the simulation information to fortran.\n");
976	<	MPIcheckPoint();
977	<	#endif // is_mpi
976	>
977	>	errorCheckPoint();
978	>
979	>	// Setup number of neighbors in neighbor list if present
980	>	if (simParams_->haveNeighborListNeighbors()) {
981	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
982	>	setNeighbors(&nlistNeighbors);
983	>	}
984	>
985	>
986		}
987
988
713	–	#ifdef IS_MPI
989		void SimInfo::setupFortranParallel() {
990	<
990	>	#ifdef IS_MPI
991		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
992		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
993		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 762 | Line 1037 | namespace oopse {
1037		}
1038
1039		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1040	<	MPIcheckPoint();
1040	>	errorCheckPoint();
1041
767	–
768	–	}
769	–
1042		#endif
771	–
772	–	double SimInfo::calcMaxCutoffRadius() {
773	–
774	–
775	–	std::set<AtomType*> atomTypes;
776	–	std::set<AtomType*>::iterator i;
777	–	std::vector<double> cutoffRadius;
778	–
779	–	//get the unique atom types
780	–	atomTypes = getUniqueAtomTypes();
781	–
782	–	//query the max cutoff radius among these atom types
783	–	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784	–	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
785	–	}
786	–
787	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
788	–	#ifdef IS_MPI
789	–	//pick the max cutoff radius among the processors
790	–	#endif
791	–
792	–	return maxCutoffRadius;
1043		}
1044
1045	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
1045	>	void SimInfo::setupCutoff() {
1046
1047	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
798	<
799	<	if (!simParams_->haveRcut()){
800	<	sprintf(painCave.errMsg,
801	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
802	<	"\tOOPSE will use a default value of 15.0 angstroms"
803	<	"\tfor the cutoffRadius.\n");
804	<	painCave.isFatal = 0;
805	<	simError();
806	<	rcut = 15.0;
807	<	} else{
808	<	rcut = simParams_->getRcut();
809	<	}
1047	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1048
1049	<	if (!simParams_->haveRsw()){
1050	<	sprintf(painCave.errMsg,
813	<	"SimCreator Warning: No value was set for switchingRadius.\n"
814	<	"\tOOPSE will use a default value of\n"
815	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
816	<	painCave.isFatal = 0;
817	<	simError();
818	<	rsw = 0.95 * rcut;
819	<	} else{
820	<	rsw = simParams_->getRsw();
821	<	}
1049	>	// Check the cutoff policy
1050	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1051
1052	<	} else {
1053	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1054	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
826	<
827	<	if (simParams_->haveRcut()) {
828	<	rcut = simParams_->getRcut();
829	<	} else {
830	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
831	<	rcut = calcMaxCutoffRadius();
832	<	}
1052	>	// Set LJ shifting bools to false
1053	>	ljsp_ = 0;
1054	>	ljsf_ = 0;
1055
1056	<	if (simParams_->haveRsw()) {
1057	<	rsw  = simParams_->getRsw();
1058	<	} else {
1059	<	rsw = rcut;
1060	<	}
839	<
1056	>	std::string myPolicy;
1057	>	if (forceFieldOptions_.haveCutoffPolicy()){
1058	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1059	>	}else if (simParams_->haveCutoffPolicy()) {
1060	>	myPolicy = simParams_->getCutoffPolicy();
1061		}
841	–	}
1062
1063	<	void SimInfo::setupCutoff() {
1064	<	getCutoff(rcut_, rsw_);
845	<	double rnblist = rcut_ + 1; // skin of neighbor list
846	<
847	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
848	<
849	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
850	<	if (simParams_->haveCutoffPolicy()) {
851	<	std::string myPolicy = simParams_->getCutoffPolicy();
1063	>	if (!myPolicy.empty()){
1064	>	toUpper(myPolicy);
1065		if (myPolicy == "MIX") {
1066		cp = MIX_CUTOFF_POLICY;
1067		} else {
#	Line 866 | Line 1079 | namespace oopse {
1079		}
1080		}
1081		}
1082	+	}
1083	+	notifyFortranCutoffPolicy(&cp);
1084	+
1085	+	// Check the Skin Thickness for neighborlists
1086	+	RealType skin;
1087	+	if (simParams_->haveSkinThickness()) {
1088	+	skin = simParams_->getSkinThickness();
1089	+	notifyFortranSkinThickness(&skin);
1090	+	}
1091	+
1092	+	// Check if the cutoff was set explicitly:
1093	+	if (simParams_->haveCutoffRadius()) {
1094	+	rcut_ = simParams_->getCutoffRadius();
1095	+	if (simParams_->haveSwitchingRadius()) {
1096	+	rsw_  = simParams_->getSwitchingRadius();
1097	+	} else {
1098	+	if (fInfo_.SIM_uses_Charges |
1099	+	fInfo_.SIM_uses_Dipoles |
1100	+	fInfo_.SIM_uses_RF) {
1101	+
1102	+	rsw_ = 0.85 * rcut_;
1103	+	sprintf(painCave.errMsg,
1104	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
1105	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1106	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1107	+	painCave.isFatal = 0;
1108	+	simError();
1109	+	} else {
1110	+	rsw_ = rcut_;
1111	+	sprintf(painCave.errMsg,
1112	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
1113	+	"\tOpenMD will use the same value as the cutoffRadius.\n"
1114	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1115	+	painCave.isFatal = 0;
1116	+	simError();
1117	+	}
1118	+	}
1119	+
1120	+	if (simParams_->haveElectrostaticSummationMethod()) {
1121	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1122	+	toUpper(myMethod);
1123	+
1124	+	if (myMethod == "SHIFTED_POTENTIAL") {
1125	+	ljsp_ = 1;
1126	+	} else if (myMethod == "SHIFTED_FORCE") {
1127	+	ljsf_ = 1;
1128	+	}
1129	+	}
1130	+
1131	+	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1132	+
1133	+	} else {
1134	+
1135	+	// For electrostatic atoms, we'll assume a large safe value:
1136	+	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1137	+	sprintf(painCave.errMsg,
1138	+	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1139	+	"\tOpenMD will use a default value of 15.0 angstroms"
1140	+	"\tfor the cutoffRadius.\n");
1141	+	painCave.isFatal = 0;
1142	+	simError();
1143	+	rcut_ = 15.0;
1144	+
1145	+	if (simParams_->haveElectrostaticSummationMethod()) {
1146	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1147	+	toUpper(myMethod);
1148	+
1149	+	// For the time being, we're tethering the LJ shifted behavior to the
1150	+	// electrostaticSummationMethod keyword options
1151	+	if (myMethod == "SHIFTED_POTENTIAL") {
1152	+	ljsp_ = 1;
1153	+	} else if (myMethod == "SHIFTED_FORCE") {
1154	+	ljsf_ = 1;
1155	+	}
1156	+	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1157	+	if (simParams_->haveSwitchingRadius()){
1158	+	sprintf(painCave.errMsg,
1159	+	"SimInfo Warning: A value was set for the switchingRadius\n"
1160	+	"\teven though the electrostaticSummationMethod was\n"
1161	+	"\tset to %s\n", myMethod.c_str());
1162	+	painCave.isFatal = 1;
1163	+	simError();
1164	+	}
1165	+	}
1166	+	}
1167	+
1168	+	if (simParams_->haveSwitchingRadius()){
1169	+	rsw_ = simParams_->getSwitchingRadius();
1170	+	} else {
1171	+	sprintf(painCave.errMsg,
1172	+	"SimCreator Warning: No value was set for switchingRadius.\n"
1173	+	"\tOpenMD will use a default value of\n"
1174	+	"\t0.85 * cutoffRadius for the switchingRadius\n");
1175	+	painCave.isFatal = 0;
1176	+	simError();
1177	+	rsw_ = 0.85 * rcut_;
1178	+	}
1179	+
1180	+	Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1181	+	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1182	+
1183	+	} else {
1184	+	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1185	+	// We'll punt and let fortran figure out the cutoffs later.
1186	+
1187	+	notifyFortranYouAreOnYourOwn();
1188	+
1189	+	}
1190		}
870	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1191		}
1192
1193	<	void SimInfo::setupCoulombicCorrection( int isError ) {
1193	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1194
1195		int errorOut;
1196	<	int cc =  NONE;
1197	<	double alphaVal;
1198	<
1196	>	ElectrostaticSummationMethod esm = NONE;
1197	>	ElectrostaticScreeningMethod sm = UNDAMPED;
1198	>	RealType alphaVal;
1199	>	RealType dielectric;
1200	>
1201		errorOut = isError;
1202
1203	<	if (simParams_->haveCoulombicCorrection()) {
1204	<	std::string myCorrection = simParams_->getCoulombicCorrection();
1205	<	if (myCorrection == "NONE") {
1206	<	cc = NONE;
1203	>	if (simParams_->haveElectrostaticSummationMethod()) {
1204	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1205	>	toUpper(myMethod);
1206	>	if (myMethod == "NONE") {
1207	>	esm = NONE;
1208		} else {
1209	<	if (myCorrection == "UNDAMPED_WOLF") {
1210	<	cc = UNDAMPED_WOLF;
1209	>	if (myMethod == "SWITCHING_FUNCTION") {
1210	>	esm = SWITCHING_FUNCTION;
1211		} else {
1212	<	if (myCorrection == "WOLF") {
1213	<	cc = WOLF;
1214	<	if (!simParams_->haveDampingAlpha()) {
1215	<	//throw error
1216	<	sprintf( painCave.errMsg,
894	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Wolf Coulombic Correction.", simParams_->getDampingAlpha());
895	<	painCave.isFatal = 0;
896	<	simError();
897	<	}
898	<	alphaVal = simParams_->getDampingAlpha();
899	<	} else {
900	<	if (myCorrection == "REACTION_FIELD") {
901	<	cc = REACTION_FIELD;
1212	>	if (myMethod == "SHIFTED_POTENTIAL") {
1213	>	esm = SHIFTED_POTENTIAL;
1214	>	} else {
1215	>	if (myMethod == "SHIFTED_FORCE") {
1216	>	esm = SHIFTED_FORCE;
1217		} else {
1218	<	// throw error
1219	<	sprintf( painCave.errMsg,
1220	<	"SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() );
1221	<	painCave.isFatal = 1;
1222	<	simError();
1223	<	}
1224	<	}
1218	>	if (myMethod == "REACTION_FIELD") {
1219	>	esm = REACTION_FIELD;
1220	>	dielectric = simParams_->getDielectric();
1221	>	if (!simParams_->haveDielectric()) {
1222	>	// throw warning
1223	>	sprintf( painCave.errMsg,
1224	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1225	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1226	>	painCave.isFatal = 0;
1227	>	simError();
1228	>	}
1229	>	} else {
1230	>	// throw error
1231	>	sprintf( painCave.errMsg,
1232	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1233	>	"\t(Input file specified %s .)\n"
1234	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1235	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1236	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1237	>	painCave.isFatal = 1;
1238	>	simError();
1239	>	}
1240	>	}
1241	>	}
1242		}
1243		}
1244		}
1245	<	initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut );
1245	>
1246	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1247	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1248	>	toUpper(myScreen);
1249	>	if (myScreen == "UNDAMPED") {
1250	>	sm = UNDAMPED;
1251	>	} else {
1252	>	if (myScreen == "DAMPED") {
1253	>	sm = DAMPED;
1254	>	if (!simParams_->haveDampingAlpha()) {
1255	>	// first set a cutoff dependent alpha value
1256	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1257	>	alphaVal = 0.5125 - rcut_* 0.025;
1258	>	// for values rcut > 20.5, alpha is zero
1259	>	if (alphaVal < 0) alphaVal = 0;
1260	>
1261	>	// throw warning
1262	>	sprintf( painCave.errMsg,
1263	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1264	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1265	>	painCave.isFatal = 0;
1266	>	simError();
1267	>	} else {
1268	>	alphaVal = simParams_->getDampingAlpha();
1269	>	}
1270	>
1271	>	} else {
1272	>	// throw error
1273	>	sprintf( painCave.errMsg,
1274	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1275	>	"\t(Input file specified %s .)\n"
1276	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1277	>	"or \"damped\".\n", myScreen.c_str() );
1278	>	painCave.isFatal = 1;
1279	>	simError();
1280	>	}
1281	>	}
1282	>	}
1283	>
1284	>
1285	>	Electrostatic::setElectrostaticSummationMethod( esm );
1286	>	Electrostatic::setElectrostaticScreeningMethod( sm );
1287	>	Electrostatic::setDampingAlpha( alphaVal );
1288	>	Electrostatic::setReactionFieldDielectric( dielectric );
1289	>	initFortranFF( &errorOut );
1290		}
1291
1292	+	void SimInfo::setupSwitchingFunction() {
1293	+	int ft = CUBIC;
1294	+
1295	+	if (simParams_->haveSwitchingFunctionType()) {
1296	+	std::string funcType = simParams_->getSwitchingFunctionType();
1297	+	toUpper(funcType);
1298	+	if (funcType == "CUBIC") {
1299	+	ft = CUBIC;
1300	+	} else {
1301	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1302	+	ft = FIFTH_ORDER_POLY;
1303	+	} else {
1304	+	// throw error
1305	+	sprintf( painCave.errMsg,
1306	+	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1307	+	painCave.isFatal = 1;
1308	+	simError();
1309	+	}
1310	+	}
1311	+	}
1312	+
1313	+	// send switching function notification to switcheroo
1314	+	setFunctionType(&ft);
1315	+
1316	+	}
1317	+
1318	+	void SimInfo::setupAccumulateBoxDipole() {
1319	+
1320	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1321	+	if ( simParams_->haveAccumulateBoxDipole() )
1322	+	if ( simParams_->getAccumulateBoxDipole() ) {
1323	+	setAccumulateBoxDipole();
1324	+	calcBoxDipole_ = true;
1325	+	}
1326	+
1327	+	}
1328	+
1329		void SimInfo::addProperty(GenericData* genData) {
1330		properties_.addProperty(genData);
1331		}
#	Line 969 | Line 1382 | namespace oopse {
1382		Molecule* mol;
1383
1384		Vector3d comVel(0.0);
1385	<	double totalMass = 0.0;
1385	>	RealType totalMass = 0.0;
1386
1387
1388		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1389	<	double mass = mol->getMass();
1389	>	RealType mass = mol->getMass();
1390		totalMass += mass;
1391		comVel += mass * mol->getComVel();
1392		}
1393
1394		#ifdef IS_MPI
1395	<	double tmpMass = totalMass;
1395	>	RealType tmpMass = totalMass;
1396		Vector3d tmpComVel(comVel);
1397	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1398	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1397	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399		#endif
1400
1401		comVel /= totalMass;
#	Line 995 | Line 1408 | namespace oopse {
1408		Molecule* mol;
1409
1410		Vector3d com(0.0);
1411	<	double totalMass = 0.0;
1411	>	RealType totalMass = 0.0;
1412
1413		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1414	<	double mass = mol->getMass();
1414	>	RealType mass = mol->getMass();
1415		totalMass += mass;
1416		com += mass * mol->getCom();
1417		}
1418
1419		#ifdef IS_MPI
1420	<	double tmpMass = totalMass;
1420	>	RealType tmpMass = totalMass;
1421		Vector3d tmpCom(com);
1422	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1423	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1422	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1423	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1424		#endif
1425
1426		com /= totalMass;
#	Line 1031 | Line 1444 | namespace oopse {
1444		Molecule* mol;
1445
1446
1447	<	double totalMass = 0.0;
1447	>	RealType totalMass = 0.0;
1448
1449
1450		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1451	<	double mass = mol->getMass();
1451	>	RealType mass = mol->getMass();
1452		totalMass += mass;
1453		com += mass * mol->getCom();
1454		comVel += mass * mol->getComVel();
1455		}
1456
1457		#ifdef IS_MPI
1458	<	double tmpMass = totalMass;
1458	>	RealType tmpMass = totalMass;
1459		Vector3d tmpCom(com);
1460		Vector3d tmpComVel(comVel);
1461	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1462	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1463	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1461	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1462	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1463	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1464		#endif
1465
1466		com /= totalMass;
#	Line 1066 | Line 1479 | namespace oopse {
1479		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1480
1481
1482	<	double xx = 0.0;
1483	<	double yy = 0.0;
1484	<	double zz = 0.0;
1485	<	double xy = 0.0;
1486	<	double xz = 0.0;
1487	<	double yz = 0.0;
1482	>	RealType xx = 0.0;
1483	>	RealType yy = 0.0;
1484	>	RealType zz = 0.0;
1485	>	RealType xy = 0.0;
1486	>	RealType xz = 0.0;
1487	>	RealType yz = 0.0;
1488		Vector3d com(0.0);
1489		Vector3d comVel(0.0);
1490
#	Line 1083 | Line 1496 | namespace oopse {
1496		Vector3d thisq(0.0);
1497		Vector3d thisv(0.0);
1498
1499	<	double thisMass = 0.0;
1499	>	RealType thisMass = 0.0;
1500
1501
1502
#	Line 1121 | Line 1534 | namespace oopse {
1534		#ifdef IS_MPI
1535		Mat3x3d tmpI(inertiaTensor);
1536		Vector3d tmpAngMom;
1537	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1538	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1537	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1538	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1539		#endif
1540
1541		return;
#	Line 1143 | Line 1556 | namespace oopse {
1556		Vector3d thisr(0.0);
1557		Vector3d thisp(0.0);
1558
1559	<	double thisMass;
1559	>	RealType thisMass;
1560
1561		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1562		thisMass = mol->getMass();
#	Line 1156 | Line 1569 | namespace oopse {
1569
1570		#ifdef IS_MPI
1571		Vector3d tmpAngMom;
1572	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1572	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1573		#endif
1574
1575		return angularMomentum;
1576		}
1577
1578	<
1579	<	}//end namespace oopse
1578	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1579	>	return IOIndexToIntegrableObject.at(index);
1580	>	}
1581	>
1582	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1583	>	IOIndexToIntegrableObject= v;
1584	>	}
1585
1586	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1587	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1588	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1589	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1590	+	*/
1591	+	void SimInfo::getGyrationalVolume(RealType &volume){
1592	+	Mat3x3d intTensor;
1593	+	RealType det;
1594	+	Vector3d dummyAngMom;
1595	+	RealType sysconstants;
1596	+	RealType geomCnst;
1597	+
1598	+	geomCnst = 3.0/2.0;
1599	+	/* Get the inertial tensor and angular momentum for free*/
1600	+	getInertiaTensor(intTensor,dummyAngMom);
1601	+
1602	+	det = intTensor.determinant();
1603	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1604	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1605	+	return;
1606	+	}
1607	+
1608	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1609	+	Mat3x3d intTensor;
1610	+	Vector3d dummyAngMom;
1611	+	RealType sysconstants;
1612	+	RealType geomCnst;
1613	+
1614	+	geomCnst = 3.0/2.0;
1615	+	/* Get the inertial tensor and angular momentum for free*/
1616	+	getInertiaTensor(intTensor,dummyAngMom);
1617	+
1618	+	detI = intTensor.determinant();
1619	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1620	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1621	+	return;
1622	+	}
1623	+	/*
1624	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1625	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1626	+	sdByGlobalIndex_ = v;
1627	+	}
1628	+
1629	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1630	+	//assert(index < nAtoms_ + nRigidBodies_);
1631	+	return sdByGlobalIndex_.at(index);
1632	+	}
1633	+	*/
1634	+	}//end namespace OpenMD
1635	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 598 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines