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 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 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 "UseTheForce/fCutoffPolicy.h"
57	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
58		#include "UseTheForce/doForces_interface.h"
58	–	#include "UseTheForce/notifyCutoffs_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62	+	#include "io/ForceFieldOptions.hpp"
63	+	#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
66		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	<	namespace oopse {
72	<
73	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
74	<	ForceField* ff, Globals* simParams) :
75	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
76	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
71	>	using namespace std;
72	>	namespace OpenMD {
73	>
74	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75	>	forceField_(ff), simParams_(simParams),
76	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
80	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
81	<	sman_(NULL), fortranInitialized_(false) {
82	<
80	<
81	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
82	<	MoleculeStamp* molStamp;
83	<	int nMolWithSameStamp;
84	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
86	<	CutoffGroupStamp* cgStamp;
87	<	RigidBodyStamp* rbStamp;
88	<	int nRigidAtoms = 0;
79	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83
84	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
85	<	molStamp = i->first;
86	<	nMolWithSameStamp = i->second;
87	<
88	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
89	<
90	<	//calculate atoms in molecules
91	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
92	<
93	<
94	<	//calculate atoms in cutoff groups
95	<	int nAtomsInGroups = 0;
96	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
97	<
98	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
99	<	cgStamp = molStamp->getCutoffGroup(j);
100	<	nAtomsInGroups += cgStamp->getNMembers();
101	<	}
102	<
103	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
104	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
105	<
106	<	//calculate atoms in rigid bodies
107	<	int nAtomsInRigidBodies = 0;
108	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
109	<
116	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
117	<	rbStamp = molStamp->getRigidBody(j);
118	<	nAtomsInRigidBodies += rbStamp->getNMembers();
119	<	}
120	<
121	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123	<
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97	>
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110		}
111	<
112	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
113	<	//therefore the total number of cutoff groups in the system is equal to
114	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
115	<	//file plus the number of cutoff groups defined in meta-data file
116	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
117	<
118	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
119	<	//therefore the total number of  integrable objects in the system is equal to
120	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
121	<	//file plus the number of  rigid bodies defined in meta-data file
122	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
123	<
124	<	nGlobalMols_ = molStampIds_.size();
125	<
126	<	#ifdef IS_MPI
127	<	molToProcMap_.resize(nGlobalMols_);
128	<	#endif
129	<
130	<	}
131	<
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128	>	}
129	>
130	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	>	//group therefore the total number of cutoff groups in the system is
132	>	//equal to the total number of atoms minus number of atoms belong to
133	>	//cutoff group defined in meta-data file plus the number of cutoff
134	>	//groups defined in meta-data file
135	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
136	>
137	>	//every free atom (atom does not belong to rigid bodies) is an
138	>	//integrable object therefore the total number of integrable objects
139	>	//in the system is equal to the total number of atoms minus number of
140	>	//atoms belong to rigid body defined in meta-data file plus the number
141	>	//of rigid bodies defined in meta-data file
142	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
143	>	+ nGlobalRigidBodies_;
144	>
145	>	nGlobalMols_ = molStampIds_.size();
146	>	molToProcMap_.resize(nGlobalMols_);
147	>	}
148	>
149		SimInfo::~SimInfo() {
150	<	std::map<int, Molecule*>::iterator i;
150	>	map<int, Molecule*>::iterator i;
151		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
152		delete i->second;
153		}
154		molecules_.clear();
155
153	–	delete stamps_;
156		delete sman_;
157		delete simParams_;
158		delete forceField_;
159		}
160
159	–	int SimInfo::getNGlobalConstraints() {
160	–	int nGlobalConstraints;
161	–	#ifdef IS_MPI
162	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
163	–	MPI_COMM_WORLD);
164	–	#else
165	–	nGlobalConstraints =  nConstraints_;
166	–	#endif
167	–	return nGlobalConstraints;
168	–	}
161
162		bool SimInfo::addMolecule(Molecule* mol) {
163		MoleculeIterator i;
164	<
164	>
165		i = molecules_.find(mol->getGlobalIndex());
166		if (i == molecules_.end() ) {
167	<
168	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
169	<
167	>
168	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
169	>
170		nAtoms_ += mol->getNAtoms();
171		nBonds_ += mol->getNBonds();
172		nBends_ += mol->getNBends();
173		nTorsions_ += mol->getNTorsions();
174	+	nInversions_ += mol->getNInversions();
175		nRigidBodies_ += mol->getNRigidBodies();
176		nIntegrableObjects_ += mol->getNIntegrableObjects();
177		nCutoffGroups_ += mol->getNCutoffGroups();
178		nConstraints_ += mol->getNConstraintPairs();
179	<
180	<	addExcludePairs(mol);
181	<
179	>
180	>	addInteractionPairs(mol);
181	>
182		return true;
183		} else {
184		return false;
185		}
186		}
187	<
187	>
188		bool SimInfo::removeMolecule(Molecule* mol) {
189		MoleculeIterator i;
190		i = molecules_.find(mol->getGlobalIndex());
#	Line 204 | Line 197 | namespace oopse {
197		nBonds_ -= mol->getNBonds();
198		nBends_ -= mol->getNBends();
199		nTorsions_ -= mol->getNTorsions();
200	+	nInversions_ -= mol->getNInversions();
201		nRigidBodies_ -= mol->getNRigidBodies();
202		nIntegrableObjects_ -= mol->getNIntegrableObjects();
203		nCutoffGroups_ -= mol->getNCutoffGroups();
204		nConstraints_ -= mol->getNConstraintPairs();
205
206	<	removeExcludePairs(mol);
206	>	removeInteractionPairs(mol);
207		molecules_.erase(mol->getGlobalIndex());
208
209		delete mol;
#	Line 218 | Line 212 | namespace oopse {
212		} else {
213		return false;
214		}
221	–
222	–
215		}
216
217
#	Line 237 | Line 229 | namespace oopse {
229		void SimInfo::calcNdf() {
230		int ndf_local;
231		MoleculeIterator i;
232	<	std::vector<StuntDouble*>::iterator j;
232	>	vector<StuntDouble*>::iterator j;
233		Molecule* mol;
234		StuntDouble* integrableObject;
235
#	Line 257 | Line 249 | namespace oopse {
249		}
250		}
251
252	<	}//end for (integrableObject)
253	<	}// end for (mol)
252	>	}
253	>	}
254
255		// n_constraints is local, so subtract them on each processor
256		ndf_local -= nConstraints_;
#	Line 275 | Line 267 | namespace oopse {
267
268		}
269
270	+	int SimInfo::getFdf() {
271	+	#ifdef IS_MPI
272	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
273	+	#else
274	+	fdf_ = fdf_local;
275	+	#endif
276	+	return fdf_;
277	+	}
278	+
279		void SimInfo::calcNdfRaw() {
280		int ndfRaw_local;
281
282		MoleculeIterator i;
283	<	std::vector<StuntDouble*>::iterator j;
283	>	vector<StuntDouble*>::iterator j;
284		Molecule* mol;
285		StuntDouble* integrableObject;
286
#	Line 326 | Line 327 | namespace oopse {
327
328		}
329
330	<	void SimInfo::addExcludePairs(Molecule* mol) {
331	<	std::vector<Bond*>::iterator bondIter;
332	<	std::vector<Bend*>::iterator bendIter;
333	<	std::vector<Torsion*>::iterator torsionIter;
330	>	void SimInfo::addInteractionPairs(Molecule* mol) {
331	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
332	>	vector<Bond*>::iterator bondIter;
333	>	vector<Bend*>::iterator bendIter;
334	>	vector<Torsion*>::iterator torsionIter;
335	>	vector<Inversion*>::iterator inversionIter;
336		Bond* bond;
337		Bend* bend;
338		Torsion* torsion;
339	+	Inversion* inversion;
340		int a;
341		int b;
342		int c;
343		int d;
344	+
345	+	// atomGroups can be used to add special interaction maps between
346	+	// groups of atoms that are in two separate rigid bodies.
347	+	// However, most site-site interactions between two rigid bodies
348	+	// are probably not special, just the ones between the physically
349	+	// bonded atoms.  Interactions *within* a single rigid body should
350	+	// always be excluded.  These are done at the bottom of this
351	+	// function.
352	+
353	+	map<int, set<int> > atomGroups;
354	+	Molecule::RigidBodyIterator rbIter;
355	+	RigidBody* rb;
356	+	Molecule::IntegrableObjectIterator ii;
357	+	StuntDouble* integrableObject;
358
359	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
359	>	for (integrableObject = mol->beginIntegrableObject(ii);
360	>	integrableObject != NULL;
361	>	integrableObject = mol->nextIntegrableObject(ii)) {
362	>
363	>	if (integrableObject->isRigidBody()) {
364	>	rb = static_cast<RigidBody*>(integrableObject);
365	>	vector<Atom*> atoms = rb->getAtoms();
366	>	set<int> rigidAtoms;
367	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
368	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
369	>	}
370	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
371	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372	>	}
373	>	} else {
374	>	set<int> oneAtomSet;
375	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
376	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377	>	}
378	>	}
379	>
380	>	for (bond= mol->beginBond(bondIter); bond != NULL;
381	>	bond = mol->nextBond(bondIter)) {
382	>
383		a = bond->getAtomA()->getGlobalIndex();
384	<	b = bond->getAtomB()->getGlobalIndex();
385	<	exclude_.addPair(a, b);
384	>	b = bond->getAtomB()->getGlobalIndex();
385	>
386	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
387	>	oneTwoInteractions_.addPair(a, b);
388	>	} else {
389	>	excludedInteractions_.addPair(a, b);
390	>	}
391		}
392
393	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
393	>	for (bend= mol->beginBend(bendIter); bend != NULL;
394	>	bend = mol->nextBend(bendIter)) {
395	>
396		a = bend->getAtomA()->getGlobalIndex();
397		b = bend->getAtomB()->getGlobalIndex();
398		c = bend->getAtomC()->getGlobalIndex();
399	<
400	<	exclude_.addPair(a, b);
401	<	exclude_.addPair(a, c);
402	<	exclude_.addPair(b, c);
399	>
400	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
401	>	oneTwoInteractions_.addPair(a, b);
402	>	oneTwoInteractions_.addPair(b, c);
403	>	} else {
404	>	excludedInteractions_.addPair(a, b);
405	>	excludedInteractions_.addPair(b, c);
406	>	}
407	>
408	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
409	>	oneThreeInteractions_.addPair(a, c);
410	>	} else {
411	>	excludedInteractions_.addPair(a, c);
412	>	}
413		}
414
415	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
415	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
416	>	torsion = mol->nextTorsion(torsionIter)) {
417	>
418		a = torsion->getAtomA()->getGlobalIndex();
419		b = torsion->getAtomB()->getGlobalIndex();
420		c = torsion->getAtomC()->getGlobalIndex();
421	<	d = torsion->getAtomD()->getGlobalIndex();
421	>	d = torsion->getAtomD()->getGlobalIndex();
422
423	<	exclude_.addPair(a, b);
424	<	exclude_.addPair(a, c);
425	<	exclude_.addPair(a, d);
426	<	exclude_.addPair(b, c);
427	<	exclude_.addPair(b, d);
428	<	exclude_.addPair(c, d);
423	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
424	>	oneTwoInteractions_.addPair(a, b);
425	>	oneTwoInteractions_.addPair(b, c);
426	>	oneTwoInteractions_.addPair(c, d);
427	>	} else {
428	>	excludedInteractions_.addPair(a, b);
429	>	excludedInteractions_.addPair(b, c);
430	>	excludedInteractions_.addPair(c, d);
431	>	}
432	>
433	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
434	>	oneThreeInteractions_.addPair(a, c);
435	>	oneThreeInteractions_.addPair(b, d);
436	>	} else {
437	>	excludedInteractions_.addPair(a, c);
438	>	excludedInteractions_.addPair(b, d);
439	>	}
440	>
441	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
442	>	oneFourInteractions_.addPair(a, d);
443	>	} else {
444	>	excludedInteractions_.addPair(a, d);
445	>	}
446		}
447
448	<	Molecule::RigidBodyIterator rbIter;
449	<	RigidBody* rb;
450	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
451	<	std::vector<Atom*> atoms = rb->getAtoms();
452	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
453	<	for (int j = i + 1; j < atoms.size(); ++j) {
448	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
449	>	inversion = mol->nextInversion(inversionIter)) {
450	>
451	>	a = inversion->getAtomA()->getGlobalIndex();
452	>	b = inversion->getAtomB()->getGlobalIndex();
453	>	c = inversion->getAtomC()->getGlobalIndex();
454	>	d = inversion->getAtomD()->getGlobalIndex();
455	>
456	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	>	oneTwoInteractions_.addPair(a, b);
458	>	oneTwoInteractions_.addPair(a, c);
459	>	oneTwoInteractions_.addPair(a, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, b);
462	>	excludedInteractions_.addPair(a, c);
463	>	excludedInteractions_.addPair(a, d);
464	>	}
465	>
466	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
467	>	oneThreeInteractions_.addPair(b, c);
468	>	oneThreeInteractions_.addPair(b, d);
469	>	oneThreeInteractions_.addPair(c, d);
470	>	} else {
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(b, d);
473	>	excludedInteractions_.addPair(c, d);
474	>	}
475	>	}
476	>
477	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478	>	rb = mol->nextRigidBody(rbIter)) {
479	>	vector<Atom*> atoms = rb->getAtoms();
480	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
481	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
482		a = atoms[i]->getGlobalIndex();
483		b = atoms[j]->getGlobalIndex();
484	<	exclude_.addPair(a, b);
484	>	excludedInteractions_.addPair(a, b);
485		}
486		}
487		}
488
489		}
490
491	<	void SimInfo::removeExcludePairs(Molecule* mol) {
492	<	std::vector<Bond*>::iterator bondIter;
493	<	std::vector<Bend*>::iterator bendIter;
494	<	std::vector<Torsion*>::iterator torsionIter;
491	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
492	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
493	>	vector<Bond*>::iterator bondIter;
494	>	vector<Bend*>::iterator bendIter;
495	>	vector<Torsion*>::iterator torsionIter;
496	>	vector<Inversion*>::iterator inversionIter;
497		Bond* bond;
498		Bend* bend;
499		Torsion* torsion;
500	+	Inversion* inversion;
501		int a;
502		int b;
503		int c;
504		int d;
505	+
506	+	map<int, set<int> > atomGroups;
507	+	Molecule::RigidBodyIterator rbIter;
508	+	RigidBody* rb;
509	+	Molecule::IntegrableObjectIterator ii;
510	+	StuntDouble* integrableObject;
511
512	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
512	>	for (integrableObject = mol->beginIntegrableObject(ii);
513	>	integrableObject != NULL;
514	>	integrableObject = mol->nextIntegrableObject(ii)) {
515	>
516	>	if (integrableObject->isRigidBody()) {
517	>	rb = static_cast<RigidBody*>(integrableObject);
518	>	vector<Atom*> atoms = rb->getAtoms();
519	>	set<int> rigidAtoms;
520	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
521	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
522	>	}
523	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
524	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525	>	}
526	>	} else {
527	>	set<int> oneAtomSet;
528	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
529	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530	>	}
531	>	}
532	>
533	>	for (bond= mol->beginBond(bondIter); bond != NULL;
534	>	bond = mol->nextBond(bondIter)) {
535	>
536		a = bond->getAtomA()->getGlobalIndex();
537	<	b = bond->getAtomB()->getGlobalIndex();
538	<	exclude_.removePair(a, b);
537	>	b = bond->getAtomB()->getGlobalIndex();
538	>
539	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
540	>	oneTwoInteractions_.removePair(a, b);
541	>	} else {
542	>	excludedInteractions_.removePair(a, b);
543	>	}
544		}
545
546	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
546	>	for (bend= mol->beginBend(bendIter); bend != NULL;
547	>	bend = mol->nextBend(bendIter)) {
548	>
549		a = bend->getAtomA()->getGlobalIndex();
550		b = bend->getAtomB()->getGlobalIndex();
551		c = bend->getAtomC()->getGlobalIndex();
552	+
553	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
554	+	oneTwoInteractions_.removePair(a, b);
555	+	oneTwoInteractions_.removePair(b, c);
556	+	} else {
557	+	excludedInteractions_.removePair(a, b);
558	+	excludedInteractions_.removePair(b, c);
559	+	}
560
561	<	exclude_.removePair(a, b);
562	<	exclude_.removePair(a, c);
563	<	exclude_.removePair(b, c);
561	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
562	>	oneThreeInteractions_.removePair(a, c);
563	>	} else {
564	>	excludedInteractions_.removePair(a, c);
565	>	}
566		}
567
568	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
568	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
569	>	torsion = mol->nextTorsion(torsionIter)) {
570	>
571		a = torsion->getAtomA()->getGlobalIndex();
572		b = torsion->getAtomB()->getGlobalIndex();
573		c = torsion->getAtomC()->getGlobalIndex();
574	<	d = torsion->getAtomD()->getGlobalIndex();
574	>	d = torsion->getAtomD()->getGlobalIndex();
575	>
576	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
577	>	oneTwoInteractions_.removePair(a, b);
578	>	oneTwoInteractions_.removePair(b, c);
579	>	oneTwoInteractions_.removePair(c, d);
580	>	} else {
581	>	excludedInteractions_.removePair(a, b);
582	>	excludedInteractions_.removePair(b, c);
583	>	excludedInteractions_.removePair(c, d);
584	>	}
585
586	<	exclude_.removePair(a, b);
587	<	exclude_.removePair(a, c);
588	<	exclude_.removePair(a, d);
589	<	exclude_.removePair(b, c);
590	<	exclude_.removePair(b, d);
591	<	exclude_.removePair(c, d);
586	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
587	>	oneThreeInteractions_.removePair(a, c);
588	>	oneThreeInteractions_.removePair(b, d);
589	>	} else {
590	>	excludedInteractions_.removePair(a, c);
591	>	excludedInteractions_.removePair(b, d);
592	>	}
593	>
594	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
595	>	oneFourInteractions_.removePair(a, d);
596	>	} else {
597	>	excludedInteractions_.removePair(a, d);
598	>	}
599		}
600
601	<	Molecule::RigidBodyIterator rbIter;
602	<	RigidBody* rb;
603	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
604	<	std::vector<Atom*> atoms = rb->getAtoms();
605	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
606	<	for (int j = i + 1; j < atoms.size(); ++j) {
601	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
602	>	inversion = mol->nextInversion(inversionIter)) {
603	>
604	>	a = inversion->getAtomA()->getGlobalIndex();
605	>	b = inversion->getAtomB()->getGlobalIndex();
606	>	c = inversion->getAtomC()->getGlobalIndex();
607	>	d = inversion->getAtomD()->getGlobalIndex();
608	>
609	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
610	>	oneTwoInteractions_.removePair(a, b);
611	>	oneTwoInteractions_.removePair(a, c);
612	>	oneTwoInteractions_.removePair(a, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, b);
615	>	excludedInteractions_.removePair(a, c);
616	>	excludedInteractions_.removePair(a, d);
617	>	}
618	>
619	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
620	>	oneThreeInteractions_.removePair(b, c);
621	>	oneThreeInteractions_.removePair(b, d);
622	>	oneThreeInteractions_.removePair(c, d);
623	>	} else {
624	>	excludedInteractions_.removePair(b, c);
625	>	excludedInteractions_.removePair(b, d);
626	>	excludedInteractions_.removePair(c, d);
627	>	}
628	>	}
629	>
630	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
631	>	rb = mol->nextRigidBody(rbIter)) {
632	>	vector<Atom*> atoms = rb->getAtoms();
633	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
634	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
635		a = atoms[i]->getGlobalIndex();
636		b = atoms[j]->getGlobalIndex();
637	<	exclude_.removePair(a, b);
637	>	excludedInteractions_.removePair(a, b);
638		}
639		}
640		}
641	<
641	>
642		}
643	<
644	<
643	>
644	>
645		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
646		int curStampId;
647	<
647	>
648		//index from 0
649		curStampId = moleculeStamps_.size();
650
#	Line 451 | Line 652 | namespace oopse {
652		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
653		}
654
454	–	void SimInfo::update() {
655
656	<	setupSimType();
657	<
658	<	#ifdef IS_MPI
659	<	setupFortranParallel();
660	<	#endif
661	<
662	<	setupFortranSim();
663	<
664	<	//setup fortran force field
465	<	/** @deprecate */
466	<	int isError = 0;
467	<
468	<	setupElectrostaticSummationMethod( isError );
469	<
470	<	if(isError){
471	<	sprintf( painCave.errMsg,
472	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
473	<	painCave.isFatal = 1;
474	<	simError();
475	<	}
476	<
477	<
478	<	setupCutoff();
479	<
656	>	/**
657	>	* update
658	>	*
659	>	*  Performs the global checks and variable settings after the
660	>	*  objects have been created.
661	>	*
662	>	*/
663	>	void SimInfo::update() {
664	>	setupSimVariables();
665		calcNdf();
666		calcNdfRaw();
667		calcNdfTrans();
483	–
484	–	fortranInitialized_ = true;
668		}
669	<
670	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
669	>
670	>	/**
671	>	* getSimulatedAtomTypes
672	>	*
673	>	* Returns an STL set of AtomType* that are actually present in this
674	>	* simulation.  Must query all processors to assemble this information.
675	>	*
676	>	*/
677	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
678		SimInfo::MoleculeIterator mi;
679		Molecule* mol;
680		Molecule::AtomIterator ai;
681		Atom* atom;
682	<	std::set<AtomType*> atomTypes;
683	<
684	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
495	<
682	>	set<AtomType*> atomTypes;
683	>
684	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
685		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
686		atomTypes.insert(atom->getAtomType());
687	<	}
688	<
500	<	}
687	>	}
688	>	}
689
690	<	return atomTypes;
503	<	}
690	>	#ifdef IS_MPI
691
692	<	void SimInfo::setupSimType() {
693	<	std::set<AtomType*>::iterator i;
507	<	std::set<AtomType*> atomTypes;
508	<	atomTypes = getUniqueAtomTypes();
509	<
510	<	int useLennardJones = 0;
511	<	int useElectrostatic = 0;
512	<	int useEAM = 0;
513	<	int useCharge = 0;
514	<	int useDirectional = 0;
515	<	int useDipole = 0;
516	<	int useGayBerne = 0;
517	<	int useSticky = 0;
518	<	int useStickyPower = 0;
519	<	int useShape = 0;
520	<	int useFLARB = 0; //it is not in AtomType yet
521	<	int useDirectionalAtom = 0;
522	<	int useElectrostatics = 0;
523	<	//usePBC and useRF are from simParams
524	<	int usePBC = simParams_->getPBC();
692	>	// loop over the found atom types on this processor, and add their
693	>	// numerical idents to a vector:
694
695	<	//loop over all of the atom types
696	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
697	<	useLennardJones |= (*i)->isLennardJones();
698	<	useElectrostatic |= (*i)->isElectrostatic();
530	<	useEAM |= (*i)->isEAM();
531	<	useCharge |= (*i)->isCharge();
532	<	useDirectional |= (*i)->isDirectional();
533	<	useDipole |= (*i)->isDipole();
534	<	useGayBerne |= (*i)->isGayBerne();
535	<	useSticky |= (*i)->isSticky();
536	<	useStickyPower |= (*i)->isStickyPower();
537	<	useShape |= (*i)->isShape();
538	<	}
695	>	vector<int> foundTypes;
696	>	set<AtomType*>::iterator i;
697	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
698	>	foundTypes.push_back( (*i)->getIdent() );
699
700	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
701	<	useDirectionalAtom = 1;
542	<	}
700	>	// count_local holds the number of found types on this processor
701	>	int count_local = foundTypes.size();
702
703	<	if (useCharge || useDipole) {
704	<	useElectrostatics = 1;
705	<	}
703	>	// count holds the total number of found types on all processors
704	>	// (some will be redundant with the ones found locally):
705	>	int count;
706	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
707
708	<	#ifdef IS_MPI
709	<	int temp;
708	>	// create a vector to hold the globally found types, and resize it:
709	>	vector<int> ftGlobal;
710	>	ftGlobal.resize(count);
711	>	vector<int> counts;
712
713	<	temp = usePBC;
714	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
713	>	int nproc = MPI::COMM_WORLD.Get_size();
714	>	counts.resize(nproc);
715	>	vector<int> disps;
716	>	disps.resize(nproc);
717
718	<	temp = useDirectionalAtom;
555	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556	<
557	<	temp = useLennardJones;
558	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
559	<
560	<	temp = useElectrostatics;
561	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
562	<
563	<	temp = useCharge;
564	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
565	<
566	<	temp = useDipole;
567	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568	<
569	<	temp = useSticky;
570	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
571	<
572	<	temp = useStickyPower;
573	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
718	>	// now spray out the foundTypes to all the other processors:
719
720	<	temp = useGayBerne;
721	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
720	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
721	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
722
723	<	temp = useEAM;
724	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
725	<
726	<	temp = useShape;
727	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
728	<
729	<	temp = useFLARB;
730	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731	<
723	>	// foundIdents is a stl set, so inserting an already found ident
724	>	// will have no effect.
725	>	set<int> foundIdents;
726	>	vector<int>::iterator j;
727	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
728	>	foundIdents.insert((*j));
729	>
730	>	// now iterate over the foundIdents and get the actual atom types
731	>	// that correspond to these:
732	>	set<int>::iterator it;
733	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
734	>	atomTypes.insert( forceField_->getAtomType((*it)) );
735	>
736		#endif
737	+
738	+	return atomTypes;
739	+	}
740
741	<	fInfo_.SIM_uses_PBC = usePBC;
742	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
743	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
744	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
745	<	fInfo_.SIM_uses_Charges = useCharge;
746	<	fInfo_.SIM_uses_Dipoles = useDipole;
747	<	fInfo_.SIM_uses_Sticky = useSticky;
596	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
597	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
598	<	fInfo_.SIM_uses_EAM = useEAM;
599	<	fInfo_.SIM_uses_Shapes = useShape;
600	<	fInfo_.SIM_uses_FLARB = useFLARB;
601	<
602	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
603	<
604	<	if (simParams_->haveDielectric()) {
605	<	fInfo_.dielect = simParams_->getDielectric();
606	<	} else {
607	<	sprintf(painCave.errMsg,
608	<	"SimSetup Error: No Dielectric constant was set.\n"
609	<	"\tYou are trying to use Reaction Field without"
610	<	"\tsetting a dielectric constant!\n");
611	<	painCave.isFatal = 1;
612	<	simError();
741	>	void SimInfo::setupSimVariables() {
742	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
743	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
744	>	calcBoxDipole_ = false;
745	>	if ( simParams_->haveAccumulateBoxDipole() )
746	>	if ( simParams_->getAccumulateBoxDipole() ) {
747	>	calcBoxDipole_ = true;
748		}
749	<
750	<	} else {
751	<	fInfo_.dielect = 0.0;
749	>
750	>	set<AtomType*>::iterator i;
751	>	set<AtomType*> atomTypes;
752	>	atomTypes = getSimulatedAtomTypes();
753	>	int usesElectrostatic = 0;
754	>	int usesMetallic = 0;
755	>	int usesDirectional = 0;
756	>	//loop over all of the atom types
757	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
758	>	usesElectrostatic |= (*i)->isElectrostatic();
759	>	usesMetallic |= (*i)->isMetal();
760	>	usesDirectional |= (*i)->isDirectional();
761		}
762
763	+	#ifdef IS_MPI
764	+	int temp;
765	+	temp = usesDirectional;
766	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	+
768	+	temp = usesMetallic;
769	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	+
771	+	temp = usesElectrostatic;
772	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	+	#endif
774	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
775	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
776	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
777	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
778	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
779	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
780		}
781
782	<	void SimInfo::setupFortranSim() {
782	>	void SimInfo::setupFortran() {
783		int isError;
784	<	int nExclude;
785	<	std::vector<int> fortranGlobalGroupMembership;
784	>	int nExclude, nOneTwo, nOneThree, nOneFour;
785	>	vector<int> fortranGlobalGroupMembership;
786
626	–	nExclude = exclude_.getSize();
787		isError = 0;
788
789		//globalGroupMembership_ is filled by SimCreator
#	Line 632 | Line 792 | namespace oopse {
792		}
793
794		//calculate mass ratio of cutoff group
795	<	std::vector<double> mfact;
795	>	vector<RealType> mfact;
796		SimInfo::MoleculeIterator mi;
797		Molecule* mol;
798		Molecule::CutoffGroupIterator ci;
799		CutoffGroup* cg;
800		Molecule::AtomIterator ai;
801		Atom* atom;
802	<	double totalMass;
802	>	RealType totalMass;
803
804		//to avoid memory reallocation, reserve enough space for mfact
805		mfact.reserve(getNCutoffGroups());
#	Line 649 | Line 809 | namespace oopse {
809
810		totalMass = cg->getMass();
811		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
812	<	mfact.push_back(atom->getMass()/totalMass);
812	>	// Check for massless groups - set mfact to 1 if true
813	>	if (totalMass != 0)
814	>	mfact.push_back(atom->getMass()/totalMass);
815	>	else
816	>	mfact.push_back( 1.0 );
817		}
654	–
818		}
819		}
820
821	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
822	<	std::vector<int> identArray;
821	>	//fill ident array of local atoms (it is actually ident of
822	>	//AtomType, it is so confusing !!!)
823	>	vector<int> identArray;
824
825		//to avoid memory reallocation, reserve enough space identArray
826		identArray.reserve(getNAtoms());
#	Line 669 | Line 833 | namespace oopse {
833
834		//fill molMembershipArray
835		//molMembershipArray is filled by SimCreator
836	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
836	>	vector<int> molMembershipArray(nGlobalAtoms_);
837		for (int i = 0; i < nGlobalAtoms_; i++) {
838		molMembershipArray[i] = globalMolMembership_[i] + 1;
839		}
840
841		//setup fortran simulation
678	–	int nGlobalExcludes = 0;
679	–	int* globalExcludes = NULL;
680	–	int* excludeList = exclude_.getExcludeList();
681	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
682	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
683	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
842
843	<	if( isError ){
843	>	nExclude = excludedInteractions_.getSize();
844	>	nOneTwo = oneTwoInteractions_.getSize();
845	>	nOneThree = oneThreeInteractions_.getSize();
846	>	nOneFour = oneFourInteractions_.getSize();
847
848	+	int* excludeList = excludedInteractions_.getPairList();
849	+	int* oneTwoList = oneTwoInteractions_.getPairList();
850	+	int* oneThreeList = oneThreeInteractions_.getPairList();
851	+	int* oneFourList = oneFourInteractions_.getPairList();
852	+
853	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
854	+	&nExclude, excludeList,
855	+	&nOneTwo, oneTwoList,
856	+	&nOneThree, oneThreeList,
857	+	&nOneFour, oneFourList,
858	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
859	+	&fortranGlobalGroupMembership[0], &isError);
860	+
861	+	if( isError ){
862	+
863		sprintf( painCave.errMsg,
864		"There was an error setting the simulation information in fortran.\n" );
865		painCave.isFatal = 1;
866	<	painCave.severity = OOPSE_ERROR;
866	>	painCave.severity = OPENMD_ERROR;
867		simError();
868		}
869	<
870	<	#ifdef IS_MPI
869	>
870	>
871		sprintf( checkPointMsg,
872		"succesfully sent the simulation information to fortran.\n");
697	–	MPIcheckPoint();
698	–	#endif // is_mpi
699	–	}
700	–
701	–
702	–	#ifdef IS_MPI
703	–	void SimInfo::setupFortranParallel() {
873
874	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
875	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
876	<	std::vector<int> localToGlobalCutoffGroupIndex;
877	<	SimInfo::MoleculeIterator mi;
878	<	Molecule::AtomIterator ai;
879	<	Molecule::CutoffGroupIterator ci;
880	<	Molecule* mol;
881	<	Atom* atom;
882	<	CutoffGroup* cg;
874	>	errorCheckPoint();
875	>
876	>	// Setup number of neighbors in neighbor list if present
877	>	if (simParams_->haveNeighborListNeighbors()) {
878	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
879	>	setNeighbors(&nlistNeighbors);
880	>	}
881	>
882	>	#ifdef IS_MPI
883	>	//SimInfo is responsible for creating localToGlobalAtomIndex and
884	>	//localToGlobalGroupIndex
885	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
886	>	vector<int> localToGlobalCutoffGroupIndex;
887		mpiSimData parallelData;
715	–	int isError;
888
889		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
890
#	Line 751 | Line 923 | namespace oopse {
923		}
924
925		sprintf(checkPointMsg, " mpiRefresh successful.\n");
926	<	MPIcheckPoint();
755	<
756	<
757	<	}
758	<
926	>	errorCheckPoint();
927		#endif
760	–
761	–	double SimInfo::calcMaxCutoffRadius() {
762	–
928
929	<	std::set<AtomType*> atomTypes;
930	<	std::set<AtomType*>::iterator i;
931	<	std::vector<double> cutoffRadius;
932	<
933	<	//get the unique atom types
934	<	atomTypes = getUniqueAtomTypes();
770	<
771	<	//query the max cutoff radius among these atom types
772	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
773	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
929	>	initFortranFF(&isError);
930	>	if (isError) {
931	>	sprintf(painCave.errMsg,
932	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
933	>	painCave.isFatal = 1;
934	>	simError();
935		}
936	<
776	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
777	<	#ifdef IS_MPI
778	<	//pick the max cutoff radius among the processors
779	<	#endif
780	<
781	<	return maxCutoffRadius;
782	<	}
783	<
784	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
785	<
786	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
787	<
788	<	if (!simParams_->haveRcut()){
789	<	sprintf(painCave.errMsg,
790	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
791	<	"\tOOPSE will use a default value of 15.0 angstroms"
792	<	"\tfor the cutoffRadius.\n");
793	<	painCave.isFatal = 0;
794	<	simError();
795	<	rcut = 15.0;
796	<	} else{
797	<	rcut = simParams_->getRcut();
798	<	}
799	<
800	<	if (!simParams_->haveRsw()){
801	<	sprintf(painCave.errMsg,
802	<	"SimCreator Warning: No value was set for switchingRadius.\n"
803	<	"\tOOPSE will use a default value of\n"
804	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
805	<	painCave.isFatal = 0;
806	<	simError();
807	<	rsw = 0.95 * rcut;
808	<	} else{
809	<	rsw = simParams_->getRsw();
810	<	}
811	<
812	<	} else {
813	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
814	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
815	<
816	<	if (simParams_->haveRcut()) {
817	<	rcut = simParams_->getRcut();
818	<	} else {
819	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
820	<	rcut = calcMaxCutoffRadius();
821	<	}
822	<
823	<	if (simParams_->haveRsw()) {
824	<	rsw  = simParams_->getRsw();
825	<	} else {
826	<	rsw = rcut;
827	<	}
828	<
829	<	}
830	<	}
831	<
832	<	void SimInfo::setupCutoff() {
833	<	getCutoff(rcut_, rsw_);
834	<	double rnblist = rcut_ + 1; // skin of neighbor list
835	<
836	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
837	<
838	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
839	<	if (simParams_->haveCutoffPolicy()) {
840	<	std::string myPolicy = simParams_->getCutoffPolicy();
841	<	if (myPolicy == "MIX") {
842	<	cp = MIX_CUTOFF_POLICY;
843	<	} else {
844	<	if (myPolicy == "MAX") {
845	<	cp = MAX_CUTOFF_POLICY;
846	<	} else {
847	<	if (myPolicy == "TRADITIONAL") {
848	<	cp = TRADITIONAL_CUTOFF_POLICY;
849	<	} else {
850	<	// throw error
851	<	sprintf( painCave.errMsg,
852	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
853	<	painCave.isFatal = 1;
854	<	simError();
855	<	}
856	<	}
857	<	}
858	<	}
859	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
860	<	}
861	<
862	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
863	<
864	<	int errorOut;
865	<	int esm =  NONE;
866	<	double alphaVal;
867	<
868	<	errorOut = isError;
869	<
870	<	if (simParams_->haveElectrostaticSummationMethod()) {
871	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
872	<	if (myMethod == "NONE") {
873	<	esm = NONE;
874	<	} else {
875	<	if (myMethod == "UNDAMPED_WOLF") {
876	<	esm = UNDAMPED_WOLF;
877	<	} else {
878	<	if (myMethod == "DAMPED_WOLF") {
879	<	esm = DAMPED_WOLF;
880	<	if (!simParams_->haveDampingAlpha()) {
881	<	//throw error
882	<	sprintf( painCave.errMsg,
883	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", simParams_->getDampingAlpha());
884	<	painCave.isFatal = 0;
885	<	simError();
886	<	}
887	<	alphaVal = simParams_->getDampingAlpha();
888	<	} else {
889	<	if (myMethod == "REACTION_FIELD") {
890	<	esm = REACTION_FIELD;
891	<	} else {
892	<	// throw error
893	<	sprintf( painCave.errMsg,
894	<	"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() );
895	<	painCave.isFatal = 1;
896	<	simError();
897	<	}
898	<	}
899	<	}
900	<	}
901	<	}
902	<	initFortranFF( &esm, &alphaVal, &errorOut );
936	>	fortranInitialized_ = true;
937		}
938
939		void SimInfo::addProperty(GenericData* genData) {
940		properties_.addProperty(genData);
941		}
942
943	<	void SimInfo::removeProperty(const std::string& propName) {
943	>	void SimInfo::removeProperty(const string& propName) {
944		properties_.removeProperty(propName);
945		}
946
#	Line 914 | Line 948 | namespace oopse {
948		properties_.clearProperties();
949		}
950
951	<	std::vector<std::string> SimInfo::getPropertyNames() {
951	>	vector<string> SimInfo::getPropertyNames() {
952		return properties_.getPropertyNames();
953		}
954
955	<	std::vector<GenericData*> SimInfo::getProperties() {
955	>	vector<GenericData*> SimInfo::getProperties() {
956		return properties_.getProperties();
957		}
958
959	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
959	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
960		return properties_.getPropertyByName(propName);
961		}
962
#	Line 958 | Line 992 | namespace oopse {
992		Molecule* mol;
993
994		Vector3d comVel(0.0);
995	<	double totalMass = 0.0;
995	>	RealType totalMass = 0.0;
996
997
998		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
999	<	double mass = mol->getMass();
999	>	RealType mass = mol->getMass();
1000		totalMass += mass;
1001		comVel += mass * mol->getComVel();
1002		}
1003
1004		#ifdef IS_MPI
1005	<	double tmpMass = totalMass;
1005	>	RealType tmpMass = totalMass;
1006		Vector3d tmpComVel(comVel);
1007	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1008	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1007	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1008	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1009		#endif
1010
1011		comVel /= totalMass;
#	Line 984 | Line 1018 | namespace oopse {
1018		Molecule* mol;
1019
1020		Vector3d com(0.0);
1021	<	double totalMass = 0.0;
1021	>	RealType totalMass = 0.0;
1022
1023		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1024	<	double mass = mol->getMass();
1024	>	RealType mass = mol->getMass();
1025		totalMass += mass;
1026		com += mass * mol->getCom();
1027		}
1028
1029		#ifdef IS_MPI
1030	<	double tmpMass = totalMass;
1030	>	RealType tmpMass = totalMass;
1031		Vector3d tmpCom(com);
1032	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1033	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1032	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1034		#endif
1035
1036		com /= totalMass;
#	Line 1005 | Line 1039 | namespace oopse {
1039
1040		}
1041
1042	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1042	>	ostream& operator <<(ostream& o, SimInfo& info) {
1043
1044		return o;
1045		}
#	Line 1020 | Line 1054 | namespace oopse {
1054		Molecule* mol;
1055
1056
1057	<	double totalMass = 0.0;
1057	>	RealType totalMass = 0.0;
1058
1059
1060		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1061	<	double mass = mol->getMass();
1061	>	RealType mass = mol->getMass();
1062		totalMass += mass;
1063		com += mass * mol->getCom();
1064		comVel += mass * mol->getComVel();
1065		}
1066
1067		#ifdef IS_MPI
1068	<	double tmpMass = totalMass;
1068	>	RealType tmpMass = totalMass;
1069		Vector3d tmpCom(com);
1070		Vector3d tmpComVel(comVel);
1071	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1072	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1073	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1071	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1072	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1073	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074		#endif
1075
1076		com /= totalMass;
#	Line 1048 | Line 1082 | namespace oopse {
1082
1083
1084		[  Ixx -Ixy  -Ixz ]
1085	<	J =| -Iyx  Iyy  -Iyz |
1085	>	J =| -Iyx  Iyy  -Iyz |
1086		[ -Izx -Iyz   Izz ]
1087		*/
1088
1089		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1090
1091
1092	<	double xx = 0.0;
1093	<	double yy = 0.0;
1094	<	double zz = 0.0;
1095	<	double xy = 0.0;
1096	<	double xz = 0.0;
1097	<	double yz = 0.0;
1092	>	RealType xx = 0.0;
1093	>	RealType yy = 0.0;
1094	>	RealType zz = 0.0;
1095	>	RealType xy = 0.0;
1096	>	RealType xz = 0.0;
1097	>	RealType yz = 0.0;
1098		Vector3d com(0.0);
1099		Vector3d comVel(0.0);
1100
#	Line 1072 | Line 1106 | namespace oopse {
1106		Vector3d thisq(0.0);
1107		Vector3d thisv(0.0);
1108
1109	<	double thisMass = 0.0;
1109	>	RealType thisMass = 0.0;
1110
1111
1112
#	Line 1110 | Line 1144 | namespace oopse {
1144		#ifdef IS_MPI
1145		Mat3x3d tmpI(inertiaTensor);
1146		Vector3d tmpAngMom;
1147	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1148	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1147	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1148	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149		#endif
1150
1151		return;
#	Line 1132 | Line 1166 | namespace oopse {
1166		Vector3d thisr(0.0);
1167		Vector3d thisp(0.0);
1168
1169	<	double thisMass;
1169	>	RealType thisMass;
1170
1171		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1172		thisMass = mol->getMass();
#	Line 1145 | Line 1179 | namespace oopse {
1179
1180		#ifdef IS_MPI
1181		Vector3d tmpAngMom;
1182	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1182	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1183		#endif
1184
1185		return angularMomentum;
1186		}
1153	–
1187
1188	<	}//end namespace oopse
1188	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1189	>	return IOIndexToIntegrableObject.at(index);
1190	>	}
1191	>
1192	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1193	>	IOIndexToIntegrableObject= v;
1194	>	}
1195
1196	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1197	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1198	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1199	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1200	+	*/
1201	+	void SimInfo::getGyrationalVolume(RealType &volume){
1202	+	Mat3x3d intTensor;
1203	+	RealType det;
1204	+	Vector3d dummyAngMom;
1205	+	RealType sysconstants;
1206	+	RealType geomCnst;
1207	+
1208	+	geomCnst = 3.0/2.0;
1209	+	/* Get the inertial tensor and angular momentum for free*/
1210	+	getInertiaTensor(intTensor,dummyAngMom);
1211	+
1212	+	det = intTensor.determinant();
1213	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1214	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1215	+	return;
1216	+	}
1217	+
1218	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1219	+	Mat3x3d intTensor;
1220	+	Vector3d dummyAngMom;
1221	+	RealType sysconstants;
1222	+	RealType geomCnst;
1223	+
1224	+	geomCnst = 3.0/2.0;
1225	+	/* Get the inertial tensor and angular momentum for free*/
1226	+	getInertiaTensor(intTensor,dummyAngMom);
1227	+
1228	+	detI = intTensor.determinant();
1229	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1230	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1231	+	return;
1232	+	}
1233	+	/*
1234	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1235	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1236	+	sdByGlobalIndex_ = v;
1237	+	}
1238	+
1239	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1240	+	//assert(index < nAtoms_ + nRigidBodies_);
1241	+	return sdByGlobalIndex_.at(index);
1242	+	}
1243	+	*/
1244	+	int SimInfo::getNGlobalConstraints() {
1245	+	int nGlobalConstraints;
1246	+	#ifdef IS_MPI
1247	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1248	+	MPI_COMM_WORLD);
1249	+	#else
1250	+	nGlobalConstraints =  nConstraints_;
1251	+	#endif
1252	+	return nGlobalConstraints;
1253	+	}
1254	+
1255	+	}//end namespace OpenMD
1256	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 608 by chrisfen, Fri Sep 16 21:07:45 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC

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

Diff Legend

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