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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 764 by gezelter, Mon Nov 21 22:59:21 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 53 | Line 54
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/fCutoffPolicy.h"
57	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	<	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	<	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60	<	#include "UseTheForce/doForces_interface.h"
61	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61	<
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
70	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
74	<	std::map<int, std::set<int> >::iterator i = container.find(index);
75	<	std::set<int> result;
76	<	if (i != container.end()) {
77	<	result = i->second;
78	<	}
79	<
80	<	return result;
81	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
72	<	ForceField* ff, Globals* simParams) :
73	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
86	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
79	<
93	<
94	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
95	<	MoleculeStamp* molStamp;
96	<	int nMolWithSameStamp;
97	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
98	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
99	<	CutoffGroupStamp* cgStamp;
100	<	RigidBodyStamp* rbStamp;
101	<	int nRigidAtoms = 0;
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80
81	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
82	<	molStamp = i->first;
83	<	nMolWithSameStamp = i->second;
84	<
85	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
86	<
87	<	//calculate atoms in molecules
88	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
89	<
90	<
91	<	//calculate atoms in cutoff groups
92	<	int nAtomsInGroups = 0;
93	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
94	<
95	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
96	<	cgStamp = molStamp->getCutoffGroup(j);
97	<	nAtomsInGroups += cgStamp->getNMembers();
98	<	}
99	<
100	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
101	<
102	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
103	<
104	<	//calculate atoms in rigid bodies
105	<	int nAtomsInRigidBodies = 0;
106	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129	<
130	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
131	<	rbStamp = molStamp->getRigidBody(j);
132	<	nAtomsInRigidBodies += rbStamp->getNMembers();
133	<	}
134	<
135	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
136	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
137	<
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107		}
108	<
109	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
110	<	//group therefore the total number of cutoff groups in the system is
111	<	//equal to the total number of atoms minus number of atoms belong to
112	<	//cutoff group defined in meta-data file plus the number of cutoff
113	<	//groups defined in meta-data file
114	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
115	<
116	<	//every free atom (atom does not belong to rigid bodies) is an
117	<	//integrable object therefore the total number of integrable objects
118	<	//in the system is equal to the total number of atoms minus number of
119	<	//atoms belong to rigid body defined in meta-data file plus the number
120	<	//of rigid bodies defined in meta-data file
121	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
122	<	+ nGlobalRigidBodies_;
123	<
124	<	nGlobalMols_ = molStampIds_.size();
156	<
157	<	#ifdef IS_MPI
158	<	molToProcMap_.resize(nGlobalMols_);
159	<	#endif
160	<
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
133	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	+
135	+	//every free atom (atom does not belong to rigid bodies) is an
136	+	//integrable object therefore the total number of integrable objects
137	+	//in the system is equal to the total number of atoms minus number of
138	+	//atoms belong to rigid body defined in meta-data file plus the number
139	+	//of rigid bodies defined in meta-data file
140	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	+	+ nGlobalRigidBodies_;
142	+
143	+	nGlobalMols_ = molStampIds_.size();
144	+	molToProcMap_.resize(nGlobalMols_);
145	+	}
146	+
147		SimInfo::~SimInfo() {
148	<	std::map<int, Molecule*>::iterator i;
148	>	map<int, Molecule*>::iterator i;
149		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150		delete i->second;
151		}
152		molecules_.clear();
153
170	–	delete stamps_;
154		delete sman_;
155		delete simParams_;
156		delete forceField_;
157		}
158
176	–	int SimInfo::getNGlobalConstraints() {
177	–	int nGlobalConstraints;
178	–	#ifdef IS_MPI
179	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180	–	MPI_COMM_WORLD);
181	–	#else
182	–	nGlobalConstraints =  nConstraints_;
183	–	#endif
184	–	return nGlobalConstraints;
185	–	}
159
160		bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168		nAtoms_ += mol->getNAtoms();
169		nBonds_ += mol->getNBonds();
170		nBends_ += mol->getNBends();
171		nTorsions_ += mol->getNTorsions();
172	+	nInversions_ += mol->getNInversions();
173		nRigidBodies_ += mol->getNRigidBodies();
174		nIntegrableObjects_ += mol->getNIntegrableObjects();
175		nCutoffGroups_ += mol->getNCutoffGroups();
176		nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
177	>
178	>	addInteractionPairs(mol);
179	>
180		return true;
181		} else {
182		return false;
183		}
184		}
185	<
185	>
186		bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
#	Line 221 | Line 195 | namespace oopse {
195		nBonds_ -= mol->getNBonds();
196		nBends_ -= mol->getNBends();
197		nTorsions_ -= mol->getNTorsions();
198	+	nInversions_ -= mol->getNInversions();
199		nRigidBodies_ -= mol->getNRigidBodies();
200		nIntegrableObjects_ -= mol->getNIntegrableObjects();
201		nCutoffGroups_ -= mol->getNCutoffGroups();
202		nConstraints_ -= mol->getNConstraintPairs();
203
204	<	removeExcludePairs(mol);
204	>	removeInteractionPairs(mol);
205		molecules_.erase(mol->getGlobalIndex());
206
207		delete mol;
#	Line 235 | Line 210 | namespace oopse {
210		} else {
211		return false;
212		}
238	–
239	–
213		}
214
215
#	Line 252 | Line 225 | namespace oopse {
225
226
227		void SimInfo::calcNdf() {
228	<	int ndf_local;
228	>	int ndf_local, nfq_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232	>
233		Molecule* mol;
234		StuntDouble* integrableObject;
235	+	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
#	Line 273 | Line 250 | namespace oopse {
250		ndf_local += 3;
251		}
252		}
253	<
254	<	}//end for (integrableObject)
255	<	}// end for (mol)
253	>	}
254	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255	>	atom = mol->nextFluctuatingCharge(k)) {
256	>	if (atom->isFluctuatingCharge()) {
257	>	nfq_local++;
258	>	}
259	>	}
260	>	}
261
262	+	ndfLocal_ = ndf_local;
263	+	cerr << "ndfLocal_ = " << ndfLocal_ << "\n";
264	+
265		// n_constraints is local, so subtract them on each processor
266		ndf_local -= nConstraints_;
267
268		#ifdef IS_MPI
269		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
271		#else
272		ndf_ = ndf_local;
273	+	nGlobalFluctuatingCharges_ = nfq_local;
274		#endif
275
276		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 292 | Line 279 | namespace oopse {
279
280		}
281
282	+	int SimInfo::getFdf() {
283	+	#ifdef IS_MPI
284	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
285	+	#else
286	+	fdf_ = fdf_local;
287	+	#endif
288	+	return fdf_;
289	+	}
290	+
291	+	unsigned int SimInfo::getNLocalCutoffGroups(){
292	+	int nLocalCutoffAtoms = 0;
293	+	Molecule* mol;
294	+	MoleculeIterator mi;
295	+	CutoffGroup* cg;
296	+	Molecule::CutoffGroupIterator ci;
297	+
298	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
299	+
300	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
301	+	cg = mol->nextCutoffGroup(ci)) {
302	+	nLocalCutoffAtoms += cg->getNumAtom();
303	+
304	+	}
305	+	}
306	+
307	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
308	+	}
309	+
310		void SimInfo::calcNdfRaw() {
311		int ndfRaw_local;
312
313		MoleculeIterator i;
314	<	std::vector<StuntDouble*>::iterator j;
314	>	vector<StuntDouble*>::iterator j;
315		Molecule* mol;
316		StuntDouble* integrableObject;
317
#	Line 343 | Line 358 | namespace oopse {
358
359		}
360
361	<	void SimInfo::addExcludePairs(Molecule* mol) {
362	<	std::vector<Bond*>::iterator bondIter;
363	<	std::vector<Bend*>::iterator bendIter;
364	<	std::vector<Torsion*>::iterator torsionIter;
361	>	void SimInfo::addInteractionPairs(Molecule* mol) {
362	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
363	>	vector<Bond*>::iterator bondIter;
364	>	vector<Bend*>::iterator bendIter;
365	>	vector<Torsion*>::iterator torsionIter;
366	>	vector<Inversion*>::iterator inversionIter;
367		Bond* bond;
368		Bend* bend;
369		Torsion* torsion;
370	+	Inversion* inversion;
371		int a;
372		int b;
373		int c;
374		int d;
375
376	<	std::map<int, std::set<int> > atomGroups;
376	>	// atomGroups can be used to add special interaction maps between
377	>	// groups of atoms that are in two separate rigid bodies.
378	>	// However, most site-site interactions between two rigid bodies
379	>	// are probably not special, just the ones between the physically
380	>	// bonded atoms.  Interactions *within* a single rigid body should
381	>	// always be excluded.  These are done at the bottom of this
382	>	// function.
383
384	+	map<int, set<int> > atomGroups;
385		Molecule::RigidBodyIterator rbIter;
386		RigidBody* rb;
387		Molecule::IntegrableObjectIterator ii;
388		StuntDouble* integrableObject;
389
390	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
391	<	integrableObject = mol->nextIntegrableObject(ii)) {
392	<
390	>	for (integrableObject = mol->beginIntegrableObject(ii);
391	>	integrableObject != NULL;
392	>	integrableObject = mol->nextIntegrableObject(ii)) {
393	>
394		if (integrableObject->isRigidBody()) {
395	<	rb = static_cast<RigidBody*>(integrableObject);
396	<	std::vector<Atom*> atoms = rb->getAtoms();
397	<	std::set<int> rigidAtoms;
398	<	for (int i = 0; i < atoms.size(); ++i) {
399	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
400	<	}
401	<	for (int i = 0; i < atoms.size(); ++i) {
402	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
403	<	}
395	>	rb = static_cast<RigidBody*>(integrableObject);
396	>	vector<Atom*> atoms = rb->getAtoms();
397	>	set<int> rigidAtoms;
398	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
399	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
400	>	}
401	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
402	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
403	>	}
404		} else {
405	<	std::set<int> oneAtomSet;
405	>	set<int> oneAtomSet;
406		oneAtomSet.insert(integrableObject->getGlobalIndex());
407	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
407	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
408		}
409		}
410	+
411	+	for (bond= mol->beginBond(bondIter); bond != NULL;
412	+	bond = mol->nextBond(bondIter)) {
413
385	–
386	–
387	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
414		a = bond->getAtomA()->getGlobalIndex();
415	<	b = bond->getAtomB()->getGlobalIndex();
416	<	exclude_.addPair(a, b);
415	>	b = bond->getAtomB()->getGlobalIndex();
416	>
417	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
418	>	oneTwoInteractions_.addPair(a, b);
419	>	} else {
420	>	excludedInteractions_.addPair(a, b);
421	>	}
422		}
423
424	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
424	>	for (bend= mol->beginBend(bendIter); bend != NULL;
425	>	bend = mol->nextBend(bendIter)) {
426	>
427		a = bend->getAtomA()->getGlobalIndex();
428		b = bend->getAtomB()->getGlobalIndex();
429		c = bend->getAtomC()->getGlobalIndex();
397	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
398	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
399	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
400	–
401	–	exclude_.addPairs(rigidSetA, rigidSetB);
402	–	exclude_.addPairs(rigidSetA, rigidSetC);
403	–	exclude_.addPairs(rigidSetB, rigidSetC);
430
431	<	//exclude_.addPair(a, b);
432	<	//exclude_.addPair(a, c);
433	<	//exclude_.addPair(b, c);
431	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
432	>	oneTwoInteractions_.addPair(a, b);
433	>	oneTwoInteractions_.addPair(b, c);
434	>	} else {
435	>	excludedInteractions_.addPair(a, b);
436	>	excludedInteractions_.addPair(b, c);
437	>	}
438	>
439	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
440	>	oneThreeInteractions_.addPair(a, c);
441	>	} else {
442	>	excludedInteractions_.addPair(a, c);
443	>	}
444		}
445
446	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
446	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
447	>	torsion = mol->nextTorsion(torsionIter)) {
448	>
449		a = torsion->getAtomA()->getGlobalIndex();
450		b = torsion->getAtomB()->getGlobalIndex();
451		c = torsion->getAtomC()->getGlobalIndex();
452	<	d = torsion->getAtomD()->getGlobalIndex();
415	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
416	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
417	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
418	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
452	>	d = torsion->getAtomD()->getGlobalIndex();
453
454	<	exclude_.addPairs(rigidSetA, rigidSetB);
455	<	exclude_.addPairs(rigidSetA, rigidSetC);
456	<	exclude_.addPairs(rigidSetA, rigidSetD);
457	<	exclude_.addPairs(rigidSetB, rigidSetC);
458	<	exclude_.addPairs(rigidSetB, rigidSetD);
459	<	exclude_.addPairs(rigidSetC, rigidSetD);
454	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
455	>	oneTwoInteractions_.addPair(a, b);
456	>	oneTwoInteractions_.addPair(b, c);
457	>	oneTwoInteractions_.addPair(c, d);
458	>	} else {
459	>	excludedInteractions_.addPair(a, b);
460	>	excludedInteractions_.addPair(b, c);
461	>	excludedInteractions_.addPair(c, d);
462	>	}
463
464	<	/*
465	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
466	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
467	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
468	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
469	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
470	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
471	<
472	<
473	<	exclude_.addPair(a, b);
474	<	exclude_.addPair(a, c);
475	<	exclude_.addPair(a, d);
476	<	exclude_.addPair(b, c);
440	<	exclude_.addPair(b, d);
441	<	exclude_.addPair(c, d);
442	<	*/
464	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
465	>	oneThreeInteractions_.addPair(a, c);
466	>	oneThreeInteractions_.addPair(b, d);
467	>	} else {
468	>	excludedInteractions_.addPair(a, c);
469	>	excludedInteractions_.addPair(b, d);
470	>	}
471	>
472	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
473	>	oneFourInteractions_.addPair(a, d);
474	>	} else {
475	>	excludedInteractions_.addPair(a, d);
476	>	}
477		}
478
479	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
480	<	std::vector<Atom*> atoms = rb->getAtoms();
481	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
482	<	for (int j = i + 1; j < atoms.size(); ++j) {
479	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
480	>	inversion = mol->nextInversion(inversionIter)) {
481	>
482	>	a = inversion->getAtomA()->getGlobalIndex();
483	>	b = inversion->getAtomB()->getGlobalIndex();
484	>	c = inversion->getAtomC()->getGlobalIndex();
485	>	d = inversion->getAtomD()->getGlobalIndex();
486	>
487	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
488	>	oneTwoInteractions_.addPair(a, b);
489	>	oneTwoInteractions_.addPair(a, c);
490	>	oneTwoInteractions_.addPair(a, d);
491	>	} else {
492	>	excludedInteractions_.addPair(a, b);
493	>	excludedInteractions_.addPair(a, c);
494	>	excludedInteractions_.addPair(a, d);
495	>	}
496	>
497	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
498	>	oneThreeInteractions_.addPair(b, c);
499	>	oneThreeInteractions_.addPair(b, d);
500	>	oneThreeInteractions_.addPair(c, d);
501	>	} else {
502	>	excludedInteractions_.addPair(b, c);
503	>	excludedInteractions_.addPair(b, d);
504	>	excludedInteractions_.addPair(c, d);
505	>	}
506	>	}
507	>
508	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
509	>	rb = mol->nextRigidBody(rbIter)) {
510	>	vector<Atom*> atoms = rb->getAtoms();
511	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
512	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
513		a = atoms[i]->getGlobalIndex();
514		b = atoms[j]->getGlobalIndex();
515	<	exclude_.addPair(a, b);
515	>	excludedInteractions_.addPair(a, b);
516		}
517		}
518		}
519
520		}
521
522	<	void SimInfo::removeExcludePairs(Molecule* mol) {
523	<	std::vector<Bond*>::iterator bondIter;
524	<	std::vector<Bend*>::iterator bendIter;
525	<	std::vector<Torsion*>::iterator torsionIter;
522	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
523	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
524	>	vector<Bond*>::iterator bondIter;
525	>	vector<Bend*>::iterator bendIter;
526	>	vector<Torsion*>::iterator torsionIter;
527	>	vector<Inversion*>::iterator inversionIter;
528		Bond* bond;
529		Bend* bend;
530		Torsion* torsion;
531	+	Inversion* inversion;
532		int a;
533		int b;
534		int c;
535		int d;
536
537	<	std::map<int, std::set<int> > atomGroups;
471	<
537	>	map<int, set<int> > atomGroups;
538		Molecule::RigidBodyIterator rbIter;
539		RigidBody* rb;
540		Molecule::IntegrableObjectIterator ii;
541		StuntDouble* integrableObject;
542
543	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
544	<	integrableObject = mol->nextIntegrableObject(ii)) {
545	<
543	>	for (integrableObject = mol->beginIntegrableObject(ii);
544	>	integrableObject != NULL;
545	>	integrableObject = mol->nextIntegrableObject(ii)) {
546	>
547		if (integrableObject->isRigidBody()) {
548	<	rb = static_cast<RigidBody*>(integrableObject);
549	<	std::vector<Atom*> atoms = rb->getAtoms();
550	<	std::set<int> rigidAtoms;
551	<	for (int i = 0; i < atoms.size(); ++i) {
552	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
553	<	}
554	<	for (int i = 0; i < atoms.size(); ++i) {
555	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556	<	}
548	>	rb = static_cast<RigidBody*>(integrableObject);
549	>	vector<Atom*> atoms = rb->getAtoms();
550	>	set<int> rigidAtoms;
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
553	>	}
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556	>	}
557		} else {
558	<	std::set<int> oneAtomSet;
558	>	set<int> oneAtomSet;
559		oneAtomSet.insert(integrableObject->getGlobalIndex());
560	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
560	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
561		}
562		}
563
564	<
565	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
564	>	for (bond= mol->beginBond(bondIter); bond != NULL;
565	>	bond = mol->nextBond(bondIter)) {
566	>
567		a = bond->getAtomA()->getGlobalIndex();
568	<	b = bond->getAtomB()->getGlobalIndex();
569	<	exclude_.removePair(a, b);
568	>	b = bond->getAtomB()->getGlobalIndex();
569	>
570	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	>	oneTwoInteractions_.removePair(a, b);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	}
575		}
576
577	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
577	>	for (bend= mol->beginBend(bendIter); bend != NULL;
578	>	bend = mol->nextBend(bendIter)) {
579	>
580		a = bend->getAtomA()->getGlobalIndex();
581		b = bend->getAtomB()->getGlobalIndex();
582		c = bend->getAtomC()->getGlobalIndex();
508	–
509	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
510	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
511	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
512	–
513	–	exclude_.removePairs(rigidSetA, rigidSetB);
514	–	exclude_.removePairs(rigidSetA, rigidSetC);
515	–	exclude_.removePairs(rigidSetB, rigidSetC);
583
584	<	//exclude_.removePair(a, b);
585	<	//exclude_.removePair(a, c);
586	<	//exclude_.removePair(b, c);
584	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
585	>	oneTwoInteractions_.removePair(a, b);
586	>	oneTwoInteractions_.removePair(b, c);
587	>	} else {
588	>	excludedInteractions_.removePair(a, b);
589	>	excludedInteractions_.removePair(b, c);
590	>	}
591	>
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	} else {
595	>	excludedInteractions_.removePair(a, c);
596	>	}
597		}
598
599	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
599	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
600	>	torsion = mol->nextTorsion(torsionIter)) {
601	>
602		a = torsion->getAtomA()->getGlobalIndex();
603		b = torsion->getAtomB()->getGlobalIndex();
604		c = torsion->getAtomC()->getGlobalIndex();
605	<	d = torsion->getAtomD()->getGlobalIndex();
605	>	d = torsion->getAtomD()->getGlobalIndex();
606	>
607	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
608	>	oneTwoInteractions_.removePair(a, b);
609	>	oneTwoInteractions_.removePair(b, c);
610	>	oneTwoInteractions_.removePair(c, d);
611	>	} else {
612	>	excludedInteractions_.removePair(a, b);
613	>	excludedInteractions_.removePair(b, c);
614	>	excludedInteractions_.removePair(c, d);
615	>	}
616
617	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
618	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
619	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
620	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
617	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
618	>	oneThreeInteractions_.removePair(a, c);
619	>	oneThreeInteractions_.removePair(b, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(b, d);
623	>	}
624
625	<	exclude_.removePairs(rigidSetA, rigidSetB);
626	<	exclude_.removePairs(rigidSetA, rigidSetC);
627	<	exclude_.removePairs(rigidSetA, rigidSetD);
628	<	exclude_.removePairs(rigidSetB, rigidSetC);
629	<	exclude_.removePairs(rigidSetB, rigidSetD);
630	<	exclude_.removePairs(rigidSetC, rigidSetD);
625	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
626	>	oneFourInteractions_.removePair(a, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, d);
629	>	}
630	>	}
631
632	<	/*
633	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
542	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
543	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
544	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
545	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
546	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
632	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
633	>	inversion = mol->nextInversion(inversionIter)) {
634
635	<
636	<	exclude_.removePair(a, b);
637	<	exclude_.removePair(a, c);
638	<	exclude_.removePair(a, d);
639	<	exclude_.removePair(b, c);
640	<	exclude_.removePair(b, d);
641	<	exclude_.removePair(c, d);
642	<	*/
635	>	a = inversion->getAtomA()->getGlobalIndex();
636	>	b = inversion->getAtomB()->getGlobalIndex();
637	>	c = inversion->getAtomC()->getGlobalIndex();
638	>	d = inversion->getAtomD()->getGlobalIndex();
639	>
640	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
641	>	oneTwoInteractions_.removePair(a, b);
642	>	oneTwoInteractions_.removePair(a, c);
643	>	oneTwoInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, b);
646	>	excludedInteractions_.removePair(a, c);
647	>	excludedInteractions_.removePair(a, d);
648	>	}
649	>
650	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
651	>	oneThreeInteractions_.removePair(b, c);
652	>	oneThreeInteractions_.removePair(b, d);
653	>	oneThreeInteractions_.removePair(c, d);
654	>	} else {
655	>	excludedInteractions_.removePair(b, c);
656	>	excludedInteractions_.removePair(b, d);
657	>	excludedInteractions_.removePair(c, d);
658	>	}
659		}
660
661	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
662	<	std::vector<Atom*> atoms = rb->getAtoms();
663	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
664	<	for (int j = i + 1; j < atoms.size(); ++j) {
661	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
662	>	rb = mol->nextRigidBody(rbIter)) {
663	>	vector<Atom*> atoms = rb->getAtoms();
664	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
665	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
666		a = atoms[i]->getGlobalIndex();
667		b = atoms[j]->getGlobalIndex();
668	<	exclude_.removePair(a, b);
668	>	excludedInteractions_.removePair(a, b);
669		}
670		}
671		}
672	<
672	>
673		}
674	<
675	<
674	>
675	>
676		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
677		int curStampId;
678	<
678	>
679		//index from 0
680		curStampId = moleculeStamps_.size();
681
#	Line 579 | Line 683 | namespace oopse {
683		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684		}
685
582	–	void SimInfo::update() {
686
687	<	setupSimType();
688	<
689	<	#ifdef IS_MPI
690	<	setupFortranParallel();
691	<	#endif
692	<
693	<	setupFortranSim();
694	<
695	<	//setup fortran force field
593	<	/** @deprecate */
594	<	int isError = 0;
595	<
596	<	setupElectrostaticSummationMethod( isError );
597	<	setupSwitchingFunction();
598	<
599	<	if(isError){
600	<	sprintf( painCave.errMsg,
601	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
602	<	painCave.isFatal = 1;
603	<	simError();
604	<	}
605	<
606	<
607	<	setupCutoff();
608	<
687	>	/**
688	>	* update
689	>	*
690	>	*  Performs the global checks and variable settings after the
691	>	*  objects have been created.
692	>	*
693	>	*/
694	>	void SimInfo::update() {
695	>	setupSimVariables();
696		calcNdf();
697		calcNdfRaw();
698		calcNdfTrans();
612	–
613	–	fortranInitialized_ = true;
699		}
700	<
701	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
700	>
701	>	/**
702	>	* getSimulatedAtomTypes
703	>	*
704	>	* Returns an STL set of AtomType* that are actually present in this
705	>	* simulation.  Must query all processors to assemble this information.
706	>	*
707	>	*/
708	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709		SimInfo::MoleculeIterator mi;
710		Molecule* mol;
711		Molecule::AtomIterator ai;
712		Atom* atom;
713	<	std::set<AtomType*> atomTypes;
714	<
713	>	set<AtomType*> atomTypes;
714	>
715		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	<
717	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
716	>	for(atom = mol->beginAtom(ai); atom != NULL;
717	>	atom = mol->nextAtom(ai)) {
718		atomTypes.insert(atom->getAtomType());
719	<	}
720	<
719	>	}
720	>	}
721	>
722	>	#ifdef IS_MPI
723	>
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726	>
727	>	vector<int> foundTypes;
728	>	set<AtomType*>::iterator i;
729	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730	>	foundTypes.push_back( (*i)->getIdent() );
731	>
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734	>
735	>	int nproc = MPI::COMM_WORLD.Get_size();
736	>
737	>	// we need arrays to hold the counts and displacement vectors for
738	>	// all processors
739	>	vector<int> counts(nproc, 0);
740	>	vector<int> disps(nproc, 0);
741	>
742	>	// fill the counts array
743	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744	>	1, MPI::INT);
745	>
746	>	// use the processor counts to compute the displacement array
747	>	disps[0] = 0;
748	>	int totalCount = counts[0];
749	>	for (int iproc = 1; iproc < nproc; iproc++) {
750	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
751	>	totalCount += counts[iproc];
752		}
753
754	<	return atomTypes;
755	<	}
633	<
634	<	void SimInfo::setupSimType() {
635	<	std::set<AtomType*>::iterator i;
636	<	std::set<AtomType*> atomTypes;
637	<	atomTypes = getUniqueAtomTypes();
754	>	// we need a (possibly redundant) set of all found types:
755	>	vector<int> ftGlobal(totalCount);
756
757	<	int useLennardJones = 0;
758	<	int useElectrostatic = 0;
759	<	int useEAM = 0;
760	<	int useSC = 0;
643	<	int useCharge = 0;
644	<	int useDirectional = 0;
645	<	int useDipole = 0;
646	<	int useGayBerne = 0;
647	<	int useSticky = 0;
648	<	int useStickyPower = 0;
649	<	int useShape = 0;
650	<	int useFLARB = 0; //it is not in AtomType yet
651	<	int useDirectionalAtom = 0;
652	<	int useElectrostatics = 0;
653	<	//usePBC and useRF are from simParams
654	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
655	<	int useRF;
656	<	int useSF;
657	<	std::string myMethod;
757	>	// now spray out the foundTypes to all the other processors:
758	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759	>	&ftGlobal[0], &counts[0], &disps[0],
760	>	MPI::INT);
761
762	<	// set the useRF logical
660	<	useRF = 0;
661	<	useSF = 0;
762	>	vector<int>::iterator j;
763
764	+	// foundIdents is a stl set, so inserting an already found ident
765	+	// will have no effect.
766	+	set<int> foundIdents;
767
768	<	if (simParams_->haveElectrostaticSummationMethod()) {
769	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
770	<	toUpper(myMethod);
771	<	if (myMethod == "REACTION_FIELD") {
772	<	useRF=1;
773	<	} else {
774	<	if (myMethod == "SHIFTED_FORCE") {
775	<	useSF = 1;
776	<	}
777	<	}
674	<	}
768	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769	>	foundIdents.insert((*j));
770	>
771	>	// now iterate over the foundIdents and get the actual atom types
772	>	// that correspond to these:
773	>	set<int>::iterator it;
774	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	>	atomTypes.insert( forceField_->getAtomType((*it)) );
776	>
777	>	#endif
778
779	+	return atomTypes;
780	+	}
781	+
782	+	void SimInfo::setupSimVariables() {
783	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
784	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	+	calcBoxDipole_ = false;
786	+	if ( simParams_->haveAccumulateBoxDipole() )
787	+	if ( simParams_->getAccumulateBoxDipole() ) {
788	+	calcBoxDipole_ = true;
789	+	}
790	+
791	+	set<AtomType*>::iterator i;
792	+	set<AtomType*> atomTypes;
793	+	atomTypes = getSimulatedAtomTypes();
794	+	int usesElectrostatic = 0;
795	+	int usesMetallic = 0;
796	+	int usesDirectional = 0;
797	+	int usesFluctuatingCharges =  0;
798		//loop over all of the atom types
799		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800	<	useLennardJones |= (*i)->isLennardJones();
801	<	useElectrostatic |= (*i)->isElectrostatic();
802	<	useEAM |= (*i)->isEAM();
803	<	useSC |= (*i)->isSC();
682	<	useCharge |= (*i)->isCharge();
683	<	useDirectional |= (*i)->isDirectional();
684	<	useDipole |= (*i)->isDipole();
685	<	useGayBerne |= (*i)->isGayBerne();
686	<	useSticky |= (*i)->isSticky();
687	<	useStickyPower |= (*i)->isStickyPower();
688	<	useShape |= (*i)->isShape();
800	>	usesElectrostatic |= (*i)->isElectrostatic();
801	>	usesMetallic |= (*i)->isMetal();
802	>	usesDirectional |= (*i)->isDirectional();
803	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804		}
805	<
691	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
692	<	useDirectionalAtom = 1;
693	<	}
694	<
695	<	if (useCharge || useDipole) {
696	<	useElectrostatics = 1;
697	<	}
698	<
805	>
806		#ifdef IS_MPI
807		int temp;
808	+	temp = usesDirectional;
809	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	+
811	+	temp = usesMetallic;
812	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	+
814	+	temp = usesElectrostatic;
815	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816
817	<	temp = usePBC;
818	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	>	temp = usesFluctuatingCharges;
818	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	#else
820
821	<	temp = useDirectionalAtom;
822	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	>	usesDirectionalAtoms_ = usesDirectional;
822	>	usesMetallicAtoms_ = usesMetallic;
823	>	usesElectrostaticAtoms_ = usesElectrostatic;
824	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
825
826	<	temp = useLennardJones;
827	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	>	#endif
827	>
828	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
829	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
830	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
831	>	}
832
711	–	temp = useElectrostatics;
712	–	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833
834	<	temp = useCharge;
835	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834	>	vector<int> SimInfo::getGlobalAtomIndices() {
835	>	SimInfo::MoleculeIterator mi;
836	>	Molecule* mol;
837	>	Molecule::AtomIterator ai;
838	>	Atom* atom;
839
840	<	temp = useDipole;
718	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
719	<
720	<	temp = useSticky;
721	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
722	<
723	<	temp = useStickyPower;
724	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
841
842	<	temp = useGayBerne;
843	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
843	>
844	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
845	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
846	>	}
847	>	}
848	>	return GlobalAtomIndices;
849	>	}
850
729	–	temp = useEAM;
730	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851
852	<	temp = useSC;
853	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	<
855	<	temp = useShape;
856	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	vector<int> SimInfo::getGlobalGroupIndices() {
853	>	SimInfo::MoleculeIterator mi;
854	>	Molecule* mol;
855	>	Molecule::CutoffGroupIterator ci;
856	>	CutoffGroup* cg;
857
858	<	temp = useFLARB;
859	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	<
741	<	temp = useRF;
742	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
743	<
744	<	temp = useSF;
745	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
746	<
747	<	#endif
748	<
749	<	fInfo_.SIM_uses_PBC = usePBC;
750	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
751	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
752	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
753	<	fInfo_.SIM_uses_Charges = useCharge;
754	<	fInfo_.SIM_uses_Dipoles = useDipole;
755	<	fInfo_.SIM_uses_Sticky = useSticky;
756	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
757	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
758	<	fInfo_.SIM_uses_EAM = useEAM;
759	<	fInfo_.SIM_uses_SC = useSC;
760	<	fInfo_.SIM_uses_Shapes = useShape;
761	<	fInfo_.SIM_uses_FLARB = useFLARB;
762	<	fInfo_.SIM_uses_RF = useRF;
763	<	fInfo_.SIM_uses_SF = useSF;
764	<
765	<	if( myMethod == "REACTION_FIELD") {
858	>	vector<int> GlobalGroupIndices;
859	>
860	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
861
862	<	if (simParams_->haveDielectric()) {
863	<	fInfo_.dielect = simParams_->getDielectric();
864	<	} else {
865	<	sprintf(painCave.errMsg,
866	<	"SimSetup Error: No Dielectric constant was set.\n"
867	<	"\tYou are trying to use Reaction Field without"
773	<	"\tsetting a dielectric constant!\n");
774	<	painCave.isFatal = 1;
775	<	simError();
776	<	}
862	>	//local index of cutoff group is trivial, it only depends on the
863	>	//order of travesing
864	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
865	>	cg = mol->nextCutoffGroup(ci)) {
866	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
867	>	}
868		}
869	<
869	>	return GlobalGroupIndices;
870		}
871
781	–	void SimInfo::setupFortranSim() {
782	–	int isError;
783	–	int nExclude;
784	–	std::vector<int> fortranGlobalGroupMembership;
785	–
786	–	nExclude = exclude_.getSize();
787	–	isError = 0;
872
873	<	//globalGroupMembership_ is filled by SimCreator
874	<	for (int i = 0; i < nGlobalAtoms_; i++) {
791	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
792	<	}
873	>	void SimInfo::prepareTopology() {
874	>	int nExclude, nOneTwo, nOneThree, nOneFour;
875
876		//calculate mass ratio of cutoff group
795	–	std::vector<double> mfact;
877		SimInfo::MoleculeIterator mi;
878		Molecule* mol;
879		Molecule::CutoffGroupIterator ci;
880		CutoffGroup* cg;
881		Molecule::AtomIterator ai;
882		Atom* atom;
883	<	double totalMass;
883	>	RealType totalMass;
884
885	<	//to avoid memory reallocation, reserve enough space for mfact
886	<	mfact.reserve(getNCutoffGroups());
885	>	/**
886	>	* The mass factor is the relative mass of an atom to the total
887	>	* mass of the cutoff group it belongs to.  By default, all atoms
888	>	* are their own cutoff groups, and therefore have mass factors of
889	>	* 1.  We need some special handling for massless atoms, which
890	>	* will be treated as carrying the entire mass of the cutoff
891	>	* group.
892	>	*/
893	>	massFactors_.clear();
894	>	massFactors_.resize(getNAtoms(), 1.0);
895
896		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
897	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
898	>	cg = mol->nextCutoffGroup(ci)) {
899
900		totalMass = cg->getMass();
901		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
902		// Check for massless groups - set mfact to 1 if true
903	<	if (totalMass != 0)
904	<	mfact.push_back(atom->getMass()/totalMass);
903	>	if (totalMass != 0)
904	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
905		else
906	<	mfact.push_back( 1.0 );
906	>	massFactors_[atom->getLocalIndex()] = 1.0;
907		}
818	–
908		}
909		}
910
911	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
823	<	std::vector<int> identArray;
911	>	// Build the identArray_
912
913	<	//to avoid memory reallocation, reserve enough space identArray
914	<	identArray.reserve(getNAtoms());
827	<
913	>	identArray_.clear();
914	>	identArray_.reserve(getNAtoms());
915		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
916		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
917	<	identArray.push_back(atom->getIdent());
917	>	identArray_.push_back(atom->getIdent());
918		}
919		}
833	–
834	–	//fill molMembershipArray
835	–	//molMembershipArray is filled by SimCreator
836	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
837	–	for (int i = 0; i < nGlobalAtoms_; i++) {
838	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
839	–	}
920
921	<	//setup fortran simulation
842	<	int nGlobalExcludes = 0;
843	<	int* globalExcludes = NULL;
844	<	int* excludeList = exclude_.getExcludeList();
845	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
846	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
847	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
921	>	//scan topology
922
923	<	if( isError ){
923	>	nExclude = excludedInteractions_.getSize();
924	>	nOneTwo = oneTwoInteractions_.getSize();
925	>	nOneThree = oneThreeInteractions_.getSize();
926	>	nOneFour = oneFourInteractions_.getSize();
927
928	<	sprintf( painCave.errMsg,
929	<	"There was an error setting the simulation information in fortran.\n" );
930	<	painCave.isFatal = 1;
931	<	painCave.severity = OOPSE_ERROR;
855	<	simError();
856	<	}
857	<
858	<	#ifdef IS_MPI
859	<	sprintf( checkPointMsg,
860	<	"succesfully sent the simulation information to fortran.\n");
861	<	MPIcheckPoint();
862	<	#endif // is_mpi
863	<	}
864	<
865	<
866	<	#ifdef IS_MPI
867	<	void SimInfo::setupFortranParallel() {
868	<
869	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
870	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
871	<	std::vector<int> localToGlobalCutoffGroupIndex;
872	<	SimInfo::MoleculeIterator mi;
873	<	Molecule::AtomIterator ai;
874	<	Molecule::CutoffGroupIterator ci;
875	<	Molecule* mol;
876	<	Atom* atom;
877	<	CutoffGroup* cg;
878	<	mpiSimData parallelData;
879	<	int isError;
880	<
881	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
882	<
883	<	//local index(index in DataStorge) of atom is important
884	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
885	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
886	<	}
887	<
888	<	//local index of cutoff group is trivial, it only depends on the order of travesing
889	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
890	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
891	<	}
892	<
893	<	}
894	<
895	<	//fill up mpiSimData struct
896	<	parallelData.nMolGlobal = getNGlobalMolecules();
897	<	parallelData.nMolLocal = getNMolecules();
898	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
899	<	parallelData.nAtomsLocal = getNAtoms();
900	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
901	<	parallelData.nGroupsLocal = getNCutoffGroups();
902	<	parallelData.myNode = worldRank;
903	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
904	<
905	<	//pass mpiSimData struct and index arrays to fortran
906	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
907	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
908	<	&localToGlobalCutoffGroupIndex[0], &isError);
909	<
910	<	if (isError) {
911	<	sprintf(painCave.errMsg,
912	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
913	<	painCave.isFatal = 1;
914	<	simError();
915	<	}
916	<
917	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
918	<	MPIcheckPoint();
919	<
928	>	int* excludeList = excludedInteractions_.getPairList();
929	>	int* oneTwoList = oneTwoInteractions_.getPairList();
930	>	int* oneThreeList = oneThreeInteractions_.getPairList();
931	>	int* oneFourList = oneFourInteractions_.getPairList();
932
933	<	}
922	<
923	<	#endif
924	<
925	<	void SimInfo::setupCutoff() {
926	<
927	<	// Check the cutoff policy
928	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
929	<	if (simParams_->haveCutoffPolicy()) {
930	<	std::string myPolicy = simParams_->getCutoffPolicy();
931	<	toUpper(myPolicy);
932	<	if (myPolicy == "MIX") {
933	<	cp = MIX_CUTOFF_POLICY;
934	<	} else {
935	<	if (myPolicy == "MAX") {
936	<	cp = MAX_CUTOFF_POLICY;
937	<	} else {
938	<	if (myPolicy == "TRADITIONAL") {
939	<	cp = TRADITIONAL_CUTOFF_POLICY;
940	<	} else {
941	<	// throw error
942	<	sprintf( painCave.errMsg,
943	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
944	<	painCave.isFatal = 1;
945	<	simError();
946	<	}
947	<	}
948	<	}
949	<	}
950	<	notifyFortranCutoffPolicy(&cp);
951	<
952	<	// Check the Skin Thickness for neighborlists
953	<	double skin;
954	<	if (simParams_->haveSkinThickness()) {
955	<	skin = simParams_->getSkinThickness();
956	<	notifyFortranSkinThickness(&skin);
957	<	}
958	<
959	<	// Check if the cutoff was set explicitly:
960	<	if (simParams_->haveCutoffRadius()) {
961	<	rcut_ = simParams_->getCutoffRadius();
962	<	if (simParams_->haveSwitchingRadius()) {
963	<	rsw_  = simParams_->getSwitchingRadius();
964	<	} else {
965	<	rsw_ = rcut_;
966	<	}
967	<	notifyFortranCutoffs(&rcut_, &rsw_);
968	<
969	<	} else {
970	<
971	<	// For electrostatic atoms, we'll assume a large safe value:
972	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
973	<	sprintf(painCave.errMsg,
974	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
975	<	"\tOOPSE will use a default value of 15.0 angstroms"
976	<	"\tfor the cutoffRadius.\n");
977	<	painCave.isFatal = 0;
978	<	simError();
979	<	rcut_ = 15.0;
980	<
981	<	if (simParams_->haveElectrostaticSummationMethod()) {
982	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
983	<	toUpper(myMethod);
984	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
985	<	if (simParams_->haveSwitchingRadius()){
986	<	sprintf(painCave.errMsg,
987	<	"SimInfo Warning: A value was set for the switchingRadius\n"
988	<	"\teven though the electrostaticSummationMethod was\n"
989	<	"\tset to %s\n", myMethod.c_str());
990	<	painCave.isFatal = 1;
991	<	simError();
992	<	}
993	<	}
994	<	}
995	<
996	<	if (simParams_->haveSwitchingRadius()){
997	<	rsw_ = simParams_->getSwitchingRadius();
998	<	} else {
999	<	sprintf(painCave.errMsg,
1000	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1001	<	"\tOOPSE will use a default value of\n"
1002	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1003	<	painCave.isFatal = 0;
1004	<	simError();
1005	<	rsw_ = 0.85 * rcut_;
1006	<	}
1007	<	notifyFortranCutoffs(&rcut_, &rsw_);
1008	<	} else {
1009	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1010	<	// We'll punt and let fortran figure out the cutoffs later.
1011	<
1012	<	notifyFortranYouAreOnYourOwn();
1013	<
1014	<	}
1015	<	}
1016	<	}
1017	<
1018	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1019	<
1020	<	int errorOut;
1021	<	int esm =  NONE;
1022	<	int sm = UNDAMPED;
1023	<	double alphaVal;
1024	<	double dielectric;
1025	<
1026	<	errorOut = isError;
1027	<	alphaVal = simParams_->getDampingAlpha();
1028	<	dielectric = simParams_->getDielectric();
1029	<
1030	<	if (simParams_->haveElectrostaticSummationMethod()) {
1031	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1032	<	toUpper(myMethod);
1033	<	if (myMethod == "NONE") {
1034	<	esm = NONE;
1035	<	} else {
1036	<	if (myMethod == "SWITCHING_FUNCTION") {
1037	<	esm = SWITCHING_FUNCTION;
1038	<	} else {
1039	<	if (myMethod == "SHIFTED_POTENTIAL") {
1040	<	esm = SHIFTED_POTENTIAL;
1041	<	} else {
1042	<	if (myMethod == "SHIFTED_FORCE") {
1043	<	esm = SHIFTED_FORCE;
1044	<	} else {
1045	<	if (myMethod == "REACTION_FIELD") {
1046	<	esm = REACTION_FIELD;
1047	<	} else {
1048	<	// throw error
1049	<	sprintf( painCave.errMsg,
1050	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1051	<	"\t(Input file specified %s .)\n"
1052	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1053	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1054	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1055	<	painCave.isFatal = 1;
1056	<	simError();
1057	<	}
1058	<	}
1059	<	}
1060	<	}
1061	<	}
1062	<	}
1063	<
1064	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1065	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1066	<	toUpper(myScreen);
1067	<	if (myScreen == "UNDAMPED") {
1068	<	sm = UNDAMPED;
1069	<	} else {
1070	<	if (myScreen == "DAMPED") {
1071	<	sm = DAMPED;
1072	<	if (!simParams_->haveDampingAlpha()) {
1073	<	//throw error
1074	<	sprintf( painCave.errMsg,
1075	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1076	<	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1077	<	painCave.isFatal = 0;
1078	<	simError();
1079	<	}
1080	<	} else {
1081	<	// throw error
1082	<	sprintf( painCave.errMsg,
1083	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1084	<	"\t(Input file specified %s .)\n"
1085	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1086	<	"or \"damped\".\n", myScreen.c_str() );
1087	<	painCave.isFatal = 1;
1088	<	simError();
1089	<	}
1090	<	}
1091	<	}
1092	<
1093	<	// let's pass some summation method variables to fortran
1094	<	setElectrostaticSummationMethod( &esm );
1095	<	notifyFortranElectrostaticMethod( &esm );
1096	<	setScreeningMethod( &sm );
1097	<	setDampingAlpha( &alphaVal );
1098	<	setReactionFieldDielectric( &dielectric );
1099	<	initFortranFF( &errorOut );
933	>	topologyDone_ = true;
934		}
935
1102	–	void SimInfo::setupSwitchingFunction() {
1103	–	int ft = CUBIC;
1104	–
1105	–	if (simParams_->haveSwitchingFunctionType()) {
1106	–	std::string funcType = simParams_->getSwitchingFunctionType();
1107	–	toUpper(funcType);
1108	–	if (funcType == "CUBIC") {
1109	–	ft = CUBIC;
1110	–	} else {
1111	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1112	–	ft = FIFTH_ORDER_POLY;
1113	–	} else {
1114	–	// throw error
1115	–	sprintf( painCave.errMsg,
1116	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1117	–	painCave.isFatal = 1;
1118	–	simError();
1119	–	}
1120	–	}
1121	–	}
1122	–
1123	–	// send switching function notification to switcheroo
1124	–	setFunctionType(&ft);
1125	–
1126	–	}
1127	–
936		void SimInfo::addProperty(GenericData* genData) {
937		properties_.addProperty(genData);
938		}
939
940	<	void SimInfo::removeProperty(const std::string& propName) {
940	>	void SimInfo::removeProperty(const string& propName) {
941		properties_.removeProperty(propName);
942		}
943
#	Line 1137 | Line 945 | namespace oopse {
945		properties_.clearProperties();
946		}
947
948	<	std::vector<std::string> SimInfo::getPropertyNames() {
948	>	vector<string> SimInfo::getPropertyNames() {
949		return properties_.getPropertyNames();
950		}
951
952	<	std::vector<GenericData*> SimInfo::getProperties() {
952	>	vector<GenericData*> SimInfo::getProperties() {
953		return properties_.getProperties();
954		}
955
956	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
956	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
957		return properties_.getPropertyByName(propName);
958		}
959
#	Line 1159 | Line 967 | namespace oopse {
967		Molecule* mol;
968		RigidBody* rb;
969		Atom* atom;
970	+	CutoffGroup* cg;
971		SimInfo::MoleculeIterator mi;
972		Molecule::RigidBodyIterator rbIter;
973	<	Molecule::AtomIterator atomIter;;
973	>	Molecule::AtomIterator atomIter;
974	>	Molecule::CutoffGroupIterator cgIter;
975
976		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
977
#	Line 1172 | Line 982 | namespace oopse {
982		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
983		rb->setSnapshotManager(sman_);
984		}
985	+
986	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
987	+	cg->setSnapshotManager(sman_);
988	+	}
989		}
990
991		}
#	Line 1181 | Line 995 | namespace oopse {
995		Molecule* mol;
996
997		Vector3d comVel(0.0);
998	<	double totalMass = 0.0;
998	>	RealType totalMass = 0.0;
999
1000
1001		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1002	<	double mass = mol->getMass();
1002	>	RealType mass = mol->getMass();
1003		totalMass += mass;
1004		comVel += mass * mol->getComVel();
1005		}
1006
1007		#ifdef IS_MPI
1008	<	double tmpMass = totalMass;
1008	>	RealType tmpMass = totalMass;
1009		Vector3d tmpComVel(comVel);
1010	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1011	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1010	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1011	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1012		#endif
1013
1014		comVel /= totalMass;
#	Line 1207 | Line 1021 | namespace oopse {
1021		Molecule* mol;
1022
1023		Vector3d com(0.0);
1024	<	double totalMass = 0.0;
1024	>	RealType totalMass = 0.0;
1025
1026		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1027	<	double mass = mol->getMass();
1027	>	RealType mass = mol->getMass();
1028		totalMass += mass;
1029		com += mass * mol->getCom();
1030		}
1031
1032		#ifdef IS_MPI
1033	<	double tmpMass = totalMass;
1033	>	RealType tmpMass = totalMass;
1034		Vector3d tmpCom(com);
1035	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1036	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1035	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1036	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1037		#endif
1038
1039		com /= totalMass;
#	Line 1228 | Line 1042 | namespace oopse {
1042
1043		}
1044
1045	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1045	>	ostream& operator <<(ostream& o, SimInfo& info) {
1046
1047		return o;
1048		}
#	Line 1243 | Line 1057 | namespace oopse {
1057		Molecule* mol;
1058
1059
1060	<	double totalMass = 0.0;
1060	>	RealType totalMass = 0.0;
1061
1062
1063		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1064	<	double mass = mol->getMass();
1064	>	RealType mass = mol->getMass();
1065		totalMass += mass;
1066		com += mass * mol->getCom();
1067		comVel += mass * mol->getComVel();
1068		}
1069
1070		#ifdef IS_MPI
1071	<	double tmpMass = totalMass;
1071	>	RealType tmpMass = totalMass;
1072		Vector3d tmpCom(com);
1073		Vector3d tmpComVel(comVel);
1074	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1075	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1076	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1074	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1075	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1076	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1077		#endif
1078
1079		com /= totalMass;
#	Line 1271 | Line 1085 | namespace oopse {
1085
1086
1087		[  Ixx -Ixy  -Ixz ]
1088	<	J =| -Iyx  Iyy  -Iyz |
1088	>	J =| -Iyx  Iyy  -Iyz |
1089		[ -Izx -Iyz   Izz ]
1090		*/
1091
1092		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1093
1094
1095	<	double xx = 0.0;
1096	<	double yy = 0.0;
1097	<	double zz = 0.0;
1098	<	double xy = 0.0;
1099	<	double xz = 0.0;
1100	<	double yz = 0.0;
1095	>	RealType xx = 0.0;
1096	>	RealType yy = 0.0;
1097	>	RealType zz = 0.0;
1098	>	RealType xy = 0.0;
1099	>	RealType xz = 0.0;
1100	>	RealType yz = 0.0;
1101		Vector3d com(0.0);
1102		Vector3d comVel(0.0);
1103
#	Line 1295 | Line 1109 | namespace oopse {
1109		Vector3d thisq(0.0);
1110		Vector3d thisv(0.0);
1111
1112	<	double thisMass = 0.0;
1112	>	RealType thisMass = 0.0;
1113
1114
1115
#	Line 1333 | Line 1147 | namespace oopse {
1147		#ifdef IS_MPI
1148		Mat3x3d tmpI(inertiaTensor);
1149		Vector3d tmpAngMom;
1150	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1151	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1150	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1152		#endif
1153
1154		return;
#	Line 1355 | Line 1169 | namespace oopse {
1169		Vector3d thisr(0.0);
1170		Vector3d thisp(0.0);
1171
1172	<	double thisMass;
1172	>	RealType thisMass;
1173
1174		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1175		thisMass = mol->getMass();
#	Line 1368 | Line 1182 | namespace oopse {
1182
1183		#ifdef IS_MPI
1184		Vector3d tmpAngMom;
1185	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1185	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1186		#endif
1187
1188		return angularMomentum;
1189		}
1190
1191	<
1192	<	}//end namespace oopse
1191	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1192	>	return IOIndexToIntegrableObject.at(index);
1193	>	}
1194	>
1195	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1196	>	IOIndexToIntegrableObject= v;
1197	>	}
1198
1199	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1200	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1201	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1202	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1203	+	*/
1204	+	void SimInfo::getGyrationalVolume(RealType &volume){
1205	+	Mat3x3d intTensor;
1206	+	RealType det;
1207	+	Vector3d dummyAngMom;
1208	+	RealType sysconstants;
1209	+	RealType geomCnst;
1210	+
1211	+	geomCnst = 3.0/2.0;
1212	+	/* Get the inertial tensor and angular momentum for free*/
1213	+	getInertiaTensor(intTensor,dummyAngMom);
1214	+
1215	+	det = intTensor.determinant();
1216	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1218	+	return;
1219	+	}
1220	+
1221	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1222	+	Mat3x3d intTensor;
1223	+	Vector3d dummyAngMom;
1224	+	RealType sysconstants;
1225	+	RealType geomCnst;
1226	+
1227	+	geomCnst = 3.0/2.0;
1228	+	/* Get the inertial tensor and angular momentum for free*/
1229	+	getInertiaTensor(intTensor,dummyAngMom);
1230	+
1231	+	detI = intTensor.determinant();
1232	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1234	+	return;
1235	+	}
1236	+	/*
1237	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1238	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1239	+	sdByGlobalIndex_ = v;
1240	+	}
1241	+
1242	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1243	+	//assert(index < nAtoms_ + nRigidBodies_);
1244	+	return sdByGlobalIndex_.at(index);
1245	+	}
1246	+	*/
1247	+	int SimInfo::getNGlobalConstraints() {
1248	+	int nGlobalConstraints;
1249	+	#ifdef IS_MPI
1250	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1251	+	MPI_COMM_WORLD);
1252	+	#else
1253	+	nGlobalConstraints =  nConstraints_;
1254	+	#endif
1255	+	return nGlobalConstraints;
1256	+	}
1257	+
1258	+	}//end namespace OpenMD
1259	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 764 by gezelter, Mon Nov 21 22:59:21 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

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