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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 809 by gezelter, Mon Dec 12 19:32:50 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1750 by gezelter, Thu Jun 7 12:53:46 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(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
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	<
80	<	MoleculeStamp* molStamp;
81	<	int nMolWithSameStamp;
82	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
84	<	CutoffGroupStamp* cgStamp;
85	<	RigidBodyStamp* rbStamp;
86	<	int nRigidAtoms = 0;
87	<	std::vector<Component*> components = simParams->getComponents();
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	>	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	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	<	molStamp = (*i)->getMoleculeStamp();
97	<	nMolWithSameStamp = (*i)->getNMol();
98	<
99	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
100	<
101	<	//calculate atoms in molecules
102	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	<
104	<	//calculate atoms in cutoff groups
105	<	int nAtomsInGroups = 0;
106	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
113	<
114	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
115	<	cgStamp = molStamp->getCutoffGroupStamp(j);
116	<	nAtomsInGroups += cgStamp->getNMembers();
117	<	}
118	<
119	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
120	<
121	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
122	<
123	<	//calculate atoms in rigid bodies
124	<	int nAtomsInRigidBodies = 0;
125	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
126	<
127	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
128	<	rbStamp = molStamp->getRigidBodyStamp(j);
129	<	nAtomsInRigidBodies += rbStamp->getNMembers();
130	<	}
131	<
132	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
133	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
134	<
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();
153	<
154	<	#ifdef IS_MPI
155	<	molToProcMap_.resize(nGlobalMols_);
156	<	#endif
157	<
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		}
#	Line 169 | Line 156 | namespace oopse {
156		delete forceField_;
157		}
158
172	–	int SimInfo::getNGlobalConstraints() {
173	–	int nGlobalConstraints;
174	–	#ifdef IS_MPI
175	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
176	–	MPI_COMM_WORLD);
177	–	#else
178	–	nGlobalConstraints =  nConstraints_;
179	–	#endif
180	–	return nGlobalConstraints;
181	–	}
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 217 | 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 231 | Line 210 | namespace oopse {
210		} else {
211		return false;
212		}
234	–
235	–
213		}
214
215
#	Line 248 | 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 269 | Line 250 | namespace oopse {
250		ndf_local += 3;
251		}
252		}
272	–
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	+
264		// n_constraints is local, so subtract them on each processor
265		ndf_local -= nConstraints_;
266
267		#ifdef IS_MPI
268		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
270		#else
271		ndf_ = ndf_local;
272	+	nGlobalFluctuatingCharges_ = nfq_local;
273		#endif
274
275		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 288 | Line 278 | namespace oopse {
278
279		}
280
281	+	int SimInfo::getFdf() {
282	+	#ifdef IS_MPI
283	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	+	#else
285	+	fdf_ = fdf_local;
286	+	#endif
287	+	return fdf_;
288	+	}
289	+
290	+	unsigned int SimInfo::getNLocalCutoffGroups(){
291	+	int nLocalCutoffAtoms = 0;
292	+	Molecule* mol;
293	+	MoleculeIterator mi;
294	+	CutoffGroup* cg;
295	+	Molecule::CutoffGroupIterator ci;
296	+
297	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
298	+
299	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
300	+	cg = mol->nextCutoffGroup(ci)) {
301	+	nLocalCutoffAtoms += cg->getNumAtom();
302	+
303	+	}
304	+	}
305	+
306	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
307	+	}
308	+
309		void SimInfo::calcNdfRaw() {
310		int ndfRaw_local;
311
312		MoleculeIterator i;
313	<	std::vector<StuntDouble*>::iterator j;
313	>	vector<StuntDouble*>::iterator j;
314		Molecule* mol;
315		StuntDouble* integrableObject;
316
#	Line 339 | Line 357 | namespace oopse {
357
358		}
359
360	<	void SimInfo::addExcludePairs(Molecule* mol) {
361	<	std::vector<Bond*>::iterator bondIter;
362	<	std::vector<Bend*>::iterator bendIter;
363	<	std::vector<Torsion*>::iterator torsionIter;
360	>	void SimInfo::addInteractionPairs(Molecule* mol) {
361	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
362	>	vector<Bond*>::iterator bondIter;
363	>	vector<Bend*>::iterator bendIter;
364	>	vector<Torsion*>::iterator torsionIter;
365	>	vector<Inversion*>::iterator inversionIter;
366		Bond* bond;
367		Bend* bend;
368		Torsion* torsion;
369	+	Inversion* inversion;
370		int a;
371		int b;
372		int c;
373		int d;
374
375	<	std::map<int, std::set<int> > atomGroups;
375	>	// atomGroups can be used to add special interaction maps between
376	>	// groups of atoms that are in two separate rigid bodies.
377	>	// However, most site-site interactions between two rigid bodies
378	>	// are probably not special, just the ones between the physically
379	>	// bonded atoms.  Interactions *within* a single rigid body should
380	>	// always be excluded.  These are done at the bottom of this
381	>	// function.
382
383	+	map<int, set<int> > atomGroups;
384		Molecule::RigidBodyIterator rbIter;
385		RigidBody* rb;
386		Molecule::IntegrableObjectIterator ii;
387		StuntDouble* integrableObject;
388
389	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
390	<	integrableObject = mol->nextIntegrableObject(ii)) {
391	<
389	>	for (integrableObject = mol->beginIntegrableObject(ii);
390	>	integrableObject != NULL;
391	>	integrableObject = mol->nextIntegrableObject(ii)) {
392	>
393		if (integrableObject->isRigidBody()) {
394	<	rb = static_cast<RigidBody*>(integrableObject);
395	<	std::vector<Atom*> atoms = rb->getAtoms();
396	<	std::set<int> rigidAtoms;
397	<	for (int i = 0; i < atoms.size(); ++i) {
398	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
399	<	}
400	<	for (int i = 0; i < atoms.size(); ++i) {
401	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
402	<	}
394	>	rb = static_cast<RigidBody*>(integrableObject);
395	>	vector<Atom*> atoms = rb->getAtoms();
396	>	set<int> rigidAtoms;
397	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
399	>	}
400	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
401	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
402	>	}
403		} else {
404	<	std::set<int> oneAtomSet;
404	>	set<int> oneAtomSet;
405		oneAtomSet.insert(integrableObject->getGlobalIndex());
406	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
406	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
407		}
408		}
409	+
410	+	for (bond= mol->beginBond(bondIter); bond != NULL;
411	+	bond = mol->nextBond(bondIter)) {
412
381	–
382	–
383	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
413		a = bond->getAtomA()->getGlobalIndex();
414	<	b = bond->getAtomB()->getGlobalIndex();
415	<	exclude_.addPair(a, b);
414	>	b = bond->getAtomB()->getGlobalIndex();
415	>
416	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
417	>	oneTwoInteractions_.addPair(a, b);
418	>	} else {
419	>	excludedInteractions_.addPair(a, b);
420	>	}
421		}
422
423	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
423	>	for (bend= mol->beginBend(bendIter); bend != NULL;
424	>	bend = mol->nextBend(bendIter)) {
425	>
426		a = bend->getAtomA()->getGlobalIndex();
427		b = bend->getAtomB()->getGlobalIndex();
428		c = bend->getAtomC()->getGlobalIndex();
393	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
394	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
395	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
396	–
397	–	exclude_.addPairs(rigidSetA, rigidSetB);
398	–	exclude_.addPairs(rigidSetA, rigidSetC);
399	–	exclude_.addPairs(rigidSetB, rigidSetC);
429
430	<	//exclude_.addPair(a, b);
431	<	//exclude_.addPair(a, c);
432	<	//exclude_.addPair(b, c);
430	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
431	>	oneTwoInteractions_.addPair(a, b);
432	>	oneTwoInteractions_.addPair(b, c);
433	>	} else {
434	>	excludedInteractions_.addPair(a, b);
435	>	excludedInteractions_.addPair(b, c);
436	>	}
437	>
438	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
439	>	oneThreeInteractions_.addPair(a, c);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	}
443		}
444
445	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
445	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
446	>	torsion = mol->nextTorsion(torsionIter)) {
447	>
448		a = torsion->getAtomA()->getGlobalIndex();
449		b = torsion->getAtomB()->getGlobalIndex();
450		c = torsion->getAtomC()->getGlobalIndex();
451	<	d = torsion->getAtomD()->getGlobalIndex();
411	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
412	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
413	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
414	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
451	>	d = torsion->getAtomD()->getGlobalIndex();
452
453	<	exclude_.addPairs(rigidSetA, rigidSetB);
454	<	exclude_.addPairs(rigidSetA, rigidSetC);
455	<	exclude_.addPairs(rigidSetA, rigidSetD);
456	<	exclude_.addPairs(rigidSetB, rigidSetC);
457	<	exclude_.addPairs(rigidSetB, rigidSetD);
458	<	exclude_.addPairs(rigidSetC, rigidSetD);
453	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
454	>	oneTwoInteractions_.addPair(a, b);
455	>	oneTwoInteractions_.addPair(b, c);
456	>	oneTwoInteractions_.addPair(c, d);
457	>	} else {
458	>	excludedInteractions_.addPair(a, b);
459	>	excludedInteractions_.addPair(b, c);
460	>	excludedInteractions_.addPair(c, d);
461	>	}
462	>
463	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
464	>	oneThreeInteractions_.addPair(a, c);
465	>	oneThreeInteractions_.addPair(b, d);
466	>	} else {
467	>	excludedInteractions_.addPair(a, c);
468	>	excludedInteractions_.addPair(b, d);
469	>	}
470
471	<	/*
472	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
473	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
474	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
475	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
428	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
429	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
430	<
431	<
432	<	exclude_.addPair(a, b);
433	<	exclude_.addPair(a, c);
434	<	exclude_.addPair(a, d);
435	<	exclude_.addPair(b, c);
436	<	exclude_.addPair(b, d);
437	<	exclude_.addPair(c, d);
438	<	*/
471	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
472	>	oneFourInteractions_.addPair(a, d);
473	>	} else {
474	>	excludedInteractions_.addPair(a, d);
475	>	}
476		}
477
478	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
479	<	std::vector<Atom*> atoms = rb->getAtoms();
480	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
481	<	for (int j = i + 1; j < atoms.size(); ++j) {
478	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
479	>	inversion = mol->nextInversion(inversionIter)) {
480	>
481	>	a = inversion->getAtomA()->getGlobalIndex();
482	>	b = inversion->getAtomB()->getGlobalIndex();
483	>	c = inversion->getAtomC()->getGlobalIndex();
484	>	d = inversion->getAtomD()->getGlobalIndex();
485	>
486	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
487	>	oneTwoInteractions_.addPair(a, b);
488	>	oneTwoInteractions_.addPair(a, c);
489	>	oneTwoInteractions_.addPair(a, d);
490	>	} else {
491	>	excludedInteractions_.addPair(a, b);
492	>	excludedInteractions_.addPair(a, c);
493	>	excludedInteractions_.addPair(a, d);
494	>	}
495	>
496	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
497	>	oneThreeInteractions_.addPair(b, c);
498	>	oneThreeInteractions_.addPair(b, d);
499	>	oneThreeInteractions_.addPair(c, d);
500	>	} else {
501	>	excludedInteractions_.addPair(b, c);
502	>	excludedInteractions_.addPair(b, d);
503	>	excludedInteractions_.addPair(c, d);
504	>	}
505	>	}
506	>
507	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
508	>	rb = mol->nextRigidBody(rbIter)) {
509	>	vector<Atom*> atoms = rb->getAtoms();
510	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
511	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
512		a = atoms[i]->getGlobalIndex();
513		b = atoms[j]->getGlobalIndex();
514	<	exclude_.addPair(a, b);
514	>	excludedInteractions_.addPair(a, b);
515		}
516		}
517		}
518
519		}
520
521	<	void SimInfo::removeExcludePairs(Molecule* mol) {
522	<	std::vector<Bond*>::iterator bondIter;
523	<	std::vector<Bend*>::iterator bendIter;
524	<	std::vector<Torsion*>::iterator torsionIter;
521	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
522	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
523	>	vector<Bond*>::iterator bondIter;
524	>	vector<Bend*>::iterator bendIter;
525	>	vector<Torsion*>::iterator torsionIter;
526	>	vector<Inversion*>::iterator inversionIter;
527		Bond* bond;
528		Bend* bend;
529		Torsion* torsion;
530	+	Inversion* inversion;
531		int a;
532		int b;
533		int c;
534		int d;
535
536	<	std::map<int, std::set<int> > atomGroups;
467	<
536	>	map<int, set<int> > atomGroups;
537		Molecule::RigidBodyIterator rbIter;
538		RigidBody* rb;
539		Molecule::IntegrableObjectIterator ii;
540		StuntDouble* integrableObject;
541
542	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
543	<	integrableObject = mol->nextIntegrableObject(ii)) {
544	<
542	>	for (integrableObject = mol->beginIntegrableObject(ii);
543	>	integrableObject != NULL;
544	>	integrableObject = mol->nextIntegrableObject(ii)) {
545	>
546		if (integrableObject->isRigidBody()) {
547	<	rb = static_cast<RigidBody*>(integrableObject);
548	<	std::vector<Atom*> atoms = rb->getAtoms();
549	<	std::set<int> rigidAtoms;
550	<	for (int i = 0; i < atoms.size(); ++i) {
551	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
552	<	}
553	<	for (int i = 0; i < atoms.size(); ++i) {
554	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555	<	}
547	>	rb = static_cast<RigidBody*>(integrableObject);
548	>	vector<Atom*> atoms = rb->getAtoms();
549	>	set<int> rigidAtoms;
550	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
552	>	}
553	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
554	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555	>	}
556		} else {
557	<	std::set<int> oneAtomSet;
557	>	set<int> oneAtomSet;
558		oneAtomSet.insert(integrableObject->getGlobalIndex());
559	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
559	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
560		}
561		}
562
563	<
564	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
563	>	for (bond= mol->beginBond(bondIter); bond != NULL;
564	>	bond = mol->nextBond(bondIter)) {
565	>
566		a = bond->getAtomA()->getGlobalIndex();
567	<	b = bond->getAtomB()->getGlobalIndex();
568	<	exclude_.removePair(a, b);
567	>	b = bond->getAtomB()->getGlobalIndex();
568	>
569	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
570	>	oneTwoInteractions_.removePair(a, b);
571	>	} else {
572	>	excludedInteractions_.removePair(a, b);
573	>	}
574		}
575
576	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
576	>	for (bend= mol->beginBend(bendIter); bend != NULL;
577	>	bend = mol->nextBend(bendIter)) {
578	>
579		a = bend->getAtomA()->getGlobalIndex();
580		b = bend->getAtomB()->getGlobalIndex();
581		c = bend->getAtomC()->getGlobalIndex();
504	–
505	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
506	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
507	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
508	–
509	–	exclude_.removePairs(rigidSetA, rigidSetB);
510	–	exclude_.removePairs(rigidSetA, rigidSetC);
511	–	exclude_.removePairs(rigidSetB, rigidSetC);
582
583	<	//exclude_.removePair(a, b);
584	<	//exclude_.removePair(a, c);
585	<	//exclude_.removePair(b, c);
583	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
584	>	oneTwoInteractions_.removePair(a, b);
585	>	oneTwoInteractions_.removePair(b, c);
586	>	} else {
587	>	excludedInteractions_.removePair(a, b);
588	>	excludedInteractions_.removePair(b, c);
589	>	}
590	>
591	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
592	>	oneThreeInteractions_.removePair(a, c);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	}
596		}
597
598	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
598	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
599	>	torsion = mol->nextTorsion(torsionIter)) {
600	>
601		a = torsion->getAtomA()->getGlobalIndex();
602		b = torsion->getAtomB()->getGlobalIndex();
603		c = torsion->getAtomC()->getGlobalIndex();
604	<	d = torsion->getAtomD()->getGlobalIndex();
604	>	d = torsion->getAtomD()->getGlobalIndex();
605	>
606	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
607	>	oneTwoInteractions_.removePair(a, b);
608	>	oneTwoInteractions_.removePair(b, c);
609	>	oneTwoInteractions_.removePair(c, d);
610	>	} else {
611	>	excludedInteractions_.removePair(a, b);
612	>	excludedInteractions_.removePair(b, c);
613	>	excludedInteractions_.removePair(c, d);
614	>	}
615
616	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
617	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
618	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
619	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
616	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
617	>	oneThreeInteractions_.removePair(a, c);
618	>	oneThreeInteractions_.removePair(b, d);
619	>	} else {
620	>	excludedInteractions_.removePair(a, c);
621	>	excludedInteractions_.removePair(b, d);
622	>	}
623
624	<	exclude_.removePairs(rigidSetA, rigidSetB);
625	<	exclude_.removePairs(rigidSetA, rigidSetC);
626	<	exclude_.removePairs(rigidSetA, rigidSetD);
627	<	exclude_.removePairs(rigidSetB, rigidSetC);
628	<	exclude_.removePairs(rigidSetB, rigidSetD);
629	<	exclude_.removePairs(rigidSetC, rigidSetD);
624	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
625	>	oneFourInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, d);
628	>	}
629	>	}
630
631	<	/*
632	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
538	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
539	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
540	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
541	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
542	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
631	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
632	>	inversion = mol->nextInversion(inversionIter)) {
633
634	<
635	<	exclude_.removePair(a, b);
636	<	exclude_.removePair(a, c);
637	<	exclude_.removePair(a, d);
638	<	exclude_.removePair(b, c);
639	<	exclude_.removePair(b, d);
640	<	exclude_.removePair(c, d);
641	<	*/
634	>	a = inversion->getAtomA()->getGlobalIndex();
635	>	b = inversion->getAtomB()->getGlobalIndex();
636	>	c = inversion->getAtomC()->getGlobalIndex();
637	>	d = inversion->getAtomD()->getGlobalIndex();
638	>
639	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
640	>	oneTwoInteractions_.removePair(a, b);
641	>	oneTwoInteractions_.removePair(a, c);
642	>	oneTwoInteractions_.removePair(a, d);
643	>	} else {
644	>	excludedInteractions_.removePair(a, b);
645	>	excludedInteractions_.removePair(a, c);
646	>	excludedInteractions_.removePair(a, d);
647	>	}
648	>
649	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
650	>	oneThreeInteractions_.removePair(b, c);
651	>	oneThreeInteractions_.removePair(b, d);
652	>	oneThreeInteractions_.removePair(c, d);
653	>	} else {
654	>	excludedInteractions_.removePair(b, c);
655	>	excludedInteractions_.removePair(b, d);
656	>	excludedInteractions_.removePair(c, d);
657	>	}
658		}
659
660	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
661	<	std::vector<Atom*> atoms = rb->getAtoms();
662	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
663	<	for (int j = i + 1; j < atoms.size(); ++j) {
660	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
661	>	rb = mol->nextRigidBody(rbIter)) {
662	>	vector<Atom*> atoms = rb->getAtoms();
663	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
664	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
665		a = atoms[i]->getGlobalIndex();
666		b = atoms[j]->getGlobalIndex();
667	<	exclude_.removePair(a, b);
667	>	excludedInteractions_.removePair(a, b);
668		}
669		}
670		}
671	<
671	>
672		}
673	<
674	<
673	>
674	>
675		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
676		int curStampId;
677	<
677	>
678		//index from 0
679		curStampId = moleculeStamps_.size();
680
#	Line 575 | Line 682 | namespace oopse {
682		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
683		}
684
578	–	void SimInfo::update() {
685
686	<	setupSimType();
687	<
688	<	#ifdef IS_MPI
689	<	setupFortranParallel();
690	<	#endif
691	<
692	<	setupFortranSim();
693	<
694	<	//setup fortran force field
589	<	/** @deprecate */
590	<	int isError = 0;
591	<
592	<	setupElectrostaticSummationMethod( isError );
593	<	setupSwitchingFunction();
594	<
595	<	if(isError){
596	<	sprintf( painCave.errMsg,
597	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
598	<	painCave.isFatal = 1;
599	<	simError();
600	<	}
601	<
602	<
603	<	setupCutoff();
604	<
686	>	/**
687	>	* update
688	>	*
689	>	*  Performs the global checks and variable settings after the
690	>	*  objects have been created.
691	>	*
692	>	*/
693	>	void SimInfo::update() {
694	>	setupSimVariables();
695		calcNdf();
696		calcNdfRaw();
697		calcNdfTrans();
608	–
609	–	fortranInitialized_ = true;
698		}
699	<
700	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
699	>
700	>	/**
701	>	* getSimulatedAtomTypes
702	>	*
703	>	* Returns an STL set of AtomType* that are actually present in this
704	>	* simulation.  Must query all processors to assemble this information.
705	>	*
706	>	*/
707	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
708		SimInfo::MoleculeIterator mi;
709		Molecule* mol;
710		Molecule::AtomIterator ai;
711		Atom* atom;
712	<	std::set<AtomType*> atomTypes;
713	<
712	>	set<AtomType*> atomTypes;
713	>
714		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
715	<
716	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
715	>	for(atom = mol->beginAtom(ai); atom != NULL;
716	>	atom = mol->nextAtom(ai)) {
717		atomTypes.insert(atom->getAtomType());
718	<	}
719	<
720	<	}
718	>	}
719	>	}
720	>
721	>	#ifdef IS_MPI
722
723	<	return atomTypes;
724	<	}
629	<
630	<	void SimInfo::setupSimType() {
631	<	std::set<AtomType*>::iterator i;
632	<	std::set<AtomType*> atomTypes;
633	<	atomTypes = getUniqueAtomTypes();
723	>	// loop over the found atom types on this processor, and add their
724	>	// numerical idents to a vector:
725
726	<	int useLennardJones = 0;
727	<	int useElectrostatic = 0;
728	<	int useEAM = 0;
729	<	int useSC = 0;
639	<	int useCharge = 0;
640	<	int useDirectional = 0;
641	<	int useDipole = 0;
642	<	int useGayBerne = 0;
643	<	int useSticky = 0;
644	<	int useStickyPower = 0;
645	<	int useShape = 0;
646	<	int useFLARB = 0; //it is not in AtomType yet
647	<	int useDirectionalAtom = 0;
648	<	int useElectrostatics = 0;
649	<	//usePBC and useRF are from simParams
650	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
651	<	int useRF;
652	<	int useSF;
653	<	std::string myMethod;
726	>	vector<int> foundTypes;
727	>	set<AtomType*>::iterator i;
728	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
729	>	foundTypes.push_back( (*i)->getIdent() );
730
731	<	// set the useRF logical
732	<	useRF = 0;
657	<	useSF = 0;
731	>	// count_local holds the number of found types on this processor
732	>	int count_local = foundTypes.size();
733
734	+	int nproc = MPI::COMM_WORLD.Get_size();
735
736	<	if (simParams_->haveElectrostaticSummationMethod()) {
737	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
738	<	toUpper(myMethod);
739	<	if (myMethod == "REACTION_FIELD") {
664	<	useRF=1;
665	<	} else {
666	<	if (myMethod == "SHIFTED_FORCE") {
667	<	useSF = 1;
668	<	}
669	<	}
670	<	}
736	>	// we need arrays to hold the counts and displacement vectors for
737	>	// all processors
738	>	vector<int> counts(nproc, 0);
739	>	vector<int> disps(nproc, 0);
740
741	<	//loop over all of the atom types
742	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
743	<	useLennardJones |= (*i)->isLennardJones();
744	<	useElectrostatic |= (*i)->isElectrostatic();
745	<	useEAM |= (*i)->isEAM();
746	<	useSC |= (*i)->isSC();
747	<	useCharge |= (*i)->isCharge();
748	<	useDirectional |= (*i)->isDirectional();
749	<	useDipole |= (*i)->isDipole();
750	<	useGayBerne |= (*i)->isGayBerne();
682	<	useSticky |= (*i)->isSticky();
683	<	useStickyPower |= (*i)->isStickyPower();
684	<	useShape |= (*i)->isShape();
741	>	// fill the counts array
742	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
743	>	1, MPI::INT);
744	>
745	>	// use the processor counts to compute the displacement array
746	>	disps[0] = 0;
747	>	int totalCount = counts[0];
748	>	for (int iproc = 1; iproc < nproc; iproc++) {
749	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
750	>	totalCount += counts[iproc];
751		}
752
753	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
754	<	useDirectionalAtom = 1;
755	<	}
753	>	// we need a (possibly redundant) set of all found types:
754	>	vector<int> ftGlobal(totalCount);
755	>
756	>	// now spray out the foundTypes to all the other processors:
757	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
758	>	&ftGlobal[0], &counts[0], &disps[0],
759	>	MPI::INT);
760
761	<	if (useCharge || useDipole) {
692	<	useElectrostatics = 1;
693	<	}
761	>	vector<int>::iterator j;
762
763	<	#ifdef IS_MPI
764	<	int temp;
763	>	// foundIdents is a stl set, so inserting an already found ident
764	>	// will have no effect.
765	>	set<int> foundIdents;
766
767	<	temp = usePBC;
768	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
768	>	foundIdents.insert((*j));
769	>
770	>	// now iterate over the foundIdents and get the actual atom types
771	>	// that correspond to these:
772	>	set<int>::iterator it;
773	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774	>	atomTypes.insert( forceField_->getAtomType((*it)) );
775	>
776	>	#endif
777
778	<	temp = useDirectionalAtom;
779	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
778	>	return atomTypes;
779	>	}
780
781	<	temp = useLennardJones;
782	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	>	void SimInfo::setupSimVariables() {
782	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
783	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
784	>	calcBoxDipole_ = false;
785	>	if ( simParams_->haveAccumulateBoxDipole() )
786	>	if ( simParams_->getAccumulateBoxDipole() ) {
787	>	calcBoxDipole_ = true;
788	>	}
789	>
790	>	set<AtomType*>::iterator i;
791	>	set<AtomType*> atomTypes;
792	>	atomTypes = getSimulatedAtomTypes();
793	>	int usesElectrostatic = 0;
794	>	int usesMetallic = 0;
795	>	int usesDirectional = 0;
796	>	int usesFluctuatingCharges =  0;
797	>	//loop over all of the atom types
798	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
799	>	usesElectrostatic |= (*i)->isElectrostatic();
800	>	usesMetallic |= (*i)->isMetal();
801	>	usesDirectional |= (*i)->isDirectional();
802	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
803	>	}
804	>
805	>	#ifdef IS_MPI
806	>	int temp;
807	>	temp = usesDirectional;
808	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	>
810	>	temp = usesMetallic;
811	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
812	>
813	>	temp = usesElectrostatic;
814	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815
816	<	temp = useElectrostatics;
817	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	temp = usesFluctuatingCharges;
817	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	>	#else
819
820	<	temp = useCharge;
821	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	>	usesDirectionalAtoms_ = usesDirectional;
821	>	usesMetallicAtoms_ = usesMetallic;
822	>	usesElectrostaticAtoms_ = usesElectrostatic;
823	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
824
825	<	temp = useDipole;
714	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
715	<
716	<	temp = useSticky;
717	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
718	<
719	<	temp = useStickyPower;
720	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
825	>	#endif
826
827	<	temp = useGayBerne;
828	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
828	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
829	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
830	>	}
831
725	–	temp = useEAM;
726	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832
833	<	temp = useSC;
834	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	>	vector<int> SimInfo::getGlobalAtomIndices() {
834	>	SimInfo::MoleculeIterator mi;
835	>	Molecule* mol;
836	>	Molecule::AtomIterator ai;
837	>	Atom* atom;
838	>
839	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
840
841	<	temp = useShape;
842	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
842	>
843	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
844	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
845	>	}
846	>	}
847	>	return GlobalAtomIndices;
848	>	}
849
734	–	temp = useFLARB;
735	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850
851	<	temp = useRF;
852	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851	>	vector<int> SimInfo::getGlobalGroupIndices() {
852	>	SimInfo::MoleculeIterator mi;
853	>	Molecule* mol;
854	>	Molecule::CutoffGroupIterator ci;
855	>	CutoffGroup* cg;
856
857	<	temp = useSF;
858	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	<
743	<	#endif
744	<
745	<	fInfo_.SIM_uses_PBC = usePBC;
746	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
747	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
748	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
749	<	fInfo_.SIM_uses_Charges = useCharge;
750	<	fInfo_.SIM_uses_Dipoles = useDipole;
751	<	fInfo_.SIM_uses_Sticky = useSticky;
752	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
753	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
754	<	fInfo_.SIM_uses_EAM = useEAM;
755	<	fInfo_.SIM_uses_SC = useSC;
756	<	fInfo_.SIM_uses_Shapes = useShape;
757	<	fInfo_.SIM_uses_FLARB = useFLARB;
758	<	fInfo_.SIM_uses_RF = useRF;
759	<	fInfo_.SIM_uses_SF = useSF;
760	<
761	<	if( myMethod == "REACTION_FIELD") {
857	>	vector<int> GlobalGroupIndices;
858	>
859	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
860
861	<	if (simParams_->haveDielectric()) {
862	<	fInfo_.dielect = simParams_->getDielectric();
863	<	} else {
864	<	sprintf(painCave.errMsg,
865	<	"SimSetup Error: No Dielectric constant was set.\n"
866	<	"\tYou are trying to use Reaction Field without"
769	<	"\tsetting a dielectric constant!\n");
770	<	painCave.isFatal = 1;
771	<	simError();
772	<	}
861	>	//local index of cutoff group is trivial, it only depends on the
862	>	//order of travesing
863	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
864	>	cg = mol->nextCutoffGroup(ci)) {
865	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
866	>	}
867		}
868	<
868	>	return GlobalGroupIndices;
869		}
870
777	–	void SimInfo::setupFortranSim() {
778	–	int isError;
779	–	int nExclude;
780	–	std::vector<int> fortranGlobalGroupMembership;
781	–
782	–	nExclude = exclude_.getSize();
783	–	isError = 0;
871
872	<	//globalGroupMembership_ is filled by SimCreator
873	<	for (int i = 0; i < nGlobalAtoms_; i++) {
787	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
788	<	}
872	>	void SimInfo::prepareTopology() {
873	>	int nExclude, nOneTwo, nOneThree, nOneFour;
874
875		//calculate mass ratio of cutoff group
791	–	std::vector<double> mfact;
876		SimInfo::MoleculeIterator mi;
877		Molecule* mol;
878		Molecule::CutoffGroupIterator ci;
879		CutoffGroup* cg;
880		Molecule::AtomIterator ai;
881		Atom* atom;
882	<	double totalMass;
882	>	RealType totalMass;
883
884	<	//to avoid memory reallocation, reserve enough space for mfact
885	<	mfact.reserve(getNCutoffGroups());
884	>	/**
885	>	* The mass factor is the relative mass of an atom to the total
886	>	* mass of the cutoff group it belongs to.  By default, all atoms
887	>	* are their own cutoff groups, and therefore have mass factors of
888	>	* 1.  We need some special handling for massless atoms, which
889	>	* will be treated as carrying the entire mass of the cutoff
890	>	* group.
891	>	*/
892	>	massFactors_.clear();
893	>	massFactors_.resize(getNAtoms(), 1.0);
894
895		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
896	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
896	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
897	>	cg = mol->nextCutoffGroup(ci)) {
898
899		totalMass = cg->getMass();
900		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
901		// Check for massless groups - set mfact to 1 if true
902	<	if (totalMass != 0)
903	<	mfact.push_back(atom->getMass()/totalMass);
902	>	if (totalMass != 0)
903	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
904		else
905	<	mfact.push_back( 1.0 );
905	>	massFactors_[atom->getLocalIndex()] = 1.0;
906		}
814	–
907		}
908		}
909
910	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
819	<	std::vector<int> identArray;
910	>	// Build the identArray_
911
912	<	//to avoid memory reallocation, reserve enough space identArray
913	<	identArray.reserve(getNAtoms());
823	<
912	>	identArray_.clear();
913	>	identArray_.reserve(getNAtoms());
914		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
915		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
916	<	identArray.push_back(atom->getIdent());
916	>	identArray_.push_back(atom->getIdent());
917		}
918		}
829	–
830	–	//fill molMembershipArray
831	–	//molMembershipArray is filled by SimCreator
832	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
833	–	for (int i = 0; i < nGlobalAtoms_; i++) {
834	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
835	–	}
919
920	<	//setup fortran simulation
838	<	int nGlobalExcludes = 0;
839	<	int* globalExcludes = NULL;
840	<	int* excludeList = exclude_.getExcludeList();
841	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
842	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
843	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
920	>	//scan topology
921
922	<	if( isError ){
922	>	nExclude = excludedInteractions_.getSize();
923	>	nOneTwo = oneTwoInteractions_.getSize();
924	>	nOneThree = oneThreeInteractions_.getSize();
925	>	nOneFour = oneFourInteractions_.getSize();
926
927	<	sprintf( painCave.errMsg,
928	<	"There was an error setting the simulation information in fortran.\n" );
929	<	painCave.isFatal = 1;
930	<	painCave.severity = OOPSE_ERROR;
851	<	simError();
852	<	}
853	<
854	<	#ifdef IS_MPI
855	<	sprintf( checkPointMsg,
856	<	"succesfully sent the simulation information to fortran.\n");
857	<	MPIcheckPoint();
858	<	#endif // is_mpi
859	<	}
860	<
861	<
862	<	#ifdef IS_MPI
863	<	void SimInfo::setupFortranParallel() {
864	<
865	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
866	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
867	<	std::vector<int> localToGlobalCutoffGroupIndex;
868	<	SimInfo::MoleculeIterator mi;
869	<	Molecule::AtomIterator ai;
870	<	Molecule::CutoffGroupIterator ci;
871	<	Molecule* mol;
872	<	Atom* atom;
873	<	CutoffGroup* cg;
874	<	mpiSimData parallelData;
875	<	int isError;
876	<
877	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
878	<
879	<	//local index(index in DataStorge) of atom is important
880	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
882	<	}
883	<
884	<	//local index of cutoff group is trivial, it only depends on the order of travesing
885	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
886	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
887	<	}
888	<
889	<	}
890	<
891	<	//fill up mpiSimData struct
892	<	parallelData.nMolGlobal = getNGlobalMolecules();
893	<	parallelData.nMolLocal = getNMolecules();
894	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
895	<	parallelData.nAtomsLocal = getNAtoms();
896	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
897	<	parallelData.nGroupsLocal = getNCutoffGroups();
898	<	parallelData.myNode = worldRank;
899	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
900	<
901	<	//pass mpiSimData struct and index arrays to fortran
902	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
903	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
904	<	&localToGlobalCutoffGroupIndex[0], &isError);
905	<
906	<	if (isError) {
907	<	sprintf(painCave.errMsg,
908	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
909	<	painCave.isFatal = 1;
910	<	simError();
911	<	}
912	<
913	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
914	<	MPIcheckPoint();
915	<
916	<
917	<	}
918	<
919	<	#endif
927	>	int* excludeList = excludedInteractions_.getPairList();
928	>	int* oneTwoList = oneTwoInteractions_.getPairList();
929	>	int* oneThreeList = oneThreeInteractions_.getPairList();
930	>	int* oneFourList = oneFourInteractions_.getPairList();
931
932	<	void SimInfo::setupCutoff() {
922	<
923	<	// Check the cutoff policy
924	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
925	<	if (simParams_->haveCutoffPolicy()) {
926	<	std::string myPolicy = simParams_->getCutoffPolicy();
927	<	toUpper(myPolicy);
928	<	if (myPolicy == "MIX") {
929	<	cp = MIX_CUTOFF_POLICY;
930	<	} else {
931	<	if (myPolicy == "MAX") {
932	<	cp = MAX_CUTOFF_POLICY;
933	<	} else {
934	<	if (myPolicy == "TRADITIONAL") {
935	<	cp = TRADITIONAL_CUTOFF_POLICY;
936	<	} else {
937	<	// throw error
938	<	sprintf( painCave.errMsg,
939	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
940	<	painCave.isFatal = 1;
941	<	simError();
942	<	}
943	<	}
944	<	}
945	<	}
946	<	notifyFortranCutoffPolicy(&cp);
947	<
948	<	// Check the Skin Thickness for neighborlists
949	<	double skin;
950	<	if (simParams_->haveSkinThickness()) {
951	<	skin = simParams_->getSkinThickness();
952	<	notifyFortranSkinThickness(&skin);
953	<	}
954	<
955	<	// Check if the cutoff was set explicitly:
956	<	if (simParams_->haveCutoffRadius()) {
957	<	rcut_ = simParams_->getCutoffRadius();
958	<	if (simParams_->haveSwitchingRadius()) {
959	<	rsw_  = simParams_->getSwitchingRadius();
960	<	} else {
961	<	rsw_ = rcut_;
962	<	}
963	<	notifyFortranCutoffs(&rcut_, &rsw_);
964	<
965	<	} else {
966	<
967	<	// For electrostatic atoms, we'll assume a large safe value:
968	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
969	<	sprintf(painCave.errMsg,
970	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
971	<	"\tOOPSE will use a default value of 15.0 angstroms"
972	<	"\tfor the cutoffRadius.\n");
973	<	painCave.isFatal = 0;
974	<	simError();
975	<	rcut_ = 15.0;
976	<
977	<	if (simParams_->haveElectrostaticSummationMethod()) {
978	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
979	<	toUpper(myMethod);
980	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
981	<	if (simParams_->haveSwitchingRadius()){
982	<	sprintf(painCave.errMsg,
983	<	"SimInfo Warning: A value was set for the switchingRadius\n"
984	<	"\teven though the electrostaticSummationMethod was\n"
985	<	"\tset to %s\n", myMethod.c_str());
986	<	painCave.isFatal = 1;
987	<	simError();
988	<	}
989	<	}
990	<	}
991	<
992	<	if (simParams_->haveSwitchingRadius()){
993	<	rsw_ = simParams_->getSwitchingRadius();
994	<	} else {
995	<	sprintf(painCave.errMsg,
996	<	"SimCreator Warning: No value was set for switchingRadius.\n"
997	<	"\tOOPSE will use a default value of\n"
998	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
999	<	painCave.isFatal = 0;
1000	<	simError();
1001	<	rsw_ = 0.85 * rcut_;
1002	<	}
1003	<	notifyFortranCutoffs(&rcut_, &rsw_);
1004	<	} else {
1005	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1006	<	// We'll punt and let fortran figure out the cutoffs later.
1007	<
1008	<	notifyFortranYouAreOnYourOwn();
1009	<
1010	<	}
1011	<	}
1012	<	}
1013	<
1014	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1015	<
1016	<	int errorOut;
1017	<	int esm =  NONE;
1018	<	int sm = UNDAMPED;
1019	<	double alphaVal;
1020	<	double dielectric;
1021	<
1022	<	errorOut = isError;
1023	<	alphaVal = simParams_->getDampingAlpha();
1024	<	dielectric = simParams_->getDielectric();
1025	<
1026	<	if (simParams_->haveElectrostaticSummationMethod()) {
1027	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028	<	toUpper(myMethod);
1029	<	if (myMethod == "NONE") {
1030	<	esm = NONE;
1031	<	} else {
1032	<	if (myMethod == "SWITCHING_FUNCTION") {
1033	<	esm = SWITCHING_FUNCTION;
1034	<	} else {
1035	<	if (myMethod == "SHIFTED_POTENTIAL") {
1036	<	esm = SHIFTED_POTENTIAL;
1037	<	} else {
1038	<	if (myMethod == "SHIFTED_FORCE") {
1039	<	esm = SHIFTED_FORCE;
1040	<	} else {
1041	<	if (myMethod == "REACTION_FIELD") {
1042	<	esm = REACTION_FIELD;
1043	<	} else {
1044	<	// throw error
1045	<	sprintf( painCave.errMsg,
1046	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1047	<	"\t(Input file specified %s .)\n"
1048	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1049	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1050	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1051	<	painCave.isFatal = 1;
1052	<	simError();
1053	<	}
1054	<	}
1055	<	}
1056	<	}
1057	<	}
1058	<	}
1059	<
1060	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1061	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1062	<	toUpper(myScreen);
1063	<	if (myScreen == "UNDAMPED") {
1064	<	sm = UNDAMPED;
1065	<	} else {
1066	<	if (myScreen == "DAMPED") {
1067	<	sm = DAMPED;
1068	<	if (!simParams_->haveDampingAlpha()) {
1069	<	//throw error
1070	<	sprintf( painCave.errMsg,
1071	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1072	<	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1073	<	painCave.isFatal = 0;
1074	<	simError();
1075	<	}
1076	<	} else {
1077	<	// throw error
1078	<	sprintf( painCave.errMsg,
1079	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1080	<	"\t(Input file specified %s .)\n"
1081	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1082	<	"or \"damped\".\n", myScreen.c_str() );
1083	<	painCave.isFatal = 1;
1084	<	simError();
1085	<	}
1086	<	}
1087	<	}
1088	<
1089	<	// let's pass some summation method variables to fortran
1090	<	setElectrostaticSumMethod( &esm );
1091	<	setFortranElectrostaticMethod( &esm );
1092	<	setScreeningMethod( &sm );
1093	<	setDampingAlpha( &alphaVal );
1094	<	setReactionFieldDielectric( &dielectric );
1095	<	initFortranFF( &errorOut );
932	>	topologyDone_ = true;
933		}
934
1098	–	void SimInfo::setupSwitchingFunction() {
1099	–	int ft = CUBIC;
1100	–
1101	–	if (simParams_->haveSwitchingFunctionType()) {
1102	–	std::string funcType = simParams_->getSwitchingFunctionType();
1103	–	toUpper(funcType);
1104	–	if (funcType == "CUBIC") {
1105	–	ft = CUBIC;
1106	–	} else {
1107	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1108	–	ft = FIFTH_ORDER_POLY;
1109	–	} else {
1110	–	// throw error
1111	–	sprintf( painCave.errMsg,
1112	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1113	–	painCave.isFatal = 1;
1114	–	simError();
1115	–	}
1116	–	}
1117	–	}
1118	–
1119	–	// send switching function notification to switcheroo
1120	–	setFunctionType(&ft);
1121	–
1122	–	}
1123	–
935		void SimInfo::addProperty(GenericData* genData) {
936		properties_.addProperty(genData);
937		}
938
939	<	void SimInfo::removeProperty(const std::string& propName) {
939	>	void SimInfo::removeProperty(const string& propName) {
940		properties_.removeProperty(propName);
941		}
942
#	Line 1133 | Line 944 | namespace oopse {
944		properties_.clearProperties();
945		}
946
947	<	std::vector<std::string> SimInfo::getPropertyNames() {
947	>	vector<string> SimInfo::getPropertyNames() {
948		return properties_.getPropertyNames();
949		}
950
951	<	std::vector<GenericData*> SimInfo::getProperties() {
951	>	vector<GenericData*> SimInfo::getProperties() {
952		return properties_.getProperties();
953		}
954
955	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
955	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
956		return properties_.getPropertyByName(propName);
957		}
958
#	Line 1155 | Line 966 | namespace oopse {
966		Molecule* mol;
967		RigidBody* rb;
968		Atom* atom;
969	+	CutoffGroup* cg;
970		SimInfo::MoleculeIterator mi;
971		Molecule::RigidBodyIterator rbIter;
972	<	Molecule::AtomIterator atomIter;;
972	>	Molecule::AtomIterator atomIter;
973	>	Molecule::CutoffGroupIterator cgIter;
974
975		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
976
#	Line 1168 | Line 981 | namespace oopse {
981		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
982		rb->setSnapshotManager(sman_);
983		}
984	+
985	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
986	+	cg->setSnapshotManager(sman_);
987	+	}
988		}
989
990		}
#	Line 1177 | Line 994 | namespace oopse {
994		Molecule* mol;
995
996		Vector3d comVel(0.0);
997	<	double totalMass = 0.0;
997	>	RealType totalMass = 0.0;
998
999
1000		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1001	<	double mass = mol->getMass();
1001	>	RealType mass = mol->getMass();
1002		totalMass += mass;
1003		comVel += mass * mol->getComVel();
1004		}
1005
1006		#ifdef IS_MPI
1007	<	double tmpMass = totalMass;
1007	>	RealType tmpMass = totalMass;
1008		Vector3d tmpComVel(comVel);
1009	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1010	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1009	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1010	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1011		#endif
1012
1013		comVel /= totalMass;
#	Line 1203 | Line 1020 | namespace oopse {
1020		Molecule* mol;
1021
1022		Vector3d com(0.0);
1023	<	double totalMass = 0.0;
1023	>	RealType totalMass = 0.0;
1024
1025		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1026	<	double mass = mol->getMass();
1026	>	RealType mass = mol->getMass();
1027		totalMass += mass;
1028		com += mass * mol->getCom();
1029		}
1030
1031		#ifdef IS_MPI
1032	<	double tmpMass = totalMass;
1032	>	RealType tmpMass = totalMass;
1033		Vector3d tmpCom(com);
1034	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1035	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1034	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1035	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1036		#endif
1037
1038		com /= totalMass;
#	Line 1224 | Line 1041 | namespace oopse {
1041
1042		}
1043
1044	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1044	>	ostream& operator <<(ostream& o, SimInfo& info) {
1045
1046		return o;
1047		}
#	Line 1239 | Line 1056 | namespace oopse {
1056		Molecule* mol;
1057
1058
1059	<	double totalMass = 0.0;
1059	>	RealType totalMass = 0.0;
1060
1061
1062		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1063	<	double mass = mol->getMass();
1063	>	RealType mass = mol->getMass();
1064		totalMass += mass;
1065		com += mass * mol->getCom();
1066		comVel += mass * mol->getComVel();
1067		}
1068
1069		#ifdef IS_MPI
1070	<	double tmpMass = totalMass;
1070	>	RealType tmpMass = totalMass;
1071		Vector3d tmpCom(com);
1072		Vector3d tmpComVel(comVel);
1073	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1074	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1075	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1073	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1075	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1076		#endif
1077
1078		com /= totalMass;
#	Line 1267 | Line 1084 | namespace oopse {
1084
1085
1086		[  Ixx -Ixy  -Ixz ]
1087	<	J =| -Iyx  Iyy  -Iyz |
1087	>	J =| -Iyx  Iyy  -Iyz |
1088		[ -Izx -Iyz   Izz ]
1089		*/
1090
1091		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1092
1093
1094	<	double xx = 0.0;
1095	<	double yy = 0.0;
1096	<	double zz = 0.0;
1097	<	double xy = 0.0;
1098	<	double xz = 0.0;
1099	<	double yz = 0.0;
1094	>	RealType xx = 0.0;
1095	>	RealType yy = 0.0;
1096	>	RealType zz = 0.0;
1097	>	RealType xy = 0.0;
1098	>	RealType xz = 0.0;
1099	>	RealType yz = 0.0;
1100		Vector3d com(0.0);
1101		Vector3d comVel(0.0);
1102
#	Line 1291 | Line 1108 | namespace oopse {
1108		Vector3d thisq(0.0);
1109		Vector3d thisv(0.0);
1110
1111	<	double thisMass = 0.0;
1111	>	RealType thisMass = 0.0;
1112
1113
1114
#	Line 1329 | Line 1146 | namespace oopse {
1146		#ifdef IS_MPI
1147		Mat3x3d tmpI(inertiaTensor);
1148		Vector3d tmpAngMom;
1149	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1150	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1149	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151		#endif
1152
1153		return;
#	Line 1351 | Line 1168 | namespace oopse {
1168		Vector3d thisr(0.0);
1169		Vector3d thisp(0.0);
1170
1171	<	double thisMass;
1171	>	RealType thisMass;
1172
1173		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1174		thisMass = mol->getMass();
#	Line 1364 | Line 1181 | namespace oopse {
1181
1182		#ifdef IS_MPI
1183		Vector3d tmpAngMom;
1184	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1184	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1185		#endif
1186
1187		return angularMomentum;
1188		}
1189
1190	<
1191	<	}//end namespace oopse
1190	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1191	>	return IOIndexToIntegrableObject.at(index);
1192	>	}
1193	>
1194	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1195	>	IOIndexToIntegrableObject= v;
1196	>	}
1197
1198	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1199	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1200	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1201	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1202	+	*/
1203	+	void SimInfo::getGyrationalVolume(RealType &volume){
1204	+	Mat3x3d intTensor;
1205	+	RealType det;
1206	+	Vector3d dummyAngMom;
1207	+	RealType sysconstants;
1208	+	RealType geomCnst;
1209	+
1210	+	geomCnst = 3.0/2.0;
1211	+	/* Get the inertial tensor and angular momentum for free*/
1212	+	getInertiaTensor(intTensor,dummyAngMom);
1213	+
1214	+	det = intTensor.determinant();
1215	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1216	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1217	+	return;
1218	+	}
1219	+
1220	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1221	+	Mat3x3d intTensor;
1222	+	Vector3d dummyAngMom;
1223	+	RealType sysconstants;
1224	+	RealType geomCnst;
1225	+
1226	+	geomCnst = 3.0/2.0;
1227	+	/* Get the inertial tensor and angular momentum for free*/
1228	+	getInertiaTensor(intTensor,dummyAngMom);
1229	+
1230	+	detI = intTensor.determinant();
1231	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1232	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1233	+	return;
1234	+	}
1235	+	/*
1236	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1237	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1238	+	sdByGlobalIndex_ = v;
1239	+	}
1240	+
1241	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1242	+	//assert(index < nAtoms_ + nRigidBodies_);
1243	+	return sdByGlobalIndex_.at(index);
1244	+	}
1245	+	*/
1246	+	int SimInfo::getNGlobalConstraints() {
1247	+	int nGlobalConstraints;
1248	+	#ifdef IS_MPI
1249	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1250	+	MPI_COMM_WORLD);
1251	+	#else
1252	+	nGlobalConstraints =  nConstraints_;
1253	+	#endif
1254	+	return nGlobalConstraints;
1255	+	}
1256	+
1257	+	}//end namespace OpenMD
1258	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 809 by gezelter, Mon Dec 12 19:32:50 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1750 by gezelter, Thu Jun 7 12:53:46 2012 UTC

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