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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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, 234107 (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 46 | Line 47
47		* @version 1.0
48		*/
49
50	+	#ifdef IS_MPI
51	+	#include <mpi.h>
52	+	#endif
53		#include <algorithm>
54		#include <set>
55		#include <map>
#	Line 54 | Line 58
58		#include "math/Vector3.hpp"
59		#include "primitives/Molecule.hpp"
60		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
61		#include "utils/MemoryUtils.hpp"
62		#include "utils/simError.h"
63		#include "selection/SelectionManager.hpp"
64		#include "io/ForceFieldOptions.hpp"
65	<	#include "UseTheForce/ForceField.hpp"
65	>	#include "brains/ForceField.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<
69	<	#ifdef IS_MPI
73	<	#include "UseTheForce/mpiComponentPlan.h"
74	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
76	<
77	<	namespace oopse {
78	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	<	std::map<int, std::set<int> >::iterator i = container.find(index);
80	<	std::set<int> result;
81	<	if (i != container.end()) {
82	<	result = i->second;
83	<	}
84	<
85	<	return result;
86	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73	<	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
74		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
75	<	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
76	<	calcBoxDipole_(false), useAtomicVirial_(true) {
75	>	nConstraints_(0), nFluctuatingCharges_(0),
76	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
79	>	nGlobalTorsions_(0), nGlobalInversions_(0), nGlobalConstraints_(0),
80	>	hasNGlobalConstraints_(false),
81	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82	>	sman_(NULL), topologyDone_(false), calcBoxDipole_(false),
83	>	calcBoxQuadrupole_(false), useAtomicVirial_(true) {
84	>
85	>	MoleculeStamp* molStamp;
86	>	int nMolWithSameStamp;
87	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
89	>	CutoffGroupStamp* cgStamp;
90	>	RigidBodyStamp* rbStamp;
91	>	int nRigidAtoms = 0;
92	>
93	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin();
96	>	i !=components.end(); ++i) {
97	>	molStamp = (*i)->getMoleculeStamp();
98	>	if ( (*i)->haveRegion() ) {
99	>	molStamp->setRegion( (*i)->getRegion() );
100	>	} else {
101	>	// set the region to a disallowed value:
102	>	molStamp->setRegion( -1 );
103	>	}
104
105	<
99	<	MoleculeStamp* molStamp;
100	<	int nMolWithSameStamp;
101	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
102	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
103	<	CutoffGroupStamp* cgStamp;
104	<	RigidBodyStamp* rbStamp;
105	<	int nRigidAtoms = 0;
106	<
107	<	std::vector<Component*> components = simParams->getComponents();
105	>	nMolWithSameStamp = (*i)->getNMol();
106
107	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108	<	molStamp = (*i)->getMoleculeStamp();
109	<	nMolWithSameStamp = (*i)->getNMol();
110	<
111	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
112	<
113	<	//calculate atoms in molecules
114	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
115	<
116	<	//calculate atoms in cutoff groups
117	<	int nAtomsInGroups = 0;
118	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	<
120	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroupStamp(j);
122	<	nAtomsInGroups += cgStamp->getNMembers();
125	<	}
126	<
127	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128	<
129	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130	<
131	<	//calculate atoms in rigid bodies
132	<	int nAtomsInRigidBodies = 0;
133	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134	<
135	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
136	<	rbStamp = molStamp->getRigidBodyStamp(j);
137	<	nAtomsInRigidBodies += rbStamp->getNMembers();
138	<	}
139	<
140	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	<
107	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
108	>
109	>	//calculate atoms in molecules
110	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
111	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
112	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
113	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
114	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
115	>
116	>	//calculate atoms in cutoff groups
117	>	int nAtomsInGroups = 0;
118	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	>
120	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122	>	nAtomsInGroups += cgStamp->getNMembers();
123		}
124	<
125	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
126	<	//group therefore the total number of cutoff groups in the system is
127	<	//equal to the total number of atoms minus number of atoms belong to
128	<	//cutoff group defined in meta-data file plus the number of cutoff
129	<	//groups defined in meta-data file
130	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
131	<
132	<	//every free atom (atom does not belong to rigid bodies) is an
133	<	//integrable object therefore the total number of integrable objects
134	<	//in the system is equal to the total number of atoms minus number of
135	<	//atoms belong to rigid body defined in meta-data file plus the number
136	<	//of rigid bodies defined in meta-data file
137	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
138	<	+ nGlobalRigidBodies_;
139	<
140	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
124	>
125	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	>
127	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128	>
129	>	//calculate atoms in rigid bodies
130	>	int nAtomsInRigidBodies = 0;
131	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	>
133	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135	>	nAtomsInRigidBodies += rbStamp->getNMembers();
136	>	}
137	>
138	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	>
141		}
142	+
143	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	+	//group therefore the total number of cutoff groups in the system is
145	+	//equal to the total number of atoms minus number of atoms belong to
146	+	//cutoff group defined in meta-data file plus the number of cutoff
147	+	//groups defined in meta-data file
148
149	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
150	+
151	+	//every free atom (atom does not belong to rigid bodies) is an
152	+	//integrable object therefore the total number of integrable objects
153	+	//in the system is equal to the total number of atoms minus number of
154	+	//atoms belong to rigid body defined in meta-data file plus the number
155	+	//of rigid bodies defined in meta-data file
156	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
157	+	+ nGlobalRigidBodies_;
158	+
159	+	nGlobalMols_ = molStampIds_.size();
160	+	molToProcMap_.resize(nGlobalMols_);
161	+	}
162	+
163		SimInfo::~SimInfo() {
164	<	std::map<int, Molecule*>::iterator i;
164	>	map<int, Molecule*>::iterator i;
165		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
166		delete i->second;
167		}
#	Line 173 | Line 172 | namespace oopse {
172		delete forceField_;
173		}
174
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	–	}
175
176		bool SimInfo::addMolecule(Molecule* mol) {
177		MoleculeIterator i;
178	<
178	>
179		i = molecules_.find(mol->getGlobalIndex());
180		if (i == molecules_.end() ) {
181	<
182	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
183	<
181	>
182	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
183	>
184		nAtoms_ += mol->getNAtoms();
185		nBonds_ += mol->getNBonds();
186		nBends_ += mol->getNBends();
#	Line 201 | Line 190 | namespace oopse {
190		nIntegrableObjects_ += mol->getNIntegrableObjects();
191		nCutoffGroups_ += mol->getNCutoffGroups();
192		nConstraints_ += mol->getNConstraintPairs();
193	<
193	>
194		addInteractionPairs(mol);
195	<
195	>
196		return true;
197		} else {
198		return false;
199		}
200		}
201	<
201	>
202		bool SimInfo::removeMolecule(Molecule* mol) {
203		MoleculeIterator i;
204		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 226 | namespace oopse {
226		} else {
227		return false;
228		}
240	–
241	–
229		}
230
231
#	Line 254 | Line 241 | namespace oopse {
241
242
243		void SimInfo::calcNdf() {
244	<	int ndf_local;
244	>	int ndf_local, nfq_local;
245		MoleculeIterator i;
246	<	std::vector<StuntDouble*>::iterator j;
246	>	vector<StuntDouble*>::iterator j;
247	>	vector<Atom*>::iterator k;
248	>
249		Molecule* mol;
250	<	StuntDouble* integrableObject;
250	>	StuntDouble* sd;
251	>	Atom* atom;
252
253		ndf_local = 0;
254	+	nfq_local = 0;
255
256		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
266	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	–	integrableObject = mol->nextIntegrableObject(j)) {
257
258	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
259	+	sd = mol->nextIntegrableObject(j)) {
260	+
261		ndf_local += 3;
262
263	<	if (integrableObject->isDirectional()) {
264	<	if (integrableObject->isLinear()) {
263	>	if (sd->isDirectional()) {
264	>	if (sd->isLinear()) {
265		ndf_local += 2;
266		} else {
267		ndf_local += 3;
268		}
269		}
278	–
270		}
271	+
272	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
273	+	atom = mol->nextFluctuatingCharge(k)) {
274	+	if (atom->isFluctuatingCharge()) {
275	+	nfq_local++;
276	+	}
277	+	}
278		}
279
280	+	ndfLocal_ = ndf_local;
281	+
282		// n_constraints is local, so subtract them on each processor
283		ndf_local -= nConstraints_;
284
285		#ifdef IS_MPI
286	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
286	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
288	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
289		#else
290		ndf_ = ndf_local;
291	+	nGlobalFluctuatingCharges_ = nfq_local;
292		#endif
293
294		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 296 | Line 299 | namespace oopse {
299
300		int SimInfo::getFdf() {
301		#ifdef IS_MPI
302	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
302	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
303		#else
304		fdf_ = fdf_local;
305		#endif
306		return fdf_;
307		}
308	+
309	+	unsigned int SimInfo::getNLocalCutoffGroups(){
310	+	int nLocalCutoffAtoms = 0;
311	+	Molecule* mol;
312	+	MoleculeIterator mi;
313	+	CutoffGroup* cg;
314	+	Molecule::CutoffGroupIterator ci;
315
316	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
317	+
318	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
319	+	cg = mol->nextCutoffGroup(ci)) {
320	+	nLocalCutoffAtoms += cg->getNumAtom();
321	+
322	+	}
323	+	}
324	+
325	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
326	+	}
327	+
328		void SimInfo::calcNdfRaw() {
329		int ndfRaw_local;
330
331		MoleculeIterator i;
332	<	std::vector<StuntDouble*>::iterator j;
332	>	vector<StuntDouble*>::iterator j;
333		Molecule* mol;
334	<	StuntDouble* integrableObject;
334	>	StuntDouble* sd;
335
336		// Raw degrees of freedom that we have to set
337		ndfRaw_local = 0;
338
339		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	–	integrableObject = mol->nextIntegrableObject(j)) {
340
341	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
342	+	sd = mol->nextIntegrableObject(j)) {
343	+
344		ndfRaw_local += 3;
345
346	<	if (integrableObject->isDirectional()) {
347	<	if (integrableObject->isLinear()) {
346	>	if (sd->isDirectional()) {
347	>	if (sd->isLinear()) {
348		ndfRaw_local += 2;
349		} else {
350		ndfRaw_local += 3;
#	Line 332 | Line 355 | namespace oopse {
355		}
356
357		#ifdef IS_MPI
358	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
358	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
359		#else
360		ndfRaw_ = ndfRaw_local;
361		#endif
#	Line 343 | Line 366 | namespace oopse {
366
367		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
368
346	–
369		#ifdef IS_MPI
370	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
370	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
371	>	MPI_COMM_WORLD);
372		#else
373		ndfTrans_ = ndfTrans_local;
374		#endif
375
376		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
354	–
377		}
378
379		void SimInfo::addInteractionPairs(Molecule* mol) {
380		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
381	<	std::vector<Bond*>::iterator bondIter;
382	<	std::vector<Bend*>::iterator bendIter;
383	<	std::vector<Torsion*>::iterator torsionIter;
384	<	std::vector<Inversion*>::iterator inversionIter;
381	>	vector<Bond*>::iterator bondIter;
382	>	vector<Bend*>::iterator bendIter;
383	>	vector<Torsion*>::iterator torsionIter;
384	>	vector<Inversion*>::iterator inversionIter;
385		Bond* bond;
386		Bend* bend;
387		Torsion* torsion;
#	Line 377 | Line 399 | namespace oopse {
399		// always be excluded.  These are done at the bottom of this
400		// function.
401
402	<	std::map<int, std::set<int> > atomGroups;
402	>	map<int, set<int> > atomGroups;
403		Molecule::RigidBodyIterator rbIter;
404		RigidBody* rb;
405		Molecule::IntegrableObjectIterator ii;
406	<	StuntDouble* integrableObject;
406	>	StuntDouble* sd;
407
408	<	for (integrableObject = mol->beginIntegrableObject(ii);
409	<	integrableObject != NULL;
388	<	integrableObject = mol->nextIntegrableObject(ii)) {
408	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
409	>	sd = mol->nextIntegrableObject(ii)) {
410
411	<	if (integrableObject->isRigidBody()) {
412	<	rb = static_cast<RigidBody*>(integrableObject);
413	<	std::vector<Atom*> atoms = rb->getAtoms();
414	<	std::set<int> rigidAtoms;
411	>	if (sd->isRigidBody()) {
412	>	rb = static_cast<RigidBody*>(sd);
413	>	vector<Atom*> atoms = rb->getAtoms();
414	>	set<int> rigidAtoms;
415		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
416		rigidAtoms.insert(atoms[i]->getGlobalIndex());
417		}
418		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
419	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
419	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
420		}
421		} else {
422	<	std::set<int> oneAtomSet;
423	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
424	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
422	>	set<int> oneAtomSet;
423	>	oneAtomSet.insert(sd->getGlobalIndex());
424	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
425		}
426		}
427	+
428
429		for (bond= mol->beginBond(bondIter); bond != NULL;
430		bond = mol->nextBond(bondIter)) {
431
432		a = bond->getAtomA()->getGlobalIndex();
433		b = bond->getAtomB()->getGlobalIndex();
434	<
434	>
435		if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436		oneTwoInteractions_.addPair(a, b);
437		} else {
#	Line 503 | Line 525 | namespace oopse {
525
526		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
527		rb = mol->nextRigidBody(rbIter)) {
528	<	std::vector<Atom*> atoms = rb->getAtoms();
528	>	vector<Atom*> atoms = rb->getAtoms();
529		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
530		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
531		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 539 | namespace oopse {
539
540		void SimInfo::removeInteractionPairs(Molecule* mol) {
541		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
542	<	std::vector<Bond*>::iterator bondIter;
543	<	std::vector<Bend*>::iterator bendIter;
544	<	std::vector<Torsion*>::iterator torsionIter;
545	<	std::vector<Inversion*>::iterator inversionIter;
542	>	vector<Bond*>::iterator bondIter;
543	>	vector<Bend*>::iterator bendIter;
544	>	vector<Torsion*>::iterator torsionIter;
545	>	vector<Inversion*>::iterator inversionIter;
546		Bond* bond;
547		Bend* bend;
548		Torsion* torsion;
#	Line 530 | Line 552 | namespace oopse {
552		int c;
553		int d;
554
555	<	std::map<int, std::set<int> > atomGroups;
555	>	map<int, set<int> > atomGroups;
556		Molecule::RigidBodyIterator rbIter;
557		RigidBody* rb;
558		Molecule::IntegrableObjectIterator ii;
559	<	StuntDouble* integrableObject;
559	>	StuntDouble* sd;
560
561	<	for (integrableObject = mol->beginIntegrableObject(ii);
562	<	integrableObject != NULL;
541	<	integrableObject = mol->nextIntegrableObject(ii)) {
561	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
562	>	sd = mol->nextIntegrableObject(ii)) {
563
564	<	if (integrableObject->isRigidBody()) {
565	<	rb = static_cast<RigidBody*>(integrableObject);
566	<	std::vector<Atom*> atoms = rb->getAtoms();
567	<	std::set<int> rigidAtoms;
564	>	if (sd->isRigidBody()) {
565	>	rb = static_cast<RigidBody*>(sd);
566	>	vector<Atom*> atoms = rb->getAtoms();
567	>	set<int> rigidAtoms;
568		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
569		rigidAtoms.insert(atoms[i]->getGlobalIndex());
570		}
571		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
572	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
572	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
573		}
574		} else {
575	<	std::set<int> oneAtomSet;
576	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
577	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
575	>	set<int> oneAtomSet;
576	>	oneAtomSet.insert(sd->getGlobalIndex());
577	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
578		}
579		}
580
#	Line 656 | Line 677 | namespace oopse {
677
678		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
679		rb = mol->nextRigidBody(rbIter)) {
680	<	std::vector<Atom*> atoms = rb->getAtoms();
680	>	vector<Atom*> atoms = rb->getAtoms();
681		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
682		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
683		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 700 | namespace oopse {
700		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
701		}
702
682	–	void SimInfo::update() {
703
704	<	setupSimType();
705	<
706	<	#ifdef IS_MPI
707	<	setupFortranParallel();
708	<	#endif
709	<
710	<	setupFortranSim();
711	<
712	<	//setup fortran force field
713	<	/** @deprecate */
694	<	int isError = 0;
695	<
696	<	setupCutoff();
697	<
698	<	setupElectrostaticSummationMethod( isError );
699	<	setupSwitchingFunction();
700	<	setupAccumulateBoxDipole();
701	<
702	<	if(isError){
703	<	sprintf( painCave.errMsg,
704	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
705	<	painCave.isFatal = 1;
706	<	simError();
707	<	}
708	<
704	>	/**
705	>	* update
706	>	*
707	>	*  Performs the global checks and variable settings after the
708	>	*  objects have been created.
709	>	*
710	>	*/
711	>	void SimInfo::update() {
712	>	setupSimVariables();
713	>	calcNConstraints();
714		calcNdf();
715		calcNdfRaw();
716		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
717		}
718	<
719	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
718	>
719	>	/**
720	>	* getSimulatedAtomTypes
721	>	*
722	>	* Returns an STL set of AtomType* that are actually present in this
723	>	* simulation.  Must query all processors to assemble this information.
724	>	*
725	>	*/
726	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
727		SimInfo::MoleculeIterator mi;
728		Molecule* mol;
729		Molecule::AtomIterator ai;
730		Atom* atom;
731	<	std::set<AtomType*> atomTypes;
732	<
731	>	set<AtomType*> atomTypes;
732	>
733		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
734	<
735	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
734	>	for(atom = mol->beginAtom(ai); atom != NULL;
735	>	atom = mol->nextAtom(ai)) {
736		atomTypes.insert(atom->getAtomType());
737	<	}
738	<
729	<	}
730	<
731	<	return atomTypes;
732	<	}
733	<
734	<	void SimInfo::setupSimType() {
735	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
737	>	}
738	>	}
739
740	<	int useLennardJones = 0;
740	<	int useElectrostatic = 0;
741	<	int useEAM = 0;
742	<	int useSC = 0;
743	<	int useCharge = 0;
744	<	int useDirectional = 0;
745	<	int useDipole = 0;
746	<	int useGayBerne = 0;
747	<	int useSticky = 0;
748	<	int useStickyPower = 0;
749	<	int useShape = 0;
750	<	int useFLARB = 0; //it is not in AtomType yet
751	<	int useDirectionalAtom = 0;
752	<	int useElectrostatics = 0;
753	<	//usePBC and useRF are from simParams
754	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755	<	int useRF;
756	<	int useSF;
757	<	int useSP;
758	<	int useBoxDipole;
740	>	#ifdef IS_MPI
741
742	<	std::string myMethod;
743	<
762	<	// set the useRF logical
763	<	useRF = 0;
764	<	useSF = 0;
765	<	useSP = 0;
766	<
767	<
768	<	if (simParams_->haveElectrostaticSummationMethod()) {
769	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
770	<	toUpper(myMethod);
771	<	if (myMethod == "REACTION_FIELD"){
772	<	useRF = 1;
773	<	} else if (myMethod == "SHIFTED_FORCE"){
774	<	useSF = 1;
775	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
776	<	useSP = 1;
777	<	}
778	<	}
742	>	// loop over the found atom types on this processor, and add their
743	>	// numerical idents to a vector:
744
745	<	if (simParams_->haveAccumulateBoxDipole())
746	<	if (simParams_->getAccumulateBoxDipole())
747	<	useBoxDipole = 1;
745	>	vector<int> foundTypes;
746	>	set<AtomType*>::iterator i;
747	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
748	>	foundTypes.push_back( (*i)->getIdent() );
749
750	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
750	>	// count_local holds the number of found types on this processor
751	>	int count_local = foundTypes.size();
752
753	<	//loop over all of the atom types
754	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
788	<	useLennardJones |= (*i)->isLennardJones();
789	<	useElectrostatic |= (*i)->isElectrostatic();
790	<	useEAM |= (*i)->isEAM();
791	<	useSC |= (*i)->isSC();
792	<	useCharge |= (*i)->isCharge();
793	<	useDirectional |= (*i)->isDirectional();
794	<	useDipole |= (*i)->isDipole();
795	<	useGayBerne |= (*i)->isGayBerne();
796	<	useSticky |= (*i)->isSticky();
797	<	useStickyPower |= (*i)->isStickyPower();
798	<	useShape |= (*i)->isShape();
799	<	}
753	>	int nproc;
754	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
755
756	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
757	<	useDirectionalAtom = 1;
758	<	}
756	>	// we need arrays to hold the counts and displacement vectors for
757	>	// all processors
758	>	vector<int> counts(nproc, 0);
759	>	vector<int> disps(nproc, 0);
760
761	<	if (useCharge || useDipole) {
762	<	useElectrostatics = 1;
761	>	// fill the counts array
762	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
763	>	1, MPI_INT, MPI_COMM_WORLD);
764	>
765	>	// use the processor counts to compute the displacement array
766	>	disps[0] = 0;
767	>	int totalCount = counts[0];
768	>	for (int iproc = 1; iproc < nproc; iproc++) {
769	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
770	>	totalCount += counts[iproc];
771		}
772
773	<	#ifdef IS_MPI
774	<	int temp;
773	>	// we need a (possibly redundant) set of all found types:
774	>	vector<int> ftGlobal(totalCount);
775	>
776	>	// now spray out the foundTypes to all the other processors:
777	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
778	>	&ftGlobal[0], &counts[0], &disps[0],
779	>	MPI_INT, MPI_COMM_WORLD);
780
781	<	temp = usePBC;
813	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	>	vector<int>::iterator j;
782
783	<	temp = useDirectionalAtom;
784	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
783	>	// foundIdents is a stl set, so inserting an already found ident
784	>	// will have no effect.
785	>	set<int> foundIdents;
786
787	<	temp = useLennardJones;
788	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
787	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
788	>	foundIdents.insert((*j));
789	>
790	>	// now iterate over the foundIdents and get the actual atom types
791	>	// that correspond to these:
792	>	set<int>::iterator it;
793	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
794	>	atomTypes.insert( forceField_->getAtomType((*it)) );
795	>
796	>	#endif
797
798	<	temp = useElectrostatics;
799	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	return atomTypes;
799	>	}
800
824	–	temp = useCharge;
825	–	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801
802	<	temp = useDipole;
803	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	>	int getGlobalCountOfType(AtomType* atype) {
803	>	/*
804	>	set<AtomType*> atypes = getSimulatedAtomTypes();
805	>	map<AtomType*, int> counts_;
806
807	<	temp = useSticky;
808	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
808	>	for(atom = mol->beginAtom(ai); atom != NULL;
809	>	atom = mol->nextAtom(ai)) {
810	>	atom->getAtomType();
811	>	}
812	>	}
813	>	*/
814	>	return 0;
815	>	}
816
817	<	temp = useStickyPower;
818	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	>	void SimInfo::setupSimVariables() {
818	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
819	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
820	>	// parameter is true
821	>	calcBoxDipole_ = false;
822	>	if ( simParams_->haveAccumulateBoxDipole() )
823	>	if ( simParams_->getAccumulateBoxDipole() ) {
824	>	calcBoxDipole_ = true;
825	>	}
826	>	// we only call setAccumulateBoxQuadrupole if the accumulateBoxQuadrupole
827	>	// parameter is true
828	>	calcBoxQuadrupole_ = false;
829	>	if ( simParams_->haveAccumulateBoxQuadrupole() )
830	>	if ( simParams_->getAccumulateBoxQuadrupole() ) {
831	>	calcBoxQuadrupole_ = true;
832	>	}
833
834	<	temp = useGayBerne;
835	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834	>	set<AtomType*>::iterator i;
835	>	set<AtomType*> atomTypes;
836	>	atomTypes = getSimulatedAtomTypes();
837	>	bool usesElectrostatic = false;
838	>	bool usesMetallic = false;
839	>	bool usesDirectional = false;
840	>	bool usesFluctuatingCharges =  false;
841	>	//loop over all of the atom types
842	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
843	>	usesElectrostatic |= (*i)->isElectrostatic();
844	>	usesMetallic |= (*i)->isMetal();
845	>	usesDirectional |= (*i)->isDirectional();
846	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
847	>	}
848
849	<	temp = useEAM;
850	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
849	>	#ifdef IS_MPI
850	>	int temp;
851
852	<	temp = useSC;
853	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	temp = usesDirectional;
853	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
854	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
855
856	<	temp = useShape;
857	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	>	temp = usesMetallic;
857	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
858	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
859
860	<	temp = useFLARB;
861	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>	temp = usesElectrostatic;
861	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
862	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
863
864	<	temp = useRF;
865	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	temp = usesFluctuatingCharges;
865	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
866	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
867	>	#else
868
869	<	temp = useSF;
870	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
869	>	usesDirectionalAtoms_ = usesDirectional;
870	>	usesMetallicAtoms_ = usesMetallic;
871	>	usesElectrostaticAtoms_ = usesElectrostatic;
872	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
873
874	<	temp = useSP;
875	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	>	#endif
875	>
876	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
877	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
878	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
879	>	}
880
860	–	temp = useBoxDipole;
861	–	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
881
882	<	temp = useAtomicVirial_;
883	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
882	>	vector<int> SimInfo::getGlobalAtomIndices() {
883	>	SimInfo::MoleculeIterator mi;
884	>	Molecule* mol;
885	>	Molecule::AtomIterator ai;
886	>	Atom* atom;
887
888	<	#endif
889	<
890	<	fInfo_.SIM_uses_PBC = usePBC;
891	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
892	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
893	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
894	<	fInfo_.SIM_uses_Charges = useCharge;
895	<	fInfo_.SIM_uses_Dipoles = useDipole;
896	<	fInfo_.SIM_uses_Sticky = useSticky;
875	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
876	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
877	<	fInfo_.SIM_uses_EAM = useEAM;
878	<	fInfo_.SIM_uses_SC = useSC;
879	<	fInfo_.SIM_uses_Shapes = useShape;
880	<	fInfo_.SIM_uses_FLARB = useFLARB;
881	<	fInfo_.SIM_uses_RF = useRF;
882	<	fInfo_.SIM_uses_SF = useSF;
883	<	fInfo_.SIM_uses_SP = useSP;
884	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
885	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
888	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
889	>
890	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
891	>
892	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
894	>	}
895	>	}
896	>	return GlobalAtomIndices;
897		}
898
888	–	void SimInfo::setupFortranSim() {
889	–	int isError;
890	–	int nExclude, nOneTwo, nOneThree, nOneFour;
891	–	std::vector<int> fortranGlobalGroupMembership;
892	–
893	–	isError = 0;
899
900	<	//globalGroupMembership_ is filled by SimCreator
901	<	for (int i = 0; i < nGlobalAtoms_; i++) {
902	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
900	>	vector<int> SimInfo::getGlobalGroupIndices() {
901	>	SimInfo::MoleculeIterator mi;
902	>	Molecule* mol;
903	>	Molecule::CutoffGroupIterator ci;
904	>	CutoffGroup* cg;
905	>
906	>	vector<int> GlobalGroupIndices;
907	>
908	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
909	>
910	>	//local index of cutoff group is trivial, it only depends on the
911	>	//order of travesing
912	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
913	>	cg = mol->nextCutoffGroup(ci)) {
914	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
915	>	}
916		}
917	+	return GlobalGroupIndices;
918	+	}
919
920	+
921	+	void SimInfo::prepareTopology() {
922	+
923		//calculate mass ratio of cutoff group
901	–	std::vector<RealType> mfact;
924		SimInfo::MoleculeIterator mi;
925		Molecule* mol;
926		Molecule::CutoffGroupIterator ci;
#	Line 907 | Line 929 | namespace oopse {
929		Atom* atom;
930		RealType totalMass;
931
932	<	//to avoid memory reallocation, reserve enough space for mfact
933	<	mfact.reserve(getNCutoffGroups());
932	>	/**
933	>	* The mass factor is the relative mass of an atom to the total
934	>	* mass of the cutoff group it belongs to.  By default, all atoms
935	>	* are their own cutoff groups, and therefore have mass factors of
936	>	* 1.  We need some special handling for massless atoms, which
937	>	* will be treated as carrying the entire mass of the cutoff
938	>	* group.
939	>	*/
940	>	massFactors_.clear();
941	>	massFactors_.resize(getNAtoms(), 1.0);
942
943		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
944	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
944	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
945	>	cg = mol->nextCutoffGroup(ci)) {
946
947		totalMass = cg->getMass();
948		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
949		// Check for massless groups - set mfact to 1 if true
950	<	if (totalMass != 0)
951	<	mfact.push_back(atom->getMass()/totalMass);
950	>	if (totalMass != 0)
951	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
952		else
953	<	mfact.push_back( 1.0 );
953	>	massFactors_[atom->getLocalIndex()] = 1.0;
954		}
955		}
956		}
957
958	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
928	<	std::vector<int> identArray;
958	>	// Build the identArray_ and regions_
959
960	<	//to avoid memory reallocation, reserve enough space identArray
961	<	identArray.reserve(getNAtoms());
962	<
963	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
960	>	identArray_.clear();
961	>	identArray_.reserve(getNAtoms());
962	>	regions_.clear();
963	>	regions_.reserve(getNAtoms());
964	>
965	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
966	>	int reg = mol->getRegion();
967		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
968	<	identArray.push_back(atom->getIdent());
968	>	identArray_.push_back(atom->getIdent());
969	>	regions_.push_back(reg);
970		}
971		}
972	+
973	+	topologyDone_ = true;
974	+	}
975
976	<	//fill molMembershipArray
977	<	//molMembershipArray is filled by SimCreator
978	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
942	<	for (int i = 0; i < nGlobalAtoms_; i++) {
943	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
944	<	}
945	<
946	<	//setup fortran simulation
976	>	void SimInfo::addProperty(GenericData* genData) {
977	>	properties_.addProperty(genData);
978	>	}
979
980	<	nExclude = excludedInteractions_.getSize();
981	<	nOneTwo = oneTwoInteractions_.getSize();
982	<	nOneThree = oneThreeInteractions_.getSize();
951	<	nOneFour = oneFourInteractions_.getSize();
980	>	void SimInfo::removeProperty(const string& propName) {
981	>	properties_.removeProperty(propName);
982	>	}
983
984	<	std::cerr << "excludedInteractions contains: " << excludedInteractions_.getSize() << " pairs \n";
985	<	std::cerr << "oneTwoInteractions contains: " << oneTwoInteractions_.getSize() << " pairs \n";
986	<	std::cerr << "oneThreeInteractions contains: " << oneThreeInteractions_.getSize() << " pairs \n";
956	<	std::cerr << "oneFourInteractions contains: " << oneFourInteractions_.getSize() << " pairs \n";
984	>	void SimInfo::clearProperties() {
985	>	properties_.clearProperties();
986	>	}
987
988	<	int* excludeList = excludedInteractions_.getPairList();
989	<	int* oneTwoList = oneTwoInteractions_.getPairList();
990	<	int* oneThreeList = oneThreeInteractions_.getPairList();
961	<	int* oneFourList = oneFourInteractions_.getPairList();
962	<
963	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
964	<	&nExclude, excludeList,
965	<	&nOneTwo, oneTwoList,
966	<	&nOneThree, oneThreeList,
967	<	&nOneFour, oneFourList,
968	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
969	<	&fortranGlobalGroupMembership[0], &isError);
970	<
971	<	if( isError ){
988	>	vector<string> SimInfo::getPropertyNames() {
989	>	return properties_.getPropertyNames();
990	>	}
991
992	<	sprintf( painCave.errMsg,
993	<	"There was an error setting the simulation information in fortran.\n" );
994	<	painCave.isFatal = 1;
976	<	painCave.severity = OOPSE_ERROR;
977	<	simError();
978	<	}
979	<
980	<
981	<	sprintf( checkPointMsg,
982	<	"succesfully sent the simulation information to fortran.\n");
983	<
984	<	errorCheckPoint();
985	<
986	<	// Setup number of neighbors in neighbor list if present
987	<	if (simParams_->haveNeighborListNeighbors()) {
988	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
989	<	setNeighbors(&nlistNeighbors);
990	<	}
991	<
992	>	vector<GenericData*> SimInfo::getProperties() {
993	>	return properties_.getProperties();
994	>	}
995
996	+	GenericData* SimInfo::getPropertyByName(const string& propName) {
997	+	return properties_.getPropertyByName(propName);
998		}
999
1000	+	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1001	+	if (sman_ == sman) {
1002	+	return;
1003	+	}
1004	+	delete sman_;
1005	+	sman_ = sman;
1006
996	–	void SimInfo::setupFortranParallel() {
997	–	#ifdef IS_MPI
998	–	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
999	–	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1000	–	std::vector<int> localToGlobalCutoffGroupIndex;
1007		SimInfo::MoleculeIterator mi;
1008		Molecule::AtomIterator ai;
1009	<	Molecule::CutoffGroupIterator ci;
1009	>	Molecule::RigidBodyIterator rbIter;
1010	>	Molecule::CutoffGroupIterator cgIter;
1011	>	Molecule::BondIterator bondIter;
1012	>	Molecule::BendIterator bendIter;
1013	>	Molecule::TorsionIterator torsionIter;
1014	>	Molecule::InversionIterator inversionIter;
1015	>
1016		Molecule* mol;
1017		Atom* atom;
1018	+	RigidBody* rb;
1019		CutoffGroup* cg;
1020	<	mpiSimData parallelData;
1021	<	int isError;
1020	>	Bond* bond;
1021	>	Bend* bend;
1022	>	Torsion* torsion;
1023	>	Inversion* inversion;
1024
1025	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1011	<
1012	<	//local index(index in DataStorge) of atom is important
1013	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1014	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1015	<	}
1016	<
1017	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1018	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1019	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1020	<	}
1025	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1026
1027	<	}
1028	<
1029	<	//fill up mpiSimData struct
1030	<	parallelData.nMolGlobal = getNGlobalMolecules();
1031	<	parallelData.nMolLocal = getNMolecules();
1032	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1033	<	parallelData.nAtomsLocal = getNAtoms();
1029	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1030	<	parallelData.nGroupsLocal = getNCutoffGroups();
1031	<	parallelData.myNode = worldRank;
1032	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1033	<
1034	<	//pass mpiSimData struct and index arrays to fortran
1035	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1036	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1037	<	&localToGlobalCutoffGroupIndex[0], &isError);
1038	<
1039	<	if (isError) {
1040	<	sprintf(painCave.errMsg,
1041	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1042	<	painCave.isFatal = 1;
1043	<	simError();
1044	<	}
1045	<
1046	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1047	<	errorCheckPoint();
1048	<
1049	<	#endif
1050	<	}
1051	<
1052	<	void SimInfo::setupCutoff() {
1053	<
1054	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1055	<
1056	<	// Check the cutoff policy
1057	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1058	<
1059	<	// Set LJ shifting bools to false
1060	<	ljsp_ = false;
1061	<	ljsf_ = false;
1062	<
1063	<	std::string myPolicy;
1064	<	if (forceFieldOptions_.haveCutoffPolicy()){
1065	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1066	<	}else if (simParams_->haveCutoffPolicy()) {
1067	<	myPolicy = simParams_->getCutoffPolicy();
1068	<	}
1069	<
1070	<	if (!myPolicy.empty()){
1071	<	toUpper(myPolicy);
1072	<	if (myPolicy == "MIX") {
1073	<	cp = MIX_CUTOFF_POLICY;
1074	<	} else {
1075	<	if (myPolicy == "MAX") {
1076	<	cp = MAX_CUTOFF_POLICY;
1077	<	} else {
1078	<	if (myPolicy == "TRADITIONAL") {
1079	<	cp = TRADITIONAL_CUTOFF_POLICY;
1080	<	} else {
1081	<	// throw error
1082	<	sprintf( painCave.errMsg,
1083	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1084	<	painCave.isFatal = 1;
1085	<	simError();
1086	<	}
1087	<	}
1027	>	for (atom = mol->beginAtom(ai); atom != NULL;
1028	>	atom = mol->nextAtom(ai)) {
1029	>	atom->setSnapshotManager(sman_);
1030	>	}
1031	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1032	>	rb = mol->nextRigidBody(rbIter)) {
1033	>	rb->setSnapshotManager(sman_);
1034		}
1035	<	}
1036	<	notifyFortranCutoffPolicy(&cp);
1037	<
1092	<	// Check the Skin Thickness for neighborlists
1093	<	RealType skin;
1094	<	if (simParams_->haveSkinThickness()) {
1095	<	skin = simParams_->getSkinThickness();
1096	<	notifyFortranSkinThickness(&skin);
1097	<	}
1098	<
1099	<	// Check if the cutoff was set explicitly:
1100	<	if (simParams_->haveCutoffRadius()) {
1101	<	rcut_ = simParams_->getCutoffRadius();
1102	<	if (simParams_->haveSwitchingRadius()) {
1103	<	rsw_  = simParams_->getSwitchingRadius();
1104	<	} else {
1105	<	if (fInfo_.SIM_uses_Charges |
1106	<	fInfo_.SIM_uses_Dipoles |
1107	<	fInfo_.SIM_uses_RF) {
1108	<
1109	<	rsw_ = 0.85 * rcut_;
1110	<	sprintf(painCave.errMsg,
1111	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1112	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1113	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1114	<	painCave.isFatal = 0;
1115	<	simError();
1116	<	} else {
1117	<	rsw_ = rcut_;
1118	<	sprintf(painCave.errMsg,
1119	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1120	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1121	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1122	<	painCave.isFatal = 0;
1123	<	simError();
1124	<	}
1035	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1036	>	cg = mol->nextCutoffGroup(cgIter)) {
1037	>	cg->setSnapshotManager(sman_);
1038		}
1039	<
1040	<	if (simParams_->haveElectrostaticSummationMethod()) {
1041	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1129	<	toUpper(myMethod);
1130	<
1131	<	if (myMethod == "SHIFTED_POTENTIAL") {
1132	<	ljsp_ = true;
1133	<	} else if (myMethod == "SHIFTED_FORCE") {
1134	<	ljsf_ = true;
1135	<	}
1039	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1040	>	bond = mol->nextBond(bondIter)) {
1041	>	bond->setSnapshotManager(sman_);
1042		}
1043	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1044	<
1045	<	} else {
1140	<
1141	<	// For electrostatic atoms, we'll assume a large safe value:
1142	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1143	<	sprintf(painCave.errMsg,
1144	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1145	<	"\tOOPSE will use a default value of 15.0 angstroms"
1146	<	"\tfor the cutoffRadius.\n");
1147	<	painCave.isFatal = 0;
1148	<	simError();
1149	<	rcut_ = 15.0;
1150	<
1151	<	if (simParams_->haveElectrostaticSummationMethod()) {
1152	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1153	<	toUpper(myMethod);
1154	<
1155	<	// For the time being, we're tethering the LJ shifted behavior to the
1156	<	// electrostaticSummationMethod keyword options
1157	<	if (myMethod == "SHIFTED_POTENTIAL") {
1158	<	ljsp_ = true;
1159	<	} else if (myMethod == "SHIFTED_FORCE") {
1160	<	ljsf_ = true;
1161	<	}
1162	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1163	<	if (simParams_->haveSwitchingRadius()){
1164	<	sprintf(painCave.errMsg,
1165	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1166	<	"\teven though the electrostaticSummationMethod was\n"
1167	<	"\tset to %s\n", myMethod.c_str());
1168	<	painCave.isFatal = 1;
1169	<	simError();
1170	<	}
1171	<	}
1172	<	}
1173	<
1174	<	if (simParams_->haveSwitchingRadius()){
1175	<	rsw_ = simParams_->getSwitchingRadius();
1176	<	} else {
1177	<	sprintf(painCave.errMsg,
1178	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1179	<	"\tOOPSE will use a default value of\n"
1180	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1181	<	painCave.isFatal = 0;
1182	<	simError();
1183	<	rsw_ = 0.85 * rcut_;
1184	<	}
1185	<
1186	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1187	<
1188	<	} else {
1189	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1190	<	// We'll punt and let fortran figure out the cutoffs later.
1191	<
1192	<	notifyFortranYouAreOnYourOwn();
1193	<
1043	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1044	>	bend = mol->nextBend(bendIter)) {
1045	>	bend->setSnapshotManager(sman_);
1046		}
1047	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1048	+	torsion = mol->nextTorsion(torsionIter)) {
1049	+	torsion->setSnapshotManager(sman_);
1050	+	}
1051	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1052	+	inversion = mol->nextInversion(inversionIter)) {
1053	+	inversion->setSnapshotManager(sman_);
1054	+	}
1055		}
1056		}
1057
1198	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1199	–
1200	–	int errorOut;
1201	–	int esm =  NONE;
1202	–	int sm = UNDAMPED;
1203	–	RealType alphaVal;
1204	–	RealType dielectric;
1205	–
1206	–	errorOut = isError;
1058
1059	<	if (simParams_->haveElectrostaticSummationMethod()) {
1209	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1210	<	toUpper(myMethod);
1211	<	if (myMethod == "NONE") {
1212	<	esm = NONE;
1213	<	} else {
1214	<	if (myMethod == "SWITCHING_FUNCTION") {
1215	<	esm = SWITCHING_FUNCTION;
1216	<	} else {
1217	<	if (myMethod == "SHIFTED_POTENTIAL") {
1218	<	esm = SHIFTED_POTENTIAL;
1219	<	} else {
1220	<	if (myMethod == "SHIFTED_FORCE") {
1221	<	esm = SHIFTED_FORCE;
1222	<	} else {
1223	<	if (myMethod == "REACTION_FIELD") {
1224	<	esm = REACTION_FIELD;
1225	<	dielectric = simParams_->getDielectric();
1226	<	if (!simParams_->haveDielectric()) {
1227	<	// throw warning
1228	<	sprintf( painCave.errMsg,
1229	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1230	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1231	<	painCave.isFatal = 0;
1232	<	simError();
1233	<	}
1234	<	} else {
1235	<	// throw error
1236	<	sprintf( painCave.errMsg,
1237	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1238	<	"\t(Input file specified %s .)\n"
1239	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1240	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1241	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1242	<	painCave.isFatal = 1;
1243	<	simError();
1244	<	}
1245	<	}
1246	<	}
1247	<	}
1248	<	}
1249	<	}
1250	<
1251	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1252	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1253	<	toUpper(myScreen);
1254	<	if (myScreen == "UNDAMPED") {
1255	<	sm = UNDAMPED;
1256	<	} else {
1257	<	if (myScreen == "DAMPED") {
1258	<	sm = DAMPED;
1259	<	if (!simParams_->haveDampingAlpha()) {
1260	<	// first set a cutoff dependent alpha value
1261	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1262	<	alphaVal = 0.5125 - rcut_* 0.025;
1263	<	// for values rcut > 20.5, alpha is zero
1264	<	if (alphaVal < 0) alphaVal = 0;
1059	>	ostream& operator <<(ostream& o, SimInfo& info) {
1060
1266	–	// throw warning
1267	–	sprintf( painCave.errMsg,
1268	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1269	–	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1270	–	painCave.isFatal = 0;
1271	–	simError();
1272	–	} else {
1273	–	alphaVal = simParams_->getDampingAlpha();
1274	–	}
1275	–
1276	–	} else {
1277	–	// throw error
1278	–	sprintf( painCave.errMsg,
1279	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1280	–	"\t(Input file specified %s .)\n"
1281	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1282	–	"or \"damped\".\n", myScreen.c_str() );
1283	–	painCave.isFatal = 1;
1284	–	simError();
1285	–	}
1286	–	}
1287	–	}
1288	–
1289	–	// let's pass some summation method variables to fortran
1290	–	setElectrostaticSummationMethod( &esm );
1291	–	setFortranElectrostaticMethod( &esm );
1292	–	setScreeningMethod( &sm );
1293	–	setDampingAlpha( &alphaVal );
1294	–	setReactionFieldDielectric( &dielectric );
1295	–	initFortranFF( &errorOut );
1296	–	}
1297	–
1298	–	void SimInfo::setupSwitchingFunction() {
1299	–	int ft = CUBIC;
1300	–
1301	–	if (simParams_->haveSwitchingFunctionType()) {
1302	–	std::string funcType = simParams_->getSwitchingFunctionType();
1303	–	toUpper(funcType);
1304	–	if (funcType == "CUBIC") {
1305	–	ft = CUBIC;
1306	–	} else {
1307	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1308	–	ft = FIFTH_ORDER_POLY;
1309	–	} else {
1310	–	// throw error
1311	–	sprintf( painCave.errMsg,
1312	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1313	–	painCave.isFatal = 1;
1314	–	simError();
1315	–	}
1316	–	}
1317	–	}
1318	–
1319	–	// send switching function notification to switcheroo
1320	–	setFunctionType(&ft);
1321	–
1322	–	}
1323	–
1324	–	void SimInfo::setupAccumulateBoxDipole() {
1325	–
1326	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1327	–	if ( simParams_->haveAccumulateBoxDipole() )
1328	–	if ( simParams_->getAccumulateBoxDipole() ) {
1329	–	setAccumulateBoxDipole();
1330	–	calcBoxDipole_ = true;
1331	–	}
1332	–
1333	–	}
1334	–
1335	–	void SimInfo::addProperty(GenericData* genData) {
1336	–	properties_.addProperty(genData);
1337	–	}
1338	–
1339	–	void SimInfo::removeProperty(const std::string& propName) {
1340	–	properties_.removeProperty(propName);
1341	–	}
1342	–
1343	–	void SimInfo::clearProperties() {
1344	–	properties_.clearProperties();
1345	–	}
1346	–
1347	–	std::vector<std::string> SimInfo::getPropertyNames() {
1348	–	return properties_.getPropertyNames();
1349	–	}
1350	–
1351	–	std::vector<GenericData*> SimInfo::getProperties() {
1352	–	return properties_.getProperties();
1353	–	}
1354	–
1355	–	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1356	–	return properties_.getPropertyByName(propName);
1357	–	}
1358	–
1359	–	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1360	–	if (sman_ == sman) {
1361	–	return;
1362	–	}
1363	–	delete sman_;
1364	–	sman_ = sman;
1365	–
1366	–	Molecule* mol;
1367	–	RigidBody* rb;
1368	–	Atom* atom;
1369	–	SimInfo::MoleculeIterator mi;
1370	–	Molecule::RigidBodyIterator rbIter;
1371	–	Molecule::AtomIterator atomIter;;
1372	–
1373	–	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1374	–
1375	–	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1376	–	atom->setSnapshotManager(sman_);
1377	–	}
1378	–
1379	–	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1380	–	rb->setSnapshotManager(sman_);
1381	–	}
1382	–	}
1383	–
1384	–	}
1385	–
1386	–	Vector3d SimInfo::getComVel(){
1387	–	SimInfo::MoleculeIterator i;
1388	–	Molecule* mol;
1389	–
1390	–	Vector3d comVel(0.0);
1391	–	RealType totalMass = 0.0;
1392	–
1393	–
1394	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1395	–	RealType mass = mol->getMass();
1396	–	totalMass += mass;
1397	–	comVel += mass * mol->getComVel();
1398	–	}
1399	–
1400	–	#ifdef IS_MPI
1401	–	RealType tmpMass = totalMass;
1402	–	Vector3d tmpComVel(comVel);
1403	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1404	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1405	–	#endif
1406	–
1407	–	comVel /= totalMass;
1408	–
1409	–	return comVel;
1410	–	}
1411	–
1412	–	Vector3d SimInfo::getCom(){
1413	–	SimInfo::MoleculeIterator i;
1414	–	Molecule* mol;
1415	–
1416	–	Vector3d com(0.0);
1417	–	RealType totalMass = 0.0;
1418	–
1419	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1420	–	RealType mass = mol->getMass();
1421	–	totalMass += mass;
1422	–	com += mass * mol->getCom();
1423	–	}
1424	–
1425	–	#ifdef IS_MPI
1426	–	RealType tmpMass = totalMass;
1427	–	Vector3d tmpCom(com);
1428	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1429	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1430	–	#endif
1431	–
1432	–	com /= totalMass;
1433	–
1434	–	return com;
1435	–
1436	–	}
1437	–
1438	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1439	–
1061		return o;
1062		}
1063
1064	<
1444	<	/*
1445	<	Returns center of mass and center of mass velocity in one function call.
1446	<	*/
1447	<
1448	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1449	<	SimInfo::MoleculeIterator i;
1450	<	Molecule* mol;
1451	<
1452	<
1453	<	RealType totalMass = 0.0;
1454	<
1455	<
1456	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1457	<	RealType mass = mol->getMass();
1458	<	totalMass += mass;
1459	<	com += mass * mol->getCom();
1460	<	comVel += mass * mol->getComVel();
1461	<	}
1462	<
1463	<	#ifdef IS_MPI
1464	<	RealType tmpMass = totalMass;
1465	<	Vector3d tmpCom(com);
1466	<	Vector3d tmpComVel(comVel);
1467	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1468	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1469	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1470	<	#endif
1471	<
1472	<	com /= totalMass;
1473	<	comVel /= totalMass;
1474	<	}
1475	<
1476	<	/*
1477	<	Return intertia tensor for entire system and angular momentum Vector.
1478	<
1479	<
1480	<	[  Ixx -Ixy  -Ixz ]
1481	<	J =| -Iyx  Iyy  -Iyz |
1482	<	[ -Izx -Iyz   Izz ]
1483	<	*/
1484	<
1485	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1486	<
1487	<
1488	<	RealType xx = 0.0;
1489	<	RealType yy = 0.0;
1490	<	RealType zz = 0.0;
1491	<	RealType xy = 0.0;
1492	<	RealType xz = 0.0;
1493	<	RealType yz = 0.0;
1494	<	Vector3d com(0.0);
1495	<	Vector3d comVel(0.0);
1496	<
1497	<	getComAll(com, comVel);
1498	<
1499	<	SimInfo::MoleculeIterator i;
1500	<	Molecule* mol;
1501	<
1502	<	Vector3d thisq(0.0);
1503	<	Vector3d thisv(0.0);
1504	<
1505	<	RealType thisMass = 0.0;
1506	<
1507	<
1508	<
1509	<
1510	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1511	<
1512	<	thisq = mol->getCom()-com;
1513	<	thisv = mol->getComVel()-comVel;
1514	<	thisMass = mol->getMass();
1515	<	// Compute moment of intertia coefficients.
1516	<	xx += thisq[0]*thisq[0]*thisMass;
1517	<	yy += thisq[1]*thisq[1]*thisMass;
1518	<	zz += thisq[2]*thisq[2]*thisMass;
1519	<
1520	<	// compute products of intertia
1521	<	xy += thisq[0]*thisq[1]*thisMass;
1522	<	xz += thisq[0]*thisq[2]*thisMass;
1523	<	yz += thisq[1]*thisq[2]*thisMass;
1524	<
1525	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1526	<
1527	<	}
1528	<
1529	<
1530	<	inertiaTensor(0,0) = yy + zz;
1531	<	inertiaTensor(0,1) = -xy;
1532	<	inertiaTensor(0,2) = -xz;
1533	<	inertiaTensor(1,0) = -xy;
1534	<	inertiaTensor(1,1) = xx + zz;
1535	<	inertiaTensor(1,2) = -yz;
1536	<	inertiaTensor(2,0) = -xz;
1537	<	inertiaTensor(2,1) = -yz;
1538	<	inertiaTensor(2,2) = xx + yy;
1539	<
1540	<	#ifdef IS_MPI
1541	<	Mat3x3d tmpI(inertiaTensor);
1542	<	Vector3d tmpAngMom;
1543	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1544	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1545	<	#endif
1546	<
1547	<	return;
1548	<	}
1549	<
1550	<	//Returns the angular momentum of the system
1551	<	Vector3d SimInfo::getAngularMomentum(){
1552	<
1553	<	Vector3d com(0.0);
1554	<	Vector3d comVel(0.0);
1555	<	Vector3d angularMomentum(0.0);
1556	<
1557	<	getComAll(com,comVel);
1558	<
1559	<	SimInfo::MoleculeIterator i;
1560	<	Molecule* mol;
1561	<
1562	<	Vector3d thisr(0.0);
1563	<	Vector3d thisp(0.0);
1564	<
1565	<	RealType thisMass;
1566	<
1567	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1568	<	thisMass = mol->getMass();
1569	<	thisr = mol->getCom()-com;
1570	<	thisp = (mol->getComVel()-comVel)*thisMass;
1571	<
1572	<	angularMomentum += cross( thisr, thisp );
1573	<
1574	<	}
1575	<
1576	<	#ifdef IS_MPI
1577	<	Vector3d tmpAngMom;
1578	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1579	<	#endif
1580	<
1581	<	return angularMomentum;
1582	<	}
1583	<
1064	>
1065		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1066	<	return IOIndexToIntegrableObject.at(index);
1066	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1067	>	sprintf(painCave.errMsg,
1068	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1069	>	"\tindex exceeds number of known objects!\n");
1070	>	painCave.isFatal = 1;
1071	>	simError();
1072	>	return NULL;
1073	>	} else
1074	>	return IOIndexToIntegrableObject.at(index);
1075		}
1076
1077	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1077	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1078		IOIndexToIntegrableObject= v;
1079		}
1080
1081	<	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1082	<	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1083	<	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1084	<	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1085	<	*/
1086	<	void SimInfo::getGyrationalVolume(RealType &volume){
1087	<	Mat3x3d intTensor;
1599	<	RealType det;
1600	<	Vector3d dummyAngMom;
1601	<	RealType sysconstants;
1602	<	RealType geomCnst;
1603	<
1604	<	geomCnst = 3.0/2.0;
1605	<	/* Get the inertial tensor and angular momentum for free*/
1606	<	getInertiaTensor(intTensor,dummyAngMom);
1607	<
1608	<	det = intTensor.determinant();
1609	<	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1610	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1611	<	return;
1081	>	void SimInfo::calcNConstraints() {
1082	>	#ifdef IS_MPI
1083	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1084	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1085	>	#else
1086	>	nGlobalConstraints_ =  nConstraints_;
1087	>	#endif
1088		}
1089
1090	<	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1615	<	Mat3x3d intTensor;
1616	<	Vector3d dummyAngMom;
1617	<	RealType sysconstants;
1618	<	RealType geomCnst;
1090	>	}//end namespace OpenMD
1091
1620	–	geomCnst = 3.0/2.0;
1621	–	/* Get the inertial tensor and angular momentum for free*/
1622	–	getInertiaTensor(intTensor,dummyAngMom);
1623	–
1624	–	detI = intTensor.determinant();
1625	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1626	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1627	–	return;
1628	–	}
1629	–	/*
1630	–	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1631	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1632	–	sdByGlobalIndex_ = v;
1633	–	}
1634	–
1635	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1636	–	//assert(index < nAtoms_ + nRigidBodies_);
1637	–	return sdByGlobalIndex_.at(index);
1638	–	}
1639	–	*/
1640	–	}//end namespace oopse
1641	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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