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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	<	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	<	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
79	<	calcBoxDipole_(false), useAtomicVirial_(true) {
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77	>	nGlobalTorsions_(0), nGlobalInversions_(0), nAtoms_(0), nBonds_(0),
78	>	nBends_(0), nTorsions_(0), nInversions_(0), nRigidBodies_(0),
79	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
80	>	nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
81	>	calcBoxDipole_(false), useAtomicVirial_(true) {
82	>
83	>	MoleculeStamp* molStamp;
84	>	int nMolWithSameStamp;
85	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
87	>	CutoffGroupStamp* cgStamp;
88	>	RigidBodyStamp* rbStamp;
89	>	int nRigidAtoms = 0;
90	>
91	>	vector<Component*> components = simParams->getComponents();
92	>
93	>	for (vector<Component*>::iterator i = components.begin();
94	>	i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	if ( (*i)->haveRegion() ) {
97	>	molStamp->setRegion( (*i)->getRegion() );
98	>	} else {
99	>	// set the region to a disallowed value:
100	>	molStamp->setRegion( -1 );
101	>	}
102
103	<
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();
103	>	nMolWithSameStamp = (*i)->getNMol();
104
105	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
106	<	molStamp = (*i)->getMoleculeStamp();
107	<	nMolWithSameStamp = (*i)->getNMol();
108	<
109	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
110	<
111	<	//calculate atoms in molecules
112	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
113	<
114	<	//calculate atoms in cutoff groups
115	<	int nAtomsInGroups = 0;
116	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
117	<
118	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
119	<	cgStamp = molStamp->getCutoffGroupStamp(j);
120	<	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	<
105	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
106	>
107	>	//calculate atoms in molecules
108	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
109	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
110	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
111	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
112	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
113	>
114	>	//calculate atoms in cutoff groups
115	>	int nAtomsInGroups = 0;
116	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
117	>
118	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
119	>	cgStamp = molStamp->getCutoffGroupStamp(j);
120	>	nAtomsInGroups += cgStamp->getNMembers();
121		}
122	<
123	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	<	//group therefore the total number of cutoff groups in the system is
125	<	//equal to the total number of atoms minus number of atoms belong to
126	<	//cutoff group defined in meta-data file plus the number of cutoff
127	<	//groups defined in meta-data file
128	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
129	<
130	<	//every free atom (atom does not belong to rigid bodies) is an
131	<	//integrable object therefore the total number of integrable objects
132	<	//in the system is equal to the total number of atoms minus number of
133	<	//atoms belong to rigid body defined in meta-data file plus the number
134	<	//of rigid bodies defined in meta-data file
135	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
136	<	+ nGlobalRigidBodies_;
137	<
138	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
122	>
123	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
124	>
125	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
126	>
127	>	//calculate atoms in rigid bodies
128	>	int nAtomsInRigidBodies = 0;
129	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130	>
131	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
132	>	rbStamp = molStamp->getRigidBodyStamp(j);
133	>	nAtomsInRigidBodies += rbStamp->getNMembers();
134	>	}
135	>
136	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138	>
139		}
140	+
141	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
142	+	//group therefore the total number of cutoff groups in the system is
143	+	//equal to the total number of atoms minus number of atoms belong to
144	+	//cutoff group defined in meta-data file plus the number of cutoff
145	+	//groups defined in meta-data file
146
147	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148	+
149	+	//every free atom (atom does not belong to rigid bodies) is an
150	+	//integrable object therefore the total number of integrable objects
151	+	//in the system is equal to the total number of atoms minus number of
152	+	//atoms belong to rigid body defined in meta-data file plus the number
153	+	//of rigid bodies defined in meta-data file
154	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	+	+ nGlobalRigidBodies_;
156	+
157	+	nGlobalMols_ = molStampIds_.size();
158	+	molToProcMap_.resize(nGlobalMols_);
159	+	}
160	+
161		SimInfo::~SimInfo() {
162	<	std::map<int, Molecule*>::iterator i;
162	>	map<int, Molecule*>::iterator i;
163		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
164		delete i->second;
165		}
#	Line 173 | Line 170 | namespace oopse {
170		delete forceField_;
171		}
172
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	–	}
173
174		bool SimInfo::addMolecule(Molecule* mol) {
175		MoleculeIterator i;
176	<
176	>
177		i = molecules_.find(mol->getGlobalIndex());
178		if (i == molecules_.end() ) {
179	<
180	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
181	<
179	>
180	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
181	>
182		nAtoms_ += mol->getNAtoms();
183		nBonds_ += mol->getNBonds();
184		nBends_ += mol->getNBends();
#	Line 201 | Line 188 | namespace oopse {
188		nIntegrableObjects_ += mol->getNIntegrableObjects();
189		nCutoffGroups_ += mol->getNCutoffGroups();
190		nConstraints_ += mol->getNConstraintPairs();
191	<
191	>
192		addInteractionPairs(mol);
193	<
193	>
194		return true;
195		} else {
196		return false;
197		}
198		}
199	<
199	>
200		bool SimInfo::removeMolecule(Molecule* mol) {
201		MoleculeIterator i;
202		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 224 | namespace oopse {
224		} else {
225		return false;
226		}
240	–
241	–
227		}
228
229
#	Line 254 | Line 239 | namespace oopse {
239
240
241		void SimInfo::calcNdf() {
242	<	int ndf_local;
242	>	int ndf_local, nfq_local;
243		MoleculeIterator i;
244	<	std::vector<StuntDouble*>::iterator j;
244	>	vector<StuntDouble*>::iterator j;
245	>	vector<Atom*>::iterator k;
246	>
247		Molecule* mol;
248	<	StuntDouble* integrableObject;
248	>	StuntDouble* sd;
249	>	Atom* atom;
250
251		ndf_local = 0;
252	+	nfq_local = 0;
253
254		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
266	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	–	integrableObject = mol->nextIntegrableObject(j)) {
255
256	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
257	+	sd = mol->nextIntegrableObject(j)) {
258	+
259		ndf_local += 3;
260
261	<	if (integrableObject->isDirectional()) {
262	<	if (integrableObject->isLinear()) {
261	>	if (sd->isDirectional()) {
262	>	if (sd->isLinear()) {
263		ndf_local += 2;
264		} else {
265		ndf_local += 3;
266		}
267		}
278	–
268		}
269	+
270	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
271	+	atom = mol->nextFluctuatingCharge(k)) {
272	+	if (atom->isFluctuatingCharge()) {
273	+	nfq_local++;
274	+	}
275	+	}
276		}
277
278	+	ndfLocal_ = ndf_local;
279	+
280		// n_constraints is local, so subtract them on each processor
281		ndf_local -= nConstraints_;
282
283		#ifdef IS_MPI
284	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
285	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
286	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287	>	// MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
288	>	// MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
289	>	//                           MPI::INT, MPI::SUM);
290		#else
291		ndf_ = ndf_local;
292	+	nGlobalFluctuatingCharges_ = nfq_local;
293		#endif
294
295		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 296 | Line 300 | namespace oopse {
300
301		int SimInfo::getFdf() {
302		#ifdef IS_MPI
303	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
303	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
304	>	// MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
305		#else
306		fdf_ = fdf_local;
307		#endif
308		return fdf_;
309		}
310	+
311	+	unsigned int SimInfo::getNLocalCutoffGroups(){
312	+	int nLocalCutoffAtoms = 0;
313	+	Molecule* mol;
314	+	MoleculeIterator mi;
315	+	CutoffGroup* cg;
316	+	Molecule::CutoffGroupIterator ci;
317
318	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
319	+
320	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
321	+	cg = mol->nextCutoffGroup(ci)) {
322	+	nLocalCutoffAtoms += cg->getNumAtom();
323	+
324	+	}
325	+	}
326	+
327	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
328	+	}
329	+
330		void SimInfo::calcNdfRaw() {
331		int ndfRaw_local;
332
333		MoleculeIterator i;
334	<	std::vector<StuntDouble*>::iterator j;
334	>	vector<StuntDouble*>::iterator j;
335		Molecule* mol;
336	<	StuntDouble* integrableObject;
336	>	StuntDouble* sd;
337
338		// Raw degrees of freedom that we have to set
339		ndfRaw_local = 0;
340
341		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	–	integrableObject = mol->nextIntegrableObject(j)) {
342
343	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
344	+	sd = mol->nextIntegrableObject(j)) {
345	+
346		ndfRaw_local += 3;
347
348	<	if (integrableObject->isDirectional()) {
349	<	if (integrableObject->isLinear()) {
348	>	if (sd->isDirectional()) {
349	>	if (sd->isLinear()) {
350		ndfRaw_local += 2;
351		} else {
352		ndfRaw_local += 3;
#	Line 332 | Line 357 | namespace oopse {
357		}
358
359		#ifdef IS_MPI
360	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
360	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
361	>	// MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
362		#else
363		ndfRaw_ = ndfRaw_local;
364		#endif
#	Line 345 | Line 371 | namespace oopse {
371
372
373		#ifdef IS_MPI
374	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
374	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1,
375	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
376	>	// MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
377	>	//                           MPI::INT, MPI::SUM);
378		#else
379		ndfTrans_ = ndfTrans_local;
380		#endif
#	Line 356 | Line 385 | namespace oopse {
385
386		void SimInfo::addInteractionPairs(Molecule* mol) {
387		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
388	<	std::vector<Bond*>::iterator bondIter;
389	<	std::vector<Bend*>::iterator bendIter;
390	<	std::vector<Torsion*>::iterator torsionIter;
391	<	std::vector<Inversion*>::iterator inversionIter;
388	>	vector<Bond*>::iterator bondIter;
389	>	vector<Bend*>::iterator bendIter;
390	>	vector<Torsion*>::iterator torsionIter;
391	>	vector<Inversion*>::iterator inversionIter;
392		Bond* bond;
393		Bend* bend;
394		Torsion* torsion;
#	Line 377 | Line 406 | namespace oopse {
406		// always be excluded.  These are done at the bottom of this
407		// function.
408
409	<	std::map<int, std::set<int> > atomGroups;
409	>	map<int, set<int> > atomGroups;
410		Molecule::RigidBodyIterator rbIter;
411		RigidBody* rb;
412		Molecule::IntegrableObjectIterator ii;
413	<	StuntDouble* integrableObject;
413	>	StuntDouble* sd;
414
415	<	for (integrableObject = mol->beginIntegrableObject(ii);
416	<	integrableObject != NULL;
388	<	integrableObject = mol->nextIntegrableObject(ii)) {
415	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
416	>	sd = mol->nextIntegrableObject(ii)) {
417
418	<	if (integrableObject->isRigidBody()) {
419	<	rb = static_cast<RigidBody*>(integrableObject);
420	<	std::vector<Atom*> atoms = rb->getAtoms();
421	<	std::set<int> rigidAtoms;
418	>	if (sd->isRigidBody()) {
419	>	rb = static_cast<RigidBody*>(sd);
420	>	vector<Atom*> atoms = rb->getAtoms();
421	>	set<int> rigidAtoms;
422		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
423		rigidAtoms.insert(atoms[i]->getGlobalIndex());
424		}
425		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
426	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
426	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
427		}
428		} else {
429	<	std::set<int> oneAtomSet;
430	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
431	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
429	>	set<int> oneAtomSet;
430	>	oneAtomSet.insert(sd->getGlobalIndex());
431	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
432		}
433		}
434	+
435
436		for (bond= mol->beginBond(bondIter); bond != NULL;
437		bond = mol->nextBond(bondIter)) {
438
439		a = bond->getAtomA()->getGlobalIndex();
440		b = bond->getAtomB()->getGlobalIndex();
441	<
441	>
442		if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
443		oneTwoInteractions_.addPair(a, b);
444		} else {
#	Line 446 | Line 475 | namespace oopse {
475		b = torsion->getAtomB()->getGlobalIndex();
476		c = torsion->getAtomC()->getGlobalIndex();
477		d = torsion->getAtomD()->getGlobalIndex();
478	<
478	>
479		if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
480		oneTwoInteractions_.addPair(a, b);
481		oneTwoInteractions_.addPair(b, c);
#	Line 503 | Line 532 | namespace oopse {
532
533		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
534		rb = mol->nextRigidBody(rbIter)) {
535	<	std::vector<Atom*> atoms = rb->getAtoms();
535	>	vector<Atom*> atoms = rb->getAtoms();
536		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
537		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
538		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 546 | namespace oopse {
546
547		void SimInfo::removeInteractionPairs(Molecule* mol) {
548		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
549	<	std::vector<Bond*>::iterator bondIter;
550	<	std::vector<Bend*>::iterator bendIter;
551	<	std::vector<Torsion*>::iterator torsionIter;
552	<	std::vector<Inversion*>::iterator inversionIter;
549	>	vector<Bond*>::iterator bondIter;
550	>	vector<Bend*>::iterator bendIter;
551	>	vector<Torsion*>::iterator torsionIter;
552	>	vector<Inversion*>::iterator inversionIter;
553		Bond* bond;
554		Bend* bend;
555		Torsion* torsion;
#	Line 530 | Line 559 | namespace oopse {
559		int c;
560		int d;
561
562	<	std::map<int, std::set<int> > atomGroups;
562	>	map<int, set<int> > atomGroups;
563		Molecule::RigidBodyIterator rbIter;
564		RigidBody* rb;
565		Molecule::IntegrableObjectIterator ii;
566	<	StuntDouble* integrableObject;
566	>	StuntDouble* sd;
567
568	<	for (integrableObject = mol->beginIntegrableObject(ii);
569	<	integrableObject != NULL;
541	<	integrableObject = mol->nextIntegrableObject(ii)) {
568	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
569	>	sd = mol->nextIntegrableObject(ii)) {
570
571	<	if (integrableObject->isRigidBody()) {
572	<	rb = static_cast<RigidBody*>(integrableObject);
573	<	std::vector<Atom*> atoms = rb->getAtoms();
574	<	std::set<int> rigidAtoms;
571	>	if (sd->isRigidBody()) {
572	>	rb = static_cast<RigidBody*>(sd);
573	>	vector<Atom*> atoms = rb->getAtoms();
574	>	set<int> rigidAtoms;
575		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
576		rigidAtoms.insert(atoms[i]->getGlobalIndex());
577		}
578		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
579	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
579	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
580		}
581		} else {
582	<	std::set<int> oneAtomSet;
583	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
584	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
582	>	set<int> oneAtomSet;
583	>	oneAtomSet.insert(sd->getGlobalIndex());
584	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
585		}
586		}
587
#	Line 656 | Line 684 | namespace oopse {
684
685		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
686		rb = mol->nextRigidBody(rbIter)) {
687	<	std::vector<Atom*> atoms = rb->getAtoms();
687	>	vector<Atom*> atoms = rb->getAtoms();
688		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
689		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
690		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 707 | namespace oopse {
707		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
708		}
709
682	–	void SimInfo::update() {
710
711	<	setupSimType();
712	<
713	<	#ifdef IS_MPI
714	<	setupFortranParallel();
715	<	#endif
716	<
717	<	setupFortranSim();
718	<
719	<	//setup fortran force field
693	<	/** @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	<
711	>	/**
712	>	* update
713	>	*
714	>	*  Performs the global checks and variable settings after the
715	>	*  objects have been created.
716	>	*
717	>	*/
718	>	void SimInfo::update() {
719	>	setupSimVariables();
720		calcNdf();
721		calcNdfRaw();
722		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
723		}
724	<
725	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
724	>
725	>	/**
726	>	* getSimulatedAtomTypes
727	>	*
728	>	* Returns an STL set of AtomType* that are actually present in this
729	>	* simulation.  Must query all processors to assemble this information.
730	>	*
731	>	*/
732	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
733		SimInfo::MoleculeIterator mi;
734		Molecule* mol;
735		Molecule::AtomIterator ai;
736		Atom* atom;
737	<	std::set<AtomType*> atomTypes;
738	<
737	>	set<AtomType*> atomTypes;
738	>
739		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
740	<
741	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
740	>	for(atom = mol->beginAtom(ai); atom != NULL;
741	>	atom = mol->nextAtom(ai)) {
742		atomTypes.insert(atom->getAtomType());
743	<	}
744	<
745	<	}
743	>	}
744	>	}
745	>
746	>	#ifdef IS_MPI
747
748	<	return atomTypes;
749	<	}
733	<
734	<	void SimInfo::setupSimType() {
735	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
748	>	// loop over the found atom types on this processor, and add their
749	>	// numerical idents to a vector:
750
751	<	int useLennardJones = 0;
752	<	int useElectrostatic = 0;
753	<	int useEAM = 0;
754	<	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;
751	>	vector<int> foundTypes;
752	>	set<AtomType*>::iterator i;
753	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
754	>	foundTypes.push_back( (*i)->getIdent() );
755
756	<	std::string myMethod;
756	>	// count_local holds the number of found types on this processor
757	>	int count_local = foundTypes.size();
758
759	<	// set the useRF logical
760	<	useRF = 0;
761	<	useSF = 0;
765	<	useSP = 0;
759	>	int nproc;
760	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
761	>	// int nproc = MPI::COMM_WORLD.Get_size();
762
763	+	// we need arrays to hold the counts and displacement vectors for
764	+	// all processors
765	+	vector<int> counts(nproc, 0);
766	+	vector<int> disps(nproc, 0);
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	<	}
768	>	// fill the counts array
769	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
770	>	1, MPI_INT, MPI_COMM_WORLD);
771	>	// MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
772	>	//                           1, MPI::INT);
773	>
774	>	// use the processor counts to compute the displacement array
775	>	disps[0] = 0;
776	>	int totalCount = counts[0];
777	>	for (int iproc = 1; iproc < nproc; iproc++) {
778	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
779	>	totalCount += counts[iproc];
780		}
781	+
782	+	// we need a (possibly redundant) set of all found types:
783	+	vector<int> ftGlobal(totalCount);
784
785	<	if (simParams_->haveAccumulateBoxDipole())
786	<	if (simParams_->getAccumulateBoxDipole())
787	<	useBoxDipole = 1;
785	>	// now spray out the foundTypes to all the other processors:
786	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
787	>	&ftGlobal[0], &counts[0], &disps[0],
788	>	MPI_INT, MPI_COMM_WORLD);
789	>	// MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
790	>	//                            &ftGlobal[0], &counts[0], &disps[0],
791	>	//                            MPI::INT);
792
793	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
793	>	vector<int>::iterator j;
794
795	<	//loop over all of the atom types
796	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
797	<	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	<	}
795	>	// foundIdents is a stl set, so inserting an already found ident
796	>	// will have no effect.
797	>	set<int> foundIdents;
798
799	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
800	<	useDirectionalAtom = 1;
801	<	}
799	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
800	>	foundIdents.insert((*j));
801	>
802	>	// now iterate over the foundIdents and get the actual atom types
803	>	// that correspond to these:
804	>	set<int>::iterator it;
805	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
806	>	atomTypes.insert( forceField_->getAtomType((*it)) );
807	>
808	>	#endif
809
810	<	if (useCharge || useDipole) {
811	<	useElectrostatics = 1;
807	<	}
810	>	return atomTypes;
811	>	}
812
809	–	#ifdef IS_MPI
810	–	int temp;
813
814	<	temp = usePBC;
815	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	int getGlobalCountOfType(AtomType* atype) {
815	>	/*
816	>	set<AtomType*> atypes = getSimulatedAtomTypes();
817	>	map<AtomType*, int> counts_;
818
819	<	temp = useDirectionalAtom;
820	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
820	>	for(atom = mol->beginAtom(ai); atom != NULL;
821	>	atom = mol->nextAtom(ai)) {
822	>	atom->getAtomType();
823	>	}
824	>	}
825	>	*/
826	>	return 0;
827	>	}
828
829	<	temp = useLennardJones;
830	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
829	>	void SimInfo::setupSimVariables() {
830	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
831	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
832	>	// parameter is true
833	>	calcBoxDipole_ = false;
834	>	if ( simParams_->haveAccumulateBoxDipole() )
835	>	if ( simParams_->getAccumulateBoxDipole() ) {
836	>	calcBoxDipole_ = true;
837	>	}
838	>
839	>	set<AtomType*>::iterator i;
840	>	set<AtomType*> atomTypes;
841	>	atomTypes = getSimulatedAtomTypes();
842	>	bool usesElectrostatic = false;
843	>	bool usesMetallic = false;
844	>	bool usesDirectional = false;
845	>	bool usesFluctuatingCharges =  false;
846	>	//loop over all of the atom types
847	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
848	>	usesElectrostatic |= (*i)->isElectrostatic();
849	>	usesMetallic |= (*i)->isMetal();
850	>	usesDirectional |= (*i)->isDirectional();
851	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
852	>	}
853
854	<	temp = useElectrostatics;
855	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	>	#ifdef IS_MPI
855	>	int temp;
856
857	<	temp = useCharge;
858	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	>	temp = usesDirectional;
858	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
859	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
860
861	<	temp = useDipole;
862	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
829	<
830	<	temp = useSticky;
831	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832	<
833	<	temp = useStickyPower;
834	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
861	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
862	>	//                           MPI::LOR);
863
864	<	temp = useGayBerne;
865	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	temp = usesMetallic;
865	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
866	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
867
868	<	temp = useEAM;
869	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841	<
842	<	temp = useSC;
843	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
868	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
869	>	//                           MPI::LOR);
870
871	<	temp = useShape;
872	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
871	>	temp = usesElectrostatic;
872	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
873	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
874
875	<	temp = useFLARB;
876	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
876	>	//                           MPI::LOR);
877
878	<	temp = useRF;
879	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
878	>	temp = usesFluctuatingCharges;
879	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
880	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
881
882	<	temp = useSF;
883	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
882	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
883	>	//                           MPI::LOR);
884
885	<	temp = useSP;
858	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885	>	#else
886
887	<	temp = useBoxDipole;
888	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
887	>	usesDirectionalAtoms_ = usesDirectional;
888	>	usesMetallicAtoms_ = usesMetallic;
889	>	usesElectrostaticAtoms_ = usesElectrostatic;
890	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
891
863	–	temp = useAtomicVirial_;
864	–	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865	–
892		#endif
893	<
894	<	fInfo_.SIM_uses_PBC = usePBC;
895	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
896	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
871	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
872	<	fInfo_.SIM_uses_Charges = useCharge;
873	<	fInfo_.SIM_uses_Dipoles = useDipole;
874	<	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_;
893	>
894	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
895	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
896	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
897		}
898
899	<	void SimInfo::setupFortranSim() {
900	<	int isError;
901	<	int nExclude, nOneTwo, nOneThree, nOneFour;
902	<	std::vector<int> fortranGlobalGroupMembership;
899	>
900	>	vector<int> SimInfo::getGlobalAtomIndices() {
901	>	SimInfo::MoleculeIterator mi;
902	>	Molecule* mol;
903	>	Molecule::AtomIterator ai;
904	>	Atom* atom;
905	>
906	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
907
908	<	isError = 0;
908	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
909	>
910	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
911	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
912	>	}
913	>	}
914	>	return GlobalAtomIndices;
915	>	}
916
917	<	//globalGroupMembership_ is filled by SimCreator
918	<	for (int i = 0; i < nGlobalAtoms_; i++) {
919	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
917	>
918	>	vector<int> SimInfo::getGlobalGroupIndices() {
919	>	SimInfo::MoleculeIterator mi;
920	>	Molecule* mol;
921	>	Molecule::CutoffGroupIterator ci;
922	>	CutoffGroup* cg;
923	>
924	>	vector<int> GlobalGroupIndices;
925	>
926	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
927	>
928	>	//local index of cutoff group is trivial, it only depends on the
929	>	//order of travesing
930	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
931	>	cg = mol->nextCutoffGroup(ci)) {
932	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
933	>	}
934		}
935	+	return GlobalGroupIndices;
936	+	}
937
938	+
939	+	void SimInfo::prepareTopology() {
940	+
941		//calculate mass ratio of cutoff group
901	–	std::vector<RealType> mfact;
942		SimInfo::MoleculeIterator mi;
943		Molecule* mol;
944		Molecule::CutoffGroupIterator ci;
#	Line 907 | Line 947 | namespace oopse {
947		Atom* atom;
948		RealType totalMass;
949
950	<	//to avoid memory reallocation, reserve enough space for mfact
951	<	mfact.reserve(getNCutoffGroups());
950	>	/**
951	>	* The mass factor is the relative mass of an atom to the total
952	>	* mass of the cutoff group it belongs to.  By default, all atoms
953	>	* are their own cutoff groups, and therefore have mass factors of
954	>	* 1.  We need some special handling for massless atoms, which
955	>	* will be treated as carrying the entire mass of the cutoff
956	>	* group.
957	>	*/
958	>	massFactors_.clear();
959	>	massFactors_.resize(getNAtoms(), 1.0);
960
961		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
962	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
962	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
963	>	cg = mol->nextCutoffGroup(ci)) {
964
965		totalMass = cg->getMass();
966		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
967		// Check for massless groups - set mfact to 1 if true
968	<	if (totalMass != 0)
969	<	mfact.push_back(atom->getMass()/totalMass);
968	>	if (totalMass != 0)
969	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
970		else
971	<	mfact.push_back( 1.0 );
971	>	massFactors_[atom->getLocalIndex()] = 1.0;
972		}
973		}
974		}
975
976	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
928	<	std::vector<int> identArray;
976	>	// Build the identArray_ and regions_
977
978	<	//to avoid memory reallocation, reserve enough space identArray
979	<	identArray.reserve(getNAtoms());
980	<
981	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
978	>	identArray_.clear();
979	>	identArray_.reserve(getNAtoms());
980	>	regions_.clear();
981	>	regions_.reserve(getNAtoms());
982	>
983	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
984	>	int reg = mol->getRegion();
985		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
986	<	identArray.push_back(atom->getIdent());
986	>	identArray_.push_back(atom->getIdent());
987	>	regions_.push_back(reg);
988		}
989		}
990	+
991	+	topologyDone_ = true;
992	+	}
993
994	<	//fill molMembershipArray
995	<	//molMembershipArray is filled by SimCreator
996	<	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
994	>	void SimInfo::addProperty(GenericData* genData) {
995	>	properties_.addProperty(genData);
996	>	}
997
998	<	nExclude = excludedInteractions_.getSize();
999	<	nOneTwo = oneTwoInteractions_.getSize();
1000	<	nOneThree = oneThreeInteractions_.getSize();
951	<	nOneFour = oneFourInteractions_.getSize();
998	>	void SimInfo::removeProperty(const string& propName) {
999	>	properties_.removeProperty(propName);
1000	>	}
1001
1002	<	std::cerr << "exculdes:\n";
1003	<	std::cerr << excludedInteractions_;
1004	<	std::cerr << "\noneTwo:\n";
956	<	std::cerr << oneTwoInteractions_;
957	<	std::cerr << "\noneThree:\n";
958	<	std::cerr << oneThreeInteractions_;
959	<	std::cerr << "\noneFour:\n";
960	<	std::cerr << oneFourInteractions_;
1002	>	void SimInfo::clearProperties() {
1003	>	properties_.clearProperties();
1004	>	}
1005
1006	<	int* excludeList = excludedInteractions_.getPairList();
1007	<	int* oneTwoList = oneTwoInteractions_.getPairList();
1008	<	int* oneThreeList = oneThreeInteractions_.getPairList();
965	<	int* oneFourList = oneFourInteractions_.getPairList();
966	<
967	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
968	<	&nExclude, excludeList,
969	<	&nOneTwo, oneTwoList,
970	<	&nOneThree, oneThreeList,
971	<	&nOneFour, oneFourList,
972	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
973	<	&fortranGlobalGroupMembership[0], &isError);
974	<
975	<	if( isError ){
1006	>	vector<string> SimInfo::getPropertyNames() {
1007	>	return properties_.getPropertyNames();
1008	>	}
1009
1010	<	sprintf( painCave.errMsg,
1011	<	"There was an error setting the simulation information in fortran.\n" );
1012	<	painCave.isFatal = 1;
980	<	painCave.severity = OOPSE_ERROR;
981	<	simError();
982	<	}
983	<
984	<
985	<	sprintf( checkPointMsg,
986	<	"succesfully sent the simulation information to fortran.\n");
987	<
988	<	errorCheckPoint();
989	<
990	<	// Setup number of neighbors in neighbor list if present
991	<	if (simParams_->haveNeighborListNeighbors()) {
992	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
993	<	setNeighbors(&nlistNeighbors);
994	<	}
995	<
1010	>	vector<GenericData*> SimInfo::getProperties() {
1011	>	return properties_.getProperties();
1012	>	}
1013
1014	+	GenericData* SimInfo::getPropertyByName(const string& propName) {
1015	+	return properties_.getPropertyByName(propName);
1016		}
1017
1018	+	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1019	+	if (sman_ == sman) {
1020	+	return;
1021	+	}
1022	+	delete sman_;
1023	+	sman_ = sman;
1024
1000	–	void SimInfo::setupFortranParallel() {
1001	–	#ifdef IS_MPI
1002	–	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1003	–	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1004	–	std::vector<int> localToGlobalCutoffGroupIndex;
1025		SimInfo::MoleculeIterator mi;
1026		Molecule::AtomIterator ai;
1027	<	Molecule::CutoffGroupIterator ci;
1027	>	Molecule::RigidBodyIterator rbIter;
1028	>	Molecule::CutoffGroupIterator cgIter;
1029	>	Molecule::BondIterator bondIter;
1030	>	Molecule::BendIterator bendIter;
1031	>	Molecule::TorsionIterator torsionIter;
1032	>	Molecule::InversionIterator inversionIter;
1033	>
1034		Molecule* mol;
1035		Atom* atom;
1036	+	RigidBody* rb;
1037		CutoffGroup* cg;
1038	<	mpiSimData parallelData;
1039	<	int isError;
1038	>	Bond* bond;
1039	>	Bend* bend;
1040	>	Torsion* torsion;
1041	>	Inversion* inversion;
1042
1043	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1015	<
1016	<	//local index(index in DataStorge) of atom is important
1017	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1018	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1019	<	}
1020	<
1021	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1022	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1023	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1024	<	}
1043	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1044
1045	<	}
1046	<
1047	<	//fill up mpiSimData struct
1048	<	parallelData.nMolGlobal = getNGlobalMolecules();
1049	<	parallelData.nMolLocal = getNMolecules();
1050	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1051	<	parallelData.nAtomsLocal = getNAtoms();
1033	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1034	<	parallelData.nGroupsLocal = getNCutoffGroups();
1035	<	parallelData.myNode = worldRank;
1036	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1037	<
1038	<	//pass mpiSimData struct and index arrays to fortran
1039	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1040	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1041	<	&localToGlobalCutoffGroupIndex[0], &isError);
1042	<
1043	<	if (isError) {
1044	<	sprintf(painCave.errMsg,
1045	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1046	<	painCave.isFatal = 1;
1047	<	simError();
1048	<	}
1049	<
1050	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1051	<	errorCheckPoint();
1052	<
1053	<	#endif
1054	<	}
1055	<
1056	<	void SimInfo::setupCutoff() {
1057	<
1058	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1059	<
1060	<	// Check the cutoff policy
1061	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1062	<
1063	<	// Set LJ shifting bools to false
1064	<	ljsp_ = false;
1065	<	ljsf_ = false;
1066	<
1067	<	std::string myPolicy;
1068	<	if (forceFieldOptions_.haveCutoffPolicy()){
1069	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1070	<	}else if (simParams_->haveCutoffPolicy()) {
1071	<	myPolicy = simParams_->getCutoffPolicy();
1072	<	}
1073	<
1074	<	if (!myPolicy.empty()){
1075	<	toUpper(myPolicy);
1076	<	if (myPolicy == "MIX") {
1077	<	cp = MIX_CUTOFF_POLICY;
1078	<	} else {
1079	<	if (myPolicy == "MAX") {
1080	<	cp = MAX_CUTOFF_POLICY;
1081	<	} else {
1082	<	if (myPolicy == "TRADITIONAL") {
1083	<	cp = TRADITIONAL_CUTOFF_POLICY;
1084	<	} else {
1085	<	// throw error
1086	<	sprintf( painCave.errMsg,
1087	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1088	<	painCave.isFatal = 1;
1089	<	simError();
1090	<	}
1091	<	}
1045	>	for (atom = mol->beginAtom(ai); atom != NULL;
1046	>	atom = mol->nextAtom(ai)) {
1047	>	atom->setSnapshotManager(sman_);
1048	>	}
1049	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1050	>	rb = mol->nextRigidBody(rbIter)) {
1051	>	rb->setSnapshotManager(sman_);
1052		}
1053	<	}
1054	<	notifyFortranCutoffPolicy(&cp);
1055	<
1096	<	// Check the Skin Thickness for neighborlists
1097	<	RealType skin;
1098	<	if (simParams_->haveSkinThickness()) {
1099	<	skin = simParams_->getSkinThickness();
1100	<	notifyFortranSkinThickness(&skin);
1101	<	}
1102	<
1103	<	// Check if the cutoff was set explicitly:
1104	<	if (simParams_->haveCutoffRadius()) {
1105	<	rcut_ = simParams_->getCutoffRadius();
1106	<	if (simParams_->haveSwitchingRadius()) {
1107	<	rsw_  = simParams_->getSwitchingRadius();
1108	<	} else {
1109	<	if (fInfo_.SIM_uses_Charges |
1110	<	fInfo_.SIM_uses_Dipoles |
1111	<	fInfo_.SIM_uses_RF) {
1112	<
1113	<	rsw_ = 0.85 * rcut_;
1114	<	sprintf(painCave.errMsg,
1115	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1117	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118	<	painCave.isFatal = 0;
1119	<	simError();
1120	<	} else {
1121	<	rsw_ = rcut_;
1122	<	sprintf(painCave.errMsg,
1123	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1124	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1125	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1126	<	painCave.isFatal = 0;
1127	<	simError();
1128	<	}
1053	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1054	>	cg = mol->nextCutoffGroup(cgIter)) {
1055	>	cg->setSnapshotManager(sman_);
1056		}
1057	<
1058	<	if (simParams_->haveElectrostaticSummationMethod()) {
1059	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1133	<	toUpper(myMethod);
1134	<
1135	<	if (myMethod == "SHIFTED_POTENTIAL") {
1136	<	ljsp_ = true;
1137	<	} else if (myMethod == "SHIFTED_FORCE") {
1138	<	ljsf_ = true;
1139	<	}
1057	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1058	>	bond = mol->nextBond(bondIter)) {
1059	>	bond->setSnapshotManager(sman_);
1060		}
1061	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1062	<
1063	<	} else {
1144	<
1145	<	// For electrostatic atoms, we'll assume a large safe value:
1146	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1147	<	sprintf(painCave.errMsg,
1148	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1149	<	"\tOOPSE will use a default value of 15.0 angstroms"
1150	<	"\tfor the cutoffRadius.\n");
1151	<	painCave.isFatal = 0;
1152	<	simError();
1153	<	rcut_ = 15.0;
1154	<
1155	<	if (simParams_->haveElectrostaticSummationMethod()) {
1156	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1157	<	toUpper(myMethod);
1158	<
1159	<	// For the time being, we're tethering the LJ shifted behavior to the
1160	<	// electrostaticSummationMethod keyword options
1161	<	if (myMethod == "SHIFTED_POTENTIAL") {
1162	<	ljsp_ = true;
1163	<	} else if (myMethod == "SHIFTED_FORCE") {
1164	<	ljsf_ = true;
1165	<	}
1166	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1167	<	if (simParams_->haveSwitchingRadius()){
1168	<	sprintf(painCave.errMsg,
1169	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1170	<	"\teven though the electrostaticSummationMethod was\n"
1171	<	"\tset to %s\n", myMethod.c_str());
1172	<	painCave.isFatal = 1;
1173	<	simError();
1174	<	}
1175	<	}
1176	<	}
1177	<
1178	<	if (simParams_->haveSwitchingRadius()){
1179	<	rsw_ = simParams_->getSwitchingRadius();
1180	<	} else {
1181	<	sprintf(painCave.errMsg,
1182	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1183	<	"\tOOPSE will use a default value of\n"
1184	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1185	<	painCave.isFatal = 0;
1186	<	simError();
1187	<	rsw_ = 0.85 * rcut_;
1188	<	}
1189	<
1190	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1191	<
1192	<	} else {
1193	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1194	<	// We'll punt and let fortran figure out the cutoffs later.
1195	<
1196	<	notifyFortranYouAreOnYourOwn();
1197	<
1061	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1062	>	bend = mol->nextBend(bendIter)) {
1063	>	bend->setSnapshotManager(sman_);
1064		}
1065	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1066	+	torsion = mol->nextTorsion(torsionIter)) {
1067	+	torsion->setSnapshotManager(sman_);
1068	+	}
1069	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1070	+	inversion = mol->nextInversion(inversionIter)) {
1071	+	inversion->setSnapshotManager(sman_);
1072	+	}
1073		}
1074		}
1075
1202	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1203	–
1204	–	int errorOut;
1205	–	int esm =  NONE;
1206	–	int sm = UNDAMPED;
1207	–	RealType alphaVal;
1208	–	RealType dielectric;
1209	–
1210	–	errorOut = isError;
1076
1077	<	if (simParams_->haveElectrostaticSummationMethod()) {
1213	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1214	<	toUpper(myMethod);
1215	<	if (myMethod == "NONE") {
1216	<	esm = NONE;
1217	<	} else {
1218	<	if (myMethod == "SWITCHING_FUNCTION") {
1219	<	esm = SWITCHING_FUNCTION;
1220	<	} else {
1221	<	if (myMethod == "SHIFTED_POTENTIAL") {
1222	<	esm = SHIFTED_POTENTIAL;
1223	<	} else {
1224	<	if (myMethod == "SHIFTED_FORCE") {
1225	<	esm = SHIFTED_FORCE;
1226	<	} else {
1227	<	if (myMethod == "REACTION_FIELD") {
1228	<	esm = REACTION_FIELD;
1229	<	dielectric = simParams_->getDielectric();
1230	<	if (!simParams_->haveDielectric()) {
1231	<	// throw warning
1232	<	sprintf( painCave.errMsg,
1233	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1234	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1235	<	painCave.isFatal = 0;
1236	<	simError();
1237	<	}
1238	<	} else {
1239	<	// throw error
1240	<	sprintf( painCave.errMsg,
1241	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1242	<	"\t(Input file specified %s .)\n"
1243	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1244	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1245	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1246	<	painCave.isFatal = 1;
1247	<	simError();
1248	<	}
1249	<	}
1250	<	}
1251	<	}
1252	<	}
1253	<	}
1254	<
1255	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1256	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1257	<	toUpper(myScreen);
1258	<	if (myScreen == "UNDAMPED") {
1259	<	sm = UNDAMPED;
1260	<	} else {
1261	<	if (myScreen == "DAMPED") {
1262	<	sm = DAMPED;
1263	<	if (!simParams_->haveDampingAlpha()) {
1264	<	// first set a cutoff dependent alpha value
1265	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1266	<	alphaVal = 0.5125 - rcut_* 0.025;
1267	<	// for values rcut > 20.5, alpha is zero
1268	<	if (alphaVal < 0) alphaVal = 0;
1077	>	ostream& operator <<(ostream& o, SimInfo& info) {
1078
1270	–	// throw warning
1271	–	sprintf( painCave.errMsg,
1272	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1273	–	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1274	–	painCave.isFatal = 0;
1275	–	simError();
1276	–	} else {
1277	–	alphaVal = simParams_->getDampingAlpha();
1278	–	}
1279	–
1280	–	} else {
1281	–	// throw error
1282	–	sprintf( painCave.errMsg,
1283	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1284	–	"\t(Input file specified %s .)\n"
1285	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1286	–	"or \"damped\".\n", myScreen.c_str() );
1287	–	painCave.isFatal = 1;
1288	–	simError();
1289	–	}
1290	–	}
1291	–	}
1292	–
1293	–	// let's pass some summation method variables to fortran
1294	–	setElectrostaticSummationMethod( &esm );
1295	–	setFortranElectrostaticMethod( &esm );
1296	–	setScreeningMethod( &sm );
1297	–	setDampingAlpha( &alphaVal );
1298	–	setReactionFieldDielectric( &dielectric );
1299	–	initFortranFF( &errorOut );
1300	–	}
1301	–
1302	–	void SimInfo::setupSwitchingFunction() {
1303	–	int ft = CUBIC;
1304	–
1305	–	if (simParams_->haveSwitchingFunctionType()) {
1306	–	std::string funcType = simParams_->getSwitchingFunctionType();
1307	–	toUpper(funcType);
1308	–	if (funcType == "CUBIC") {
1309	–	ft = CUBIC;
1310	–	} else {
1311	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1312	–	ft = FIFTH_ORDER_POLY;
1313	–	} else {
1314	–	// throw error
1315	–	sprintf( painCave.errMsg,
1316	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1317	–	painCave.isFatal = 1;
1318	–	simError();
1319	–	}
1320	–	}
1321	–	}
1322	–
1323	–	// send switching function notification to switcheroo
1324	–	setFunctionType(&ft);
1325	–
1326	–	}
1327	–
1328	–	void SimInfo::setupAccumulateBoxDipole() {
1329	–
1330	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1331	–	if ( simParams_->haveAccumulateBoxDipole() )
1332	–	if ( simParams_->getAccumulateBoxDipole() ) {
1333	–	setAccumulateBoxDipole();
1334	–	calcBoxDipole_ = true;
1335	–	}
1336	–
1337	–	}
1338	–
1339	–	void SimInfo::addProperty(GenericData* genData) {
1340	–	properties_.addProperty(genData);
1341	–	}
1342	–
1343	–	void SimInfo::removeProperty(const std::string& propName) {
1344	–	properties_.removeProperty(propName);
1345	–	}
1346	–
1347	–	void SimInfo::clearProperties() {
1348	–	properties_.clearProperties();
1349	–	}
1350	–
1351	–	std::vector<std::string> SimInfo::getPropertyNames() {
1352	–	return properties_.getPropertyNames();
1353	–	}
1354	–
1355	–	std::vector<GenericData*> SimInfo::getProperties() {
1356	–	return properties_.getProperties();
1357	–	}
1358	–
1359	–	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1360	–	return properties_.getPropertyByName(propName);
1361	–	}
1362	–
1363	–	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1364	–	if (sman_ == sman) {
1365	–	return;
1366	–	}
1367	–	delete sman_;
1368	–	sman_ = sman;
1369	–
1370	–	Molecule* mol;
1371	–	RigidBody* rb;
1372	–	Atom* atom;
1373	–	SimInfo::MoleculeIterator mi;
1374	–	Molecule::RigidBodyIterator rbIter;
1375	–	Molecule::AtomIterator atomIter;;
1376	–
1377	–	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1378	–
1379	–	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1380	–	atom->setSnapshotManager(sman_);
1381	–	}
1382	–
1383	–	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1384	–	rb->setSnapshotManager(sman_);
1385	–	}
1386	–	}
1387	–
1388	–	}
1389	–
1390	–	Vector3d SimInfo::getComVel(){
1391	–	SimInfo::MoleculeIterator i;
1392	–	Molecule* mol;
1393	–
1394	–	Vector3d comVel(0.0);
1395	–	RealType totalMass = 0.0;
1396	–
1397	–
1398	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1399	–	RealType mass = mol->getMass();
1400	–	totalMass += mass;
1401	–	comVel += mass * mol->getComVel();
1402	–	}
1403	–
1404	–	#ifdef IS_MPI
1405	–	RealType tmpMass = totalMass;
1406	–	Vector3d tmpComVel(comVel);
1407	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1408	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1409	–	#endif
1410	–
1411	–	comVel /= totalMass;
1412	–
1413	–	return comVel;
1414	–	}
1415	–
1416	–	Vector3d SimInfo::getCom(){
1417	–	SimInfo::MoleculeIterator i;
1418	–	Molecule* mol;
1419	–
1420	–	Vector3d com(0.0);
1421	–	RealType totalMass = 0.0;
1422	–
1423	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1424	–	RealType mass = mol->getMass();
1425	–	totalMass += mass;
1426	–	com += mass * mol->getCom();
1427	–	}
1428	–
1429	–	#ifdef IS_MPI
1430	–	RealType tmpMass = totalMass;
1431	–	Vector3d tmpCom(com);
1432	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1433	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1434	–	#endif
1435	–
1436	–	com /= totalMass;
1437	–
1438	–	return com;
1439	–
1440	–	}
1441	–
1442	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1443	–
1079		return o;
1080		}
1081
1082	<
1448	<	/*
1449	<	Returns center of mass and center of mass velocity in one function call.
1450	<	*/
1451	<
1452	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1453	<	SimInfo::MoleculeIterator i;
1454	<	Molecule* mol;
1455	<
1456	<
1457	<	RealType totalMass = 0.0;
1458	<
1459	<
1460	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1461	<	RealType mass = mol->getMass();
1462	<	totalMass += mass;
1463	<	com += mass * mol->getCom();
1464	<	comVel += mass * mol->getComVel();
1465	<	}
1466	<
1467	<	#ifdef IS_MPI
1468	<	RealType tmpMass = totalMass;
1469	<	Vector3d tmpCom(com);
1470	<	Vector3d tmpComVel(comVel);
1471	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1472	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1473	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1474	<	#endif
1475	<
1476	<	com /= totalMass;
1477	<	comVel /= totalMass;
1478	<	}
1479	<
1480	<	/*
1481	<	Return intertia tensor for entire system and angular momentum Vector.
1482	<
1483	<
1484	<	[  Ixx -Ixy  -Ixz ]
1485	<	J =| -Iyx  Iyy  -Iyz |
1486	<	[ -Izx -Iyz   Izz ]
1487	<	*/
1488	<
1489	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1490	<
1491	<
1492	<	RealType xx = 0.0;
1493	<	RealType yy = 0.0;
1494	<	RealType zz = 0.0;
1495	<	RealType xy = 0.0;
1496	<	RealType xz = 0.0;
1497	<	RealType yz = 0.0;
1498	<	Vector3d com(0.0);
1499	<	Vector3d comVel(0.0);
1500	<
1501	<	getComAll(com, comVel);
1502	<
1503	<	SimInfo::MoleculeIterator i;
1504	<	Molecule* mol;
1505	<
1506	<	Vector3d thisq(0.0);
1507	<	Vector3d thisv(0.0);
1508	<
1509	<	RealType thisMass = 0.0;
1510	<
1511	<
1512	<
1513	<
1514	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1515	<
1516	<	thisq = mol->getCom()-com;
1517	<	thisv = mol->getComVel()-comVel;
1518	<	thisMass = mol->getMass();
1519	<	// Compute moment of intertia coefficients.
1520	<	xx += thisq[0]*thisq[0]*thisMass;
1521	<	yy += thisq[1]*thisq[1]*thisMass;
1522	<	zz += thisq[2]*thisq[2]*thisMass;
1523	<
1524	<	// compute products of intertia
1525	<	xy += thisq[0]*thisq[1]*thisMass;
1526	<	xz += thisq[0]*thisq[2]*thisMass;
1527	<	yz += thisq[1]*thisq[2]*thisMass;
1528	<
1529	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1530	<
1531	<	}
1532	<
1533	<
1534	<	inertiaTensor(0,0) = yy + zz;
1535	<	inertiaTensor(0,1) = -xy;
1536	<	inertiaTensor(0,2) = -xz;
1537	<	inertiaTensor(1,0) = -xy;
1538	<	inertiaTensor(1,1) = xx + zz;
1539	<	inertiaTensor(1,2) = -yz;
1540	<	inertiaTensor(2,0) = -xz;
1541	<	inertiaTensor(2,1) = -yz;
1542	<	inertiaTensor(2,2) = xx + yy;
1543	<
1544	<	#ifdef IS_MPI
1545	<	Mat3x3d tmpI(inertiaTensor);
1546	<	Vector3d tmpAngMom;
1547	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1548	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1549	<	#endif
1550	<
1551	<	return;
1552	<	}
1553	<
1554	<	//Returns the angular momentum of the system
1555	<	Vector3d SimInfo::getAngularMomentum(){
1556	<
1557	<	Vector3d com(0.0);
1558	<	Vector3d comVel(0.0);
1559	<	Vector3d angularMomentum(0.0);
1560	<
1561	<	getComAll(com,comVel);
1562	<
1563	<	SimInfo::MoleculeIterator i;
1564	<	Molecule* mol;
1565	<
1566	<	Vector3d thisr(0.0);
1567	<	Vector3d thisp(0.0);
1568	<
1569	<	RealType thisMass;
1570	<
1571	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1572	<	thisMass = mol->getMass();
1573	<	thisr = mol->getCom()-com;
1574	<	thisp = (mol->getComVel()-comVel)*thisMass;
1575	<
1576	<	angularMomentum += cross( thisr, thisp );
1577	<
1578	<	}
1579	<
1580	<	#ifdef IS_MPI
1581	<	Vector3d tmpAngMom;
1582	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1583	<	#endif
1584	<
1585	<	return angularMomentum;
1586	<	}
1587	<
1082	>
1083		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1084	<	return IOIndexToIntegrableObject.at(index);
1084	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1085	>	sprintf(painCave.errMsg,
1086	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1087	>	"\tindex exceeds number of known objects!\n");
1088	>	painCave.isFatal = 1;
1089	>	simError();
1090	>	return NULL;
1091	>	} else
1092	>	return IOIndexToIntegrableObject.at(index);
1093		}
1094
1095	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1095	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1096		IOIndexToIntegrableObject= v;
1097		}
1098
1099	<	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1100	<	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1101	<	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1102	<	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1103	<	*/
1104	<	void SimInfo::getGyrationalVolume(RealType &volume){
1105	<	Mat3x3d intTensor;
1106	<	RealType det;
1107	<	Vector3d dummyAngMom;
1108	<	RealType sysconstants;
1109	<	RealType geomCnst;
1607	<
1608	<	geomCnst = 3.0/2.0;
1609	<	/* Get the inertial tensor and angular momentum for free*/
1610	<	getInertiaTensor(intTensor,dummyAngMom);
1611	<
1612	<	det = intTensor.determinant();
1613	<	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1614	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1615	<	return;
1099	>	int SimInfo::getNGlobalConstraints() {
1100	>	int nGlobalConstraints;
1101	>	#ifdef IS_MPI
1102	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1103	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1104	>	// MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1105	>	//                           MPI::INT, MPI::SUM);
1106	>	#else
1107	>	nGlobalConstraints =  nConstraints_;
1108	>	#endif
1109	>	return nGlobalConstraints;
1110		}
1111
1112	<	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1619	<	Mat3x3d intTensor;
1620	<	Vector3d dummyAngMom;
1621	<	RealType sysconstants;
1622	<	RealType geomCnst;
1112	>	}//end namespace OpenMD
1113
1624	–	geomCnst = 3.0/2.0;
1625	–	/* Get the inertial tensor and angular momentum for free*/
1626	–	getInertiaTensor(intTensor,dummyAngMom);
1627	–
1628	–	detI = intTensor.determinant();
1629	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1630	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1631	–	return;
1632	–	}
1633	–	/*
1634	–	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1635	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1636	–	sdByGlobalIndex_ = v;
1637	–	}
1638	–
1639	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1640	–	//assert(index < nAtoms_ + nRigidBodies_);
1641	–	return sdByGlobalIndex_.at(index);
1642	–	}
1643	–	*/
1644	–	}//end namespace oopse
1645	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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