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root/OpenMD/trunk/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 701 by chrisfen, Wed Oct 26 23:32:25 2005 UTC vs.
Revision 1930 by gezelter, Mon Aug 19 13:51:04 2013 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 48 | Line 49
49
50		#include <algorithm>
51		#include <set>
52	+	#include <map>
53
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/fCutoffPolicy.h"
56	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57	<	#include "UseTheForce/doForces_interface.h"
58	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
59	<	#include "UseTheForce/notifyCutoffs_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61	<
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
67	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<
70	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	<	ForceField* ff, Globals* simParams) :
72	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
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), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
79	<
81	<
82	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
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;
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80
81	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
82	<	molStamp = i->first;
83	<	nMolWithSameStamp = i->second;
84	<
85	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
86	<
87	<	//calculate atoms in molecules
88	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
89	<
90	<
91	<	//calculate atoms in cutoff groups
92	<	int nAtomsInGroups = 0;
93	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
94	<
95	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
96	<	cgStamp = molStamp->getCutoffGroup(j);
97	<	nAtomsInGroups += cgStamp->getNMembers();
98	<	}
109	<
110	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111	<
112	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113	<
114	<	//calculate atoms in rigid bodies
115	<	int nAtomsInRigidBodies = 0;
116	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	<
118	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	<	rbStamp = molStamp->getRigidBody(j);
120	<	nAtomsInRigidBodies += rbStamp->getNMembers();
121	<	}
122	<
123	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	<
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin();
92	>	i !=components.end(); ++i) {
93	>	molStamp = (*i)->getMoleculeStamp();
94	>	if ( (*i)->haveRegion() ) {
95	>	molStamp->setRegion( (*i)->getRegion() );
96	>	} else {
97	>	// set the region to a disallowed value:
98	>	molStamp->setRegion( -1 );
99		}
100
101	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
102	<	//group therefore the total number of cutoff groups in the system is
103	<	//equal to the total number of atoms minus number of atoms belong to
104	<	//cutoff group defined in meta-data file plus the number of cutoff
105	<	//groups defined in meta-data file
106	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
107	<
108	<	//every free atom (atom does not belong to rigid bodies) is an
109	<	//integrable object therefore the total number of integrable objects
110	<	//in the system is equal to the total number of atoms minus number of
111	<	//atoms belong to rigid body defined in meta-data file plus the number
112	<	//of rigid bodies defined in meta-data file
113	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
114	<	+ nGlobalRigidBodies_;
115	<
116	<	nGlobalMols_ = molStampIds_.size();
117	<
118	<	#ifdef IS_MPI
119	<	molToProcMap_.resize(nGlobalMols_);
120	<	#endif
121	<
101	>	nMolWithSameStamp = (*i)->getNMol();
102	>
103	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
104	>
105	>	//calculate atoms in molecules
106	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	>
108	>	//calculate atoms in cutoff groups
109	>	int nAtomsInGroups = 0;
110	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
111	>
112	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
113	>	cgStamp = molStamp->getCutoffGroupStamp(j);
114	>	nAtomsInGroups += cgStamp->getNMembers();
115	>	}
116	>
117	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
118	>
119	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
120	>
121	>	//calculate atoms in rigid bodies
122	>	int nAtomsInRigidBodies = 0;
123	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
124	>
125	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
126	>	rbStamp = molStamp->getRigidBodyStamp(j);
127	>	nAtomsInRigidBodies += rbStamp->getNMembers();
128	>	}
129	>
130	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
131	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
132	>
133		}
134	+
135	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
136	+	//group therefore the total number of cutoff groups in the system is
137	+	//equal to the total number of atoms minus number of atoms belong to
138	+	//cutoff group defined in meta-data file plus the number of cutoff
139	+	//groups defined in meta-data file
140
141	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
142	+
143	+	//every free atom (atom does not belong to rigid bodies) is an
144	+	//integrable object therefore the total number of integrable objects
145	+	//in the system is equal to the total number of atoms minus number of
146	+	//atoms belong to rigid body defined in meta-data file plus the number
147	+	//of rigid bodies defined in meta-data file
148	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	+	+ nGlobalRigidBodies_;
150	+
151	+	nGlobalMols_ = molStampIds_.size();
152	+	molToProcMap_.resize(nGlobalMols_);
153	+	}
154	+
155		SimInfo::~SimInfo() {
156	<	std::map<int, Molecule*>::iterator i;
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158		delete i->second;
159		}
160		molecules_.clear();
161
158	–	delete stamps_;
162		delete sman_;
163		delete simParams_;
164		delete forceField_;
165		}
166
164	–	int SimInfo::getNGlobalConstraints() {
165	–	int nGlobalConstraints;
166	–	#ifdef IS_MPI
167	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
168	–	MPI_COMM_WORLD);
169	–	#else
170	–	nGlobalConstraints =  nConstraints_;
171	–	#endif
172	–	return nGlobalConstraints;
173	–	}
167
168		bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176		nAtoms_ += mol->getNAtoms();
177		nBonds_ += mol->getNBonds();
178		nBends_ += mol->getNBends();
179		nTorsions_ += mol->getNTorsions();
180	+	nInversions_ += mol->getNInversions();
181		nRigidBodies_ += mol->getNRigidBodies();
182		nIntegrableObjects_ += mol->getNIntegrableObjects();
183		nCutoffGroups_ += mol->getNCutoffGroups();
184		nConstraints_ += mol->getNConstraintPairs();
185	<
186	<	addExcludePairs(mol);
187	<
185	>
186	>	addInteractionPairs(mol);
187	>
188		return true;
189		} else {
190		return false;
191		}
192		}
193	<
193	>
194		bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
#	Line 209 | Line 203 | namespace oopse {
203		nBonds_ -= mol->getNBonds();
204		nBends_ -= mol->getNBends();
205		nTorsions_ -= mol->getNTorsions();
206	+	nInversions_ -= mol->getNInversions();
207		nRigidBodies_ -= mol->getNRigidBodies();
208		nIntegrableObjects_ -= mol->getNIntegrableObjects();
209		nCutoffGroups_ -= mol->getNCutoffGroups();
210		nConstraints_ -= mol->getNConstraintPairs();
211
212	<	removeExcludePairs(mol);
212	>	removeInteractionPairs(mol);
213		molecules_.erase(mol->getGlobalIndex());
214
215		delete mol;
#	Line 223 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
226	–
227	–
221		}
222
223
#	Line 240 | Line 233 | namespace oopse {
233
234
235		void SimInfo::calcNdf() {
236	<	int ndf_local;
236	>	int ndf_local, nfq_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239	>	vector<Atom*>::iterator k;
240	>
241		Molecule* mol;
242	<	StuntDouble* integrableObject;
242	>	StuntDouble* sd;
243	>	Atom* atom;
244
245		ndf_local = 0;
246	+	nfq_local = 0;
247
248		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
252	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
253	–	integrableObject = mol->nextIntegrableObject(j)) {
249
250	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
251	+	sd = mol->nextIntegrableObject(j)) {
252	+
253		ndf_local += 3;
254
255	<	if (integrableObject->isDirectional()) {
256	<	if (integrableObject->isLinear()) {
255	>	if (sd->isDirectional()) {
256	>	if (sd->isLinear()) {
257		ndf_local += 2;
258		} else {
259		ndf_local += 3;
260		}
261		}
262	<
263	<	}//end for (integrableObject)
264	<	}// end for (mol)
262	>	}
263	>
264	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
265	>	atom = mol->nextFluctuatingCharge(k)) {
266	>	if (atom->isFluctuatingCharge()) {
267	>	nfq_local++;
268	>	}
269	>	}
270	>	}
271
272	+	ndfLocal_ = ndf_local;
273	+
274		// n_constraints is local, so subtract them on each processor
275		ndf_local -= nConstraints_;
276
277		#ifdef IS_MPI
278	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
278	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
279	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
280	>	MPI::INT, MPI::SUM);
281		#else
282		ndf_ = ndf_local;
283	+	nGlobalFluctuatingCharges_ = nfq_local;
284		#endif
285
286		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 280 | Line 289 | namespace oopse {
289
290		}
291
292	+	int SimInfo::getFdf() {
293	+	#ifdef IS_MPI
294	+	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
295	+	#else
296	+	fdf_ = fdf_local;
297	+	#endif
298	+	return fdf_;
299	+	}
300	+
301	+	unsigned int SimInfo::getNLocalCutoffGroups(){
302	+	int nLocalCutoffAtoms = 0;
303	+	Molecule* mol;
304	+	MoleculeIterator mi;
305	+	CutoffGroup* cg;
306	+	Molecule::CutoffGroupIterator ci;
307	+
308	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
309	+
310	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
311	+	cg = mol->nextCutoffGroup(ci)) {
312	+	nLocalCutoffAtoms += cg->getNumAtom();
313	+
314	+	}
315	+	}
316	+
317	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
318	+	}
319	+
320		void SimInfo::calcNdfRaw() {
321		int ndfRaw_local;
322
323		MoleculeIterator i;
324	<	std::vector<StuntDouble*>::iterator j;
324	>	vector<StuntDouble*>::iterator j;
325		Molecule* mol;
326	<	StuntDouble* integrableObject;
326	>	StuntDouble* sd;
327
328		// Raw degrees of freedom that we have to set
329		ndfRaw_local = 0;
330
331		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
295	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
296	–	integrableObject = mol->nextIntegrableObject(j)) {
332
333	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
334	+	sd = mol->nextIntegrableObject(j)) {
335	+
336		ndfRaw_local += 3;
337
338	<	if (integrableObject->isDirectional()) {
339	<	if (integrableObject->isLinear()) {
338	>	if (sd->isDirectional()) {
339	>	if (sd->isLinear()) {
340		ndfRaw_local += 2;
341		} else {
342		ndfRaw_local += 3;
#	Line 309 | Line 347 | namespace oopse {
347		}
348
349		#ifdef IS_MPI
350	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
351		#else
352		ndfRaw_ = ndfRaw_local;
353		#endif
#	Line 322 | Line 360 | namespace oopse {
360
361
362		#ifdef IS_MPI
363	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
363	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
364	>	MPI::INT, MPI::SUM);
365		#else
366		ndfTrans_ = ndfTrans_local;
367		#endif
#	Line 331 | Line 370 | namespace oopse {
370
371		}
372
373	<	void SimInfo::addExcludePairs(Molecule* mol) {
374	<	std::vector<Bond*>::iterator bondIter;
375	<	std::vector<Bend*>::iterator bendIter;
376	<	std::vector<Torsion*>::iterator torsionIter;
373	>	void SimInfo::addInteractionPairs(Molecule* mol) {
374	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
375	>	vector<Atom*>::iterator atomIter;
376	>	vector<Bond*>::iterator bondIter;
377	>	vector<Bend*>::iterator bendIter;
378	>	vector<Torsion*>::iterator torsionIter;
379	>	vector<Inversion*>::iterator inversionIter;
380	>	Atom* atom;
381		Bond* bond;
382		Bend* bend;
383		Torsion* torsion;
384	+	Inversion* inversion;
385		int a;
386		int b;
387		int c;
388		int d;
389	+
390	+	// atomGroups can be used to add special interaction maps between
391	+	// groups of atoms that are in two separate rigid bodies.
392	+	// However, most site-site interactions between two rigid bodies
393	+	// are probably not special, just the ones between the physically
394	+	// bonded atoms.  Interactions *within* a single rigid body should
395	+	// always be excluded.  These are done at the bottom of this
396	+	// function.
397	+
398	+	map<int, set<int> > atomGroups;
399	+	Molecule::RigidBodyIterator rbIter;
400	+	RigidBody* rb;
401	+	Molecule::IntegrableObjectIterator ii;
402	+	StuntDouble* sd;
403
404	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
404	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
405	>	sd = mol->nextIntegrableObject(ii)) {
406	>
407	>	if (sd->isRigidBody()) {
408	>	rb = static_cast<RigidBody*>(sd);
409	>	vector<Atom*> atoms = rb->getAtoms();
410	>	set<int> rigidAtoms;
411	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
412	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
413	>	}
414	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
416	>	}
417	>	} else {
418	>	set<int> oneAtomSet;
419	>	oneAtomSet.insert(sd->getGlobalIndex());
420	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
421	>	}
422	>	}
423	>
424	>
425	>	for (bond= mol->beginBond(bondIter); bond != NULL;
426	>	bond = mol->nextBond(bondIter)) {
427	>
428		a = bond->getAtomA()->getGlobalIndex();
429	<	b = bond->getAtomB()->getGlobalIndex();
430	<	exclude_.addPair(a, b);
429	>	b = bond->getAtomB()->getGlobalIndex();
430	>
431	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
432	>	oneTwoInteractions_.addPair(a, b);
433	>	} else {
434	>	excludedInteractions_.addPair(a, b);
435	>	}
436		}
437
438	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
438	>	for (bend= mol->beginBend(bendIter); bend != NULL;
439	>	bend = mol->nextBend(bendIter)) {
440	>
441		a = bend->getAtomA()->getGlobalIndex();
442		b = bend->getAtomB()->getGlobalIndex();
443		c = bend->getAtomC()->getGlobalIndex();
444	+
445	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
446	+	oneTwoInteractions_.addPair(a, b);
447	+	oneTwoInteractions_.addPair(b, c);
448	+	} else {
449	+	excludedInteractions_.addPair(a, b);
450	+	excludedInteractions_.addPair(b, c);
451	+	}
452
453	<	exclude_.addPair(a, b);
454	<	exclude_.addPair(a, c);
455	<	exclude_.addPair(b, c);
453	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
454	>	oneThreeInteractions_.addPair(a, c);
455	>	} else {
456	>	excludedInteractions_.addPair(a, c);
457	>	}
458		}
459
460	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
460	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
461	>	torsion = mol->nextTorsion(torsionIter)) {
462	>
463		a = torsion->getAtomA()->getGlobalIndex();
464		b = torsion->getAtomB()->getGlobalIndex();
465		c = torsion->getAtomC()->getGlobalIndex();
466	<	d = torsion->getAtomD()->getGlobalIndex();
466	>	d = torsion->getAtomD()->getGlobalIndex();
467
468	<	exclude_.addPair(a, b);
469	<	exclude_.addPair(a, c);
470	<	exclude_.addPair(a, d);
471	<	exclude_.addPair(b, c);
472	<	exclude_.addPair(b, d);
473	<	exclude_.addPair(c, d);
468	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
469	>	oneTwoInteractions_.addPair(a, b);
470	>	oneTwoInteractions_.addPair(b, c);
471	>	oneTwoInteractions_.addPair(c, d);
472	>	} else {
473	>	excludedInteractions_.addPair(a, b);
474	>	excludedInteractions_.addPair(b, c);
475	>	excludedInteractions_.addPair(c, d);
476	>	}
477	>
478	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
479	>	oneThreeInteractions_.addPair(a, c);
480	>	oneThreeInteractions_.addPair(b, d);
481	>	} else {
482	>	excludedInteractions_.addPair(a, c);
483	>	excludedInteractions_.addPair(b, d);
484	>	}
485	>
486	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
487	>	oneFourInteractions_.addPair(a, d);
488	>	} else {
489	>	excludedInteractions_.addPair(a, d);
490	>	}
491		}
492
493	<	Molecule::RigidBodyIterator rbIter;
494	<	RigidBody* rb;
495	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
496	<	std::vector<Atom*> atoms = rb->getAtoms();
497	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
498	<	for (int j = i + 1; j < atoms.size(); ++j) {
493	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
494	>	inversion = mol->nextInversion(inversionIter)) {
495	>
496	>	a = inversion->getAtomA()->getGlobalIndex();
497	>	b = inversion->getAtomB()->getGlobalIndex();
498	>	c = inversion->getAtomC()->getGlobalIndex();
499	>	d = inversion->getAtomD()->getGlobalIndex();
500	>
501	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
502	>	oneTwoInteractions_.addPair(a, b);
503	>	oneTwoInteractions_.addPair(a, c);
504	>	oneTwoInteractions_.addPair(a, d);
505	>	} else {
506	>	excludedInteractions_.addPair(a, b);
507	>	excludedInteractions_.addPair(a, c);
508	>	excludedInteractions_.addPair(a, d);
509	>	}
510	>
511	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
512	>	oneThreeInteractions_.addPair(b, c);
513	>	oneThreeInteractions_.addPair(b, d);
514	>	oneThreeInteractions_.addPair(c, d);
515	>	} else {
516	>	excludedInteractions_.addPair(b, c);
517	>	excludedInteractions_.addPair(b, d);
518	>	excludedInteractions_.addPair(c, d);
519	>	}
520	>	}
521	>
522	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
523	>	rb = mol->nextRigidBody(rbIter)) {
524	>	vector<Atom*> atoms = rb->getAtoms();
525	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
526	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
527		a = atoms[i]->getGlobalIndex();
528		b = atoms[j]->getGlobalIndex();
529	<	exclude_.addPair(a, b);
529	>	excludedInteractions_.addPair(a, b);
530		}
531		}
532		}
533
534		}
535
536	<	void SimInfo::removeExcludePairs(Molecule* mol) {
537	<	std::vector<Bond*>::iterator bondIter;
538	<	std::vector<Bend*>::iterator bendIter;
539	<	std::vector<Torsion*>::iterator torsionIter;
536	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
537	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
538	>	vector<Bond*>::iterator bondIter;
539	>	vector<Bend*>::iterator bendIter;
540	>	vector<Torsion*>::iterator torsionIter;
541	>	vector<Inversion*>::iterator inversionIter;
542		Bond* bond;
543		Bend* bend;
544		Torsion* torsion;
545	+	Inversion* inversion;
546		int a;
547		int b;
548		int c;
549		int d;
550	+
551	+	map<int, set<int> > atomGroups;
552	+	Molecule::RigidBodyIterator rbIter;
553	+	RigidBody* rb;
554	+	Molecule::IntegrableObjectIterator ii;
555	+	StuntDouble* sd;
556
557	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
557	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
558	>	sd = mol->nextIntegrableObject(ii)) {
559	>
560	>	if (sd->isRigidBody()) {
561	>	rb = static_cast<RigidBody*>(sd);
562	>	vector<Atom*> atoms = rb->getAtoms();
563	>	set<int> rigidAtoms;
564	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
565	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
566	>	}
567	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
569	>	}
570	>	} else {
571	>	set<int> oneAtomSet;
572	>	oneAtomSet.insert(sd->getGlobalIndex());
573	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
574	>	}
575	>	}
576	>
577	>	for (bond= mol->beginBond(bondIter); bond != NULL;
578	>	bond = mol->nextBond(bondIter)) {
579	>
580		a = bond->getAtomA()->getGlobalIndex();
581	<	b = bond->getAtomB()->getGlobalIndex();
582	<	exclude_.removePair(a, b);
581	>	b = bond->getAtomB()->getGlobalIndex();
582	>
583	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
584	>	oneTwoInteractions_.removePair(a, b);
585	>	} else {
586	>	excludedInteractions_.removePair(a, b);
587	>	}
588		}
589
590	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
590	>	for (bend= mol->beginBend(bendIter); bend != NULL;
591	>	bend = mol->nextBend(bendIter)) {
592	>
593		a = bend->getAtomA()->getGlobalIndex();
594		b = bend->getAtomB()->getGlobalIndex();
595		c = bend->getAtomC()->getGlobalIndex();
596	+
597	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
598	+	oneTwoInteractions_.removePair(a, b);
599	+	oneTwoInteractions_.removePair(b, c);
600	+	} else {
601	+	excludedInteractions_.removePair(a, b);
602	+	excludedInteractions_.removePair(b, c);
603	+	}
604
605	<	exclude_.removePair(a, b);
606	<	exclude_.removePair(a, c);
607	<	exclude_.removePair(b, c);
605	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
606	>	oneThreeInteractions_.removePair(a, c);
607	>	} else {
608	>	excludedInteractions_.removePair(a, c);
609	>	}
610		}
611
612	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
612	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
613	>	torsion = mol->nextTorsion(torsionIter)) {
614	>
615		a = torsion->getAtomA()->getGlobalIndex();
616		b = torsion->getAtomB()->getGlobalIndex();
617		c = torsion->getAtomC()->getGlobalIndex();
618	<	d = torsion->getAtomD()->getGlobalIndex();
618	>	d = torsion->getAtomD()->getGlobalIndex();
619	>
620	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
621	>	oneTwoInteractions_.removePair(a, b);
622	>	oneTwoInteractions_.removePair(b, c);
623	>	oneTwoInteractions_.removePair(c, d);
624	>	} else {
625	>	excludedInteractions_.removePair(a, b);
626	>	excludedInteractions_.removePair(b, c);
627	>	excludedInteractions_.removePair(c, d);
628	>	}
629
630	<	exclude_.removePair(a, b);
631	<	exclude_.removePair(a, c);
632	<	exclude_.removePair(a, d);
633	<	exclude_.removePair(b, c);
634	<	exclude_.removePair(b, d);
635	<	exclude_.removePair(c, d);
630	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
631	>	oneThreeInteractions_.removePair(a, c);
632	>	oneThreeInteractions_.removePair(b, d);
633	>	} else {
634	>	excludedInteractions_.removePair(a, c);
635	>	excludedInteractions_.removePair(b, d);
636	>	}
637	>
638	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
639	>	oneFourInteractions_.removePair(a, d);
640	>	} else {
641	>	excludedInteractions_.removePair(a, d);
642	>	}
643		}
644
645	<	Molecule::RigidBodyIterator rbIter;
646	<	RigidBody* rb;
647	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
648	<	std::vector<Atom*> atoms = rb->getAtoms();
649	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
650	<	for (int j = i + 1; j < atoms.size(); ++j) {
645	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
646	>	inversion = mol->nextInversion(inversionIter)) {
647	>
648	>	a = inversion->getAtomA()->getGlobalIndex();
649	>	b = inversion->getAtomB()->getGlobalIndex();
650	>	c = inversion->getAtomC()->getGlobalIndex();
651	>	d = inversion->getAtomD()->getGlobalIndex();
652	>
653	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
654	>	oneTwoInteractions_.removePair(a, b);
655	>	oneTwoInteractions_.removePair(a, c);
656	>	oneTwoInteractions_.removePair(a, d);
657	>	} else {
658	>	excludedInteractions_.removePair(a, b);
659	>	excludedInteractions_.removePair(a, c);
660	>	excludedInteractions_.removePair(a, d);
661	>	}
662	>
663	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
664	>	oneThreeInteractions_.removePair(b, c);
665	>	oneThreeInteractions_.removePair(b, d);
666	>	oneThreeInteractions_.removePair(c, d);
667	>	} else {
668	>	excludedInteractions_.removePair(b, c);
669	>	excludedInteractions_.removePair(b, d);
670	>	excludedInteractions_.removePair(c, d);
671	>	}
672	>	}
673	>
674	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
675	>	rb = mol->nextRigidBody(rbIter)) {
676	>	vector<Atom*> atoms = rb->getAtoms();
677	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
678	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
679		a = atoms[i]->getGlobalIndex();
680		b = atoms[j]->getGlobalIndex();
681	<	exclude_.removePair(a, b);
681	>	excludedInteractions_.removePair(a, b);
682		}
683		}
684		}
685	<
685	>
686		}
687	<
688	<
687	>
688	>
689		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
690		int curStampId;
691	<
691	>
692		//index from 0
693		curStampId = moleculeStamps_.size();
694
#	Line 456 | Line 696 | namespace oopse {
696		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
697		}
698
459	–	void SimInfo::update() {
699
700	<	setupSimType();
701	<
702	<	#ifdef IS_MPI
703	<	setupFortranParallel();
704	<	#endif
705	<
706	<	setupFortranSim();
707	<
708	<	//setup fortran force field
470	<	/** @deprecate */
471	<	int isError = 0;
472	<
473	<	setupElectrostaticSummationMethod( isError );
474	<
475	<	if(isError){
476	<	sprintf( painCave.errMsg,
477	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
478	<	painCave.isFatal = 1;
479	<	simError();
480	<	}
481	<
482	<
483	<	setupCutoff();
484	<
700	>	/**
701	>	* update
702	>	*
703	>	*  Performs the global checks and variable settings after the
704	>	*  objects have been created.
705	>	*
706	>	*/
707	>	void SimInfo::update() {
708	>	setupSimVariables();
709		calcNdf();
710		calcNdfRaw();
711		calcNdfTrans();
488	–
489	–	fortranInitialized_ = true;
712		}
713	<
714	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
713	>
714	>	/**
715	>	* getSimulatedAtomTypes
716	>	*
717	>	* Returns an STL set of AtomType* that are actually present in this
718	>	* simulation.  Must query all processors to assemble this information.
719	>	*
720	>	*/
721	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
722		SimInfo::MoleculeIterator mi;
723		Molecule* mol;
724		Molecule::AtomIterator ai;
725		Atom* atom;
726	<	std::set<AtomType*> atomTypes;
727	<
726	>	set<AtomType*> atomTypes;
727	>
728		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
729	<
730	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
729	>	for(atom = mol->beginAtom(ai); atom != NULL;
730	>	atom = mol->nextAtom(ai)) {
731		atomTypes.insert(atom->getAtomType());
732	<	}
733	<
734	<	}
732	>	}
733	>	}
734	>
735	>	#ifdef IS_MPI
736
737	<	return atomTypes;
738	<	}
509	<
510	<	void SimInfo::setupSimType() {
511	<	std::set<AtomType*>::iterator i;
512	<	std::set<AtomType*> atomTypes;
513	<	atomTypes = getUniqueAtomTypes();
737	>	// loop over the found atom types on this processor, and add their
738	>	// numerical idents to a vector:
739
740	<	int useLennardJones = 0;
741	<	int useElectrostatic = 0;
742	<	int useEAM = 0;
743	<	int useCharge = 0;
519	<	int useDirectional = 0;
520	<	int useDipole = 0;
521	<	int useGayBerne = 0;
522	<	int useSticky = 0;
523	<	int useStickyPower = 0;
524	<	int useShape = 0;
525	<	int useFLARB = 0; //it is not in AtomType yet
526	<	int useDirectionalAtom = 0;
527	<	int useElectrostatics = 0;
528	<	//usePBC and useRF are from simParams
529	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
530	<	int useRF;
531	<	std::string myMethod;
740	>	vector<int> foundTypes;
741	>	set<AtomType*>::iterator i;
742	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
743	>	foundTypes.push_back( (*i)->getIdent() );
744
745	<	// set the useRF logical
746	<	useRF = 0;
745	>	// count_local holds the number of found types on this processor
746	>	int count_local = foundTypes.size();
747
748	+	int nproc = MPI::COMM_WORLD.Get_size();
749
750	<	if (simParams_->haveElectrostaticSummationMethod()) {
751	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
752	<	toUpper(myMethod);
753	<	if (myMethod == "REACTION_FIELD") {
754	<	useRF=1;
755	<	}
750	>	// we need arrays to hold the counts and displacement vectors for
751	>	// all processors
752	>	vector<int> counts(nproc, 0);
753	>	vector<int> disps(nproc, 0);
754	>
755	>	// fill the counts array
756	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
757	>	1, MPI::INT);
758	>
759	>	// use the processor counts to compute the displacement array
760	>	disps[0] = 0;
761	>	int totalCount = counts[0];
762	>	for (int iproc = 1; iproc < nproc; iproc++) {
763	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
764	>	totalCount += counts[iproc];
765		}
766	+
767	+	// we need a (possibly redundant) set of all found types:
768	+	vector<int> ftGlobal(totalCount);
769	+
770	+	// now spray out the foundTypes to all the other processors:
771	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
772	+	&ftGlobal[0], &counts[0], &disps[0],
773	+	MPI::INT);
774	+
775	+	vector<int>::iterator j;
776	+
777	+	// foundIdents is a stl set, so inserting an already found ident
778	+	// will have no effect.
779	+	set<int> foundIdents;
780	+
781	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
782	+	foundIdents.insert((*j));
783	+
784	+	// now iterate over the foundIdents and get the actual atom types
785	+	// that correspond to these:
786	+	set<int>::iterator it;
787	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
788	+	atomTypes.insert( forceField_->getAtomType((*it)) );
789	+
790	+	#endif
791
792	<	//loop over all of the atom types
793	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
547	<	useLennardJones |= (*i)->isLennardJones();
548	<	useElectrostatic |= (*i)->isElectrostatic();
549	<	useEAM |= (*i)->isEAM();
550	<	useCharge |= (*i)->isCharge();
551	<	useDirectional |= (*i)->isDirectional();
552	<	useDipole |= (*i)->isDipole();
553	<	useGayBerne |= (*i)->isGayBerne();
554	<	useSticky |= (*i)->isSticky();
555	<	useStickyPower |= (*i)->isStickyPower();
556	<	useShape |= (*i)->isShape();
557	<	}
792	>	return atomTypes;
793	>	}
794
559	–	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
560	–	useDirectionalAtom = 1;
561	–	}
795
796	<	if (useCharge || useDipole) {
797	<	useElectrostatics = 1;
798	<	}
796	>	int getGlobalCountOfType(AtomType* atype) {
797	>	/*
798	>	set<AtomType*> atypes = getSimulatedAtomTypes();
799	>	map<AtomType*, int> counts_;
800
801	<	#ifdef IS_MPI
802	<	int temp;
801	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
802	>	for(atom = mol->beginAtom(ai); atom != NULL;
803	>	atom = mol->nextAtom(ai)) {
804	>	atom->getAtomType();
805	>	}
806	>	}
807	>	*/
808	>	return 0;
809	>	}
810
811	<	temp = usePBC;
812	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	void SimInfo::setupSimVariables() {
812	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
813	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
814	>	// parameter is true
815	>	calcBoxDipole_ = false;
816	>	if ( simParams_->haveAccumulateBoxDipole() )
817	>	if ( simParams_->getAccumulateBoxDipole() ) {
818	>	calcBoxDipole_ = true;
819	>	}
820	>
821	>	set<AtomType*>::iterator i;
822	>	set<AtomType*> atomTypes;
823	>	atomTypes = getSimulatedAtomTypes();
824	>	bool usesElectrostatic = false;
825	>	bool usesMetallic = false;
826	>	bool usesDirectional = false;
827	>	bool usesFluctuatingCharges =  false;
828	>	//loop over all of the atom types
829	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
830	>	usesElectrostatic |= (*i)->isElectrostatic();
831	>	usesMetallic |= (*i)->isMetal();
832	>	usesDirectional |= (*i)->isDirectional();
833	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
834	>	}
835
836	<	temp = useDirectionalAtom;
837	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836	>	#ifdef IS_MPI
837	>	bool temp;
838	>	temp = usesDirectional;
839	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
840	>	MPI::LOR);
841	>
842	>	temp = usesMetallic;
843	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
844	>	MPI::LOR);
845	>
846	>	temp = usesElectrostatic;
847	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
848	>	MPI::LOR);
849
850	<	temp = useLennardJones;
851	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	>	temp = usesFluctuatingCharges;
851	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
852	>	MPI::LOR);
853	>	#else
854
855	<	temp = useElectrostatics;
856	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
855	>	usesDirectionalAtoms_ = usesDirectional;
856	>	usesMetallicAtoms_ = usesMetallic;
857	>	usesElectrostaticAtoms_ = usesElectrostatic;
858	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
859
860	<	temp = useCharge;
861	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>	#endif
861	>
862	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
863	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
864	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
865	>	}
866
585	–	temp = useDipole;
586	–	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
867
868	<	temp = useSticky;
869	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
868	>	vector<int> SimInfo::getGlobalAtomIndices() {
869	>	SimInfo::MoleculeIterator mi;
870	>	Molecule* mol;
871	>	Molecule::AtomIterator ai;
872	>	Atom* atom;
873
874	<	temp = useStickyPower;
592	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
875
876	<	temp = useGayBerne;
877	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
876	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
877	>
878	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
879	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
880	>	}
881	>	}
882	>	return GlobalAtomIndices;
883	>	}
884
597	–	temp = useEAM;
598	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885
886	<	temp = useShape;
887	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886	>	vector<int> SimInfo::getGlobalGroupIndices() {
887	>	SimInfo::MoleculeIterator mi;
888	>	Molecule* mol;
889	>	Molecule::CutoffGroupIterator ci;
890	>	CutoffGroup* cg;
891
892	<	temp = useFLARB;
893	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
894	<
606	<	temp = useRF;
607	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
608	<
609	<	#endif
610	<
611	<	fInfo_.SIM_uses_PBC = usePBC;
612	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
613	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
614	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
615	<	fInfo_.SIM_uses_Charges = useCharge;
616	<	fInfo_.SIM_uses_Dipoles = useDipole;
617	<	fInfo_.SIM_uses_Sticky = useSticky;
618	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
619	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
620	<	fInfo_.SIM_uses_EAM = useEAM;
621	<	fInfo_.SIM_uses_Shapes = useShape;
622	<	fInfo_.SIM_uses_FLARB = useFLARB;
623	<	fInfo_.SIM_uses_RF = useRF;
624	<
625	<	if( myMethod == "REACTION_FIELD") {
892	>	vector<int> GlobalGroupIndices;
893	>
894	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
895
896	<	if (simParams_->haveDielectric()) {
897	<	fInfo_.dielect = simParams_->getDielectric();
898	<	} else {
899	<	sprintf(painCave.errMsg,
900	<	"SimSetup Error: No Dielectric constant was set.\n"
901	<	"\tYou are trying to use Reaction Field without"
633	<	"\tsetting a dielectric constant!\n");
634	<	painCave.isFatal = 1;
635	<	simError();
636	<	}
896	>	//local index of cutoff group is trivial, it only depends on the
897	>	//order of travesing
898	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
899	>	cg = mol->nextCutoffGroup(ci)) {
900	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
901	>	}
902		}
903	+	return GlobalGroupIndices;
904		}
905
640	–	void SimInfo::setupFortranSim() {
641	–	int isError;
642	–	int nExclude;
643	–	std::vector<int> fortranGlobalGroupMembership;
644	–
645	–	nExclude = exclude_.getSize();
646	–	isError = 0;
906
907	<	//globalGroupMembership_ is filled by SimCreator
649	<	for (int i = 0; i < nGlobalAtoms_; i++) {
650	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
651	<	}
907	>	void SimInfo::prepareTopology() {
908
909		//calculate mass ratio of cutoff group
654	–	std::vector<double> mfact;
910		SimInfo::MoleculeIterator mi;
911		Molecule* mol;
912		Molecule::CutoffGroupIterator ci;
913		CutoffGroup* cg;
914		Molecule::AtomIterator ai;
915		Atom* atom;
916	<	double totalMass;
916	>	RealType totalMass;
917
918	<	//to avoid memory reallocation, reserve enough space for mfact
919	<	mfact.reserve(getNCutoffGroups());
918	>	/**
919	>	* The mass factor is the relative mass of an atom to the total
920	>	* mass of the cutoff group it belongs to.  By default, all atoms
921	>	* are their own cutoff groups, and therefore have mass factors of
922	>	* 1.  We need some special handling for massless atoms, which
923	>	* will be treated as carrying the entire mass of the cutoff
924	>	* group.
925	>	*/
926	>	massFactors_.clear();
927	>	massFactors_.resize(getNAtoms(), 1.0);
928
929		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
930	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
930	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
931	>	cg = mol->nextCutoffGroup(ci)) {
932
933		totalMass = cg->getMass();
934		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
935		// Check for massless groups - set mfact to 1 if true
936	<	if (totalMass != 0)
937	<	mfact.push_back(atom->getMass()/totalMass);
936	>	if (totalMass != 0)
937	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
938		else
939	<	mfact.push_back( 1.0 );
939	>	massFactors_[atom->getLocalIndex()] = 1.0;
940		}
677	–
941		}
942		}
943
944	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
682	<	std::vector<int> identArray;
944	>	// Build the identArray_ and regions_
945
946	<	//to avoid memory reallocation, reserve enough space identArray
947	<	identArray.reserve(getNAtoms());
948	<
949	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
946	>	identArray_.clear();
947	>	identArray_.reserve(getNAtoms());
948	>	regions_.clear();
949	>	regions_.reserve(getNAtoms());
950	>
951	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
952	>	int reg = mol->getRegion();
953		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
954	<	identArray.push_back(atom->getIdent());
954	>	identArray_.push_back(atom->getIdent());
955	>	regions_.push_back(reg);
956		}
957		}
958	<
959	<	//fill molMembershipArray
694	<	//molMembershipArray is filled by SimCreator
695	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
696	<	for (int i = 0; i < nGlobalAtoms_; i++) {
697	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
698	<	}
699	<
700	<	//setup fortran simulation
701	<	int nGlobalExcludes = 0;
702	<	int* globalExcludes = NULL;
703	<	int* excludeList = exclude_.getExcludeList();
704	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
705	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
706	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
707	<
708	<	if( isError ){
709	<
710	<	sprintf( painCave.errMsg,
711	<	"There was an error setting the simulation information in fortran.\n" );
712	<	painCave.isFatal = 1;
713	<	painCave.severity = OOPSE_ERROR;
714	<	simError();
715	<	}
716	<
717	<	#ifdef IS_MPI
718	<	sprintf( checkPointMsg,
719	<	"succesfully sent the simulation information to fortran.\n");
720	<	MPIcheckPoint();
721	<	#endif // is_mpi
722	<	}
723	<
724	<
725	<	#ifdef IS_MPI
726	<	void SimInfo::setupFortranParallel() {
727	<
728	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
729	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
730	<	std::vector<int> localToGlobalCutoffGroupIndex;
731	<	SimInfo::MoleculeIterator mi;
732	<	Molecule::AtomIterator ai;
733	<	Molecule::CutoffGroupIterator ci;
734	<	Molecule* mol;
735	<	Atom* atom;
736	<	CutoffGroup* cg;
737	<	mpiSimData parallelData;
738	<	int isError;
739	<
740	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
741	<
742	<	//local index(index in DataStorge) of atom is important
743	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
744	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
745	<	}
746	<
747	<	//local index of cutoff group is trivial, it only depends on the order of travesing
748	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
749	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
750	<	}
751	<
752	<	}
753	<
754	<	//fill up mpiSimData struct
755	<	parallelData.nMolGlobal = getNGlobalMolecules();
756	<	parallelData.nMolLocal = getNMolecules();
757	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
758	<	parallelData.nAtomsLocal = getNAtoms();
759	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
760	<	parallelData.nGroupsLocal = getNCutoffGroups();
761	<	parallelData.myNode = worldRank;
762	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
763	<
764	<	//pass mpiSimData struct and index arrays to fortran
765	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
766	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
767	<	&localToGlobalCutoffGroupIndex[0], &isError);
768	<
769	<	if (isError) {
770	<	sprintf(painCave.errMsg,
771	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
775	<
776	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
777	<	MPIcheckPoint();
778	<
779	<
780	<	}
781	<
782	<	#endif
783	<
784	<	double SimInfo::calcMaxCutoffRadius() {
785	<
786	<
787	<	std::set<AtomType*> atomTypes;
788	<	std::set<AtomType*>::iterator i;
789	<	std::vector<double> cutoffRadius;
790	<
791	<	//get the unique atom types
792	<	atomTypes = getUniqueAtomTypes();
793	<
794	<	//query the max cutoff radius among these atom types
795	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
796	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
797	<	}
798	<
799	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
800	<	#ifdef IS_MPI
801	<	//pick the max cutoff radius among the processors
802	<	#endif
803	<
804	<	return maxCutoffRadius;
805	<	}
806	<
807	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
808	<
809	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
810	<
811	<	if (!simParams_->haveCutoffRadius()){
812	<	sprintf(painCave.errMsg,
813	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
814	<	"\tOOPSE will use a default value of 15.0 angstroms"
815	<	"\tfor the cutoffRadius.\n");
816	<	painCave.isFatal = 0;
817	<	simError();
818	<	rcut = 15.0;
819	<	} else{
820	<	rcut = simParams_->getCutoffRadius();
821	<	}
822	<
823	<	if (!simParams_->haveSwitchingRadius()){
824	<	sprintf(painCave.errMsg,
825	<	"SimCreator Warning: No value was set for switchingRadius.\n"
826	<	"\tOOPSE will use a default value of\n"
827	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
828	<	painCave.isFatal = 0;
829	<	simError();
830	<	rsw = 0.85 * rcut;
831	<	} else{
832	<	rsw = simParams_->getSwitchingRadius();
833	<	}
834	<
835	<	} else {
836	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
837	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
838	<
839	<	if (simParams_->haveCutoffRadius()) {
840	<	rcut = simParams_->getCutoffRadius();
841	<	} else {
842	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
843	<	rcut = calcMaxCutoffRadius();
844	<	}
845	<
846	<	if (simParams_->haveSwitchingRadius()) {
847	<	rsw  = simParams_->getSwitchingRadius();
848	<	} else {
849	<	rsw = rcut;
850	<	}
851	<
852	<	}
958	>
959	>	topologyDone_ = true;
960		}
961
855	–	void SimInfo::setupCutoff() {
856	–	getCutoff(rcut_, rsw_);
857	–	double rnblist = rcut_ + 1; // skin of neighbor list
858	–
859	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
860	–
861	–	int cp =  TRADITIONAL_CUTOFF_POLICY;
862	–	if (simParams_->haveCutoffPolicy()) {
863	–	std::string myPolicy = simParams_->getCutoffPolicy();
864	–	toUpper(myPolicy);
865	–	if (myPolicy == "MIX") {
866	–	cp = MIX_CUTOFF_POLICY;
867	–	} else {
868	–	if (myPolicy == "MAX") {
869	–	cp = MAX_CUTOFF_POLICY;
870	–	} else {
871	–	if (myPolicy == "TRADITIONAL") {
872	–	cp = TRADITIONAL_CUTOFF_POLICY;
873	–	} else {
874	–	// throw error
875	–	sprintf( painCave.errMsg,
876	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
877	–	painCave.isFatal = 1;
878	–	simError();
879	–	}
880	–	}
881	–	}
882	–	}
883	–
884	–
885	–	if (simParams_->haveSkinThickness()) {
886	–	double skinThickness = simParams_->getSkinThickness();
887	–	}
888	–
889	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
890	–	// also send cutoff notification to electrostatics
891	–	setElectrostaticCutoffRadius(&rcut_, &rsw_);
892	–	}
893	–
894	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
895	–
896	–	int errorOut;
897	–	int esm =  NONE;
898	–	double alphaVal;
899	–	double dielectric;
900	–
901	–	errorOut = isError;
902	–	alphaVal = simParams_->getDampingAlpha();
903	–	dielectric = simParams_->getDielectric();
904	–
905	–	if (simParams_->haveElectrostaticSummationMethod()) {
906	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
907	–	toUpper(myMethod);
908	–	if (myMethod == "NONE") {
909	–	esm = NONE;
910	–	} else {
911	–	if (myMethod == "UNDAMPED_WOLF") {
912	–	esm = UNDAMPED_WOLF;
913	–	} else {
914	–	if (myMethod == "DAMPED_WOLF") {
915	–	esm = DAMPED_WOLF;
916	–	if (!simParams_->haveDampingAlpha()) {
917	–	//throw error
918	–	sprintf( painCave.errMsg,
919	–	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal);
920	–	painCave.isFatal = 0;
921	–	simError();
922	–	}
923	–	} else {
924	–	if (myMethod == "REACTION_FIELD") {
925	–	esm = REACTION_FIELD;
926	–	} else {
927	–	// throw error
928	–	sprintf( painCave.errMsg,
929	–	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
930	–	painCave.isFatal = 1;
931	–	simError();
932	–	}
933	–	}
934	–	}
935	–	}
936	–	}
937	–	// let's pass some summation method variables to fortran
938	–	setElectrostaticSummationMethod( &esm );
939	–	setDampedWolfAlpha( &alphaVal );
940	–	setReactionFieldDielectric( &dielectric );
941	–	initFortranFF( &esm, &errorOut );
942	–	}
943	–
962		void SimInfo::addProperty(GenericData* genData) {
963		properties_.addProperty(genData);
964		}
965
966	<	void SimInfo::removeProperty(const std::string& propName) {
966	>	void SimInfo::removeProperty(const string& propName) {
967		properties_.removeProperty(propName);
968		}
969
#	Line 953 | Line 971 | namespace oopse {
971		properties_.clearProperties();
972		}
973
974	<	std::vector<std::string> SimInfo::getPropertyNames() {
974	>	vector<string> SimInfo::getPropertyNames() {
975		return properties_.getPropertyNames();
976		}
977
978	<	std::vector<GenericData*> SimInfo::getProperties() {
978	>	vector<GenericData*> SimInfo::getProperties() {
979		return properties_.getProperties();
980		}
981
982	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
982	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
983		return properties_.getPropertyByName(propName);
984		}
985
#	Line 975 | Line 993 | namespace oopse {
993		Molecule* mol;
994		RigidBody* rb;
995		Atom* atom;
996	+	CutoffGroup* cg;
997		SimInfo::MoleculeIterator mi;
998		Molecule::RigidBodyIterator rbIter;
999	<	Molecule::AtomIterator atomIter;;
999	>	Molecule::AtomIterator atomIter;
1000	>	Molecule::CutoffGroupIterator cgIter;
1001
1002		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1003
1004	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1004	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
1005	>	atom = mol->nextAtom(atomIter)) {
1006		atom->setSnapshotManager(sman_);
1007		}
1008
1009	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1009	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1010	>	rb = mol->nextRigidBody(rbIter)) {
1011		rb->setSnapshotManager(sman_);
1012		}
1013	+
1014	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1015	+	cg = mol->nextCutoffGroup(cgIter)) {
1016	+	cg->setSnapshotManager(sman_);
1017	+	}
1018		}
1019
1020		}
1021
995	–	Vector3d SimInfo::getComVel(){
996	–	SimInfo::MoleculeIterator i;
997	–	Molecule* mol;
1022
1023	<	Vector3d comVel(0.0);
1000	<	double totalMass = 0.0;
1001	<
1002	<
1003	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1004	<	double mass = mol->getMass();
1005	<	totalMass += mass;
1006	<	comVel += mass * mol->getComVel();
1007	<	}
1023	>	ostream& operator <<(ostream& o, SimInfo& info) {
1024
1009	–	#ifdef IS_MPI
1010	–	double tmpMass = totalMass;
1011	–	Vector3d tmpComVel(comVel);
1012	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1013	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1014	–	#endif
1015	–
1016	–	comVel /= totalMass;
1017	–
1018	–	return comVel;
1019	–	}
1020	–
1021	–	Vector3d SimInfo::getCom(){
1022	–	SimInfo::MoleculeIterator i;
1023	–	Molecule* mol;
1024	–
1025	–	Vector3d com(0.0);
1026	–	double totalMass = 0.0;
1027	–
1028	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1029	–	double mass = mol->getMass();
1030	–	totalMass += mass;
1031	–	com += mass * mol->getCom();
1032	–	}
1033	–
1034	–	#ifdef IS_MPI
1035	–	double tmpMass = totalMass;
1036	–	Vector3d tmpCom(com);
1037	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1038	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1039	–	#endif
1040	–
1041	–	com /= totalMass;
1042	–
1043	–	return com;
1044	–
1045	–	}
1046	–
1047	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1048	–
1025		return o;
1026		}
1027
1028	<
1029	<	/*
1030	<	Returns center of mass and center of mass velocity in one function call.
1031	<	*/
1032	<
1033	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1034	<	SimInfo::MoleculeIterator i;
1035	<	Molecule* mol;
1036	<
1037	<
1038	<	double totalMass = 0.0;
1039	<
1028	>
1029	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1030	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1031	>	sprintf(painCave.errMsg,
1032	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1033	>	"\tindex exceeds number of known objects!\n");
1034	>	painCave.isFatal = 1;
1035	>	simError();
1036	>	return NULL;
1037	>	} else
1038	>	return IOIndexToIntegrableObject.at(index);
1039	>	}
1040	>
1041	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1042	>	IOIndexToIntegrableObject= v;
1043	>	}
1044
1045	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1046	<	double mass = mol->getMass();
1067	<	totalMass += mass;
1068	<	com += mass * mol->getCom();
1069	<	comVel += mass * mol->getComVel();
1070	<	}
1071	<
1045	>	int SimInfo::getNGlobalConstraints() {
1046	>	int nGlobalConstraints;
1047		#ifdef IS_MPI
1048	<	double tmpMass = totalMass;
1049	<	Vector3d tmpCom(com);
1050	<	Vector3d tmpComVel(comVel);
1051	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1077	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1078	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1048	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1049	>	MPI::INT, MPI::SUM);
1050	>	#else
1051	>	nGlobalConstraints =  nConstraints_;
1052		#endif
1053	<
1054	<	com /= totalMass;
1082	<	comVel /= totalMass;
1083	<	}
1084	<
1085	<	/*
1086	<	Return intertia tensor for entire system and angular momentum Vector.
1053	>	return nGlobalConstraints;
1054	>	}
1055
1056	+	}//end namespace OpenMD
1057
1089	–	[  Ixx -Ixy  -Ixz ]
1090	–	J =| -Iyx  Iyy  -Iyz |
1091	–	[ -Izx -Iyz   Izz ]
1092	–	*/
1093	–
1094	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1095	–
1096	–
1097	–	double xx = 0.0;
1098	–	double yy = 0.0;
1099	–	double zz = 0.0;
1100	–	double xy = 0.0;
1101	–	double xz = 0.0;
1102	–	double yz = 0.0;
1103	–	Vector3d com(0.0);
1104	–	Vector3d comVel(0.0);
1105	–
1106	–	getComAll(com, comVel);
1107	–
1108	–	SimInfo::MoleculeIterator i;
1109	–	Molecule* mol;
1110	–
1111	–	Vector3d thisq(0.0);
1112	–	Vector3d thisv(0.0);
1113	–
1114	–	double thisMass = 0.0;
1115	–
1116	–
1117	–
1118	–
1119	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1120	–
1121	–	thisq = mol->getCom()-com;
1122	–	thisv = mol->getComVel()-comVel;
1123	–	thisMass = mol->getMass();
1124	–	// Compute moment of intertia coefficients.
1125	–	xx += thisq[0]*thisq[0]*thisMass;
1126	–	yy += thisq[1]*thisq[1]*thisMass;
1127	–	zz += thisq[2]*thisq[2]*thisMass;
1128	–
1129	–	// compute products of intertia
1130	–	xy += thisq[0]*thisq[1]*thisMass;
1131	–	xz += thisq[0]*thisq[2]*thisMass;
1132	–	yz += thisq[1]*thisq[2]*thisMass;
1133	–
1134	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1135	–
1136	–	}
1137	–
1138	–
1139	–	inertiaTensor(0,0) = yy + zz;
1140	–	inertiaTensor(0,1) = -xy;
1141	–	inertiaTensor(0,2) = -xz;
1142	–	inertiaTensor(1,0) = -xy;
1143	–	inertiaTensor(1,1) = xx + zz;
1144	–	inertiaTensor(1,2) = -yz;
1145	–	inertiaTensor(2,0) = -xz;
1146	–	inertiaTensor(2,1) = -yz;
1147	–	inertiaTensor(2,2) = xx + yy;
1148	–
1149	–	#ifdef IS_MPI
1150	–	Mat3x3d tmpI(inertiaTensor);
1151	–	Vector3d tmpAngMom;
1152	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1153	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1154	–	#endif
1155	–
1156	–	return;
1157	–	}
1158	–
1159	–	//Returns the angular momentum of the system
1160	–	Vector3d SimInfo::getAngularMomentum(){
1161	–
1162	–	Vector3d com(0.0);
1163	–	Vector3d comVel(0.0);
1164	–	Vector3d angularMomentum(0.0);
1165	–
1166	–	getComAll(com,comVel);
1167	–
1168	–	SimInfo::MoleculeIterator i;
1169	–	Molecule* mol;
1170	–
1171	–	Vector3d thisr(0.0);
1172	–	Vector3d thisp(0.0);
1173	–
1174	–	double thisMass;
1175	–
1176	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1177	–	thisMass = mol->getMass();
1178	–	thisr = mol->getCom()-com;
1179	–	thisp = (mol->getComVel()-comVel)*thisMass;
1180	–
1181	–	angularMomentum += cross( thisr, thisp );
1182	–
1183	–	}
1184	–
1185	–	#ifdef IS_MPI
1186	–	Vector3d tmpAngMom;
1187	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1188	–	#endif
1189	–
1190	–	return angularMomentum;
1191	–	}
1192	–
1193	–
1194	–	}//end namespace oopse
1195	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 701 by chrisfen, Wed Oct 26 23:32:25 2005 UTC vs.
Revision 1930 by gezelter, Mon Aug 19 13:51:04 2013 UTC

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