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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC vs.
Revision 1929 by gezelter, Mon Aug 19 13:12:00 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 54 | Line 55
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57		#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"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61		#include "io/ForceFieldOptions.hpp"
62	<	#include "UseTheForce/ForceField.hpp"
63	<
71	<
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"
75	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
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), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
79	<	useAtomicVirial_(true) {
80	<
81	<	MoleculeStamp* molStamp;
82	<	int nMolWithSameStamp;
83	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
85	<	CutoffGroupStamp* cgStamp;
86	<	RigidBodyStamp* rbStamp;
87	<	int nRigidAtoms = 0;
88	<	std::vector<Component*> components = simParams->getComponents();
89	<
90	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91	<	molStamp = (*i)->getMoleculeStamp();
92	<	nMolWithSameStamp = (*i)->getNMol();
93	<
94	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
95	<
96	<	//calculate atoms in molecules
97	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
98	<
116	<	//calculate atoms in cutoff groups
117	<	int nAtomsInGroups = 0;
118	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	<
120	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroupStamp(j);
122	<	nAtomsInGroups += cgStamp->getNMembers();
123	<	}
124	<
125	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	<
127	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128	<
129	<	//calculate atoms in rigid bodies
130	<	int nAtomsInRigidBodies = 0;
131	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	<
133	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	<	rbStamp = molStamp->getRigidBodyStamp(j);
135	<	nAtomsInRigidBodies += rbStamp->getNMembers();
136	<	}
137	<
138	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	<
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin();
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		}
#	Line 175 | Line 164 | namespace oopse {
164		delete forceField_;
165		}
166
178	–	int SimInfo::getNGlobalConstraints() {
179	–	int nGlobalConstraints;
180	–	#ifdef IS_MPI
181	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
182	–	MPI_COMM_WORLD);
183	–	#else
184	–	nGlobalConstraints =  nConstraints_;
185	–	#endif
186	–	return nGlobalConstraints;
187	–	}
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 223 | 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 237 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
240	–
241	–
221		}
222
223
#	Line 254 | 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)) {
266	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	–	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	<
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 296 | Line 291 | namespace oopse {
291
292		int SimInfo::getFdf() {
293		#ifdef IS_MPI
294	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
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)) {
318	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	–	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 332 | 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 345 | 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 354 | 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<Bond*>::iterator bondIter;
376	>	vector<Bend*>::iterator bendIter;
377	>	vector<Torsion*>::iterator torsionIter;
378	>	vector<Inversion*>::iterator inversionIter;
379		Bond* bond;
380		Bend* bend;
381		Torsion* torsion;
382	+	Inversion* inversion;
383		int a;
384		int b;
385		int c;
386		int d;
387
388	<	std::map<int, std::set<int> > atomGroups;
388	>	// atomGroups can be used to add special interaction maps between
389	>	// groups of atoms that are in two separate rigid bodies.
390	>	// However, most site-site interactions between two rigid bodies
391	>	// are probably not special, just the ones between the physically
392	>	// bonded atoms.  Interactions *within* a single rigid body should
393	>	// always be excluded.  These are done at the bottom of this
394	>	// function.
395
396	+	map<int, set<int> > atomGroups;
397		Molecule::RigidBodyIterator rbIter;
398		RigidBody* rb;
399		Molecule::IntegrableObjectIterator ii;
400	<	StuntDouble* integrableObject;
400	>	StuntDouble* sd;
401
402	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
403	<	integrableObject = mol->nextIntegrableObject(ii)) {
404	<
405	<	if (integrableObject->isRigidBody()) {
406	<	rb = static_cast<RigidBody*>(integrableObject);
407	<	std::vector<Atom*> atoms = rb->getAtoms();
408	<	std::set<int> rigidAtoms;
409	<	for (int i = 0; i < atoms.size(); ++i) {
410	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
411	<	}
412	<	for (int i = 0; i < atoms.size(); ++i) {
413	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
414	<	}
402	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
403	>	sd = mol->nextIntegrableObject(ii)) {
404	>
405	>	if (sd->isRigidBody()) {
406	>	rb = static_cast<RigidBody*>(sd);
407	>	vector<Atom*> atoms = rb->getAtoms();
408	>	set<int> rigidAtoms;
409	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
410	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
411	>	}
412	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
413	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
414	>	}
415		} else {
416	<	std::set<int> oneAtomSet;
417	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
418	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
416	>	set<int> oneAtomSet;
417	>	oneAtomSet.insert(sd->getGlobalIndex());
418	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
419		}
420		}
421	+
422	+	for (bond= mol->beginBond(bondIter); bond != NULL;
423	+	bond = mol->nextBond(bondIter)) {
424
396	–
397	–
398	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
425		a = bond->getAtomA()->getGlobalIndex();
426	<	b = bond->getAtomB()->getGlobalIndex();
427	<	exclude_.addPair(a, b);
426	>	b = bond->getAtomB()->getGlobalIndex();
427	>
428	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
429	>	oneTwoInteractions_.addPair(a, b);
430	>	} else {
431	>	excludedInteractions_.addPair(a, b);
432	>	}
433		}
434
435	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
435	>	for (bend= mol->beginBend(bendIter); bend != NULL;
436	>	bend = mol->nextBend(bendIter)) {
437	>
438		a = bend->getAtomA()->getGlobalIndex();
439		b = bend->getAtomB()->getGlobalIndex();
440		c = bend->getAtomC()->getGlobalIndex();
408	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
409	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
410	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
411	–
412	–	exclude_.addPairs(rigidSetA, rigidSetB);
413	–	exclude_.addPairs(rigidSetA, rigidSetC);
414	–	exclude_.addPairs(rigidSetB, rigidSetC);
441
442	<	//exclude_.addPair(a, b);
443	<	//exclude_.addPair(a, c);
444	<	//exclude_.addPair(b, c);
442	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
443	>	oneTwoInteractions_.addPair(a, b);
444	>	oneTwoInteractions_.addPair(b, c);
445	>	} else {
446	>	excludedInteractions_.addPair(a, b);
447	>	excludedInteractions_.addPair(b, c);
448	>	}
449	>
450	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
451	>	oneThreeInteractions_.addPair(a, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, c);
454	>	}
455		}
456
457	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
457	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
458	>	torsion = mol->nextTorsion(torsionIter)) {
459	>
460		a = torsion->getAtomA()->getGlobalIndex();
461		b = torsion->getAtomB()->getGlobalIndex();
462		c = torsion->getAtomC()->getGlobalIndex();
463	<	d = torsion->getAtomD()->getGlobalIndex();
426	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
427	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
428	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
429	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
463	>	d = torsion->getAtomD()->getGlobalIndex();
464
465	<	exclude_.addPairs(rigidSetA, rigidSetB);
466	<	exclude_.addPairs(rigidSetA, rigidSetC);
467	<	exclude_.addPairs(rigidSetA, rigidSetD);
468	<	exclude_.addPairs(rigidSetB, rigidSetC);
469	<	exclude_.addPairs(rigidSetB, rigidSetD);
470	<	exclude_.addPairs(rigidSetC, rigidSetD);
465	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
466	>	oneTwoInteractions_.addPair(a, b);
467	>	oneTwoInteractions_.addPair(b, c);
468	>	oneTwoInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(a, b);
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474
475	<	/*
476	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
477	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
478	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
479	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
480	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
481	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
482	<
483	<
484	<	exclude_.addPair(a, b);
485	<	exclude_.addPair(a, c);
486	<	exclude_.addPair(a, d);
487	<	exclude_.addPair(b, c);
451	<	exclude_.addPair(b, d);
452	<	exclude_.addPair(c, d);
453	<	*/
475	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
476	>	oneThreeInteractions_.addPair(a, c);
477	>	oneThreeInteractions_.addPair(b, d);
478	>	} else {
479	>	excludedInteractions_.addPair(a, c);
480	>	excludedInteractions_.addPair(b, d);
481	>	}
482	>
483	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
484	>	oneFourInteractions_.addPair(a, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, d);
487	>	}
488		}
489
490	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
491	<	std::vector<Atom*> atoms = rb->getAtoms();
492	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
493	<	for (int j = i + 1; j < atoms.size(); ++j) {
490	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
491	>	inversion = mol->nextInversion(inversionIter)) {
492	>
493	>	a = inversion->getAtomA()->getGlobalIndex();
494	>	b = inversion->getAtomB()->getGlobalIndex();
495	>	c = inversion->getAtomC()->getGlobalIndex();
496	>	d = inversion->getAtomD()->getGlobalIndex();
497	>
498	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
499	>	oneTwoInteractions_.addPair(a, b);
500	>	oneTwoInteractions_.addPair(a, c);
501	>	oneTwoInteractions_.addPair(a, d);
502	>	} else {
503	>	excludedInteractions_.addPair(a, b);
504	>	excludedInteractions_.addPair(a, c);
505	>	excludedInteractions_.addPair(a, d);
506	>	}
507	>
508	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
509	>	oneThreeInteractions_.addPair(b, c);
510	>	oneThreeInteractions_.addPair(b, d);
511	>	oneThreeInteractions_.addPair(c, d);
512	>	} else {
513	>	excludedInteractions_.addPair(b, c);
514	>	excludedInteractions_.addPair(b, d);
515	>	excludedInteractions_.addPair(c, d);
516	>	}
517	>	}
518	>
519	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
520	>	rb = mol->nextRigidBody(rbIter)) {
521	>	vector<Atom*> atoms = rb->getAtoms();
522	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
523	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
524		a = atoms[i]->getGlobalIndex();
525		b = atoms[j]->getGlobalIndex();
526	<	exclude_.addPair(a, b);
526	>	excludedInteractions_.addPair(a, b);
527		}
528		}
529		}
530
531		}
532
533	<	void SimInfo::removeExcludePairs(Molecule* mol) {
534	<	std::vector<Bond*>::iterator bondIter;
535	<	std::vector<Bend*>::iterator bendIter;
536	<	std::vector<Torsion*>::iterator torsionIter;
533	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
534	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
535	>	vector<Bond*>::iterator bondIter;
536	>	vector<Bend*>::iterator bendIter;
537	>	vector<Torsion*>::iterator torsionIter;
538	>	vector<Inversion*>::iterator inversionIter;
539		Bond* bond;
540		Bend* bend;
541		Torsion* torsion;
542	+	Inversion* inversion;
543		int a;
544		int b;
545		int c;
546		int d;
547
548	<	std::map<int, std::set<int> > atomGroups;
482	<
548	>	map<int, set<int> > atomGroups;
549		Molecule::RigidBodyIterator rbIter;
550		RigidBody* rb;
551		Molecule::IntegrableObjectIterator ii;
552	<	StuntDouble* integrableObject;
552	>	StuntDouble* sd;
553
554	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
555	<	integrableObject = mol->nextIntegrableObject(ii)) {
556	<
557	<	if (integrableObject->isRigidBody()) {
558	<	rb = static_cast<RigidBody*>(integrableObject);
559	<	std::vector<Atom*> atoms = rb->getAtoms();
560	<	std::set<int> rigidAtoms;
561	<	for (int i = 0; i < atoms.size(); ++i) {
562	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
563	<	}
564	<	for (int i = 0; i < atoms.size(); ++i) {
565	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
566	<	}
554	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
555	>	sd = mol->nextIntegrableObject(ii)) {
556	>
557	>	if (sd->isRigidBody()) {
558	>	rb = static_cast<RigidBody*>(sd);
559	>	vector<Atom*> atoms = rb->getAtoms();
560	>	set<int> rigidAtoms;
561	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
562	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
563	>	}
564	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
565	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
566	>	}
567		} else {
568	<	std::set<int> oneAtomSet;
569	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
570	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
568	>	set<int> oneAtomSet;
569	>	oneAtomSet.insert(sd->getGlobalIndex());
570	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
571		}
572		}
573
574	<
575	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
574	>	for (bond= mol->beginBond(bondIter); bond != NULL;
575	>	bond = mol->nextBond(bondIter)) {
576	>
577		a = bond->getAtomA()->getGlobalIndex();
578	<	b = bond->getAtomB()->getGlobalIndex();
579	<	exclude_.removePair(a, b);
578	>	b = bond->getAtomB()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	} else {
583	>	excludedInteractions_.removePair(a, b);
584	>	}
585		}
586
587	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
587	>	for (bend= mol->beginBend(bendIter); bend != NULL;
588	>	bend = mol->nextBend(bendIter)) {
589	>
590		a = bend->getAtomA()->getGlobalIndex();
591		b = bend->getAtomB()->getGlobalIndex();
592		c = bend->getAtomC()->getGlobalIndex();
519	–
520	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
521	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
522	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
523	–
524	–	exclude_.removePairs(rigidSetA, rigidSetB);
525	–	exclude_.removePairs(rigidSetA, rigidSetC);
526	–	exclude_.removePairs(rigidSetB, rigidSetC);
593
594	<	//exclude_.removePair(a, b);
595	<	//exclude_.removePair(a, c);
596	<	//exclude_.removePair(b, c);
594	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
595	>	oneTwoInteractions_.removePair(a, b);
596	>	oneTwoInteractions_.removePair(b, c);
597	>	} else {
598	>	excludedInteractions_.removePair(a, b);
599	>	excludedInteractions_.removePair(b, c);
600	>	}
601	>
602	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
603	>	oneThreeInteractions_.removePair(a, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, c);
606	>	}
607		}
608
609	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
609	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
610	>	torsion = mol->nextTorsion(torsionIter)) {
611	>
612		a = torsion->getAtomA()->getGlobalIndex();
613		b = torsion->getAtomB()->getGlobalIndex();
614		c = torsion->getAtomC()->getGlobalIndex();
615	<	d = torsion->getAtomD()->getGlobalIndex();
615	>	d = torsion->getAtomD()->getGlobalIndex();
616	>
617	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
618	>	oneTwoInteractions_.removePair(a, b);
619	>	oneTwoInteractions_.removePair(b, c);
620	>	oneTwoInteractions_.removePair(c, d);
621	>	} else {
622	>	excludedInteractions_.removePair(a, b);
623	>	excludedInteractions_.removePair(b, c);
624	>	excludedInteractions_.removePair(c, d);
625	>	}
626
627	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
628	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
629	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
630	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
627	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
628	>	oneThreeInteractions_.removePair(a, c);
629	>	oneThreeInteractions_.removePair(b, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, c);
632	>	excludedInteractions_.removePair(b, d);
633	>	}
634
635	<	exclude_.removePairs(rigidSetA, rigidSetB);
636	<	exclude_.removePairs(rigidSetA, rigidSetC);
637	<	exclude_.removePairs(rigidSetA, rigidSetD);
638	<	exclude_.removePairs(rigidSetB, rigidSetC);
639	<	exclude_.removePairs(rigidSetB, rigidSetD);
640	<	exclude_.removePairs(rigidSetC, rigidSetD);
635	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
636	>	oneFourInteractions_.removePair(a, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, d);
639	>	}
640	>	}
641
642	<	/*
643	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
553	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
554	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
555	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
556	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
557	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
642	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
643	>	inversion = mol->nextInversion(inversionIter)) {
644
645	<
646	<	exclude_.removePair(a, b);
647	<	exclude_.removePair(a, c);
648	<	exclude_.removePair(a, d);
649	<	exclude_.removePair(b, c);
650	<	exclude_.removePair(b, d);
651	<	exclude_.removePair(c, d);
652	<	*/
645	>	a = inversion->getAtomA()->getGlobalIndex();
646	>	b = inversion->getAtomB()->getGlobalIndex();
647	>	c = inversion->getAtomC()->getGlobalIndex();
648	>	d = inversion->getAtomD()->getGlobalIndex();
649	>
650	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
651	>	oneTwoInteractions_.removePair(a, b);
652	>	oneTwoInteractions_.removePair(a, c);
653	>	oneTwoInteractions_.removePair(a, d);
654	>	} else {
655	>	excludedInteractions_.removePair(a, b);
656	>	excludedInteractions_.removePair(a, c);
657	>	excludedInteractions_.removePair(a, d);
658	>	}
659	>
660	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
661	>	oneThreeInteractions_.removePair(b, c);
662	>	oneThreeInteractions_.removePair(b, d);
663	>	oneThreeInteractions_.removePair(c, d);
664	>	} else {
665	>	excludedInteractions_.removePair(b, c);
666	>	excludedInteractions_.removePair(b, d);
667	>	excludedInteractions_.removePair(c, d);
668	>	}
669		}
670
671	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
672	<	std::vector<Atom*> atoms = rb->getAtoms();
673	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
674	<	for (int j = i + 1; j < atoms.size(); ++j) {
671	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
672	>	rb = mol->nextRigidBody(rbIter)) {
673	>	vector<Atom*> atoms = rb->getAtoms();
674	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
675	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
676		a = atoms[i]->getGlobalIndex();
677		b = atoms[j]->getGlobalIndex();
678	<	exclude_.removePair(a, b);
678	>	excludedInteractions_.removePair(a, b);
679		}
680		}
681		}
682	<
682	>
683		}
684	<
685	<
684	>
685	>
686		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
687		int curStampId;
688	<
688	>
689		//index from 0
690		curStampId = moleculeStamps_.size();
691
#	Line 590 | Line 693 | namespace oopse {
693		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
694		}
695
593	–	void SimInfo::update() {
696
697	<	setupSimType();
698	<
699	<	#ifdef IS_MPI
700	<	setupFortranParallel();
701	<	#endif
702	<
703	<	setupFortranSim();
704	<
705	<	//setup fortran force field
604	<	/** @deprecate */
605	<	int isError = 0;
606	<
607	<	setupCutoff();
608	<
609	<	setupElectrostaticSummationMethod( isError );
610	<	setupSwitchingFunction();
611	<	setupAccumulateBoxDipole();
612	<
613	<	if(isError){
614	<	sprintf( painCave.errMsg,
615	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
616	<	painCave.isFatal = 1;
617	<	simError();
618	<	}
619	<
697	>	/**
698	>	* update
699	>	*
700	>	*  Performs the global checks and variable settings after the
701	>	*  objects have been created.
702	>	*
703	>	*/
704	>	void SimInfo::update() {
705	>	setupSimVariables();
706		calcNdf();
707		calcNdfRaw();
708		calcNdfTrans();
623	–
624	–	fortranInitialized_ = true;
709		}
710	<
711	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
710	>
711	>	/**
712	>	* getSimulatedAtomTypes
713	>	*
714	>	* Returns an STL set of AtomType* that are actually present in this
715	>	* simulation.  Must query all processors to assemble this information.
716	>	*
717	>	*/
718	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
719		SimInfo::MoleculeIterator mi;
720		Molecule* mol;
721		Molecule::AtomIterator ai;
722		Atom* atom;
723	<	std::set<AtomType*> atomTypes;
724	<
723	>	set<AtomType*> atomTypes;
724	>
725		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
726	<
727	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
726	>	for(atom = mol->beginAtom(ai); atom != NULL;
727	>	atom = mol->nextAtom(ai)) {
728		atomTypes.insert(atom->getAtomType());
729	<	}
730	<
640	<	}
641	<
642	<	return atomTypes;
643	<	}
644	<
645	<	void SimInfo::setupSimType() {
646	<	std::set<AtomType*>::iterator i;
647	<	std::set<AtomType*> atomTypes;
648	<	atomTypes = getUniqueAtomTypes();
729	>	}
730	>	}
731
732	<	int useLennardJones = 0;
651	<	int useElectrostatic = 0;
652	<	int useEAM = 0;
653	<	int useSC = 0;
654	<	int useCharge = 0;
655	<	int useDirectional = 0;
656	<	int useDipole = 0;
657	<	int useGayBerne = 0;
658	<	int useSticky = 0;
659	<	int useStickyPower = 0;
660	<	int useShape = 0;
661	<	int useFLARB = 0; //it is not in AtomType yet
662	<	int useDirectionalAtom = 0;
663	<	int useElectrostatics = 0;
664	<	//usePBC and useRF are from simParams
665	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666	<	int useRF;
667	<	int useSF;
668	<	int useSP;
669	<	int useBoxDipole;
732	>	#ifdef IS_MPI
733
734	<	std::string myMethod;
735	<
673	<	// set the useRF logical
674	<	useRF = 0;
675	<	useSF = 0;
676	<	useSP = 0;
677	<
678	<
679	<	if (simParams_->haveElectrostaticSummationMethod()) {
680	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
681	<	toUpper(myMethod);
682	<	if (myMethod == "REACTION_FIELD"){
683	<	useRF = 1;
684	<	} else if (myMethod == "SHIFTED_FORCE"){
685	<	useSF = 1;
686	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
687	<	useSP = 1;
688	<	}
689	<	}
734	>	// loop over the found atom types on this processor, and add their
735	>	// numerical idents to a vector:
736
737	<	if (simParams_->haveAccumulateBoxDipole())
738	<	if (simParams_->getAccumulateBoxDipole())
739	<	useBoxDipole = 1;
737	>	vector<int> foundTypes;
738	>	set<AtomType*>::iterator i;
739	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
740	>	foundTypes.push_back( (*i)->getIdent() );
741
742	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
742	>	// count_local holds the number of found types on this processor
743	>	int count_local = foundTypes.size();
744
745	<	//loop over all of the atom types
698	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
699	<	useLennardJones |= (*i)->isLennardJones();
700	<	useElectrostatic |= (*i)->isElectrostatic();
701	<	useEAM |= (*i)->isEAM();
702	<	useSC |= (*i)->isSC();
703	<	useCharge |= (*i)->isCharge();
704	<	useDirectional |= (*i)->isDirectional();
705	<	useDipole |= (*i)->isDipole();
706	<	useGayBerne |= (*i)->isGayBerne();
707	<	useSticky |= (*i)->isSticky();
708	<	useStickyPower |= (*i)->isStickyPower();
709	<	useShape |= (*i)->isShape();
710	<	}
745	>	int nproc = MPI::COMM_WORLD.Get_size();
746
747	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
748	<	useDirectionalAtom = 1;
749	<	}
747	>	// we need arrays to hold the counts and displacement vectors for
748	>	// all processors
749	>	vector<int> counts(nproc, 0);
750	>	vector<int> disps(nproc, 0);
751
752	<	if (useCharge || useDipole) {
753	<	useElectrostatics = 1;
752	>	// fill the counts array
753	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
754	>	1, MPI::INT);
755	>
756	>	// use the processor counts to compute the displacement array
757	>	disps[0] = 0;
758	>	int totalCount = counts[0];
759	>	for (int iproc = 1; iproc < nproc; iproc++) {
760	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
761	>	totalCount += counts[iproc];
762		}
763
764	<	#ifdef IS_MPI
765	<	int temp;
764	>	// we need a (possibly redundant) set of all found types:
765	>	vector<int> ftGlobal(totalCount);
766	>
767	>	// now spray out the foundTypes to all the other processors:
768	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
769	>	&ftGlobal[0], &counts[0], &disps[0],
770	>	MPI::INT);
771
772	<	temp = usePBC;
724	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	>	vector<int>::iterator j;
773
774	<	temp = useDirectionalAtom;
775	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
774	>	// foundIdents is a stl set, so inserting an already found ident
775	>	// will have no effect.
776	>	set<int> foundIdents;
777
778	<	temp = useLennardJones;
779	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
778	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
779	>	foundIdents.insert((*j));
780	>
781	>	// now iterate over the foundIdents and get the actual atom types
782	>	// that correspond to these:
783	>	set<int>::iterator it;
784	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
785	>	atomTypes.insert( forceField_->getAtomType((*it)) );
786	>
787	>	#endif
788
789	<	temp = useElectrostatics;
790	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
789	>	return atomTypes;
790	>	}
791
735	–	temp = useCharge;
736	–	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
792
793	<	temp = useDipole;
794	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793	>	int getGlobalCountOfType(AtomType* atype) {
794	>	/*
795	>	set<AtomType*> atypes = getSimulatedAtomTypes();
796	>	map<AtomType*, int> counts_;
797
798	<	temp = useSticky;
799	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
799	>	for(atom = mol->beginAtom(ai); atom != NULL;
800	>	atom = mol->nextAtom(ai)) {
801	>	atom->getAtomType();
802	>	}
803	>	}
804	>	*/
805	>	return 0;
806	>	}
807
808	<	temp = useStickyPower;
809	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	void SimInfo::setupSimVariables() {
809	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
810	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
811	>	// parameter is true
812	>	calcBoxDipole_ = false;
813	>	if ( simParams_->haveAccumulateBoxDipole() )
814	>	if ( simParams_->getAccumulateBoxDipole() ) {
815	>	calcBoxDipole_ = true;
816	>	}
817
818	<	temp = useGayBerne;
819	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	>	set<AtomType*>::iterator i;
819	>	set<AtomType*> atomTypes;
820	>	atomTypes = getSimulatedAtomTypes();
821	>	bool usesElectrostatic = false;
822	>	bool usesMetallic = false;
823	>	bool usesDirectional = false;
824	>	bool usesFluctuatingCharges =  false;
825	>	//loop over all of the atom types
826	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
827	>	usesElectrostatic |= (*i)->isElectrostatic();
828	>	usesMetallic |= (*i)->isMetal();
829	>	usesDirectional |= (*i)->isDirectional();
830	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
831	>	}
832
833	<	temp = useEAM;
834	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
835	<
836	<	temp = useSC;
837	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	>	#ifdef IS_MPI
834	>	bool temp;
835	>	temp = usesDirectional;
836	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
837	>	MPI::LOR);
838	>
839	>	temp = usesMetallic;
840	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
841	>	MPI::LOR);
842
843	<	temp = useShape;
844	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
843	>	temp = usesElectrostatic;
844	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
845	>	MPI::LOR);
846
847	<	temp = useFLARB;
848	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
847	>	temp = usesFluctuatingCharges;
848	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
849	>	MPI::LOR);
850	>	#else
851
852	<	temp = useRF;
853	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	usesDirectionalAtoms_ = usesDirectional;
853	>	usesMetallicAtoms_ = usesMetallic;
854	>	usesElectrostaticAtoms_ = usesElectrostatic;
855	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
856
765	–	temp = useSF;
766	–	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	–
768	–	temp = useSP;
769	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	–
771	–	temp = useBoxDipole;
772	–	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	–
774	–	temp = useAtomicVirial_;
775	–	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	–
857		#endif
858	<
859	<	fInfo_.SIM_uses_PBC = usePBC;
860	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
861	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
782	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
783	<	fInfo_.SIM_uses_Charges = useCharge;
784	<	fInfo_.SIM_uses_Dipoles = useDipole;
785	<	fInfo_.SIM_uses_Sticky = useSticky;
786	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
787	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
788	<	fInfo_.SIM_uses_EAM = useEAM;
789	<	fInfo_.SIM_uses_SC = useSC;
790	<	fInfo_.SIM_uses_Shapes = useShape;
791	<	fInfo_.SIM_uses_FLARB = useFLARB;
792	<	fInfo_.SIM_uses_RF = useRF;
793	<	fInfo_.SIM_uses_SF = useSF;
794	<	fInfo_.SIM_uses_SP = useSP;
795	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
858	>
859	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
860	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
861	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
862		}
863
799	–	void SimInfo::setupFortranSim() {
800	–	int isError;
801	–	int nExclude;
802	–	std::vector<int> fortranGlobalGroupMembership;
803	–
804	–	nExclude = exclude_.getSize();
805	–	isError = 0;
864
865	<	//globalGroupMembership_ is filled by SimCreator
808	<	for (int i = 0; i < nGlobalAtoms_; i++) {
809	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
810	<	}
811	<
812	<	//calculate mass ratio of cutoff group
813	<	std::vector<RealType> mfact;
865	>	vector<int> SimInfo::getGlobalAtomIndices() {
866		SimInfo::MoleculeIterator mi;
867		Molecule* mol;
816	–	Molecule::CutoffGroupIterator ci;
817	–	CutoffGroup* cg;
868		Molecule::AtomIterator ai;
869		Atom* atom;
820	–	RealType totalMass;
870
871	<	//to avoid memory reallocation, reserve enough space for mfact
823	<	mfact.reserve(getNCutoffGroups());
871	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
872
873	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
874	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
875	<
876	<	totalMass = cg->getMass();
829	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
830	<	// Check for massless groups - set mfact to 1 if true
831	<	if (totalMass != 0)
832	<	mfact.push_back(atom->getMass()/totalMass);
833	<	else
834	<	mfact.push_back( 1.0 );
835	<	}
836	<
837	<	}
838	<	}
839	<
840	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
841	<	std::vector<int> identArray;
842	<
843	<	//to avoid memory reallocation, reserve enough space identArray
844	<	identArray.reserve(getNAtoms());
845	<
846	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
847	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
848	<	identArray.push_back(atom->getIdent());
873	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
874	>
875	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
876	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
877		}
850	–	}
851	–
852	–	//fill molMembershipArray
853	–	//molMembershipArray is filled by SimCreator
854	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
855	–	for (int i = 0; i < nGlobalAtoms_; i++) {
856	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
878		}
879	<
859	<	//setup fortran simulation
860	<	int nGlobalExcludes = 0;
861	<	int* globalExcludes = NULL;
862	<	int* excludeList = exclude_.getExcludeList();
863	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
864	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
865	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
866	<
867	<	if( isError ){
868	<
869	<	sprintf( painCave.errMsg,
870	<	"There was an error setting the simulation information in fortran.\n" );
871	<	painCave.isFatal = 1;
872	<	painCave.severity = OOPSE_ERROR;
873	<	simError();
874	<	}
875	<
876	<	#ifdef IS_MPI
877	<	sprintf( checkPointMsg,
878	<	"succesfully sent the simulation information to fortran.\n");
879	<	MPIcheckPoint();
880	<	#endif // is_mpi
881	<
882	<	// Setup number of neighbors in neighbor list if present
883	<	if (simParams_->haveNeighborListNeighbors()) {
884	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
885	<	setNeighbors(&nlistNeighbors);
886	<	}
887	<
888	<
879	>	return GlobalAtomIndices;
880		}
881
882
883	<	#ifdef IS_MPI
893	<	void SimInfo::setupFortranParallel() {
894	<
895	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
896	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
897	<	std::vector<int> localToGlobalCutoffGroupIndex;
883	>	vector<int> SimInfo::getGlobalGroupIndices() {
884		SimInfo::MoleculeIterator mi;
899	–	Molecule::AtomIterator ai;
900	–	Molecule::CutoffGroupIterator ci;
885		Molecule* mol;
886	<	Atom* atom;
886	>	Molecule::CutoffGroupIterator ci;
887		CutoffGroup* cg;
904	–	mpiSimData parallelData;
905	–	int isError;
888
889	+	vector<int> GlobalGroupIndices;
890	+
891		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
892	<
893	<	//local index(index in DataStorge) of atom is important
894	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
895	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
896	<	}
897	<
914	<	//local index of cutoff group is trivial, it only depends on the order of travesing
915	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
916	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
892	>
893	>	//local index of cutoff group is trivial, it only depends on the
894	>	//order of travesing
895	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
896	>	cg = mol->nextCutoffGroup(ci)) {
897	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
898		}
918	–
899		}
900	+	return GlobalGroupIndices;
901	+	}
902
921	–	//fill up mpiSimData struct
922	–	parallelData.nMolGlobal = getNGlobalMolecules();
923	–	parallelData.nMolLocal = getNMolecules();
924	–	parallelData.nAtomsGlobal = getNGlobalAtoms();
925	–	parallelData.nAtomsLocal = getNAtoms();
926	–	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
927	–	parallelData.nGroupsLocal = getNCutoffGroups();
928	–	parallelData.myNode = worldRank;
929	–	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
903
904	<	//pass mpiSimData struct and index arrays to fortran
932	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
933	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
934	<	&localToGlobalCutoffGroupIndex[0], &isError);
904	>	void SimInfo::prepareTopology() {
905
906	<	if (isError) {
907	<	sprintf(painCave.errMsg,
908	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
909	<	painCave.isFatal = 1;
910	<	simError();
911	<	}
906	>	//calculate mass ratio of cutoff group
907	>	SimInfo::MoleculeIterator mi;
908	>	Molecule* mol;
909	>	Molecule::CutoffGroupIterator ci;
910	>	CutoffGroup* cg;
911	>	Molecule::AtomIterator ai;
912	>	Atom* atom;
913	>	RealType totalMass;
914
915	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
916	<	MPIcheckPoint();
917	<
918	<
919	<	}
920	<
921	<	#endif
922	<
923	<	void SimInfo::setupCutoff() {
915	>	/**
916	>	* The mass factor is the relative mass of an atom to the total
917	>	* mass of the cutoff group it belongs to.  By default, all atoms
918	>	* are their own cutoff groups, and therefore have mass factors of
919	>	* 1.  We need some special handling for massless atoms, which
920	>	* will be treated as carrying the entire mass of the cutoff
921	>	* group.
922	>	*/
923	>	massFactors_.clear();
924	>	massFactors_.resize(getNAtoms(), 1.0);
925
926	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
927	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
928	>	cg = mol->nextCutoffGroup(ci)) {
929
930	<	// Check the cutoff policy
931	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
932	<
933	<	// Set LJ shifting bools to false
934	<	ljsp_ = false;
935	<	ljsf_ = false;
936	<
962	<	std::string myPolicy;
963	<	if (forceFieldOptions_.haveCutoffPolicy()){
964	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
965	<	}else if (simParams_->haveCutoffPolicy()) {
966	<	myPolicy = simParams_->getCutoffPolicy();
967	<	}
968	<
969	<	if (!myPolicy.empty()){
970	<	toUpper(myPolicy);
971	<	if (myPolicy == "MIX") {
972	<	cp = MIX_CUTOFF_POLICY;
973	<	} else {
974	<	if (myPolicy == "MAX") {
975	<	cp = MAX_CUTOFF_POLICY;
976	<	} else {
977	<	if (myPolicy == "TRADITIONAL") {
978	<	cp = TRADITIONAL_CUTOFF_POLICY;
979	<	} else {
980	<	// throw error
981	<	sprintf( painCave.errMsg,
982	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
983	<	painCave.isFatal = 1;
984	<	simError();
985	<	}
986	<	}
987	<	}
988	<	}
989	<	notifyFortranCutoffPolicy(&cp);
990	<
991	<	// Check the Skin Thickness for neighborlists
992	<	RealType skin;
993	<	if (simParams_->haveSkinThickness()) {
994	<	skin = simParams_->getSkinThickness();
995	<	notifyFortranSkinThickness(&skin);
996	<	}
997	<
998	<	// Check if the cutoff was set explicitly:
999	<	if (simParams_->haveCutoffRadius()) {
1000	<	rcut_ = simParams_->getCutoffRadius();
1001	<	if (simParams_->haveSwitchingRadius()) {
1002	<	rsw_  = simParams_->getSwitchingRadius();
1003	<	} else {
1004	<	if (fInfo_.SIM_uses_Charges |
1005	<	fInfo_.SIM_uses_Dipoles |
1006	<	fInfo_.SIM_uses_RF) {
1007	<
1008	<	rsw_ = 0.85 * rcut_;
1009	<	sprintf(painCave.errMsg,
1010	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1011	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1012	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1013	<	painCave.isFatal = 0;
1014	<	simError();
1015	<	} else {
1016	<	rsw_ = rcut_;
1017	<	sprintf(painCave.errMsg,
1018	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1019	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1020	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1021	<	painCave.isFatal = 0;
1022	<	simError();
930	>	totalMass = cg->getMass();
931	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
932	>	// Check for massless groups - set mfact to 1 if true
933	>	if (totalMass != 0)
934	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
935	>	else
936	>	massFactors_[atom->getLocalIndex()] = 1.0;
937		}
938	<	}
1025	<
1026	<	if (simParams_->haveElectrostaticSummationMethod()) {
1027	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028	<	toUpper(myMethod);
1029	<
1030	<	if (myMethod == "SHIFTED_POTENTIAL") {
1031	<	ljsp_ = true;
1032	<	} else if (myMethod == "SHIFTED_FORCE") {
1033	<	ljsf_ = true;
1034	<	}
1035	<	}
1036	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1037	<
1038	<	} else {
1039	<
1040	<	// For electrostatic atoms, we'll assume a large safe value:
1041	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1042	<	sprintf(painCave.errMsg,
1043	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1044	<	"\tOOPSE will use a default value of 15.0 angstroms"
1045	<	"\tfor the cutoffRadius.\n");
1046	<	painCave.isFatal = 0;
1047	<	simError();
1048	<	rcut_ = 15.0;
1049	<
1050	<	if (simParams_->haveElectrostaticSummationMethod()) {
1051	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1052	<	toUpper(myMethod);
1053	<
1054	<	// For the time being, we're tethering the LJ shifted behavior to the
1055	<	// electrostaticSummationMethod keyword options
1056	<	if (myMethod == "SHIFTED_POTENTIAL") {
1057	<	ljsp_ = true;
1058	<	} else if (myMethod == "SHIFTED_FORCE") {
1059	<	ljsf_ = true;
1060	<	}
1061	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1062	<	if (simParams_->haveSwitchingRadius()){
1063	<	sprintf(painCave.errMsg,
1064	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1065	<	"\teven though the electrostaticSummationMethod was\n"
1066	<	"\tset to %s\n", myMethod.c_str());
1067	<	painCave.isFatal = 1;
1068	<	simError();
1069	<	}
1070	<	}
1071	<	}
1072	<
1073	<	if (simParams_->haveSwitchingRadius()){
1074	<	rsw_ = simParams_->getSwitchingRadius();
1075	<	} else {
1076	<	sprintf(painCave.errMsg,
1077	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1078	<	"\tOOPSE will use a default value of\n"
1079	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1080	<	painCave.isFatal = 0;
1081	<	simError();
1082	<	rsw_ = 0.85 * rcut_;
1083	<	}
1084	<
1085	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1086	<
1087	<	} else {
1088	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1089	<	// We'll punt and let fortran figure out the cutoffs later.
1090	<
1091	<	notifyFortranYouAreOnYourOwn();
1092	<
1093	<	}
938	>	}
939		}
1095	–	}
940
941	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1098	<
1099	<	int errorOut;
1100	<	int esm =  NONE;
1101	<	int sm = UNDAMPED;
1102	<	RealType alphaVal;
1103	<	RealType dielectric;
1104	<
1105	<	errorOut = isError;
941	>	// Build the identArray_ and regions_
942
943	<	if (simParams_->haveElectrostaticSummationMethod()) {
944	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
945	<	toUpper(myMethod);
946	<	if (myMethod == "NONE") {
947	<	esm = NONE;
948	<	} else {
949	<	if (myMethod == "SWITCHING_FUNCTION") {
950	<	esm = SWITCHING_FUNCTION;
951	<	} else {
952	<	if (myMethod == "SHIFTED_POTENTIAL") {
1117	<	esm = SHIFTED_POTENTIAL;
1118	<	} else {
1119	<	if (myMethod == "SHIFTED_FORCE") {
1120	<	esm = SHIFTED_FORCE;
1121	<	} else {
1122	<	if (myMethod == "REACTION_FIELD") {
1123	<	esm = REACTION_FIELD;
1124	<	dielectric = simParams_->getDielectric();
1125	<	if (!simParams_->haveDielectric()) {
1126	<	// throw warning
1127	<	sprintf( painCave.errMsg,
1128	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1129	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1130	<	painCave.isFatal = 0;
1131	<	simError();
1132	<	}
1133	<	} else {
1134	<	// throw error
1135	<	sprintf( painCave.errMsg,
1136	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1137	<	"\t(Input file specified %s .)\n"
1138	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1139	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1140	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1141	<	painCave.isFatal = 1;
1142	<	simError();
1143	<	}
1144	<	}
1145	<	}
1146	<	}
943	>	identArray_.clear();
944	>	identArray_.reserve(getNAtoms());
945	>	regions_.clear();
946	>	regions_.reserve(getNAtoms());
947	>
948	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
949	>	int reg = mol->getRegion();
950	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
951	>	identArray_.push_back(atom->getIdent());
952	>	regions_.push_back(reg);
953		}
954	<	}
955	<
956	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1151	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1152	<	toUpper(myScreen);
1153	<	if (myScreen == "UNDAMPED") {
1154	<	sm = UNDAMPED;
1155	<	} else {
1156	<	if (myScreen == "DAMPED") {
1157	<	sm = DAMPED;
1158	<	if (!simParams_->haveDampingAlpha()) {
1159	<	// first set a cutoff dependent alpha value
1160	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1161	<	alphaVal = 0.5125 - rcut_* 0.025;
1162	<	// for values rcut > 20.5, alpha is zero
1163	<	if (alphaVal < 0) alphaVal = 0;
1164	<
1165	<	// throw warning
1166	<	sprintf( painCave.errMsg,
1167	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1168	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1169	<	painCave.isFatal = 0;
1170	<	simError();
1171	<	} else {
1172	<	alphaVal = simParams_->getDampingAlpha();
1173	<	}
1174	<
1175	<	} else {
1176	<	// throw error
1177	<	sprintf( painCave.errMsg,
1178	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1179	<	"\t(Input file specified %s .)\n"
1180	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1181	<	"or \"damped\".\n", myScreen.c_str() );
1182	<	painCave.isFatal = 1;
1183	<	simError();
1184	<	}
1185	<	}
1186	<	}
1187	<
1188	<	// let's pass some summation method variables to fortran
1189	<	setElectrostaticSummationMethod( &esm );
1190	<	setFortranElectrostaticMethod( &esm );
1191	<	setScreeningMethod( &sm );
1192	<	setDampingAlpha( &alphaVal );
1193	<	setReactionFieldDielectric( &dielectric );
1194	<	initFortranFF( &errorOut );
954	>	}
955	>
956	>	topologyDone_ = true;
957		}
958
1197	–	void SimInfo::setupSwitchingFunction() {
1198	–	int ft = CUBIC;
1199	–
1200	–	if (simParams_->haveSwitchingFunctionType()) {
1201	–	std::string funcType = simParams_->getSwitchingFunctionType();
1202	–	toUpper(funcType);
1203	–	if (funcType == "CUBIC") {
1204	–	ft = CUBIC;
1205	–	} else {
1206	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1207	–	ft = FIFTH_ORDER_POLY;
1208	–	} else {
1209	–	// throw error
1210	–	sprintf( painCave.errMsg,
1211	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1212	–	painCave.isFatal = 1;
1213	–	simError();
1214	–	}
1215	–	}
1216	–	}
1217	–
1218	–	// send switching function notification to switcheroo
1219	–	setFunctionType(&ft);
1220	–
1221	–	}
1222	–
1223	–	void SimInfo::setupAccumulateBoxDipole() {
1224	–
1225	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1226	–	if ( simParams_->haveAccumulateBoxDipole() )
1227	–	if ( simParams_->getAccumulateBoxDipole() ) {
1228	–	setAccumulateBoxDipole();
1229	–	calcBoxDipole_ = true;
1230	–	}
1231	–
1232	–	}
1233	–
959		void SimInfo::addProperty(GenericData* genData) {
960		properties_.addProperty(genData);
961		}
962
963	<	void SimInfo::removeProperty(const std::string& propName) {
963	>	void SimInfo::removeProperty(const string& propName) {
964		properties_.removeProperty(propName);
965		}
966
#	Line 1243 | Line 968 | namespace oopse {
968		properties_.clearProperties();
969		}
970
971	<	std::vector<std::string> SimInfo::getPropertyNames() {
971	>	vector<string> SimInfo::getPropertyNames() {
972		return properties_.getPropertyNames();
973		}
974
975	<	std::vector<GenericData*> SimInfo::getProperties() {
975	>	vector<GenericData*> SimInfo::getProperties() {
976		return properties_.getProperties();
977		}
978
979	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
979	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
980		return properties_.getPropertyByName(propName);
981		}
982
#	Line 1265 | Line 990 | namespace oopse {
990		Molecule* mol;
991		RigidBody* rb;
992		Atom* atom;
993	+	CutoffGroup* cg;
994		SimInfo::MoleculeIterator mi;
995		Molecule::RigidBodyIterator rbIter;
996	<	Molecule::AtomIterator atomIter;;
996	>	Molecule::AtomIterator atomIter;
997	>	Molecule::CutoffGroupIterator cgIter;
998
999		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1000
1001	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1001	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
1002	>	atom = mol->nextAtom(atomIter)) {
1003		atom->setSnapshotManager(sman_);
1004		}
1005
1006	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1006	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1007	>	rb = mol->nextRigidBody(rbIter)) {
1008		rb->setSnapshotManager(sman_);
1009		}
1010	+
1011	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1012	+	cg = mol->nextCutoffGroup(cgIter)) {
1013	+	cg->setSnapshotManager(sman_);
1014	+	}
1015		}
1016
1017		}
1018
1285	–	Vector3d SimInfo::getComVel(){
1286	–	SimInfo::MoleculeIterator i;
1287	–	Molecule* mol;
1019
1020	<	Vector3d comVel(0.0);
1290	<	RealType totalMass = 0.0;
1291	<
1292	<
1293	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1294	<	RealType mass = mol->getMass();
1295	<	totalMass += mass;
1296	<	comVel += mass * mol->getComVel();
1297	<	}
1298	<
1299	<	#ifdef IS_MPI
1300	<	RealType tmpMass = totalMass;
1301	<	Vector3d tmpComVel(comVel);
1302	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1303	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304	<	#endif
1305	<
1306	<	comVel /= totalMass;
1307	<
1308	<	return comVel;
1309	<	}
1310	<
1311	<	Vector3d SimInfo::getCom(){
1312	<	SimInfo::MoleculeIterator i;
1313	<	Molecule* mol;
1314	<
1315	<	Vector3d com(0.0);
1316	<	RealType totalMass = 0.0;
1317	<
1318	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1319	<	RealType mass = mol->getMass();
1320	<	totalMass += mass;
1321	<	com += mass * mol->getCom();
1322	<	}
1323	<
1324	<	#ifdef IS_MPI
1325	<	RealType tmpMass = totalMass;
1326	<	Vector3d tmpCom(com);
1327	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1328	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1329	<	#endif
1330	<
1331	<	com /= totalMass;
1332	<
1333	<	return com;
1334	<
1335	<	}
1336	<
1337	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1020	>	ostream& operator <<(ostream& o, SimInfo& info) {
1021
1022		return o;
1023		}
1024
1025	<
1343	<	/*
1344	<	Returns center of mass and center of mass velocity in one function call.
1345	<	*/
1346	<
1347	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1348	<	SimInfo::MoleculeIterator i;
1349	<	Molecule* mol;
1350	<
1351	<
1352	<	RealType totalMass = 0.0;
1353	<
1354	<
1355	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1356	<	RealType mass = mol->getMass();
1357	<	totalMass += mass;
1358	<	com += mass * mol->getCom();
1359	<	comVel += mass * mol->getComVel();
1360	<	}
1361	<
1362	<	#ifdef IS_MPI
1363	<	RealType tmpMass = totalMass;
1364	<	Vector3d tmpCom(com);
1365	<	Vector3d tmpComVel(comVel);
1366	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1367	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1368	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1369	<	#endif
1370	<
1371	<	com /= totalMass;
1372	<	comVel /= totalMass;
1373	<	}
1374	<
1375	<	/*
1376	<	Return intertia tensor for entire system and angular momentum Vector.
1377	<
1378	<
1379	<	[  Ixx -Ixy  -Ixz ]
1380	<	J =| -Iyx  Iyy  -Iyz |
1381	<	[ -Izx -Iyz   Izz ]
1382	<	*/
1383	<
1384	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1385	<
1386	<
1387	<	RealType xx = 0.0;
1388	<	RealType yy = 0.0;
1389	<	RealType zz = 0.0;
1390	<	RealType xy = 0.0;
1391	<	RealType xz = 0.0;
1392	<	RealType yz = 0.0;
1393	<	Vector3d com(0.0);
1394	<	Vector3d comVel(0.0);
1395	<
1396	<	getComAll(com, comVel);
1397	<
1398	<	SimInfo::MoleculeIterator i;
1399	<	Molecule* mol;
1400	<
1401	<	Vector3d thisq(0.0);
1402	<	Vector3d thisv(0.0);
1403	<
1404	<	RealType thisMass = 0.0;
1405	<
1406	<
1407	<
1408	<
1409	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1410	<
1411	<	thisq = mol->getCom()-com;
1412	<	thisv = mol->getComVel()-comVel;
1413	<	thisMass = mol->getMass();
1414	<	// Compute moment of intertia coefficients.
1415	<	xx += thisq[0]*thisq[0]*thisMass;
1416	<	yy += thisq[1]*thisq[1]*thisMass;
1417	<	zz += thisq[2]*thisq[2]*thisMass;
1418	<
1419	<	// compute products of intertia
1420	<	xy += thisq[0]*thisq[1]*thisMass;
1421	<	xz += thisq[0]*thisq[2]*thisMass;
1422	<	yz += thisq[1]*thisq[2]*thisMass;
1423	<
1424	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1425	<
1426	<	}
1427	<
1428	<
1429	<	inertiaTensor(0,0) = yy + zz;
1430	<	inertiaTensor(0,1) = -xy;
1431	<	inertiaTensor(0,2) = -xz;
1432	<	inertiaTensor(1,0) = -xy;
1433	<	inertiaTensor(1,1) = xx + zz;
1434	<	inertiaTensor(1,2) = -yz;
1435	<	inertiaTensor(2,0) = -xz;
1436	<	inertiaTensor(2,1) = -yz;
1437	<	inertiaTensor(2,2) = xx + yy;
1438	<
1439	<	#ifdef IS_MPI
1440	<	Mat3x3d tmpI(inertiaTensor);
1441	<	Vector3d tmpAngMom;
1442	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1443	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1444	<	#endif
1445	<
1446	<	return;
1447	<	}
1448	<
1449	<	//Returns the angular momentum of the system
1450	<	Vector3d SimInfo::getAngularMomentum(){
1451	<
1452	<	Vector3d com(0.0);
1453	<	Vector3d comVel(0.0);
1454	<	Vector3d angularMomentum(0.0);
1455	<
1456	<	getComAll(com,comVel);
1457	<
1458	<	SimInfo::MoleculeIterator i;
1459	<	Molecule* mol;
1460	<
1461	<	Vector3d thisr(0.0);
1462	<	Vector3d thisp(0.0);
1463	<
1464	<	RealType thisMass;
1465	<
1466	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1467	<	thisMass = mol->getMass();
1468	<	thisr = mol->getCom()-com;
1469	<	thisp = (mol->getComVel()-comVel)*thisMass;
1470	<
1471	<	angularMomentum += cross( thisr, thisp );
1472	<
1473	<	}
1474	<
1475	<	#ifdef IS_MPI
1476	<	Vector3d tmpAngMom;
1477	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1478	<	#endif
1479	<
1480	<	return angularMomentum;
1481	<	}
1482	<
1025	>
1026		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1027	<	return IOIndexToIntegrableObject.at(index);
1027	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1028	>	sprintf(painCave.errMsg,
1029	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1030	>	"\tindex exceeds number of known objects!\n");
1031	>	painCave.isFatal = 1;
1032	>	simError();
1033	>	return NULL;
1034	>	} else
1035	>	return IOIndexToIntegrableObject.at(index);
1036		}
1037
1038	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1038	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1039		IOIndexToIntegrableObject= v;
1040		}
1041
1042	<	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1043	<	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1044	<	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1045	<	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1046	<	*/
1047	<	void SimInfo::getGyrationalVolume(RealType &volume){
1048	<	Mat3x3d intTensor;
1049	<	RealType det;
1050	<	Vector3d dummyAngMom;
1500	<	RealType sysconstants;
1501	<	RealType geomCnst;
1502	<
1503	<	geomCnst = 3.0/2.0;
1504	<	/* Get the inertial tensor and angular momentum for free*/
1505	<	getInertiaTensor(intTensor,dummyAngMom);
1506	<
1507	<	det = intTensor.determinant();
1508	<	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1509	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1510	<	return;
1042	>	int SimInfo::getNGlobalConstraints() {
1043	>	int nGlobalConstraints;
1044	>	#ifdef IS_MPI
1045	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1046	>	MPI::INT, MPI::SUM);
1047	>	#else
1048	>	nGlobalConstraints =  nConstraints_;
1049	>	#endif
1050	>	return nGlobalConstraints;
1051		}
1052
1053	<	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1514	<	Mat3x3d intTensor;
1515	<	Vector3d dummyAngMom;
1516	<	RealType sysconstants;
1517	<	RealType geomCnst;
1053	>	}//end namespace OpenMD
1054
1519	–	geomCnst = 3.0/2.0;
1520	–	/* Get the inertial tensor and angular momentum for free*/
1521	–	getInertiaTensor(intTensor,dummyAngMom);
1522	–
1523	–	detI = intTensor.determinant();
1524	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1525	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1526	–	return;
1527	–	}
1528	–	/*
1529	–	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1530	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1531	–	sdByGlobalIndex_ = v;
1532	–	}
1533	–
1534	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1535	–	//assert(index < nAtoms_ + nRigidBodies_);
1536	–	return sdByGlobalIndex_.at(index);
1537	–	}
1538	–	*/
1539	–	}//end namespace oopse
1540	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 UTC vs.
Revision 1929 by gezelter, Mon Aug 19 13:12:00 2013 UTC

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