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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1103 by chuckv, Fri Dec 29 20:21:53 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 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	<
80	<	MoleculeStamp* molStamp;
81	<	int nMolWithSameStamp;
82	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
84	<	CutoffGroupStamp* cgStamp;
85	<	RigidBodyStamp* rbStamp;
86	<	int nRigidAtoms = 0;
87	<	std::vector<Component*> components = simParams->getComponents();
88	<
89	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
90	<	molStamp = (*i)->getMoleculeStamp();
91	<	nMolWithSameStamp = (*i)->getNMol();
92	<
93	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
94	<
95	<	//calculate atoms in molecules
96	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
97	<
98	<	//calculate atoms in cutoff groups
99	<	int nAtomsInGroups = 0;
100	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
101	<
102	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
103	<	cgStamp = molStamp->getCutoffGroupStamp(j);
104	<	nAtomsInGroups += cgStamp->getNMembers();
105	<	}
106	<
107	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
108	<
109	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
110	<
111	<	//calculate atoms in rigid bodies
112	<	int nAtomsInRigidBodies = 0;
113	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
114	<
115	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
116	<	rbStamp = molStamp->getRigidBodyStamp(j);
117	<	nAtomsInRigidBodies += rbStamp->getNMembers();
118	<	}
119	<
120	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
121	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
122	<
123	<	}
124	<
125	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	<	//group therefore the total number of cutoff groups in the system is
144	<	//equal to the total number of atoms minus number of atoms belong to
145	<	//cutoff group defined in meta-data file plus the number of cutoff
146	<	//groups defined in meta-data file
147	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148	<
149	<	//every free atom (atom does not belong to rigid bodies) is an
150	<	//integrable object therefore the total number of integrable objects
151	<	//in the system is equal to the total number of atoms minus number of
152	<	//atoms belong to rigid body defined in meta-data file plus the number
153	<	//of rigid bodies defined in meta-data file
154	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	<	+ nGlobalRigidBodies_;
156	<
157	<	nGlobalMols_ = molStampIds_.size();
158	<
159	<	#ifdef IS_MPI
160	<	molToProcMap_.resize(nGlobalMols_);
161	<	#endif
162	<
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	>	nMolWithSameStamp = (*i)->getNMol();
95	>
96	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
97	>
98	>	//calculate atoms in molecules
99	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100	>
101	>	//calculate atoms in cutoff groups
102	>	int nAtomsInGroups = 0;
103	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
104	>
105	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
106	>	cgStamp = molStamp->getCutoffGroupStamp(j);
107	>	nAtomsInGroups += cgStamp->getNMembers();
108	>	}
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->getRigidBodyStamp(j);
120	>	nAtomsInRigidBodies += rbStamp->getNMembers();
121	>	}
122	>
123	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	>
126		}
127	+
128	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
129	+	//group therefore the total number of cutoff groups in the system is
130	+	//equal to the total number of atoms minus number of atoms belong to
131	+	//cutoff group defined in meta-data file plus the number of cutoff
132	+	//groups defined in meta-data file
133
134	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135	+
136	+	//every free atom (atom does not belong to rigid bodies) is an
137	+	//integrable object therefore the total number of integrable objects
138	+	//in the system is equal to the total number of atoms minus number of
139	+	//atoms belong to rigid body defined in meta-data file plus the number
140	+	//of rigid bodies defined in meta-data file
141	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	+	+ nGlobalRigidBodies_;
143	+
144	+	nGlobalMols_ = molStampIds_.size();
145	+	molToProcMap_.resize(nGlobalMols_);
146	+	}
147	+
148		SimInfo::~SimInfo() {
149	<	std::map<int, Molecule*>::iterator i;
149	>	map<int, Molecule*>::iterator i;
150		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151		delete i->second;
152		}
#	Line 174 | Line 157 | namespace oopse {
157		delete forceField_;
158		}
159
177	–	int SimInfo::getNGlobalConstraints() {
178	–	int nGlobalConstraints;
179	–	#ifdef IS_MPI
180	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
181	–	MPI_COMM_WORLD);
182	–	#else
183	–	nGlobalConstraints =  nConstraints_;
184	–	#endif
185	–	return nGlobalConstraints;
186	–	}
160
161		bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169		nAtoms_ += mol->getNAtoms();
170		nBonds_ += mol->getNBonds();
171		nBends_ += mol->getNBends();
172		nTorsions_ += mol->getNTorsions();
173	+	nInversions_ += mol->getNInversions();
174		nRigidBodies_ += mol->getNRigidBodies();
175		nIntegrableObjects_ += mol->getNIntegrableObjects();
176		nCutoffGroups_ += mol->getNCutoffGroups();
177		nConstraints_ += mol->getNConstraintPairs();
178	<
179	<	addExcludePairs(mol);
180	<
178	>
179	>	addInteractionPairs(mol);
180	>
181		return true;
182		} else {
183		return false;
184		}
185		}
186	<
186	>
187		bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
#	Line 222 | Line 196 | namespace oopse {
196		nBonds_ -= mol->getNBonds();
197		nBends_ -= mol->getNBends();
198		nTorsions_ -= mol->getNTorsions();
199	+	nInversions_ -= mol->getNInversions();
200		nRigidBodies_ -= mol->getNRigidBodies();
201		nIntegrableObjects_ -= mol->getNIntegrableObjects();
202		nCutoffGroups_ -= mol->getNCutoffGroups();
203		nConstraints_ -= mol->getNConstraintPairs();
204
205	<	removeExcludePairs(mol);
205	>	removeInteractionPairs(mol);
206		molecules_.erase(mol->getGlobalIndex());
207
208		delete mol;
#	Line 236 | Line 211 | namespace oopse {
211		} else {
212		return false;
213		}
239	–
240	–
214		}
215
216
#	Line 253 | Line 226 | namespace oopse {
226
227
228		void SimInfo::calcNdf() {
229	<	int ndf_local;
229	>	int ndf_local, nfq_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232	>	vector<Atom*>::iterator k;
233	>
234		Molecule* mol;
235	<	StuntDouble* integrableObject;
235	>	StuntDouble* sd;
236	>	Atom* atom;
237
238		ndf_local = 0;
239	+	nfq_local = 0;
240
241		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
265	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
266	–	integrableObject = mol->nextIntegrableObject(j)) {
242
243	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
244	+	sd = mol->nextIntegrableObject(j)) {
245	+
246		ndf_local += 3;
247
248	<	if (integrableObject->isDirectional()) {
249	<	if (integrableObject->isLinear()) {
248	>	if (sd->isDirectional()) {
249	>	if (sd->isLinear()) {
250		ndf_local += 2;
251		} else {
252		ndf_local += 3;
253		}
254		}
277	–
255		}
256	+
257	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258	+	atom = mol->nextFluctuatingCharge(k)) {
259	+	if (atom->isFluctuatingCharge()) {
260	+	nfq_local++;
261	+	}
262	+	}
263		}
264
265	+	ndfLocal_ = ndf_local;
266	+
267		// n_constraints is local, so subtract them on each processor
268		ndf_local -= nConstraints_;
269
270		#ifdef IS_MPI
271	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
272	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
273	>	MPI::INT, MPI::SUM);
274		#else
275		ndf_ = ndf_local;
276	+	nGlobalFluctuatingCharges_ = nfq_local;
277		#endif
278
279		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 295 | Line 284 | namespace oopse {
284
285		int SimInfo::getFdf() {
286		#ifdef IS_MPI
287	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
287	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
288		#else
289		fdf_ = fdf_local;
290		#endif
291		return fdf_;
292		}
293	+
294	+	unsigned int SimInfo::getNLocalCutoffGroups(){
295	+	int nLocalCutoffAtoms = 0;
296	+	Molecule* mol;
297	+	MoleculeIterator mi;
298	+	CutoffGroup* cg;
299	+	Molecule::CutoffGroupIterator ci;
300
301	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
302	+
303	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
304	+	cg = mol->nextCutoffGroup(ci)) {
305	+	nLocalCutoffAtoms += cg->getNumAtom();
306	+
307	+	}
308	+	}
309	+
310	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
311	+	}
312	+
313		void SimInfo::calcNdfRaw() {
314		int ndfRaw_local;
315
316		MoleculeIterator i;
317	<	std::vector<StuntDouble*>::iterator j;
317	>	vector<StuntDouble*>::iterator j;
318		Molecule* mol;
319	<	StuntDouble* integrableObject;
319	>	StuntDouble* sd;
320
321		// Raw degrees of freedom that we have to set
322		ndfRaw_local = 0;
323
324		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
317	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
318	–	integrableObject = mol->nextIntegrableObject(j)) {
325
326	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
327	+	sd = mol->nextIntegrableObject(j)) {
328	+
329		ndfRaw_local += 3;
330
331	<	if (integrableObject->isDirectional()) {
332	<	if (integrableObject->isLinear()) {
331	>	if (sd->isDirectional()) {
332	>	if (sd->isLinear()) {
333		ndfRaw_local += 2;
334		} else {
335		ndfRaw_local += 3;
#	Line 331 | Line 340 | namespace oopse {
340		}
341
342		#ifdef IS_MPI
343	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
344		#else
345		ndfRaw_ = ndfRaw_local;
346		#endif
#	Line 344 | Line 353 | namespace oopse {
353
354
355		#ifdef IS_MPI
356	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
357	>	MPI::INT, MPI::SUM);
358		#else
359		ndfTrans_ = ndfTrans_local;
360		#endif
#	Line 353 | Line 363 | namespace oopse {
363
364		}
365
366	<	void SimInfo::addExcludePairs(Molecule* mol) {
367	<	std::vector<Bond*>::iterator bondIter;
368	<	std::vector<Bend*>::iterator bendIter;
369	<	std::vector<Torsion*>::iterator torsionIter;
366	>	void SimInfo::addInteractionPairs(Molecule* mol) {
367	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
368	>	vector<Bond*>::iterator bondIter;
369	>	vector<Bend*>::iterator bendIter;
370	>	vector<Torsion*>::iterator torsionIter;
371	>	vector<Inversion*>::iterator inversionIter;
372		Bond* bond;
373		Bend* bend;
374		Torsion* torsion;
375	+	Inversion* inversion;
376		int a;
377		int b;
378		int c;
379		int d;
380
381	<	std::map<int, std::set<int> > atomGroups;
381	>	// atomGroups can be used to add special interaction maps between
382	>	// groups of atoms that are in two separate rigid bodies.
383	>	// However, most site-site interactions between two rigid bodies
384	>	// are probably not special, just the ones between the physically
385	>	// bonded atoms.  Interactions *within* a single rigid body should
386	>	// always be excluded.  These are done at the bottom of this
387	>	// function.
388
389	+	map<int, set<int> > atomGroups;
390		Molecule::RigidBodyIterator rbIter;
391		RigidBody* rb;
392		Molecule::IntegrableObjectIterator ii;
393	<	StuntDouble* integrableObject;
393	>	StuntDouble* sd;
394
395	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
396	<	integrableObject = mol->nextIntegrableObject(ii)) {
397	<
398	<	if (integrableObject->isRigidBody()) {
399	<	rb = static_cast<RigidBody*>(integrableObject);
400	<	std::vector<Atom*> atoms = rb->getAtoms();
401	<	std::set<int> rigidAtoms;
402	<	for (int i = 0; i < atoms.size(); ++i) {
403	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
404	<	}
405	<	for (int i = 0; i < atoms.size(); ++i) {
406	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
407	<	}
395	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
396	>	sd = mol->nextIntegrableObject(ii)) {
397	>
398	>	if (sd->isRigidBody()) {
399	>	rb = static_cast<RigidBody*>(sd);
400	>	vector<Atom*> atoms = rb->getAtoms();
401	>	set<int> rigidAtoms;
402	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
403	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
404	>	}
405	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
406	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
407	>	}
408		} else {
409	<	std::set<int> oneAtomSet;
410	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
411	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
409	>	set<int> oneAtomSet;
410	>	oneAtomSet.insert(sd->getGlobalIndex());
411	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
412		}
413		}
414	+
415	+	for (bond= mol->beginBond(bondIter); bond != NULL;
416	+	bond = mol->nextBond(bondIter)) {
417
395	–
396	–
397	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
418		a = bond->getAtomA()->getGlobalIndex();
419	<	b = bond->getAtomB()->getGlobalIndex();
420	<	exclude_.addPair(a, b);
419	>	b = bond->getAtomB()->getGlobalIndex();
420	>
421	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
422	>	oneTwoInteractions_.addPair(a, b);
423	>	} else {
424	>	excludedInteractions_.addPair(a, b);
425	>	}
426		}
427
428	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
428	>	for (bend= mol->beginBend(bendIter); bend != NULL;
429	>	bend = mol->nextBend(bendIter)) {
430	>
431		a = bend->getAtomA()->getGlobalIndex();
432		b = bend->getAtomB()->getGlobalIndex();
433		c = bend->getAtomC()->getGlobalIndex();
407	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
408	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
409	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
410	–
411	–	exclude_.addPairs(rigidSetA, rigidSetB);
412	–	exclude_.addPairs(rigidSetA, rigidSetC);
413	–	exclude_.addPairs(rigidSetB, rigidSetC);
434
435	<	//exclude_.addPair(a, b);
436	<	//exclude_.addPair(a, c);
437	<	//exclude_.addPair(b, c);
435	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436	>	oneTwoInteractions_.addPair(a, b);
437	>	oneTwoInteractions_.addPair(b, c);
438	>	} else {
439	>	excludedInteractions_.addPair(a, b);
440	>	excludedInteractions_.addPair(b, c);
441	>	}
442	>
443	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
444	>	oneThreeInteractions_.addPair(a, c);
445	>	} else {
446	>	excludedInteractions_.addPair(a, c);
447	>	}
448		}
449
450	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
450	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
451	>	torsion = mol->nextTorsion(torsionIter)) {
452	>
453		a = torsion->getAtomA()->getGlobalIndex();
454		b = torsion->getAtomB()->getGlobalIndex();
455		c = torsion->getAtomC()->getGlobalIndex();
456	<	d = torsion->getAtomD()->getGlobalIndex();
425	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
426	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
427	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
428	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
456	>	d = torsion->getAtomD()->getGlobalIndex();
457
458	<	exclude_.addPairs(rigidSetA, rigidSetB);
459	<	exclude_.addPairs(rigidSetA, rigidSetC);
460	<	exclude_.addPairs(rigidSetA, rigidSetD);
461	<	exclude_.addPairs(rigidSetB, rigidSetC);
462	<	exclude_.addPairs(rigidSetB, rigidSetD);
463	<	exclude_.addPairs(rigidSetC, rigidSetD);
458	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
459	>	oneTwoInteractions_.addPair(a, b);
460	>	oneTwoInteractions_.addPair(b, c);
461	>	oneTwoInteractions_.addPair(c, d);
462	>	} else {
463	>	excludedInteractions_.addPair(a, b);
464	>	excludedInteractions_.addPair(b, c);
465	>	excludedInteractions_.addPair(c, d);
466	>	}
467
468	<	/*
469	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
470	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
471	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
472	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
473	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
474	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
475	<
476	<
477	<	exclude_.addPair(a, b);
478	<	exclude_.addPair(a, c);
479	<	exclude_.addPair(a, d);
480	<	exclude_.addPair(b, c);
450	<	exclude_.addPair(b, d);
451	<	exclude_.addPair(c, d);
452	<	*/
468	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
469	>	oneThreeInteractions_.addPair(a, c);
470	>	oneThreeInteractions_.addPair(b, d);
471	>	} else {
472	>	excludedInteractions_.addPair(a, c);
473	>	excludedInteractions_.addPair(b, d);
474	>	}
475	>
476	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
477	>	oneFourInteractions_.addPair(a, d);
478	>	} else {
479	>	excludedInteractions_.addPair(a, d);
480	>	}
481		}
482
483	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
484	<	std::vector<Atom*> atoms = rb->getAtoms();
485	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
486	<	for (int j = i + 1; j < atoms.size(); ++j) {
483	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
484	>	inversion = mol->nextInversion(inversionIter)) {
485	>
486	>	a = inversion->getAtomA()->getGlobalIndex();
487	>	b = inversion->getAtomB()->getGlobalIndex();
488	>	c = inversion->getAtomC()->getGlobalIndex();
489	>	d = inversion->getAtomD()->getGlobalIndex();
490	>
491	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
492	>	oneTwoInteractions_.addPair(a, b);
493	>	oneTwoInteractions_.addPair(a, c);
494	>	oneTwoInteractions_.addPair(a, d);
495	>	} else {
496	>	excludedInteractions_.addPair(a, b);
497	>	excludedInteractions_.addPair(a, c);
498	>	excludedInteractions_.addPair(a, d);
499	>	}
500	>
501	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
502	>	oneThreeInteractions_.addPair(b, c);
503	>	oneThreeInteractions_.addPair(b, d);
504	>	oneThreeInteractions_.addPair(c, d);
505	>	} else {
506	>	excludedInteractions_.addPair(b, c);
507	>	excludedInteractions_.addPair(b, d);
508	>	excludedInteractions_.addPair(c, d);
509	>	}
510	>	}
511	>
512	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
513	>	rb = mol->nextRigidBody(rbIter)) {
514	>	vector<Atom*> atoms = rb->getAtoms();
515	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
516	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
517		a = atoms[i]->getGlobalIndex();
518		b = atoms[j]->getGlobalIndex();
519	<	exclude_.addPair(a, b);
519	>	excludedInteractions_.addPair(a, b);
520		}
521		}
522		}
523
524		}
525
526	<	void SimInfo::removeExcludePairs(Molecule* mol) {
527	<	std::vector<Bond*>::iterator bondIter;
528	<	std::vector<Bend*>::iterator bendIter;
529	<	std::vector<Torsion*>::iterator torsionIter;
526	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
527	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
528	>	vector<Bond*>::iterator bondIter;
529	>	vector<Bend*>::iterator bendIter;
530	>	vector<Torsion*>::iterator torsionIter;
531	>	vector<Inversion*>::iterator inversionIter;
532		Bond* bond;
533		Bend* bend;
534		Torsion* torsion;
535	+	Inversion* inversion;
536		int a;
537		int b;
538		int c;
539		int d;
540
541	<	std::map<int, std::set<int> > atomGroups;
481	<
541	>	map<int, set<int> > atomGroups;
542		Molecule::RigidBodyIterator rbIter;
543		RigidBody* rb;
544		Molecule::IntegrableObjectIterator ii;
545	<	StuntDouble* integrableObject;
545	>	StuntDouble* sd;
546
547	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
548	<	integrableObject = mol->nextIntegrableObject(ii)) {
549	<
550	<	if (integrableObject->isRigidBody()) {
551	<	rb = static_cast<RigidBody*>(integrableObject);
552	<	std::vector<Atom*> atoms = rb->getAtoms();
553	<	std::set<int> rigidAtoms;
554	<	for (int i = 0; i < atoms.size(); ++i) {
555	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
556	<	}
557	<	for (int i = 0; i < atoms.size(); ++i) {
558	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
559	<	}
547	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
548	>	sd = mol->nextIntegrableObject(ii)) {
549	>
550	>	if (sd->isRigidBody()) {
551	>	rb = static_cast<RigidBody*>(sd);
552	>	vector<Atom*> atoms = rb->getAtoms();
553	>	set<int> rigidAtoms;
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
556	>	}
557	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
558	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
559	>	}
560		} else {
561	<	std::set<int> oneAtomSet;
562	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
563	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
561	>	set<int> oneAtomSet;
562	>	oneAtomSet.insert(sd->getGlobalIndex());
563	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
564		}
565		}
566
567	<
568	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
567	>	for (bond= mol->beginBond(bondIter); bond != NULL;
568	>	bond = mol->nextBond(bondIter)) {
569	>
570		a = bond->getAtomA()->getGlobalIndex();
571	<	b = bond->getAtomB()->getGlobalIndex();
572	<	exclude_.removePair(a, b);
571	>	b = bond->getAtomB()->getGlobalIndex();
572	>
573	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
574	>	oneTwoInteractions_.removePair(a, b);
575	>	} else {
576	>	excludedInteractions_.removePair(a, b);
577	>	}
578		}
579
580	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
580	>	for (bend= mol->beginBend(bendIter); bend != NULL;
581	>	bend = mol->nextBend(bendIter)) {
582	>
583		a = bend->getAtomA()->getGlobalIndex();
584		b = bend->getAtomB()->getGlobalIndex();
585		c = bend->getAtomC()->getGlobalIndex();
518	–
519	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
520	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
521	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
522	–
523	–	exclude_.removePairs(rigidSetA, rigidSetB);
524	–	exclude_.removePairs(rigidSetA, rigidSetC);
525	–	exclude_.removePairs(rigidSetB, rigidSetC);
586
587	<	//exclude_.removePair(a, b);
588	<	//exclude_.removePair(a, c);
589	<	//exclude_.removePair(b, c);
587	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
588	>	oneTwoInteractions_.removePair(a, b);
589	>	oneTwoInteractions_.removePair(b, c);
590	>	} else {
591	>	excludedInteractions_.removePair(a, b);
592	>	excludedInteractions_.removePair(b, c);
593	>	}
594	>
595	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
596	>	oneThreeInteractions_.removePair(a, c);
597	>	} else {
598	>	excludedInteractions_.removePair(a, c);
599	>	}
600		}
601
602	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
602	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
603	>	torsion = mol->nextTorsion(torsionIter)) {
604	>
605		a = torsion->getAtomA()->getGlobalIndex();
606		b = torsion->getAtomB()->getGlobalIndex();
607		c = torsion->getAtomC()->getGlobalIndex();
608	<	d = torsion->getAtomD()->getGlobalIndex();
608	>	d = torsion->getAtomD()->getGlobalIndex();
609	>
610	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
611	>	oneTwoInteractions_.removePair(a, b);
612	>	oneTwoInteractions_.removePair(b, c);
613	>	oneTwoInteractions_.removePair(c, d);
614	>	} else {
615	>	excludedInteractions_.removePair(a, b);
616	>	excludedInteractions_.removePair(b, c);
617	>	excludedInteractions_.removePair(c, d);
618	>	}
619
620	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
621	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
622	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
623	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
620	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
621	>	oneThreeInteractions_.removePair(a, c);
622	>	oneThreeInteractions_.removePair(b, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, c);
625	>	excludedInteractions_.removePair(b, d);
626	>	}
627
628	<	exclude_.removePairs(rigidSetA, rigidSetB);
629	<	exclude_.removePairs(rigidSetA, rigidSetC);
630	<	exclude_.removePairs(rigidSetA, rigidSetD);
631	<	exclude_.removePairs(rigidSetB, rigidSetC);
632	<	exclude_.removePairs(rigidSetB, rigidSetD);
633	<	exclude_.removePairs(rigidSetC, rigidSetD);
628	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
629	>	oneFourInteractions_.removePair(a, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, d);
632	>	}
633	>	}
634
635	<	/*
636	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
552	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
553	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
554	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
555	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
556	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
635	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
636	>	inversion = mol->nextInversion(inversionIter)) {
637
638	<
639	<	exclude_.removePair(a, b);
640	<	exclude_.removePair(a, c);
641	<	exclude_.removePair(a, d);
642	<	exclude_.removePair(b, c);
643	<	exclude_.removePair(b, d);
644	<	exclude_.removePair(c, d);
645	<	*/
638	>	a = inversion->getAtomA()->getGlobalIndex();
639	>	b = inversion->getAtomB()->getGlobalIndex();
640	>	c = inversion->getAtomC()->getGlobalIndex();
641	>	d = inversion->getAtomD()->getGlobalIndex();
642	>
643	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
644	>	oneTwoInteractions_.removePair(a, b);
645	>	oneTwoInteractions_.removePair(a, c);
646	>	oneTwoInteractions_.removePair(a, d);
647	>	} else {
648	>	excludedInteractions_.removePair(a, b);
649	>	excludedInteractions_.removePair(a, c);
650	>	excludedInteractions_.removePair(a, d);
651	>	}
652	>
653	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
654	>	oneThreeInteractions_.removePair(b, c);
655	>	oneThreeInteractions_.removePair(b, d);
656	>	oneThreeInteractions_.removePair(c, d);
657	>	} else {
658	>	excludedInteractions_.removePair(b, c);
659	>	excludedInteractions_.removePair(b, d);
660	>	excludedInteractions_.removePair(c, d);
661	>	}
662		}
663
664	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
665	<	std::vector<Atom*> atoms = rb->getAtoms();
666	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
667	<	for (int j = i + 1; j < atoms.size(); ++j) {
664	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
665	>	rb = mol->nextRigidBody(rbIter)) {
666	>	vector<Atom*> atoms = rb->getAtoms();
667	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
668	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
669		a = atoms[i]->getGlobalIndex();
670		b = atoms[j]->getGlobalIndex();
671	<	exclude_.removePair(a, b);
671	>	excludedInteractions_.removePair(a, b);
672		}
673		}
674		}
675	<
675	>
676		}
677	<
678	<
677	>
678	>
679		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
680		int curStampId;
681	<
681	>
682		//index from 0
683		curStampId = moleculeStamps_.size();
684
#	Line 589 | Line 686 | namespace oopse {
686		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
687		}
688
592	–	void SimInfo::update() {
689
690	<	setupSimType();
691	<
692	<	#ifdef IS_MPI
693	<	setupFortranParallel();
694	<	#endif
695	<
696	<	setupFortranSim();
697	<
698	<	//setup fortran force field
603	<	/** @deprecate */
604	<	int isError = 0;
605	<
606	<	setupCutoff();
607	<
608	<	setupElectrostaticSummationMethod( isError );
609	<	setupSwitchingFunction();
610	<	setupAccumulateBoxDipole();
611	<
612	<	if(isError){
613	<	sprintf( painCave.errMsg,
614	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
615	<	painCave.isFatal = 1;
616	<	simError();
617	<	}
618	<
690	>	/**
691	>	* update
692	>	*
693	>	*  Performs the global checks and variable settings after the
694	>	*  objects have been created.
695	>	*
696	>	*/
697	>	void SimInfo::update() {
698	>	setupSimVariables();
699		calcNdf();
700		calcNdfRaw();
701		calcNdfTrans();
622	–
623	–	fortranInitialized_ = true;
702		}
703	<
704	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
703	>
704	>	/**
705	>	* getSimulatedAtomTypes
706	>	*
707	>	* Returns an STL set of AtomType* that are actually present in this
708	>	* simulation.  Must query all processors to assemble this information.
709	>	*
710	>	*/
711	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
712		SimInfo::MoleculeIterator mi;
713		Molecule* mol;
714		Molecule::AtomIterator ai;
715		Atom* atom;
716	<	std::set<AtomType*> atomTypes;
717	<
716	>	set<AtomType*> atomTypes;
717	>
718		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
719	<
720	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
719	>	for(atom = mol->beginAtom(ai); atom != NULL;
720	>	atom = mol->nextAtom(ai)) {
721		atomTypes.insert(atom->getAtomType());
722	<	}
723	<
724	<	}
722	>	}
723	>	}
724	>
725	>	#ifdef IS_MPI
726
727	<	return atomTypes;
728	<	}
643	<
644	<	void SimInfo::setupSimType() {
645	<	std::set<AtomType*>::iterator i;
646	<	std::set<AtomType*> atomTypes;
647	<	atomTypes = getUniqueAtomTypes();
727	>	// loop over the found atom types on this processor, and add their
728	>	// numerical idents to a vector:
729
730	<	int useLennardJones = 0;
731	<	int useElectrostatic = 0;
732	<	int useEAM = 0;
733	<	int useSC = 0;
653	<	int useCharge = 0;
654	<	int useDirectional = 0;
655	<	int useDipole = 0;
656	<	int useGayBerne = 0;
657	<	int useSticky = 0;
658	<	int useStickyPower = 0;
659	<	int useShape = 0;
660	<	int useFLARB = 0; //it is not in AtomType yet
661	<	int useDirectionalAtom = 0;
662	<	int useElectrostatics = 0;
663	<	//usePBC and useRF are from simParams
664	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
665	<	int useRF;
666	<	int useSF;
667	<	int useSP;
668	<	int useBoxDipole;
669	<	std::string myMethod;
730	>	vector<int> foundTypes;
731	>	set<AtomType*>::iterator i;
732	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
733	>	foundTypes.push_back( (*i)->getIdent() );
734
735	<	// set the useRF logical
736	<	useRF = 0;
673	<	useSF = 0;
674	<	useSP = 0;
735	>	// count_local holds the number of found types on this processor
736	>	int count_local = foundTypes.size();
737
738	+	int nproc = MPI::COMM_WORLD.Get_size();
739
740	<	if (simParams_->haveElectrostaticSummationMethod()) {
741	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
742	<	toUpper(myMethod);
743	<	if (myMethod == "REACTION_FIELD"){
681	<	useRF = 1;
682	<	} else if (myMethod == "SHIFTED_FORCE"){
683	<	useSF = 1;
684	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
685	<	useSP = 1;
686	<	}
687	<	}
688	<
689	<	if (simParams_->haveAccumulateBoxDipole())
690	<	if (simParams_->getAccumulateBoxDipole())
691	<	useBoxDipole = 1;
740	>	// we need arrays to hold the counts and displacement vectors for
741	>	// all processors
742	>	vector<int> counts(nproc, 0);
743	>	vector<int> disps(nproc, 0);
744
745	<	//loop over all of the atom types
746	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
747	<	useLennardJones |= (*i)->isLennardJones();
748	<	useElectrostatic |= (*i)->isElectrostatic();
749	<	useEAM |= (*i)->isEAM();
750	<	useSC |= (*i)->isSC();
751	<	useCharge |= (*i)->isCharge();
752	<	useDirectional |= (*i)->isDirectional();
753	<	useDipole |= (*i)->isDipole();
754	<	useGayBerne |= (*i)->isGayBerne();
703	<	useSticky |= (*i)->isSticky();
704	<	useStickyPower |= (*i)->isStickyPower();
705	<	useShape |= (*i)->isShape();
745	>	// fill the counts array
746	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
747	>	1, MPI::INT);
748	>
749	>	// use the processor counts to compute the displacement array
750	>	disps[0] = 0;
751	>	int totalCount = counts[0];
752	>	for (int iproc = 1; iproc < nproc; iproc++) {
753	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
754	>	totalCount += counts[iproc];
755		}
756
757	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
758	<	useDirectionalAtom = 1;
759	<	}
757	>	// we need a (possibly redundant) set of all found types:
758	>	vector<int> ftGlobal(totalCount);
759	>
760	>	// now spray out the foundTypes to all the other processors:
761	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
762	>	&ftGlobal[0], &counts[0], &disps[0],
763	>	MPI::INT);
764
765	<	if (useCharge || useDipole) {
713	<	useElectrostatics = 1;
714	<	}
765	>	vector<int>::iterator j;
766
767	<	#ifdef IS_MPI
768	<	int temp;
767	>	// foundIdents is a stl set, so inserting an already found ident
768	>	// will have no effect.
769	>	set<int> foundIdents;
770
771	<	temp = usePBC;
772	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
771	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
772	>	foundIdents.insert((*j));
773	>
774	>	// now iterate over the foundIdents and get the actual atom types
775	>	// that correspond to these:
776	>	set<int>::iterator it;
777	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
778	>	atomTypes.insert( forceField_->getAtomType((*it)) );
779	>
780	>	#endif
781
782	<	temp = useDirectionalAtom;
783	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	return atomTypes;
783	>	}
784
725	–	temp = useLennardJones;
726	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
785
786	<	temp = useElectrostatics;
787	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786	>	int getGlobalCountOfType(AtomType* atype) {
787	>	/*
788	>	set<AtomType*> atypes = getSimulatedAtomTypes();
789	>	map<AtomType*, int> counts_;
790
791	<	temp = useCharge;
792	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
791	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
792	>	for(atom = mol->beginAtom(ai); atom != NULL;
793	>	atom = mol->nextAtom(ai)) {
794	>	atom->getAtomType();
795	>	}
796	>	}
797	>	*/
798	>	return 0;
799	>	}
800
801	<	temp = useDipole;
802	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	void SimInfo::setupSimVariables() {
802	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
803	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
804	>	// parameter is true
805	>	calcBoxDipole_ = false;
806	>	if ( simParams_->haveAccumulateBoxDipole() )
807	>	if ( simParams_->getAccumulateBoxDipole() ) {
808	>	calcBoxDipole_ = true;
809	>	}
810	>
811	>	set<AtomType*>::iterator i;
812	>	set<AtomType*> atomTypes;
813	>	atomTypes = getSimulatedAtomTypes();
814	>	bool usesElectrostatic = false;
815	>	bool usesMetallic = false;
816	>	bool usesDirectional = false;
817	>	bool usesFluctuatingCharges =  false;
818	>	//loop over all of the atom types
819	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
820	>	usesElectrostatic |= (*i)->isElectrostatic();
821	>	usesMetallic |= (*i)->isMetal();
822	>	usesDirectional |= (*i)->isDirectional();
823	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
824	>	}
825
826	<	temp = useSticky;
827	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828	<
829	<	temp = useStickyPower;
830	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	>	#ifdef IS_MPI
827	>	bool temp;
828	>	temp = usesDirectional;
829	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
830	>	MPI::LOR);
831	>
832	>	temp = usesMetallic;
833	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
834	>	MPI::LOR);
835
836	<	temp = useGayBerne;
837	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836	>	temp = usesElectrostatic;
837	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
838	>	MPI::LOR);
839
840	<	temp = useEAM;
841	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	>	temp = usesFluctuatingCharges;
841	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
842	>	MPI::LOR);
843	>	#else
844
845	<	temp = useSC;
846	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845	>	usesDirectionalAtoms_ = usesDirectional;
846	>	usesMetallicAtoms_ = usesMetallic;
847	>	usesElectrostaticAtoms_ = usesElectrostatic;
848	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
849	>
850	>	#endif
851
852	<	temp = useShape;
853	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
853	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
854	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
855	>	}
856
755	–	temp = useFLARB;
756	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857
858	<	temp = useRF;
859	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
858	>	vector<int> SimInfo::getGlobalAtomIndices() {
859	>	SimInfo::MoleculeIterator mi;
860	>	Molecule* mol;
861	>	Molecule::AtomIterator ai;
862	>	Atom* atom;
863
864	<	temp = useSF;
865	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
865	>
866	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
867	>
868	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
869	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
870	>	}
871	>	}
872	>	return GlobalAtomIndices;
873	>	}
874
764	–	temp = useSP;
765	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875
876	<	temp = useBoxDipole;
877	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
876	>	vector<int> SimInfo::getGlobalGroupIndices() {
877	>	SimInfo::MoleculeIterator mi;
878	>	Molecule* mol;
879	>	Molecule::CutoffGroupIterator ci;
880	>	CutoffGroup* cg;
881
882	<	#endif
883	<
884	<	fInfo_.SIM_uses_PBC = usePBC;
885	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
886	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
887	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
888	<	fInfo_.SIM_uses_Charges = useCharge;
889	<	fInfo_.SIM_uses_Dipoles = useDipole;
890	<	fInfo_.SIM_uses_Sticky = useSticky;
891	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
892	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
893	<	fInfo_.SIM_uses_EAM = useEAM;
782	<	fInfo_.SIM_uses_SC = useSC;
783	<	fInfo_.SIM_uses_Shapes = useShape;
784	<	fInfo_.SIM_uses_FLARB = useFLARB;
785	<	fInfo_.SIM_uses_RF = useRF;
786	<	fInfo_.SIM_uses_SF = useSF;
787	<	fInfo_.SIM_uses_SP = useSP;
788	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
882	>	vector<int> GlobalGroupIndices;
883	>
884	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
885	>
886	>	//local index of cutoff group is trivial, it only depends on the
887	>	//order of travesing
888	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
889	>	cg = mol->nextCutoffGroup(ci)) {
890	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
891	>	}
892	>	}
893	>	return GlobalGroupIndices;
894		}
895
791	–	void SimInfo::setupFortranSim() {
792	–	int isError;
793	–	int nExclude;
794	–	std::vector<int> fortranGlobalGroupMembership;
795	–
796	–	nExclude = exclude_.getSize();
797	–	isError = 0;
896
897	<	//globalGroupMembership_ is filled by SimCreator
800	<	for (int i = 0; i < nGlobalAtoms_; i++) {
801	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
802	<	}
897	>	void SimInfo::prepareTopology() {
898
899		//calculate mass ratio of cutoff group
805	–	std::vector<RealType> mfact;
900		SimInfo::MoleculeIterator mi;
901		Molecule* mol;
902		Molecule::CutoffGroupIterator ci;
#	Line 811 | Line 905 | namespace oopse {
905		Atom* atom;
906		RealType totalMass;
907
908	<	//to avoid memory reallocation, reserve enough space for mfact
909	<	mfact.reserve(getNCutoffGroups());
908	>	/**
909	>	* The mass factor is the relative mass of an atom to the total
910	>	* mass of the cutoff group it belongs to.  By default, all atoms
911	>	* are their own cutoff groups, and therefore have mass factors of
912	>	* 1.  We need some special handling for massless atoms, which
913	>	* will be treated as carrying the entire mass of the cutoff
914	>	* group.
915	>	*/
916	>	massFactors_.clear();
917	>	massFactors_.resize(getNAtoms(), 1.0);
918
919		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
920	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
921	>	cg = mol->nextCutoffGroup(ci)) {
922
923		totalMass = cg->getMass();
924		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
925		// Check for massless groups - set mfact to 1 if true
926	<	if (totalMass != 0)
927	<	mfact.push_back(atom->getMass()/totalMass);
926	>	if (totalMass != 0)
927	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
928		else
929	<	mfact.push_back( 1.0 );
929	>	massFactors_[atom->getLocalIndex()] = 1.0;
930		}
828	–
931		}
932		}
933
934	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
833	<	std::vector<int> identArray;
934	>	// Build the identArray_
935
936	<	//to avoid memory reallocation, reserve enough space identArray
937	<	identArray.reserve(getNAtoms());
837	<
936	>	identArray_.clear();
937	>	identArray_.reserve(getNAtoms());
938		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
939		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
940	<	identArray.push_back(atom->getIdent());
940	>	identArray_.push_back(atom->getIdent());
941		}
942		}
843	–
844	–	//fill molMembershipArray
845	–	//molMembershipArray is filled by SimCreator
846	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
847	–	for (int i = 0; i < nGlobalAtoms_; i++) {
848	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
849	–	}
943
944	<	//setup fortran simulation
852	<	int nGlobalExcludes = 0;
853	<	int* globalExcludes = NULL;
854	<	int* excludeList = exclude_.getExcludeList();
855	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
856	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
857	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
858	<
859	<	if( isError ){
860	<
861	<	sprintf( painCave.errMsg,
862	<	"There was an error setting the simulation information in fortran.\n" );
863	<	painCave.isFatal = 1;
864	<	painCave.severity = OOPSE_ERROR;
865	<	simError();
866	<	}
867	<
868	<	#ifdef IS_MPI
869	<	sprintf( checkPointMsg,
870	<	"succesfully sent the simulation information to fortran.\n");
871	<	MPIcheckPoint();
872	<	#endif // is_mpi
873	<
874	<	// Setup number of neighbors in neighbor list if present
875	<	if (simParams_->haveNeighborListNeighbors()) {
876	<	setNeighbors(simParams_->getNeighborListNeighbors());
877	<	}
878	<
879	<
880	<	}
881	<
882	<
883	<	#ifdef IS_MPI
884	<	void SimInfo::setupFortranParallel() {
885	<
886	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
887	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
888	<	std::vector<int> localToGlobalCutoffGroupIndex;
889	<	SimInfo::MoleculeIterator mi;
890	<	Molecule::AtomIterator ai;
891	<	Molecule::CutoffGroupIterator ci;
892	<	Molecule* mol;
893	<	Atom* atom;
894	<	CutoffGroup* cg;
895	<	mpiSimData parallelData;
896	<	int isError;
897	<
898	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
899	<
900	<	//local index(index in DataStorge) of atom is important
901	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
902	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
903	<	}
904	<
905	<	//local index of cutoff group is trivial, it only depends on the order of travesing
906	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
907	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
908	<	}
909	<
910	<	}
911	<
912	<	//fill up mpiSimData struct
913	<	parallelData.nMolGlobal = getNGlobalMolecules();
914	<	parallelData.nMolLocal = getNMolecules();
915	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
916	<	parallelData.nAtomsLocal = getNAtoms();
917	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
918	<	parallelData.nGroupsLocal = getNCutoffGroups();
919	<	parallelData.myNode = worldRank;
920	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
921	<
922	<	//pass mpiSimData struct and index arrays to fortran
923	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
924	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
925	<	&localToGlobalCutoffGroupIndex[0], &isError);
926	<
927	<	if (isError) {
928	<	sprintf(painCave.errMsg,
929	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
930	<	painCave.isFatal = 1;
931	<	simError();
932	<	}
933	<
934	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
935	<	MPIcheckPoint();
936	<
937	<
938	<	}
939	<
940	<	#endif
941	<
942	<	void SimInfo::setupCutoff() {
943	<
944	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
945	<
946	<	// Check the cutoff policy
947	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
948	<
949	<	std::string myPolicy;
950	<	if (forceFieldOptions_.haveCutoffPolicy()){
951	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
952	<	}else if (simParams_->haveCutoffPolicy()) {
953	<	myPolicy = simParams_->getCutoffPolicy();
954	<	}
955	<
956	<	if (!myPolicy.empty()){
957	<	toUpper(myPolicy);
958	<	if (myPolicy == "MIX") {
959	<	cp = MIX_CUTOFF_POLICY;
960	<	} else {
961	<	if (myPolicy == "MAX") {
962	<	cp = MAX_CUTOFF_POLICY;
963	<	} else {
964	<	if (myPolicy == "TRADITIONAL") {
965	<	cp = TRADITIONAL_CUTOFF_POLICY;
966	<	} else {
967	<	// throw error
968	<	sprintf( painCave.errMsg,
969	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
970	<	painCave.isFatal = 1;
971	<	simError();
972	<	}
973	<	}
974	<	}
975	<	}
976	<	notifyFortranCutoffPolicy(&cp);
977	<
978	<	// Check the Skin Thickness for neighborlists
979	<	RealType skin;
980	<	if (simParams_->haveSkinThickness()) {
981	<	skin = simParams_->getSkinThickness();
982	<	notifyFortranSkinThickness(&skin);
983	<	}
984	<
985	<	// Check if the cutoff was set explicitly:
986	<	if (simParams_->haveCutoffRadius()) {
987	<	rcut_ = simParams_->getCutoffRadius();
988	<	if (simParams_->haveSwitchingRadius()) {
989	<	rsw_  = simParams_->getSwitchingRadius();
990	<	} else {
991	<	if (fInfo_.SIM_uses_Charges |
992	<	fInfo_.SIM_uses_Dipoles |
993	<	fInfo_.SIM_uses_RF) {
994	<
995	<	rsw_ = 0.85 * rcut_;
996	<	sprintf(painCave.errMsg,
997	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
998	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
999	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1000	<	painCave.isFatal = 0;
1001	<	simError();
1002	<	} else {
1003	<	rsw_ = rcut_;
1004	<	sprintf(painCave.errMsg,
1005	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1006	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1007	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1008	<	painCave.isFatal = 0;
1009	<	simError();
1010	<	}
1011	<	}
1012	<
1013	<	notifyFortranCutoffs(&rcut_, &rsw_);
1014	<
1015	<	} else {
1016	<
1017	<	// For electrostatic atoms, we'll assume a large safe value:
1018	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1019	<	sprintf(painCave.errMsg,
1020	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1021	<	"\tOOPSE will use a default value of 15.0 angstroms"
1022	<	"\tfor the cutoffRadius.\n");
1023	<	painCave.isFatal = 0;
1024	<	simError();
1025	<	rcut_ = 15.0;
1026	<
1027	<	if (simParams_->haveElectrostaticSummationMethod()) {
1028	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1029	<	toUpper(myMethod);
1030	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1031	<	if (simParams_->haveSwitchingRadius()){
1032	<	sprintf(painCave.errMsg,
1033	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1034	<	"\teven though the electrostaticSummationMethod was\n"
1035	<	"\tset to %s\n", myMethod.c_str());
1036	<	painCave.isFatal = 1;
1037	<	simError();
1038	<	}
1039	<	}
1040	<	}
1041	<
1042	<	if (simParams_->haveSwitchingRadius()){
1043	<	rsw_ = simParams_->getSwitchingRadius();
1044	<	} else {
1045	<	sprintf(painCave.errMsg,
1046	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1047	<	"\tOOPSE will use a default value of\n"
1048	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1049	<	painCave.isFatal = 0;
1050	<	simError();
1051	<	rsw_ = 0.85 * rcut_;
1052	<	}
1053	<	notifyFortranCutoffs(&rcut_, &rsw_);
1054	<	} else {
1055	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1056	<	// We'll punt and let fortran figure out the cutoffs later.
1057	<
1058	<	notifyFortranYouAreOnYourOwn();
1059	<
1060	<	}
1061	<	}
1062	<	}
1063	<
1064	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1065	<
1066	<	int errorOut;
1067	<	int esm =  NONE;
1068	<	int sm = UNDAMPED;
1069	<	RealType alphaVal;
1070	<	RealType dielectric;
1071	<
1072	<	errorOut = isError;
1073	<
1074	<	if (simParams_->haveElectrostaticSummationMethod()) {
1075	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1076	<	toUpper(myMethod);
1077	<	if (myMethod == "NONE") {
1078	<	esm = NONE;
1079	<	} else {
1080	<	if (myMethod == "SWITCHING_FUNCTION") {
1081	<	esm = SWITCHING_FUNCTION;
1082	<	} else {
1083	<	if (myMethod == "SHIFTED_POTENTIAL") {
1084	<	esm = SHIFTED_POTENTIAL;
1085	<	} else {
1086	<	if (myMethod == "SHIFTED_FORCE") {
1087	<	esm = SHIFTED_FORCE;
1088	<	} else {
1089	<	if (myMethod == "REACTION_FIELD") {
1090	<	esm = REACTION_FIELD;
1091	<	dielectric = simParams_->getDielectric();
1092	<	if (!simParams_->haveDielectric()) {
1093	<	// throw warning
1094	<	sprintf( painCave.errMsg,
1095	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1096	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1097	<	painCave.isFatal = 0;
1098	<	simError();
1099	<	}
1100	<	} else {
1101	<	// throw error
1102	<	sprintf( painCave.errMsg,
1103	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1104	<	"\t(Input file specified %s .)\n"
1105	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1106	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1107	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1108	<	painCave.isFatal = 1;
1109	<	simError();
1110	<	}
1111	<	}
1112	<	}
1113	<	}
1114	<	}
1115	<	}
1116	<
1117	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1118	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1119	<	toUpper(myScreen);
1120	<	if (myScreen == "UNDAMPED") {
1121	<	sm = UNDAMPED;
1122	<	} else {
1123	<	if (myScreen == "DAMPED") {
1124	<	sm = DAMPED;
1125	<	if (!simParams_->haveDampingAlpha()) {
1126	<	// first set a cutoff dependent alpha value
1127	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1128	<	alphaVal = 0.5125 - rcut_* 0.025;
1129	<	// for values rcut > 20.5, alpha is zero
1130	<	if (alphaVal < 0) alphaVal = 0;
1131	<
1132	<	// throw warning
1133	<	sprintf( painCave.errMsg,
1134	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1135	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1136	<	painCave.isFatal = 0;
1137	<	simError();
1138	<	} else {
1139	<	alphaVal = simParams_->getDampingAlpha();
1140	<	}
1141	<
1142	<	} else {
1143	<	// throw error
1144	<	sprintf( painCave.errMsg,
1145	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1146	<	"\t(Input file specified %s .)\n"
1147	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1148	<	"or \"damped\".\n", myScreen.c_str() );
1149	<	painCave.isFatal = 1;
1150	<	simError();
1151	<	}
1152	<	}
1153	<	}
1154	<
1155	<	// let's pass some summation method variables to fortran
1156	<	setElectrostaticSummationMethod( &esm );
1157	<	setFortranElectrostaticMethod( &esm );
1158	<	setScreeningMethod( &sm );
1159	<	setDampingAlpha( &alphaVal );
1160	<	setReactionFieldDielectric( &dielectric );
1161	<	initFortranFF( &errorOut );
944	>	topologyDone_ = true;
945		}
946
1164	–	void SimInfo::setupSwitchingFunction() {
1165	–	int ft = CUBIC;
1166	–
1167	–	if (simParams_->haveSwitchingFunctionType()) {
1168	–	std::string funcType = simParams_->getSwitchingFunctionType();
1169	–	toUpper(funcType);
1170	–	if (funcType == "CUBIC") {
1171	–	ft = CUBIC;
1172	–	} else {
1173	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1174	–	ft = FIFTH_ORDER_POLY;
1175	–	} else {
1176	–	// throw error
1177	–	sprintf( painCave.errMsg,
1178	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1179	–	painCave.isFatal = 1;
1180	–	simError();
1181	–	}
1182	–	}
1183	–	}
1184	–
1185	–	// send switching function notification to switcheroo
1186	–	setFunctionType(&ft);
1187	–
1188	–	}
1189	–
1190	–	void SimInfo::setupAccumulateBoxDipole() {
1191	–
1192	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1193	–	if ( simParams_->haveAccumulateBoxDipole() )
1194	–	if ( simParams_->getAccumulateBoxDipole() ) {
1195	–	setAccumulateBoxDipole();
1196	–	calcBoxDipole_ = true;
1197	–	}
1198	–
1199	–	}
1200	–
947		void SimInfo::addProperty(GenericData* genData) {
948		properties_.addProperty(genData);
949		}
950
951	<	void SimInfo::removeProperty(const std::string& propName) {
951	>	void SimInfo::removeProperty(const string& propName) {
952		properties_.removeProperty(propName);
953		}
954
#	Line 1210 | Line 956 | namespace oopse {
956		properties_.clearProperties();
957		}
958
959	<	std::vector<std::string> SimInfo::getPropertyNames() {
959	>	vector<string> SimInfo::getPropertyNames() {
960		return properties_.getPropertyNames();
961		}
962
963	<	std::vector<GenericData*> SimInfo::getProperties() {
963	>	vector<GenericData*> SimInfo::getProperties() {
964		return properties_.getProperties();
965		}
966
967	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
967	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
968		return properties_.getPropertyByName(propName);
969		}
970
#	Line 1232 | Line 978 | namespace oopse {
978		Molecule* mol;
979		RigidBody* rb;
980		Atom* atom;
981	+	CutoffGroup* cg;
982		SimInfo::MoleculeIterator mi;
983		Molecule::RigidBodyIterator rbIter;
984	<	Molecule::AtomIterator atomIter;;
984	>	Molecule::AtomIterator atomIter;
985	>	Molecule::CutoffGroupIterator cgIter;
986
987		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
988
989	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
989	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
990	>	atom = mol->nextAtom(atomIter)) {
991		atom->setSnapshotManager(sman_);
992		}
993
994	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
994	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
995	>	rb = mol->nextRigidBody(rbIter)) {
996		rb->setSnapshotManager(sman_);
997		}
998	+
999	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1000	+	cg = mol->nextCutoffGroup(cgIter)) {
1001	+	cg->setSnapshotManager(sman_);
1002	+	}
1003		}
1004
1005		}
1006
1252	–	Vector3d SimInfo::getComVel(){
1253	–	SimInfo::MoleculeIterator i;
1254	–	Molecule* mol;
1007
1008	<	Vector3d comVel(0.0);
1257	<	RealType totalMass = 0.0;
1258	<
1259	<
1260	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1261	<	RealType mass = mol->getMass();
1262	<	totalMass += mass;
1263	<	comVel += mass * mol->getComVel();
1264	<	}
1008	>	ostream& operator <<(ostream& o, SimInfo& info) {
1009
1266	–	#ifdef IS_MPI
1267	–	RealType tmpMass = totalMass;
1268	–	Vector3d tmpComVel(comVel);
1269	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1270	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1271	–	#endif
1272	–
1273	–	comVel /= totalMass;
1274	–
1275	–	return comVel;
1276	–	}
1277	–
1278	–	Vector3d SimInfo::getCom(){
1279	–	SimInfo::MoleculeIterator i;
1280	–	Molecule* mol;
1281	–
1282	–	Vector3d com(0.0);
1283	–	RealType totalMass = 0.0;
1284	–
1285	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1286	–	RealType mass = mol->getMass();
1287	–	totalMass += mass;
1288	–	com += mass * mol->getCom();
1289	–	}
1290	–
1291	–	#ifdef IS_MPI
1292	–	RealType tmpMass = totalMass;
1293	–	Vector3d tmpCom(com);
1294	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1295	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1296	–	#endif
1297	–
1298	–	com /= totalMass;
1299	–
1300	–	return com;
1301	–
1302	–	}
1303	–
1304	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1305	–
1010		return o;
1011		}
1308	–
1309	–
1310	–	/*
1311	–	Returns center of mass and center of mass velocity in one function call.
1312	–	*/
1313	–
1314	–	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1315	–	SimInfo::MoleculeIterator i;
1316	–	Molecule* mol;
1317	–
1318	–
1319	–	RealType totalMass = 0.0;
1320	–
1321	–
1322	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1323	–	RealType mass = mol->getMass();
1324	–	totalMass += mass;
1325	–	com += mass * mol->getCom();
1326	–	comVel += mass * mol->getComVel();
1327	–	}
1328	–
1329	–	#ifdef IS_MPI
1330	–	RealType tmpMass = totalMass;
1331	–	Vector3d tmpCom(com);
1332	–	Vector3d tmpComVel(comVel);
1333	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1334	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1335	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1336	–	#endif
1337	–
1338	–	com /= totalMass;
1339	–	comVel /= totalMass;
1340	–	}
1012
1013	<	/*
1343	<	Return intertia tensor for entire system and angular momentum Vector.
1344	<
1345	<
1346	<	[  Ixx -Ixy  -Ixz ]
1347	<	J =| -Iyx  Iyy  -Iyz |
1348	<	[ -Izx -Iyz   Izz ]
1349	<	*/
1350	<
1351	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1352	<
1353	<
1354	<	RealType xx = 0.0;
1355	<	RealType yy = 0.0;
1356	<	RealType zz = 0.0;
1357	<	RealType xy = 0.0;
1358	<	RealType xz = 0.0;
1359	<	RealType yz = 0.0;
1360	<	Vector3d com(0.0);
1361	<	Vector3d comVel(0.0);
1362	<
1363	<	getComAll(com, comVel);
1364	<
1365	<	SimInfo::MoleculeIterator i;
1366	<	Molecule* mol;
1367	<
1368	<	Vector3d thisq(0.0);
1369	<	Vector3d thisv(0.0);
1370	<
1371	<	RealType thisMass = 0.0;
1372	<
1373	<
1374	<
1375	<
1376	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1377	<
1378	<	thisq = mol->getCom()-com;
1379	<	thisv = mol->getComVel()-comVel;
1380	<	thisMass = mol->getMass();
1381	<	// Compute moment of intertia coefficients.
1382	<	xx += thisq[0]*thisq[0]*thisMass;
1383	<	yy += thisq[1]*thisq[1]*thisMass;
1384	<	zz += thisq[2]*thisq[2]*thisMass;
1385	<
1386	<	// compute products of intertia
1387	<	xy += thisq[0]*thisq[1]*thisMass;
1388	<	xz += thisq[0]*thisq[2]*thisMass;
1389	<	yz += thisq[1]*thisq[2]*thisMass;
1390	<
1391	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1392	<
1393	<	}
1394	<
1395	<
1396	<	inertiaTensor(0,0) = yy + zz;
1397	<	inertiaTensor(0,1) = -xy;
1398	<	inertiaTensor(0,2) = -xz;
1399	<	inertiaTensor(1,0) = -xy;
1400	<	inertiaTensor(1,1) = xx + zz;
1401	<	inertiaTensor(1,2) = -yz;
1402	<	inertiaTensor(2,0) = -xz;
1403	<	inertiaTensor(2,1) = -yz;
1404	<	inertiaTensor(2,2) = xx + yy;
1405	<
1406	<	#ifdef IS_MPI
1407	<	Mat3x3d tmpI(inertiaTensor);
1408	<	Vector3d tmpAngMom;
1409	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1410	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1411	<	#endif
1412	<
1413	<	return;
1414	<	}
1415	<
1416	<	//Returns the angular momentum of the system
1417	<	Vector3d SimInfo::getAngularMomentum(){
1418	<
1419	<	Vector3d com(0.0);
1420	<	Vector3d comVel(0.0);
1421	<	Vector3d angularMomentum(0.0);
1422	<
1423	<	getComAll(com,comVel);
1424	<
1425	<	SimInfo::MoleculeIterator i;
1426	<	Molecule* mol;
1427	<
1428	<	Vector3d thisr(0.0);
1429	<	Vector3d thisp(0.0);
1430	<
1431	<	RealType thisMass;
1432	<
1433	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1434	<	thisMass = mol->getMass();
1435	<	thisr = mol->getCom()-com;
1436	<	thisp = (mol->getComVel()-comVel)*thisMass;
1437	<
1438	<	angularMomentum += cross( thisr, thisp );
1439	<
1440	<	}
1441	<
1442	<	#ifdef IS_MPI
1443	<	Vector3d tmpAngMom;
1444	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1445	<	#endif
1446	<
1447	<	return angularMomentum;
1448	<	}
1449	<
1013	>
1014		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1015	<	return IOIndexToIntegrableObject.at(index);
1015	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1016	>	sprintf(painCave.errMsg,
1017	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1018	>	"\tindex exceeds number of known objects!\n");
1019	>	painCave.isFatal = 1;
1020	>	simError();
1021	>	return NULL;
1022	>	} else
1023	>	return IOIndexToIntegrableObject.at(index);
1024		}
1025
1026	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1026	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1027		IOIndexToIntegrableObject= v;
1028		}
1029
1030	<	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1031	<	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1032	<	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1033	<	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1034	<	*/
1035	<	void SimInfo::getGyrationalVolume(RealType &volume){
1036	<	Mat3x3d intTensor;
1037	<	RealType det;
1038	<	Vector3d dummyAngMom;
1467	<	RealType sysconstants;
1468	<	RealType geomCnst;
1469	<
1470	<	geomCnst = 3.0/2.0;
1471	<	/* Get the inertial tensor and angular momentum for free*/
1472	<	getInertiaTensor(intTensor,dummyAngMom);
1473	<
1474	<	det = intTensor.determinant();
1475	<	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1476	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1477	<	return;
1030	>	int SimInfo::getNGlobalConstraints() {
1031	>	int nGlobalConstraints;
1032	>	#ifdef IS_MPI
1033	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1034	>	MPI::INT, MPI::SUM);
1035	>	#else
1036	>	nGlobalConstraints =  nConstraints_;
1037	>	#endif
1038	>	return nGlobalConstraints;
1039		}
1040
1041	<	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1481	<	Mat3x3d intTensor;
1482	<	Vector3d dummyAngMom;
1483	<	RealType sysconstants;
1484	<	RealType geomCnst;
1041	>	}//end namespace OpenMD
1042
1486	–	geomCnst = 3.0/2.0;
1487	–	/* Get the inertial tensor and angular momentum for free*/
1488	–	getInertiaTensor(intTensor,dummyAngMom);
1489	–
1490	–	detI = intTensor.determinant();
1491	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1492	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1493	–	return;
1494	–	}
1495	–	/*
1496	–	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1497	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1498	–	sdByGlobalIndex_ = v;
1499	–	}
1500	–
1501	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1502	–	//assert(index < nAtoms_ + nRigidBodies_);
1503	–	return sdByGlobalIndex_.at(index);
1504	–	}
1505	–	*/
1506	–	}//end namespace oopse
1507	–

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1103 by chuckv, Fri Dec 29 20:21:53 2006 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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