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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 834 by chuckv, Fri Dec 30 23:15:59 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 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, 24107 (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 53 | Line 54
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/fCutoffPolicy.h"
57	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	<	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	<	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60	<	#include "UseTheForce/doForces_interface.h"
61	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
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	<
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"
72	<	#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) {
76	<	std::map<int, std::set<int> >::iterator i = container.find(index);
77	<	std::set<int> result;
78	<	if (i != container.end()) {
79	<	result = i->second;
80	<	}
81	<
82	<	return result;
83	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
79	<
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();
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(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94
95	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	<	molStamp = (*i)->getMoleculeStamp();
97	<	nMolWithSameStamp = (*i)->getNMol();
98	<
99	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
100	<
101	<	//calculate atoms in molecules
102	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	<
104	<	//calculate atoms in cutoff groups
105	<	int nAtomsInGroups = 0;
106	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
115	<
116	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
117	<	cgStamp = molStamp->getCutoffGroupStamp(j);
118	<	nAtomsInGroups += cgStamp->getNMembers();
119	<	}
120	<
121	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
122	<
123	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
124	<
125	<	//calculate atoms in rigid bodies
126	<	int nAtomsInRigidBodies = 0;
127	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128	<
129	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
130	<	rbStamp = molStamp->getRigidBodyStamp(j);
131	<	nAtomsInRigidBodies += rbStamp->getNMembers();
132	<	}
133	<
134	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
135	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
136	<
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107		}
108	<
109	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
110	<	//group therefore the total number of cutoff groups in the system is
111	<	//equal to the total number of atoms minus number of atoms belong to
112	<	//cutoff group defined in meta-data file plus the number of cutoff
113	<	//groups defined in meta-data file
114	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
115	<
116	<	//every free atom (atom does not belong to rigid bodies) is an
117	<	//integrable object therefore the total number of integrable objects
118	<	//in the system is equal to the total number of atoms minus number of
119	<	//atoms belong to rigid body defined in meta-data file plus the number
120	<	//of rigid bodies defined in meta-data file
121	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
122	<	+ nGlobalRigidBodies_;
123	<
124	<	nGlobalMols_ = molStampIds_.size();
155	<
156	<	#ifdef IS_MPI
157	<	molToProcMap_.resize(nGlobalMols_);
158	<	#endif
159	<
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
133	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	+
135	+	//every free atom (atom does not belong to rigid bodies) is an
136	+	//integrable object therefore the total number of integrable objects
137	+	//in the system is equal to the total number of atoms minus number of
138	+	//atoms belong to rigid body defined in meta-data file plus the number
139	+	//of rigid bodies defined in meta-data file
140	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	+	+ nGlobalRigidBodies_;
142	+
143	+	nGlobalMols_ = molStampIds_.size();
144	+	molToProcMap_.resize(nGlobalMols_);
145	+	}
146	+
147		SimInfo::~SimInfo() {
148	<	std::map<int, Molecule*>::iterator i;
148	>	map<int, Molecule*>::iterator i;
149		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150		delete i->second;
151		}
#	Line 171 | Line 156 | namespace oopse {
156		delete forceField_;
157		}
158
174	–	int SimInfo::getNGlobalConstraints() {
175	–	int nGlobalConstraints;
176	–	#ifdef IS_MPI
177	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
178	–	MPI_COMM_WORLD);
179	–	#else
180	–	nGlobalConstraints =  nConstraints_;
181	–	#endif
182	–	return nGlobalConstraints;
183	–	}
159
160		bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168		nAtoms_ += mol->getNAtoms();
169		nBonds_ += mol->getNBonds();
170		nBends_ += mol->getNBends();
171		nTorsions_ += mol->getNTorsions();
172	+	nInversions_ += mol->getNInversions();
173		nRigidBodies_ += mol->getNRigidBodies();
174		nIntegrableObjects_ += mol->getNIntegrableObjects();
175		nCutoffGroups_ += mol->getNCutoffGroups();
176		nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
177	>
178	>	addInteractionPairs(mol);
179	>
180		return true;
181		} else {
182		return false;
183		}
184		}
185	<
185	>
186		bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
#	Line 219 | Line 195 | namespace oopse {
195		nBonds_ -= mol->getNBonds();
196		nBends_ -= mol->getNBends();
197		nTorsions_ -= mol->getNTorsions();
198	+	nInversions_ -= mol->getNInversions();
199		nRigidBodies_ -= mol->getNRigidBodies();
200		nIntegrableObjects_ -= mol->getNIntegrableObjects();
201		nCutoffGroups_ -= mol->getNCutoffGroups();
202		nConstraints_ -= mol->getNConstraintPairs();
203
204	<	removeExcludePairs(mol);
204	>	removeInteractionPairs(mol);
205		molecules_.erase(mol->getGlobalIndex());
206
207		delete mol;
#	Line 233 | Line 210 | namespace oopse {
210		} else {
211		return false;
212		}
236	–
237	–
213		}
214
215
#	Line 250 | Line 225 | namespace oopse {
225
226
227		void SimInfo::calcNdf() {
228	<	int ndf_local;
228	>	int ndf_local, nfq_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232	>
233		Molecule* mol;
234	<	StuntDouble* integrableObject;
234	>	StuntDouble* sd;
235	>	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
262	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	–	integrableObject = mol->nextIntegrableObject(j)) {
241
242	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
243	+	sd = mol->nextIntegrableObject(j)) {
244	+
245		ndf_local += 3;
246
247	<	if (integrableObject->isDirectional()) {
248	<	if (integrableObject->isLinear()) {
247	>	if (sd->isDirectional()) {
248	>	if (sd->isLinear()) {
249		ndf_local += 2;
250		} else {
251		ndf_local += 3;
252		}
253		}
274	–
254		}
255	+
256	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
257	+	atom = mol->nextFluctuatingCharge(k)) {
258	+	if (atom->isFluctuatingCharge()) {
259	+	nfq_local++;
260	+	}
261	+	}
262		}
263
264	+	ndfLocal_ = ndf_local;
265	+
266		// n_constraints is local, so subtract them on each processor
267		ndf_local -= nConstraints_;
268
269		#ifdef IS_MPI
270		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
272		#else
273		ndf_ = ndf_local;
274	+	nGlobalFluctuatingCharges_ = nfq_local;
275		#endif
276
277		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 290 | Line 280 | namespace oopse {
280
281		}
282
283	+	int SimInfo::getFdf() {
284	+	#ifdef IS_MPI
285	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
286	+	#else
287	+	fdf_ = fdf_local;
288	+	#endif
289	+	return fdf_;
290	+	}
291	+
292	+	unsigned int SimInfo::getNLocalCutoffGroups(){
293	+	int nLocalCutoffAtoms = 0;
294	+	Molecule* mol;
295	+	MoleculeIterator mi;
296	+	CutoffGroup* cg;
297	+	Molecule::CutoffGroupIterator ci;
298	+
299	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
300	+
301	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
302	+	cg = mol->nextCutoffGroup(ci)) {
303	+	nLocalCutoffAtoms += cg->getNumAtom();
304	+
305	+	}
306	+	}
307	+
308	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
309	+	}
310	+
311		void SimInfo::calcNdfRaw() {
312		int ndfRaw_local;
313
314		MoleculeIterator i;
315	<	std::vector<StuntDouble*>::iterator j;
315	>	vector<StuntDouble*>::iterator j;
316		Molecule* mol;
317	<	StuntDouble* integrableObject;
317	>	StuntDouble* sd;
318
319		// Raw degrees of freedom that we have to set
320		ndfRaw_local = 0;
321
322		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
305	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
306	–	integrableObject = mol->nextIntegrableObject(j)) {
323
324	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
325	+	sd = mol->nextIntegrableObject(j)) {
326	+
327		ndfRaw_local += 3;
328
329	<	if (integrableObject->isDirectional()) {
330	<	if (integrableObject->isLinear()) {
329	>	if (sd->isDirectional()) {
330	>	if (sd->isLinear()) {
331		ndfRaw_local += 2;
332		} else {
333		ndfRaw_local += 3;
#	Line 341 | Line 360 | namespace oopse {
360
361		}
362
363	<	void SimInfo::addExcludePairs(Molecule* mol) {
364	<	std::vector<Bond*>::iterator bondIter;
365	<	std::vector<Bend*>::iterator bendIter;
366	<	std::vector<Torsion*>::iterator torsionIter;
363	>	void SimInfo::addInteractionPairs(Molecule* mol) {
364	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
365	>	vector<Bond*>::iterator bondIter;
366	>	vector<Bend*>::iterator bendIter;
367	>	vector<Torsion*>::iterator torsionIter;
368	>	vector<Inversion*>::iterator inversionIter;
369		Bond* bond;
370		Bend* bend;
371		Torsion* torsion;
372	+	Inversion* inversion;
373		int a;
374		int b;
375		int c;
376		int d;
377
378	<	std::map<int, std::set<int> > atomGroups;
378	>	// atomGroups can be used to add special interaction maps between
379	>	// groups of atoms that are in two separate rigid bodies.
380	>	// However, most site-site interactions between two rigid bodies
381	>	// are probably not special, just the ones between the physically
382	>	// bonded atoms.  Interactions *within* a single rigid body should
383	>	// always be excluded.  These are done at the bottom of this
384	>	// function.
385
386	+	map<int, set<int> > atomGroups;
387		Molecule::RigidBodyIterator rbIter;
388		RigidBody* rb;
389		Molecule::IntegrableObjectIterator ii;
390	<	StuntDouble* integrableObject;
390	>	StuntDouble* sd;
391
392	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
393	<	integrableObject = mol->nextIntegrableObject(ii)) {
394	<
395	<	if (integrableObject->isRigidBody()) {
396	<	rb = static_cast<RigidBody*>(integrableObject);
397	<	std::vector<Atom*> atoms = rb->getAtoms();
398	<	std::set<int> rigidAtoms;
399	<	for (int i = 0; i < atoms.size(); ++i) {
400	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
401	<	}
402	<	for (int i = 0; i < atoms.size(); ++i) {
403	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
404	<	}
392	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
393	>	sd = mol->nextIntegrableObject(ii)) {
394	>
395	>	if (sd->isRigidBody()) {
396	>	rb = static_cast<RigidBody*>(sd);
397	>	vector<Atom*> atoms = rb->getAtoms();
398	>	set<int> rigidAtoms;
399	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
400	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
401	>	}
402	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
403	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
404	>	}
405		} else {
406	<	std::set<int> oneAtomSet;
407	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
408	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
406	>	set<int> oneAtomSet;
407	>	oneAtomSet.insert(sd->getGlobalIndex());
408	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
409		}
410		}
411	+
412	+	for (bond= mol->beginBond(bondIter); bond != NULL;
413	+	bond = mol->nextBond(bondIter)) {
414
383	–
384	–
385	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
415		a = bond->getAtomA()->getGlobalIndex();
416	<	b = bond->getAtomB()->getGlobalIndex();
417	<	exclude_.addPair(a, b);
416	>	b = bond->getAtomB()->getGlobalIndex();
417	>
418	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
419	>	oneTwoInteractions_.addPair(a, b);
420	>	} else {
421	>	excludedInteractions_.addPair(a, b);
422	>	}
423		}
424
425	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
425	>	for (bend= mol->beginBend(bendIter); bend != NULL;
426	>	bend = mol->nextBend(bendIter)) {
427	>
428		a = bend->getAtomA()->getGlobalIndex();
429		b = bend->getAtomB()->getGlobalIndex();
430		c = bend->getAtomC()->getGlobalIndex();
395	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
396	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
397	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
398	–
399	–	exclude_.addPairs(rigidSetA, rigidSetB);
400	–	exclude_.addPairs(rigidSetA, rigidSetC);
401	–	exclude_.addPairs(rigidSetB, rigidSetC);
431
432	<	//exclude_.addPair(a, b);
433	<	//exclude_.addPair(a, c);
434	<	//exclude_.addPair(b, c);
432	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
433	>	oneTwoInteractions_.addPair(a, b);
434	>	oneTwoInteractions_.addPair(b, c);
435	>	} else {
436	>	excludedInteractions_.addPair(a, b);
437	>	excludedInteractions_.addPair(b, c);
438	>	}
439	>
440	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
441	>	oneThreeInteractions_.addPair(a, c);
442	>	} else {
443	>	excludedInteractions_.addPair(a, c);
444	>	}
445		}
446
447	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
447	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
448	>	torsion = mol->nextTorsion(torsionIter)) {
449	>
450		a = torsion->getAtomA()->getGlobalIndex();
451		b = torsion->getAtomB()->getGlobalIndex();
452		c = torsion->getAtomC()->getGlobalIndex();
453	<	d = torsion->getAtomD()->getGlobalIndex();
413	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
414	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
415	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
416	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
453	>	d = torsion->getAtomD()->getGlobalIndex();
454
455	<	exclude_.addPairs(rigidSetA, rigidSetB);
456	<	exclude_.addPairs(rigidSetA, rigidSetC);
457	<	exclude_.addPairs(rigidSetA, rigidSetD);
458	<	exclude_.addPairs(rigidSetB, rigidSetC);
459	<	exclude_.addPairs(rigidSetB, rigidSetD);
460	<	exclude_.addPairs(rigidSetC, rigidSetD);
455	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
456	>	oneTwoInteractions_.addPair(a, b);
457	>	oneTwoInteractions_.addPair(b, c);
458	>	oneTwoInteractions_.addPair(c, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(b, c);
462	>	excludedInteractions_.addPair(c, d);
463	>	}
464
465	<	/*
466	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
467	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
468	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
469	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
470	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
471	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
472	<
473	<
474	<	exclude_.addPair(a, b);
475	<	exclude_.addPair(a, c);
476	<	exclude_.addPair(a, d);
477	<	exclude_.addPair(b, c);
438	<	exclude_.addPair(b, d);
439	<	exclude_.addPair(c, d);
440	<	*/
465	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
466	>	oneThreeInteractions_.addPair(a, c);
467	>	oneThreeInteractions_.addPair(b, d);
468	>	} else {
469	>	excludedInteractions_.addPair(a, c);
470	>	excludedInteractions_.addPair(b, d);
471	>	}
472	>
473	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
474	>	oneFourInteractions_.addPair(a, d);
475	>	} else {
476	>	excludedInteractions_.addPair(a, d);
477	>	}
478		}
479
480	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
481	<	std::vector<Atom*> atoms = rb->getAtoms();
482	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
483	<	for (int j = i + 1; j < atoms.size(); ++j) {
480	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
481	>	inversion = mol->nextInversion(inversionIter)) {
482	>
483	>	a = inversion->getAtomA()->getGlobalIndex();
484	>	b = inversion->getAtomB()->getGlobalIndex();
485	>	c = inversion->getAtomC()->getGlobalIndex();
486	>	d = inversion->getAtomD()->getGlobalIndex();
487	>
488	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
489	>	oneTwoInteractions_.addPair(a, b);
490	>	oneTwoInteractions_.addPair(a, c);
491	>	oneTwoInteractions_.addPair(a, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, b);
494	>	excludedInteractions_.addPair(a, c);
495	>	excludedInteractions_.addPair(a, d);
496	>	}
497	>
498	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
499	>	oneThreeInteractions_.addPair(b, c);
500	>	oneThreeInteractions_.addPair(b, d);
501	>	oneThreeInteractions_.addPair(c, d);
502	>	} else {
503	>	excludedInteractions_.addPair(b, c);
504	>	excludedInteractions_.addPair(b, d);
505	>	excludedInteractions_.addPair(c, d);
506	>	}
507	>	}
508	>
509	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
510	>	rb = mol->nextRigidBody(rbIter)) {
511	>	vector<Atom*> atoms = rb->getAtoms();
512	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
513	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
514		a = atoms[i]->getGlobalIndex();
515		b = atoms[j]->getGlobalIndex();
516	<	exclude_.addPair(a, b);
516	>	excludedInteractions_.addPair(a, b);
517		}
518		}
519		}
520
521		}
522
523	<	void SimInfo::removeExcludePairs(Molecule* mol) {
524	<	std::vector<Bond*>::iterator bondIter;
525	<	std::vector<Bend*>::iterator bendIter;
526	<	std::vector<Torsion*>::iterator torsionIter;
523	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
524	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
525	>	vector<Bond*>::iterator bondIter;
526	>	vector<Bend*>::iterator bendIter;
527	>	vector<Torsion*>::iterator torsionIter;
528	>	vector<Inversion*>::iterator inversionIter;
529		Bond* bond;
530		Bend* bend;
531		Torsion* torsion;
532	+	Inversion* inversion;
533		int a;
534		int b;
535		int c;
536		int d;
537
538	<	std::map<int, std::set<int> > atomGroups;
469	<
538	>	map<int, set<int> > atomGroups;
539		Molecule::RigidBodyIterator rbIter;
540		RigidBody* rb;
541		Molecule::IntegrableObjectIterator ii;
542	<	StuntDouble* integrableObject;
542	>	StuntDouble* sd;
543
544	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
545	<	integrableObject = mol->nextIntegrableObject(ii)) {
546	<
547	<	if (integrableObject->isRigidBody()) {
548	<	rb = static_cast<RigidBody*>(integrableObject);
549	<	std::vector<Atom*> atoms = rb->getAtoms();
550	<	std::set<int> rigidAtoms;
551	<	for (int i = 0; i < atoms.size(); ++i) {
552	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
553	<	}
554	<	for (int i = 0; i < atoms.size(); ++i) {
555	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556	<	}
544	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
545	>	sd = mol->nextIntegrableObject(ii)) {
546	>
547	>	if (sd->isRigidBody()) {
548	>	rb = static_cast<RigidBody*>(sd);
549	>	vector<Atom*> atoms = rb->getAtoms();
550	>	set<int> rigidAtoms;
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
553	>	}
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556	>	}
557		} else {
558	<	std::set<int> oneAtomSet;
559	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
560	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
558	>	set<int> oneAtomSet;
559	>	oneAtomSet.insert(sd->getGlobalIndex());
560	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
561		}
562		}
563
564	<
565	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
564	>	for (bond= mol->beginBond(bondIter); bond != NULL;
565	>	bond = mol->nextBond(bondIter)) {
566	>
567		a = bond->getAtomA()->getGlobalIndex();
568	<	b = bond->getAtomB()->getGlobalIndex();
569	<	exclude_.removePair(a, b);
568	>	b = bond->getAtomB()->getGlobalIndex();
569	>
570	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	>	oneTwoInteractions_.removePair(a, b);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	}
575		}
576
577	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
577	>	for (bend= mol->beginBend(bendIter); bend != NULL;
578	>	bend = mol->nextBend(bendIter)) {
579	>
580		a = bend->getAtomA()->getGlobalIndex();
581		b = bend->getAtomB()->getGlobalIndex();
582		c = bend->getAtomC()->getGlobalIndex();
506	–
507	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
508	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
509	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
510	–
511	–	exclude_.removePairs(rigidSetA, rigidSetB);
512	–	exclude_.removePairs(rigidSetA, rigidSetC);
513	–	exclude_.removePairs(rigidSetB, rigidSetC);
583
584	<	//exclude_.removePair(a, b);
585	<	//exclude_.removePair(a, c);
586	<	//exclude_.removePair(b, c);
584	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
585	>	oneTwoInteractions_.removePair(a, b);
586	>	oneTwoInteractions_.removePair(b, c);
587	>	} else {
588	>	excludedInteractions_.removePair(a, b);
589	>	excludedInteractions_.removePair(b, c);
590	>	}
591	>
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	} else {
595	>	excludedInteractions_.removePair(a, c);
596	>	}
597		}
598
599	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
599	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
600	>	torsion = mol->nextTorsion(torsionIter)) {
601	>
602		a = torsion->getAtomA()->getGlobalIndex();
603		b = torsion->getAtomB()->getGlobalIndex();
604		c = torsion->getAtomC()->getGlobalIndex();
605	<	d = torsion->getAtomD()->getGlobalIndex();
605	>	d = torsion->getAtomD()->getGlobalIndex();
606	>
607	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
608	>	oneTwoInteractions_.removePair(a, b);
609	>	oneTwoInteractions_.removePair(b, c);
610	>	oneTwoInteractions_.removePair(c, d);
611	>	} else {
612	>	excludedInteractions_.removePair(a, b);
613	>	excludedInteractions_.removePair(b, c);
614	>	excludedInteractions_.removePair(c, d);
615	>	}
616
617	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
618	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
619	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
620	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
617	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
618	>	oneThreeInteractions_.removePair(a, c);
619	>	oneThreeInteractions_.removePair(b, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(b, d);
623	>	}
624
625	<	exclude_.removePairs(rigidSetA, rigidSetB);
626	<	exclude_.removePairs(rigidSetA, rigidSetC);
627	<	exclude_.removePairs(rigidSetA, rigidSetD);
628	<	exclude_.removePairs(rigidSetB, rigidSetC);
629	<	exclude_.removePairs(rigidSetB, rigidSetD);
630	<	exclude_.removePairs(rigidSetC, rigidSetD);
625	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
626	>	oneFourInteractions_.removePair(a, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, d);
629	>	}
630	>	}
631
632	<	/*
633	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
540	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
541	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
542	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
543	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
544	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
632	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
633	>	inversion = mol->nextInversion(inversionIter)) {
634
635	<
636	<	exclude_.removePair(a, b);
637	<	exclude_.removePair(a, c);
638	<	exclude_.removePair(a, d);
639	<	exclude_.removePair(b, c);
640	<	exclude_.removePair(b, d);
641	<	exclude_.removePair(c, d);
642	<	*/
635	>	a = inversion->getAtomA()->getGlobalIndex();
636	>	b = inversion->getAtomB()->getGlobalIndex();
637	>	c = inversion->getAtomC()->getGlobalIndex();
638	>	d = inversion->getAtomD()->getGlobalIndex();
639	>
640	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
641	>	oneTwoInteractions_.removePair(a, b);
642	>	oneTwoInteractions_.removePair(a, c);
643	>	oneTwoInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, b);
646	>	excludedInteractions_.removePair(a, c);
647	>	excludedInteractions_.removePair(a, d);
648	>	}
649	>
650	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
651	>	oneThreeInteractions_.removePair(b, c);
652	>	oneThreeInteractions_.removePair(b, d);
653	>	oneThreeInteractions_.removePair(c, d);
654	>	} else {
655	>	excludedInteractions_.removePair(b, c);
656	>	excludedInteractions_.removePair(b, d);
657	>	excludedInteractions_.removePair(c, d);
658	>	}
659		}
660
661	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
662	<	std::vector<Atom*> atoms = rb->getAtoms();
663	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
664	<	for (int j = i + 1; j < atoms.size(); ++j) {
661	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
662	>	rb = mol->nextRigidBody(rbIter)) {
663	>	vector<Atom*> atoms = rb->getAtoms();
664	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
665	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
666		a = atoms[i]->getGlobalIndex();
667		b = atoms[j]->getGlobalIndex();
668	<	exclude_.removePair(a, b);
668	>	excludedInteractions_.removePair(a, b);
669		}
670		}
671		}
672	<
672	>
673		}
674	<
675	<
674	>
675	>
676		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
677		int curStampId;
678	<
678	>
679		//index from 0
680		curStampId = moleculeStamps_.size();
681
#	Line 577 | Line 683 | namespace oopse {
683		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684		}
685
580	–	void SimInfo::update() {
686
687	<	setupSimType();
688	<
689	<	#ifdef IS_MPI
690	<	setupFortranParallel();
691	<	#endif
692	<
693	<	setupFortranSim();
694	<
695	<	//setup fortran force field
591	<	/** @deprecate */
592	<	int isError = 0;
593	<
594	<	setupElectrostaticSummationMethod( isError );
595	<	setupSwitchingFunction();
596	<
597	<	if(isError){
598	<	sprintf( painCave.errMsg,
599	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
600	<	painCave.isFatal = 1;
601	<	simError();
602	<	}
603	<
604	<
605	<	setupCutoff();
606	<
687	>	/**
688	>	* update
689	>	*
690	>	*  Performs the global checks and variable settings after the
691	>	*  objects have been created.
692	>	*
693	>	*/
694	>	void SimInfo::update() {
695	>	setupSimVariables();
696		calcNdf();
697		calcNdfRaw();
698		calcNdfTrans();
610	–
611	–	fortranInitialized_ = true;
699		}
700	<
701	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
700	>
701	>	/**
702	>	* getSimulatedAtomTypes
703	>	*
704	>	* Returns an STL set of AtomType* that are actually present in this
705	>	* simulation.  Must query all processors to assemble this information.
706	>	*
707	>	*/
708	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709		SimInfo::MoleculeIterator mi;
710		Molecule* mol;
711		Molecule::AtomIterator ai;
712		Atom* atom;
713	<	std::set<AtomType*> atomTypes;
714	<
713	>	set<AtomType*> atomTypes;
714	>
715		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	<
717	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
716	>	for(atom = mol->beginAtom(ai); atom != NULL;
717	>	atom = mol->nextAtom(ai)) {
718		atomTypes.insert(atom->getAtomType());
719	<	}
720	<
721	<	}
719	>	}
720	>	}
721	>
722	>	#ifdef IS_MPI
723
724	<	return atomTypes;
725	<	}
631	<
632	<	void SimInfo::setupSimType() {
633	<	std::set<AtomType*>::iterator i;
634	<	std::set<AtomType*> atomTypes;
635	<	atomTypes = getUniqueAtomTypes();
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726
727	<	int useLennardJones = 0;
728	<	int useElectrostatic = 0;
729	<	int useEAM = 0;
730	<	int useSC = 0;
641	<	int useCharge = 0;
642	<	int useDirectional = 0;
643	<	int useDipole = 0;
644	<	int useGayBerne = 0;
645	<	int useSticky = 0;
646	<	int useStickyPower = 0;
647	<	int useShape = 0;
648	<	int useFLARB = 0; //it is not in AtomType yet
649	<	int useDirectionalAtom = 0;
650	<	int useElectrostatics = 0;
651	<	//usePBC and useRF are from simParams
652	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
653	<	int useRF;
654	<	int useSF;
655	<	std::string myMethod;
727	>	vector<int> foundTypes;
728	>	set<AtomType*>::iterator i;
729	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730	>	foundTypes.push_back( (*i)->getIdent() );
731
732	<	// set the useRF logical
733	<	useRF = 0;
659	<	useSF = 0;
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734
735	+	int nproc = MPI::COMM_WORLD.Get_size();
736
737	<	if (simParams_->haveElectrostaticSummationMethod()) {
738	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
739	<	toUpper(myMethod);
740	<	if (myMethod == "REACTION_FIELD") {
741	<	useRF=1;
742	<	} else {
743	<	if (myMethod == "SHIFTED_FORCE") {
744	<	useSF = 1;
745	<	}
746	<	}
737	>	// we need arrays to hold the counts and displacement vectors for
738	>	// all processors
739	>	vector<int> counts(nproc, 0);
740	>	vector<int> disps(nproc, 0);
741	>
742	>	// fill the counts array
743	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744	>	1, MPI::INT);
745	>
746	>	// use the processor counts to compute the displacement array
747	>	disps[0] = 0;
748	>	int totalCount = counts[0];
749	>	for (int iproc = 1; iproc < nproc; iproc++) {
750	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
751	>	totalCount += counts[iproc];
752		}
753	+
754	+	// we need a (possibly redundant) set of all found types:
755	+	vector<int> ftGlobal(totalCount);
756	+
757	+	// now spray out the foundTypes to all the other processors:
758	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759	+	&ftGlobal[0], &counts[0], &disps[0],
760	+	MPI::INT);
761	+
762	+	vector<int>::iterator j;
763	+
764	+	// foundIdents is a stl set, so inserting an already found ident
765	+	// will have no effect.
766	+	set<int> foundIdents;
767
768	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769	+	foundIdents.insert((*j));
770	+
771	+	// now iterate over the foundIdents and get the actual atom types
772	+	// that correspond to these:
773	+	set<int>::iterator it;
774	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	+	atomTypes.insert( forceField_->getAtomType((*it)) );
776	+
777	+	#endif
778	+
779	+	return atomTypes;
780	+	}
781	+
782	+	void SimInfo::setupSimVariables() {
783	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
784	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	+	calcBoxDipole_ = false;
786	+	if ( simParams_->haveAccumulateBoxDipole() )
787	+	if ( simParams_->getAccumulateBoxDipole() ) {
788	+	calcBoxDipole_ = true;
789	+	}
790	+
791	+	set<AtomType*>::iterator i;
792	+	set<AtomType*> atomTypes;
793	+	atomTypes = getSimulatedAtomTypes();
794	+	bool usesElectrostatic = false;
795	+	bool usesMetallic = false;
796	+	bool usesDirectional = false;
797	+	bool usesFluctuatingCharges =  false;
798		//loop over all of the atom types
799		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800	<	useLennardJones |= (*i)->isLennardJones();
801	<	useElectrostatic |= (*i)->isElectrostatic();
802	<	useEAM |= (*i)->isEAM();
803	<	useSC |= (*i)->isSC();
680	<	useCharge |= (*i)->isCharge();
681	<	useDirectional |= (*i)->isDirectional();
682	<	useDipole |= (*i)->isDipole();
683	<	useGayBerne |= (*i)->isGayBerne();
684	<	useSticky |= (*i)->isSticky();
685	<	useStickyPower |= (*i)->isStickyPower();
686	<	useShape |= (*i)->isShape();
800	>	usesElectrostatic |= (*i)->isElectrostatic();
801	>	usesMetallic |= (*i)->isMetal();
802	>	usesDirectional |= (*i)->isDirectional();
803	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804		}
805
806	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
807	<	useDirectionalAtom = 1;
808	<	}
806	>	#ifdef IS_MPI
807	>	bool temp;
808	>	temp = usesDirectional;
809	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
810	>	MPI::LOR);
811	>
812	>	temp = usesMetallic;
813	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
814	>	MPI::LOR);
815	>
816	>	temp = usesElectrostatic;
817	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
818	>	MPI::LOR);
819
820	<	if (useCharge || useDipole) {
821	<	useElectrostatics = 1;
822	<	}
820	>	temp = usesFluctuatingCharges;
821	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
822	>	MPI::LOR);
823	>	#else
824
825	<	#ifdef IS_MPI
826	<	int temp;
825	>	usesDirectionalAtoms_ = usesDirectional;
826	>	usesMetallicAtoms_ = usesMetallic;
827	>	usesElectrostaticAtoms_ = usesElectrostatic;
828	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
829
830	<	temp = usePBC;
831	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	>	#endif
831	>
832	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
833	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
834	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
835	>	}
836
703	–	temp = useDirectionalAtom;
704	–	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837
838	<	temp = useLennardJones;
839	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838	>	vector<int> SimInfo::getGlobalAtomIndices() {
839	>	SimInfo::MoleculeIterator mi;
840	>	Molecule* mol;
841	>	Molecule::AtomIterator ai;
842	>	Atom* atom;
843
844	<	temp = useElectrostatics;
710	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
711	<
712	<	temp = useCharge;
713	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
714	<
715	<	temp = useDipole;
716	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
717	<
718	<	temp = useSticky;
719	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
720	<
721	<	temp = useStickyPower;
722	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
845
846	<	temp = useGayBerne;
847	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
847	>
848	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
849	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
850	>	}
851	>	}
852	>	return GlobalAtomIndices;
853	>	}
854
727	–	temp = useEAM;
728	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
855
856	<	temp = useSC;
857	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
858	<
859	<	temp = useShape;
860	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	>	vector<int> SimInfo::getGlobalGroupIndices() {
857	>	SimInfo::MoleculeIterator mi;
858	>	Molecule* mol;
859	>	Molecule::CutoffGroupIterator ci;
860	>	CutoffGroup* cg;
861
862	<	temp = useFLARB;
863	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	<
739	<	temp = useRF;
740	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741	<
742	<	temp = useSF;
743	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744	<
745	<	#endif
746	<
747	<	fInfo_.SIM_uses_PBC = usePBC;
748	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
749	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
750	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
751	<	fInfo_.SIM_uses_Charges = useCharge;
752	<	fInfo_.SIM_uses_Dipoles = useDipole;
753	<	fInfo_.SIM_uses_Sticky = useSticky;
754	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
755	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
756	<	fInfo_.SIM_uses_EAM = useEAM;
757	<	fInfo_.SIM_uses_SC = useSC;
758	<	fInfo_.SIM_uses_Shapes = useShape;
759	<	fInfo_.SIM_uses_FLARB = useFLARB;
760	<	fInfo_.SIM_uses_RF = useRF;
761	<	fInfo_.SIM_uses_SF = useSF;
762	<
763	<	if( myMethod == "REACTION_FIELD") {
862	>	vector<int> GlobalGroupIndices;
863	>
864	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
865
866	<	if (simParams_->haveDielectric()) {
867	<	fInfo_.dielect = simParams_->getDielectric();
868	<	} else {
869	<	sprintf(painCave.errMsg,
870	<	"SimSetup Error: No Dielectric constant was set.\n"
871	<	"\tYou are trying to use Reaction Field without"
771	<	"\tsetting a dielectric constant!\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
866	>	//local index of cutoff group is trivial, it only depends on the
867	>	//order of travesing
868	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
869	>	cg = mol->nextCutoffGroup(ci)) {
870	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
871	>	}
872		}
873	<
873	>	return GlobalGroupIndices;
874		}
875
779	–	void SimInfo::setupFortranSim() {
780	–	int isError;
781	–	int nExclude;
782	–	std::vector<int> fortranGlobalGroupMembership;
783	–
784	–	nExclude = exclude_.getSize();
785	–	isError = 0;
876
877	<	//globalGroupMembership_ is filled by SimCreator
878	<	for (int i = 0; i < nGlobalAtoms_; i++) {
789	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
790	<	}
877	>	void SimInfo::prepareTopology() {
878	>	int nExclude, nOneTwo, nOneThree, nOneFour;
879
880		//calculate mass ratio of cutoff group
793	–	std::vector<double> mfact;
881		SimInfo::MoleculeIterator mi;
882		Molecule* mol;
883		Molecule::CutoffGroupIterator ci;
884		CutoffGroup* cg;
885		Molecule::AtomIterator ai;
886		Atom* atom;
887	<	double totalMass;
887	>	RealType totalMass;
888
889	<	//to avoid memory reallocation, reserve enough space for mfact
890	<	mfact.reserve(getNCutoffGroups());
889	>	/**
890	>	* The mass factor is the relative mass of an atom to the total
891	>	* mass of the cutoff group it belongs to.  By default, all atoms
892	>	* are their own cutoff groups, and therefore have mass factors of
893	>	* 1.  We need some special handling for massless atoms, which
894	>	* will be treated as carrying the entire mass of the cutoff
895	>	* group.
896	>	*/
897	>	massFactors_.clear();
898	>	massFactors_.resize(getNAtoms(), 1.0);
899
900		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
901	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
901	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
902	>	cg = mol->nextCutoffGroup(ci)) {
903
904		totalMass = cg->getMass();
905		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906		// Check for massless groups - set mfact to 1 if true
907	<	if (totalMass != 0)
908	<	mfact.push_back(atom->getMass()/totalMass);
907	>	if (totalMass != 0)
908	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
909		else
910	<	mfact.push_back( 1.0 );
910	>	massFactors_[atom->getLocalIndex()] = 1.0;
911		}
816	–
912		}
913		}
914
915	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
821	<	std::vector<int> identArray;
915	>	// Build the identArray_
916
917	<	//to avoid memory reallocation, reserve enough space identArray
918	<	identArray.reserve(getNAtoms());
825	<
917	>	identArray_.clear();
918	>	identArray_.reserve(getNAtoms());
919		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
921	<	identArray.push_back(atom->getIdent());
921	>	identArray_.push_back(atom->getIdent());
922		}
923		}
831	–
832	–	//fill molMembershipArray
833	–	//molMembershipArray is filled by SimCreator
834	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
835	–	for (int i = 0; i < nGlobalAtoms_; i++) {
836	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
837	–	}
924
925	<	//setup fortran simulation
840	<	int nGlobalExcludes = 0;
841	<	int* globalExcludes = NULL;
842	<	int* excludeList = exclude_.getExcludeList();
843	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
844	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
845	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
925	>	//scan topology
926
927	<	if( isError ){
927	>	nExclude = excludedInteractions_.getSize();
928	>	nOneTwo = oneTwoInteractions_.getSize();
929	>	nOneThree = oneThreeInteractions_.getSize();
930	>	nOneFour = oneFourInteractions_.getSize();
931
932	<	sprintf( painCave.errMsg,
933	<	"There was an error setting the simulation information in fortran.\n" );
934	<	painCave.isFatal = 1;
935	<	painCave.severity = OOPSE_ERROR;
853	<	simError();
854	<	}
932	>	int* excludeList = excludedInteractions_.getPairList();
933	>	int* oneTwoList = oneTwoInteractions_.getPairList();
934	>	int* oneThreeList = oneThreeInteractions_.getPairList();
935	>	int* oneFourList = oneFourInteractions_.getPairList();
936
937	<	#ifdef IS_MPI
857	<	sprintf( checkPointMsg,
858	<	"succesfully sent the simulation information to fortran.\n");
859	<	MPIcheckPoint();
860	<	#endif // is_mpi
861	<	}
862	<
863	<
864	<	#ifdef IS_MPI
865	<	void SimInfo::setupFortranParallel() {
866	<
867	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
868	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
869	<	std::vector<int> localToGlobalCutoffGroupIndex;
870	<	SimInfo::MoleculeIterator mi;
871	<	Molecule::AtomIterator ai;
872	<	Molecule::CutoffGroupIterator ci;
873	<	Molecule* mol;
874	<	Atom* atom;
875	<	CutoffGroup* cg;
876	<	mpiSimData parallelData;
877	<	int isError;
878	<
879	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
880	<
881	<	//local index(index in DataStorge) of atom is important
882	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
884	<	}
885	<
886	<	//local index of cutoff group is trivial, it only depends on the order of travesing
887	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
888	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
889	<	}
890	<
891	<	}
892	<
893	<	//fill up mpiSimData struct
894	<	parallelData.nMolGlobal = getNGlobalMolecules();
895	<	parallelData.nMolLocal = getNMolecules();
896	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
897	<	parallelData.nAtomsLocal = getNAtoms();
898	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
899	<	parallelData.nGroupsLocal = getNCutoffGroups();
900	<	parallelData.myNode = worldRank;
901	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
902	<
903	<	//pass mpiSimData struct and index arrays to fortran
904	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
905	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
906	<	&localToGlobalCutoffGroupIndex[0], &isError);
907	<
908	<	if (isError) {
909	<	sprintf(painCave.errMsg,
910	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
911	<	painCave.isFatal = 1;
912	<	simError();
913	<	}
914	<
915	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
916	<	MPIcheckPoint();
917	<
918	<
919	<	}
920	<
921	<	#endif
922	<
923	<	void SimInfo::setupCutoff() {
924	<
925	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926	<
927	<	// Check the cutoff policy
928	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929	<
930	<	std::string myPolicy;
931	<	if (forceFieldOptions_.haveCutoffPolicy()){
932	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
933	<	}else if (simParams_->haveCutoffPolicy()) {
934	<	myPolicy = simParams_->getCutoffPolicy();
935	<	}
936	<
937	<	if (!myPolicy.empty()){
938	<	toUpper(myPolicy);
939	<	if (myPolicy == "MIX") {
940	<	cp = MIX_CUTOFF_POLICY;
941	<	} else {
942	<	if (myPolicy == "MAX") {
943	<	cp = MAX_CUTOFF_POLICY;
944	<	} else {
945	<	if (myPolicy == "TRADITIONAL") {
946	<	cp = TRADITIONAL_CUTOFF_POLICY;
947	<	} else {
948	<	// throw error
949	<	sprintf( painCave.errMsg,
950	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
951	<	painCave.isFatal = 1;
952	<	simError();
953	<	}
954	<	}
955	<	}
956	<	}
957	<	notifyFortranCutoffPolicy(&cp);
958	<
959	<	// Check the Skin Thickness for neighborlists
960	<	double skin;
961	<	if (simParams_->haveSkinThickness()) {
962	<	skin = simParams_->getSkinThickness();
963	<	notifyFortranSkinThickness(&skin);
964	<	}
965	<
966	<	// Check if the cutoff was set explicitly:
967	<	if (simParams_->haveCutoffRadius()) {
968	<	rcut_ = simParams_->getCutoffRadius();
969	<	if (simParams_->haveSwitchingRadius()) {
970	<	rsw_  = simParams_->getSwitchingRadius();
971	<	} else {
972	<	rsw_ = rcut_;
973	<	}
974	<	notifyFortranCutoffs(&rcut_, &rsw_);
975	<
976	<	} else {
977	<
978	<	// For electrostatic atoms, we'll assume a large safe value:
979	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
980	<	sprintf(painCave.errMsg,
981	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
982	<	"\tOOPSE will use a default value of 15.0 angstroms"
983	<	"\tfor the cutoffRadius.\n");
984	<	painCave.isFatal = 0;
985	<	simError();
986	<	rcut_ = 15.0;
987	<
988	<	if (simParams_->haveElectrostaticSummationMethod()) {
989	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
990	<	toUpper(myMethod);
991	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
992	<	if (simParams_->haveSwitchingRadius()){
993	<	sprintf(painCave.errMsg,
994	<	"SimInfo Warning: A value was set for the switchingRadius\n"
995	<	"\teven though the electrostaticSummationMethod was\n"
996	<	"\tset to %s\n", myMethod.c_str());
997	<	painCave.isFatal = 1;
998	<	simError();
999	<	}
1000	<	}
1001	<	}
1002	<
1003	<	if (simParams_->haveSwitchingRadius()){
1004	<	rsw_ = simParams_->getSwitchingRadius();
1005	<	} else {
1006	<	sprintf(painCave.errMsg,
1007	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1008	<	"\tOOPSE will use a default value of\n"
1009	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1010	<	painCave.isFatal = 0;
1011	<	simError();
1012	<	rsw_ = 0.85 * rcut_;
1013	<	}
1014	<	notifyFortranCutoffs(&rcut_, &rsw_);
1015	<	} else {
1016	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1017	<	// We'll punt and let fortran figure out the cutoffs later.
1018	<
1019	<	notifyFortranYouAreOnYourOwn();
1020	<
1021	<	}
1022	<	}
937	>	topologyDone_ = true;
938		}
939
1025	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1026	–
1027	–	int errorOut;
1028	–	int esm =  NONE;
1029	–	int sm = UNDAMPED;
1030	–	double alphaVal;
1031	–	double dielectric;
1032	–
1033	–	errorOut = isError;
1034	–	alphaVal = simParams_->getDampingAlpha();
1035	–	dielectric = simParams_->getDielectric();
1036	–
1037	–	if (simParams_->haveElectrostaticSummationMethod()) {
1038	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1039	–	toUpper(myMethod);
1040	–	if (myMethod == "NONE") {
1041	–	esm = NONE;
1042	–	} else {
1043	–	if (myMethod == "SWITCHING_FUNCTION") {
1044	–	esm = SWITCHING_FUNCTION;
1045	–	} else {
1046	–	if (myMethod == "SHIFTED_POTENTIAL") {
1047	–	esm = SHIFTED_POTENTIAL;
1048	–	} else {
1049	–	if (myMethod == "SHIFTED_FORCE") {
1050	–	esm = SHIFTED_FORCE;
1051	–	} else {
1052	–	if (myMethod == "REACTION_FIELD") {
1053	–	esm = REACTION_FIELD;
1054	–	} else {
1055	–	// throw error
1056	–	sprintf( painCave.errMsg,
1057	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1058	–	"\t(Input file specified %s .)\n"
1059	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1060	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1061	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1062	–	painCave.isFatal = 1;
1063	–	simError();
1064	–	}
1065	–	}
1066	–	}
1067	–	}
1068	–	}
1069	–	}
1070	–
1071	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1072	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1073	–	toUpper(myScreen);
1074	–	if (myScreen == "UNDAMPED") {
1075	–	sm = UNDAMPED;
1076	–	} else {
1077	–	if (myScreen == "DAMPED") {
1078	–	sm = DAMPED;
1079	–	if (!simParams_->haveDampingAlpha()) {
1080	–	//throw error
1081	–	sprintf( painCave.errMsg,
1082	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1083	–	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1084	–	painCave.isFatal = 0;
1085	–	simError();
1086	–	}
1087	–	} else {
1088	–	// throw error
1089	–	sprintf( painCave.errMsg,
1090	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1091	–	"\t(Input file specified %s .)\n"
1092	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1093	–	"or \"damped\".\n", myScreen.c_str() );
1094	–	painCave.isFatal = 1;
1095	–	simError();
1096	–	}
1097	–	}
1098	–	}
1099	–
1100	–	// let's pass some summation method variables to fortran
1101	–	setElectrostaticSumMethod( &esm );
1102	–	setFortranElectrostaticMethod( &esm );
1103	–	setScreeningMethod( &sm );
1104	–	setDampingAlpha( &alphaVal );
1105	–	setReactionFieldDielectric( &dielectric );
1106	–	initFortranFF( &errorOut );
1107	–	}
1108	–
1109	–	void SimInfo::setupSwitchingFunction() {
1110	–	int ft = CUBIC;
1111	–
1112	–	if (simParams_->haveSwitchingFunctionType()) {
1113	–	std::string funcType = simParams_->getSwitchingFunctionType();
1114	–	toUpper(funcType);
1115	–	if (funcType == "CUBIC") {
1116	–	ft = CUBIC;
1117	–	} else {
1118	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1119	–	ft = FIFTH_ORDER_POLY;
1120	–	} else {
1121	–	// throw error
1122	–	sprintf( painCave.errMsg,
1123	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1124	–	painCave.isFatal = 1;
1125	–	simError();
1126	–	}
1127	–	}
1128	–	}
1129	–
1130	–	// send switching function notification to switcheroo
1131	–	setFunctionType(&ft);
1132	–
1133	–	}
1134	–
940		void SimInfo::addProperty(GenericData* genData) {
941		properties_.addProperty(genData);
942		}
943
944	<	void SimInfo::removeProperty(const std::string& propName) {
944	>	void SimInfo::removeProperty(const string& propName) {
945		properties_.removeProperty(propName);
946		}
947
#	Line 1144 | Line 949 | namespace oopse {
949		properties_.clearProperties();
950		}
951
952	<	std::vector<std::string> SimInfo::getPropertyNames() {
952	>	vector<string> SimInfo::getPropertyNames() {
953		return properties_.getPropertyNames();
954		}
955
956	<	std::vector<GenericData*> SimInfo::getProperties() {
956	>	vector<GenericData*> SimInfo::getProperties() {
957		return properties_.getProperties();
958		}
959
960	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
960	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
961		return properties_.getPropertyByName(propName);
962		}
963
#	Line 1166 | Line 971 | namespace oopse {
971		Molecule* mol;
972		RigidBody* rb;
973		Atom* atom;
974	+	CutoffGroup* cg;
975		SimInfo::MoleculeIterator mi;
976		Molecule::RigidBodyIterator rbIter;
977	<	Molecule::AtomIterator atomIter;;
977	>	Molecule::AtomIterator atomIter;
978	>	Molecule::CutoffGroupIterator cgIter;
979
980		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
981
#	Line 1179 | Line 986 | namespace oopse {
986		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
987		rb->setSnapshotManager(sman_);
988		}
989	+
990	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
991	+	cg->setSnapshotManager(sman_);
992	+	}
993		}
994
995		}
996
1186	–	Vector3d SimInfo::getComVel(){
1187	–	SimInfo::MoleculeIterator i;
1188	–	Molecule* mol;
997
998	<	Vector3d comVel(0.0);
1191	<	double totalMass = 0.0;
1192	<
1193	<
1194	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1195	<	double mass = mol->getMass();
1196	<	totalMass += mass;
1197	<	comVel += mass * mol->getComVel();
1198	<	}
998	>	ostream& operator <<(ostream& o, SimInfo& info) {
999
1200	–	#ifdef IS_MPI
1201	–	double tmpMass = totalMass;
1202	–	Vector3d tmpComVel(comVel);
1203	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1204	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1205	–	#endif
1206	–
1207	–	comVel /= totalMass;
1208	–
1209	–	return comVel;
1210	–	}
1211	–
1212	–	Vector3d SimInfo::getCom(){
1213	–	SimInfo::MoleculeIterator i;
1214	–	Molecule* mol;
1215	–
1216	–	Vector3d com(0.0);
1217	–	double totalMass = 0.0;
1218	–
1219	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1220	–	double mass = mol->getMass();
1221	–	totalMass += mass;
1222	–	com += mass * mol->getCom();
1223	–	}
1224	–
1225	–	#ifdef IS_MPI
1226	–	double tmpMass = totalMass;
1227	–	Vector3d tmpCom(com);
1228	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1229	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1230	–	#endif
1231	–
1232	–	com /= totalMass;
1233	–
1234	–	return com;
1235	–
1236	–	}
1237	–
1238	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1239	–
1000		return o;
1001		}
1002
1003	<
1004	<	/*
1005	<	Returns center of mass and center of mass velocity in one function call.
1006	<	*/
1007	<
1008	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1009	<	SimInfo::MoleculeIterator i;
1010	<	Molecule* mol;
1011	<
1012	<
1013	<	double totalMass = 0.0;
1014	<
1003	>
1004	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005	>	return IOIndexToIntegrableObject.at(index);
1006	>	}
1007	>
1008	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009	>	IOIndexToIntegrableObject= v;
1010	>	}
1011	>	/*
1012	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1014	>	sdByGlobalIndex_ = v;
1015	>	}
1016
1017	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1018	<	double mass = mol->getMass();
1019	<	totalMass += mass;
1020	<	com += mass * mol->getCom();
1021	<	comVel += mass * mol->getComVel();
1022	<	}
1023	<
1017	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1018	>	//assert(index < nAtoms_ + nRigidBodies_);
1019	>	return sdByGlobalIndex_.at(index);
1020	>	}
1021	>	*/
1022	>	int SimInfo::getNGlobalConstraints() {
1023	>	int nGlobalConstraints;
1024		#ifdef IS_MPI
1025	<	double tmpMass = totalMass;
1026	<	Vector3d tmpCom(com);
1027	<	Vector3d tmpComVel(comVel);
1028	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1268	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1269	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1025	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1026	>	MPI_COMM_WORLD);
1027	>	#else
1028	>	nGlobalConstraints =  nConstraints_;
1029		#endif
1030	<
1031	<	com /= totalMass;
1273	<	comVel /= totalMass;
1274	<	}
1275	<
1276	<	/*
1277	<	Return intertia tensor for entire system and angular momentum Vector.
1030	>	return nGlobalConstraints;
1031	>	}
1032
1033	+	}//end namespace OpenMD
1034
1280	–	[  Ixx -Ixy  -Ixz ]
1281	–	J =| -Iyx  Iyy  -Iyz |
1282	–	[ -Izx -Iyz   Izz ]
1283	–	*/
1284	–
1285	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1286	–
1287	–
1288	–	double xx = 0.0;
1289	–	double yy = 0.0;
1290	–	double zz = 0.0;
1291	–	double xy = 0.0;
1292	–	double xz = 0.0;
1293	–	double yz = 0.0;
1294	–	Vector3d com(0.0);
1295	–	Vector3d comVel(0.0);
1296	–
1297	–	getComAll(com, comVel);
1298	–
1299	–	SimInfo::MoleculeIterator i;
1300	–	Molecule* mol;
1301	–
1302	–	Vector3d thisq(0.0);
1303	–	Vector3d thisv(0.0);
1304	–
1305	–	double thisMass = 0.0;
1306	–
1307	–
1308	–
1309	–
1310	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1311	–
1312	–	thisq = mol->getCom()-com;
1313	–	thisv = mol->getComVel()-comVel;
1314	–	thisMass = mol->getMass();
1315	–	// Compute moment of intertia coefficients.
1316	–	xx += thisq[0]*thisq[0]*thisMass;
1317	–	yy += thisq[1]*thisq[1]*thisMass;
1318	–	zz += thisq[2]*thisq[2]*thisMass;
1319	–
1320	–	// compute products of intertia
1321	–	xy += thisq[0]*thisq[1]*thisMass;
1322	–	xz += thisq[0]*thisq[2]*thisMass;
1323	–	yz += thisq[1]*thisq[2]*thisMass;
1324	–
1325	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1326	–
1327	–	}
1328	–
1329	–
1330	–	inertiaTensor(0,0) = yy + zz;
1331	–	inertiaTensor(0,1) = -xy;
1332	–	inertiaTensor(0,2) = -xz;
1333	–	inertiaTensor(1,0) = -xy;
1334	–	inertiaTensor(1,1) = xx + zz;
1335	–	inertiaTensor(1,2) = -yz;
1336	–	inertiaTensor(2,0) = -xz;
1337	–	inertiaTensor(2,1) = -yz;
1338	–	inertiaTensor(2,2) = xx + yy;
1339	–
1340	–	#ifdef IS_MPI
1341	–	Mat3x3d tmpI(inertiaTensor);
1342	–	Vector3d tmpAngMom;
1343	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1344	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1345	–	#endif
1346	–
1347	–	return;
1348	–	}
1349	–
1350	–	//Returns the angular momentum of the system
1351	–	Vector3d SimInfo::getAngularMomentum(){
1352	–
1353	–	Vector3d com(0.0);
1354	–	Vector3d comVel(0.0);
1355	–	Vector3d angularMomentum(0.0);
1356	–
1357	–	getComAll(com,comVel);
1358	–
1359	–	SimInfo::MoleculeIterator i;
1360	–	Molecule* mol;
1361	–
1362	–	Vector3d thisr(0.0);
1363	–	Vector3d thisp(0.0);
1364	–
1365	–	double thisMass;
1366	–
1367	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1368	–	thisMass = mol->getMass();
1369	–	thisr = mol->getCom()-com;
1370	–	thisp = (mol->getComVel()-comVel)*thisMass;
1371	–
1372	–	angularMomentum += cross( thisr, thisp );
1373	–
1374	–	}
1375	–
1376	–	#ifdef IS_MPI
1377	–	Vector3d tmpAngMom;
1378	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1379	–	#endif
1380	–
1381	–	return angularMomentum;
1382	–	}
1383	–
1384	–
1385	–	}//end namespace oopse
1386	–

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 834 by chuckv, Fri Dec 30 23:15:59 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

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