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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1715 by gezelter, Tue May 22 21:55:31 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 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	<
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),
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), sman_(NULL), fortranInitialized_(false),
79	<	calcBoxDipole_(false), useAtomicVirial_(true) {
80	<
81	<
82	<	MoleculeStamp* molStamp;
83	<	int nMolWithSameStamp;
84	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
86	<	CutoffGroupStamp* cgStamp;
87	<	RigidBodyStamp* rbStamp;
88	<	int nRigidAtoms = 0;
89	<
90	<	std::vector<Component*> components = simParams->getComponents();
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();
121	<
122	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	<	cgStamp = molStamp->getCutoffGroupStamp(j);
124	<	nAtomsInGroups += cgStamp->getNMembers();
125	<	}
126	<
127	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128	<
129	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130	<
131	<	//calculate atoms in rigid bodies
132	<	int nAtomsInRigidBodies = 0;
133	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134	<
135	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
136	<	rbStamp = molStamp->getRigidBodyStamp(j);
137	<	nAtomsInRigidBodies += rbStamp->getNMembers();
138	<	}
139	<
140	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	<
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();
161	<	molToProcMap_.resize(nGlobalMols_);
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 173 | Line 156 | namespace oopse {
156		delete forceField_;
157		}
158
176	–	int SimInfo::getNGlobalConstraints() {
177	–	int nGlobalConstraints;
178	–	#ifdef IS_MPI
179	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180	–	MPI_COMM_WORLD);
181	–	#else
182	–	nGlobalConstraints =  nConstraints_;
183	–	#endif
184	–	return nGlobalConstraints;
185	–	}
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();
#	Line 201 | Line 174 | namespace oopse {
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 228 | Line 201 | namespace oopse {
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 237 | Line 210 | namespace oopse {
210		} else {
211		return false;
212		}
240	–
241	–
213		}
214
215
#	Line 254 | 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;
235	+	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
#	Line 275 | Line 250 | namespace oopse {
250		ndf_local += 3;
251		}
252		}
278	–
253		}
254	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255	+	atom = mol->nextFluctuatingCharge(k)) {
256	+	if (atom->isFluctuatingCharge()) {
257	+	nfq_local++;
258	+	}
259	+	}
260		}
261
262		// n_constraints is local, so subtract them on each processor
#	Line 284 | Line 264 | namespace oopse {
264
265		#ifdef IS_MPI
266		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
268		#else
269		ndf_ = ndf_local;
270	+	nGlobalFluctuatingCharges_ = nfq_local;
271		#endif
272
273		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 302 | Line 284 | namespace oopse {
284		#endif
285		return fdf_;
286		}
287	+
288	+	unsigned int SimInfo::getNLocalCutoffGroups(){
289	+	int nLocalCutoffAtoms = 0;
290	+	Molecule* mol;
291	+	MoleculeIterator mi;
292	+	CutoffGroup* cg;
293	+	Molecule::CutoffGroupIterator ci;
294
295	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
296	+
297	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
298	+	cg = mol->nextCutoffGroup(ci)) {
299	+	nLocalCutoffAtoms += cg->getNumAtom();
300	+
301	+	}
302	+	}
303	+
304	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
305	+	}
306	+
307		void SimInfo::calcNdfRaw() {
308		int ndfRaw_local;
309
310		MoleculeIterator i;
311	<	std::vector<StuntDouble*>::iterator j;
311	>	vector<StuntDouble*>::iterator j;
312		Molecule* mol;
313		StuntDouble* integrableObject;
314
#	Line 354 | Line 355 | namespace oopse {
355
356		}
357
358	<	void SimInfo::addExcludePairs(Molecule* mol) {
359	<	std::vector<Bond*>::iterator bondIter;
360	<	std::vector<Bend*>::iterator bendIter;
361	<	std::vector<Torsion*>::iterator torsionIter;
362	<	std::vector<Inversion*>::iterator inversionIter;
358	>	void SimInfo::addInteractionPairs(Molecule* mol) {
359	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
360	>	vector<Bond*>::iterator bondIter;
361	>	vector<Bend*>::iterator bendIter;
362	>	vector<Torsion*>::iterator torsionIter;
363	>	vector<Inversion*>::iterator inversionIter;
364		Bond* bond;
365		Bend* bend;
366		Torsion* torsion;
#	Line 368 | Line 370 | namespace oopse {
370		int c;
371		int d;
372
373	<	std::map<int, std::set<int> > atomGroups;
373	>	// atomGroups can be used to add special interaction maps between
374	>	// groups of atoms that are in two separate rigid bodies.
375	>	// However, most site-site interactions between two rigid bodies
376	>	// are probably not special, just the ones between the physically
377	>	// bonded atoms.  Interactions *within* a single rigid body should
378	>	// always be excluded.  These are done at the bottom of this
379	>	// function.
380
381	+	map<int, set<int> > atomGroups;
382		Molecule::RigidBodyIterator rbIter;
383		RigidBody* rb;
384		Molecule::IntegrableObjectIterator ii;
385		StuntDouble* integrableObject;
386
387	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
388	<	integrableObject = mol->nextIntegrableObject(ii)) {
389	<
387	>	for (integrableObject = mol->beginIntegrableObject(ii);
388	>	integrableObject != NULL;
389	>	integrableObject = mol->nextIntegrableObject(ii)) {
390	>
391		if (integrableObject->isRigidBody()) {
392	<	rb = static_cast<RigidBody*>(integrableObject);
393	<	std::vector<Atom*> atoms = rb->getAtoms();
394	<	std::set<int> rigidAtoms;
395	<	for (int i = 0; i < atoms.size(); ++i) {
396	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
397	<	}
398	<	for (int i = 0; i < atoms.size(); ++i) {
399	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
400	<	}
392	>	rb = static_cast<RigidBody*>(integrableObject);
393	>	vector<Atom*> atoms = rb->getAtoms();
394	>	set<int> rigidAtoms;
395	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
396	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
397	>	}
398	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
399	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
400	>	}
401		} else {
402	<	std::set<int> oneAtomSet;
402	>	set<int> oneAtomSet;
403		oneAtomSet.insert(integrableObject->getGlobalIndex());
404	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
404	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
405		}
406		}
407	+
408	+	for (bond= mol->beginBond(bondIter); bond != NULL;
409	+	bond = mol->nextBond(bondIter)) {
410
398	–
399	–
400	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
411		a = bond->getAtomA()->getGlobalIndex();
412	<	b = bond->getAtomB()->getGlobalIndex();
413	<	exclude_.addPair(a, b);
412	>	b = bond->getAtomB()->getGlobalIndex();
413	>
414	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
415	>	oneTwoInteractions_.addPair(a, b);
416	>	} else {
417	>	excludedInteractions_.addPair(a, b);
418	>	}
419		}
420
421	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
421	>	for (bend= mol->beginBend(bendIter); bend != NULL;
422	>	bend = mol->nextBend(bendIter)) {
423	>
424		a = bend->getAtomA()->getGlobalIndex();
425		b = bend->getAtomB()->getGlobalIndex();
426		c = bend->getAtomC()->getGlobalIndex();
410	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
411	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
412	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
413	–
414	–	exclude_.addPairs(rigidSetA, rigidSetB);
415	–	exclude_.addPairs(rigidSetA, rigidSetC);
416	–	exclude_.addPairs(rigidSetB, rigidSetC);
427
428	<	//exclude_.addPair(a, b);
429	<	//exclude_.addPair(a, c);
430	<	//exclude_.addPair(b, c);
428	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
429	>	oneTwoInteractions_.addPair(a, b);
430	>	oneTwoInteractions_.addPair(b, c);
431	>	} else {
432	>	excludedInteractions_.addPair(a, b);
433	>	excludedInteractions_.addPair(b, c);
434	>	}
435	>
436	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
437	>	oneThreeInteractions_.addPair(a, c);
438	>	} else {
439	>	excludedInteractions_.addPair(a, c);
440	>	}
441		}
442
443	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
443	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
444	>	torsion = mol->nextTorsion(torsionIter)) {
445	>
446		a = torsion->getAtomA()->getGlobalIndex();
447		b = torsion->getAtomB()->getGlobalIndex();
448		c = torsion->getAtomC()->getGlobalIndex();
449	<	d = torsion->getAtomD()->getGlobalIndex();
428	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
429	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
430	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
431	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
449	>	d = torsion->getAtomD()->getGlobalIndex();
450
451	<	exclude_.addPairs(rigidSetA, rigidSetB);
452	<	exclude_.addPairs(rigidSetA, rigidSetC);
453	<	exclude_.addPairs(rigidSetA, rigidSetD);
454	<	exclude_.addPairs(rigidSetB, rigidSetC);
455	<	exclude_.addPairs(rigidSetB, rigidSetD);
456	<	exclude_.addPairs(rigidSetC, rigidSetD);
451	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
452	>	oneTwoInteractions_.addPair(a, b);
453	>	oneTwoInteractions_.addPair(b, c);
454	>	oneTwoInteractions_.addPair(c, d);
455	>	} else {
456	>	excludedInteractions_.addPair(a, b);
457	>	excludedInteractions_.addPair(b, c);
458	>	excludedInteractions_.addPair(c, d);
459	>	}
460
461	<	/*
462	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
463	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
464	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
465	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
466	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
467	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
468	<
469	<
470	<	exclude_.addPair(a, b);
471	<	exclude_.addPair(a, c);
472	<	exclude_.addPair(a, d);
473	<	exclude_.addPair(b, c);
453	<	exclude_.addPair(b, d);
454	<	exclude_.addPair(c, d);
455	<	*/
461	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
462	>	oneThreeInteractions_.addPair(a, c);
463	>	oneThreeInteractions_.addPair(b, d);
464	>	} else {
465	>	excludedInteractions_.addPair(a, c);
466	>	excludedInteractions_.addPair(b, d);
467	>	}
468	>
469	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
470	>	oneFourInteractions_.addPair(a, d);
471	>	} else {
472	>	excludedInteractions_.addPair(a, d);
473	>	}
474		}
475
476		for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
477		inversion = mol->nextInversion(inversionIter)) {
478	+
479		a = inversion->getAtomA()->getGlobalIndex();
480		b = inversion->getAtomB()->getGlobalIndex();
481		c = inversion->getAtomC()->getGlobalIndex();
482		d = inversion->getAtomD()->getGlobalIndex();
464	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
465	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
466	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
467	–	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
483
484	<	exclude_.addPairs(rigidSetA, rigidSetB);
485	<	exclude_.addPairs(rigidSetA, rigidSetC);
486	<	exclude_.addPairs(rigidSetA, rigidSetD);
487	<	exclude_.addPairs(rigidSetB, rigidSetC);
488	<	exclude_.addPairs(rigidSetB, rigidSetD);
489	<	exclude_.addPairs(rigidSetC, rigidSetD);
484	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
485	>	oneTwoInteractions_.addPair(a, b);
486	>	oneTwoInteractions_.addPair(a, c);
487	>	oneTwoInteractions_.addPair(a, d);
488	>	} else {
489	>	excludedInteractions_.addPair(a, b);
490	>	excludedInteractions_.addPair(a, c);
491	>	excludedInteractions_.addPair(a, d);
492	>	}
493
494	<	/*
495	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
496	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
497	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
498	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
499	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
500	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
501	<
502	<
485	<	exclude_.addPair(a, b);
486	<	exclude_.addPair(a, c);
487	<	exclude_.addPair(a, d);
488	<	exclude_.addPair(b, c);
489	<	exclude_.addPair(b, d);
490	<	exclude_.addPair(c, d);
491	<	*/
494	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
495	>	oneThreeInteractions_.addPair(b, c);
496	>	oneThreeInteractions_.addPair(b, d);
497	>	oneThreeInteractions_.addPair(c, d);
498	>	} else {
499	>	excludedInteractions_.addPair(b, c);
500	>	excludedInteractions_.addPair(b, d);
501	>	excludedInteractions_.addPair(c, d);
502	>	}
503		}
504
505	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
506	<	std::vector<Atom*> atoms = rb->getAtoms();
507	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
508	<	for (int j = i + 1; j < atoms.size(); ++j) {
505	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
506	>	rb = mol->nextRigidBody(rbIter)) {
507	>	vector<Atom*> atoms = rb->getAtoms();
508	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
509	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
510		a = atoms[i]->getGlobalIndex();
511		b = atoms[j]->getGlobalIndex();
512	<	exclude_.addPair(a, b);
512	>	excludedInteractions_.addPair(a, b);
513		}
514		}
515		}
516
517		}
518
519	<	void SimInfo::removeExcludePairs(Molecule* mol) {
520	<	std::vector<Bond*>::iterator bondIter;
521	<	std::vector<Bend*>::iterator bendIter;
522	<	std::vector<Torsion*>::iterator torsionIter;
523	<	std::vector<Inversion*>::iterator inversionIter;
519	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
520	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
521	>	vector<Bond*>::iterator bondIter;
522	>	vector<Bend*>::iterator bendIter;
523	>	vector<Torsion*>::iterator torsionIter;
524	>	vector<Inversion*>::iterator inversionIter;
525		Bond* bond;
526		Bend* bend;
527		Torsion* torsion;
#	Line 518 | Line 531 | namespace oopse {
531		int c;
532		int d;
533
534	<	std::map<int, std::set<int> > atomGroups;
522	<
534	>	map<int, set<int> > atomGroups;
535		Molecule::RigidBodyIterator rbIter;
536		RigidBody* rb;
537		Molecule::IntegrableObjectIterator ii;
538		StuntDouble* integrableObject;
539
540	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
541	<	integrableObject = mol->nextIntegrableObject(ii)) {
542	<
540	>	for (integrableObject = mol->beginIntegrableObject(ii);
541	>	integrableObject != NULL;
542	>	integrableObject = mol->nextIntegrableObject(ii)) {
543	>
544		if (integrableObject->isRigidBody()) {
545	<	rb = static_cast<RigidBody*>(integrableObject);
546	<	std::vector<Atom*> atoms = rb->getAtoms();
547	<	std::set<int> rigidAtoms;
548	<	for (int i = 0; i < atoms.size(); ++i) {
549	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
550	<	}
551	<	for (int i = 0; i < atoms.size(); ++i) {
552	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
553	<	}
545	>	rb = static_cast<RigidBody*>(integrableObject);
546	>	vector<Atom*> atoms = rb->getAtoms();
547	>	set<int> rigidAtoms;
548	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
549	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
550	>	}
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
553	>	}
554		} else {
555	<	std::set<int> oneAtomSet;
555	>	set<int> oneAtomSet;
556		oneAtomSet.insert(integrableObject->getGlobalIndex());
557	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
557	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
558		}
559		}
560
561	<
562	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
561	>	for (bond= mol->beginBond(bondIter); bond != NULL;
562	>	bond = mol->nextBond(bondIter)) {
563	>
564		a = bond->getAtomA()->getGlobalIndex();
565	<	b = bond->getAtomB()->getGlobalIndex();
566	<	exclude_.removePair(a, b);
565	>	b = bond->getAtomB()->getGlobalIndex();
566	>
567	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
568	>	oneTwoInteractions_.removePair(a, b);
569	>	} else {
570	>	excludedInteractions_.removePair(a, b);
571	>	}
572		}
573
574	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
574	>	for (bend= mol->beginBend(bendIter); bend != NULL;
575	>	bend = mol->nextBend(bendIter)) {
576	>
577		a = bend->getAtomA()->getGlobalIndex();
578		b = bend->getAtomB()->getGlobalIndex();
579		c = bend->getAtomC()->getGlobalIndex();
559	–
560	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
561	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
562	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
563	–
564	–	exclude_.removePairs(rigidSetA, rigidSetB);
565	–	exclude_.removePairs(rigidSetA, rigidSetC);
566	–	exclude_.removePairs(rigidSetB, rigidSetC);
580
581	<	//exclude_.removePair(a, b);
582	<	//exclude_.removePair(a, c);
583	<	//exclude_.removePair(b, c);
581	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
582	>	oneTwoInteractions_.removePair(a, b);
583	>	oneTwoInteractions_.removePair(b, c);
584	>	} else {
585	>	excludedInteractions_.removePair(a, b);
586	>	excludedInteractions_.removePair(b, c);
587	>	}
588	>
589	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
590	>	oneThreeInteractions_.removePair(a, c);
591	>	} else {
592	>	excludedInteractions_.removePair(a, c);
593	>	}
594		}
595
596	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
596	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
597	>	torsion = mol->nextTorsion(torsionIter)) {
598	>
599		a = torsion->getAtomA()->getGlobalIndex();
600		b = torsion->getAtomB()->getGlobalIndex();
601		c = torsion->getAtomC()->getGlobalIndex();
602	<	d = torsion->getAtomD()->getGlobalIndex();
602	>	d = torsion->getAtomD()->getGlobalIndex();
603	>
604	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
605	>	oneTwoInteractions_.removePair(a, b);
606	>	oneTwoInteractions_.removePair(b, c);
607	>	oneTwoInteractions_.removePair(c, d);
608	>	} else {
609	>	excludedInteractions_.removePair(a, b);
610	>	excludedInteractions_.removePair(b, c);
611	>	excludedInteractions_.removePair(c, d);
612	>	}
613
614	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
615	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
616	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
617	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
614	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
615	>	oneThreeInteractions_.removePair(a, c);
616	>	oneThreeInteractions_.removePair(b, d);
617	>	} else {
618	>	excludedInteractions_.removePair(a, c);
619	>	excludedInteractions_.removePair(b, d);
620	>	}
621
622	<	exclude_.removePairs(rigidSetA, rigidSetB);
623	<	exclude_.removePairs(rigidSetA, rigidSetC);
624	<	exclude_.removePairs(rigidSetA, rigidSetD);
625	<	exclude_.removePairs(rigidSetB, rigidSetC);
626	<	exclude_.removePairs(rigidSetB, rigidSetD);
589	<	exclude_.removePairs(rigidSetC, rigidSetD);
590	<
591	<	/*
592	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
593	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
594	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
595	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
596	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
597	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
598	<
599	<
600	<	exclude_.removePair(a, b);
601	<	exclude_.removePair(a, c);
602	<	exclude_.removePair(a, d);
603	<	exclude_.removePair(b, c);
604	<	exclude_.removePair(b, d);
605	<	exclude_.removePair(c, d);
606	<	*/
622	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
623	>	oneFourInteractions_.removePair(a, d);
624	>	} else {
625	>	excludedInteractions_.removePair(a, d);
626	>	}
627		}
628
629	<	for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
629	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
630	>	inversion = mol->nextInversion(inversionIter)) {
631	>
632		a = inversion->getAtomA()->getGlobalIndex();
633		b = inversion->getAtomB()->getGlobalIndex();
634		c = inversion->getAtomC()->getGlobalIndex();
635		d = inversion->getAtomD()->getGlobalIndex();
636
637	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
638	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
639	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
640	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
637	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
638	>	oneTwoInteractions_.removePair(a, b);
639	>	oneTwoInteractions_.removePair(a, c);
640	>	oneTwoInteractions_.removePair(a, d);
641	>	} else {
642	>	excludedInteractions_.removePair(a, b);
643	>	excludedInteractions_.removePair(a, c);
644	>	excludedInteractions_.removePair(a, d);
645	>	}
646
647	<	exclude_.removePairs(rigidSetA, rigidSetB);
648	<	exclude_.removePairs(rigidSetA, rigidSetC);
649	<	exclude_.removePairs(rigidSetA, rigidSetD);
650	<	exclude_.removePairs(rigidSetB, rigidSetC);
651	<	exclude_.removePairs(rigidSetB, rigidSetD);
652	<	exclude_.removePairs(rigidSetC, rigidSetD);
653	<
654	<	/*
655	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
629	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
630	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
631	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
632	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
633	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
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	<	*/
647	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
648	>	oneThreeInteractions_.removePair(b, c);
649	>	oneThreeInteractions_.removePair(b, d);
650	>	oneThreeInteractions_.removePair(c, d);
651	>	} else {
652	>	excludedInteractions_.removePair(b, c);
653	>	excludedInteractions_.removePair(b, d);
654	>	excludedInteractions_.removePair(c, d);
655	>	}
656		}
657
658	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
659	<	std::vector<Atom*> atoms = rb->getAtoms();
660	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
661	<	for (int j = i + 1; j < atoms.size(); ++j) {
658	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
659	>	rb = mol->nextRigidBody(rbIter)) {
660	>	vector<Atom*> atoms = rb->getAtoms();
661	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
662	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
663		a = atoms[i]->getGlobalIndex();
664		b = atoms[j]->getGlobalIndex();
665	<	exclude_.removePair(a, b);
665	>	excludedInteractions_.removePair(a, b);
666		}
667		}
668		}
669	<
669	>
670		}
671	<
672	<
671	>
672	>
673		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
674		int curStampId;
675	<
675	>
676		//index from 0
677		curStampId = moleculeStamps_.size();
678
#	Line 666 | Line 680 | namespace oopse {
680		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
681		}
682
669	–	void SimInfo::update() {
683
684	<	setupSimType();
685	<
686	<	#ifdef IS_MPI
687	<	setupFortranParallel();
688	<	#endif
689	<
690	<	setupFortranSim();
691	<
692	<	//setup fortran force field
680	<	/** @deprecate */
681	<	int isError = 0;
682	<
683	<	setupCutoff();
684	<
685	<	setupElectrostaticSummationMethod( isError );
686	<	setupSwitchingFunction();
687	<	setupAccumulateBoxDipole();
688	<
689	<	if(isError){
690	<	sprintf( painCave.errMsg,
691	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
692	<	painCave.isFatal = 1;
693	<	simError();
694	<	}
695	<
684	>	/**
685	>	* update
686	>	*
687	>	*  Performs the global checks and variable settings after the
688	>	*  objects have been created.
689	>	*
690	>	*/
691	>	void SimInfo::update() {
692	>	setupSimVariables();
693		calcNdf();
694		calcNdfRaw();
695		calcNdfTrans();
699	–
700	–	fortranInitialized_ = true;
696		}
697	<
698	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
697	>
698	>	/**
699	>	* getSimulatedAtomTypes
700	>	*
701	>	* Returns an STL set of AtomType* that are actually present in this
702	>	* simulation.  Must query all processors to assemble this information.
703	>	*
704	>	*/
705	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
706		SimInfo::MoleculeIterator mi;
707		Molecule* mol;
708		Molecule::AtomIterator ai;
709		Atom* atom;
710	<	std::set<AtomType*> atomTypes;
711	<
710	>	set<AtomType*> atomTypes;
711	>
712		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
713	<
714	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
713	>	for(atom = mol->beginAtom(ai); atom != NULL;
714	>	atom = mol->nextAtom(ai)) {
715		atomTypes.insert(atom->getAtomType());
716	<	}
717	<
718	<	}
716	>	}
717	>	}
718	>
719	>	#ifdef IS_MPI
720
721	<	return atomTypes;
722	<	}
720	<
721	<	void SimInfo::setupSimType() {
722	<	std::set<AtomType*>::iterator i;
723	<	std::set<AtomType*> atomTypes;
724	<	atomTypes = getUniqueAtomTypes();
721	>	// loop over the found atom types on this processor, and add their
722	>	// numerical idents to a vector:
723
724	<	int useLennardJones = 0;
725	<	int useElectrostatic = 0;
726	<	int useEAM = 0;
727	<	int useSC = 0;
730	<	int useCharge = 0;
731	<	int useDirectional = 0;
732	<	int useDipole = 0;
733	<	int useGayBerne = 0;
734	<	int useSticky = 0;
735	<	int useStickyPower = 0;
736	<	int useShape = 0;
737	<	int useFLARB = 0; //it is not in AtomType yet
738	<	int useDirectionalAtom = 0;
739	<	int useElectrostatics = 0;
740	<	//usePBC and useRF are from simParams
741	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
742	<	int useRF;
743	<	int useSF;
744	<	int useSP;
745	<	int useBoxDipole;
724	>	vector<int> foundTypes;
725	>	set<AtomType*>::iterator i;
726	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
727	>	foundTypes.push_back( (*i)->getIdent() );
728
729	<	std::string myMethod;
729	>	// count_local holds the number of found types on this processor
730	>	int count_local = foundTypes.size();
731
732	<	// set the useRF logical
750	<	useRF = 0;
751	<	useSF = 0;
752	<	useSP = 0;
732	>	int nproc = MPI::COMM_WORLD.Get_size();
733
734	+	// we need arrays to hold the counts and displacement vectors for
735	+	// all processors
736	+	vector<int> counts(nproc, 0);
737	+	vector<int> disps(nproc, 0);
738
739	<	if (simParams_->haveElectrostaticSummationMethod()) {
740	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
741	<	toUpper(myMethod);
742	<	if (myMethod == "REACTION_FIELD"){
743	<	useRF = 1;
744	<	} else if (myMethod == "SHIFTED_FORCE"){
745	<	useSF = 1;
746	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
747	<	useSP = 1;
748	<	}
739	>	// fill the counts array
740	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
741	>	1, MPI::INT);
742	>
743	>	// use the processor counts to compute the displacement array
744	>	disps[0] = 0;
745	>	int totalCount = counts[0];
746	>	for (int iproc = 1; iproc < nproc; iproc++) {
747	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
748	>	totalCount += counts[iproc];
749		}
750	+
751	+	// we need a (possibly redundant) set of all found types:
752	+	vector<int> ftGlobal(totalCount);
753
754	<	if (simParams_->haveAccumulateBoxDipole())
755	<	if (simParams_->getAccumulateBoxDipole())
756	<	useBoxDipole = 1;
754	>	// now spray out the foundTypes to all the other processors:
755	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
756	>	&ftGlobal[0], &counts[0], &disps[0],
757	>	MPI::INT);
758
759	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
759	>	vector<int>::iterator j;
760
761	<	//loop over all of the atom types
762	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
763	<	useLennardJones |= (*i)->isLennardJones();
776	<	useElectrostatic |= (*i)->isElectrostatic();
777	<	useEAM |= (*i)->isEAM();
778	<	useSC |= (*i)->isSC();
779	<	useCharge |= (*i)->isCharge();
780	<	useDirectional |= (*i)->isDirectional();
781	<	useDipole |= (*i)->isDipole();
782	<	useGayBerne |= (*i)->isGayBerne();
783	<	useSticky |= (*i)->isSticky();
784	<	useStickyPower |= (*i)->isStickyPower();
785	<	useShape |= (*i)->isShape();
786	<	}
761	>	// foundIdents is a stl set, so inserting an already found ident
762	>	// will have no effect.
763	>	set<int> foundIdents;
764
765	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
766	<	useDirectionalAtom = 1;
767	<	}
765	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
766	>	foundIdents.insert((*j));
767	>
768	>	// now iterate over the foundIdents and get the actual atom types
769	>	// that correspond to these:
770	>	set<int>::iterator it;
771	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
772	>	atomTypes.insert( forceField_->getAtomType((*it)) );
773	>
774	>	#endif
775
776	<	if (useCharge || useDipole) {
777	<	useElectrostatics = 1;
794	<	}
776	>	return atomTypes;
777	>	}
778
779	+	void SimInfo::setupSimVariables() {
780	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
781	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
782	+	calcBoxDipole_ = false;
783	+	if ( simParams_->haveAccumulateBoxDipole() )
784	+	if ( simParams_->getAccumulateBoxDipole() ) {
785	+	calcBoxDipole_ = true;
786	+	}
787	+
788	+	set<AtomType*>::iterator i;
789	+	set<AtomType*> atomTypes;
790	+	atomTypes = getSimulatedAtomTypes();
791	+	int usesElectrostatic = 0;
792	+	int usesMetallic = 0;
793	+	int usesDirectional = 0;
794	+	int usesFluctuatingCharges =  0;
795	+	//loop over all of the atom types
796	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
797	+	usesElectrostatic |= (*i)->isElectrostatic();
798	+	usesMetallic |= (*i)->isMetal();
799	+	usesDirectional |= (*i)->isDirectional();
800	+	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
801	+	}
802	+
803		#ifdef IS_MPI
804		int temp;
805	<
806	<	temp = usePBC;
800	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	<
802	<	temp = useDirectionalAtom;
803	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
804	<
805	<	temp = useLennardJones;
806	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	<
808	<	temp = useElectrostatics;
809	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	<
811	<	temp = useCharge;
812	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	<
814	<	temp = useDipole;
815	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	<
817	<	temp = useSticky;
818	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	<
820	<	temp = useStickyPower;
821	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
805	>	temp = usesDirectional;
806	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807
808	<	temp = useGayBerne;
809	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
825	<
826	<	temp = useEAM;
827	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828	<
829	<	temp = useSC;
830	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	temp = usesMetallic;
809	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810
811	<	temp = useShape;
812	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	temp = usesElectrostatic;
812	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useFLARB;
815	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	temp = usesFluctuatingCharges;
815	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	#else
817
818	<	temp = useRF;
819	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	>	usesDirectionalAtoms_ = usesDirectional;
819	>	usesMetallicAtoms_ = usesMetallic;
820	>	usesElectrostaticAtoms_ = usesElectrostatic;
821	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
822
823	<	temp = useSF;
824	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
823	>	#endif
824	>
825	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
826	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
827	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
828	>	}
829
844	–	temp = useSP;
845	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830
831	<	temp = useBoxDipole;
832	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831	>	vector<int> SimInfo::getGlobalAtomIndices() {
832	>	SimInfo::MoleculeIterator mi;
833	>	Molecule* mol;
834	>	Molecule::AtomIterator ai;
835	>	Atom* atom;
836
837	<	temp = useAtomicVirial_;
838	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
838	>
839	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840	>
841	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
842	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
843	>	}
844	>	}
845	>	return GlobalAtomIndices;
846	>	}
847
853	–	#endif
848
849	<	fInfo_.SIM_uses_PBC = usePBC;
850	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
851	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
852	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
853	<	fInfo_.SIM_uses_Charges = useCharge;
860	<	fInfo_.SIM_uses_Dipoles = useDipole;
861	<	fInfo_.SIM_uses_Sticky = useSticky;
862	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
863	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
864	<	fInfo_.SIM_uses_EAM = useEAM;
865	<	fInfo_.SIM_uses_SC = useSC;
866	<	fInfo_.SIM_uses_Shapes = useShape;
867	<	fInfo_.SIM_uses_FLARB = useFLARB;
868	<	fInfo_.SIM_uses_RF = useRF;
869	<	fInfo_.SIM_uses_SF = useSF;
870	<	fInfo_.SIM_uses_SP = useSP;
871	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
872	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
873	<	}
849	>	vector<int> SimInfo::getGlobalGroupIndices() {
850	>	SimInfo::MoleculeIterator mi;
851	>	Molecule* mol;
852	>	Molecule::CutoffGroupIterator ci;
853	>	CutoffGroup* cg;
854
855	<	void SimInfo::setupFortranSim() {
876	<	int isError;
877	<	int nExclude;
878	<	std::vector<int> fortranGlobalGroupMembership;
855	>	vector<int> GlobalGroupIndices;
856
857	<	nExclude = exclude_.getSize();
858	<	isError = 0;
859	<
860	<	//globalGroupMembership_ is filled by SimCreator
861	<	for (int i = 0; i < nGlobalAtoms_; i++) {
862	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
857	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
858	>
859	>	//local index of cutoff group is trivial, it only depends on the
860	>	//order of travesing
861	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
862	>	cg = mol->nextCutoffGroup(ci)) {
863	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
864	>	}
865		}
866	+	return GlobalGroupIndices;
867	+	}
868
869	+
870	+	void SimInfo::prepareTopology() {
871	+	int nExclude, nOneTwo, nOneThree, nOneFour;
872	+
873		//calculate mass ratio of cutoff group
889	–	std::vector<RealType> mfact;
874		SimInfo::MoleculeIterator mi;
875		Molecule* mol;
876		Molecule::CutoffGroupIterator ci;
#	Line 895 | Line 879 | namespace oopse {
879		Atom* atom;
880		RealType totalMass;
881
882	<	//to avoid memory reallocation, reserve enough space for mfact
883	<	mfact.reserve(getNCutoffGroups());
882	>	/**
883	>	* The mass factor is the relative mass of an atom to the total
884	>	* mass of the cutoff group it belongs to.  By default, all atoms
885	>	* are their own cutoff groups, and therefore have mass factors of
886	>	* 1.  We need some special handling for massless atoms, which
887	>	* will be treated as carrying the entire mass of the cutoff
888	>	* group.
889	>	*/
890	>	massFactors_.clear();
891	>	massFactors_.resize(getNAtoms(), 1.0);
892
893		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
894	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
894	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
895	>	cg = mol->nextCutoffGroup(ci)) {
896
897		totalMass = cg->getMass();
898		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
899		// Check for massless groups - set mfact to 1 if true
900	<	if (totalMass != 0)
901	<	mfact.push_back(atom->getMass()/totalMass);
900	>	if (totalMass != 0)
901	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
902		else
903	<	mfact.push_back( 1.0 );
903	>	massFactors_[atom->getLocalIndex()] = 1.0;
904		}
912	–
905		}
906		}
907
908	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
917	<	std::vector<int> identArray;
908	>	// Build the identArray_
909
910	<	//to avoid memory reallocation, reserve enough space identArray
911	<	identArray.reserve(getNAtoms());
921	<
910	>	identArray_.clear();
911	>	identArray_.reserve(getNAtoms());
912		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
913		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
914	<	identArray.push_back(atom->getIdent());
914	>	identArray_.push_back(atom->getIdent());
915		}
916		}
927	–
928	–	//fill molMembershipArray
929	–	//molMembershipArray is filled by SimCreator
930	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
931	–	for (int i = 0; i < nGlobalAtoms_; i++) {
932	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
933	–	}
917
918	<	//setup fortran simulation
936	<	int nGlobalExcludes = 0;
937	<	int* globalExcludes = NULL;
938	<	int* excludeList = exclude_.getExcludeList();
939	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
940	<	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
941	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
942	<	&fortranGlobalGroupMembership[0], &isError);
943	<
944	<	if( isError ){
945	<
946	<	sprintf( painCave.errMsg,
947	<	"There was an error setting the simulation information in fortran.\n" );
948	<	painCave.isFatal = 1;
949	<	painCave.severity = OOPSE_ERROR;
950	<	simError();
951	<	}
952	<
953	<
954	<	sprintf( checkPointMsg,
955	<	"succesfully sent the simulation information to fortran.\n");
956	<
957	<	errorCheckPoint();
958	<
959	<	// Setup number of neighbors in neighbor list if present
960	<	if (simParams_->haveNeighborListNeighbors()) {
961	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
962	<	setNeighbors(&nlistNeighbors);
963	<	}
964	<
918	>	//scan topology
919
920	<	}
920	>	nExclude = excludedInteractions_.getSize();
921	>	nOneTwo = oneTwoInteractions_.getSize();
922	>	nOneThree = oneThreeInteractions_.getSize();
923	>	nOneFour = oneFourInteractions_.getSize();
924
925	<
926	<	void SimInfo::setupFortranParallel() {
927	<	#ifdef IS_MPI
928	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
972	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
973	<	std::vector<int> localToGlobalCutoffGroupIndex;
974	<	SimInfo::MoleculeIterator mi;
975	<	Molecule::AtomIterator ai;
976	<	Molecule::CutoffGroupIterator ci;
977	<	Molecule* mol;
978	<	Atom* atom;
979	<	CutoffGroup* cg;
980	<	mpiSimData parallelData;
981	<	int isError;
982	<
983	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
984	<
985	<	//local index(index in DataStorge) of atom is important
986	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
987	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
988	<	}
989	<
990	<	//local index of cutoff group is trivial, it only depends on the order of travesing
991	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
992	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
993	<	}
994	<
995	<	}
925	>	int* excludeList = excludedInteractions_.getPairList();
926	>	int* oneTwoList = oneTwoInteractions_.getPairList();
927	>	int* oneThreeList = oneThreeInteractions_.getPairList();
928	>	int* oneFourList = oneFourInteractions_.getPairList();
929
930	<	//fill up mpiSimData struct
998	<	parallelData.nMolGlobal = getNGlobalMolecules();
999	<	parallelData.nMolLocal = getNMolecules();
1000	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1001	<	parallelData.nAtomsLocal = getNAtoms();
1002	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1003	<	parallelData.nGroupsLocal = getNCutoffGroups();
1004	<	parallelData.myNode = worldRank;
1005	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1006	<
1007	<	//pass mpiSimData struct and index arrays to fortran
1008	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1009	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1010	<	&localToGlobalCutoffGroupIndex[0], &isError);
1011	<
1012	<	if (isError) {
1013	<	sprintf(painCave.errMsg,
1014	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1015	<	painCave.isFatal = 1;
1016	<	simError();
1017	<	}
1018	<
1019	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1020	<	errorCheckPoint();
1021	<
1022	<	#endif
1023	<	}
1024	<
1025	<	void SimInfo::setupCutoff() {
1026	<
1027	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1028	<
1029	<	// Check the cutoff policy
1030	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1031	<
1032	<	// Set LJ shifting bools to false
1033	<	ljsp_ = false;
1034	<	ljsf_ = false;
1035	<
1036	<	std::string myPolicy;
1037	<	if (forceFieldOptions_.haveCutoffPolicy()){
1038	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1039	<	}else if (simParams_->haveCutoffPolicy()) {
1040	<	myPolicy = simParams_->getCutoffPolicy();
1041	<	}
1042	<
1043	<	if (!myPolicy.empty()){
1044	<	toUpper(myPolicy);
1045	<	if (myPolicy == "MIX") {
1046	<	cp = MIX_CUTOFF_POLICY;
1047	<	} else {
1048	<	if (myPolicy == "MAX") {
1049	<	cp = MAX_CUTOFF_POLICY;
1050	<	} else {
1051	<	if (myPolicy == "TRADITIONAL") {
1052	<	cp = TRADITIONAL_CUTOFF_POLICY;
1053	<	} else {
1054	<	// throw error
1055	<	sprintf( painCave.errMsg,
1056	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1057	<	painCave.isFatal = 1;
1058	<	simError();
1059	<	}
1060	<	}
1061	<	}
1062	<	}
1063	<	notifyFortranCutoffPolicy(&cp);
1064	<
1065	<	// Check the Skin Thickness for neighborlists
1066	<	RealType skin;
1067	<	if (simParams_->haveSkinThickness()) {
1068	<	skin = simParams_->getSkinThickness();
1069	<	notifyFortranSkinThickness(&skin);
1070	<	}
1071	<
1072	<	// Check if the cutoff was set explicitly:
1073	<	if (simParams_->haveCutoffRadius()) {
1074	<	rcut_ = simParams_->getCutoffRadius();
1075	<	if (simParams_->haveSwitchingRadius()) {
1076	<	rsw_  = simParams_->getSwitchingRadius();
1077	<	} else {
1078	<	if (fInfo_.SIM_uses_Charges |
1079	<	fInfo_.SIM_uses_Dipoles |
1080	<	fInfo_.SIM_uses_RF) {
1081	<
1082	<	rsw_ = 0.85 * rcut_;
1083	<	sprintf(painCave.errMsg,
1084	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1085	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1086	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1087	<	painCave.isFatal = 0;
1088	<	simError();
1089	<	} else {
1090	<	rsw_ = rcut_;
1091	<	sprintf(painCave.errMsg,
1092	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1093	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1094	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1095	<	painCave.isFatal = 0;
1096	<	simError();
1097	<	}
1098	<	}
1099	<
1100	<	if (simParams_->haveElectrostaticSummationMethod()) {
1101	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1102	<	toUpper(myMethod);
1103	<
1104	<	if (myMethod == "SHIFTED_POTENTIAL") {
1105	<	ljsp_ = true;
1106	<	} else if (myMethod == "SHIFTED_FORCE") {
1107	<	ljsf_ = true;
1108	<	}
1109	<	}
1110	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1111	<
1112	<	} else {
1113	<
1114	<	// For electrostatic atoms, we'll assume a large safe value:
1115	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1116	<	sprintf(painCave.errMsg,
1117	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1118	<	"\tOOPSE will use a default value of 15.0 angstroms"
1119	<	"\tfor the cutoffRadius.\n");
1120	<	painCave.isFatal = 0;
1121	<	simError();
1122	<	rcut_ = 15.0;
1123	<
1124	<	if (simParams_->haveElectrostaticSummationMethod()) {
1125	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1126	<	toUpper(myMethod);
1127	<
1128	<	// For the time being, we're tethering the LJ shifted behavior to the
1129	<	// electrostaticSummationMethod keyword options
1130	<	if (myMethod == "SHIFTED_POTENTIAL") {
1131	<	ljsp_ = true;
1132	<	} else if (myMethod == "SHIFTED_FORCE") {
1133	<	ljsf_ = true;
1134	<	}
1135	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1136	<	if (simParams_->haveSwitchingRadius()){
1137	<	sprintf(painCave.errMsg,
1138	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1139	<	"\teven though the electrostaticSummationMethod was\n"
1140	<	"\tset to %s\n", myMethod.c_str());
1141	<	painCave.isFatal = 1;
1142	<	simError();
1143	<	}
1144	<	}
1145	<	}
1146	<
1147	<	if (simParams_->haveSwitchingRadius()){
1148	<	rsw_ = simParams_->getSwitchingRadius();
1149	<	} else {
1150	<	sprintf(painCave.errMsg,
1151	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1152	<	"\tOOPSE will use a default value of\n"
1153	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1154	<	painCave.isFatal = 0;
1155	<	simError();
1156	<	rsw_ = 0.85 * rcut_;
1157	<	}
1158	<
1159	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1160	<
1161	<	} else {
1162	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1163	<	// We'll punt and let fortran figure out the cutoffs later.
1164	<
1165	<	notifyFortranYouAreOnYourOwn();
1166	<
1167	<	}
1168	<	}
1169	<	}
1170	<
1171	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1172	<
1173	<	int errorOut;
1174	<	int esm =  NONE;
1175	<	int sm = UNDAMPED;
1176	<	RealType alphaVal;
1177	<	RealType dielectric;
1178	<
1179	<	errorOut = isError;
1180	<
1181	<	if (simParams_->haveElectrostaticSummationMethod()) {
1182	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1183	<	toUpper(myMethod);
1184	<	if (myMethod == "NONE") {
1185	<	esm = NONE;
1186	<	} else {
1187	<	if (myMethod == "SWITCHING_FUNCTION") {
1188	<	esm = SWITCHING_FUNCTION;
1189	<	} else {
1190	<	if (myMethod == "SHIFTED_POTENTIAL") {
1191	<	esm = SHIFTED_POTENTIAL;
1192	<	} else {
1193	<	if (myMethod == "SHIFTED_FORCE") {
1194	<	esm = SHIFTED_FORCE;
1195	<	} else {
1196	<	if (myMethod == "REACTION_FIELD") {
1197	<	esm = REACTION_FIELD;
1198	<	dielectric = simParams_->getDielectric();
1199	<	if (!simParams_->haveDielectric()) {
1200	<	// throw warning
1201	<	sprintf( painCave.errMsg,
1202	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1203	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1204	<	painCave.isFatal = 0;
1205	<	simError();
1206	<	}
1207	<	} else {
1208	<	// throw error
1209	<	sprintf( painCave.errMsg,
1210	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1211	<	"\t(Input file specified %s .)\n"
1212	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1213	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1214	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1215	<	painCave.isFatal = 1;
1216	<	simError();
1217	<	}
1218	<	}
1219	<	}
1220	<	}
1221	<	}
1222	<	}
1223	<
1224	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1225	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1226	<	toUpper(myScreen);
1227	<	if (myScreen == "UNDAMPED") {
1228	<	sm = UNDAMPED;
1229	<	} else {
1230	<	if (myScreen == "DAMPED") {
1231	<	sm = DAMPED;
1232	<	if (!simParams_->haveDampingAlpha()) {
1233	<	// first set a cutoff dependent alpha value
1234	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1235	<	alphaVal = 0.5125 - rcut_* 0.025;
1236	<	// for values rcut > 20.5, alpha is zero
1237	<	if (alphaVal < 0) alphaVal = 0;
1238	<
1239	<	// throw warning
1240	<	sprintf( painCave.errMsg,
1241	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1242	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1243	<	painCave.isFatal = 0;
1244	<	simError();
1245	<	} else {
1246	<	alphaVal = simParams_->getDampingAlpha();
1247	<	}
1248	<
1249	<	} else {
1250	<	// throw error
1251	<	sprintf( painCave.errMsg,
1252	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1253	<	"\t(Input file specified %s .)\n"
1254	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1255	<	"or \"damped\".\n", myScreen.c_str() );
1256	<	painCave.isFatal = 1;
1257	<	simError();
1258	<	}
1259	<	}
1260	<	}
1261	<
1262	<	// let's pass some summation method variables to fortran
1263	<	setElectrostaticSummationMethod( &esm );
1264	<	setFortranElectrostaticMethod( &esm );
1265	<	setScreeningMethod( &sm );
1266	<	setDampingAlpha( &alphaVal );
1267	<	setReactionFieldDielectric( &dielectric );
1268	<	initFortranFF( &errorOut );
930	>	topologyDone_ = true;
931		}
932
1271	–	void SimInfo::setupSwitchingFunction() {
1272	–	int ft = CUBIC;
1273	–
1274	–	if (simParams_->haveSwitchingFunctionType()) {
1275	–	std::string funcType = simParams_->getSwitchingFunctionType();
1276	–	toUpper(funcType);
1277	–	if (funcType == "CUBIC") {
1278	–	ft = CUBIC;
1279	–	} else {
1280	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1281	–	ft = FIFTH_ORDER_POLY;
1282	–	} else {
1283	–	// throw error
1284	–	sprintf( painCave.errMsg,
1285	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1286	–	painCave.isFatal = 1;
1287	–	simError();
1288	–	}
1289	–	}
1290	–	}
1291	–
1292	–	// send switching function notification to switcheroo
1293	–	setFunctionType(&ft);
1294	–
1295	–	}
1296	–
1297	–	void SimInfo::setupAccumulateBoxDipole() {
1298	–
1299	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1300	–	if ( simParams_->haveAccumulateBoxDipole() )
1301	–	if ( simParams_->getAccumulateBoxDipole() ) {
1302	–	setAccumulateBoxDipole();
1303	–	calcBoxDipole_ = true;
1304	–	}
1305	–
1306	–	}
1307	–
933		void SimInfo::addProperty(GenericData* genData) {
934		properties_.addProperty(genData);
935		}
936
937	<	void SimInfo::removeProperty(const std::string& propName) {
937	>	void SimInfo::removeProperty(const string& propName) {
938		properties_.removeProperty(propName);
939		}
940
#	Line 1317 | Line 942 | namespace oopse {
942		properties_.clearProperties();
943		}
944
945	<	std::vector<std::string> SimInfo::getPropertyNames() {
945	>	vector<string> SimInfo::getPropertyNames() {
946		return properties_.getPropertyNames();
947		}
948
949	<	std::vector<GenericData*> SimInfo::getProperties() {
949	>	vector<GenericData*> SimInfo::getProperties() {
950		return properties_.getProperties();
951		}
952
953	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
953	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
954		return properties_.getPropertyByName(propName);
955		}
956
#	Line 1339 | Line 964 | namespace oopse {
964		Molecule* mol;
965		RigidBody* rb;
966		Atom* atom;
967	+	CutoffGroup* cg;
968		SimInfo::MoleculeIterator mi;
969		Molecule::RigidBodyIterator rbIter;
970	<	Molecule::AtomIterator atomIter;;
970	>	Molecule::AtomIterator atomIter;
971	>	Molecule::CutoffGroupIterator cgIter;
972
973		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
974
#	Line 1352 | Line 979 | namespace oopse {
979		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
980		rb->setSnapshotManager(sman_);
981		}
982	+
983	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
984	+	cg->setSnapshotManager(sman_);
985	+	}
986		}
987
988		}
#	Line 1408 | Line 1039 | namespace oopse {
1039
1040		}
1041
1042	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1042	>	ostream& operator <<(ostream& o, SimInfo& info) {
1043
1044		return o;
1045		}
#	Line 1451 | Line 1082 | namespace oopse {
1082
1083
1084		[  Ixx -Ixy  -Ixz ]
1085	<	J =| -Iyx  Iyy  -Iyz |
1085	>	J =| -Iyx  Iyy  -Iyz |
1086		[ -Izx -Iyz   Izz ]
1087		*/
1088
#	Line 1558 | Line 1189 | namespace oopse {
1189		return IOIndexToIntegrableObject.at(index);
1190		}
1191
1192	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1192	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1193		IOIndexToIntegrableObject= v;
1194		}
1195
#	Line 1580 | Line 1211 | namespace oopse {
1211
1212		det = intTensor.determinant();
1213		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1214	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1214	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1215		return;
1216		}
1217
#	Line 1596 | Line 1227 | namespace oopse {
1227
1228		detI = intTensor.determinant();
1229		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1230	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1230	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1231		return;
1232		}
1233		/*
1234	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1234	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1235		assert( v.size() == nAtoms_ + nRigidBodies_);
1236		sdByGlobalIndex_ = v;
1237		}
#	Line 1610 | Line 1241 | namespace oopse {
1241		return sdByGlobalIndex_.at(index);
1242		}
1243		*/
1244	<	}//end namespace oopse
1244	>	int SimInfo::getNGlobalConstraints() {
1245	>	int nGlobalConstraints;
1246	>	#ifdef IS_MPI
1247	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1248	>	MPI_COMM_WORLD);
1249	>	#else
1250	>	nGlobalConstraints =  nConstraints_;
1251	>	#endif
1252	>	return nGlobalConstraints;
1253	>	}
1254
1255	+	}//end namespace OpenMD
1256	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

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