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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1767 by gezelter, Fri Jul 6 22:01:58 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	<
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	<	std::map<int, std::set<int> >::iterator i = container.find(index);
80	<	std::set<int> result;
81	<	if (i != container.end()) {
82	<	result = i->second;
83	<	}
84	<
85	<	return result;
86	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
79	<	useAtomicVirial_(true) {
80	<
81	<	MoleculeStamp* molStamp;
82	<	int nMolWithSameStamp;
83	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
85	<	CutoffGroupStamp* cgStamp;
86	<	RigidBodyStamp* rbStamp;
87	<	int nRigidAtoms = 0;
88	<	std::vector<Component*> components = simParams->getComponents();
89	<
90	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91	<	molStamp = (*i)->getMoleculeStamp();
92	<	nMolWithSameStamp = (*i)->getNMol();
93	<
94	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
95	<
96	<	//calculate atoms in molecules
97	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
98	<
99	<	//calculate atoms in cutoff groups
100	<	int nAtomsInGroups = 0;
101	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102	<
103	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
104	<	cgStamp = molStamp->getCutoffGroupStamp(j);
105	<	nAtomsInGroups += cgStamp->getNMembers();
106	<	}
107	<
108	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109	<
110	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
111	<
112	<	//calculate atoms in rigid bodies
113	<	int nAtomsInRigidBodies = 0;
114	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
115	<
116	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
117	<	rbStamp = molStamp->getRigidBodyStamp(j);
118	<	nAtomsInRigidBodies += rbStamp->getNMembers();
119	<	}
120	<
121	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123	<
124	<	}
142	<
143	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	<	//group therefore the total number of cutoff groups in the system is
145	<	//equal to the total number of atoms minus number of atoms belong to
146	<	//cutoff group defined in meta-data file plus the number of cutoff
147	<	//groups defined in meta-data file
148	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149	<
150	<	//every free atom (atom does not belong to rigid bodies) is an
151	<	//integrable object therefore the total number of integrable objects
152	<	//in the system is equal to the total number of atoms minus number of
153	<	//atoms belong to rigid body defined in meta-data file plus the number
154	<	//of rigid bodies defined in meta-data file
155	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	<	+ nGlobalRigidBodies_;
157	<
158	<	nGlobalMols_ = molStampIds_.size();
159	<	molToProcMap_.resize(nGlobalMols_);
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	>	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	>	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;
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 271 | Line 250 | namespace oopse {
250		ndf_local += 3;
251		}
252		}
274	–
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	+	ndfLocal_ = ndf_local;
263	+
264		// n_constraints is local, so subtract them on each processor
265		ndf_local -= nConstraints_;
266
267		#ifdef IS_MPI
268		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
270		#else
271		ndf_ = ndf_local;
272	+	nGlobalFluctuatingCharges_ = nfq_local;
273		#endif
274
275		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 298 | Line 286 | namespace oopse {
286		#endif
287		return fdf_;
288		}
289	+
290	+	unsigned int SimInfo::getNLocalCutoffGroups(){
291	+	int nLocalCutoffAtoms = 0;
292	+	Molecule* mol;
293	+	MoleculeIterator mi;
294	+	CutoffGroup* cg;
295	+	Molecule::CutoffGroupIterator ci;
296
297	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
298	+
299	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
300	+	cg = mol->nextCutoffGroup(ci)) {
301	+	nLocalCutoffAtoms += cg->getNumAtom();
302	+
303	+	}
304	+	}
305	+
306	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
307	+	}
308	+
309		void SimInfo::calcNdfRaw() {
310		int ndfRaw_local;
311
312		MoleculeIterator i;
313	<	std::vector<StuntDouble*>::iterator j;
313	>	vector<StuntDouble*>::iterator j;
314		Molecule* mol;
315		StuntDouble* integrableObject;
316
#	Line 350 | Line 357 | namespace oopse {
357
358		}
359
360	<	void SimInfo::addExcludePairs(Molecule* mol) {
361	<	std::vector<Bond*>::iterator bondIter;
362	<	std::vector<Bend*>::iterator bendIter;
363	<	std::vector<Torsion*>::iterator torsionIter;
360	>	void SimInfo::addInteractionPairs(Molecule* mol) {
361	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
362	>	vector<Bond*>::iterator bondIter;
363	>	vector<Bend*>::iterator bendIter;
364	>	vector<Torsion*>::iterator torsionIter;
365	>	vector<Inversion*>::iterator inversionIter;
366		Bond* bond;
367		Bend* bend;
368		Torsion* torsion;
369	+	Inversion* inversion;
370		int a;
371		int b;
372		int c;
373		int d;
374
375	<	std::map<int, std::set<int> > atomGroups;
375	>	// atomGroups can be used to add special interaction maps between
376	>	// groups of atoms that are in two separate rigid bodies.
377	>	// However, most site-site interactions between two rigid bodies
378	>	// are probably not special, just the ones between the physically
379	>	// bonded atoms.  Interactions *within* a single rigid body should
380	>	// always be excluded.  These are done at the bottom of this
381	>	// function.
382
383	+	map<int, set<int> > atomGroups;
384		Molecule::RigidBodyIterator rbIter;
385		RigidBody* rb;
386		Molecule::IntegrableObjectIterator ii;
387		StuntDouble* integrableObject;
388
389	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
390	<	integrableObject = mol->nextIntegrableObject(ii)) {
391	<
389	>	for (integrableObject = mol->beginIntegrableObject(ii);
390	>	integrableObject != NULL;
391	>	integrableObject = mol->nextIntegrableObject(ii)) {
392	>
393		if (integrableObject->isRigidBody()) {
394	<	rb = static_cast<RigidBody*>(integrableObject);
395	<	std::vector<Atom*> atoms = rb->getAtoms();
396	<	std::set<int> rigidAtoms;
397	<	for (int i = 0; i < atoms.size(); ++i) {
398	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
399	<	}
400	<	for (int i = 0; i < atoms.size(); ++i) {
401	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
402	<	}
394	>	rb = static_cast<RigidBody*>(integrableObject);
395	>	vector<Atom*> atoms = rb->getAtoms();
396	>	set<int> rigidAtoms;
397	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
399	>	}
400	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
401	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
402	>	}
403		} else {
404	<	std::set<int> oneAtomSet;
404	>	set<int> oneAtomSet;
405		oneAtomSet.insert(integrableObject->getGlobalIndex());
406	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
406	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
407		}
408		}
409	+
410	+	for (bond= mol->beginBond(bondIter); bond != NULL;
411	+	bond = mol->nextBond(bondIter)) {
412
392	–
393	–
394	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
413		a = bond->getAtomA()->getGlobalIndex();
414	<	b = bond->getAtomB()->getGlobalIndex();
415	<	exclude_.addPair(a, b);
414	>	b = bond->getAtomB()->getGlobalIndex();
415	>
416	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
417	>	oneTwoInteractions_.addPair(a, b);
418	>	} else {
419	>	excludedInteractions_.addPair(a, b);
420	>	}
421		}
422
423	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
423	>	for (bend= mol->beginBend(bendIter); bend != NULL;
424	>	bend = mol->nextBend(bendIter)) {
425	>
426		a = bend->getAtomA()->getGlobalIndex();
427		b = bend->getAtomB()->getGlobalIndex();
428		c = bend->getAtomC()->getGlobalIndex();
404	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407	–
408	–	exclude_.addPairs(rigidSetA, rigidSetB);
409	–	exclude_.addPairs(rigidSetA, rigidSetC);
410	–	exclude_.addPairs(rigidSetB, rigidSetC);
429
430	<	//exclude_.addPair(a, b);
431	<	//exclude_.addPair(a, c);
432	<	//exclude_.addPair(b, c);
430	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
431	>	oneTwoInteractions_.addPair(a, b);
432	>	oneTwoInteractions_.addPair(b, c);
433	>	} else {
434	>	excludedInteractions_.addPair(a, b);
435	>	excludedInteractions_.addPair(b, c);
436	>	}
437	>
438	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
439	>	oneThreeInteractions_.addPair(a, c);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	}
443		}
444
445	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
445	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
446	>	torsion = mol->nextTorsion(torsionIter)) {
447	>
448		a = torsion->getAtomA()->getGlobalIndex();
449		b = torsion->getAtomB()->getGlobalIndex();
450		c = torsion->getAtomC()->getGlobalIndex();
451	<	d = torsion->getAtomD()->getGlobalIndex();
422	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
451	>	d = torsion->getAtomD()->getGlobalIndex();
452
453	<	exclude_.addPairs(rigidSetA, rigidSetB);
454	<	exclude_.addPairs(rigidSetA, rigidSetC);
455	<	exclude_.addPairs(rigidSetA, rigidSetD);
456	<	exclude_.addPairs(rigidSetB, rigidSetC);
457	<	exclude_.addPairs(rigidSetB, rigidSetD);
458	<	exclude_.addPairs(rigidSetC, rigidSetD);
453	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
454	>	oneTwoInteractions_.addPair(a, b);
455	>	oneTwoInteractions_.addPair(b, c);
456	>	oneTwoInteractions_.addPair(c, d);
457	>	} else {
458	>	excludedInteractions_.addPair(a, b);
459	>	excludedInteractions_.addPair(b, c);
460	>	excludedInteractions_.addPair(c, d);
461	>	}
462
463	<	/*
464	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
465	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
466	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
467	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
468	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
469	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
470	<
471	<
472	<	exclude_.addPair(a, b);
473	<	exclude_.addPair(a, c);
474	<	exclude_.addPair(a, d);
475	<	exclude_.addPair(b, c);
447	<	exclude_.addPair(b, d);
448	<	exclude_.addPair(c, d);
449	<	*/
463	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
464	>	oneThreeInteractions_.addPair(a, c);
465	>	oneThreeInteractions_.addPair(b, d);
466	>	} else {
467	>	excludedInteractions_.addPair(a, c);
468	>	excludedInteractions_.addPair(b, d);
469	>	}
470	>
471	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
472	>	oneFourInteractions_.addPair(a, d);
473	>	} else {
474	>	excludedInteractions_.addPair(a, d);
475	>	}
476		}
477
478	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
479	<	std::vector<Atom*> atoms = rb->getAtoms();
480	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
481	<	for (int j = i + 1; j < atoms.size(); ++j) {
478	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
479	>	inversion = mol->nextInversion(inversionIter)) {
480	>
481	>	a = inversion->getAtomA()->getGlobalIndex();
482	>	b = inversion->getAtomB()->getGlobalIndex();
483	>	c = inversion->getAtomC()->getGlobalIndex();
484	>	d = inversion->getAtomD()->getGlobalIndex();
485	>
486	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
487	>	oneTwoInteractions_.addPair(a, b);
488	>	oneTwoInteractions_.addPair(a, c);
489	>	oneTwoInteractions_.addPair(a, d);
490	>	} else {
491	>	excludedInteractions_.addPair(a, b);
492	>	excludedInteractions_.addPair(a, c);
493	>	excludedInteractions_.addPair(a, d);
494	>	}
495	>
496	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
497	>	oneThreeInteractions_.addPair(b, c);
498	>	oneThreeInteractions_.addPair(b, d);
499	>	oneThreeInteractions_.addPair(c, d);
500	>	} else {
501	>	excludedInteractions_.addPair(b, c);
502	>	excludedInteractions_.addPair(b, d);
503	>	excludedInteractions_.addPair(c, d);
504	>	}
505	>	}
506	>
507	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
508	>	rb = mol->nextRigidBody(rbIter)) {
509	>	vector<Atom*> atoms = rb->getAtoms();
510	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
511	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
512		a = atoms[i]->getGlobalIndex();
513		b = atoms[j]->getGlobalIndex();
514	<	exclude_.addPair(a, b);
514	>	excludedInteractions_.addPair(a, b);
515		}
516		}
517		}
518
519		}
520
521	<	void SimInfo::removeExcludePairs(Molecule* mol) {
522	<	std::vector<Bond*>::iterator bondIter;
523	<	std::vector<Bend*>::iterator bendIter;
524	<	std::vector<Torsion*>::iterator torsionIter;
521	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
522	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
523	>	vector<Bond*>::iterator bondIter;
524	>	vector<Bend*>::iterator bendIter;
525	>	vector<Torsion*>::iterator torsionIter;
526	>	vector<Inversion*>::iterator inversionIter;
527		Bond* bond;
528		Bend* bend;
529		Torsion* torsion;
530	+	Inversion* inversion;
531		int a;
532		int b;
533		int c;
534		int d;
535
536	<	std::map<int, std::set<int> > atomGroups;
478	<
536	>	map<int, set<int> > atomGroups;
537		Molecule::RigidBodyIterator rbIter;
538		RigidBody* rb;
539		Molecule::IntegrableObjectIterator ii;
540		StuntDouble* integrableObject;
541
542	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
543	<	integrableObject = mol->nextIntegrableObject(ii)) {
544	<
542	>	for (integrableObject = mol->beginIntegrableObject(ii);
543	>	integrableObject != NULL;
544	>	integrableObject = mol->nextIntegrableObject(ii)) {
545	>
546		if (integrableObject->isRigidBody()) {
547	<	rb = static_cast<RigidBody*>(integrableObject);
548	<	std::vector<Atom*> atoms = rb->getAtoms();
549	<	std::set<int> rigidAtoms;
550	<	for (int i = 0; i < atoms.size(); ++i) {
551	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
552	<	}
553	<	for (int i = 0; i < atoms.size(); ++i) {
554	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555	<	}
547	>	rb = static_cast<RigidBody*>(integrableObject);
548	>	vector<Atom*> atoms = rb->getAtoms();
549	>	set<int> rigidAtoms;
550	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
552	>	}
553	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
554	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555	>	}
556		} else {
557	<	std::set<int> oneAtomSet;
557	>	set<int> oneAtomSet;
558		oneAtomSet.insert(integrableObject->getGlobalIndex());
559	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
559	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
560		}
561		}
562
563	<
564	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
563	>	for (bond= mol->beginBond(bondIter); bond != NULL;
564	>	bond = mol->nextBond(bondIter)) {
565	>
566		a = bond->getAtomA()->getGlobalIndex();
567	<	b = bond->getAtomB()->getGlobalIndex();
568	<	exclude_.removePair(a, b);
567	>	b = bond->getAtomB()->getGlobalIndex();
568	>
569	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
570	>	oneTwoInteractions_.removePair(a, b);
571	>	} else {
572	>	excludedInteractions_.removePair(a, b);
573	>	}
574		}
575
576	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
576	>	for (bend= mol->beginBend(bendIter); bend != NULL;
577	>	bend = mol->nextBend(bendIter)) {
578	>
579		a = bend->getAtomA()->getGlobalIndex();
580		b = bend->getAtomB()->getGlobalIndex();
581		c = bend->getAtomC()->getGlobalIndex();
515	–
516	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	–
520	–	exclude_.removePairs(rigidSetA, rigidSetB);
521	–	exclude_.removePairs(rigidSetA, rigidSetC);
522	–	exclude_.removePairs(rigidSetB, rigidSetC);
582
583	<	//exclude_.removePair(a, b);
584	<	//exclude_.removePair(a, c);
585	<	//exclude_.removePair(b, c);
583	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
584	>	oneTwoInteractions_.removePair(a, b);
585	>	oneTwoInteractions_.removePair(b, c);
586	>	} else {
587	>	excludedInteractions_.removePair(a, b);
588	>	excludedInteractions_.removePair(b, c);
589	>	}
590	>
591	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
592	>	oneThreeInteractions_.removePair(a, c);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	}
596		}
597
598	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
598	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
599	>	torsion = mol->nextTorsion(torsionIter)) {
600	>
601		a = torsion->getAtomA()->getGlobalIndex();
602		b = torsion->getAtomB()->getGlobalIndex();
603		c = torsion->getAtomC()->getGlobalIndex();
604	<	d = torsion->getAtomD()->getGlobalIndex();
604	>	d = torsion->getAtomD()->getGlobalIndex();
605	>
606	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
607	>	oneTwoInteractions_.removePair(a, b);
608	>	oneTwoInteractions_.removePair(b, c);
609	>	oneTwoInteractions_.removePair(c, d);
610	>	} else {
611	>	excludedInteractions_.removePair(a, b);
612	>	excludedInteractions_.removePair(b, c);
613	>	excludedInteractions_.removePair(c, d);
614	>	}
615
616	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
617	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
618	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
619	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
616	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
617	>	oneThreeInteractions_.removePair(a, c);
618	>	oneThreeInteractions_.removePair(b, d);
619	>	} else {
620	>	excludedInteractions_.removePair(a, c);
621	>	excludedInteractions_.removePair(b, d);
622	>	}
623
624	<	exclude_.removePairs(rigidSetA, rigidSetB);
625	<	exclude_.removePairs(rigidSetA, rigidSetC);
626	<	exclude_.removePairs(rigidSetA, rigidSetD);
627	<	exclude_.removePairs(rigidSetB, rigidSetC);
628	<	exclude_.removePairs(rigidSetB, rigidSetD);
629	<	exclude_.removePairs(rigidSetC, rigidSetD);
624	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
625	>	oneFourInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, d);
628	>	}
629	>	}
630
631	<	/*
632	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
631	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
632	>	inversion = mol->nextInversion(inversionIter)) {
633
634	<
635	<	exclude_.removePair(a, b);
636	<	exclude_.removePair(a, c);
637	<	exclude_.removePair(a, d);
638	<	exclude_.removePair(b, c);
639	<	exclude_.removePair(b, d);
640	<	exclude_.removePair(c, d);
641	<	*/
634	>	a = inversion->getAtomA()->getGlobalIndex();
635	>	b = inversion->getAtomB()->getGlobalIndex();
636	>	c = inversion->getAtomC()->getGlobalIndex();
637	>	d = inversion->getAtomD()->getGlobalIndex();
638	>
639	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
640	>	oneTwoInteractions_.removePair(a, b);
641	>	oneTwoInteractions_.removePair(a, c);
642	>	oneTwoInteractions_.removePair(a, d);
643	>	} else {
644	>	excludedInteractions_.removePair(a, b);
645	>	excludedInteractions_.removePair(a, c);
646	>	excludedInteractions_.removePair(a, d);
647	>	}
648	>
649	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
650	>	oneThreeInteractions_.removePair(b, c);
651	>	oneThreeInteractions_.removePair(b, d);
652	>	oneThreeInteractions_.removePair(c, d);
653	>	} else {
654	>	excludedInteractions_.removePair(b, c);
655	>	excludedInteractions_.removePair(b, d);
656	>	excludedInteractions_.removePair(c, d);
657	>	}
658		}
659
660	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
661	<	std::vector<Atom*> atoms = rb->getAtoms();
662	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
663	<	for (int j = i + 1; j < atoms.size(); ++j) {
660	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
661	>	rb = mol->nextRigidBody(rbIter)) {
662	>	vector<Atom*> atoms = rb->getAtoms();
663	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
664	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
665		a = atoms[i]->getGlobalIndex();
666		b = atoms[j]->getGlobalIndex();
667	<	exclude_.removePair(a, b);
667	>	excludedInteractions_.removePair(a, b);
668		}
669		}
670		}
671	<
671	>
672		}
673	<
674	<
673	>
674	>
675		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
676		int curStampId;
677	<
677	>
678		//index from 0
679		curStampId = moleculeStamps_.size();
680
#	Line 586 | Line 682 | namespace oopse {
682		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
683		}
684
589	–	void SimInfo::update() {
590	–
591	–	setupSimType();
592	–
593	–	#ifdef IS_MPI
594	–	setupFortranParallel();
595	–	#endif
596	–
597	–	setupFortranSim();
598	–
599	–	//setup fortran force field
600	–	/** @deprecate */
601	–	int isError = 0;
602	–
603	–	setupCutoff();
604	–
605	–	setupElectrostaticSummationMethod( isError );
606	–	setupSwitchingFunction();
607	–	setupAccumulateBoxDipole();
608	–
609	–	if(isError){
610	–	sprintf( painCave.errMsg,
611	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
612	–	painCave.isFatal = 1;
613	–	simError();
614	–	}
685
686	+	/**
687	+	* update
688	+	*
689	+	*  Performs the global checks and variable settings after the
690	+	*  objects have been created.
691	+	*
692	+	*/
693	+	void SimInfo::update() {
694	+	setupSimVariables();
695		calcNdf();
696		calcNdfRaw();
697		calcNdfTrans();
619	–
620	–	fortranInitialized_ = true;
698		}
699	<
700	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
699	>
700	>	/**
701	>	* getSimulatedAtomTypes
702	>	*
703	>	* Returns an STL set of AtomType* that are actually present in this
704	>	* simulation.  Must query all processors to assemble this information.
705	>	*
706	>	*/
707	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
708		SimInfo::MoleculeIterator mi;
709		Molecule* mol;
710		Molecule::AtomIterator ai;
711		Atom* atom;
712	<	std::set<AtomType*> atomTypes;
713	<
712	>	set<AtomType*> atomTypes;
713	>
714		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
715	<
716	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
715	>	for(atom = mol->beginAtom(ai); atom != NULL;
716	>	atom = mol->nextAtom(ai)) {
717		atomTypes.insert(atom->getAtomType());
718	<	}
719	<
636	<	}
637	<
638	<	return atomTypes;
639	<	}
640	<
641	<	void SimInfo::setupSimType() {
642	<	std::set<AtomType*>::iterator i;
643	<	std::set<AtomType*> atomTypes;
644	<	atomTypes = getUniqueAtomTypes();
718	>	}
719	>	}
720
721	<	int useLennardJones = 0;
647	<	int useElectrostatic = 0;
648	<	int useEAM = 0;
649	<	int useSC = 0;
650	<	int useCharge = 0;
651	<	int useDirectional = 0;
652	<	int useDipole = 0;
653	<	int useGayBerne = 0;
654	<	int useSticky = 0;
655	<	int useStickyPower = 0;
656	<	int useShape = 0;
657	<	int useFLARB = 0; //it is not in AtomType yet
658	<	int useDirectionalAtom = 0;
659	<	int useElectrostatics = 0;
660	<	//usePBC and useRF are from simParams
661	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662	<	int useRF;
663	<	int useSF;
664	<	int useSP;
665	<	int useBoxDipole;
721	>	#ifdef IS_MPI
722
723	<	std::string myMethod;
724	<
669	<	// set the useRF logical
670	<	useRF = 0;
671	<	useSF = 0;
672	<	useSP = 0;
673	<
674	<
675	<	if (simParams_->haveElectrostaticSummationMethod()) {
676	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
677	<	toUpper(myMethod);
678	<	if (myMethod == "REACTION_FIELD"){
679	<	useRF = 1;
680	<	} else if (myMethod == "SHIFTED_FORCE"){
681	<	useSF = 1;
682	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
683	<	useSP = 1;
684	<	}
685	<	}
723	>	// loop over the found atom types on this processor, and add their
724	>	// numerical idents to a vector:
725
726	<	if (simParams_->haveAccumulateBoxDipole())
727	<	if (simParams_->getAccumulateBoxDipole())
728	<	useBoxDipole = 1;
726	>	vector<int> foundTypes;
727	>	set<AtomType*>::iterator i;
728	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
729	>	foundTypes.push_back( (*i)->getIdent() );
730
731	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
731	>	// count_local holds the number of found types on this processor
732	>	int count_local = foundTypes.size();
733
734	<	//loop over all of the atom types
694	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
695	<	useLennardJones |= (*i)->isLennardJones();
696	<	useElectrostatic |= (*i)->isElectrostatic();
697	<	useEAM |= (*i)->isEAM();
698	<	useSC |= (*i)->isSC();
699	<	useCharge |= (*i)->isCharge();
700	<	useDirectional |= (*i)->isDirectional();
701	<	useDipole |= (*i)->isDipole();
702	<	useGayBerne |= (*i)->isGayBerne();
703	<	useSticky |= (*i)->isSticky();
704	<	useStickyPower |= (*i)->isStickyPower();
705	<	useShape |= (*i)->isShape();
706	<	}
734	>	int nproc = MPI::COMM_WORLD.Get_size();
735
736	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
737	<	useDirectionalAtom = 1;
738	<	}
736	>	// we need arrays to hold the counts and displacement vectors for
737	>	// all processors
738	>	vector<int> counts(nproc, 0);
739	>	vector<int> disps(nproc, 0);
740
741	<	if (useCharge || useDipole) {
742	<	useElectrostatics = 1;
741	>	// fill the counts array
742	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
743	>	1, MPI::INT);
744	>
745	>	// use the processor counts to compute the displacement array
746	>	disps[0] = 0;
747	>	int totalCount = counts[0];
748	>	for (int iproc = 1; iproc < nproc; iproc++) {
749	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
750	>	totalCount += counts[iproc];
751		}
752
753	<	#ifdef IS_MPI
754	<	int temp;
753	>	// we need a (possibly redundant) set of all found types:
754	>	vector<int> ftGlobal(totalCount);
755	>
756	>	// now spray out the foundTypes to all the other processors:
757	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
758	>	&ftGlobal[0], &counts[0], &disps[0],
759	>	MPI::INT);
760
761	<	temp = usePBC;
720	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
761	>	vector<int>::iterator j;
762
763	<	temp = useDirectionalAtom;
764	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763	>	// foundIdents is a stl set, so inserting an already found ident
764	>	// will have no effect.
765	>	set<int> foundIdents;
766
767	<	temp = useLennardJones;
768	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
727	<
728	<	temp = useElectrostatics;
729	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
730	<
731	<	temp = useCharge;
732	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
733	<
734	<	temp = useDipole;
735	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
736	<
737	<	temp = useSticky;
738	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739	<
740	<	temp = useStickyPower;
741	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
768	>	foundIdents.insert((*j));
769
770	<	temp = useGayBerne;
771	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	// now iterate over the foundIdents and get the actual atom types
771	>	// that correspond to these:
772	>	set<int>::iterator it;
773	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774	>	atomTypes.insert( forceField_->getAtomType((*it)) );
775	>
776	>	#endif
777
778	<	temp = useEAM;
779	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
778	>	return atomTypes;
779	>	}
780
781	<	temp = useSC;
782	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	>	void SimInfo::setupSimVariables() {
782	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
783	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
784	>	calcBoxDipole_ = false;
785	>	if ( simParams_->haveAccumulateBoxDipole() )
786	>	if ( simParams_->getAccumulateBoxDipole() ) {
787	>	calcBoxDipole_ = true;
788	>	}
789
790	<	temp = useShape;
791	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
790	>	set<AtomType*>::iterator i;
791	>	set<AtomType*> atomTypes;
792	>	atomTypes = getSimulatedAtomTypes();
793	>	bool usesElectrostatic = false;
794	>	bool usesMetallic = false;
795	>	bool usesDirectional = false;
796	>	bool usesFluctuatingCharges =  false;
797	>	//loop over all of the atom types
798	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
799	>	usesElectrostatic |= (*i)->isElectrostatic();
800	>	usesMetallic |= (*i)->isMetal();
801	>	usesDirectional |= (*i)->isDirectional();
802	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
803	>	}
804
805	<	temp = useFLARB;
806	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
805	>	#ifdef IS_MPI
806	>	bool temp;
807	>	temp = usesDirectional;
808	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
809	>	MPI::LOR);
810	>
811	>	temp = usesMetallic;
812	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
813	>	MPI::LOR);
814	>
815	>	temp = usesElectrostatic;
816	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
817	>	MPI::LOR);
818
819	<	temp = useRF;
820	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	temp = usesFluctuatingCharges;
820	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
821	>	MPI::LOR);
822	>	#else
823
824	<	temp = useSF;
825	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
824	>	usesDirectionalAtoms_ = usesDirectional;
825	>	usesMetallicAtoms_ = usesMetallic;
826	>	usesElectrostaticAtoms_ = usesElectrostatic;
827	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
828
829	<	temp = useSP;
830	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
829	>	#endif
830	>
831	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
832	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
833	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
834	>	}
835
767	–	temp = useBoxDipole;
768	–	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836
837	<	temp = useAtomicVirial_;
838	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837	>	vector<int> SimInfo::getGlobalAtomIndices() {
838	>	SimInfo::MoleculeIterator mi;
839	>	Molecule* mol;
840	>	Molecule::AtomIterator ai;
841	>	Atom* atom;
842
843	<	#endif
844	<
845	<	fInfo_.SIM_uses_PBC = usePBC;
846	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
847	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
848	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
849	<	fInfo_.SIM_uses_Charges = useCharge;
850	<	fInfo_.SIM_uses_Dipoles = useDipole;
851	<	fInfo_.SIM_uses_Sticky = useSticky;
782	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
783	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
784	<	fInfo_.SIM_uses_EAM = useEAM;
785	<	fInfo_.SIM_uses_SC = useSC;
786	<	fInfo_.SIM_uses_Shapes = useShape;
787	<	fInfo_.SIM_uses_FLARB = useFLARB;
788	<	fInfo_.SIM_uses_RF = useRF;
789	<	fInfo_.SIM_uses_SF = useSF;
790	<	fInfo_.SIM_uses_SP = useSP;
791	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
792	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
843	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
844	>
845	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
846	>
847	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
848	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
849	>	}
850	>	}
851	>	return GlobalAtomIndices;
852		}
853
795	–	void SimInfo::setupFortranSim() {
796	–	int isError;
797	–	int nExclude;
798	–	std::vector<int> fortranGlobalGroupMembership;
799	–
800	–	nExclude = exclude_.getSize();
801	–	isError = 0;
854
855	<	//globalGroupMembership_ is filled by SimCreator
856	<	for (int i = 0; i < nGlobalAtoms_; i++) {
857	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
855	>	vector<int> SimInfo::getGlobalGroupIndices() {
856	>	SimInfo::MoleculeIterator mi;
857	>	Molecule* mol;
858	>	Molecule::CutoffGroupIterator ci;
859	>	CutoffGroup* cg;
860	>
861	>	vector<int> GlobalGroupIndices;
862	>
863	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
864	>
865	>	//local index of cutoff group is trivial, it only depends on the
866	>	//order of travesing
867	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
868	>	cg = mol->nextCutoffGroup(ci)) {
869	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
870	>	}
871		}
872	+	return GlobalGroupIndices;
873	+	}
874
875	+
876	+	void SimInfo::prepareTopology() {
877	+	int nExclude, nOneTwo, nOneThree, nOneFour;
878	+
879		//calculate mass ratio of cutoff group
809	–	std::vector<RealType> mfact;
880		SimInfo::MoleculeIterator mi;
881		Molecule* mol;
882		Molecule::CutoffGroupIterator ci;
#	Line 815 | Line 885 | namespace oopse {
885		Atom* atom;
886		RealType totalMass;
887
888	<	//to avoid memory reallocation, reserve enough space for mfact
889	<	mfact.reserve(getNCutoffGroups());
888	>	/**
889	>	* The mass factor is the relative mass of an atom to the total
890	>	* mass of the cutoff group it belongs to.  By default, all atoms
891	>	* are their own cutoff groups, and therefore have mass factors of
892	>	* 1.  We need some special handling for massless atoms, which
893	>	* will be treated as carrying the entire mass of the cutoff
894	>	* group.
895	>	*/
896	>	massFactors_.clear();
897	>	massFactors_.resize(getNAtoms(), 1.0);
898
899		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
900	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
900	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
901	>	cg = mol->nextCutoffGroup(ci)) {
902
903		totalMass = cg->getMass();
904		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
905		// Check for massless groups - set mfact to 1 if true
906	<	if (totalMass != 0)
907	<	mfact.push_back(atom->getMass()/totalMass);
906	>	if (totalMass != 0)
907	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
908		else
909	<	mfact.push_back( 1.0 );
909	>	massFactors_[atom->getLocalIndex()] = 1.0;
910		}
832	–
911		}
912		}
913
914	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
837	<	std::vector<int> identArray;
914	>	// Build the identArray_
915
916	<	//to avoid memory reallocation, reserve enough space identArray
917	<	identArray.reserve(getNAtoms());
841	<
916	>	identArray_.clear();
917	>	identArray_.reserve(getNAtoms());
918		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
919		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
920	<	identArray.push_back(atom->getIdent());
920	>	identArray_.push_back(atom->getIdent());
921		}
922		}
847	–
848	–	//fill molMembershipArray
849	–	//molMembershipArray is filled by SimCreator
850	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
851	–	for (int i = 0; i < nGlobalAtoms_; i++) {
852	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
853	–	}
923
924	<	//setup fortran simulation
856	<	int nGlobalExcludes = 0;
857	<	int* globalExcludes = NULL;
858	<	int* excludeList = exclude_.getExcludeList();
859	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
860	<	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
861	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862	<	&fortranGlobalGroupMembership[0], &isError);
863	<
864	<	if( isError ){
865	<
866	<	sprintf( painCave.errMsg,
867	<	"There was an error setting the simulation information in fortran.\n" );
868	<	painCave.isFatal = 1;
869	<	painCave.severity = OOPSE_ERROR;
870	<	simError();
871	<	}
872	<
873	<
874	<	sprintf( checkPointMsg,
875	<	"succesfully sent the simulation information to fortran.\n");
876	<
877	<	errorCheckPoint();
878	<
879	<	// Setup number of neighbors in neighbor list if present
880	<	if (simParams_->haveNeighborListNeighbors()) {
881	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
882	<	setNeighbors(&nlistNeighbors);
883	<	}
884	<
924	>	//scan topology
925
926	<	}
926	>	nExclude = excludedInteractions_.getSize();
927	>	nOneTwo = oneTwoInteractions_.getSize();
928	>	nOneThree = oneThreeInteractions_.getSize();
929	>	nOneFour = oneFourInteractions_.getSize();
930
931	<
932	<	void SimInfo::setupFortranParallel() {
933	<	#ifdef IS_MPI
934	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
892	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
893	<	std::vector<int> localToGlobalCutoffGroupIndex;
894	<	SimInfo::MoleculeIterator mi;
895	<	Molecule::AtomIterator ai;
896	<	Molecule::CutoffGroupIterator ci;
897	<	Molecule* mol;
898	<	Atom* atom;
899	<	CutoffGroup* cg;
900	<	mpiSimData parallelData;
901	<	int isError;
902	<
903	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
904	<
905	<	//local index(index in DataStorge) of atom is important
906	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
908	<	}
909	<
910	<	//local index of cutoff group is trivial, it only depends on the order of travesing
911	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
912	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
913	<	}
914	<
915	<	}
916	<
917	<	//fill up mpiSimData struct
918	<	parallelData.nMolGlobal = getNGlobalMolecules();
919	<	parallelData.nMolLocal = getNMolecules();
920	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
921	<	parallelData.nAtomsLocal = getNAtoms();
922	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
923	<	parallelData.nGroupsLocal = getNCutoffGroups();
924	<	parallelData.myNode = worldRank;
925	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
926	<
927	<	//pass mpiSimData struct and index arrays to fortran
928	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
929	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
930	<	&localToGlobalCutoffGroupIndex[0], &isError);
931	<
932	<	if (isError) {
933	<	sprintf(painCave.errMsg,
934	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
935	<	painCave.isFatal = 1;
936	<	simError();
937	<	}
938	<
939	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
940	<	errorCheckPoint();
941	<
942	<	#endif
943	<	}
944	<
945	<	void SimInfo::setupCutoff() {
946	<
947	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
948	<
949	<	// Check the cutoff policy
950	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
951	<
952	<	// Set LJ shifting bools to false
953	<	ljsp_ = false;
954	<	ljsf_ = false;
955	<
956	<	std::string myPolicy;
957	<	if (forceFieldOptions_.haveCutoffPolicy()){
958	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
959	<	}else if (simParams_->haveCutoffPolicy()) {
960	<	myPolicy = simParams_->getCutoffPolicy();
961	<	}
962	<
963	<	if (!myPolicy.empty()){
964	<	toUpper(myPolicy);
965	<	if (myPolicy == "MIX") {
966	<	cp = MIX_CUTOFF_POLICY;
967	<	} else {
968	<	if (myPolicy == "MAX") {
969	<	cp = MAX_CUTOFF_POLICY;
970	<	} else {
971	<	if (myPolicy == "TRADITIONAL") {
972	<	cp = TRADITIONAL_CUTOFF_POLICY;
973	<	} else {
974	<	// throw error
975	<	sprintf( painCave.errMsg,
976	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
977	<	painCave.isFatal = 1;
978	<	simError();
979	<	}
980	<	}
981	<	}
982	<	}
983	<	notifyFortranCutoffPolicy(&cp);
984	<
985	<	// Check the Skin Thickness for neighborlists
986	<	RealType skin;
987	<	if (simParams_->haveSkinThickness()) {
988	<	skin = simParams_->getSkinThickness();
989	<	notifyFortranSkinThickness(&skin);
990	<	}
991	<
992	<	// Check if the cutoff was set explicitly:
993	<	if (simParams_->haveCutoffRadius()) {
994	<	rcut_ = simParams_->getCutoffRadius();
995	<	if (simParams_->haveSwitchingRadius()) {
996	<	rsw_  = simParams_->getSwitchingRadius();
997	<	} else {
998	<	if (fInfo_.SIM_uses_Charges |
999	<	fInfo_.SIM_uses_Dipoles |
1000	<	fInfo_.SIM_uses_RF) {
1001	<
1002	<	rsw_ = 0.85 * rcut_;
1003	<	sprintf(painCave.errMsg,
1004	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1005	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1006	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1007	<	painCave.isFatal = 0;
1008	<	simError();
1009	<	} else {
1010	<	rsw_ = rcut_;
1011	<	sprintf(painCave.errMsg,
1012	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1013	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1014	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1015	<	painCave.isFatal = 0;
1016	<	simError();
1017	<	}
1018	<	}
1019	<
1020	<	if (simParams_->haveElectrostaticSummationMethod()) {
1021	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1022	<	toUpper(myMethod);
1023	<
1024	<	if (myMethod == "SHIFTED_POTENTIAL") {
1025	<	ljsp_ = true;
1026	<	} else if (myMethod == "SHIFTED_FORCE") {
1027	<	ljsf_ = true;
1028	<	}
1029	<	}
1030	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1031	<
1032	<	} else {
1033	<
1034	<	// For electrostatic atoms, we'll assume a large safe value:
1035	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1036	<	sprintf(painCave.errMsg,
1037	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1038	<	"\tOOPSE will use a default value of 15.0 angstroms"
1039	<	"\tfor the cutoffRadius.\n");
1040	<	painCave.isFatal = 0;
1041	<	simError();
1042	<	rcut_ = 15.0;
1043	<
1044	<	if (simParams_->haveElectrostaticSummationMethod()) {
1045	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1046	<	toUpper(myMethod);
1047	<
1048	<	// For the time being, we're tethering the LJ shifted behavior to the
1049	<	// electrostaticSummationMethod keyword options
1050	<	if (myMethod == "SHIFTED_POTENTIAL") {
1051	<	ljsp_ = true;
1052	<	} else if (myMethod == "SHIFTED_FORCE") {
1053	<	ljsf_ = true;
1054	<	}
1055	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1056	<	if (simParams_->haveSwitchingRadius()){
1057	<	sprintf(painCave.errMsg,
1058	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1059	<	"\teven though the electrostaticSummationMethod was\n"
1060	<	"\tset to %s\n", myMethod.c_str());
1061	<	painCave.isFatal = 1;
1062	<	simError();
1063	<	}
1064	<	}
1065	<	}
1066	<
1067	<	if (simParams_->haveSwitchingRadius()){
1068	<	rsw_ = simParams_->getSwitchingRadius();
1069	<	} else {
1070	<	sprintf(painCave.errMsg,
1071	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1072	<	"\tOOPSE will use a default value of\n"
1073	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1074	<	painCave.isFatal = 0;
1075	<	simError();
1076	<	rsw_ = 0.85 * rcut_;
1077	<	}
1078	<
1079	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1080	<
1081	<	} else {
1082	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1083	<	// We'll punt and let fortran figure out the cutoffs later.
1084	<
1085	<	notifyFortranYouAreOnYourOwn();
1086	<
1087	<	}
1088	<	}
1089	<	}
931	>	int* excludeList = excludedInteractions_.getPairList();
932	>	int* oneTwoList = oneTwoInteractions_.getPairList();
933	>	int* oneThreeList = oneThreeInteractions_.getPairList();
934	>	int* oneFourList = oneFourInteractions_.getPairList();
935
936	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1092	<
1093	<	int errorOut;
1094	<	int esm =  NONE;
1095	<	int sm = UNDAMPED;
1096	<	RealType alphaVal;
1097	<	RealType dielectric;
1098	<
1099	<	errorOut = isError;
1100	<
1101	<	if (simParams_->haveElectrostaticSummationMethod()) {
1102	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1103	<	toUpper(myMethod);
1104	<	if (myMethod == "NONE") {
1105	<	esm = NONE;
1106	<	} else {
1107	<	if (myMethod == "SWITCHING_FUNCTION") {
1108	<	esm = SWITCHING_FUNCTION;
1109	<	} else {
1110	<	if (myMethod == "SHIFTED_POTENTIAL") {
1111	<	esm = SHIFTED_POTENTIAL;
1112	<	} else {
1113	<	if (myMethod == "SHIFTED_FORCE") {
1114	<	esm = SHIFTED_FORCE;
1115	<	} else {
1116	<	if (myMethod == "REACTION_FIELD") {
1117	<	esm = REACTION_FIELD;
1118	<	dielectric = simParams_->getDielectric();
1119	<	if (!simParams_->haveDielectric()) {
1120	<	// throw warning
1121	<	sprintf( painCave.errMsg,
1122	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1123	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1124	<	painCave.isFatal = 0;
1125	<	simError();
1126	<	}
1127	<	} else {
1128	<	// throw error
1129	<	sprintf( painCave.errMsg,
1130	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1131	<	"\t(Input file specified %s .)\n"
1132	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1133	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1134	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1135	<	painCave.isFatal = 1;
1136	<	simError();
1137	<	}
1138	<	}
1139	<	}
1140	<	}
1141	<	}
1142	<	}
1143	<
1144	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1145	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1146	<	toUpper(myScreen);
1147	<	if (myScreen == "UNDAMPED") {
1148	<	sm = UNDAMPED;
1149	<	} else {
1150	<	if (myScreen == "DAMPED") {
1151	<	sm = DAMPED;
1152	<	if (!simParams_->haveDampingAlpha()) {
1153	<	// first set a cutoff dependent alpha value
1154	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1155	<	alphaVal = 0.5125 - rcut_* 0.025;
1156	<	// for values rcut > 20.5, alpha is zero
1157	<	if (alphaVal < 0) alphaVal = 0;
1158	<
1159	<	// throw warning
1160	<	sprintf( painCave.errMsg,
1161	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1162	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1163	<	painCave.isFatal = 0;
1164	<	simError();
1165	<	} else {
1166	<	alphaVal = simParams_->getDampingAlpha();
1167	<	}
1168	<
1169	<	} else {
1170	<	// throw error
1171	<	sprintf( painCave.errMsg,
1172	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1173	<	"\t(Input file specified %s .)\n"
1174	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1175	<	"or \"damped\".\n", myScreen.c_str() );
1176	<	painCave.isFatal = 1;
1177	<	simError();
1178	<	}
1179	<	}
1180	<	}
1181	<
1182	<	// let's pass some summation method variables to fortran
1183	<	setElectrostaticSummationMethod( &esm );
1184	<	setFortranElectrostaticMethod( &esm );
1185	<	setScreeningMethod( &sm );
1186	<	setDampingAlpha( &alphaVal );
1187	<	setReactionFieldDielectric( &dielectric );
1188	<	initFortranFF( &errorOut );
936	>	topologyDone_ = true;
937		}
938
1191	–	void SimInfo::setupSwitchingFunction() {
1192	–	int ft = CUBIC;
1193	–
1194	–	if (simParams_->haveSwitchingFunctionType()) {
1195	–	std::string funcType = simParams_->getSwitchingFunctionType();
1196	–	toUpper(funcType);
1197	–	if (funcType == "CUBIC") {
1198	–	ft = CUBIC;
1199	–	} else {
1200	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1201	–	ft = FIFTH_ORDER_POLY;
1202	–	} else {
1203	–	// throw error
1204	–	sprintf( painCave.errMsg,
1205	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1206	–	painCave.isFatal = 1;
1207	–	simError();
1208	–	}
1209	–	}
1210	–	}
1211	–
1212	–	// send switching function notification to switcheroo
1213	–	setFunctionType(&ft);
1214	–
1215	–	}
1216	–
1217	–	void SimInfo::setupAccumulateBoxDipole() {
1218	–
1219	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1220	–	if ( simParams_->haveAccumulateBoxDipole() )
1221	–	if ( simParams_->getAccumulateBoxDipole() ) {
1222	–	setAccumulateBoxDipole();
1223	–	calcBoxDipole_ = true;
1224	–	}
1225	–
1226	–	}
1227	–
939		void SimInfo::addProperty(GenericData* genData) {
940		properties_.addProperty(genData);
941		}
942
943	<	void SimInfo::removeProperty(const std::string& propName) {
943	>	void SimInfo::removeProperty(const string& propName) {
944		properties_.removeProperty(propName);
945		}
946
#	Line 1237 | Line 948 | namespace oopse {
948		properties_.clearProperties();
949		}
950
951	<	std::vector<std::string> SimInfo::getPropertyNames() {
951	>	vector<string> SimInfo::getPropertyNames() {
952		return properties_.getPropertyNames();
953		}
954
955	<	std::vector<GenericData*> SimInfo::getProperties() {
955	>	vector<GenericData*> SimInfo::getProperties() {
956		return properties_.getProperties();
957		}
958
959	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
959	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
960		return properties_.getPropertyByName(propName);
961		}
962
#	Line 1259 | Line 970 | namespace oopse {
970		Molecule* mol;
971		RigidBody* rb;
972		Atom* atom;
973	+	CutoffGroup* cg;
974		SimInfo::MoleculeIterator mi;
975		Molecule::RigidBodyIterator rbIter;
976	<	Molecule::AtomIterator atomIter;;
976	>	Molecule::AtomIterator atomIter;
977	>	Molecule::CutoffGroupIterator cgIter;
978
979		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
980
#	Line 1272 | Line 985 | namespace oopse {
985		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
986		rb->setSnapshotManager(sman_);
987		}
988	+
989	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
990	+	cg->setSnapshotManager(sman_);
991	+	}
992		}
993
994		}
995
1279	–	Vector3d SimInfo::getComVel(){
1280	–	SimInfo::MoleculeIterator i;
1281	–	Molecule* mol;
996
997	<	Vector3d comVel(0.0);
1284	<	RealType totalMass = 0.0;
1285	<
1286	<
1287	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1288	<	RealType mass = mol->getMass();
1289	<	totalMass += mass;
1290	<	comVel += mass * mol->getComVel();
1291	<	}
1292	<
1293	<	#ifdef IS_MPI
1294	<	RealType tmpMass = totalMass;
1295	<	Vector3d tmpComVel(comVel);
1296	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1298	<	#endif
1299	<
1300	<	comVel /= totalMass;
1301	<
1302	<	return comVel;
1303	<	}
1304	<
1305	<	Vector3d SimInfo::getCom(){
1306	<	SimInfo::MoleculeIterator i;
1307	<	Molecule* mol;
1308	<
1309	<	Vector3d com(0.0);
1310	<	RealType totalMass = 0.0;
1311	<
1312	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	<	RealType mass = mol->getMass();
1314	<	totalMass += mass;
1315	<	com += mass * mol->getCom();
1316	<	}
1317	<
1318	<	#ifdef IS_MPI
1319	<	RealType tmpMass = totalMass;
1320	<	Vector3d tmpCom(com);
1321	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323	<	#endif
1324	<
1325	<	com /= totalMass;
1326	<
1327	<	return com;
997	>	ostream& operator <<(ostream& o, SimInfo& info) {
998
1329	–	}
1330	–
1331	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1332	–
999		return o;
1000		}
1001
1002	<
1337	<	/*
1338	<	Returns center of mass and center of mass velocity in one function call.
1339	<	*/
1340	<
1341	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1342	<	SimInfo::MoleculeIterator i;
1343	<	Molecule* mol;
1344	<
1345	<
1346	<	RealType totalMass = 0.0;
1347	<
1348	<
1349	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1350	<	RealType mass = mol->getMass();
1351	<	totalMass += mass;
1352	<	com += mass * mol->getCom();
1353	<	comVel += mass * mol->getComVel();
1354	<	}
1355	<
1356	<	#ifdef IS_MPI
1357	<	RealType tmpMass = totalMass;
1358	<	Vector3d tmpCom(com);
1359	<	Vector3d tmpComVel(comVel);
1360	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1361	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1362	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1363	<	#endif
1364	<
1365	<	com /= totalMass;
1366	<	comVel /= totalMass;
1367	<	}
1368	<
1369	<	/*
1370	<	Return intertia tensor for entire system and angular momentum Vector.
1371	<
1372	<
1373	<	[  Ixx -Ixy  -Ixz ]
1374	<	J =| -Iyx  Iyy  -Iyz |
1375	<	[ -Izx -Iyz   Izz ]
1376	<	*/
1377	<
1378	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1379	<
1380	<
1381	<	RealType xx = 0.0;
1382	<	RealType yy = 0.0;
1383	<	RealType zz = 0.0;
1384	<	RealType xy = 0.0;
1385	<	RealType xz = 0.0;
1386	<	RealType yz = 0.0;
1387	<	Vector3d com(0.0);
1388	<	Vector3d comVel(0.0);
1389	<
1390	<	getComAll(com, comVel);
1391	<
1392	<	SimInfo::MoleculeIterator i;
1393	<	Molecule* mol;
1394	<
1395	<	Vector3d thisq(0.0);
1396	<	Vector3d thisv(0.0);
1397	<
1398	<	RealType thisMass = 0.0;
1399	<
1400	<
1401	<
1402	<
1403	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1404	<
1405	<	thisq = mol->getCom()-com;
1406	<	thisv = mol->getComVel()-comVel;
1407	<	thisMass = mol->getMass();
1408	<	// Compute moment of intertia coefficients.
1409	<	xx += thisq[0]*thisq[0]*thisMass;
1410	<	yy += thisq[1]*thisq[1]*thisMass;
1411	<	zz += thisq[2]*thisq[2]*thisMass;
1412	<
1413	<	// compute products of intertia
1414	<	xy += thisq[0]*thisq[1]*thisMass;
1415	<	xz += thisq[0]*thisq[2]*thisMass;
1416	<	yz += thisq[1]*thisq[2]*thisMass;
1417	<
1418	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1419	<
1420	<	}
1421	<
1422	<
1423	<	inertiaTensor(0,0) = yy + zz;
1424	<	inertiaTensor(0,1) = -xy;
1425	<	inertiaTensor(0,2) = -xz;
1426	<	inertiaTensor(1,0) = -xy;
1427	<	inertiaTensor(1,1) = xx + zz;
1428	<	inertiaTensor(1,2) = -yz;
1429	<	inertiaTensor(2,0) = -xz;
1430	<	inertiaTensor(2,1) = -yz;
1431	<	inertiaTensor(2,2) = xx + yy;
1432	<
1433	<	#ifdef IS_MPI
1434	<	Mat3x3d tmpI(inertiaTensor);
1435	<	Vector3d tmpAngMom;
1436	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1437	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1438	<	#endif
1439	<
1440	<	return;
1441	<	}
1442	<
1443	<	//Returns the angular momentum of the system
1444	<	Vector3d SimInfo::getAngularMomentum(){
1445	<
1446	<	Vector3d com(0.0);
1447	<	Vector3d comVel(0.0);
1448	<	Vector3d angularMomentum(0.0);
1449	<
1450	<	getComAll(com,comVel);
1451	<
1452	<	SimInfo::MoleculeIterator i;
1453	<	Molecule* mol;
1454	<
1455	<	Vector3d thisr(0.0);
1456	<	Vector3d thisp(0.0);
1457	<
1458	<	RealType thisMass;
1459	<
1460	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1461	<	thisMass = mol->getMass();
1462	<	thisr = mol->getCom()-com;
1463	<	thisp = (mol->getComVel()-comVel)*thisMass;
1464	<
1465	<	angularMomentum += cross( thisr, thisp );
1466	<
1467	<	}
1468	<
1469	<	#ifdef IS_MPI
1470	<	Vector3d tmpAngMom;
1471	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1472	<	#endif
1473	<
1474	<	return angularMomentum;
1475	<	}
1476	<
1002	>
1003		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1004		return IOIndexToIntegrableObject.at(index);
1005		}
1006
1007	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1007	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1008		IOIndexToIntegrableObject= v;
1009		}
1484	–
1485	–	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1486	–	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1487	–	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1488	–	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1489	–	*/
1490	–	void SimInfo::getGyrationalVolume(RealType &volume){
1491	–	Mat3x3d intTensor;
1492	–	RealType det;
1493	–	Vector3d dummyAngMom;
1494	–	RealType sysconstants;
1495	–	RealType geomCnst;
1496	–
1497	–	geomCnst = 3.0/2.0;
1498	–	/* Get the inertial tensor and angular momentum for free*/
1499	–	getInertiaTensor(intTensor,dummyAngMom);
1500	–
1501	–	det = intTensor.determinant();
1502	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1503	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1504	–	return;
1505	–	}
1506	–
1507	–	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1508	–	Mat3x3d intTensor;
1509	–	Vector3d dummyAngMom;
1510	–	RealType sysconstants;
1511	–	RealType geomCnst;
1512	–
1513	–	geomCnst = 3.0/2.0;
1514	–	/* Get the inertial tensor and angular momentum for free*/
1515	–	getInertiaTensor(intTensor,dummyAngMom);
1516	–
1517	–	detI = intTensor.determinant();
1518	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1519	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1520	–	return;
1521	–	}
1010		/*
1011	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1011	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1012		assert( v.size() == nAtoms_ + nRigidBodies_);
1013		sdByGlobalIndex_ = v;
1014		}
#	Line 1530 | Line 1018 | namespace oopse {
1018		return sdByGlobalIndex_.at(index);
1019		}
1020		*/
1021	<	}//end namespace oopse
1021	>	int SimInfo::getNGlobalConstraints() {
1022	>	int nGlobalConstraints;
1023	>	#ifdef IS_MPI
1024	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1025	>	MPI_COMM_WORLD);
1026	>	#else
1027	>	nGlobalConstraints =  nConstraints_;
1028	>	#endif
1029	>	return nGlobalConstraints;
1030	>	}
1031
1032	+	}//end namespace OpenMD
1033	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

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