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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
Revision 1930 by gezelter, Mon Aug 19 13:51:04 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 53 | Line 54
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/fCutoffPolicy.h"
57	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	<	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	<	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60	<	#include "UseTheForce/doForces_interface.h"
61	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61		#include "io/ForceFieldOptions.hpp"
62	<	#include "UseTheForce/ForceField.hpp"
63	<
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
72	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	<	std::map<int, std::set<int> >::iterator i = container.find(index);
77	<	std::set<int> result;
78	<	if (i != container.end()) {
79	<	result = i->second;
80	<	}
81	<
82	<	return result;
83	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73		ndf_(0), 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) {
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin();
92	>	i !=components.end(); ++i) {
93	>	molStamp = (*i)->getMoleculeStamp();
94	>	if ( (*i)->haveRegion() ) {
95	>	molStamp->setRegion( (*i)->getRegion() );
96	>	} else {
97	>	// set the region to a disallowed value:
98	>	molStamp->setRegion( -1 );
99	>	}
100
101	<	MoleculeStamp* molStamp;
95	<	int nMolWithSameStamp;
96	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
97	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
98	<	CutoffGroupStamp* cgStamp;
99	<	RigidBodyStamp* rbStamp;
100	<	int nRigidAtoms = 0;
101	<	std::vector<Component*> components = simParams->getComponents();
101	>	nMolWithSameStamp = (*i)->getNMol();
102
103	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104	<	molStamp = (*i)->getMoleculeStamp();
105	<	nMolWithSameStamp = (*i)->getNMol();
106	<
107	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
108	<
109	<	//calculate atoms in molecules
110	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
111	<
112	<	//calculate atoms in cutoff groups
113	<	int nAtomsInGroups = 0;
114	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
115	<
116	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
117	<	cgStamp = molStamp->getCutoffGroupStamp(j);
118	<	nAtomsInGroups += cgStamp->getNMembers();
119	<	}
120	<
121	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
122	<
123	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
124	<
125	<	//calculate atoms in rigid bodies
126	<	int nAtomsInRigidBodies = 0;
127	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128	<
129	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
130	<	rbStamp = molStamp->getRigidBodyStamp(j);
131	<	nAtomsInRigidBodies += rbStamp->getNMembers();
132	<	}
133	<
134	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
135	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
136	<
103	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
104	>
105	>	//calculate atoms in molecules
106	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	>
108	>	//calculate atoms in cutoff groups
109	>	int nAtomsInGroups = 0;
110	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
111	>
112	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
113	>	cgStamp = molStamp->getCutoffGroupStamp(j);
114	>	nAtomsInGroups += cgStamp->getNMembers();
115		}
116	<
117	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
118	<	//group therefore the total number of cutoff groups in the system is
119	<	//equal to the total number of atoms minus number of atoms belong to
120	<	//cutoff group defined in meta-data file plus the number of cutoff
121	<	//groups defined in meta-data file
122	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
123	<
124	<	//every free atom (atom does not belong to rigid bodies) is an
125	<	//integrable object therefore the total number of integrable objects
126	<	//in the system is equal to the total number of atoms minus number of
127	<	//atoms belong to rigid body defined in meta-data file plus the number
128	<	//of rigid bodies defined in meta-data file
129	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
130	<	+ nGlobalRigidBodies_;
131	<
132	<	nGlobalMols_ = molStampIds_.size();
155	<
156	<	#ifdef IS_MPI
157	<	molToProcMap_.resize(nGlobalMols_);
158	<	#endif
159	<
116	>
117	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
118	>
119	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
120	>
121	>	//calculate atoms in rigid bodies
122	>	int nAtomsInRigidBodies = 0;
123	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
124	>
125	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
126	>	rbStamp = molStamp->getRigidBodyStamp(j);
127	>	nAtomsInRigidBodies += rbStamp->getNMembers();
128	>	}
129	>
130	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
131	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
132	>
133		}
134	+
135	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
136	+	//group therefore the total number of cutoff groups in the system is
137	+	//equal to the total number of atoms minus number of atoms belong to
138	+	//cutoff group defined in meta-data file plus the number of cutoff
139	+	//groups defined in meta-data file
140
141	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
142	+
143	+	//every free atom (atom does not belong to rigid bodies) is an
144	+	//integrable object therefore the total number of integrable objects
145	+	//in the system is equal to the total number of atoms minus number of
146	+	//atoms belong to rigid body defined in meta-data file plus the number
147	+	//of rigid bodies defined in meta-data file
148	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	+	+ nGlobalRigidBodies_;
150	+
151	+	nGlobalMols_ = molStampIds_.size();
152	+	molToProcMap_.resize(nGlobalMols_);
153	+	}
154	+
155		SimInfo::~SimInfo() {
156	<	std::map<int, Molecule*>::iterator i;
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158		delete i->second;
159		}
#	Line 171 | Line 164 | namespace oopse {
164		delete forceField_;
165		}
166
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	–	}
167
168		bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176		nAtoms_ += mol->getNAtoms();
177		nBonds_ += mol->getNBonds();
178		nBends_ += mol->getNBends();
179		nTorsions_ += mol->getNTorsions();
180	+	nInversions_ += mol->getNInversions();
181		nRigidBodies_ += mol->getNRigidBodies();
182		nIntegrableObjects_ += mol->getNIntegrableObjects();
183		nCutoffGroups_ += mol->getNCutoffGroups();
184		nConstraints_ += mol->getNConstraintPairs();
185	<
186	<	addExcludePairs(mol);
187	<
185	>
186	>	addInteractionPairs(mol);
187	>
188		return true;
189		} else {
190		return false;
191		}
192		}
193	<
193	>
194		bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
#	Line 219 | Line 203 | namespace oopse {
203		nBonds_ -= mol->getNBonds();
204		nBends_ -= mol->getNBends();
205		nTorsions_ -= mol->getNTorsions();
206	+	nInversions_ -= mol->getNInversions();
207		nRigidBodies_ -= mol->getNRigidBodies();
208		nIntegrableObjects_ -= mol->getNIntegrableObjects();
209		nCutoffGroups_ -= mol->getNCutoffGroups();
210		nConstraints_ -= mol->getNConstraintPairs();
211
212	<	removeExcludePairs(mol);
212	>	removeInteractionPairs(mol);
213		molecules_.erase(mol->getGlobalIndex());
214
215		delete mol;
#	Line 233 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
236	–
237	–
221		}
222
223
#	Line 250 | Line 233 | namespace oopse {
233
234
235		void SimInfo::calcNdf() {
236	<	int ndf_local;
236	>	int ndf_local, nfq_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239	>	vector<Atom*>::iterator k;
240	>
241		Molecule* mol;
242	<	StuntDouble* integrableObject;
242	>	StuntDouble* sd;
243	>	Atom* atom;
244
245		ndf_local = 0;
246	+	nfq_local = 0;
247
248		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
262	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	–	integrableObject = mol->nextIntegrableObject(j)) {
249
250	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
251	+	sd = mol->nextIntegrableObject(j)) {
252	+
253		ndf_local += 3;
254
255	<	if (integrableObject->isDirectional()) {
256	<	if (integrableObject->isLinear()) {
255	>	if (sd->isDirectional()) {
256	>	if (sd->isLinear()) {
257		ndf_local += 2;
258		} else {
259		ndf_local += 3;
260		}
261		}
274	–
262		}
263	+
264	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
265	+	atom = mol->nextFluctuatingCharge(k)) {
266	+	if (atom->isFluctuatingCharge()) {
267	+	nfq_local++;
268	+	}
269	+	}
270		}
271
272	+	ndfLocal_ = ndf_local;
273	+
274		// n_constraints is local, so subtract them on each processor
275		ndf_local -= nConstraints_;
276
277		#ifdef IS_MPI
278	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
278	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
279	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
280	>	MPI::INT, MPI::SUM);
281		#else
282		ndf_ = ndf_local;
283	+	nGlobalFluctuatingCharges_ = nfq_local;
284		#endif
285
286		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 292 | Line 291 | namespace oopse {
291
292		int SimInfo::getFdf() {
293		#ifdef IS_MPI
294	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
294	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
295		#else
296		fdf_ = fdf_local;
297		#endif
298		return fdf_;
299		}
300	+
301	+	unsigned int SimInfo::getNLocalCutoffGroups(){
302	+	int nLocalCutoffAtoms = 0;
303	+	Molecule* mol;
304	+	MoleculeIterator mi;
305	+	CutoffGroup* cg;
306	+	Molecule::CutoffGroupIterator ci;
307
308	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
309	+
310	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
311	+	cg = mol->nextCutoffGroup(ci)) {
312	+	nLocalCutoffAtoms += cg->getNumAtom();
313	+
314	+	}
315	+	}
316	+
317	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
318	+	}
319	+
320		void SimInfo::calcNdfRaw() {
321		int ndfRaw_local;
322
323		MoleculeIterator i;
324	<	std::vector<StuntDouble*>::iterator j;
324	>	vector<StuntDouble*>::iterator j;
325		Molecule* mol;
326	<	StuntDouble* integrableObject;
326	>	StuntDouble* sd;
327
328		// Raw degrees of freedom that we have to set
329		ndfRaw_local = 0;
330
331		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
314	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
315	–	integrableObject = mol->nextIntegrableObject(j)) {
332
333	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
334	+	sd = mol->nextIntegrableObject(j)) {
335	+
336		ndfRaw_local += 3;
337
338	<	if (integrableObject->isDirectional()) {
339	<	if (integrableObject->isLinear()) {
338	>	if (sd->isDirectional()) {
339	>	if (sd->isLinear()) {
340		ndfRaw_local += 2;
341		} else {
342		ndfRaw_local += 3;
#	Line 328 | Line 347 | namespace oopse {
347		}
348
349		#ifdef IS_MPI
350	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
351		#else
352		ndfRaw_ = ndfRaw_local;
353		#endif
#	Line 341 | Line 360 | namespace oopse {
360
361
362		#ifdef IS_MPI
363	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
363	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
364	>	MPI::INT, MPI::SUM);
365		#else
366		ndfTrans_ = ndfTrans_local;
367		#endif
#	Line 350 | Line 370 | namespace oopse {
370
371		}
372
373	<	void SimInfo::addExcludePairs(Molecule* mol) {
374	<	std::vector<Bond*>::iterator bondIter;
375	<	std::vector<Bend*>::iterator bendIter;
376	<	std::vector<Torsion*>::iterator torsionIter;
373	>	void SimInfo::addInteractionPairs(Molecule* mol) {
374	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
375	>	vector<Atom*>::iterator atomIter;
376	>	vector<Bond*>::iterator bondIter;
377	>	vector<Bend*>::iterator bendIter;
378	>	vector<Torsion*>::iterator torsionIter;
379	>	vector<Inversion*>::iterator inversionIter;
380	>	Atom* atom;
381		Bond* bond;
382		Bend* bend;
383		Torsion* torsion;
384	+	Inversion* inversion;
385		int a;
386		int b;
387		int c;
388		int d;
389
390	<	std::map<int, std::set<int> > atomGroups;
390	>	// atomGroups can be used to add special interaction maps between
391	>	// groups of atoms that are in two separate rigid bodies.
392	>	// However, most site-site interactions between two rigid bodies
393	>	// are probably not special, just the ones between the physically
394	>	// bonded atoms.  Interactions *within* a single rigid body should
395	>	// always be excluded.  These are done at the bottom of this
396	>	// function.
397
398	+	map<int, set<int> > atomGroups;
399		Molecule::RigidBodyIterator rbIter;
400		RigidBody* rb;
401		Molecule::IntegrableObjectIterator ii;
402	<	StuntDouble* integrableObject;
402	>	StuntDouble* sd;
403
404	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
405	<	integrableObject = mol->nextIntegrableObject(ii)) {
406	<
407	<	if (integrableObject->isRigidBody()) {
408	<	rb = static_cast<RigidBody*>(integrableObject);
409	<	std::vector<Atom*> atoms = rb->getAtoms();
410	<	std::set<int> rigidAtoms;
411	<	for (int i = 0; i < atoms.size(); ++i) {
412	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
413	<	}
414	<	for (int i = 0; i < atoms.size(); ++i) {
415	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
416	<	}
404	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
405	>	sd = mol->nextIntegrableObject(ii)) {
406	>
407	>	if (sd->isRigidBody()) {
408	>	rb = static_cast<RigidBody*>(sd);
409	>	vector<Atom*> atoms = rb->getAtoms();
410	>	set<int> rigidAtoms;
411	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
412	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
413	>	}
414	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
416	>	}
417		} else {
418	<	std::set<int> oneAtomSet;
419	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
420	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
418	>	set<int> oneAtomSet;
419	>	oneAtomSet.insert(sd->getGlobalIndex());
420	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
421		}
422		}
423
424	<
425	<
426	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
424	>
425	>	for (bond= mol->beginBond(bondIter); bond != NULL;
426	>	bond = mol->nextBond(bondIter)) {
427	>
428		a = bond->getAtomA()->getGlobalIndex();
429	<	b = bond->getAtomB()->getGlobalIndex();
430	<	exclude_.addPair(a, b);
429	>	b = bond->getAtomB()->getGlobalIndex();
430	>
431	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
432	>	oneTwoInteractions_.addPair(a, b);
433	>	} else {
434	>	excludedInteractions_.addPair(a, b);
435	>	}
436		}
437
438	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
438	>	for (bend= mol->beginBend(bendIter); bend != NULL;
439	>	bend = mol->nextBend(bendIter)) {
440	>
441		a = bend->getAtomA()->getGlobalIndex();
442		b = bend->getAtomB()->getGlobalIndex();
443		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);
444
445	<	//exclude_.addPair(a, b);
446	<	//exclude_.addPair(a, c);
447	<	//exclude_.addPair(b, c);
445	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
446	>	oneTwoInteractions_.addPair(a, b);
447	>	oneTwoInteractions_.addPair(b, c);
448	>	} else {
449	>	excludedInteractions_.addPair(a, b);
450	>	excludedInteractions_.addPair(b, c);
451	>	}
452	>
453	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
454	>	oneThreeInteractions_.addPair(a, c);
455	>	} else {
456	>	excludedInteractions_.addPair(a, c);
457	>	}
458		}
459
460	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
460	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
461	>	torsion = mol->nextTorsion(torsionIter)) {
462	>
463		a = torsion->getAtomA()->getGlobalIndex();
464		b = torsion->getAtomB()->getGlobalIndex();
465		c = torsion->getAtomC()->getGlobalIndex();
466	<	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);
466	>	d = torsion->getAtomD()->getGlobalIndex();
467
468	<	exclude_.addPairs(rigidSetA, rigidSetB);
469	<	exclude_.addPairs(rigidSetA, rigidSetC);
470	<	exclude_.addPairs(rigidSetA, rigidSetD);
471	<	exclude_.addPairs(rigidSetB, rigidSetC);
472	<	exclude_.addPairs(rigidSetB, rigidSetD);
473	<	exclude_.addPairs(rigidSetC, rigidSetD);
468	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
469	>	oneTwoInteractions_.addPair(a, b);
470	>	oneTwoInteractions_.addPair(b, c);
471	>	oneTwoInteractions_.addPair(c, d);
472	>	} else {
473	>	excludedInteractions_.addPair(a, b);
474	>	excludedInteractions_.addPair(b, c);
475	>	excludedInteractions_.addPair(c, d);
476	>	}
477
478	<	/*
479	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
480	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
481	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
482	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
483	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
484	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
485	<
486	<
487	<	exclude_.addPair(a, b);
488	<	exclude_.addPair(a, c);
489	<	exclude_.addPair(a, d);
490	<	exclude_.addPair(b, c);
447	<	exclude_.addPair(b, d);
448	<	exclude_.addPair(c, d);
449	<	*/
478	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
479	>	oneThreeInteractions_.addPair(a, c);
480	>	oneThreeInteractions_.addPair(b, d);
481	>	} else {
482	>	excludedInteractions_.addPair(a, c);
483	>	excludedInteractions_.addPair(b, d);
484	>	}
485	>
486	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
487	>	oneFourInteractions_.addPair(a, d);
488	>	} else {
489	>	excludedInteractions_.addPair(a, d);
490	>	}
491		}
492
493	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
494	<	std::vector<Atom*> atoms = rb->getAtoms();
495	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
496	<	for (int j = i + 1; j < atoms.size(); ++j) {
493	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
494	>	inversion = mol->nextInversion(inversionIter)) {
495	>
496	>	a = inversion->getAtomA()->getGlobalIndex();
497	>	b = inversion->getAtomB()->getGlobalIndex();
498	>	c = inversion->getAtomC()->getGlobalIndex();
499	>	d = inversion->getAtomD()->getGlobalIndex();
500	>
501	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
502	>	oneTwoInteractions_.addPair(a, b);
503	>	oneTwoInteractions_.addPair(a, c);
504	>	oneTwoInteractions_.addPair(a, d);
505	>	} else {
506	>	excludedInteractions_.addPair(a, b);
507	>	excludedInteractions_.addPair(a, c);
508	>	excludedInteractions_.addPair(a, d);
509	>	}
510	>
511	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
512	>	oneThreeInteractions_.addPair(b, c);
513	>	oneThreeInteractions_.addPair(b, d);
514	>	oneThreeInteractions_.addPair(c, d);
515	>	} else {
516	>	excludedInteractions_.addPair(b, c);
517	>	excludedInteractions_.addPair(b, d);
518	>	excludedInteractions_.addPair(c, d);
519	>	}
520	>	}
521	>
522	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
523	>	rb = mol->nextRigidBody(rbIter)) {
524	>	vector<Atom*> atoms = rb->getAtoms();
525	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
526	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
527		a = atoms[i]->getGlobalIndex();
528		b = atoms[j]->getGlobalIndex();
529	<	exclude_.addPair(a, b);
529	>	excludedInteractions_.addPair(a, b);
530		}
531		}
532		}
533
534		}
535
536	<	void SimInfo::removeExcludePairs(Molecule* mol) {
537	<	std::vector<Bond*>::iterator bondIter;
538	<	std::vector<Bend*>::iterator bendIter;
539	<	std::vector<Torsion*>::iterator torsionIter;
536	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
537	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
538	>	vector<Bond*>::iterator bondIter;
539	>	vector<Bend*>::iterator bendIter;
540	>	vector<Torsion*>::iterator torsionIter;
541	>	vector<Inversion*>::iterator inversionIter;
542		Bond* bond;
543		Bend* bend;
544		Torsion* torsion;
545	+	Inversion* inversion;
546		int a;
547		int b;
548		int c;
549		int d;
550
551	<	std::map<int, std::set<int> > atomGroups;
478	<
551	>	map<int, set<int> > atomGroups;
552		Molecule::RigidBodyIterator rbIter;
553		RigidBody* rb;
554		Molecule::IntegrableObjectIterator ii;
555	<	StuntDouble* integrableObject;
555	>	StuntDouble* sd;
556
557	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
558	<	integrableObject = mol->nextIntegrableObject(ii)) {
559	<
560	<	if (integrableObject->isRigidBody()) {
561	<	rb = static_cast<RigidBody*>(integrableObject);
562	<	std::vector<Atom*> atoms = rb->getAtoms();
563	<	std::set<int> rigidAtoms;
564	<	for (int i = 0; i < atoms.size(); ++i) {
565	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
566	<	}
567	<	for (int i = 0; i < atoms.size(); ++i) {
568	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
569	<	}
557	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
558	>	sd = mol->nextIntegrableObject(ii)) {
559	>
560	>	if (sd->isRigidBody()) {
561	>	rb = static_cast<RigidBody*>(sd);
562	>	vector<Atom*> atoms = rb->getAtoms();
563	>	set<int> rigidAtoms;
564	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
565	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
566	>	}
567	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
569	>	}
570		} else {
571	<	std::set<int> oneAtomSet;
572	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
573	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
571	>	set<int> oneAtomSet;
572	>	oneAtomSet.insert(sd->getGlobalIndex());
573	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
574		}
575		}
576
577	<
578	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
577	>	for (bond= mol->beginBond(bondIter); bond != NULL;
578	>	bond = mol->nextBond(bondIter)) {
579	>
580		a = bond->getAtomA()->getGlobalIndex();
581	<	b = bond->getAtomB()->getGlobalIndex();
582	<	exclude_.removePair(a, b);
581	>	b = bond->getAtomB()->getGlobalIndex();
582	>
583	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
584	>	oneTwoInteractions_.removePair(a, b);
585	>	} else {
586	>	excludedInteractions_.removePair(a, b);
587	>	}
588		}
589
590	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
590	>	for (bend= mol->beginBend(bendIter); bend != NULL;
591	>	bend = mol->nextBend(bendIter)) {
592	>
593		a = bend->getAtomA()->getGlobalIndex();
594		b = bend->getAtomB()->getGlobalIndex();
595		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);
596
597	<	//exclude_.removePair(a, b);
598	<	//exclude_.removePair(a, c);
599	<	//exclude_.removePair(b, c);
597	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
598	>	oneTwoInteractions_.removePair(a, b);
599	>	oneTwoInteractions_.removePair(b, c);
600	>	} else {
601	>	excludedInteractions_.removePair(a, b);
602	>	excludedInteractions_.removePair(b, c);
603	>	}
604	>
605	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
606	>	oneThreeInteractions_.removePair(a, c);
607	>	} else {
608	>	excludedInteractions_.removePair(a, c);
609	>	}
610		}
611
612	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
612	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
613	>	torsion = mol->nextTorsion(torsionIter)) {
614	>
615		a = torsion->getAtomA()->getGlobalIndex();
616		b = torsion->getAtomB()->getGlobalIndex();
617		c = torsion->getAtomC()->getGlobalIndex();
618	<	d = torsion->getAtomD()->getGlobalIndex();
618	>	d = torsion->getAtomD()->getGlobalIndex();
619	>
620	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
621	>	oneTwoInteractions_.removePair(a, b);
622	>	oneTwoInteractions_.removePair(b, c);
623	>	oneTwoInteractions_.removePair(c, d);
624	>	} else {
625	>	excludedInteractions_.removePair(a, b);
626	>	excludedInteractions_.removePair(b, c);
627	>	excludedInteractions_.removePair(c, d);
628	>	}
629
630	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
631	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
632	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
633	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
630	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
631	>	oneThreeInteractions_.removePair(a, c);
632	>	oneThreeInteractions_.removePair(b, d);
633	>	} else {
634	>	excludedInteractions_.removePair(a, c);
635	>	excludedInteractions_.removePair(b, d);
636	>	}
637
638	<	exclude_.removePairs(rigidSetA, rigidSetB);
639	<	exclude_.removePairs(rigidSetA, rigidSetC);
640	<	exclude_.removePairs(rigidSetA, rigidSetD);
641	<	exclude_.removePairs(rigidSetB, rigidSetC);
642	<	exclude_.removePairs(rigidSetB, rigidSetD);
643	<	exclude_.removePairs(rigidSetC, rigidSetD);
638	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
639	>	oneFourInteractions_.removePair(a, d);
640	>	} else {
641	>	excludedInteractions_.removePair(a, d);
642	>	}
643	>	}
644
645	<	/*
646	<	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());
645	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
646	>	inversion = mol->nextInversion(inversionIter)) {
647
648	<
649	<	exclude_.removePair(a, b);
650	<	exclude_.removePair(a, c);
651	<	exclude_.removePair(a, d);
652	<	exclude_.removePair(b, c);
653	<	exclude_.removePair(b, d);
654	<	exclude_.removePair(c, d);
655	<	*/
648	>	a = inversion->getAtomA()->getGlobalIndex();
649	>	b = inversion->getAtomB()->getGlobalIndex();
650	>	c = inversion->getAtomC()->getGlobalIndex();
651	>	d = inversion->getAtomD()->getGlobalIndex();
652	>
653	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
654	>	oneTwoInteractions_.removePair(a, b);
655	>	oneTwoInteractions_.removePair(a, c);
656	>	oneTwoInteractions_.removePair(a, d);
657	>	} else {
658	>	excludedInteractions_.removePair(a, b);
659	>	excludedInteractions_.removePair(a, c);
660	>	excludedInteractions_.removePair(a, d);
661	>	}
662	>
663	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
664	>	oneThreeInteractions_.removePair(b, c);
665	>	oneThreeInteractions_.removePair(b, d);
666	>	oneThreeInteractions_.removePair(c, d);
667	>	} else {
668	>	excludedInteractions_.removePair(b, c);
669	>	excludedInteractions_.removePair(b, d);
670	>	excludedInteractions_.removePair(c, d);
671	>	}
672		}
673
674	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
675	<	std::vector<Atom*> atoms = rb->getAtoms();
676	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
677	<	for (int j = i + 1; j < atoms.size(); ++j) {
674	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
675	>	rb = mol->nextRigidBody(rbIter)) {
676	>	vector<Atom*> atoms = rb->getAtoms();
677	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
678	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
679		a = atoms[i]->getGlobalIndex();
680		b = atoms[j]->getGlobalIndex();
681	<	exclude_.removePair(a, b);
681	>	excludedInteractions_.removePair(a, b);
682		}
683		}
684		}
685	<
685	>
686		}
687	<
688	<
687	>
688	>
689		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
690		int curStampId;
691	<
691	>
692		//index from 0
693		curStampId = moleculeStamps_.size();
694
#	Line 586 | Line 696 | namespace oopse {
696		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
697		}
698
589	–	void SimInfo::update() {
699
700	<	setupSimType();
701	<
702	<	#ifdef IS_MPI
703	<	setupFortranParallel();
704	<	#endif
705	<
706	<	setupFortranSim();
707	<
708	<	//setup fortran force field
600	<	/** @deprecate */
601	<	int isError = 0;
602	<
603	<	setupElectrostaticSummationMethod( isError );
604	<	setupSwitchingFunction();
605	<	setupAccumulateBoxDipole();
606	<
607	<	if(isError){
608	<	sprintf( painCave.errMsg,
609	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
610	<	painCave.isFatal = 1;
611	<	simError();
612	<	}
613	<
614	<
615	<	setupCutoff();
616	<
700	>	/**
701	>	* update
702	>	*
703	>	*  Performs the global checks and variable settings after the
704	>	*  objects have been created.
705	>	*
706	>	*/
707	>	void SimInfo::update() {
708	>	setupSimVariables();
709		calcNdf();
710		calcNdfRaw();
711		calcNdfTrans();
620	–
621	–	fortranInitialized_ = true;
712		}
713	<
714	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
713	>
714	>	/**
715	>	* getSimulatedAtomTypes
716	>	*
717	>	* Returns an STL set of AtomType* that are actually present in this
718	>	* simulation.  Must query all processors to assemble this information.
719	>	*
720	>	*/
721	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
722		SimInfo::MoleculeIterator mi;
723		Molecule* mol;
724		Molecule::AtomIterator ai;
725		Atom* atom;
726	<	std::set<AtomType*> atomTypes;
727	<
726	>	set<AtomType*> atomTypes;
727	>
728		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
729	<
730	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
729	>	for(atom = mol->beginAtom(ai); atom != NULL;
730	>	atom = mol->nextAtom(ai)) {
731		atomTypes.insert(atom->getAtomType());
732	<	}
733	<
734	<	}
732	>	}
733	>	}
734	>
735	>	#ifdef IS_MPI
736
737	<	return atomTypes;
738	<	}
641	<
642	<	void SimInfo::setupSimType() {
643	<	std::set<AtomType*>::iterator i;
644	<	std::set<AtomType*> atomTypes;
645	<	atomTypes = getUniqueAtomTypes();
737	>	// loop over the found atom types on this processor, and add their
738	>	// numerical idents to a vector:
739
740	<	int useLennardJones = 0;
741	<	int useElectrostatic = 0;
742	<	int useEAM = 0;
743	<	int useSC = 0;
651	<	int useCharge = 0;
652	<	int useDirectional = 0;
653	<	int useDipole = 0;
654	<	int useGayBerne = 0;
655	<	int useSticky = 0;
656	<	int useStickyPower = 0;
657	<	int useShape = 0;
658	<	int useFLARB = 0; //it is not in AtomType yet
659	<	int useDirectionalAtom = 0;
660	<	int useElectrostatics = 0;
661	<	//usePBC and useRF are from simParams
662	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663	<	int useRF;
664	<	int useSF;
665	<	int useSP;
666	<	int useBoxDipole;
667	<	std::string myMethod;
740	>	vector<int> foundTypes;
741	>	set<AtomType*>::iterator i;
742	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
743	>	foundTypes.push_back( (*i)->getIdent() );
744
745	<	// set the useRF logical
746	<	useRF = 0;
671	<	useSF = 0;
745	>	// count_local holds the number of found types on this processor
746	>	int count_local = foundTypes.size();
747
748	+	int nproc = MPI::COMM_WORLD.Get_size();
749
750	<	if (simParams_->haveElectrostaticSummationMethod()) {
751	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
752	<	toUpper(myMethod);
753	<	if (myMethod == "REACTION_FIELD"){
754	<	useRF=1;
755	<	} else if (myMethod == "SHIFTED_FORCE"){
756	<	useSF = 1;
757	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
758	<	useSP = 1;
759	<	}
750	>	// we need arrays to hold the counts and displacement vectors for
751	>	// all processors
752	>	vector<int> counts(nproc, 0);
753	>	vector<int> disps(nproc, 0);
754	>
755	>	// fill the counts array
756	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
757	>	1, MPI::INT);
758	>
759	>	// use the processor counts to compute the displacement array
760	>	disps[0] = 0;
761	>	int totalCount = counts[0];
762	>	for (int iproc = 1; iproc < nproc; iproc++) {
763	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
764	>	totalCount += counts[iproc];
765		}
766	+
767	+	// we need a (possibly redundant) set of all found types:
768	+	vector<int> ftGlobal(totalCount);
769
770	<	if (simParams_->haveAccumulateBoxDipole())
771	<	if (simParams_->getAccumulateBoxDipole())
772	<	useBoxDipole = 1;
770	>	// now spray out the foundTypes to all the other processors:
771	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
772	>	&ftGlobal[0], &counts[0], &disps[0],
773	>	MPI::INT);
774
775	<	//loop over all of the atom types
691	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
692	<	useLennardJones |= (*i)->isLennardJones();
693	<	useElectrostatic |= (*i)->isElectrostatic();
694	<	useEAM |= (*i)->isEAM();
695	<	useSC |= (*i)->isSC();
696	<	useCharge |= (*i)->isCharge();
697	<	useDirectional |= (*i)->isDirectional();
698	<	useDipole |= (*i)->isDipole();
699	<	useGayBerne |= (*i)->isGayBerne();
700	<	useSticky |= (*i)->isSticky();
701	<	useStickyPower |= (*i)->isStickyPower();
702	<	useShape |= (*i)->isShape();
703	<	}
775	>	vector<int>::iterator j;
776
777	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
778	<	useDirectionalAtom = 1;
779	<	}
777	>	// foundIdents is a stl set, so inserting an already found ident
778	>	// will have no effect.
779	>	set<int> foundIdents;
780
781	<	if (useCharge || useDipole) {
782	<	useElectrostatics = 1;
783	<	}
781	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
782	>	foundIdents.insert((*j));
783	>
784	>	// now iterate over the foundIdents and get the actual atom types
785	>	// that correspond to these:
786	>	set<int>::iterator it;
787	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
788	>	atomTypes.insert( forceField_->getAtomType((*it)) );
789	>
790	>	#endif
791
792	<	#ifdef IS_MPI
793	<	int temp;
792	>	return atomTypes;
793	>	}
794
716	–	temp = usePBC;
717	–	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
795
796	<	temp = useDirectionalAtom;
797	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	>	int getGlobalCountOfType(AtomType* atype) {
797	>	/*
798	>	set<AtomType*> atypes = getSimulatedAtomTypes();
799	>	map<AtomType*, int> counts_;
800
801	<	temp = useLennardJones;
802	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
802	>	for(atom = mol->beginAtom(ai); atom != NULL;
803	>	atom = mol->nextAtom(ai)) {
804	>	atom->getAtomType();
805	>	}
806	>	}
807	>	*/
808	>	return 0;
809	>	}
810
811	<	temp = useElectrostatics;
812	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	<
814	<	temp = useCharge;
815	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	<
817	<	temp = useDipole;
818	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	<
734	<	temp = useSticky;
735	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
736	<
737	<	temp = useStickyPower;
738	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	void SimInfo::setupSimVariables() {
812	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
813	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
814	>	// parameter is true
815	>	calcBoxDipole_ = false;
816	>	if ( simParams_->haveAccumulateBoxDipole() )
817	>	if ( simParams_->getAccumulateBoxDipole() ) {
818	>	calcBoxDipole_ = true;
819	>	}
820
821	<	temp = useGayBerne;
822	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	>	set<AtomType*>::iterator i;
822	>	set<AtomType*> atomTypes;
823	>	atomTypes = getSimulatedAtomTypes();
824	>	bool usesElectrostatic = false;
825	>	bool usesMetallic = false;
826	>	bool usesDirectional = false;
827	>	bool usesFluctuatingCharges =  false;
828	>	//loop over all of the atom types
829	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
830	>	usesElectrostatic |= (*i)->isElectrostatic();
831	>	usesMetallic |= (*i)->isMetal();
832	>	usesDirectional |= (*i)->isDirectional();
833	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
834	>	}
835
836	<	temp = useEAM;
837	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838	<
839	<	temp = useSC;
840	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836	>	#ifdef IS_MPI
837	>	bool temp;
838	>	temp = usesDirectional;
839	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
840	>	MPI::LOR);
841	>
842	>	temp = usesMetallic;
843	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
844	>	MPI::LOR);
845
846	<	temp = useShape;
847	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	>	temp = usesElectrostatic;
847	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
848	>	MPI::LOR);
849
850	<	temp = useFLARB;
851	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	>	temp = usesFluctuatingCharges;
851	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
852	>	MPI::LOR);
853	>	#else
854
855	<	temp = useRF;
856	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
855	>	usesDirectionalAtoms_ = usesDirectional;
856	>	usesMetallicAtoms_ = usesMetallic;
857	>	usesElectrostaticAtoms_ = usesElectrostatic;
858	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
859
860	<	temp = useSF;
861	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>	#endif
861	>
862	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
863	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
864	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
865	>	}
866
761	–	temp = useSP;
762	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
867
868	<	temp = useBoxDipole;
869	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
868	>	vector<int> SimInfo::getGlobalAtomIndices() {
869	>	SimInfo::MoleculeIterator mi;
870	>	Molecule* mol;
871	>	Molecule::AtomIterator ai;
872	>	Atom* atom;
873
874	<	#endif
874	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
875	>
876	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
877	>
878	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
879	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
880	>	}
881	>	}
882	>	return GlobalAtomIndices;
883	>	}
884
769	–	fInfo_.SIM_uses_PBC = usePBC;
770	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
771	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
772	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
773	–	fInfo_.SIM_uses_Charges = useCharge;
774	–	fInfo_.SIM_uses_Dipoles = useDipole;
775	–	fInfo_.SIM_uses_Sticky = useSticky;
776	–	fInfo_.SIM_uses_StickyPower = useStickyPower;
777	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
778	–	fInfo_.SIM_uses_EAM = useEAM;
779	–	fInfo_.SIM_uses_SC = useSC;
780	–	fInfo_.SIM_uses_Shapes = useShape;
781	–	fInfo_.SIM_uses_FLARB = useFLARB;
782	–	fInfo_.SIM_uses_RF = useRF;
783	–	fInfo_.SIM_uses_SF = useSF;
784	–	fInfo_.SIM_uses_SP = useSP;
785	–	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
885
886	<	if( myMethod == "REACTION_FIELD") {
886	>	vector<int> SimInfo::getGlobalGroupIndices() {
887	>	SimInfo::MoleculeIterator mi;
888	>	Molecule* mol;
889	>	Molecule::CutoffGroupIterator ci;
890	>	CutoffGroup* cg;
891	>
892	>	vector<int> GlobalGroupIndices;
893	>
894	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
895
896	<	if (simParams_->haveDielectric()) {
897	<	fInfo_.dielect = simParams_->getDielectric();
898	<	} else {
899	<	sprintf(painCave.errMsg,
900	<	"SimSetup Error: No Dielectric constant was set.\n"
901	<	"\tYou are trying to use Reaction Field without"
795	<	"\tsetting a dielectric constant!\n");
796	<	painCave.isFatal = 1;
797	<	simError();
798	<	}
896	>	//local index of cutoff group is trivial, it only depends on the
897	>	//order of travesing
898	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
899	>	cg = mol->nextCutoffGroup(ci)) {
900	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
901	>	}
902		}
903	<
903	>	return GlobalGroupIndices;
904		}
905
803	–	void SimInfo::setupFortranSim() {
804	–	int isError;
805	–	int nExclude;
806	–	std::vector<int> fortranGlobalGroupMembership;
807	–
808	–	nExclude = exclude_.getSize();
809	–	isError = 0;
906
907	<	//globalGroupMembership_ is filled by SimCreator
812	<	for (int i = 0; i < nGlobalAtoms_; i++) {
813	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
814	<	}
907	>	void SimInfo::prepareTopology() {
908
909		//calculate mass ratio of cutoff group
817	–	std::vector<RealType> mfact;
910		SimInfo::MoleculeIterator mi;
911		Molecule* mol;
912		Molecule::CutoffGroupIterator ci;
#	Line 823 | Line 915 | namespace oopse {
915		Atom* atom;
916		RealType totalMass;
917
918	<	//to avoid memory reallocation, reserve enough space for mfact
919	<	mfact.reserve(getNCutoffGroups());
918	>	/**
919	>	* The mass factor is the relative mass of an atom to the total
920	>	* mass of the cutoff group it belongs to.  By default, all atoms
921	>	* are their own cutoff groups, and therefore have mass factors of
922	>	* 1.  We need some special handling for massless atoms, which
923	>	* will be treated as carrying the entire mass of the cutoff
924	>	* group.
925	>	*/
926	>	massFactors_.clear();
927	>	massFactors_.resize(getNAtoms(), 1.0);
928
929		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
930	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
930	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
931	>	cg = mol->nextCutoffGroup(ci)) {
932
933		totalMass = cg->getMass();
934		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
935		// Check for massless groups - set mfact to 1 if true
936	<	if (totalMass != 0)
937	<	mfact.push_back(atom->getMass()/totalMass);
936	>	if (totalMass != 0)
937	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
938		else
939	<	mfact.push_back( 1.0 );
939	>	massFactors_[atom->getLocalIndex()] = 1.0;
940		}
840	–
941		}
942		}
943
944	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
845	<	std::vector<int> identArray;
944	>	// Build the identArray_ and regions_
945
946	<	//to avoid memory reallocation, reserve enough space identArray
947	<	identArray.reserve(getNAtoms());
948	<
949	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
946	>	identArray_.clear();
947	>	identArray_.reserve(getNAtoms());
948	>	regions_.clear();
949	>	regions_.reserve(getNAtoms());
950	>
951	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
952	>	int reg = mol->getRegion();
953		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
954	<	identArray.push_back(atom->getIdent());
954	>	identArray_.push_back(atom->getIdent());
955	>	regions_.push_back(reg);
956		}
957		}
958	<
959	<	//fill molMembershipArray
857	<	//molMembershipArray is filled by SimCreator
858	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
859	<	for (int i = 0; i < nGlobalAtoms_; i++) {
860	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
861	<	}
862	<
863	<	//setup fortran simulation
864	<	int nGlobalExcludes = 0;
865	<	int* globalExcludes = NULL;
866	<	int* excludeList = exclude_.getExcludeList();
867	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
868	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
869	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
870	<
871	<	if( isError ){
872	<
873	<	sprintf( painCave.errMsg,
874	<	"There was an error setting the simulation information in fortran.\n" );
875	<	painCave.isFatal = 1;
876	<	painCave.severity = OOPSE_ERROR;
877	<	simError();
878	<	}
879	<
880	<	#ifdef IS_MPI
881	<	sprintf( checkPointMsg,
882	<	"succesfully sent the simulation information to fortran.\n");
883	<	MPIcheckPoint();
884	<	#endif // is_mpi
885	<	}
886	<
887	<
888	<	#ifdef IS_MPI
889	<	void SimInfo::setupFortranParallel() {
890	<
891	<	//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	<	MPIcheckPoint();
941	<
942	<
943	<	}
944	<
945	<	#endif
946	<
947	<	void SimInfo::setupCutoff() {
948	<
949	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
950	<
951	<	// Check the cutoff policy
952	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
953	<
954	<	std::string myPolicy;
955	<	if (forceFieldOptions_.haveCutoffPolicy()){
956	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
957	<	}else if (simParams_->haveCutoffPolicy()) {
958	<	myPolicy = simParams_->getCutoffPolicy();
959	<	}
960	<
961	<	if (!myPolicy.empty()){
962	<	toUpper(myPolicy);
963	<	if (myPolicy == "MIX") {
964	<	cp = MIX_CUTOFF_POLICY;
965	<	} else {
966	<	if (myPolicy == "MAX") {
967	<	cp = MAX_CUTOFF_POLICY;
968	<	} else {
969	<	if (myPolicy == "TRADITIONAL") {
970	<	cp = TRADITIONAL_CUTOFF_POLICY;
971	<	} else {
972	<	// throw error
973	<	sprintf( painCave.errMsg,
974	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
975	<	painCave.isFatal = 1;
976	<	simError();
977	<	}
978	<	}
979	<	}
980	<	}
981	<	notifyFortranCutoffPolicy(&cp);
982	<
983	<	// Check the Skin Thickness for neighborlists
984	<	RealType skin;
985	<	if (simParams_->haveSkinThickness()) {
986	<	skin = simParams_->getSkinThickness();
987	<	notifyFortranSkinThickness(&skin);
988	<	}
989	<
990	<	// Check if the cutoff was set explicitly:
991	<	if (simParams_->haveCutoffRadius()) {
992	<	rcut_ = simParams_->getCutoffRadius();
993	<	if (simParams_->haveSwitchingRadius()) {
994	<	rsw_  = simParams_->getSwitchingRadius();
995	<	} else {
996	<	if (fInfo_.SIM_uses_Charges |
997	<	fInfo_.SIM_uses_Dipoles |
998	<	fInfo_.SIM_uses_RF) {
999	<
1000	<	rsw_ = 0.85 * rcut_;
1001	<	sprintf(painCave.errMsg,
1002	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1003	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1004	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1005	<	painCave.isFatal = 0;
1006	<	simError();
1007	<	} else {
1008	<	rsw_ = rcut_;
1009	<	sprintf(painCave.errMsg,
1010	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1011	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1012	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1013	<	painCave.isFatal = 0;
1014	<	simError();
1015	<	}
1016	<	}
1017	<
1018	<	notifyFortranCutoffs(&rcut_, &rsw_);
1019	<
1020	<	} else {
1021	<
1022	<	// For electrostatic atoms, we'll assume a large safe value:
1023	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1024	<	sprintf(painCave.errMsg,
1025	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1026	<	"\tOOPSE will use a default value of 15.0 angstroms"
1027	<	"\tfor the cutoffRadius.\n");
1028	<	painCave.isFatal = 0;
1029	<	simError();
1030	<	rcut_ = 15.0;
1031	<
1032	<	if (simParams_->haveElectrostaticSummationMethod()) {
1033	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1034	<	toUpper(myMethod);
1035	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1036	<	if (simParams_->haveSwitchingRadius()){
1037	<	sprintf(painCave.errMsg,
1038	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1039	<	"\teven though the electrostaticSummationMethod was\n"
1040	<	"\tset to %s\n", myMethod.c_str());
1041	<	painCave.isFatal = 1;
1042	<	simError();
1043	<	}
1044	<	}
1045	<	}
1046	<
1047	<	if (simParams_->haveSwitchingRadius()){
1048	<	rsw_ = simParams_->getSwitchingRadius();
1049	<	} else {
1050	<	sprintf(painCave.errMsg,
1051	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1052	<	"\tOOPSE will use a default value of\n"
1053	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1054	<	painCave.isFatal = 0;
1055	<	simError();
1056	<	rsw_ = 0.85 * rcut_;
1057	<	}
1058	<	notifyFortranCutoffs(&rcut_, &rsw_);
1059	<	} else {
1060	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1061	<	// We'll punt and let fortran figure out the cutoffs later.
1062	<
1063	<	notifyFortranYouAreOnYourOwn();
1064	<
1065	<	}
1066	<	}
958	>
959	>	topologyDone_ = true;
960		}
961
1069	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1070	–
1071	–	int errorOut;
1072	–	int esm =  NONE;
1073	–	int sm = UNDAMPED;
1074	–	RealType alphaVal;
1075	–	RealType dielectric;
1076	–
1077	–	errorOut = isError;
1078	–	alphaVal = simParams_->getDampingAlpha();
1079	–	dielectric = simParams_->getDielectric();
1080	–
1081	–	if (simParams_->haveElectrostaticSummationMethod()) {
1082	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1083	–	toUpper(myMethod);
1084	–	if (myMethod == "NONE") {
1085	–	esm = NONE;
1086	–	} else {
1087	–	if (myMethod == "SWITCHING_FUNCTION") {
1088	–	esm = SWITCHING_FUNCTION;
1089	–	} else {
1090	–	if (myMethod == "SHIFTED_POTENTIAL") {
1091	–	esm = SHIFTED_POTENTIAL;
1092	–	} else {
1093	–	if (myMethod == "SHIFTED_FORCE") {
1094	–	esm = SHIFTED_FORCE;
1095	–	} else {
1096	–	if (myMethod == "REACTION_FIELD") {
1097	–	esm = REACTION_FIELD;
1098	–	} else {
1099	–	// throw error
1100	–	sprintf( painCave.errMsg,
1101	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1102	–	"\t(Input file specified %s .)\n"
1103	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1104	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1105	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1106	–	painCave.isFatal = 1;
1107	–	simError();
1108	–	}
1109	–	}
1110	–	}
1111	–	}
1112	–	}
1113	–	}
1114	–
1115	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1116	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1117	–	toUpper(myScreen);
1118	–	if (myScreen == "UNDAMPED") {
1119	–	sm = UNDAMPED;
1120	–	} else {
1121	–	if (myScreen == "DAMPED") {
1122	–	sm = DAMPED;
1123	–	if (!simParams_->haveDampingAlpha()) {
1124	–	//throw error
1125	–	sprintf( painCave.errMsg,
1126	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1127	–	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1128	–	painCave.isFatal = 0;
1129	–	simError();
1130	–	}
1131	–	} else {
1132	–	// throw error
1133	–	sprintf( painCave.errMsg,
1134	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1135	–	"\t(Input file specified %s .)\n"
1136	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1137	–	"or \"damped\".\n", myScreen.c_str() );
1138	–	painCave.isFatal = 1;
1139	–	simError();
1140	–	}
1141	–	}
1142	–	}
1143	–
1144	–	// let's pass some summation method variables to fortran
1145	–	setElectrostaticSummationMethod( &esm );
1146	–	setFortranElectrostaticMethod( &esm );
1147	–	setScreeningMethod( &sm );
1148	–	setDampingAlpha( &alphaVal );
1149	–	setReactionFieldDielectric( &dielectric );
1150	–	initFortranFF( &errorOut );
1151	–	}
1152	–
1153	–	void SimInfo::setupSwitchingFunction() {
1154	–	int ft = CUBIC;
1155	–
1156	–	if (simParams_->haveSwitchingFunctionType()) {
1157	–	std::string funcType = simParams_->getSwitchingFunctionType();
1158	–	toUpper(funcType);
1159	–	if (funcType == "CUBIC") {
1160	–	ft = CUBIC;
1161	–	} else {
1162	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1163	–	ft = FIFTH_ORDER_POLY;
1164	–	} else {
1165	–	// throw error
1166	–	sprintf( painCave.errMsg,
1167	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1168	–	painCave.isFatal = 1;
1169	–	simError();
1170	–	}
1171	–	}
1172	–	}
1173	–
1174	–	// send switching function notification to switcheroo
1175	–	setFunctionType(&ft);
1176	–
1177	–	}
1178	–
1179	–	void SimInfo::setupAccumulateBoxDipole() {
1180	–
1181	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1182	–	if ( simParams_->haveAccumulateBoxDipole() )
1183	–	if ( simParams_->getAccumulateBoxDipole() ) {
1184	–	setAccumulateBoxDipole();
1185	–	calcBoxDipole_ = true;
1186	–	}
1187	–
1188	–	}
1189	–
962		void SimInfo::addProperty(GenericData* genData) {
963		properties_.addProperty(genData);
964		}
965
966	<	void SimInfo::removeProperty(const std::string& propName) {
966	>	void SimInfo::removeProperty(const string& propName) {
967		properties_.removeProperty(propName);
968		}
969
#	Line 1199 | Line 971 | namespace oopse {
971		properties_.clearProperties();
972		}
973
974	<	std::vector<std::string> SimInfo::getPropertyNames() {
974	>	vector<string> SimInfo::getPropertyNames() {
975		return properties_.getPropertyNames();
976		}
977
978	<	std::vector<GenericData*> SimInfo::getProperties() {
978	>	vector<GenericData*> SimInfo::getProperties() {
979		return properties_.getProperties();
980		}
981
982	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
982	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
983		return properties_.getPropertyByName(propName);
984		}
985
#	Line 1221 | Line 993 | namespace oopse {
993		Molecule* mol;
994		RigidBody* rb;
995		Atom* atom;
996	+	CutoffGroup* cg;
997		SimInfo::MoleculeIterator mi;
998		Molecule::RigidBodyIterator rbIter;
999	<	Molecule::AtomIterator atomIter;;
999	>	Molecule::AtomIterator atomIter;
1000	>	Molecule::CutoffGroupIterator cgIter;
1001
1002		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1003
1004	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1004	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
1005	>	atom = mol->nextAtom(atomIter)) {
1006		atom->setSnapshotManager(sman_);
1007		}
1008
1009	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1009	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1010	>	rb = mol->nextRigidBody(rbIter)) {
1011		rb->setSnapshotManager(sman_);
1012		}
1013	+
1014	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1015	+	cg = mol->nextCutoffGroup(cgIter)) {
1016	+	cg->setSnapshotManager(sman_);
1017	+	}
1018		}
1019
1020		}
1021
1241	–	Vector3d SimInfo::getComVel(){
1242	–	SimInfo::MoleculeIterator i;
1243	–	Molecule* mol;
1022
1023	<	Vector3d comVel(0.0);
1246	<	RealType totalMass = 0.0;
1247	<
1248	<
1249	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1250	<	RealType mass = mol->getMass();
1251	<	totalMass += mass;
1252	<	comVel += mass * mol->getComVel();
1253	<	}
1023	>	ostream& operator <<(ostream& o, SimInfo& info) {
1024
1255	–	#ifdef IS_MPI
1256	–	RealType tmpMass = totalMass;
1257	–	Vector3d tmpComVel(comVel);
1258	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1259	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1260	–	#endif
1261	–
1262	–	comVel /= totalMass;
1263	–
1264	–	return comVel;
1265	–	}
1266	–
1267	–	Vector3d SimInfo::getCom(){
1268	–	SimInfo::MoleculeIterator i;
1269	–	Molecule* mol;
1270	–
1271	–	Vector3d com(0.0);
1272	–	RealType totalMass = 0.0;
1273	–
1274	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1275	–	RealType mass = mol->getMass();
1276	–	totalMass += mass;
1277	–	com += mass * mol->getCom();
1278	–	}
1279	–
1280	–	#ifdef IS_MPI
1281	–	RealType tmpMass = totalMass;
1282	–	Vector3d tmpCom(com);
1283	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1284	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1285	–	#endif
1286	–
1287	–	com /= totalMass;
1288	–
1289	–	return com;
1290	–
1291	–	}
1292	–
1293	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1294	–
1025		return o;
1026		}
1027
1028	<
1029	<	/*
1030	<	Returns center of mass and center of mass velocity in one function call.
1031	<	*/
1032	<
1033	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1034	<	SimInfo::MoleculeIterator i;
1035	<	Molecule* mol;
1036	<
1037	<
1038	<	RealType totalMass = 0.0;
1039	<
1028	>
1029	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1030	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1031	>	sprintf(painCave.errMsg,
1032	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1033	>	"\tindex exceeds number of known objects!\n");
1034	>	painCave.isFatal = 1;
1035	>	simError();
1036	>	return NULL;
1037	>	} else
1038	>	return IOIndexToIntegrableObject.at(index);
1039	>	}
1040	>
1041	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1042	>	IOIndexToIntegrableObject= v;
1043	>	}
1044
1045	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1046	<	RealType mass = mol->getMass();
1313	<	totalMass += mass;
1314	<	com += mass * mol->getCom();
1315	<	comVel += mass * mol->getComVel();
1316	<	}
1317	<
1045	>	int SimInfo::getNGlobalConstraints() {
1046	>	int nGlobalConstraints;
1047		#ifdef IS_MPI
1048	<	RealType tmpMass = totalMass;
1049	<	Vector3d tmpCom(com);
1050	<	Vector3d tmpComVel(comVel);
1051	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1048	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1049	>	MPI::INT, MPI::SUM);
1050	>	#else
1051	>	nGlobalConstraints =  nConstraints_;
1052		#endif
1053	<
1054	<	com /= totalMass;
1328	<	comVel /= totalMass;
1329	<	}
1330	<
1331	<	/*
1332	<	Return intertia tensor for entire system and angular momentum Vector.
1053	>	return nGlobalConstraints;
1054	>	}
1055
1056	+	}//end namespace OpenMD
1057
1335	–	[  Ixx -Ixy  -Ixz ]
1336	–	J =| -Iyx  Iyy  -Iyz |
1337	–	[ -Izx -Iyz   Izz ]
1338	–	*/
1339	–
1340	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1341	–
1342	–
1343	–	RealType xx = 0.0;
1344	–	RealType yy = 0.0;
1345	–	RealType zz = 0.0;
1346	–	RealType xy = 0.0;
1347	–	RealType xz = 0.0;
1348	–	RealType yz = 0.0;
1349	–	Vector3d com(0.0);
1350	–	Vector3d comVel(0.0);
1351	–
1352	–	getComAll(com, comVel);
1353	–
1354	–	SimInfo::MoleculeIterator i;
1355	–	Molecule* mol;
1356	–
1357	–	Vector3d thisq(0.0);
1358	–	Vector3d thisv(0.0);
1359	–
1360	–	RealType thisMass = 0.0;
1361	–
1362	–
1363	–
1364	–
1365	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1366	–
1367	–	thisq = mol->getCom()-com;
1368	–	thisv = mol->getComVel()-comVel;
1369	–	thisMass = mol->getMass();
1370	–	// Compute moment of intertia coefficients.
1371	–	xx += thisq[0]*thisq[0]*thisMass;
1372	–	yy += thisq[1]*thisq[1]*thisMass;
1373	–	zz += thisq[2]*thisq[2]*thisMass;
1374	–
1375	–	// compute products of intertia
1376	–	xy += thisq[0]*thisq[1]*thisMass;
1377	–	xz += thisq[0]*thisq[2]*thisMass;
1378	–	yz += thisq[1]*thisq[2]*thisMass;
1379	–
1380	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1381	–
1382	–	}
1383	–
1384	–
1385	–	inertiaTensor(0,0) = yy + zz;
1386	–	inertiaTensor(0,1) = -xy;
1387	–	inertiaTensor(0,2) = -xz;
1388	–	inertiaTensor(1,0) = -xy;
1389	–	inertiaTensor(1,1) = xx + zz;
1390	–	inertiaTensor(1,2) = -yz;
1391	–	inertiaTensor(2,0) = -xz;
1392	–	inertiaTensor(2,1) = -yz;
1393	–	inertiaTensor(2,2) = xx + yy;
1394	–
1395	–	#ifdef IS_MPI
1396	–	Mat3x3d tmpI(inertiaTensor);
1397	–	Vector3d tmpAngMom;
1398	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1400	–	#endif
1401	–
1402	–	return;
1403	–	}
1404	–
1405	–	//Returns the angular momentum of the system
1406	–	Vector3d SimInfo::getAngularMomentum(){
1407	–
1408	–	Vector3d com(0.0);
1409	–	Vector3d comVel(0.0);
1410	–	Vector3d angularMomentum(0.0);
1411	–
1412	–	getComAll(com,comVel);
1413	–
1414	–	SimInfo::MoleculeIterator i;
1415	–	Molecule* mol;
1416	–
1417	–	Vector3d thisr(0.0);
1418	–	Vector3d thisp(0.0);
1419	–
1420	–	RealType thisMass;
1421	–
1422	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1423	–	thisMass = mol->getMass();
1424	–	thisr = mol->getCom()-com;
1425	–	thisp = (mol->getComVel()-comVel)*thisMass;
1426	–
1427	–	angularMomentum += cross( thisr, thisp );
1428	–
1429	–	}
1430	–
1431	–	#ifdef IS_MPI
1432	–	Vector3d tmpAngMom;
1433	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1434	–	#endif
1435	–
1436	–	return angularMomentum;
1437	–	}
1438	–
1439	–
1440	–	}//end namespace oopse
1441	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
Revision 1930 by gezelter, Mon Aug 19 13:51:04 2013 UTC

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