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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 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 46 | Line 47
47		* @version 1.0
48		*/
49
50	+	#ifdef IS_MPI
51	+	#include <mpi.h>
52	+	#endif
53		#include <algorithm>
54		#include <set>
55		#include <map>
#	Line 53 | Line 57
57		#include "brains/SimInfo.hpp"
58		#include "math/Vector3.hpp"
59		#include "primitives/Molecule.hpp"
60	<	#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/notifyCutoffs_interface.h"
63	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
60	>	#include "primitives/StuntDouble.hpp"
61		#include "utils/MemoryUtils.hpp"
62		#include "utils/simError.h"
63		#include "selection/SelectionManager.hpp"
64	+	#include "io/ForceFieldOptions.hpp"
65	+	#include "brains/ForceField.hpp"
66	+	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	#ifdef IS_MPI
69	<	#include "UseTheForce/mpiComponentPlan.h"
70	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
71	<	#endif
72	<
73	<	namespace oopse {
74	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
75	<	std::map<int, std::set<int> >::iterator i = container.find(index);
76	<	std::set<int> result;
77	<	if (i != container.end()) {
78	<	result = i->second;
79	<	}
80	<
81	<	return result;
82	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
72	<	ForceField* ff, Globals* simParams) :
73	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
87	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
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) {
79	<
80	<
81	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
96	<	MoleculeStamp* molStamp;
97	<	int nMolWithSameStamp;
98	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
99	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
100	<	CutoffGroupStamp* cgStamp;
101	<	RigidBodyStamp* rbStamp;
102	<	int nRigidAtoms = 0;
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77	>	nGlobalTorsions_(0), nGlobalInversions_(0), nAtoms_(0), nBonds_(0),
78	>	nBends_(0), nTorsions_(0), nInversions_(0), nRigidBodies_(0),
79	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
80	>	nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
81	>	calcBoxDipole_(false), useAtomicVirial_(true) {
82
83	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
84	<	molStamp = i->first;
85	<	nMolWithSameStamp = i->second;
86	<
87	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
88	<
89	<	//calculate atoms in molecules
90	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
91	<
92	<
93	<	//calculate atoms in cutoff groups
94	<	int nAtomsInGroups = 0;
95	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
96	<
97	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
98	<	cgStamp = molStamp->getCutoffGroup(j);
99	<	nAtomsInGroups += cgStamp->getNMembers();
100	<	}
122	<
123	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
124	<
125	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
126	<
127	<	//calculate atoms in rigid bodies
128	<	int nAtomsInRigidBodies = 0;
129	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130	<
131	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
132	<	rbStamp = molStamp->getRigidBody(j);
133	<	nAtomsInRigidBodies += rbStamp->getNMembers();
134	<	}
135	<
136	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138	<
83	>	MoleculeStamp* molStamp;
84	>	int nMolWithSameStamp;
85	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
87	>	CutoffGroupStamp* cgStamp;
88	>	RigidBodyStamp* rbStamp;
89	>	int nRigidAtoms = 0;
90	>
91	>	vector<Component*> components = simParams->getComponents();
92	>
93	>	for (vector<Component*>::iterator i = components.begin();
94	>	i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	if ( (*i)->haveRegion() ) {
97	>	molStamp->setRegion( (*i)->getRegion() );
98	>	} else {
99	>	// set the region to a disallowed value:
100	>	molStamp->setRegion( -1 );
101		}
102
103	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
104	<	//group therefore the total number of cutoff groups in the system is
105	<	//equal to the total number of atoms minus number of atoms belong to
106	<	//cutoff group defined in meta-data file plus the number of cutoff
107	<	//groups defined in meta-data file
108	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
109	<
110	<	//every free atom (atom does not belong to rigid bodies) is an
111	<	//integrable object therefore the total number of integrable objects
112	<	//in the system is equal to the total number of atoms minus number of
113	<	//atoms belong to rigid body defined in meta-data file plus the number
114	<	//of rigid bodies defined in meta-data file
115	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
116	<	+ nGlobalRigidBodies_;
117	<
118	<	nGlobalMols_ = molStampIds_.size();
119	<
120	<	#ifdef IS_MPI
121	<	molToProcMap_.resize(nGlobalMols_);
122	<	#endif
123	<
103	>	nMolWithSameStamp = (*i)->getNMol();
104	>
105	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
106	>
107	>	//calculate atoms in molecules
108	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
109	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
110	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
111	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
112	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
113	>
114	>	//calculate atoms in cutoff groups
115	>	int nAtomsInGroups = 0;
116	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
117	>
118	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
119	>	cgStamp = molStamp->getCutoffGroupStamp(j);
120	>	nAtomsInGroups += cgStamp->getNMembers();
121	>	}
122	>
123	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
124	>
125	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
126	>
127	>	//calculate atoms in rigid bodies
128	>	int nAtomsInRigidBodies = 0;
129	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130	>
131	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
132	>	rbStamp = molStamp->getRigidBodyStamp(j);
133	>	nAtomsInRigidBodies += rbStamp->getNMembers();
134	>	}
135	>
136	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138	>
139		}
140	+
141	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
142	+	//group therefore the total number of cutoff groups in the system is
143	+	//equal to the total number of atoms minus number of atoms belong to
144	+	//cutoff group defined in meta-data file plus the number of cutoff
145	+	//groups defined in meta-data file
146
147	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148	+
149	+	//every free atom (atom does not belong to rigid bodies) is an
150	+	//integrable object therefore the total number of integrable objects
151	+	//in the system is equal to the total number of atoms minus number of
152	+	//atoms belong to rigid body defined in meta-data file plus the number
153	+	//of rigid bodies defined in meta-data file
154	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	+	+ nGlobalRigidBodies_;
156	+
157	+	nGlobalMols_ = molStampIds_.size();
158	+	molToProcMap_.resize(nGlobalMols_);
159	+	}
160	+
161		SimInfo::~SimInfo() {
162	<	std::map<int, Molecule*>::iterator i;
162	>	map<int, Molecule*>::iterator i;
163		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
164		delete i->second;
165		}
166		molecules_.clear();
167
171	–	delete stamps_;
168		delete sman_;
169		delete simParams_;
170		delete forceField_;
171		}
172
177	–	int SimInfo::getNGlobalConstraints() {
178	–	int nGlobalConstraints;
179	–	#ifdef IS_MPI
180	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
181	–	MPI_COMM_WORLD);
182	–	#else
183	–	nGlobalConstraints =  nConstraints_;
184	–	#endif
185	–	return nGlobalConstraints;
186	–	}
173
174		bool SimInfo::addMolecule(Molecule* mol) {
175		MoleculeIterator i;
176	<
176	>
177		i = molecules_.find(mol->getGlobalIndex());
178		if (i == molecules_.end() ) {
179	<
180	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
181	<
179	>
180	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
181	>
182		nAtoms_ += mol->getNAtoms();
183		nBonds_ += mol->getNBonds();
184		nBends_ += mol->getNBends();
185		nTorsions_ += mol->getNTorsions();
186	+	nInversions_ += mol->getNInversions();
187		nRigidBodies_ += mol->getNRigidBodies();
188		nIntegrableObjects_ += mol->getNIntegrableObjects();
189		nCutoffGroups_ += mol->getNCutoffGroups();
190		nConstraints_ += mol->getNConstraintPairs();
191	<
192	<	addExcludePairs(mol);
193	<
191	>
192	>	addInteractionPairs(mol);
193	>
194		return true;
195		} else {
196		return false;
197		}
198		}
199	<
199	>
200		bool SimInfo::removeMolecule(Molecule* mol) {
201		MoleculeIterator i;
202		i = molecules_.find(mol->getGlobalIndex());
#	Line 222 | Line 209 | namespace oopse {
209		nBonds_ -= mol->getNBonds();
210		nBends_ -= mol->getNBends();
211		nTorsions_ -= mol->getNTorsions();
212	+	nInversions_ -= mol->getNInversions();
213		nRigidBodies_ -= mol->getNRigidBodies();
214		nIntegrableObjects_ -= mol->getNIntegrableObjects();
215		nCutoffGroups_ -= mol->getNCutoffGroups();
216		nConstraints_ -= mol->getNConstraintPairs();
217
218	<	removeExcludePairs(mol);
218	>	removeInteractionPairs(mol);
219		molecules_.erase(mol->getGlobalIndex());
220
221		delete mol;
#	Line 236 | Line 224 | namespace oopse {
224		} else {
225		return false;
226		}
239	–
240	–
227		}
228
229
#	Line 253 | Line 239 | namespace oopse {
239
240
241		void SimInfo::calcNdf() {
242	<	int ndf_local;
242	>	int ndf_local, nfq_local;
243		MoleculeIterator i;
244	<	std::vector<StuntDouble*>::iterator j;
244	>	vector<StuntDouble*>::iterator j;
245	>	vector<Atom*>::iterator k;
246	>
247		Molecule* mol;
248	<	StuntDouble* integrableObject;
248	>	StuntDouble* sd;
249	>	Atom* atom;
250
251		ndf_local = 0;
252	+	nfq_local = 0;
253
254		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
265	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
266	–	integrableObject = mol->nextIntegrableObject(j)) {
255
256	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
257	+	sd = mol->nextIntegrableObject(j)) {
258	+
259		ndf_local += 3;
260
261	<	if (integrableObject->isDirectional()) {
262	<	if (integrableObject->isLinear()) {
261	>	if (sd->isDirectional()) {
262	>	if (sd->isLinear()) {
263		ndf_local += 2;
264		} else {
265		ndf_local += 3;
266		}
267		}
268	<
269	<	}//end for (integrableObject)
270	<	}// end for (mol)
268	>	}
269	>
270	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
271	>	atom = mol->nextFluctuatingCharge(k)) {
272	>	if (atom->isFluctuatingCharge()) {
273	>	nfq_local++;
274	>	}
275	>	}
276	>	}
277
278	+	ndfLocal_ = ndf_local;
279	+
280		// n_constraints is local, so subtract them on each processor
281		ndf_local -= nConstraints_;
282
283		#ifdef IS_MPI
284	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
285	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
286	>	MPI::INT, MPI::SUM);
287		#else
288		ndf_ = ndf_local;
289	+	nGlobalFluctuatingCharges_ = nfq_local;
290		#endif
291
292		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 293 | Line 295 | namespace oopse {
295
296		}
297
298	+	int SimInfo::getFdf() {
299	+	#ifdef IS_MPI
300	+	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
301	+	#else
302	+	fdf_ = fdf_local;
303	+	#endif
304	+	return fdf_;
305	+	}
306	+
307	+	unsigned int SimInfo::getNLocalCutoffGroups(){
308	+	int nLocalCutoffAtoms = 0;
309	+	Molecule* mol;
310	+	MoleculeIterator mi;
311	+	CutoffGroup* cg;
312	+	Molecule::CutoffGroupIterator ci;
313	+
314	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
315	+
316	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
317	+	cg = mol->nextCutoffGroup(ci)) {
318	+	nLocalCutoffAtoms += cg->getNumAtom();
319	+
320	+	}
321	+	}
322	+
323	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
324	+	}
325	+
326		void SimInfo::calcNdfRaw() {
327		int ndfRaw_local;
328
329		MoleculeIterator i;
330	<	std::vector<StuntDouble*>::iterator j;
330	>	vector<StuntDouble*>::iterator j;
331		Molecule* mol;
332	<	StuntDouble* integrableObject;
332	>	StuntDouble* sd;
333
334		// Raw degrees of freedom that we have to set
335		ndfRaw_local = 0;
336
337		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
308	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
309	–	integrableObject = mol->nextIntegrableObject(j)) {
338
339	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
340	+	sd = mol->nextIntegrableObject(j)) {
341	+
342		ndfRaw_local += 3;
343
344	<	if (integrableObject->isDirectional()) {
345	<	if (integrableObject->isLinear()) {
344	>	if (sd->isDirectional()) {
345	>	if (sd->isLinear()) {
346		ndfRaw_local += 2;
347		} else {
348		ndfRaw_local += 3;
#	Line 322 | Line 353 | namespace oopse {
353		}
354
355		#ifdef IS_MPI
356	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
357		#else
358		ndfRaw_ = ndfRaw_local;
359		#endif
#	Line 335 | Line 366 | namespace oopse {
366
367
368		#ifdef IS_MPI
369	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
369	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
370	>	MPI::INT, MPI::SUM);
371		#else
372		ndfTrans_ = ndfTrans_local;
373		#endif
#	Line 344 | Line 376 | namespace oopse {
376
377		}
378
379	<	void SimInfo::addExcludePairs(Molecule* mol) {
380	<	std::vector<Bond*>::iterator bondIter;
381	<	std::vector<Bend*>::iterator bendIter;
382	<	std::vector<Torsion*>::iterator torsionIter;
379	>	void SimInfo::addInteractionPairs(Molecule* mol) {
380	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
381	>	vector<Bond*>::iterator bondIter;
382	>	vector<Bend*>::iterator bendIter;
383	>	vector<Torsion*>::iterator torsionIter;
384	>	vector<Inversion*>::iterator inversionIter;
385		Bond* bond;
386		Bend* bend;
387		Torsion* torsion;
388	+	Inversion* inversion;
389		int a;
390		int b;
391		int c;
392		int d;
393
394	<	std::map<int, std::set<int> > atomGroups;
394	>	// atomGroups can be used to add special interaction maps between
395	>	// groups of atoms that are in two separate rigid bodies.
396	>	// However, most site-site interactions between two rigid bodies
397	>	// are probably not special, just the ones between the physically
398	>	// bonded atoms.  Interactions *within* a single rigid body should
399	>	// always be excluded.  These are done at the bottom of this
400	>	// function.
401
402	+	map<int, set<int> > atomGroups;
403		Molecule::RigidBodyIterator rbIter;
404		RigidBody* rb;
405		Molecule::IntegrableObjectIterator ii;
406	<	StuntDouble* integrableObject;
406	>	StuntDouble* sd;
407
408	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
409	<	integrableObject = mol->nextIntegrableObject(ii)) {
410	<
411	<	if (integrableObject->isRigidBody()) {
412	<	rb = static_cast<RigidBody*>(integrableObject);
413	<	std::vector<Atom*> atoms = rb->getAtoms();
414	<	std::set<int> rigidAtoms;
415	<	for (int i = 0; i < atoms.size(); ++i) {
416	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
417	<	}
418	<	for (int i = 0; i < atoms.size(); ++i) {
419	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
420	<	}
408	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
409	>	sd = mol->nextIntegrableObject(ii)) {
410	>
411	>	if (sd->isRigidBody()) {
412	>	rb = static_cast<RigidBody*>(sd);
413	>	vector<Atom*> atoms = rb->getAtoms();
414	>	set<int> rigidAtoms;
415	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
416	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
417	>	}
418	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
419	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
420	>	}
421		} else {
422	<	std::set<int> oneAtomSet;
423	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
424	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
422	>	set<int> oneAtomSet;
423	>	oneAtomSet.insert(sd->getGlobalIndex());
424	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
425		}
426		}
427
428	<
429	<
430	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
428	>
429	>	for (bond= mol->beginBond(bondIter); bond != NULL;
430	>	bond = mol->nextBond(bondIter)) {
431	>
432		a = bond->getAtomA()->getGlobalIndex();
433	<	b = bond->getAtomB()->getGlobalIndex();
434	<	exclude_.addPair(a, b);
433	>	b = bond->getAtomB()->getGlobalIndex();
434	>
435	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436	>	oneTwoInteractions_.addPair(a, b);
437	>	} else {
438	>	excludedInteractions_.addPair(a, b);
439	>	}
440		}
441
442	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
442	>	for (bend= mol->beginBend(bendIter); bend != NULL;
443	>	bend = mol->nextBend(bendIter)) {
444	>
445		a = bend->getAtomA()->getGlobalIndex();
446		b = bend->getAtomB()->getGlobalIndex();
447		c = bend->getAtomC()->getGlobalIndex();
398	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
399	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
400	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
401	–
402	–	exclude_.addPairs(rigidSetA, rigidSetB);
403	–	exclude_.addPairs(rigidSetA, rigidSetC);
404	–	exclude_.addPairs(rigidSetB, rigidSetC);
448
449	<	//exclude_.addPair(a, b);
450	<	//exclude_.addPair(a, c);
451	<	//exclude_.addPair(b, c);
449	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
450	>	oneTwoInteractions_.addPair(a, b);
451	>	oneTwoInteractions_.addPair(b, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, b);
454	>	excludedInteractions_.addPair(b, c);
455	>	}
456	>
457	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
458	>	oneThreeInteractions_.addPair(a, c);
459	>	} else {
460	>	excludedInteractions_.addPair(a, c);
461	>	}
462		}
463
464	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
464	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
465	>	torsion = mol->nextTorsion(torsionIter)) {
466	>
467		a = torsion->getAtomA()->getGlobalIndex();
468		b = torsion->getAtomB()->getGlobalIndex();
469		c = torsion->getAtomC()->getGlobalIndex();
470	<	d = torsion->getAtomD()->getGlobalIndex();
416	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
417	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
418	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
419	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
470	>	d = torsion->getAtomD()->getGlobalIndex();
471
472	<	exclude_.addPairs(rigidSetA, rigidSetB);
473	<	exclude_.addPairs(rigidSetA, rigidSetC);
474	<	exclude_.addPairs(rigidSetA, rigidSetD);
475	<	exclude_.addPairs(rigidSetB, rigidSetC);
476	<	exclude_.addPairs(rigidSetB, rigidSetD);
477	<	exclude_.addPairs(rigidSetC, rigidSetD);
472	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
473	>	oneTwoInteractions_.addPair(a, b);
474	>	oneTwoInteractions_.addPair(b, c);
475	>	oneTwoInteractions_.addPair(c, d);
476	>	} else {
477	>	excludedInteractions_.addPair(a, b);
478	>	excludedInteractions_.addPair(b, c);
479	>	excludedInteractions_.addPair(c, d);
480	>	}
481
482	<	/*
483	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
484	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
485	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
486	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
487	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
488	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
489	<
490	<
491	<	exclude_.addPair(a, b);
492	<	exclude_.addPair(a, c);
493	<	exclude_.addPair(a, d);
494	<	exclude_.addPair(b, c);
441	<	exclude_.addPair(b, d);
442	<	exclude_.addPair(c, d);
443	<	*/
482	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
483	>	oneThreeInteractions_.addPair(a, c);
484	>	oneThreeInteractions_.addPair(b, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, c);
487	>	excludedInteractions_.addPair(b, d);
488	>	}
489	>
490	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
491	>	oneFourInteractions_.addPair(a, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, d);
494	>	}
495		}
496
497	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
498	<	std::vector<Atom*> atoms = rb->getAtoms();
499	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
500	<	for (int j = i + 1; j < atoms.size(); ++j) {
497	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
498	>	inversion = mol->nextInversion(inversionIter)) {
499	>
500	>	a = inversion->getAtomA()->getGlobalIndex();
501	>	b = inversion->getAtomB()->getGlobalIndex();
502	>	c = inversion->getAtomC()->getGlobalIndex();
503	>	d = inversion->getAtomD()->getGlobalIndex();
504	>
505	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
506	>	oneTwoInteractions_.addPair(a, b);
507	>	oneTwoInteractions_.addPair(a, c);
508	>	oneTwoInteractions_.addPair(a, d);
509	>	} else {
510	>	excludedInteractions_.addPair(a, b);
511	>	excludedInteractions_.addPair(a, c);
512	>	excludedInteractions_.addPair(a, d);
513	>	}
514	>
515	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
516	>	oneThreeInteractions_.addPair(b, c);
517	>	oneThreeInteractions_.addPair(b, d);
518	>	oneThreeInteractions_.addPair(c, d);
519	>	} else {
520	>	excludedInteractions_.addPair(b, c);
521	>	excludedInteractions_.addPair(b, d);
522	>	excludedInteractions_.addPair(c, d);
523	>	}
524	>	}
525	>
526	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
527	>	rb = mol->nextRigidBody(rbIter)) {
528	>	vector<Atom*> atoms = rb->getAtoms();
529	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
530	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
531		a = atoms[i]->getGlobalIndex();
532		b = atoms[j]->getGlobalIndex();
533	<	exclude_.addPair(a, b);
533	>	excludedInteractions_.addPair(a, b);
534		}
535		}
536		}
537
538		}
539
540	<	void SimInfo::removeExcludePairs(Molecule* mol) {
541	<	std::vector<Bond*>::iterator bondIter;
542	<	std::vector<Bend*>::iterator bendIter;
543	<	std::vector<Torsion*>::iterator torsionIter;
540	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
541	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
542	>	vector<Bond*>::iterator bondIter;
543	>	vector<Bend*>::iterator bendIter;
544	>	vector<Torsion*>::iterator torsionIter;
545	>	vector<Inversion*>::iterator inversionIter;
546		Bond* bond;
547		Bend* bend;
548		Torsion* torsion;
549	+	Inversion* inversion;
550		int a;
551		int b;
552		int c;
553		int d;
554
555	<	std::map<int, std::set<int> > atomGroups;
472	<
555	>	map<int, set<int> > atomGroups;
556		Molecule::RigidBodyIterator rbIter;
557		RigidBody* rb;
558		Molecule::IntegrableObjectIterator ii;
559	<	StuntDouble* integrableObject;
559	>	StuntDouble* sd;
560
561	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
562	<	integrableObject = mol->nextIntegrableObject(ii)) {
563	<
564	<	if (integrableObject->isRigidBody()) {
565	<	rb = static_cast<RigidBody*>(integrableObject);
566	<	std::vector<Atom*> atoms = rb->getAtoms();
567	<	std::set<int> rigidAtoms;
568	<	for (int i = 0; i < atoms.size(); ++i) {
569	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
570	<	}
571	<	for (int i = 0; i < atoms.size(); ++i) {
572	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
573	<	}
561	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
562	>	sd = mol->nextIntegrableObject(ii)) {
563	>
564	>	if (sd->isRigidBody()) {
565	>	rb = static_cast<RigidBody*>(sd);
566	>	vector<Atom*> atoms = rb->getAtoms();
567	>	set<int> rigidAtoms;
568	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
569	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
570	>	}
571	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
572	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
573	>	}
574		} else {
575	<	std::set<int> oneAtomSet;
576	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
577	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
575	>	set<int> oneAtomSet;
576	>	oneAtomSet.insert(sd->getGlobalIndex());
577	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
578		}
579		}
580
581	<
582	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
581	>	for (bond= mol->beginBond(bondIter); bond != NULL;
582	>	bond = mol->nextBond(bondIter)) {
583	>
584		a = bond->getAtomA()->getGlobalIndex();
585	<	b = bond->getAtomB()->getGlobalIndex();
586	<	exclude_.removePair(a, b);
585	>	b = bond->getAtomB()->getGlobalIndex();
586	>
587	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
588	>	oneTwoInteractions_.removePair(a, b);
589	>	} else {
590	>	excludedInteractions_.removePair(a, b);
591	>	}
592		}
593
594	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
594	>	for (bend= mol->beginBend(bendIter); bend != NULL;
595	>	bend = mol->nextBend(bendIter)) {
596	>
597		a = bend->getAtomA()->getGlobalIndex();
598		b = bend->getAtomB()->getGlobalIndex();
599		c = bend->getAtomC()->getGlobalIndex();
509	–
510	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
511	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
512	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
513	–
514	–	exclude_.removePairs(rigidSetA, rigidSetB);
515	–	exclude_.removePairs(rigidSetA, rigidSetC);
516	–	exclude_.removePairs(rigidSetB, rigidSetC);
600
601	<	//exclude_.removePair(a, b);
602	<	//exclude_.removePair(a, c);
603	<	//exclude_.removePair(b, c);
601	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
602	>	oneTwoInteractions_.removePair(a, b);
603	>	oneTwoInteractions_.removePair(b, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, b);
606	>	excludedInteractions_.removePair(b, c);
607	>	}
608	>
609	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
610	>	oneThreeInteractions_.removePair(a, c);
611	>	} else {
612	>	excludedInteractions_.removePair(a, c);
613	>	}
614		}
615
616	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
616	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
617	>	torsion = mol->nextTorsion(torsionIter)) {
618	>
619		a = torsion->getAtomA()->getGlobalIndex();
620		b = torsion->getAtomB()->getGlobalIndex();
621		c = torsion->getAtomC()->getGlobalIndex();
622	<	d = torsion->getAtomD()->getGlobalIndex();
622	>	d = torsion->getAtomD()->getGlobalIndex();
623	>
624	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
625	>	oneTwoInteractions_.removePair(a, b);
626	>	oneTwoInteractions_.removePair(b, c);
627	>	oneTwoInteractions_.removePair(c, d);
628	>	} else {
629	>	excludedInteractions_.removePair(a, b);
630	>	excludedInteractions_.removePair(b, c);
631	>	excludedInteractions_.removePair(c, d);
632	>	}
633
634	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
635	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
636	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
637	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
634	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
635	>	oneThreeInteractions_.removePair(a, c);
636	>	oneThreeInteractions_.removePair(b, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, c);
639	>	excludedInteractions_.removePair(b, d);
640	>	}
641
642	<	exclude_.removePairs(rigidSetA, rigidSetB);
643	<	exclude_.removePairs(rigidSetA, rigidSetC);
644	<	exclude_.removePairs(rigidSetA, rigidSetD);
645	<	exclude_.removePairs(rigidSetB, rigidSetC);
646	<	exclude_.removePairs(rigidSetB, rigidSetD);
647	<	exclude_.removePairs(rigidSetC, rigidSetD);
642	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
643	>	oneFourInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, d);
646	>	}
647	>	}
648
649	<	/*
650	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
651	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
652	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
653	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
654	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
655	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
649	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
650	>	inversion = mol->nextInversion(inversionIter)) {
651	>
652	>	a = inversion->getAtomA()->getGlobalIndex();
653	>	b = inversion->getAtomB()->getGlobalIndex();
654	>	c = inversion->getAtomC()->getGlobalIndex();
655	>	d = inversion->getAtomD()->getGlobalIndex();
656
657	<
658	<	exclude_.removePair(a, b);
659	<	exclude_.removePair(a, c);
660	<	exclude_.removePair(a, d);
661	<	exclude_.removePair(b, c);
662	<	exclude_.removePair(b, d);
663	<	exclude_.removePair(c, d);
664	<	*/
657	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
658	>	oneTwoInteractions_.removePair(a, b);
659	>	oneTwoInteractions_.removePair(a, c);
660	>	oneTwoInteractions_.removePair(a, d);
661	>	} else {
662	>	excludedInteractions_.removePair(a, b);
663	>	excludedInteractions_.removePair(a, c);
664	>	excludedInteractions_.removePair(a, d);
665	>	}
666	>
667	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
668	>	oneThreeInteractions_.removePair(b, c);
669	>	oneThreeInteractions_.removePair(b, d);
670	>	oneThreeInteractions_.removePair(c, d);
671	>	} else {
672	>	excludedInteractions_.removePair(b, c);
673	>	excludedInteractions_.removePair(b, d);
674	>	excludedInteractions_.removePair(c, d);
675	>	}
676		}
677
678	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
679	<	std::vector<Atom*> atoms = rb->getAtoms();
680	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
681	<	for (int j = i + 1; j < atoms.size(); ++j) {
678	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
679	>	rb = mol->nextRigidBody(rbIter)) {
680	>	vector<Atom*> atoms = rb->getAtoms();
681	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
682	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
683		a = atoms[i]->getGlobalIndex();
684		b = atoms[j]->getGlobalIndex();
685	<	exclude_.removePair(a, b);
685	>	excludedInteractions_.removePair(a, b);
686		}
687		}
688		}
689	<
689	>
690		}
691	<
692	<
691	>
692	>
693		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
694		int curStampId;
695	<
695	>
696		//index from 0
697		curStampId = moleculeStamps_.size();
698
#	Line 580 | Line 700 | namespace oopse {
700		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
701		}
702
583	–	void SimInfo::update() {
703
704	<	setupSimType();
705	<
706	<	#ifdef IS_MPI
707	<	setupFortranParallel();
708	<	#endif
709	<
710	<	setupFortranSim();
711	<
712	<	//setup fortran force field
594	<	/** @deprecate */
595	<	int isError = 0;
596	<
597	<	setupElectrostaticSummationMethod( isError );
598	<	setupSwitchingFunction();
599	<
600	<	if(isError){
601	<	sprintf( painCave.errMsg,
602	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
603	<	painCave.isFatal = 1;
604	<	simError();
605	<	}
606	<
607	<
608	<	setupCutoff();
609	<
704	>	/**
705	>	* update
706	>	*
707	>	*  Performs the global checks and variable settings after the
708	>	*  objects have been created.
709	>	*
710	>	*/
711	>	void SimInfo::update() {
712	>	setupSimVariables();
713		calcNdf();
714		calcNdfRaw();
715		calcNdfTrans();
613	–
614	–	fortranInitialized_ = true;
716		}
717	<
718	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
717	>
718	>	/**
719	>	* getSimulatedAtomTypes
720	>	*
721	>	* Returns an STL set of AtomType* that are actually present in this
722	>	* simulation.  Must query all processors to assemble this information.
723	>	*
724	>	*/
725	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
726		SimInfo::MoleculeIterator mi;
727		Molecule* mol;
728		Molecule::AtomIterator ai;
729		Atom* atom;
730	<	std::set<AtomType*> atomTypes;
731	<
730	>	set<AtomType*> atomTypes;
731	>
732		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
733	<
734	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
733	>	for(atom = mol->beginAtom(ai); atom != NULL;
734	>	atom = mol->nextAtom(ai)) {
735		atomTypes.insert(atom->getAtomType());
736	<	}
737	<
736	>	}
737	>	}
738	>
739	>	#ifdef IS_MPI
740	>
741	>	// loop over the found atom types on this processor, and add their
742	>	// numerical idents to a vector:
743	>
744	>	vector<int> foundTypes;
745	>	set<AtomType*>::iterator i;
746	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
747	>	foundTypes.push_back( (*i)->getIdent() );
748	>
749	>	// count_local holds the number of found types on this processor
750	>	int count_local = foundTypes.size();
751	>
752	>	int nproc = MPI::COMM_WORLD.Get_size();
753	>
754	>	// we need arrays to hold the counts and displacement vectors for
755	>	// all processors
756	>	vector<int> counts(nproc, 0);
757	>	vector<int> disps(nproc, 0);
758	>
759	>	// fill the counts array
760	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
761	>	1, MPI::INT);
762	>
763	>	// use the processor counts to compute the displacement array
764	>	disps[0] = 0;
765	>	int totalCount = counts[0];
766	>	for (int iproc = 1; iproc < nproc; iproc++) {
767	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
768	>	totalCount += counts[iproc];
769		}
770
771	+	// we need a (possibly redundant) set of all found types:
772	+	vector<int> ftGlobal(totalCount);
773	+
774	+	// now spray out the foundTypes to all the other processors:
775	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
776	+	&ftGlobal[0], &counts[0], &disps[0],
777	+	MPI::INT);
778	+
779	+	vector<int>::iterator j;
780	+
781	+	// foundIdents is a stl set, so inserting an already found ident
782	+	// will have no effect.
783	+	set<int> foundIdents;
784	+
785	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
786	+	foundIdents.insert((*j));
787	+
788	+	// now iterate over the foundIdents and get the actual atom types
789	+	// that correspond to these:
790	+	set<int>::iterator it;
791	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
792	+	atomTypes.insert( forceField_->getAtomType((*it)) );
793	+
794	+	#endif
795	+
796		return atomTypes;
797		}
798
635	–	void SimInfo::setupSimType() {
636	–	std::set<AtomType*>::iterator i;
637	–	std::set<AtomType*> atomTypes;
638	–	atomTypes = getUniqueAtomTypes();
639	–
640	–	int useLennardJones = 0;
641	–	int useElectrostatic = 0;
642	–	int useEAM = 0;
643	–	int useSC = 0;
644	–	int useCharge = 0;
645	–	int useDirectional = 0;
646	–	int useDipole = 0;
647	–	int useGayBerne = 0;
648	–	int useSticky = 0;
649	–	int useStickyPower = 0;
650	–	int useShape = 0;
651	–	int useFLARB = 0; //it is not in AtomType yet
652	–	int useDirectionalAtom = 0;
653	–	int useElectrostatics = 0;
654	–	//usePBC and useRF are from simParams
655	–	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
656	–	int useRF;
657	–	int useSF;
658	–	std::string myMethod;
799
800	<	// set the useRF logical
801	<	useRF = 0;
802	<	useSF = 0;
800	>	int getGlobalCountOfType(AtomType* atype) {
801	>	/*
802	>	set<AtomType*> atypes = getSimulatedAtomTypes();
803	>	map<AtomType*, int> counts_;
804
805	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
806	+	for(atom = mol->beginAtom(ai); atom != NULL;
807	+	atom = mol->nextAtom(ai)) {
808	+	atom->getAtomType();
809	+	}
810	+	}
811	+	*/
812	+	return 0;
813	+	}
814
815	<	if (simParams_->haveElectrostaticSummationMethod()) {
816	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
817	<	toUpper(myMethod);
818	<	if (myMethod == "REACTION_FIELD") {
819	<	useRF=1;
820	<	} else {
821	<	if (myMethod == "SHIFTED_FORCE") {
822	<	useSF = 1;
673	<	}
815	>	void SimInfo::setupSimVariables() {
816	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
817	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
818	>	// parameter is true
819	>	calcBoxDipole_ = false;
820	>	if ( simParams_->haveAccumulateBoxDipole() )
821	>	if ( simParams_->getAccumulateBoxDipole() ) {
822	>	calcBoxDipole_ = true;
823		}
824	<	}
825	<
824	>
825	>	set<AtomType*>::iterator i;
826	>	set<AtomType*> atomTypes;
827	>	atomTypes = getSimulatedAtomTypes();
828	>	bool usesElectrostatic = false;
829	>	bool usesMetallic = false;
830	>	bool usesDirectional = false;
831	>	bool usesFluctuatingCharges =  false;
832		//loop over all of the atom types
833		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
834	<	useLennardJones |= (*i)->isLennardJones();
835	<	useElectrostatic |= (*i)->isElectrostatic();
836	<	useEAM |= (*i)->isEAM();
837	<	useSC |= (*i)->isSC();
683	<	useCharge |= (*i)->isCharge();
684	<	useDirectional |= (*i)->isDirectional();
685	<	useDipole |= (*i)->isDipole();
686	<	useGayBerne |= (*i)->isGayBerne();
687	<	useSticky |= (*i)->isSticky();
688	<	useStickyPower |= (*i)->isStickyPower();
689	<	useShape |= (*i)->isShape();
834	>	usesElectrostatic |= (*i)->isElectrostatic();
835	>	usesMetallic |= (*i)->isMetal();
836	>	usesDirectional |= (*i)->isDirectional();
837	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
838		}
839
840	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
841	<	useDirectionalAtom = 1;
842	<	}
840	>	#ifdef IS_MPI
841	>	bool temp;
842	>	temp = usesDirectional;
843	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
844	>	MPI::LOR);
845	>
846	>	temp = usesMetallic;
847	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
848	>	MPI::LOR);
849	>
850	>	temp = usesElectrostatic;
851	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
852	>	MPI::LOR);
853
854	<	if (useCharge || useDipole) {
855	<	useElectrostatics = 1;
856	<	}
854	>	temp = usesFluctuatingCharges;
855	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
856	>	MPI::LOR);
857	>	#else
858
859	<	#ifdef IS_MPI
860	<	int temp;
859	>	usesDirectionalAtoms_ = usesDirectional;
860	>	usesMetallicAtoms_ = usesMetallic;
861	>	usesElectrostaticAtoms_ = usesElectrostatic;
862	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
863
864	<	temp = usePBC;
865	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	#endif
865	>
866	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
867	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
868	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
869	>	}
870
706	–	temp = useDirectionalAtom;
707	–	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
871
872	<	temp = useLennardJones;
873	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
872	>	vector<int> SimInfo::getGlobalAtomIndices() {
873	>	SimInfo::MoleculeIterator mi;
874	>	Molecule* mol;
875	>	Molecule::AtomIterator ai;
876	>	Atom* atom;
877
878	<	temp = useElectrostatics;
713	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
714	<
715	<	temp = useCharge;
716	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
717	<
718	<	temp = useDipole;
719	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
720	<
721	<	temp = useSticky;
722	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
723	<
724	<	temp = useStickyPower;
725	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
878	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
879
880	<	temp = useGayBerne;
881	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
880	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
881	>
882	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
884	>	}
885	>	}
886	>	return GlobalAtomIndices;
887	>	}
888
730	–	temp = useEAM;
731	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
889
890	<	temp = useSC;
891	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
892	<
893	<	temp = useShape;
894	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
890	>	vector<int> SimInfo::getGlobalGroupIndices() {
891	>	SimInfo::MoleculeIterator mi;
892	>	Molecule* mol;
893	>	Molecule::CutoffGroupIterator ci;
894	>	CutoffGroup* cg;
895
896	<	temp = useFLARB;
897	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
898	<
742	<	temp = useRF;
743	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744	<
745	<	temp = useSF;
746	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
747	<
748	<	#endif
749	<
750	<	fInfo_.SIM_uses_PBC = usePBC;
751	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
752	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
753	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
754	<	fInfo_.SIM_uses_Charges = useCharge;
755	<	fInfo_.SIM_uses_Dipoles = useDipole;
756	<	fInfo_.SIM_uses_Sticky = useSticky;
757	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
758	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
759	<	fInfo_.SIM_uses_EAM = useEAM;
760	<	fInfo_.SIM_uses_SC = useSC;
761	<	fInfo_.SIM_uses_Shapes = useShape;
762	<	fInfo_.SIM_uses_FLARB = useFLARB;
763	<	fInfo_.SIM_uses_RF = useRF;
764	<	fInfo_.SIM_uses_SF = useSF;
765	<
766	<	if( myMethod == "REACTION_FIELD") {
896	>	vector<int> GlobalGroupIndices;
897	>
898	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
899
900	<	if (simParams_->haveDielectric()) {
901	<	fInfo_.dielect = simParams_->getDielectric();
902	<	} else {
903	<	sprintf(painCave.errMsg,
904	<	"SimSetup Error: No Dielectric constant was set.\n"
905	<	"\tYou are trying to use Reaction Field without"
774	<	"\tsetting a dielectric constant!\n");
775	<	painCave.isFatal = 1;
776	<	simError();
777	<	}
900	>	//local index of cutoff group is trivial, it only depends on the
901	>	//order of travesing
902	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
903	>	cg = mol->nextCutoffGroup(ci)) {
904	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
905	>	}
906		}
907	<
907	>	return GlobalGroupIndices;
908		}
909
782	–	void SimInfo::setupFortranSim() {
783	–	int isError;
784	–	int nExclude;
785	–	std::vector<int> fortranGlobalGroupMembership;
786	–
787	–	nExclude = exclude_.getSize();
788	–	isError = 0;
910
911	<	//globalGroupMembership_ is filled by SimCreator
791	<	for (int i = 0; i < nGlobalAtoms_; i++) {
792	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
793	<	}
911	>	void SimInfo::prepareTopology() {
912
913		//calculate mass ratio of cutoff group
796	–	std::vector<double> mfact;
914		SimInfo::MoleculeIterator mi;
915		Molecule* mol;
916		Molecule::CutoffGroupIterator ci;
917		CutoffGroup* cg;
918		Molecule::AtomIterator ai;
919		Atom* atom;
920	<	double totalMass;
920	>	RealType totalMass;
921
922	<	//to avoid memory reallocation, reserve enough space for mfact
923	<	mfact.reserve(getNCutoffGroups());
922	>	/**
923	>	* The mass factor is the relative mass of an atom to the total
924	>	* mass of the cutoff group it belongs to.  By default, all atoms
925	>	* are their own cutoff groups, and therefore have mass factors of
926	>	* 1.  We need some special handling for massless atoms, which
927	>	* will be treated as carrying the entire mass of the cutoff
928	>	* group.
929	>	*/
930	>	massFactors_.clear();
931	>	massFactors_.resize(getNAtoms(), 1.0);
932
933		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
934	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
934	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
935	>	cg = mol->nextCutoffGroup(ci)) {
936
937		totalMass = cg->getMass();
938		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
939		// Check for massless groups - set mfact to 1 if true
940	<	if (totalMass != 0)
941	<	mfact.push_back(atom->getMass()/totalMass);
940	>	if (totalMass != 0)
941	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
942		else
943	<	mfact.push_back( 1.0 );
943	>	massFactors_[atom->getLocalIndex()] = 1.0;
944		}
819	–
945		}
946		}
947
948	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
824	<	std::vector<int> identArray;
948	>	// Build the identArray_ and regions_
949
950	<	//to avoid memory reallocation, reserve enough space identArray
951	<	identArray.reserve(getNAtoms());
952	<
953	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
950	>	identArray_.clear();
951	>	identArray_.reserve(getNAtoms());
952	>	regions_.clear();
953	>	regions_.reserve(getNAtoms());
954	>
955	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956	>	int reg = mol->getRegion();
957		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
958	<	identArray.push_back(atom->getIdent());
958	>	identArray_.push_back(atom->getIdent());
959	>	regions_.push_back(reg);
960		}
961		}
962	<
963	<	//fill molMembershipArray
836	<	//molMembershipArray is filled by SimCreator
837	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
838	<	for (int i = 0; i < nGlobalAtoms_; i++) {
839	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
840	<	}
841	<
842	<	//setup fortran simulation
843	<	int nGlobalExcludes = 0;
844	<	int* globalExcludes = NULL;
845	<	int* excludeList = exclude_.getExcludeList();
846	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
847	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
848	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
849	<
850	<	if( isError ){
851	<
852	<	sprintf( painCave.errMsg,
853	<	"There was an error setting the simulation information in fortran.\n" );
854	<	painCave.isFatal = 1;
855	<	painCave.severity = OOPSE_ERROR;
856	<	simError();
857	<	}
858	<
859	<	#ifdef IS_MPI
860	<	sprintf( checkPointMsg,
861	<	"succesfully sent the simulation information to fortran.\n");
862	<	MPIcheckPoint();
863	<	#endif // is_mpi
864	<	}
865	<
866	<
867	<	#ifdef IS_MPI
868	<	void SimInfo::setupFortranParallel() {
869	<
870	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
871	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
872	<	std::vector<int> localToGlobalCutoffGroupIndex;
873	<	SimInfo::MoleculeIterator mi;
874	<	Molecule::AtomIterator ai;
875	<	Molecule::CutoffGroupIterator ci;
876	<	Molecule* mol;
877	<	Atom* atom;
878	<	CutoffGroup* cg;
879	<	mpiSimData parallelData;
880	<	int isError;
881	<
882	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
883	<
884	<	//local index(index in DataStorge) of atom is important
885	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
886	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
887	<	}
888	<
889	<	//local index of cutoff group is trivial, it only depends on the order of travesing
890	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
891	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
892	<	}
893	<
894	<	}
895	<
896	<	//fill up mpiSimData struct
897	<	parallelData.nMolGlobal = getNGlobalMolecules();
898	<	parallelData.nMolLocal = getNMolecules();
899	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
900	<	parallelData.nAtomsLocal = getNAtoms();
901	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
902	<	parallelData.nGroupsLocal = getNCutoffGroups();
903	<	parallelData.myNode = worldRank;
904	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
905	<
906	<	//pass mpiSimData struct and index arrays to fortran
907	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
908	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
909	<	&localToGlobalCutoffGroupIndex[0], &isError);
910	<
911	<	if (isError) {
912	<	sprintf(painCave.errMsg,
913	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
914	<	painCave.isFatal = 1;
915	<	simError();
916	<	}
917	<
918	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
919	<	MPIcheckPoint();
920	<
921	<
922	<	}
923	<
924	<	#endif
925	<
926	<	double SimInfo::calcMaxCutoffRadius() {
927	<
928	<
929	<	std::set<AtomType*> atomTypes;
930	<	std::set<AtomType*>::iterator i;
931	<	std::vector<double> cutoffRadius;
932	<
933	<	//get the unique atom types
934	<	atomTypes = getUniqueAtomTypes();
935	<
936	<	//query the max cutoff radius among these atom types
937	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
938	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939	<	}
940	<
941	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
942	<	#ifdef IS_MPI
943	<	//pick the max cutoff radius among the processors
944	<	#endif
945	<
946	<	return maxCutoffRadius;
947	<	}
948	<
949	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
950	<
951	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
952	<
953	<	if (!simParams_->haveCutoffRadius()){
954	<	sprintf(painCave.errMsg,
955	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
956	<	"\tOOPSE will use a default value of 15.0 angstroms"
957	<	"\tfor the cutoffRadius.\n");
958	<	painCave.isFatal = 0;
959	<	simError();
960	<	rcut = 15.0;
961	<	} else{
962	<	rcut = simParams_->getCutoffRadius();
963	<	}
964	<
965	<	if (!simParams_->haveSwitchingRadius()){
966	<	sprintf(painCave.errMsg,
967	<	"SimCreator Warning: No value was set for switchingRadius.\n"
968	<	"\tOOPSE will use a default value of\n"
969	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
970	<	painCave.isFatal = 0;
971	<	simError();
972	<	rsw = 0.85 * rcut;
973	<	} else{
974	<	rsw = simParams_->getSwitchingRadius();
975	<	}
976	<
977	<	} else {
978	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
979	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
980	<
981	<	if (simParams_->haveCutoffRadius()) {
982	<	rcut = simParams_->getCutoffRadius();
983	<	} else {
984	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
985	<	rcut = calcMaxCutoffRadius();
986	<	}
987	<
988	<	if (simParams_->haveSwitchingRadius()) {
989	<	rsw  = simParams_->getSwitchingRadius();
990	<	} else {
991	<	rsw = rcut;
992	<	}
993	<
994	<	}
995	<	}
996	<
997	<	void SimInfo::setupCutoff() {
998	<	getCutoff(rcut_, rsw_);
999	<	double rnblist = rcut_ + 1; // skin of neighbor list
1000	<
1001	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1002	<
1003	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
1004	<	if (simParams_->haveCutoffPolicy()) {
1005	<	std::string myPolicy = simParams_->getCutoffPolicy();
1006	<	toUpper(myPolicy);
1007	<	if (myPolicy == "MIX") {
1008	<	cp = MIX_CUTOFF_POLICY;
1009	<	} else {
1010	<	if (myPolicy == "MAX") {
1011	<	cp = MAX_CUTOFF_POLICY;
1012	<	} else {
1013	<	if (myPolicy == "TRADITIONAL") {
1014	<	cp = TRADITIONAL_CUTOFF_POLICY;
1015	<	} else {
1016	<	// throw error
1017	<	sprintf( painCave.errMsg,
1018	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1019	<	painCave.isFatal = 1;
1020	<	simError();
1021	<	}
1022	<	}
1023	<	}
1024	<	}
1025	<
1026	<
1027	<	if (simParams_->haveSkinThickness()) {
1028	<	double skinThickness = simParams_->getSkinThickness();
1029	<	}
1030	<
1031	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1032	<	// also send cutoff notification to electrostatics
1033	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
962	>
963	>	topologyDone_ = true;
964		}
965
1036	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1037	–
1038	–	int errorOut;
1039	–	int esm =  NONE;
1040	–	int sm = UNDAMPED;
1041	–	double alphaVal;
1042	–	double dielectric;
1043	–
1044	–	errorOut = isError;
1045	–	alphaVal = simParams_->getDampingAlpha();
1046	–	dielectric = simParams_->getDielectric();
1047	–
1048	–	if (simParams_->haveElectrostaticSummationMethod()) {
1049	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1050	–	toUpper(myMethod);
1051	–	if (myMethod == "NONE") {
1052	–	esm = NONE;
1053	–	} else {
1054	–	if (myMethod == "SWITCHING_FUNCTION") {
1055	–	esm = SWITCHING_FUNCTION;
1056	–	} else {
1057	–	if (myMethod == "SHIFTED_POTENTIAL") {
1058	–	esm = SHIFTED_POTENTIAL;
1059	–	} else {
1060	–	if (myMethod == "SHIFTED_FORCE") {
1061	–	esm = SHIFTED_FORCE;
1062	–	} else {
1063	–	if (myMethod == "REACTION_FIELD") {
1064	–	esm = REACTION_FIELD;
1065	–	} else {
1066	–	// throw error
1067	–	sprintf( painCave.errMsg,
1068	–	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1069	–	painCave.isFatal = 1;
1070	–	simError();
1071	–	}
1072	–	}
1073	–	}
1074	–	}
1075	–	}
1076	–	}
1077	–
1078	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1079	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1080	–	toUpper(myScreen);
1081	–	if (myScreen == "UNDAMPED") {
1082	–	sm = UNDAMPED;
1083	–	} else {
1084	–	if (myScreen == "DAMPED") {
1085	–	sm = DAMPED;
1086	–	if (!simParams_->haveDampingAlpha()) {
1087	–	//throw error
1088	–	sprintf( painCave.errMsg,
1089	–	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1090	–	painCave.isFatal = 0;
1091	–	simError();
1092	–	}
1093	–	} else {
1094	–	// throw error
1095	–	sprintf( painCave.errMsg,
1096	–	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1097	–	painCave.isFatal = 1;
1098	–	simError();
1099	–	}
1100	–	}
1101	–	}
1102	–
1103	–	// let's pass some summation method variables to fortran
1104	–	setElectrostaticSummationMethod( &esm );
1105	–	setScreeningMethod( &sm );
1106	–	setDampingAlpha( &alphaVal );
1107	–	setReactionFieldDielectric( &dielectric );
1108	–	initFortranFF( &esm, &errorOut );
1109	–	}
1110	–
1111	–	void SimInfo::setupSwitchingFunction() {
1112	–	int ft = CUBIC;
1113	–
1114	–	if (simParams_->haveSwitchingFunctionType()) {
1115	–	std::string funcType = simParams_->getSwitchingFunctionType();
1116	–	toUpper(funcType);
1117	–	if (funcType == "CUBIC") {
1118	–	ft = CUBIC;
1119	–	} else {
1120	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1121	–	ft = FIFTH_ORDER_POLY;
1122	–	} else {
1123	–	// throw error
1124	–	sprintf( painCave.errMsg,
1125	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1126	–	painCave.isFatal = 1;
1127	–	simError();
1128	–	}
1129	–	}
1130	–	}
1131	–
1132	–	// send switching function notification to switcheroo
1133	–	setFunctionType(&ft);
1134	–
1135	–	}
1136	–
966		void SimInfo::addProperty(GenericData* genData) {
967		properties_.addProperty(genData);
968		}
969
970	<	void SimInfo::removeProperty(const std::string& propName) {
970	>	void SimInfo::removeProperty(const string& propName) {
971		properties_.removeProperty(propName);
972		}
973
#	Line 1146 | Line 975 | namespace oopse {
975		properties_.clearProperties();
976		}
977
978	<	std::vector<std::string> SimInfo::getPropertyNames() {
978	>	vector<string> SimInfo::getPropertyNames() {
979		return properties_.getPropertyNames();
980		}
981
982	<	std::vector<GenericData*> SimInfo::getProperties() {
982	>	vector<GenericData*> SimInfo::getProperties() {
983		return properties_.getProperties();
984		}
985
986	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
986	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
987		return properties_.getPropertyByName(propName);
988		}
989
#	Line 1165 | Line 994 | namespace oopse {
994		delete sman_;
995		sman_ = sman;
996
1168	–	Molecule* mol;
1169	–	RigidBody* rb;
1170	–	Atom* atom;
997		SimInfo::MoleculeIterator mi;
998	+	Molecule::AtomIterator ai;
999		Molecule::RigidBodyIterator rbIter;
1000	<	Molecule::AtomIterator atomIter;;
1000	>	Molecule::CutoffGroupIterator cgIter;
1001	>	Molecule::BondIterator bondIter;
1002	>	Molecule::BendIterator bendIter;
1003	>	Molecule::TorsionIterator torsionIter;
1004	>	Molecule::InversionIterator inversionIter;
1005
1006	+	Molecule* mol;
1007	+	Atom* atom;
1008	+	RigidBody* rb;
1009	+	CutoffGroup* cg;
1010	+	Bond* bond;
1011	+	Bend* bend;
1012	+	Torsion* torsion;
1013	+	Inversion* inversion;
1014	+
1015		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1016
1017	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1017	>	for (atom = mol->beginAtom(ai); atom != NULL;
1018	>	atom = mol->nextAtom(ai)) {
1019		atom->setSnapshotManager(sman_);
1020	<	}
1021	<
1022	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1020	>	}
1021	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1022	>	rb = mol->nextRigidBody(rbIter)) {
1023		rb->setSnapshotManager(sman_);
1024		}
1025	<	}
1026	<
1025	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1026	>	cg = mol->nextCutoffGroup(cgIter)) {
1027	>	cg->setSnapshotManager(sman_);
1028	>	}
1029	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1030	>	bond = mol->nextBond(bondIter)) {
1031	>	bond->setSnapshotManager(sman_);
1032	>	}
1033	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1034	>	bend = mol->nextBend(bendIter)) {
1035	>	bend->setSnapshotManager(sman_);
1036	>	}
1037	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1038	>	torsion = mol->nextTorsion(torsionIter)) {
1039	>	torsion->setSnapshotManager(sman_);
1040	>	}
1041	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1042	>	inversion = mol->nextInversion(inversionIter)) {
1043	>	inversion->setSnapshotManager(sman_);
1044	>	}
1045	>	}
1046		}
1047
1188	–	Vector3d SimInfo::getComVel(){
1189	–	SimInfo::MoleculeIterator i;
1190	–	Molecule* mol;
1048
1049	<	Vector3d comVel(0.0);
1193	<	double totalMass = 0.0;
1194	<
1195	<
1196	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1197	<	double mass = mol->getMass();
1198	<	totalMass += mass;
1199	<	comVel += mass * mol->getComVel();
1200	<	}
1049	>	ostream& operator <<(ostream& o, SimInfo& info) {
1050
1202	–	#ifdef IS_MPI
1203	–	double tmpMass = totalMass;
1204	–	Vector3d tmpComVel(comVel);
1205	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1206	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1207	–	#endif
1208	–
1209	–	comVel /= totalMass;
1210	–
1211	–	return comVel;
1212	–	}
1213	–
1214	–	Vector3d SimInfo::getCom(){
1215	–	SimInfo::MoleculeIterator i;
1216	–	Molecule* mol;
1217	–
1218	–	Vector3d com(0.0);
1219	–	double totalMass = 0.0;
1220	–
1221	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1222	–	double mass = mol->getMass();
1223	–	totalMass += mass;
1224	–	com += mass * mol->getCom();
1225	–	}
1226	–
1227	–	#ifdef IS_MPI
1228	–	double tmpMass = totalMass;
1229	–	Vector3d tmpCom(com);
1230	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1231	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1232	–	#endif
1233	–
1234	–	com /= totalMass;
1235	–
1236	–	return com;
1237	–
1238	–	}
1239	–
1240	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1241	–
1051		return o;
1052		}
1053
1054	<
1055	<	/*
1056	<	Returns center of mass and center of mass velocity in one function call.
1057	<	*/
1058	<
1059	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1060	<	SimInfo::MoleculeIterator i;
1061	<	Molecule* mol;
1062	<
1063	<
1064	<	double totalMass = 0.0;
1065	<
1054	>
1055	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1056	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1057	>	sprintf(painCave.errMsg,
1058	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1059	>	"\tindex exceeds number of known objects!\n");
1060	>	painCave.isFatal = 1;
1061	>	simError();
1062	>	return NULL;
1063	>	} else
1064	>	return IOIndexToIntegrableObject.at(index);
1065	>	}
1066	>
1067	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1068	>	IOIndexToIntegrableObject= v;
1069	>	}
1070
1071	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1072	<	double mass = mol->getMass();
1260	<	totalMass += mass;
1261	<	com += mass * mol->getCom();
1262	<	comVel += mass * mol->getComVel();
1263	<	}
1264	<
1071	>	int SimInfo::getNGlobalConstraints() {
1072	>	int nGlobalConstraints;
1073		#ifdef IS_MPI
1074	<	double tmpMass = totalMass;
1075	<	Vector3d tmpCom(com);
1076	<	Vector3d tmpComVel(comVel);
1077	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1271	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1074	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1075	>	MPI::INT, MPI::SUM);
1076	>	#else
1077	>	nGlobalConstraints =  nConstraints_;
1078		#endif
1079	<
1080	<	com /= totalMass;
1275	<	comVel /= totalMass;
1276	<	}
1277	<
1278	<	/*
1279	<	Return intertia tensor for entire system and angular momentum Vector.
1079	>	return nGlobalConstraints;
1080	>	}
1081
1082	+	}//end namespace OpenMD
1083
1282	–	[  Ixx -Ixy  -Ixz ]
1283	–	J =| -Iyx  Iyy  -Iyz |
1284	–	[ -Izx -Iyz   Izz ]
1285	–	*/
1286	–
1287	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1288	–
1289	–
1290	–	double xx = 0.0;
1291	–	double yy = 0.0;
1292	–	double zz = 0.0;
1293	–	double xy = 0.0;
1294	–	double xz = 0.0;
1295	–	double yz = 0.0;
1296	–	Vector3d com(0.0);
1297	–	Vector3d comVel(0.0);
1298	–
1299	–	getComAll(com, comVel);
1300	–
1301	–	SimInfo::MoleculeIterator i;
1302	–	Molecule* mol;
1303	–
1304	–	Vector3d thisq(0.0);
1305	–	Vector3d thisv(0.0);
1306	–
1307	–	double thisMass = 0.0;
1308	–
1309	–
1310	–
1311	–
1312	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	–
1314	–	thisq = mol->getCom()-com;
1315	–	thisv = mol->getComVel()-comVel;
1316	–	thisMass = mol->getMass();
1317	–	// Compute moment of intertia coefficients.
1318	–	xx += thisq[0]*thisq[0]*thisMass;
1319	–	yy += thisq[1]*thisq[1]*thisMass;
1320	–	zz += thisq[2]*thisq[2]*thisMass;
1321	–
1322	–	// compute products of intertia
1323	–	xy += thisq[0]*thisq[1]*thisMass;
1324	–	xz += thisq[0]*thisq[2]*thisMass;
1325	–	yz += thisq[1]*thisq[2]*thisMass;
1326	–
1327	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1328	–
1329	–	}
1330	–
1331	–
1332	–	inertiaTensor(0,0) = yy + zz;
1333	–	inertiaTensor(0,1) = -xy;
1334	–	inertiaTensor(0,2) = -xz;
1335	–	inertiaTensor(1,0) = -xy;
1336	–	inertiaTensor(1,1) = xx + zz;
1337	–	inertiaTensor(1,2) = -yz;
1338	–	inertiaTensor(2,0) = -xz;
1339	–	inertiaTensor(2,1) = -yz;
1340	–	inertiaTensor(2,2) = xx + yy;
1341	–
1342	–	#ifdef IS_MPI
1343	–	Mat3x3d tmpI(inertiaTensor);
1344	–	Vector3d tmpAngMom;
1345	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1346	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1347	–	#endif
1348	–
1349	–	return;
1350	–	}
1351	–
1352	–	//Returns the angular momentum of the system
1353	–	Vector3d SimInfo::getAngularMomentum(){
1354	–
1355	–	Vector3d com(0.0);
1356	–	Vector3d comVel(0.0);
1357	–	Vector3d angularMomentum(0.0);
1358	–
1359	–	getComAll(com,comVel);
1360	–
1361	–	SimInfo::MoleculeIterator i;
1362	–	Molecule* mol;
1363	–
1364	–	Vector3d thisr(0.0);
1365	–	Vector3d thisp(0.0);
1366	–
1367	–	double thisMass;
1368	–
1369	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1370	–	thisMass = mol->getMass();
1371	–	thisr = mol->getCom()-com;
1372	–	thisp = (mol->getComVel()-comVel)*thisMass;
1373	–
1374	–	angularMomentum += cross( thisr, thisp );
1375	–
1376	–	}
1377	–
1378	–	#ifdef IS_MPI
1379	–	Vector3d tmpAngMom;
1380	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1381	–	#endif
1382	–
1383	–	return angularMomentum;
1384	–	}
1385	–
1386	–
1387	–	}//end namespace oopse
1388	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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