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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 879 by chrisfen, Wed Feb 1 21:06:43 2006 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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/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 "UseTheForce/ForceField.hpp"
65	>	#include "brains/ForceField.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	#ifdef IS_MPI
69	<	#include "UseTheForce/mpiComponentPlan.h"
71	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
72	<	#endif
73	<
74	<	namespace oopse {
75	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	<	std::map<int, std::set<int> >::iterator i = container.find(index);
77	<	std::set<int> result;
78	<	if (i != container.end()) {
79	<	result = i->second;
80	<	}
81	<
82	<	return result;
83	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
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	>	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	<	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();
103	>	nMolWithSameStamp = (*i)->getNMol();
104
105	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
106	<	molStamp = (*i)->getMoleculeStamp();
107	<	nMolWithSameStamp = (*i)->getNMol();
108	<
109	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
110	<
111	<	//calculate atoms in molecules
112	<	nGlobalAtoms_ += molStamp->getNAtoms() *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();
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	<
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	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	<	//group therefore the total number of cutoff groups in the system is
125	<	//equal to the total number of atoms minus number of atoms belong to
126	<	//cutoff group defined in meta-data file plus the number of cutoff
127	<	//groups defined in meta-data file
128	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
129	<
130	<	//every free atom (atom does not belong to rigid bodies) is an
131	<	//integrable object therefore the total number of integrable objects
132	<	//in the system is equal to the total number of atoms minus number of
133	<	//atoms belong to rigid body defined in meta-data file plus the number
134	<	//of rigid bodies defined in meta-data file
135	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
136	<	+ nGlobalRigidBodies_;
137	<
138	<	nGlobalMols_ = molStampIds_.size();
155	<
156	<	#ifdef IS_MPI
157	<	molToProcMap_.resize(nGlobalMols_);
158	<	#endif
159	<
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		}
#	Line 171 | Line 170 | namespace oopse {
170		delete forceField_;
171		}
172
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	–	}
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 219 | 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 233 | Line 224 | namespace oopse {
224		} else {
225		return false;
226		}
236	–
237	–
227		}
228
229
#	Line 250 | 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)) {
262	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	–	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		}
274	–
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_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
285	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
286	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287	>	// MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
288	>	// MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
289	>	//                           MPI::INT, MPI::SUM);
290		#else
291		ndf_ = ndf_local;
292	+	nGlobalFluctuatingCharges_ = nfq_local;
293		#endif
294
295		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 290 | Line 298 | namespace oopse {
298
299		}
300
301	+	int SimInfo::getFdf() {
302	+	#ifdef IS_MPI
303	+	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
304	+	// MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
305	+	#else
306	+	fdf_ = fdf_local;
307	+	#endif
308	+	return fdf_;
309	+	}
310	+
311	+	unsigned int SimInfo::getNLocalCutoffGroups(){
312	+	int nLocalCutoffAtoms = 0;
313	+	Molecule* mol;
314	+	MoleculeIterator mi;
315	+	CutoffGroup* cg;
316	+	Molecule::CutoffGroupIterator ci;
317	+
318	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
319	+
320	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
321	+	cg = mol->nextCutoffGroup(ci)) {
322	+	nLocalCutoffAtoms += cg->getNumAtom();
323	+
324	+	}
325	+	}
326	+
327	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
328	+	}
329	+
330		void SimInfo::calcNdfRaw() {
331		int ndfRaw_local;
332
333		MoleculeIterator i;
334	<	std::vector<StuntDouble*>::iterator j;
334	>	vector<StuntDouble*>::iterator j;
335		Molecule* mol;
336	<	StuntDouble* integrableObject;
336	>	StuntDouble* sd;
337
338		// Raw degrees of freedom that we have to set
339		ndfRaw_local = 0;
340
341		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
305	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
306	–	integrableObject = mol->nextIntegrableObject(j)) {
342
343	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
344	+	sd = mol->nextIntegrableObject(j)) {
345	+
346		ndfRaw_local += 3;
347
348	<	if (integrableObject->isDirectional()) {
349	<	if (integrableObject->isLinear()) {
348	>	if (sd->isDirectional()) {
349	>	if (sd->isLinear()) {
350		ndfRaw_local += 2;
351		} else {
352		ndfRaw_local += 3;
#	Line 319 | Line 357 | namespace oopse {
357		}
358
359		#ifdef IS_MPI
360	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
360	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
361	>	// MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
362		#else
363		ndfRaw_ = ndfRaw_local;
364		#endif
#	Line 332 | Line 371 | namespace oopse {
371
372
373		#ifdef IS_MPI
374	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
374	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1,
375	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
376	>	// MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
377	>	//                           MPI::INT, MPI::SUM);
378		#else
379		ndfTrans_ = ndfTrans_local;
380		#endif
#	Line 341 | Line 383 | namespace oopse {
383
384		}
385
386	<	void SimInfo::addExcludePairs(Molecule* mol) {
387	<	std::vector<Bond*>::iterator bondIter;
388	<	std::vector<Bend*>::iterator bendIter;
389	<	std::vector<Torsion*>::iterator torsionIter;
386	>	void SimInfo::addInteractionPairs(Molecule* mol) {
387	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
388	>	vector<Bond*>::iterator bondIter;
389	>	vector<Bend*>::iterator bendIter;
390	>	vector<Torsion*>::iterator torsionIter;
391	>	vector<Inversion*>::iterator inversionIter;
392		Bond* bond;
393		Bend* bend;
394		Torsion* torsion;
395	+	Inversion* inversion;
396		int a;
397		int b;
398		int c;
399		int d;
400
401	<	std::map<int, std::set<int> > atomGroups;
401	>	// atomGroups can be used to add special interaction maps between
402	>	// groups of atoms that are in two separate rigid bodies.
403	>	// However, most site-site interactions between two rigid bodies
404	>	// are probably not special, just the ones between the physically
405	>	// bonded atoms.  Interactions *within* a single rigid body should
406	>	// always be excluded.  These are done at the bottom of this
407	>	// function.
408
409	+	map<int, set<int> > atomGroups;
410		Molecule::RigidBodyIterator rbIter;
411		RigidBody* rb;
412		Molecule::IntegrableObjectIterator ii;
413	<	StuntDouble* integrableObject;
413	>	StuntDouble* sd;
414
415	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
416	<	integrableObject = mol->nextIntegrableObject(ii)) {
417	<
418	<	if (integrableObject->isRigidBody()) {
419	<	rb = static_cast<RigidBody*>(integrableObject);
420	<	std::vector<Atom*> atoms = rb->getAtoms();
421	<	std::set<int> rigidAtoms;
422	<	for (int i = 0; i < atoms.size(); ++i) {
423	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
424	<	}
425	<	for (int i = 0; i < atoms.size(); ++i) {
426	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
427	<	}
415	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
416	>	sd = mol->nextIntegrableObject(ii)) {
417	>
418	>	if (sd->isRigidBody()) {
419	>	rb = static_cast<RigidBody*>(sd);
420	>	vector<Atom*> atoms = rb->getAtoms();
421	>	set<int> rigidAtoms;
422	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
423	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
424	>	}
425	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
426	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
427	>	}
428		} else {
429	<	std::set<int> oneAtomSet;
430	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
431	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
429	>	set<int> oneAtomSet;
430	>	oneAtomSet.insert(sd->getGlobalIndex());
431	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
432		}
433		}
434
435	<
436	<
437	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
435	>
436	>	for (bond= mol->beginBond(bondIter); bond != NULL;
437	>	bond = mol->nextBond(bondIter)) {
438	>
439		a = bond->getAtomA()->getGlobalIndex();
440	<	b = bond->getAtomB()->getGlobalIndex();
441	<	exclude_.addPair(a, b);
440	>	b = bond->getAtomB()->getGlobalIndex();
441	>
442	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
443	>	oneTwoInteractions_.addPair(a, b);
444	>	} else {
445	>	excludedInteractions_.addPair(a, b);
446	>	}
447		}
448
449	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
449	>	for (bend= mol->beginBend(bendIter); bend != NULL;
450	>	bend = mol->nextBend(bendIter)) {
451	>
452		a = bend->getAtomA()->getGlobalIndex();
453		b = bend->getAtomB()->getGlobalIndex();
454		c = bend->getAtomC()->getGlobalIndex();
395	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
396	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
397	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
398	–
399	–	exclude_.addPairs(rigidSetA, rigidSetB);
400	–	exclude_.addPairs(rigidSetA, rigidSetC);
401	–	exclude_.addPairs(rigidSetB, rigidSetC);
455
456	<	//exclude_.addPair(a, b);
457	<	//exclude_.addPair(a, c);
458	<	//exclude_.addPair(b, c);
456	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	>	oneTwoInteractions_.addPair(a, b);
458	>	oneTwoInteractions_.addPair(b, c);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(b, c);
462	>	}
463	>
464	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
465	>	oneThreeInteractions_.addPair(a, c);
466	>	} else {
467	>	excludedInteractions_.addPair(a, c);
468	>	}
469		}
470
471	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
471	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
472	>	torsion = mol->nextTorsion(torsionIter)) {
473	>
474		a = torsion->getAtomA()->getGlobalIndex();
475		b = torsion->getAtomB()->getGlobalIndex();
476		c = torsion->getAtomC()->getGlobalIndex();
477	<	d = torsion->getAtomD()->getGlobalIndex();
413	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
414	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
415	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
416	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
477	>	d = torsion->getAtomD()->getGlobalIndex();
478
479	<	exclude_.addPairs(rigidSetA, rigidSetB);
480	<	exclude_.addPairs(rigidSetA, rigidSetC);
481	<	exclude_.addPairs(rigidSetA, rigidSetD);
482	<	exclude_.addPairs(rigidSetB, rigidSetC);
483	<	exclude_.addPairs(rigidSetB, rigidSetD);
484	<	exclude_.addPairs(rigidSetC, rigidSetD);
479	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
480	>	oneTwoInteractions_.addPair(a, b);
481	>	oneTwoInteractions_.addPair(b, c);
482	>	oneTwoInteractions_.addPair(c, d);
483	>	} else {
484	>	excludedInteractions_.addPair(a, b);
485	>	excludedInteractions_.addPair(b, c);
486	>	excludedInteractions_.addPair(c, d);
487	>	}
488
489	<	/*
490	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
491	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
492	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
493	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
494	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
495	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
496	<
497	<
498	<	exclude_.addPair(a, b);
499	<	exclude_.addPair(a, c);
500	<	exclude_.addPair(a, d);
501	<	exclude_.addPair(b, c);
438	<	exclude_.addPair(b, d);
439	<	exclude_.addPair(c, d);
440	<	*/
489	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
490	>	oneThreeInteractions_.addPair(a, c);
491	>	oneThreeInteractions_.addPair(b, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, c);
494	>	excludedInteractions_.addPair(b, d);
495	>	}
496	>
497	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
498	>	oneFourInteractions_.addPair(a, d);
499	>	} else {
500	>	excludedInteractions_.addPair(a, d);
501	>	}
502		}
503
504	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
505	<	std::vector<Atom*> atoms = rb->getAtoms();
506	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
507	<	for (int j = i + 1; j < atoms.size(); ++j) {
504	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
505	>	inversion = mol->nextInversion(inversionIter)) {
506	>
507	>	a = inversion->getAtomA()->getGlobalIndex();
508	>	b = inversion->getAtomB()->getGlobalIndex();
509	>	c = inversion->getAtomC()->getGlobalIndex();
510	>	d = inversion->getAtomD()->getGlobalIndex();
511	>
512	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
513	>	oneTwoInteractions_.addPair(a, b);
514	>	oneTwoInteractions_.addPair(a, c);
515	>	oneTwoInteractions_.addPair(a, d);
516	>	} else {
517	>	excludedInteractions_.addPair(a, b);
518	>	excludedInteractions_.addPair(a, c);
519	>	excludedInteractions_.addPair(a, d);
520	>	}
521	>
522	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
523	>	oneThreeInteractions_.addPair(b, c);
524	>	oneThreeInteractions_.addPair(b, d);
525	>	oneThreeInteractions_.addPair(c, d);
526	>	} else {
527	>	excludedInteractions_.addPair(b, c);
528	>	excludedInteractions_.addPair(b, d);
529	>	excludedInteractions_.addPair(c, d);
530	>	}
531	>	}
532	>
533	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
534	>	rb = mol->nextRigidBody(rbIter)) {
535	>	vector<Atom*> atoms = rb->getAtoms();
536	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
537	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
538		a = atoms[i]->getGlobalIndex();
539		b = atoms[j]->getGlobalIndex();
540	<	exclude_.addPair(a, b);
540	>	excludedInteractions_.addPair(a, b);
541		}
542		}
543		}
544
545		}
546
547	<	void SimInfo::removeExcludePairs(Molecule* mol) {
548	<	std::vector<Bond*>::iterator bondIter;
549	<	std::vector<Bend*>::iterator bendIter;
550	<	std::vector<Torsion*>::iterator torsionIter;
547	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
548	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
549	>	vector<Bond*>::iterator bondIter;
550	>	vector<Bend*>::iterator bendIter;
551	>	vector<Torsion*>::iterator torsionIter;
552	>	vector<Inversion*>::iterator inversionIter;
553		Bond* bond;
554		Bend* bend;
555		Torsion* torsion;
556	+	Inversion* inversion;
557		int a;
558		int b;
559		int c;
560		int d;
561
562	<	std::map<int, std::set<int> > atomGroups;
469	<
562	>	map<int, set<int> > atomGroups;
563		Molecule::RigidBodyIterator rbIter;
564		RigidBody* rb;
565		Molecule::IntegrableObjectIterator ii;
566	<	StuntDouble* integrableObject;
566	>	StuntDouble* sd;
567
568	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
569	<	integrableObject = mol->nextIntegrableObject(ii)) {
570	<
571	<	if (integrableObject->isRigidBody()) {
572	<	rb = static_cast<RigidBody*>(integrableObject);
573	<	std::vector<Atom*> atoms = rb->getAtoms();
574	<	std::set<int> rigidAtoms;
575	<	for (int i = 0; i < atoms.size(); ++i) {
576	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
577	<	}
578	<	for (int i = 0; i < atoms.size(); ++i) {
579	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
580	<	}
568	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
569	>	sd = mol->nextIntegrableObject(ii)) {
570	>
571	>	if (sd->isRigidBody()) {
572	>	rb = static_cast<RigidBody*>(sd);
573	>	vector<Atom*> atoms = rb->getAtoms();
574	>	set<int> rigidAtoms;
575	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
576	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
577	>	}
578	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
579	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
580	>	}
581		} else {
582	<	std::set<int> oneAtomSet;
583	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
584	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
582	>	set<int> oneAtomSet;
583	>	oneAtomSet.insert(sd->getGlobalIndex());
584	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
585		}
586		}
587
588	<
589	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
588	>	for (bond= mol->beginBond(bondIter); bond != NULL;
589	>	bond = mol->nextBond(bondIter)) {
590	>
591		a = bond->getAtomA()->getGlobalIndex();
592	<	b = bond->getAtomB()->getGlobalIndex();
593	<	exclude_.removePair(a, b);
592	>	b = bond->getAtomB()->getGlobalIndex();
593	>
594	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
595	>	oneTwoInteractions_.removePair(a, b);
596	>	} else {
597	>	excludedInteractions_.removePair(a, b);
598	>	}
599		}
600
601	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
601	>	for (bend= mol->beginBend(bendIter); bend != NULL;
602	>	bend = mol->nextBend(bendIter)) {
603	>
604		a = bend->getAtomA()->getGlobalIndex();
605		b = bend->getAtomB()->getGlobalIndex();
606		c = bend->getAtomC()->getGlobalIndex();
506	–
507	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
508	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
509	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
510	–
511	–	exclude_.removePairs(rigidSetA, rigidSetB);
512	–	exclude_.removePairs(rigidSetA, rigidSetC);
513	–	exclude_.removePairs(rigidSetB, rigidSetC);
607
608	<	//exclude_.removePair(a, b);
609	<	//exclude_.removePair(a, c);
610	<	//exclude_.removePair(b, c);
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(b, c);
611	>	} else {
612	>	excludedInteractions_.removePair(a, b);
613	>	excludedInteractions_.removePair(b, c);
614	>	}
615	>
616	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
617	>	oneThreeInteractions_.removePair(a, c);
618	>	} else {
619	>	excludedInteractions_.removePair(a, c);
620	>	}
621		}
622
623	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
623	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
624	>	torsion = mol->nextTorsion(torsionIter)) {
625	>
626		a = torsion->getAtomA()->getGlobalIndex();
627		b = torsion->getAtomB()->getGlobalIndex();
628		c = torsion->getAtomC()->getGlobalIndex();
629	<	d = torsion->getAtomD()->getGlobalIndex();
629	>	d = torsion->getAtomD()->getGlobalIndex();
630	>
631	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
632	>	oneTwoInteractions_.removePair(a, b);
633	>	oneTwoInteractions_.removePair(b, c);
634	>	oneTwoInteractions_.removePair(c, d);
635	>	} else {
636	>	excludedInteractions_.removePair(a, b);
637	>	excludedInteractions_.removePair(b, c);
638	>	excludedInteractions_.removePair(c, d);
639	>	}
640
641	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
642	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
643	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
644	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
641	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
642	>	oneThreeInteractions_.removePair(a, c);
643	>	oneThreeInteractions_.removePair(b, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, c);
646	>	excludedInteractions_.removePair(b, d);
647	>	}
648
649	<	exclude_.removePairs(rigidSetA, rigidSetB);
650	<	exclude_.removePairs(rigidSetA, rigidSetC);
651	<	exclude_.removePairs(rigidSetA, rigidSetD);
652	<	exclude_.removePairs(rigidSetB, rigidSetC);
653	<	exclude_.removePairs(rigidSetB, rigidSetD);
654	<	exclude_.removePairs(rigidSetC, rigidSetD);
649	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
650	>	oneFourInteractions_.removePair(a, d);
651	>	} else {
652	>	excludedInteractions_.removePair(a, d);
653	>	}
654	>	}
655
656	<	/*
657	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
540	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
541	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
542	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
543	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
544	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
656	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
657	>	inversion = mol->nextInversion(inversionIter)) {
658
659	<
660	<	exclude_.removePair(a, b);
661	<	exclude_.removePair(a, c);
662	<	exclude_.removePair(a, d);
663	<	exclude_.removePair(b, c);
664	<	exclude_.removePair(b, d);
665	<	exclude_.removePair(c, d);
666	<	*/
659	>	a = inversion->getAtomA()->getGlobalIndex();
660	>	b = inversion->getAtomB()->getGlobalIndex();
661	>	c = inversion->getAtomC()->getGlobalIndex();
662	>	d = inversion->getAtomD()->getGlobalIndex();
663	>
664	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
665	>	oneTwoInteractions_.removePair(a, b);
666	>	oneTwoInteractions_.removePair(a, c);
667	>	oneTwoInteractions_.removePair(a, d);
668	>	} else {
669	>	excludedInteractions_.removePair(a, b);
670	>	excludedInteractions_.removePair(a, c);
671	>	excludedInteractions_.removePair(a, d);
672	>	}
673	>
674	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
675	>	oneThreeInteractions_.removePair(b, c);
676	>	oneThreeInteractions_.removePair(b, d);
677	>	oneThreeInteractions_.removePair(c, d);
678	>	} else {
679	>	excludedInteractions_.removePair(b, c);
680	>	excludedInteractions_.removePair(b, d);
681	>	excludedInteractions_.removePair(c, d);
682	>	}
683		}
684
685	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
686	<	std::vector<Atom*> atoms = rb->getAtoms();
687	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
688	<	for (int j = i + 1; j < atoms.size(); ++j) {
685	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
686	>	rb = mol->nextRigidBody(rbIter)) {
687	>	vector<Atom*> atoms = rb->getAtoms();
688	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
689	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
690		a = atoms[i]->getGlobalIndex();
691		b = atoms[j]->getGlobalIndex();
692	<	exclude_.removePair(a, b);
692	>	excludedInteractions_.removePair(a, b);
693		}
694		}
695		}
696	<
696	>
697		}
698	<
699	<
698	>
699	>
700		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
701		int curStampId;
702	<
702	>
703		//index from 0
704		curStampId = moleculeStamps_.size();
705
#	Line 577 | Line 707 | namespace oopse {
707		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
708		}
709
580	–	void SimInfo::update() {
710
711	<	setupSimType();
712	<
713	<	#ifdef IS_MPI
714	<	setupFortranParallel();
715	<	#endif
716	<
717	<	setupFortranSim();
718	<
719	<	//setup fortran force field
591	<	/** @deprecate */
592	<	int isError = 0;
593	<
594	<	setupElectrostaticSummationMethod( isError );
595	<	setupSwitchingFunction();
596	<
597	<	if(isError){
598	<	sprintf( painCave.errMsg,
599	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
600	<	painCave.isFatal = 1;
601	<	simError();
602	<	}
603	<
604	<
605	<	setupCutoff();
606	<
711	>	/**
712	>	* update
713	>	*
714	>	*  Performs the global checks and variable settings after the
715	>	*  objects have been created.
716	>	*
717	>	*/
718	>	void SimInfo::update() {
719	>	setupSimVariables();
720		calcNdf();
721		calcNdfRaw();
722		calcNdfTrans();
610	–
611	–	fortranInitialized_ = true;
723		}
724	<
725	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
724	>
725	>	/**
726	>	* getSimulatedAtomTypes
727	>	*
728	>	* Returns an STL set of AtomType* that are actually present in this
729	>	* simulation.  Must query all processors to assemble this information.
730	>	*
731	>	*/
732	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
733		SimInfo::MoleculeIterator mi;
734		Molecule* mol;
735		Molecule::AtomIterator ai;
736		Atom* atom;
737	<	std::set<AtomType*> atomTypes;
738	<
737	>	set<AtomType*> atomTypes;
738	>
739		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
740	<
741	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
740	>	for(atom = mol->beginAtom(ai); atom != NULL;
741	>	atom = mol->nextAtom(ai)) {
742		atomTypes.insert(atom->getAtomType());
743	<	}
744	<
743	>	}
744	>	}
745	>
746	>	#ifdef IS_MPI
747	>
748	>	// loop over the found atom types on this processor, and add their
749	>	// numerical idents to a vector:
750	>
751	>	vector<int> foundTypes;
752	>	set<AtomType*>::iterator i;
753	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
754	>	foundTypes.push_back( (*i)->getIdent() );
755	>
756	>	// count_local holds the number of found types on this processor
757	>	int count_local = foundTypes.size();
758	>
759	>	int nproc;
760	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
761	>	// int nproc = MPI::COMM_WORLD.Get_size();
762	>
763	>	// we need arrays to hold the counts and displacement vectors for
764	>	// all processors
765	>	vector<int> counts(nproc, 0);
766	>	vector<int> disps(nproc, 0);
767	>
768	>	// fill the counts array
769	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
770	>	1, MPI_INT, MPI_COMM_WORLD);
771	>	// MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
772	>	//                           1, MPI::INT);
773	>
774	>	// use the processor counts to compute the displacement array
775	>	disps[0] = 0;
776	>	int totalCount = counts[0];
777	>	for (int iproc = 1; iproc < nproc; iproc++) {
778	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
779	>	totalCount += counts[iproc];
780		}
781
782	<	return atomTypes;
783	<	}
782	>	// we need a (possibly redundant) set of all found types:
783	>	vector<int> ftGlobal(totalCount);
784	>
785	>	// now spray out the foundTypes to all the other processors:
786	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
787	>	&ftGlobal[0], &counts[0], &disps[0],
788	>	MPI_INT, MPI_COMM_WORLD);
789	>	// MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
790	>	//                            &ftGlobal[0], &counts[0], &disps[0],
791	>	//                            MPI::INT);
792
793	<	void SimInfo::setupSimType() {
794	<	std::set<AtomType*>::iterator i;
795	<	std::set<AtomType*> atomTypes;
796	<	atomTypes = getUniqueAtomTypes();
793	>	vector<int>::iterator j;
794	>
795	>	// foundIdents is a stl set, so inserting an already found ident
796	>	// will have no effect.
797	>	set<int> foundIdents;
798	>
799	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
800	>	foundIdents.insert((*j));
801
802	<	int useLennardJones = 0;
803	<	int useElectrostatic = 0;
804	<	int useEAM = 0;
805	<	int useSC = 0;
806	<	int useCharge = 0;
807	<	int useDirectional = 0;
808	<	int useDipole = 0;
644	<	int useGayBerne = 0;
645	<	int useSticky = 0;
646	<	int useStickyPower = 0;
647	<	int useShape = 0;
648	<	int useFLARB = 0; //it is not in AtomType yet
649	<	int useDirectionalAtom = 0;
650	<	int useElectrostatics = 0;
651	<	//usePBC and useRF are from simParams
652	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
653	<	int useRF;
654	<	int useSF;
655	<	std::string myMethod;
802	>	// now iterate over the foundIdents and get the actual atom types
803	>	// that correspond to these:
804	>	set<int>::iterator it;
805	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
806	>	atomTypes.insert( forceField_->getAtomType((*it)) );
807	>
808	>	#endif
809
810	<	// set the useRF logical
811	<	useRF = 0;
659	<	useSF = 0;
810	>	return atomTypes;
811	>	}
812
813
814	<	if (simParams_->haveElectrostaticSummationMethod()) {
815	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
816	<	toUpper(myMethod);
817	<	if (myMethod == "REACTION_FIELD") {
666	<	useRF=1;
667	<	} else {
668	<	if (myMethod == "SHIFTED_FORCE") {
669	<	useSF = 1;
670	<	}
671	<	}
672	<	}
814	>	int getGlobalCountOfType(AtomType* atype) {
815	>	/*
816	>	set<AtomType*> atypes = getSimulatedAtomTypes();
817	>	map<AtomType*, int> counts_;
818
819	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
820	+	for(atom = mol->beginAtom(ai); atom != NULL;
821	+	atom = mol->nextAtom(ai)) {
822	+	atom->getAtomType();
823	+	}
824	+	}
825	+	*/
826	+	return 0;
827	+	}
828	+
829	+	void SimInfo::setupSimVariables() {
830	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
831	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
832	+	// parameter is true
833	+	calcBoxDipole_ = false;
834	+	if ( simParams_->haveAccumulateBoxDipole() )
835	+	if ( simParams_->getAccumulateBoxDipole() ) {
836	+	calcBoxDipole_ = true;
837	+	}
838	+
839	+	set<AtomType*>::iterator i;
840	+	set<AtomType*> atomTypes;
841	+	atomTypes = getSimulatedAtomTypes();
842	+	bool usesElectrostatic = false;
843	+	bool usesMetallic = false;
844	+	bool usesDirectional = false;
845	+	bool usesFluctuatingCharges =  false;
846		//loop over all of the atom types
847		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
848	<	useLennardJones |= (*i)->isLennardJones();
849	<	useElectrostatic |= (*i)->isElectrostatic();
850	<	useEAM |= (*i)->isEAM();
851	<	useSC |= (*i)->isSC();
680	<	useCharge |= (*i)->isCharge();
681	<	useDirectional |= (*i)->isDirectional();
682	<	useDipole |= (*i)->isDipole();
683	<	useGayBerne |= (*i)->isGayBerne();
684	<	useSticky |= (*i)->isSticky();
685	<	useStickyPower |= (*i)->isStickyPower();
686	<	useShape |= (*i)->isShape();
848	>	usesElectrostatic |= (*i)->isElectrostatic();
849	>	usesMetallic |= (*i)->isMetal();
850	>	usesDirectional |= (*i)->isDirectional();
851	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
852		}
853
854	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
690	<	useDirectionalAtom = 1;
691	<	}
692	<
693	<	if (useCharge || useDipole) {
694	<	useElectrostatics = 1;
695	<	}
696	<
697	<	#ifdef IS_MPI
854	>	#ifdef IS_MPI
855		int temp;
856
857	<	temp = usePBC;
858	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	>	temp = usesDirectional;
858	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
859	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
860
861	<	temp = useDirectionalAtom;
862	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
861	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
862	>	//                           MPI::LOR);
863	>
864	>	temp = usesMetallic;
865	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
866	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
867
868	<	temp = useLennardJones;
869	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
868	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
869	>	//                           MPI::LOR);
870	>
871	>	temp = usesElectrostatic;
872	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
873	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
874
875	<	temp = useElectrostatics;
876	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
876	>	//                           MPI::LOR);
877
878	<	temp = useCharge;
879	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
878	>	temp = usesFluctuatingCharges;
879	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
880	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
881
882	<	temp = useDipole;
883	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
882	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
883	>	//                           MPI::LOR);
884
885	<	temp = useSticky;
719	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885	>	#else
886
887	<	temp = useStickyPower;
888	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
889	<
890	<	temp = useGayBerne;
725	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
887	>	usesDirectionalAtoms_ = usesDirectional;
888	>	usesMetallicAtoms_ = usesMetallic;
889	>	usesElectrostaticAtoms_ = usesElectrostatic;
890	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
891
892	<	temp = useEAM;
728	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729	<
730	<	temp = useSC;
731	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
892	>	#endif
893
894	<	temp = useShape;
895	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
894	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
895	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
896	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
897	>	}
898
736	–	temp = useFLARB;
737	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
899
900	<	temp = useRF;
901	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
900	>	vector<int> SimInfo::getGlobalAtomIndices() {
901	>	SimInfo::MoleculeIterator mi;
902	>	Molecule* mol;
903	>	Molecule::AtomIterator ai;
904	>	Atom* atom;
905
906	<	temp = useSF;
907	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
906	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
907	>
908	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
909	>
910	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
911	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
912	>	}
913	>	}
914	>	return GlobalAtomIndices;
915	>	}
916
745	–	#endif
917
918	<	fInfo_.SIM_uses_PBC = usePBC;
919	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
920	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
921	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
922	<	fInfo_.SIM_uses_Charges = useCharge;
752	<	fInfo_.SIM_uses_Dipoles = useDipole;
753	<	fInfo_.SIM_uses_Sticky = useSticky;
754	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
755	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
756	<	fInfo_.SIM_uses_EAM = useEAM;
757	<	fInfo_.SIM_uses_SC = useSC;
758	<	fInfo_.SIM_uses_Shapes = useShape;
759	<	fInfo_.SIM_uses_FLARB = useFLARB;
760	<	fInfo_.SIM_uses_RF = useRF;
761	<	fInfo_.SIM_uses_SF = useSF;
918	>	vector<int> SimInfo::getGlobalGroupIndices() {
919	>	SimInfo::MoleculeIterator mi;
920	>	Molecule* mol;
921	>	Molecule::CutoffGroupIterator ci;
922	>	CutoffGroup* cg;
923
924	<	if( myMethod == "REACTION_FIELD") {
924	>	vector<int> GlobalGroupIndices;
925	>
926	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
927
928	<	if (simParams_->haveDielectric()) {
929	<	fInfo_.dielect = simParams_->getDielectric();
930	<	} else {
931	<	sprintf(painCave.errMsg,
932	<	"SimSetup Error: No Dielectric constant was set.\n"
933	<	"\tYou are trying to use Reaction Field without"
771	<	"\tsetting a dielectric constant!\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
928	>	//local index of cutoff group is trivial, it only depends on the
929	>	//order of travesing
930	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
931	>	cg = mol->nextCutoffGroup(ci)) {
932	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
933	>	}
934		}
935	<
935	>	return GlobalGroupIndices;
936		}
937
779	–	void SimInfo::setupFortranSim() {
780	–	int isError;
781	–	int nExclude;
782	–	std::vector<int> fortranGlobalGroupMembership;
783	–
784	–	nExclude = exclude_.getSize();
785	–	isError = 0;
938
939	<	//globalGroupMembership_ is filled by SimCreator
788	<	for (int i = 0; i < nGlobalAtoms_; i++) {
789	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
790	<	}
939	>	void SimInfo::prepareTopology() {
940
941		//calculate mass ratio of cutoff group
793	–	std::vector<double> mfact;
942		SimInfo::MoleculeIterator mi;
943		Molecule* mol;
944		Molecule::CutoffGroupIterator ci;
945		CutoffGroup* cg;
946		Molecule::AtomIterator ai;
947		Atom* atom;
948	<	double totalMass;
948	>	RealType totalMass;
949
950	<	//to avoid memory reallocation, reserve enough space for mfact
951	<	mfact.reserve(getNCutoffGroups());
950	>	/**
951	>	* The mass factor is the relative mass of an atom to the total
952	>	* mass of the cutoff group it belongs to.  By default, all atoms
953	>	* are their own cutoff groups, and therefore have mass factors of
954	>	* 1.  We need some special handling for massless atoms, which
955	>	* will be treated as carrying the entire mass of the cutoff
956	>	* group.
957	>	*/
958	>	massFactors_.clear();
959	>	massFactors_.resize(getNAtoms(), 1.0);
960
961		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
962	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
962	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
963	>	cg = mol->nextCutoffGroup(ci)) {
964
965		totalMass = cg->getMass();
966		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
967		// Check for massless groups - set mfact to 1 if true
968	<	if (totalMass != 0)
969	<	mfact.push_back(atom->getMass()/totalMass);
968	>	if (totalMass != 0)
969	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
970		else
971	<	mfact.push_back( 1.0 );
971	>	massFactors_[atom->getLocalIndex()] = 1.0;
972		}
816	–
973		}
974		}
975
976	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
977	<	std::vector<int> identArray;
978	<
979	<	//to avoid memory reallocation, reserve enough space identArray
980	<	identArray.reserve(getNAtoms());
981	<
982	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
976	>	// Build the identArray_ and regions_
977	>
978	>	identArray_.clear();
979	>	identArray_.reserve(getNAtoms());
980	>	regions_.clear();
981	>	regions_.reserve(getNAtoms());
982	>
983	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
984	>	int reg = mol->getRegion();
985		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
986	<	identArray.push_back(atom->getIdent());
986	>	identArray_.push_back(atom->getIdent());
987	>	regions_.push_back(reg);
988		}
989		}
990	<
991	<	//fill molMembershipArray
833	<	//molMembershipArray is filled by SimCreator
834	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
835	<	for (int i = 0; i < nGlobalAtoms_; i++) {
836	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
837	<	}
838	<
839	<	//setup fortran simulation
840	<	int nGlobalExcludes = 0;
841	<	int* globalExcludes = NULL;
842	<	int* excludeList = exclude_.getExcludeList();
843	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
844	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
845	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
846	<
847	<	if( isError ){
848	<
849	<	sprintf( painCave.errMsg,
850	<	"There was an error setting the simulation information in fortran.\n" );
851	<	painCave.isFatal = 1;
852	<	painCave.severity = OOPSE_ERROR;
853	<	simError();
854	<	}
855	<
856	<	#ifdef IS_MPI
857	<	sprintf( checkPointMsg,
858	<	"succesfully sent the simulation information to fortran.\n");
859	<	MPIcheckPoint();
860	<	#endif // is_mpi
861	<	}
862	<
863	<
864	<	#ifdef IS_MPI
865	<	void SimInfo::setupFortranParallel() {
866	<
867	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
868	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
869	<	std::vector<int> localToGlobalCutoffGroupIndex;
870	<	SimInfo::MoleculeIterator mi;
871	<	Molecule::AtomIterator ai;
872	<	Molecule::CutoffGroupIterator ci;
873	<	Molecule* mol;
874	<	Atom* atom;
875	<	CutoffGroup* cg;
876	<	mpiSimData parallelData;
877	<	int isError;
878	<
879	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
880	<
881	<	//local index(index in DataStorge) of atom is important
882	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
884	<	}
885	<
886	<	//local index of cutoff group is trivial, it only depends on the order of travesing
887	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
888	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
889	<	}
890	<
891	<	}
892	<
893	<	//fill up mpiSimData struct
894	<	parallelData.nMolGlobal = getNGlobalMolecules();
895	<	parallelData.nMolLocal = getNMolecules();
896	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
897	<	parallelData.nAtomsLocal = getNAtoms();
898	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
899	<	parallelData.nGroupsLocal = getNCutoffGroups();
900	<	parallelData.myNode = worldRank;
901	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
902	<
903	<	//pass mpiSimData struct and index arrays to fortran
904	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
905	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
906	<	&localToGlobalCutoffGroupIndex[0], &isError);
907	<
908	<	if (isError) {
909	<	sprintf(painCave.errMsg,
910	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
911	<	painCave.isFatal = 1;
912	<	simError();
913	<	}
914	<
915	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
916	<	MPIcheckPoint();
917	<
918	<
919	<	}
920	<
921	<	#endif
922	<
923	<	void SimInfo::setupCutoff() {
924	<
925	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926	<
927	<	// Check the cutoff policy
928	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929	<
930	<	std::string myPolicy;
931	<	if (forceFieldOptions_.haveCutoffPolicy()){
932	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
933	<	}else if (simParams_->haveCutoffPolicy()) {
934	<	myPolicy = simParams_->getCutoffPolicy();
935	<	}
936	<
937	<	if (!myPolicy.empty()){
938	<	toUpper(myPolicy);
939	<	if (myPolicy == "MIX") {
940	<	cp = MIX_CUTOFF_POLICY;
941	<	} else {
942	<	if (myPolicy == "MAX") {
943	<	cp = MAX_CUTOFF_POLICY;
944	<	} else {
945	<	if (myPolicy == "TRADITIONAL") {
946	<	cp = TRADITIONAL_CUTOFF_POLICY;
947	<	} else {
948	<	// throw error
949	<	sprintf( painCave.errMsg,
950	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
951	<	painCave.isFatal = 1;
952	<	simError();
953	<	}
954	<	}
955	<	}
956	<	}
957	<	notifyFortranCutoffPolicy(&cp);
958	<
959	<	// Check the Skin Thickness for neighborlists
960	<	double skin;
961	<	if (simParams_->haveSkinThickness()) {
962	<	skin = simParams_->getSkinThickness();
963	<	notifyFortranSkinThickness(&skin);
964	<	}
965	<
966	<	// Check if the cutoff was set explicitly:
967	<	if (simParams_->haveCutoffRadius()) {
968	<	rcut_ = simParams_->getCutoffRadius();
969	<	if (simParams_->haveSwitchingRadius()) {
970	<	rsw_  = simParams_->getSwitchingRadius();
971	<	} else {
972	<	if (fInfo_.SIM_uses_Charges |
973	<	fInfo_.SIM_uses_Dipoles |
974	<	fInfo_.SIM_uses_RF) {
975	<
976	<	rsw_ = 0.85 * rcut_;
977	<	sprintf(painCave.errMsg,
978	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
979	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
980	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
981	<	painCave.isFatal = 0;
982	<	simError();
983	<	} else {
984	<	rsw_ = rcut_;
985	<	sprintf(painCave.errMsg,
986	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
987	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
988	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
989	<	painCave.isFatal = 0;
990	<	simError();
991	<	}
992	<	}
993	<
994	<	notifyFortranCutoffs(&rcut_, &rsw_);
995	<
996	<	} else {
997	<
998	<	// For electrostatic atoms, we'll assume a large safe value:
999	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1000	<	sprintf(painCave.errMsg,
1001	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1002	<	"\tOOPSE will use a default value of 15.0 angstroms"
1003	<	"\tfor the cutoffRadius.\n");
1004	<	painCave.isFatal = 0;
1005	<	simError();
1006	<	rcut_ = 15.0;
1007	<
1008	<	if (simParams_->haveElectrostaticSummationMethod()) {
1009	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1010	<	toUpper(myMethod);
1011	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1012	<	if (simParams_->haveSwitchingRadius()){
1013	<	sprintf(painCave.errMsg,
1014	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1015	<	"\teven though the electrostaticSummationMethod was\n"
1016	<	"\tset to %s\n", myMethod.c_str());
1017	<	painCave.isFatal = 1;
1018	<	simError();
1019	<	}
1020	<	}
1021	<	}
1022	<
1023	<	if (simParams_->haveSwitchingRadius()){
1024	<	rsw_ = simParams_->getSwitchingRadius();
1025	<	} else {
1026	<	sprintf(painCave.errMsg,
1027	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1028	<	"\tOOPSE will use a default value of\n"
1029	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1030	<	painCave.isFatal = 0;
1031	<	simError();
1032	<	rsw_ = 0.85 * rcut_;
1033	<	}
1034	<	notifyFortranCutoffs(&rcut_, &rsw_);
1035	<	} else {
1036	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1037	<	// We'll punt and let fortran figure out the cutoffs later.
1038	<
1039	<	notifyFortranYouAreOnYourOwn();
1040	<
1041	<	}
1042	<	}
990	>
991	>	topologyDone_ = true;
992		}
993
1045	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1046	–
1047	–	int errorOut;
1048	–	int esm =  NONE;
1049	–	int sm = UNDAMPED;
1050	–	double alphaVal;
1051	–	double dielectric;
1052	–
1053	–	errorOut = isError;
1054	–	alphaVal = simParams_->getDampingAlpha();
1055	–	dielectric = simParams_->getDielectric();
1056	–
1057	–	if (simParams_->haveElectrostaticSummationMethod()) {
1058	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1059	–	toUpper(myMethod);
1060	–	if (myMethod == "NONE") {
1061	–	esm = NONE;
1062	–	} else {
1063	–	if (myMethod == "SWITCHING_FUNCTION") {
1064	–	esm = SWITCHING_FUNCTION;
1065	–	} else {
1066	–	if (myMethod == "SHIFTED_POTENTIAL") {
1067	–	esm = SHIFTED_POTENTIAL;
1068	–	} else {
1069	–	if (myMethod == "SHIFTED_FORCE") {
1070	–	esm = SHIFTED_FORCE;
1071	–	} else {
1072	–	if (myMethod == "REACTION_FIELD") {
1073	–	esm = REACTION_FIELD;
1074	–	} else {
1075	–	// throw error
1076	–	sprintf( painCave.errMsg,
1077	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1078	–	"\t(Input file specified %s .)\n"
1079	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1080	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1081	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1082	–	painCave.isFatal = 1;
1083	–	simError();
1084	–	}
1085	–	}
1086	–	}
1087	–	}
1088	–	}
1089	–	}
1090	–
1091	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1092	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1093	–	toUpper(myScreen);
1094	–	if (myScreen == "UNDAMPED") {
1095	–	sm = UNDAMPED;
1096	–	} else {
1097	–	if (myScreen == "DAMPED") {
1098	–	sm = DAMPED;
1099	–	if (!simParams_->haveDampingAlpha()) {
1100	–	//throw error
1101	–	sprintf( painCave.errMsg,
1102	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1103	–	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1104	–	painCave.isFatal = 0;
1105	–	simError();
1106	–	}
1107	–	} else {
1108	–	// throw error
1109	–	sprintf( painCave.errMsg,
1110	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1111	–	"\t(Input file specified %s .)\n"
1112	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1113	–	"or \"damped\".\n", myScreen.c_str() );
1114	–	painCave.isFatal = 1;
1115	–	simError();
1116	–	}
1117	–	}
1118	–	}
1119	–
1120	–	// let's pass some summation method variables to fortran
1121	–	setElectrostaticSummationMethod( &esm );
1122	–	setFortranElectrostaticMethod( &esm );
1123	–	setScreeningMethod( &sm );
1124	–	setDampingAlpha( &alphaVal );
1125	–	setReactionFieldDielectric( &dielectric );
1126	–	initFortranFF( &errorOut );
1127	–	}
1128	–
1129	–	void SimInfo::setupSwitchingFunction() {
1130	–	int ft = CUBIC;
1131	–
1132	–	if (simParams_->haveSwitchingFunctionType()) {
1133	–	std::string funcType = simParams_->getSwitchingFunctionType();
1134	–	toUpper(funcType);
1135	–	if (funcType == "CUBIC") {
1136	–	ft = CUBIC;
1137	–	} else {
1138	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1139	–	ft = FIFTH_ORDER_POLY;
1140	–	} else {
1141	–	// throw error
1142	–	sprintf( painCave.errMsg,
1143	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1144	–	painCave.isFatal = 1;
1145	–	simError();
1146	–	}
1147	–	}
1148	–	}
1149	–
1150	–	// send switching function notification to switcheroo
1151	–	setFunctionType(&ft);
1152	–
1153	–	}
1154	–
994		void SimInfo::addProperty(GenericData* genData) {
995		properties_.addProperty(genData);
996		}
997
998	<	void SimInfo::removeProperty(const std::string& propName) {
998	>	void SimInfo::removeProperty(const string& propName) {
999		properties_.removeProperty(propName);
1000		}
1001
#	Line 1164 | Line 1003 | namespace oopse {
1003		properties_.clearProperties();
1004		}
1005
1006	<	std::vector<std::string> SimInfo::getPropertyNames() {
1006	>	vector<string> SimInfo::getPropertyNames() {
1007		return properties_.getPropertyNames();
1008		}
1009
1010	<	std::vector<GenericData*> SimInfo::getProperties() {
1010	>	vector<GenericData*> SimInfo::getProperties() {
1011		return properties_.getProperties();
1012		}
1013
1014	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1014	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1015		return properties_.getPropertyByName(propName);
1016		}
1017
#	Line 1183 | Line 1022 | namespace oopse {
1022		delete sman_;
1023		sman_ = sman;
1024
1186	–	Molecule* mol;
1187	–	RigidBody* rb;
1188	–	Atom* atom;
1025		SimInfo::MoleculeIterator mi;
1026	+	Molecule::AtomIterator ai;
1027		Molecule::RigidBodyIterator rbIter;
1028	<	Molecule::AtomIterator atomIter;;
1028	>	Molecule::CutoffGroupIterator cgIter;
1029	>	Molecule::BondIterator bondIter;
1030	>	Molecule::BendIterator bendIter;
1031	>	Molecule::TorsionIterator torsionIter;
1032	>	Molecule::InversionIterator inversionIter;
1033
1034	+	Molecule* mol;
1035	+	Atom* atom;
1036	+	RigidBody* rb;
1037	+	CutoffGroup* cg;
1038	+	Bond* bond;
1039	+	Bend* bend;
1040	+	Torsion* torsion;
1041	+	Inversion* inversion;
1042	+
1043		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1044
1045	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1045	>	for (atom = mol->beginAtom(ai); atom != NULL;
1046	>	atom = mol->nextAtom(ai)) {
1047		atom->setSnapshotManager(sman_);
1048	<	}
1049	<
1050	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1048	>	}
1049	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1050	>	rb = mol->nextRigidBody(rbIter)) {
1051		rb->setSnapshotManager(sman_);
1052		}
1053	<	}
1054	<
1053	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1054	>	cg = mol->nextCutoffGroup(cgIter)) {
1055	>	cg->setSnapshotManager(sman_);
1056	>	}
1057	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1058	>	bond = mol->nextBond(bondIter)) {
1059	>	bond->setSnapshotManager(sman_);
1060	>	}
1061	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1062	>	bend = mol->nextBend(bendIter)) {
1063	>	bend->setSnapshotManager(sman_);
1064	>	}
1065	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1066	>	torsion = mol->nextTorsion(torsionIter)) {
1067	>	torsion->setSnapshotManager(sman_);
1068	>	}
1069	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1070	>	inversion = mol->nextInversion(inversionIter)) {
1071	>	inversion->setSnapshotManager(sman_);
1072	>	}
1073	>	}
1074		}
1075
1206	–	Vector3d SimInfo::getComVel(){
1207	–	SimInfo::MoleculeIterator i;
1208	–	Molecule* mol;
1076
1077	<	Vector3d comVel(0.0);
1211	<	double totalMass = 0.0;
1212	<
1213	<
1214	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1215	<	double mass = mol->getMass();
1216	<	totalMass += mass;
1217	<	comVel += mass * mol->getComVel();
1218	<	}
1077	>	ostream& operator <<(ostream& o, SimInfo& info) {
1078
1220	–	#ifdef IS_MPI
1221	–	double tmpMass = totalMass;
1222	–	Vector3d tmpComVel(comVel);
1223	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1224	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1225	–	#endif
1226	–
1227	–	comVel /= totalMass;
1228	–
1229	–	return comVel;
1230	–	}
1231	–
1232	–	Vector3d SimInfo::getCom(){
1233	–	SimInfo::MoleculeIterator i;
1234	–	Molecule* mol;
1235	–
1236	–	Vector3d com(0.0);
1237	–	double totalMass = 0.0;
1238	–
1239	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1240	–	double mass = mol->getMass();
1241	–	totalMass += mass;
1242	–	com += mass * mol->getCom();
1243	–	}
1244	–
1245	–	#ifdef IS_MPI
1246	–	double tmpMass = totalMass;
1247	–	Vector3d tmpCom(com);
1248	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1249	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1250	–	#endif
1251	–
1252	–	com /= totalMass;
1253	–
1254	–	return com;
1255	–
1256	–	}
1257	–
1258	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1259	–
1079		return o;
1080		}
1081
1082	<
1083	<	/*
1084	<	Returns center of mass and center of mass velocity in one function call.
1085	<	*/
1086	<
1087	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1088	<	SimInfo::MoleculeIterator i;
1089	<	Molecule* mol;
1090	<
1091	<
1092	<	double totalMass = 0.0;
1093	<
1082	>
1083	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1084	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1085	>	sprintf(painCave.errMsg,
1086	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1087	>	"\tindex exceeds number of known objects!\n");
1088	>	painCave.isFatal = 1;
1089	>	simError();
1090	>	return NULL;
1091	>	} else
1092	>	return IOIndexToIntegrableObject.at(index);
1093	>	}
1094	>
1095	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1096	>	IOIndexToIntegrableObject= v;
1097	>	}
1098
1099	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1100	<	double mass = mol->getMass();
1278	<	totalMass += mass;
1279	<	com += mass * mol->getCom();
1280	<	comVel += mass * mol->getComVel();
1281	<	}
1282	<
1099	>	int SimInfo::getNGlobalConstraints() {
1100	>	int nGlobalConstraints;
1101		#ifdef IS_MPI
1102	<	double tmpMass = totalMass;
1103	<	Vector3d tmpCom(com);
1104	<	Vector3d tmpComVel(comVel);
1105	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1106	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1107	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1102	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1103	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1104	>	// MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1105	>	//                           MPI::INT, MPI::SUM);
1106	>	#else
1107	>	nGlobalConstraints =  nConstraints_;
1108		#endif
1109	<
1110	<	com /= totalMass;
1293	<	comVel /= totalMass;
1294	<	}
1295	<
1296	<	/*
1297	<	Return intertia tensor for entire system and angular momentum Vector.
1109	>	return nGlobalConstraints;
1110	>	}
1111
1112	+	}//end namespace OpenMD
1113
1300	–	[  Ixx -Ixy  -Ixz ]
1301	–	J =| -Iyx  Iyy  -Iyz |
1302	–	[ -Izx -Iyz   Izz ]
1303	–	*/
1304	–
1305	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1306	–
1307	–
1308	–	double xx = 0.0;
1309	–	double yy = 0.0;
1310	–	double zz = 0.0;
1311	–	double xy = 0.0;
1312	–	double xz = 0.0;
1313	–	double yz = 0.0;
1314	–	Vector3d com(0.0);
1315	–	Vector3d comVel(0.0);
1316	–
1317	–	getComAll(com, comVel);
1318	–
1319	–	SimInfo::MoleculeIterator i;
1320	–	Molecule* mol;
1321	–
1322	–	Vector3d thisq(0.0);
1323	–	Vector3d thisv(0.0);
1324	–
1325	–	double thisMass = 0.0;
1326	–
1327	–
1328	–
1329	–
1330	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1331	–
1332	–	thisq = mol->getCom()-com;
1333	–	thisv = mol->getComVel()-comVel;
1334	–	thisMass = mol->getMass();
1335	–	// Compute moment of intertia coefficients.
1336	–	xx += thisq[0]*thisq[0]*thisMass;
1337	–	yy += thisq[1]*thisq[1]*thisMass;
1338	–	zz += thisq[2]*thisq[2]*thisMass;
1339	–
1340	–	// compute products of intertia
1341	–	xy += thisq[0]*thisq[1]*thisMass;
1342	–	xz += thisq[0]*thisq[2]*thisMass;
1343	–	yz += thisq[1]*thisq[2]*thisMass;
1344	–
1345	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1346	–
1347	–	}
1348	–
1349	–
1350	–	inertiaTensor(0,0) = yy + zz;
1351	–	inertiaTensor(0,1) = -xy;
1352	–	inertiaTensor(0,2) = -xz;
1353	–	inertiaTensor(1,0) = -xy;
1354	–	inertiaTensor(1,1) = xx + zz;
1355	–	inertiaTensor(1,2) = -yz;
1356	–	inertiaTensor(2,0) = -xz;
1357	–	inertiaTensor(2,1) = -yz;
1358	–	inertiaTensor(2,2) = xx + yy;
1359	–
1360	–	#ifdef IS_MPI
1361	–	Mat3x3d tmpI(inertiaTensor);
1362	–	Vector3d tmpAngMom;
1363	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1364	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1365	–	#endif
1366	–
1367	–	return;
1368	–	}
1369	–
1370	–	//Returns the angular momentum of the system
1371	–	Vector3d SimInfo::getAngularMomentum(){
1372	–
1373	–	Vector3d com(0.0);
1374	–	Vector3d comVel(0.0);
1375	–	Vector3d angularMomentum(0.0);
1376	–
1377	–	getComAll(com,comVel);
1378	–
1379	–	SimInfo::MoleculeIterator i;
1380	–	Molecule* mol;
1381	–
1382	–	Vector3d thisr(0.0);
1383	–	Vector3d thisp(0.0);
1384	–
1385	–	double thisMass;
1386	–
1387	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1388	–	thisMass = mol->getMass();
1389	–	thisr = mol->getCom()-com;
1390	–	thisp = (mol->getComVel()-comVel)*thisMass;
1391	–
1392	–	angularMomentum += cross( thisr, thisp );
1393	–
1394	–	}
1395	–
1396	–	#ifdef IS_MPI
1397	–	Vector3d tmpAngMom;
1398	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1399	–	#endif
1400	–
1401	–	return angularMomentum;
1402	–	}
1403	–
1404	–
1405	–	}//end namespace oopse
1406	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 879 by chrisfen, Wed Feb 1 21:06:43 2006 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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