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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 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 "brains/ForceField.hpp"
66	+	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	#ifdef IS_MPI
69	<	#include "UseTheForce/mpiComponentPlan.h"
69	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
70	<	#endif
71	<
72	<	namespace oopse {
73	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
74	<	std::map<int, std::set<int> >::iterator i = container.find(index);
75	<	std::set<int> result;
76	<	if (i != container.end()) {
77	<	result = i->second;
78	<	}
79	<
80	<	return result;
81	<	}
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), nGlobalConstraints_(0),
78	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
79	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
80	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL),
81	>	topologyDone_(false), calcBoxDipole_(false), useAtomicVirial_(true),
82	>	hasNGlobalConstraints_(false) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin();
95	>	i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	if ( (*i)->haveRegion() ) {
98	>	molStamp->setRegion( (*i)->getRegion() );
99	>	} else {
100	>	// set the region to a disallowed value:
101	>	molStamp->setRegion( -1 );
102	>	}
103
104	<	MoleculeStamp* molStamp;
93	<	int nMolWithSameStamp;
94	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
95	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
96	<	CutoffGroupStamp* cgStamp;
97	<	RigidBodyStamp* rbStamp;
98	<	int nRigidAtoms = 0;
99	<	std::vector<Component*> components = simParams->getComponents();
104	>	nMolWithSameStamp = (*i)->getNMol();
105
106	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
107	<	molStamp = (*i)->getMoleculeStamp();
108	<	nMolWithSameStamp = (*i)->getNMol();
109	<
110	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
111	<
112	<	//calculate atoms in molecules
113	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114	<
115	<	//calculate atoms in cutoff groups
116	<	int nAtomsInGroups = 0;
117	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	<
119	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroupStamp(j);
121	<	nAtomsInGroups += cgStamp->getNMembers();
117	<	}
118	<
119	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
120	<
121	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
122	<
123	<	//calculate atoms in rigid bodies
124	<	int nAtomsInRigidBodies = 0;
125	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
126	<
127	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
128	<	rbStamp = molStamp->getRigidBodyStamp(j);
129	<	nAtomsInRigidBodies += rbStamp->getNMembers();
130	<	}
131	<
132	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
133	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
134	<
106	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
107	>
108	>	//calculate atoms in molecules
109	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
110	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
111	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
112	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
113	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
114	>
115	>	//calculate atoms in cutoff groups
116	>	int nAtomsInGroups = 0;
117	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	>
119	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121	>	nAtomsInGroups += cgStamp->getNMembers();
122		}
123	<
124	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
125	<	//group therefore the total number of cutoff groups in the system is
126	<	//equal to the total number of atoms minus number of atoms belong to
127	<	//cutoff group defined in meta-data file plus the number of cutoff
128	<	//groups defined in meta-data file
129	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130	<
131	<	//every free atom (atom does not belong to rigid bodies) is an
132	<	//integrable object therefore the total number of integrable objects
133	<	//in the system is equal to the total number of atoms minus number of
134	<	//atoms belong to rigid body defined in meta-data file plus the number
135	<	//of rigid bodies defined in meta-data file
136	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137	<	+ nGlobalRigidBodies_;
138	<
139	<	nGlobalMols_ = molStampIds_.size();
153	<
154	<	#ifdef IS_MPI
155	<	molToProcMap_.resize(nGlobalMols_);
156	<	#endif
157	<
123	>
124	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	>
126	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127	>
128	>	//calculate atoms in rigid bodies
129	>	int nAtomsInRigidBodies = 0;
130	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	>
132	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134	>	nAtomsInRigidBodies += rbStamp->getNMembers();
135	>	}
136	>
137	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	>
140		}
141	+
142	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	+	//group therefore the total number of cutoff groups in the system is
144	+	//equal to the total number of atoms minus number of atoms belong to
145	+	//cutoff group defined in meta-data file plus the number of cutoff
146	+	//groups defined in meta-data file
147
148	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149	+
150	+	//every free atom (atom does not belong to rigid bodies) is an
151	+	//integrable object therefore the total number of integrable objects
152	+	//in the system is equal to the total number of atoms minus number of
153	+	//atoms belong to rigid body defined in meta-data file plus the number
154	+	//of rigid bodies defined in meta-data file
155	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	+	+ nGlobalRigidBodies_;
157	+
158	+	nGlobalMols_ = molStampIds_.size();
159	+	molToProcMap_.resize(nGlobalMols_);
160	+	}
161	+
162		SimInfo::~SimInfo() {
163	<	std::map<int, Molecule*>::iterator i;
163	>	map<int, Molecule*>::iterator i;
164		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165		delete i->second;
166		}
#	Line 169 | Line 171 | namespace oopse {
171		delete forceField_;
172		}
173
172	–	int SimInfo::getNGlobalConstraints() {
173	–	int nGlobalConstraints;
174	–	#ifdef IS_MPI
175	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
176	–	MPI_COMM_WORLD);
177	–	#else
178	–	nGlobalConstraints =  nConstraints_;
179	–	#endif
180	–	return nGlobalConstraints;
181	–	}
174
175		bool SimInfo::addMolecule(Molecule* mol) {
176		MoleculeIterator i;
177	<
177	>
178		i = molecules_.find(mol->getGlobalIndex());
179		if (i == molecules_.end() ) {
180	<
181	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
182	<
180	>
181	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
182	>
183		nAtoms_ += mol->getNAtoms();
184		nBonds_ += mol->getNBonds();
185		nBends_ += mol->getNBends();
186		nTorsions_ += mol->getNTorsions();
187	+	nInversions_ += mol->getNInversions();
188		nRigidBodies_ += mol->getNRigidBodies();
189		nIntegrableObjects_ += mol->getNIntegrableObjects();
190		nCutoffGroups_ += mol->getNCutoffGroups();
191		nConstraints_ += mol->getNConstraintPairs();
192	<
193	<	addExcludePairs(mol);
194	<
192	>
193	>	addInteractionPairs(mol);
194	>
195		return true;
196		} else {
197		return false;
198		}
199		}
200	<
200	>
201		bool SimInfo::removeMolecule(Molecule* mol) {
202		MoleculeIterator i;
203		i = molecules_.find(mol->getGlobalIndex());
#	Line 217 | Line 210 | namespace oopse {
210		nBonds_ -= mol->getNBonds();
211		nBends_ -= mol->getNBends();
212		nTorsions_ -= mol->getNTorsions();
213	+	nInversions_ -= mol->getNInversions();
214		nRigidBodies_ -= mol->getNRigidBodies();
215		nIntegrableObjects_ -= mol->getNIntegrableObjects();
216		nCutoffGroups_ -= mol->getNCutoffGroups();
217		nConstraints_ -= mol->getNConstraintPairs();
218
219	<	removeExcludePairs(mol);
219	>	removeInteractionPairs(mol);
220		molecules_.erase(mol->getGlobalIndex());
221
222		delete mol;
#	Line 231 | Line 225 | namespace oopse {
225		} else {
226		return false;
227		}
234	–
235	–
228		}
229
230
#	Line 248 | Line 240 | namespace oopse {
240
241
242		void SimInfo::calcNdf() {
243	<	int ndf_local;
243	>	int ndf_local, nfq_local;
244		MoleculeIterator i;
245	<	std::vector<StuntDouble*>::iterator j;
245	>	vector<StuntDouble*>::iterator j;
246	>	vector<Atom*>::iterator k;
247	>
248		Molecule* mol;
249	<	StuntDouble* integrableObject;
249	>	StuntDouble* sd;
250	>	Atom* atom;
251
252		ndf_local = 0;
253	+	nfq_local = 0;
254
255		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
260	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
261	–	integrableObject = mol->nextIntegrableObject(j)) {
256
257	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
258	+	sd = mol->nextIntegrableObject(j)) {
259	+
260		ndf_local += 3;
261
262	<	if (integrableObject->isDirectional()) {
263	<	if (integrableObject->isLinear()) {
262	>	if (sd->isDirectional()) {
263	>	if (sd->isLinear()) {
264		ndf_local += 2;
265		} else {
266		ndf_local += 3;
267		}
268		}
272	–
269		}
270	+
271	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
272	+	atom = mol->nextFluctuatingCharge(k)) {
273	+	if (atom->isFluctuatingCharge()) {
274	+	nfq_local++;
275	+	}
276	+	}
277		}
278
279	+	ndfLocal_ = ndf_local;
280	+
281		// n_constraints is local, so subtract them on each processor
282		ndf_local -= nConstraints_;
283
284		#ifdef IS_MPI
285	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
285	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
286	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
287	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
288		#else
289		ndf_ = ndf_local;
290	+	nGlobalFluctuatingCharges_ = nfq_local;
291		#endif
292
293		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 288 | Line 296 | namespace oopse {
296
297		}
298
299	+	int SimInfo::getFdf() {
300	+	#ifdef IS_MPI
301	+	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
302	+	#else
303	+	fdf_ = fdf_local;
304	+	#endif
305	+	return fdf_;
306	+	}
307	+
308	+	unsigned int SimInfo::getNLocalCutoffGroups(){
309	+	int nLocalCutoffAtoms = 0;
310	+	Molecule* mol;
311	+	MoleculeIterator mi;
312	+	CutoffGroup* cg;
313	+	Molecule::CutoffGroupIterator ci;
314	+
315	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
316	+
317	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
318	+	cg = mol->nextCutoffGroup(ci)) {
319	+	nLocalCutoffAtoms += cg->getNumAtom();
320	+
321	+	}
322	+	}
323	+
324	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
325	+	}
326	+
327		void SimInfo::calcNdfRaw() {
328		int ndfRaw_local;
329
330		MoleculeIterator i;
331	<	std::vector<StuntDouble*>::iterator j;
331	>	vector<StuntDouble*>::iterator j;
332		Molecule* mol;
333	<	StuntDouble* integrableObject;
333	>	StuntDouble* sd;
334
335		// Raw degrees of freedom that we have to set
336		ndfRaw_local = 0;
337
338		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
303	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
304	–	integrableObject = mol->nextIntegrableObject(j)) {
339
340	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
341	+	sd = mol->nextIntegrableObject(j)) {
342	+
343		ndfRaw_local += 3;
344
345	<	if (integrableObject->isDirectional()) {
346	<	if (integrableObject->isLinear()) {
345	>	if (sd->isDirectional()) {
346	>	if (sd->isLinear()) {
347		ndfRaw_local += 2;
348		} else {
349		ndfRaw_local += 3;
#	Line 317 | Line 354 | namespace oopse {
354		}
355
356		#ifdef IS_MPI
357	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
357	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
358		#else
359		ndfRaw_ = ndfRaw_local;
360		#endif
#	Line 328 | Line 365 | namespace oopse {
365
366		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
367
331	–
368		#ifdef IS_MPI
369	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
369	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
370	>	MPI_COMM_WORLD);
371		#else
372		ndfTrans_ = ndfTrans_local;
373		#endif
374
375		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
339	–
376		}
377
378	<	void SimInfo::addExcludePairs(Molecule* mol) {
379	<	std::vector<Bond*>::iterator bondIter;
380	<	std::vector<Bend*>::iterator bendIter;
381	<	std::vector<Torsion*>::iterator torsionIter;
378	>	void SimInfo::addInteractionPairs(Molecule* mol) {
379	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
380	>	vector<Bond*>::iterator bondIter;
381	>	vector<Bend*>::iterator bendIter;
382	>	vector<Torsion*>::iterator torsionIter;
383	>	vector<Inversion*>::iterator inversionIter;
384		Bond* bond;
385		Bend* bend;
386		Torsion* torsion;
387	+	Inversion* inversion;
388		int a;
389		int b;
390		int c;
391		int d;
392
393	<	std::map<int, std::set<int> > atomGroups;
393	>	// atomGroups can be used to add special interaction maps between
394	>	// groups of atoms that are in two separate rigid bodies.
395	>	// However, most site-site interactions between two rigid bodies
396	>	// are probably not special, just the ones between the physically
397	>	// bonded atoms.  Interactions *within* a single rigid body should
398	>	// always be excluded.  These are done at the bottom of this
399	>	// function.
400
401	+	map<int, set<int> > atomGroups;
402		Molecule::RigidBodyIterator rbIter;
403		RigidBody* rb;
404		Molecule::IntegrableObjectIterator ii;
405	<	StuntDouble* integrableObject;
405	>	StuntDouble* sd;
406
407	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
408	<	integrableObject = mol->nextIntegrableObject(ii)) {
409	<
410	<	if (integrableObject->isRigidBody()) {
411	<	rb = static_cast<RigidBody*>(integrableObject);
412	<	std::vector<Atom*> atoms = rb->getAtoms();
413	<	std::set<int> rigidAtoms;
414	<	for (int i = 0; i < atoms.size(); ++i) {
415	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
416	<	}
417	<	for (int i = 0; i < atoms.size(); ++i) {
418	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
419	<	}
407	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
408	>	sd = mol->nextIntegrableObject(ii)) {
409	>
410	>	if (sd->isRigidBody()) {
411	>	rb = static_cast<RigidBody*>(sd);
412	>	vector<Atom*> atoms = rb->getAtoms();
413	>	set<int> rigidAtoms;
414	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
416	>	}
417	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
418	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
419	>	}
420		} else {
421	<	std::set<int> oneAtomSet;
422	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
423	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
421	>	set<int> oneAtomSet;
422	>	oneAtomSet.insert(sd->getGlobalIndex());
423	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
424		}
425		}
426
427	<
428	<
429	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
427	>
428	>	for (bond= mol->beginBond(bondIter); bond != NULL;
429	>	bond = mol->nextBond(bondIter)) {
430	>
431		a = bond->getAtomA()->getGlobalIndex();
432	<	b = bond->getAtomB()->getGlobalIndex();
433	<	exclude_.addPair(a, b);
432	>	b = bond->getAtomB()->getGlobalIndex();
433	>
434	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
435	>	oneTwoInteractions_.addPair(a, b);
436	>	} else {
437	>	excludedInteractions_.addPair(a, b);
438	>	}
439		}
440
441	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
441	>	for (bend= mol->beginBend(bendIter); bend != NULL;
442	>	bend = mol->nextBend(bendIter)) {
443	>
444		a = bend->getAtomA()->getGlobalIndex();
445		b = bend->getAtomB()->getGlobalIndex();
446		c = bend->getAtomC()->getGlobalIndex();
393	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
394	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
395	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
396	–
397	–	exclude_.addPairs(rigidSetA, rigidSetB);
398	–	exclude_.addPairs(rigidSetA, rigidSetC);
399	–	exclude_.addPairs(rigidSetB, rigidSetC);
447
448	<	//exclude_.addPair(a, b);
449	<	//exclude_.addPair(a, c);
450	<	//exclude_.addPair(b, c);
448	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
449	>	oneTwoInteractions_.addPair(a, b);
450	>	oneTwoInteractions_.addPair(b, c);
451	>	} else {
452	>	excludedInteractions_.addPair(a, b);
453	>	excludedInteractions_.addPair(b, c);
454	>	}
455	>
456	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
457	>	oneThreeInteractions_.addPair(a, c);
458	>	} else {
459	>	excludedInteractions_.addPair(a, c);
460	>	}
461		}
462
463	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
463	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
464	>	torsion = mol->nextTorsion(torsionIter)) {
465	>
466		a = torsion->getAtomA()->getGlobalIndex();
467		b = torsion->getAtomB()->getGlobalIndex();
468		c = torsion->getAtomC()->getGlobalIndex();
469	<	d = torsion->getAtomD()->getGlobalIndex();
411	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
412	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
413	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
414	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
469	>	d = torsion->getAtomD()->getGlobalIndex();
470
471	<	exclude_.addPairs(rigidSetA, rigidSetB);
472	<	exclude_.addPairs(rigidSetA, rigidSetC);
473	<	exclude_.addPairs(rigidSetA, rigidSetD);
474	<	exclude_.addPairs(rigidSetB, rigidSetC);
475	<	exclude_.addPairs(rigidSetB, rigidSetD);
476	<	exclude_.addPairs(rigidSetC, rigidSetD);
471	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
472	>	oneTwoInteractions_.addPair(a, b);
473	>	oneTwoInteractions_.addPair(b, c);
474	>	oneTwoInteractions_.addPair(c, d);
475	>	} else {
476	>	excludedInteractions_.addPair(a, b);
477	>	excludedInteractions_.addPair(b, c);
478	>	excludedInteractions_.addPair(c, d);
479	>	}
480
481	<	/*
482	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
483	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
484	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
485	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
486	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
487	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
488	<
489	<
490	<	exclude_.addPair(a, b);
491	<	exclude_.addPair(a, c);
492	<	exclude_.addPair(a, d);
493	<	exclude_.addPair(b, c);
436	<	exclude_.addPair(b, d);
437	<	exclude_.addPair(c, d);
438	<	*/
481	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
482	>	oneThreeInteractions_.addPair(a, c);
483	>	oneThreeInteractions_.addPair(b, d);
484	>	} else {
485	>	excludedInteractions_.addPair(a, c);
486	>	excludedInteractions_.addPair(b, d);
487	>	}
488	>
489	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
490	>	oneFourInteractions_.addPair(a, d);
491	>	} else {
492	>	excludedInteractions_.addPair(a, d);
493	>	}
494		}
495
496	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
497	<	std::vector<Atom*> atoms = rb->getAtoms();
498	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
499	<	for (int j = i + 1; j < atoms.size(); ++j) {
496	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
497	>	inversion = mol->nextInversion(inversionIter)) {
498	>
499	>	a = inversion->getAtomA()->getGlobalIndex();
500	>	b = inversion->getAtomB()->getGlobalIndex();
501	>	c = inversion->getAtomC()->getGlobalIndex();
502	>	d = inversion->getAtomD()->getGlobalIndex();
503	>
504	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
505	>	oneTwoInteractions_.addPair(a, b);
506	>	oneTwoInteractions_.addPair(a, c);
507	>	oneTwoInteractions_.addPair(a, d);
508	>	} else {
509	>	excludedInteractions_.addPair(a, b);
510	>	excludedInteractions_.addPair(a, c);
511	>	excludedInteractions_.addPair(a, d);
512	>	}
513	>
514	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
515	>	oneThreeInteractions_.addPair(b, c);
516	>	oneThreeInteractions_.addPair(b, d);
517	>	oneThreeInteractions_.addPair(c, d);
518	>	} else {
519	>	excludedInteractions_.addPair(b, c);
520	>	excludedInteractions_.addPair(b, d);
521	>	excludedInteractions_.addPair(c, d);
522	>	}
523	>	}
524	>
525	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
526	>	rb = mol->nextRigidBody(rbIter)) {
527	>	vector<Atom*> atoms = rb->getAtoms();
528	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
529	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
530		a = atoms[i]->getGlobalIndex();
531		b = atoms[j]->getGlobalIndex();
532	<	exclude_.addPair(a, b);
532	>	excludedInteractions_.addPair(a, b);
533		}
534		}
535		}
536
537		}
538
539	<	void SimInfo::removeExcludePairs(Molecule* mol) {
540	<	std::vector<Bond*>::iterator bondIter;
541	<	std::vector<Bend*>::iterator bendIter;
542	<	std::vector<Torsion*>::iterator torsionIter;
539	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
540	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
541	>	vector<Bond*>::iterator bondIter;
542	>	vector<Bend*>::iterator bendIter;
543	>	vector<Torsion*>::iterator torsionIter;
544	>	vector<Inversion*>::iterator inversionIter;
545		Bond* bond;
546		Bend* bend;
547		Torsion* torsion;
548	+	Inversion* inversion;
549		int a;
550		int b;
551		int c;
552		int d;
553
554	<	std::map<int, std::set<int> > atomGroups;
467	<
554	>	map<int, set<int> > atomGroups;
555		Molecule::RigidBodyIterator rbIter;
556		RigidBody* rb;
557		Molecule::IntegrableObjectIterator ii;
558	<	StuntDouble* integrableObject;
558	>	StuntDouble* sd;
559
560	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
561	<	integrableObject = mol->nextIntegrableObject(ii)) {
562	<
563	<	if (integrableObject->isRigidBody()) {
564	<	rb = static_cast<RigidBody*>(integrableObject);
565	<	std::vector<Atom*> atoms = rb->getAtoms();
566	<	std::set<int> rigidAtoms;
567	<	for (int i = 0; i < atoms.size(); ++i) {
568	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
569	<	}
570	<	for (int i = 0; i < atoms.size(); ++i) {
571	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
572	<	}
560	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
561	>	sd = mol->nextIntegrableObject(ii)) {
562	>
563	>	if (sd->isRigidBody()) {
564	>	rb = static_cast<RigidBody*>(sd);
565	>	vector<Atom*> atoms = rb->getAtoms();
566	>	set<int> rigidAtoms;
567	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
569	>	}
570	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
571	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
572	>	}
573		} else {
574	<	std::set<int> oneAtomSet;
575	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
576	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
574	>	set<int> oneAtomSet;
575	>	oneAtomSet.insert(sd->getGlobalIndex());
576	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
577		}
578		}
579
580	<
581	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
580	>	for (bond= mol->beginBond(bondIter); bond != NULL;
581	>	bond = mol->nextBond(bondIter)) {
582	>
583		a = bond->getAtomA()->getGlobalIndex();
584	<	b = bond->getAtomB()->getGlobalIndex();
585	<	exclude_.removePair(a, b);
584	>	b = bond->getAtomB()->getGlobalIndex();
585	>
586	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
587	>	oneTwoInteractions_.removePair(a, b);
588	>	} else {
589	>	excludedInteractions_.removePair(a, b);
590	>	}
591		}
592
593	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
593	>	for (bend= mol->beginBend(bendIter); bend != NULL;
594	>	bend = mol->nextBend(bendIter)) {
595	>
596		a = bend->getAtomA()->getGlobalIndex();
597		b = bend->getAtomB()->getGlobalIndex();
598		c = bend->getAtomC()->getGlobalIndex();
504	–
505	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
506	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
507	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
508	–
509	–	exclude_.removePairs(rigidSetA, rigidSetB);
510	–	exclude_.removePairs(rigidSetA, rigidSetC);
511	–	exclude_.removePairs(rigidSetB, rigidSetC);
599
600	<	//exclude_.removePair(a, b);
601	<	//exclude_.removePair(a, c);
602	<	//exclude_.removePair(b, c);
600	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
601	>	oneTwoInteractions_.removePair(a, b);
602	>	oneTwoInteractions_.removePair(b, c);
603	>	} else {
604	>	excludedInteractions_.removePair(a, b);
605	>	excludedInteractions_.removePair(b, c);
606	>	}
607	>
608	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
609	>	oneThreeInteractions_.removePair(a, c);
610	>	} else {
611	>	excludedInteractions_.removePair(a, c);
612	>	}
613		}
614
615	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
615	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
616	>	torsion = mol->nextTorsion(torsionIter)) {
617	>
618		a = torsion->getAtomA()->getGlobalIndex();
619		b = torsion->getAtomB()->getGlobalIndex();
620		c = torsion->getAtomC()->getGlobalIndex();
621	<	d = torsion->getAtomD()->getGlobalIndex();
621	>	d = torsion->getAtomD()->getGlobalIndex();
622	>
623	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
624	>	oneTwoInteractions_.removePair(a, b);
625	>	oneTwoInteractions_.removePair(b, c);
626	>	oneTwoInteractions_.removePair(c, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, b);
629	>	excludedInteractions_.removePair(b, c);
630	>	excludedInteractions_.removePair(c, d);
631	>	}
632
633	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
634	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
635	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
636	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
633	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
634	>	oneThreeInteractions_.removePair(a, c);
635	>	oneThreeInteractions_.removePair(b, d);
636	>	} else {
637	>	excludedInteractions_.removePair(a, c);
638	>	excludedInteractions_.removePair(b, d);
639	>	}
640
641	<	exclude_.removePairs(rigidSetA, rigidSetB);
642	<	exclude_.removePairs(rigidSetA, rigidSetC);
643	<	exclude_.removePairs(rigidSetA, rigidSetD);
644	<	exclude_.removePairs(rigidSetB, rigidSetC);
645	<	exclude_.removePairs(rigidSetB, rigidSetD);
646	<	exclude_.removePairs(rigidSetC, rigidSetD);
641	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
642	>	oneFourInteractions_.removePair(a, d);
643	>	} else {
644	>	excludedInteractions_.removePair(a, d);
645	>	}
646	>	}
647
648	<	/*
649	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
538	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
539	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
540	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
541	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
542	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
648	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
649	>	inversion = mol->nextInversion(inversionIter)) {
650
651	<
652	<	exclude_.removePair(a, b);
653	<	exclude_.removePair(a, c);
654	<	exclude_.removePair(a, d);
655	<	exclude_.removePair(b, c);
656	<	exclude_.removePair(b, d);
657	<	exclude_.removePair(c, d);
658	<	*/
651	>	a = inversion->getAtomA()->getGlobalIndex();
652	>	b = inversion->getAtomB()->getGlobalIndex();
653	>	c = inversion->getAtomC()->getGlobalIndex();
654	>	d = inversion->getAtomD()->getGlobalIndex();
655	>
656	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
657	>	oneTwoInteractions_.removePair(a, b);
658	>	oneTwoInteractions_.removePair(a, c);
659	>	oneTwoInteractions_.removePair(a, d);
660	>	} else {
661	>	excludedInteractions_.removePair(a, b);
662	>	excludedInteractions_.removePair(a, c);
663	>	excludedInteractions_.removePair(a, d);
664	>	}
665	>
666	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
667	>	oneThreeInteractions_.removePair(b, c);
668	>	oneThreeInteractions_.removePair(b, d);
669	>	oneThreeInteractions_.removePair(c, d);
670	>	} else {
671	>	excludedInteractions_.removePair(b, c);
672	>	excludedInteractions_.removePair(b, d);
673	>	excludedInteractions_.removePair(c, d);
674	>	}
675		}
676
677	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
678	<	std::vector<Atom*> atoms = rb->getAtoms();
679	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
680	<	for (int j = i + 1; j < atoms.size(); ++j) {
677	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
678	>	rb = mol->nextRigidBody(rbIter)) {
679	>	vector<Atom*> atoms = rb->getAtoms();
680	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
681	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
682		a = atoms[i]->getGlobalIndex();
683		b = atoms[j]->getGlobalIndex();
684	<	exclude_.removePair(a, b);
684	>	excludedInteractions_.removePair(a, b);
685		}
686		}
687		}
688	<
688	>
689		}
690	<
691	<
690	>
691	>
692		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
693		int curStampId;
694	<
694	>
695		//index from 0
696		curStampId = moleculeStamps_.size();
697
#	Line 575 | Line 699 | namespace oopse {
699		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
700		}
701
578	–	void SimInfo::update() {
702
703	<	setupSimType();
704	<
705	<	#ifdef IS_MPI
706	<	setupFortranParallel();
707	<	#endif
708	<
709	<	setupFortranSim();
710	<
711	<	//setup fortran force field
712	<	/** @deprecate */
590	<	int isError = 0;
591	<
592	<	setupElectrostaticSummationMethod( isError );
593	<	setupSwitchingFunction();
594	<
595	<	if(isError){
596	<	sprintf( painCave.errMsg,
597	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
598	<	painCave.isFatal = 1;
599	<	simError();
600	<	}
601	<
602	<
603	<	setupCutoff();
604	<
703	>	/**
704	>	* update
705	>	*
706	>	*  Performs the global checks and variable settings after the
707	>	*  objects have been created.
708	>	*
709	>	*/
710	>	void SimInfo::update() {
711	>	setupSimVariables();
712	>	calcNConstraints();
713		calcNdf();
714		calcNdfRaw();
715		calcNdfTrans();
608	–
609	–	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	<
738	<	}
736	>	}
737	>	}
738	>
739	>	#ifdef IS_MPI
740
741	<	return atomTypes;
742	<	}
629	<
630	<	void SimInfo::setupSimType() {
631	<	std::set<AtomType*>::iterator i;
632	<	std::set<AtomType*> atomTypes;
633	<	atomTypes = getUniqueAtomTypes();
741	>	// loop over the found atom types on this processor, and add their
742	>	// numerical idents to a vector:
743
744	<	int useLennardJones = 0;
745	<	int useElectrostatic = 0;
746	<	int useEAM = 0;
747	<	int useSC = 0;
639	<	int useCharge = 0;
640	<	int useDirectional = 0;
641	<	int useDipole = 0;
642	<	int useGayBerne = 0;
643	<	int useSticky = 0;
644	<	int useStickyPower = 0;
645	<	int useShape = 0;
646	<	int useFLARB = 0; //it is not in AtomType yet
647	<	int useDirectionalAtom = 0;
648	<	int useElectrostatics = 0;
649	<	//usePBC and useRF are from simParams
650	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
651	<	int useRF;
652	<	int useSF;
653	<	std::string myMethod;
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	<	// set the useRF logical
750	<	useRF = 0;
657	<	useSF = 0;
749	>	// count_local holds the number of found types on this processor
750	>	int count_local = foundTypes.size();
751
752	+	int nproc;
753	+	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
754	+	// int nproc = MPI::COMM_WORLD.Get_size();
755
756	<	if (simParams_->haveElectrostaticSummationMethod()) {
757	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
758	<	toUpper(myMethod);
759	<	if (myMethod == "REACTION_FIELD") {
664	<	useRF=1;
665	<	} else {
666	<	if (myMethod == "SHIFTED_FORCE") {
667	<	useSF = 1;
668	<	}
669	<	}
670	<	}
756	>	// we need arrays to hold the counts and displacement vectors for
757	>	// all processors
758	>	vector<int> counts(nproc, 0);
759	>	vector<int> disps(nproc, 0);
760
761	<	//loop over all of the atom types
762	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
763	<	useLennardJones |= (*i)->isLennardJones();
764	<	useElectrostatic |= (*i)->isElectrostatic();
765	<	useEAM |= (*i)->isEAM();
766	<	useSC |= (*i)->isSC();
767	<	useCharge |= (*i)->isCharge();
768	<	useDirectional |= (*i)->isDirectional();
769	<	useDipole |= (*i)->isDipole();
770	<	useGayBerne |= (*i)->isGayBerne();
771	<	useSticky |= (*i)->isSticky();
772	<	useStickyPower |= (*i)->isStickyPower();
684	<	useShape |= (*i)->isShape();
761	>	// fill the counts array
762	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
763	>	1, MPI_INT, MPI_COMM_WORLD);
764	>	// MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
765	>	//                           1, MPI::INT);
766	>
767	>	// use the processor counts to compute the displacement array
768	>	disps[0] = 0;
769	>	int totalCount = counts[0];
770	>	for (int iproc = 1; iproc < nproc; iproc++) {
771	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
772	>	totalCount += counts[iproc];
773		}
774
775	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
776	<	useDirectionalAtom = 1;
777	<	}
775	>	// we need a (possibly redundant) set of all found types:
776	>	vector<int> ftGlobal(totalCount);
777	>
778	>	// now spray out the foundTypes to all the other processors:
779	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
780	>	&ftGlobal[0], &counts[0], &disps[0],
781	>	MPI_INT, MPI_COMM_WORLD);
782	>	// MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
783	>	//                            &ftGlobal[0], &counts[0], &disps[0],
784	>	//                            MPI::INT);
785
786	<	if (useCharge || useDipole) {
692	<	useElectrostatics = 1;
693	<	}
786	>	vector<int>::iterator j;
787
788	<	#ifdef IS_MPI
789	<	int temp;
788	>	// foundIdents is a stl set, so inserting an already found ident
789	>	// will have no effect.
790	>	set<int> foundIdents;
791
792	<	temp = usePBC;
793	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
792	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
793	>	foundIdents.insert((*j));
794	>
795	>	// now iterate over the foundIdents and get the actual atom types
796	>	// that correspond to these:
797	>	set<int>::iterator it;
798	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
799	>	atomTypes.insert( forceField_->getAtomType((*it)) );
800	>
801	>	#endif
802
803	<	temp = useDirectionalAtom;
804	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
803	>	return atomTypes;
804	>	}
805
704	–	temp = useLennardJones;
705	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806
807	<	temp = useElectrostatics;
808	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>	int getGlobalCountOfType(AtomType* atype) {
808	>	/*
809	>	set<AtomType*> atypes = getSimulatedAtomTypes();
810	>	map<AtomType*, int> counts_;
811
812	<	temp = useCharge;
813	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
812	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
813	>	for(atom = mol->beginAtom(ai); atom != NULL;
814	>	atom = mol->nextAtom(ai)) {
815	>	atom->getAtomType();
816	>	}
817	>	}
818	>	*/
819	>	return 0;
820	>	}
821
822	<	temp = useDipole;
823	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
824	<
825	<	temp = useSticky;
826	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	<
828	<	temp = useStickyPower;
829	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
822	>	void SimInfo::setupSimVariables() {
823	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
824	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
825	>	// parameter is true
826	>	calcBoxDipole_ = false;
827	>	if ( simParams_->haveAccumulateBoxDipole() )
828	>	if ( simParams_->getAccumulateBoxDipole() ) {
829	>	calcBoxDipole_ = true;
830	>	}
831
832	<	temp = useGayBerne;
833	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832	>	set<AtomType*>::iterator i;
833	>	set<AtomType*> atomTypes;
834	>	atomTypes = getSimulatedAtomTypes();
835	>	bool usesElectrostatic = false;
836	>	bool usesMetallic = false;
837	>	bool usesDirectional = false;
838	>	bool usesFluctuatingCharges =  false;
839	>	//loop over all of the atom types
840	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
841	>	usesElectrostatic |= (*i)->isElectrostatic();
842	>	usesMetallic |= (*i)->isMetal();
843	>	usesDirectional |= (*i)->isDirectional();
844	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
845	>	}
846
847	<	temp = useEAM;
848	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
847	>	#ifdef IS_MPI
848	>	int temp;
849
850	<	temp = useSC;
851	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	>	temp = usesDirectional;
851	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
852	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
853
854	<	temp = useShape;
855	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	>	temp = usesMetallic;
855	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
856	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
857
858	<	temp = useFLARB;
859	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
858	>	temp = usesElectrostatic;
859	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
860	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
861
862	<	temp = useRF;
863	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	>	temp = usesFluctuatingCharges;
863	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
864	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
865	>	#else
866
867	<	temp = useSF;
868	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
867	>	usesDirectionalAtoms_ = usesDirectional;
868	>	usesMetallicAtoms_ = usesMetallic;
869	>	usesElectrostaticAtoms_ = usesElectrostatic;
870	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
871
872		#endif
873	+
874	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
875	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
876	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
877	+	}
878
745	–	fInfo_.SIM_uses_PBC = usePBC;
746	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
747	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
748	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
749	–	fInfo_.SIM_uses_Charges = useCharge;
750	–	fInfo_.SIM_uses_Dipoles = useDipole;
751	–	fInfo_.SIM_uses_Sticky = useSticky;
752	–	fInfo_.SIM_uses_StickyPower = useStickyPower;
753	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
754	–	fInfo_.SIM_uses_EAM = useEAM;
755	–	fInfo_.SIM_uses_SC = useSC;
756	–	fInfo_.SIM_uses_Shapes = useShape;
757	–	fInfo_.SIM_uses_FLARB = useFLARB;
758	–	fInfo_.SIM_uses_RF = useRF;
759	–	fInfo_.SIM_uses_SF = useSF;
879
880	<	if( myMethod == "REACTION_FIELD") {
880	>	vector<int> SimInfo::getGlobalAtomIndices() {
881	>	SimInfo::MoleculeIterator mi;
882	>	Molecule* mol;
883	>	Molecule::AtomIterator ai;
884	>	Atom* atom;
885	>
886	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
887	>
888	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889
890	<	if (simParams_->haveDielectric()) {
891	<	fInfo_.dielect = simParams_->getDielectric();
892	<	} else {
766	<	sprintf(painCave.errMsg,
767	<	"SimSetup Error: No Dielectric constant was set.\n"
768	<	"\tYou are trying to use Reaction Field without"
769	<	"\tsetting a dielectric constant!\n");
770	<	painCave.isFatal = 1;
771	<	simError();
772	<	}
890	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
891	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
892	>	}
893		}
894	<
894	>	return GlobalAtomIndices;
895		}
896
777	–	void SimInfo::setupFortranSim() {
778	–	int isError;
779	–	int nExclude;
780	–	std::vector<int> fortranGlobalGroupMembership;
781	–
782	–	nExclude = exclude_.getSize();
783	–	isError = 0;
897
898	<	//globalGroupMembership_ is filled by SimCreator
899	<	for (int i = 0; i < nGlobalAtoms_; i++) {
900	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
898	>	vector<int> SimInfo::getGlobalGroupIndices() {
899	>	SimInfo::MoleculeIterator mi;
900	>	Molecule* mol;
901	>	Molecule::CutoffGroupIterator ci;
902	>	CutoffGroup* cg;
903	>
904	>	vector<int> GlobalGroupIndices;
905	>
906	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
907	>
908	>	//local index of cutoff group is trivial, it only depends on the
909	>	//order of travesing
910	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
911	>	cg = mol->nextCutoffGroup(ci)) {
912	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
913	>	}
914		}
915	+	return GlobalGroupIndices;
916	+	}
917
918	+
919	+	void SimInfo::prepareTopology() {
920	+
921		//calculate mass ratio of cutoff group
791	–	std::vector<double> mfact;
922		SimInfo::MoleculeIterator mi;
923		Molecule* mol;
924		Molecule::CutoffGroupIterator ci;
925		CutoffGroup* cg;
926		Molecule::AtomIterator ai;
927		Atom* atom;
928	<	double totalMass;
928	>	RealType totalMass;
929
930	<	//to avoid memory reallocation, reserve enough space for mfact
931	<	mfact.reserve(getNCutoffGroups());
930	>	/**
931	>	* The mass factor is the relative mass of an atom to the total
932	>	* mass of the cutoff group it belongs to.  By default, all atoms
933	>	* are their own cutoff groups, and therefore have mass factors of
934	>	* 1.  We need some special handling for massless atoms, which
935	>	* will be treated as carrying the entire mass of the cutoff
936	>	* group.
937	>	*/
938	>	massFactors_.clear();
939	>	massFactors_.resize(getNAtoms(), 1.0);
940
941		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
942	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
942	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
943	>	cg = mol->nextCutoffGroup(ci)) {
944
945		totalMass = cg->getMass();
946		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
947		// Check for massless groups - set mfact to 1 if true
948	<	if (totalMass != 0)
949	<	mfact.push_back(atom->getMass()/totalMass);
948	>	if (totalMass != 0)
949	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
950		else
951	<	mfact.push_back( 1.0 );
951	>	massFactors_[atom->getLocalIndex()] = 1.0;
952		}
814	–
953		}
954		}
955
956	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
819	<	std::vector<int> identArray;
956	>	// Build the identArray_ and regions_
957
958	<	//to avoid memory reallocation, reserve enough space identArray
959	<	identArray.reserve(getNAtoms());
960	<
961	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
958	>	identArray_.clear();
959	>	identArray_.reserve(getNAtoms());
960	>	regions_.clear();
961	>	regions_.reserve(getNAtoms());
962	>
963	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
964	>	int reg = mol->getRegion();
965		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
966	<	identArray.push_back(atom->getIdent());
966	>	identArray_.push_back(atom->getIdent());
967	>	regions_.push_back(reg);
968		}
969		}
970	<
971	<	//fill molMembershipArray
831	<	//molMembershipArray is filled by SimCreator
832	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
833	<	for (int i = 0; i < nGlobalAtoms_; i++) {
834	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
835	<	}
836	<
837	<	//setup fortran simulation
838	<	int nGlobalExcludes = 0;
839	<	int* globalExcludes = NULL;
840	<	int* excludeList = exclude_.getExcludeList();
841	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
842	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
843	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
844	<
845	<	if( isError ){
846	<
847	<	sprintf( painCave.errMsg,
848	<	"There was an error setting the simulation information in fortran.\n" );
849	<	painCave.isFatal = 1;
850	<	painCave.severity = OOPSE_ERROR;
851	<	simError();
852	<	}
853	<
854	<	#ifdef IS_MPI
855	<	sprintf( checkPointMsg,
856	<	"succesfully sent the simulation information to fortran.\n");
857	<	MPIcheckPoint();
858	<	#endif // is_mpi
859	<	}
860	<
861	<
862	<	#ifdef IS_MPI
863	<	void SimInfo::setupFortranParallel() {
864	<
865	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
866	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
867	<	std::vector<int> localToGlobalCutoffGroupIndex;
868	<	SimInfo::MoleculeIterator mi;
869	<	Molecule::AtomIterator ai;
870	<	Molecule::CutoffGroupIterator ci;
871	<	Molecule* mol;
872	<	Atom* atom;
873	<	CutoffGroup* cg;
874	<	mpiSimData parallelData;
875	<	int isError;
876	<
877	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
878	<
879	<	//local index(index in DataStorge) of atom is important
880	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
882	<	}
883	<
884	<	//local index of cutoff group is trivial, it only depends on the order of travesing
885	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
886	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
887	<	}
888	<
889	<	}
890	<
891	<	//fill up mpiSimData struct
892	<	parallelData.nMolGlobal = getNGlobalMolecules();
893	<	parallelData.nMolLocal = getNMolecules();
894	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
895	<	parallelData.nAtomsLocal = getNAtoms();
896	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
897	<	parallelData.nGroupsLocal = getNCutoffGroups();
898	<	parallelData.myNode = worldRank;
899	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
900	<
901	<	//pass mpiSimData struct and index arrays to fortran
902	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
903	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
904	<	&localToGlobalCutoffGroupIndex[0], &isError);
905	<
906	<	if (isError) {
907	<	sprintf(painCave.errMsg,
908	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
909	<	painCave.isFatal = 1;
910	<	simError();
911	<	}
912	<
913	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
914	<	MPIcheckPoint();
915	<
916	<
917	<	}
918	<
919	<	#endif
920	<
921	<	void SimInfo::setupCutoff() {
922	<
923	<	// Check the cutoff policy
924	<	int cp =  TRADITIONAL_CUTOFF_POLICY;
925	<	if (simParams_->haveCutoffPolicy()) {
926	<	std::string myPolicy = simParams_->getCutoffPolicy();
927	<	toUpper(myPolicy);
928	<	if (myPolicy == "MIX") {
929	<	cp = MIX_CUTOFF_POLICY;
930	<	} else {
931	<	if (myPolicy == "MAX") {
932	<	cp = MAX_CUTOFF_POLICY;
933	<	} else {
934	<	if (myPolicy == "TRADITIONAL") {
935	<	cp = TRADITIONAL_CUTOFF_POLICY;
936	<	} else {
937	<	// throw error
938	<	sprintf( painCave.errMsg,
939	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
940	<	painCave.isFatal = 1;
941	<	simError();
942	<	}
943	<	}
944	<	}
945	<	}
946	<	notifyFortranCutoffPolicy(&cp);
947	<
948	<	// Check the Skin Thickness for neighborlists
949	<	double skin;
950	<	if (simParams_->haveSkinThickness()) {
951	<	skin = simParams_->getSkinThickness();
952	<	notifyFortranSkinThickness(&skin);
953	<	}
954	<
955	<	// Check if the cutoff was set explicitly:
956	<	if (simParams_->haveCutoffRadius()) {
957	<	rcut_ = simParams_->getCutoffRadius();
958	<	if (simParams_->haveSwitchingRadius()) {
959	<	rsw_  = simParams_->getSwitchingRadius();
960	<	} else {
961	<	rsw_ = rcut_;
962	<	}
963	<	notifyFortranCutoffs(&rcut_, &rsw_);
964	<
965	<	} else {
966	<
967	<	// For electrostatic atoms, we'll assume a large safe value:
968	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
969	<	sprintf(painCave.errMsg,
970	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
971	<	"\tOOPSE will use a default value of 15.0 angstroms"
972	<	"\tfor the cutoffRadius.\n");
973	<	painCave.isFatal = 0;
974	<	simError();
975	<	rcut_ = 15.0;
976	<
977	<	if (simParams_->haveElectrostaticSummationMethod()) {
978	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
979	<	toUpper(myMethod);
980	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
981	<	if (simParams_->haveSwitchingRadius()){
982	<	sprintf(painCave.errMsg,
983	<	"SimInfo Warning: A value was set for the switchingRadius\n"
984	<	"\teven though the electrostaticSummationMethod was\n"
985	<	"\tset to %s\n", myMethod.c_str());
986	<	painCave.isFatal = 1;
987	<	simError();
988	<	}
989	<	}
990	<	}
991	<
992	<	if (simParams_->haveSwitchingRadius()){
993	<	rsw_ = simParams_->getSwitchingRadius();
994	<	} else {
995	<	sprintf(painCave.errMsg,
996	<	"SimCreator Warning: No value was set for switchingRadius.\n"
997	<	"\tOOPSE will use a default value of\n"
998	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
999	<	painCave.isFatal = 0;
1000	<	simError();
1001	<	rsw_ = 0.85 * rcut_;
1002	<	}
1003	<	notifyFortranCutoffs(&rcut_, &rsw_);
1004	<	} else {
1005	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1006	<	// We'll punt and let fortran figure out the cutoffs later.
1007	<
1008	<	notifyFortranYouAreOnYourOwn();
1009	<
1010	<	}
1011	<	}
970	>
971	>	topologyDone_ = true;
972		}
973
1014	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1015	–
1016	–	int errorOut;
1017	–	int esm =  NONE;
1018	–	int sm = UNDAMPED;
1019	–	double alphaVal;
1020	–	double dielectric;
1021	–
1022	–	errorOut = isError;
1023	–	alphaVal = simParams_->getDampingAlpha();
1024	–	dielectric = simParams_->getDielectric();
1025	–
1026	–	if (simParams_->haveElectrostaticSummationMethod()) {
1027	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028	–	toUpper(myMethod);
1029	–	if (myMethod == "NONE") {
1030	–	esm = NONE;
1031	–	} else {
1032	–	if (myMethod == "SWITCHING_FUNCTION") {
1033	–	esm = SWITCHING_FUNCTION;
1034	–	} else {
1035	–	if (myMethod == "SHIFTED_POTENTIAL") {
1036	–	esm = SHIFTED_POTENTIAL;
1037	–	} else {
1038	–	if (myMethod == "SHIFTED_FORCE") {
1039	–	esm = SHIFTED_FORCE;
1040	–	} else {
1041	–	if (myMethod == "REACTION_FIELD") {
1042	–	esm = REACTION_FIELD;
1043	–	} else {
1044	–	// throw error
1045	–	sprintf( painCave.errMsg,
1046	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1047	–	"\t(Input file specified %s .)\n"
1048	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1049	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1050	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1051	–	painCave.isFatal = 1;
1052	–	simError();
1053	–	}
1054	–	}
1055	–	}
1056	–	}
1057	–	}
1058	–	}
1059	–
1060	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1061	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1062	–	toUpper(myScreen);
1063	–	if (myScreen == "UNDAMPED") {
1064	–	sm = UNDAMPED;
1065	–	} else {
1066	–	if (myScreen == "DAMPED") {
1067	–	sm = DAMPED;
1068	–	if (!simParams_->haveDampingAlpha()) {
1069	–	//throw error
1070	–	sprintf( painCave.errMsg,
1071	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1072	–	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1073	–	painCave.isFatal = 0;
1074	–	simError();
1075	–	}
1076	–	} else {
1077	–	// throw error
1078	–	sprintf( painCave.errMsg,
1079	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1080	–	"\t(Input file specified %s .)\n"
1081	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1082	–	"or \"damped\".\n", myScreen.c_str() );
1083	–	painCave.isFatal = 1;
1084	–	simError();
1085	–	}
1086	–	}
1087	–	}
1088	–
1089	–	// let's pass some summation method variables to fortran
1090	–	setElectrostaticSummationMethod( &esm );
1091	–	notifyFortranElectrostaticMethod( &esm );
1092	–	setScreeningMethod( &sm );
1093	–	setDampingAlpha( &alphaVal );
1094	–	setReactionFieldDielectric( &dielectric );
1095	–	initFortranFF( &errorOut );
1096	–	}
1097	–
1098	–	void SimInfo::setupSwitchingFunction() {
1099	–	int ft = CUBIC;
1100	–
1101	–	if (simParams_->haveSwitchingFunctionType()) {
1102	–	std::string funcType = simParams_->getSwitchingFunctionType();
1103	–	toUpper(funcType);
1104	–	if (funcType == "CUBIC") {
1105	–	ft = CUBIC;
1106	–	} else {
1107	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1108	–	ft = FIFTH_ORDER_POLY;
1109	–	} else {
1110	–	// throw error
1111	–	sprintf( painCave.errMsg,
1112	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1113	–	painCave.isFatal = 1;
1114	–	simError();
1115	–	}
1116	–	}
1117	–	}
1118	–
1119	–	// send switching function notification to switcheroo
1120	–	setFunctionType(&ft);
1121	–
1122	–	}
1123	–
974		void SimInfo::addProperty(GenericData* genData) {
975		properties_.addProperty(genData);
976		}
977
978	<	void SimInfo::removeProperty(const std::string& propName) {
978	>	void SimInfo::removeProperty(const string& propName) {
979		properties_.removeProperty(propName);
980		}
981
#	Line 1133 | Line 983 | namespace oopse {
983		properties_.clearProperties();
984		}
985
986	<	std::vector<std::string> SimInfo::getPropertyNames() {
986	>	vector<string> SimInfo::getPropertyNames() {
987		return properties_.getPropertyNames();
988		}
989
990	<	std::vector<GenericData*> SimInfo::getProperties() {
990	>	vector<GenericData*> SimInfo::getProperties() {
991		return properties_.getProperties();
992		}
993
994	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
994	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
995		return properties_.getPropertyByName(propName);
996		}
997
#	Line 1152 | Line 1002 | namespace oopse {
1002		delete sman_;
1003		sman_ = sman;
1004
1155	–	Molecule* mol;
1156	–	RigidBody* rb;
1157	–	Atom* atom;
1005		SimInfo::MoleculeIterator mi;
1006	+	Molecule::AtomIterator ai;
1007		Molecule::RigidBodyIterator rbIter;
1008	<	Molecule::AtomIterator atomIter;;
1008	>	Molecule::CutoffGroupIterator cgIter;
1009	>	Molecule::BondIterator bondIter;
1010	>	Molecule::BendIterator bendIter;
1011	>	Molecule::TorsionIterator torsionIter;
1012	>	Molecule::InversionIterator inversionIter;
1013
1014	+	Molecule* mol;
1015	+	Atom* atom;
1016	+	RigidBody* rb;
1017	+	CutoffGroup* cg;
1018	+	Bond* bond;
1019	+	Bend* bend;
1020	+	Torsion* torsion;
1021	+	Inversion* inversion;
1022	+
1023		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1024
1025	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1025	>	for (atom = mol->beginAtom(ai); atom != NULL;
1026	>	atom = mol->nextAtom(ai)) {
1027		atom->setSnapshotManager(sman_);
1028	<	}
1029	<
1030	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1028	>	}
1029	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1030	>	rb = mol->nextRigidBody(rbIter)) {
1031		rb->setSnapshotManager(sman_);
1032		}
1033	<	}
1034	<
1033	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1034	>	cg = mol->nextCutoffGroup(cgIter)) {
1035	>	cg->setSnapshotManager(sman_);
1036	>	}
1037	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1038	>	bond = mol->nextBond(bondIter)) {
1039	>	bond->setSnapshotManager(sman_);
1040	>	}
1041	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1042	>	bend = mol->nextBend(bendIter)) {
1043	>	bend->setSnapshotManager(sman_);
1044	>	}
1045	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1046	>	torsion = mol->nextTorsion(torsionIter)) {
1047	>	torsion->setSnapshotManager(sman_);
1048	>	}
1049	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1050	>	inversion = mol->nextInversion(inversionIter)) {
1051	>	inversion->setSnapshotManager(sman_);
1052	>	}
1053	>	}
1054		}
1055
1175	–	Vector3d SimInfo::getComVel(){
1176	–	SimInfo::MoleculeIterator i;
1177	–	Molecule* mol;
1056
1057	<	Vector3d comVel(0.0);
1180	<	double totalMass = 0.0;
1181	<
1182	<
1183	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1184	<	double mass = mol->getMass();
1185	<	totalMass += mass;
1186	<	comVel += mass * mol->getComVel();
1187	<	}
1057	>	ostream& operator <<(ostream& o, SimInfo& info) {
1058
1189	–	#ifdef IS_MPI
1190	–	double tmpMass = totalMass;
1191	–	Vector3d tmpComVel(comVel);
1192	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1193	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1194	–	#endif
1195	–
1196	–	comVel /= totalMass;
1197	–
1198	–	return comVel;
1199	–	}
1200	–
1201	–	Vector3d SimInfo::getCom(){
1202	–	SimInfo::MoleculeIterator i;
1203	–	Molecule* mol;
1204	–
1205	–	Vector3d com(0.0);
1206	–	double totalMass = 0.0;
1207	–
1208	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1209	–	double mass = mol->getMass();
1210	–	totalMass += mass;
1211	–	com += mass * mol->getCom();
1212	–	}
1213	–
1214	–	#ifdef IS_MPI
1215	–	double tmpMass = totalMass;
1216	–	Vector3d tmpCom(com);
1217	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1218	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1219	–	#endif
1220	–
1221	–	com /= totalMass;
1222	–
1223	–	return com;
1224	–
1225	–	}
1226	–
1227	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1228	–
1059		return o;
1060		}
1061
1062	<
1063	<	/*
1064	<	Returns center of mass and center of mass velocity in one function call.
1065	<	*/
1066	<
1067	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1068	<	SimInfo::MoleculeIterator i;
1069	<	Molecule* mol;
1070	<
1071	<
1072	<	double totalMass = 0.0;
1073	<
1062	>
1063	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1064	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1065	>	sprintf(painCave.errMsg,
1066	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1067	>	"\tindex exceeds number of known objects!\n");
1068	>	painCave.isFatal = 1;
1069	>	simError();
1070	>	return NULL;
1071	>	} else
1072	>	return IOIndexToIntegrableObject.at(index);
1073	>	}
1074	>
1075	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1076	>	IOIndexToIntegrableObject= v;
1077	>	}
1078
1079	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1246	<	double mass = mol->getMass();
1247	<	totalMass += mass;
1248	<	com += mass * mol->getCom();
1249	<	comVel += mass * mol->getComVel();
1250	<	}
1251	<
1079	>	void SimInfo::calcNConstraints() {
1080		#ifdef IS_MPI
1081	<	double tmpMass = totalMass;
1082	<	Vector3d tmpCom(com);
1083	<	Vector3d tmpComVel(comVel);
1084	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1081	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1082	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1083	>	#else
1084	>	nGlobalConstraints_ =  nConstraints_;
1085		#endif
1086	<
1261	<	com /= totalMass;
1262	<	comVel /= totalMass;
1263	<	}
1264	<
1265	<	/*
1266	<	Return intertia tensor for entire system and angular momentum Vector.
1086	>	}
1087
1088	+	}//end namespace OpenMD
1089
1269	–	[  Ixx -Ixy  -Ixz ]
1270	–	J =| -Iyx  Iyy  -Iyz |
1271	–	[ -Izx -Iyz   Izz ]
1272	–	*/
1273	–
1274	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1275	–
1276	–
1277	–	double xx = 0.0;
1278	–	double yy = 0.0;
1279	–	double zz = 0.0;
1280	–	double xy = 0.0;
1281	–	double xz = 0.0;
1282	–	double yz = 0.0;
1283	–	Vector3d com(0.0);
1284	–	Vector3d comVel(0.0);
1285	–
1286	–	getComAll(com, comVel);
1287	–
1288	–	SimInfo::MoleculeIterator i;
1289	–	Molecule* mol;
1290	–
1291	–	Vector3d thisq(0.0);
1292	–	Vector3d thisv(0.0);
1293	–
1294	–	double thisMass = 0.0;
1295	–
1296	–
1297	–
1298	–
1299	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1300	–
1301	–	thisq = mol->getCom()-com;
1302	–	thisv = mol->getComVel()-comVel;
1303	–	thisMass = mol->getMass();
1304	–	// Compute moment of intertia coefficients.
1305	–	xx += thisq[0]*thisq[0]*thisMass;
1306	–	yy += thisq[1]*thisq[1]*thisMass;
1307	–	zz += thisq[2]*thisq[2]*thisMass;
1308	–
1309	–	// compute products of intertia
1310	–	xy += thisq[0]*thisq[1]*thisMass;
1311	–	xz += thisq[0]*thisq[2]*thisMass;
1312	–	yz += thisq[1]*thisq[2]*thisMass;
1313	–
1314	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1315	–
1316	–	}
1317	–
1318	–
1319	–	inertiaTensor(0,0) = yy + zz;
1320	–	inertiaTensor(0,1) = -xy;
1321	–	inertiaTensor(0,2) = -xz;
1322	–	inertiaTensor(1,0) = -xy;
1323	–	inertiaTensor(1,1) = xx + zz;
1324	–	inertiaTensor(1,2) = -yz;
1325	–	inertiaTensor(2,0) = -xz;
1326	–	inertiaTensor(2,1) = -yz;
1327	–	inertiaTensor(2,2) = xx + yy;
1328	–
1329	–	#ifdef IS_MPI
1330	–	Mat3x3d tmpI(inertiaTensor);
1331	–	Vector3d tmpAngMom;
1332	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1333	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1334	–	#endif
1335	–
1336	–	return;
1337	–	}
1338	–
1339	–	//Returns the angular momentum of the system
1340	–	Vector3d SimInfo::getAngularMomentum(){
1341	–
1342	–	Vector3d com(0.0);
1343	–	Vector3d comVel(0.0);
1344	–	Vector3d angularMomentum(0.0);
1345	–
1346	–	getComAll(com,comVel);
1347	–
1348	–	SimInfo::MoleculeIterator i;
1349	–	Molecule* mol;
1350	–
1351	–	Vector3d thisr(0.0);
1352	–	Vector3d thisp(0.0);
1353	–
1354	–	double thisMass;
1355	–
1356	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1357	–	thisMass = mol->getMass();
1358	–	thisr = mol->getCom()-com;
1359	–	thisp = (mol->getComVel()-comVel)*thisMass;
1360	–
1361	–	angularMomentum += cross( thisr, thisp );
1362	–
1363	–	}
1364	–
1365	–	#ifdef IS_MPI
1366	–	Vector3d tmpAngMom;
1367	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1368	–	#endif
1369	–
1370	–	return angularMomentum;
1371	–	}
1372	–
1373	–
1374	–	}//end namespace oopse
1375	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

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