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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1121 by chuckv, Mon Feb 26 04:45:42 2007 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 46 | Line 47
47		* @version 1.0
48		*/
49
50	+	#ifdef IS_MPI
51	+	#include <mpi.h>
52	+	#endif
53		#include <algorithm>
54		#include <set>
55		#include <map>
#	Line 54 | Line 58
58		#include "math/Vector3.hpp"
59		#include "primitives/Molecule.hpp"
60		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
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	<
69	<	#ifdef IS_MPI
73	<	#include "UseTheForce/mpiComponentPlan.h"
74	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
76	<
77	<	namespace oopse {
78	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	<	std::map<int, std::set<int> >::iterator i = container.find(index);
80	<	std::set<int> result;
81	<	if (i != container.end()) {
82	<	result = i->second;
83	<	}
84	<
85	<	return result;
86	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin();
92	>	i !=components.end(); ++i) {
93	>	molStamp = (*i)->getMoleculeStamp();
94	>	if ( (*i)->haveRegion() ) {
95	>	molStamp->setRegion( (*i)->getRegion() );
96	>	} else {
97	>	// set the region to a disallowed value:
98	>	molStamp->setRegion( -1 );
99	>	}
100
101	<	MoleculeStamp* molStamp;
98	<	int nMolWithSameStamp;
99	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
100	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
101	<	CutoffGroupStamp* cgStamp;
102	<	RigidBodyStamp* rbStamp;
103	<	int nRigidAtoms = 0;
104	<	std::vector<Component*> components = simParams->getComponents();
101	>	nMolWithSameStamp = (*i)->getNMol();
102
103	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104	<	molStamp = (*i)->getMoleculeStamp();
105	<	nMolWithSameStamp = (*i)->getNMol();
106	<
107	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
108	<
109	<	//calculate atoms in molecules
110	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
111	<
112	<	//calculate atoms in cutoff groups
113	<	int nAtomsInGroups = 0;
114	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	<
119	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroupStamp(j);
121	<	nAtomsInGroups += cgStamp->getNMembers();
122	<	}
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	<
103	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
104	>
105	>	//calculate atoms in molecules
106	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	>
108	>	//calculate atoms in cutoff groups
109	>	int nAtomsInGroups = 0;
110	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
111	>
112	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
113	>	cgStamp = molStamp->getCutoffGroupStamp(j);
114	>	nAtomsInGroups += cgStamp->getNMembers();
115		}
116	<
117	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
118	<	//group therefore the total number of cutoff groups in the system is
119	<	//equal to the total number of atoms minus number of atoms belong to
120	<	//cutoff group defined in meta-data file plus the number of cutoff
121	<	//groups defined in meta-data file
122	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
123	<
124	<	//every free atom (atom does not belong to rigid bodies) is an
125	<	//integrable object therefore the total number of integrable objects
126	<	//in the system is equal to the total number of atoms minus number of
127	<	//atoms belong to rigid body defined in meta-data file plus the number
128	<	//of rigid bodies defined in meta-data file
129	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
130	<	+ nGlobalRigidBodies_;
131	<
132	<	nGlobalMols_ = molStampIds_.size();
158	<
159	<	#ifdef IS_MPI
160	<	molToProcMap_.resize(nGlobalMols_);
161	<	#endif
162	<
116	>
117	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
118	>
119	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
120	>
121	>	//calculate atoms in rigid bodies
122	>	int nAtomsInRigidBodies = 0;
123	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
124	>
125	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
126	>	rbStamp = molStamp->getRigidBodyStamp(j);
127	>	nAtomsInRigidBodies += rbStamp->getNMembers();
128	>	}
129	>
130	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
131	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
132	>
133		}
134	+
135	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
136	+	//group therefore the total number of cutoff groups in the system is
137	+	//equal to the total number of atoms minus number of atoms belong to
138	+	//cutoff group defined in meta-data file plus the number of cutoff
139	+	//groups defined in meta-data file
140
141	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
142	+
143	+	//every free atom (atom does not belong to rigid bodies) is an
144	+	//integrable object therefore the total number of integrable objects
145	+	//in the system is equal to the total number of atoms minus number of
146	+	//atoms belong to rigid body defined in meta-data file plus the number
147	+	//of rigid bodies defined in meta-data file
148	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	+	+ nGlobalRigidBodies_;
150	+
151	+	nGlobalMols_ = molStampIds_.size();
152	+	molToProcMap_.resize(nGlobalMols_);
153	+	}
154	+
155		SimInfo::~SimInfo() {
156	<	std::map<int, Molecule*>::iterator i;
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158		delete i->second;
159		}
#	Line 174 | Line 164 | namespace oopse {
164		delete forceField_;
165		}
166
177	–	int SimInfo::getNGlobalConstraints() {
178	–	int nGlobalConstraints;
179	–	#ifdef IS_MPI
180	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
181	–	MPI_COMM_WORLD);
182	–	#else
183	–	nGlobalConstraints =  nConstraints_;
184	–	#endif
185	–	return nGlobalConstraints;
186	–	}
167
168		bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176		nAtoms_ += mol->getNAtoms();
177		nBonds_ += mol->getNBonds();
178		nBends_ += mol->getNBends();
179		nTorsions_ += mol->getNTorsions();
180	+	nInversions_ += mol->getNInversions();
181		nRigidBodies_ += mol->getNRigidBodies();
182		nIntegrableObjects_ += mol->getNIntegrableObjects();
183		nCutoffGroups_ += mol->getNCutoffGroups();
184		nConstraints_ += mol->getNConstraintPairs();
185	<
186	<	addExcludePairs(mol);
187	<
185	>
186	>	addInteractionPairs(mol);
187	>
188		return true;
189		} else {
190		return false;
191		}
192		}
193	<
193	>
194		bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
#	Line 222 | Line 203 | namespace oopse {
203		nBonds_ -= mol->getNBonds();
204		nBends_ -= mol->getNBends();
205		nTorsions_ -= mol->getNTorsions();
206	+	nInversions_ -= mol->getNInversions();
207		nRigidBodies_ -= mol->getNRigidBodies();
208		nIntegrableObjects_ -= mol->getNIntegrableObjects();
209		nCutoffGroups_ -= mol->getNCutoffGroups();
210		nConstraints_ -= mol->getNConstraintPairs();
211
212	<	removeExcludePairs(mol);
212	>	removeInteractionPairs(mol);
213		molecules_.erase(mol->getGlobalIndex());
214
215		delete mol;
#	Line 236 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
239	–
240	–
221		}
222
223
#	Line 253 | Line 233 | namespace oopse {
233
234
235		void SimInfo::calcNdf() {
236	<	int ndf_local;
236	>	int ndf_local, nfq_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239	>	vector<Atom*>::iterator k;
240	>
241		Molecule* mol;
242	<	StuntDouble* integrableObject;
242	>	StuntDouble* sd;
243	>	Atom* atom;
244
245		ndf_local = 0;
246	+	nfq_local = 0;
247
248		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
265	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
266	–	integrableObject = mol->nextIntegrableObject(j)) {
249
250	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
251	+	sd = mol->nextIntegrableObject(j)) {
252	+
253		ndf_local += 3;
254
255	<	if (integrableObject->isDirectional()) {
256	<	if (integrableObject->isLinear()) {
255	>	if (sd->isDirectional()) {
256	>	if (sd->isLinear()) {
257		ndf_local += 2;
258		} else {
259		ndf_local += 3;
260		}
261		}
277	–
262		}
263	+
264	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
265	+	atom = mol->nextFluctuatingCharge(k)) {
266	+	if (atom->isFluctuatingCharge()) {
267	+	nfq_local++;
268	+	}
269	+	}
270		}
271
272	+	ndfLocal_ = ndf_local;
273	+
274		// n_constraints is local, so subtract them on each processor
275		ndf_local -= nConstraints_;
276
277		#ifdef IS_MPI
278	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
278	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
279	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
280	>	MPI::INT, MPI::SUM);
281		#else
282		ndf_ = ndf_local;
283	+	nGlobalFluctuatingCharges_ = nfq_local;
284		#endif
285
286		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 295 | Line 291 | namespace oopse {
291
292		int SimInfo::getFdf() {
293		#ifdef IS_MPI
294	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
294	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
295		#else
296		fdf_ = fdf_local;
297		#endif
298		return fdf_;
299		}
300	+
301	+	unsigned int SimInfo::getNLocalCutoffGroups(){
302	+	int nLocalCutoffAtoms = 0;
303	+	Molecule* mol;
304	+	MoleculeIterator mi;
305	+	CutoffGroup* cg;
306	+	Molecule::CutoffGroupIterator ci;
307
308	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
309	+
310	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
311	+	cg = mol->nextCutoffGroup(ci)) {
312	+	nLocalCutoffAtoms += cg->getNumAtom();
313	+
314	+	}
315	+	}
316	+
317	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
318	+	}
319	+
320		void SimInfo::calcNdfRaw() {
321		int ndfRaw_local;
322
323		MoleculeIterator i;
324	<	std::vector<StuntDouble*>::iterator j;
324	>	vector<StuntDouble*>::iterator j;
325		Molecule* mol;
326	<	StuntDouble* integrableObject;
326	>	StuntDouble* sd;
327
328		// Raw degrees of freedom that we have to set
329		ndfRaw_local = 0;
330
331		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
317	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
318	–	integrableObject = mol->nextIntegrableObject(j)) {
332
333	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
334	+	sd = mol->nextIntegrableObject(j)) {
335	+
336		ndfRaw_local += 3;
337
338	<	if (integrableObject->isDirectional()) {
339	<	if (integrableObject->isLinear()) {
338	>	if (sd->isDirectional()) {
339	>	if (sd->isLinear()) {
340		ndfRaw_local += 2;
341		} else {
342		ndfRaw_local += 3;
#	Line 331 | Line 347 | namespace oopse {
347		}
348
349		#ifdef IS_MPI
350	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
351		#else
352		ndfRaw_ = ndfRaw_local;
353		#endif
#	Line 344 | Line 360 | namespace oopse {
360
361
362		#ifdef IS_MPI
363	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
363	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
364	>	MPI::INT, MPI::SUM);
365		#else
366		ndfTrans_ = ndfTrans_local;
367		#endif
#	Line 353 | Line 370 | namespace oopse {
370
371		}
372
373	<	void SimInfo::addExcludePairs(Molecule* mol) {
374	<	std::vector<Bond*>::iterator bondIter;
375	<	std::vector<Bend*>::iterator bendIter;
376	<	std::vector<Torsion*>::iterator torsionIter;
373	>	void SimInfo::addInteractionPairs(Molecule* mol) {
374	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
375	>	vector<Atom*>::iterator atomIter;
376	>	vector<Bond*>::iterator bondIter;
377	>	vector<Bend*>::iterator bendIter;
378	>	vector<Torsion*>::iterator torsionIter;
379	>	vector<Inversion*>::iterator inversionIter;
380	>	Atom* atom;
381		Bond* bond;
382		Bend* bend;
383		Torsion* torsion;
384	+	Inversion* inversion;
385		int a;
386		int b;
387		int c;
388		int d;
389
390	<	std::map<int, std::set<int> > atomGroups;
390	>	// atomGroups can be used to add special interaction maps between
391	>	// groups of atoms that are in two separate rigid bodies.
392	>	// However, most site-site interactions between two rigid bodies
393	>	// are probably not special, just the ones between the physically
394	>	// bonded atoms.  Interactions *within* a single rigid body should
395	>	// always be excluded.  These are done at the bottom of this
396	>	// function.
397
398	+	map<int, set<int> > atomGroups;
399		Molecule::RigidBodyIterator rbIter;
400		RigidBody* rb;
401		Molecule::IntegrableObjectIterator ii;
402	<	StuntDouble* integrableObject;
402	>	StuntDouble* sd;
403
404	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
405	<	integrableObject = mol->nextIntegrableObject(ii)) {
406	<
407	<	if (integrableObject->isRigidBody()) {
408	<	rb = static_cast<RigidBody*>(integrableObject);
409	<	std::vector<Atom*> atoms = rb->getAtoms();
410	<	std::set<int> rigidAtoms;
411	<	for (int i = 0; i < atoms.size(); ++i) {
412	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
413	<	}
414	<	for (int i = 0; i < atoms.size(); ++i) {
415	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
416	<	}
404	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
405	>	sd = mol->nextIntegrableObject(ii)) {
406	>
407	>	if (sd->isRigidBody()) {
408	>	rb = static_cast<RigidBody*>(sd);
409	>	vector<Atom*> atoms = rb->getAtoms();
410	>	set<int> rigidAtoms;
411	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
412	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
413	>	}
414	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
416	>	}
417		} else {
418	<	std::set<int> oneAtomSet;
419	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
420	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
418	>	set<int> oneAtomSet;
419	>	oneAtomSet.insert(sd->getGlobalIndex());
420	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
421		}
422		}
423
424	<
425	<
426	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
424	>
425	>	for (bond= mol->beginBond(bondIter); bond != NULL;
426	>	bond = mol->nextBond(bondIter)) {
427	>
428		a = bond->getAtomA()->getGlobalIndex();
429	<	b = bond->getAtomB()->getGlobalIndex();
430	<	exclude_.addPair(a, b);
429	>	b = bond->getAtomB()->getGlobalIndex();
430	>
431	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
432	>	oneTwoInteractions_.addPair(a, b);
433	>	} else {
434	>	excludedInteractions_.addPair(a, b);
435	>	}
436		}
437
438	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
438	>	for (bend= mol->beginBend(bendIter); bend != NULL;
439	>	bend = mol->nextBend(bendIter)) {
440	>
441		a = bend->getAtomA()->getGlobalIndex();
442		b = bend->getAtomB()->getGlobalIndex();
443		c = bend->getAtomC()->getGlobalIndex();
407	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
408	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
409	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
410	–
411	–	exclude_.addPairs(rigidSetA, rigidSetB);
412	–	exclude_.addPairs(rigidSetA, rigidSetC);
413	–	exclude_.addPairs(rigidSetB, rigidSetC);
444
445	<	//exclude_.addPair(a, b);
446	<	//exclude_.addPair(a, c);
447	<	//exclude_.addPair(b, c);
445	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
446	>	oneTwoInteractions_.addPair(a, b);
447	>	oneTwoInteractions_.addPair(b, c);
448	>	} else {
449	>	excludedInteractions_.addPair(a, b);
450	>	excludedInteractions_.addPair(b, c);
451	>	}
452	>
453	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
454	>	oneThreeInteractions_.addPair(a, c);
455	>	} else {
456	>	excludedInteractions_.addPair(a, c);
457	>	}
458		}
459
460	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
460	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
461	>	torsion = mol->nextTorsion(torsionIter)) {
462	>
463		a = torsion->getAtomA()->getGlobalIndex();
464		b = torsion->getAtomB()->getGlobalIndex();
465		c = torsion->getAtomC()->getGlobalIndex();
466	<	d = torsion->getAtomD()->getGlobalIndex();
425	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
426	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
427	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
428	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
466	>	d = torsion->getAtomD()->getGlobalIndex();
467
468	<	exclude_.addPairs(rigidSetA, rigidSetB);
469	<	exclude_.addPairs(rigidSetA, rigidSetC);
470	<	exclude_.addPairs(rigidSetA, rigidSetD);
471	<	exclude_.addPairs(rigidSetB, rigidSetC);
472	<	exclude_.addPairs(rigidSetB, rigidSetD);
473	<	exclude_.addPairs(rigidSetC, rigidSetD);
468	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
469	>	oneTwoInteractions_.addPair(a, b);
470	>	oneTwoInteractions_.addPair(b, c);
471	>	oneTwoInteractions_.addPair(c, d);
472	>	} else {
473	>	excludedInteractions_.addPair(a, b);
474	>	excludedInteractions_.addPair(b, c);
475	>	excludedInteractions_.addPair(c, d);
476	>	}
477
478	<	/*
479	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
480	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
481	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
482	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
483	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
484	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
485	<
486	<
487	<	exclude_.addPair(a, b);
488	<	exclude_.addPair(a, c);
489	<	exclude_.addPair(a, d);
490	<	exclude_.addPair(b, c);
450	<	exclude_.addPair(b, d);
451	<	exclude_.addPair(c, d);
452	<	*/
478	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
479	>	oneThreeInteractions_.addPair(a, c);
480	>	oneThreeInteractions_.addPair(b, d);
481	>	} else {
482	>	excludedInteractions_.addPair(a, c);
483	>	excludedInteractions_.addPair(b, d);
484	>	}
485	>
486	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
487	>	oneFourInteractions_.addPair(a, d);
488	>	} else {
489	>	excludedInteractions_.addPair(a, d);
490	>	}
491		}
492
493	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
494	<	std::vector<Atom*> atoms = rb->getAtoms();
495	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
496	<	for (int j = i + 1; j < atoms.size(); ++j) {
493	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
494	>	inversion = mol->nextInversion(inversionIter)) {
495	>
496	>	a = inversion->getAtomA()->getGlobalIndex();
497	>	b = inversion->getAtomB()->getGlobalIndex();
498	>	c = inversion->getAtomC()->getGlobalIndex();
499	>	d = inversion->getAtomD()->getGlobalIndex();
500	>
501	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
502	>	oneTwoInteractions_.addPair(a, b);
503	>	oneTwoInteractions_.addPair(a, c);
504	>	oneTwoInteractions_.addPair(a, d);
505	>	} else {
506	>	excludedInteractions_.addPair(a, b);
507	>	excludedInteractions_.addPair(a, c);
508	>	excludedInteractions_.addPair(a, d);
509	>	}
510	>
511	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
512	>	oneThreeInteractions_.addPair(b, c);
513	>	oneThreeInteractions_.addPair(b, d);
514	>	oneThreeInteractions_.addPair(c, d);
515	>	} else {
516	>	excludedInteractions_.addPair(b, c);
517	>	excludedInteractions_.addPair(b, d);
518	>	excludedInteractions_.addPair(c, d);
519	>	}
520	>	}
521	>
522	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
523	>	rb = mol->nextRigidBody(rbIter)) {
524	>	vector<Atom*> atoms = rb->getAtoms();
525	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
526	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
527		a = atoms[i]->getGlobalIndex();
528		b = atoms[j]->getGlobalIndex();
529	<	exclude_.addPair(a, b);
529	>	excludedInteractions_.addPair(a, b);
530		}
531		}
532		}
533
534		}
535
536	<	void SimInfo::removeExcludePairs(Molecule* mol) {
537	<	std::vector<Bond*>::iterator bondIter;
538	<	std::vector<Bend*>::iterator bendIter;
539	<	std::vector<Torsion*>::iterator torsionIter;
536	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
537	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
538	>	vector<Bond*>::iterator bondIter;
539	>	vector<Bend*>::iterator bendIter;
540	>	vector<Torsion*>::iterator torsionIter;
541	>	vector<Inversion*>::iterator inversionIter;
542		Bond* bond;
543		Bend* bend;
544		Torsion* torsion;
545	+	Inversion* inversion;
546		int a;
547		int b;
548		int c;
549		int d;
550
551	<	std::map<int, std::set<int> > atomGroups;
481	<
551	>	map<int, set<int> > atomGroups;
552		Molecule::RigidBodyIterator rbIter;
553		RigidBody* rb;
554		Molecule::IntegrableObjectIterator ii;
555	<	StuntDouble* integrableObject;
555	>	StuntDouble* sd;
556
557	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
558	<	integrableObject = mol->nextIntegrableObject(ii)) {
559	<
560	<	if (integrableObject->isRigidBody()) {
561	<	rb = static_cast<RigidBody*>(integrableObject);
562	<	std::vector<Atom*> atoms = rb->getAtoms();
563	<	std::set<int> rigidAtoms;
564	<	for (int i = 0; i < atoms.size(); ++i) {
565	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
566	<	}
567	<	for (int i = 0; i < atoms.size(); ++i) {
568	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
569	<	}
557	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
558	>	sd = mol->nextIntegrableObject(ii)) {
559	>
560	>	if (sd->isRigidBody()) {
561	>	rb = static_cast<RigidBody*>(sd);
562	>	vector<Atom*> atoms = rb->getAtoms();
563	>	set<int> rigidAtoms;
564	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
565	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
566	>	}
567	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
569	>	}
570		} else {
571	<	std::set<int> oneAtomSet;
572	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
573	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
571	>	set<int> oneAtomSet;
572	>	oneAtomSet.insert(sd->getGlobalIndex());
573	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
574		}
575		}
576
577	<
578	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
577	>	for (bond= mol->beginBond(bondIter); bond != NULL;
578	>	bond = mol->nextBond(bondIter)) {
579	>
580		a = bond->getAtomA()->getGlobalIndex();
581	<	b = bond->getAtomB()->getGlobalIndex();
582	<	exclude_.removePair(a, b);
581	>	b = bond->getAtomB()->getGlobalIndex();
582	>
583	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
584	>	oneTwoInteractions_.removePair(a, b);
585	>	} else {
586	>	excludedInteractions_.removePair(a, b);
587	>	}
588		}
589
590	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
590	>	for (bend= mol->beginBend(bendIter); bend != NULL;
591	>	bend = mol->nextBend(bendIter)) {
592	>
593		a = bend->getAtomA()->getGlobalIndex();
594		b = bend->getAtomB()->getGlobalIndex();
595		c = bend->getAtomC()->getGlobalIndex();
518	–
519	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
520	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
521	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
522	–
523	–	exclude_.removePairs(rigidSetA, rigidSetB);
524	–	exclude_.removePairs(rigidSetA, rigidSetC);
525	–	exclude_.removePairs(rigidSetB, rigidSetC);
596
597	<	//exclude_.removePair(a, b);
598	<	//exclude_.removePair(a, c);
599	<	//exclude_.removePair(b, c);
597	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
598	>	oneTwoInteractions_.removePair(a, b);
599	>	oneTwoInteractions_.removePair(b, c);
600	>	} else {
601	>	excludedInteractions_.removePair(a, b);
602	>	excludedInteractions_.removePair(b, c);
603	>	}
604	>
605	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
606	>	oneThreeInteractions_.removePair(a, c);
607	>	} else {
608	>	excludedInteractions_.removePair(a, c);
609	>	}
610		}
611
612	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
612	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
613	>	torsion = mol->nextTorsion(torsionIter)) {
614	>
615		a = torsion->getAtomA()->getGlobalIndex();
616		b = torsion->getAtomB()->getGlobalIndex();
617		c = torsion->getAtomC()->getGlobalIndex();
618	<	d = torsion->getAtomD()->getGlobalIndex();
618	>	d = torsion->getAtomD()->getGlobalIndex();
619	>
620	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
621	>	oneTwoInteractions_.removePair(a, b);
622	>	oneTwoInteractions_.removePair(b, c);
623	>	oneTwoInteractions_.removePair(c, d);
624	>	} else {
625	>	excludedInteractions_.removePair(a, b);
626	>	excludedInteractions_.removePair(b, c);
627	>	excludedInteractions_.removePair(c, d);
628	>	}
629
630	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
631	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
632	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
633	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
630	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
631	>	oneThreeInteractions_.removePair(a, c);
632	>	oneThreeInteractions_.removePair(b, d);
633	>	} else {
634	>	excludedInteractions_.removePair(a, c);
635	>	excludedInteractions_.removePair(b, d);
636	>	}
637
638	<	exclude_.removePairs(rigidSetA, rigidSetB);
639	<	exclude_.removePairs(rigidSetA, rigidSetC);
640	<	exclude_.removePairs(rigidSetA, rigidSetD);
641	<	exclude_.removePairs(rigidSetB, rigidSetC);
642	<	exclude_.removePairs(rigidSetB, rigidSetD);
643	<	exclude_.removePairs(rigidSetC, rigidSetD);
638	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
639	>	oneFourInteractions_.removePair(a, d);
640	>	} else {
641	>	excludedInteractions_.removePair(a, d);
642	>	}
643	>	}
644
645	<	/*
646	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
552	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
553	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
554	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
555	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
556	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
645	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
646	>	inversion = mol->nextInversion(inversionIter)) {
647
648	<
649	<	exclude_.removePair(a, b);
650	<	exclude_.removePair(a, c);
651	<	exclude_.removePair(a, d);
652	<	exclude_.removePair(b, c);
653	<	exclude_.removePair(b, d);
654	<	exclude_.removePair(c, d);
655	<	*/
648	>	a = inversion->getAtomA()->getGlobalIndex();
649	>	b = inversion->getAtomB()->getGlobalIndex();
650	>	c = inversion->getAtomC()->getGlobalIndex();
651	>	d = inversion->getAtomD()->getGlobalIndex();
652	>
653	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
654	>	oneTwoInteractions_.removePair(a, b);
655	>	oneTwoInteractions_.removePair(a, c);
656	>	oneTwoInteractions_.removePair(a, d);
657	>	} else {
658	>	excludedInteractions_.removePair(a, b);
659	>	excludedInteractions_.removePair(a, c);
660	>	excludedInteractions_.removePair(a, d);
661	>	}
662	>
663	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
664	>	oneThreeInteractions_.removePair(b, c);
665	>	oneThreeInteractions_.removePair(b, d);
666	>	oneThreeInteractions_.removePair(c, d);
667	>	} else {
668	>	excludedInteractions_.removePair(b, c);
669	>	excludedInteractions_.removePair(b, d);
670	>	excludedInteractions_.removePair(c, d);
671	>	}
672		}
673
674	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
675	<	std::vector<Atom*> atoms = rb->getAtoms();
676	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
677	<	for (int j = i + 1; j < atoms.size(); ++j) {
674	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
675	>	rb = mol->nextRigidBody(rbIter)) {
676	>	vector<Atom*> atoms = rb->getAtoms();
677	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
678	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
679		a = atoms[i]->getGlobalIndex();
680		b = atoms[j]->getGlobalIndex();
681	<	exclude_.removePair(a, b);
681	>	excludedInteractions_.removePair(a, b);
682		}
683		}
684		}
685	<
685	>
686		}
687	<
688	<
687	>
688	>
689		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
690		int curStampId;
691	<
691	>
692		//index from 0
693		curStampId = moleculeStamps_.size();
694
#	Line 589 | Line 696 | namespace oopse {
696		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
697		}
698
592	–	void SimInfo::update() {
699
700	<	setupSimType();
701	<
702	<	#ifdef IS_MPI
703	<	setupFortranParallel();
704	<	#endif
705	<
706	<	setupFortranSim();
707	<
708	<	//setup fortran force field
603	<	/** @deprecate */
604	<	int isError = 0;
605	<
606	<	setupCutoff();
607	<
608	<	setupElectrostaticSummationMethod( isError );
609	<	setupSwitchingFunction();
610	<	setupAccumulateBoxDipole();
611	<
612	<	if(isError){
613	<	sprintf( painCave.errMsg,
614	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
615	<	painCave.isFatal = 1;
616	<	simError();
617	<	}
618	<
700	>	/**
701	>	* update
702	>	*
703	>	*  Performs the global checks and variable settings after the
704	>	*  objects have been created.
705	>	*
706	>	*/
707	>	void SimInfo::update() {
708	>	setupSimVariables();
709		calcNdf();
710		calcNdfRaw();
711		calcNdfTrans();
622	–
623	–	fortranInitialized_ = true;
712		}
713	<
714	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
713	>
714	>	/**
715	>	* getSimulatedAtomTypes
716	>	*
717	>	* Returns an STL set of AtomType* that are actually present in this
718	>	* simulation.  Must query all processors to assemble this information.
719	>	*
720	>	*/
721	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
722		SimInfo::MoleculeIterator mi;
723		Molecule* mol;
724		Molecule::AtomIterator ai;
725		Atom* atom;
726	<	std::set<AtomType*> atomTypes;
727	<
726	>	set<AtomType*> atomTypes;
727	>
728		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
729	<
730	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
729	>	for(atom = mol->beginAtom(ai); atom != NULL;
730	>	atom = mol->nextAtom(ai)) {
731		atomTypes.insert(atom->getAtomType());
732	<	}
733	<
734	<	}
732	>	}
733	>	}
734	>
735	>	#ifdef IS_MPI
736
737	<	return atomTypes;
738	<	}
643	<
644	<	void SimInfo::setupSimType() {
645	<	std::set<AtomType*>::iterator i;
646	<	std::set<AtomType*> atomTypes;
647	<	atomTypes = getUniqueAtomTypes();
737	>	// loop over the found atom types on this processor, and add their
738	>	// numerical idents to a vector:
739
740	<	int useLennardJones = 0;
741	<	int useElectrostatic = 0;
742	<	int useEAM = 0;
743	<	int useSC = 0;
653	<	int useCharge = 0;
654	<	int useDirectional = 0;
655	<	int useDipole = 0;
656	<	int useGayBerne = 0;
657	<	int useSticky = 0;
658	<	int useStickyPower = 0;
659	<	int useShape = 0;
660	<	int useFLARB = 0; //it is not in AtomType yet
661	<	int useDirectionalAtom = 0;
662	<	int useElectrostatics = 0;
663	<	//usePBC and useRF are from simParams
664	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
665	<	int useRF;
666	<	int useSF;
667	<	int useSP;
668	<	int useBoxDipole;
669	<	std::string myMethod;
740	>	vector<int> foundTypes;
741	>	set<AtomType*>::iterator i;
742	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
743	>	foundTypes.push_back( (*i)->getIdent() );
744
745	<	// set the useRF logical
746	<	useRF = 0;
673	<	useSF = 0;
674	<	useSP = 0;
745	>	// count_local holds the number of found types on this processor
746	>	int count_local = foundTypes.size();
747
748	+	int nproc = MPI::COMM_WORLD.Get_size();
749
750	<	if (simParams_->haveElectrostaticSummationMethod()) {
751	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
752	<	toUpper(myMethod);
753	<	if (myMethod == "REACTION_FIELD"){
681	<	useRF = 1;
682	<	} else if (myMethod == "SHIFTED_FORCE"){
683	<	useSF = 1;
684	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
685	<	useSP = 1;
686	<	}
687	<	}
688	<
689	<	if (simParams_->haveAccumulateBoxDipole())
690	<	if (simParams_->getAccumulateBoxDipole())
691	<	useBoxDipole = 1;
750	>	// we need arrays to hold the counts and displacement vectors for
751	>	// all processors
752	>	vector<int> counts(nproc, 0);
753	>	vector<int> disps(nproc, 0);
754
755	<	//loop over all of the atom types
756	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	<	useLennardJones |= (*i)->isLennardJones();
758	<	useElectrostatic |= (*i)->isElectrostatic();
759	<	useEAM |= (*i)->isEAM();
760	<	useSC |= (*i)->isSC();
761	<	useCharge |= (*i)->isCharge();
762	<	useDirectional |= (*i)->isDirectional();
763	<	useDipole |= (*i)->isDipole();
764	<	useGayBerne |= (*i)->isGayBerne();
703	<	useSticky |= (*i)->isSticky();
704	<	useStickyPower |= (*i)->isStickyPower();
705	<	useShape |= (*i)->isShape();
755	>	// fill the counts array
756	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
757	>	1, MPI::INT);
758	>
759	>	// use the processor counts to compute the displacement array
760	>	disps[0] = 0;
761	>	int totalCount = counts[0];
762	>	for (int iproc = 1; iproc < nproc; iproc++) {
763	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
764	>	totalCount += counts[iproc];
765		}
766
767	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
768	<	useDirectionalAtom = 1;
769	<	}
767	>	// we need a (possibly redundant) set of all found types:
768	>	vector<int> ftGlobal(totalCount);
769	>
770	>	// now spray out the foundTypes to all the other processors:
771	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
772	>	&ftGlobal[0], &counts[0], &disps[0],
773	>	MPI::INT);
774
775	<	if (useCharge || useDipole) {
713	<	useElectrostatics = 1;
714	<	}
775	>	vector<int>::iterator j;
776
777	<	#ifdef IS_MPI
778	<	int temp;
777	>	// foundIdents is a stl set, so inserting an already found ident
778	>	// will have no effect.
779	>	set<int> foundIdents;
780
781	<	temp = usePBC;
782	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
782	>	foundIdents.insert((*j));
783	>
784	>	// now iterate over the foundIdents and get the actual atom types
785	>	// that correspond to these:
786	>	set<int>::iterator it;
787	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
788	>	atomTypes.insert( forceField_->getAtomType((*it)) );
789	>
790	>	#endif
791
792	<	temp = useDirectionalAtom;
793	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
792	>	return atomTypes;
793	>	}
794
725	–	temp = useLennardJones;
726	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
795
796	<	temp = useElectrostatics;
797	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	>	int getGlobalCountOfType(AtomType* atype) {
797	>	/*
798	>	set<AtomType*> atypes = getSimulatedAtomTypes();
799	>	map<AtomType*, int> counts_;
800
801	<	temp = useCharge;
802	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
802	>	for(atom = mol->beginAtom(ai); atom != NULL;
803	>	atom = mol->nextAtom(ai)) {
804	>	atom->getAtomType();
805	>	}
806	>	}
807	>	*/
808	>	return 0;
809	>	}
810
811	<	temp = useDipole;
812	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	void SimInfo::setupSimVariables() {
812	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
813	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
814	>	// parameter is true
815	>	calcBoxDipole_ = false;
816	>	if ( simParams_->haveAccumulateBoxDipole() )
817	>	if ( simParams_->getAccumulateBoxDipole() ) {
818	>	calcBoxDipole_ = true;
819	>	}
820	>
821	>	set<AtomType*>::iterator i;
822	>	set<AtomType*> atomTypes;
823	>	atomTypes = getSimulatedAtomTypes();
824	>	bool usesElectrostatic = false;
825	>	bool usesMetallic = false;
826	>	bool usesDirectional = false;
827	>	bool usesFluctuatingCharges =  false;
828	>	//loop over all of the atom types
829	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
830	>	usesElectrostatic |= (*i)->isElectrostatic();
831	>	usesMetallic |= (*i)->isMetal();
832	>	usesDirectional |= (*i)->isDirectional();
833	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
834	>	}
835
836	<	temp = useSticky;
837	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838	<
839	<	temp = useStickyPower;
840	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836	>	#ifdef IS_MPI
837	>	bool temp;
838	>	temp = usesDirectional;
839	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
840	>	MPI::LOR);
841	>
842	>	temp = usesMetallic;
843	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
844	>	MPI::LOR);
845
846	<	temp = useGayBerne;
847	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	>	temp = usesElectrostatic;
847	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
848	>	MPI::LOR);
849
850	<	temp = useEAM;
851	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	>	temp = usesFluctuatingCharges;
851	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
852	>	MPI::LOR);
853	>	#else
854
855	<	temp = useSC;
856	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
855	>	usesDirectionalAtoms_ = usesDirectional;
856	>	usesMetallicAtoms_ = usesMetallic;
857	>	usesElectrostaticAtoms_ = usesElectrostatic;
858	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
859	>
860	>	#endif
861
862	<	temp = useShape;
863	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
863	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
864	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
865	>	}
866
755	–	temp = useFLARB;
756	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
867
868	<	temp = useRF;
869	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
868	>	vector<int> SimInfo::getGlobalAtomIndices() {
869	>	SimInfo::MoleculeIterator mi;
870	>	Molecule* mol;
871	>	Molecule::AtomIterator ai;
872	>	Atom* atom;
873
874	<	temp = useSF;
875	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
875	>
876	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
877	>
878	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
879	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
880	>	}
881	>	}
882	>	return GlobalAtomIndices;
883	>	}
884
764	–	temp = useSP;
765	–	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885
886	<	temp = useBoxDipole;
887	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886	>	vector<int> SimInfo::getGlobalGroupIndices() {
887	>	SimInfo::MoleculeIterator mi;
888	>	Molecule* mol;
889	>	Molecule::CutoffGroupIterator ci;
890	>	CutoffGroup* cg;
891
892	<	#endif
893	<
894	<	fInfo_.SIM_uses_PBC = usePBC;
895	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
896	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
897	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
898	<	fInfo_.SIM_uses_Charges = useCharge;
899	<	fInfo_.SIM_uses_Dipoles = useDipole;
900	<	fInfo_.SIM_uses_Sticky = useSticky;
901	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
902	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
903	<	fInfo_.SIM_uses_EAM = useEAM;
782	<	fInfo_.SIM_uses_SC = useSC;
783	<	fInfo_.SIM_uses_Shapes = useShape;
784	<	fInfo_.SIM_uses_FLARB = useFLARB;
785	<	fInfo_.SIM_uses_RF = useRF;
786	<	fInfo_.SIM_uses_SF = useSF;
787	<	fInfo_.SIM_uses_SP = useSP;
788	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
892	>	vector<int> GlobalGroupIndices;
893	>
894	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
895	>
896	>	//local index of cutoff group is trivial, it only depends on the
897	>	//order of travesing
898	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
899	>	cg = mol->nextCutoffGroup(ci)) {
900	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
901	>	}
902	>	}
903	>	return GlobalGroupIndices;
904		}
905
791	–	void SimInfo::setupFortranSim() {
792	–	int isError;
793	–	int nExclude;
794	–	std::vector<int> fortranGlobalGroupMembership;
795	–
796	–	nExclude = exclude_.getSize();
797	–	isError = 0;
906
907	<	//globalGroupMembership_ is filled by SimCreator
800	<	for (int i = 0; i < nGlobalAtoms_; i++) {
801	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
802	<	}
907	>	void SimInfo::prepareTopology() {
908
909		//calculate mass ratio of cutoff group
805	–	std::vector<RealType> mfact;
910		SimInfo::MoleculeIterator mi;
911		Molecule* mol;
912		Molecule::CutoffGroupIterator ci;
#	Line 811 | Line 915 | namespace oopse {
915		Atom* atom;
916		RealType totalMass;
917
918	<	//to avoid memory reallocation, reserve enough space for mfact
919	<	mfact.reserve(getNCutoffGroups());
918	>	/**
919	>	* The mass factor is the relative mass of an atom to the total
920	>	* mass of the cutoff group it belongs to.  By default, all atoms
921	>	* are their own cutoff groups, and therefore have mass factors of
922	>	* 1.  We need some special handling for massless atoms, which
923	>	* will be treated as carrying the entire mass of the cutoff
924	>	* group.
925	>	*/
926	>	massFactors_.clear();
927	>	massFactors_.resize(getNAtoms(), 1.0);
928
929		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
930	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
930	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
931	>	cg = mol->nextCutoffGroup(ci)) {
932
933		totalMass = cg->getMass();
934		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
935		// Check for massless groups - set mfact to 1 if true
936	<	if (totalMass != 0)
937	<	mfact.push_back(atom->getMass()/totalMass);
936	>	if (totalMass != 0)
937	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
938		else
939	<	mfact.push_back( 1.0 );
939	>	massFactors_[atom->getLocalIndex()] = 1.0;
940		}
828	–
941		}
942		}
943
944	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
833	<	std::vector<int> identArray;
944	>	// Build the identArray_ and regions_
945
946	<	//to avoid memory reallocation, reserve enough space identArray
947	<	identArray.reserve(getNAtoms());
948	<
949	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
946	>	identArray_.clear();
947	>	identArray_.reserve(getNAtoms());
948	>	regions_.clear();
949	>	regions_.reserve(getNAtoms());
950	>
951	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
952	>	int reg = mol->getRegion();
953		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
954	<	identArray.push_back(atom->getIdent());
954	>	identArray_.push_back(atom->getIdent());
955	>	regions_.push_back(reg);
956		}
957		}
958	<
959	<	//fill molMembershipArray
845	<	//molMembershipArray is filled by SimCreator
846	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
847	<	for (int i = 0; i < nGlobalAtoms_; i++) {
848	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
849	<	}
850	<
851	<	//setup fortran simulation
852	<	int nGlobalExcludes = 0;
853	<	int* globalExcludes = NULL;
854	<	int* excludeList = exclude_.getExcludeList();
855	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
856	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
857	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
858	<
859	<	if( isError ){
860	<
861	<	sprintf( painCave.errMsg,
862	<	"There was an error setting the simulation information in fortran.\n" );
863	<	painCave.isFatal = 1;
864	<	painCave.severity = OOPSE_ERROR;
865	<	simError();
866	<	}
867	<
868	<	#ifdef IS_MPI
869	<	sprintf( checkPointMsg,
870	<	"succesfully sent the simulation information to fortran.\n");
871	<	MPIcheckPoint();
872	<	#endif // is_mpi
873	<
874	<	// Setup number of neighbors in neighbor list if present
875	<	if (simParams_->haveNeighborListNeighbors()) {
876	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
877	<	setNeighbors(&nlistNeighbors);
878	<	}
879	<
880	<
881	<	}
882	<
883	<
884	<	#ifdef IS_MPI
885	<	void SimInfo::setupFortranParallel() {
886	<
887	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
888	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
889	<	std::vector<int> localToGlobalCutoffGroupIndex;
890	<	SimInfo::MoleculeIterator mi;
891	<	Molecule::AtomIterator ai;
892	<	Molecule::CutoffGroupIterator ci;
893	<	Molecule* mol;
894	<	Atom* atom;
895	<	CutoffGroup* cg;
896	<	mpiSimData parallelData;
897	<	int isError;
898	<
899	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
900	<
901	<	//local index(index in DataStorge) of atom is important
902	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
903	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
904	<	}
905	<
906	<	//local index of cutoff group is trivial, it only depends on the order of travesing
907	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
908	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
909	<	}
910	<
911	<	}
912	<
913	<	//fill up mpiSimData struct
914	<	parallelData.nMolGlobal = getNGlobalMolecules();
915	<	parallelData.nMolLocal = getNMolecules();
916	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
917	<	parallelData.nAtomsLocal = getNAtoms();
918	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
919	<	parallelData.nGroupsLocal = getNCutoffGroups();
920	<	parallelData.myNode = worldRank;
921	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
922	<
923	<	//pass mpiSimData struct and index arrays to fortran
924	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
925	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
926	<	&localToGlobalCutoffGroupIndex[0], &isError);
927	<
928	<	if (isError) {
929	<	sprintf(painCave.errMsg,
930	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
931	<	painCave.isFatal = 1;
932	<	simError();
933	<	}
934	<
935	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
936	<	MPIcheckPoint();
937	<
938	<
939	<	}
940	<
941	<	#endif
942	<
943	<	void SimInfo::setupCutoff() {
944	<
945	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
946	<
947	<	// Check the cutoff policy
948	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
949	<
950	<	std::string myPolicy;
951	<	if (forceFieldOptions_.haveCutoffPolicy()){
952	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
953	<	}else if (simParams_->haveCutoffPolicy()) {
954	<	myPolicy = simParams_->getCutoffPolicy();
955	<	}
956	<
957	<	if (!myPolicy.empty()){
958	<	toUpper(myPolicy);
959	<	if (myPolicy == "MIX") {
960	<	cp = MIX_CUTOFF_POLICY;
961	<	} else {
962	<	if (myPolicy == "MAX") {
963	<	cp = MAX_CUTOFF_POLICY;
964	<	} else {
965	<	if (myPolicy == "TRADITIONAL") {
966	<	cp = TRADITIONAL_CUTOFF_POLICY;
967	<	} else {
968	<	// throw error
969	<	sprintf( painCave.errMsg,
970	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
971	<	painCave.isFatal = 1;
972	<	simError();
973	<	}
974	<	}
975	<	}
976	<	}
977	<	notifyFortranCutoffPolicy(&cp);
978	<
979	<	// Check the Skin Thickness for neighborlists
980	<	RealType skin;
981	<	if (simParams_->haveSkinThickness()) {
982	<	skin = simParams_->getSkinThickness();
983	<	notifyFortranSkinThickness(&skin);
984	<	}
985	<
986	<	// Check if the cutoff was set explicitly:
987	<	if (simParams_->haveCutoffRadius()) {
988	<	rcut_ = simParams_->getCutoffRadius();
989	<	if (simParams_->haveSwitchingRadius()) {
990	<	rsw_  = simParams_->getSwitchingRadius();
991	<	} else {
992	<	if (fInfo_.SIM_uses_Charges |
993	<	fInfo_.SIM_uses_Dipoles |
994	<	fInfo_.SIM_uses_RF) {
995	<
996	<	rsw_ = 0.85 * rcut_;
997	<	sprintf(painCave.errMsg,
998	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
999	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1000	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1001	<	painCave.isFatal = 0;
1002	<	simError();
1003	<	} else {
1004	<	rsw_ = rcut_;
1005	<	sprintf(painCave.errMsg,
1006	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1007	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1008	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1009	<	painCave.isFatal = 0;
1010	<	simError();
1011	<	}
1012	<	}
1013	<
1014	<	notifyFortranCutoffs(&rcut_, &rsw_);
1015	<
1016	<	} else {
1017	<
1018	<	// For electrostatic atoms, we'll assume a large safe value:
1019	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1020	<	sprintf(painCave.errMsg,
1021	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1022	<	"\tOOPSE will use a default value of 15.0 angstroms"
1023	<	"\tfor the cutoffRadius.\n");
1024	<	painCave.isFatal = 0;
1025	<	simError();
1026	<	rcut_ = 15.0;
1027	<
1028	<	if (simParams_->haveElectrostaticSummationMethod()) {
1029	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1030	<	toUpper(myMethod);
1031	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1032	<	if (simParams_->haveSwitchingRadius()){
1033	<	sprintf(painCave.errMsg,
1034	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1035	<	"\teven though the electrostaticSummationMethod was\n"
1036	<	"\tset to %s\n", myMethod.c_str());
1037	<	painCave.isFatal = 1;
1038	<	simError();
1039	<	}
1040	<	}
1041	<	}
1042	<
1043	<	if (simParams_->haveSwitchingRadius()){
1044	<	rsw_ = simParams_->getSwitchingRadius();
1045	<	} else {
1046	<	sprintf(painCave.errMsg,
1047	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1048	<	"\tOOPSE will use a default value of\n"
1049	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1050	<	painCave.isFatal = 0;
1051	<	simError();
1052	<	rsw_ = 0.85 * rcut_;
1053	<	}
1054	<	notifyFortranCutoffs(&rcut_, &rsw_);
1055	<	} else {
1056	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1057	<	// We'll punt and let fortran figure out the cutoffs later.
1058	<
1059	<	notifyFortranYouAreOnYourOwn();
1060	<
1061	<	}
1062	<	}
1063	<	}
1064	<
1065	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1066	<
1067	<	int errorOut;
1068	<	int esm =  NONE;
1069	<	int sm = UNDAMPED;
1070	<	RealType alphaVal;
1071	<	RealType dielectric;
1072	<
1073	<	errorOut = isError;
1074	<
1075	<	if (simParams_->haveElectrostaticSummationMethod()) {
1076	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1077	<	toUpper(myMethod);
1078	<	if (myMethod == "NONE") {
1079	<	esm = NONE;
1080	<	} else {
1081	<	if (myMethod == "SWITCHING_FUNCTION") {
1082	<	esm = SWITCHING_FUNCTION;
1083	<	} else {
1084	<	if (myMethod == "SHIFTED_POTENTIAL") {
1085	<	esm = SHIFTED_POTENTIAL;
1086	<	} else {
1087	<	if (myMethod == "SHIFTED_FORCE") {
1088	<	esm = SHIFTED_FORCE;
1089	<	} else {
1090	<	if (myMethod == "REACTION_FIELD") {
1091	<	esm = REACTION_FIELD;
1092	<	dielectric = simParams_->getDielectric();
1093	<	if (!simParams_->haveDielectric()) {
1094	<	// throw warning
1095	<	sprintf( painCave.errMsg,
1096	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1097	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1098	<	painCave.isFatal = 0;
1099	<	simError();
1100	<	}
1101	<	} else {
1102	<	// throw error
1103	<	sprintf( painCave.errMsg,
1104	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1105	<	"\t(Input file specified %s .)\n"
1106	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1107	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1108	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1109	<	painCave.isFatal = 1;
1110	<	simError();
1111	<	}
1112	<	}
1113	<	}
1114	<	}
1115	<	}
1116	<	}
1117	<
1118	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1119	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1120	<	toUpper(myScreen);
1121	<	if (myScreen == "UNDAMPED") {
1122	<	sm = UNDAMPED;
1123	<	} else {
1124	<	if (myScreen == "DAMPED") {
1125	<	sm = DAMPED;
1126	<	if (!simParams_->haveDampingAlpha()) {
1127	<	// first set a cutoff dependent alpha value
1128	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1129	<	alphaVal = 0.5125 - rcut_* 0.025;
1130	<	// for values rcut > 20.5, alpha is zero
1131	<	if (alphaVal < 0) alphaVal = 0;
1132	<
1133	<	// throw warning
1134	<	sprintf( painCave.errMsg,
1135	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1136	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1137	<	painCave.isFatal = 0;
1138	<	simError();
1139	<	} else {
1140	<	alphaVal = simParams_->getDampingAlpha();
1141	<	}
1142	<
1143	<	} else {
1144	<	// throw error
1145	<	sprintf( painCave.errMsg,
1146	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1147	<	"\t(Input file specified %s .)\n"
1148	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1149	<	"or \"damped\".\n", myScreen.c_str() );
1150	<	painCave.isFatal = 1;
1151	<	simError();
1152	<	}
1153	<	}
1154	<	}
1155	<
1156	<	// let's pass some summation method variables to fortran
1157	<	setElectrostaticSummationMethod( &esm );
1158	<	setFortranElectrostaticMethod( &esm );
1159	<	setScreeningMethod( &sm );
1160	<	setDampingAlpha( &alphaVal );
1161	<	setReactionFieldDielectric( &dielectric );
1162	<	initFortranFF( &errorOut );
958	>
959	>	topologyDone_ = true;
960		}
961
1165	–	void SimInfo::setupSwitchingFunction() {
1166	–	int ft = CUBIC;
1167	–
1168	–	if (simParams_->haveSwitchingFunctionType()) {
1169	–	std::string funcType = simParams_->getSwitchingFunctionType();
1170	–	toUpper(funcType);
1171	–	if (funcType == "CUBIC") {
1172	–	ft = CUBIC;
1173	–	} else {
1174	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1175	–	ft = FIFTH_ORDER_POLY;
1176	–	} else {
1177	–	// throw error
1178	–	sprintf( painCave.errMsg,
1179	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1180	–	painCave.isFatal = 1;
1181	–	simError();
1182	–	}
1183	–	}
1184	–	}
1185	–
1186	–	// send switching function notification to switcheroo
1187	–	setFunctionType(&ft);
1188	–
1189	–	}
1190	–
1191	–	void SimInfo::setupAccumulateBoxDipole() {
1192	–
1193	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1194	–	if ( simParams_->haveAccumulateBoxDipole() )
1195	–	if ( simParams_->getAccumulateBoxDipole() ) {
1196	–	setAccumulateBoxDipole();
1197	–	calcBoxDipole_ = true;
1198	–	}
1199	–
1200	–	}
1201	–
962		void SimInfo::addProperty(GenericData* genData) {
963		properties_.addProperty(genData);
964		}
965
966	<	void SimInfo::removeProperty(const std::string& propName) {
966	>	void SimInfo::removeProperty(const string& propName) {
967		properties_.removeProperty(propName);
968		}
969
#	Line 1211 | Line 971 | namespace oopse {
971		properties_.clearProperties();
972		}
973
974	<	std::vector<std::string> SimInfo::getPropertyNames() {
974	>	vector<string> SimInfo::getPropertyNames() {
975		return properties_.getPropertyNames();
976		}
977
978	<	std::vector<GenericData*> SimInfo::getProperties() {
978	>	vector<GenericData*> SimInfo::getProperties() {
979		return properties_.getProperties();
980		}
981
982	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
982	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
983		return properties_.getPropertyByName(propName);
984		}
985
#	Line 1233 | Line 993 | namespace oopse {
993		Molecule* mol;
994		RigidBody* rb;
995		Atom* atom;
996	+	CutoffGroup* cg;
997		SimInfo::MoleculeIterator mi;
998		Molecule::RigidBodyIterator rbIter;
999	<	Molecule::AtomIterator atomIter;;
999	>	Molecule::AtomIterator atomIter;
1000	>	Molecule::CutoffGroupIterator cgIter;
1001
1002		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1003
1004	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1004	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
1005	>	atom = mol->nextAtom(atomIter)) {
1006		atom->setSnapshotManager(sman_);
1007		}
1008
1009	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1009	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1010	>	rb = mol->nextRigidBody(rbIter)) {
1011		rb->setSnapshotManager(sman_);
1012		}
1013	+
1014	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1015	+	cg = mol->nextCutoffGroup(cgIter)) {
1016	+	cg->setSnapshotManager(sman_);
1017	+	}
1018		}
1019
1020		}
1021
1253	–	Vector3d SimInfo::getComVel(){
1254	–	SimInfo::MoleculeIterator i;
1255	–	Molecule* mol;
1022
1023	<	Vector3d comVel(0.0);
1258	<	RealType totalMass = 0.0;
1259	<
1260	<
1261	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1262	<	RealType mass = mol->getMass();
1263	<	totalMass += mass;
1264	<	comVel += mass * mol->getComVel();
1265	<	}
1023	>	ostream& operator <<(ostream& o, SimInfo& info) {
1024
1267	–	#ifdef IS_MPI
1268	–	RealType tmpMass = totalMass;
1269	–	Vector3d tmpComVel(comVel);
1270	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1271	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1272	–	#endif
1273	–
1274	–	comVel /= totalMass;
1275	–
1276	–	return comVel;
1277	–	}
1278	–
1279	–	Vector3d SimInfo::getCom(){
1280	–	SimInfo::MoleculeIterator i;
1281	–	Molecule* mol;
1282	–
1283	–	Vector3d com(0.0);
1284	–	RealType totalMass = 0.0;
1285	–
1286	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1287	–	RealType mass = mol->getMass();
1288	–	totalMass += mass;
1289	–	com += mass * mol->getCom();
1290	–	}
1291	–
1292	–	#ifdef IS_MPI
1293	–	RealType tmpMass = totalMass;
1294	–	Vector3d tmpCom(com);
1295	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1296	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297	–	#endif
1298	–
1299	–	com /= totalMass;
1300	–
1301	–	return com;
1302	–
1303	–	}
1304	–
1305	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1306	–
1025		return o;
1026		}
1027
1028	<
1311	<	/*
1312	<	Returns center of mass and center of mass velocity in one function call.
1313	<	*/
1314	<
1315	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1316	<	SimInfo::MoleculeIterator i;
1317	<	Molecule* mol;
1318	<
1319	<
1320	<	RealType totalMass = 0.0;
1321	<
1322	<
1323	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1324	<	RealType mass = mol->getMass();
1325	<	totalMass += mass;
1326	<	com += mass * mol->getCom();
1327	<	comVel += mass * mol->getComVel();
1328	<	}
1329	<
1330	<	#ifdef IS_MPI
1331	<	RealType tmpMass = totalMass;
1332	<	Vector3d tmpCom(com);
1333	<	Vector3d tmpComVel(comVel);
1334	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1335	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1336	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1337	<	#endif
1338	<
1339	<	com /= totalMass;
1340	<	comVel /= totalMass;
1341	<	}
1342	<
1343	<	/*
1344	<	Return intertia tensor for entire system and angular momentum Vector.
1345	<
1346	<
1347	<	[  Ixx -Ixy  -Ixz ]
1348	<	J =| -Iyx  Iyy  -Iyz |
1349	<	[ -Izx -Iyz   Izz ]
1350	<	*/
1351	<
1352	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1353	<
1354	<
1355	<	RealType xx = 0.0;
1356	<	RealType yy = 0.0;
1357	<	RealType zz = 0.0;
1358	<	RealType xy = 0.0;
1359	<	RealType xz = 0.0;
1360	<	RealType yz = 0.0;
1361	<	Vector3d com(0.0);
1362	<	Vector3d comVel(0.0);
1363	<
1364	<	getComAll(com, comVel);
1365	<
1366	<	SimInfo::MoleculeIterator i;
1367	<	Molecule* mol;
1368	<
1369	<	Vector3d thisq(0.0);
1370	<	Vector3d thisv(0.0);
1371	<
1372	<	RealType thisMass = 0.0;
1373	<
1374	<
1375	<
1376	<
1377	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1378	<
1379	<	thisq = mol->getCom()-com;
1380	<	thisv = mol->getComVel()-comVel;
1381	<	thisMass = mol->getMass();
1382	<	// Compute moment of intertia coefficients.
1383	<	xx += thisq[0]*thisq[0]*thisMass;
1384	<	yy += thisq[1]*thisq[1]*thisMass;
1385	<	zz += thisq[2]*thisq[2]*thisMass;
1386	<
1387	<	// compute products of intertia
1388	<	xy += thisq[0]*thisq[1]*thisMass;
1389	<	xz += thisq[0]*thisq[2]*thisMass;
1390	<	yz += thisq[1]*thisq[2]*thisMass;
1391	<
1392	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1393	<
1394	<	}
1395	<
1396	<
1397	<	inertiaTensor(0,0) = yy + zz;
1398	<	inertiaTensor(0,1) = -xy;
1399	<	inertiaTensor(0,2) = -xz;
1400	<	inertiaTensor(1,0) = -xy;
1401	<	inertiaTensor(1,1) = xx + zz;
1402	<	inertiaTensor(1,2) = -yz;
1403	<	inertiaTensor(2,0) = -xz;
1404	<	inertiaTensor(2,1) = -yz;
1405	<	inertiaTensor(2,2) = xx + yy;
1406	<
1407	<	#ifdef IS_MPI
1408	<	Mat3x3d tmpI(inertiaTensor);
1409	<	Vector3d tmpAngMom;
1410	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1411	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1412	<	#endif
1413	<
1414	<	return;
1415	<	}
1416	<
1417	<	//Returns the angular momentum of the system
1418	<	Vector3d SimInfo::getAngularMomentum(){
1419	<
1420	<	Vector3d com(0.0);
1421	<	Vector3d comVel(0.0);
1422	<	Vector3d angularMomentum(0.0);
1423	<
1424	<	getComAll(com,comVel);
1425	<
1426	<	SimInfo::MoleculeIterator i;
1427	<	Molecule* mol;
1428	<
1429	<	Vector3d thisr(0.0);
1430	<	Vector3d thisp(0.0);
1431	<
1432	<	RealType thisMass;
1433	<
1434	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1435	<	thisMass = mol->getMass();
1436	<	thisr = mol->getCom()-com;
1437	<	thisp = (mol->getComVel()-comVel)*thisMass;
1438	<
1439	<	angularMomentum += cross( thisr, thisp );
1440	<
1441	<	}
1442	<
1443	<	#ifdef IS_MPI
1444	<	Vector3d tmpAngMom;
1445	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1446	<	#endif
1447	<
1448	<	return angularMomentum;
1449	<	}
1450	<
1028	>
1029		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1030	<	return IOIndexToIntegrableObject.at(index);
1030	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1031	>	sprintf(painCave.errMsg,
1032	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1033	>	"\tindex exceeds number of known objects!\n");
1034	>	painCave.isFatal = 1;
1035	>	simError();
1036	>	return NULL;
1037	>	} else
1038	>	return IOIndexToIntegrableObject.at(index);
1039		}
1040
1041	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1041	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1042		IOIndexToIntegrableObject= v;
1043		}
1044
1045	<	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1046	<	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1047	<	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1048	<	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1049	<	*/
1050	<	void SimInfo::getGyrationalVolume(RealType &volume){
1051	<	Mat3x3d intTensor;
1052	<	RealType det;
1053	<	Vector3d dummyAngMom;
1468	<	RealType sysconstants;
1469	<	RealType geomCnst;
1470	<
1471	<	geomCnst = 3.0/2.0;
1472	<	/* Get the inertial tensor and angular momentum for free*/
1473	<	getInertiaTensor(intTensor,dummyAngMom);
1474	<
1475	<	det = intTensor.determinant();
1476	<	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1477	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1478	<	return;
1045	>	int SimInfo::getNGlobalConstraints() {
1046	>	int nGlobalConstraints;
1047	>	#ifdef IS_MPI
1048	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1049	>	MPI::INT, MPI::SUM);
1050	>	#else
1051	>	nGlobalConstraints =  nConstraints_;
1052	>	#endif
1053	>	return nGlobalConstraints;
1054		}
1055
1056	<	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1482	<	Mat3x3d intTensor;
1483	<	Vector3d dummyAngMom;
1484	<	RealType sysconstants;
1485	<	RealType geomCnst;
1056	>	}//end namespace OpenMD
1057
1487	–	geomCnst = 3.0/2.0;
1488	–	/* Get the inertial tensor and angular momentum for free*/
1489	–	getInertiaTensor(intTensor,dummyAngMom);
1490	–
1491	–	detI = intTensor.determinant();
1492	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1493	–	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1494	–	return;
1495	–	}
1496	–	/*
1497	–	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1498	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1499	–	sdByGlobalIndex_ = v;
1500	–	}
1501	–
1502	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1503	–	//assert(index < nAtoms_ + nRigidBodies_);
1504	–	return sdByGlobalIndex_.at(index);
1505	–	}
1506	–	*/
1507	–	}//end namespace oopse
1508	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 1121 by chuckv, Mon Feb 26 04:45:42 2007 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

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