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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 53 | Line 54
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/fCutoffPolicy.h"
57	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	<	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	<	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60	<	#include "UseTheForce/doForces_interface.h"
61	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	<	#include "UseTheForce/notifyCutoffs_interface.h"
63	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61	<
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
71	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
75	<	std::map<int, std::set<int> >::iterator i = container.find(index);
76	<	std::set<int> result;
77	<	if (i != container.end()) {
78	<	result = i->second;
79	<	}
80	<
81	<	return result;
82	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
72	<	ForceField* ff, Globals* simParams) :
73	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
87	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
79	<
94	<
95	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
96	<	MoleculeStamp* molStamp;
97	<	int nMolWithSameStamp;
98	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
99	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
100	<	CutoffGroupStamp* cgStamp;
101	<	RigidBodyStamp* rbStamp;
102	<	int nRigidAtoms = 0;
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), 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	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
82	<	molStamp = i->first;
83	<	nMolWithSameStamp = i->second;
84	<
85	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
86	<
87	<	//calculate atoms in molecules
88	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
89	<
90	<
91	<	//calculate atoms in cutoff groups
92	<	int nAtomsInGroups = 0;
93	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
94	<
95	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
96	<	cgStamp = molStamp->getCutoffGroup(j);
97	<	nAtomsInGroups += cgStamp->getNMembers();
98	<	}
122	<
123	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
124	<
125	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
126	<
127	<	//calculate atoms in rigid bodies
128	<	int nAtomsInRigidBodies = 0;
129	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130	<
131	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
132	<	rbStamp = molStamp->getRigidBody(j);
133	<	nAtomsInRigidBodies += rbStamp->getNMembers();
134	<	}
135	<
136	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138	<
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	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
102	<	//group therefore the total number of cutoff groups in the system is
103	<	//equal to the total number of atoms minus number of atoms belong to
104	<	//cutoff group defined in meta-data file plus the number of cutoff
105	<	//groups defined in meta-data file
106	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
107	<
108	<	//every free atom (atom does not belong to rigid bodies) is an
109	<	//integrable object therefore the total number of integrable objects
110	<	//in the system is equal to the total number of atoms minus number of
111	<	//atoms belong to rigid body defined in meta-data file plus the number
112	<	//of rigid bodies defined in meta-data file
113	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
114	<	+ nGlobalRigidBodies_;
115	<
116	<	nGlobalMols_ = molStampIds_.size();
117	<
118	<	#ifdef IS_MPI
119	<	molToProcMap_.resize(nGlobalMols_);
120	<	#endif
121	<
101	>	nMolWithSameStamp = (*i)->getNMol();
102	>
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	>	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		}
160		molecules_.clear();
161
171	–	delete stamps_;
162		delete sman_;
163		delete simParams_;
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		}
262	<
263	<	}//end for (integrableObject)
264	<	}// end for (mol)
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 293 | Line 289 | namespace oopse {
289
290		}
291
292	+	int SimInfo::getFdf() {
293	+	#ifdef IS_MPI
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)) {
308	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
309	–	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 322 | 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 335 | 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 344 | 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<Bond*>::iterator bondIter;
376	>	vector<Bend*>::iterator bendIter;
377	>	vector<Torsion*>::iterator torsionIter;
378	>	vector<Inversion*>::iterator inversionIter;
379		Bond* bond;
380		Bend* bend;
381		Torsion* torsion;
382	+	Inversion* inversion;
383		int a;
384		int b;
385		int c;
386		int d;
387
388	<	std::map<int, std::set<int> > atomGroups;
388	>	// atomGroups can be used to add special interaction maps between
389	>	// groups of atoms that are in two separate rigid bodies.
390	>	// However, most site-site interactions between two rigid bodies
391	>	// are probably not special, just the ones between the physically
392	>	// bonded atoms.  Interactions *within* a single rigid body should
393	>	// always be excluded.  These are done at the bottom of this
394	>	// function.
395
396	+	map<int, set<int> > atomGroups;
397		Molecule::RigidBodyIterator rbIter;
398		RigidBody* rb;
399		Molecule::IntegrableObjectIterator ii;
400	<	StuntDouble* integrableObject;
400	>	StuntDouble* sd;
401
402	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
403	<	integrableObject = mol->nextIntegrableObject(ii)) {
404	<
405	<	if (integrableObject->isRigidBody()) {
406	<	rb = static_cast<RigidBody*>(integrableObject);
407	<	std::vector<Atom*> atoms = rb->getAtoms();
408	<	std::set<int> rigidAtoms;
409	<	for (int i = 0; i < atoms.size(); ++i) {
410	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
411	<	}
412	<	for (int i = 0; i < atoms.size(); ++i) {
413	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
414	<	}
402	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
403	>	sd = mol->nextIntegrableObject(ii)) {
404	>
405	>	if (sd->isRigidBody()) {
406	>	rb = static_cast<RigidBody*>(sd);
407	>	vector<Atom*> atoms = rb->getAtoms();
408	>	set<int> rigidAtoms;
409	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
410	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
411	>	}
412	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
413	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
414	>	}
415		} else {
416	<	std::set<int> oneAtomSet;
417	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
418	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
416	>	set<int> oneAtomSet;
417	>	oneAtomSet.insert(sd->getGlobalIndex());
418	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
419		}
420		}
421	+
422	+	for (bond= mol->beginBond(bondIter); bond != NULL;
423	+	bond = mol->nextBond(bondIter)) {
424
386	–
387	–
388	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
425		a = bond->getAtomA()->getGlobalIndex();
426	<	b = bond->getAtomB()->getGlobalIndex();
427	<	exclude_.addPair(a, b);
426	>	b = bond->getAtomB()->getGlobalIndex();
427	>
428	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
429	>	oneTwoInteractions_.addPair(a, b);
430	>	} else {
431	>	excludedInteractions_.addPair(a, b);
432	>	}
433		}
434
435	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
435	>	for (bend= mol->beginBend(bendIter); bend != NULL;
436	>	bend = mol->nextBend(bendIter)) {
437	>
438		a = bend->getAtomA()->getGlobalIndex();
439		b = bend->getAtomB()->getGlobalIndex();
440		c = bend->getAtomC()->getGlobalIndex();
398	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
399	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
400	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
401	–
402	–	exclude_.addPairs(rigidSetA, rigidSetB);
403	–	exclude_.addPairs(rigidSetA, rigidSetC);
404	–	exclude_.addPairs(rigidSetB, rigidSetC);
441
442	<	//exclude_.addPair(a, b);
443	<	//exclude_.addPair(a, c);
444	<	//exclude_.addPair(b, c);
442	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
443	>	oneTwoInteractions_.addPair(a, b);
444	>	oneTwoInteractions_.addPair(b, c);
445	>	} else {
446	>	excludedInteractions_.addPair(a, b);
447	>	excludedInteractions_.addPair(b, c);
448	>	}
449	>
450	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
451	>	oneThreeInteractions_.addPair(a, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, c);
454	>	}
455		}
456
457	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
457	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
458	>	torsion = mol->nextTorsion(torsionIter)) {
459	>
460		a = torsion->getAtomA()->getGlobalIndex();
461		b = torsion->getAtomB()->getGlobalIndex();
462		c = torsion->getAtomC()->getGlobalIndex();
463	<	d = torsion->getAtomD()->getGlobalIndex();
416	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
417	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
418	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
419	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
463	>	d = torsion->getAtomD()->getGlobalIndex();
464
465	<	exclude_.addPairs(rigidSetA, rigidSetB);
466	<	exclude_.addPairs(rigidSetA, rigidSetC);
467	<	exclude_.addPairs(rigidSetA, rigidSetD);
468	<	exclude_.addPairs(rigidSetB, rigidSetC);
469	<	exclude_.addPairs(rigidSetB, rigidSetD);
470	<	exclude_.addPairs(rigidSetC, rigidSetD);
465	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
466	>	oneTwoInteractions_.addPair(a, b);
467	>	oneTwoInteractions_.addPair(b, c);
468	>	oneTwoInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(a, b);
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474
475	<	/*
476	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
477	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
478	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
479	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
480	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
481	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
482	<
483	<
484	<	exclude_.addPair(a, b);
485	<	exclude_.addPair(a, c);
486	<	exclude_.addPair(a, d);
487	<	exclude_.addPair(b, c);
441	<	exclude_.addPair(b, d);
442	<	exclude_.addPair(c, d);
443	<	*/
475	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
476	>	oneThreeInteractions_.addPair(a, c);
477	>	oneThreeInteractions_.addPair(b, d);
478	>	} else {
479	>	excludedInteractions_.addPair(a, c);
480	>	excludedInteractions_.addPair(b, d);
481	>	}
482	>
483	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
484	>	oneFourInteractions_.addPair(a, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, d);
487	>	}
488		}
489
490	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
491	<	std::vector<Atom*> atoms = rb->getAtoms();
492	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
493	<	for (int j = i + 1; j < atoms.size(); ++j) {
490	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
491	>	inversion = mol->nextInversion(inversionIter)) {
492	>
493	>	a = inversion->getAtomA()->getGlobalIndex();
494	>	b = inversion->getAtomB()->getGlobalIndex();
495	>	c = inversion->getAtomC()->getGlobalIndex();
496	>	d = inversion->getAtomD()->getGlobalIndex();
497	>
498	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
499	>	oneTwoInteractions_.addPair(a, b);
500	>	oneTwoInteractions_.addPair(a, c);
501	>	oneTwoInteractions_.addPair(a, d);
502	>	} else {
503	>	excludedInteractions_.addPair(a, b);
504	>	excludedInteractions_.addPair(a, c);
505	>	excludedInteractions_.addPair(a, d);
506	>	}
507	>
508	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
509	>	oneThreeInteractions_.addPair(b, c);
510	>	oneThreeInteractions_.addPair(b, d);
511	>	oneThreeInteractions_.addPair(c, d);
512	>	} else {
513	>	excludedInteractions_.addPair(b, c);
514	>	excludedInteractions_.addPair(b, d);
515	>	excludedInteractions_.addPair(c, d);
516	>	}
517	>	}
518	>
519	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
520	>	rb = mol->nextRigidBody(rbIter)) {
521	>	vector<Atom*> atoms = rb->getAtoms();
522	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
523	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
524		a = atoms[i]->getGlobalIndex();
525		b = atoms[j]->getGlobalIndex();
526	<	exclude_.addPair(a, b);
526	>	excludedInteractions_.addPair(a, b);
527		}
528		}
529		}
530
531		}
532
533	<	void SimInfo::removeExcludePairs(Molecule* mol) {
534	<	std::vector<Bond*>::iterator bondIter;
535	<	std::vector<Bend*>::iterator bendIter;
536	<	std::vector<Torsion*>::iterator torsionIter;
533	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
534	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
535	>	vector<Bond*>::iterator bondIter;
536	>	vector<Bend*>::iterator bendIter;
537	>	vector<Torsion*>::iterator torsionIter;
538	>	vector<Inversion*>::iterator inversionIter;
539		Bond* bond;
540		Bend* bend;
541		Torsion* torsion;
542	+	Inversion* inversion;
543		int a;
544		int b;
545		int c;
546		int d;
547
548	<	std::map<int, std::set<int> > atomGroups;
472	<
548	>	map<int, set<int> > atomGroups;
549		Molecule::RigidBodyIterator rbIter;
550		RigidBody* rb;
551		Molecule::IntegrableObjectIterator ii;
552	<	StuntDouble* integrableObject;
552	>	StuntDouble* sd;
553
554	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
555	<	integrableObject = mol->nextIntegrableObject(ii)) {
556	<
557	<	if (integrableObject->isRigidBody()) {
558	<	rb = static_cast<RigidBody*>(integrableObject);
559	<	std::vector<Atom*> atoms = rb->getAtoms();
560	<	std::set<int> rigidAtoms;
561	<	for (int i = 0; i < atoms.size(); ++i) {
562	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
563	<	}
564	<	for (int i = 0; i < atoms.size(); ++i) {
565	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
566	<	}
554	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
555	>	sd = mol->nextIntegrableObject(ii)) {
556	>
557	>	if (sd->isRigidBody()) {
558	>	rb = static_cast<RigidBody*>(sd);
559	>	vector<Atom*> atoms = rb->getAtoms();
560	>	set<int> rigidAtoms;
561	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
562	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
563	>	}
564	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
565	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
566	>	}
567		} else {
568	<	std::set<int> oneAtomSet;
569	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
570	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
568	>	set<int> oneAtomSet;
569	>	oneAtomSet.insert(sd->getGlobalIndex());
570	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
571		}
572		}
573
574	<
575	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
574	>	for (bond= mol->beginBond(bondIter); bond != NULL;
575	>	bond = mol->nextBond(bondIter)) {
576	>
577		a = bond->getAtomA()->getGlobalIndex();
578	<	b = bond->getAtomB()->getGlobalIndex();
579	<	exclude_.removePair(a, b);
578	>	b = bond->getAtomB()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	} else {
583	>	excludedInteractions_.removePair(a, b);
584	>	}
585		}
586
587	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
587	>	for (bend= mol->beginBend(bendIter); bend != NULL;
588	>	bend = mol->nextBend(bendIter)) {
589	>
590		a = bend->getAtomA()->getGlobalIndex();
591		b = bend->getAtomB()->getGlobalIndex();
592		c = bend->getAtomC()->getGlobalIndex();
509	–
510	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
511	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
512	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
513	–
514	–	exclude_.removePairs(rigidSetA, rigidSetB);
515	–	exclude_.removePairs(rigidSetA, rigidSetC);
516	–	exclude_.removePairs(rigidSetB, rigidSetC);
593
594	<	//exclude_.removePair(a, b);
595	<	//exclude_.removePair(a, c);
596	<	//exclude_.removePair(b, c);
594	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
595	>	oneTwoInteractions_.removePair(a, b);
596	>	oneTwoInteractions_.removePair(b, c);
597	>	} else {
598	>	excludedInteractions_.removePair(a, b);
599	>	excludedInteractions_.removePair(b, c);
600	>	}
601	>
602	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
603	>	oneThreeInteractions_.removePair(a, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, c);
606	>	}
607		}
608
609	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
609	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
610	>	torsion = mol->nextTorsion(torsionIter)) {
611	>
612		a = torsion->getAtomA()->getGlobalIndex();
613		b = torsion->getAtomB()->getGlobalIndex();
614		c = torsion->getAtomC()->getGlobalIndex();
615	<	d = torsion->getAtomD()->getGlobalIndex();
615	>	d = torsion->getAtomD()->getGlobalIndex();
616	>
617	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
618	>	oneTwoInteractions_.removePair(a, b);
619	>	oneTwoInteractions_.removePair(b, c);
620	>	oneTwoInteractions_.removePair(c, d);
621	>	} else {
622	>	excludedInteractions_.removePair(a, b);
623	>	excludedInteractions_.removePair(b, c);
624	>	excludedInteractions_.removePair(c, d);
625	>	}
626
627	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
628	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
629	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
630	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
627	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
628	>	oneThreeInteractions_.removePair(a, c);
629	>	oneThreeInteractions_.removePair(b, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, c);
632	>	excludedInteractions_.removePair(b, d);
633	>	}
634
635	<	exclude_.removePairs(rigidSetA, rigidSetB);
636	<	exclude_.removePairs(rigidSetA, rigidSetC);
637	<	exclude_.removePairs(rigidSetA, rigidSetD);
638	<	exclude_.removePairs(rigidSetB, rigidSetC);
639	<	exclude_.removePairs(rigidSetB, rigidSetD);
640	<	exclude_.removePairs(rigidSetC, rigidSetD);
540	<
541	<	/*
542	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
543	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
544	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
545	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
546	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
547	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
635	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
636	>	oneFourInteractions_.removePair(a, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, d);
639	>	}
640	>	}
641
642	<
643	<	exclude_.removePair(a, b);
644	<	exclude_.removePair(a, c);
645	<	exclude_.removePair(a, d);
646	<	exclude_.removePair(b, c);
647	<	exclude_.removePair(b, d);
648	<	exclude_.removePair(c, d);
649	<	*/
642	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
643	>	inversion = mol->nextInversion(inversionIter)) {
644	>
645	>	a = inversion->getAtomA()->getGlobalIndex();
646	>	b = inversion->getAtomB()->getGlobalIndex();
647	>	c = inversion->getAtomC()->getGlobalIndex();
648	>	d = inversion->getAtomD()->getGlobalIndex();
649	>
650	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
651	>	oneTwoInteractions_.removePair(a, b);
652	>	oneTwoInteractions_.removePair(a, c);
653	>	oneTwoInteractions_.removePair(a, d);
654	>	} else {
655	>	excludedInteractions_.removePair(a, b);
656	>	excludedInteractions_.removePair(a, c);
657	>	excludedInteractions_.removePair(a, d);
658	>	}
659	>
660	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
661	>	oneThreeInteractions_.removePair(b, c);
662	>	oneThreeInteractions_.removePair(b, d);
663	>	oneThreeInteractions_.removePair(c, d);
664	>	} else {
665	>	excludedInteractions_.removePair(b, c);
666	>	excludedInteractions_.removePair(b, d);
667	>	excludedInteractions_.removePair(c, d);
668	>	}
669		}
670
671	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
672	<	std::vector<Atom*> atoms = rb->getAtoms();
673	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
674	<	for (int j = i + 1; j < atoms.size(); ++j) {
671	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
672	>	rb = mol->nextRigidBody(rbIter)) {
673	>	vector<Atom*> atoms = rb->getAtoms();
674	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
675	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
676		a = atoms[i]->getGlobalIndex();
677		b = atoms[j]->getGlobalIndex();
678	<	exclude_.removePair(a, b);
678	>	excludedInteractions_.removePair(a, b);
679		}
680		}
681		}
682	<
682	>
683		}
684	<
685	<
684	>
685	>
686		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
687		int curStampId;
688	<
688	>
689		//index from 0
690		curStampId = moleculeStamps_.size();
691
#	Line 580 | Line 693 | namespace oopse {
693		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
694		}
695
583	–	void SimInfo::update() {
696
697	<	setupSimType();
698	<
699	<	#ifdef IS_MPI
700	<	setupFortranParallel();
701	<	#endif
702	<
703	<	setupFortranSim();
704	<
705	<	//setup fortran force field
594	<	/** @deprecate */
595	<	int isError = 0;
596	<
597	<	setupElectrostaticSummationMethod( isError );
598	<	setupSwitchingFunction();
599	<
600	<	if(isError){
601	<	sprintf( painCave.errMsg,
602	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
603	<	painCave.isFatal = 1;
604	<	simError();
605	<	}
606	<
607	<
608	<	setupCutoff();
609	<
697	>	/**
698	>	* update
699	>	*
700	>	*  Performs the global checks and variable settings after the
701	>	*  objects have been created.
702	>	*
703	>	*/
704	>	void SimInfo::update() {
705	>	setupSimVariables();
706		calcNdf();
707		calcNdfRaw();
708		calcNdfTrans();
613	–
614	–	fortranInitialized_ = true;
709		}
710	<
711	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
710	>
711	>	/**
712	>	* getSimulatedAtomTypes
713	>	*
714	>	* Returns an STL set of AtomType* that are actually present in this
715	>	* simulation.  Must query all processors to assemble this information.
716	>	*
717	>	*/
718	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
719		SimInfo::MoleculeIterator mi;
720		Molecule* mol;
721		Molecule::AtomIterator ai;
722		Atom* atom;
723	<	std::set<AtomType*> atomTypes;
724	<
723	>	set<AtomType*> atomTypes;
724	>
725		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
726	<
727	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
726	>	for(atom = mol->beginAtom(ai); atom != NULL;
727	>	atom = mol->nextAtom(ai)) {
728		atomTypes.insert(atom->getAtomType());
729	<	}
730	<
731	<	}
729	>	}
730	>	}
731	>
732	>	#ifdef IS_MPI
733
734	<	return atomTypes;
735	<	}
634	<
635	<	void SimInfo::setupSimType() {
636	<	std::set<AtomType*>::iterator i;
637	<	std::set<AtomType*> atomTypes;
638	<	atomTypes = getUniqueAtomTypes();
734	>	// loop over the found atom types on this processor, and add their
735	>	// numerical idents to a vector:
736
737	<	int useLennardJones = 0;
738	<	int useElectrostatic = 0;
739	<	int useEAM = 0;
740	<	int useSC = 0;
644	<	int useCharge = 0;
645	<	int useDirectional = 0;
646	<	int useDipole = 0;
647	<	int useGayBerne = 0;
648	<	int useSticky = 0;
649	<	int useStickyPower = 0;
650	<	int useShape = 0;
651	<	int useFLARB = 0; //it is not in AtomType yet
652	<	int useDirectionalAtom = 0;
653	<	int useElectrostatics = 0;
654	<	//usePBC and useRF are from simParams
655	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
656	<	int useRF;
657	<	int useSF;
658	<	std::string myMethod;
737	>	vector<int> foundTypes;
738	>	set<AtomType*>::iterator i;
739	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
740	>	foundTypes.push_back( (*i)->getIdent() );
741
742	<	// set the useRF logical
743	<	useRF = 0;
662	<	useSF = 0;
742	>	// count_local holds the number of found types on this processor
743	>	int count_local = foundTypes.size();
744
745	+	int nproc = MPI::COMM_WORLD.Get_size();
746
747	<	if (simParams_->haveElectrostaticSummationMethod()) {
748	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
749	<	toUpper(myMethod);
750	<	if (myMethod == "REACTION_FIELD") {
751	<	useRF=1;
752	<	} else {
753	<	if (myMethod == "SHIFTED_FORCE") {
754	<	useSF = 1;
755	<	}
756	<	}
747	>	// we need arrays to hold the counts and displacement vectors for
748	>	// all processors
749	>	vector<int> counts(nproc, 0);
750	>	vector<int> disps(nproc, 0);
751	>
752	>	// fill the counts array
753	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
754	>	1, MPI::INT);
755	>
756	>	// use the processor counts to compute the displacement array
757	>	disps[0] = 0;
758	>	int totalCount = counts[0];
759	>	for (int iproc = 1; iproc < nproc; iproc++) {
760	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
761	>	totalCount += counts[iproc];
762		}
763
764	<	//loop over all of the atom types
765	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
766	<	useLennardJones |= (*i)->isLennardJones();
767	<	useElectrostatic |= (*i)->isElectrostatic();
768	<	useEAM |= (*i)->isEAM();
769	<	useSC |= (*i)->isSC();
770	<	useCharge |= (*i)->isCharge();
684	<	useDirectional |= (*i)->isDirectional();
685	<	useDipole |= (*i)->isDipole();
686	<	useGayBerne |= (*i)->isGayBerne();
687	<	useSticky |= (*i)->isSticky();
688	<	useStickyPower |= (*i)->isStickyPower();
689	<	useShape |= (*i)->isShape();
690	<	}
764	>	// we need a (possibly redundant) set of all found types:
765	>	vector<int> ftGlobal(totalCount);
766	>
767	>	// now spray out the foundTypes to all the other processors:
768	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
769	>	&ftGlobal[0], &counts[0], &disps[0],
770	>	MPI::INT);
771
772	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
693	<	useDirectionalAtom = 1;
694	<	}
772	>	vector<int>::iterator j;
773
774	<	if (useCharge || useDipole) {
775	<	useElectrostatics = 1;
776	<	}
774	>	// foundIdents is a stl set, so inserting an already found ident
775	>	// will have no effect.
776	>	set<int> foundIdents;
777
778	<	#ifdef IS_MPI
779	<	int temp;
778	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
779	>	foundIdents.insert((*j));
780	>
781	>	// now iterate over the foundIdents and get the actual atom types
782	>	// that correspond to these:
783	>	set<int>::iterator it;
784	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
785	>	atomTypes.insert( forceField_->getAtomType((*it)) );
786	>
787	>	#endif
788
789	<	temp = usePBC;
790	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
789	>	return atomTypes;
790	>	}
791
706	–	temp = useDirectionalAtom;
707	–	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
792
793	<	temp = useLennardJones;
794	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793	>	int getGlobalCountOfType(AtomType* atype) {
794	>	/*
795	>	set<AtomType*> atypes = getSimulatedAtomTypes();
796	>	map<AtomType*, int> counts_;
797
798	<	temp = useElectrostatics;
799	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
799	>	for(atom = mol->beginAtom(ai); atom != NULL;
800	>	atom = mol->nextAtom(ai)) {
801	>	atom->getAtomType();
802	>	}
803	>	}
804	>	*/
805	>	return 0;
806	>	}
807
808	<	temp = useCharge;
809	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	void SimInfo::setupSimVariables() {
809	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
810	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
811	>	// parameter is true
812	>	calcBoxDipole_ = false;
813	>	if ( simParams_->haveAccumulateBoxDipole() )
814	>	if ( simParams_->getAccumulateBoxDipole() ) {
815	>	calcBoxDipole_ = true;
816	>	}
817	>
818	>	set<AtomType*>::iterator i;
819	>	set<AtomType*> atomTypes;
820	>	atomTypes = getSimulatedAtomTypes();
821	>	bool usesElectrostatic = false;
822	>	bool usesMetallic = false;
823	>	bool usesDirectional = false;
824	>	bool usesFluctuatingCharges =  false;
825	>	//loop over all of the atom types
826	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
827	>	usesElectrostatic |= (*i)->isElectrostatic();
828	>	usesMetallic |= (*i)->isMetal();
829	>	usesDirectional |= (*i)->isDirectional();
830	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
831	>	}
832
833	<	temp = useDipole;
834	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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);
833	>	#ifdef IS_MPI
834	>	bool temp;
835	>	temp = usesDirectional;
836	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
837	>	MPI::LOR);
838	>
839	>	temp = usesMetallic;
840	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
841	>	MPI::LOR);
842
843	<	temp = useGayBerne;
844	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
843	>	temp = usesElectrostatic;
844	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
845	>	MPI::LOR);
846
847	<	temp = useEAM;
848	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
847	>	temp = usesFluctuatingCharges;
848	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
849	>	MPI::LOR);
850	>	#else
851
852	<	temp = useSC;
853	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	usesDirectionalAtoms_ = usesDirectional;
853	>	usesMetallicAtoms_ = usesMetallic;
854	>	usesElectrostaticAtoms_ = usesElectrostatic;
855	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
856	>
857	>	#endif
858
859	<	temp = useShape;
860	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
860	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
861	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
862	>	}
863
739	–	temp = useFLARB;
740	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864
865	<	temp = useRF;
866	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865	>	vector<int> SimInfo::getGlobalAtomIndices() {
866	>	SimInfo::MoleculeIterator mi;
867	>	Molecule* mol;
868	>	Molecule::AtomIterator ai;
869	>	Atom* atom;
870
871	<	temp = useSF;
872	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
871	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
872	>
873	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
874	>
875	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
876	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
877	>	}
878	>	}
879	>	return GlobalAtomIndices;
880	>	}
881
748	–	#endif
882
883	<	fInfo_.SIM_uses_PBC = usePBC;
884	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
885	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
886	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
887	<	fInfo_.SIM_uses_Charges = useCharge;
755	<	fInfo_.SIM_uses_Dipoles = useDipole;
756	<	fInfo_.SIM_uses_Sticky = useSticky;
757	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
758	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
759	<	fInfo_.SIM_uses_EAM = useEAM;
760	<	fInfo_.SIM_uses_SC = useSC;
761	<	fInfo_.SIM_uses_Shapes = useShape;
762	<	fInfo_.SIM_uses_FLARB = useFLARB;
763	<	fInfo_.SIM_uses_RF = useRF;
764	<	fInfo_.SIM_uses_SF = useSF;
883	>	vector<int> SimInfo::getGlobalGroupIndices() {
884	>	SimInfo::MoleculeIterator mi;
885	>	Molecule* mol;
886	>	Molecule::CutoffGroupIterator ci;
887	>	CutoffGroup* cg;
888
889	<	if( myMethod == "REACTION_FIELD") {
889	>	vector<int> GlobalGroupIndices;
890	>
891	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
892
893	<	if (simParams_->haveDielectric()) {
894	<	fInfo_.dielect = simParams_->getDielectric();
895	<	} else {
896	<	sprintf(painCave.errMsg,
897	<	"SimSetup Error: No Dielectric constant was set.\n"
898	<	"\tYou are trying to use Reaction Field without"
774	<	"\tsetting a dielectric constant!\n");
775	<	painCave.isFatal = 1;
776	<	simError();
777	<	}
893	>	//local index of cutoff group is trivial, it only depends on the
894	>	//order of travesing
895	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
896	>	cg = mol->nextCutoffGroup(ci)) {
897	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
898	>	}
899		}
900	<
900	>	return GlobalGroupIndices;
901		}
902
782	–	void SimInfo::setupFortranSim() {
783	–	int isError;
784	–	int nExclude;
785	–	std::vector<int> fortranGlobalGroupMembership;
786	–
787	–	nExclude = exclude_.getSize();
788	–	isError = 0;
903
904	<	//globalGroupMembership_ is filled by SimCreator
791	<	for (int i = 0; i < nGlobalAtoms_; i++) {
792	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
793	<	}
904	>	void SimInfo::prepareTopology() {
905
906		//calculate mass ratio of cutoff group
796	–	std::vector<double> mfact;
907		SimInfo::MoleculeIterator mi;
908		Molecule* mol;
909		Molecule::CutoffGroupIterator ci;
910		CutoffGroup* cg;
911		Molecule::AtomIterator ai;
912		Atom* atom;
913	<	double totalMass;
913	>	RealType totalMass;
914
915	<	//to avoid memory reallocation, reserve enough space for mfact
916	<	mfact.reserve(getNCutoffGroups());
915	>	/**
916	>	* The mass factor is the relative mass of an atom to the total
917	>	* mass of the cutoff group it belongs to.  By default, all atoms
918	>	* are their own cutoff groups, and therefore have mass factors of
919	>	* 1.  We need some special handling for massless atoms, which
920	>	* will be treated as carrying the entire mass of the cutoff
921	>	* group.
922	>	*/
923	>	massFactors_.clear();
924	>	massFactors_.resize(getNAtoms(), 1.0);
925
926		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
927	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
927	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
928	>	cg = mol->nextCutoffGroup(ci)) {
929
930		totalMass = cg->getMass();
931		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
932		// Check for massless groups - set mfact to 1 if true
933	<	if (totalMass != 0)
934	<	mfact.push_back(atom->getMass()/totalMass);
933	>	if (totalMass != 0)
934	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
935		else
936	<	mfact.push_back( 1.0 );
936	>	massFactors_[atom->getLocalIndex()] = 1.0;
937		}
819	–
938		}
939		}
940
941	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
824	<	std::vector<int> identArray;
941	>	// Build the identArray_
942
943	<	//to avoid memory reallocation, reserve enough space identArray
944	<	identArray.reserve(getNAtoms());
828	<
943	>	identArray_.clear();
944	>	identArray_.reserve(getNAtoms());
945		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
946		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
947	<	identArray.push_back(atom->getIdent());
947	>	identArray_.push_back(atom->getIdent());
948		}
949		}
834	–
835	–	//fill molMembershipArray
836	–	//molMembershipArray is filled by SimCreator
837	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
838	–	for (int i = 0; i < nGlobalAtoms_; i++) {
839	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
840	–	}
841	–
842	–	//setup fortran simulation
843	–	int nGlobalExcludes = 0;
844	–	int* globalExcludes = NULL;
845	–	int* excludeList = exclude_.getExcludeList();
846	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
847	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
848	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
849	–
850	–	if( isError ){
851	–
852	–	sprintf( painCave.errMsg,
853	–	"There was an error setting the simulation information in fortran.\n" );
854	–	painCave.isFatal = 1;
855	–	painCave.severity = OOPSE_ERROR;
856	–	simError();
857	–	}
858	–
859	–	#ifdef IS_MPI
860	–	sprintf( checkPointMsg,
861	–	"succesfully sent the simulation information to fortran.\n");
862	–	MPIcheckPoint();
863	–	#endif // is_mpi
864	–	}
865	–
866	–
867	–	#ifdef IS_MPI
868	–	void SimInfo::setupFortranParallel() {
869	–
870	–	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
871	–	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
872	–	std::vector<int> localToGlobalCutoffGroupIndex;
873	–	SimInfo::MoleculeIterator mi;
874	–	Molecule::AtomIterator ai;
875	–	Molecule::CutoffGroupIterator ci;
876	–	Molecule* mol;
877	–	Atom* atom;
878	–	CutoffGroup* cg;
879	–	mpiSimData parallelData;
880	–	int isError;
881	–
882	–	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
883	–
884	–	//local index(index in DataStorge) of atom is important
885	–	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
886	–	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
887	–	}
888	–
889	–	//local index of cutoff group is trivial, it only depends on the order of travesing
890	–	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
891	–	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
892	–	}
893	–
894	–	}
895	–
896	–	//fill up mpiSimData struct
897	–	parallelData.nMolGlobal = getNGlobalMolecules();
898	–	parallelData.nMolLocal = getNMolecules();
899	–	parallelData.nAtomsGlobal = getNGlobalAtoms();
900	–	parallelData.nAtomsLocal = getNAtoms();
901	–	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
902	–	parallelData.nGroupsLocal = getNCutoffGroups();
903	–	parallelData.myNode = worldRank;
904	–	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
905	–
906	–	//pass mpiSimData struct and index arrays to fortran
907	–	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
908	–	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
909	–	&localToGlobalCutoffGroupIndex[0], &isError);
910	–
911	–	if (isError) {
912	–	sprintf(painCave.errMsg,
913	–	"mpiRefresh errror: fortran didn't like something we gave it.\n");
914	–	painCave.isFatal = 1;
915	–	simError();
916	–	}
917	–
918	–	sprintf(checkPointMsg, " mpiRefresh successful.\n");
919	–	MPIcheckPoint();
920	–
921	–
922	–	}
923	–
924	–	#endif
925	–
926	–	double SimInfo::calcMaxCutoffRadius() {
927	–
928	–
929	–	std::set<AtomType*> atomTypes;
930	–	std::set<AtomType*>::iterator i;
931	–	std::vector<double> cutoffRadius;
932	–
933	–	//get the unique atom types
934	–	atomTypes = getUniqueAtomTypes();
935	–
936	–	//query the max cutoff radius among these atom types
937	–	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
938	–	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939	–	}
940	–
941	–	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
942	–	#ifdef IS_MPI
943	–	//pick the max cutoff radius among the processors
944	–	#endif
945	–
946	–	return maxCutoffRadius;
947	–	}
948	–
949	–	void SimInfo::getCutoff(double& rcut, double& rsw) {
950	–
951	–	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
952	–
953	–	if (!simParams_->haveCutoffRadius()){
954	–	sprintf(painCave.errMsg,
955	–	"SimCreator Warning: No value was set for the cutoffRadius.\n"
956	–	"\tOOPSE will use a default value of 15.0 angstroms"
957	–	"\tfor the cutoffRadius.\n");
958	–	painCave.isFatal = 0;
959	–	simError();
960	–	rcut = 15.0;
961	–	} else{
962	–	rcut = simParams_->getCutoffRadius();
963	–	}
964	–
965	–	if (!simParams_->haveSwitchingRadius()){
966	–	sprintf(painCave.errMsg,
967	–	"SimCreator Warning: No value was set for switchingRadius.\n"
968	–	"\tOOPSE will use a default value of\n"
969	–	"\t0.85 * cutoffRadius for the switchingRadius\n");
970	–	painCave.isFatal = 0;
971	–	simError();
972	–	rsw = 0.85 * rcut;
973	–	} else{
974	–	rsw = simParams_->getSwitchingRadius();
975	–	}
976	–
977	–	} else {
978	–	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
979	–	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
980	–
981	–	if (simParams_->haveCutoffRadius()) {
982	–	rcut = simParams_->getCutoffRadius();
983	–	} else {
984	–	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
985	–	rcut = calcMaxCutoffRadius();
986	–	}
987	–
988	–	if (simParams_->haveSwitchingRadius()) {
989	–	rsw  = simParams_->getSwitchingRadius();
990	–	} else {
991	–	rsw = rcut;
992	–	}
950
951	<	}
951	>	topologyDone_ = true;
952		}
953
997	–	void SimInfo::setupCutoff() {
998	–	getCutoff(rcut_, rsw_);
999	–	double rnblist = rcut_ + 1; // skin of neighbor list
1000	–
1001	–	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1002	–
1003	–	int cp =  TRADITIONAL_CUTOFF_POLICY;
1004	–	if (simParams_->haveCutoffPolicy()) {
1005	–	std::string myPolicy = simParams_->getCutoffPolicy();
1006	–	toUpper(myPolicy);
1007	–	if (myPolicy == "MIX") {
1008	–	cp = MIX_CUTOFF_POLICY;
1009	–	} else {
1010	–	if (myPolicy == "MAX") {
1011	–	cp = MAX_CUTOFF_POLICY;
1012	–	} else {
1013	–	if (myPolicy == "TRADITIONAL") {
1014	–	cp = TRADITIONAL_CUTOFF_POLICY;
1015	–	} else {
1016	–	// throw error
1017	–	sprintf( painCave.errMsg,
1018	–	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1019	–	painCave.isFatal = 1;
1020	–	simError();
1021	–	}
1022	–	}
1023	–	}
1024	–	}
1025	–
1026	–
1027	–	if (simParams_->haveSkinThickness()) {
1028	–	double skinThickness = simParams_->getSkinThickness();
1029	–	}
1030	–
1031	–	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1032	–	// also send cutoff notification to electrostatics
1033	–	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1034	–	}
1035	–
1036	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1037	–
1038	–	int errorOut;
1039	–	int esm =  NONE;
1040	–	int sm = UNDAMPED;
1041	–	double alphaVal;
1042	–	double dielectric;
1043	–
1044	–	errorOut = isError;
1045	–	alphaVal = simParams_->getDampingAlpha();
1046	–	dielectric = simParams_->getDielectric();
1047	–
1048	–	if (simParams_->haveElectrostaticSummationMethod()) {
1049	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1050	–	toUpper(myMethod);
1051	–	if (myMethod == "NONE") {
1052	–	esm = NONE;
1053	–	} else {
1054	–	if (myMethod == "SWITCHING_FUNCTION") {
1055	–	esm = SWITCHING_FUNCTION;
1056	–	} else {
1057	–	if (myMethod == "SHIFTED_POTENTIAL") {
1058	–	esm = SHIFTED_POTENTIAL;
1059	–	} else {
1060	–	if (myMethod == "SHIFTED_FORCE") {
1061	–	esm = SHIFTED_FORCE;
1062	–	} else {
1063	–	if (myMethod == "REACTION_FIELD") {
1064	–	esm = REACTION_FIELD;
1065	–	} else {
1066	–	// throw error
1067	–	sprintf( painCave.errMsg,
1068	–	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1069	–	painCave.isFatal = 1;
1070	–	simError();
1071	–	}
1072	–	}
1073	–	}
1074	–	}
1075	–	}
1076	–	}
1077	–
1078	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1079	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1080	–	toUpper(myScreen);
1081	–	if (myScreen == "UNDAMPED") {
1082	–	sm = UNDAMPED;
1083	–	} else {
1084	–	if (myScreen == "DAMPED") {
1085	–	sm = DAMPED;
1086	–	if (!simParams_->haveDampingAlpha()) {
1087	–	//throw error
1088	–	sprintf( painCave.errMsg,
1089	–	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1090	–	painCave.isFatal = 0;
1091	–	simError();
1092	–	}
1093	–	} else {
1094	–	// throw error
1095	–	sprintf( painCave.errMsg,
1096	–	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1097	–	painCave.isFatal = 1;
1098	–	simError();
1099	–	}
1100	–	}
1101	–	}
1102	–
1103	–	// let's pass some summation method variables to fortran
1104	–	setElectrostaticSummationMethod( &esm );
1105	–	setScreeningMethod( &sm );
1106	–	setDampingAlpha( &alphaVal );
1107	–	setReactionFieldDielectric( &dielectric );
1108	–	initFortranFF( &esm, &errorOut );
1109	–	}
1110	–
1111	–	void SimInfo::setupSwitchingFunction() {
1112	–	int ft = CUBIC;
1113	–
1114	–	if (simParams_->haveSwitchingFunctionType()) {
1115	–	std::string funcType = simParams_->getSwitchingFunctionType();
1116	–	toUpper(funcType);
1117	–	if (funcType == "CUBIC") {
1118	–	ft = CUBIC;
1119	–	} else {
1120	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1121	–	ft = FIFTH_ORDER_POLY;
1122	–	} else {
1123	–	// throw error
1124	–	sprintf( painCave.errMsg,
1125	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1126	–	painCave.isFatal = 1;
1127	–	simError();
1128	–	}
1129	–	}
1130	–	}
1131	–
1132	–	// send switching function notification to switcheroo
1133	–	setFunctionType(&ft);
1134	–
1135	–	}
1136	–
954		void SimInfo::addProperty(GenericData* genData) {
955		properties_.addProperty(genData);
956		}
957
958	<	void SimInfo::removeProperty(const std::string& propName) {
958	>	void SimInfo::removeProperty(const string& propName) {
959		properties_.removeProperty(propName);
960		}
961
#	Line 1146 | Line 963 | namespace oopse {
963		properties_.clearProperties();
964		}
965
966	<	std::vector<std::string> SimInfo::getPropertyNames() {
966	>	vector<string> SimInfo::getPropertyNames() {
967		return properties_.getPropertyNames();
968		}
969
970	<	std::vector<GenericData*> SimInfo::getProperties() {
970	>	vector<GenericData*> SimInfo::getProperties() {
971		return properties_.getProperties();
972		}
973
974	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
974	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
975		return properties_.getPropertyByName(propName);
976		}
977
#	Line 1168 | Line 985 | namespace oopse {
985		Molecule* mol;
986		RigidBody* rb;
987		Atom* atom;
988	+	CutoffGroup* cg;
989		SimInfo::MoleculeIterator mi;
990		Molecule::RigidBodyIterator rbIter;
991	<	Molecule::AtomIterator atomIter;;
991	>	Molecule::AtomIterator atomIter;
992	>	Molecule::CutoffGroupIterator cgIter;
993
994		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
995
996	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
996	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
997	>	atom = mol->nextAtom(atomIter)) {
998		atom->setSnapshotManager(sman_);
999		}
1000
1001	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1001	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1002	>	rb = mol->nextRigidBody(rbIter)) {
1003		rb->setSnapshotManager(sman_);
1004		}
1005	+
1006	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1007	+	cg = mol->nextCutoffGroup(cgIter)) {
1008	+	cg->setSnapshotManager(sman_);
1009	+	}
1010		}
1011
1012		}
1013
1188	–	Vector3d SimInfo::getComVel(){
1189	–	SimInfo::MoleculeIterator i;
1190	–	Molecule* mol;
1014
1015	<	Vector3d comVel(0.0);
1193	<	double totalMass = 0.0;
1194	<
1195	<
1196	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1197	<	double mass = mol->getMass();
1198	<	totalMass += mass;
1199	<	comVel += mass * mol->getComVel();
1200	<	}
1015	>	ostream& operator <<(ostream& o, SimInfo& info) {
1016
1202	–	#ifdef IS_MPI
1203	–	double tmpMass = totalMass;
1204	–	Vector3d tmpComVel(comVel);
1205	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1206	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1207	–	#endif
1208	–
1209	–	comVel /= totalMass;
1210	–
1211	–	return comVel;
1212	–	}
1213	–
1214	–	Vector3d SimInfo::getCom(){
1215	–	SimInfo::MoleculeIterator i;
1216	–	Molecule* mol;
1217	–
1218	–	Vector3d com(0.0);
1219	–	double totalMass = 0.0;
1220	–
1221	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1222	–	double mass = mol->getMass();
1223	–	totalMass += mass;
1224	–	com += mass * mol->getCom();
1225	–	}
1226	–
1227	–	#ifdef IS_MPI
1228	–	double tmpMass = totalMass;
1229	–	Vector3d tmpCom(com);
1230	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1231	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1232	–	#endif
1233	–
1234	–	com /= totalMass;
1235	–
1236	–	return com;
1237	–
1238	–	}
1239	–
1240	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1241	–
1017		return o;
1018		}
1019
1020	<
1021	<	/*
1022	<	Returns center of mass and center of mass velocity in one function call.
1023	<	*/
1024	<
1025	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1026	<	SimInfo::MoleculeIterator i;
1027	<	Molecule* mol;
1028	<
1029	<
1030	<	double totalMass = 0.0;
1031	<
1020	>
1021	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1022	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1023	>	sprintf(painCave.errMsg,
1024	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1025	>	"\tindex exceeds number of known objects!\n");
1026	>	painCave.isFatal = 1;
1027	>	simError();
1028	>	return NULL;
1029	>	} else
1030	>	return IOIndexToIntegrableObject.at(index);
1031	>	}
1032	>
1033	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1034	>	IOIndexToIntegrableObject= v;
1035	>	}
1036
1037	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1038	<	double mass = mol->getMass();
1260	<	totalMass += mass;
1261	<	com += mass * mol->getCom();
1262	<	comVel += mass * mol->getComVel();
1263	<	}
1264	<
1037	>	int SimInfo::getNGlobalConstraints() {
1038	>	int nGlobalConstraints;
1039		#ifdef IS_MPI
1040	<	double tmpMass = totalMass;
1041	<	Vector3d tmpCom(com);
1042	<	Vector3d tmpComVel(comVel);
1043	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1271	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1040	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1041	>	MPI::INT, MPI::SUM);
1042	>	#else
1043	>	nGlobalConstraints =  nConstraints_;
1044		#endif
1045	<
1046	<	com /= totalMass;
1275	<	comVel /= totalMass;
1276	<	}
1277	<
1278	<	/*
1279	<	Return intertia tensor for entire system and angular momentum Vector.
1045	>	return nGlobalConstraints;
1046	>	}
1047
1048	+	}//end namespace OpenMD
1049
1282	–	[  Ixx -Ixy  -Ixz ]
1283	–	J =| -Iyx  Iyy  -Iyz |
1284	–	[ -Izx -Iyz   Izz ]
1285	–	*/
1286	–
1287	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1288	–
1289	–
1290	–	double xx = 0.0;
1291	–	double yy = 0.0;
1292	–	double zz = 0.0;
1293	–	double xy = 0.0;
1294	–	double xz = 0.0;
1295	–	double yz = 0.0;
1296	–	Vector3d com(0.0);
1297	–	Vector3d comVel(0.0);
1298	–
1299	–	getComAll(com, comVel);
1300	–
1301	–	SimInfo::MoleculeIterator i;
1302	–	Molecule* mol;
1303	–
1304	–	Vector3d thisq(0.0);
1305	–	Vector3d thisv(0.0);
1306	–
1307	–	double thisMass = 0.0;
1308	–
1309	–
1310	–
1311	–
1312	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	–
1314	–	thisq = mol->getCom()-com;
1315	–	thisv = mol->getComVel()-comVel;
1316	–	thisMass = mol->getMass();
1317	–	// Compute moment of intertia coefficients.
1318	–	xx += thisq[0]*thisq[0]*thisMass;
1319	–	yy += thisq[1]*thisq[1]*thisMass;
1320	–	zz += thisq[2]*thisq[2]*thisMass;
1321	–
1322	–	// compute products of intertia
1323	–	xy += thisq[0]*thisq[1]*thisMass;
1324	–	xz += thisq[0]*thisq[2]*thisMass;
1325	–	yz += thisq[1]*thisq[2]*thisMass;
1326	–
1327	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1328	–
1329	–	}
1330	–
1331	–
1332	–	inertiaTensor(0,0) = yy + zz;
1333	–	inertiaTensor(0,1) = -xy;
1334	–	inertiaTensor(0,2) = -xz;
1335	–	inertiaTensor(1,0) = -xy;
1336	–	inertiaTensor(1,1) = xx + zz;
1337	–	inertiaTensor(1,2) = -yz;
1338	–	inertiaTensor(2,0) = -xz;
1339	–	inertiaTensor(2,1) = -yz;
1340	–	inertiaTensor(2,2) = xx + yy;
1341	–
1342	–	#ifdef IS_MPI
1343	–	Mat3x3d tmpI(inertiaTensor);
1344	–	Vector3d tmpAngMom;
1345	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1346	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1347	–	#endif
1348	–
1349	–	return;
1350	–	}
1351	–
1352	–	//Returns the angular momentum of the system
1353	–	Vector3d SimInfo::getAngularMomentum(){
1354	–
1355	–	Vector3d com(0.0);
1356	–	Vector3d comVel(0.0);
1357	–	Vector3d angularMomentum(0.0);
1358	–
1359	–	getComAll(com,comVel);
1360	–
1361	–	SimInfo::MoleculeIterator i;
1362	–	Molecule* mol;
1363	–
1364	–	Vector3d thisr(0.0);
1365	–	Vector3d thisp(0.0);
1366	–
1367	–	double thisMass;
1368	–
1369	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1370	–	thisMass = mol->getMass();
1371	–	thisr = mol->getCom()-com;
1372	–	thisp = (mol->getComVel()-comVel)*thisMass;
1373	–
1374	–	angularMomentum += cross( thisr, thisp );
1375	–
1376	–	}
1377	–
1378	–	#ifdef IS_MPI
1379	–	Vector3d tmpAngMom;
1380	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1381	–	#endif
1382	–
1383	–	return angularMomentum;
1384	–	}
1385	–
1386	–
1387	–	}//end namespace oopse
1388	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

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