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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 834 by chuckv, Fri Dec 30 23:15:59 2005 UTC vs.
Revision 1940 by gezelter, Fri Nov 1 19:31:41 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 46 | Line 47
47		* @version 1.0
48		*/
49
50	+	#ifdef IS_MPI
51	+	#include <mpi.h>
52	+	#endif
53		#include <algorithm>
54		#include <set>
55		#include <map>
#	Line 53 | Line 57
57		#include "brains/SimInfo.hpp"
58		#include "math/Vector3.hpp"
59		#include "primitives/Molecule.hpp"
60	<	#include "UseTheForce/fCutoffPolicy.h"
57	<	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	<	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	<	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60	<	#include "UseTheForce/doForces_interface.h"
61	<	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
60	>	#include "primitives/StuntDouble.hpp"
61		#include "utils/MemoryUtils.hpp"
62		#include "utils/simError.h"
63		#include "selection/SelectionManager.hpp"
64		#include "io/ForceFieldOptions.hpp"
65	<	#include "UseTheForce/ForceField.hpp"
65	>	#include "brains/ForceField.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	#ifdef IS_MPI
69	<	#include "UseTheForce/mpiComponentPlan.h"
71	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
72	<	#endif
73	<
74	<	namespace oopse {
75	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	<	std::map<int, std::set<int> >::iterator i = container.find(index);
77	<	std::set<int> result;
78	<	if (i != container.end()) {
79	<	result = i->second;
80	<	}
81	<
82	<	return result;
83	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), 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;
95	<	int nMolWithSameStamp;
96	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
97	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
98	<	CutoffGroupStamp* cgStamp;
99	<	RigidBodyStamp* rbStamp;
100	<	int nRigidAtoms = 0;
101	<	std::vector<Component*> components = simParams->getComponents();
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();
115	<
116	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
117	<	cgStamp = molStamp->getCutoffGroupStamp(j);
118	<	nAtomsInGroups += cgStamp->getNMembers();
119	<	}
120	<
121	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
122	<
123	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
124	<
125	<	//calculate atoms in rigid bodies
126	<	int nAtomsInRigidBodies = 0;
127	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128	<
129	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
130	<	rbStamp = molStamp->getRigidBodyStamp(j);
131	<	nAtomsInRigidBodies += rbStamp->getNMembers();
132	<	}
133	<
134	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
135	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
136	<
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();
155	<
156	<	#ifdef IS_MPI
157	<	molToProcMap_.resize(nGlobalMols_);
158	<	#endif
159	<
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 171 | Line 164 | namespace oopse {
164		delete forceField_;
165		}
166
174	–	int SimInfo::getNGlobalConstraints() {
175	–	int nGlobalConstraints;
176	–	#ifdef IS_MPI
177	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
178	–	MPI_COMM_WORLD);
179	–	#else
180	–	nGlobalConstraints =  nConstraints_;
181	–	#endif
182	–	return nGlobalConstraints;
183	–	}
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 219 | 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 233 | Line 218 | namespace oopse {
218		} else {
219		return false;
220		}
236	–
237	–
221		}
222
223
#	Line 250 | 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)) {
262	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	–	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		}
274	–
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 290 | 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)) {
305	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
306	–	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 319 | 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 332 | 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 341 | 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	<
423	<
424	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
422	>
423	>	for (bond= mol->beginBond(bondIter); bond != NULL;
424	>	bond = mol->nextBond(bondIter)) {
425	>
426		a = bond->getAtomA()->getGlobalIndex();
427	<	b = bond->getAtomB()->getGlobalIndex();
428	<	exclude_.addPair(a, b);
427	>	b = bond->getAtomB()->getGlobalIndex();
428	>
429	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
430	>	oneTwoInteractions_.addPair(a, b);
431	>	} else {
432	>	excludedInteractions_.addPair(a, b);
433	>	}
434		}
435
436	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
436	>	for (bend= mol->beginBend(bendIter); bend != NULL;
437	>	bend = mol->nextBend(bendIter)) {
438	>
439		a = bend->getAtomA()->getGlobalIndex();
440		b = bend->getAtomB()->getGlobalIndex();
441		c = bend->getAtomC()->getGlobalIndex();
395	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
396	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
397	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
398	–
399	–	exclude_.addPairs(rigidSetA, rigidSetB);
400	–	exclude_.addPairs(rigidSetA, rigidSetC);
401	–	exclude_.addPairs(rigidSetB, rigidSetC);
442
443	<	//exclude_.addPair(a, b);
444	<	//exclude_.addPair(a, c);
445	<	//exclude_.addPair(b, c);
443	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
444	>	oneTwoInteractions_.addPair(a, b);
445	>	oneTwoInteractions_.addPair(b, c);
446	>	} else {
447	>	excludedInteractions_.addPair(a, b);
448	>	excludedInteractions_.addPair(b, c);
449	>	}
450	>
451	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
452	>	oneThreeInteractions_.addPair(a, c);
453	>	} else {
454	>	excludedInteractions_.addPair(a, c);
455	>	}
456		}
457
458	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
458	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
459	>	torsion = mol->nextTorsion(torsionIter)) {
460	>
461		a = torsion->getAtomA()->getGlobalIndex();
462		b = torsion->getAtomB()->getGlobalIndex();
463		c = torsion->getAtomC()->getGlobalIndex();
464	<	d = torsion->getAtomD()->getGlobalIndex();
413	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
414	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
415	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
416	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
464	>	d = torsion->getAtomD()->getGlobalIndex();
465
466	<	exclude_.addPairs(rigidSetA, rigidSetB);
467	<	exclude_.addPairs(rigidSetA, rigidSetC);
468	<	exclude_.addPairs(rigidSetA, rigidSetD);
469	<	exclude_.addPairs(rigidSetB, rigidSetC);
470	<	exclude_.addPairs(rigidSetB, rigidSetD);
471	<	exclude_.addPairs(rigidSetC, rigidSetD);
466	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
467	>	oneTwoInteractions_.addPair(a, b);
468	>	oneTwoInteractions_.addPair(b, c);
469	>	oneTwoInteractions_.addPair(c, d);
470	>	} else {
471	>	excludedInteractions_.addPair(a, b);
472	>	excludedInteractions_.addPair(b, c);
473	>	excludedInteractions_.addPair(c, d);
474	>	}
475	>
476	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
477	>	oneThreeInteractions_.addPair(a, c);
478	>	oneThreeInteractions_.addPair(b, d);
479	>	} else {
480	>	excludedInteractions_.addPair(a, c);
481	>	excludedInteractions_.addPair(b, d);
482	>	}
483
484	<	/*
485	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
486	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
487	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
488	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
430	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
431	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
432	<
433	<
434	<	exclude_.addPair(a, b);
435	<	exclude_.addPair(a, c);
436	<	exclude_.addPair(a, d);
437	<	exclude_.addPair(b, c);
438	<	exclude_.addPair(b, d);
439	<	exclude_.addPair(c, d);
440	<	*/
484	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
485	>	oneFourInteractions_.addPair(a, d);
486	>	} else {
487	>	excludedInteractions_.addPair(a, d);
488	>	}
489		}
490
491	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
492	<	std::vector<Atom*> atoms = rb->getAtoms();
493	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
494	<	for (int j = i + 1; j < atoms.size(); ++j) {
491	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
492	>	inversion = mol->nextInversion(inversionIter)) {
493	>
494	>	a = inversion->getAtomA()->getGlobalIndex();
495	>	b = inversion->getAtomB()->getGlobalIndex();
496	>	c = inversion->getAtomC()->getGlobalIndex();
497	>	d = inversion->getAtomD()->getGlobalIndex();
498	>
499	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
500	>	oneTwoInteractions_.addPair(a, b);
501	>	oneTwoInteractions_.addPair(a, c);
502	>	oneTwoInteractions_.addPair(a, d);
503	>	} else {
504	>	excludedInteractions_.addPair(a, b);
505	>	excludedInteractions_.addPair(a, c);
506	>	excludedInteractions_.addPair(a, d);
507	>	}
508	>
509	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
510	>	oneThreeInteractions_.addPair(b, c);
511	>	oneThreeInteractions_.addPair(b, d);
512	>	oneThreeInteractions_.addPair(c, d);
513	>	} else {
514	>	excludedInteractions_.addPair(b, c);
515	>	excludedInteractions_.addPair(b, d);
516	>	excludedInteractions_.addPair(c, d);
517	>	}
518	>	}
519	>
520	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
521	>	rb = mol->nextRigidBody(rbIter)) {
522	>	vector<Atom*> atoms = rb->getAtoms();
523	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
524	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
525		a = atoms[i]->getGlobalIndex();
526		b = atoms[j]->getGlobalIndex();
527	<	exclude_.addPair(a, b);
527	>	excludedInteractions_.addPair(a, b);
528		}
529		}
530		}
531
532		}
533
534	<	void SimInfo::removeExcludePairs(Molecule* mol) {
535	<	std::vector<Bond*>::iterator bondIter;
536	<	std::vector<Bend*>::iterator bendIter;
537	<	std::vector<Torsion*>::iterator torsionIter;
534	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
535	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
536	>	vector<Bond*>::iterator bondIter;
537	>	vector<Bend*>::iterator bendIter;
538	>	vector<Torsion*>::iterator torsionIter;
539	>	vector<Inversion*>::iterator inversionIter;
540		Bond* bond;
541		Bend* bend;
542		Torsion* torsion;
543	+	Inversion* inversion;
544		int a;
545		int b;
546		int c;
547		int d;
548
549	<	std::map<int, std::set<int> > atomGroups;
469	<
549	>	map<int, set<int> > atomGroups;
550		Molecule::RigidBodyIterator rbIter;
551		RigidBody* rb;
552		Molecule::IntegrableObjectIterator ii;
553	<	StuntDouble* integrableObject;
553	>	StuntDouble* sd;
554
555	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
556	<	integrableObject = mol->nextIntegrableObject(ii)) {
557	<
558	<	if (integrableObject->isRigidBody()) {
559	<	rb = static_cast<RigidBody*>(integrableObject);
560	<	std::vector<Atom*> atoms = rb->getAtoms();
561	<	std::set<int> rigidAtoms;
562	<	for (int i = 0; i < atoms.size(); ++i) {
563	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
564	<	}
565	<	for (int i = 0; i < atoms.size(); ++i) {
566	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
567	<	}
555	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
556	>	sd = mol->nextIntegrableObject(ii)) {
557	>
558	>	if (sd->isRigidBody()) {
559	>	rb = static_cast<RigidBody*>(sd);
560	>	vector<Atom*> atoms = rb->getAtoms();
561	>	set<int> rigidAtoms;
562	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
563	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
564	>	}
565	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
566	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
567	>	}
568		} else {
569	<	std::set<int> oneAtomSet;
570	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
571	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
569	>	set<int> oneAtomSet;
570	>	oneAtomSet.insert(sd->getGlobalIndex());
571	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
572		}
573		}
574
575	<
576	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
575	>	for (bond= mol->beginBond(bondIter); bond != NULL;
576	>	bond = mol->nextBond(bondIter)) {
577	>
578		a = bond->getAtomA()->getGlobalIndex();
579	<	b = bond->getAtomB()->getGlobalIndex();
580	<	exclude_.removePair(a, b);
579	>	b = bond->getAtomB()->getGlobalIndex();
580	>
581	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
582	>	oneTwoInteractions_.removePair(a, b);
583	>	} else {
584	>	excludedInteractions_.removePair(a, b);
585	>	}
586		}
587
588	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
588	>	for (bend= mol->beginBend(bendIter); bend != NULL;
589	>	bend = mol->nextBend(bendIter)) {
590	>
591		a = bend->getAtomA()->getGlobalIndex();
592		b = bend->getAtomB()->getGlobalIndex();
593		c = bend->getAtomC()->getGlobalIndex();
506	–
507	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
508	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
509	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
510	–
511	–	exclude_.removePairs(rigidSetA, rigidSetB);
512	–	exclude_.removePairs(rigidSetA, rigidSetC);
513	–	exclude_.removePairs(rigidSetB, rigidSetC);
594
595	<	//exclude_.removePair(a, b);
596	<	//exclude_.removePair(a, c);
597	<	//exclude_.removePair(b, c);
595	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
596	>	oneTwoInteractions_.removePair(a, b);
597	>	oneTwoInteractions_.removePair(b, c);
598	>	} else {
599	>	excludedInteractions_.removePair(a, b);
600	>	excludedInteractions_.removePair(b, c);
601	>	}
602	>
603	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
604	>	oneThreeInteractions_.removePair(a, c);
605	>	} else {
606	>	excludedInteractions_.removePair(a, c);
607	>	}
608		}
609
610	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
610	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
611	>	torsion = mol->nextTorsion(torsionIter)) {
612	>
613		a = torsion->getAtomA()->getGlobalIndex();
614		b = torsion->getAtomB()->getGlobalIndex();
615		c = torsion->getAtomC()->getGlobalIndex();
616	<	d = torsion->getAtomD()->getGlobalIndex();
616	>	d = torsion->getAtomD()->getGlobalIndex();
617	>
618	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
619	>	oneTwoInteractions_.removePair(a, b);
620	>	oneTwoInteractions_.removePair(b, c);
621	>	oneTwoInteractions_.removePair(c, d);
622	>	} else {
623	>	excludedInteractions_.removePair(a, b);
624	>	excludedInteractions_.removePair(b, c);
625	>	excludedInteractions_.removePair(c, d);
626	>	}
627
628	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
629	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
630	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
631	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
628	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
629	>	oneThreeInteractions_.removePair(a, c);
630	>	oneThreeInteractions_.removePair(b, d);
631	>	} else {
632	>	excludedInteractions_.removePair(a, c);
633	>	excludedInteractions_.removePair(b, d);
634	>	}
635
636	<	exclude_.removePairs(rigidSetA, rigidSetB);
637	<	exclude_.removePairs(rigidSetA, rigidSetC);
638	<	exclude_.removePairs(rigidSetA, rigidSetD);
639	<	exclude_.removePairs(rigidSetB, rigidSetC);
640	<	exclude_.removePairs(rigidSetB, rigidSetD);
641	<	exclude_.removePairs(rigidSetC, rigidSetD);
636	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
637	>	oneFourInteractions_.removePair(a, d);
638	>	} else {
639	>	excludedInteractions_.removePair(a, d);
640	>	}
641	>	}
642
643	<	/*
644	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
540	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
541	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
542	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
543	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
544	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
643	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
644	>	inversion = mol->nextInversion(inversionIter)) {
645
646	<
647	<	exclude_.removePair(a, b);
648	<	exclude_.removePair(a, c);
649	<	exclude_.removePair(a, d);
650	<	exclude_.removePair(b, c);
651	<	exclude_.removePair(b, d);
652	<	exclude_.removePair(c, d);
653	<	*/
646	>	a = inversion->getAtomA()->getGlobalIndex();
647	>	b = inversion->getAtomB()->getGlobalIndex();
648	>	c = inversion->getAtomC()->getGlobalIndex();
649	>	d = inversion->getAtomD()->getGlobalIndex();
650	>
651	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
652	>	oneTwoInteractions_.removePair(a, b);
653	>	oneTwoInteractions_.removePair(a, c);
654	>	oneTwoInteractions_.removePair(a, d);
655	>	} else {
656	>	excludedInteractions_.removePair(a, b);
657	>	excludedInteractions_.removePair(a, c);
658	>	excludedInteractions_.removePair(a, d);
659	>	}
660	>
661	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
662	>	oneThreeInteractions_.removePair(b, c);
663	>	oneThreeInteractions_.removePair(b, d);
664	>	oneThreeInteractions_.removePair(c, d);
665	>	} else {
666	>	excludedInteractions_.removePair(b, c);
667	>	excludedInteractions_.removePair(b, d);
668	>	excludedInteractions_.removePair(c, d);
669	>	}
670		}
671
672	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
673	<	std::vector<Atom*> atoms = rb->getAtoms();
674	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
675	<	for (int j = i + 1; j < atoms.size(); ++j) {
672	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
673	>	rb = mol->nextRigidBody(rbIter)) {
674	>	vector<Atom*> atoms = rb->getAtoms();
675	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
676	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
677		a = atoms[i]->getGlobalIndex();
678		b = atoms[j]->getGlobalIndex();
679	<	exclude_.removePair(a, b);
679	>	excludedInteractions_.removePair(a, b);
680		}
681		}
682		}
683	<
683	>
684		}
685	<
686	<
685	>
686	>
687		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
688		int curStampId;
689	<
689	>
690		//index from 0
691		curStampId = moleculeStamps_.size();
692
#	Line 577 | Line 694 | namespace oopse {
694		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
695		}
696
580	–	void SimInfo::update() {
697
698	<	setupSimType();
699	<
700	<	#ifdef IS_MPI
701	<	setupFortranParallel();
702	<	#endif
703	<
704	<	setupFortranSim();
705	<
706	<	//setup fortran force field
591	<	/** @deprecate */
592	<	int isError = 0;
593	<
594	<	setupElectrostaticSummationMethod( isError );
595	<	setupSwitchingFunction();
596	<
597	<	if(isError){
598	<	sprintf( painCave.errMsg,
599	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
600	<	painCave.isFatal = 1;
601	<	simError();
602	<	}
603	<
604	<
605	<	setupCutoff();
606	<
698	>	/**
699	>	* update
700	>	*
701	>	*  Performs the global checks and variable settings after the
702	>	*  objects have been created.
703	>	*
704	>	*/
705	>	void SimInfo::update() {
706	>	setupSimVariables();
707		calcNdf();
708		calcNdfRaw();
709		calcNdfTrans();
610	–
611	–	fortranInitialized_ = true;
710		}
711	<
712	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
711	>
712	>	/**
713	>	* getSimulatedAtomTypes
714	>	*
715	>	* Returns an STL set of AtomType* that are actually present in this
716	>	* simulation.  Must query all processors to assemble this information.
717	>	*
718	>	*/
719	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
720		SimInfo::MoleculeIterator mi;
721		Molecule* mol;
722		Molecule::AtomIterator ai;
723		Atom* atom;
724	<	std::set<AtomType*> atomTypes;
725	<
724	>	set<AtomType*> atomTypes;
725	>
726		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
727	<
728	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
727	>	for(atom = mol->beginAtom(ai); atom != NULL;
728	>	atom = mol->nextAtom(ai)) {
729		atomTypes.insert(atom->getAtomType());
730	<	}
731	<
732	<	}
730	>	}
731	>	}
732	>
733	>	#ifdef IS_MPI
734
735	<	return atomTypes;
736	<	}
631	<
632	<	void SimInfo::setupSimType() {
633	<	std::set<AtomType*>::iterator i;
634	<	std::set<AtomType*> atomTypes;
635	<	atomTypes = getUniqueAtomTypes();
735	>	// loop over the found atom types on this processor, and add their
736	>	// numerical idents to a vector:
737
738	<	int useLennardJones = 0;
739	<	int useElectrostatic = 0;
740	<	int useEAM = 0;
741	<	int useSC = 0;
641	<	int useCharge = 0;
642	<	int useDirectional = 0;
643	<	int useDipole = 0;
644	<	int useGayBerne = 0;
645	<	int useSticky = 0;
646	<	int useStickyPower = 0;
647	<	int useShape = 0;
648	<	int useFLARB = 0; //it is not in AtomType yet
649	<	int useDirectionalAtom = 0;
650	<	int useElectrostatics = 0;
651	<	//usePBC and useRF are from simParams
652	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
653	<	int useRF;
654	<	int useSF;
655	<	std::string myMethod;
738	>	vector<int> foundTypes;
739	>	set<AtomType*>::iterator i;
740	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
741	>	foundTypes.push_back( (*i)->getIdent() );
742
743	<	// set the useRF logical
744	<	useRF = 0;
659	<	useSF = 0;
743	>	// count_local holds the number of found types on this processor
744	>	int count_local = foundTypes.size();
745
746	+	int nproc = MPI::COMM_WORLD.Get_size();
747
748	<	if (simParams_->haveElectrostaticSummationMethod()) {
749	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
750	<	toUpper(myMethod);
751	<	if (myMethod == "REACTION_FIELD") {
752	<	useRF=1;
753	<	} else {
754	<	if (myMethod == "SHIFTED_FORCE") {
755	<	useSF = 1;
756	<	}
757	<	}
748	>	// we need arrays to hold the counts and displacement vectors for
749	>	// all processors
750	>	vector<int> counts(nproc, 0);
751	>	vector<int> disps(nproc, 0);
752	>
753	>	// fill the counts array
754	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
755	>	1, MPI::INT);
756	>
757	>	// use the processor counts to compute the displacement array
758	>	disps[0] = 0;
759	>	int totalCount = counts[0];
760	>	for (int iproc = 1; iproc < nproc; iproc++) {
761	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
762	>	totalCount += counts[iproc];
763		}
764
765	<	//loop over all of the atom types
766	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
767	<	useLennardJones |= (*i)->isLennardJones();
768	<	useElectrostatic |= (*i)->isElectrostatic();
769	<	useEAM |= (*i)->isEAM();
770	<	useSC |= (*i)->isSC();
771	<	useCharge |= (*i)->isCharge();
772	<	useDirectional |= (*i)->isDirectional();
773	<	useDipole |= (*i)->isDipole();
774	<	useGayBerne |= (*i)->isGayBerne();
775	<	useSticky |= (*i)->isSticky();
776	<	useStickyPower |= (*i)->isStickyPower();
777	<	useShape |= (*i)->isShape();
687	<	}
765	>	// we need a (possibly redundant) set of all found types:
766	>	vector<int> ftGlobal(totalCount);
767	>
768	>	// now spray out the foundTypes to all the other processors:
769	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
770	>	&ftGlobal[0], &counts[0], &disps[0],
771	>	MPI::INT);
772	>
773	>	vector<int>::iterator j;
774	>
775	>	// foundIdents is a stl set, so inserting an already found ident
776	>	// will have no effect.
777	>	set<int> foundIdents;
778
779	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
780	<	useDirectionalAtom = 1;
781	<	}
779	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
780	>	foundIdents.insert((*j));
781	>
782	>	// now iterate over the foundIdents and get the actual atom types
783	>	// that correspond to these:
784	>	set<int>::iterator it;
785	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
786	>	atomTypes.insert( forceField_->getAtomType((*it)) );
787	>
788	>	#endif
789
790	<	if (useCharge || useDipole) {
791	<	useElectrostatics = 1;
695	<	}
790	>	return atomTypes;
791	>	}
792
697	–	#ifdef IS_MPI
698	–	int temp;
793
794	<	temp = usePBC;
795	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
794	>	int getGlobalCountOfType(AtomType* atype) {
795	>	/*
796	>	set<AtomType*> atypes = getSimulatedAtomTypes();
797	>	map<AtomType*, int> counts_;
798
799	<	temp = useDirectionalAtom;
800	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
800	>	for(atom = mol->beginAtom(ai); atom != NULL;
801	>	atom = mol->nextAtom(ai)) {
802	>	atom->getAtomType();
803	>	}
804	>	}
805	>	*/
806	>	return 0;
807	>	}
808
809	<	temp = useLennardJones;
810	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	>	void SimInfo::setupSimVariables() {
810	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
811	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
812	>	// parameter is true
813	>	calcBoxDipole_ = false;
814	>	if ( simParams_->haveAccumulateBoxDipole() )
815	>	if ( simParams_->getAccumulateBoxDipole() ) {
816	>	calcBoxDipole_ = true;
817	>	}
818	>
819	>	set<AtomType*>::iterator i;
820	>	set<AtomType*> atomTypes;
821	>	atomTypes = getSimulatedAtomTypes();
822	>	bool usesElectrostatic = false;
823	>	bool usesMetallic = false;
824	>	bool usesDirectional = false;
825	>	bool usesFluctuatingCharges =  false;
826	>	//loop over all of the atom types
827	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
828	>	usesElectrostatic |= (*i)->isElectrostatic();
829	>	usesMetallic |= (*i)->isMetal();
830	>	usesDirectional |= (*i)->isDirectional();
831	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
832	>	}
833
834	<	temp = useElectrostatics;
835	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834	>	#ifdef IS_MPI
835	>	bool temp;
836	>	temp = usesDirectional;
837	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
838	>	MPI::LOR);
839	>
840	>	temp = usesMetallic;
841	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
842	>	MPI::LOR);
843	>
844	>	temp = usesElectrostatic;
845	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
846	>	MPI::LOR);
847
848	<	temp = useCharge;
849	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
848	>	temp = usesFluctuatingCharges;
849	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
850	>	MPI::LOR);
851	>	#else
852
853	<	temp = useDipole;
854	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853	>	usesDirectionalAtoms_ = usesDirectional;
854	>	usesMetallicAtoms_ = usesMetallic;
855	>	usesElectrostaticAtoms_ = usesElectrostatic;
856	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
857
858	<	temp = useSticky;
719	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
720	<
721	<	temp = useStickyPower;
722	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
858	>	#endif
859
860	<	temp = useGayBerne;
861	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
861	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
862	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
863	>	}
864
727	–	temp = useEAM;
728	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865
866	<	temp = useSC;
867	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	>	vector<int> SimInfo::getGlobalAtomIndices() {
867	>	SimInfo::MoleculeIterator mi;
868	>	Molecule* mol;
869	>	Molecule::AtomIterator ai;
870	>	Atom* atom;
871	>
872	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
873
874	<	temp = useShape;
875	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
875	>
876	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
877	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
878	>	}
879	>	}
880	>	return GlobalAtomIndices;
881	>	}
882
736	–	temp = useFLARB;
737	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
883
884	<	temp = useRF;
885	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
884	>	vector<int> SimInfo::getGlobalGroupIndices() {
885	>	SimInfo::MoleculeIterator mi;
886	>	Molecule* mol;
887	>	Molecule::CutoffGroupIterator ci;
888	>	CutoffGroup* cg;
889
890	<	temp = useSF;
891	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
892	<
745	<	#endif
746	<
747	<	fInfo_.SIM_uses_PBC = usePBC;
748	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
749	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
750	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
751	<	fInfo_.SIM_uses_Charges = useCharge;
752	<	fInfo_.SIM_uses_Dipoles = useDipole;
753	<	fInfo_.SIM_uses_Sticky = useSticky;
754	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
755	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
756	<	fInfo_.SIM_uses_EAM = useEAM;
757	<	fInfo_.SIM_uses_SC = useSC;
758	<	fInfo_.SIM_uses_Shapes = useShape;
759	<	fInfo_.SIM_uses_FLARB = useFLARB;
760	<	fInfo_.SIM_uses_RF = useRF;
761	<	fInfo_.SIM_uses_SF = useSF;
762	<
763	<	if( myMethod == "REACTION_FIELD") {
890	>	vector<int> GlobalGroupIndices;
891	>
892	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
893
894	<	if (simParams_->haveDielectric()) {
895	<	fInfo_.dielect = simParams_->getDielectric();
896	<	} else {
897	<	sprintf(painCave.errMsg,
898	<	"SimSetup Error: No Dielectric constant was set.\n"
899	<	"\tYou are trying to use Reaction Field without"
771	<	"\tsetting a dielectric constant!\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
894	>	//local index of cutoff group is trivial, it only depends on the
895	>	//order of travesing
896	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
897	>	cg = mol->nextCutoffGroup(ci)) {
898	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
899	>	}
900		}
901	<
901	>	return GlobalGroupIndices;
902		}
903
779	–	void SimInfo::setupFortranSim() {
780	–	int isError;
781	–	int nExclude;
782	–	std::vector<int> fortranGlobalGroupMembership;
783	–
784	–	nExclude = exclude_.getSize();
785	–	isError = 0;
904
905	<	//globalGroupMembership_ is filled by SimCreator
788	<	for (int i = 0; i < nGlobalAtoms_; i++) {
789	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
790	<	}
905	>	void SimInfo::prepareTopology() {
906
907		//calculate mass ratio of cutoff group
793	–	std::vector<double> mfact;
908		SimInfo::MoleculeIterator mi;
909		Molecule* mol;
910		Molecule::CutoffGroupIterator ci;
911		CutoffGroup* cg;
912		Molecule::AtomIterator ai;
913		Atom* atom;
914	<	double totalMass;
914	>	RealType totalMass;
915
916	<	//to avoid memory reallocation, reserve enough space for mfact
917	<	mfact.reserve(getNCutoffGroups());
916	>	/**
917	>	* The mass factor is the relative mass of an atom to the total
918	>	* mass of the cutoff group it belongs to.  By default, all atoms
919	>	* are their own cutoff groups, and therefore have mass factors of
920	>	* 1.  We need some special handling for massless atoms, which
921	>	* will be treated as carrying the entire mass of the cutoff
922	>	* group.
923	>	*/
924	>	massFactors_.clear();
925	>	massFactors_.resize(getNAtoms(), 1.0);
926
927		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
928	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
928	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
929	>	cg = mol->nextCutoffGroup(ci)) {
930
931		totalMass = cg->getMass();
932		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
933		// Check for massless groups - set mfact to 1 if true
934	<	if (totalMass != 0)
935	<	mfact.push_back(atom->getMass()/totalMass);
934	>	if (totalMass != 0)
935	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
936		else
937	<	mfact.push_back( 1.0 );
937	>	massFactors_[atom->getLocalIndex()] = 1.0;
938		}
816	–
939		}
940		}
941
942	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
821	<	std::vector<int> identArray;
942	>	// Build the identArray_ and regions_
943
944	<	//to avoid memory reallocation, reserve enough space identArray
945	<	identArray.reserve(getNAtoms());
946	<
947	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
944	>	identArray_.clear();
945	>	identArray_.reserve(getNAtoms());
946	>	regions_.clear();
947	>	regions_.reserve(getNAtoms());
948	>
949	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
950	>	int reg = mol->getRegion();
951		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
952	<	identArray.push_back(atom->getIdent());
952	>	identArray_.push_back(atom->getIdent());
953	>	regions_.push_back(reg);
954		}
955		}
956	<
957	<	//fill molMembershipArray
833	<	//molMembershipArray is filled by SimCreator
834	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
835	<	for (int i = 0; i < nGlobalAtoms_; i++) {
836	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
837	<	}
838	<
839	<	//setup fortran simulation
840	<	int nGlobalExcludes = 0;
841	<	int* globalExcludes = NULL;
842	<	int* excludeList = exclude_.getExcludeList();
843	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
844	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
845	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
846	<
847	<	if( isError ){
848	<
849	<	sprintf( painCave.errMsg,
850	<	"There was an error setting the simulation information in fortran.\n" );
851	<	painCave.isFatal = 1;
852	<	painCave.severity = OOPSE_ERROR;
853	<	simError();
854	<	}
855	<
856	<	#ifdef IS_MPI
857	<	sprintf( checkPointMsg,
858	<	"succesfully sent the simulation information to fortran.\n");
859	<	MPIcheckPoint();
860	<	#endif // is_mpi
861	<	}
862	<
863	<
864	<	#ifdef IS_MPI
865	<	void SimInfo::setupFortranParallel() {
866	<
867	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
868	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
869	<	std::vector<int> localToGlobalCutoffGroupIndex;
870	<	SimInfo::MoleculeIterator mi;
871	<	Molecule::AtomIterator ai;
872	<	Molecule::CutoffGroupIterator ci;
873	<	Molecule* mol;
874	<	Atom* atom;
875	<	CutoffGroup* cg;
876	<	mpiSimData parallelData;
877	<	int isError;
878	<
879	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
880	<
881	<	//local index(index in DataStorge) of atom is important
882	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
884	<	}
885	<
886	<	//local index of cutoff group is trivial, it only depends on the order of travesing
887	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
888	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
889	<	}
890	<
891	<	}
892	<
893	<	//fill up mpiSimData struct
894	<	parallelData.nMolGlobal = getNGlobalMolecules();
895	<	parallelData.nMolLocal = getNMolecules();
896	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
897	<	parallelData.nAtomsLocal = getNAtoms();
898	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
899	<	parallelData.nGroupsLocal = getNCutoffGroups();
900	<	parallelData.myNode = worldRank;
901	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
902	<
903	<	//pass mpiSimData struct and index arrays to fortran
904	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
905	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
906	<	&localToGlobalCutoffGroupIndex[0], &isError);
907	<
908	<	if (isError) {
909	<	sprintf(painCave.errMsg,
910	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
911	<	painCave.isFatal = 1;
912	<	simError();
913	<	}
914	<
915	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
916	<	MPIcheckPoint();
917	<
918	<
919	<	}
920	<
921	<	#endif
922	<
923	<	void SimInfo::setupCutoff() {
924	<
925	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926	<
927	<	// Check the cutoff policy
928	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929	<
930	<	std::string myPolicy;
931	<	if (forceFieldOptions_.haveCutoffPolicy()){
932	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
933	<	}else if (simParams_->haveCutoffPolicy()) {
934	<	myPolicy = simParams_->getCutoffPolicy();
935	<	}
936	<
937	<	if (!myPolicy.empty()){
938	<	toUpper(myPolicy);
939	<	if (myPolicy == "MIX") {
940	<	cp = MIX_CUTOFF_POLICY;
941	<	} else {
942	<	if (myPolicy == "MAX") {
943	<	cp = MAX_CUTOFF_POLICY;
944	<	} else {
945	<	if (myPolicy == "TRADITIONAL") {
946	<	cp = TRADITIONAL_CUTOFF_POLICY;
947	<	} else {
948	<	// throw error
949	<	sprintf( painCave.errMsg,
950	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
951	<	painCave.isFatal = 1;
952	<	simError();
953	<	}
954	<	}
955	<	}
956	<	}
957	<	notifyFortranCutoffPolicy(&cp);
958	<
959	<	// Check the Skin Thickness for neighborlists
960	<	double skin;
961	<	if (simParams_->haveSkinThickness()) {
962	<	skin = simParams_->getSkinThickness();
963	<	notifyFortranSkinThickness(&skin);
964	<	}
965	<
966	<	// Check if the cutoff was set explicitly:
967	<	if (simParams_->haveCutoffRadius()) {
968	<	rcut_ = simParams_->getCutoffRadius();
969	<	if (simParams_->haveSwitchingRadius()) {
970	<	rsw_  = simParams_->getSwitchingRadius();
971	<	} else {
972	<	rsw_ = rcut_;
973	<	}
974	<	notifyFortranCutoffs(&rcut_, &rsw_);
975	<
976	<	} else {
977	<
978	<	// For electrostatic atoms, we'll assume a large safe value:
979	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
980	<	sprintf(painCave.errMsg,
981	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
982	<	"\tOOPSE will use a default value of 15.0 angstroms"
983	<	"\tfor the cutoffRadius.\n");
984	<	painCave.isFatal = 0;
985	<	simError();
986	<	rcut_ = 15.0;
987	<
988	<	if (simParams_->haveElectrostaticSummationMethod()) {
989	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
990	<	toUpper(myMethod);
991	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
992	<	if (simParams_->haveSwitchingRadius()){
993	<	sprintf(painCave.errMsg,
994	<	"SimInfo Warning: A value was set for the switchingRadius\n"
995	<	"\teven though the electrostaticSummationMethod was\n"
996	<	"\tset to %s\n", myMethod.c_str());
997	<	painCave.isFatal = 1;
998	<	simError();
999	<	}
1000	<	}
1001	<	}
1002	<
1003	<	if (simParams_->haveSwitchingRadius()){
1004	<	rsw_ = simParams_->getSwitchingRadius();
1005	<	} else {
1006	<	sprintf(painCave.errMsg,
1007	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1008	<	"\tOOPSE will use a default value of\n"
1009	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1010	<	painCave.isFatal = 0;
1011	<	simError();
1012	<	rsw_ = 0.85 * rcut_;
1013	<	}
1014	<	notifyFortranCutoffs(&rcut_, &rsw_);
1015	<	} else {
1016	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1017	<	// We'll punt and let fortran figure out the cutoffs later.
1018	<
1019	<	notifyFortranYouAreOnYourOwn();
1020	<
1021	<	}
1022	<	}
956	>
957	>	topologyDone_ = true;
958		}
959
1025	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1026	–
1027	–	int errorOut;
1028	–	int esm =  NONE;
1029	–	int sm = UNDAMPED;
1030	–	double alphaVal;
1031	–	double dielectric;
1032	–
1033	–	errorOut = isError;
1034	–	alphaVal = simParams_->getDampingAlpha();
1035	–	dielectric = simParams_->getDielectric();
1036	–
1037	–	if (simParams_->haveElectrostaticSummationMethod()) {
1038	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1039	–	toUpper(myMethod);
1040	–	if (myMethod == "NONE") {
1041	–	esm = NONE;
1042	–	} else {
1043	–	if (myMethod == "SWITCHING_FUNCTION") {
1044	–	esm = SWITCHING_FUNCTION;
1045	–	} else {
1046	–	if (myMethod == "SHIFTED_POTENTIAL") {
1047	–	esm = SHIFTED_POTENTIAL;
1048	–	} else {
1049	–	if (myMethod == "SHIFTED_FORCE") {
1050	–	esm = SHIFTED_FORCE;
1051	–	} else {
1052	–	if (myMethod == "REACTION_FIELD") {
1053	–	esm = REACTION_FIELD;
1054	–	} else {
1055	–	// throw error
1056	–	sprintf( painCave.errMsg,
1057	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1058	–	"\t(Input file specified %s .)\n"
1059	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1060	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1061	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1062	–	painCave.isFatal = 1;
1063	–	simError();
1064	–	}
1065	–	}
1066	–	}
1067	–	}
1068	–	}
1069	–	}
1070	–
1071	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1072	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1073	–	toUpper(myScreen);
1074	–	if (myScreen == "UNDAMPED") {
1075	–	sm = UNDAMPED;
1076	–	} else {
1077	–	if (myScreen == "DAMPED") {
1078	–	sm = DAMPED;
1079	–	if (!simParams_->haveDampingAlpha()) {
1080	–	//throw error
1081	–	sprintf( painCave.errMsg,
1082	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1083	–	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1084	–	painCave.isFatal = 0;
1085	–	simError();
1086	–	}
1087	–	} else {
1088	–	// throw error
1089	–	sprintf( painCave.errMsg,
1090	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1091	–	"\t(Input file specified %s .)\n"
1092	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1093	–	"or \"damped\".\n", myScreen.c_str() );
1094	–	painCave.isFatal = 1;
1095	–	simError();
1096	–	}
1097	–	}
1098	–	}
1099	–
1100	–	// let's pass some summation method variables to fortran
1101	–	setElectrostaticSumMethod( &esm );
1102	–	setFortranElectrostaticMethod( &esm );
1103	–	setScreeningMethod( &sm );
1104	–	setDampingAlpha( &alphaVal );
1105	–	setReactionFieldDielectric( &dielectric );
1106	–	initFortranFF( &errorOut );
1107	–	}
1108	–
1109	–	void SimInfo::setupSwitchingFunction() {
1110	–	int ft = CUBIC;
1111	–
1112	–	if (simParams_->haveSwitchingFunctionType()) {
1113	–	std::string funcType = simParams_->getSwitchingFunctionType();
1114	–	toUpper(funcType);
1115	–	if (funcType == "CUBIC") {
1116	–	ft = CUBIC;
1117	–	} else {
1118	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1119	–	ft = FIFTH_ORDER_POLY;
1120	–	} else {
1121	–	// throw error
1122	–	sprintf( painCave.errMsg,
1123	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1124	–	painCave.isFatal = 1;
1125	–	simError();
1126	–	}
1127	–	}
1128	–	}
1129	–
1130	–	// send switching function notification to switcheroo
1131	–	setFunctionType(&ft);
1132	–
1133	–	}
1134	–
960		void SimInfo::addProperty(GenericData* genData) {
961		properties_.addProperty(genData);
962		}
963
964	<	void SimInfo::removeProperty(const std::string& propName) {
964	>	void SimInfo::removeProperty(const string& propName) {
965		properties_.removeProperty(propName);
966		}
967
#	Line 1144 | Line 969 | namespace oopse {
969		properties_.clearProperties();
970		}
971
972	<	std::vector<std::string> SimInfo::getPropertyNames() {
972	>	vector<string> SimInfo::getPropertyNames() {
973		return properties_.getPropertyNames();
974		}
975
976	<	std::vector<GenericData*> SimInfo::getProperties() {
976	>	vector<GenericData*> SimInfo::getProperties() {
977		return properties_.getProperties();
978		}
979
980	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
980	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
981		return properties_.getPropertyByName(propName);
982		}
983
#	Line 1166 | Line 991 | namespace oopse {
991		Molecule* mol;
992		RigidBody* rb;
993		Atom* atom;
994	+	CutoffGroup* cg;
995		SimInfo::MoleculeIterator mi;
996		Molecule::RigidBodyIterator rbIter;
997	<	Molecule::AtomIterator atomIter;;
997	>	Molecule::AtomIterator atomIter;
998	>	Molecule::CutoffGroupIterator cgIter;
999
1000		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1001
1002	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1002	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
1003	>	atom = mol->nextAtom(atomIter)) {
1004		atom->setSnapshotManager(sman_);
1005		}
1006
1007	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1007	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1008	>	rb = mol->nextRigidBody(rbIter)) {
1009		rb->setSnapshotManager(sman_);
1010		}
1011	+
1012	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1013	+	cg = mol->nextCutoffGroup(cgIter)) {
1014	+	cg->setSnapshotManager(sman_);
1015	+	}
1016		}
1017
1018		}
1019
1186	–	Vector3d SimInfo::getComVel(){
1187	–	SimInfo::MoleculeIterator i;
1188	–	Molecule* mol;
1020
1021	<	Vector3d comVel(0.0);
1191	<	double totalMass = 0.0;
1192	<
1193	<
1194	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1195	<	double mass = mol->getMass();
1196	<	totalMass += mass;
1197	<	comVel += mass * mol->getComVel();
1198	<	}
1021	>	ostream& operator <<(ostream& o, SimInfo& info) {
1022
1200	–	#ifdef IS_MPI
1201	–	double tmpMass = totalMass;
1202	–	Vector3d tmpComVel(comVel);
1203	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1204	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1205	–	#endif
1206	–
1207	–	comVel /= totalMass;
1208	–
1209	–	return comVel;
1210	–	}
1211	–
1212	–	Vector3d SimInfo::getCom(){
1213	–	SimInfo::MoleculeIterator i;
1214	–	Molecule* mol;
1215	–
1216	–	Vector3d com(0.0);
1217	–	double totalMass = 0.0;
1218	–
1219	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1220	–	double mass = mol->getMass();
1221	–	totalMass += mass;
1222	–	com += mass * mol->getCom();
1223	–	}
1224	–
1225	–	#ifdef IS_MPI
1226	–	double tmpMass = totalMass;
1227	–	Vector3d tmpCom(com);
1228	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1229	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1230	–	#endif
1231	–
1232	–	com /= totalMass;
1233	–
1234	–	return com;
1235	–
1236	–	}
1237	–
1238	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1239	–
1023		return o;
1024		}
1025
1026	<
1027	<	/*
1028	<	Returns center of mass and center of mass velocity in one function call.
1029	<	*/
1030	<
1031	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1032	<	SimInfo::MoleculeIterator i;
1033	<	Molecule* mol;
1034	<
1035	<
1036	<	double totalMass = 0.0;
1037	<
1026	>
1027	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1028	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1029	>	sprintf(painCave.errMsg,
1030	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1031	>	"\tindex exceeds number of known objects!\n");
1032	>	painCave.isFatal = 1;
1033	>	simError();
1034	>	return NULL;
1035	>	} else
1036	>	return IOIndexToIntegrableObject.at(index);
1037	>	}
1038	>
1039	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1040	>	IOIndexToIntegrableObject= v;
1041	>	}
1042
1043	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1044	<	double mass = mol->getMass();
1258	<	totalMass += mass;
1259	<	com += mass * mol->getCom();
1260	<	comVel += mass * mol->getComVel();
1261	<	}
1262	<
1043	>	int SimInfo::getNGlobalConstraints() {
1044	>	int nGlobalConstraints;
1045		#ifdef IS_MPI
1046	<	double tmpMass = totalMass;
1047	<	Vector3d tmpCom(com);
1048	<	Vector3d tmpComVel(comVel);
1049	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1268	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1269	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1046	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1047	>	MPI::INT, MPI::SUM);
1048	>	#else
1049	>	nGlobalConstraints =  nConstraints_;
1050		#endif
1051	<
1052	<	com /= totalMass;
1273	<	comVel /= totalMass;
1274	<	}
1275	<
1276	<	/*
1277	<	Return intertia tensor for entire system and angular momentum Vector.
1051	>	return nGlobalConstraints;
1052	>	}
1053
1054	+	}//end namespace OpenMD
1055
1280	–	[  Ixx -Ixy  -Ixz ]
1281	–	J =| -Iyx  Iyy  -Iyz |
1282	–	[ -Izx -Iyz   Izz ]
1283	–	*/
1284	–
1285	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1286	–
1287	–
1288	–	double xx = 0.0;
1289	–	double yy = 0.0;
1290	–	double zz = 0.0;
1291	–	double xy = 0.0;
1292	–	double xz = 0.0;
1293	–	double yz = 0.0;
1294	–	Vector3d com(0.0);
1295	–	Vector3d comVel(0.0);
1296	–
1297	–	getComAll(com, comVel);
1298	–
1299	–	SimInfo::MoleculeIterator i;
1300	–	Molecule* mol;
1301	–
1302	–	Vector3d thisq(0.0);
1303	–	Vector3d thisv(0.0);
1304	–
1305	–	double thisMass = 0.0;
1306	–
1307	–
1308	–
1309	–
1310	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1311	–
1312	–	thisq = mol->getCom()-com;
1313	–	thisv = mol->getComVel()-comVel;
1314	–	thisMass = mol->getMass();
1315	–	// Compute moment of intertia coefficients.
1316	–	xx += thisq[0]*thisq[0]*thisMass;
1317	–	yy += thisq[1]*thisq[1]*thisMass;
1318	–	zz += thisq[2]*thisq[2]*thisMass;
1319	–
1320	–	// compute products of intertia
1321	–	xy += thisq[0]*thisq[1]*thisMass;
1322	–	xz += thisq[0]*thisq[2]*thisMass;
1323	–	yz += thisq[1]*thisq[2]*thisMass;
1324	–
1325	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1326	–
1327	–	}
1328	–
1329	–
1330	–	inertiaTensor(0,0) = yy + zz;
1331	–	inertiaTensor(0,1) = -xy;
1332	–	inertiaTensor(0,2) = -xz;
1333	–	inertiaTensor(1,0) = -xy;
1334	–	inertiaTensor(1,1) = xx + zz;
1335	–	inertiaTensor(1,2) = -yz;
1336	–	inertiaTensor(2,0) = -xz;
1337	–	inertiaTensor(2,1) = -yz;
1338	–	inertiaTensor(2,2) = xx + yy;
1339	–
1340	–	#ifdef IS_MPI
1341	–	Mat3x3d tmpI(inertiaTensor);
1342	–	Vector3d tmpAngMom;
1343	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1344	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1345	–	#endif
1346	–
1347	–	return;
1348	–	}
1349	–
1350	–	//Returns the angular momentum of the system
1351	–	Vector3d SimInfo::getAngularMomentum(){
1352	–
1353	–	Vector3d com(0.0);
1354	–	Vector3d comVel(0.0);
1355	–	Vector3d angularMomentum(0.0);
1356	–
1357	–	getComAll(com,comVel);
1358	–
1359	–	SimInfo::MoleculeIterator i;
1360	–	Molecule* mol;
1361	–
1362	–	Vector3d thisr(0.0);
1363	–	Vector3d thisp(0.0);
1364	–
1365	–	double thisMass;
1366	–
1367	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1368	–	thisMass = mol->getMass();
1369	–	thisr = mol->getCom()-com;
1370	–	thisp = (mol->getComVel()-comVel)*thisMass;
1371	–
1372	–	angularMomentum += cross( thisr, thisp );
1373	–
1374	–	}
1375	–
1376	–	#ifdef IS_MPI
1377	–	Vector3d tmpAngMom;
1378	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1379	–	#endif
1380	–
1381	–	return angularMomentum;
1382	–	}
1383	–
1384	–
1385	–	}//end namespace oopse
1386	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 834 by chuckv, Fri Dec 30 23:15:59 2005 UTC vs.
Revision 1940 by gezelter, Fri Nov 1 19:31:41 2013 UTC

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