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root/OpenMD/trunk/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 46 | Line 47
47		* @version 1.0
48		*/
49
50	+	#ifdef IS_MPI
51	+	#include <mpi.h>
52	+	#endif
53		#include <algorithm>
54		#include <set>
55		#include <map>
#	Line 54 | Line 58
58		#include "math/Vector3.hpp"
59		#include "primitives/Molecule.hpp"
60		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
63	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
61		#include "utils/MemoryUtils.hpp"
62		#include "utils/simError.h"
63		#include "selection/SelectionManager.hpp"
64		#include "io/ForceFieldOptions.hpp"
65	<	#include "UseTheForce/ForceField.hpp"
65	>	#include "brains/ForceField.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	#ifdef IS_MPI
69	<	#include "UseTheForce/mpiComponentPlan.h"
72	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
73	<	#endif
74	<
75	<	namespace oopse {
76	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
77	<	std::map<int, std::set<int> >::iterator i = container.find(index);
78	<	std::set<int> result;
79	<	if (i != container.end()) {
80	<	result = i->second;
81	<	}
82	<
83	<	return result;
84	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77	>	nGlobalTorsions_(0), nGlobalInversions_(0), nGlobalConstraints_(0),
78	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
79	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
80	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL),
81	>	topologyDone_(false), calcBoxDipole_(false), useAtomicVirial_(true),
82	>	hasNGlobalConstraints_(false) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin();
95	>	i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	if ( (*i)->haveRegion() ) {
98	>	molStamp->setRegion( (*i)->getRegion() );
99	>	} else {
100	>	// set the region to a disallowed value:
101	>	molStamp->setRegion( -1 );
102	>	}
103
104	<	MoleculeStamp* molStamp;
96	<	int nMolWithSameStamp;
97	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
98	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
99	<	CutoffGroupStamp* cgStamp;
100	<	RigidBodyStamp* rbStamp;
101	<	int nRigidAtoms = 0;
102	<	std::vector<Component*> components = simParams->getComponents();
104	>	nMolWithSameStamp = (*i)->getNMol();
105
106	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
107	<	molStamp = (*i)->getMoleculeStamp();
108	<	nMolWithSameStamp = (*i)->getNMol();
109	<
110	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
111	<
112	<	//calculate atoms in molecules
113	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114	<
115	<	//calculate atoms in cutoff groups
116	<	int nAtomsInGroups = 0;
117	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	<
119	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroupStamp(j);
121	<	nAtomsInGroups += cgStamp->getNMembers();
120	<	}
121	<
122	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123	<
124	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
125	<
126	<	//calculate atoms in rigid bodies
127	<	int nAtomsInRigidBodies = 0;
128	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129	<
130	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
131	<	rbStamp = molStamp->getRigidBodyStamp(j);
132	<	nAtomsInRigidBodies += rbStamp->getNMembers();
133	<	}
134	<
135	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
136	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
137	<
106	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
107	>
108	>	//calculate atoms in molecules
109	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
110	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
111	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
112	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
113	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
114	>
115	>	//calculate atoms in cutoff groups
116	>	int nAtomsInGroups = 0;
117	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	>
119	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121	>	nAtomsInGroups += cgStamp->getNMembers();
122		}
123	<
124	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
125	<	//group therefore the total number of cutoff groups in the system is
126	<	//equal to the total number of atoms minus number of atoms belong to
127	<	//cutoff group defined in meta-data file plus the number of cutoff
128	<	//groups defined in meta-data file
129	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130	<
131	<	//every free atom (atom does not belong to rigid bodies) is an
132	<	//integrable object therefore the total number of integrable objects
133	<	//in the system is equal to the total number of atoms minus number of
134	<	//atoms belong to rigid body defined in meta-data file plus the number
135	<	//of rigid bodies defined in meta-data file
136	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137	<	+ nGlobalRigidBodies_;
138	<
139	<	nGlobalMols_ = molStampIds_.size();
156	<
157	<	#ifdef IS_MPI
158	<	molToProcMap_.resize(nGlobalMols_);
159	<	#endif
160	<
123	>
124	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	>
126	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127	>
128	>	//calculate atoms in rigid bodies
129	>	int nAtomsInRigidBodies = 0;
130	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	>
132	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134	>	nAtomsInRigidBodies += rbStamp->getNMembers();
135	>	}
136	>
137	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	>
140		}
141	+
142	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	+	//group therefore the total number of cutoff groups in the system is
144	+	//equal to the total number of atoms minus number of atoms belong to
145	+	//cutoff group defined in meta-data file plus the number of cutoff
146	+	//groups defined in meta-data file
147
148	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149	+
150	+	//every free atom (atom does not belong to rigid bodies) is an
151	+	//integrable object therefore the total number of integrable objects
152	+	//in the system is equal to the total number of atoms minus number of
153	+	//atoms belong to rigid body defined in meta-data file plus the number
154	+	//of rigid bodies defined in meta-data file
155	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	+	+ nGlobalRigidBodies_;
157	+
158	+	nGlobalMols_ = molStampIds_.size();
159	+	molToProcMap_.resize(nGlobalMols_);
160	+	}
161	+
162		SimInfo::~SimInfo() {
163	<	std::map<int, Molecule*>::iterator i;
163	>	map<int, Molecule*>::iterator i;
164		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165		delete i->second;
166		}
#	Line 172 | Line 171 | namespace oopse {
171		delete forceField_;
172		}
173
175	–	int SimInfo::getNGlobalConstraints() {
176	–	int nGlobalConstraints;
177	–	#ifdef IS_MPI
178	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
179	–	MPI_COMM_WORLD);
180	–	#else
181	–	nGlobalConstraints =  nConstraints_;
182	–	#endif
183	–	return nGlobalConstraints;
184	–	}
174
175		bool SimInfo::addMolecule(Molecule* mol) {
176		MoleculeIterator i;
177	<
177	>
178		i = molecules_.find(mol->getGlobalIndex());
179		if (i == molecules_.end() ) {
180	<
181	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
182	<
180	>
181	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
182	>
183		nAtoms_ += mol->getNAtoms();
184		nBonds_ += mol->getNBonds();
185		nBends_ += mol->getNBends();
186		nTorsions_ += mol->getNTorsions();
187	+	nInversions_ += mol->getNInversions();
188		nRigidBodies_ += mol->getNRigidBodies();
189		nIntegrableObjects_ += mol->getNIntegrableObjects();
190		nCutoffGroups_ += mol->getNCutoffGroups();
191		nConstraints_ += mol->getNConstraintPairs();
192	<
193	<	addExcludePairs(mol);
194	<
192	>
193	>	addInteractionPairs(mol);
194	>
195		return true;
196		} else {
197		return false;
198		}
199		}
200	<
200	>
201		bool SimInfo::removeMolecule(Molecule* mol) {
202		MoleculeIterator i;
203		i = molecules_.find(mol->getGlobalIndex());
#	Line 220 | Line 210 | namespace oopse {
210		nBonds_ -= mol->getNBonds();
211		nBends_ -= mol->getNBends();
212		nTorsions_ -= mol->getNTorsions();
213	+	nInversions_ -= mol->getNInversions();
214		nRigidBodies_ -= mol->getNRigidBodies();
215		nIntegrableObjects_ -= mol->getNIntegrableObjects();
216		nCutoffGroups_ -= mol->getNCutoffGroups();
217		nConstraints_ -= mol->getNConstraintPairs();
218
219	<	removeExcludePairs(mol);
219	>	removeInteractionPairs(mol);
220		molecules_.erase(mol->getGlobalIndex());
221
222		delete mol;
#	Line 234 | Line 225 | namespace oopse {
225		} else {
226		return false;
227		}
237	–
238	–
228		}
229
230
#	Line 251 | Line 240 | namespace oopse {
240
241
242		void SimInfo::calcNdf() {
243	<	int ndf_local;
243	>	int ndf_local, nfq_local;
244		MoleculeIterator i;
245	<	std::vector<StuntDouble*>::iterator j;
245	>	vector<StuntDouble*>::iterator j;
246	>	vector<Atom*>::iterator k;
247	>
248		Molecule* mol;
249	<	StuntDouble* integrableObject;
249	>	StuntDouble* sd;
250	>	Atom* atom;
251
252		ndf_local = 0;
253	+	nfq_local = 0;
254
255		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
263	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
264	–	integrableObject = mol->nextIntegrableObject(j)) {
256
257	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
258	+	sd = mol->nextIntegrableObject(j)) {
259	+
260		ndf_local += 3;
261
262	<	if (integrableObject->isDirectional()) {
263	<	if (integrableObject->isLinear()) {
262	>	if (sd->isDirectional()) {
263	>	if (sd->isLinear()) {
264		ndf_local += 2;
265		} else {
266		ndf_local += 3;
267		}
268		}
275	–
269		}
270	+
271	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
272	+	atom = mol->nextFluctuatingCharge(k)) {
273	+	if (atom->isFluctuatingCharge()) {
274	+	nfq_local++;
275	+	}
276	+	}
277		}
278
279	+	ndfLocal_ = ndf_local;
280	+
281		// n_constraints is local, so subtract them on each processor
282		ndf_local -= nConstraints_;
283
284		#ifdef IS_MPI
285	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
285	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
286	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
287	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
288		#else
289		ndf_ = ndf_local;
290	+	nGlobalFluctuatingCharges_ = nfq_local;
291		#endif
292
293		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 293 | Line 298 | namespace oopse {
298
299		int SimInfo::getFdf() {
300		#ifdef IS_MPI
301	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
301	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
302		#else
303		fdf_ = fdf_local;
304		#endif
305		return fdf_;
306		}
307	+
308	+	unsigned int SimInfo::getNLocalCutoffGroups(){
309	+	int nLocalCutoffAtoms = 0;
310	+	Molecule* mol;
311	+	MoleculeIterator mi;
312	+	CutoffGroup* cg;
313	+	Molecule::CutoffGroupIterator ci;
314
315	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
316	+
317	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
318	+	cg = mol->nextCutoffGroup(ci)) {
319	+	nLocalCutoffAtoms += cg->getNumAtom();
320	+
321	+	}
322	+	}
323	+
324	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
325	+	}
326	+
327		void SimInfo::calcNdfRaw() {
328		int ndfRaw_local;
329
330		MoleculeIterator i;
331	<	std::vector<StuntDouble*>::iterator j;
331	>	vector<StuntDouble*>::iterator j;
332		Molecule* mol;
333	<	StuntDouble* integrableObject;
333	>	StuntDouble* sd;
334
335		// Raw degrees of freedom that we have to set
336		ndfRaw_local = 0;
337
338		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
315	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
316	–	integrableObject = mol->nextIntegrableObject(j)) {
339
340	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
341	+	sd = mol->nextIntegrableObject(j)) {
342	+
343		ndfRaw_local += 3;
344
345	<	if (integrableObject->isDirectional()) {
346	<	if (integrableObject->isLinear()) {
345	>	if (sd->isDirectional()) {
346	>	if (sd->isLinear()) {
347		ndfRaw_local += 2;
348		} else {
349		ndfRaw_local += 3;
#	Line 329 | Line 354 | namespace oopse {
354		}
355
356		#ifdef IS_MPI
357	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
357	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
358		#else
359		ndfRaw_ = ndfRaw_local;
360		#endif
#	Line 340 | Line 365 | namespace oopse {
365
366		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
367
343	–
368		#ifdef IS_MPI
369	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
369	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
370	>	MPI_COMM_WORLD);
371		#else
372		ndfTrans_ = ndfTrans_local;
373		#endif
374
375		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
351	–
376		}
377
378	<	void SimInfo::addExcludePairs(Molecule* mol) {
379	<	std::vector<Bond*>::iterator bondIter;
380	<	std::vector<Bend*>::iterator bendIter;
381	<	std::vector<Torsion*>::iterator torsionIter;
378	>	void SimInfo::addInteractionPairs(Molecule* mol) {
379	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
380	>	vector<Bond*>::iterator bondIter;
381	>	vector<Bend*>::iterator bendIter;
382	>	vector<Torsion*>::iterator torsionIter;
383	>	vector<Inversion*>::iterator inversionIter;
384		Bond* bond;
385		Bend* bend;
386		Torsion* torsion;
387	+	Inversion* inversion;
388		int a;
389		int b;
390		int c;
391		int d;
392
393	<	std::map<int, std::set<int> > atomGroups;
393	>	// atomGroups can be used to add special interaction maps between
394	>	// groups of atoms that are in two separate rigid bodies.
395	>	// However, most site-site interactions between two rigid bodies
396	>	// are probably not special, just the ones between the physically
397	>	// bonded atoms.  Interactions *within* a single rigid body should
398	>	// always be excluded.  These are done at the bottom of this
399	>	// function.
400
401	+	map<int, set<int> > atomGroups;
402		Molecule::RigidBodyIterator rbIter;
403		RigidBody* rb;
404		Molecule::IntegrableObjectIterator ii;
405	<	StuntDouble* integrableObject;
405	>	StuntDouble* sd;
406
407	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
408	<	integrableObject = mol->nextIntegrableObject(ii)) {
409	<
410	<	if (integrableObject->isRigidBody()) {
411	<	rb = static_cast<RigidBody*>(integrableObject);
412	<	std::vector<Atom*> atoms = rb->getAtoms();
413	<	std::set<int> rigidAtoms;
414	<	for (int i = 0; i < atoms.size(); ++i) {
415	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
416	<	}
417	<	for (int i = 0; i < atoms.size(); ++i) {
418	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
419	<	}
407	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
408	>	sd = mol->nextIntegrableObject(ii)) {
409	>
410	>	if (sd->isRigidBody()) {
411	>	rb = static_cast<RigidBody*>(sd);
412	>	vector<Atom*> atoms = rb->getAtoms();
413	>	set<int> rigidAtoms;
414	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
416	>	}
417	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
418	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
419	>	}
420		} else {
421	<	std::set<int> oneAtomSet;
422	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
423	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
421	>	set<int> oneAtomSet;
422	>	oneAtomSet.insert(sd->getGlobalIndex());
423	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
424		}
425		}
426
427	<
428	<
429	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
427	>
428	>	for (bond= mol->beginBond(bondIter); bond != NULL;
429	>	bond = mol->nextBond(bondIter)) {
430	>
431		a = bond->getAtomA()->getGlobalIndex();
432	<	b = bond->getAtomB()->getGlobalIndex();
433	<	exclude_.addPair(a, b);
432	>	b = bond->getAtomB()->getGlobalIndex();
433	>
434	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
435	>	oneTwoInteractions_.addPair(a, b);
436	>	} else {
437	>	excludedInteractions_.addPair(a, b);
438	>	}
439		}
440
441	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
441	>	for (bend= mol->beginBend(bendIter); bend != NULL;
442	>	bend = mol->nextBend(bendIter)) {
443	>
444		a = bend->getAtomA()->getGlobalIndex();
445		b = bend->getAtomB()->getGlobalIndex();
446		c = bend->getAtomC()->getGlobalIndex();
405	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
406	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
407	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
408	–
409	–	exclude_.addPairs(rigidSetA, rigidSetB);
410	–	exclude_.addPairs(rigidSetA, rigidSetC);
411	–	exclude_.addPairs(rigidSetB, rigidSetC);
447
448	<	//exclude_.addPair(a, b);
449	<	//exclude_.addPair(a, c);
450	<	//exclude_.addPair(b, c);
448	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
449	>	oneTwoInteractions_.addPair(a, b);
450	>	oneTwoInteractions_.addPair(b, c);
451	>	} else {
452	>	excludedInteractions_.addPair(a, b);
453	>	excludedInteractions_.addPair(b, c);
454	>	}
455	>
456	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
457	>	oneThreeInteractions_.addPair(a, c);
458	>	} else {
459	>	excludedInteractions_.addPair(a, c);
460	>	}
461		}
462
463	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
463	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
464	>	torsion = mol->nextTorsion(torsionIter)) {
465	>
466		a = torsion->getAtomA()->getGlobalIndex();
467		b = torsion->getAtomB()->getGlobalIndex();
468		c = torsion->getAtomC()->getGlobalIndex();
469	<	d = torsion->getAtomD()->getGlobalIndex();
423	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
424	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
425	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
426	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
469	>	d = torsion->getAtomD()->getGlobalIndex();
470
471	<	exclude_.addPairs(rigidSetA, rigidSetB);
472	<	exclude_.addPairs(rigidSetA, rigidSetC);
473	<	exclude_.addPairs(rigidSetA, rigidSetD);
474	<	exclude_.addPairs(rigidSetB, rigidSetC);
475	<	exclude_.addPairs(rigidSetB, rigidSetD);
476	<	exclude_.addPairs(rigidSetC, rigidSetD);
471	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
472	>	oneTwoInteractions_.addPair(a, b);
473	>	oneTwoInteractions_.addPair(b, c);
474	>	oneTwoInteractions_.addPair(c, d);
475	>	} else {
476	>	excludedInteractions_.addPair(a, b);
477	>	excludedInteractions_.addPair(b, c);
478	>	excludedInteractions_.addPair(c, d);
479	>	}
480
481	<	/*
482	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
483	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
484	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
485	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
486	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
487	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
488	<
489	<
490	<	exclude_.addPair(a, b);
491	<	exclude_.addPair(a, c);
492	<	exclude_.addPair(a, d);
493	<	exclude_.addPair(b, c);
448	<	exclude_.addPair(b, d);
449	<	exclude_.addPair(c, d);
450	<	*/
481	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
482	>	oneThreeInteractions_.addPair(a, c);
483	>	oneThreeInteractions_.addPair(b, d);
484	>	} else {
485	>	excludedInteractions_.addPair(a, c);
486	>	excludedInteractions_.addPair(b, d);
487	>	}
488	>
489	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
490	>	oneFourInteractions_.addPair(a, d);
491	>	} else {
492	>	excludedInteractions_.addPair(a, d);
493	>	}
494		}
495
496	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
497	<	std::vector<Atom*> atoms = rb->getAtoms();
498	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
499	<	for (int j = i + 1; j < atoms.size(); ++j) {
496	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
497	>	inversion = mol->nextInversion(inversionIter)) {
498	>
499	>	a = inversion->getAtomA()->getGlobalIndex();
500	>	b = inversion->getAtomB()->getGlobalIndex();
501	>	c = inversion->getAtomC()->getGlobalIndex();
502	>	d = inversion->getAtomD()->getGlobalIndex();
503	>
504	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
505	>	oneTwoInteractions_.addPair(a, b);
506	>	oneTwoInteractions_.addPair(a, c);
507	>	oneTwoInteractions_.addPair(a, d);
508	>	} else {
509	>	excludedInteractions_.addPair(a, b);
510	>	excludedInteractions_.addPair(a, c);
511	>	excludedInteractions_.addPair(a, d);
512	>	}
513	>
514	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
515	>	oneThreeInteractions_.addPair(b, c);
516	>	oneThreeInteractions_.addPair(b, d);
517	>	oneThreeInteractions_.addPair(c, d);
518	>	} else {
519	>	excludedInteractions_.addPair(b, c);
520	>	excludedInteractions_.addPair(b, d);
521	>	excludedInteractions_.addPair(c, d);
522	>	}
523	>	}
524	>
525	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
526	>	rb = mol->nextRigidBody(rbIter)) {
527	>	vector<Atom*> atoms = rb->getAtoms();
528	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
529	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
530		a = atoms[i]->getGlobalIndex();
531		b = atoms[j]->getGlobalIndex();
532	<	exclude_.addPair(a, b);
532	>	excludedInteractions_.addPair(a, b);
533		}
534		}
535		}
536
537		}
538
539	<	void SimInfo::removeExcludePairs(Molecule* mol) {
540	<	std::vector<Bond*>::iterator bondIter;
541	<	std::vector<Bend*>::iterator bendIter;
542	<	std::vector<Torsion*>::iterator torsionIter;
539	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
540	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
541	>	vector<Bond*>::iterator bondIter;
542	>	vector<Bend*>::iterator bendIter;
543	>	vector<Torsion*>::iterator torsionIter;
544	>	vector<Inversion*>::iterator inversionIter;
545		Bond* bond;
546		Bend* bend;
547		Torsion* torsion;
548	+	Inversion* inversion;
549		int a;
550		int b;
551		int c;
552		int d;
553
554	<	std::map<int, std::set<int> > atomGroups;
479	<
554	>	map<int, set<int> > atomGroups;
555		Molecule::RigidBodyIterator rbIter;
556		RigidBody* rb;
557		Molecule::IntegrableObjectIterator ii;
558	<	StuntDouble* integrableObject;
558	>	StuntDouble* sd;
559
560	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
561	<	integrableObject = mol->nextIntegrableObject(ii)) {
562	<
563	<	if (integrableObject->isRigidBody()) {
564	<	rb = static_cast<RigidBody*>(integrableObject);
565	<	std::vector<Atom*> atoms = rb->getAtoms();
566	<	std::set<int> rigidAtoms;
567	<	for (int i = 0; i < atoms.size(); ++i) {
568	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
569	<	}
570	<	for (int i = 0; i < atoms.size(); ++i) {
571	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
572	<	}
560	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
561	>	sd = mol->nextIntegrableObject(ii)) {
562	>
563	>	if (sd->isRigidBody()) {
564	>	rb = static_cast<RigidBody*>(sd);
565	>	vector<Atom*> atoms = rb->getAtoms();
566	>	set<int> rigidAtoms;
567	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
569	>	}
570	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
571	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
572	>	}
573		} else {
574	<	std::set<int> oneAtomSet;
575	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
576	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
574	>	set<int> oneAtomSet;
575	>	oneAtomSet.insert(sd->getGlobalIndex());
576	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
577		}
578		}
579
580	<
581	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
580	>	for (bond= mol->beginBond(bondIter); bond != NULL;
581	>	bond = mol->nextBond(bondIter)) {
582	>
583		a = bond->getAtomA()->getGlobalIndex();
584	<	b = bond->getAtomB()->getGlobalIndex();
585	<	exclude_.removePair(a, b);
584	>	b = bond->getAtomB()->getGlobalIndex();
585	>
586	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
587	>	oneTwoInteractions_.removePair(a, b);
588	>	} else {
589	>	excludedInteractions_.removePair(a, b);
590	>	}
591		}
592
593	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
593	>	for (bend= mol->beginBend(bendIter); bend != NULL;
594	>	bend = mol->nextBend(bendIter)) {
595	>
596		a = bend->getAtomA()->getGlobalIndex();
597		b = bend->getAtomB()->getGlobalIndex();
598		c = bend->getAtomC()->getGlobalIndex();
516	–
517	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
518	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
519	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
520	–
521	–	exclude_.removePairs(rigidSetA, rigidSetB);
522	–	exclude_.removePairs(rigidSetA, rigidSetC);
523	–	exclude_.removePairs(rigidSetB, rigidSetC);
599
600	<	//exclude_.removePair(a, b);
601	<	//exclude_.removePair(a, c);
602	<	//exclude_.removePair(b, c);
600	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
601	>	oneTwoInteractions_.removePair(a, b);
602	>	oneTwoInteractions_.removePair(b, c);
603	>	} else {
604	>	excludedInteractions_.removePair(a, b);
605	>	excludedInteractions_.removePair(b, c);
606	>	}
607	>
608	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
609	>	oneThreeInteractions_.removePair(a, c);
610	>	} else {
611	>	excludedInteractions_.removePair(a, c);
612	>	}
613		}
614
615	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
615	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
616	>	torsion = mol->nextTorsion(torsionIter)) {
617	>
618		a = torsion->getAtomA()->getGlobalIndex();
619		b = torsion->getAtomB()->getGlobalIndex();
620		c = torsion->getAtomC()->getGlobalIndex();
621	<	d = torsion->getAtomD()->getGlobalIndex();
621	>	d = torsion->getAtomD()->getGlobalIndex();
622	>
623	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
624	>	oneTwoInteractions_.removePair(a, b);
625	>	oneTwoInteractions_.removePair(b, c);
626	>	oneTwoInteractions_.removePair(c, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, b);
629	>	excludedInteractions_.removePair(b, c);
630	>	excludedInteractions_.removePair(c, d);
631	>	}
632
633	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
634	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
635	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
636	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
633	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
634	>	oneThreeInteractions_.removePair(a, c);
635	>	oneThreeInteractions_.removePair(b, d);
636	>	} else {
637	>	excludedInteractions_.removePair(a, c);
638	>	excludedInteractions_.removePair(b, d);
639	>	}
640
641	<	exclude_.removePairs(rigidSetA, rigidSetB);
642	<	exclude_.removePairs(rigidSetA, rigidSetC);
643	<	exclude_.removePairs(rigidSetA, rigidSetD);
644	<	exclude_.removePairs(rigidSetB, rigidSetC);
645	<	exclude_.removePairs(rigidSetB, rigidSetD);
646	<	exclude_.removePairs(rigidSetC, rigidSetD);
641	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
642	>	oneFourInteractions_.removePair(a, d);
643	>	} else {
644	>	excludedInteractions_.removePair(a, d);
645	>	}
646	>	}
647
648	<	/*
649	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
550	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
551	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
552	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
553	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
554	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
648	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
649	>	inversion = mol->nextInversion(inversionIter)) {
650
651	<
652	<	exclude_.removePair(a, b);
653	<	exclude_.removePair(a, c);
654	<	exclude_.removePair(a, d);
655	<	exclude_.removePair(b, c);
656	<	exclude_.removePair(b, d);
657	<	exclude_.removePair(c, d);
658	<	*/
651	>	a = inversion->getAtomA()->getGlobalIndex();
652	>	b = inversion->getAtomB()->getGlobalIndex();
653	>	c = inversion->getAtomC()->getGlobalIndex();
654	>	d = inversion->getAtomD()->getGlobalIndex();
655	>
656	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
657	>	oneTwoInteractions_.removePair(a, b);
658	>	oneTwoInteractions_.removePair(a, c);
659	>	oneTwoInteractions_.removePair(a, d);
660	>	} else {
661	>	excludedInteractions_.removePair(a, b);
662	>	excludedInteractions_.removePair(a, c);
663	>	excludedInteractions_.removePair(a, d);
664	>	}
665	>
666	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
667	>	oneThreeInteractions_.removePair(b, c);
668	>	oneThreeInteractions_.removePair(b, d);
669	>	oneThreeInteractions_.removePair(c, d);
670	>	} else {
671	>	excludedInteractions_.removePair(b, c);
672	>	excludedInteractions_.removePair(b, d);
673	>	excludedInteractions_.removePair(c, d);
674	>	}
675		}
676
677	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
678	<	std::vector<Atom*> atoms = rb->getAtoms();
679	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
680	<	for (int j = i + 1; j < atoms.size(); ++j) {
677	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
678	>	rb = mol->nextRigidBody(rbIter)) {
679	>	vector<Atom*> atoms = rb->getAtoms();
680	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
681	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
682		a = atoms[i]->getGlobalIndex();
683		b = atoms[j]->getGlobalIndex();
684	<	exclude_.removePair(a, b);
684	>	excludedInteractions_.removePair(a, b);
685		}
686		}
687		}
688	<
688	>
689		}
690	<
691	<
690	>
691	>
692		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
693		int curStampId;
694	<
694	>
695		//index from 0
696		curStampId = moleculeStamps_.size();
697
#	Line 587 | Line 699 | namespace oopse {
699		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
700		}
701
590	–	void SimInfo::update() {
702
703	<	setupSimType();
704	<
705	<	#ifdef IS_MPI
706	<	setupFortranParallel();
707	<	#endif
708	<
709	<	setupFortranSim();
710	<
711	<	//setup fortran force field
712	<	/** @deprecate */
602	<	int isError = 0;
603	<
604	<	setupCutoff();
605	<
606	<	setupElectrostaticSummationMethod( isError );
607	<	setupSwitchingFunction();
608	<	setupAccumulateBoxDipole();
609	<
610	<	if(isError){
611	<	sprintf( painCave.errMsg,
612	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
613	<	painCave.isFatal = 1;
614	<	simError();
615	<	}
616	<
703	>	/**
704	>	* update
705	>	*
706	>	*  Performs the global checks and variable settings after the
707	>	*  objects have been created.
708	>	*
709	>	*/
710	>	void SimInfo::update() {
711	>	setupSimVariables();
712	>	calcNConstraints();
713		calcNdf();
714		calcNdfRaw();
715		calcNdfTrans();
620	–
621	–	fortranInitialized_ = true;
716		}
717	<
718	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
717	>
718	>	/**
719	>	* getSimulatedAtomTypes
720	>	*
721	>	* Returns an STL set of AtomType* that are actually present in this
722	>	* simulation.  Must query all processors to assemble this information.
723	>	*
724	>	*/
725	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
726		SimInfo::MoleculeIterator mi;
727		Molecule* mol;
728		Molecule::AtomIterator ai;
729		Atom* atom;
730	<	std::set<AtomType*> atomTypes;
731	<
730	>	set<AtomType*> atomTypes;
731	>
732		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
733	<
734	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
733	>	for(atom = mol->beginAtom(ai); atom != NULL;
734	>	atom = mol->nextAtom(ai)) {
735		atomTypes.insert(atom->getAtomType());
736	<	}
737	<
736	>	}
737	>	}
738	>
739	>	#ifdef IS_MPI
740	>
741	>	// loop over the found atom types on this processor, and add their
742	>	// numerical idents to a vector:
743	>
744	>	vector<int> foundTypes;
745	>	set<AtomType*>::iterator i;
746	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
747	>	foundTypes.push_back( (*i)->getIdent() );
748	>
749	>	// count_local holds the number of found types on this processor
750	>	int count_local = foundTypes.size();
751	>
752	>	int nproc;
753	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
754	>	// int nproc = MPI::COMM_WORLD.Get_size();
755	>
756	>	// we need arrays to hold the counts and displacement vectors for
757	>	// all processors
758	>	vector<int> counts(nproc, 0);
759	>	vector<int> disps(nproc, 0);
760	>
761	>	// fill the counts array
762	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
763	>	1, MPI_INT, MPI_COMM_WORLD);
764	>	// MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
765	>	//                           1, MPI::INT);
766	>
767	>	// use the processor counts to compute the displacement array
768	>	disps[0] = 0;
769	>	int totalCount = counts[0];
770	>	for (int iproc = 1; iproc < nproc; iproc++) {
771	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
772	>	totalCount += counts[iproc];
773		}
774
775	+	// we need a (possibly redundant) set of all found types:
776	+	vector<int> ftGlobal(totalCount);
777	+
778	+	// now spray out the foundTypes to all the other processors:
779	+	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
780	+	&ftGlobal[0], &counts[0], &disps[0],
781	+	MPI_INT, MPI_COMM_WORLD);
782	+	// MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
783	+	//                            &ftGlobal[0], &counts[0], &disps[0],
784	+	//                            MPI::INT);
785	+
786	+	vector<int>::iterator j;
787	+
788	+	// foundIdents is a stl set, so inserting an already found ident
789	+	// will have no effect.
790	+	set<int> foundIdents;
791	+
792	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
793	+	foundIdents.insert((*j));
794	+
795	+	// now iterate over the foundIdents and get the actual atom types
796	+	// that correspond to these:
797	+	set<int>::iterator it;
798	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
799	+	atomTypes.insert( forceField_->getAtomType((*it)) );
800	+
801	+	#endif
802	+
803		return atomTypes;
804		}
805
642	–	void SimInfo::setupSimType() {
643	–	std::set<AtomType*>::iterator i;
644	–	std::set<AtomType*> atomTypes;
645	–	atomTypes = getUniqueAtomTypes();
646	–
647	–	int useLennardJones = 0;
648	–	int useElectrostatic = 0;
649	–	int useEAM = 0;
650	–	int useSC = 0;
651	–	int useCharge = 0;
652	–	int useDirectional = 0;
653	–	int useDipole = 0;
654	–	int useGayBerne = 0;
655	–	int useSticky = 0;
656	–	int useStickyPower = 0;
657	–	int useShape = 0;
658	–	int useFLARB = 0; //it is not in AtomType yet
659	–	int useDirectionalAtom = 0;
660	–	int useElectrostatics = 0;
661	–	//usePBC and useRF are from simParams
662	–	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663	–	int useRF;
664	–	int useSF;
665	–	int useSP;
666	–	int useBoxDipole;
667	–	std::string myMethod;
806
807	<	// set the useRF logical
808	<	useRF = 0;
809	<	useSF = 0;
807	>	int getGlobalCountOfType(AtomType* atype) {
808	>	/*
809	>	set<AtomType*> atypes = getSimulatedAtomTypes();
810	>	map<AtomType*, int> counts_;
811
812	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
813	+	for(atom = mol->beginAtom(ai); atom != NULL;
814	+	atom = mol->nextAtom(ai)) {
815	+	atom->getAtomType();
816	+	}
817	+	}
818	+	*/
819	+	return 0;
820	+	}
821
822	<	if (simParams_->haveElectrostaticSummationMethod()) {
823	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
824	<	toUpper(myMethod);
825	<	if (myMethod == "REACTION_FIELD"){
826	<	useRF=1;
827	<	} else if (myMethod == "SHIFTED_FORCE"){
828	<	useSF = 1;
829	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
830	<	useSP = 1;
683	<	}
684	<	}
822	>	void SimInfo::setupSimVariables() {
823	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
824	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
825	>	// parameter is true
826	>	calcBoxDipole_ = false;
827	>	if ( simParams_->haveAccumulateBoxDipole() )
828	>	if ( simParams_->getAccumulateBoxDipole() ) {
829	>	calcBoxDipole_ = true;
830	>	}
831
832	<	if (simParams_->haveAccumulateBoxDipole())
833	<	if (simParams_->getAccumulateBoxDipole())
834	<	useBoxDipole = 1;
835	<
832	>	set<AtomType*>::iterator i;
833	>	set<AtomType*> atomTypes;
834	>	atomTypes = getSimulatedAtomTypes();
835	>	bool usesElectrostatic = false;
836	>	bool usesMetallic = false;
837	>	bool usesDirectional = false;
838	>	bool usesFluctuatingCharges =  false;
839		//loop over all of the atom types
840		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
841	<	useLennardJones |= (*i)->isLennardJones();
842	<	useElectrostatic |= (*i)->isElectrostatic();
843	<	useEAM |= (*i)->isEAM();
844	<	useSC |= (*i)->isSC();
696	<	useCharge |= (*i)->isCharge();
697	<	useDirectional |= (*i)->isDirectional();
698	<	useDipole |= (*i)->isDipole();
699	<	useGayBerne |= (*i)->isGayBerne();
700	<	useSticky |= (*i)->isSticky();
701	<	useStickyPower |= (*i)->isStickyPower();
702	<	useShape |= (*i)->isShape();
841	>	usesElectrostatic |= (*i)->isElectrostatic();
842	>	usesMetallic |= (*i)->isMetal();
843	>	usesDirectional |= (*i)->isDirectional();
844	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
845		}
846
847	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
706	<	useDirectionalAtom = 1;
707	<	}
708	<
709	<	if (useCharge || useDipole) {
710	<	useElectrostatics = 1;
711	<	}
712	<
713	<	#ifdef IS_MPI
847	>	#ifdef IS_MPI
848		int temp;
849
850	<	temp = usePBC;
851	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850	>	temp = usesDirectional;
851	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
852	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
853	>
854	>	temp = usesMetallic;
855	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
856	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
857
858	<	temp = useDirectionalAtom;
859	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
858	>	temp = usesElectrostatic;
859	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
860	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
861
862	<	temp = useLennardJones;
863	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	>	temp = usesFluctuatingCharges;
863	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
864	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
865	>	#else
866
867	<	temp = useElectrostatics;
868	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
867	>	usesDirectionalAtoms_ = usesDirectional;
868	>	usesMetallicAtoms_ = usesMetallic;
869	>	usesElectrostaticAtoms_ = usesElectrostatic;
870	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
871
872	<	temp = useCharge;
873	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
872	>	#endif
873	>
874	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
875	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
876	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
877	>	}
878
731	–	temp = useDipole;
732	–	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
879
880	<	temp = useSticky;
881	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
880	>	vector<int> SimInfo::getGlobalAtomIndices() {
881	>	SimInfo::MoleculeIterator mi;
882	>	Molecule* mol;
883	>	Molecule::AtomIterator ai;
884	>	Atom* atom;
885
886	<	temp = useStickyPower;
738	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
887
888	<	temp = useGayBerne;
889	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
888	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889	>
890	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
891	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
892	>	}
893	>	}
894	>	return GlobalAtomIndices;
895	>	}
896
743	–	temp = useEAM;
744	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
897
898	<	temp = useSC;
899	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
900	<
901	<	temp = useShape;
902	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
898	>	vector<int> SimInfo::getGlobalGroupIndices() {
899	>	SimInfo::MoleculeIterator mi;
900	>	Molecule* mol;
901	>	Molecule::CutoffGroupIterator ci;
902	>	CutoffGroup* cg;
903
904	<	temp = useFLARB;
905	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
906	<
907	<	temp = useRF;
908	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
909	<
910	<	temp = useSF;
911	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
912	<
913	<	temp = useSP;
914	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
915	<
764	<	temp = useBoxDipole;
765	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	<
767	<	#endif
768	<
769	<	fInfo_.SIM_uses_PBC = usePBC;
770	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
771	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
772	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
773	<	fInfo_.SIM_uses_Charges = useCharge;
774	<	fInfo_.SIM_uses_Dipoles = useDipole;
775	<	fInfo_.SIM_uses_Sticky = useSticky;
776	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
777	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
778	<	fInfo_.SIM_uses_EAM = useEAM;
779	<	fInfo_.SIM_uses_SC = useSC;
780	<	fInfo_.SIM_uses_Shapes = useShape;
781	<	fInfo_.SIM_uses_FLARB = useFLARB;
782	<	fInfo_.SIM_uses_RF = useRF;
783	<	fInfo_.SIM_uses_SF = useSF;
784	<	fInfo_.SIM_uses_SP = useSP;
785	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
904	>	vector<int> GlobalGroupIndices;
905	>
906	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
907	>
908	>	//local index of cutoff group is trivial, it only depends on the
909	>	//order of travesing
910	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
911	>	cg = mol->nextCutoffGroup(ci)) {
912	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
913	>	}
914	>	}
915	>	return GlobalGroupIndices;
916		}
917
788	–	void SimInfo::setupFortranSim() {
789	–	int isError;
790	–	int nExclude;
791	–	std::vector<int> fortranGlobalGroupMembership;
792	–
793	–	nExclude = exclude_.getSize();
794	–	isError = 0;
918
919	<	//globalGroupMembership_ is filled by SimCreator
797	<	for (int i = 0; i < nGlobalAtoms_; i++) {
798	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
799	<	}
919	>	void SimInfo::prepareTopology() {
920
921		//calculate mass ratio of cutoff group
802	–	std::vector<RealType> mfact;
922		SimInfo::MoleculeIterator mi;
923		Molecule* mol;
924		Molecule::CutoffGroupIterator ci;
#	Line 808 | Line 927 | namespace oopse {
927		Atom* atom;
928		RealType totalMass;
929
930	<	//to avoid memory reallocation, reserve enough space for mfact
931	<	mfact.reserve(getNCutoffGroups());
930	>	/**
931	>	* The mass factor is the relative mass of an atom to the total
932	>	* mass of the cutoff group it belongs to.  By default, all atoms
933	>	* are their own cutoff groups, and therefore have mass factors of
934	>	* 1.  We need some special handling for massless atoms, which
935	>	* will be treated as carrying the entire mass of the cutoff
936	>	* group.
937	>	*/
938	>	massFactors_.clear();
939	>	massFactors_.resize(getNAtoms(), 1.0);
940
941		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
942	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
942	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
943	>	cg = mol->nextCutoffGroup(ci)) {
944
945		totalMass = cg->getMass();
946		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
947		// Check for massless groups - set mfact to 1 if true
948	<	if (totalMass != 0)
949	<	mfact.push_back(atom->getMass()/totalMass);
948	>	if (totalMass != 0)
949	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
950		else
951	<	mfact.push_back( 1.0 );
951	>	massFactors_[atom->getLocalIndex()] = 1.0;
952		}
825	–
953		}
954		}
955
956	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
830	<	std::vector<int> identArray;
956	>	// Build the identArray_ and regions_
957
958	<	//to avoid memory reallocation, reserve enough space identArray
959	<	identArray.reserve(getNAtoms());
960	<
961	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
958	>	identArray_.clear();
959	>	identArray_.reserve(getNAtoms());
960	>	regions_.clear();
961	>	regions_.reserve(getNAtoms());
962	>
963	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
964	>	int reg = mol->getRegion();
965		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
966	<	identArray.push_back(atom->getIdent());
966	>	identArray_.push_back(atom->getIdent());
967	>	regions_.push_back(reg);
968		}
969		}
970	<
971	<	//fill molMembershipArray
842	<	//molMembershipArray is filled by SimCreator
843	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
844	<	for (int i = 0; i < nGlobalAtoms_; i++) {
845	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
846	<	}
847	<
848	<	//setup fortran simulation
849	<	int nGlobalExcludes = 0;
850	<	int* globalExcludes = NULL;
851	<	int* excludeList = exclude_.getExcludeList();
852	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
853	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
854	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
855	<
856	<	if( isError ){
857	<
858	<	sprintf( painCave.errMsg,
859	<	"There was an error setting the simulation information in fortran.\n" );
860	<	painCave.isFatal = 1;
861	<	painCave.severity = OOPSE_ERROR;
862	<	simError();
863	<	}
864	<
865	<	#ifdef IS_MPI
866	<	sprintf( checkPointMsg,
867	<	"succesfully sent the simulation information to fortran.\n");
868	<	MPIcheckPoint();
869	<	#endif // is_mpi
870	<	}
871	<
872	<
873	<	#ifdef IS_MPI
874	<	void SimInfo::setupFortranParallel() {
875	<
876	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
877	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
878	<	std::vector<int> localToGlobalCutoffGroupIndex;
879	<	SimInfo::MoleculeIterator mi;
880	<	Molecule::AtomIterator ai;
881	<	Molecule::CutoffGroupIterator ci;
882	<	Molecule* mol;
883	<	Atom* atom;
884	<	CutoffGroup* cg;
885	<	mpiSimData parallelData;
886	<	int isError;
887	<
888	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889	<
890	<	//local index(index in DataStorge) of atom is important
891	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893	<	}
894	<
895	<	//local index of cutoff group is trivial, it only depends on the order of travesing
896	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898	<	}
899	<
900	<	}
901	<
902	<	//fill up mpiSimData struct
903	<	parallelData.nMolGlobal = getNGlobalMolecules();
904	<	parallelData.nMolLocal = getNMolecules();
905	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
906	<	parallelData.nAtomsLocal = getNAtoms();
907	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
908	<	parallelData.nGroupsLocal = getNCutoffGroups();
909	<	parallelData.myNode = worldRank;
910	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
911	<
912	<	//pass mpiSimData struct and index arrays to fortran
913	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
914	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
915	<	&localToGlobalCutoffGroupIndex[0], &isError);
916	<
917	<	if (isError) {
918	<	sprintf(painCave.errMsg,
919	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
920	<	painCave.isFatal = 1;
921	<	simError();
922	<	}
923	<
924	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
925	<	MPIcheckPoint();
926	<
927	<
928	<	}
929	<
930	<	#endif
931	<
932	<	void SimInfo::setupCutoff() {
933	<
934	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935	<
936	<	// Check the cutoff policy
937	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
938	<
939	<	std::string myPolicy;
940	<	if (forceFieldOptions_.haveCutoffPolicy()){
941	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
942	<	}else if (simParams_->haveCutoffPolicy()) {
943	<	myPolicy = simParams_->getCutoffPolicy();
944	<	}
945	<
946	<	if (!myPolicy.empty()){
947	<	toUpper(myPolicy);
948	<	if (myPolicy == "MIX") {
949	<	cp = MIX_CUTOFF_POLICY;
950	<	} else {
951	<	if (myPolicy == "MAX") {
952	<	cp = MAX_CUTOFF_POLICY;
953	<	} else {
954	<	if (myPolicy == "TRADITIONAL") {
955	<	cp = TRADITIONAL_CUTOFF_POLICY;
956	<	} else {
957	<	// throw error
958	<	sprintf( painCave.errMsg,
959	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
960	<	painCave.isFatal = 1;
961	<	simError();
962	<	}
963	<	}
964	<	}
965	<	}
966	<	notifyFortranCutoffPolicy(&cp);
967	<
968	<	// Check the Skin Thickness for neighborlists
969	<	RealType skin;
970	<	if (simParams_->haveSkinThickness()) {
971	<	skin = simParams_->getSkinThickness();
972	<	notifyFortranSkinThickness(&skin);
973	<	}
974	<
975	<	// Check if the cutoff was set explicitly:
976	<	if (simParams_->haveCutoffRadius()) {
977	<	rcut_ = simParams_->getCutoffRadius();
978	<	if (simParams_->haveSwitchingRadius()) {
979	<	rsw_  = simParams_->getSwitchingRadius();
980	<	} else {
981	<	if (fInfo_.SIM_uses_Charges |
982	<	fInfo_.SIM_uses_Dipoles |
983	<	fInfo_.SIM_uses_RF) {
984	<
985	<	rsw_ = 0.85 * rcut_;
986	<	sprintf(painCave.errMsg,
987	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
988	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
990	<	painCave.isFatal = 0;
991	<	simError();
992	<	} else {
993	<	rsw_ = rcut_;
994	<	sprintf(painCave.errMsg,
995	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
996	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
997	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
998	<	painCave.isFatal = 0;
999	<	simError();
1000	<	}
1001	<	}
1002	<
1003	<	notifyFortranCutoffs(&rcut_, &rsw_);
1004	<
1005	<	} else {
1006	<
1007	<	// For electrostatic atoms, we'll assume a large safe value:
1008	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1009	<	sprintf(painCave.errMsg,
1010	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1011	<	"\tOOPSE will use a default value of 15.0 angstroms"
1012	<	"\tfor the cutoffRadius.\n");
1013	<	painCave.isFatal = 0;
1014	<	simError();
1015	<	rcut_ = 15.0;
1016	<
1017	<	if (simParams_->haveElectrostaticSummationMethod()) {
1018	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1019	<	toUpper(myMethod);
1020	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1021	<	if (simParams_->haveSwitchingRadius()){
1022	<	sprintf(painCave.errMsg,
1023	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1024	<	"\teven though the electrostaticSummationMethod was\n"
1025	<	"\tset to %s\n", myMethod.c_str());
1026	<	painCave.isFatal = 1;
1027	<	simError();
1028	<	}
1029	<	}
1030	<	}
1031	<
1032	<	if (simParams_->haveSwitchingRadius()){
1033	<	rsw_ = simParams_->getSwitchingRadius();
1034	<	} else {
1035	<	sprintf(painCave.errMsg,
1036	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1037	<	"\tOOPSE will use a default value of\n"
1038	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1039	<	painCave.isFatal = 0;
1040	<	simError();
1041	<	rsw_ = 0.85 * rcut_;
1042	<	}
1043	<	notifyFortranCutoffs(&rcut_, &rsw_);
1044	<	} else {
1045	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1046	<	// We'll punt and let fortran figure out the cutoffs later.
1047	<
1048	<	notifyFortranYouAreOnYourOwn();
1049	<
1050	<	}
1051	<	}
1052	<	}
1053	<
1054	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1055	<
1056	<	int errorOut;
1057	<	int esm =  NONE;
1058	<	int sm = UNDAMPED;
1059	<	RealType alphaVal;
1060	<	RealType dielectric;
1061	<
1062	<	errorOut = isError;
1063	<
1064	<	if (simParams_->haveElectrostaticSummationMethod()) {
1065	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1066	<	toUpper(myMethod);
1067	<	if (myMethod == "NONE") {
1068	<	esm = NONE;
1069	<	} else {
1070	<	if (myMethod == "SWITCHING_FUNCTION") {
1071	<	esm = SWITCHING_FUNCTION;
1072	<	} else {
1073	<	if (myMethod == "SHIFTED_POTENTIAL") {
1074	<	esm = SHIFTED_POTENTIAL;
1075	<	} else {
1076	<	if (myMethod == "SHIFTED_FORCE") {
1077	<	esm = SHIFTED_FORCE;
1078	<	} else {
1079	<	if (myMethod == "REACTION_FIELD") {
1080	<	esm = REACTION_FIELD;
1081	<	dielectric = simParams_->getDielectric();
1082	<	if (!simParams_->haveDielectric()) {
1083	<	// throw warning
1084	<	sprintf( painCave.errMsg,
1085	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1086	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1087	<	painCave.isFatal = 0;
1088	<	simError();
1089	<	}
1090	<	} else {
1091	<	// throw error
1092	<	sprintf( painCave.errMsg,
1093	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1094	<	"\t(Input file specified %s .)\n"
1095	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1096	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1097	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1098	<	painCave.isFatal = 1;
1099	<	simError();
1100	<	}
1101	<	}
1102	<	}
1103	<	}
1104	<	}
1105	<	}
1106	<
1107	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1108	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1109	<	toUpper(myScreen);
1110	<	if (myScreen == "UNDAMPED") {
1111	<	sm = UNDAMPED;
1112	<	} else {
1113	<	if (myScreen == "DAMPED") {
1114	<	sm = DAMPED;
1115	<	if (!simParams_->haveDampingAlpha()) {
1116	<	// first set a cutoff dependent alpha value
1117	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1118	<	alphaVal = 0.5125 - rcut_* 0.025;
1119	<	// for values rcut > 20.5, alpha is zero
1120	<	if (alphaVal < 0) alphaVal = 0;
1121	<
1122	<	// throw warning
1123	<	sprintf( painCave.errMsg,
1124	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1125	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1126	<	painCave.isFatal = 0;
1127	<	simError();
1128	<	}
1129	<	} else {
1130	<	// throw error
1131	<	sprintf( painCave.errMsg,
1132	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1133	<	"\t(Input file specified %s .)\n"
1134	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1135	<	"or \"damped\".\n", myScreen.c_str() );
1136	<	painCave.isFatal = 1;
1137	<	simError();
1138	<	}
1139	<	}
1140	<	}
1141	<
1142	<	// let's pass some summation method variables to fortran
1143	<	setElectrostaticSummationMethod( &esm );
1144	<	setFortranElectrostaticMethod( &esm );
1145	<	setScreeningMethod( &sm );
1146	<	setDampingAlpha( &alphaVal );
1147	<	setReactionFieldDielectric( &dielectric );
1148	<	initFortranFF( &errorOut );
970	>
971	>	topologyDone_ = true;
972		}
973
1151	–	void SimInfo::setupSwitchingFunction() {
1152	–	int ft = CUBIC;
1153	–
1154	–	if (simParams_->haveSwitchingFunctionType()) {
1155	–	std::string funcType = simParams_->getSwitchingFunctionType();
1156	–	toUpper(funcType);
1157	–	if (funcType == "CUBIC") {
1158	–	ft = CUBIC;
1159	–	} else {
1160	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1161	–	ft = FIFTH_ORDER_POLY;
1162	–	} else {
1163	–	// throw error
1164	–	sprintf( painCave.errMsg,
1165	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1166	–	painCave.isFatal = 1;
1167	–	simError();
1168	–	}
1169	–	}
1170	–	}
1171	–
1172	–	// send switching function notification to switcheroo
1173	–	setFunctionType(&ft);
1174	–
1175	–	}
1176	–
1177	–	void SimInfo::setupAccumulateBoxDipole() {
1178	–
1179	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1180	–	if ( simParams_->haveAccumulateBoxDipole() )
1181	–	if ( simParams_->getAccumulateBoxDipole() ) {
1182	–	setAccumulateBoxDipole();
1183	–	calcBoxDipole_ = true;
1184	–	}
1185	–
1186	–	}
1187	–
974		void SimInfo::addProperty(GenericData* genData) {
975		properties_.addProperty(genData);
976		}
977
978	<	void SimInfo::removeProperty(const std::string& propName) {
978	>	void SimInfo::removeProperty(const string& propName) {
979		properties_.removeProperty(propName);
980		}
981
#	Line 1197 | Line 983 | namespace oopse {
983		properties_.clearProperties();
984		}
985
986	<	std::vector<std::string> SimInfo::getPropertyNames() {
986	>	vector<string> SimInfo::getPropertyNames() {
987		return properties_.getPropertyNames();
988		}
989
990	<	std::vector<GenericData*> SimInfo::getProperties() {
990	>	vector<GenericData*> SimInfo::getProperties() {
991		return properties_.getProperties();
992		}
993
994	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
994	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
995		return properties_.getPropertyByName(propName);
996		}
997
#	Line 1216 | Line 1002 | namespace oopse {
1002		delete sman_;
1003		sman_ = sman;
1004
1219	–	Molecule* mol;
1220	–	RigidBody* rb;
1221	–	Atom* atom;
1005		SimInfo::MoleculeIterator mi;
1006	+	Molecule::AtomIterator ai;
1007		Molecule::RigidBodyIterator rbIter;
1008	<	Molecule::AtomIterator atomIter;;
1008	>	Molecule::CutoffGroupIterator cgIter;
1009	>	Molecule::BondIterator bondIter;
1010	>	Molecule::BendIterator bendIter;
1011	>	Molecule::TorsionIterator torsionIter;
1012	>	Molecule::InversionIterator inversionIter;
1013
1014	+	Molecule* mol;
1015	+	Atom* atom;
1016	+	RigidBody* rb;
1017	+	CutoffGroup* cg;
1018	+	Bond* bond;
1019	+	Bend* bend;
1020	+	Torsion* torsion;
1021	+	Inversion* inversion;
1022	+
1023		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1024
1025	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1025	>	for (atom = mol->beginAtom(ai); atom != NULL;
1026	>	atom = mol->nextAtom(ai)) {
1027		atom->setSnapshotManager(sman_);
1028	<	}
1029	<
1030	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1028	>	}
1029	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1030	>	rb = mol->nextRigidBody(rbIter)) {
1031		rb->setSnapshotManager(sman_);
1032		}
1033	<	}
1034	<
1033	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1034	>	cg = mol->nextCutoffGroup(cgIter)) {
1035	>	cg->setSnapshotManager(sman_);
1036	>	}
1037	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1038	>	bond = mol->nextBond(bondIter)) {
1039	>	bond->setSnapshotManager(sman_);
1040	>	}
1041	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1042	>	bend = mol->nextBend(bendIter)) {
1043	>	bend->setSnapshotManager(sman_);
1044	>	}
1045	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1046	>	torsion = mol->nextTorsion(torsionIter)) {
1047	>	torsion->setSnapshotManager(sman_);
1048	>	}
1049	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1050	>	inversion = mol->nextInversion(inversionIter)) {
1051	>	inversion->setSnapshotManager(sman_);
1052	>	}
1053	>	}
1054		}
1055
1239	–	Vector3d SimInfo::getComVel(){
1240	–	SimInfo::MoleculeIterator i;
1241	–	Molecule* mol;
1056
1057	<	Vector3d comVel(0.0);
1244	<	RealType totalMass = 0.0;
1245	<
1246	<
1247	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1248	<	RealType mass = mol->getMass();
1249	<	totalMass += mass;
1250	<	comVel += mass * mol->getComVel();
1251	<	}
1252	<
1253	<	#ifdef IS_MPI
1254	<	RealType tmpMass = totalMass;
1255	<	Vector3d tmpComVel(comVel);
1256	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1257	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258	<	#endif
1259	<
1260	<	comVel /= totalMass;
1261	<
1262	<	return comVel;
1263	<	}
1264	<
1265	<	Vector3d SimInfo::getCom(){
1266	<	SimInfo::MoleculeIterator i;
1267	<	Molecule* mol;
1057	>	ostream& operator <<(ostream& o, SimInfo& info) {
1058
1269	–	Vector3d com(0.0);
1270	–	RealType totalMass = 0.0;
1271	–
1272	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1273	–	RealType mass = mol->getMass();
1274	–	totalMass += mass;
1275	–	com += mass * mol->getCom();
1276	–	}
1277	–
1278	–	#ifdef IS_MPI
1279	–	RealType tmpMass = totalMass;
1280	–	Vector3d tmpCom(com);
1281	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1282	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1283	–	#endif
1284	–
1285	–	com /= totalMass;
1286	–
1287	–	return com;
1288	–
1289	–	}
1290	–
1291	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1292	–
1059		return o;
1060		}
1061
1062	<
1297	<	/*
1298	<	Returns center of mass and center of mass velocity in one function call.
1299	<	*/
1300	<
1301	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1302	<	SimInfo::MoleculeIterator i;
1303	<	Molecule* mol;
1304	<
1305	<
1306	<	RealType totalMass = 0.0;
1307	<
1308	<
1309	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1310	<	RealType mass = mol->getMass();
1311	<	totalMass += mass;
1312	<	com += mass * mol->getCom();
1313	<	comVel += mass * mol->getComVel();
1314	<	}
1315	<
1316	<	#ifdef IS_MPI
1317	<	RealType tmpMass = totalMass;
1318	<	Vector3d tmpCom(com);
1319	<	Vector3d tmpComVel(comVel);
1320	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1321	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323	<	#endif
1324	<
1325	<	com /= totalMass;
1326	<	comVel /= totalMass;
1327	<	}
1328	<
1329	<	/*
1330	<	Return intertia tensor for entire system and angular momentum Vector.
1331	<
1332	<
1333	<	[  Ixx -Ixy  -Ixz ]
1334	<	J =| -Iyx  Iyy  -Iyz |
1335	<	[ -Izx -Iyz   Izz ]
1336	<	*/
1337	<
1338	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1339	<
1340	<
1341	<	RealType xx = 0.0;
1342	<	RealType yy = 0.0;
1343	<	RealType zz = 0.0;
1344	<	RealType xy = 0.0;
1345	<	RealType xz = 0.0;
1346	<	RealType yz = 0.0;
1347	<	Vector3d com(0.0);
1348	<	Vector3d comVel(0.0);
1349	<
1350	<	getComAll(com, comVel);
1351	<
1352	<	SimInfo::MoleculeIterator i;
1353	<	Molecule* mol;
1354	<
1355	<	Vector3d thisq(0.0);
1356	<	Vector3d thisv(0.0);
1357	<
1358	<	RealType thisMass = 0.0;
1359	<
1360	<
1361	<
1362	<
1363	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1364	<
1365	<	thisq = mol->getCom()-com;
1366	<	thisv = mol->getComVel()-comVel;
1367	<	thisMass = mol->getMass();
1368	<	// Compute moment of intertia coefficients.
1369	<	xx += thisq[0]*thisq[0]*thisMass;
1370	<	yy += thisq[1]*thisq[1]*thisMass;
1371	<	zz += thisq[2]*thisq[2]*thisMass;
1372	<
1373	<	// compute products of intertia
1374	<	xy += thisq[0]*thisq[1]*thisMass;
1375	<	xz += thisq[0]*thisq[2]*thisMass;
1376	<	yz += thisq[1]*thisq[2]*thisMass;
1377	<
1378	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1379	<
1380	<	}
1381	<
1382	<
1383	<	inertiaTensor(0,0) = yy + zz;
1384	<	inertiaTensor(0,1) = -xy;
1385	<	inertiaTensor(0,2) = -xz;
1386	<	inertiaTensor(1,0) = -xy;
1387	<	inertiaTensor(1,1) = xx + zz;
1388	<	inertiaTensor(1,2) = -yz;
1389	<	inertiaTensor(2,0) = -xz;
1390	<	inertiaTensor(2,1) = -yz;
1391	<	inertiaTensor(2,2) = xx + yy;
1392	<
1393	<	#ifdef IS_MPI
1394	<	Mat3x3d tmpI(inertiaTensor);
1395	<	Vector3d tmpAngMom;
1396	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1397	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398	<	#endif
1399	<
1400	<	return;
1401	<	}
1402	<
1403	<	//Returns the angular momentum of the system
1404	<	Vector3d SimInfo::getAngularMomentum(){
1405	<
1406	<	Vector3d com(0.0);
1407	<	Vector3d comVel(0.0);
1408	<	Vector3d angularMomentum(0.0);
1409	<
1410	<	getComAll(com,comVel);
1411	<
1412	<	SimInfo::MoleculeIterator i;
1413	<	Molecule* mol;
1414	<
1415	<	Vector3d thisr(0.0);
1416	<	Vector3d thisp(0.0);
1417	<
1418	<	RealType thisMass;
1419	<
1420	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1421	<	thisMass = mol->getMass();
1422	<	thisr = mol->getCom()-com;
1423	<	thisp = (mol->getComVel()-comVel)*thisMass;
1424	<
1425	<	angularMomentum += cross( thisr, thisp );
1426	<
1427	<	}
1428	<
1429	<	#ifdef IS_MPI
1430	<	Vector3d tmpAngMom;
1431	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1432	<	#endif
1433	<
1434	<	return angularMomentum;
1435	<	}
1436	<
1062	>
1063		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1064	<	return IOIndexToIntegrableObject.at(index);
1064	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1065	>	sprintf(painCave.errMsg,
1066	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1067	>	"\tindex exceeds number of known objects!\n");
1068	>	painCave.isFatal = 1;
1069	>	simError();
1070	>	return NULL;
1071	>	} else
1072	>	return IOIndexToIntegrableObject.at(index);
1073		}
1074
1075	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1075	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1076		IOIndexToIntegrableObject= v;
1077		}
1078
1079	<	/*
1080	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1081	<	assert( v.size() == nAtoms_ + nRigidBodies_);
1082	<	sdByGlobalIndex_ = v;
1083	<	}
1079	>	void SimInfo::calcNConstraints() {
1080	>	#ifdef IS_MPI
1081	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1082	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1083	>	#else
1084	>	nGlobalConstraints_ =  nConstraints_;
1085	>	#endif
1086	>	}
1087
1088	<	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1452	<	//assert(index < nAtoms_ + nRigidBodies_);
1453	<	return sdByGlobalIndex_.at(index);
1454	<	}
1455	<	*/
1456	<	}//end namespace oopse
1088	>	}//end namespace OpenMD
1089

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

#	Line 0 | Line 1
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