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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
74	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
75	>	nConstraints_(0), nFluctuatingCharges_(0),
76		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
79	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
80	<	sman_(NULL), fortranInitialized_(false) {
77	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
79	>	nGlobalTorsions_(0), nGlobalInversions_(0), nGlobalConstraints_(0),
80	>	hasNGlobalConstraints_(false),
81	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82	>	sman_(NULL), topologyDone_(false), calcBoxDipole_(false),
83	>	calcBoxQuadrupole_(false), useAtomicVirial_(true) {
84	>
85	>	MoleculeStamp* molStamp;
86	>	int nMolWithSameStamp;
87	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
89	>	CutoffGroupStamp* cgStamp;
90	>	RigidBodyStamp* rbStamp;
91	>	int nRigidAtoms = 0;
92	>
93	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin();
96	>	i !=components.end(); ++i) {
97	>	molStamp = (*i)->getMoleculeStamp();
98	>	if ( (*i)->haveRegion() ) {
99	>	molStamp->setRegion( (*i)->getRegion() );
100	>	} else {
101	>	// set the region to a disallowed value:
102	>	molStamp->setRegion( -1 );
103	>	}
104
105	<	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();
105	>	nMolWithSameStamp = (*i)->getNMol();
106
107	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108	<	molStamp = (*i)->getMoleculeStamp();
109	<	nMolWithSameStamp = (*i)->getNMol();
110	<
111	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
112	<
113	<	//calculate atoms in molecules
114	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
115	<
116	<	//calculate atoms in cutoff groups
117	<	int nAtomsInGroups = 0;
118	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	<
120	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroupStamp(j);
122	<	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	<
107	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
108	>
109	>	//calculate atoms in molecules
110	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
111	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
112	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
113	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
114	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
115	>
116	>	//calculate atoms in cutoff groups
117	>	int nAtomsInGroups = 0;
118	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	>
120	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122	>	nAtomsInGroups += cgStamp->getNMembers();
123		}
124	<
125	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
126	<	//group therefore the total number of cutoff groups in the system is
127	<	//equal to the total number of atoms minus number of atoms belong to
128	<	//cutoff group defined in meta-data file plus the number of cutoff
129	<	//groups defined in meta-data file
130	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
131	<
132	<	//every free atom (atom does not belong to rigid bodies) is an
133	<	//integrable object therefore the total number of integrable objects
134	<	//in the system is equal to the total number of atoms minus number of
135	<	//atoms belong to rigid body defined in meta-data file plus the number
136	<	//of rigid bodies defined in meta-data file
137	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
138	<	+ nGlobalRigidBodies_;
139	<
140	<	nGlobalMols_ = molStampIds_.size();
155	<
156	<	#ifdef IS_MPI
157	<	molToProcMap_.resize(nGlobalMols_);
158	<	#endif
159	<
124	>
125	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	>
127	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128	>
129	>	//calculate atoms in rigid bodies
130	>	int nAtomsInRigidBodies = 0;
131	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	>
133	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135	>	nAtomsInRigidBodies += rbStamp->getNMembers();
136	>	}
137	>
138	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	>
141		}
142	+
143	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	+	//group therefore the total number of cutoff groups in the system is
145	+	//equal to the total number of atoms minus number of atoms belong to
146	+	//cutoff group defined in meta-data file plus the number of cutoff
147	+	//groups defined in meta-data file
148
149	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
150	+
151	+	//every free atom (atom does not belong to rigid bodies) is an
152	+	//integrable object therefore the total number of integrable objects
153	+	//in the system is equal to the total number of atoms minus number of
154	+	//atoms belong to rigid body defined in meta-data file plus the number
155	+	//of rigid bodies defined in meta-data file
156	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
157	+	+ nGlobalRigidBodies_;
158	+
159	+	nGlobalMols_ = molStampIds_.size();
160	+	molToProcMap_.resize(nGlobalMols_);
161	+	}
162	+
163		SimInfo::~SimInfo() {
164	<	std::map<int, Molecule*>::iterator i;
164	>	map<int, Molecule*>::iterator i;
165		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
166		delete i->second;
167		}
#	Line 171 | Line 172 | namespace oopse {
172		delete forceField_;
173		}
174
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	–	}
175
176		bool SimInfo::addMolecule(Molecule* mol) {
177		MoleculeIterator i;
178	<
178	>
179		i = molecules_.find(mol->getGlobalIndex());
180		if (i == molecules_.end() ) {
181	<
182	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
183	<
181	>
182	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
183	>
184		nAtoms_ += mol->getNAtoms();
185		nBonds_ += mol->getNBonds();
186		nBends_ += mol->getNBends();
187		nTorsions_ += mol->getNTorsions();
188	+	nInversions_ += mol->getNInversions();
189		nRigidBodies_ += mol->getNRigidBodies();
190		nIntegrableObjects_ += mol->getNIntegrableObjects();
191		nCutoffGroups_ += mol->getNCutoffGroups();
192		nConstraints_ += mol->getNConstraintPairs();
193	<
194	<	addExcludePairs(mol);
195	<
193	>
194	>	addInteractionPairs(mol);
195	>
196		return true;
197		} else {
198		return false;
199		}
200		}
201	<
201	>
202		bool SimInfo::removeMolecule(Molecule* mol) {
203		MoleculeIterator i;
204		i = molecules_.find(mol->getGlobalIndex());
#	Line 219 | Line 211 | namespace oopse {
211		nBonds_ -= mol->getNBonds();
212		nBends_ -= mol->getNBends();
213		nTorsions_ -= mol->getNTorsions();
214	+	nInversions_ -= mol->getNInversions();
215		nRigidBodies_ -= mol->getNRigidBodies();
216		nIntegrableObjects_ -= mol->getNIntegrableObjects();
217		nCutoffGroups_ -= mol->getNCutoffGroups();
218		nConstraints_ -= mol->getNConstraintPairs();
219
220	<	removeExcludePairs(mol);
220	>	removeInteractionPairs(mol);
221		molecules_.erase(mol->getGlobalIndex());
222
223		delete mol;
#	Line 233 | Line 226 | namespace oopse {
226		} else {
227		return false;
228		}
236	–
237	–
229		}
230
231
#	Line 250 | Line 241 | namespace oopse {
241
242
243		void SimInfo::calcNdf() {
244	<	int ndf_local;
244	>	int ndf_local, nfq_local;
245		MoleculeIterator i;
246	<	std::vector<StuntDouble*>::iterator j;
246	>	vector<StuntDouble*>::iterator j;
247	>	vector<Atom*>::iterator k;
248	>
249		Molecule* mol;
250	<	StuntDouble* integrableObject;
250	>	StuntDouble* sd;
251	>	Atom* atom;
252
253		ndf_local = 0;
254	+	nfq_local = 0;
255
256		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
262	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	–	integrableObject = mol->nextIntegrableObject(j)) {
257
258	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
259	+	sd = mol->nextIntegrableObject(j)) {
260	+
261		ndf_local += 3;
262
263	<	if (integrableObject->isDirectional()) {
264	<	if (integrableObject->isLinear()) {
263	>	if (sd->isDirectional()) {
264	>	if (sd->isLinear()) {
265		ndf_local += 2;
266		} else {
267		ndf_local += 3;
268		}
269		}
274	–
270		}
271	+
272	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
273	+	atom = mol->nextFluctuatingCharge(k)) {
274	+	if (atom->isFluctuatingCharge()) {
275	+	nfq_local++;
276	+	}
277	+	}
278		}
279
280	+	ndfLocal_ = ndf_local;
281	+
282		// n_constraints is local, so subtract them on each processor
283		ndf_local -= nConstraints_;
284
285		#ifdef IS_MPI
286	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
286	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
288	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
289		#else
290		ndf_ = ndf_local;
291	+	nGlobalFluctuatingCharges_ = nfq_local;
292		#endif
293
294		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 292 | Line 299 | namespace oopse {
299
300		int SimInfo::getFdf() {
301		#ifdef IS_MPI
302	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
302	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
303		#else
304		fdf_ = fdf_local;
305		#endif
306		return fdf_;
307		}
308	+
309	+	unsigned int SimInfo::getNLocalCutoffGroups(){
310	+	int nLocalCutoffAtoms = 0;
311	+	Molecule* mol;
312	+	MoleculeIterator mi;
313	+	CutoffGroup* cg;
314	+	Molecule::CutoffGroupIterator ci;
315
316	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
317	+
318	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
319	+	cg = mol->nextCutoffGroup(ci)) {
320	+	nLocalCutoffAtoms += cg->getNumAtom();
321	+
322	+	}
323	+	}
324	+
325	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
326	+	}
327	+
328		void SimInfo::calcNdfRaw() {
329		int ndfRaw_local;
330
331		MoleculeIterator i;
332	<	std::vector<StuntDouble*>::iterator j;
332	>	vector<StuntDouble*>::iterator j;
333		Molecule* mol;
334	<	StuntDouble* integrableObject;
334	>	StuntDouble* sd;
335
336		// Raw degrees of freedom that we have to set
337		ndfRaw_local = 0;
338
339		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
314	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
315	–	integrableObject = mol->nextIntegrableObject(j)) {
340
341	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
342	+	sd = mol->nextIntegrableObject(j)) {
343	+
344		ndfRaw_local += 3;
345
346	<	if (integrableObject->isDirectional()) {
347	<	if (integrableObject->isLinear()) {
346	>	if (sd->isDirectional()) {
347	>	if (sd->isLinear()) {
348		ndfRaw_local += 2;
349		} else {
350		ndfRaw_local += 3;
#	Line 328 | Line 355 | namespace oopse {
355		}
356
357		#ifdef IS_MPI
358	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
358	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
359		#else
360		ndfRaw_ = ndfRaw_local;
361		#endif
#	Line 339 | Line 366 | namespace oopse {
366
367		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
368
342	–
369		#ifdef IS_MPI
370	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
370	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
371	>	MPI_COMM_WORLD);
372		#else
373		ndfTrans_ = ndfTrans_local;
374		#endif
375
376		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
350	–
377		}
378
379	<	void SimInfo::addExcludePairs(Molecule* mol) {
380	<	std::vector<Bond*>::iterator bondIter;
381	<	std::vector<Bend*>::iterator bendIter;
382	<	std::vector<Torsion*>::iterator torsionIter;
379	>	void SimInfo::addInteractionPairs(Molecule* mol) {
380	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
381	>	vector<Bond*>::iterator bondIter;
382	>	vector<Bend*>::iterator bendIter;
383	>	vector<Torsion*>::iterator torsionIter;
384	>	vector<Inversion*>::iterator inversionIter;
385		Bond* bond;
386		Bend* bend;
387		Torsion* torsion;
388	+	Inversion* inversion;
389		int a;
390		int b;
391		int c;
392		int d;
393
394	<	std::map<int, std::set<int> > atomGroups;
394	>	// atomGroups can be used to add special interaction maps between
395	>	// groups of atoms that are in two separate rigid bodies.
396	>	// However, most site-site interactions between two rigid bodies
397	>	// are probably not special, just the ones between the physically
398	>	// bonded atoms.  Interactions *within* a single rigid body should
399	>	// always be excluded.  These are done at the bottom of this
400	>	// function.
401
402	+	map<int, set<int> > atomGroups;
403		Molecule::RigidBodyIterator rbIter;
404		RigidBody* rb;
405		Molecule::IntegrableObjectIterator ii;
406	<	StuntDouble* integrableObject;
406	>	StuntDouble* sd;
407
408	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
409	<	integrableObject = mol->nextIntegrableObject(ii)) {
410	<
411	<	if (integrableObject->isRigidBody()) {
412	<	rb = static_cast<RigidBody*>(integrableObject);
413	<	std::vector<Atom*> atoms = rb->getAtoms();
414	<	std::set<int> rigidAtoms;
415	<	for (int i = 0; i < atoms.size(); ++i) {
416	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
417	<	}
418	<	for (int i = 0; i < atoms.size(); ++i) {
419	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
420	<	}
408	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
409	>	sd = mol->nextIntegrableObject(ii)) {
410	>
411	>	if (sd->isRigidBody()) {
412	>	rb = static_cast<RigidBody*>(sd);
413	>	vector<Atom*> atoms = rb->getAtoms();
414	>	set<int> rigidAtoms;
415	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
416	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
417	>	}
418	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
419	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
420	>	}
421		} else {
422	<	std::set<int> oneAtomSet;
423	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
424	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
422	>	set<int> oneAtomSet;
423	>	oneAtomSet.insert(sd->getGlobalIndex());
424	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
425		}
426		}
427
428	<
429	<
430	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
428	>
429	>	for (bond= mol->beginBond(bondIter); bond != NULL;
430	>	bond = mol->nextBond(bondIter)) {
431	>
432		a = bond->getAtomA()->getGlobalIndex();
433	<	b = bond->getAtomB()->getGlobalIndex();
434	<	exclude_.addPair(a, b);
433	>	b = bond->getAtomB()->getGlobalIndex();
434	>
435	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436	>	oneTwoInteractions_.addPair(a, b);
437	>	} else {
438	>	excludedInteractions_.addPair(a, b);
439	>	}
440		}
441
442	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
442	>	for (bend= mol->beginBend(bendIter); bend != NULL;
443	>	bend = mol->nextBend(bendIter)) {
444	>
445		a = bend->getAtomA()->getGlobalIndex();
446		b = bend->getAtomB()->getGlobalIndex();
447		c = bend->getAtomC()->getGlobalIndex();
404	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407	–
408	–	exclude_.addPairs(rigidSetA, rigidSetB);
409	–	exclude_.addPairs(rigidSetA, rigidSetC);
410	–	exclude_.addPairs(rigidSetB, rigidSetC);
448
449	<	//exclude_.addPair(a, b);
450	<	//exclude_.addPair(a, c);
451	<	//exclude_.addPair(b, c);
449	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
450	>	oneTwoInteractions_.addPair(a, b);
451	>	oneTwoInteractions_.addPair(b, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, b);
454	>	excludedInteractions_.addPair(b, c);
455	>	}
456	>
457	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
458	>	oneThreeInteractions_.addPair(a, c);
459	>	} else {
460	>	excludedInteractions_.addPair(a, c);
461	>	}
462		}
463
464	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
464	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
465	>	torsion = mol->nextTorsion(torsionIter)) {
466	>
467		a = torsion->getAtomA()->getGlobalIndex();
468		b = torsion->getAtomB()->getGlobalIndex();
469		c = torsion->getAtomC()->getGlobalIndex();
470	<	d = torsion->getAtomD()->getGlobalIndex();
422	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
470	>	d = torsion->getAtomD()->getGlobalIndex();
471
472	<	exclude_.addPairs(rigidSetA, rigidSetB);
473	<	exclude_.addPairs(rigidSetA, rigidSetC);
474	<	exclude_.addPairs(rigidSetA, rigidSetD);
475	<	exclude_.addPairs(rigidSetB, rigidSetC);
476	<	exclude_.addPairs(rigidSetB, rigidSetD);
477	<	exclude_.addPairs(rigidSetC, rigidSetD);
472	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
473	>	oneTwoInteractions_.addPair(a, b);
474	>	oneTwoInteractions_.addPair(b, c);
475	>	oneTwoInteractions_.addPair(c, d);
476	>	} else {
477	>	excludedInteractions_.addPair(a, b);
478	>	excludedInteractions_.addPair(b, c);
479	>	excludedInteractions_.addPair(c, d);
480	>	}
481
482	<	/*
483	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
484	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
485	<	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
486	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
487	<	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
488	<	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
489	<
490	<
491	<	exclude_.addPair(a, b);
492	<	exclude_.addPair(a, c);
493	<	exclude_.addPair(a, d);
494	<	exclude_.addPair(b, c);
447	<	exclude_.addPair(b, d);
448	<	exclude_.addPair(c, d);
449	<	*/
482	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
483	>	oneThreeInteractions_.addPair(a, c);
484	>	oneThreeInteractions_.addPair(b, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, c);
487	>	excludedInteractions_.addPair(b, d);
488	>	}
489	>
490	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
491	>	oneFourInteractions_.addPair(a, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, d);
494	>	}
495		}
496
497	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
498	<	std::vector<Atom*> atoms = rb->getAtoms();
499	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
500	<	for (int j = i + 1; j < atoms.size(); ++j) {
497	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
498	>	inversion = mol->nextInversion(inversionIter)) {
499	>
500	>	a = inversion->getAtomA()->getGlobalIndex();
501	>	b = inversion->getAtomB()->getGlobalIndex();
502	>	c = inversion->getAtomC()->getGlobalIndex();
503	>	d = inversion->getAtomD()->getGlobalIndex();
504	>
505	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
506	>	oneTwoInteractions_.addPair(a, b);
507	>	oneTwoInteractions_.addPair(a, c);
508	>	oneTwoInteractions_.addPair(a, d);
509	>	} else {
510	>	excludedInteractions_.addPair(a, b);
511	>	excludedInteractions_.addPair(a, c);
512	>	excludedInteractions_.addPair(a, d);
513	>	}
514	>
515	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
516	>	oneThreeInteractions_.addPair(b, c);
517	>	oneThreeInteractions_.addPair(b, d);
518	>	oneThreeInteractions_.addPair(c, d);
519	>	} else {
520	>	excludedInteractions_.addPair(b, c);
521	>	excludedInteractions_.addPair(b, d);
522	>	excludedInteractions_.addPair(c, d);
523	>	}
524	>	}
525	>
526	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
527	>	rb = mol->nextRigidBody(rbIter)) {
528	>	vector<Atom*> atoms = rb->getAtoms();
529	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
530	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
531		a = atoms[i]->getGlobalIndex();
532		b = atoms[j]->getGlobalIndex();
533	<	exclude_.addPair(a, b);
533	>	excludedInteractions_.addPair(a, b);
534		}
535		}
536		}
537
538		}
539
540	<	void SimInfo::removeExcludePairs(Molecule* mol) {
541	<	std::vector<Bond*>::iterator bondIter;
542	<	std::vector<Bend*>::iterator bendIter;
543	<	std::vector<Torsion*>::iterator torsionIter;
540	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
541	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
542	>	vector<Bond*>::iterator bondIter;
543	>	vector<Bend*>::iterator bendIter;
544	>	vector<Torsion*>::iterator torsionIter;
545	>	vector<Inversion*>::iterator inversionIter;
546		Bond* bond;
547		Bend* bend;
548		Torsion* torsion;
549	+	Inversion* inversion;
550		int a;
551		int b;
552		int c;
553		int d;
554
555	<	std::map<int, std::set<int> > atomGroups;
478	<
555	>	map<int, set<int> > atomGroups;
556		Molecule::RigidBodyIterator rbIter;
557		RigidBody* rb;
558		Molecule::IntegrableObjectIterator ii;
559	<	StuntDouble* integrableObject;
559	>	StuntDouble* sd;
560
561	<	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
562	<	integrableObject = mol->nextIntegrableObject(ii)) {
563	<
564	<	if (integrableObject->isRigidBody()) {
565	<	rb = static_cast<RigidBody*>(integrableObject);
566	<	std::vector<Atom*> atoms = rb->getAtoms();
567	<	std::set<int> rigidAtoms;
568	<	for (int i = 0; i < atoms.size(); ++i) {
569	<	rigidAtoms.insert(atoms[i]->getGlobalIndex());
570	<	}
571	<	for (int i = 0; i < atoms.size(); ++i) {
572	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
573	<	}
561	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
562	>	sd = mol->nextIntegrableObject(ii)) {
563	>
564	>	if (sd->isRigidBody()) {
565	>	rb = static_cast<RigidBody*>(sd);
566	>	vector<Atom*> atoms = rb->getAtoms();
567	>	set<int> rigidAtoms;
568	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
569	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
570	>	}
571	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
572	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
573	>	}
574		} else {
575	<	std::set<int> oneAtomSet;
576	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
577	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
575	>	set<int> oneAtomSet;
576	>	oneAtomSet.insert(sd->getGlobalIndex());
577	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
578		}
579		}
580
581	<
582	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
581	>	for (bond= mol->beginBond(bondIter); bond != NULL;
582	>	bond = mol->nextBond(bondIter)) {
583	>
584		a = bond->getAtomA()->getGlobalIndex();
585	<	b = bond->getAtomB()->getGlobalIndex();
586	<	exclude_.removePair(a, b);
585	>	b = bond->getAtomB()->getGlobalIndex();
586	>
587	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
588	>	oneTwoInteractions_.removePair(a, b);
589	>	} else {
590	>	excludedInteractions_.removePair(a, b);
591	>	}
592		}
593
594	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
594	>	for (bend= mol->beginBend(bendIter); bend != NULL;
595	>	bend = mol->nextBend(bendIter)) {
596	>
597		a = bend->getAtomA()->getGlobalIndex();
598		b = bend->getAtomB()->getGlobalIndex();
599		c = bend->getAtomC()->getGlobalIndex();
515	–
516	–	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	–	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	–	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	–
520	–	exclude_.removePairs(rigidSetA, rigidSetB);
521	–	exclude_.removePairs(rigidSetA, rigidSetC);
522	–	exclude_.removePairs(rigidSetB, rigidSetC);
600
601	<	//exclude_.removePair(a, b);
602	<	//exclude_.removePair(a, c);
603	<	//exclude_.removePair(b, c);
601	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
602	>	oneTwoInteractions_.removePair(a, b);
603	>	oneTwoInteractions_.removePair(b, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, b);
606	>	excludedInteractions_.removePair(b, c);
607	>	}
608	>
609	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
610	>	oneThreeInteractions_.removePair(a, c);
611	>	} else {
612	>	excludedInteractions_.removePair(a, c);
613	>	}
614		}
615
616	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
616	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
617	>	torsion = mol->nextTorsion(torsionIter)) {
618	>
619		a = torsion->getAtomA()->getGlobalIndex();
620		b = torsion->getAtomB()->getGlobalIndex();
621		c = torsion->getAtomC()->getGlobalIndex();
622	<	d = torsion->getAtomD()->getGlobalIndex();
622	>	d = torsion->getAtomD()->getGlobalIndex();
623	>
624	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
625	>	oneTwoInteractions_.removePair(a, b);
626	>	oneTwoInteractions_.removePair(b, c);
627	>	oneTwoInteractions_.removePair(c, d);
628	>	} else {
629	>	excludedInteractions_.removePair(a, b);
630	>	excludedInteractions_.removePair(b, c);
631	>	excludedInteractions_.removePair(c, d);
632	>	}
633
634	<	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
635	<	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
636	<	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
637	<	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
634	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
635	>	oneThreeInteractions_.removePair(a, c);
636	>	oneThreeInteractions_.removePair(b, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, c);
639	>	excludedInteractions_.removePair(b, d);
640	>	}
641
642	<	exclude_.removePairs(rigidSetA, rigidSetB);
643	<	exclude_.removePairs(rigidSetA, rigidSetC);
644	<	exclude_.removePairs(rigidSetA, rigidSetD);
645	<	exclude_.removePairs(rigidSetB, rigidSetC);
646	<	exclude_.removePairs(rigidSetB, rigidSetD);
647	<	exclude_.removePairs(rigidSetC, rigidSetD);
642	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
643	>	oneFourInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, d);
646	>	}
647	>	}
648
649	<	/*
650	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	<	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	<	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	<	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
649	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
650	>	inversion = mol->nextInversion(inversionIter)) {
651
652	<
653	<	exclude_.removePair(a, b);
654	<	exclude_.removePair(a, c);
655	<	exclude_.removePair(a, d);
656	<	exclude_.removePair(b, c);
657	<	exclude_.removePair(b, d);
658	<	exclude_.removePair(c, d);
659	<	*/
652	>	a = inversion->getAtomA()->getGlobalIndex();
653	>	b = inversion->getAtomB()->getGlobalIndex();
654	>	c = inversion->getAtomC()->getGlobalIndex();
655	>	d = inversion->getAtomD()->getGlobalIndex();
656	>
657	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
658	>	oneTwoInteractions_.removePair(a, b);
659	>	oneTwoInteractions_.removePair(a, c);
660	>	oneTwoInteractions_.removePair(a, d);
661	>	} else {
662	>	excludedInteractions_.removePair(a, b);
663	>	excludedInteractions_.removePair(a, c);
664	>	excludedInteractions_.removePair(a, d);
665	>	}
666	>
667	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
668	>	oneThreeInteractions_.removePair(b, c);
669	>	oneThreeInteractions_.removePair(b, d);
670	>	oneThreeInteractions_.removePair(c, d);
671	>	} else {
672	>	excludedInteractions_.removePair(b, c);
673	>	excludedInteractions_.removePair(b, d);
674	>	excludedInteractions_.removePair(c, d);
675	>	}
676		}
677
678	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
679	<	std::vector<Atom*> atoms = rb->getAtoms();
680	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
681	<	for (int j = i + 1; j < atoms.size(); ++j) {
678	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
679	>	rb = mol->nextRigidBody(rbIter)) {
680	>	vector<Atom*> atoms = rb->getAtoms();
681	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
682	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
683		a = atoms[i]->getGlobalIndex();
684		b = atoms[j]->getGlobalIndex();
685	<	exclude_.removePair(a, b);
685	>	excludedInteractions_.removePair(a, b);
686		}
687		}
688		}
689	<
689	>
690		}
691	<
692	<
691	>
692	>
693		void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
694		int curStampId;
695	<
695	>
696		//index from 0
697		curStampId = moleculeStamps_.size();
698
#	Line 586 | Line 700 | namespace oopse {
700		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
701		}
702
589	–	void SimInfo::update() {
703
704	<	setupSimType();
705	<
706	<	#ifdef IS_MPI
707	<	setupFortranParallel();
708	<	#endif
709	<
710	<	setupFortranSim();
711	<
712	<	//setup fortran force field
713	<	/** @deprecate */
601	<	int isError = 0;
602	<
603	<	setupElectrostaticSummationMethod( isError );
604	<	setupSwitchingFunction();
605	<
606	<	if(isError){
607	<	sprintf( painCave.errMsg,
608	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
609	<	painCave.isFatal = 1;
610	<	simError();
611	<	}
612	<
613	<
614	<	setupCutoff();
615	<
704	>	/**
705	>	* update
706	>	*
707	>	*  Performs the global checks and variable settings after the
708	>	*  objects have been created.
709	>	*
710	>	*/
711	>	void SimInfo::update() {
712	>	setupSimVariables();
713	>	calcNConstraints();
714		calcNdf();
715		calcNdfRaw();
716		calcNdfTrans();
619	–
620	–	fortranInitialized_ = true;
717		}
718	<
719	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
718	>
719	>	/**
720	>	* getSimulatedAtomTypes
721	>	*
722	>	* Returns an STL set of AtomType* that are actually present in this
723	>	* simulation.  Must query all processors to assemble this information.
724	>	*
725	>	*/
726	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
727		SimInfo::MoleculeIterator mi;
728		Molecule* mol;
729		Molecule::AtomIterator ai;
730		Atom* atom;
731	<	std::set<AtomType*> atomTypes;
732	<
731	>	set<AtomType*> atomTypes;
732	>
733		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
734	<
735	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
734	>	for(atom = mol->beginAtom(ai); atom != NULL;
735	>	atom = mol->nextAtom(ai)) {
736		atomTypes.insert(atom->getAtomType());
737	<	}
738	<
737	>	}
738	>	}
739	>
740	>	#ifdef IS_MPI
741	>
742	>	// loop over the found atom types on this processor, and add their
743	>	// numerical idents to a vector:
744	>
745	>	vector<int> foundTypes;
746	>	set<AtomType*>::iterator i;
747	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
748	>	foundTypes.push_back( (*i)->getIdent() );
749	>
750	>	// count_local holds the number of found types on this processor
751	>	int count_local = foundTypes.size();
752	>
753	>	int nproc;
754	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
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	>
765	>	// use the processor counts to compute the displacement array
766	>	disps[0] = 0;
767	>	int totalCount = counts[0];
768	>	for (int iproc = 1; iproc < nproc; iproc++) {
769	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
770	>	totalCount += counts[iproc];
771		}
772
773	<	return atomTypes;
774	<	}
773	>	// we need a (possibly redundant) set of all found types:
774	>	vector<int> ftGlobal(totalCount);
775	>
776	>	// now spray out the foundTypes to all the other processors:
777	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
778	>	&ftGlobal[0], &counts[0], &disps[0],
779	>	MPI_INT, MPI_COMM_WORLD);
780
781	<	void SimInfo::setupSimType() {
782	<	std::set<AtomType*>::iterator i;
783	<	std::set<AtomType*> atomTypes;
784	<	atomTypes = getUniqueAtomTypes();
781	>	vector<int>::iterator j;
782	>
783	>	// foundIdents is a stl set, so inserting an already found ident
784	>	// will have no effect.
785	>	set<int> foundIdents;
786	>
787	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
788	>	foundIdents.insert((*j));
789
790	<	int useLennardJones = 0;
791	<	int useElectrostatic = 0;
792	<	int useEAM = 0;
793	<	int useSC = 0;
794	<	int useCharge = 0;
795	<	int useDirectional = 0;
796	<	int useDipole = 0;
653	<	int useGayBerne = 0;
654	<	int useSticky = 0;
655	<	int useStickyPower = 0;
656	<	int useShape = 0;
657	<	int useFLARB = 0; //it is not in AtomType yet
658	<	int useDirectionalAtom = 0;
659	<	int useElectrostatics = 0;
660	<	//usePBC and useRF are from simParams
661	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662	<	int useRF;
663	<	int useSF;
664	<	std::string myMethod;
790	>	// now iterate over the foundIdents and get the actual atom types
791	>	// that correspond to these:
792	>	set<int>::iterator it;
793	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
794	>	atomTypes.insert( forceField_->getAtomType((*it)) );
795	>
796	>	#endif
797
798	<	// set the useRF logical
799	<	useRF = 0;
668	<	useSF = 0;
798	>	return atomTypes;
799	>	}
800
801
802	<	if (simParams_->haveElectrostaticSummationMethod()) {
803	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
804	<	toUpper(myMethod);
805	<	if (myMethod == "REACTION_FIELD") {
806	<	useRF=1;
807	<	} else {
808	<	if (myMethod == "SHIFTED_FORCE") {
809	<	useSF = 1;
810	<	}
811	<	}
812	<	}
802	>	int getGlobalCountOfType(AtomType* atype) {
803	>	/*
804	>	set<AtomType*> atypes = getSimulatedAtomTypes();
805	>	map<AtomType*, int> counts_;
806	>
807	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
808	>	for(atom = mol->beginAtom(ai); atom != NULL;
809	>	atom = mol->nextAtom(ai)) {
810	>	atom->getAtomType();
811	>	}
812	>	}
813	>	*/
814	>	return 0;
815	>	}
816
817	+	void SimInfo::setupSimVariables() {
818	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
819	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
820	+	// parameter is true
821	+	calcBoxDipole_ = false;
822	+	if ( simParams_->haveAccumulateBoxDipole() )
823	+	if ( simParams_->getAccumulateBoxDipole() ) {
824	+	calcBoxDipole_ = true;
825	+	}
826	+	// we only call setAccumulateBoxQuadrupole if the accumulateBoxQuadrupole
827	+	// parameter is true
828	+	calcBoxQuadrupole_ = false;
829	+	if ( simParams_->haveAccumulateBoxQuadrupole() )
830	+	if ( simParams_->getAccumulateBoxQuadrupole() ) {
831	+	calcBoxQuadrupole_ = true;
832	+	}
833	+
834	+	set<AtomType*>::iterator i;
835	+	set<AtomType*> atomTypes;
836	+	atomTypes = getSimulatedAtomTypes();
837	+	bool usesElectrostatic = false;
838	+	bool usesMetallic = false;
839	+	bool usesDirectional = false;
840	+	bool usesFluctuatingCharges =  false;
841		//loop over all of the atom types
842		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
843	<	useLennardJones |= (*i)->isLennardJones();
844	<	useElectrostatic |= (*i)->isElectrostatic();
845	<	useEAM |= (*i)->isEAM();
846	<	useSC |= (*i)->isSC();
689	<	useCharge |= (*i)->isCharge();
690	<	useDirectional |= (*i)->isDirectional();
691	<	useDipole |= (*i)->isDipole();
692	<	useGayBerne |= (*i)->isGayBerne();
693	<	useSticky |= (*i)->isSticky();
694	<	useStickyPower |= (*i)->isStickyPower();
695	<	useShape |= (*i)->isShape();
843	>	usesElectrostatic |= (*i)->isElectrostatic();
844	>	usesMetallic |= (*i)->isMetal();
845	>	usesDirectional |= (*i)->isDirectional();
846	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
847		}
848
849	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
699	<	useDirectionalAtom = 1;
700	<	}
701	<
702	<	if (useCharge || useDipole) {
703	<	useElectrostatics = 1;
704	<	}
705	<
706	<	#ifdef IS_MPI
849	>	#ifdef IS_MPI
850		int temp;
851
852	<	temp = usePBC;
853	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	temp = usesDirectional;
853	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
854	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
855	>
856	>	temp = usesMetallic;
857	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
858	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
859
860	<	temp = useDirectionalAtom;
861	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>	temp = usesElectrostatic;
861	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
862	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
863
864	<	temp = useLennardJones;
865	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	temp = usesFluctuatingCharges;
865	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
866	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
867	>	#else
868
869	<	temp = useElectrostatics;
870	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
869	>	usesDirectionalAtoms_ = usesDirectional;
870	>	usesMetallicAtoms_ = usesMetallic;
871	>	usesElectrostaticAtoms_ = usesElectrostatic;
872	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
873
874	<	temp = useCharge;
875	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	>	#endif
875	>
876	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
877	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
878	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
879	>	}
880
724	–	temp = useDipole;
725	–	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
881
882	<	temp = useSticky;
883	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
882	>	vector<int> SimInfo::getGlobalAtomIndices() {
883	>	SimInfo::MoleculeIterator mi;
884	>	Molecule* mol;
885	>	Molecule::AtomIterator ai;
886	>	Atom* atom;
887
888	<	temp = useStickyPower;
731	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
888	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
889
890	<	temp = useGayBerne;
891	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
890	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
891	>
892	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
894	>	}
895	>	}
896	>	return GlobalAtomIndices;
897	>	}
898
736	–	temp = useEAM;
737	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
899
900	<	temp = useSC;
901	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
902	<
903	<	temp = useShape;
904	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
900	>	vector<int> SimInfo::getGlobalGroupIndices() {
901	>	SimInfo::MoleculeIterator mi;
902	>	Molecule* mol;
903	>	Molecule::CutoffGroupIterator ci;
904	>	CutoffGroup* cg;
905
906	<	temp = useFLARB;
907	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
908	<
748	<	temp = useRF;
749	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
750	<
751	<	temp = useSF;
752	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
753	<
754	<	#endif
755	<
756	<	fInfo_.SIM_uses_PBC = usePBC;
757	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
758	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
759	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
760	<	fInfo_.SIM_uses_Charges = useCharge;
761	<	fInfo_.SIM_uses_Dipoles = useDipole;
762	<	fInfo_.SIM_uses_Sticky = useSticky;
763	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
764	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
765	<	fInfo_.SIM_uses_EAM = useEAM;
766	<	fInfo_.SIM_uses_SC = useSC;
767	<	fInfo_.SIM_uses_Shapes = useShape;
768	<	fInfo_.SIM_uses_FLARB = useFLARB;
769	<	fInfo_.SIM_uses_RF = useRF;
770	<	fInfo_.SIM_uses_SF = useSF;
771	<
772	<	if( myMethod == "REACTION_FIELD") {
906	>	vector<int> GlobalGroupIndices;
907	>
908	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
909
910	<	if (simParams_->haveDielectric()) {
911	<	fInfo_.dielect = simParams_->getDielectric();
912	<	} else {
913	<	sprintf(painCave.errMsg,
914	<	"SimSetup Error: No Dielectric constant was set.\n"
915	<	"\tYou are trying to use Reaction Field without"
780	<	"\tsetting a dielectric constant!\n");
781	<	painCave.isFatal = 1;
782	<	simError();
783	<	}
910	>	//local index of cutoff group is trivial, it only depends on the
911	>	//order of travesing
912	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
913	>	cg = mol->nextCutoffGroup(ci)) {
914	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
915	>	}
916		}
917	<
917	>	return GlobalGroupIndices;
918		}
919
788	–	void SimInfo::setupFortranSim() {
789	–	int isError;
790	–	int nExclude;
791	–	std::vector<int> fortranGlobalGroupMembership;
792	–
793	–	nExclude = exclude_.getSize();
794	–	isError = 0;
920
921	<	//globalGroupMembership_ is filled by SimCreator
797	<	for (int i = 0; i < nGlobalAtoms_; i++) {
798	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
799	<	}
921	>	void SimInfo::prepareTopology() {
922
923		//calculate mass ratio of cutoff group
802	–	std::vector<double> mfact;
924		SimInfo::MoleculeIterator mi;
925		Molecule* mol;
926		Molecule::CutoffGroupIterator ci;
927		CutoffGroup* cg;
928		Molecule::AtomIterator ai;
929		Atom* atom;
930	<	double totalMass;
930	>	RealType totalMass;
931
932	<	//to avoid memory reallocation, reserve enough space for mfact
933	<	mfact.reserve(getNCutoffGroups());
932	>	/**
933	>	* The mass factor is the relative mass of an atom to the total
934	>	* mass of the cutoff group it belongs to.  By default, all atoms
935	>	* are their own cutoff groups, and therefore have mass factors of
936	>	* 1.  We need some special handling for massless atoms, which
937	>	* will be treated as carrying the entire mass of the cutoff
938	>	* group.
939	>	*/
940	>	massFactors_.clear();
941	>	massFactors_.resize(getNAtoms(), 1.0);
942
943		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
944	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
944	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
945	>	cg = mol->nextCutoffGroup(ci)) {
946
947		totalMass = cg->getMass();
948		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
949		// Check for massless groups - set mfact to 1 if true
950	<	if (totalMass != 0)
951	<	mfact.push_back(atom->getMass()/totalMass);
950	>	if (totalMass != 0)
951	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
952		else
953	<	mfact.push_back( 1.0 );
953	>	massFactors_[atom->getLocalIndex()] = 1.0;
954		}
825	–
955		}
956		}
957
958	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
830	<	std::vector<int> identArray;
958	>	// Build the identArray_ and regions_
959
960	<	//to avoid memory reallocation, reserve enough space identArray
961	<	identArray.reserve(getNAtoms());
962	<
963	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
960	>	identArray_.clear();
961	>	identArray_.reserve(getNAtoms());
962	>	regions_.clear();
963	>	regions_.reserve(getNAtoms());
964	>
965	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
966	>	int reg = mol->getRegion();
967		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
968	<	identArray.push_back(atom->getIdent());
968	>	identArray_.push_back(atom->getIdent());
969	>	regions_.push_back(reg);
970		}
971		}
972	<
973	<	//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	<	double 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	<	}
972	>
973	>	topologyDone_ = true;
974		}
975
1054	–	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1055	–
1056	–	int errorOut;
1057	–	int esm =  NONE;
1058	–	int sm = UNDAMPED;
1059	–	double alphaVal;
1060	–	double dielectric;
1061	–
1062	–	errorOut = isError;
1063	–	alphaVal = simParams_->getDampingAlpha();
1064	–	dielectric = simParams_->getDielectric();
1065	–
1066	–	if (simParams_->haveElectrostaticSummationMethod()) {
1067	–	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1068	–	toUpper(myMethod);
1069	–	if (myMethod == "NONE") {
1070	–	esm = NONE;
1071	–	} else {
1072	–	if (myMethod == "SWITCHING_FUNCTION") {
1073	–	esm = SWITCHING_FUNCTION;
1074	–	} else {
1075	–	if (myMethod == "SHIFTED_POTENTIAL") {
1076	–	esm = SHIFTED_POTENTIAL;
1077	–	} else {
1078	–	if (myMethod == "SHIFTED_FORCE") {
1079	–	esm = SHIFTED_FORCE;
1080	–	} else {
1081	–	if (myMethod == "REACTION_FIELD") {
1082	–	esm = REACTION_FIELD;
1083	–	} else {
1084	–	// throw error
1085	–	sprintf( painCave.errMsg,
1086	–	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1087	–	"\t(Input file specified %s .)\n"
1088	–	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1089	–	"\t\"shifted_potential\", \"shifted_force\", or \n"
1090	–	"\t\"reaction_field\".\n", myMethod.c_str() );
1091	–	painCave.isFatal = 1;
1092	–	simError();
1093	–	}
1094	–	}
1095	–	}
1096	–	}
1097	–	}
1098	–	}
1099	–
1100	–	if (simParams_->haveElectrostaticScreeningMethod()) {
1101	–	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1102	–	toUpper(myScreen);
1103	–	if (myScreen == "UNDAMPED") {
1104	–	sm = UNDAMPED;
1105	–	} else {
1106	–	if (myScreen == "DAMPED") {
1107	–	sm = DAMPED;
1108	–	if (!simParams_->haveDampingAlpha()) {
1109	–	//throw error
1110	–	sprintf( painCave.errMsg,
1111	–	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1112	–	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1113	–	painCave.isFatal = 0;
1114	–	simError();
1115	–	}
1116	–	} else {
1117	–	// throw error
1118	–	sprintf( painCave.errMsg,
1119	–	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1120	–	"\t(Input file specified %s .)\n"
1121	–	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1122	–	"or \"damped\".\n", myScreen.c_str() );
1123	–	painCave.isFatal = 1;
1124	–	simError();
1125	–	}
1126	–	}
1127	–	}
1128	–
1129	–	// let's pass some summation method variables to fortran
1130	–	setElectrostaticSummationMethod( &esm );
1131	–	setFortranElectrostaticMethod( &esm );
1132	–	setScreeningMethod( &sm );
1133	–	setDampingAlpha( &alphaVal );
1134	–	setReactionFieldDielectric( &dielectric );
1135	–	initFortranFF( &errorOut );
1136	–	}
1137	–
1138	–	void SimInfo::setupSwitchingFunction() {
1139	–	int ft = CUBIC;
1140	–
1141	–	if (simParams_->haveSwitchingFunctionType()) {
1142	–	std::string funcType = simParams_->getSwitchingFunctionType();
1143	–	toUpper(funcType);
1144	–	if (funcType == "CUBIC") {
1145	–	ft = CUBIC;
1146	–	} else {
1147	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1148	–	ft = FIFTH_ORDER_POLY;
1149	–	} else {
1150	–	// throw error
1151	–	sprintf( painCave.errMsg,
1152	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1153	–	painCave.isFatal = 1;
1154	–	simError();
1155	–	}
1156	–	}
1157	–	}
1158	–
1159	–	// send switching function notification to switcheroo
1160	–	setFunctionType(&ft);
1161	–
1162	–	}
1163	–
976		void SimInfo::addProperty(GenericData* genData) {
977		properties_.addProperty(genData);
978		}
979
980	<	void SimInfo::removeProperty(const std::string& propName) {
980	>	void SimInfo::removeProperty(const string& propName) {
981		properties_.removeProperty(propName);
982		}
983
#	Line 1173 | Line 985 | namespace oopse {
985		properties_.clearProperties();
986		}
987
988	<	std::vector<std::string> SimInfo::getPropertyNames() {
988	>	vector<string> SimInfo::getPropertyNames() {
989		return properties_.getPropertyNames();
990		}
991
992	<	std::vector<GenericData*> SimInfo::getProperties() {
992	>	vector<GenericData*> SimInfo::getProperties() {
993		return properties_.getProperties();
994		}
995
996	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
996	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
997		return properties_.getPropertyByName(propName);
998		}
999
#	Line 1192 | Line 1004 | namespace oopse {
1004		delete sman_;
1005		sman_ = sman;
1006
1195	–	Molecule* mol;
1196	–	RigidBody* rb;
1197	–	Atom* atom;
1007		SimInfo::MoleculeIterator mi;
1008	+	Molecule::AtomIterator ai;
1009		Molecule::RigidBodyIterator rbIter;
1010	<	Molecule::AtomIterator atomIter;;
1010	>	Molecule::CutoffGroupIterator cgIter;
1011	>	Molecule::BondIterator bondIter;
1012	>	Molecule::BendIterator bendIter;
1013	>	Molecule::TorsionIterator torsionIter;
1014	>	Molecule::InversionIterator inversionIter;
1015
1016	+	Molecule* mol;
1017	+	Atom* atom;
1018	+	RigidBody* rb;
1019	+	CutoffGroup* cg;
1020	+	Bond* bond;
1021	+	Bend* bend;
1022	+	Torsion* torsion;
1023	+	Inversion* inversion;
1024	+
1025		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1026
1027	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1027	>	for (atom = mol->beginAtom(ai); atom != NULL;
1028	>	atom = mol->nextAtom(ai)) {
1029		atom->setSnapshotManager(sman_);
1030	<	}
1031	<
1032	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1030	>	}
1031	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1032	>	rb = mol->nextRigidBody(rbIter)) {
1033		rb->setSnapshotManager(sman_);
1034		}
1035	<	}
1036	<
1035	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1036	>	cg = mol->nextCutoffGroup(cgIter)) {
1037	>	cg->setSnapshotManager(sman_);
1038	>	}
1039	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1040	>	bond = mol->nextBond(bondIter)) {
1041	>	bond->setSnapshotManager(sman_);
1042	>	}
1043	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1044	>	bend = mol->nextBend(bendIter)) {
1045	>	bend->setSnapshotManager(sman_);
1046	>	}
1047	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1048	>	torsion = mol->nextTorsion(torsionIter)) {
1049	>	torsion->setSnapshotManager(sman_);
1050	>	}
1051	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1052	>	inversion = mol->nextInversion(inversionIter)) {
1053	>	inversion->setSnapshotManager(sman_);
1054	>	}
1055	>	}
1056		}
1057
1215	–	Vector3d SimInfo::getComVel(){
1216	–	SimInfo::MoleculeIterator i;
1217	–	Molecule* mol;
1058
1059	<	Vector3d comVel(0.0);
1220	<	double totalMass = 0.0;
1221	<
1222	<
1223	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1224	<	double mass = mol->getMass();
1225	<	totalMass += mass;
1226	<	comVel += mass * mol->getComVel();
1227	<	}
1059	>	ostream& operator <<(ostream& o, SimInfo& info) {
1060
1229	–	#ifdef IS_MPI
1230	–	double tmpMass = totalMass;
1231	–	Vector3d tmpComVel(comVel);
1232	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1233	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1234	–	#endif
1235	–
1236	–	comVel /= totalMass;
1237	–
1238	–	return comVel;
1239	–	}
1240	–
1241	–	Vector3d SimInfo::getCom(){
1242	–	SimInfo::MoleculeIterator i;
1243	–	Molecule* mol;
1244	–
1245	–	Vector3d com(0.0);
1246	–	double totalMass = 0.0;
1247	–
1248	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249	–	double mass = mol->getMass();
1250	–	totalMass += mass;
1251	–	com += mass * mol->getCom();
1252	–	}
1253	–
1254	–	#ifdef IS_MPI
1255	–	double tmpMass = totalMass;
1256	–	Vector3d tmpCom(com);
1257	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1259	–	#endif
1260	–
1261	–	com /= totalMass;
1262	–
1263	–	return com;
1264	–
1265	–	}
1266	–
1267	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1268	–
1061		return o;
1062		}
1063
1064	<
1065	<	/*
1066	<	Returns center of mass and center of mass velocity in one function call.
1067	<	*/
1068	<
1069	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1070	<	SimInfo::MoleculeIterator i;
1071	<	Molecule* mol;
1072	<
1073	<
1074	<	double totalMass = 0.0;
1075	<
1064	>
1065	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1066	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1067	>	sprintf(painCave.errMsg,
1068	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1069	>	"\tindex exceeds number of known objects!\n");
1070	>	painCave.isFatal = 1;
1071	>	simError();
1072	>	return NULL;
1073	>	} else
1074	>	return IOIndexToIntegrableObject.at(index);
1075	>	}
1076	>
1077	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1078	>	IOIndexToIntegrableObject= v;
1079	>	}
1080
1081	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1286	<	double mass = mol->getMass();
1287	<	totalMass += mass;
1288	<	com += mass * mol->getCom();
1289	<	comVel += mass * mol->getComVel();
1290	<	}
1291	<
1081	>	void SimInfo::calcNConstraints() {
1082		#ifdef IS_MPI
1083	<	double tmpMass = totalMass;
1084	<	Vector3d tmpCom(com);
1085	<	Vector3d tmpComVel(comVel);
1086	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1297	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1298	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1083	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1084	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1085	>	#else
1086	>	nGlobalConstraints_ =  nConstraints_;
1087		#endif
1088	<
1301	<	com /= totalMass;
1302	<	comVel /= totalMass;
1303	<	}
1304	<
1305	<	/*
1306	<	Return intertia tensor for entire system and angular momentum Vector.
1088	>	}
1089
1090	+	}//end namespace OpenMD
1091
1309	–	[  Ixx -Ixy  -Ixz ]
1310	–	J =| -Iyx  Iyy  -Iyz |
1311	–	[ -Izx -Iyz   Izz ]
1312	–	*/
1313	–
1314	–	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1315	–
1316	–
1317	–	double xx = 0.0;
1318	–	double yy = 0.0;
1319	–	double zz = 0.0;
1320	–	double xy = 0.0;
1321	–	double xz = 0.0;
1322	–	double yz = 0.0;
1323	–	Vector3d com(0.0);
1324	–	Vector3d comVel(0.0);
1325	–
1326	–	getComAll(com, comVel);
1327	–
1328	–	SimInfo::MoleculeIterator i;
1329	–	Molecule* mol;
1330	–
1331	–	Vector3d thisq(0.0);
1332	–	Vector3d thisv(0.0);
1333	–
1334	–	double thisMass = 0.0;
1335	–
1336	–
1337	–
1338	–
1339	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1340	–
1341	–	thisq = mol->getCom()-com;
1342	–	thisv = mol->getComVel()-comVel;
1343	–	thisMass = mol->getMass();
1344	–	// Compute moment of intertia coefficients.
1345	–	xx += thisq[0]*thisq[0]*thisMass;
1346	–	yy += thisq[1]*thisq[1]*thisMass;
1347	–	zz += thisq[2]*thisq[2]*thisMass;
1348	–
1349	–	// compute products of intertia
1350	–	xy += thisq[0]*thisq[1]*thisMass;
1351	–	xz += thisq[0]*thisq[2]*thisMass;
1352	–	yz += thisq[1]*thisq[2]*thisMass;
1353	–
1354	–	angularMomentum += cross( thisq, thisv ) * thisMass;
1355	–
1356	–	}
1357	–
1358	–
1359	–	inertiaTensor(0,0) = yy + zz;
1360	–	inertiaTensor(0,1) = -xy;
1361	–	inertiaTensor(0,2) = -xz;
1362	–	inertiaTensor(1,0) = -xy;
1363	–	inertiaTensor(1,1) = xx + zz;
1364	–	inertiaTensor(1,2) = -yz;
1365	–	inertiaTensor(2,0) = -xz;
1366	–	inertiaTensor(2,1) = -yz;
1367	–	inertiaTensor(2,2) = xx + yy;
1368	–
1369	–	#ifdef IS_MPI
1370	–	Mat3x3d tmpI(inertiaTensor);
1371	–	Vector3d tmpAngMom;
1372	–	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1373	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1374	–	#endif
1375	–
1376	–	return;
1377	–	}
1378	–
1379	–	//Returns the angular momentum of the system
1380	–	Vector3d SimInfo::getAngularMomentum(){
1381	–
1382	–	Vector3d com(0.0);
1383	–	Vector3d comVel(0.0);
1384	–	Vector3d angularMomentum(0.0);
1385	–
1386	–	getComAll(com,comVel);
1387	–
1388	–	SimInfo::MoleculeIterator i;
1389	–	Molecule* mol;
1390	–
1391	–	Vector3d thisr(0.0);
1392	–	Vector3d thisp(0.0);
1393	–
1394	–	double thisMass;
1395	–
1396	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1397	–	thisMass = mol->getMass();
1398	–	thisr = mol->getCom()-com;
1399	–	thisp = (mol->getComVel()-comVel)*thisMass;
1400	–
1401	–	angularMomentum += cross( thisr, thisp );
1402	–
1403	–	}
1404	–
1405	–	#ifdef IS_MPI
1406	–	Vector3d tmpAngMom;
1407	–	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1408	–	#endif
1409	–
1410	–	return angularMomentum;
1411	–	}
1412	–
1413	–
1414	–	}//end namespace oopse
1415	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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