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root/OpenMD/branches/development/src/brains/SimInfo.cpp

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trunk/src/brains/SimInfo.cpp (file contents), Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 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, 24107 (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 54 | Line 55
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	–	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	–	#include "UseTheForce/doForces_interface.h"
62	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	–	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61		#include "io/ForceFieldOptions.hpp"
62	<	#include "UseTheForce/ForceField.hpp"
63	<
71	<
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	<	std::map<int, std::set<int> >::iterator i = container.find(index);
80	<	std::set<int> result;
81	<	if (i != container.end()) {
82	<	result = i->second;
83	<	}
84	<
85	<	return result;
86	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
73		ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76		nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77		nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	<	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
79	<	calcBoxDipole_(false), useAtomicVirial_(true) {
80	<
81	<
82	<	MoleculeStamp* molStamp;
83	<	int nMolWithSameStamp;
84	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85	<	int nGroups = 0;      //total cutoff groups defined in meta-data file
86	<	CutoffGroupStamp* cgStamp;
87	<	RigidBodyStamp* rbStamp;
88	<	int nRigidAtoms = 0;
89	<
90	<	std::vector<Component*> components = simParams->getComponents();
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94
95	<	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	<	molStamp = (*i)->getMoleculeStamp();
97	<	nMolWithSameStamp = (*i)->getNMol();
98	<
99	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
100	<
101	<	//calculate atoms in molecules
102	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	<
104	<	//calculate atoms in cutoff groups
105	<	int nAtomsInGroups = 0;
106	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107	<
108	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
109	<	cgStamp = molStamp->getCutoffGroupStamp(j);
110	<	nAtomsInGroups += cgStamp->getNMembers();
111	<	}
112	<
113	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114	<
115	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
116	<
117	<	//calculate atoms in rigid bodies
118	<	int nAtomsInRigidBodies = 0;
119	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120	<
121	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
122	<	rbStamp = molStamp->getRigidBodyStamp(j);
123	<	nAtomsInRigidBodies += rbStamp->getNMembers();
124	<	}
139	<
140	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	<
143	<	}
144	<
145	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
146	<	//group therefore the total number of cutoff groups in the system is
147	<	//equal to the total number of atoms minus number of atoms belong to
148	<	//cutoff group defined in meta-data file plus the number of cutoff
149	<	//groups defined in meta-data file
150	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
151	<
152	<	//every free atom (atom does not belong to rigid bodies) is an
153	<	//integrable object therefore the total number of integrable objects
154	<	//in the system is equal to the total number of atoms minus number of
155	<	//atoms belong to rigid body defined in meta-data file plus the number
156	<	//of rigid bodies defined in meta-data file
157	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
158	<	+ nGlobalRigidBodies_;
159	<
160	<	nGlobalMols_ = molStampIds_.size();
161	<	molToProcMap_.resize(nGlobalMols_);
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107	>	}
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
133	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	+
135	+	//every free atom (atom does not belong to rigid bodies) is an
136	+	//integrable object therefore the total number of integrable objects
137	+	//in the system is equal to the total number of atoms minus number of
138	+	//atoms belong to rigid body defined in meta-data file plus the number
139	+	//of rigid bodies defined in meta-data file
140	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	+	+ nGlobalRigidBodies_;
142	+
143	+	nGlobalMols_ = molStampIds_.size();
144	+	molToProcMap_.resize(nGlobalMols_);
145	+	}
146	+
147		SimInfo::~SimInfo() {
148	<	std::map<int, Molecule*>::iterator i;
148	>	map<int, Molecule*>::iterator i;
149		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150		delete i->second;
151		}
#	Line 173 | Line 156 | namespace oopse {
156		delete forceField_;
157		}
158
176	–	int SimInfo::getNGlobalConstraints() {
177	–	int nGlobalConstraints;
178	–	#ifdef IS_MPI
179	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180	–	MPI_COMM_WORLD);
181	–	#else
182	–	nGlobalConstraints =  nConstraints_;
183	–	#endif
184	–	return nGlobalConstraints;
185	–	}
159
160		bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168		nAtoms_ += mol->getNAtoms();
169		nBonds_ += mol->getNBonds();
170		nBends_ += mol->getNBends();
#	Line 201 | Line 174 | namespace oopse {
174		nIntegrableObjects_ += mol->getNIntegrableObjects();
175		nCutoffGroups_ += mol->getNCutoffGroups();
176		nConstraints_ += mol->getNConstraintPairs();
177	<
177	>
178		addInteractionPairs(mol);
179	<
179	>
180		return true;
181		} else {
182		return false;
183		}
184		}
185	<
185	>
186		bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
#	Line 237 | Line 210 | namespace oopse {
210		} else {
211		return false;
212		}
240	–
241	–
213		}
214
215
#	Line 254 | Line 225 | namespace oopse {
225
226
227		void SimInfo::calcNdf() {
228	<	int ndf_local;
228	>	int ndf_local, nfq_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232	>
233		Molecule* mol;
234		StuntDouble* integrableObject;
235	+	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
#	Line 275 | Line 250 | namespace oopse {
250		ndf_local += 3;
251		}
252		}
278	–
253		}
254	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255	+	atom = mol->nextFluctuatingCharge(k)) {
256	+	if (atom->isFluctuatingCharge()) {
257	+	nfq_local++;
258	+	}
259	+	}
260		}
261
262	+	ndfLocal_ = ndf_local;
263	+	cerr << "ndfLocal_ = " << ndfLocal_ << "\n";
264	+
265		// n_constraints is local, so subtract them on each processor
266		ndf_local -= nConstraints_;
267
268		#ifdef IS_MPI
269		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
271		#else
272		ndf_ = ndf_local;
273	+	nGlobalFluctuatingCharges_ = nfq_local;
274		#endif
275
276		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 302 | Line 287 | namespace oopse {
287		#endif
288		return fdf_;
289		}
290	+
291	+	unsigned int SimInfo::getNLocalCutoffGroups(){
292	+	int nLocalCutoffAtoms = 0;
293	+	Molecule* mol;
294	+	MoleculeIterator mi;
295	+	CutoffGroup* cg;
296	+	Molecule::CutoffGroupIterator ci;
297
298	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
299	+
300	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
301	+	cg = mol->nextCutoffGroup(ci)) {
302	+	nLocalCutoffAtoms += cg->getNumAtom();
303	+
304	+	}
305	+	}
306	+
307	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
308	+	}
309	+
310		void SimInfo::calcNdfRaw() {
311		int ndfRaw_local;
312
313		MoleculeIterator i;
314	<	std::vector<StuntDouble*>::iterator j;
314	>	vector<StuntDouble*>::iterator j;
315		Molecule* mol;
316		StuntDouble* integrableObject;
317
#	Line 356 | Line 360 | namespace oopse {
360
361		void SimInfo::addInteractionPairs(Molecule* mol) {
362		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
363	<	std::vector<Bond*>::iterator bondIter;
364	<	std::vector<Bend*>::iterator bendIter;
365	<	std::vector<Torsion*>::iterator torsionIter;
366	<	std::vector<Inversion*>::iterator inversionIter;
363	>	vector<Bond*>::iterator bondIter;
364	>	vector<Bend*>::iterator bendIter;
365	>	vector<Torsion*>::iterator torsionIter;
366	>	vector<Inversion*>::iterator inversionIter;
367		Bond* bond;
368		Bend* bend;
369		Torsion* torsion;
#	Line 377 | Line 381 | namespace oopse {
381		// always be excluded.  These are done at the bottom of this
382		// function.
383
384	<	std::map<int, std::set<int> > atomGroups;
384	>	map<int, set<int> > atomGroups;
385		Molecule::RigidBodyIterator rbIter;
386		RigidBody* rb;
387		Molecule::IntegrableObjectIterator ii;
#	Line 389 | Line 393 | namespace oopse {
393
394		if (integrableObject->isRigidBody()) {
395		rb = static_cast<RigidBody*>(integrableObject);
396	<	std::vector<Atom*> atoms = rb->getAtoms();
397	<	std::set<int> rigidAtoms;
396	>	vector<Atom*> atoms = rb->getAtoms();
397	>	set<int> rigidAtoms;
398		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
399		rigidAtoms.insert(atoms[i]->getGlobalIndex());
400		}
401		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
402	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
402	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
403		}
404		} else {
405	<	std::set<int> oneAtomSet;
405	>	set<int> oneAtomSet;
406		oneAtomSet.insert(integrableObject->getGlobalIndex());
407	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
407	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
408		}
409		}
410
#	Line 503 | Line 507 | namespace oopse {
507
508		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
509		rb = mol->nextRigidBody(rbIter)) {
510	<	std::vector<Atom*> atoms = rb->getAtoms();
510	>	vector<Atom*> atoms = rb->getAtoms();
511		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
512		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
513		a = atoms[i]->getGlobalIndex();
#	Line 517 | Line 521 | namespace oopse {
521
522		void SimInfo::removeInteractionPairs(Molecule* mol) {
523		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
524	<	std::vector<Bond*>::iterator bondIter;
525	<	std::vector<Bend*>::iterator bendIter;
526	<	std::vector<Torsion*>::iterator torsionIter;
527	<	std::vector<Inversion*>::iterator inversionIter;
524	>	vector<Bond*>::iterator bondIter;
525	>	vector<Bend*>::iterator bendIter;
526	>	vector<Torsion*>::iterator torsionIter;
527	>	vector<Inversion*>::iterator inversionIter;
528		Bond* bond;
529		Bend* bend;
530		Torsion* torsion;
#	Line 530 | Line 534 | namespace oopse {
534		int c;
535		int d;
536
537	<	std::map<int, std::set<int> > atomGroups;
537	>	map<int, set<int> > atomGroups;
538		Molecule::RigidBodyIterator rbIter;
539		RigidBody* rb;
540		Molecule::IntegrableObjectIterator ii;
#	Line 542 | Line 546 | namespace oopse {
546
547		if (integrableObject->isRigidBody()) {
548		rb = static_cast<RigidBody*>(integrableObject);
549	<	std::vector<Atom*> atoms = rb->getAtoms();
550	<	std::set<int> rigidAtoms;
549	>	vector<Atom*> atoms = rb->getAtoms();
550	>	set<int> rigidAtoms;
551		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552		rigidAtoms.insert(atoms[i]->getGlobalIndex());
553		}
554		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556		}
557		} else {
558	<	std::set<int> oneAtomSet;
558	>	set<int> oneAtomSet;
559		oneAtomSet.insert(integrableObject->getGlobalIndex());
560	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
560	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
561		}
562		}
563
#	Line 656 | Line 660 | namespace oopse {
660
661		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
662		rb = mol->nextRigidBody(rbIter)) {
663	<	std::vector<Atom*> atoms = rb->getAtoms();
663	>	vector<Atom*> atoms = rb->getAtoms();
664		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
665		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
666		a = atoms[i]->getGlobalIndex();
#	Line 679 | Line 683 | namespace oopse {
683		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684		}
685
682	–	void SimInfo::update() {
686
687	<	setupSimType();
688	<
689	<	#ifdef IS_MPI
690	<	setupFortranParallel();
691	<	#endif
692	<
693	<	setupFortranSim();
694	<
695	<	//setup fortran force field
693	<	/** @deprecate */
694	<	int isError = 0;
695	<
696	<	setupCutoff();
697	<
698	<	setupElectrostaticSummationMethod( isError );
699	<	setupSwitchingFunction();
700	<	setupAccumulateBoxDipole();
701	<
702	<	if(isError){
703	<	sprintf( painCave.errMsg,
704	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
705	<	painCave.isFatal = 1;
706	<	simError();
707	<	}
708	<
687	>	/**
688	>	* update
689	>	*
690	>	*  Performs the global checks and variable settings after the
691	>	*  objects have been created.
692	>	*
693	>	*/
694	>	void SimInfo::update() {
695	>	setupSimVariables();
696		calcNdf();
697		calcNdfRaw();
698		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
699		}
700	<
701	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
700	>
701	>	/**
702	>	* getSimulatedAtomTypes
703	>	*
704	>	* Returns an STL set of AtomType* that are actually present in this
705	>	* simulation.  Must query all processors to assemble this information.
706	>	*
707	>	*/
708	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709		SimInfo::MoleculeIterator mi;
710		Molecule* mol;
711		Molecule::AtomIterator ai;
712		Atom* atom;
713	<	std::set<AtomType*> atomTypes;
714	<
713	>	set<AtomType*> atomTypes;
714	>
715		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	<
717	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
716	>	for(atom = mol->beginAtom(ai); atom != NULL;
717	>	atom = mol->nextAtom(ai)) {
718		atomTypes.insert(atom->getAtomType());
719	<	}
720	<
721	<	}
719	>	}
720	>	}
721	>
722	>	#ifdef IS_MPI
723
724	<	return atomTypes;
725	<	}
733	<
734	<	void SimInfo::setupSimType() {
735	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726
727	<	int useLennardJones = 0;
728	<	int useElectrostatic = 0;
729	<	int useEAM = 0;
730	<	int useSC = 0;
743	<	int useCharge = 0;
744	<	int useDirectional = 0;
745	<	int useDipole = 0;
746	<	int useGayBerne = 0;
747	<	int useSticky = 0;
748	<	int useStickyPower = 0;
749	<	int useShape = 0;
750	<	int useFLARB = 0; //it is not in AtomType yet
751	<	int useDirectionalAtom = 0;
752	<	int useElectrostatics = 0;
753	<	//usePBC and useRF are from simParams
754	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755	<	int useRF;
756	<	int useSF;
757	<	int useSP;
758	<	int useBoxDipole;
727	>	vector<int> foundTypes;
728	>	set<AtomType*>::iterator i;
729	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730	>	foundTypes.push_back( (*i)->getIdent() );
731
732	<	std::string myMethod;
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734
735	<	// set the useRF logical
763	<	useRF = 0;
764	<	useSF = 0;
765	<	useSP = 0;
735	>	int nproc = MPI::COMM_WORLD.Get_size();
736
737	+	// we need arrays to hold the counts and displacement vectors for
738	+	// all processors
739	+	vector<int> counts(nproc, 0);
740	+	vector<int> disps(nproc, 0);
741
742	<	if (simParams_->haveElectrostaticSummationMethod()) {
743	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
744	<	toUpper(myMethod);
745	<	if (myMethod == "REACTION_FIELD"){
746	<	useRF = 1;
747	<	} else if (myMethod == "SHIFTED_FORCE"){
748	<	useSF = 1;
749	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
750	<	useSP = 1;
751	<	}
742	>	// fill the counts array
743	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744	>	1, MPI::INT);
745	>
746	>	// use the processor counts to compute the displacement array
747	>	disps[0] = 0;
748	>	int totalCount = counts[0];
749	>	for (int iproc = 1; iproc < nproc; iproc++) {
750	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
751	>	totalCount += counts[iproc];
752		}
753	+
754	+	// we need a (possibly redundant) set of all found types:
755	+	vector<int> ftGlobal(totalCount);
756
757	<	if (simParams_->haveAccumulateBoxDipole())
758	<	if (simParams_->getAccumulateBoxDipole())
759	<	useBoxDipole = 1;
757	>	// now spray out the foundTypes to all the other processors:
758	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759	>	&ftGlobal[0], &counts[0], &disps[0],
760	>	MPI::INT);
761
762	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
762	>	vector<int>::iterator j;
763
764	<	//loop over all of the atom types
765	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
766	<	useLennardJones |= (*i)->isLennardJones();
789	<	useElectrostatic |= (*i)->isElectrostatic();
790	<	useEAM |= (*i)->isEAM();
791	<	useSC |= (*i)->isSC();
792	<	useCharge |= (*i)->isCharge();
793	<	useDirectional |= (*i)->isDirectional();
794	<	useDipole |= (*i)->isDipole();
795	<	useGayBerne |= (*i)->isGayBerne();
796	<	useSticky |= (*i)->isSticky();
797	<	useStickyPower |= (*i)->isStickyPower();
798	<	useShape |= (*i)->isShape();
799	<	}
764	>	// foundIdents is a stl set, so inserting an already found ident
765	>	// will have no effect.
766	>	set<int> foundIdents;
767
768	<	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
769	<	useDirectionalAtom = 1;
770	<	}
768	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769	>	foundIdents.insert((*j));
770	>
771	>	// now iterate over the foundIdents and get the actual atom types
772	>	// that correspond to these:
773	>	set<int>::iterator it;
774	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	>	atomTypes.insert( forceField_->getAtomType((*it)) );
776	>
777	>	#endif
778
779	<	if (useCharge || useDipole) {
780	<	useElectrostatics = 1;
807	<	}
779	>	return atomTypes;
780	>	}
781
782	+	void SimInfo::setupSimVariables() {
783	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
784	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	+	calcBoxDipole_ = false;
786	+	if ( simParams_->haveAccumulateBoxDipole() )
787	+	if ( simParams_->getAccumulateBoxDipole() ) {
788	+	calcBoxDipole_ = true;
789	+	}
790	+
791	+	set<AtomType*>::iterator i;
792	+	set<AtomType*> atomTypes;
793	+	atomTypes = getSimulatedAtomTypes();
794	+	int usesElectrostatic = 0;
795	+	int usesMetallic = 0;
796	+	int usesDirectional = 0;
797	+	int usesFluctuatingCharges =  0;
798	+	//loop over all of the atom types
799	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800	+	usesElectrostatic |= (*i)->isElectrostatic();
801	+	usesMetallic |= (*i)->isMetal();
802	+	usesDirectional |= (*i)->isDirectional();
803	+	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804	+	}
805	+
806		#ifdef IS_MPI
807		int temp;
808	<
809	<	temp = usePBC;
813	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	<
815	<	temp = useDirectionalAtom;
816	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	<
818	<	temp = useLennardJones;
819	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	<
821	<	temp = useElectrostatics;
822	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
823	<
824	<	temp = useCharge;
825	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	<
827	<	temp = useDipole;
828	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
829	<
830	<	temp = useSticky;
831	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832	<
833	<	temp = useStickyPower;
834	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
808	>	temp = usesDirectional;
809	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810
811	<	temp = useGayBerne;
812	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838	<
839	<	temp = useEAM;
840	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841	<
842	<	temp = useSC;
843	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811	>	temp = usesMetallic;
812	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useShape;
815	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	temp = usesElectrostatic;
815	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816
817	<	temp = useFLARB;
818	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	<
851	<	temp = useRF;
852	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853	<
854	<	temp = useSF;
855	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	<
857	<	temp = useSP;
858	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	>	temp = usesFluctuatingCharges;
818	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	#else
820
821	<	temp = useBoxDipole;
822	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	>	usesDirectionalAtoms_ = usesDirectional;
822	>	usesMetallicAtoms_ = usesMetallic;
823	>	usesElectrostaticAtoms_ = usesElectrostatic;
824	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
825
863	–	temp = useAtomicVirial_;
864	–	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865	–
826		#endif
827	<
828	<	fInfo_.SIM_uses_PBC = usePBC;
829	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
830	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
871	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
872	<	fInfo_.SIM_uses_Charges = useCharge;
873	<	fInfo_.SIM_uses_Dipoles = useDipole;
874	<	fInfo_.SIM_uses_Sticky = useSticky;
875	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
876	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
877	<	fInfo_.SIM_uses_EAM = useEAM;
878	<	fInfo_.SIM_uses_SC = useSC;
879	<	fInfo_.SIM_uses_Shapes = useShape;
880	<	fInfo_.SIM_uses_FLARB = useFLARB;
881	<	fInfo_.SIM_uses_RF = useRF;
882	<	fInfo_.SIM_uses_SF = useSF;
883	<	fInfo_.SIM_uses_SP = useSP;
884	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
885	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
827	>
828	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
829	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
830	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
831		}
832
833	<	void SimInfo::setupFortranSim() {
834	<	int isError;
835	<	int nExclude, nOneTwo, nOneThree, nOneFour;
836	<	std::vector<int> fortranGlobalGroupMembership;
833	>
834	>	vector<int> SimInfo::getGlobalAtomIndices() {
835	>	SimInfo::MoleculeIterator mi;
836	>	Molecule* mol;
837	>	Molecule::AtomIterator ai;
838	>	Atom* atom;
839	>
840	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
841
842	<	isError = 0;
842	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
843	>
844	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
845	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
846	>	}
847	>	}
848	>	return GlobalAtomIndices;
849	>	}
850
851	<	//globalGroupMembership_ is filled by SimCreator
852	<	for (int i = 0; i < nGlobalAtoms_; i++) {
853	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
851	>
852	>	vector<int> SimInfo::getGlobalGroupIndices() {
853	>	SimInfo::MoleculeIterator mi;
854	>	Molecule* mol;
855	>	Molecule::CutoffGroupIterator ci;
856	>	CutoffGroup* cg;
857	>
858	>	vector<int> GlobalGroupIndices;
859	>
860	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
861	>
862	>	//local index of cutoff group is trivial, it only depends on the
863	>	//order of travesing
864	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
865	>	cg = mol->nextCutoffGroup(ci)) {
866	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
867	>	}
868		}
869	+	return GlobalGroupIndices;
870	+	}
871
872	+
873	+	void SimInfo::prepareTopology() {
874	+	int nExclude, nOneTwo, nOneThree, nOneFour;
875	+
876		//calculate mass ratio of cutoff group
901	–	std::vector<RealType> mfact;
877		SimInfo::MoleculeIterator mi;
878		Molecule* mol;
879		Molecule::CutoffGroupIterator ci;
#	Line 907 | Line 882 | namespace oopse {
882		Atom* atom;
883		RealType totalMass;
884
885	<	//to avoid memory reallocation, reserve enough space for mfact
886	<	mfact.reserve(getNCutoffGroups());
885	>	/**
886	>	* The mass factor is the relative mass of an atom to the total
887	>	* mass of the cutoff group it belongs to.  By default, all atoms
888	>	* are their own cutoff groups, and therefore have mass factors of
889	>	* 1.  We need some special handling for massless atoms, which
890	>	* will be treated as carrying the entire mass of the cutoff
891	>	* group.
892	>	*/
893	>	massFactors_.clear();
894	>	massFactors_.resize(getNAtoms(), 1.0);
895
896		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
897	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
898	>	cg = mol->nextCutoffGroup(ci)) {
899
900		totalMass = cg->getMass();
901		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
902		// Check for massless groups - set mfact to 1 if true
903	<	if (totalMass != 0)
904	<	mfact.push_back(atom->getMass()/totalMass);
903	>	if (totalMass != 0)
904	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
905		else
906	<	mfact.push_back( 1.0 );
906	>	massFactors_[atom->getLocalIndex()] = 1.0;
907		}
908		}
909		}
910
911	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
928	<	std::vector<int> identArray;
911	>	// Build the identArray_
912
913	<	//to avoid memory reallocation, reserve enough space identArray
914	<	identArray.reserve(getNAtoms());
932	<
913	>	identArray_.clear();
914	>	identArray_.reserve(getNAtoms());
915		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
916		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
917	<	identArray.push_back(atom->getIdent());
917	>	identArray_.push_back(atom->getIdent());
918		}
919		}
938	–
939	–	//fill molMembershipArray
940	–	//molMembershipArray is filled by SimCreator
941	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
942	–	for (int i = 0; i < nGlobalAtoms_; i++) {
943	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
944	–	}
920
921	<	//setup fortran simulation
921	>	//scan topology
922
923		nExclude = excludedInteractions_.getSize();
924		nOneTwo = oneTwoInteractions_.getSize();
925		nOneThree = oneThreeInteractions_.getSize();
926		nOneFour = oneFourInteractions_.getSize();
927
953	–	std::cerr << "excludedInteractions contains: " << excludedInteractions_.getSize() << " pairs \n";
954	–	std::cerr << "oneTwoInteractions contains: " << oneTwoInteractions_.getSize() << " pairs \n";
955	–	std::cerr << "oneThreeInteractions contains: " << oneThreeInteractions_.getSize() << " pairs \n";
956	–	std::cerr << "oneFourInteractions contains: " << oneFourInteractions_.getSize() << " pairs \n";
957	–
928		int* excludeList = excludedInteractions_.getPairList();
929		int* oneTwoList = oneTwoInteractions_.getPairList();
930		int* oneThreeList = oneThreeInteractions_.getPairList();
931		int* oneFourList = oneFourInteractions_.getPairList();
932
933	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
964	<	&nExclude, excludeList,
965	<	&nOneTwo, oneTwoList,
966	<	&nOneThree, oneThreeList,
967	<	&nOneFour, oneFourList,
968	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
969	<	&fortranGlobalGroupMembership[0], &isError);
970	<
971	<	if( isError ){
972	<
973	<	sprintf( painCave.errMsg,
974	<	"There was an error setting the simulation information in fortran.\n" );
975	<	painCave.isFatal = 1;
976	<	painCave.severity = OOPSE_ERROR;
977	<	simError();
978	<	}
979	<
980	<
981	<	sprintf( checkPointMsg,
982	<	"succesfully sent the simulation information to fortran.\n");
983	<
984	<	errorCheckPoint();
985	<
986	<	// Setup number of neighbors in neighbor list if present
987	<	if (simParams_->haveNeighborListNeighbors()) {
988	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
989	<	setNeighbors(&nlistNeighbors);
990	<	}
991	<
992	<
993	<	}
994	<
995	<
996	<	void SimInfo::setupFortranParallel() {
997	<	#ifdef IS_MPI
998	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
999	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1000	<	std::vector<int> localToGlobalCutoffGroupIndex;
1001	<	SimInfo::MoleculeIterator mi;
1002	<	Molecule::AtomIterator ai;
1003	<	Molecule::CutoffGroupIterator ci;
1004	<	Molecule* mol;
1005	<	Atom* atom;
1006	<	CutoffGroup* cg;
1007	<	mpiSimData parallelData;
1008	<	int isError;
1009	<
1010	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1011	<
1012	<	//local index(index in DataStorge) of atom is important
1013	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1014	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1015	<	}
1016	<
1017	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1018	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1019	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1020	<	}
1021	<
1022	<	}
1023	<
1024	<	//fill up mpiSimData struct
1025	<	parallelData.nMolGlobal = getNGlobalMolecules();
1026	<	parallelData.nMolLocal = getNMolecules();
1027	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1028	<	parallelData.nAtomsLocal = getNAtoms();
1029	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1030	<	parallelData.nGroupsLocal = getNCutoffGroups();
1031	<	parallelData.myNode = worldRank;
1032	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1033	<
1034	<	//pass mpiSimData struct and index arrays to fortran
1035	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1036	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1037	<	&localToGlobalCutoffGroupIndex[0], &isError);
1038	<
1039	<	if (isError) {
1040	<	sprintf(painCave.errMsg,
1041	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1042	<	painCave.isFatal = 1;
1043	<	simError();
1044	<	}
1045	<
1046	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1047	<	errorCheckPoint();
1048	<
1049	<	#endif
1050	<	}
1051	<
1052	<	void SimInfo::setupCutoff() {
1053	<
1054	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1055	<
1056	<	// Check the cutoff policy
1057	<	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1058	<
1059	<	// Set LJ shifting bools to false
1060	<	ljsp_ = false;
1061	<	ljsf_ = false;
1062	<
1063	<	std::string myPolicy;
1064	<	if (forceFieldOptions_.haveCutoffPolicy()){
1065	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1066	<	}else if (simParams_->haveCutoffPolicy()) {
1067	<	myPolicy = simParams_->getCutoffPolicy();
1068	<	}
1069	<
1070	<	if (!myPolicy.empty()){
1071	<	toUpper(myPolicy);
1072	<	if (myPolicy == "MIX") {
1073	<	cp = MIX_CUTOFF_POLICY;
1074	<	} else {
1075	<	if (myPolicy == "MAX") {
1076	<	cp = MAX_CUTOFF_POLICY;
1077	<	} else {
1078	<	if (myPolicy == "TRADITIONAL") {
1079	<	cp = TRADITIONAL_CUTOFF_POLICY;
1080	<	} else {
1081	<	// throw error
1082	<	sprintf( painCave.errMsg,
1083	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1084	<	painCave.isFatal = 1;
1085	<	simError();
1086	<	}
1087	<	}
1088	<	}
1089	<	}
1090	<	notifyFortranCutoffPolicy(&cp);
1091	<
1092	<	// Check the Skin Thickness for neighborlists
1093	<	RealType skin;
1094	<	if (simParams_->haveSkinThickness()) {
1095	<	skin = simParams_->getSkinThickness();
1096	<	notifyFortranSkinThickness(&skin);
1097	<	}
1098	<
1099	<	// Check if the cutoff was set explicitly:
1100	<	if (simParams_->haveCutoffRadius()) {
1101	<	rcut_ = simParams_->getCutoffRadius();
1102	<	if (simParams_->haveSwitchingRadius()) {
1103	<	rsw_  = simParams_->getSwitchingRadius();
1104	<	} else {
1105	<	if (fInfo_.SIM_uses_Charges |
1106	<	fInfo_.SIM_uses_Dipoles |
1107	<	fInfo_.SIM_uses_RF) {
1108	<
1109	<	rsw_ = 0.85 * rcut_;
1110	<	sprintf(painCave.errMsg,
1111	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1112	<	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1113	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1114	<	painCave.isFatal = 0;
1115	<	simError();
1116	<	} else {
1117	<	rsw_ = rcut_;
1118	<	sprintf(painCave.errMsg,
1119	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1120	<	"\tOOPSE will use the same value as the cutoffRadius.\n"
1121	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1122	<	painCave.isFatal = 0;
1123	<	simError();
1124	<	}
1125	<	}
1126	<
1127	<	if (simParams_->haveElectrostaticSummationMethod()) {
1128	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1129	<	toUpper(myMethod);
1130	<
1131	<	if (myMethod == "SHIFTED_POTENTIAL") {
1132	<	ljsp_ = true;
1133	<	} else if (myMethod == "SHIFTED_FORCE") {
1134	<	ljsf_ = true;
1135	<	}
1136	<	}
1137	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1138	<
1139	<	} else {
1140	<
1141	<	// For electrostatic atoms, we'll assume a large safe value:
1142	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1143	<	sprintf(painCave.errMsg,
1144	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1145	<	"\tOOPSE will use a default value of 15.0 angstroms"
1146	<	"\tfor the cutoffRadius.\n");
1147	<	painCave.isFatal = 0;
1148	<	simError();
1149	<	rcut_ = 15.0;
1150	<
1151	<	if (simParams_->haveElectrostaticSummationMethod()) {
1152	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1153	<	toUpper(myMethod);
1154	<
1155	<	// For the time being, we're tethering the LJ shifted behavior to the
1156	<	// electrostaticSummationMethod keyword options
1157	<	if (myMethod == "SHIFTED_POTENTIAL") {
1158	<	ljsp_ = true;
1159	<	} else if (myMethod == "SHIFTED_FORCE") {
1160	<	ljsf_ = true;
1161	<	}
1162	<	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1163	<	if (simParams_->haveSwitchingRadius()){
1164	<	sprintf(painCave.errMsg,
1165	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1166	<	"\teven though the electrostaticSummationMethod was\n"
1167	<	"\tset to %s\n", myMethod.c_str());
1168	<	painCave.isFatal = 1;
1169	<	simError();
1170	<	}
1171	<	}
1172	<	}
1173	<
1174	<	if (simParams_->haveSwitchingRadius()){
1175	<	rsw_ = simParams_->getSwitchingRadius();
1176	<	} else {
1177	<	sprintf(painCave.errMsg,
1178	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1179	<	"\tOOPSE will use a default value of\n"
1180	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1181	<	painCave.isFatal = 0;
1182	<	simError();
1183	<	rsw_ = 0.85 * rcut_;
1184	<	}
1185	<
1186	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1187	<
1188	<	} else {
1189	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1190	<	// We'll punt and let fortran figure out the cutoffs later.
1191	<
1192	<	notifyFortranYouAreOnYourOwn();
1193	<
1194	<	}
1195	<	}
1196	<	}
1197	<
1198	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1199	<
1200	<	int errorOut;
1201	<	int esm =  NONE;
1202	<	int sm = UNDAMPED;
1203	<	RealType alphaVal;
1204	<	RealType dielectric;
1205	<
1206	<	errorOut = isError;
1207	<
1208	<	if (simParams_->haveElectrostaticSummationMethod()) {
1209	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1210	<	toUpper(myMethod);
1211	<	if (myMethod == "NONE") {
1212	<	esm = NONE;
1213	<	} else {
1214	<	if (myMethod == "SWITCHING_FUNCTION") {
1215	<	esm = SWITCHING_FUNCTION;
1216	<	} else {
1217	<	if (myMethod == "SHIFTED_POTENTIAL") {
1218	<	esm = SHIFTED_POTENTIAL;
1219	<	} else {
1220	<	if (myMethod == "SHIFTED_FORCE") {
1221	<	esm = SHIFTED_FORCE;
1222	<	} else {
1223	<	if (myMethod == "REACTION_FIELD") {
1224	<	esm = REACTION_FIELD;
1225	<	dielectric = simParams_->getDielectric();
1226	<	if (!simParams_->haveDielectric()) {
1227	<	// throw warning
1228	<	sprintf( painCave.errMsg,
1229	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1230	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1231	<	painCave.isFatal = 0;
1232	<	simError();
1233	<	}
1234	<	} else {
1235	<	// throw error
1236	<	sprintf( painCave.errMsg,
1237	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1238	<	"\t(Input file specified %s .)\n"
1239	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1240	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1241	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1242	<	painCave.isFatal = 1;
1243	<	simError();
1244	<	}
1245	<	}
1246	<	}
1247	<	}
1248	<	}
1249	<	}
1250	<
1251	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1252	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1253	<	toUpper(myScreen);
1254	<	if (myScreen == "UNDAMPED") {
1255	<	sm = UNDAMPED;
1256	<	} else {
1257	<	if (myScreen == "DAMPED") {
1258	<	sm = DAMPED;
1259	<	if (!simParams_->haveDampingAlpha()) {
1260	<	// first set a cutoff dependent alpha value
1261	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1262	<	alphaVal = 0.5125 - rcut_* 0.025;
1263	<	// for values rcut > 20.5, alpha is zero
1264	<	if (alphaVal < 0) alphaVal = 0;
1265	<
1266	<	// throw warning
1267	<	sprintf( painCave.errMsg,
1268	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1269	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1270	<	painCave.isFatal = 0;
1271	<	simError();
1272	<	} else {
1273	<	alphaVal = simParams_->getDampingAlpha();
1274	<	}
1275	<
1276	<	} else {
1277	<	// throw error
1278	<	sprintf( painCave.errMsg,
1279	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1280	<	"\t(Input file specified %s .)\n"
1281	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1282	<	"or \"damped\".\n", myScreen.c_str() );
1283	<	painCave.isFatal = 1;
1284	<	simError();
1285	<	}
1286	<	}
1287	<	}
1288	<
1289	<	// let's pass some summation method variables to fortran
1290	<	setElectrostaticSummationMethod( &esm );
1291	<	setFortranElectrostaticMethod( &esm );
1292	<	setScreeningMethod( &sm );
1293	<	setDampingAlpha( &alphaVal );
1294	<	setReactionFieldDielectric( &dielectric );
1295	<	initFortranFF( &errorOut );
1296	<	}
1297	<
1298	<	void SimInfo::setupSwitchingFunction() {
1299	<	int ft = CUBIC;
1300	<
1301	<	if (simParams_->haveSwitchingFunctionType()) {
1302	<	std::string funcType = simParams_->getSwitchingFunctionType();
1303	<	toUpper(funcType);
1304	<	if (funcType == "CUBIC") {
1305	<	ft = CUBIC;
1306	<	} else {
1307	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1308	<	ft = FIFTH_ORDER_POLY;
1309	<	} else {
1310	<	// throw error
1311	<	sprintf( painCave.errMsg,
1312	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1313	<	painCave.isFatal = 1;
1314	<	simError();
1315	<	}
1316	<	}
1317	<	}
1318	<
1319	<	// send switching function notification to switcheroo
1320	<	setFunctionType(&ft);
1321	<
933	>	topologyDone_ = true;
934		}
935
1324	–	void SimInfo::setupAccumulateBoxDipole() {
1325	–
1326	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1327	–	if ( simParams_->haveAccumulateBoxDipole() )
1328	–	if ( simParams_->getAccumulateBoxDipole() ) {
1329	–	setAccumulateBoxDipole();
1330	–	calcBoxDipole_ = true;
1331	–	}
1332	–
1333	–	}
1334	–
936		void SimInfo::addProperty(GenericData* genData) {
937		properties_.addProperty(genData);
938		}
939
940	<	void SimInfo::removeProperty(const std::string& propName) {
940	>	void SimInfo::removeProperty(const string& propName) {
941		properties_.removeProperty(propName);
942		}
943
#	Line 1344 | Line 945 | namespace oopse {
945		properties_.clearProperties();
946		}
947
948	<	std::vector<std::string> SimInfo::getPropertyNames() {
948	>	vector<string> SimInfo::getPropertyNames() {
949		return properties_.getPropertyNames();
950		}
951
952	<	std::vector<GenericData*> SimInfo::getProperties() {
952	>	vector<GenericData*> SimInfo::getProperties() {
953		return properties_.getProperties();
954		}
955
956	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
956	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
957		return properties_.getPropertyByName(propName);
958		}
959
#	Line 1366 | Line 967 | namespace oopse {
967		Molecule* mol;
968		RigidBody* rb;
969		Atom* atom;
970	+	CutoffGroup* cg;
971		SimInfo::MoleculeIterator mi;
972		Molecule::RigidBodyIterator rbIter;
973	<	Molecule::AtomIterator atomIter;;
973	>	Molecule::AtomIterator atomIter;
974	>	Molecule::CutoffGroupIterator cgIter;
975
976		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
977
#	Line 1378 | Line 981 | namespace oopse {
981
982		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
983		rb->setSnapshotManager(sman_);
984	+	}
985	+
986	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
987	+	cg->setSnapshotManager(sman_);
988		}
989		}
990
#	Line 1435 | Line 1042 | namespace oopse {
1042
1043		}
1044
1045	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1045	>	ostream& operator <<(ostream& o, SimInfo& info) {
1046
1047		return o;
1048		}
#	Line 1478 | Line 1085 | namespace oopse {
1085
1086
1087		[  Ixx -Ixy  -Ixz ]
1088	<	J =| -Iyx  Iyy  -Iyz |
1088	>	J =| -Iyx  Iyy  -Iyz |
1089		[ -Izx -Iyz   Izz ]
1090		*/
1091
#	Line 1585 | Line 1192 | namespace oopse {
1192		return IOIndexToIntegrableObject.at(index);
1193		}
1194
1195	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1195	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1196		IOIndexToIntegrableObject= v;
1197		}
1198
#	Line 1607 | Line 1214 | namespace oopse {
1214
1215		det = intTensor.determinant();
1216		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1217	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1218		return;
1219		}
1220
#	Line 1623 | Line 1230 | namespace oopse {
1230
1231		detI = intTensor.determinant();
1232		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233	<	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1233	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1234		return;
1235		}
1236		/*
1237	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1237	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1238		assert( v.size() == nAtoms_ + nRigidBodies_);
1239		sdByGlobalIndex_ = v;
1240		}
#	Line 1637 | Line 1244 | namespace oopse {
1244		return sdByGlobalIndex_.at(index);
1245		}
1246		*/
1247	<	}//end namespace oopse
1247	>	int SimInfo::getNGlobalConstraints() {
1248	>	int nGlobalConstraints;
1249	>	#ifdef IS_MPI
1250	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1251	>	MPI_COMM_WORLD);
1252	>	#else
1253	>	nGlobalConstraints =  nConstraints_;
1254	>	#endif
1255	>	return nGlobalConstraints;
1256	>	}
1257
1258	+	}//end namespace OpenMD
1259	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

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