[ViewVC] Diff of: OpenMD/branches/development/src/brains/SimInfo.cpp

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs.
Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

#	Line 36 \| Line 36
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] Vardeman & Gezelter, in progress (2009).
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/fSwitchingFunctionType.h"
59	–	#include "UseTheForce/doForces_interface.h"
60	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61	–	#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	<
68	<
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"
72	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	+	using namespace std;
69		namespace OpenMD {
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	–	}
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();
118	<
119	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroupStamp(j);
121	<	nAtomsInGroups += cgStamp->getNMembers();
122	<	}
123	<
124	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	<
126	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127	<
128	<	//calculate atoms in rigid bodies
129	<	int nAtomsInRigidBodies = 0;
130	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	<
132	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	<	rbStamp = molStamp->getRigidBodyStamp(j);
134	<	nAtomsInRigidBodies += rbStamp->getNMembers();
135	<	}
136	<
137	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	<
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	<	//every free atom (atom does not belong to cutoff groups) is a cutoff
110	<	//group therefore the total number of cutoff groups in the system is
111	<	//equal to the total number of atoms minus number of atoms belong to
112	<	//cutoff group defined in meta-data file plus the number of cutoff
113	<	//groups defined in meta-data file
114	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
115	<
116	<	//every free atom (atom does not belong to rigid bodies) is an
117	<	//integrable object therefore the total number of integrable objects
118	<	//in the system is equal to the total number of atoms minus number of
119	<	//atoms belong to rigid body defined in meta-data file plus the number
120	<	//of rigid bodies defined in meta-data file
121	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
122	<	+ nGlobalRigidBodies_;
123	<
124	<	nGlobalMols_ = molStampIds_.size();
158	<	molToProcMap_.resize(nGlobalMols_);
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 170 \| Line 156 \| namespace OpenMD {
156		delete forceField_;
157		}
158
173	–	int SimInfo::getNGlobalConstraints() {
174	–	int nGlobalConstraints;
175	–	#ifdef IS_MPI
176	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
177	–	MPI_COMM_WORLD);
178	–	#else
179	–	nGlobalConstraints = nConstraints_;
180	–	#endif
181	–	return nGlobalConstraints;
182	–	}
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 198 \| Line 174 \| namespace OpenMD {
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 234 \| Line 210 \| namespace OpenMD {
210		} else {
211		return false;
212		}
237	–
238	–
213		}
214
215
#	Line 251 \| Line 225 \| namespace OpenMD {
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 272 \| Line 250 \| namespace OpenMD {
250		ndf_local += 3;
251		}
252		}
275	–
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 298 \| Line 286 \| namespace OpenMD {
286		fdf_ = fdf_local;
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 353 \| Line 360 \| namespace OpenMD {
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 374 \| Line 381 \| namespace OpenMD {
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 386 \| Line 393 \| namespace OpenMD {
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 500 \| Line 507 \| namespace OpenMD {
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 514 \| Line 521 \| namespace OpenMD {
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 527 \| Line 534 \| namespace OpenMD {
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 539 \| Line 546 \| namespace OpenMD {
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 653 \| Line 660 \| namespace OpenMD {
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 676 \| Line 683 \| namespace OpenMD {
683		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684		}
685
679	–	void SimInfo::update() {
680	–
681	–	setupSimType();
682	–
683	–	#ifdef IS_MPI
684	–	setupFortranParallel();
685	–	#endif
686	–
687	–	setupFortranSim();
686
687	<	//setup fortran force field
688	<	/** @deprecate */
689	<	int isError = 0;
690	<
691	<	setupCutoff();
692	<
693	<	setupElectrostaticSummationMethod( isError );
694	<	setupSwitchingFunction();
695	<	setupAccumulateBoxDipole();
698	<
699	<	if(isError){
700	<	sprintf( painCave.errMsg,
701	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
702	<	painCave.isFatal = 1;
703	<	simError();
704	<	}
705	<
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();
709	–
710	–	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	<	}
730	<
731	<	void SimInfo::setupSimType() {
732	<	std::set<AtomType*>::iterator i;
733	<	std::set<AtomType*> atomTypes;
734	<	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;
740	<	int useCharge = 0;
741	<	int useDirectional = 0;
742	<	int useDipole = 0;
743	<	int useGayBerne = 0;
744	<	int useSticky = 0;
745	<	int useStickyPower = 0;
746	<	int useShape = 0;
747	<	int useFLARB = 0; //it is not in AtomType yet
748	<	int useDirectionalAtom = 0;
749	<	int useElectrostatics = 0;
750	<	//usePBC and useRF are from simParams
751	<	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
752	<	int useRF;
753	<	int useSF;
754	<	int useSP;
755	<	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
760	<	useRF = 0;
761	<	useSF = 0;
762	<	useSP = 0;
763	<	useBoxDipole = 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();
787	<	useElectrostatic \|= (*i)->isElectrostatic();
788	<	useEAM \|= (*i)->isEAM();
789	<	useSC \|= (*i)->isSC();
790	<	useCharge \|= (*i)->isCharge();
791	<	useDirectional \|= (*i)->isDirectional();
792	<	useDipole \|= (*i)->isDipole();
793	<	useGayBerne \|= (*i)->isGayBerne();
794	<	useSticky \|= (*i)->isSticky();
795	<	useStickyPower \|= (*i)->isStickyPower();
796	<	useShape \|= (*i)->isShape();
797	<	}
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;
805	<	}
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	+	temp = usesDirectional;
809	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	+
811	+	temp = usesMetallic;
812	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	+
814	+	temp = usesElectrostatic;
815	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816
817	<	temp = usePBC;
818	<	MPI_Allreduce(&temp, &usePBC, 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 = useDirectionalAtom;
822	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	>	usesDirectionalAtoms_ = usesDirectional;
822	>	usesMetallicAtoms_ = usesMetallic;
823	>	usesElectrostaticAtoms_ = usesElectrostatic;
824	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
825
826	<	temp = useLennardJones;
827	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	>	#endif
827	>
828	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
829	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
830	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
831	>	}
832
819	–	temp = useElectrostatics;
820	–	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833
834	<	temp = useCharge;
835	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834	>	vector<int> SimInfo::getGlobalAtomIndices() {
835	>	SimInfo::MoleculeIterator mi;
836	>	Molecule* mol;
837	>	Molecule::AtomIterator ai;
838	>	Atom* atom;
839
840	<	temp = useDipole;
826	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	<
828	<	temp = useSticky;
829	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	<
831	<	temp = useStickyPower;
832	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
841
842	<	temp = useGayBerne;
843	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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
837	–	temp = useEAM;
838	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851
852	<	temp = useSC;
853	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	<
855	<	temp = useShape;
856	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	vector<int> SimInfo::getGlobalGroupIndices() {
853	>	SimInfo::MoleculeIterator mi;
854	>	Molecule* mol;
855	>	Molecule::CutoffGroupIterator ci;
856	>	CutoffGroup* cg;
857
858	<	temp = useFLARB;
859	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	<
861	<	temp = useRF;
862	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	<
864	<	temp = useSF;
865	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	<
867	<	temp = useSP;
868	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
869	<
858	<	temp = useBoxDipole;
859	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	<
861	<	temp = useAtomicVirial_;
862	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	<
864	<	#endif
865	<
866	<	fInfo_.SIM_uses_PBC = usePBC;
867	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
868	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
869	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
870	<	fInfo_.SIM_uses_Charges = useCharge;
871	<	fInfo_.SIM_uses_Dipoles = useDipole;
872	<	fInfo_.SIM_uses_Sticky = useSticky;
873	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
874	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
875	<	fInfo_.SIM_uses_EAM = useEAM;
876	<	fInfo_.SIM_uses_SC = useSC;
877	<	fInfo_.SIM_uses_Shapes = useShape;
878	<	fInfo_.SIM_uses_FLARB = useFLARB;
879	<	fInfo_.SIM_uses_RF = useRF;
880	<	fInfo_.SIM_uses_SF = useSF;
881	<	fInfo_.SIM_uses_SP = useSP;
882	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
883	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
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	<	void SimInfo::setupFortranSim() {
873	<	int isError;
872	>
873	>	void SimInfo::prepareTopology() {
874		int nExclude, nOneTwo, nOneThree, nOneFour;
889	–	std::vector<int> fortranGlobalGroupMembership;
890	–
891	–	isError = 0;
875
893	–	//globalGroupMembership_ is filled by SimCreator
894	–	for (int i = 0; i < nGlobalAtoms_; i++) {
895	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
896	–	}
897	–
876		//calculate mass ratio of cutoff group
899	–	std::vector<RealType> mfact;
877		SimInfo::MoleculeIterator mi;
878		Molecule* mol;
879		Molecule::CutoffGroupIterator ci;
#	Line 905 \| Line 882 \| namespace OpenMD {
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 !!!)
926	<	std::vector<int> identArray;
911	>	// Build the identArray_
912
913	<	//to avoid memory reallocation, reserve enough space identArray
914	<	identArray.reserve(getNAtoms());
930	<
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		}
936	–
937	–	//fill molMembershipArray
938	–	//molMembershipArray is filled by SimCreator
939	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
940	–	for (int i = 0; i < nGlobalAtoms_; i++) {
941	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
942	–	}
920
921	<	//setup fortran simulation
921	>	//scan topology
922
923		nExclude = excludedInteractions_.getSize();
924		nOneTwo = oneTwoInteractions_.getSize();
#	Line 953 \| Line 930 \| namespace OpenMD {
930		int* oneThreeList = oneThreeInteractions_.getPairList();
931		int* oneFourList = oneFourInteractions_.getPairList();
932
933	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
957	<	&nExclude, excludeList,
958	<	&nOneTwo, oneTwoList,
959	<	&nOneThree, oneThreeList,
960	<	&nOneFour, oneFourList,
961	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
962	<	&fortranGlobalGroupMembership[0], &isError);
963	<
964	<	if( isError ){
965	<
966	<	sprintf( painCave.errMsg,
967	<	"There was an error setting the simulation information in fortran.\n" );
968	<	painCave.isFatal = 1;
969	<	painCave.severity = OPENMD_ERROR;
970	<	simError();
971	<	}
972	<
973	<
974	<	sprintf( checkPointMsg,
975	<	"succesfully sent the simulation information to fortran.\n");
976	<
977	<	errorCheckPoint();
978	<
979	<	// Setup number of neighbors in neighbor list if present
980	<	if (simParams_->haveNeighborListNeighbors()) {
981	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
982	<	setNeighbors(&nlistNeighbors);
983	<	}
984	<
985	<
986	<	}
987	<
988	<
989	<	void SimInfo::setupFortranParallel() {
990	<	#ifdef IS_MPI
991	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
992	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
993	<	std::vector<int> localToGlobalCutoffGroupIndex;
994	<	SimInfo::MoleculeIterator mi;
995	<	Molecule::AtomIterator ai;
996	<	Molecule::CutoffGroupIterator ci;
997	<	Molecule* mol;
998	<	Atom* atom;
999	<	CutoffGroup* cg;
1000	<	mpiSimData parallelData;
1001	<	int isError;
1002	<
1003	<	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1004	<
1005	<	//local index(index in DataStorge) of atom is important
1006	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1007	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1008	<	}
1009	<
1010	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1011	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1012	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1013	<	}
1014	<
1015	<	}
1016	<
1017	<	//fill up mpiSimData struct
1018	<	parallelData.nMolGlobal = getNGlobalMolecules();
1019	<	parallelData.nMolLocal = getNMolecules();
1020	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1021	<	parallelData.nAtomsLocal = getNAtoms();
1022	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1023	<	parallelData.nGroupsLocal = getNCutoffGroups();
1024	<	parallelData.myNode = worldRank;
1025	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1026	<
1027	<	//pass mpiSimData struct and index arrays to fortran
1028	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1029	<	&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
1030	<	&localToGlobalCutoffGroupIndex[0], &isError);
1031	<
1032	<	if (isError) {
1033	<	sprintf(painCave.errMsg,
1034	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1035	<	painCave.isFatal = 1;
1036	<	simError();
1037	<	}
1038	<
1039	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1040	<	errorCheckPoint();
1041	<
1042	<	#endif
1043	<	}
1044	<
1045	<	void SimInfo::setupCutoff() {
1046	<
1047	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1048	<
1049	<	// Check the cutoff policy
1050	<	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1051	<
1052	<	// Set LJ shifting bools to false
1053	<	ljsp_ = 0;
1054	<	ljsf_ = 0;
1055	<
1056	<	std::string myPolicy;
1057	<	if (forceFieldOptions_.haveCutoffPolicy()){
1058	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1059	<	}else if (simParams_->haveCutoffPolicy()) {
1060	<	myPolicy = simParams_->getCutoffPolicy();
1061	<	}
1062	<
1063	<	if (!myPolicy.empty()){
1064	<	toUpper(myPolicy);
1065	<	if (myPolicy == "MIX") {
1066	<	cp = MIX_CUTOFF_POLICY;
1067	<	} else {
1068	<	if (myPolicy == "MAX") {
1069	<	cp = MAX_CUTOFF_POLICY;
1070	<	} else {
1071	<	if (myPolicy == "TRADITIONAL") {
1072	<	cp = TRADITIONAL_CUTOFF_POLICY;
1073	<	} else {
1074	<	// throw error
1075	<	sprintf( painCave.errMsg,
1076	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1077	<	painCave.isFatal = 1;
1078	<	simError();
1079	<	}
1080	<	}
1081	<	}
1082	<	}
1083	<	notifyFortranCutoffPolicy(&cp);
1084	<
1085	<	// Check the Skin Thickness for neighborlists
1086	<	RealType skin;
1087	<	if (simParams_->haveSkinThickness()) {
1088	<	skin = simParams_->getSkinThickness();
1089	<	notifyFortranSkinThickness(&skin);
1090	<	}
1091	<
1092	<	// Check if the cutoff was set explicitly:
1093	<	if (simParams_->haveCutoffRadius()) {
1094	<	rcut_ = simParams_->getCutoffRadius();
1095	<	if (simParams_->haveSwitchingRadius()) {
1096	<	rsw_ = simParams_->getSwitchingRadius();
1097	<	} else {
1098	<	if (fInfo_.SIM_uses_Charges \|
1099	<	fInfo_.SIM_uses_Dipoles \|
1100	<	fInfo_.SIM_uses_RF) {
1101	<
1102	<	rsw_ = 0.85 * rcut_;
1103	<	sprintf(painCave.errMsg,
1104	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1105	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1106	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1107	<	painCave.isFatal = 0;
1108	<	simError();
1109	<	} else {
1110	<	rsw_ = rcut_;
1111	<	sprintf(painCave.errMsg,
1112	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1113	<	"\tOpenMD will use the same value as the cutoffRadius.\n"
1114	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1115	<	painCave.isFatal = 0;
1116	<	simError();
1117	<	}
1118	<	}
1119	<
1120	<	if (simParams_->haveElectrostaticSummationMethod()) {
1121	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1122	<	toUpper(myMethod);
1123	<
1124	<	if (myMethod == "SHIFTED_POTENTIAL") {
1125	<	ljsp_ = 1;
1126	<	} else if (myMethod == "SHIFTED_FORCE") {
1127	<	ljsf_ = 1;
1128	<	}
1129	<	}
1130	<
1131	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1132	<
1133	<	} else {
1134	<
1135	<	// For electrostatic atoms, we'll assume a large safe value:
1136	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1137	<	sprintf(painCave.errMsg,
1138	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1139	<	"\tOpenMD will use a default value of 15.0 angstroms"
1140	<	"\tfor the cutoffRadius.\n");
1141	<	painCave.isFatal = 0;
1142	<	simError();
1143	<	rcut_ = 15.0;
1144	<
1145	<	if (simParams_->haveElectrostaticSummationMethod()) {
1146	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1147	<	toUpper(myMethod);
1148	<
1149	<	// For the time being, we're tethering the LJ shifted behavior to the
1150	<	// electrostaticSummationMethod keyword options
1151	<	if (myMethod == "SHIFTED_POTENTIAL") {
1152	<	ljsp_ = 1;
1153	<	} else if (myMethod == "SHIFTED_FORCE") {
1154	<	ljsf_ = 1;
1155	<	}
1156	<	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1157	<	if (simParams_->haveSwitchingRadius()){
1158	<	sprintf(painCave.errMsg,
1159	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1160	<	"\teven though the electrostaticSummationMethod was\n"
1161	<	"\tset to %s\n", myMethod.c_str());
1162	<	painCave.isFatal = 1;
1163	<	simError();
1164	<	}
1165	<	}
1166	<	}
1167	<
1168	<	if (simParams_->haveSwitchingRadius()){
1169	<	rsw_ = simParams_->getSwitchingRadius();
1170	<	} else {
1171	<	sprintf(painCave.errMsg,
1172	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1173	<	"\tOpenMD will use a default value of\n"
1174	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1175	<	painCave.isFatal = 0;
1176	<	simError();
1177	<	rsw_ = 0.85 * rcut_;
1178	<	}
1179	<
1180	<	Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1181	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1182	<
1183	<	} else {
1184	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1185	<	// We'll punt and let fortran figure out the cutoffs later.
1186	<
1187	<	notifyFortranYouAreOnYourOwn();
1188	<
1189	<	}
1190	<	}
1191	<	}
1192	<
1193	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1194	<
1195	<	int errorOut;
1196	<	ElectrostaticSummationMethod esm = NONE;
1197	<	ElectrostaticScreeningMethod sm = UNDAMPED;
1198	<	RealType alphaVal;
1199	<	RealType dielectric;
1200	<
1201	<	errorOut = isError;
1202	<
1203	<	if (simParams_->haveElectrostaticSummationMethod()) {
1204	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1205	<	toUpper(myMethod);
1206	<	if (myMethod == "NONE") {
1207	<	esm = NONE;
1208	<	} else {
1209	<	if (myMethod == "SWITCHING_FUNCTION") {
1210	<	esm = SWITCHING_FUNCTION;
1211	<	} else {
1212	<	if (myMethod == "SHIFTED_POTENTIAL") {
1213	<	esm = SHIFTED_POTENTIAL;
1214	<	} else {
1215	<	if (myMethod == "SHIFTED_FORCE") {
1216	<	esm = SHIFTED_FORCE;
1217	<	} else {
1218	<	if (myMethod == "REACTION_FIELD") {
1219	<	esm = REACTION_FIELD;
1220	<	dielectric = simParams_->getDielectric();
1221	<	if (!simParams_->haveDielectric()) {
1222	<	// throw warning
1223	<	sprintf( painCave.errMsg,
1224	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1225	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1226	<	painCave.isFatal = 0;
1227	<	simError();
1228	<	}
1229	<	} else {
1230	<	// throw error
1231	<	sprintf( painCave.errMsg,
1232	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1233	<	"\t(Input file specified %s .)\n"
1234	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1235	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1236	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1237	<	painCave.isFatal = 1;
1238	<	simError();
1239	<	}
1240	<	}
1241	<	}
1242	<	}
1243	<	}
1244	<	}
1245	<
1246	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1247	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1248	<	toUpper(myScreen);
1249	<	if (myScreen == "UNDAMPED") {
1250	<	sm = UNDAMPED;
1251	<	} else {
1252	<	if (myScreen == "DAMPED") {
1253	<	sm = DAMPED;
1254	<	if (!simParams_->haveDampingAlpha()) {
1255	<	// first set a cutoff dependent alpha value
1256	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1257	<	alphaVal = 0.5125 - rcut_* 0.025;
1258	<	// for values rcut > 20.5, alpha is zero
1259	<	if (alphaVal < 0) alphaVal = 0;
1260	<
1261	<	// throw warning
1262	<	sprintf( painCave.errMsg,
1263	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1264	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1265	<	painCave.isFatal = 0;
1266	<	simError();
1267	<	} else {
1268	<	alphaVal = simParams_->getDampingAlpha();
1269	<	}
1270	<
1271	<	} else {
1272	<	// throw error
1273	<	sprintf( painCave.errMsg,
1274	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1275	<	"\t(Input file specified %s .)\n"
1276	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1277	<	"or \"damped\".\n", myScreen.c_str() );
1278	<	painCave.isFatal = 1;
1279	<	simError();
1280	<	}
1281	<	}
1282	<	}
1283	<
1284	<
1285	<	Electrostatic::setElectrostaticSummationMethod( esm );
1286	<	Electrostatic::setElectrostaticScreeningMethod( sm );
1287	<	Electrostatic::setDampingAlpha( alphaVal );
1288	<	Electrostatic::setReactionFieldDielectric( dielectric );
1289	<	initFortranFF( &errorOut );
933	>	topologyDone_ = true;
934		}
935
1292	–	void SimInfo::setupSwitchingFunction() {
1293	–	int ft = CUBIC;
1294	–
1295	–	if (simParams_->haveSwitchingFunctionType()) {
1296	–	std::string funcType = simParams_->getSwitchingFunctionType();
1297	–	toUpper(funcType);
1298	–	if (funcType == "CUBIC") {
1299	–	ft = CUBIC;
1300	–	} else {
1301	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1302	–	ft = FIFTH_ORDER_POLY;
1303	–	} else {
1304	–	// throw error
1305	–	sprintf( painCave.errMsg,
1306	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1307	–	painCave.isFatal = 1;
1308	–	simError();
1309	–	}
1310	–	}
1311	–	}
1312	–
1313	–	// send switching function notification to switcheroo
1314	–	setFunctionType(&ft);
1315	–
1316	–	}
1317	–
1318	–	void SimInfo::setupAccumulateBoxDipole() {
1319	–
1320	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1321	–	if ( simParams_->haveAccumulateBoxDipole() )
1322	–	if ( simParams_->getAccumulateBoxDipole() ) {
1323	–	setAccumulateBoxDipole();
1324	–	calcBoxDipole_ = true;
1325	–	}
1326	–
1327	–	}
1328	–
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 1338 \| Line 945 \| namespace OpenMD {
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 1360 \| Line 967 \| namespace OpenMD {
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 1372 \| Line 981 \| namespace OpenMD {
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 1429 \| Line 1042 \| namespace OpenMD {
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 1472 \| Line 1085 \| namespace OpenMD {
1085
1086
1087		[ Ixx -Ixy -Ixz ]
1088	<	J =\| -Iyx Iyy -Iyz \|
1088	>	J =\| -Iyx Iyy -Iyz \|
1089		[ -Izx -Iyz Izz ]
1090		*/
1091
#	Line 1579 \| Line 1192 \| namespace OpenMD {
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 1601 \| Line 1214 \| namespace OpenMD {
1214
1215		det = intTensor.determinant();
1216		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217	<	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1217	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,geomCnst)*sqrt(det);
1218		return;
1219		}
1220
#	Line 1617 \| Line 1230 \| namespace OpenMD {
1230
1231		detI = intTensor.determinant();
1232		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233	<	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1233	>	volume = 4.0/3.0NumericConstant::PIpow(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 1631 \| Line 1244 \| namespace OpenMD {
1244		return sdByGlobalIndex_.at(index);
1245		}
1246		*/
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

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Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs. Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs.
Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC