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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1668 by gezelter, Fri Jan 6 19:03:05 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/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	<
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	+	using namespace std;
69		namespace OpenMD {
78	–	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	–	}
70
71		SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72		forceField_(ff), simParams_(simParams),
#	Line 92 \| Line 75 \| namespace OpenMD {
75		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(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), 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();
121	<
122	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	<	cgStamp = molStamp->getCutoffGroupStamp(j);
124	<	nAtomsInGroups += cgStamp->getNMembers();
125	<	}
126	<
127	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128	<
129	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130	<
131	<	//calculate atoms in rigid bodies
132	<	int nAtomsInRigidBodies = 0;
133	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134	<
135	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
136	<	rbStamp = molStamp->getRigidBodyStamp(j);
137	<	nAtomsInRigidBodies += rbStamp->getNMembers();
138	<	}
139	<
140	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	<
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();
161	<	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 173 \| Line 156 \| namespace OpenMD {
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 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 237 \| Line 210 \| namespace OpenMD {
210		} else {
211		return false;
212		}
240	–
241	–
213		}
214
215
#	Line 256 \| Line 227 \| namespace OpenMD {
227		void SimInfo::calcNdf() {
228		int ndf_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231		Molecule* mol;
232		StuntDouble* integrableObject;
233
#	Line 302 \| Line 273 \| namespace OpenMD {
273		#endif
274		return fdf_;
275		}
276	+
277	+	unsigned int SimInfo::getNLocalCutoffGroups(){
278	+	int nLocalCutoffAtoms = 0;
279	+	Molecule* mol;
280	+	MoleculeIterator mi;
281	+	CutoffGroup* cg;
282	+	Molecule::CutoffGroupIterator ci;
283
284	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
285	+
286	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
287	+	cg = mol->nextCutoffGroup(ci)) {
288	+	nLocalCutoffAtoms += cg->getNumAtom();
289	+
290	+	}
291	+	}
292	+
293	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
294	+	}
295	+
296		void SimInfo::calcNdfRaw() {
297		int ndfRaw_local;
298
299		MoleculeIterator i;
300	<	std::vector<StuntDouble*>::iterator j;
300	>	vector<StuntDouble*>::iterator j;
301		Molecule* mol;
302		StuntDouble* integrableObject;
303
#	Line 356 \| Line 346 \| namespace OpenMD {
346
347		void SimInfo::addInteractionPairs(Molecule* mol) {
348		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
349	<	std::vector<Bond*>::iterator bondIter;
350	<	std::vector<Bend*>::iterator bendIter;
351	<	std::vector<Torsion*>::iterator torsionIter;
352	<	std::vector<Inversion*>::iterator inversionIter;
349	>	vector<Bond*>::iterator bondIter;
350	>	vector<Bend*>::iterator bendIter;
351	>	vector<Torsion*>::iterator torsionIter;
352	>	vector<Inversion*>::iterator inversionIter;
353		Bond* bond;
354		Bend* bend;
355		Torsion* torsion;
#	Line 377 \| Line 367 \| namespace OpenMD {
367		// always be excluded. These are done at the bottom of this
368		// function.
369
370	<	std::map<int, std::set<int> > atomGroups;
370	>	map<int, set<int> > atomGroups;
371		Molecule::RigidBodyIterator rbIter;
372		RigidBody* rb;
373		Molecule::IntegrableObjectIterator ii;
#	Line 389 \| Line 379 \| namespace OpenMD {
379
380		if (integrableObject->isRigidBody()) {
381		rb = static_cast<RigidBody*>(integrableObject);
382	<	std::vector<Atom*> atoms = rb->getAtoms();
383	<	std::set<int> rigidAtoms;
382	>	vector<Atom*> atoms = rb->getAtoms();
383	>	set<int> rigidAtoms;
384		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
385		rigidAtoms.insert(atoms[i]->getGlobalIndex());
386		}
387		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
388	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
389		}
390		} else {
391	<	std::set<int> oneAtomSet;
391	>	set<int> oneAtomSet;
392		oneAtomSet.insert(integrableObject->getGlobalIndex());
393	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
393	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
394		}
395		}
396
#	Line 503 \| Line 493 \| namespace OpenMD {
493
494		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
495		rb = mol->nextRigidBody(rbIter)) {
496	<	std::vector<Atom*> atoms = rb->getAtoms();
496	>	vector<Atom*> atoms = rb->getAtoms();
497		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
498		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
499		a = atoms[i]->getGlobalIndex();
#	Line 517 \| Line 507 \| namespace OpenMD {
507
508		void SimInfo::removeInteractionPairs(Molecule* mol) {
509		ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
510	<	std::vector<Bond*>::iterator bondIter;
511	<	std::vector<Bend*>::iterator bendIter;
512	<	std::vector<Torsion*>::iterator torsionIter;
513	<	std::vector<Inversion*>::iterator inversionIter;
510	>	vector<Bond*>::iterator bondIter;
511	>	vector<Bend*>::iterator bendIter;
512	>	vector<Torsion*>::iterator torsionIter;
513	>	vector<Inversion*>::iterator inversionIter;
514		Bond* bond;
515		Bend* bend;
516		Torsion* torsion;
#	Line 530 \| Line 520 \| namespace OpenMD {
520		int c;
521		int d;
522
523	<	std::map<int, std::set<int> > atomGroups;
523	>	map<int, set<int> > atomGroups;
524		Molecule::RigidBodyIterator rbIter;
525		RigidBody* rb;
526		Molecule::IntegrableObjectIterator ii;
#	Line 542 \| Line 532 \| namespace OpenMD {
532
533		if (integrableObject->isRigidBody()) {
534		rb = static_cast<RigidBody*>(integrableObject);
535	<	std::vector<Atom*> atoms = rb->getAtoms();
536	<	std::set<int> rigidAtoms;
535	>	vector<Atom*> atoms = rb->getAtoms();
536	>	set<int> rigidAtoms;
537		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
538		rigidAtoms.insert(atoms[i]->getGlobalIndex());
539		}
540		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
541	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
541	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
542		}
543		} else {
544	<	std::set<int> oneAtomSet;
544	>	set<int> oneAtomSet;
545		oneAtomSet.insert(integrableObject->getGlobalIndex());
546	<	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
546	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
547		}
548		}
549
#	Line 656 \| Line 646 \| namespace OpenMD {
646
647		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
648		rb = mol->nextRigidBody(rbIter)) {
649	<	std::vector<Atom*> atoms = rb->getAtoms();
649	>	vector<Atom*> atoms = rb->getAtoms();
650		for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
651		for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
652		a = atoms[i]->getGlobalIndex();
#	Line 679 \| Line 669 \| namespace OpenMD {
669		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
670		}
671
682	–	void SimInfo::update() {
672
673	<	setupSimType();
674	<
675	<	#ifdef IS_MPI
676	<	setupFortranParallel();
677	<	#endif
678	<
679	<	setupFortranSim();
680	<
681	<	//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	<
673	>	/**
674	>	* update
675	>	*
676	>	* Performs the global checks and variable settings after the
677	>	* objects have been created.
678	>	*
679	>	*/
680	>	void SimInfo::update() {
681	>	setupSimVariables();
682		calcNdf();
683		calcNdfRaw();
684		calcNdfTrans();
712	–
713	–	fortranInitialized_ = true;
685		}
686	<
687	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
686	>
687	>	/**
688	>	* getSimulatedAtomTypes
689	>	*
690	>	* Returns an STL set of AtomType* that are actually present in this
691	>	* simulation. Must query all processors to assemble this information.
692	>	*
693	>	*/
694	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
695		SimInfo::MoleculeIterator mi;
696		Molecule* mol;
697		Molecule::AtomIterator ai;
698		Atom* atom;
699	<	std::set<AtomType*> atomTypes;
700	<
699	>	set<AtomType*> atomTypes;
700	>
701		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
702	<
703	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
702	>	for(atom = mol->beginAtom(ai); atom != NULL;
703	>	atom = mol->nextAtom(ai)) {
704		atomTypes.insert(atom->getAtomType());
705	<	}
706	<
707	<	}
705	>	}
706	>	}
707	>
708	>	#ifdef IS_MPI
709
710	<	return atomTypes;
711	<	}
733	<
734	<	void SimInfo::setupSimType() {
735	<	std::set<AtomType*>::iterator i;
736	<	std::set<AtomType*> atomTypes;
737	<	atomTypes = getUniqueAtomTypes();
710	>	// loop over the found atom types on this processor, and add their
711	>	// numerical idents to a vector:
712
713	<	int useLennardJones = 0;
714	<	int useElectrostatic = 0;
715	<	int useEAM = 0;
716	<	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;
713	>	vector<int> foundTypes;
714	>	set<AtomType*>::iterator i;
715	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
716	>	foundTypes.push_back( (*i)->getIdent() );
717
718	<	std::string myMethod;
718	>	// count_local holds the number of found types on this processor
719	>	int count_local = foundTypes.size();
720
721	<	// set the useRF logical
763	<	useRF = 0;
764	<	useSF = 0;
765	<	useSP = 0;
766	<	useBoxDipole = 0;
721	>	int nproc = MPI::COMM_WORLD.Get_size();
722
723	+	// we need arrays to hold the counts and displacement vectors for
724	+	// all processors
725	+	vector<int> counts(nproc, 0);
726	+	vector<int> disps(nproc, 0);
727
728	<	if (simParams_->haveElectrostaticSummationMethod()) {
729	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
730	<	toUpper(myMethod);
731	<	if (myMethod == "REACTION_FIELD"){
732	<	useRF = 1;
733	<	} else if (myMethod == "SHIFTED_FORCE"){
734	<	useSF = 1;
735	<	} else if (myMethod == "SHIFTED_POTENTIAL"){
736	<	useSP = 1;
737	<	}
728	>	// fill the counts array
729	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
730	>	1, MPI::INT);
731	>
732	>	// use the processor counts to compute the displacement array
733	>	disps[0] = 0;
734	>	int totalCount = counts[0];
735	>	for (int iproc = 1; iproc < nproc; iproc++) {
736	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
737	>	totalCount += counts[iproc];
738		}
739	+
740	+	// we need a (possibly redundant) set of all found types:
741	+	vector<int> ftGlobal(totalCount);
742
743	<	if (simParams_->haveAccumulateBoxDipole())
744	<	if (simParams_->getAccumulateBoxDipole())
745	<	useBoxDipole = 1;
743	>	// now spray out the foundTypes to all the other processors:
744	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
745	>	&ftGlobal[0], &counts[0], &disps[0],
746	>	MPI::INT);
747
748	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
748	>	vector<int>::iterator j;
749
750	<	//loop over all of the atom types
751	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
752	<	useLennardJones \|= (*i)->isLennardJones();
790	<	useElectrostatic \|= (*i)->isElectrostatic();
791	<	useEAM \|= (*i)->isEAM();
792	<	useSC \|= (*i)->isSC();
793	<	useCharge \|= (*i)->isCharge();
794	<	useDirectional \|= (*i)->isDirectional();
795	<	useDipole \|= (*i)->isDipole();
796	<	useGayBerne \|= (*i)->isGayBerne();
797	<	useSticky \|= (*i)->isSticky();
798	<	useStickyPower \|= (*i)->isStickyPower();
799	<	useShape \|= (*i)->isShape();
800	<	}
750	>	// foundIdents is a stl set, so inserting an already found ident
751	>	// will have no effect.
752	>	set<int> foundIdents;
753
754	<	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
755	<	useDirectionalAtom = 1;
756	<	}
754	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
755	>	foundIdents.insert((*j));
756	>
757	>	// now iterate over the foundIdents and get the actual atom types
758	>	// that correspond to these:
759	>	set<int>::iterator it;
760	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
761	>	atomTypes.insert( forceField_->getAtomType((*it)) );
762	>
763	>	#endif
764
765	<	if (useCharge \|\| useDipole) {
766	<	useElectrostatics = 1;
808	<	}
765	>	return atomTypes;
766	>	}
767
768	+	void SimInfo::setupSimVariables() {
769	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
770	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
771	+	calcBoxDipole_ = false;
772	+	if ( simParams_->haveAccumulateBoxDipole() )
773	+	if ( simParams_->getAccumulateBoxDipole() ) {
774	+	calcBoxDipole_ = true;
775	+	}
776	+
777	+	set<AtomType*>::iterator i;
778	+	set<AtomType*> atomTypes;
779	+	atomTypes = getSimulatedAtomTypes();
780	+	int usesElectrostatic = 0;
781	+	int usesMetallic = 0;
782	+	int usesDirectional = 0;
783	+	//loop over all of the atom types
784	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785	+	usesElectrostatic \|= (*i)->isElectrostatic();
786	+	usesMetallic \|= (*i)->isMetal();
787	+	usesDirectional \|= (*i)->isDirectional();
788	+	}
789	+
790		#ifdef IS_MPI
791		int temp;
792	+	temp = usesDirectional;
793	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
794	+
795	+	temp = usesMetallic;
796	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
797	+
798	+	temp = usesElectrostatic;
799	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800	+	#else
801
802	<	temp = usePBC;
803	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	>	usesDirectionalAtoms_ = usesDirectional;
803	>	usesMetallicAtoms_ = usesMetallic;
804	>	usesElectrostaticAtoms_ = usesElectrostatic;
805
806	<	temp = useDirectionalAtom;
807	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	#endif
807	>
808	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
809	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
810	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
811	>	}
812
819	–	temp = useLennardJones;
820	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813
814	<	temp = useElectrostatics;
815	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	vector<int> SimInfo::getGlobalAtomIndices() {
815	>	SimInfo::MoleculeIterator mi;
816	>	Molecule* mol;
817	>	Molecule::AtomIterator ai;
818	>	Atom* atom;
819
820	<	temp = useCharge;
826	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	<
828	<	temp = useDipole;
829	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	<
831	<	temp = useSticky;
832	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	<
834	<	temp = useStickyPower;
835	<	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
821
822	<	temp = useGayBerne;
823	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
822	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
823	>
824	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
825	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
826	>	}
827	>	}
828	>	return GlobalAtomIndices;
829	>	}
830
840	–	temp = useEAM;
841	–	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831
832	<	temp = useSC;
833	<	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834	<
835	<	temp = useShape;
836	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832	>	vector<int> SimInfo::getGlobalGroupIndices() {
833	>	SimInfo::MoleculeIterator mi;
834	>	Molecule* mol;
835	>	Molecule::CutoffGroupIterator ci;
836	>	CutoffGroup* cg;
837
838	<	temp = useFLARB;
839	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	<
841	<	temp = useRF;
842	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
843	<
844	<	temp = useSF;
845	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	<
847	<	temp = useSP;
848	<	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
849	<
861	<	temp = useBoxDipole;
862	<	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	<
864	<	temp = useAtomicVirial_;
865	<	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	<
867	<	#endif
868	<
869	<	fInfo_.SIM_uses_PBC = usePBC;
870	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
871	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
872	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
873	<	fInfo_.SIM_uses_Charges = useCharge;
874	<	fInfo_.SIM_uses_Dipoles = useDipole;
875	<	fInfo_.SIM_uses_Sticky = useSticky;
876	<	fInfo_.SIM_uses_StickyPower = useStickyPower;
877	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
878	<	fInfo_.SIM_uses_EAM = useEAM;
879	<	fInfo_.SIM_uses_SC = useSC;
880	<	fInfo_.SIM_uses_Shapes = useShape;
881	<	fInfo_.SIM_uses_FLARB = useFLARB;
882	<	fInfo_.SIM_uses_RF = useRF;
883	<	fInfo_.SIM_uses_SF = useSF;
884	<	fInfo_.SIM_uses_SP = useSP;
885	<	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
886	<	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
838	>	vector<int> GlobalGroupIndices;
839	>
840	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
841	>
842	>	//local index of cutoff group is trivial, it only depends on the
843	>	//order of travesing
844	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
845	>	cg = mol->nextCutoffGroup(ci)) {
846	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
847	>	}
848	>	}
849	>	return GlobalGroupIndices;
850		}
851
852	<	void SimInfo::setupFortranSim() {
853	<	int isError;
852	>
853	>	void SimInfo::prepareTopology() {
854		int nExclude, nOneTwo, nOneThree, nOneFour;
892	–	std::vector<int> fortranGlobalGroupMembership;
893	–
894	–	isError = 0;
855
896	–	//globalGroupMembership_ is filled by SimCreator
897	–	for (int i = 0; i < nGlobalAtoms_; i++) {
898	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
899	–	}
900	–
856		//calculate mass ratio of cutoff group
902	–	std::vector<RealType> mfact;
857		SimInfo::MoleculeIterator mi;
858		Molecule* mol;
859		Molecule::CutoffGroupIterator ci;
#	Line 908 \| Line 862 \| namespace OpenMD {
862		Atom* atom;
863		RealType totalMass;
864
865	<	//to avoid memory reallocation, reserve enough space for mfact
866	<	mfact.reserve(getNCutoffGroups());
865	>	/**
866	>	* The mass factor is the relative mass of an atom to the total
867	>	* mass of the cutoff group it belongs to. By default, all atoms
868	>	* are their own cutoff groups, and therefore have mass factors of
869	>	* 1. We need some special handling for massless atoms, which
870	>	* will be treated as carrying the entire mass of the cutoff
871	>	* group.
872	>	*/
873	>	massFactors_.clear();
874	>	massFactors_.resize(getNAtoms(), 1.0);
875
876		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
877	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
877	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
878	>	cg = mol->nextCutoffGroup(ci)) {
879
880		totalMass = cg->getMass();
881		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
882		// Check for massless groups - set mfact to 1 if true
883	<	if (totalMass != 0)
884	<	mfact.push_back(atom->getMass()/totalMass);
883	>	if (totalMass != 0)
884	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
885		else
886	<	mfact.push_back( 1.0 );
886	>	massFactors_[atom->getLocalIndex()] = 1.0;
887		}
888		}
889		}
890
891	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929	<	std::vector<int> identArray;
891	>	// Build the identArray_
892
893	<	//to avoid memory reallocation, reserve enough space identArray
894	<	identArray.reserve(getNAtoms());
933	<
893	>	identArray_.clear();
894	>	identArray_.reserve(getNAtoms());
895		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
896		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
897	<	identArray.push_back(atom->getIdent());
897	>	identArray_.push_back(atom->getIdent());
898		}
899		}
939	–
940	–	//fill molMembershipArray
941	–	//molMembershipArray is filled by SimCreator
942	–	std::vector<int> molMembershipArray(nGlobalAtoms_);
943	–	for (int i = 0; i < nGlobalAtoms_; i++) {
944	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
945	–	}
900
901	<	//setup fortran simulation
901	>	//scan topology
902
903		nExclude = excludedInteractions_.getSize();
904		nOneTwo = oneTwoInteractions_.getSize();
#	Line 956 \| Line 910 \| namespace OpenMD {
910		int* oneThreeList = oneThreeInteractions_.getPairList();
911		int* oneFourList = oneFourInteractions_.getPairList();
912
913	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
960	<	&nExclude, excludeList,
961	<	&nOneTwo, oneTwoList,
962	<	&nOneThree, oneThreeList,
963	<	&nOneFour, oneFourList,
964	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965	<	&fortranGlobalGroupMembership[0], &isError);
966	<
967	<	if( isError ){
968	<
969	<	sprintf( painCave.errMsg,
970	<	"There was an error setting the simulation information in fortran.\n" );
971	<	painCave.isFatal = 1;
972	<	painCave.severity = OPENMD_ERROR;
973	<	simError();
974	<	}
975	<
976	<
977	<	sprintf( checkPointMsg,
978	<	"succesfully sent the simulation information to fortran.\n");
979	<
980	<	errorCheckPoint();
981	<
982	<	// Setup number of neighbors in neighbor list if present
983	<	if (simParams_->haveNeighborListNeighbors()) {
984	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
985	<	setNeighbors(&nlistNeighbors);
986	<	}
987	<
988	<
989	<	}
990	<
991	<
992	<	void SimInfo::setupFortranParallel() {
993	<	#ifdef IS_MPI
994	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
995	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
996	<	std::vector<int> localToGlobalCutoffGroupIndex;
997	<	SimInfo::MoleculeIterator mi;
998	<	Molecule::AtomIterator ai;
999	<	Molecule::CutoffGroupIterator ci;
1000	<	Molecule* mol;
1001	<	Atom* atom;
1002	<	CutoffGroup* cg;
1003	<	mpiSimData parallelData;
1004	<	int isError;
1005	<
1006	<	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1007	<
1008	<	//local index(index in DataStorge) of atom is important
1009	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1010	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1011	<	}
1012	<
1013	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1014	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1015	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1016	<	}
1017	<
1018	<	}
1019	<
1020	<	//fill up mpiSimData struct
1021	<	parallelData.nMolGlobal = getNGlobalMolecules();
1022	<	parallelData.nMolLocal = getNMolecules();
1023	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1024	<	parallelData.nAtomsLocal = getNAtoms();
1025	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1026	<	parallelData.nGroupsLocal = getNCutoffGroups();
1027	<	parallelData.myNode = worldRank;
1028	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1029	<
1030	<	//pass mpiSimData struct and index arrays to fortran
1031	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1032	<	&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
1033	<	&localToGlobalCutoffGroupIndex[0], &isError);
1034	<
1035	<	if (isError) {
1036	<	sprintf(painCave.errMsg,
1037	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1038	<	painCave.isFatal = 1;
1039	<	simError();
1040	<	}
1041	<
1042	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1043	<	errorCheckPoint();
1044	<
1045	<	#endif
1046	<	}
1047	<
1048	<	void SimInfo::setupCutoff() {
1049	<
1050	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1051	<
1052	<	// Check the cutoff policy
1053	<	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054	<
1055	<	// Set LJ shifting bools to false
1056	<	ljsp_ = 0;
1057	<	ljsf_ = 0;
1058	<
1059	<	std::string myPolicy;
1060	<	if (forceFieldOptions_.haveCutoffPolicy()){
1061	<	myPolicy = forceFieldOptions_.getCutoffPolicy();
1062	<	}else if (simParams_->haveCutoffPolicy()) {
1063	<	myPolicy = simParams_->getCutoffPolicy();
1064	<	}
1065	<
1066	<	if (!myPolicy.empty()){
1067	<	toUpper(myPolicy);
1068	<	if (myPolicy == "MIX") {
1069	<	cp = MIX_CUTOFF_POLICY;
1070	<	} else {
1071	<	if (myPolicy == "MAX") {
1072	<	cp = MAX_CUTOFF_POLICY;
1073	<	} else {
1074	<	if (myPolicy == "TRADITIONAL") {
1075	<	cp = TRADITIONAL_CUTOFF_POLICY;
1076	<	} else {
1077	<	// throw error
1078	<	sprintf( painCave.errMsg,
1079	<	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1080	<	painCave.isFatal = 1;
1081	<	simError();
1082	<	}
1083	<	}
1084	<	}
1085	<	}
1086	<	notifyFortranCutoffPolicy(&cp);
1087	<
1088	<	// Check the Skin Thickness for neighborlists
1089	<	RealType skin;
1090	<	if (simParams_->haveSkinThickness()) {
1091	<	skin = simParams_->getSkinThickness();
1092	<	notifyFortranSkinThickness(&skin);
1093	<	}
1094	<
1095	<	// Check if the cutoff was set explicitly:
1096	<	if (simParams_->haveCutoffRadius()) {
1097	<	rcut_ = simParams_->getCutoffRadius();
1098	<	if (simParams_->haveSwitchingRadius()) {
1099	<	rsw_ = simParams_->getSwitchingRadius();
1100	<	} else {
1101	<	if (fInfo_.SIM_uses_Charges \|
1102	<	fInfo_.SIM_uses_Dipoles \|
1103	<	fInfo_.SIM_uses_RF) {
1104	<
1105	<	rsw_ = 0.85 * rcut_;
1106	<	sprintf(painCave.errMsg,
1107	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1108	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1109	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1110	<	painCave.isFatal = 0;
1111	<	simError();
1112	<	} else {
1113	<	rsw_ = rcut_;
1114	<	sprintf(painCave.errMsg,
1115	<	"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	<	"\tOpenMD will use the same value as the cutoffRadius.\n"
1117	<	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118	<	painCave.isFatal = 0;
1119	<	simError();
1120	<	}
1121	<	}
1122	<
1123	<	if (simParams_->haveElectrostaticSummationMethod()) {
1124	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1125	<	toUpper(myMethod);
1126	<
1127	<	if (myMethod == "SHIFTED_POTENTIAL") {
1128	<	ljsp_ = 1;
1129	<	} else if (myMethod == "SHIFTED_FORCE") {
1130	<	ljsf_ = 1;
1131	<	}
1132	<	}
1133	<
1134	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1135	<
1136	<	} else {
1137	<
1138	<	// For electrostatic atoms, we'll assume a large safe value:
1139	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1140	<	sprintf(painCave.errMsg,
1141	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1142	<	"\tOpenMD will use a default value of 15.0 angstroms"
1143	<	"\tfor the cutoffRadius.\n");
1144	<	painCave.isFatal = 0;
1145	<	simError();
1146	<	rcut_ = 15.0;
1147	<
1148	<	if (simParams_->haveElectrostaticSummationMethod()) {
1149	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1150	<	toUpper(myMethod);
1151	<
1152	<	// For the time being, we're tethering the LJ shifted behavior to the
1153	<	// electrostaticSummationMethod keyword options
1154	<	if (myMethod == "SHIFTED_POTENTIAL") {
1155	<	ljsp_ = 1;
1156	<	} else if (myMethod == "SHIFTED_FORCE") {
1157	<	ljsf_ = 1;
1158	<	}
1159	<	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1160	<	if (simParams_->haveSwitchingRadius()){
1161	<	sprintf(painCave.errMsg,
1162	<	"SimInfo Warning: A value was set for the switchingRadius\n"
1163	<	"\teven though the electrostaticSummationMethod was\n"
1164	<	"\tset to %s\n", myMethod.c_str());
1165	<	painCave.isFatal = 1;
1166	<	simError();
1167	<	}
1168	<	}
1169	<	}
1170	<
1171	<	if (simParams_->haveSwitchingRadius()){
1172	<	rsw_ = simParams_->getSwitchingRadius();
1173	<	} else {
1174	<	sprintf(painCave.errMsg,
1175	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1176	<	"\tOpenMD will use a default value of\n"
1177	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
1178	<	painCave.isFatal = 0;
1179	<	simError();
1180	<	rsw_ = 0.85 * rcut_;
1181	<	}
1182	<
1183	<	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1184	<
1185	<	} else {
1186	<	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1187	<	// We'll punt and let fortran figure out the cutoffs later.
1188	<
1189	<	notifyFortranYouAreOnYourOwn();
1190	<
1191	<	}
1192	<	}
1193	<	}
1194	<
1195	<	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1196	<
1197	<	int errorOut;
1198	<	int esm = NONE;
1199	<	int sm = UNDAMPED;
1200	<	RealType alphaVal;
1201	<	RealType dielectric;
1202	<
1203	<	errorOut = isError;
1204	<
1205	<	if (simParams_->haveElectrostaticSummationMethod()) {
1206	<	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1207	<	toUpper(myMethod);
1208	<	if (myMethod == "NONE") {
1209	<	esm = NONE;
1210	<	} else {
1211	<	if (myMethod == "SWITCHING_FUNCTION") {
1212	<	esm = SWITCHING_FUNCTION;
1213	<	} else {
1214	<	if (myMethod == "SHIFTED_POTENTIAL") {
1215	<	esm = SHIFTED_POTENTIAL;
1216	<	} else {
1217	<	if (myMethod == "SHIFTED_FORCE") {
1218	<	esm = SHIFTED_FORCE;
1219	<	} else {
1220	<	if (myMethod == "REACTION_FIELD") {
1221	<	esm = REACTION_FIELD;
1222	<	dielectric = simParams_->getDielectric();
1223	<	if (!simParams_->haveDielectric()) {
1224	<	// throw warning
1225	<	sprintf( painCave.errMsg,
1226	<	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1227	<	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1228	<	painCave.isFatal = 0;
1229	<	simError();
1230	<	}
1231	<	} else {
1232	<	// throw error
1233	<	sprintf( painCave.errMsg,
1234	<	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1235	<	"\t(Input file specified %s .)\n"
1236	<	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1237	<	"\t\"shifted_potential\", \"shifted_force\", or \n"
1238	<	"\t\"reaction_field\".\n", myMethod.c_str() );
1239	<	painCave.isFatal = 1;
1240	<	simError();
1241	<	}
1242	<	}
1243	<	}
1244	<	}
1245	<	}
1246	<	}
1247	<
1248	<	if (simParams_->haveElectrostaticScreeningMethod()) {
1249	<	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1250	<	toUpper(myScreen);
1251	<	if (myScreen == "UNDAMPED") {
1252	<	sm = UNDAMPED;
1253	<	} else {
1254	<	if (myScreen == "DAMPED") {
1255	<	sm = DAMPED;
1256	<	if (!simParams_->haveDampingAlpha()) {
1257	<	// first set a cutoff dependent alpha value
1258	<	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1259	<	alphaVal = 0.5125 - rcut_* 0.025;
1260	<	// for values rcut > 20.5, alpha is zero
1261	<	if (alphaVal < 0) alphaVal = 0;
1262	<
1263	<	// throw warning
1264	<	sprintf( painCave.errMsg,
1265	<	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1266	<	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1267	<	painCave.isFatal = 0;
1268	<	simError();
1269	<	} else {
1270	<	alphaVal = simParams_->getDampingAlpha();
1271	<	}
1272	<
1273	<	} else {
1274	<	// throw error
1275	<	sprintf( painCave.errMsg,
1276	<	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1277	<	"\t(Input file specified %s .)\n"
1278	<	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1279	<	"or \"damped\".\n", myScreen.c_str() );
1280	<	painCave.isFatal = 1;
1281	<	simError();
1282	<	}
1283	<	}
1284	<	}
1285	<
1286	<	// let's pass some summation method variables to fortran
1287	<	setElectrostaticSummationMethod( &esm );
1288	<	setFortranElectrostaticMethod( &esm );
1289	<	setScreeningMethod( &sm );
1290	<	setDampingAlpha( &alphaVal );
1291	<	setReactionFieldDielectric( &dielectric );
1292	<	initFortranFF( &errorOut );
1293	<	}
1294	<
1295	<	void SimInfo::setupSwitchingFunction() {
1296	<	int ft = CUBIC;
1297	<
1298	<	if (simParams_->haveSwitchingFunctionType()) {
1299	<	std::string funcType = simParams_->getSwitchingFunctionType();
1300	<	toUpper(funcType);
1301	<	if (funcType == "CUBIC") {
1302	<	ft = CUBIC;
1303	<	} else {
1304	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1305	<	ft = FIFTH_ORDER_POLY;
1306	<	} else {
1307	<	// throw error
1308	<	sprintf( painCave.errMsg,
1309	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1310	<	painCave.isFatal = 1;
1311	<	simError();
1312	<	}
1313	<	}
1314	<	}
1315	<
1316	<	// send switching function notification to switcheroo
1317	<	setFunctionType(&ft);
1318	<
913	>	topologyDone_ = true;
914		}
915
1321	–	void SimInfo::setupAccumulateBoxDipole() {
1322	–
1323	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1324	–	if ( simParams_->haveAccumulateBoxDipole() )
1325	–	if ( simParams_->getAccumulateBoxDipole() ) {
1326	–	setAccumulateBoxDipole();
1327	–	calcBoxDipole_ = true;
1328	–	}
1329	–
1330	–	}
1331	–
916		void SimInfo::addProperty(GenericData* genData) {
917		properties_.addProperty(genData);
918		}
919
920	<	void SimInfo::removeProperty(const std::string& propName) {
920	>	void SimInfo::removeProperty(const string& propName) {
921		properties_.removeProperty(propName);
922		}
923
#	Line 1341 \| Line 925 \| namespace OpenMD {
925		properties_.clearProperties();
926		}
927
928	<	std::vector<std::string> SimInfo::getPropertyNames() {
928	>	vector<string> SimInfo::getPropertyNames() {
929		return properties_.getPropertyNames();
930		}
931
932	<	std::vector<GenericData*> SimInfo::getProperties() {
932	>	vector<GenericData*> SimInfo::getProperties() {
933		return properties_.getProperties();
934		}
935
936	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
936	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
937		return properties_.getPropertyByName(propName);
938		}
939
#	Line 1363 \| Line 947 \| namespace OpenMD {
947		Molecule* mol;
948		RigidBody* rb;
949		Atom* atom;
950	+	CutoffGroup* cg;
951		SimInfo::MoleculeIterator mi;
952		Molecule::RigidBodyIterator rbIter;
953	<	Molecule::AtomIterator atomIter;;
953	>	Molecule::AtomIterator atomIter;
954	>	Molecule::CutoffGroupIterator cgIter;
955
956		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
957
#	Line 1376 \| Line 962 \| namespace OpenMD {
962		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
963		rb->setSnapshotManager(sman_);
964		}
965	+
966	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
967	+	cg->setSnapshotManager(sman_);
968	+	}
969		}
970
971		}
#	Line 1432 \| Line 1022 \| namespace OpenMD {
1022
1023		}
1024
1025	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1025	>	ostream& operator <<(ostream& o, SimInfo& info) {
1026
1027		return o;
1028		}
#	Line 1475 \| Line 1065 \| namespace OpenMD {
1065
1066
1067		[ Ixx -Ixy -Ixz ]
1068	<	J =\| -Iyx Iyy -Iyz \|
1068	>	J =\| -Iyx Iyy -Iyz \|
1069		[ -Izx -Iyz Izz ]
1070		*/
1071
#	Line 1582 \| Line 1172 \| namespace OpenMD {
1172		return IOIndexToIntegrableObject.at(index);
1173		}
1174
1175	<	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1175	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1176		IOIndexToIntegrableObject= v;
1177		}
1178
#	Line 1604 \| Line 1194 \| namespace OpenMD {
1194
1195		det = intTensor.determinant();
1196		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1197	<	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1197	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,geomCnst)*sqrt(det);
1198		return;
1199		}
1200
#	Line 1620 \| Line 1210 \| namespace OpenMD {
1210
1211		detI = intTensor.determinant();
1212		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1213	<	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1213	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,geomCnst)*sqrt(detI);
1214		return;
1215		}
1216		/*
1217	<	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1217	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1218		assert( v.size() == nAtoms_ + nRigidBodies_);
1219		sdByGlobalIndex_ = v;
1220		}
#	Line 1634 \| Line 1224 \| namespace OpenMD {
1224		return sdByGlobalIndex_.at(index);
1225		}
1226		*/
1227	+	int SimInfo::getNGlobalConstraints() {
1228	+	int nGlobalConstraints;
1229	+	#ifdef IS_MPI
1230	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1231	+	MPI_COMM_WORLD);
1232	+	#else
1233	+	nGlobalConstraints = nConstraints_;
1234	+	#endif
1235	+	return nGlobalConstraints;
1236	+	}
1237	+
1238		}//end namespace OpenMD
1239

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Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs. Revision 1668 by gezelter, Fri Jan 6 19:03:05 2012 UTC

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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1668 by gezelter, Fri Jan 6 19:03:05 2012 UTC