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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC vs.
Revision 1779 by gezelter, Mon Aug 20 17:51:39 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/DarkSide/neighborLists_interface.h"
58	–	#include "UseTheForce/doForces_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"
62	>	#include "brains/ForceField.hpp"
63		#include "nonbonded/SwitchingFunction.hpp"
65	–
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
69	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68		using namespace std;
69		namespace OpenMD {
#	Line 75 \| Line 72 \| namespace OpenMD {
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),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79		calcBoxDipole_(false), useAtomicVirial_(true) {
80
81		MoleculeStamp* molStamp;
#	Line 91 \| Line 88 \| namespace OpenMD {
88
89		vector<Component*> components = simParams->getComponents();
90
91	<	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91	>	for (vector<Component*>::iterator i = components.begin();
92	>	i !=components.end(); ++i) {
93		molStamp = (*i)->getMoleculeStamp();
94		nMolWithSameStamp = (*i)->getNMol();
95
#	Line 132 \| Line 130 \| namespace OpenMD {
130		//equal to the total number of atoms minus number of atoms belong to
131		//cutoff group defined in meta-data file plus the number of cutoff
132		//groups defined in meta-data file
133	+
134		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135
136		//every free atom (atom does not belong to rigid bodies) is an
#	Line 227 \| Line 226 \| namespace OpenMD {
226
227
228		void SimInfo::calcNdf() {
229	<	int ndf_local;
229	>	int ndf_local, nfq_local;
230		MoleculeIterator i;
231		vector<StuntDouble*>::iterator j;
232	+	vector<Atom*>::iterator k;
233	+
234		Molecule* mol;
235	<	StuntDouble* integrableObject;
235	>	StuntDouble* sd;
236	>	Atom* atom;
237
238		ndf_local = 0;
239	+	nfq_local = 0;
240
241		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
239	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
240	–	integrableObject = mol->nextIntegrableObject(j)) {
242
243	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
244	+	sd = mol->nextIntegrableObject(j)) {
245	+
246		ndf_local += 3;
247
248	<	if (integrableObject->isDirectional()) {
249	<	if (integrableObject->isLinear()) {
248	>	if (sd->isDirectional()) {
249	>	if (sd->isLinear()) {
250		ndf_local += 2;
251		} else {
252		ndf_local += 3;
253		}
254		}
251	–
255		}
256	+
257	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258	+	atom = mol->nextFluctuatingCharge(k)) {
259	+	if (atom->isFluctuatingCharge()) {
260	+	nfq_local++;
261	+	}
262	+	}
263		}
264
265	+	ndfLocal_ = ndf_local;
266	+
267		// n_constraints is local, so subtract them on each processor
268		ndf_local -= nConstraints_;
269
270		#ifdef IS_MPI
271		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
273		#else
274		ndf_ = ndf_local;
275	+	nGlobalFluctuatingCharges_ = nfq_local;
276		#endif
277
278		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 275 \| Line 289 \| namespace OpenMD {
289		#endif
290		return fdf_;
291		}
292	+
293	+	unsigned int SimInfo::getNLocalCutoffGroups(){
294	+	int nLocalCutoffAtoms = 0;
295	+	Molecule* mol;
296	+	MoleculeIterator mi;
297	+	CutoffGroup* cg;
298	+	Molecule::CutoffGroupIterator ci;
299
300	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
301	+
302	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
303	+	cg = mol->nextCutoffGroup(ci)) {
304	+	nLocalCutoffAtoms += cg->getNumAtom();
305	+
306	+	}
307	+	}
308	+
309	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
310	+	}
311	+
312		void SimInfo::calcNdfRaw() {
313		int ndfRaw_local;
314
315		MoleculeIterator i;
316		vector<StuntDouble*>::iterator j;
317		Molecule* mol;
318	<	StuntDouble* integrableObject;
318	>	StuntDouble* sd;
319
320		// Raw degrees of freedom that we have to set
321		ndfRaw_local = 0;
322
323		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
291	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292	–	integrableObject = mol->nextIntegrableObject(j)) {
324
325	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
326	+	sd = mol->nextIntegrableObject(j)) {
327	+
328		ndfRaw_local += 3;
329
330	<	if (integrableObject->isDirectional()) {
331	<	if (integrableObject->isLinear()) {
330	>	if (sd->isDirectional()) {
331	>	if (sd->isLinear()) {
332		ndfRaw_local += 2;
333		} else {
334		ndfRaw_local += 3;
#	Line 354 \| Line 388 \| namespace OpenMD {
388		Molecule::RigidBodyIterator rbIter;
389		RigidBody* rb;
390		Molecule::IntegrableObjectIterator ii;
391	<	StuntDouble* integrableObject;
391	>	StuntDouble* sd;
392
393	<	for (integrableObject = mol->beginIntegrableObject(ii);
394	<	integrableObject != NULL;
361	<	integrableObject = mol->nextIntegrableObject(ii)) {
393	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
394	>	sd = mol->nextIntegrableObject(ii)) {
395
396	<	if (integrableObject->isRigidBody()) {
397	<	rb = static_cast<RigidBody*>(integrableObject);
396	>	if (sd->isRigidBody()) {
397	>	rb = static_cast<RigidBody*>(sd);
398		vector<Atom*> atoms = rb->getAtoms();
399		set<int> rigidAtoms;
400		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
#	Line 372 \| Line 405 \| namespace OpenMD {
405		}
406		} else {
407		set<int> oneAtomSet;
408	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
409	<	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
408	>	oneAtomSet.insert(sd->getGlobalIndex());
409	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
410		}
411		}
412
#	Line 507 \| Line 540 \| namespace OpenMD {
540		Molecule::RigidBodyIterator rbIter;
541		RigidBody* rb;
542		Molecule::IntegrableObjectIterator ii;
543	<	StuntDouble* integrableObject;
543	>	StuntDouble* sd;
544
545	<	for (integrableObject = mol->beginIntegrableObject(ii);
546	<	integrableObject != NULL;
514	<	integrableObject = mol->nextIntegrableObject(ii)) {
545	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
546	>	sd = mol->nextIntegrableObject(ii)) {
547
548	<	if (integrableObject->isRigidBody()) {
549	<	rb = static_cast<RigidBody*>(integrableObject);
548	>	if (sd->isRigidBody()) {
549	>	rb = static_cast<RigidBody*>(sd);
550		vector<Atom*> atoms = rb->getAtoms();
551		set<int> rigidAtoms;
552		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
#	Line 525 \| Line 557 \| namespace OpenMD {
557		}
558		} else {
559		set<int> oneAtomSet;
560	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
561	<	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
560	>	oneAtomSet.insert(sd->getGlobalIndex());
561	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
562		}
563		}
564
#	Line 681 \| Line 713 \| namespace OpenMD {
713		Atom* atom;
714		set<AtomType*> atomTypes;
715
716	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
717	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
716	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
717	>	for(atom = mol->beginAtom(ai); atom != NULL;
718	>	atom = mol->nextAtom(ai)) {
719		atomTypes.insert(atom->getAtomType());
720		}
721		}
722	<
722	>
723		#ifdef IS_MPI
724
725		// loop over the found atom types on this processor, and add their
726		// numerical idents to a vector:
727	<
727	>
728		vector<int> foundTypes;
729		set<AtomType*>::iterator i;
730		for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
#	Line 700 \| Line 733 \| namespace OpenMD {
733		// count_local holds the number of found types on this processor
734		int count_local = foundTypes.size();
735
703	–	// count holds the total number of found types on all processors
704	–	// (some will be redundant with the ones found locally):
705	–	int count;
706	–	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
707	–
708	–	// create a vector to hold the globally found types, and resize it:
709	–	vector<int> ftGlobal;
710	–	ftGlobal.resize(count);
711	–	vector<int> counts;
712	–
736		int nproc = MPI::COMM_WORLD.Get_size();
714	–	counts.resize(nproc);
715	–	vector<int> disps;
716	–	disps.resize(nproc);
737
738	<	// now spray out the foundTypes to all the other processors:
738	>	// we need arrays to hold the counts and displacement vectors for
739	>	// all processors
740	>	vector<int> counts(nproc, 0);
741	>	vector<int> disps(nproc, 0);
742	>
743	>	// fill the counts array
744	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
745	>	1, MPI::INT);
746	>
747	>	// use the processor counts to compute the displacement array
748	>	disps[0] = 0;
749	>	int totalCount = counts[0];
750	>	for (int iproc = 1; iproc < nproc; iproc++) {
751	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
752	>	totalCount += counts[iproc];
753	>	}
754	>
755	>	// we need a (possibly redundant) set of all found types:
756	>	vector<int> ftGlobal(totalCount);
757
758	+	// now spray out the foundTypes to all the other processors:
759		MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
760	<	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
760	>	&ftGlobal[0], &counts[0], &disps[0],
761	>	MPI::INT);
762
763	+	vector<int>::iterator j;
764	+
765		// foundIdents is a stl set, so inserting an already found ident
766		// will have no effect.
767		set<int> foundIdents;
768	<	vector<int>::iterator j;
768	>
769		for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
770		foundIdents.insert((*j));
771
772		// now iterate over the foundIdents and get the actual atom types
773		// that correspond to these:
774		set<int>::iterator it;
775	<	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
776		atomTypes.insert( forceField_->getAtomType((*it)) );
777
778		#endif
779	<
779	>
780		return atomTypes;
781		}
782
783		void SimInfo::setupSimVariables() {
784		useAtomicVirial_ = simParams_->getUseAtomicVirial();
785	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
786	>	// parameter is true
787		calcBoxDipole_ = false;
788		if ( simParams_->haveAccumulateBoxDipole() )
789		if ( simParams_->getAccumulateBoxDipole() ) {
790		calcBoxDipole_ = true;
791		}
792	<
792	>
793		set<AtomType*>::iterator i;
794		set<AtomType*> atomTypes;
795		atomTypes = getSimulatedAtomTypes();
796	<	int usesElectrostatic = 0;
797	<	int usesMetallic = 0;
798	<	int usesDirectional = 0;
796	>	bool usesElectrostatic = false;
797	>	bool usesMetallic = false;
798	>	bool usesDirectional = false;
799	>	bool usesFluctuatingCharges = false;
800		//loop over all of the atom types
801		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
802		usesElectrostatic \|= (*i)->isElectrostatic();
803		usesMetallic \|= (*i)->isMetal();
804		usesDirectional \|= (*i)->isDirectional();
805	+	usesFluctuatingCharges \|= (*i)->isFluctuatingCharge();
806		}
807
808	<	#ifdef IS_MPI
809	<	int temp;
808	>	#ifdef IS_MPI
809	>	bool temp;
810		temp = usesDirectional;
811	<	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
812	<
811	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
812	>	MPI::LOR);
813	>
814		temp = usesMetallic;
815	<	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	<
815	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
816	>	MPI::LOR);
817	>
818		temp = usesElectrostatic;
819	<	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
820	>	MPI::LOR);
821	>
822	>	temp = usesFluctuatingCharges;
823	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
824	>	MPI::LOR);
825	>	#else
826	>
827	>	usesDirectionalAtoms_ = usesDirectional;
828	>	usesMetallicAtoms_ = usesMetallic;
829	>	usesElectrostaticAtoms_ = usesElectrostatic;
830	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
831	>
832		#endif
833	<	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
834	<	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
835	<	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
836	<	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
778	<	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
779	<	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
833	>
834	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
835	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
836	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
837		}
838
839	<	void SimInfo::setupFortran() {
840	<	int isError;
841	<	int nExclude, nOneTwo, nOneThree, nOneFour;
842	<	vector<int> fortranGlobalGroupMembership;
839	>
840	>	vector<int> SimInfo::getGlobalAtomIndices() {
841	>	SimInfo::MoleculeIterator mi;
842	>	Molecule* mol;
843	>	Molecule::AtomIterator ai;
844	>	Atom* atom;
845	>
846	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
847
848	<	isError = 0;
848	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
849	>
850	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
851	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
852	>	}
853	>	}
854	>	return GlobalAtomIndices;
855	>	}
856
857	<	//globalGroupMembership_ is filled by SimCreator
858	<	for (int i = 0; i < nGlobalAtoms_; i++) {
859	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
857	>
858	>	vector<int> SimInfo::getGlobalGroupIndices() {
859	>	SimInfo::MoleculeIterator mi;
860	>	Molecule* mol;
861	>	Molecule::CutoffGroupIterator ci;
862	>	CutoffGroup* cg;
863	>
864	>	vector<int> GlobalGroupIndices;
865	>
866	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
867	>
868	>	//local index of cutoff group is trivial, it only depends on the
869	>	//order of travesing
870	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
871	>	cg = mol->nextCutoffGroup(ci)) {
872	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
873	>	}
874		}
875	+	return GlobalGroupIndices;
876	+	}
877
878	+
879	+	void SimInfo::prepareTopology() {
880	+	int nExclude, nOneTwo, nOneThree, nOneFour;
881	+
882		//calculate mass ratio of cutoff group
795	–	vector<RealType> mfact;
883		SimInfo::MoleculeIterator mi;
884		Molecule* mol;
885		Molecule::CutoffGroupIterator ci;
#	Line 801 \| Line 888 \| namespace OpenMD {
888		Atom* atom;
889		RealType totalMass;
890
891	<	//to avoid memory reallocation, reserve enough space for mfact
892	<	mfact.reserve(getNCutoffGroups());
891	>	/**
892	>	* The mass factor is the relative mass of an atom to the total
893	>	* mass of the cutoff group it belongs to. By default, all atoms
894	>	* are their own cutoff groups, and therefore have mass factors of
895	>	* 1. We need some special handling for massless atoms, which
896	>	* will be treated as carrying the entire mass of the cutoff
897	>	* group.
898	>	*/
899	>	massFactors_.clear();
900	>	massFactors_.resize(getNAtoms(), 1.0);
901
902		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
903	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
903	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
904	>	cg = mol->nextCutoffGroup(ci)) {
905
906		totalMass = cg->getMass();
907		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
908		// Check for massless groups - set mfact to 1 if true
909	<	if (totalMass != 0)
910	<	mfact.push_back(atom->getMass()/totalMass);
909	>	if (totalMass != 0)
910	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
911		else
912	<	mfact.push_back( 1.0 );
912	>	massFactors_[atom->getLocalIndex()] = 1.0;
913		}
914		}
915		}
916
917	<	//fill ident array of local atoms (it is actually ident of
822	<	//AtomType, it is so confusing !!!)
823	<	vector<int> identArray;
917	>	// Build the identArray_
918
919	<	//to avoid memory reallocation, reserve enough space identArray
920	<	identArray.reserve(getNAtoms());
827	<
919	>	identArray_.clear();
920	>	identArray_.reserve(getNAtoms());
921		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
922		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
923	<	identArray.push_back(atom->getIdent());
923	>	identArray_.push_back(atom->getIdent());
924		}
925		}
833	–
834	–	//fill molMembershipArray
835	–	//molMembershipArray is filled by SimCreator
836	–	vector<int> molMembershipArray(nGlobalAtoms_);
837	–	for (int i = 0; i < nGlobalAtoms_; i++) {
838	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
839	–	}
926
927	<	//setup fortran simulation
927	>	//scan topology
928
929		nExclude = excludedInteractions_.getSize();
930		nOneTwo = oneTwoInteractions_.getSize();
#	Line 850 \| Line 936 \| namespace OpenMD {
936		int* oneThreeList = oneThreeInteractions_.getPairList();
937		int* oneFourList = oneFourInteractions_.getPairList();
938
939	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
854	<	&nExclude, excludeList,
855	<	&nOneTwo, oneTwoList,
856	<	&nOneThree, oneThreeList,
857	<	&nOneFour, oneFourList,
858	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
859	<	&fortranGlobalGroupMembership[0], &isError);
860	<
861	<	if( isError ){
862	<
863	<	sprintf( painCave.errMsg,
864	<	"There was an error setting the simulation information in fortran.\n" );
865	<	painCave.isFatal = 1;
866	<	painCave.severity = OPENMD_ERROR;
867	<	simError();
868	<	}
869	<
870	<
871	<	sprintf( checkPointMsg,
872	<	"succesfully sent the simulation information to fortran.\n");
873	<
874	<	errorCheckPoint();
875	<
876	<	// Setup number of neighbors in neighbor list if present
877	<	if (simParams_->haveNeighborListNeighbors()) {
878	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
879	<	setNeighbors(&nlistNeighbors);
880	<	}
881	<
882	<	#ifdef IS_MPI
883	<	//SimInfo is responsible for creating localToGlobalAtomIndex and
884	<	//localToGlobalGroupIndex
885	<	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
886	<	vector<int> localToGlobalCutoffGroupIndex;
887	<	mpiSimData parallelData;
888	<
889	<	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
890	<
891	<	//local index(index in DataStorge) of atom is important
892	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
894	<	}
895	<
896	<	//local index of cutoff group is trivial, it only depends on the order of travesing
897	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
898	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
899	<	}
900	<
901	<	}
902	<
903	<	//fill up mpiSimData struct
904	<	parallelData.nMolGlobal = getNGlobalMolecules();
905	<	parallelData.nMolLocal = getNMolecules();
906	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
907	<	parallelData.nAtomsLocal = getNAtoms();
908	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
909	<	parallelData.nGroupsLocal = getNCutoffGroups();
910	<	parallelData.myNode = worldRank;
911	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
912	<
913	<	//pass mpiSimData struct and index arrays to fortran
914	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
915	<	&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
916	<	&localToGlobalCutoffGroupIndex[0], &isError);
917	<
918	<	if (isError) {
919	<	sprintf(painCave.errMsg,
920	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
921	<	painCave.isFatal = 1;
922	<	simError();
923	<	}
924	<
925	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
926	<	errorCheckPoint();
927	<	#endif
928	<
929	<	initFortranFF(&isError);
930	<	if (isError) {
931	<	sprintf(painCave.errMsg,
932	<	"initFortranFF errror: fortran didn't like something we gave it.\n");
933	<	painCave.isFatal = 1;
934	<	simError();
935	<	}
936	<	fortranInitialized_ = true;
939	>	topologyDone_ = true;
940		}
941
942		void SimInfo::addProperty(GenericData* genData) {
#	Line 970 \| Line 973 \| namespace OpenMD {
973		Molecule* mol;
974		RigidBody* rb;
975		Atom* atom;
976	+	CutoffGroup* cg;
977		SimInfo::MoleculeIterator mi;
978		Molecule::RigidBodyIterator rbIter;
979	<	Molecule::AtomIterator atomIter;;
979	>	Molecule::AtomIterator atomIter;
980	>	Molecule::CutoffGroupIterator cgIter;
981
982		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
983
984	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
984	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
985	>	atom = mol->nextAtom(atomIter)) {
986		atom->setSnapshotManager(sman_);
987		}
988
989	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
989	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
990	>	rb = mol->nextRigidBody(rbIter)) {
991		rb->setSnapshotManager(sman_);
992		}
993	+
994	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
995	+	cg = mol->nextCutoffGroup(cgIter)) {
996	+	cg->setSnapshotManager(sman_);
997	+	}
998		}
999
1000		}
1001
990	–	Vector3d SimInfo::getComVel(){
991	–	SimInfo::MoleculeIterator i;
992	–	Molecule* mol;
1002
994	–	Vector3d comVel(0.0);
995	–	RealType totalMass = 0.0;
996	–
997	–
998	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
999	–	RealType mass = mol->getMass();
1000	–	totalMass += mass;
1001	–	comVel += mass * mol->getComVel();
1002	–	}
1003	–
1004	–	#ifdef IS_MPI
1005	–	RealType tmpMass = totalMass;
1006	–	Vector3d tmpComVel(comVel);
1007	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1008	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1009	–	#endif
1010	–
1011	–	comVel /= totalMass;
1012	–
1013	–	return comVel;
1014	–	}
1015	–
1016	–	Vector3d SimInfo::getCom(){
1017	–	SimInfo::MoleculeIterator i;
1018	–	Molecule* mol;
1019	–
1020	–	Vector3d com(0.0);
1021	–	RealType totalMass = 0.0;
1022	–
1023	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1024	–	RealType mass = mol->getMass();
1025	–	totalMass += mass;
1026	–	com += mass * mol->getCom();
1027	–	}
1028	–
1029	–	#ifdef IS_MPI
1030	–	RealType tmpMass = totalMass;
1031	–	Vector3d tmpCom(com);
1032	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1034	–	#endif
1035	–
1036	–	com /= totalMass;
1037	–
1038	–	return com;
1039	–
1040	–	}
1041	–
1003		ostream& operator <<(ostream& o, SimInfo& info) {
1004
1005		return o;
1006		}
1007
1008	<
1048	<	/*
1049	<	Returns center of mass and center of mass velocity in one function call.
1050	<	*/
1051	<
1052	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1053	<	SimInfo::MoleculeIterator i;
1054	<	Molecule* mol;
1055	<
1056	<
1057	<	RealType totalMass = 0.0;
1058	<
1059	<
1060	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1061	<	RealType mass = mol->getMass();
1062	<	totalMass += mass;
1063	<	com += mass * mol->getCom();
1064	<	comVel += mass * mol->getComVel();
1065	<	}
1066	<
1067	<	#ifdef IS_MPI
1068	<	RealType tmpMass = totalMass;
1069	<	Vector3d tmpCom(com);
1070	<	Vector3d tmpComVel(comVel);
1071	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1072	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1073	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074	<	#endif
1075	<
1076	<	com /= totalMass;
1077	<	comVel /= totalMass;
1078	<	}
1079	<
1080	<	/*
1081	<	Return intertia tensor for entire system and angular momentum Vector.
1082	<
1083	<
1084	<	[ Ixx -Ixy -Ixz ]
1085	<	J =\| -Iyx Iyy -Iyz \|
1086	<	[ -Izx -Iyz Izz ]
1087	<	*/
1088	<
1089	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1090	<
1091	<
1092	<	RealType xx = 0.0;
1093	<	RealType yy = 0.0;
1094	<	RealType zz = 0.0;
1095	<	RealType xy = 0.0;
1096	<	RealType xz = 0.0;
1097	<	RealType yz = 0.0;
1098	<	Vector3d com(0.0);
1099	<	Vector3d comVel(0.0);
1100	<
1101	<	getComAll(com, comVel);
1102	<
1103	<	SimInfo::MoleculeIterator i;
1104	<	Molecule* mol;
1105	<
1106	<	Vector3d thisq(0.0);
1107	<	Vector3d thisv(0.0);
1108	<
1109	<	RealType thisMass = 0.0;
1110	<
1111	<
1112	<
1113	<
1114	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1115	<
1116	<	thisq = mol->getCom()-com;
1117	<	thisv = mol->getComVel()-comVel;
1118	<	thisMass = mol->getMass();
1119	<	// Compute moment of intertia coefficients.
1120	<	xx += thisq[0]thisq[0]thisMass;
1121	<	yy += thisq[1]thisq[1]thisMass;
1122	<	zz += thisq[2]thisq[2]thisMass;
1123	<
1124	<	// compute products of intertia
1125	<	xy += thisq[0]thisq[1]thisMass;
1126	<	xz += thisq[0]thisq[2]thisMass;
1127	<	yz += thisq[1]thisq[2]thisMass;
1128	<
1129	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1130	<
1131	<	}
1132	<
1133	<
1134	<	inertiaTensor(0,0) = yy + zz;
1135	<	inertiaTensor(0,1) = -xy;
1136	<	inertiaTensor(0,2) = -xz;
1137	<	inertiaTensor(1,0) = -xy;
1138	<	inertiaTensor(1,1) = xx + zz;
1139	<	inertiaTensor(1,2) = -yz;
1140	<	inertiaTensor(2,0) = -xz;
1141	<	inertiaTensor(2,1) = -yz;
1142	<	inertiaTensor(2,2) = xx + yy;
1143	<
1144	<	#ifdef IS_MPI
1145	<	Mat3x3d tmpI(inertiaTensor);
1146	<	Vector3d tmpAngMom;
1147	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1148	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149	<	#endif
1150	<
1151	<	return;
1152	<	}
1153	<
1154	<	//Returns the angular momentum of the system
1155	<	Vector3d SimInfo::getAngularMomentum(){
1156	<
1157	<	Vector3d com(0.0);
1158	<	Vector3d comVel(0.0);
1159	<	Vector3d angularMomentum(0.0);
1160	<
1161	<	getComAll(com,comVel);
1162	<
1163	<	SimInfo::MoleculeIterator i;
1164	<	Molecule* mol;
1165	<
1166	<	Vector3d thisr(0.0);
1167	<	Vector3d thisp(0.0);
1168	<
1169	<	RealType thisMass;
1170	<
1171	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1172	<	thisMass = mol->getMass();
1173	<	thisr = mol->getCom()-com;
1174	<	thisp = (mol->getComVel()-comVel)*thisMass;
1175	<
1176	<	angularMomentum += cross( thisr, thisp );
1177	<
1178	<	}
1179	<
1180	<	#ifdef IS_MPI
1181	<	Vector3d tmpAngMom;
1182	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1183	<	#endif
1184	<
1185	<	return angularMomentum;
1186	<	}
1187	<
1008	>
1009		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1010	<	return IOIndexToIntegrableObject.at(index);
1010	>	if (index >= IOIndexToIntegrableObject.size()) {
1011	>	sprintf(painCave.errMsg,
1012	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1013	>	"\tindex exceeds number of known objects!\n");
1014	>	painCave.isFatal = 1;
1015	>	simError();
1016	>	return NULL;
1017	>	} else
1018	>	return IOIndexToIntegrableObject.at(index);
1019		}
1020
1021		void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1022		IOIndexToIntegrableObject= v;
1023		}
1024
1196	–	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1197	–	based on the radius of gyration V=4/3PiR_1R_2R_3
1198	–	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1199	–	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1200	–	*/
1201	–	void SimInfo::getGyrationalVolume(RealType &volume){
1202	–	Mat3x3d intTensor;
1203	–	RealType det;
1204	–	Vector3d dummyAngMom;
1205	–	RealType sysconstants;
1206	–	RealType geomCnst;
1207	–
1208	–	geomCnst = 3.0/2.0;
1209	–	/* Get the inertial tensor and angular momentum for free*/
1210	–	getInertiaTensor(intTensor,dummyAngMom);
1211	–
1212	–	det = intTensor.determinant();
1213	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1214	–	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1215	–	return;
1216	–	}
1217	–
1218	–	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1219	–	Mat3x3d intTensor;
1220	–	Vector3d dummyAngMom;
1221	–	RealType sysconstants;
1222	–	RealType geomCnst;
1223	–
1224	–	geomCnst = 3.0/2.0;
1225	–	/* Get the inertial tensor and angular momentum for free*/
1226	–	getInertiaTensor(intTensor,dummyAngMom);
1227	–
1228	–	detI = intTensor.determinant();
1229	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1230	–	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1231	–	return;
1232	–	}
1233	–	/*
1234	–	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1235	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1236	–	sdByGlobalIndex_ = v;
1237	–	}
1238	–
1239	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1240	–	//assert(index < nAtoms_ + nRigidBodies_);
1241	–	return sdByGlobalIndex_.at(index);
1242	–	}
1243	–	*/
1025		int SimInfo::getNGlobalConstraints() {
1026		int nGlobalConstraints;
1027		#ifdef IS_MPI

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Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC vs. Revision 1779 by gezelter, Mon Aug 20 17:51:39 2012 UTC

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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC vs.
Revision 1779 by gezelter, Mon Aug 20 17:51:39 2012 UTC