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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

#	Line 35 \| Line 35
35		*
36		* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4] Vardeman & Gezelter, in progress (2009).
38	>	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	>	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 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 "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"
64	–
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
68	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68		using namespace std;
69		namespace OpenMD {
#	Line 74 \| 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 90 \| 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 131 \| 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 226 \| 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)) {
238	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
239	–	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		}
250	–
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);
271	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
272	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
273	>	MPI::INT, MPI::SUM);
274		#else
275		ndf_ = ndf_local;
276	+	nGlobalFluctuatingCharges_ = nfq_local;
277		#endif
278
279		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 268 \| Line 284 \| namespace OpenMD {
284
285		int SimInfo::getFdf() {
286		#ifdef IS_MPI
287	<	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
287	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
288		#else
289		fdf_ = fdf_local;
290		#endif
291		return fdf_;
292		}
293	+
294	+	unsigned int SimInfo::getNLocalCutoffGroups(){
295	+	int nLocalCutoffAtoms = 0;
296	+	Molecule* mol;
297	+	MoleculeIterator mi;
298	+	CutoffGroup* cg;
299	+	Molecule::CutoffGroupIterator ci;
300
301	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
302	+
303	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
304	+	cg = mol->nextCutoffGroup(ci)) {
305	+	nLocalCutoffAtoms += cg->getNumAtom();
306	+
307	+	}
308	+	}
309	+
310	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
311	+	}
312	+
313		void SimInfo::calcNdfRaw() {
314		int ndfRaw_local;
315
316		MoleculeIterator i;
317		vector<StuntDouble*>::iterator j;
318		Molecule* mol;
319	<	StuntDouble* integrableObject;
319	>	StuntDouble* sd;
320
321		// Raw degrees of freedom that we have to set
322		ndfRaw_local = 0;
323
324		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
290	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	–	integrableObject = mol->nextIntegrableObject(j)) {
325
326	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
327	+	sd = mol->nextIntegrableObject(j)) {
328	+
329		ndfRaw_local += 3;
330
331	<	if (integrableObject->isDirectional()) {
332	<	if (integrableObject->isLinear()) {
331	>	if (sd->isDirectional()) {
332	>	if (sd->isLinear()) {
333		ndfRaw_local += 2;
334		} else {
335		ndfRaw_local += 3;
#	Line 304 \| Line 340 \| namespace OpenMD {
340		}
341
342		#ifdef IS_MPI
343	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
344		#else
345		ndfRaw_ = ndfRaw_local;
346		#endif
#	Line 317 \| Line 353 \| namespace OpenMD {
353
354
355		#ifdef IS_MPI
356	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
357	>	MPI::INT, MPI::SUM);
358		#else
359		ndfTrans_ = ndfTrans_local;
360		#endif
#	Line 353 \| Line 390 \| namespace OpenMD {
390		Molecule::RigidBodyIterator rbIter;
391		RigidBody* rb;
392		Molecule::IntegrableObjectIterator ii;
393	<	StuntDouble* integrableObject;
393	>	StuntDouble* sd;
394
395	<	for (integrableObject = mol->beginIntegrableObject(ii);
396	<	integrableObject != NULL;
360	<	integrableObject = mol->nextIntegrableObject(ii)) {
395	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
396	>	sd = mol->nextIntegrableObject(ii)) {
397
398	<	if (integrableObject->isRigidBody()) {
399	<	rb = static_cast<RigidBody*>(integrableObject);
398	>	if (sd->isRigidBody()) {
399	>	rb = static_cast<RigidBody*>(sd);
400		vector<Atom*> atoms = rb->getAtoms();
401		set<int> rigidAtoms;
402		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
#	Line 371 \| Line 407 \| namespace OpenMD {
407		}
408		} else {
409		set<int> oneAtomSet;
410	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
411	<	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
410	>	oneAtomSet.insert(sd->getGlobalIndex());
411	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
412		}
413		}
414
#	Line 506 \| Line 542 \| namespace OpenMD {
542		Molecule::RigidBodyIterator rbIter;
543		RigidBody* rb;
544		Molecule::IntegrableObjectIterator ii;
545	<	StuntDouble* integrableObject;
545	>	StuntDouble* sd;
546
547	<	for (integrableObject = mol->beginIntegrableObject(ii);
548	<	integrableObject != NULL;
513	<	integrableObject = mol->nextIntegrableObject(ii)) {
547	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
548	>	sd = mol->nextIntegrableObject(ii)) {
549
550	<	if (integrableObject->isRigidBody()) {
551	<	rb = static_cast<RigidBody*>(integrableObject);
550	>	if (sd->isRigidBody()) {
551	>	rb = static_cast<RigidBody*>(sd);
552		vector<Atom*> atoms = rb->getAtoms();
553		set<int> rigidAtoms;
554		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
#	Line 524 \| Line 559 \| namespace OpenMD {
559		}
560		} else {
561		set<int> oneAtomSet;
562	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
563	<	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
562	>	oneAtomSet.insert(sd->getGlobalIndex());
563	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
564		}
565		}
566
#	Line 680 \| Line 715 \| namespace OpenMD {
715		Atom* atom;
716		set<AtomType*> atomTypes;
717
718	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
719	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
718	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
719	>	for(atom = mol->beginAtom(ai); atom != NULL;
720	>	atom = mol->nextAtom(ai)) {
721		atomTypes.insert(atom->getAtomType());
722		}
723		}
724	<
724	>
725		#ifdef IS_MPI
726
727		// loop over the found atom types on this processor, and add their
728		// numerical idents to a vector:
729	<
729	>
730		vector<int> foundTypes;
731		set<AtomType*>::iterator i;
732		for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
#	Line 699 \| Line 735 \| namespace OpenMD {
735		// count_local holds the number of found types on this processor
736		int count_local = foundTypes.size();
737
702	–	// count holds the total number of found types on all processors
703	–	// (some will be redundant with the ones found locally):
704	–	int count;
705	–	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706	–
707	–	// create a vector to hold the globally found types, and resize it:
708	–	vector<int> ftGlobal;
709	–	ftGlobal.resize(count);
710	–	vector<int> counts;
711	–
738		int nproc = MPI::COMM_WORLD.Get_size();
739	<	counts.resize(nproc);
740	<	vector<int> disps;
741	<	disps.resize(nproc);
739	>
740	>	// we need arrays to hold the counts and displacement vectors for
741	>	// all processors
742	>	vector<int> counts(nproc, 0);
743	>	vector<int> disps(nproc, 0);
744
745	<	// now spray out the foundTypes to all the other processors:
745	>	// fill the counts array
746	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
747	>	1, MPI::INT);
748	>
749	>	// use the processor counts to compute the displacement array
750	>	disps[0] = 0;
751	>	int totalCount = counts[0];
752	>	for (int iproc = 1; iproc < nproc; iproc++) {
753	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
754	>	totalCount += counts[iproc];
755	>	}
756	>
757	>	// we need a (possibly redundant) set of all found types:
758	>	vector<int> ftGlobal(totalCount);
759
760	+	// now spray out the foundTypes to all the other processors:
761		MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
762	<	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
762	>	&ftGlobal[0], &counts[0], &disps[0],
763	>	MPI::INT);
764
765	+	vector<int>::iterator j;
766	+
767		// foundIdents is a stl set, so inserting an already found ident
768		// will have no effect.
769		set<int> foundIdents;
770	<	vector<int>::iterator j;
770	>
771		for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
772		foundIdents.insert((*j));
773
774		// now iterate over the foundIdents and get the actual atom types
775		// that correspond to these:
776		set<int>::iterator it;
777	<	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
777	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
778		atomTypes.insert( forceField_->getAtomType((*it)) );
779
780		#endif
781	<
781	>
782		return atomTypes;
783		}
784
785	+
786	+	int getGlobalCountOfType(AtomType* atype) {
787	+	/*
788	+	set<AtomType*> atypes = getSimulatedAtomTypes();
789	+	map<AtomType*, int> counts_;
790	+
791	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
792	+	for(atom = mol->beginAtom(ai); atom != NULL;
793	+	atom = mol->nextAtom(ai)) {
794	+	atom->getAtomType();
795	+	}
796	+	}
797	+	*/
798	+	return 0;
799	+	}
800	+
801		void SimInfo::setupSimVariables() {
802		useAtomicVirial_ = simParams_->getUseAtomicVirial();
803	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
803	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
804	>	// parameter is true
805		calcBoxDipole_ = false;
806		if ( simParams_->haveAccumulateBoxDipole() )
807		if ( simParams_->getAccumulateBoxDipole() ) {
808		calcBoxDipole_ = true;
809		}
810	<
810	>
811		set<AtomType*>::iterator i;
812		set<AtomType*> atomTypes;
813		atomTypes = getSimulatedAtomTypes();
814	<	int usesElectrostatic = 0;
815	<	int usesMetallic = 0;
816	<	int usesDirectional = 0;
814	>	bool usesElectrostatic = false;
815	>	bool usesMetallic = false;
816	>	bool usesDirectional = false;
817	>	bool usesFluctuatingCharges = false;
818		//loop over all of the atom types
819		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
820		usesElectrostatic \|= (*i)->isElectrostatic();
821		usesMetallic \|= (*i)->isMetal();
822		usesDirectional \|= (*i)->isDirectional();
823	+	usesFluctuatingCharges \|= (*i)->isFluctuatingCharge();
824		}
825
826	<	#ifdef IS_MPI
827	<	int temp;
826	>	#ifdef IS_MPI
827	>	bool temp;
828		temp = usesDirectional;
829	<	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	<
829	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
830	>	MPI::LOR);
831	>
832		temp = usesMetallic;
833	<	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834	<
833	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
834	>	MPI::LOR);
835	>
836		temp = usesElectrostatic;
837	<	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
838	>	MPI::LOR);
839	>
840	>	temp = usesFluctuatingCharges;
841	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
842	>	MPI::LOR);
843	>	#else
844	>
845	>	usesDirectionalAtoms_ = usesDirectional;
846	>	usesMetallicAtoms_ = usesMetallic;
847	>	usesElectrostaticAtoms_ = usesElectrostatic;
848	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
849	>
850		#endif
851	<	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
852	<	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
853	<	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
854	<	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
777	<	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
778	<	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
851	>
852	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
853	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
854	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
855		}
856
857	<	void SimInfo::setupFortran() {
858	<	int isError;
859	<	int nExclude, nOneTwo, nOneThree, nOneFour;
860	<	vector<int> fortranGlobalGroupMembership;
857	>
858	>	vector<int> SimInfo::getGlobalAtomIndices() {
859	>	SimInfo::MoleculeIterator mi;
860	>	Molecule* mol;
861	>	Molecule::AtomIterator ai;
862	>	Atom* atom;
863	>
864	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
865
866	<	isError = 0;
866	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
867	>
868	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
869	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
870	>	}
871	>	}
872	>	return GlobalAtomIndices;
873	>	}
874
875	<	//globalGroupMembership_ is filled by SimCreator
876	<	for (int i = 0; i < nGlobalAtoms_; i++) {
877	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
875	>
876	>	vector<int> SimInfo::getGlobalGroupIndices() {
877	>	SimInfo::MoleculeIterator mi;
878	>	Molecule* mol;
879	>	Molecule::CutoffGroupIterator ci;
880	>	CutoffGroup* cg;
881	>
882	>	vector<int> GlobalGroupIndices;
883	>
884	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
885	>
886	>	//local index of cutoff group is trivial, it only depends on the
887	>	//order of travesing
888	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
889	>	cg = mol->nextCutoffGroup(ci)) {
890	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
891	>	}
892		}
893	+	return GlobalGroupIndices;
894	+	}
895
896	+
897	+	void SimInfo::prepareTopology() {
898	+
899		//calculate mass ratio of cutoff group
794	–	vector<RealType> mfact;
900		SimInfo::MoleculeIterator mi;
901		Molecule* mol;
902		Molecule::CutoffGroupIterator ci;
#	Line 800 \| Line 905 \| namespace OpenMD {
905		Atom* atom;
906		RealType totalMass;
907
908	<	//to avoid memory reallocation, reserve enough space for mfact
909	<	mfact.reserve(getNCutoffGroups());
908	>	/**
909	>	* The mass factor is the relative mass of an atom to the total
910	>	* mass of the cutoff group it belongs to. By default, all atoms
911	>	* are their own cutoff groups, and therefore have mass factors of
912	>	* 1. We need some special handling for massless atoms, which
913	>	* will be treated as carrying the entire mass of the cutoff
914	>	* group.
915	>	*/
916	>	massFactors_.clear();
917	>	massFactors_.resize(getNAtoms(), 1.0);
918
919		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
920	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
921	>	cg = mol->nextCutoffGroup(ci)) {
922
923		totalMass = cg->getMass();
924		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
925		// Check for massless groups - set mfact to 1 if true
926	<	if (totalMass != 0)
927	<	mfact.push_back(atom->getMass()/totalMass);
926	>	if (totalMass != 0)
927	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
928		else
929	<	mfact.push_back( 1.0 );
929	>	massFactors_[atom->getLocalIndex()] = 1.0;
930		}
931		}
932		}
933
934	<	//fill ident array of local atoms (it is actually ident of
821	<	//AtomType, it is so confusing !!!)
822	<	vector<int> identArray;
934	>	// Build the identArray_
935
936	<	//to avoid memory reallocation, reserve enough space identArray
937	<	identArray.reserve(getNAtoms());
826	<
936	>	identArray_.clear();
937	>	identArray_.reserve(getNAtoms());
938		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
939		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
940	<	identArray.push_back(atom->getIdent());
940	>	identArray_.push_back(atom->getIdent());
941		}
942		}
832	–
833	–	//fill molMembershipArray
834	–	//molMembershipArray is filled by SimCreator
835	–	vector<int> molMembershipArray(nGlobalAtoms_);
836	–	for (int i = 0; i < nGlobalAtoms_; i++) {
837	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
838	–	}
943
944	<	//setup fortran simulation
841	<
842	<	nExclude = excludedInteractions_.getSize();
843	<	nOneTwo = oneTwoInteractions_.getSize();
844	<	nOneThree = oneThreeInteractions_.getSize();
845	<	nOneFour = oneFourInteractions_.getSize();
846	<
847	<	int* excludeList = excludedInteractions_.getPairList();
848	<	int* oneTwoList = oneTwoInteractions_.getPairList();
849	<	int* oneThreeList = oneThreeInteractions_.getPairList();
850	<	int* oneFourList = oneFourInteractions_.getPairList();
851	<
852	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
853	<	&nExclude, excludeList,
854	<	&nOneTwo, oneTwoList,
855	<	&nOneThree, oneThreeList,
856	<	&nOneFour, oneFourList,
857	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
858	<	&fortranGlobalGroupMembership[0], &isError);
859	<
860	<	if( isError ){
861	<
862	<	sprintf( painCave.errMsg,
863	<	"There was an error setting the simulation information in fortran.\n" );
864	<	painCave.isFatal = 1;
865	<	painCave.severity = OPENMD_ERROR;
866	<	simError();
867	<	}
868	<
869	<
870	<	sprintf( checkPointMsg,
871	<	"succesfully sent the simulation information to fortran.\n");
872	<
873	<	errorCheckPoint();
874	<
875	<	// Setup number of neighbors in neighbor list if present
876	<	if (simParams_->haveNeighborListNeighbors()) {
877	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
878	<	setNeighbors(&nlistNeighbors);
879	<	}
880	<
881	<	#ifdef IS_MPI
882	<	//SimInfo is responsible for creating localToGlobalAtomIndex and
883	<	//localToGlobalGroupIndex
884	<	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
885	<	vector<int> localToGlobalCutoffGroupIndex;
886	<	mpiSimData parallelData;
887	<
888	<	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
889	<
890	<	//local index(index in DataStorge) of atom is important
891	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893	<	}
894	<
895	<	//local index of cutoff group is trivial, it only depends on the order of travesing
896	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898	<	}
899	<
900	<	}
901	<
902	<	//fill up mpiSimData struct
903	<	parallelData.nMolGlobal = getNGlobalMolecules();
904	<	parallelData.nMolLocal = getNMolecules();
905	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
906	<	parallelData.nAtomsLocal = getNAtoms();
907	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
908	<	parallelData.nGroupsLocal = getNCutoffGroups();
909	<	parallelData.myNode = worldRank;
910	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
911	<
912	<	//pass mpiSimData struct and index arrays to fortran
913	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
914	<	&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
915	<	&localToGlobalCutoffGroupIndex[0], &isError);
916	<
917	<	if (isError) {
918	<	sprintf(painCave.errMsg,
919	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
920	<	painCave.isFatal = 1;
921	<	simError();
922	<	}
923	<
924	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
925	<	errorCheckPoint();
926	<	#endif
927	<	fortranInitialized_ = true;
944	>	topologyDone_ = true;
945		}
946
947		void SimInfo::addProperty(GenericData* genData) {
#	Line 961 \| Line 978 \| namespace OpenMD {
978		Molecule* mol;
979		RigidBody* rb;
980		Atom* atom;
981	+	CutoffGroup* cg;
982		SimInfo::MoleculeIterator mi;
983		Molecule::RigidBodyIterator rbIter;
984	<	Molecule::AtomIterator atomIter;;
984	>	Molecule::AtomIterator atomIter;
985	>	Molecule::CutoffGroupIterator cgIter;
986
987		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
988
989	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
989	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
990	>	atom = mol->nextAtom(atomIter)) {
991		atom->setSnapshotManager(sman_);
992		}
993
994	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
994	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
995	>	rb = mol->nextRigidBody(rbIter)) {
996		rb->setSnapshotManager(sman_);
997		}
998	+
999	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1000	+	cg = mol->nextCutoffGroup(cgIter)) {
1001	+	cg->setSnapshotManager(sman_);
1002	+	}
1003		}
1004
1005		}
1006
981	–	Vector3d SimInfo::getComVel(){
982	–	SimInfo::MoleculeIterator i;
983	–	Molecule* mol;
1007
985	–	Vector3d comVel(0.0);
986	–	RealType totalMass = 0.0;
987	–
988	–
989	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
990	–	RealType mass = mol->getMass();
991	–	totalMass += mass;
992	–	comVel += mass * mol->getComVel();
993	–	}
994	–
995	–	#ifdef IS_MPI
996	–	RealType tmpMass = totalMass;
997	–	Vector3d tmpComVel(comVel);
998	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
999	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1000	–	#endif
1001	–
1002	–	comVel /= totalMass;
1003	–
1004	–	return comVel;
1005	–	}
1006	–
1007	–	Vector3d SimInfo::getCom(){
1008	–	SimInfo::MoleculeIterator i;
1009	–	Molecule* mol;
1010	–
1011	–	Vector3d com(0.0);
1012	–	RealType totalMass = 0.0;
1013	–
1014	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1015	–	RealType mass = mol->getMass();
1016	–	totalMass += mass;
1017	–	com += mass * mol->getCom();
1018	–	}
1019	–
1020	–	#ifdef IS_MPI
1021	–	RealType tmpMass = totalMass;
1022	–	Vector3d tmpCom(com);
1023	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1024	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1025	–	#endif
1026	–
1027	–	com /= totalMass;
1028	–
1029	–	return com;
1030	–
1031	–	}
1032	–
1008		ostream& operator <<(ostream& o, SimInfo& info) {
1009
1010		return o;
1011		}
1012
1013	<
1039	<	/*
1040	<	Returns center of mass and center of mass velocity in one function call.
1041	<	*/
1042	<
1043	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1044	<	SimInfo::MoleculeIterator i;
1045	<	Molecule* mol;
1046	<
1047	<
1048	<	RealType totalMass = 0.0;
1049	<
1050	<
1051	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1052	<	RealType mass = mol->getMass();
1053	<	totalMass += mass;
1054	<	com += mass * mol->getCom();
1055	<	comVel += mass * mol->getComVel();
1056	<	}
1057	<
1058	<	#ifdef IS_MPI
1059	<	RealType tmpMass = totalMass;
1060	<	Vector3d tmpCom(com);
1061	<	Vector3d tmpComVel(comVel);
1062	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1063	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1064	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1065	<	#endif
1066	<
1067	<	com /= totalMass;
1068	<	comVel /= totalMass;
1069	<	}
1070	<
1071	<	/*
1072	<	Return intertia tensor for entire system and angular momentum Vector.
1073	<
1074	<
1075	<	[ Ixx -Ixy -Ixz ]
1076	<	J =\| -Iyx Iyy -Iyz \|
1077	<	[ -Izx -Iyz Izz ]
1078	<	*/
1079	<
1080	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1081	<
1082	<
1083	<	RealType xx = 0.0;
1084	<	RealType yy = 0.0;
1085	<	RealType zz = 0.0;
1086	<	RealType xy = 0.0;
1087	<	RealType xz = 0.0;
1088	<	RealType yz = 0.0;
1089	<	Vector3d com(0.0);
1090	<	Vector3d comVel(0.0);
1091	<
1092	<	getComAll(com, comVel);
1093	<
1094	<	SimInfo::MoleculeIterator i;
1095	<	Molecule* mol;
1096	<
1097	<	Vector3d thisq(0.0);
1098	<	Vector3d thisv(0.0);
1099	<
1100	<	RealType thisMass = 0.0;
1101	<
1102	<
1103	<
1104	<
1105	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1106	<
1107	<	thisq = mol->getCom()-com;
1108	<	thisv = mol->getComVel()-comVel;
1109	<	thisMass = mol->getMass();
1110	<	// Compute moment of intertia coefficients.
1111	<	xx += thisq[0]thisq[0]thisMass;
1112	<	yy += thisq[1]thisq[1]thisMass;
1113	<	zz += thisq[2]thisq[2]thisMass;
1114	<
1115	<	// compute products of intertia
1116	<	xy += thisq[0]thisq[1]thisMass;
1117	<	xz += thisq[0]thisq[2]thisMass;
1118	<	yz += thisq[1]thisq[2]thisMass;
1119	<
1120	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1121	<
1122	<	}
1123	<
1124	<
1125	<	inertiaTensor(0,0) = yy + zz;
1126	<	inertiaTensor(0,1) = -xy;
1127	<	inertiaTensor(0,2) = -xz;
1128	<	inertiaTensor(1,0) = -xy;
1129	<	inertiaTensor(1,1) = xx + zz;
1130	<	inertiaTensor(1,2) = -yz;
1131	<	inertiaTensor(2,0) = -xz;
1132	<	inertiaTensor(2,1) = -yz;
1133	<	inertiaTensor(2,2) = xx + yy;
1134	<
1135	<	#ifdef IS_MPI
1136	<	Mat3x3d tmpI(inertiaTensor);
1137	<	Vector3d tmpAngMom;
1138	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1139	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1140	<	#endif
1141	<
1142	<	return;
1143	<	}
1144	<
1145	<	//Returns the angular momentum of the system
1146	<	Vector3d SimInfo::getAngularMomentum(){
1147	<
1148	<	Vector3d com(0.0);
1149	<	Vector3d comVel(0.0);
1150	<	Vector3d angularMomentum(0.0);
1151	<
1152	<	getComAll(com,comVel);
1153	<
1154	<	SimInfo::MoleculeIterator i;
1155	<	Molecule* mol;
1156	<
1157	<	Vector3d thisr(0.0);
1158	<	Vector3d thisp(0.0);
1159	<
1160	<	RealType thisMass;
1161	<
1162	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1163	<	thisMass = mol->getMass();
1164	<	thisr = mol->getCom()-com;
1165	<	thisp = (mol->getComVel()-comVel)*thisMass;
1166	<
1167	<	angularMomentum += cross( thisr, thisp );
1168	<
1169	<	}
1170	<
1171	<	#ifdef IS_MPI
1172	<	Vector3d tmpAngMom;
1173	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1174	<	#endif
1175	<
1176	<	return angularMomentum;
1177	<	}
1178	<
1013	>
1014		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1015	<	return IOIndexToIntegrableObject.at(index);
1015	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1016	>	sprintf(painCave.errMsg,
1017	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1018	>	"\tindex exceeds number of known objects!\n");
1019	>	painCave.isFatal = 1;
1020	>	simError();
1021	>	return NULL;
1022	>	} else
1023	>	return IOIndexToIntegrableObject.at(index);
1024		}
1025
1026		void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1027		IOIndexToIntegrableObject= v;
1028		}
1029
1187	–	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1188	–	based on the radius of gyration V=4/3PiR_1R_2R_3
1189	–	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1190	–	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1191	–	*/
1192	–	void SimInfo::getGyrationalVolume(RealType &volume){
1193	–	Mat3x3d intTensor;
1194	–	RealType det;
1195	–	Vector3d dummyAngMom;
1196	–	RealType sysconstants;
1197	–	RealType geomCnst;
1198	–
1199	–	geomCnst = 3.0/2.0;
1200	–	/* Get the inertial tensor and angular momentum for free*/
1201	–	getInertiaTensor(intTensor,dummyAngMom);
1202	–
1203	–	det = intTensor.determinant();
1204	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1205	–	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1206	–	return;
1207	–	}
1208	–
1209	–	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1210	–	Mat3x3d intTensor;
1211	–	Vector3d dummyAngMom;
1212	–	RealType sysconstants;
1213	–	RealType geomCnst;
1214	–
1215	–	geomCnst = 3.0/2.0;
1216	–	/* Get the inertial tensor and angular momentum for free*/
1217	–	getInertiaTensor(intTensor,dummyAngMom);
1218	–
1219	–	detI = intTensor.determinant();
1220	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1221	–	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1222	–	return;
1223	–	}
1224	–	/*
1225	–	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1226	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1227	–	sdByGlobalIndex_ = v;
1228	–	}
1229	–
1230	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1231	–	//assert(index < nAtoms_ + nRigidBodies_);
1232	–	return sdByGlobalIndex_.at(index);
1233	–	}
1234	–	*/
1030		int SimInfo::getNGlobalConstraints() {
1031		int nGlobalConstraints;
1032		#ifdef IS_MPI
1033	<	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1034	<	MPI_COMM_WORLD);
1033	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1034	>	MPI::INT, MPI::SUM);
1035		#else
1036		nGlobalConstraints = nConstraints_;
1037		#endif

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Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC vs. Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC