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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC vs.
Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 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
135	–	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136	–	std::cerr << "nCA = " << nCutoffAtoms << "\n";
137	–	std::cerr << "nG = " << nGroups << "\n";
133
134		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	–
141	–	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
135
136		//every free atom (atom does not belong to rigid bodies) is an
137		//integrable object therefore the total number of integrable objects
#	Line 233 \| 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)) {
245	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	–	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		}
255	<
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 275 \| 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)) {
297	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
298	–	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 311 \| 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 324 \| 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 360 \| 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;
367	<	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 378 \| 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 513 \| 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;
520	<	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 531 \| 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 687 \| 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 706 \| Line 735 \| namespace OpenMD {
735		// count_local holds the number of found types on this processor
736		int count_local = foundTypes.size();
737
738	<	// count holds the total number of found types on all processors
710	<	// (some will be redundant with the ones found locally):
711	<	int count;
712	<	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
738	>	int nproc = MPI::COMM_WORLD.Get_size();
739
740	<	// create a vector to hold the globally found types, and resize it:
741	<	vector<int> ftGlobal;
742	<	ftGlobal.resize(count);
743	<	vector<int> counts;
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	<	int nproc = MPI::COMM_WORLD.Get_size();
746	<	counts.resize(nproc);
747	<	vector<int> disps;
748	<	disps.resize(nproc);
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	<	// now spray out the foundTypes to all the other processors:
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		void SimInfo::setupSimVariables() {
786		useAtomicVirial_ = simParams_->getUseAtomicVirial();
787	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
787	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
788	>	// parameter is true
789		calcBoxDipole_ = false;
790		if ( simParams_->haveAccumulateBoxDipole() )
791		if ( simParams_->getAccumulateBoxDipole() ) {
792		calcBoxDipole_ = true;
793		}
794	<
794	>
795		set<AtomType*>::iterator i;
796		set<AtomType*> atomTypes;
797		atomTypes = getSimulatedAtomTypes();
798	<	int usesElectrostatic = 0;
799	<	int usesMetallic = 0;
800	<	int usesDirectional = 0;
798	>	bool usesElectrostatic = false;
799	>	bool usesMetallic = false;
800	>	bool usesDirectional = false;
801	>	bool usesFluctuatingCharges = false;
802		//loop over all of the atom types
803		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
804		usesElectrostatic \|= (*i)->isElectrostatic();
805		usesMetallic \|= (*i)->isMetal();
806		usesDirectional \|= (*i)->isDirectional();
807	+	usesFluctuatingCharges \|= (*i)->isFluctuatingCharge();
808		}
809
810	<	#ifdef IS_MPI
811	<	int temp;
810	>	#ifdef IS_MPI
811	>	bool temp;
812		temp = usesDirectional;
813	<	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	<
813	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
814	>	MPI::LOR);
815	>
816		temp = usesMetallic;
817	<	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	<
817	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
818	>	MPI::LOR);
819	>
820		temp = usesElectrostatic;
821	<	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
822	>	MPI::LOR);
823	>
824	>	temp = usesFluctuatingCharges;
825	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
826	>	MPI::LOR);
827	>	#else
828	>
829	>	usesDirectionalAtoms_ = usesDirectional;
830	>	usesMetallicAtoms_ = usesMetallic;
831	>	usesElectrostaticAtoms_ = usesElectrostatic;
832	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
833	>
834		#endif
835	<	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
836	<	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
837	<	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
838	<	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784	<	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785	<	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
835	>
836	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
837	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
838	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
839		}
840
841	<	void SimInfo::setupFortran() {
842	<	int isError;
843	<	int nExclude, nOneTwo, nOneThree, nOneFour;
844	<	vector<int> fortranGlobalGroupMembership;
841	>
842	>	vector<int> SimInfo::getGlobalAtomIndices() {
843	>	SimInfo::MoleculeIterator mi;
844	>	Molecule* mol;
845	>	Molecule::AtomIterator ai;
846	>	Atom* atom;
847	>
848	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
849
850	<	isError = 0;
850	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
851	>
852	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
853	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
854	>	}
855	>	}
856	>	return GlobalAtomIndices;
857	>	}
858
859	<	//globalGroupMembership_ is filled by SimCreator
860	<	for (int i = 0; i < nGlobalAtoms_; i++) {
861	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
859	>
860	>	vector<int> SimInfo::getGlobalGroupIndices() {
861	>	SimInfo::MoleculeIterator mi;
862	>	Molecule* mol;
863	>	Molecule::CutoffGroupIterator ci;
864	>	CutoffGroup* cg;
865	>
866	>	vector<int> GlobalGroupIndices;
867	>
868	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
869	>
870	>	//local index of cutoff group is trivial, it only depends on the
871	>	//order of travesing
872	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
873	>	cg = mol->nextCutoffGroup(ci)) {
874	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
875	>	}
876		}
877	+	return GlobalGroupIndices;
878	+	}
879
880	+
881	+	void SimInfo::prepareTopology() {
882	+
883		//calculate mass ratio of cutoff group
801	–	vector<RealType> mfact;
884		SimInfo::MoleculeIterator mi;
885		Molecule* mol;
886		Molecule::CutoffGroupIterator ci;
#	Line 807 \| Line 889 \| namespace OpenMD {
889		Atom* atom;
890		RealType totalMass;
891
892	<	//to avoid memory reallocation, reserve enough space for mfact
893	<	mfact.reserve(getNCutoffGroups());
892	>	/**
893	>	* The mass factor is the relative mass of an atom to the total
894	>	* mass of the cutoff group it belongs to. By default, all atoms
895	>	* are their own cutoff groups, and therefore have mass factors of
896	>	* 1. We need some special handling for massless atoms, which
897	>	* will be treated as carrying the entire mass of the cutoff
898	>	* group.
899	>	*/
900	>	massFactors_.clear();
901	>	massFactors_.resize(getNAtoms(), 1.0);
902
903		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
904	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
904	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
905	>	cg = mol->nextCutoffGroup(ci)) {
906
907		totalMass = cg->getMass();
908		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
909		// Check for massless groups - set mfact to 1 if true
910	<	if (totalMass != 0)
911	<	mfact.push_back(atom->getMass()/totalMass);
910	>	if (totalMass != 0)
911	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
912		else
913	<	mfact.push_back( 1.0 );
913	>	massFactors_[atom->getLocalIndex()] = 1.0;
914		}
915		}
916		}
#	Line 833 \| Line 924 \| namespace OpenMD {
924		identArray_.push_back(atom->getIdent());
925		}
926		}
836	–
837	–	//fill molMembershipArray
838	–	//molMembershipArray is filled by SimCreator
839	–	vector<int> molMembershipArray(nGlobalAtoms_);
840	–	for (int i = 0; i < nGlobalAtoms_; i++) {
841	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
842	–	}
927
928	<	//setup fortran simulation
928	>	//scan topology
929
846	–	nExclude = excludedInteractions_.getSize();
847	–	nOneTwo = oneTwoInteractions_.getSize();
848	–	nOneThree = oneThreeInteractions_.getSize();
849	–	nOneFour = oneFourInteractions_.getSize();
850	–
930		int* excludeList = excludedInteractions_.getPairList();
931		int* oneTwoList = oneTwoInteractions_.getPairList();
932		int* oneThreeList = oneThreeInteractions_.getPairList();
933		int* oneFourList = oneFourInteractions_.getPairList();
934
935	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
857	<	&nExclude, excludeList,
858	<	&nOneTwo, oneTwoList,
859	<	&nOneThree, oneThreeList,
860	<	&nOneFour, oneFourList,
861	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862	<	&fortranGlobalGroupMembership[0], &isError);
863	<
864	<	if( isError ){
865	<
866	<	sprintf( painCave.errMsg,
867	<	"There was an error setting the simulation information in fortran.\n" );
868	<	painCave.isFatal = 1;
869	<	painCave.severity = OPENMD_ERROR;
870	<	simError();
871	<	}
872	<
873	<
874	<	sprintf( checkPointMsg,
875	<	"succesfully sent the simulation information to fortran.\n");
876	<
877	<	errorCheckPoint();
878	<
879	<	// Setup number of neighbors in neighbor list if present
880	<	if (simParams_->haveNeighborListNeighbors()) {
881	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
882	<	setNeighbors(&nlistNeighbors);
883	<	}
884	<
885	<	#ifdef IS_MPI
886	<	//SimInfo is responsible for creating localToGlobalAtomIndex and
887	<	//localToGlobalGroupIndex
888	<	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
889	<	vector<int> localToGlobalCutoffGroupIndex;
890	<	mpiSimData parallelData;
891	<
892	<	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
893	<
894	<	//local index(index in DataStorge) of atom is important
895	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
897	<	}
898	<
899	<	//local index of cutoff group is trivial, it only depends on the order of travesing
900	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
901	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
902	<	}
903	<
904	<	}
905	<
906	<	//fill up mpiSimData struct
907	<	parallelData.nMolGlobal = getNGlobalMolecules();
908	<	parallelData.nMolLocal = getNMolecules();
909	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
910	<	parallelData.nAtomsLocal = getNAtoms();
911	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
912	<	parallelData.nGroupsLocal = getNCutoffGroups();
913	<	parallelData.myNode = worldRank;
914	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
915	<
916	<	//pass mpiSimData struct and index arrays to fortran
917	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
918	<	&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
919	<	&localToGlobalCutoffGroupIndex[0], &isError);
920	<
921	<	if (isError) {
922	<	sprintf(painCave.errMsg,
923	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
924	<	painCave.isFatal = 1;
925	<	simError();
926	<	}
927	<
928	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
929	<	errorCheckPoint();
930	<	#endif
931	<
932	<	initFortranFF(&isError);
933	<	if (isError) {
934	<	sprintf(painCave.errMsg,
935	<	"initFortranFF errror: fortran didn't like something we gave it.\n");
936	<	painCave.isFatal = 1;
937	<	simError();
938	<	}
939	<	fortranInitialized_ = true;
935	>	topologyDone_ = true;
936		}
937
938		void SimInfo::addProperty(GenericData* genData) {
#	Line 981 \| Line 977 \| namespace OpenMD {
977
978		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
979
980	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
980	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
981	>	atom = mol->nextAtom(atomIter)) {
982		atom->setSnapshotManager(sman_);
983		}
984
985	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
985	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
986	>	rb = mol->nextRigidBody(rbIter)) {
987		rb->setSnapshotManager(sman_);
988		}
989
990	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
990	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
991	>	cg = mol->nextCutoffGroup(cgIter)) {
992		cg->setSnapshotManager(sman_);
993		}
994		}
995
996		}
997
999	–	Vector3d SimInfo::getComVel(){
1000	–	SimInfo::MoleculeIterator i;
1001	–	Molecule* mol;
998
1003	–	Vector3d comVel(0.0);
1004	–	RealType totalMass = 0.0;
1005	–
1006	–
1007	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1008	–	RealType mass = mol->getMass();
1009	–	totalMass += mass;
1010	–	comVel += mass * mol->getComVel();
1011	–	}
1012	–
1013	–	#ifdef IS_MPI
1014	–	RealType tmpMass = totalMass;
1015	–	Vector3d tmpComVel(comVel);
1016	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1017	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1018	–	#endif
1019	–
1020	–	comVel /= totalMass;
1021	–
1022	–	return comVel;
1023	–	}
1024	–
1025	–	Vector3d SimInfo::getCom(){
1026	–	SimInfo::MoleculeIterator i;
1027	–	Molecule* mol;
1028	–
1029	–	Vector3d com(0.0);
1030	–	RealType totalMass = 0.0;
1031	–
1032	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1033	–	RealType mass = mol->getMass();
1034	–	totalMass += mass;
1035	–	com += mass * mol->getCom();
1036	–	}
1037	–
1038	–	#ifdef IS_MPI
1039	–	RealType tmpMass = totalMass;
1040	–	Vector3d tmpCom(com);
1041	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1042	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1043	–	#endif
1044	–
1045	–	com /= totalMass;
1046	–
1047	–	return com;
1048	–
1049	–	}
1050	–
999		ostream& operator <<(ostream& o, SimInfo& info) {
1000
1001		return o;
1002		}
1003
1004	<
1057	<	/*
1058	<	Returns center of mass and center of mass velocity in one function call.
1059	<	*/
1060	<
1061	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1062	<	SimInfo::MoleculeIterator i;
1063	<	Molecule* mol;
1064	<
1065	<
1066	<	RealType totalMass = 0.0;
1067	<
1068	<
1069	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1070	<	RealType mass = mol->getMass();
1071	<	totalMass += mass;
1072	<	com += mass * mol->getCom();
1073	<	comVel += mass * mol->getComVel();
1074	<	}
1075	<
1076	<	#ifdef IS_MPI
1077	<	RealType tmpMass = totalMass;
1078	<	Vector3d tmpCom(com);
1079	<	Vector3d tmpComVel(comVel);
1080	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1081	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1082	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1083	<	#endif
1084	<
1085	<	com /= totalMass;
1086	<	comVel /= totalMass;
1087	<	}
1088	<
1089	<	/*
1090	<	Return intertia tensor for entire system and angular momentum Vector.
1091	<
1092	<
1093	<	[ Ixx -Ixy -Ixz ]
1094	<	J =\| -Iyx Iyy -Iyz \|
1095	<	[ -Izx -Iyz Izz ]
1096	<	*/
1097	<
1098	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1099	<
1100	<
1101	<	RealType xx = 0.0;
1102	<	RealType yy = 0.0;
1103	<	RealType zz = 0.0;
1104	<	RealType xy = 0.0;
1105	<	RealType xz = 0.0;
1106	<	RealType yz = 0.0;
1107	<	Vector3d com(0.0);
1108	<	Vector3d comVel(0.0);
1109	<
1110	<	getComAll(com, comVel);
1111	<
1112	<	SimInfo::MoleculeIterator i;
1113	<	Molecule* mol;
1114	<
1115	<	Vector3d thisq(0.0);
1116	<	Vector3d thisv(0.0);
1117	<
1118	<	RealType thisMass = 0.0;
1119	<
1120	<
1121	<
1122	<
1123	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1124	<
1125	<	thisq = mol->getCom()-com;
1126	<	thisv = mol->getComVel()-comVel;
1127	<	thisMass = mol->getMass();
1128	<	// Compute moment of intertia coefficients.
1129	<	xx += thisq[0]thisq[0]thisMass;
1130	<	yy += thisq[1]thisq[1]thisMass;
1131	<	zz += thisq[2]thisq[2]thisMass;
1132	<
1133	<	// compute products of intertia
1134	<	xy += thisq[0]thisq[1]thisMass;
1135	<	xz += thisq[0]thisq[2]thisMass;
1136	<	yz += thisq[1]thisq[2]thisMass;
1137	<
1138	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1139	<
1140	<	}
1141	<
1142	<
1143	<	inertiaTensor(0,0) = yy + zz;
1144	<	inertiaTensor(0,1) = -xy;
1145	<	inertiaTensor(0,2) = -xz;
1146	<	inertiaTensor(1,0) = -xy;
1147	<	inertiaTensor(1,1) = xx + zz;
1148	<	inertiaTensor(1,2) = -yz;
1149	<	inertiaTensor(2,0) = -xz;
1150	<	inertiaTensor(2,1) = -yz;
1151	<	inertiaTensor(2,2) = xx + yy;
1152	<
1153	<	#ifdef IS_MPI
1154	<	Mat3x3d tmpI(inertiaTensor);
1155	<	Vector3d tmpAngMom;
1156	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1157	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1158	<	#endif
1159	<
1160	<	return;
1161	<	}
1162	<
1163	<	//Returns the angular momentum of the system
1164	<	Vector3d SimInfo::getAngularMomentum(){
1165	<
1166	<	Vector3d com(0.0);
1167	<	Vector3d comVel(0.0);
1168	<	Vector3d angularMomentum(0.0);
1169	<
1170	<	getComAll(com,comVel);
1171	<
1172	<	SimInfo::MoleculeIterator i;
1173	<	Molecule* mol;
1174	<
1175	<	Vector3d thisr(0.0);
1176	<	Vector3d thisp(0.0);
1177	<
1178	<	RealType thisMass;
1179	<
1180	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1181	<	thisMass = mol->getMass();
1182	<	thisr = mol->getCom()-com;
1183	<	thisp = (mol->getComVel()-comVel)*thisMass;
1184	<
1185	<	angularMomentum += cross( thisr, thisp );
1186	<
1187	<	}
1188	<
1189	<	#ifdef IS_MPI
1190	<	Vector3d tmpAngMom;
1191	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1192	<	#endif
1193	<
1194	<	return angularMomentum;
1195	<	}
1196	<
1004	>
1005		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1006	<	return IOIndexToIntegrableObject.at(index);
1006	>	if (index >= IOIndexToIntegrableObject.size()) {
1007	>	sprintf(painCave.errMsg,
1008	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1009	>	"\tindex exceeds number of known objects!\n");
1010	>	painCave.isFatal = 1;
1011	>	simError();
1012	>	return NULL;
1013	>	} else
1014	>	return IOIndexToIntegrableObject.at(index);
1015		}
1016
1017		void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1018		IOIndexToIntegrableObject= v;
1019		}
1020
1205	–	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1206	–	based on the radius of gyration V=4/3PiR_1R_2R_3
1207	–	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1208	–	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1209	–	*/
1210	–	void SimInfo::getGyrationalVolume(RealType &volume){
1211	–	Mat3x3d intTensor;
1212	–	RealType det;
1213	–	Vector3d dummyAngMom;
1214	–	RealType sysconstants;
1215	–	RealType geomCnst;
1216	–
1217	–	geomCnst = 3.0/2.0;
1218	–	/* Get the inertial tensor and angular momentum for free*/
1219	–	getInertiaTensor(intTensor,dummyAngMom);
1220	–
1221	–	det = intTensor.determinant();
1222	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1223	–	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1224	–	return;
1225	–	}
1226	–
1227	–	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1228	–	Mat3x3d intTensor;
1229	–	Vector3d dummyAngMom;
1230	–	RealType sysconstants;
1231	–	RealType geomCnst;
1232	–
1233	–	geomCnst = 3.0/2.0;
1234	–	/* Get the inertial tensor and angular momentum for free*/
1235	–	getInertiaTensor(intTensor,dummyAngMom);
1236	–
1237	–	detI = intTensor.determinant();
1238	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1239	–	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1240	–	return;
1241	–	}
1242	–	/*
1243	–	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1244	–	assert( v.size() == nAtoms_ + nRigidBodies_);
1245	–	sdByGlobalIndex_ = v;
1246	–	}
1247	–
1248	–	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1249	–	//assert(index < nAtoms_ + nRigidBodies_);
1250	–	return sdByGlobalIndex_.at(index);
1251	–	}
1252	–	*/
1021		int SimInfo::getNGlobalConstraints() {
1022		int nGlobalConstraints;
1023		#ifdef IS_MPI
1024	<	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1025	<	MPI_COMM_WORLD);
1024	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1025	>	MPI::INT, MPI::SUM);
1026		#else
1027		nGlobalConstraints = nConstraints_;
1028		#endif

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Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC vs. Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC vs.
Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC