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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC vs.
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

#	Line 36 \| Line 36
36		* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4] Vardeman & Gezelter, in progress (2009).
39	>	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	>	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 54 \| Line 55
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57		#include "primitives/StuntDouble.hpp"
57	–	#include "UseTheForce/fCutoffPolicy.h"
58	–	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59	–	#include "UseTheForce/doForces_interface.h"
60	–	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61		#include "io/ForceFieldOptions.hpp"
62	<	#include "UseTheForce/ForceField.hpp"
63	<	#include "nonbonded/InteractionManager.hpp"
68	<
69	<
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
73	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68		using namespace std;
69		namespace OpenMD {
#	Line 79 \| 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 136 \| Line 129 \| namespace OpenMD {
129		//equal to the total number of atoms minus number of atoms belong to
130		//cutoff group defined in meta-data file plus the number of cutoff
131		//groups defined in meta-data file
132	+
133		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134
135		//every free atom (atom does not belong to rigid bodies) is an
#	Line 231 \| Line 225 \| namespace OpenMD {
225
226
227		void SimInfo::calcNdf() {
228	<	int ndf_local;
228	>	int ndf_local, nfq_local;
229		MoleculeIterator i;
230		vector<StuntDouble*>::iterator j;
231	+	vector<Atom*>::iterator k;
232	+
233		Molecule* mol;
234	<	StuntDouble* integrableObject;
234	>	StuntDouble* sd;
235	>	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
243	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
244	–	integrableObject = mol->nextIntegrableObject(j)) {
241
242	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
243	+	sd = mol->nextIntegrableObject(j)) {
244	+
245		ndf_local += 3;
246
247	<	if (integrableObject->isDirectional()) {
248	<	if (integrableObject->isLinear()) {
247	>	if (sd->isDirectional()) {
248	>	if (sd->isLinear()) {
249		ndf_local += 2;
250		} else {
251		ndf_local += 3;
252		}
253		}
255	–
254		}
255	+
256	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
257	+	atom = mol->nextFluctuatingCharge(k)) {
258	+	if (atom->isFluctuatingCharge()) {
259	+	nfq_local++;
260	+	}
261	+	}
262		}
263
264	+	ndfLocal_ = ndf_local;
265	+
266		// n_constraints is local, so subtract them on each processor
267		ndf_local -= nConstraints_;
268
269		#ifdef IS_MPI
270		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
272		#else
273		ndf_ = ndf_local;
274	+	nGlobalFluctuatingCharges_ = nfq_local;
275		#endif
276
277		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 278 \| Line 287 \| namespace OpenMD {
287		fdf_ = fdf_local;
288		#endif
289		return fdf_;
290	+	}
291	+
292	+	unsigned int SimInfo::getNLocalCutoffGroups(){
293	+	int nLocalCutoffAtoms = 0;
294	+	Molecule* mol;
295	+	MoleculeIterator mi;
296	+	CutoffGroup* cg;
297	+	Molecule::CutoffGroupIterator ci;
298	+
299	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
300	+
301	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
302	+	cg = mol->nextCutoffGroup(ci)) {
303	+	nLocalCutoffAtoms += cg->getNumAtom();
304	+
305	+	}
306	+	}
307	+
308	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
309		}
310
311		void SimInfo::calcNdfRaw() {
#	Line 286 \| Line 314 \| namespace OpenMD {
314		MoleculeIterator i;
315		vector<StuntDouble*>::iterator j;
316		Molecule* mol;
317	<	StuntDouble* integrableObject;
317	>	StuntDouble* sd;
318
319		// Raw degrees of freedom that we have to set
320		ndfRaw_local = 0;
321
322		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
295	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
296	–	integrableObject = mol->nextIntegrableObject(j)) {
323
324	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
325	+	sd = mol->nextIntegrableObject(j)) {
326	+
327		ndfRaw_local += 3;
328
329	<	if (integrableObject->isDirectional()) {
330	<	if (integrableObject->isLinear()) {
329	>	if (sd->isDirectional()) {
330	>	if (sd->isLinear()) {
331		ndfRaw_local += 2;
332		} else {
333		ndfRaw_local += 3;
#	Line 358 \| Line 387 \| namespace OpenMD {
387		Molecule::RigidBodyIterator rbIter;
388		RigidBody* rb;
389		Molecule::IntegrableObjectIterator ii;
390	<	StuntDouble* integrableObject;
390	>	StuntDouble* sd;
391
392	<	for (integrableObject = mol->beginIntegrableObject(ii);
393	<	integrableObject != NULL;
365	<	integrableObject = mol->nextIntegrableObject(ii)) {
392	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
393	>	sd = mol->nextIntegrableObject(ii)) {
394
395	<	if (integrableObject->isRigidBody()) {
396	<	rb = static_cast<RigidBody*>(integrableObject);
395	>	if (sd->isRigidBody()) {
396	>	rb = static_cast<RigidBody*>(sd);
397		vector<Atom*> atoms = rb->getAtoms();
398		set<int> rigidAtoms;
399		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
#	Line 376 \| Line 404 \| namespace OpenMD {
404		}
405		} else {
406		set<int> oneAtomSet;
407	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
408	<	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
407	>	oneAtomSet.insert(sd->getGlobalIndex());
408	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
409		}
410		}
411
#	Line 511 \| Line 539 \| namespace OpenMD {
539		Molecule::RigidBodyIterator rbIter;
540		RigidBody* rb;
541		Molecule::IntegrableObjectIterator ii;
542	<	StuntDouble* integrableObject;
542	>	StuntDouble* sd;
543
544	<	for (integrableObject = mol->beginIntegrableObject(ii);
545	<	integrableObject != NULL;
518	<	integrableObject = mol->nextIntegrableObject(ii)) {
544	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
545	>	sd = mol->nextIntegrableObject(ii)) {
546
547	<	if (integrableObject->isRigidBody()) {
548	<	rb = static_cast<RigidBody*>(integrableObject);
547	>	if (sd->isRigidBody()) {
548	>	rb = static_cast<RigidBody*>(sd);
549		vector<Atom*> atoms = rb->getAtoms();
550		set<int> rigidAtoms;
551		for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
#	Line 529 \| Line 556 \| namespace OpenMD {
556		}
557		} else {
558		set<int> oneAtomSet;
559	<	oneAtomSet.insert(integrableObject->getGlobalIndex());
560	<	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
559	>	oneAtomSet.insert(sd->getGlobalIndex());
560	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
561		}
562		}
563
#	Line 656 \| Line 683 \| namespace OpenMD {
683		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684		}
685
659	–	void SimInfo::update() {
686
687	<	setupSimType();
688	<	setupCutoffRadius();
689	<	setupSwitchingRadius();
690	<	setupCutoffMethod();
691	<	setupSkinThickness();
692	<	setupSwitchingFunction();
693	<	setupAccumulateBoxDipole();
694	<
695	<	#ifdef IS_MPI
670	<	setupFortranParallel();
671	<	#endif
672	<	setupFortranSim();
673	<	fortranInitialized_ = true;
674	<
687	>	/**
688	>	* update
689	>	*
690	>	* Performs the global checks and variable settings after the
691	>	* objects have been created.
692	>	*
693	>	*/
694	>	void SimInfo::update() {
695	>	setupSimVariables();
696		calcNdf();
697		calcNdfRaw();
698		calcNdfTrans();
699		}
700
701	+	/**
702	+	* getSimulatedAtomTypes
703	+	*
704	+	* Returns an STL set of AtomType* that are actually present in this
705	+	* simulation. Must query all processors to assemble this information.
706	+	*
707	+	*/
708		set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709		SimInfo::MoleculeIterator mi;
710		Molecule* mol;
#	Line 684 \| Line 712 \| namespace OpenMD {
712		Atom* atom;
713		set<AtomType*> atomTypes;
714
715	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
715	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	>	for(atom = mol->beginAtom(ai); atom != NULL;
717	>	atom = mol->nextAtom(ai)) {
718		atomTypes.insert(atom->getAtomType());
719		}
720		}
692	–	return atomTypes;
693	–	}
694	–
695	–	/**
696	–	* setupCutoffRadius
697	–	*
698	–	* If the cutoffRadius was explicitly set, use that value.
699	–	* If the cutoffRadius was not explicitly set:
700	–	* Are there electrostatic atoms? Use 12.0 Angstroms.
701	–	* No electrostatic atoms? Poll the atom types present in the
702	–	* simulation for suggested cutoff values (e.g. 2.5 * sigma).
703	–	* Use the maximum suggested value that was found.
704	–	*/
705	–	void SimInfo::setupCutoffRadius() {
721
722	<	if (simParams_->haveCutoffRadius()) {
708	<	cutoffRadius_ = simParams_->getCutoffRadius();
709	<	} else {
710	<	if (usesElectrostaticAtoms_) {
711	<	sprintf(painCave.errMsg,
712	<	"SimInfo Warning: No value was set for the cutoffRadius.\n"
713	<	"\tOpenMD will use a default value of 12.0 angstroms"
714	<	"\tfor the cutoffRadius.\n");
715	<	painCave.isFatal = 0;
716	<	simError();
717	<	cutoffRadius_ = 12.0;
718	<	} else {
719	<	RealType thisCut;
720	<	set<AtomType*>::iterator i;
721	<	set<AtomType*> atomTypes;
722	<	atomTypes = getSimulatedAtomTypes();
723	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
724	<	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
725	<	cutoffRadius_ = max(thisCut, cutoffRadius_);
726	<	}
727	<	sprintf(painCave.errMsg,
728	<	"SimInfo Warning: No value was set for the cutoffRadius.\n"
729	<	"\tOpenMD will use %lf angstroms.\n",
730	<	cutoffRadius_);
731	<	painCave.isFatal = 0;
732	<	simError();
733	<	}
734	<	}
722	>	#ifdef IS_MPI
723
724	<	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
725	<	}
738	<
739	<	/**
740	<	* setupSwitchingRadius
741	<	*
742	<	* If the switchingRadius was explicitly set, use that value (but check it)
743	<	* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
744	<	*/
745	<	void SimInfo::setupSwitchingRadius() {
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726
727	<	if (simParams_->haveSwitchingRadius()) {
728	<	switchingRadius_ = simParams_->getSwitchingRadius();
729	<	if (switchingRadius_ > cutoffRadius_) {
730	<	sprintf(painCave.errMsg,
731	<	"SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
732	<	switchingRadius_, cutoffRadius_);
733	<	painCave.isFatal = 1;
754	<	simError();
727	>	vector<int> foundTypes;
728	>	set<AtomType*>::iterator i;
729	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730	>	foundTypes.push_back( (*i)->getIdent() );
731	>
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734
735	<	}
757	<	} else {
758	<	switchingRadius_ = 0.85 * cutoffRadius_;
759	<	sprintf(painCave.errMsg,
760	<	"SimInfo Warning: No value was set for the switchingRadius.\n"
761	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
762	<	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
763	<	painCave.isFatal = 0;
764	<	simError();
765	<	}
766	<	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
767	<	}
735	>	int nproc = MPI::COMM_WORLD.Get_size();
736
737	<	/**
738	<	* setupSkinThickness
739	<	*
740	<	* If the skinThickness was explicitly set, use that value (but check it)
741	<	* If the skinThickness was not explicitly set: use 1.0 angstroms
742	<	*/
743	<	void SimInfo::setupSkinThickness() {
744	<	if (simParams_->haveSkinThickness()) {
745	<	skinThickness_ = simParams_->getSkinThickness();
746	<	} else {
747	<	skinThickness_ = 1.0;
748	<	sprintf(painCave.errMsg,
749	<	"SimInfo Warning: No value was set for the skinThickness.\n"
750	<	"\tOpenMD will use a default value of %f Angstroms\n"
751	<	"\tfor this simulation\n", skinThickness_);
752	<	painCave.isFatal = 0;
753	<	simError();
754	<	}
737	>	// we need arrays to hold the counts and displacement vectors for
738	>	// all processors
739	>	vector<int> counts(nproc, 0);
740	>	vector<int> disps(nproc, 0);
741	>
742	>	// fill the counts array
743	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744	>	1, MPI::INT);
745	>
746	>	// use the processor counts to compute the displacement array
747	>	disps[0] = 0;
748	>	int totalCount = counts[0];
749	>	for (int iproc = 1; iproc < nproc; iproc++) {
750	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
751	>	totalCount += counts[iproc];
752	>	}
753	>
754	>	// we need a (possibly redundant) set of all found types:
755	>	vector<int> ftGlobal(totalCount);
756	>
757	>	// now spray out the foundTypes to all the other processors:
758	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759	>	&ftGlobal[0], &counts[0], &disps[0],
760	>	MPI::INT);
761	>
762	>	vector<int>::iterator j;
763	>
764	>	// foundIdents is a stl set, so inserting an already found ident
765	>	// will have no effect.
766	>	set<int> foundIdents;
767	>
768	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769	>	foundIdents.insert((*j));
770	>
771	>	// now iterate over the foundIdents and get the actual atom types
772	>	// that correspond to these:
773	>	set<int>::iterator it;
774	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	>	atomTypes.insert( forceField_->getAtomType((*it)) );
776	>
777	>	#endif
778	>
779	>	return atomTypes;
780		}
781
782	<	void SimInfo::setupSimType() {
782	>	void SimInfo::setupSimVariables() {
783	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
784	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	>	calcBoxDipole_ = false;
786	>	if ( simParams_->haveAccumulateBoxDipole() )
787	>	if ( simParams_->getAccumulateBoxDipole() ) {
788	>	calcBoxDipole_ = true;
789	>	}
790	>
791		set<AtomType*>::iterator i;
792		set<AtomType*> atomTypes;
793	<	atomTypes = getSimulatedAtomTypes();
794	<
795	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
796	<
797	<	int usesElectrostatic = 0;
797	<	int usesMetallic = 0;
798	<	int usesDirectional = 0;
793	>	atomTypes = getSimulatedAtomTypes();
794	>	bool usesElectrostatic = false;
795	>	bool usesMetallic = false;
796	>	bool usesDirectional = false;
797	>	bool usesFluctuatingCharges = false;
798		//loop over all of the atom types
799		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800		usesElectrostatic \|= (*i)->isElectrostatic();
801		usesMetallic \|= (*i)->isMetal();
802		usesDirectional \|= (*i)->isDirectional();
803	+	usesFluctuatingCharges \|= (*i)->isFluctuatingCharge();
804		}
805
806	<	#ifdef IS_MPI
807	<	int temp;
806	>	#ifdef IS_MPI
807	>	bool temp;
808		temp = usesDirectional;
809	<	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	<
809	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
810	>	MPI::LOR);
811	>
812		temp = usesMetallic;
813	<	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	<
813	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
814	>	MPI::LOR);
815	>
816		temp = usesElectrostatic;
817	<	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
818	>	MPI::LOR);
819	>
820	>	temp = usesFluctuatingCharges;
821	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
822	>	MPI::LOR);
823	>	#else
824	>
825	>	usesDirectionalAtoms_ = usesDirectional;
826	>	usesMetallicAtoms_ = usesMetallic;
827	>	usesElectrostaticAtoms_ = usesElectrostatic;
828	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
829	>
830		#endif
831	<	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
832	<	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
833	<	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
834	<	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
821	<	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
822	<	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
831	>
832	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
833	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
834	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
835		}
836
837	<	void SimInfo::setupFortranSim() {
838	<	int isError;
839	<	int nExclude, nOneTwo, nOneThree, nOneFour;
840	<	vector<int> fortranGlobalGroupMembership;
837	>
838	>	vector<int> SimInfo::getGlobalAtomIndices() {
839	>	SimInfo::MoleculeIterator mi;
840	>	Molecule* mol;
841	>	Molecule::AtomIterator ai;
842	>	Atom* atom;
843	>
844	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
845
846	<	notifyFortranSkinThickness(&skinThickness_);
846	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
847	>
848	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
849	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
850	>	}
851	>	}
852	>	return GlobalAtomIndices;
853	>	}
854
832	–	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
833	–	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
834	–	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
855
856	<	isError = 0;
856	>	vector<int> SimInfo::getGlobalGroupIndices() {
857	>	SimInfo::MoleculeIterator mi;
858	>	Molecule* mol;
859	>	Molecule::CutoffGroupIterator ci;
860	>	CutoffGroup* cg;
861
862	<	//globalGroupMembership_ is filled by SimCreator
863	<	for (int i = 0; i < nGlobalAtoms_; i++) {
864	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
862	>	vector<int> GlobalGroupIndices;
863	>
864	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
865	>
866	>	//local index of cutoff group is trivial, it only depends on the
867	>	//order of travesing
868	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
869	>	cg = mol->nextCutoffGroup(ci)) {
870	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
871	>	}
872		}
873	+	return GlobalGroupIndices;
874	+	}
875
876	+
877	+	void SimInfo::prepareTopology() {
878	+	int nExclude, nOneTwo, nOneThree, nOneFour;
879	+
880		//calculate mass ratio of cutoff group
844	–	vector<RealType> mfact;
881		SimInfo::MoleculeIterator mi;
882		Molecule* mol;
883		Molecule::CutoffGroupIterator ci;
#	Line 850 \| Line 886 \| namespace OpenMD {
886		Atom* atom;
887		RealType totalMass;
888
889	<	//to avoid memory reallocation, reserve enough space for mfact
890	<	mfact.reserve(getNCutoffGroups());
889	>	/**
890	>	* The mass factor is the relative mass of an atom to the total
891	>	* mass of the cutoff group it belongs to. By default, all atoms
892	>	* are their own cutoff groups, and therefore have mass factors of
893	>	* 1. We need some special handling for massless atoms, which
894	>	* will be treated as carrying the entire mass of the cutoff
895	>	* group.
896	>	*/
897	>	massFactors_.clear();
898	>	massFactors_.resize(getNAtoms(), 1.0);
899
900		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
901	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
901	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
902	>	cg = mol->nextCutoffGroup(ci)) {
903
904		totalMass = cg->getMass();
905		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906		// Check for massless groups - set mfact to 1 if true
907	<	if (totalMass != 0)
908	<	mfact.push_back(atom->getMass()/totalMass);
907	>	if (totalMass != 0)
908	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
909		else
910	<	mfact.push_back( 1.0 );
910	>	massFactors_[atom->getLocalIndex()] = 1.0;
911		}
912		}
913		}
914
915	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
871	<	vector<int> identArray;
915	>	// Build the identArray_
916
917	<	//to avoid memory reallocation, reserve enough space identArray
918	<	identArray.reserve(getNAtoms());
875	<
917	>	identArray_.clear();
918	>	identArray_.reserve(getNAtoms());
919		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
921	<	identArray.push_back(atom->getIdent());
921	>	identArray_.push_back(atom->getIdent());
922		}
923		}
881	–
882	–	//fill molMembershipArray
883	–	//molMembershipArray is filled by SimCreator
884	–	vector<int> molMembershipArray(nGlobalAtoms_);
885	–	for (int i = 0; i < nGlobalAtoms_; i++) {
886	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
887	–	}
924
925	<	//setup fortran simulation
925	>	//scan topology
926
927		nExclude = excludedInteractions_.getSize();
928		nOneTwo = oneTwoInteractions_.getSize();
#	Line 898 \| Line 934 \| namespace OpenMD {
934		int* oneThreeList = oneThreeInteractions_.getPairList();
935		int* oneFourList = oneFourInteractions_.getPairList();
936
937	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
902	<	&nExclude, excludeList,
903	<	&nOneTwo, oneTwoList,
904	<	&nOneThree, oneThreeList,
905	<	&nOneFour, oneFourList,
906	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
907	<	&fortranGlobalGroupMembership[0], &isError);
908	<
909	<	if( isError ){
910	<
911	<	sprintf( painCave.errMsg,
912	<	"There was an error setting the simulation information in fortran.\n" );
913	<	painCave.isFatal = 1;
914	<	painCave.severity = OPENMD_ERROR;
915	<	simError();
916	<	}
917	<
918	<
919	<	sprintf( checkPointMsg,
920	<	"succesfully sent the simulation information to fortran.\n");
921	<
922	<	errorCheckPoint();
923	<
924	<	// Setup number of neighbors in neighbor list if present
925	<	if (simParams_->haveNeighborListNeighbors()) {
926	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
927	<	setNeighbors(&nlistNeighbors);
928	<	}
929	<
930	<
937	>	topologyDone_ = true;
938		}
939
933	–
934	–	void SimInfo::setupFortranParallel() {
935	–	#ifdef IS_MPI
936	–	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
937	–	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
938	–	vector<int> localToGlobalCutoffGroupIndex;
939	–	SimInfo::MoleculeIterator mi;
940	–	Molecule::AtomIterator ai;
941	–	Molecule::CutoffGroupIterator ci;
942	–	Molecule* mol;
943	–	Atom* atom;
944	–	CutoffGroup* cg;
945	–	mpiSimData parallelData;
946	–	int isError;
947	–
948	–	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
949	–
950	–	//local index(index in DataStorge) of atom is important
951	–	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
952	–	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
953	–	}
954	–
955	–	//local index of cutoff group is trivial, it only depends on the order of travesing
956	–	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
957	–	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
958	–	}
959	–
960	–	}
961	–
962	–	//fill up mpiSimData struct
963	–	parallelData.nMolGlobal = getNGlobalMolecules();
964	–	parallelData.nMolLocal = getNMolecules();
965	–	parallelData.nAtomsGlobal = getNGlobalAtoms();
966	–	parallelData.nAtomsLocal = getNAtoms();
967	–	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
968	–	parallelData.nGroupsLocal = getNCutoffGroups();
969	–	parallelData.myNode = worldRank;
970	–	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
971	–
972	–	//pass mpiSimData struct and index arrays to fortran
973	–	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
974	–	&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
975	–	&localToGlobalCutoffGroupIndex[0], &isError);
976	–
977	–	if (isError) {
978	–	sprintf(painCave.errMsg,
979	–	"mpiRefresh errror: fortran didn't like something we gave it.\n");
980	–	painCave.isFatal = 1;
981	–	simError();
982	–	}
983	–
984	–	sprintf(checkPointMsg, " mpiRefresh successful.\n");
985	–	errorCheckPoint();
986	–
987	–	#endif
988	–	}
989	–
990	–
991	–	void SimInfo::setupSwitchingFunction() {
992	–	int ft = CUBIC;
993	–
994	–	if (simParams_->haveSwitchingFunctionType()) {
995	–	string funcType = simParams_->getSwitchingFunctionType();
996	–	toUpper(funcType);
997	–	if (funcType == "CUBIC") {
998	–	ft = CUBIC;
999	–	} else {
1000	–	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1001	–	ft = FIFTH_ORDER_POLY;
1002	–	} else {
1003	–	// throw error
1004	–	sprintf( painCave.errMsg,
1005	–	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n"
1006	–	"\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".",
1007	–	funcType.c_str() );
1008	–	painCave.isFatal = 1;
1009	–	simError();
1010	–	}
1011	–	}
1012	–	}
1013	–
1014	–	// send switching function notification to switcheroo
1015	–	setFunctionType(&ft);
1016	–
1017	–	}
1018	–
1019	–	void SimInfo::setupAccumulateBoxDipole() {
1020	–
1021	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1022	–	if ( simParams_->haveAccumulateBoxDipole() )
1023	–	if ( simParams_->getAccumulateBoxDipole() ) {
1024	–	calcBoxDipole_ = true;
1025	–	}
1026	–
1027	–	}
1028	–
940		void SimInfo::addProperty(GenericData* genData) {
941		properties_.addProperty(genData);
942		}
#	Line 1060 \| Line 971 \| namespace OpenMD {
971		Molecule* mol;
972		RigidBody* rb;
973		Atom* atom;
974	+	CutoffGroup* cg;
975		SimInfo::MoleculeIterator mi;
976		Molecule::RigidBodyIterator rbIter;
977	<	Molecule::AtomIterator atomIter;;
977	>	Molecule::AtomIterator atomIter;
978	>	Molecule::CutoffGroupIterator cgIter;
979
980		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
981
#	Line 1073 \| Line 986 \| namespace OpenMD {
986		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
987		rb->setSnapshotManager(sman_);
988		}
989	+
990	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
991	+	cg->setSnapshotManager(sman_);
992	+	}
993		}
994
995		}
996
1080	–	Vector3d SimInfo::getComVel(){
1081	–	SimInfo::MoleculeIterator i;
1082	–	Molecule* mol;
997
1084	–	Vector3d comVel(0.0);
1085	–	RealType totalMass = 0.0;
1086	–
1087	–
1088	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1089	–	RealType mass = mol->getMass();
1090	–	totalMass += mass;
1091	–	comVel += mass * mol->getComVel();
1092	–	}
1093	–
1094	–	#ifdef IS_MPI
1095	–	RealType tmpMass = totalMass;
1096	–	Vector3d tmpComVel(comVel);
1097	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1098	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1099	–	#endif
1100	–
1101	–	comVel /= totalMass;
1102	–
1103	–	return comVel;
1104	–	}
1105	–
1106	–	Vector3d SimInfo::getCom(){
1107	–	SimInfo::MoleculeIterator i;
1108	–	Molecule* mol;
1109	–
1110	–	Vector3d com(0.0);
1111	–	RealType totalMass = 0.0;
1112	–
1113	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1114	–	RealType mass = mol->getMass();
1115	–	totalMass += mass;
1116	–	com += mass * mol->getCom();
1117	–	}
1118	–
1119	–	#ifdef IS_MPI
1120	–	RealType tmpMass = totalMass;
1121	–	Vector3d tmpCom(com);
1122	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1123	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1124	–	#endif
1125	–
1126	–	com /= totalMass;
1127	–
1128	–	return com;
1129	–
1130	–	}
1131	–
998		ostream& operator <<(ostream& o, SimInfo& info) {
999
1000		return o;
1001		}
1002
1003	<
1138	<	/*
1139	<	Returns center of mass and center of mass velocity in one function call.
1140	<	*/
1141	<
1142	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1143	<	SimInfo::MoleculeIterator i;
1144	<	Molecule* mol;
1145	<
1146	<
1147	<	RealType totalMass = 0.0;
1148	<
1149	<
1150	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1151	<	RealType mass = mol->getMass();
1152	<	totalMass += mass;
1153	<	com += mass * mol->getCom();
1154	<	comVel += mass * mol->getComVel();
1155	<	}
1156	<
1157	<	#ifdef IS_MPI
1158	<	RealType tmpMass = totalMass;
1159	<	Vector3d tmpCom(com);
1160	<	Vector3d tmpComVel(comVel);
1161	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1162	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1163	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1164	<	#endif
1165	<
1166	<	com /= totalMass;
1167	<	comVel /= totalMass;
1168	<	}
1169	<
1170	<	/*
1171	<	Return intertia tensor for entire system and angular momentum Vector.
1172	<
1173	<
1174	<	[ Ixx -Ixy -Ixz ]
1175	<	J =\| -Iyx Iyy -Iyz \|
1176	<	[ -Izx -Iyz Izz ]
1177	<	*/
1178	<
1179	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1180	<
1181	<
1182	<	RealType xx = 0.0;
1183	<	RealType yy = 0.0;
1184	<	RealType zz = 0.0;
1185	<	RealType xy = 0.0;
1186	<	RealType xz = 0.0;
1187	<	RealType yz = 0.0;
1188	<	Vector3d com(0.0);
1189	<	Vector3d comVel(0.0);
1190	<
1191	<	getComAll(com, comVel);
1192	<
1193	<	SimInfo::MoleculeIterator i;
1194	<	Molecule* mol;
1195	<
1196	<	Vector3d thisq(0.0);
1197	<	Vector3d thisv(0.0);
1198	<
1199	<	RealType thisMass = 0.0;
1200	<
1201	<
1202	<
1203	<
1204	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1205	<
1206	<	thisq = mol->getCom()-com;
1207	<	thisv = mol->getComVel()-comVel;
1208	<	thisMass = mol->getMass();
1209	<	// Compute moment of intertia coefficients.
1210	<	xx += thisq[0]thisq[0]thisMass;
1211	<	yy += thisq[1]thisq[1]thisMass;
1212	<	zz += thisq[2]thisq[2]thisMass;
1213	<
1214	<	// compute products of intertia
1215	<	xy += thisq[0]thisq[1]thisMass;
1216	<	xz += thisq[0]thisq[2]thisMass;
1217	<	yz += thisq[1]thisq[2]thisMass;
1218	<
1219	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1220	<
1221	<	}
1222	<
1223	<
1224	<	inertiaTensor(0,0) = yy + zz;
1225	<	inertiaTensor(0,1) = -xy;
1226	<	inertiaTensor(0,2) = -xz;
1227	<	inertiaTensor(1,0) = -xy;
1228	<	inertiaTensor(1,1) = xx + zz;
1229	<	inertiaTensor(1,2) = -yz;
1230	<	inertiaTensor(2,0) = -xz;
1231	<	inertiaTensor(2,1) = -yz;
1232	<	inertiaTensor(2,2) = xx + yy;
1233	<
1234	<	#ifdef IS_MPI
1235	<	Mat3x3d tmpI(inertiaTensor);
1236	<	Vector3d tmpAngMom;
1237	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1238	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1239	<	#endif
1240	<
1241	<	return;
1242	<	}
1243	<
1244	<	//Returns the angular momentum of the system
1245	<	Vector3d SimInfo::getAngularMomentum(){
1246	<
1247	<	Vector3d com(0.0);
1248	<	Vector3d comVel(0.0);
1249	<	Vector3d angularMomentum(0.0);
1250	<
1251	<	getComAll(com,comVel);
1252	<
1253	<	SimInfo::MoleculeIterator i;
1254	<	Molecule* mol;
1255	<
1256	<	Vector3d thisr(0.0);
1257	<	Vector3d thisp(0.0);
1258	<
1259	<	RealType thisMass;
1260	<
1261	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1262	<	thisMass = mol->getMass();
1263	<	thisr = mol->getCom()-com;
1264	<	thisp = (mol->getComVel()-comVel)*thisMass;
1265	<
1266	<	angularMomentum += cross( thisr, thisp );
1267	<
1268	<	}
1269	<
1270	<	#ifdef IS_MPI
1271	<	Vector3d tmpAngMom;
1272	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1273	<	#endif
1274	<
1275	<	return angularMomentum;
1276	<	}
1277	<
1003	>
1004		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005		return IOIndexToIntegrableObject.at(index);
1006		}
#	Line 1282 \| Line 1008 \| namespace OpenMD {
1008		void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009		IOIndexToIntegrableObject= v;
1010		}
1285	–
1286	–	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1287	–	based on the radius of gyration V=4/3PiR_1R_2R_3
1288	–	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1289	–	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1290	–	*/
1291	–	void SimInfo::getGyrationalVolume(RealType &volume){
1292	–	Mat3x3d intTensor;
1293	–	RealType det;
1294	–	Vector3d dummyAngMom;
1295	–	RealType sysconstants;
1296	–	RealType geomCnst;
1297	–
1298	–	geomCnst = 3.0/2.0;
1299	–	/* Get the inertial tensor and angular momentum for free*/
1300	–	getInertiaTensor(intTensor,dummyAngMom);
1301	–
1302	–	det = intTensor.determinant();
1303	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1304	–	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1305	–	return;
1306	–	}
1307	–
1308	–	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1309	–	Mat3x3d intTensor;
1310	–	Vector3d dummyAngMom;
1311	–	RealType sysconstants;
1312	–	RealType geomCnst;
1313	–
1314	–	geomCnst = 3.0/2.0;
1315	–	/* Get the inertial tensor and angular momentum for free*/
1316	–	getInertiaTensor(intTensor,dummyAngMom);
1317	–
1318	–	detI = intTensor.determinant();
1319	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1320	–	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1321	–	return;
1322	–	}
1011		/*
1012		void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013		assert( v.size() == nAtoms_ + nRigidBodies_);

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Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC vs. Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC vs.
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC