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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1534 by gezelter, Wed Dec 29 21:53:28 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/doForces_interface.h"
58	–	#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"
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 132 \| 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 227 \| 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)) {
239	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
240	–	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		}
251	–
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 275 \| Line 288 \| namespace OpenMD {
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() {
312		int ndfRaw_local;
313
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)) {
291	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292	–	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 354 \| 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;
361	<	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 372 \| 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 507 \| 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;
514	<	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 525 \| 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 687 \| namespace OpenMD {
687		/**
688		* update
689		*
690	<	* Performs the global checks and variable settings after the objects have been
691	<	* created.
690	>	* Performs the global checks and variable settings after the
691	>	* objects have been created.
692		*
693		*/
694	<	void SimInfo::update() {
664	<
694	>	void SimInfo::update() {
695		setupSimVariables();
666	–	setupCutoffs();
667	–	setupSwitching();
668	–	setupElectrostatics();
669	–	setupNeighborlists();
670	–
671	–	#ifdef IS_MPI
672	–	setupFortranParallel();
673	–	#endif
674	–	setupFortranSim();
675	–	fortranInitialized_ = true;
676	–
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 686 \| 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		}
721	<	return atomTypes;
722	<	}
721	>
722	>	#ifdef IS_MPI
723
724	<	/**
725	<	* setupCutoffs
699	<	*
700	<	* Sets the values of cutoffRadius and cutoffMethod
701	<	*
702	<	* cutoffRadius : realType
703	<	* If the cutoffRadius was explicitly set, use that value.
704	<	* If the cutoffRadius was not explicitly set:
705	<	* Are there electrostatic atoms? Use 12.0 Angstroms.
706	<	* No electrostatic atoms? Poll the atom types present in the
707	<	* simulation for suggested cutoff values (e.g. 2.5 * sigma).
708	<	* Use the maximum suggested value that was found.
709	<	*
710	<	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
711	<	* If cutoffMethod was explicitly set, use that choice.
712	<	* If cutoffMethod was not explicitly set, use SHIFTED_FORCE
713	<	*/
714	<	void SimInfo::setupCutoffs() {
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726
727	<	if (simParams_->haveCutoffRadius()) {
728	<	cutoffRadius_ = simParams_->getCutoffRadius();
729	<	} else {
730	<	if (usesElectrostaticAtoms_) {
720	<	sprintf(painCave.errMsg,
721	<	"SimInfo: No value was set for the cutoffRadius.\n"
722	<	"\tOpenMD will use a default value of 12.0 angstroms"
723	<	"\tfor the cutoffRadius.\n");
724	<	painCave.isFatal = 0;
725	<	painCave.severity = OPENMD_INFO;
726	<	simError();
727	<	cutoffRadius_ = 12.0;
728	<	} else {
729	<	RealType thisCut;
730	<	set<AtomType*>::iterator i;
731	<	set<AtomType*> atomTypes;
732	<	atomTypes = getSimulatedAtomTypes();
733	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734	<	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
735	<	cutoffRadius_ = max(thisCut, cutoffRadius_);
736	<	}
737	<	sprintf(painCave.errMsg,
738	<	"SimInfo: No value was set for the cutoffRadius.\n"
739	<	"\tOpenMD will use %lf angstroms.\n",
740	<	cutoffRadius_);
741	<	painCave.isFatal = 0;
742	<	painCave.severity = OPENMD_INFO;
743	<	simError();
744	<	}
745	<	}
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	<	map<string, CutoffMethod> stringToCutoffMethod;
733	<	stringToCutoffMethod["HARD"] = HARD;
734	<	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
735	<	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
736	<	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734	>
735	>	int nproc = MPI::COMM_WORLD.Get_size();
736	>
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	<	if (simParams_->haveCutoffMethod()) {
747	<	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
748	<	map<string, CutoffMethod>::iterator i;
749	<	i = stringToCutoffMethod.find(cutMeth);
750	<	if (i == stringToCutoffMethod.end()) {
751	<	sprintf(painCave.errMsg,
759	<	"SimInfo: Could not find chosen cutoffMethod %s\n"
760	<	"\tShould be one of: "
761	<	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
762	<	cutMeth.c_str());
763	<	painCave.isFatal = 1;
764	<	painCave.severity = OPENMD_ERROR;
765	<	simError();
766	<	} else {
767	<	cutoffMethod_ = i->second;
768	<	}
769	<	} else {
770	<	sprintf(painCave.errMsg,
771	<	"SimInfo: No value was set for the cutoffMethod.\n"
772	<	"\tOpenMD will use SHIFTED_FORCE.\n");
773	<	painCave.isFatal = 0;
774	<	painCave.severity = OPENMD_INFO;
775	<	simError();
776	<	cutoffMethod_ = SHIFTED_FORCE;
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	<
755	<	/**
781	<	* setupSwitching
782	<	*
783	<	* Sets the values of switchingRadius and
784	<	* If the switchingRadius was explicitly set, use that value (but check it)
785	<	* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
786	<	*/
787	<	void SimInfo::setupSwitching() {
753	>
754	>	// we need a (possibly redundant) set of all found types:
755	>	vector<int> ftGlobal(totalCount);
756
757	<	if (simParams_->haveSwitchingRadius()) {
758	<	switchingRadius_ = simParams_->getSwitchingRadius();
759	<	if (switchingRadius_ > cutoffRadius_) {
760	<	sprintf(painCave.errMsg,
761	<	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
762	<	switchingRadius_, cutoffRadius_);
763	<	painCave.isFatal = 1;
764	<	painCave.severity = OPENMD_ERROR;
765	<	simError();
766	<	}
767	<	} else {
768	<	switchingRadius_ = 0.85 * cutoffRadius_;
769	<	sprintf(painCave.errMsg,
802	<	"SimInfo: No value was set for the switchingRadius.\n"
803	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
804	<	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
805	<	painCave.isFatal = 0;
806	<	painCave.severity = OPENMD_WARNING;
807	<	simError();
808	<	}
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	<	if (simParams_->haveSwitchingFunctionType()) {
772	<	string funcType = simParams_->getSwitchingFunctionType();
773	<	toUpper(funcType);
774	<	if (funcType == "CUBIC") {
775	<	sft_ = cubic;
776	<	} else {
777	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
817	<	sft_ = fifth_order_poly;
818	<	} else {
819	<	// throw error
820	<	sprintf( painCave.errMsg,
821	<	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
822	<	"\tswitchingFunctionType must be one of: "
823	<	"\"cubic\" or \"fifth_order_polynomial\".",
824	<	funcType.c_str() );
825	<	painCave.isFatal = 1;
826	<	painCave.severity = OPENMD_ERROR;
827	<	simError();
828	<	}
829	<	}
830	<	}
831	<	}
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	<	/**
834	<	* setupNeighborlists
835	<	*
836	<	* If the skinThickness was explicitly set, use that value (but check it)
837	<	* If the skinThickness was not explicitly set: use 1.0 angstroms
838	<	*/
839	<	void SimInfo::setupNeighborlists() {
840	<	if (simParams_->haveSkinThickness()) {
841	<	skinThickness_ = simParams_->getSkinThickness();
842	<	} else {
843	<	skinThickness_ = 1.0;
844	<	sprintf(painCave.errMsg,
845	<	"SimInfo: No value was set for the skinThickness.\n"
846	<	"\tOpenMD will use a default value of %f Angstroms\n"
847	<	"\tfor this simulation\n", skinThickness_);
848	<	painCave.severity = OPENMD_INFO;
849	<	painCave.isFatal = 0;
850	<	simError();
851	<	}
779	>	return atomTypes;
780		}
781
782		void SimInfo::setupSimVariables() {
#	Line 859 \| Line 787 \| namespace OpenMD {
787		if ( simParams_->getAccumulateBoxDipole() ) {
788		calcBoxDipole_ = true;
789		}
790	<
790	>
791		set<AtomType*>::iterator i;
792		set<AtomType*> atomTypes;
793		atomTypes = getSimulatedAtomTypes();
794	<	int usesElectrostatic = 0;
795	<	int usesMetallic = 0;
796	<	int usesDirectional = 0;
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_;
891	<	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892	<	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
831	>
832	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
833	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
834	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
835		}
836
895	–	void SimInfo::setupFortranSim() {
896	–	int isError;
897	–	int nExclude, nOneTwo, nOneThree, nOneFour;
898	–	vector<int> fortranGlobalGroupMembership;
899	–
900	–	notifyFortranSkinThickness(&skinThickness_);
837
838	<	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
839	<	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
840	<	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
838	>	vector<int> SimInfo::getGlobalAtomIndices() {
839	>	SimInfo::MoleculeIterator mi;
840	>	Molecule* mol;
841	>	Molecule::AtomIterator ai;
842	>	Atom* atom;
843
844	<	isError = 0;
845	<
846	<	//globalGroupMembership_ is filled by SimCreator
847	<	for (int i = 0; i < nGlobalAtoms_; i++) {
848	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
844	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
845	>
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
855	+
856	+	vector<int> SimInfo::getGlobalGroupIndices() {
857	+	SimInfo::MoleculeIterator mi;
858	+	Molecule* mol;
859	+	Molecule::CutoffGroupIterator ci;
860	+	CutoffGroup* cg;
861	+
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
914	–	vector<RealType> mfact;
881		SimInfo::MoleculeIterator mi;
882		Molecule* mol;
883		Molecule::CutoffGroupIterator ci;
#	Line 920 \| 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 !!!)
941	<	vector<int> identArray;
915	>	// Build the identArray_
916
917	<	//to avoid memory reallocation, reserve enough space identArray
918	<	identArray.reserve(getNAtoms());
945	<
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		}
951	–
952	–	//fill molMembershipArray
953	–	//molMembershipArray is filled by SimCreator
954	–	vector<int> molMembershipArray(nGlobalAtoms_);
955	–	for (int i = 0; i < nGlobalAtoms_; i++) {
956	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
957	–	}
924
925	<	//setup fortran simulation
925	>	//scan topology
926
927		nExclude = excludedInteractions_.getSize();
928		nOneTwo = oneTwoInteractions_.getSize();
#	Line 968 \| Line 934 \| namespace OpenMD {
934		int* oneThreeList = oneThreeInteractions_.getPairList();
935		int* oneFourList = oneFourInteractions_.getPairList();
936
937	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
972	<	&nExclude, excludeList,
973	<	&nOneTwo, oneTwoList,
974	<	&nOneThree, oneThreeList,
975	<	&nOneFour, oneFourList,
976	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
977	<	&fortranGlobalGroupMembership[0], &isError);
978	<
979	<	if( isError ){
980	<
981	<	sprintf( painCave.errMsg,
982	<	"There was an error setting the simulation information in fortran.\n" );
983	<	painCave.isFatal = 1;
984	<	painCave.severity = OPENMD_ERROR;
985	<	simError();
986	<	}
987	<
988	<
989	<	sprintf( checkPointMsg,
990	<	"succesfully sent the simulation information to fortran.\n");
991	<
992	<	errorCheckPoint();
993	<
994	<	// Setup number of neighbors in neighbor list if present
995	<	if (simParams_->haveNeighborListNeighbors()) {
996	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
997	<	setNeighbors(&nlistNeighbors);
998	<	}
999	<
1000	<
937	>	topologyDone_ = true;
938		}
939
1003	–
1004	–	void SimInfo::setupFortranParallel() {
1005	–	#ifdef IS_MPI
1006	–	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1007	–	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008	–	vector<int> localToGlobalCutoffGroupIndex;
1009	–	SimInfo::MoleculeIterator mi;
1010	–	Molecule::AtomIterator ai;
1011	–	Molecule::CutoffGroupIterator ci;
1012	–	Molecule* mol;
1013	–	Atom* atom;
1014	–	CutoffGroup* cg;
1015	–	mpiSimData parallelData;
1016	–	int isError;
1017	–
1018	–	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1019	–
1020	–	//local index(index in DataStorge) of atom is important
1021	–	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1022	–	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1023	–	}
1024	–
1025	–	//local index of cutoff group is trivial, it only depends on the order of travesing
1026	–	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1027	–	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1028	–	}
1029	–
1030	–	}
1031	–
1032	–	//fill up mpiSimData struct
1033	–	parallelData.nMolGlobal = getNGlobalMolecules();
1034	–	parallelData.nMolLocal = getNMolecules();
1035	–	parallelData.nAtomsGlobal = getNGlobalAtoms();
1036	–	parallelData.nAtomsLocal = getNAtoms();
1037	–	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1038	–	parallelData.nGroupsLocal = getNCutoffGroups();
1039	–	parallelData.myNode = worldRank;
1040	–	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1041	–
1042	–	//pass mpiSimData struct and index arrays to fortran
1043	–	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1044	–	&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
1045	–	&localToGlobalCutoffGroupIndex[0], &isError);
1046	–
1047	–	if (isError) {
1048	–	sprintf(painCave.errMsg,
1049	–	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1050	–	painCave.isFatal = 1;
1051	–	simError();
1052	–	}
1053	–
1054	–	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1055	–	errorCheckPoint();
1056	–
1057	–	#endif
1058	–	}
1059	–
1060	–
1061	–	void SimInfo::setupAccumulateBoxDipole() {
1062	–
1063	–
1064	–	}
1065	–
940		void SimInfo::addProperty(GenericData* genData) {
941		properties_.addProperty(genData);
942		}
#	Line 1097 \| 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 1110 \| 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
1117	–	Vector3d SimInfo::getComVel(){
1118	–	SimInfo::MoleculeIterator i;
1119	–	Molecule* mol;
997
1121	–	Vector3d comVel(0.0);
1122	–	RealType totalMass = 0.0;
1123	–
1124	–
1125	–	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1126	–	RealType mass = mol->getMass();
1127	–	totalMass += mass;
1128	–	comVel += mass * mol->getComVel();
1129	–	}
1130	–
1131	–	#ifdef IS_MPI
1132	–	RealType tmpMass = totalMass;
1133	–	Vector3d tmpComVel(comVel);
1134	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1135	–	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1136	–	#endif
1137	–
1138	–	comVel /= totalMass;
1139	–
1140	–	return comVel;
1141	–	}
1142	–
1143	–	Vector3d SimInfo::getCom(){
1144	–	SimInfo::MoleculeIterator i;
1145	–	Molecule* mol;
1146	–
1147	–	Vector3d com(0.0);
1148	–	RealType totalMass = 0.0;
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	–	}
1155	–
1156	–	#ifdef IS_MPI
1157	–	RealType tmpMass = totalMass;
1158	–	Vector3d tmpCom(com);
1159	–	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1160	–	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1161	–	#endif
1162	–
1163	–	com /= totalMass;
1164	–
1165	–	return com;
1166	–
1167	–	}
1168	–
998		ostream& operator <<(ostream& o, SimInfo& info) {
999
1000		return o;
1001		}
1002
1003	<
1175	<	/*
1176	<	Returns center of mass and center of mass velocity in one function call.
1177	<	*/
1178	<
1179	<	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1180	<	SimInfo::MoleculeIterator i;
1181	<	Molecule* mol;
1182	<
1183	<
1184	<	RealType totalMass = 0.0;
1185	<
1186	<
1187	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1188	<	RealType mass = mol->getMass();
1189	<	totalMass += mass;
1190	<	com += mass * mol->getCom();
1191	<	comVel += mass * mol->getComVel();
1192	<	}
1193	<
1194	<	#ifdef IS_MPI
1195	<	RealType tmpMass = totalMass;
1196	<	Vector3d tmpCom(com);
1197	<	Vector3d tmpComVel(comVel);
1198	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1199	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1200	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1201	<	#endif
1202	<
1203	<	com /= totalMass;
1204	<	comVel /= totalMass;
1205	<	}
1206	<
1207	<	/*
1208	<	Return intertia tensor for entire system and angular momentum Vector.
1209	<
1210	<
1211	<	[ Ixx -Ixy -Ixz ]
1212	<	J =\| -Iyx Iyy -Iyz \|
1213	<	[ -Izx -Iyz Izz ]
1214	<	*/
1215	<
1216	<	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1217	<
1218	<
1219	<	RealType xx = 0.0;
1220	<	RealType yy = 0.0;
1221	<	RealType zz = 0.0;
1222	<	RealType xy = 0.0;
1223	<	RealType xz = 0.0;
1224	<	RealType yz = 0.0;
1225	<	Vector3d com(0.0);
1226	<	Vector3d comVel(0.0);
1227	<
1228	<	getComAll(com, comVel);
1229	<
1230	<	SimInfo::MoleculeIterator i;
1231	<	Molecule* mol;
1232	<
1233	<	Vector3d thisq(0.0);
1234	<	Vector3d thisv(0.0);
1235	<
1236	<	RealType thisMass = 0.0;
1237	<
1238	<
1239	<
1240	<
1241	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1242	<
1243	<	thisq = mol->getCom()-com;
1244	<	thisv = mol->getComVel()-comVel;
1245	<	thisMass = mol->getMass();
1246	<	// Compute moment of intertia coefficients.
1247	<	xx += thisq[0]thisq[0]thisMass;
1248	<	yy += thisq[1]thisq[1]thisMass;
1249	<	zz += thisq[2]thisq[2]thisMass;
1250	<
1251	<	// compute products of intertia
1252	<	xy += thisq[0]thisq[1]thisMass;
1253	<	xz += thisq[0]thisq[2]thisMass;
1254	<	yz += thisq[1]thisq[2]thisMass;
1255	<
1256	<	angularMomentum += cross( thisq, thisv ) * thisMass;
1257	<
1258	<	}
1259	<
1260	<
1261	<	inertiaTensor(0,0) = yy + zz;
1262	<	inertiaTensor(0,1) = -xy;
1263	<	inertiaTensor(0,2) = -xz;
1264	<	inertiaTensor(1,0) = -xy;
1265	<	inertiaTensor(1,1) = xx + zz;
1266	<	inertiaTensor(1,2) = -yz;
1267	<	inertiaTensor(2,0) = -xz;
1268	<	inertiaTensor(2,1) = -yz;
1269	<	inertiaTensor(2,2) = xx + yy;
1270	<
1271	<	#ifdef IS_MPI
1272	<	Mat3x3d tmpI(inertiaTensor);
1273	<	Vector3d tmpAngMom;
1274	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1275	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1276	<	#endif
1277	<
1278	<	return;
1279	<	}
1280	<
1281	<	//Returns the angular momentum of the system
1282	<	Vector3d SimInfo::getAngularMomentum(){
1283	<
1284	<	Vector3d com(0.0);
1285	<	Vector3d comVel(0.0);
1286	<	Vector3d angularMomentum(0.0);
1287	<
1288	<	getComAll(com,comVel);
1289	<
1290	<	SimInfo::MoleculeIterator i;
1291	<	Molecule* mol;
1292	<
1293	<	Vector3d thisr(0.0);
1294	<	Vector3d thisp(0.0);
1295	<
1296	<	RealType thisMass;
1297	<
1298	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1299	<	thisMass = mol->getMass();
1300	<	thisr = mol->getCom()-com;
1301	<	thisp = (mol->getComVel()-comVel)*thisMass;
1302	<
1303	<	angularMomentum += cross( thisr, thisp );
1304	<
1305	<	}
1306	<
1307	<	#ifdef IS_MPI
1308	<	Vector3d tmpAngMom;
1309	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1310	<	#endif
1311	<
1312	<	return angularMomentum;
1313	<	}
1314	<
1003	>
1004		StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005		return IOIndexToIntegrableObject.at(index);
1006		}
#	Line 1319 \| Line 1008 \| namespace OpenMD {
1008		void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009		IOIndexToIntegrableObject= v;
1010		}
1322	–
1323	–	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1324	–	based on the radius of gyration V=4/3PiR_1R_2R_3
1325	–	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1326	–	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1327	–	*/
1328	–	void SimInfo::getGyrationalVolume(RealType &volume){
1329	–	Mat3x3d intTensor;
1330	–	RealType det;
1331	–	Vector3d dummyAngMom;
1332	–	RealType sysconstants;
1333	–	RealType geomCnst;
1334	–
1335	–	geomCnst = 3.0/2.0;
1336	–	/* Get the inertial tensor and angular momentum for free*/
1337	–	getInertiaTensor(intTensor,dummyAngMom);
1338	–
1339	–	det = intTensor.determinant();
1340	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1341	–	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1342	–	return;
1343	–	}
1344	–
1345	–	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1346	–	Mat3x3d intTensor;
1347	–	Vector3d dummyAngMom;
1348	–	RealType sysconstants;
1349	–	RealType geomCnst;
1350	–
1351	–	geomCnst = 3.0/2.0;
1352	–	/* Get the inertial tensor and angular momentum for free*/
1353	–	getInertiaTensor(intTensor,dummyAngMom);
1354	–
1355	–	detI = intTensor.determinant();
1356	–	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1357	–	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1358	–	return;
1359	–	}
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 1534 by gezelter, Wed Dec 29 21:53:28 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 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC vs.
Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC