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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs.
Revision 1750 by gezelter, Thu Jun 7 12:53:46 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	–
66	–
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
70	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68		using namespace std;
69		namespace OpenMD {
#	Line 76 \| 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 133 \| 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 228 \| 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;
235	+	Atom* atom;
236
237		ndf_local = 0;
238	+	nfq_local = 0;
239
240		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241		for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
#	Line 249 \| Line 250 \| namespace OpenMD {
250		ndf_local += 3;
251		}
252		}
252	–
253		}
254	+	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255	+	atom = mol->nextFluctuatingCharge(k)) {
256	+	if (atom->isFluctuatingCharge()) {
257	+	nfq_local++;
258	+	}
259	+	}
260		}
261
262	+	ndfLocal_ = ndf_local;
263	+
264		// n_constraints is local, so subtract them on each processor
265		ndf_local -= nConstraints_;
266
267		#ifdef IS_MPI
268		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
270		#else
271		ndf_ = ndf_local;
272	+	nGlobalFluctuatingCharges_ = nfq_local;
273		#endif
274
275		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 276 \| Line 286 \| namespace OpenMD {
286		#endif
287		return fdf_;
288		}
289	+
290	+	unsigned int SimInfo::getNLocalCutoffGroups(){
291	+	int nLocalCutoffAtoms = 0;
292	+	Molecule* mol;
293	+	MoleculeIterator mi;
294	+	CutoffGroup* cg;
295	+	Molecule::CutoffGroupIterator ci;
296	+
297	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
298	+
299	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
300	+	cg = mol->nextCutoffGroup(ci)) {
301	+	nLocalCutoffAtoms += cg->getNumAtom();
302	+
303	+	}
304	+	}
305	+
306	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
307	+	}
308
309		void SimInfo::calcNdfRaw() {
310		int ndfRaw_local;
#	Line 657 \| Line 686 \| namespace OpenMD {
686		/**
687		* update
688		*
689	<	* Performs the global checks and variable settings after the objects have been
690	<	* created.
689	>	* Performs the global checks and variable settings after the
690	>	* objects have been created.
691		*
692		*/
693	<	void SimInfo::update() {
665	<
693	>	void SimInfo::update() {
694		setupSimVariables();
667	–	setupCutoffs();
668	–	setupSwitching();
669	–	setupElectrostatics();
670	–	setupNeighborlists();
671	–
672	–	#ifdef IS_MPI
673	–	setupFortranParallel();
674	–	#endif
675	–	setupFortranSim();
676	–	fortranInitialized_ = true;
677	–
695		calcNdf();
696		calcNdfRaw();
697		calcNdfTrans();
698		}
699
700	+	/**
701	+	* getSimulatedAtomTypes
702	+	*
703	+	* Returns an STL set of AtomType* that are actually present in this
704	+	* simulation. Must query all processors to assemble this information.
705	+	*
706	+	*/
707		set<AtomType*> SimInfo::getSimulatedAtomTypes() {
708		SimInfo::MoleculeIterator mi;
709		Molecule* mol;
#	Line 687 \| Line 711 \| namespace OpenMD {
711		Atom* atom;
712		set<AtomType*> atomTypes;
713
714	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
715	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
714	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
715	>	for(atom = mol->beginAtom(ai); atom != NULL;
716	>	atom = mol->nextAtom(ai)) {
717		atomTypes.insert(atom->getAtomType());
718		}
719		}
695	–	return atomTypes;
696	–	}
697	–
698	–	/**
699	–	* setupCutoffs
700	–	*
701	–	* Sets the values of cutoffRadius and cutoffMethod
702	–	*
703	–	* cutoffRadius : realType
704	–	* If the cutoffRadius was explicitly set, use that value.
705	–	* If the cutoffRadius was not explicitly set:
706	–	* Are there electrostatic atoms? Use 12.0 Angstroms.
707	–	* No electrostatic atoms? Poll the atom types present in the
708	–	* simulation for suggested cutoff values (e.g. 2.5 * sigma).
709	–	* Use the maximum suggested value that was found.
710	–	*
711	–	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712	–	* If cutoffMethod was explicitly set, use that choice.
713	–	* If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714	–	*/
715	–	void SimInfo::setupCutoffs() {
720
721	<	if (simParams_->haveCutoffRadius()) {
718	<	cutoffRadius_ = simParams_->getCutoffRadius();
719	<	} else {
720	<	if (usesElectrostaticAtoms_) {
721	<	sprintf(painCave.errMsg,
722	<	"SimInfo: No value was set for the cutoffRadius.\n"
723	<	"\tOpenMD will use a default value of 12.0 angstroms"
724	<	"\tfor the cutoffRadius.\n");
725	<	painCave.isFatal = 0;
726	<	painCave.severity = OPENMD_INFO;
727	<	simError();
728	<	cutoffRadius_ = 12.0;
729	<	} else {
730	<	RealType thisCut;
731	<	set<AtomType*>::iterator i;
732	<	set<AtomType*> atomTypes;
733	<	atomTypes = getSimulatedAtomTypes();
734	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735	<	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736	<	cutoffRadius_ = max(thisCut, cutoffRadius_);
737	<	}
738	<	sprintf(painCave.errMsg,
739	<	"SimInfo: No value was set for the cutoffRadius.\n"
740	<	"\tOpenMD will use %lf angstroms.\n",
741	<	cutoffRadius_);
742	<	painCave.isFatal = 0;
743	<	painCave.severity = OPENMD_INFO;
744	<	simError();
745	<	}
746	<	}
721	>	#ifdef IS_MPI
722
723	<	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
723	>	// loop over the found atom types on this processor, and add their
724	>	// numerical idents to a vector:
725	>
726	>	vector<int> foundTypes;
727	>	set<AtomType*>::iterator i;
728	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
729	>	foundTypes.push_back( (*i)->getIdent() );
730
731	<	map<string, CutoffMethod> stringToCutoffMethod;
732	<	stringToCutoffMethod["HARD"] = HARD;
733	<	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
734	<	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
735	<	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
731	>	// count_local holds the number of found types on this processor
732	>	int count_local = foundTypes.size();
733	>
734	>	int nproc = MPI::COMM_WORLD.Get_size();
735	>
736	>	// we need arrays to hold the counts and displacement vectors for
737	>	// all processors
738	>	vector<int> counts(nproc, 0);
739	>	vector<int> disps(nproc, 0);
740	>
741	>	// fill the counts array
742	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
743	>	1, MPI::INT);
744
745	<	if (simParams_->haveCutoffMethod()) {
746	<	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
747	<	map<string, CutoffMethod>::iterator i;
748	<	i = stringToCutoffMethod.find(cutMeth);
749	<	if (i == stringToCutoffMethod.end()) {
750	<	sprintf(painCave.errMsg,
762	<	"SimInfo: Could not find chosen cutoffMethod %s\n"
763	<	"\tShould be one of: "
764	<	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765	<	cutMeth.c_str());
766	<	painCave.isFatal = 1;
767	<	painCave.severity = OPENMD_ERROR;
768	<	simError();
769	<	} else {
770	<	cutoffMethod_ = i->second;
771	<	}
772	<	} else {
773	<	sprintf(painCave.errMsg,
774	<	"SimInfo: No value was set for the cutoffMethod.\n"
775	<	"\tOpenMD will use SHIFTED_FORCE.\n");
776	<	painCave.isFatal = 0;
777	<	painCave.severity = OPENMD_INFO;
778	<	simError();
779	<	cutoffMethod_ = SHIFTED_FORCE;
745	>	// use the processor counts to compute the displacement array
746	>	disps[0] = 0;
747	>	int totalCount = counts[0];
748	>	for (int iproc = 1; iproc < nproc; iproc++) {
749	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
750	>	totalCount += counts[iproc];
751		}
752
753	<	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
754	<	}
784	<
785	<	/**
786	<	* setupSwitching
787	<	*
788	<	* Sets the values of switchingRadius and
789	<	* If the switchingRadius was explicitly set, use that value (but check it)
790	<	* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791	<	*/
792	<	void SimInfo::setupSwitching() {
753	>	// we need a (possibly redundant) set of all found types:
754	>	vector<int> ftGlobal(totalCount);
755
756	<	if (simParams_->haveSwitchingRadius()) {
757	<	switchingRadius_ = simParams_->getSwitchingRadius();
758	<	if (switchingRadius_ > cutoffRadius_) {
759	<	sprintf(painCave.errMsg,
798	<	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799	<	switchingRadius_, cutoffRadius_);
800	<	painCave.isFatal = 1;
801	<	painCave.severity = OPENMD_ERROR;
802	<	simError();
803	<	}
804	<	} else {
805	<	switchingRadius_ = 0.85 * cutoffRadius_;
806	<	sprintf(painCave.errMsg,
807	<	"SimInfo: No value was set for the switchingRadius.\n"
808	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809	<	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810	<	painCave.isFatal = 0;
811	<	painCave.severity = OPENMD_WARNING;
812	<	simError();
813	<	}
814	<
815	<	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
756	>	// now spray out the foundTypes to all the other processors:
757	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
758	>	&ftGlobal[0], &counts[0], &disps[0],
759	>	MPI::INT);
760
761	<	SwitchingFunctionType ft;
818	<
819	<	if (simParams_->haveSwitchingFunctionType()) {
820	<	string funcType = simParams_->getSwitchingFunctionType();
821	<	toUpper(funcType);
822	<	if (funcType == "CUBIC") {
823	<	ft = cubic;
824	<	} else {
825	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826	<	ft = fifth_order_poly;
827	<	} else {
828	<	// throw error
829	<	sprintf( painCave.errMsg,
830	<	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831	<	"\tswitchingFunctionType must be one of: "
832	<	"\"cubic\" or \"fifth_order_polynomial\".",
833	<	funcType.c_str() );
834	<	painCave.isFatal = 1;
835	<	painCave.severity = OPENMD_ERROR;
836	<	simError();
837	<	}
838	<	}
839	<	}
761	>	vector<int>::iterator j;
762
763	<	InteractionManager::Instance()->setSwitchingFunctionType(ft);
764	<	}
763	>	// foundIdents is a stl set, so inserting an already found ident
764	>	// will have no effect.
765	>	set<int> foundIdents;
766
767	<	/**
768	<	* setupSkinThickness
769	<	*
770	<	* If the skinThickness was explicitly set, use that value (but check it)
771	<	* If the skinThickness was not explicitly set: use 1.0 angstroms
772	<	*/
773	<	void SimInfo::setupSkinThickness() {
774	<	if (simParams_->haveSkinThickness()) {
775	<	skinThickness_ = simParams_->getSkinThickness();
776	<	} else {
777	<	skinThickness_ = 1.0;
778	<	sprintf(painCave.errMsg,
856	<	"SimInfo Warning: No value was set for the skinThickness.\n"
857	<	"\tOpenMD will use a default value of %f Angstroms\n"
858	<	"\tfor this simulation\n", skinThickness_);
859	<	painCave.isFatal = 0;
860	<	simError();
861	<	}
767	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
768	>	foundIdents.insert((*j));
769	>
770	>	// now iterate over the foundIdents and get the actual atom types
771	>	// that correspond to these:
772	>	set<int>::iterator it;
773	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774	>	atomTypes.insert( forceField_->getAtomType((*it)) );
775	>
776	>	#endif
777	>
778	>	return atomTypes;
779		}
780
781	<	void SimInfo::setupSimType() {
781	>	void SimInfo::setupSimVariables() {
782	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
783	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
784	>	calcBoxDipole_ = false;
785	>	if ( simParams_->haveAccumulateBoxDipole() )
786	>	if ( simParams_->getAccumulateBoxDipole() ) {
787	>	calcBoxDipole_ = true;
788	>	}
789	>
790		set<AtomType*>::iterator i;
791		set<AtomType*> atomTypes;
792	<	atomTypes = getSimulatedAtomTypes();
868	<
869	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
870	<
792	>	atomTypes = getSimulatedAtomTypes();
793		int usesElectrostatic = 0;
794		int usesMetallic = 0;
795		int usesDirectional = 0;
796	+	int usesFluctuatingCharges = 0;
797		//loop over all of the atom types
798		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
799		usesElectrostatic \|= (*i)->isElectrostatic();
800		usesMetallic \|= (*i)->isMetal();
801		usesDirectional \|= (*i)->isDirectional();
802	+	usesFluctuatingCharges \|= (*i)->isFluctuatingCharge();
803		}
804	<
804	>
805		#ifdef IS_MPI
806		int temp;
807		temp = usesDirectional;
808		MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	<
809	>
810		temp = usesMetallic;
811		MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
812	<
812	>
813		temp = usesElectrostatic;
814		MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815	+
816	+	temp = usesFluctuatingCharges;
817	+	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	+	#else
819	+
820	+	usesDirectionalAtoms_ = usesDirectional;
821	+	usesMetallicAtoms_ = usesMetallic;
822	+	usesElectrostaticAtoms_ = usesElectrostatic;
823	+	usesFluctuatingCharges_ = usesFluctuatingCharges;
824	+
825		#endif
826	<	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
827	<	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
828	<	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
829	<	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
896	<	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897	<	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
826	>
827	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
828	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
829	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
830		}
831
832	<	void SimInfo::setupFortranSim() {
833	<	int isError;
834	<	int nExclude, nOneTwo, nOneThree, nOneFour;
835	<	vector<int> fortranGlobalGroupMembership;
832	>
833	>	vector<int> SimInfo::getGlobalAtomIndices() {
834	>	SimInfo::MoleculeIterator mi;
835	>	Molecule* mol;
836	>	Molecule::AtomIterator ai;
837	>	Atom* atom;
838	>
839	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
840
841	<	notifyFortranSkinThickness(&skinThickness_);
841	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
842	>
843	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
844	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
845	>	}
846	>	}
847	>	return GlobalAtomIndices;
848	>	}
849
907	–	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908	–	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909	–	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
850
851	<	isError = 0;
851	>	vector<int> SimInfo::getGlobalGroupIndices() {
852	>	SimInfo::MoleculeIterator mi;
853	>	Molecule* mol;
854	>	Molecule::CutoffGroupIterator ci;
855	>	CutoffGroup* cg;
856
857	<	//globalGroupMembership_ is filled by SimCreator
858	<	for (int i = 0; i < nGlobalAtoms_; i++) {
859	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
857	>	vector<int> GlobalGroupIndices;
858	>
859	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
860	>
861	>	//local index of cutoff group is trivial, it only depends on the
862	>	//order of travesing
863	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
864	>	cg = mol->nextCutoffGroup(ci)) {
865	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
866	>	}
867		}
868	+	return GlobalGroupIndices;
869	+	}
870
871	+
872	+	void SimInfo::prepareTopology() {
873	+	int nExclude, nOneTwo, nOneThree, nOneFour;
874	+
875		//calculate mass ratio of cutoff group
919	–	vector<RealType> mfact;
876		SimInfo::MoleculeIterator mi;
877		Molecule* mol;
878		Molecule::CutoffGroupIterator ci;
#	Line 925 \| Line 881 \| namespace OpenMD {
881		Atom* atom;
882		RealType totalMass;
883
884	<	//to avoid memory reallocation, reserve enough space for mfact
885	<	mfact.reserve(getNCutoffGroups());
884	>	/**
885	>	* The mass factor is the relative mass of an atom to the total
886	>	* mass of the cutoff group it belongs to. By default, all atoms
887	>	* are their own cutoff groups, and therefore have mass factors of
888	>	* 1. We need some special handling for massless atoms, which
889	>	* will be treated as carrying the entire mass of the cutoff
890	>	* group.
891	>	*/
892	>	massFactors_.clear();
893	>	massFactors_.resize(getNAtoms(), 1.0);
894
895		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
896	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
896	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
897	>	cg = mol->nextCutoffGroup(ci)) {
898
899		totalMass = cg->getMass();
900		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
901		// Check for massless groups - set mfact to 1 if true
902	<	if (totalMass != 0)
903	<	mfact.push_back(atom->getMass()/totalMass);
902	>	if (totalMass != 0)
903	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
904		else
905	<	mfact.push_back( 1.0 );
905	>	massFactors_[atom->getLocalIndex()] = 1.0;
906		}
907		}
908		}
909
910	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946	<	vector<int> identArray;
910	>	// Build the identArray_
911
912	<	//to avoid memory reallocation, reserve enough space identArray
913	<	identArray.reserve(getNAtoms());
950	<
912	>	identArray_.clear();
913	>	identArray_.reserve(getNAtoms());
914		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
915		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
916	<	identArray.push_back(atom->getIdent());
916	>	identArray_.push_back(atom->getIdent());
917		}
918		}
956	–
957	–	//fill molMembershipArray
958	–	//molMembershipArray is filled by SimCreator
959	–	vector<int> molMembershipArray(nGlobalAtoms_);
960	–	for (int i = 0; i < nGlobalAtoms_; i++) {
961	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
962	–	}
919
920	<	//setup fortran simulation
920	>	//scan topology
921
922		nExclude = excludedInteractions_.getSize();
923		nOneTwo = oneTwoInteractions_.getSize();
#	Line 973 \| Line 929 \| namespace OpenMD {
929		int* oneThreeList = oneThreeInteractions_.getPairList();
930		int* oneFourList = oneFourInteractions_.getPairList();
931
932	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
977	<	&nExclude, excludeList,
978	<	&nOneTwo, oneTwoList,
979	<	&nOneThree, oneThreeList,
980	<	&nOneFour, oneFourList,
981	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
982	<	&fortranGlobalGroupMembership[0], &isError);
983	<
984	<	if( isError ){
985	<
986	<	sprintf( painCave.errMsg,
987	<	"There was an error setting the simulation information in fortran.\n" );
988	<	painCave.isFatal = 1;
989	<	painCave.severity = OPENMD_ERROR;
990	<	simError();
991	<	}
992	<
993	<
994	<	sprintf( checkPointMsg,
995	<	"succesfully sent the simulation information to fortran.\n");
996	<
997	<	errorCheckPoint();
998	<
999	<	// Setup number of neighbors in neighbor list if present
1000	<	if (simParams_->haveNeighborListNeighbors()) {
1001	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
1002	<	setNeighbors(&nlistNeighbors);
1003	<	}
1004	<
1005	<
1006	<	}
1007	<
1008	<
1009	<	void SimInfo::setupFortranParallel() {
1010	<	#ifdef IS_MPI
1011	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1012	<	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	<	vector<int> localToGlobalCutoffGroupIndex;
1014	<	SimInfo::MoleculeIterator mi;
1015	<	Molecule::AtomIterator ai;
1016	<	Molecule::CutoffGroupIterator ci;
1017	<	Molecule* mol;
1018	<	Atom* atom;
1019	<	CutoffGroup* cg;
1020	<	mpiSimData parallelData;
1021	<	int isError;
1022	<
1023	<	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1024	<
1025	<	//local index(index in DataStorge) of atom is important
1026	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1027	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1028	<	}
1029	<
1030	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1031	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1032	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1033	<	}
1034	<
1035	<	}
1036	<
1037	<	//fill up mpiSimData struct
1038	<	parallelData.nMolGlobal = getNGlobalMolecules();
1039	<	parallelData.nMolLocal = getNMolecules();
1040	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
1041	<	parallelData.nAtomsLocal = getNAtoms();
1042	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1043	<	parallelData.nGroupsLocal = getNCutoffGroups();
1044	<	parallelData.myNode = worldRank;
1045	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1046	<
1047	<	//pass mpiSimData struct and index arrays to fortran
1048	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1049	<	&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
1050	<	&localToGlobalCutoffGroupIndex[0], &isError);
1051	<
1052	<	if (isError) {
1053	<	sprintf(painCave.errMsg,
1054	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1055	<	painCave.isFatal = 1;
1056	<	simError();
1057	<	}
1058	<
1059	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1060	<	errorCheckPoint();
1061	<
1062	<	#endif
932	>	topologyDone_ = true;
933		}
934
1065	–
1066	–	void SimInfo::setupSwitchingFunction() {
1067	–
1068	–	}
1069	–
1070	–	void SimInfo::setupAccumulateBoxDipole() {
1071	–
1072	–	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073	–	if ( simParams_->haveAccumulateBoxDipole() )
1074	–	if ( simParams_->getAccumulateBoxDipole() ) {
1075	–	calcBoxDipole_ = true;
1076	–	}
1077	–
1078	–	}
1079	–
935		void SimInfo::addProperty(GenericData* genData) {
936		properties_.addProperty(genData);
937		}
#	Line 1111 \| Line 966 \| namespace OpenMD {
966		Molecule* mol;
967		RigidBody* rb;
968		Atom* atom;
969	+	CutoffGroup* cg;
970		SimInfo::MoleculeIterator mi;
971		Molecule::RigidBodyIterator rbIter;
972	<	Molecule::AtomIterator atomIter;;
972	>	Molecule::AtomIterator atomIter;
973	>	Molecule::CutoffGroupIterator cgIter;
974
975		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
976
#	Line 1124 \| Line 981 \| namespace OpenMD {
981		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
982		rb->setSnapshotManager(sman_);
983		}
984	+
985	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
986	+	cg->setSnapshotManager(sman_);
987	+	}
988		}
989
990		}
#	Line 1352 \| Line 1213 \| namespace OpenMD {
1213
1214		det = intTensor.determinant();
1215		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1216	<	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1216	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,geomCnst)*sqrt(det);
1217		return;
1218		}
1219
#	Line 1368 \| Line 1229 \| namespace OpenMD {
1229
1230		detI = intTensor.determinant();
1231		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1232	<	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1232	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,geomCnst)*sqrt(detI);
1233		return;
1234		}
1235		/*

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Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs. Revision 1750 by gezelter, Thu Jun 7 12:53:46 2012 UTC

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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC vs.
Revision 1750 by gezelter, Thu Jun 7 12:53:46 2012 UTC