[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 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	–
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;
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 248 \| Line 250 \| namespace OpenMD {
250		ndf_local += 3;
251		}
252		}
251	–
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 274 \| Line 285 \| namespace OpenMD {
285		fdf_ = fdf_local;
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() {
#	Line 656 \| 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() {
664	<
693	>	void SimInfo::update() {
694		setupSimVariables();
666	–	setupCutoffs();
667	–	setupSwitching();
668	–	setupElectrostatics();
669	–	setupNeighborlists();
670	–
671	–	#ifdef IS_MPI
672	–	setupFortranParallel();
673	–	#endif
674	–	setupFortranSim();
675	–	fortranInitialized_ = true;
676	–
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 686 \| 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		}
720	<	return atomTypes;
721	<	}
720	>
721	>	#ifdef IS_MPI
722
723	<	/**
724	<	* 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() {
723	>	// loop over the found atom types on this processor, and add their
724	>	// numerical idents to a vector:
725
726	<	if (simParams_->haveCutoffRadius()) {
727	<	cutoffRadius_ = simParams_->getCutoffRadius();
728	<	} else {
729	<	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	<	}
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,
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;
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	<
754	<	/**
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() {
752	>
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,
760	<	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
761	<	switchingRadius_, cutoffRadius_);
762	<	painCave.isFatal = 1;
763	<	painCave.severity = OPENMD_ERROR;
764	<	simError();
765	<	}
766	<	} else {
767	<	switchingRadius_ = 0.85 * cutoffRadius_;
768	<	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	<	}
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	>	vector<int>::iterator j;
762	>
763	>	// foundIdents is a stl set, so inserting an already found ident
764	>	// will have no effect.
765	>	set<int> foundIdents;
766	>
767	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
768	>	foundIdents.insert((*j));
769
770	<	if (simParams_->haveSwitchingFunctionType()) {
771	<	string funcType = simParams_->getSwitchingFunctionType();
772	<	toUpper(funcType);
773	<	if (funcType == "CUBIC") {
774	<	sft_ = cubic;
775	<	} else {
776	<	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	<	}
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	<	/**
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	<	}
778	>	return atomTypes;
779		}
780
781		void SimInfo::setupSimVariables() {
#	Line 859 \| Line 786 \| namespace OpenMD {
786		if ( simParams_->getAccumulateBoxDipole() ) {
787		calcBoxDipole_ = true;
788		}
789	<
789	>
790		set<AtomType*>::iterator i;
791		set<AtomType*> atomTypes;
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_;
891	<	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892	<	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
902	–	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
903	–	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
904	–	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
914	–	vector<RealType> mfact;
876		SimInfo::MoleculeIterator mi;
877		Molecule* mol;
878		Molecule::CutoffGroupIterator ci;
#	Line 920 \| 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 !!!)
941	<	vector<int> identArray;
910	>	// Build the identArray_
911
912	<	//to avoid memory reallocation, reserve enough space identArray
913	<	identArray.reserve(getNAtoms());
945	<
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		}
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	–	}
919
920	<	//setup fortran simulation
920	>	//scan topology
921
922		nExclude = excludedInteractions_.getSize();
923		nOneTwo = oneTwoInteractions_.getSize();
#	Line 968 \| Line 929 \| namespace OpenMD {
929		int* oneThreeList = oneThreeInteractions_.getPairList();
930		int* oneFourList = oneFourInteractions_.getPairList();
931
932	<	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	<
1001	<	}
1002	<
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
932	>	topologyDone_ = true;
933		}
934
1060	–
1061	–	void SimInfo::setupAccumulateBoxDipole() {
1062	–
1063	–
1064	–	}
1065	–
935		void SimInfo::addProperty(GenericData* genData) {
936		properties_.addProperty(genData);
937		}
#	Line 1097 \| 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 1109 \| Line 980 \| namespace OpenMD {
980
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
#	Line 1338 \| 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 1354 \| 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 1534 by gezelter, Wed Dec 29 21:53:28 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 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC vs.
Revision 1750 by gezelter, Thu Jun 7 12:53:46 2012 UTC