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

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1744 by gezelter, Tue Jun 5 18:07:08 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;
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 252 \| Line 250 \| namespace OpenMD {
250		ndf_local += 3;
251		}
252		}
253	<
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	+	cerr << "ndfLocal_ = " << ndfLocal_ << "\n";
264	+
265		// n_constraints is local, so subtract them on each processor
266		ndf_local -= nConstraints_;
267
268		#ifdef IS_MPI
269		MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270	+	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
271		#else
272		ndf_ = ndf_local;
273	+	nGlobalFluctuatingCharges_ = nfq_local;
274		#endif
275
276		// nZconstraints_ is global, as are the 3 COM translations for the
#	Line 278 \| Line 286 \| namespace OpenMD {
286		fdf_ = fdf_local;
287		#endif
288		return fdf_;
289	+	}
290	+
291	+	unsigned int SimInfo::getNLocalCutoffGroups(){
292	+	int nLocalCutoffAtoms = 0;
293	+	Molecule* mol;
294	+	MoleculeIterator mi;
295	+	CutoffGroup* cg;
296	+	Molecule::CutoffGroupIterator ci;
297	+
298	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
299	+
300	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
301	+	cg = mol->nextCutoffGroup(ci)) {
302	+	nLocalCutoffAtoms += cg->getNumAtom();
303	+
304	+	}
305	+	}
306	+
307	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
308		}
309
310		void SimInfo::calcNdfRaw() {
#	Line 655 \| Line 682 \| namespace OpenMD {
682		moleculeStamps_.push_back(molStamp);
683		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684		}
658	–
659	–	void SimInfo::update() {
685
661	–	setupSimType();
662	–	setupCutoffRadius();
663	–	setupSwitchingRadius();
664	–	setupCutoffMethod();
665	–	setupSkinThickness();
666	–	setupSwitchingFunction();
667	–	setupAccumulateBoxDipole();
686
687	<	#ifdef IS_MPI
688	<	setupFortranParallel();
689	<	#endif
690	<	setupFortranSim();
691	<	fortranInitialized_ = true;
692	<
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 685 \| Line 713 \| namespace OpenMD {
713		set<AtomType*> atomTypes;
714
715		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	<
717	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
716	>	for(atom = mol->beginAtom(ai); atom != NULL;
717	>	atom = mol->nextAtom(ai)) {
718		atomTypes.insert(atom->getAtomType());
719	<	}
720	<
693	<	}
719	>	}
720	>	}
721
722	<	return atomTypes;
696	<	}
722	>	#ifdef IS_MPI
723
724	<	/**
725	<	* setupCutoffRadius
700	<	*
701	<	* If the cutoffRadius was explicitly set, use that value.
702	<	* If the cutoffRadius was not explicitly set:
703	<	* Are there electrostatic atoms? Use 12.0 Angstroms.
704	<	* No electrostatic atoms? Poll the atom types present in the
705	<	* simulation for suggested cutoff values (e.g. 2.5 * sigma).
706	<	* Use the maximum suggested value that was found.
707	<	*/
708	<	void SimInfo::setupCutoffRadius() {
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_) {
714	<	sprintf(painCave.errMsg,
715	<	"SimInfo Warning: No value was set for the cutoffRadius.\n"
716	<	"\tOpenMD will use a default value of 12.0 angstroms"
717	<	"\tfor the cutoffRadius.\n");
718	<	painCave.isFatal = 0;
719	<	simError();
720	<	cutoffRadius_ = 12.0;
721	<	} else {
722	<	RealType thisCut;
723	<	set<AtomType*>::iterator i;
724	<	set<AtomType*> atomTypes;
725	<	atomTypes = getSimulatedAtomTypes();
726	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
727	<	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
728	<	cutoffRadius_ = max(thisCut, cutoffRadius_);
729	<	}
730	<	sprintf(painCave.errMsg,
731	<	"SimInfo Warning: No value was set for the cutoffRadius.\n"
732	<	"\tOpenMD will use %lf angstroms.\n",
733	<	cutoffRadius_);
734	<	painCave.isFatal = 0;
735	<	simError();
736	<	}
737	<	}
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	<	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
733	<	}
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	<	/**
747	<	* setupSwitchingRadius
748	<	*
749	<	* If the switchingRadius was explicitly set, use that value (but check it)
750	<	* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
751	<	*/
752	<	void SimInfo::setupSwitchingRadius() {
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	<	if (simParams_->haveSwitchingRadius()) {
758	<	switchingRadius_ = simParams_->getSwitchingRadius();
759	<	if (switchingRadius_ > cutoffRadius_) {
760	<	sprintf(painCave.errMsg,
754	<	"SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
755	<	switchingRadius_, cutoffRadius_);
756	<	painCave.isFatal = 1;
757	<	simError();
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	<	}
760	<	} else {
761	<	switchingRadius_ = 0.85 * cutoffRadius_;
762	<	sprintf(painCave.errMsg,
763	<	"SimInfo Warning: No value was set for the switchingRadius.\n"
764	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
765	<	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
766	<	painCave.isFatal = 0;
767	<	simError();
768	<	}
769	<	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
770	<	}
762	>	vector<int>::iterator j;
763
764	<	/**
765	<	* setupSkinThickness
766	<	*
767	<	* If the skinThickness was explicitly set, use that value (but check it)
768	<	* If the skinThickness was not explicitly set: use 1.0 angstroms
769	<	*/
770	<	void SimInfo::setupSkinThickness() {
771	<	if (simParams_->haveSkinThickness()) {
772	<	skinThickness_ = simParams_->getSkinThickness();
773	<	} else {
774	<	skinThickness_ = 1.0;
775	<	sprintf(painCave.errMsg,
776	<	"SimInfo Warning: No value was set for the skinThickness.\n"
777	<	"\tOpenMD will use a default value of %f Angstroms\n"
778	<	"\tfor this simulation\n", skinThickness_);
779	<	painCave.isFatal = 0;
788	<	simError();
789	<	}
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();
796	<
797	<	useAtomicVirial_ = simParams_->getUseAtomicVirial();
798	<
793	>	atomTypes = getSimulatedAtomTypes();
794		int usesElectrostatic = 0;
795		int usesMetallic = 0;
796		int usesDirectional = 0;
797	+	int usesFluctuatingCharges = 0;
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	<
805	>
806		#ifdef IS_MPI
807		int temp;
808		temp = usesDirectional;
809		MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	<
810	>
811		temp = usesMetallic;
812		MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	<
813	>
814		temp = usesElectrostatic;
815		MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	+
817	+	temp = usesFluctuatingCharges;
818	+	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	+	#else
820	+
821	+	usesDirectionalAtoms_ = usesDirectional;
822	+	usesMetallicAtoms_ = usesMetallic;
823	+	usesElectrostaticAtoms_ = usesElectrostatic;
824	+	usesFluctuatingCharges_ = usesFluctuatingCharges;
825	+
826		#endif
827	<	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
828	<	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
829	<	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
830	<	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
824	<	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
825	<	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
827	>
828	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
829	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
830	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
831		}
832
833	<	void SimInfo::setupFortranSim() {
834	<	int isError;
835	<	int nExclude, nOneTwo, nOneThree, nOneFour;
836	<	vector<int> fortranGlobalGroupMembership;
833	>
834	>	vector<int> SimInfo::getGlobalAtomIndices() {
835	>	SimInfo::MoleculeIterator mi;
836	>	Molecule* mol;
837	>	Molecule::AtomIterator ai;
838	>	Atom* atom;
839	>
840	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
841
842	<	notifyFortranSkinThickness(&skinThickness_);
842	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
843	>
844	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
845	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
846	>	}
847	>	}
848	>	return GlobalAtomIndices;
849	>	}
850
835	–	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
836	–	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
837	–	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
851
852	<	isError = 0;
852	>	vector<int> SimInfo::getGlobalGroupIndices() {
853	>	SimInfo::MoleculeIterator mi;
854	>	Molecule* mol;
855	>	Molecule::CutoffGroupIterator ci;
856	>	CutoffGroup* cg;
857
858	<	//globalGroupMembership_ is filled by SimCreator
859	<	for (int i = 0; i < nGlobalAtoms_; i++) {
860	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
858	>	vector<int> GlobalGroupIndices;
859	>
860	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
861	>
862	>	//local index of cutoff group is trivial, it only depends on the
863	>	//order of travesing
864	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
865	>	cg = mol->nextCutoffGroup(ci)) {
866	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
867	>	}
868		}
869	+	return GlobalGroupIndices;
870	+	}
871
872	+
873	+	void SimInfo::prepareTopology() {
874	+	int nExclude, nOneTwo, nOneThree, nOneFour;
875	+
876		//calculate mass ratio of cutoff group
847	–	vector<RealType> mfact;
877		SimInfo::MoleculeIterator mi;
878		Molecule* mol;
879		Molecule::CutoffGroupIterator ci;
#	Line 853 \| Line 882 \| namespace OpenMD {
882		Atom* atom;
883		RealType totalMass;
884
885	<	//to avoid memory reallocation, reserve enough space for mfact
886	<	mfact.reserve(getNCutoffGroups());
885	>	/**
886	>	* The mass factor is the relative mass of an atom to the total
887	>	* mass of the cutoff group it belongs to. By default, all atoms
888	>	* are their own cutoff groups, and therefore have mass factors of
889	>	* 1. We need some special handling for massless atoms, which
890	>	* will be treated as carrying the entire mass of the cutoff
891	>	* group.
892	>	*/
893	>	massFactors_.clear();
894	>	massFactors_.resize(getNAtoms(), 1.0);
895
896		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
897	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
898	>	cg = mol->nextCutoffGroup(ci)) {
899
900		totalMass = cg->getMass();
901		for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
902		// Check for massless groups - set mfact to 1 if true
903	<	if (totalMass != 0)
904	<	mfact.push_back(atom->getMass()/totalMass);
903	>	if (totalMass != 0)
904	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
905		else
906	<	mfact.push_back( 1.0 );
906	>	massFactors_[atom->getLocalIndex()] = 1.0;
907		}
908		}
909		}
910
911	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
874	<	vector<int> identArray;
911	>	// Build the identArray_
912
913	<	//to avoid memory reallocation, reserve enough space identArray
914	<	identArray.reserve(getNAtoms());
878	<
913	>	identArray_.clear();
914	>	identArray_.reserve(getNAtoms());
915		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
916		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
917	<	identArray.push_back(atom->getIdent());
917	>	identArray_.push_back(atom->getIdent());
918		}
919		}
884	–
885	–	//fill molMembershipArray
886	–	//molMembershipArray is filled by SimCreator
887	–	vector<int> molMembershipArray(nGlobalAtoms_);
888	–	for (int i = 0; i < nGlobalAtoms_; i++) {
889	–	molMembershipArray[i] = globalMolMembership_[i] + 1;
890	–	}
920
921	<	//setup fortran simulation
921	>	//scan topology
922
923		nExclude = excludedInteractions_.getSize();
924		nOneTwo = oneTwoInteractions_.getSize();
#	Line 901 \| Line 930 \| namespace OpenMD {
930		int* oneThreeList = oneThreeInteractions_.getPairList();
931		int* oneFourList = oneFourInteractions_.getPairList();
932
933	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
905	<	&nExclude, excludeList,
906	<	&nOneTwo, oneTwoList,
907	<	&nOneThree, oneThreeList,
908	<	&nOneFour, oneFourList,
909	<	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
910	<	&fortranGlobalGroupMembership[0], &isError);
911	<
912	<	if( isError ){
913	<
914	<	sprintf( painCave.errMsg,
915	<	"There was an error setting the simulation information in fortran.\n" );
916	<	painCave.isFatal = 1;
917	<	painCave.severity = OPENMD_ERROR;
918	<	simError();
919	<	}
920	<
921	<
922	<	sprintf( checkPointMsg,
923	<	"succesfully sent the simulation information to fortran.\n");
924	<
925	<	errorCheckPoint();
926	<
927	<	// Setup number of neighbors in neighbor list if present
928	<	if (simParams_->haveNeighborListNeighbors()) {
929	<	int nlistNeighbors = simParams_->getNeighborListNeighbors();
930	<	setNeighbors(&nlistNeighbors);
931	<	}
932	<
933	<
934	<	}
935	<
936	<
937	<	void SimInfo::setupFortranParallel() {
938	<	#ifdef IS_MPI
939	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
940	<	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
941	<	vector<int> localToGlobalCutoffGroupIndex;
942	<	SimInfo::MoleculeIterator mi;
943	<	Molecule::AtomIterator ai;
944	<	Molecule::CutoffGroupIterator ci;
945	<	Molecule* mol;
946	<	Atom* atom;
947	<	CutoffGroup* cg;
948	<	mpiSimData parallelData;
949	<	int isError;
950	<
951	<	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
952	<
953	<	//local index(index in DataStorge) of atom is important
954	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
955	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
956	<	}
957	<
958	<	//local index of cutoff group is trivial, it only depends on the order of travesing
959	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
960	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
961	<	}
962	<
963	<	}
964	<
965	<	//fill up mpiSimData struct
966	<	parallelData.nMolGlobal = getNGlobalMolecules();
967	<	parallelData.nMolLocal = getNMolecules();
968	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
969	<	parallelData.nAtomsLocal = getNAtoms();
970	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
971	<	parallelData.nGroupsLocal = getNCutoffGroups();
972	<	parallelData.myNode = worldRank;
973	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
974	<
975	<	//pass mpiSimData struct and index arrays to fortran
976	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
977	<	&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal),
978	<	&localToGlobalCutoffGroupIndex[0], &isError);
979	<
980	<	if (isError) {
981	<	sprintf(painCave.errMsg,
982	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
983	<	painCave.isFatal = 1;
984	<	simError();
985	<	}
986	<
987	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
988	<	errorCheckPoint();
989	<
990	<	#endif
991	<	}
992	<
993	<
994	<	void SimInfo::setupSwitchingFunction() {
995	<	int ft = CUBIC;
996	<
997	<	if (simParams_->haveSwitchingFunctionType()) {
998	<	string funcType = simParams_->getSwitchingFunctionType();
999	<	toUpper(funcType);
1000	<	if (funcType == "CUBIC") {
1001	<	ft = CUBIC;
1002	<	} else {
1003	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1004	<	ft = FIFTH_ORDER_POLY;
1005	<	} else {
1006	<	// throw error
1007	<	sprintf( painCave.errMsg,
1008	<	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1009	<	painCave.isFatal = 1;
1010	<	simError();
1011	<	}
1012	<	}
1013	<	}
1014	<
1015	<	// send switching function notification to switcheroo
1016	<	setFunctionType(&ft);
1017	<
1018	<	}
1019	<
1020	<	void SimInfo::setupAccumulateBoxDipole() {
1021	<
1022	<	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1023	<	if ( simParams_->haveAccumulateBoxDipole() )
1024	<	if ( simParams_->getAccumulateBoxDipole() ) {
1025	<	calcBoxDipole_ = true;
1026	<	}
1027	<
933	>	topologyDone_ = true;
934		}
935
936		void SimInfo::addProperty(GenericData* genData) {
#	Line 1061 \| Line 967 \| namespace OpenMD {
967		Molecule* mol;
968		RigidBody* rb;
969		Atom* atom;
970	+	CutoffGroup* cg;
971		SimInfo::MoleculeIterator mi;
972		Molecule::RigidBodyIterator rbIter;
973	<	Molecule::AtomIterator atomIter;;
973	>	Molecule::AtomIterator atomIter;
974	>	Molecule::CutoffGroupIterator cgIter;
975
976		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
977
#	Line 1073 \| Line 981 \| namespace OpenMD {
981
982		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
983		rb->setSnapshotManager(sman_);
984	+	}
985	+
986	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
987	+	cg->setSnapshotManager(sman_);
988		}
989		}
990
#	Line 1302 \| Line 1214 \| namespace OpenMD {
1214
1215		det = intTensor.determinant();
1216		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217	<	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1217	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,geomCnst)*sqrt(det);
1218		return;
1219		}
1220
#	Line 1318 \| Line 1230 \| namespace OpenMD {
1230
1231		detI = intTensor.determinant();
1232		sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233	<	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1233	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,geomCnst)*sqrt(detI);
1234		return;
1235		}
1236		/*

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing branches/development/src/brains/SimInfo.cpp (file contents): Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs. Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

Diff Legend

Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC