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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 1103 by chuckv, Fri Dec 29 20:21:53 2006 UTC

#	Line 53 \| Line 53
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	+	#include "primitives/StuntDouble.hpp"
57		#include "UseTheForce/fCutoffPolicy.h"
58		#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59		#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60		#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61		#include "UseTheForce/doForces_interface.h"
62	+	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63		#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	–	#include "UseTheForce/notifyCutoffs_interface.h"
64		#include "UseTheForce/DarkSide/switcheroo_interface.h"
65		#include "utils/MemoryUtils.hpp"
66		#include "utils/simError.h"
67		#include "selection/SelectionManager.hpp"
68	+	#include "io/ForceFieldOptions.hpp"
69	+	#include "UseTheForce/ForceField.hpp"
70
71	+
72		#ifdef IS_MPI
73		#include "UseTheForce/mpiComponentPlan.h"
74		#include "UseTheForce/DarkSide/simParallel_interface.h"
#	Line 81 \| Line 85 \| namespace oopse {
85		return result;
86		}
87
88	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
89	<	ForceField* ff, Globals* simParams) :
90	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
87	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89	>	forceField_(ff), simParams_(simParams),
90	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
94		nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
95	<	sman_(NULL), fortranInitialized_(false) {
95	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
96
94	–
95	–	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
97		MoleculeStamp* molStamp;
98		int nMolWithSameStamp;
99		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
#	Line 100 \| Line 101 \| namespace oopse {
101		CutoffGroupStamp* cgStamp;
102		RigidBodyStamp* rbStamp;
103		int nRigidAtoms = 0;
104	<
105	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
106	<	molStamp = i->first;
107	<	nMolWithSameStamp = i->second;
104	>	std::vector<Component*> components = simParams->getComponents();
105	>
106	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
107	>	molStamp = (*i)->getMoleculeStamp();
108	>	nMolWithSameStamp = (*i)->getNMol();
109
110		addMoleculeStamp(molStamp, nMolWithSameStamp);
111
112		//calculate atoms in molecules
113		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114
113	–
115		//calculate atoms in cutoff groups
116		int nAtomsInGroups = 0;
117		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118
119		for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroup(j);
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121		nAtomsInGroups += cgStamp->getNMembers();
122		}
123
#	Line 129 \| Line 130 \| namespace oopse {
130		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131
132		for (int j=0; j < nRigidBodiesInStamp; j++) {
133	<	rbStamp = molStamp->getRigidBody(j);
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134		nAtomsInRigidBodies += rbStamp->getNMembers();
135		}
136
#	Line 168 \| Line 169 \| namespace oopse {
169		}
170		molecules_.clear();
171
171	–	delete stamps_;
172		delete sman_;
173		delete simParams_;
174		delete forceField_;
#	Line 275 \| Line 275 \| namespace oopse {
275		}
276		}
277
278	<	}//end for (integrableObject)
279	<	}// end for (mol)
278	>	}
279	>	}
280
281		// n_constraints is local, so subtract them on each processor
282		ndf_local -= nConstraints_;
#	Line 293 \| Line 293 \| namespace oopse {
293
294		}
295
296	+	int SimInfo::getFdf() {
297	+	#ifdef IS_MPI
298	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
299	+	#else
300	+	fdf_ = fdf_local;
301	+	#endif
302	+	return fdf_;
303	+	}
304	+
305		void SimInfo::calcNdfRaw() {
306		int ndfRaw_local;
307
#	Line 593 \| Line 602 \| namespace oopse {
602		//setup fortran force field
603		/** @deprecate */
604		int isError = 0;
605	+
606	+	setupCutoff();
607
608		setupElectrostaticSummationMethod( isError );
609		setupSwitchingFunction();
610	+	setupAccumulateBoxDipole();
611
612		if(isError){
613		sprintf( painCave.errMsg,
#	Line 603 \| Line 615 \| namespace oopse {
615		painCave.isFatal = 1;
616		simError();
617		}
606	–
607	–
608	–	setupCutoff();
618
619		calcNdf();
620		calcNdfRaw();
#	Line 655 \| Line 664 \| namespace oopse {
664		int usePBC = simParams_->getUsePeriodicBoundaryConditions();
665		int useRF;
666		int useSF;
667	+	int useSP;
668	+	int useBoxDipole;
669		std::string myMethod;
670
671		// set the useRF logical
672		useRF = 0;
673		useSF = 0;
674	+	useSP = 0;
675
676
677		if (simParams_->haveElectrostaticSummationMethod()) {
678		std::string myMethod = simParams_->getElectrostaticSummationMethod();
679		toUpper(myMethod);
680	<	if (myMethod == "REACTION_FIELD") {
681	<	useRF=1;
682	<	} else {
683	<	if (myMethod == "SHIFTED_FORCE") {
684	<	useSF = 1;
685	<	}
680	>	if (myMethod == "REACTION_FIELD"){
681	>	useRF = 1;
682	>	} else if (myMethod == "SHIFTED_FORCE"){
683	>	useSF = 1;
684	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
685	>	useSP = 1;
686		}
687		}
688	+
689	+	if (simParams_->haveAccumulateBoxDipole())
690	+	if (simParams_->getAccumulateBoxDipole())
691	+	useBoxDipole = 1;
692
693		//loop over all of the atom types
694		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
#	Line 743 \| Line 759 \| namespace oopse {
759		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760
761		temp = useSF;
762	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
762	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763
764	+	temp = useSP;
765	+	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	+
767	+	temp = useBoxDipole;
768	+	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	+
770		#endif
771
772		fInfo_.SIM_uses_PBC = usePBC;
#	Line 762 \| Line 784 \| namespace oopse {
784		fInfo_.SIM_uses_FLARB = useFLARB;
785		fInfo_.SIM_uses_RF = useRF;
786		fInfo_.SIM_uses_SF = useSF;
787	<
788	<	if( myMethod == "REACTION_FIELD") {
767	<
768	<	if (simParams_->haveDielectric()) {
769	<	fInfo_.dielect = simParams_->getDielectric();
770	<	} else {
771	<	sprintf(painCave.errMsg,
772	<	"SimSetup Error: No Dielectric constant was set.\n"
773	<	"\tYou are trying to use Reaction Field without"
774	<	"\tsetting a dielectric constant!\n");
775	<	painCave.isFatal = 1;
776	<	simError();
777	<	}
778	<	}
779	<
787	>	fInfo_.SIM_uses_SP = useSP;
788	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
789		}
790
791		void SimInfo::setupFortranSim() {
#	Line 793 \| Line 802 \| namespace oopse {
802		}
803
804		//calculate mass ratio of cutoff group
805	<	std::vector<double> mfact;
805	>	std::vector<RealType> mfact;
806		SimInfo::MoleculeIterator mi;
807		Molecule* mol;
808		Molecule::CutoffGroupIterator ci;
809		CutoffGroup* cg;
810		Molecule::AtomIterator ai;
811		Atom* atom;
812	<	double totalMass;
812	>	RealType totalMass;
813
814		//to avoid memory reallocation, reserve enough space for mfact
815		mfact.reserve(getNCutoffGroups());
#	Line 861 \| Line 870 \| namespace oopse {
870		"succesfully sent the simulation information to fortran.\n");
871		MPIcheckPoint();
872		#endif // is_mpi
873	+
874	+	// Setup number of neighbors in neighbor list if present
875	+	if (simParams_->haveNeighborListNeighbors()) {
876	+	setNeighbors(simParams_->getNeighborListNeighbors());
877	+	}
878	+
879	+
880		}
881
882
#	Line 923 \| Line 939 \| namespace oopse {
939
940		#endif
941
942	<	double SimInfo::calcMaxCutoffRadius() {
942	>	void SimInfo::setupCutoff() {
943	>
944	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
945
946	+	// Check the cutoff policy
947	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
948
949	<	std::set<AtomType*> atomTypes;
950	<	std::set<AtomType*>::iterator i;
951	<	std::vector<double> cutoffRadius;
952	<
953	<	//get the unique atom types
934	<	atomTypes = getUniqueAtomTypes();
935	<
936	<	//query the max cutoff radius among these atom types
937	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
938	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
949	>	std::string myPolicy;
950	>	if (forceFieldOptions_.haveCutoffPolicy()){
951	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
952	>	}else if (simParams_->haveCutoffPolicy()) {
953	>	myPolicy = simParams_->getCutoffPolicy();
954		}
955
956	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
942	<	#ifdef IS_MPI
943	<	//pick the max cutoff radius among the processors
944	<	#endif
945	<
946	<	return maxCutoffRadius;
947	<	}
948	<
949	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
950	<
951	<	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
952	<
953	<	if (!simParams_->haveCutoffRadius()){
954	<	sprintf(painCave.errMsg,
955	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
956	<	"\tOOPSE will use a default value of 15.0 angstroms"
957	<	"\tfor the cutoffRadius.\n");
958	<	painCave.isFatal = 0;
959	<	simError();
960	<	rcut = 15.0;
961	<	} else{
962	<	rcut = simParams_->getCutoffRadius();
963	<	}
964	<
965	<	if (!simParams_->haveSwitchingRadius()){
966	<	sprintf(painCave.errMsg,
967	<	"SimCreator Warning: No value was set for switchingRadius.\n"
968	<	"\tOOPSE will use a default value of\n"
969	<	"\t0.85 * cutoffRadius for the switchingRadius\n");
970	<	painCave.isFatal = 0;
971	<	simError();
972	<	rsw = 0.85 * rcut;
973	<	} else{
974	<	rsw = simParams_->getSwitchingRadius();
975	<	}
976	<
977	<	} else {
978	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
979	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
980	<
981	<	if (simParams_->haveCutoffRadius()) {
982	<	rcut = simParams_->getCutoffRadius();
983	<	} else {
984	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
985	<	rcut = calcMaxCutoffRadius();
986	<	}
987	<
988	<	if (simParams_->haveSwitchingRadius()) {
989	<	rsw = simParams_->getSwitchingRadius();
990	<	} else {
991	<	rsw = rcut;
992	<	}
993	<
994	<	}
995	<	}
996	<
997	<	void SimInfo::setupCutoff() {
998	<	getCutoff(rcut_, rsw_);
999	<	double rnblist = rcut_ + 1; // skin of neighbor list
1000	<
1001	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1002	<
1003	<	int cp = TRADITIONAL_CUTOFF_POLICY;
1004	<	if (simParams_->haveCutoffPolicy()) {
1005	<	std::string myPolicy = simParams_->getCutoffPolicy();
956	>	if (!myPolicy.empty()){
957		toUpper(myPolicy);
958		if (myPolicy == "MIX") {
959		cp = MIX_CUTOFF_POLICY;
#	Line 1021 \| Line 972 \| namespace oopse {
972		}
973		}
974		}
975	<	}
975	>	}
976	>	notifyFortranCutoffPolicy(&cp);
977
978	<
978	>	// Check the Skin Thickness for neighborlists
979	>	RealType skin;
980		if (simParams_->haveSkinThickness()) {
981	<	double skinThickness = simParams_->getSkinThickness();
982	<	}
981	>	skin = simParams_->getSkinThickness();
982	>	notifyFortranSkinThickness(&skin);
983	>	}
984	>
985	>	// Check if the cutoff was set explicitly:
986	>	if (simParams_->haveCutoffRadius()) {
987	>	rcut_ = simParams_->getCutoffRadius();
988	>	if (simParams_->haveSwitchingRadius()) {
989	>	rsw_ = simParams_->getSwitchingRadius();
990	>	} else {
991	>	if (fInfo_.SIM_uses_Charges \|
992	>	fInfo_.SIM_uses_Dipoles \|
993	>	fInfo_.SIM_uses_RF) {
994	>
995	>	rsw_ = 0.85 * rcut_;
996	>	sprintf(painCave.errMsg,
997	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
998	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
999	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1000	>	painCave.isFatal = 0;
1001	>	simError();
1002	>	} else {
1003	>	rsw_ = rcut_;
1004	>	sprintf(painCave.errMsg,
1005	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1006	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1007	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1008	>	painCave.isFatal = 0;
1009	>	simError();
1010	>	}
1011	>	}
1012	>
1013	>	notifyFortranCutoffs(&rcut_, &rsw_);
1014	>
1015	>	} else {
1016	>
1017	>	// For electrostatic atoms, we'll assume a large safe value:
1018	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1019	>	sprintf(painCave.errMsg,
1020	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1021	>	"\tOOPSE will use a default value of 15.0 angstroms"
1022	>	"\tfor the cutoffRadius.\n");
1023	>	painCave.isFatal = 0;
1024	>	simError();
1025	>	rcut_ = 15.0;
1026	>
1027	>	if (simParams_->haveElectrostaticSummationMethod()) {
1028	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1029	>	toUpper(myMethod);
1030	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1031	>	if (simParams_->haveSwitchingRadius()){
1032	>	sprintf(painCave.errMsg,
1033	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1034	>	"\teven though the electrostaticSummationMethod was\n"
1035	>	"\tset to %s\n", myMethod.c_str());
1036	>	painCave.isFatal = 1;
1037	>	simError();
1038	>	}
1039	>	}
1040	>	}
1041	>
1042	>	if (simParams_->haveSwitchingRadius()){
1043	>	rsw_ = simParams_->getSwitchingRadius();
1044	>	} else {
1045	>	sprintf(painCave.errMsg,
1046	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1047	>	"\tOOPSE will use a default value of\n"
1048	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1049	>	painCave.isFatal = 0;
1050	>	simError();
1051	>	rsw_ = 0.85 * rcut_;
1052	>	}
1053	>	notifyFortranCutoffs(&rcut_, &rsw_);
1054	>	} else {
1055	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1056	>	// We'll punt and let fortran figure out the cutoffs later.
1057	>
1058	>	notifyFortranYouAreOnYourOwn();
1059
1060	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1061	<	// also send cutoff notification to electrostatics
1033	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1060	>	}
1061	>	}
1062		}
1063
1064		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
#	Line 1038 \| Line 1066 \| namespace oopse {
1066		int errorOut;
1067		int esm = NONE;
1068		int sm = UNDAMPED;
1069	<	double alphaVal;
1070	<	double dielectric;
1071	<
1069	>	RealType alphaVal;
1070	>	RealType dielectric;
1071	>
1072		errorOut = isError;
1045	–	alphaVal = simParams_->getDampingAlpha();
1046	–	dielectric = simParams_->getDielectric();
1073
1074		if (simParams_->haveElectrostaticSummationMethod()) {
1075		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 1060 \| Line 1086 \| namespace oopse {
1086		if (myMethod == "SHIFTED_FORCE") {
1087		esm = SHIFTED_FORCE;
1088		} else {
1089	<	if (myMethod == "REACTION_FIELD") {
1089	>	if (myMethod == "REACTION_FIELD") {
1090		esm = REACTION_FIELD;
1091	+	dielectric = simParams_->getDielectric();
1092	+	if (!simParams_->haveDielectric()) {
1093	+	// throw warning
1094	+	sprintf( painCave.errMsg,
1095	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1096	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1097	+	painCave.isFatal = 0;
1098	+	simError();
1099	+	}
1100		} else {
1101		// throw error
1102		sprintf( painCave.errMsg,
1103	<	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1103	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1104	>	"\t(Input file specified %s .)\n"
1105	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1106	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1107	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1108		painCave.isFatal = 1;
1109		simError();
1110		}
#	Line 1084 \| Line 1123 \| namespace oopse {
1123		if (myScreen == "DAMPED") {
1124		sm = DAMPED;
1125		if (!simParams_->haveDampingAlpha()) {
1126	<	//throw error
1126	>	// first set a cutoff dependent alpha value
1127	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1128	>	alphaVal = 0.5125 - rcut_* 0.025;
1129	>	// for values rcut > 20.5, alpha is zero
1130	>	if (alphaVal < 0) alphaVal = 0;
1131	>
1132	>	// throw warning
1133		sprintf( painCave.errMsg,
1134	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1134	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1135	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1136		painCave.isFatal = 0;
1137		simError();
1138	+	} else {
1139	+	alphaVal = simParams_->getDampingAlpha();
1140		}
1141	+
1142		} else {
1143		// throw error
1144		sprintf( painCave.errMsg,
1145	<	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1145	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1146	>	"\t(Input file specified %s .)\n"
1147	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1148	>	"or \"damped\".\n", myScreen.c_str() );
1149		painCave.isFatal = 1;
1150		simError();
1151		}
#	Line 1102 \| Line 1154 \| namespace oopse {
1154
1155		// let's pass some summation method variables to fortran
1156		setElectrostaticSummationMethod( &esm );
1157	+	setFortranElectrostaticMethod( &esm );
1158		setScreeningMethod( &sm );
1159		setDampingAlpha( &alphaVal );
1160		setReactionFieldDielectric( &dielectric );
1161	<	initFortranFF( &esm, &errorOut );
1161	>	initFortranFF( &errorOut );
1162		}
1163
1164		void SimInfo::setupSwitchingFunction() {
#	Line 1134 \| Line 1187 \| namespace oopse {
1187
1188		}
1189
1190	+	void SimInfo::setupAccumulateBoxDipole() {
1191	+
1192	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1193	+	if ( simParams_->haveAccumulateBoxDipole() )
1194	+	if ( simParams_->getAccumulateBoxDipole() ) {
1195	+	setAccumulateBoxDipole();
1196	+	calcBoxDipole_ = true;
1197	+	}
1198	+
1199	+	}
1200	+
1201		void SimInfo::addProperty(GenericData* genData) {
1202		properties_.addProperty(genData);
1203		}
#	Line 1190 \| Line 1254 \| namespace oopse {
1254		Molecule* mol;
1255
1256		Vector3d comVel(0.0);
1257	<	double totalMass = 0.0;
1257	>	RealType totalMass = 0.0;
1258
1259
1260		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1261	<	double mass = mol->getMass();
1261	>	RealType mass = mol->getMass();
1262		totalMass += mass;
1263		comVel += mass * mol->getComVel();
1264		}
1265
1266		#ifdef IS_MPI
1267	<	double tmpMass = totalMass;
1267	>	RealType tmpMass = totalMass;
1268		Vector3d tmpComVel(comVel);
1269	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1269	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1270	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1271		#endif
1272
1273		comVel /= totalMass;
#	Line 1216 \| Line 1280 \| namespace oopse {
1280		Molecule* mol;
1281
1282		Vector3d com(0.0);
1283	<	double totalMass = 0.0;
1283	>	RealType totalMass = 0.0;
1284
1285		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1286	<	double mass = mol->getMass();
1286	>	RealType mass = mol->getMass();
1287		totalMass += mass;
1288		com += mass * mol->getCom();
1289		}
1290
1291		#ifdef IS_MPI
1292	<	double tmpMass = totalMass;
1292	>	RealType tmpMass = totalMass;
1293		Vector3d tmpCom(com);
1294	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1295	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1294	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1295	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1296		#endif
1297
1298		com /= totalMass;
#	Line 1252 \| Line 1316 \| namespace oopse {
1316		Molecule* mol;
1317
1318
1319	<	double totalMass = 0.0;
1319	>	RealType totalMass = 0.0;
1320
1321
1322		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1323	<	double mass = mol->getMass();
1323	>	RealType mass = mol->getMass();
1324		totalMass += mass;
1325		com += mass * mol->getCom();
1326		comVel += mass * mol->getComVel();
1327		}
1328
1329		#ifdef IS_MPI
1330	<	double tmpMass = totalMass;
1330	>	RealType tmpMass = totalMass;
1331		Vector3d tmpCom(com);
1332		Vector3d tmpComVel(comVel);
1333	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1334	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1335	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1333	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1334	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1335	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1336		#endif
1337
1338		com /= totalMass;
#	Line 1287 \| Line 1351 \| namespace oopse {
1351		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1352
1353
1354	<	double xx = 0.0;
1355	<	double yy = 0.0;
1356	<	double zz = 0.0;
1357	<	double xy = 0.0;
1358	<	double xz = 0.0;
1359	<	double yz = 0.0;
1354	>	RealType xx = 0.0;
1355	>	RealType yy = 0.0;
1356	>	RealType zz = 0.0;
1357	>	RealType xy = 0.0;
1358	>	RealType xz = 0.0;
1359	>	RealType yz = 0.0;
1360		Vector3d com(0.0);
1361		Vector3d comVel(0.0);
1362
#	Line 1304 \| Line 1368 \| namespace oopse {
1368		Vector3d thisq(0.0);
1369		Vector3d thisv(0.0);
1370
1371	<	double thisMass = 0.0;
1371	>	RealType thisMass = 0.0;
1372
1373
1374
#	Line 1342 \| Line 1406 \| namespace oopse {
1406		#ifdef IS_MPI
1407		Mat3x3d tmpI(inertiaTensor);
1408		Vector3d tmpAngMom;
1409	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1410	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1409	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1410	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1411		#endif
1412
1413		return;
#	Line 1364 \| Line 1428 \| namespace oopse {
1428		Vector3d thisr(0.0);
1429		Vector3d thisp(0.0);
1430
1431	<	double thisMass;
1431	>	RealType thisMass;
1432
1433		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1434		thisMass = mol->getMass();
#	Line 1377 \| Line 1441 \| namespace oopse {
1441
1442		#ifdef IS_MPI
1443		Vector3d tmpAngMom;
1444	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1444	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1445		#endif
1446
1447		return angularMomentum;
1448		}
1449
1450	<
1450	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1451	>	return IOIndexToIntegrableObject.at(index);
1452	>	}
1453	>
1454	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1455	>	IOIndexToIntegrableObject= v;
1456	>	}
1457	>
1458	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1459	>	based on the radius of gyration V=4/3PiR_1R_2R_3
1460	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1461	>	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1462	>	*/
1463	>	void SimInfo::getGyrationalVolume(RealType &volume){
1464	>	Mat3x3d intTensor;
1465	>	RealType det;
1466	>	Vector3d dummyAngMom;
1467	>	RealType sysconstants;
1468	>	RealType geomCnst;
1469	>
1470	>	geomCnst = 3.0/2.0;
1471	>	/* Get the inertial tensor and angular momentum for free*/
1472	>	getInertiaTensor(intTensor,dummyAngMom);
1473	>
1474	>	det = intTensor.determinant();
1475	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1476	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1477	>	return;
1478	>	}
1479	>
1480	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1481	>	Mat3x3d intTensor;
1482	>	Vector3d dummyAngMom;
1483	>	RealType sysconstants;
1484	>	RealType geomCnst;
1485	>
1486	>	geomCnst = 3.0/2.0;
1487	>	/* Get the inertial tensor and angular momentum for free*/
1488	>	getInertiaTensor(intTensor,dummyAngMom);
1489	>
1490	>	detI = intTensor.determinant();
1491	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1492	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1493	>	return;
1494	>	}
1495	>	/*
1496	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1497	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1498	>	sdByGlobalIndex_ = v;
1499	>	}
1500	>
1501	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1502	>	//assert(index < nAtoms_ + nRigidBodies_);
1503	>	return sdByGlobalIndex_.at(index);
1504	>	}
1505	>	*/
1506		}//end namespace oopse
1507

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs. Revision 1103 by chuckv, Fri Dec 29 20:21:53 2006 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 1103 by chuckv, Fri Dec 29 20:21:53 2006 UTC