[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 1126 by gezelter, Fri Apr 6 21:53:43 2007 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	>	useAtomicVirial_(true) {
97
94	–
95	–	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
98		MoleculeStamp* molStamp;
99		int nMolWithSameStamp;
100		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
#	Line 100 \| Line 102 \| namespace oopse {
102		CutoffGroupStamp* cgStamp;
103		RigidBodyStamp* rbStamp;
104		int nRigidAtoms = 0;
105	<
106	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
107	<	molStamp = i->first;
108	<	nMolWithSameStamp = i->second;
105	>	std::vector<Component*> components = simParams->getComponents();
106	>
107	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108	>	molStamp = (*i)->getMoleculeStamp();
109	>	nMolWithSameStamp = (*i)->getNMol();
110
111		addMoleculeStamp(molStamp, nMolWithSameStamp);
112
113		//calculate atoms in molecules
114		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
115
113	–
116		//calculate atoms in cutoff groups
117		int nAtomsInGroups = 0;
118		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119
120		for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroup(j);
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122		nAtomsInGroups += cgStamp->getNMembers();
123		}
124
#	Line 129 \| Line 131 \| namespace oopse {
131		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132
133		for (int j=0; j < nRigidBodiesInStamp; j++) {
134	<	rbStamp = molStamp->getRigidBody(j);
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135		nAtomsInRigidBodies += rbStamp->getNMembers();
136		}
137
#	Line 168 \| Line 170 \| namespace oopse {
170		}
171		molecules_.clear();
172
171	–	delete stamps_;
173		delete sman_;
174		delete simParams_;
175		delete forceField_;
#	Line 275 \| Line 276 \| namespace oopse {
276		}
277		}
278
279	<	}//end for (integrableObject)
280	<	}// end for (mol)
279	>	}
280	>	}
281
282		// n_constraints is local, so subtract them on each processor
283		ndf_local -= nConstraints_;
#	Line 293 \| Line 294 \| namespace oopse {
294
295		}
296
297	+	int SimInfo::getFdf() {
298	+	#ifdef IS_MPI
299	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300	+	#else
301	+	fdf_ = fdf_local;
302	+	#endif
303	+	return fdf_;
304	+	}
305	+
306		void SimInfo::calcNdfRaw() {
307		int ndfRaw_local;
308
#	Line 593 \| Line 603 \| namespace oopse {
603		//setup fortran force field
604		/** @deprecate */
605		int isError = 0;
606	+
607	+	setupCutoff();
608
609		setupElectrostaticSummationMethod( isError );
610		setupSwitchingFunction();
611	+	setupAccumulateBoxDipole();
612
613		if(isError){
614		sprintf( painCave.errMsg,
#	Line 603 \| Line 616 \| namespace oopse {
616		painCave.isFatal = 1;
617		simError();
618		}
606	–
607	–
608	–	setupCutoff();
619
620		calcNdf();
621		calcNdfRaw();
#	Line 655 \| Line 665 \| namespace oopse {
665		int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666		int useRF;
667		int useSF;
668	+	int useSP;
669	+	int useBoxDipole;
670	+
671		std::string myMethod;
672
673		// set the useRF logical
674		useRF = 0;
675		useSF = 0;
676	+	useSP = 0;
677
678
679		if (simParams_->haveElectrostaticSummationMethod()) {
680		std::string myMethod = simParams_->getElectrostaticSummationMethod();
681		toUpper(myMethod);
682	<	if (myMethod == "REACTION_FIELD") {
683	<	useRF=1;
684	<	} else {
685	<	if (myMethod == "SHIFTED_FORCE") {
686	<	useSF = 1;
687	<	}
682	>	if (myMethod == "REACTION_FIELD"){
683	>	useRF = 1;
684	>	} else if (myMethod == "SHIFTED_FORCE"){
685	>	useSF = 1;
686	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
687	>	useSP = 1;
688		}
689		}
690	+
691	+	if (simParams_->haveAccumulateBoxDipole())
692	+	if (simParams_->getAccumulateBoxDipole())
693	+	useBoxDipole = 1;
694
695	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
696	+
697		//loop over all of the atom types
698		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
699		useLennardJones \|= (*i)->isLennardJones();
#	Line 743 \| Line 763 \| namespace oopse {
763		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764
765		temp = useSF;
766	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767
768	+	temp = useSP;
769	+	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	+
771	+	temp = useBoxDipole;
772	+	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	+
774	+	temp = useAtomicVirial_;
775	+	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	+
777		#endif
778
779		fInfo_.SIM_uses_PBC = usePBC;
#	Line 762 \| Line 791 \| namespace oopse {
791		fInfo_.SIM_uses_FLARB = useFLARB;
792		fInfo_.SIM_uses_RF = useRF;
793		fInfo_.SIM_uses_SF = useSF;
794	<
795	<	if( myMethod == "REACTION_FIELD") {
796	<
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	<
794	>	fInfo_.SIM_uses_SP = useSP;
795	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
797		}
798
799		void SimInfo::setupFortranSim() {
#	Line 793 \| Line 810 \| namespace oopse {
810		}
811
812		//calculate mass ratio of cutoff group
813	<	std::vector<double> mfact;
813	>	std::vector<RealType> mfact;
814		SimInfo::MoleculeIterator mi;
815		Molecule* mol;
816		Molecule::CutoffGroupIterator ci;
817		CutoffGroup* cg;
818		Molecule::AtomIterator ai;
819		Atom* atom;
820	<	double totalMass;
820	>	RealType totalMass;
821
822		//to avoid memory reallocation, reserve enough space for mfact
823		mfact.reserve(getNCutoffGroups());
#	Line 861 \| Line 878 \| namespace oopse {
878		"succesfully sent the simulation information to fortran.\n");
879		MPIcheckPoint();
880		#endif // is_mpi
881	+
882	+	// Setup number of neighbors in neighbor list if present
883	+	if (simParams_->haveNeighborListNeighbors()) {
884	+	int nlistNeighbors = simParams_->getNeighborListNeighbors();
885	+	setNeighbors(&nlistNeighbors);
886	+	}
887	+
888	+
889		}
890
891
#	Line 923 \| Line 948 \| namespace oopse {
948
949		#endif
950
951	<	double SimInfo::calcMaxCutoffRadius() {
951	>	void SimInfo::setupCutoff() {
952	>
953	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
954
955	+	// Check the cutoff policy
956	+	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957
958	<	std::set<AtomType*> atomTypes;
959	<	std::set<AtomType*>::iterator i;
960	<	std::vector<double> cutoffRadius;
961	<
962	<	//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));
958	>	std::string myPolicy;
959	>	if (forceFieldOptions_.haveCutoffPolicy()){
960	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
961	>	}else if (simParams_->haveCutoffPolicy()) {
962	>	myPolicy = simParams_->getCutoffPolicy();
963		}
964
965	<	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();
965	>	if (!myPolicy.empty()){
966		toUpper(myPolicy);
967		if (myPolicy == "MIX") {
968		cp = MIX_CUTOFF_POLICY;
#	Line 1021 \| Line 981 \| namespace oopse {
981		}
982		}
983		}
984	<	}
984	>	}
985	>	notifyFortranCutoffPolicy(&cp);
986
987	<
987	>	// Check the Skin Thickness for neighborlists
988	>	RealType skin;
989		if (simParams_->haveSkinThickness()) {
990	<	double skinThickness = simParams_->getSkinThickness();
991	<	}
990	>	skin = simParams_->getSkinThickness();
991	>	notifyFortranSkinThickness(&skin);
992	>	}
993	>
994	>	// Check if the cutoff was set explicitly:
995	>	if (simParams_->haveCutoffRadius()) {
996	>	rcut_ = simParams_->getCutoffRadius();
997	>	if (simParams_->haveSwitchingRadius()) {
998	>	rsw_ = simParams_->getSwitchingRadius();
999	>	} else {
1000	>	if (fInfo_.SIM_uses_Charges \|
1001	>	fInfo_.SIM_uses_Dipoles \|
1002	>	fInfo_.SIM_uses_RF) {
1003	>
1004	>	rsw_ = 0.85 * rcut_;
1005	>	sprintf(painCave.errMsg,
1006	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1007	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1008	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1009	>	painCave.isFatal = 0;
1010	>	simError();
1011	>	} else {
1012	>	rsw_ = rcut_;
1013	>	sprintf(painCave.errMsg,
1014	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1015	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1016	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1017	>	painCave.isFatal = 0;
1018	>	simError();
1019	>	}
1020	>	}
1021	>
1022	>	notifyFortranCutoffs(&rcut_, &rsw_);
1023	>
1024	>	} else {
1025	>
1026	>	// For electrostatic atoms, we'll assume a large safe value:
1027	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1028	>	sprintf(painCave.errMsg,
1029	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1030	>	"\tOOPSE will use a default value of 15.0 angstroms"
1031	>	"\tfor the cutoffRadius.\n");
1032	>	painCave.isFatal = 0;
1033	>	simError();
1034	>	rcut_ = 15.0;
1035	>
1036	>	if (simParams_->haveElectrostaticSummationMethod()) {
1037	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1038	>	toUpper(myMethod);
1039	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1040	>	if (simParams_->haveSwitchingRadius()){
1041	>	sprintf(painCave.errMsg,
1042	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1043	>	"\teven though the electrostaticSummationMethod was\n"
1044	>	"\tset to %s\n", myMethod.c_str());
1045	>	painCave.isFatal = 1;
1046	>	simError();
1047	>	}
1048	>	}
1049	>	}
1050	>
1051	>	if (simParams_->haveSwitchingRadius()){
1052	>	rsw_ = simParams_->getSwitchingRadius();
1053	>	} else {
1054	>	sprintf(painCave.errMsg,
1055	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1056	>	"\tOOPSE will use a default value of\n"
1057	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1058	>	painCave.isFatal = 0;
1059	>	simError();
1060	>	rsw_ = 0.85 * rcut_;
1061	>	}
1062	>	notifyFortranCutoffs(&rcut_, &rsw_);
1063	>	} else {
1064	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1065	>	// We'll punt and let fortran figure out the cutoffs later.
1066	>
1067	>	notifyFortranYouAreOnYourOwn();
1068
1069	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1070	<	// also send cutoff notification to electrostatics
1033	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1069	>	}
1070	>	}
1071		}
1072
1073		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
#	Line 1038 \| Line 1075 \| namespace oopse {
1075		int errorOut;
1076		int esm = NONE;
1077		int sm = UNDAMPED;
1078	<	double alphaVal;
1079	<	double dielectric;
1080	<
1078	>	RealType alphaVal;
1079	>	RealType dielectric;
1080	>
1081		errorOut = isError;
1045	–	alphaVal = simParams_->getDampingAlpha();
1046	–	dielectric = simParams_->getDielectric();
1082
1083		if (simParams_->haveElectrostaticSummationMethod()) {
1084		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 1060 \| Line 1095 \| namespace oopse {
1095		if (myMethod == "SHIFTED_FORCE") {
1096		esm = SHIFTED_FORCE;
1097		} else {
1098	<	if (myMethod == "REACTION_FIELD") {
1098	>	if (myMethod == "REACTION_FIELD") {
1099		esm = REACTION_FIELD;
1100	+	dielectric = simParams_->getDielectric();
1101	+	if (!simParams_->haveDielectric()) {
1102	+	// throw warning
1103	+	sprintf( painCave.errMsg,
1104	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1105	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1106	+	painCave.isFatal = 0;
1107	+	simError();
1108	+	}
1109		} else {
1110		// throw error
1111		sprintf( painCave.errMsg,
1112	<	"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() );
1112	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1113	>	"\t(Input file specified %s .)\n"
1114	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1115	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1116	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1117		painCave.isFatal = 1;
1118		simError();
1119		}
#	Line 1084 \| Line 1132 \| namespace oopse {
1132		if (myScreen == "DAMPED") {
1133		sm = DAMPED;
1134		if (!simParams_->haveDampingAlpha()) {
1135	<	//throw error
1135	>	// first set a cutoff dependent alpha value
1136	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1137	>	alphaVal = 0.5125 - rcut_* 0.025;
1138	>	// for values rcut > 20.5, alpha is zero
1139	>	if (alphaVal < 0) alphaVal = 0;
1140	>
1141	>	// throw warning
1142		sprintf( painCave.errMsg,
1143	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1143	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1144	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1145		painCave.isFatal = 0;
1146		simError();
1147	+	} else {
1148	+	alphaVal = simParams_->getDampingAlpha();
1149		}
1150	+
1151		} else {
1152		// throw error
1153		sprintf( painCave.errMsg,
1154	<	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1154	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1155	>	"\t(Input file specified %s .)\n"
1156	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1157	>	"or \"damped\".\n", myScreen.c_str() );
1158		painCave.isFatal = 1;
1159		simError();
1160		}
#	Line 1102 \| Line 1163 \| namespace oopse {
1163
1164		// let's pass some summation method variables to fortran
1165		setElectrostaticSummationMethod( &esm );
1166	+	setFortranElectrostaticMethod( &esm );
1167		setScreeningMethod( &sm );
1168		setDampingAlpha( &alphaVal );
1169		setReactionFieldDielectric( &dielectric );
1170	<	initFortranFF( &esm, &errorOut );
1170	>	initFortranFF( &errorOut );
1171		}
1172
1173		void SimInfo::setupSwitchingFunction() {
#	Line 1134 \| Line 1196 \| namespace oopse {
1196
1197		}
1198
1199	+	void SimInfo::setupAccumulateBoxDipole() {
1200	+
1201	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1202	+	if ( simParams_->haveAccumulateBoxDipole() )
1203	+	if ( simParams_->getAccumulateBoxDipole() ) {
1204	+	setAccumulateBoxDipole();
1205	+	calcBoxDipole_ = true;
1206	+	}
1207	+
1208	+	}
1209	+
1210		void SimInfo::addProperty(GenericData* genData) {
1211		properties_.addProperty(genData);
1212		}
#	Line 1190 \| Line 1263 \| namespace oopse {
1263		Molecule* mol;
1264
1265		Vector3d comVel(0.0);
1266	<	double totalMass = 0.0;
1266	>	RealType totalMass = 0.0;
1267
1268
1269		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1270	<	double mass = mol->getMass();
1270	>	RealType mass = mol->getMass();
1271		totalMass += mass;
1272		comVel += mass * mol->getComVel();
1273		}
1274
1275		#ifdef IS_MPI
1276	<	double tmpMass = totalMass;
1276	>	RealType tmpMass = totalMass;
1277		Vector3d tmpComVel(comVel);
1278	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1279	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1278	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1279	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1280		#endif
1281
1282		comVel /= totalMass;
#	Line 1216 \| Line 1289 \| namespace oopse {
1289		Molecule* mol;
1290
1291		Vector3d com(0.0);
1292	<	double totalMass = 0.0;
1292	>	RealType totalMass = 0.0;
1293
1294		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1295	<	double mass = mol->getMass();
1295	>	RealType mass = mol->getMass();
1296		totalMass += mass;
1297		com += mass * mol->getCom();
1298		}
1299
1300		#ifdef IS_MPI
1301	<	double tmpMass = totalMass;
1301	>	RealType tmpMass = totalMass;
1302		Vector3d tmpCom(com);
1303	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1304	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1303	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1305		#endif
1306
1307		com /= totalMass;
#	Line 1252 \| Line 1325 \| namespace oopse {
1325		Molecule* mol;
1326
1327
1328	<	double totalMass = 0.0;
1328	>	RealType totalMass = 0.0;
1329
1330
1331		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1332	<	double mass = mol->getMass();
1332	>	RealType mass = mol->getMass();
1333		totalMass += mass;
1334		com += mass * mol->getCom();
1335		comVel += mass * mol->getComVel();
1336		}
1337
1338		#ifdef IS_MPI
1339	<	double tmpMass = totalMass;
1339	>	RealType tmpMass = totalMass;
1340		Vector3d tmpCom(com);
1341		Vector3d tmpComVel(comVel);
1342	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1343	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1344	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1342	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1343	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1344	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1345		#endif
1346
1347		com /= totalMass;
#	Line 1287 \| Line 1360 \| namespace oopse {
1360		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1361
1362
1363	<	double xx = 0.0;
1364	<	double yy = 0.0;
1365	<	double zz = 0.0;
1366	<	double xy = 0.0;
1367	<	double xz = 0.0;
1368	<	double yz = 0.0;
1363	>	RealType xx = 0.0;
1364	>	RealType yy = 0.0;
1365	>	RealType zz = 0.0;
1366	>	RealType xy = 0.0;
1367	>	RealType xz = 0.0;
1368	>	RealType yz = 0.0;
1369		Vector3d com(0.0);
1370		Vector3d comVel(0.0);
1371
#	Line 1304 \| Line 1377 \| namespace oopse {
1377		Vector3d thisq(0.0);
1378		Vector3d thisv(0.0);
1379
1380	<	double thisMass = 0.0;
1380	>	RealType thisMass = 0.0;
1381
1382
1383
#	Line 1342 \| Line 1415 \| namespace oopse {
1415		#ifdef IS_MPI
1416		Mat3x3d tmpI(inertiaTensor);
1417		Vector3d tmpAngMom;
1418	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1419	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1418	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1419	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1420		#endif
1421
1422		return;
#	Line 1364 \| Line 1437 \| namespace oopse {
1437		Vector3d thisr(0.0);
1438		Vector3d thisp(0.0);
1439
1440	<	double thisMass;
1440	>	RealType thisMass;
1441
1442		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1443		thisMass = mol->getMass();
#	Line 1377 \| Line 1450 \| namespace oopse {
1450
1451		#ifdef IS_MPI
1452		Vector3d tmpAngMom;
1453	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1453	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1454		#endif
1455
1456		return angularMomentum;
1457		}
1458
1459	<
1459	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1460	>	return IOIndexToIntegrableObject.at(index);
1461	>	}
1462	>
1463	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1464	>	IOIndexToIntegrableObject= v;
1465	>	}
1466	>
1467	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1468	>	based on the radius of gyration V=4/3PiR_1R_2R_3
1469	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1470	>	V = 4/3Pi(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1471	>	*/
1472	>	void SimInfo::getGyrationalVolume(RealType &volume){
1473	>	Mat3x3d intTensor;
1474	>	RealType det;
1475	>	Vector3d dummyAngMom;
1476	>	RealType sysconstants;
1477	>	RealType geomCnst;
1478	>
1479	>	geomCnst = 3.0/2.0;
1480	>	/* Get the inertial tensor and angular momentum for free*/
1481	>	getInertiaTensor(intTensor,dummyAngMom);
1482	>
1483	>	det = intTensor.determinant();
1484	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1485	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(det);
1486	>	return;
1487	>	}
1488	>
1489	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1490	>	Mat3x3d intTensor;
1491	>	Vector3d dummyAngMom;
1492	>	RealType sysconstants;
1493	>	RealType geomCnst;
1494	>
1495	>	geomCnst = 3.0/2.0;
1496	>	/* Get the inertial tensor and angular momentum for free*/
1497	>	getInertiaTensor(intTensor,dummyAngMom);
1498	>
1499	>	detI = intTensor.determinant();
1500	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1501	>	volume = 4.0/3.0NumericConstant::PIpow(sysconstants,3.0/2.0)*sqrt(detI);
1502	>	return;
1503	>	}
1504	>	/*
1505	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1506	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1507	>	sdByGlobalIndex_ = v;
1508	>	}
1509	>
1510	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1511	>	//assert(index < nAtoms_ + nRigidBodies_);
1512	>	return sdByGlobalIndex_.at(index);
1513	>	}
1514	>	*/
1515		}//end namespace oopse
1516

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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 1126 by gezelter, Fri Apr 6 21:53:43 2007 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 1126 by gezelter, Fri Apr 6 21:53:43 2007 UTC