[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 1050 by chrisfen, Fri Sep 22 22:19:59 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/electrostatic_interface.h"
62	–	#include "UseTheForce/notifyCutoffs_interface.h"
63		#include "UseTheForce/DarkSide/switcheroo_interface.h"
64		#include "utils/MemoryUtils.hpp"
65		#include "utils/simError.h"
66		#include "selection/SelectionManager.hpp"
67	+	#include "io/ForceFieldOptions.hpp"
68	+	#include "UseTheForce/ForceField.hpp"
69
70		#ifdef IS_MPI
71		#include "UseTheForce/mpiComponentPlan.h"
#	Line 81 \| Line 83 \| namespace oopse {
83		return result;
84		}
85
86	<	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
87	<	ForceField* ff, Globals* simParams) :
88	<	stamps_(stamps), forceField_(ff), simParams_(simParams),
87	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
86	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
87	>	forceField_(ff), simParams_(simParams),
88	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
89		nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
90		nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
91		nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
92		nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
93	<	sman_(NULL), fortranInitialized_(false) {
93	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
94
94	–
95	–	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
95		MoleculeStamp* molStamp;
96		int nMolWithSameStamp;
97		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
#	Line 100 \| Line 99 \| namespace oopse {
99		CutoffGroupStamp* cgStamp;
100		RigidBodyStamp* rbStamp;
101		int nRigidAtoms = 0;
102	<
103	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
104	<	molStamp = i->first;
105	<	nMolWithSameStamp = i->second;
102	>	std::vector<Component*> components = simParams->getComponents();
103	>
104	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
105	>	molStamp = (*i)->getMoleculeStamp();
106	>	nMolWithSameStamp = (*i)->getNMol();
107
108		addMoleculeStamp(molStamp, nMolWithSameStamp);
109
110		//calculate atoms in molecules
111		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
112
113	–
113		//calculate atoms in cutoff groups
114		int nAtomsInGroups = 0;
115		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
116
117		for (int j=0; j < nCutoffGroupsInStamp; j++) {
118	<	cgStamp = molStamp->getCutoffGroup(j);
118	>	cgStamp = molStamp->getCutoffGroupStamp(j);
119		nAtomsInGroups += cgStamp->getNMembers();
120		}
121
#	Line 129 \| Line 128 \| namespace oopse {
128		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129
130		for (int j=0; j < nRigidBodiesInStamp; j++) {
131	<	rbStamp = molStamp->getRigidBody(j);
131	>	rbStamp = molStamp->getRigidBodyStamp(j);
132		nAtomsInRigidBodies += rbStamp->getNMembers();
133		}
134
#	Line 168 \| Line 167 \| namespace oopse {
167		}
168		molecules_.clear();
169
171	–	delete stamps_;
170		delete sman_;
171		delete simParams_;
172		delete forceField_;
#	Line 275 \| Line 273 \| namespace oopse {
273		}
274		}
275
276	<	}//end for (integrableObject)
277	<	}// end for (mol)
276	>	}
277	>	}
278
279		// n_constraints is local, so subtract them on each processor
280		ndf_local -= nConstraints_;
#	Line 293 \| Line 291 \| namespace oopse {
291
292		}
293
294	+	int SimInfo::getFdf() {
295	+	#ifdef IS_MPI
296	+	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297	+	#else
298	+	fdf_ = fdf_local;
299	+	#endif
300	+	return fdf_;
301	+	}
302	+
303		void SimInfo::calcNdfRaw() {
304		int ndfRaw_local;
305
#	Line 594 \| Line 601 \| namespace oopse {
601		/** @deprecate */
602		int isError = 0;
603
604	+	setupCutoff();
605	+
606		setupElectrostaticSummationMethod( isError );
607		setupSwitchingFunction();
608	+	setupAccumulateBoxDipole();
609
610		if(isError){
611		sprintf( painCave.errMsg,
#	Line 603 \| Line 613 \| namespace oopse {
613		painCave.isFatal = 1;
614		simError();
615		}
606	–
607	–
608	–	setupCutoff();
616
617		calcNdf();
618		calcNdfRaw();
#	Line 655 \| Line 662 \| namespace oopse {
662		int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663		int useRF;
664		int useSF;
665	+	int useSP;
666	+	int useBoxDipole;
667		std::string myMethod;
668
669		// set the useRF logical
#	Line 665 \| Line 674 \| namespace oopse {
674		if (simParams_->haveElectrostaticSummationMethod()) {
675		std::string myMethod = simParams_->getElectrostaticSummationMethod();
676		toUpper(myMethod);
677	<	if (myMethod == "REACTION_FIELD") {
677	>	if (myMethod == "REACTION_FIELD"){
678		useRF=1;
679	<	} else {
680	<	if (myMethod == "SHIFTED_FORCE") {
681	<	useSF = 1;
682	<	}
679	>	} else if (myMethod == "SHIFTED_FORCE"){
680	>	useSF = 1;
681	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
682	>	useSP = 1;
683		}
684		}
685	+
686	+	if (simParams_->haveAccumulateBoxDipole())
687	+	if (simParams_->getAccumulateBoxDipole())
688	+	useBoxDipole = 1;
689
690		//loop over all of the atom types
691		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
#	Line 743 \| Line 756 \| namespace oopse {
756		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
757
758		temp = useSF;
759	<	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
759	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760
761	+	temp = useSP;
762	+	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763	+
764	+	temp = useBoxDipole;
765	+	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	+
767		#endif
768
769		fInfo_.SIM_uses_PBC = usePBC;
#	Line 762 \| Line 781 \| namespace oopse {
781		fInfo_.SIM_uses_FLARB = useFLARB;
782		fInfo_.SIM_uses_RF = useRF;
783		fInfo_.SIM_uses_SF = useSF;
784	<
785	<	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	<
784	>	fInfo_.SIM_uses_SP = useSP;
785	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
786		}
787
788		void SimInfo::setupFortranSim() {
#	Line 793 \| Line 799 \| namespace oopse {
799		}
800
801		//calculate mass ratio of cutoff group
802	<	std::vector<double> mfact;
802	>	std::vector<RealType> mfact;
803		SimInfo::MoleculeIterator mi;
804		Molecule* mol;
805		Molecule::CutoffGroupIterator ci;
806		CutoffGroup* cg;
807		Molecule::AtomIterator ai;
808		Atom* atom;
809	<	double totalMass;
809	>	RealType totalMass;
810
811		//to avoid memory reallocation, reserve enough space for mfact
812		mfact.reserve(getNCutoffGroups());
#	Line 923 \| Line 929 \| namespace oopse {
929
930		#endif
931
932	<	double SimInfo::calcMaxCutoffRadius() {
932	>	void SimInfo::setupCutoff() {
933	>
934	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935
936	<
937	<	std::set<AtomType*> atomTypes;
930	<	std::set<AtomType*>::iterator i;
931	<	std::vector<double> cutoffRadius;
936	>	// Check the cutoff policy
937	>	int cp = TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
938
939	<	//get the unique atom types
940	<	atomTypes = getUniqueAtomTypes();
941	<
942	<	//query the max cutoff radius among these atom types
943	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
938	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939	>	std::string myPolicy;
940	>	if (forceFieldOptions_.haveCutoffPolicy()){
941	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
942	>	}else if (simParams_->haveCutoffPolicy()) {
943	>	myPolicy = simParams_->getCutoffPolicy();
944		}
945
946	<	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();
946	>	if (!myPolicy.empty()){
947		toUpper(myPolicy);
948		if (myPolicy == "MIX") {
949		cp = MIX_CUTOFF_POLICY;
#	Line 1021 \| Line 962 \| namespace oopse {
962		}
963		}
964		}
965	<	}
965	>	}
966	>	notifyFortranCutoffPolicy(&cp);
967
968	<
968	>	// Check the Skin Thickness for neighborlists
969	>	RealType skin;
970		if (simParams_->haveSkinThickness()) {
971	<	double skinThickness = simParams_->getSkinThickness();
972	<	}
971	>	skin = simParams_->getSkinThickness();
972	>	notifyFortranSkinThickness(&skin);
973	>	}
974	>
975	>	// Check if the cutoff was set explicitly:
976	>	if (simParams_->haveCutoffRadius()) {
977	>	rcut_ = simParams_->getCutoffRadius();
978	>	if (simParams_->haveSwitchingRadius()) {
979	>	rsw_ = simParams_->getSwitchingRadius();
980	>	} else {
981	>	if (fInfo_.SIM_uses_Charges \|
982	>	fInfo_.SIM_uses_Dipoles \|
983	>	fInfo_.SIM_uses_RF) {
984	>
985	>	rsw_ = 0.85 * rcut_;
986	>	sprintf(painCave.errMsg,
987	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
988	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
990	>	painCave.isFatal = 0;
991	>	simError();
992	>	} else {
993	>	rsw_ = rcut_;
994	>	sprintf(painCave.errMsg,
995	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
996	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
997	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
998	>	painCave.isFatal = 0;
999	>	simError();
1000	>	}
1001	>	}
1002	>
1003	>	notifyFortranCutoffs(&rcut_, &rsw_);
1004	>
1005	>	} else {
1006	>
1007	>	// For electrostatic atoms, we'll assume a large safe value:
1008	>	if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
1009	>	sprintf(painCave.errMsg,
1010	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1011	>	"\tOOPSE will use a default value of 15.0 angstroms"
1012	>	"\tfor the cutoffRadius.\n");
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	rcut_ = 15.0;
1016	>
1017	>	if (simParams_->haveElectrostaticSummationMethod()) {
1018	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1019	>	toUpper(myMethod);
1020	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
1021	>	if (simParams_->haveSwitchingRadius()){
1022	>	sprintf(painCave.errMsg,
1023	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1024	>	"\teven though the electrostaticSummationMethod was\n"
1025	>	"\tset to %s\n", myMethod.c_str());
1026	>	painCave.isFatal = 1;
1027	>	simError();
1028	>	}
1029	>	}
1030	>	}
1031	>
1032	>	if (simParams_->haveSwitchingRadius()){
1033	>	rsw_ = simParams_->getSwitchingRadius();
1034	>	} else {
1035	>	sprintf(painCave.errMsg,
1036	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1037	>	"\tOOPSE will use a default value of\n"
1038	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1039	>	painCave.isFatal = 0;
1040	>	simError();
1041	>	rsw_ = 0.85 * rcut_;
1042	>	}
1043	>	notifyFortranCutoffs(&rcut_, &rsw_);
1044	>	} else {
1045	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1046	>	// We'll punt and let fortran figure out the cutoffs later.
1047	>
1048	>	notifyFortranYouAreOnYourOwn();
1049
1050	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1051	<	// also send cutoff notification to electrostatics
1033	<	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1050	>	}
1051	>	}
1052		}
1053
1054		void SimInfo::setupElectrostaticSummationMethod( int isError ) {
#	Line 1038 \| Line 1056 \| namespace oopse {
1056		int errorOut;
1057		int esm = NONE;
1058		int sm = UNDAMPED;
1059	<	double alphaVal;
1060	<	double dielectric;
1061	<
1059	>	RealType alphaVal;
1060	>	RealType dielectric;
1061	>
1062		errorOut = isError;
1045	–	alphaVal = simParams_->getDampingAlpha();
1046	–	dielectric = simParams_->getDielectric();
1063
1064		if (simParams_->haveElectrostaticSummationMethod()) {
1065		std::string myMethod = simParams_->getElectrostaticSummationMethod();
#	Line 1060 \| Line 1076 \| namespace oopse {
1076		if (myMethod == "SHIFTED_FORCE") {
1077		esm = SHIFTED_FORCE;
1078		} else {
1079	<	if (myMethod == "REACTION_FIELD") {
1079	>	if (myMethod == "REACTION_FIELD") {
1080		esm = REACTION_FIELD;
1081	+	dielectric = simParams_->getDielectric();
1082	+	if (!simParams_->haveDielectric()) {
1083	+	// throw warning
1084	+	sprintf( painCave.errMsg,
1085	+	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1086	+	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1087	+	painCave.isFatal = 0;
1088	+	simError();
1089	+	}
1090		} else {
1091		// throw error
1092		sprintf( painCave.errMsg,
1093	<	"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() );
1093	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1094	>	"\t(Input file specified %s .)\n"
1095	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1096	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1097	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1098		painCave.isFatal = 1;
1099		simError();
1100		}
#	Line 1084 \| Line 1113 \| namespace oopse {
1113		if (myScreen == "DAMPED") {
1114		sm = DAMPED;
1115		if (!simParams_->haveDampingAlpha()) {
1116	<	//throw error
1116	>	// first set a cutoff dependent alpha value
1117	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1118	>	alphaVal = 0.5125 - rcut_* 0.025;
1119	>	// for values rcut > 20.5, alpha is zero
1120	>	if (alphaVal < 0) alphaVal = 0;
1121	>
1122	>	// throw warning
1123		sprintf( painCave.errMsg,
1124	<	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1124	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1125	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1126		painCave.isFatal = 0;
1127		simError();
1128		}
1129		} else {
1130		// throw error
1131		sprintf( painCave.errMsg,
1132	<	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1132	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1133	>	"\t(Input file specified %s .)\n"
1134	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1135	>	"or \"damped\".\n", myScreen.c_str() );
1136		painCave.isFatal = 1;
1137		simError();
1138		}
#	Line 1102 \| Line 1141 \| namespace oopse {
1141
1142		// let's pass some summation method variables to fortran
1143		setElectrostaticSummationMethod( &esm );
1144	+	setFortranElectrostaticMethod( &esm );
1145		setScreeningMethod( &sm );
1146		setDampingAlpha( &alphaVal );
1147		setReactionFieldDielectric( &dielectric );
1148	<	initFortranFF( &esm, &errorOut );
1148	>	initFortranFF( &errorOut );
1149		}
1150
1151		void SimInfo::setupSwitchingFunction() {
#	Line 1134 \| Line 1174 \| namespace oopse {
1174
1175		}
1176
1177	+	void SimInfo::setupAccumulateBoxDipole() {
1178	+
1179	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1180	+	if ( simParams_->haveAccumulateBoxDipole() )
1181	+	if ( simParams_->getAccumulateBoxDipole() ) {
1182	+	setAccumulateBoxDipole();
1183	+	calcBoxDipole_ = true;
1184	+	}
1185	+
1186	+	}
1187	+
1188		void SimInfo::addProperty(GenericData* genData) {
1189		properties_.addProperty(genData);
1190		}
#	Line 1190 \| Line 1241 \| namespace oopse {
1241		Molecule* mol;
1242
1243		Vector3d comVel(0.0);
1244	<	double totalMass = 0.0;
1244	>	RealType totalMass = 0.0;
1245
1246
1247		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1248	<	double mass = mol->getMass();
1248	>	RealType mass = mol->getMass();
1249		totalMass += mass;
1250		comVel += mass * mol->getComVel();
1251		}
1252
1253		#ifdef IS_MPI
1254	<	double tmpMass = totalMass;
1254	>	RealType tmpMass = totalMass;
1255		Vector3d tmpComVel(comVel);
1256	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1256	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1257	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258		#endif
1259
1260		comVel /= totalMass;
#	Line 1216 \| Line 1267 \| namespace oopse {
1267		Molecule* mol;
1268
1269		Vector3d com(0.0);
1270	<	double totalMass = 0.0;
1270	>	RealType totalMass = 0.0;
1271
1272		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1273	<	double mass = mol->getMass();
1273	>	RealType mass = mol->getMass();
1274		totalMass += mass;
1275		com += mass * mol->getCom();
1276		}
1277
1278		#ifdef IS_MPI
1279	<	double tmpMass = totalMass;
1279	>	RealType tmpMass = totalMass;
1280		Vector3d tmpCom(com);
1281	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1282	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1281	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1282	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1283		#endif
1284
1285		com /= totalMass;
#	Line 1252 \| Line 1303 \| namespace oopse {
1303		Molecule* mol;
1304
1305
1306	<	double totalMass = 0.0;
1306	>	RealType totalMass = 0.0;
1307
1308
1309		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1310	<	double mass = mol->getMass();
1310	>	RealType mass = mol->getMass();
1311		totalMass += mass;
1312		com += mass * mol->getCom();
1313		comVel += mass * mol->getComVel();
1314		}
1315
1316		#ifdef IS_MPI
1317	<	double tmpMass = totalMass;
1317	>	RealType tmpMass = totalMass;
1318		Vector3d tmpCom(com);
1319		Vector3d tmpComVel(comVel);
1320	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1321	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1322	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1320	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1321	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323		#endif
1324
1325		com /= totalMass;
#	Line 1287 \| Line 1338 \| namespace oopse {
1338		void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1339
1340
1341	<	double xx = 0.0;
1342	<	double yy = 0.0;
1343	<	double zz = 0.0;
1344	<	double xy = 0.0;
1345	<	double xz = 0.0;
1346	<	double yz = 0.0;
1341	>	RealType xx = 0.0;
1342	>	RealType yy = 0.0;
1343	>	RealType zz = 0.0;
1344	>	RealType xy = 0.0;
1345	>	RealType xz = 0.0;
1346	>	RealType yz = 0.0;
1347		Vector3d com(0.0);
1348		Vector3d comVel(0.0);
1349
#	Line 1304 \| Line 1355 \| namespace oopse {
1355		Vector3d thisq(0.0);
1356		Vector3d thisv(0.0);
1357
1358	<	double thisMass = 0.0;
1358	>	RealType thisMass = 0.0;
1359
1360
1361
#	Line 1342 \| Line 1393 \| namespace oopse {
1393		#ifdef IS_MPI
1394		Mat3x3d tmpI(inertiaTensor);
1395		Vector3d tmpAngMom;
1396	<	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1397	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1396	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1397	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398		#endif
1399
1400		return;
#	Line 1364 \| Line 1415 \| namespace oopse {
1415		Vector3d thisr(0.0);
1416		Vector3d thisp(0.0);
1417
1418	<	double thisMass;
1418	>	RealType thisMass;
1419
1420		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1421		thisMass = mol->getMass();
#	Line 1377 \| Line 1428 \| namespace oopse {
1428
1429		#ifdef IS_MPI
1430		Vector3d tmpAngMom;
1431	<	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1431	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1432		#endif
1433
1434		return angularMomentum;
1435		}
1436
1437	<
1437	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1438	>	return IOIndexToIntegrableObject.at(index);
1439	>	}
1440	>
1441	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1442	>	IOIndexToIntegrableObject= v;
1443	>	}
1444	>
1445	>	/*
1446	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1447	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1448	>	sdByGlobalIndex_ = v;
1449	>	}
1450	>
1451	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1452	>	//assert(index < nAtoms_ + nRigidBodies_);
1453	>	return sdByGlobalIndex_.at(index);
1454	>	}
1455	>	*/
1456		}//end namespace oopse
1457

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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 1050 by chrisfen, Fri Sep 22 22:19:59 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 1050 by chrisfen, Fri Sep 22 22:19:59 2006 UTC