52 |
|
#include "brains/SimInfo.hpp" |
53 |
|
#include "math/Vector3.hpp" |
54 |
|
#include "primitives/Molecule.hpp" |
55 |
+ |
#include "UseTheForce/fCutoffPolicy.h" |
56 |
+ |
#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
57 |
+ |
#include "UseTheForce/DarkSide/fScreeningMethod.h" |
58 |
|
#include "UseTheForce/doForces_interface.h" |
59 |
+ |
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
60 |
|
#include "UseTheForce/notifyCutoffs_interface.h" |
61 |
|
#include "utils/MemoryUtils.hpp" |
62 |
|
#include "utils/simError.h" |
84 |
|
MoleculeStamp* molStamp; |
85 |
|
int nMolWithSameStamp; |
86 |
|
int nCutoffAtoms = 0; // number of atoms belong to cutoff groups |
87 |
< |
int nGroups = 0; //total cutoff groups defined in meta-data file |
87 |
> |
int nGroups = 0; //total cutoff groups defined in meta-data file |
88 |
|
CutoffGroupStamp* cgStamp; |
89 |
|
RigidBodyStamp* rbStamp; |
90 |
|
int nRigidAtoms = 0; |
109 |
|
} |
110 |
|
|
111 |
|
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
112 |
+ |
|
113 |
|
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
114 |
|
|
115 |
|
//calculate atoms in rigid bodies |
126 |
|
|
127 |
|
} |
128 |
|
|
129 |
< |
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
130 |
< |
//therefore the total number of cutoff groups in the system is equal to |
131 |
< |
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
132 |
< |
//file plus the number of cutoff groups defined in meta-data file |
129 |
> |
//every free atom (atom does not belong to cutoff groups) is a cutoff |
130 |
> |
//group therefore the total number of cutoff groups in the system is |
131 |
> |
//equal to the total number of atoms minus number of atoms belong to |
132 |
> |
//cutoff group defined in meta-data file plus the number of cutoff |
133 |
> |
//groups defined in meta-data file |
134 |
|
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
135 |
|
|
136 |
< |
//every free atom (atom does not belong to rigid bodies) is an integrable object |
137 |
< |
//therefore the total number of integrable objects in the system is equal to |
138 |
< |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
139 |
< |
//file plus the number of rigid bodies defined in meta-data file |
140 |
< |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
141 |
< |
|
136 |
> |
//every free atom (atom does not belong to rigid bodies) is an |
137 |
> |
//integrable object therefore the total number of integrable objects |
138 |
> |
//in the system is equal to the total number of atoms minus number of |
139 |
> |
//atoms belong to rigid body defined in meta-data file plus the number |
140 |
> |
//of rigid bodies defined in meta-data file |
141 |
> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms |
142 |
> |
+ nGlobalRigidBodies_; |
143 |
> |
|
144 |
|
nGlobalMols_ = molStampIds_.size(); |
145 |
|
|
146 |
|
#ifdef IS_MPI |
470 |
|
//setup fortran force field |
471 |
|
/** @deprecate */ |
472 |
|
int isError = 0; |
473 |
< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
473 |
> |
|
474 |
> |
setupElectrostaticSummationMethod( isError ); |
475 |
> |
|
476 |
|
if(isError){ |
477 |
|
sprintf( painCave.errMsg, |
478 |
|
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
521 |
|
int useDipole = 0; |
522 |
|
int useGayBerne = 0; |
523 |
|
int useSticky = 0; |
524 |
+ |
int useStickyPower = 0; |
525 |
|
int useShape = 0; |
526 |
|
int useFLARB = 0; //it is not in AtomType yet |
527 |
|
int useDirectionalAtom = 0; |
528 |
|
int useElectrostatics = 0; |
529 |
|
//usePBC and useRF are from simParams |
530 |
< |
int usePBC = simParams_->getPBC(); |
531 |
< |
int useRF = simParams_->getUseRF(); |
530 |
> |
int usePBC = simParams_->getUsePeriodicBoundaryConditions(); |
531 |
> |
int useRF; |
532 |
> |
int useDW; |
533 |
> |
std::string myMethod; |
534 |
> |
|
535 |
> |
// set the useRF logical |
536 |
> |
useRF = 0; |
537 |
> |
useDW = 0; |
538 |
> |
|
539 |
|
|
540 |
+ |
if (simParams_->haveElectrostaticSummationMethod()) { |
541 |
+ |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
542 |
+ |
toUpper(myMethod); |
543 |
+ |
if (myMethod == "REACTION_FIELD") { |
544 |
+ |
useRF=1; |
545 |
+ |
} else { |
546 |
+ |
if (myMethod == "SHIFTED_POTENTIAL") { |
547 |
+ |
useDW = 1; |
548 |
+ |
} |
549 |
+ |
} |
550 |
+ |
} |
551 |
+ |
|
552 |
|
//loop over all of the atom types |
553 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
554 |
|
useLennardJones |= (*i)->isLennardJones(); |
559 |
|
useDipole |= (*i)->isDipole(); |
560 |
|
useGayBerne |= (*i)->isGayBerne(); |
561 |
|
useSticky |= (*i)->isSticky(); |
562 |
+ |
useStickyPower |= (*i)->isStickyPower(); |
563 |
|
useShape |= (*i)->isShape(); |
564 |
|
} |
565 |
|
|
566 |
< |
if (useSticky || useDipole || useGayBerne || useShape) { |
566 |
> |
if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { |
567 |
|
useDirectionalAtom = 1; |
568 |
|
} |
569 |
|
|
595 |
|
temp = useSticky; |
596 |
|
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
597 |
|
|
598 |
+ |
temp = useStickyPower; |
599 |
+ |
MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
600 |
+ |
|
601 |
|
temp = useGayBerne; |
602 |
|
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
603 |
|
|
612 |
|
|
613 |
|
temp = useRF; |
614 |
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
615 |
< |
|
615 |
> |
|
616 |
> |
temp = useDW; |
617 |
> |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
618 |
> |
|
619 |
|
#endif |
620 |
|
|
621 |
|
fInfo_.SIM_uses_PBC = usePBC; |
625 |
|
fInfo_.SIM_uses_Charges = useCharge; |
626 |
|
fInfo_.SIM_uses_Dipoles = useDipole; |
627 |
|
fInfo_.SIM_uses_Sticky = useSticky; |
628 |
+ |
fInfo_.SIM_uses_StickyPower = useStickyPower; |
629 |
|
fInfo_.SIM_uses_GayBerne = useGayBerne; |
630 |
|
fInfo_.SIM_uses_EAM = useEAM; |
631 |
|
fInfo_.SIM_uses_Shapes = useShape; |
632 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
633 |
|
fInfo_.SIM_uses_RF = useRF; |
634 |
+ |
fInfo_.SIM_uses_DampedWolf = useDW; |
635 |
|
|
636 |
< |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
637 |
< |
|
636 |
> |
if( myMethod == "REACTION_FIELD") { |
637 |
> |
|
638 |
|
if (simParams_->haveDielectric()) { |
639 |
|
fInfo_.dielect = simParams_->getDielectric(); |
640 |
|
} else { |
644 |
|
"\tsetting a dielectric constant!\n"); |
645 |
|
painCave.isFatal = 1; |
646 |
|
simError(); |
647 |
< |
} |
609 |
< |
|
610 |
< |
} else { |
611 |
< |
fInfo_.dielect = 0.0; |
647 |
> |
} |
648 |
|
} |
649 |
|
|
650 |
|
} |
680 |
|
|
681 |
|
totalMass = cg->getMass(); |
682 |
|
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
683 |
< |
mfact.push_back(atom->getMass()/totalMass); |
683 |
> |
// Check for massless groups - set mfact to 1 if true |
684 |
> |
if (totalMass != 0) |
685 |
> |
mfact.push_back(atom->getMass()/totalMass); |
686 |
> |
else |
687 |
> |
mfact.push_back( 1.0 ); |
688 |
|
} |
689 |
|
|
690 |
|
} |
820 |
|
|
821 |
|
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
822 |
|
|
823 |
< |
if (!simParams_->haveRcut()){ |
823 |
> |
if (!simParams_->haveCutoffRadius()){ |
824 |
|
sprintf(painCave.errMsg, |
825 |
|
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
826 |
|
"\tOOPSE will use a default value of 15.0 angstroms" |
829 |
|
simError(); |
830 |
|
rcut = 15.0; |
831 |
|
} else{ |
832 |
< |
rcut = simParams_->getRcut(); |
832 |
> |
rcut = simParams_->getCutoffRadius(); |
833 |
|
} |
834 |
|
|
835 |
< |
if (!simParams_->haveRsw()){ |
835 |
> |
if (!simParams_->haveSwitchingRadius()){ |
836 |
|
sprintf(painCave.errMsg, |
837 |
|
"SimCreator Warning: No value was set for switchingRadius.\n" |
838 |
|
"\tOOPSE will use a default value of\n" |
839 |
< |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
839 |
> |
"\t0.85 * cutoffRadius for the switchingRadius\n"); |
840 |
|
painCave.isFatal = 0; |
841 |
|
simError(); |
842 |
< |
rsw = 0.95 * rcut; |
842 |
> |
rsw = 0.85 * rcut; |
843 |
|
} else{ |
844 |
< |
rsw = simParams_->getRsw(); |
844 |
> |
rsw = simParams_->getSwitchingRadius(); |
845 |
|
} |
846 |
|
|
847 |
|
} else { |
848 |
|
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
849 |
|
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
850 |
|
|
851 |
< |
if (simParams_->haveRcut()) { |
852 |
< |
rcut = simParams_->getRcut(); |
851 |
> |
if (simParams_->haveCutoffRadius()) { |
852 |
> |
rcut = simParams_->getCutoffRadius(); |
853 |
|
} else { |
854 |
|
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
855 |
|
rcut = calcMaxCutoffRadius(); |
856 |
|
} |
857 |
|
|
858 |
< |
if (simParams_->haveRsw()) { |
859 |
< |
rsw = simParams_->getRsw(); |
858 |
> |
if (simParams_->haveSwitchingRadius()) { |
859 |
> |
rsw = simParams_->getSwitchingRadius(); |
860 |
|
} else { |
861 |
|
rsw = rcut; |
862 |
|
} |
864 |
|
} |
865 |
|
} |
866 |
|
|
867 |
< |
void SimInfo::setupCutoff() { |
867 |
> |
void SimInfo::setupCutoff() { |
868 |
|
getCutoff(rcut_, rsw_); |
869 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
870 |
|
|
871 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
872 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
872 |
> |
|
873 |
> |
int cp = TRADITIONAL_CUTOFF_POLICY; |
874 |
> |
if (simParams_->haveCutoffPolicy()) { |
875 |
> |
std::string myPolicy = simParams_->getCutoffPolicy(); |
876 |
> |
toUpper(myPolicy); |
877 |
> |
if (myPolicy == "MIX") { |
878 |
> |
cp = MIX_CUTOFF_POLICY; |
879 |
> |
} else { |
880 |
> |
if (myPolicy == "MAX") { |
881 |
> |
cp = MAX_CUTOFF_POLICY; |
882 |
> |
} else { |
883 |
> |
if (myPolicy == "TRADITIONAL") { |
884 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
885 |
> |
} else { |
886 |
> |
// throw error |
887 |
> |
sprintf( painCave.errMsg, |
888 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
889 |
> |
painCave.isFatal = 1; |
890 |
> |
simError(); |
891 |
> |
} |
892 |
> |
} |
893 |
> |
} |
894 |
> |
} |
895 |
> |
|
896 |
> |
|
897 |
> |
if (simParams_->haveSkinThickness()) { |
898 |
> |
double skinThickness = simParams_->getSkinThickness(); |
899 |
> |
} |
900 |
> |
|
901 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
902 |
> |
// also send cutoff notification to electrostatics |
903 |
> |
setElectrostaticCutoffRadius(&rcut_, &rsw_); |
904 |
|
} |
905 |
|
|
906 |
+ |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
907 |
+ |
|
908 |
+ |
int errorOut; |
909 |
+ |
int esm = NONE; |
910 |
+ |
int sm = UNDAMPED; |
911 |
+ |
double alphaVal; |
912 |
+ |
double dielectric; |
913 |
+ |
|
914 |
+ |
errorOut = isError; |
915 |
+ |
alphaVal = simParams_->getDampingAlpha(); |
916 |
+ |
dielectric = simParams_->getDielectric(); |
917 |
+ |
|
918 |
+ |
if (simParams_->haveElectrostaticSummationMethod()) { |
919 |
+ |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
920 |
+ |
toUpper(myMethod); |
921 |
+ |
if (myMethod == "NONE") { |
922 |
+ |
esm = NONE; |
923 |
+ |
} else { |
924 |
+ |
if (myMethod == "SWITCHING_FUNCTION") { |
925 |
+ |
esm = SWITCHING_FUNCTION; |
926 |
+ |
} else { |
927 |
+ |
if (myMethod == "SHIFTED_POTENTIAL") { |
928 |
+ |
esm = SHIFTED_POTENTIAL; |
929 |
+ |
} else { |
930 |
+ |
if (myMethod == "SHIFTED_FORCE") { |
931 |
+ |
esm = SHIFTED_FORCE; |
932 |
+ |
} else { |
933 |
+ |
if (myMethod == "REACTION_FIELD") { |
934 |
+ |
esm = REACTION_FIELD; |
935 |
+ |
} else { |
936 |
+ |
// throw error |
937 |
+ |
sprintf( painCave.errMsg, |
938 |
+ |
"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() ); |
939 |
+ |
painCave.isFatal = 1; |
940 |
+ |
simError(); |
941 |
+ |
} |
942 |
+ |
} |
943 |
+ |
} |
944 |
+ |
} |
945 |
+ |
} |
946 |
+ |
} |
947 |
+ |
|
948 |
+ |
if (simParams_->haveScreeningMethod()) { |
949 |
+ |
std::string myScreen = simParams_->getScreeningMethod(); |
950 |
+ |
toUpper(myScreen); |
951 |
+ |
if (myScreen == "UNDAMPED") { |
952 |
+ |
sm = UNDAMPED; |
953 |
+ |
} else { |
954 |
+ |
if (myScreen == "DAMPED") { |
955 |
+ |
sm = DAMPED; |
956 |
+ |
if (!simParams_->haveDampingAlpha()) { |
957 |
+ |
//throw error |
958 |
+ |
sprintf( painCave.errMsg, |
959 |
+ |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal); |
960 |
+ |
painCave.isFatal = 0; |
961 |
+ |
simError(); |
962 |
+ |
} else { |
963 |
+ |
// throw error |
964 |
+ |
sprintf( painCave.errMsg, |
965 |
+ |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() ); |
966 |
+ |
painCave.isFatal = 1; |
967 |
+ |
simError(); |
968 |
+ |
} |
969 |
+ |
} |
970 |
+ |
} |
971 |
+ |
} |
972 |
+ |
// let's pass some summation method variables to fortran |
973 |
+ |
setElectrostaticSummationMethod( &esm ); |
974 |
+ |
setScreeningMethod( &sm ); |
975 |
+ |
setDampingAlpha( &alphaVal ); |
976 |
+ |
setReactionFieldDielectric( &dielectric ); |
977 |
+ |
initFortranFF( &esm, &errorOut ); |
978 |
+ |
} |
979 |
+ |
|
980 |
|
void SimInfo::addProperty(GenericData* genData) { |
981 |
|
properties_.addProperty(genData); |
982 |
|
} |
1084 |
|
|
1085 |
|
return o; |
1086 |
|
} |
1087 |
+ |
|
1088 |
+ |
|
1089 |
+ |
/* |
1090 |
+ |
Returns center of mass and center of mass velocity in one function call. |
1091 |
+ |
*/ |
1092 |
+ |
|
1093 |
+ |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1094 |
+ |
SimInfo::MoleculeIterator i; |
1095 |
+ |
Molecule* mol; |
1096 |
+ |
|
1097 |
+ |
|
1098 |
+ |
double totalMass = 0.0; |
1099 |
+ |
|
1100 |
|
|
1101 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1102 |
+ |
double mass = mol->getMass(); |
1103 |
+ |
totalMass += mass; |
1104 |
+ |
com += mass * mol->getCom(); |
1105 |
+ |
comVel += mass * mol->getComVel(); |
1106 |
+ |
} |
1107 |
+ |
|
1108 |
+ |
#ifdef IS_MPI |
1109 |
+ |
double tmpMass = totalMass; |
1110 |
+ |
Vector3d tmpCom(com); |
1111 |
+ |
Vector3d tmpComVel(comVel); |
1112 |
+ |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1113 |
+ |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1114 |
+ |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1115 |
+ |
#endif |
1116 |
+ |
|
1117 |
+ |
com /= totalMass; |
1118 |
+ |
comVel /= totalMass; |
1119 |
+ |
} |
1120 |
+ |
|
1121 |
+ |
/* |
1122 |
+ |
Return intertia tensor for entire system and angular momentum Vector. |
1123 |
+ |
|
1124 |
+ |
|
1125 |
+ |
[ Ixx -Ixy -Ixz ] |
1126 |
+ |
J =| -Iyx Iyy -Iyz | |
1127 |
+ |
[ -Izx -Iyz Izz ] |
1128 |
+ |
*/ |
1129 |
+ |
|
1130 |
+ |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1131 |
+ |
|
1132 |
+ |
|
1133 |
+ |
double xx = 0.0; |
1134 |
+ |
double yy = 0.0; |
1135 |
+ |
double zz = 0.0; |
1136 |
+ |
double xy = 0.0; |
1137 |
+ |
double xz = 0.0; |
1138 |
+ |
double yz = 0.0; |
1139 |
+ |
Vector3d com(0.0); |
1140 |
+ |
Vector3d comVel(0.0); |
1141 |
+ |
|
1142 |
+ |
getComAll(com, comVel); |
1143 |
+ |
|
1144 |
+ |
SimInfo::MoleculeIterator i; |
1145 |
+ |
Molecule* mol; |
1146 |
+ |
|
1147 |
+ |
Vector3d thisq(0.0); |
1148 |
+ |
Vector3d thisv(0.0); |
1149 |
+ |
|
1150 |
+ |
double thisMass = 0.0; |
1151 |
+ |
|
1152 |
+ |
|
1153 |
+ |
|
1154 |
+ |
|
1155 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1156 |
+ |
|
1157 |
+ |
thisq = mol->getCom()-com; |
1158 |
+ |
thisv = mol->getComVel()-comVel; |
1159 |
+ |
thisMass = mol->getMass(); |
1160 |
+ |
// Compute moment of intertia coefficients. |
1161 |
+ |
xx += thisq[0]*thisq[0]*thisMass; |
1162 |
+ |
yy += thisq[1]*thisq[1]*thisMass; |
1163 |
+ |
zz += thisq[2]*thisq[2]*thisMass; |
1164 |
+ |
|
1165 |
+ |
// compute products of intertia |
1166 |
+ |
xy += thisq[0]*thisq[1]*thisMass; |
1167 |
+ |
xz += thisq[0]*thisq[2]*thisMass; |
1168 |
+ |
yz += thisq[1]*thisq[2]*thisMass; |
1169 |
+ |
|
1170 |
+ |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1171 |
+ |
|
1172 |
+ |
} |
1173 |
+ |
|
1174 |
+ |
|
1175 |
+ |
inertiaTensor(0,0) = yy + zz; |
1176 |
+ |
inertiaTensor(0,1) = -xy; |
1177 |
+ |
inertiaTensor(0,2) = -xz; |
1178 |
+ |
inertiaTensor(1,0) = -xy; |
1179 |
+ |
inertiaTensor(1,1) = xx + zz; |
1180 |
+ |
inertiaTensor(1,2) = -yz; |
1181 |
+ |
inertiaTensor(2,0) = -xz; |
1182 |
+ |
inertiaTensor(2,1) = -yz; |
1183 |
+ |
inertiaTensor(2,2) = xx + yy; |
1184 |
+ |
|
1185 |
+ |
#ifdef IS_MPI |
1186 |
+ |
Mat3x3d tmpI(inertiaTensor); |
1187 |
+ |
Vector3d tmpAngMom; |
1188 |
+ |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1189 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1190 |
+ |
#endif |
1191 |
+ |
|
1192 |
+ |
return; |
1193 |
+ |
} |
1194 |
+ |
|
1195 |
+ |
//Returns the angular momentum of the system |
1196 |
+ |
Vector3d SimInfo::getAngularMomentum(){ |
1197 |
+ |
|
1198 |
+ |
Vector3d com(0.0); |
1199 |
+ |
Vector3d comVel(0.0); |
1200 |
+ |
Vector3d angularMomentum(0.0); |
1201 |
+ |
|
1202 |
+ |
getComAll(com,comVel); |
1203 |
+ |
|
1204 |
+ |
SimInfo::MoleculeIterator i; |
1205 |
+ |
Molecule* mol; |
1206 |
+ |
|
1207 |
+ |
Vector3d thisr(0.0); |
1208 |
+ |
Vector3d thisp(0.0); |
1209 |
+ |
|
1210 |
+ |
double thisMass; |
1211 |
+ |
|
1212 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1213 |
+ |
thisMass = mol->getMass(); |
1214 |
+ |
thisr = mol->getCom()-com; |
1215 |
+ |
thisp = (mol->getComVel()-comVel)*thisMass; |
1216 |
+ |
|
1217 |
+ |
angularMomentum += cross( thisr, thisp ); |
1218 |
+ |
|
1219 |
+ |
} |
1220 |
+ |
|
1221 |
+ |
#ifdef IS_MPI |
1222 |
+ |
Vector3d tmpAngMom; |
1223 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1224 |
+ |
#endif |
1225 |
+ |
|
1226 |
+ |
return angularMomentum; |
1227 |
+ |
} |
1228 |
+ |
|
1229 |
+ |
|
1230 |
|
}//end namespace oopse |
1231 |
|
|