52 |
|
#include "brains/SimInfo.hpp" |
53 |
|
#include "math/Vector3.hpp" |
54 |
|
#include "primitives/Molecule.hpp" |
55 |
+ |
#include "UseTheForce/fCutoffPolicy.h" |
56 |
|
#include "UseTheForce/doForces_interface.h" |
57 |
|
#include "UseTheForce/notifyCutoffs_interface.h" |
58 |
|
#include "utils/MemoryUtils.hpp" |
463 |
|
//setup fortran force field |
464 |
|
/** @deprecate */ |
465 |
|
int isError = 0; |
466 |
< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
466 |
> |
initFortranFF( &fInfo_.SIM_uses_RF, &fInfo_.SIM_uses_UW, |
467 |
> |
&fInfo_.SIM_uses_DW, &isError ); |
468 |
|
if(isError){ |
469 |
|
sprintf( painCave.errMsg, |
470 |
|
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
521 |
|
//usePBC and useRF are from simParams |
522 |
|
int usePBC = simParams_->getPBC(); |
523 |
|
int useRF = simParams_->getUseRF(); |
524 |
+ |
int useUW = simParams_->getUseUndampedWolf(); |
525 |
+ |
int useDW = simParams_->getUseDampedWolf(); |
526 |
|
|
527 |
|
//loop over all of the atom types |
528 |
|
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
587 |
|
|
588 |
|
temp = useRF; |
589 |
|
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
590 |
+ |
|
591 |
+ |
temp = useUW; |
592 |
+ |
MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
593 |
+ |
|
594 |
+ |
temp = useDW; |
595 |
+ |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
596 |
|
|
597 |
|
#endif |
598 |
|
|
609 |
|
fInfo_.SIM_uses_Shapes = useShape; |
610 |
|
fInfo_.SIM_uses_FLARB = useFLARB; |
611 |
|
fInfo_.SIM_uses_RF = useRF; |
612 |
+ |
fInfo_.SIM_uses_UW = useUW; |
613 |
+ |
fInfo_.SIM_uses_DW = useDW; |
614 |
|
|
615 |
|
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
616 |
|
|
842 |
|
} |
843 |
|
} |
844 |
|
|
845 |
< |
void SimInfo::setupCutoff() { |
845 |
> |
void SimInfo::setupCutoff() { |
846 |
|
getCutoff(rcut_, rsw_); |
847 |
|
double rnblist = rcut_ + 1; // skin of neighbor list |
848 |
|
|
849 |
|
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
850 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
850 |
> |
|
851 |
> |
int cp = TRADITIONAL_CUTOFF_POLICY; |
852 |
> |
if (simParams_->haveCutoffPolicy()) { |
853 |
> |
std::string myPolicy = simParams_->getCutoffPolicy(); |
854 |
> |
if (myPolicy == "MIX") { |
855 |
> |
cp = MIX_CUTOFF_POLICY; |
856 |
> |
} else { |
857 |
> |
if (myPolicy == "MAX") { |
858 |
> |
cp = MAX_CUTOFF_POLICY; |
859 |
> |
} else { |
860 |
> |
if (myPolicy == "TRADITIONAL") { |
861 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
862 |
> |
} else { |
863 |
> |
// throw error |
864 |
> |
sprintf( painCave.errMsg, |
865 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
866 |
> |
painCave.isFatal = 1; |
867 |
> |
simError(); |
868 |
> |
} |
869 |
> |
} |
870 |
> |
} |
871 |
> |
} |
872 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
873 |
|
} |
874 |
|
|
875 |
|
void SimInfo::addProperty(GenericData* genData) { |
979 |
|
|
980 |
|
return o; |
981 |
|
} |
982 |
+ |
|
983 |
+ |
|
984 |
+ |
/* |
985 |
+ |
Returns center of mass and center of mass velocity in one function call. |
986 |
+ |
*/ |
987 |
+ |
|
988 |
+ |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
989 |
+ |
SimInfo::MoleculeIterator i; |
990 |
+ |
Molecule* mol; |
991 |
+ |
|
992 |
+ |
|
993 |
+ |
double totalMass = 0.0; |
994 |
+ |
|
995 |
+ |
|
996 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
997 |
+ |
double mass = mol->getMass(); |
998 |
+ |
totalMass += mass; |
999 |
+ |
com += mass * mol->getCom(); |
1000 |
+ |
comVel += mass * mol->getComVel(); |
1001 |
+ |
} |
1002 |
+ |
|
1003 |
+ |
#ifdef IS_MPI |
1004 |
+ |
double tmpMass = totalMass; |
1005 |
+ |
Vector3d tmpCom(com); |
1006 |
+ |
Vector3d tmpComVel(comVel); |
1007 |
+ |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1008 |
+ |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1009 |
+ |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1010 |
+ |
#endif |
1011 |
+ |
|
1012 |
+ |
com /= totalMass; |
1013 |
+ |
comVel /= totalMass; |
1014 |
+ |
} |
1015 |
+ |
|
1016 |
+ |
/* |
1017 |
+ |
Return intertia tensor for entire system and angular momentum Vector. |
1018 |
+ |
|
1019 |
+ |
|
1020 |
+ |
[ Ixx -Ixy -Ixz ] |
1021 |
+ |
J =| -Iyx Iyy -Iyz | |
1022 |
+ |
[ -Izx -Iyz Izz ] |
1023 |
+ |
*/ |
1024 |
+ |
|
1025 |
+ |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1026 |
+ |
|
1027 |
+ |
|
1028 |
+ |
double xx = 0.0; |
1029 |
+ |
double yy = 0.0; |
1030 |
+ |
double zz = 0.0; |
1031 |
+ |
double xy = 0.0; |
1032 |
+ |
double xz = 0.0; |
1033 |
+ |
double yz = 0.0; |
1034 |
+ |
Vector3d com(0.0); |
1035 |
+ |
Vector3d comVel(0.0); |
1036 |
+ |
|
1037 |
+ |
getComAll(com, comVel); |
1038 |
+ |
|
1039 |
+ |
SimInfo::MoleculeIterator i; |
1040 |
+ |
Molecule* mol; |
1041 |
+ |
|
1042 |
+ |
Vector3d thisq(0.0); |
1043 |
+ |
Vector3d thisv(0.0); |
1044 |
|
|
1045 |
+ |
double thisMass = 0.0; |
1046 |
+ |
|
1047 |
+ |
|
1048 |
+ |
|
1049 |
+ |
|
1050 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1051 |
+ |
|
1052 |
+ |
thisq = mol->getCom()-com; |
1053 |
+ |
thisv = mol->getComVel()-comVel; |
1054 |
+ |
thisMass = mol->getMass(); |
1055 |
+ |
// Compute moment of intertia coefficients. |
1056 |
+ |
xx += thisq[0]*thisq[0]*thisMass; |
1057 |
+ |
yy += thisq[1]*thisq[1]*thisMass; |
1058 |
+ |
zz += thisq[2]*thisq[2]*thisMass; |
1059 |
+ |
|
1060 |
+ |
// compute products of intertia |
1061 |
+ |
xy += thisq[0]*thisq[1]*thisMass; |
1062 |
+ |
xz += thisq[0]*thisq[2]*thisMass; |
1063 |
+ |
yz += thisq[1]*thisq[2]*thisMass; |
1064 |
+ |
|
1065 |
+ |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1066 |
+ |
|
1067 |
+ |
} |
1068 |
+ |
|
1069 |
+ |
|
1070 |
+ |
inertiaTensor(0,0) = yy + zz; |
1071 |
+ |
inertiaTensor(0,1) = -xy; |
1072 |
+ |
inertiaTensor(0,2) = -xz; |
1073 |
+ |
inertiaTensor(1,0) = -xy; |
1074 |
+ |
inertiaTensor(1,1) = xx + zz; |
1075 |
+ |
inertiaTensor(1,2) = -yz; |
1076 |
+ |
inertiaTensor(2,0) = -xz; |
1077 |
+ |
inertiaTensor(2,1) = -yz; |
1078 |
+ |
inertiaTensor(2,2) = xx + yy; |
1079 |
+ |
|
1080 |
+ |
#ifdef IS_MPI |
1081 |
+ |
Mat3x3d tmpI(inertiaTensor); |
1082 |
+ |
Vector3d tmpAngMom; |
1083 |
+ |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1084 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1085 |
+ |
#endif |
1086 |
+ |
|
1087 |
+ |
return; |
1088 |
+ |
} |
1089 |
+ |
|
1090 |
+ |
//Returns the angular momentum of the system |
1091 |
+ |
Vector3d SimInfo::getAngularMomentum(){ |
1092 |
+ |
|
1093 |
+ |
Vector3d com(0.0); |
1094 |
+ |
Vector3d comVel(0.0); |
1095 |
+ |
Vector3d angularMomentum(0.0); |
1096 |
+ |
|
1097 |
+ |
getComAll(com,comVel); |
1098 |
+ |
|
1099 |
+ |
SimInfo::MoleculeIterator i; |
1100 |
+ |
Molecule* mol; |
1101 |
+ |
|
1102 |
+ |
Vector3d thisr(0.0); |
1103 |
+ |
Vector3d thisp(0.0); |
1104 |
+ |
|
1105 |
+ |
double thisMass; |
1106 |
+ |
|
1107 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1108 |
+ |
thisMass = mol->getMass(); |
1109 |
+ |
thisr = mol->getCom()-com; |
1110 |
+ |
thisp = (mol->getComVel()-comVel)*thisMass; |
1111 |
+ |
|
1112 |
+ |
angularMomentum += cross( thisr, thisp ); |
1113 |
+ |
|
1114 |
+ |
} |
1115 |
+ |
|
1116 |
+ |
#ifdef IS_MPI |
1117 |
+ |
Vector3d tmpAngMom; |
1118 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1119 |
+ |
#endif |
1120 |
+ |
|
1121 |
+ |
return angularMomentum; |
1122 |
+ |
} |
1123 |
+ |
|
1124 |
+ |
|
1125 |
|
}//end namespace oopse |
1126 |
|
|