52 |
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#include "brains/SimInfo.hpp" |
53 |
|
#include "math/Vector3.hpp" |
54 |
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#include "primitives/Molecule.hpp" |
55 |
+ |
#include "UseTheForce/fCutoffPolicy.h" |
56 |
+ |
#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
57 |
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#include "UseTheForce/doForces_interface.h" |
58 |
+ |
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
59 |
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#include "UseTheForce/notifyCutoffs_interface.h" |
60 |
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#include "utils/MemoryUtils.hpp" |
61 |
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#include "utils/simError.h" |
465 |
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//setup fortran force field |
466 |
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/** @deprecate */ |
467 |
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int isError = 0; |
468 |
< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
468 |
> |
|
469 |
> |
setupElectrostaticSummationMethod( isError ); |
470 |
> |
|
471 |
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if(isError){ |
472 |
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sprintf( painCave.errMsg, |
473 |
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"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
516 |
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int useDipole = 0; |
517 |
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int useGayBerne = 0; |
518 |
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int useSticky = 0; |
519 |
+ |
int useStickyPower = 0; |
520 |
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int useShape = 0; |
521 |
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int useFLARB = 0; //it is not in AtomType yet |
522 |
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int useDirectionalAtom = 0; |
523 |
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int useElectrostatics = 0; |
524 |
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//usePBC and useRF are from simParams |
525 |
|
int usePBC = simParams_->getPBC(); |
520 |
– |
int useRF = simParams_->getUseRF(); |
526 |
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|
527 |
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//loop over all of the atom types |
528 |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
534 |
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useDipole |= (*i)->isDipole(); |
535 |
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useGayBerne |= (*i)->isGayBerne(); |
536 |
|
useSticky |= (*i)->isSticky(); |
537 |
+ |
useStickyPower |= (*i)->isStickyPower(); |
538 |
|
useShape |= (*i)->isShape(); |
539 |
|
} |
540 |
|
|
541 |
< |
if (useSticky || useDipole || useGayBerne || useShape) { |
541 |
> |
if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { |
542 |
|
useDirectionalAtom = 1; |
543 |
|
} |
544 |
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|
570 |
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temp = useSticky; |
571 |
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MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
572 |
|
|
573 |
+ |
temp = useStickyPower; |
574 |
+ |
MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
575 |
+ |
|
576 |
|
temp = useGayBerne; |
577 |
|
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
578 |
|
|
585 |
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temp = useFLARB; |
586 |
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MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
587 |
|
|
579 |
– |
temp = useRF; |
580 |
– |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
581 |
– |
|
588 |
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#endif |
589 |
|
|
590 |
|
fInfo_.SIM_uses_PBC = usePBC; |
594 |
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fInfo_.SIM_uses_Charges = useCharge; |
595 |
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fInfo_.SIM_uses_Dipoles = useDipole; |
596 |
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fInfo_.SIM_uses_Sticky = useSticky; |
597 |
+ |
fInfo_.SIM_uses_StickyPower = useStickyPower; |
598 |
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fInfo_.SIM_uses_GayBerne = useGayBerne; |
599 |
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fInfo_.SIM_uses_EAM = useEAM; |
600 |
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fInfo_.SIM_uses_Shapes = useShape; |
601 |
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fInfo_.SIM_uses_FLARB = useFLARB; |
595 |
– |
fInfo_.SIM_uses_RF = useRF; |
602 |
|
|
603 |
|
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
604 |
|
|
830 |
|
} |
831 |
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} |
832 |
|
|
833 |
< |
void SimInfo::setupCutoff() { |
833 |
> |
void SimInfo::setupCutoff() { |
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getCutoff(rcut_, rsw_); |
835 |
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double rnblist = rcut_ + 1; // skin of neighbor list |
836 |
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|
837 |
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//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
838 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
838 |
> |
|
839 |
> |
int cp = TRADITIONAL_CUTOFF_POLICY; |
840 |
> |
if (simParams_->haveCutoffPolicy()) { |
841 |
> |
std::string myPolicy = simParams_->getCutoffPolicy(); |
842 |
> |
if (myPolicy == "MIX") { |
843 |
> |
cp = MIX_CUTOFF_POLICY; |
844 |
> |
} else { |
845 |
> |
if (myPolicy == "MAX") { |
846 |
> |
cp = MAX_CUTOFF_POLICY; |
847 |
> |
} else { |
848 |
> |
if (myPolicy == "TRADITIONAL") { |
849 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
850 |
> |
} else { |
851 |
> |
// throw error |
852 |
> |
sprintf( painCave.errMsg, |
853 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
854 |
> |
painCave.isFatal = 1; |
855 |
> |
simError(); |
856 |
> |
} |
857 |
> |
} |
858 |
> |
} |
859 |
> |
} |
860 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
861 |
> |
// also send cutoff notification to electrostatics |
862 |
> |
setElectrostaticCutoffRadius(&rcut_); |
863 |
|
} |
864 |
|
|
865 |
+ |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
866 |
+ |
|
867 |
+ |
int errorOut; |
868 |
+ |
int esm = NONE; |
869 |
+ |
double alphaVal; |
870 |
+ |
double dielectric; |
871 |
+ |
|
872 |
+ |
errorOut = isError; |
873 |
+ |
alphaVal = simParams_->getDampingAlpha(); |
874 |
+ |
dielectric = simParams_->getDielectric(); |
875 |
+ |
|
876 |
+ |
if (simParams_->haveElectrostaticSummationMethod()) { |
877 |
+ |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
878 |
+ |
if (myMethod == "NONE") { |
879 |
+ |
esm = NONE; |
880 |
+ |
} else { |
881 |
+ |
if (myMethod == "UNDAMPED_WOLF") { |
882 |
+ |
esm = UNDAMPED_WOLF; |
883 |
+ |
} else { |
884 |
+ |
if (myMethod == "DAMPED_WOLF") { |
885 |
+ |
esm = DAMPED_WOLF; |
886 |
+ |
if (!simParams_->haveDampingAlpha()) { |
887 |
+ |
//throw error |
888 |
+ |
sprintf( painCave.errMsg, |
889 |
+ |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal); |
890 |
+ |
painCave.isFatal = 0; |
891 |
+ |
simError(); |
892 |
+ |
} |
893 |
+ |
} else { |
894 |
+ |
if (myMethod == "REACTION_FIELD") { |
895 |
+ |
esm = REACTION_FIELD; |
896 |
+ |
} else { |
897 |
+ |
// throw error |
898 |
+ |
sprintf( painCave.errMsg, |
899 |
+ |
"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() ); |
900 |
+ |
painCave.isFatal = 1; |
901 |
+ |
simError(); |
902 |
+ |
} |
903 |
+ |
} |
904 |
+ |
} |
905 |
+ |
} |
906 |
+ |
} |
907 |
+ |
// let's pass some summation method variables to fortran |
908 |
+ |
setElectrostaticSummationMethod( &esm ); |
909 |
+ |
setDampedWolfAlpha( &alphaVal ); |
910 |
+ |
setReactionFieldDielectric( &dielectric ); |
911 |
+ |
initFortranFF( &esm, &errorOut ); |
912 |
+ |
} |
913 |
+ |
|
914 |
|
void SimInfo::addProperty(GenericData* genData) { |
915 |
|
properties_.addProperty(genData); |
916 |
|
} |
1018 |
|
|
1019 |
|
return o; |
1020 |
|
} |
1021 |
+ |
|
1022 |
+ |
|
1023 |
+ |
/* |
1024 |
+ |
Returns center of mass and center of mass velocity in one function call. |
1025 |
+ |
*/ |
1026 |
+ |
|
1027 |
+ |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1028 |
+ |
SimInfo::MoleculeIterator i; |
1029 |
+ |
Molecule* mol; |
1030 |
+ |
|
1031 |
+ |
|
1032 |
+ |
double totalMass = 0.0; |
1033 |
+ |
|
1034 |
|
|
1035 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1036 |
+ |
double mass = mol->getMass(); |
1037 |
+ |
totalMass += mass; |
1038 |
+ |
com += mass * mol->getCom(); |
1039 |
+ |
comVel += mass * mol->getComVel(); |
1040 |
+ |
} |
1041 |
+ |
|
1042 |
+ |
#ifdef IS_MPI |
1043 |
+ |
double tmpMass = totalMass; |
1044 |
+ |
Vector3d tmpCom(com); |
1045 |
+ |
Vector3d tmpComVel(comVel); |
1046 |
+ |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1047 |
+ |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1048 |
+ |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1049 |
+ |
#endif |
1050 |
+ |
|
1051 |
+ |
com /= totalMass; |
1052 |
+ |
comVel /= totalMass; |
1053 |
+ |
} |
1054 |
+ |
|
1055 |
+ |
/* |
1056 |
+ |
Return intertia tensor for entire system and angular momentum Vector. |
1057 |
+ |
|
1058 |
+ |
|
1059 |
+ |
[ Ixx -Ixy -Ixz ] |
1060 |
+ |
J =| -Iyx Iyy -Iyz | |
1061 |
+ |
[ -Izx -Iyz Izz ] |
1062 |
+ |
*/ |
1063 |
+ |
|
1064 |
+ |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1065 |
+ |
|
1066 |
+ |
|
1067 |
+ |
double xx = 0.0; |
1068 |
+ |
double yy = 0.0; |
1069 |
+ |
double zz = 0.0; |
1070 |
+ |
double xy = 0.0; |
1071 |
+ |
double xz = 0.0; |
1072 |
+ |
double yz = 0.0; |
1073 |
+ |
Vector3d com(0.0); |
1074 |
+ |
Vector3d comVel(0.0); |
1075 |
+ |
|
1076 |
+ |
getComAll(com, comVel); |
1077 |
+ |
|
1078 |
+ |
SimInfo::MoleculeIterator i; |
1079 |
+ |
Molecule* mol; |
1080 |
+ |
|
1081 |
+ |
Vector3d thisq(0.0); |
1082 |
+ |
Vector3d thisv(0.0); |
1083 |
+ |
|
1084 |
+ |
double thisMass = 0.0; |
1085 |
+ |
|
1086 |
+ |
|
1087 |
+ |
|
1088 |
+ |
|
1089 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1090 |
+ |
|
1091 |
+ |
thisq = mol->getCom()-com; |
1092 |
+ |
thisv = mol->getComVel()-comVel; |
1093 |
+ |
thisMass = mol->getMass(); |
1094 |
+ |
// Compute moment of intertia coefficients. |
1095 |
+ |
xx += thisq[0]*thisq[0]*thisMass; |
1096 |
+ |
yy += thisq[1]*thisq[1]*thisMass; |
1097 |
+ |
zz += thisq[2]*thisq[2]*thisMass; |
1098 |
+ |
|
1099 |
+ |
// compute products of intertia |
1100 |
+ |
xy += thisq[0]*thisq[1]*thisMass; |
1101 |
+ |
xz += thisq[0]*thisq[2]*thisMass; |
1102 |
+ |
yz += thisq[1]*thisq[2]*thisMass; |
1103 |
+ |
|
1104 |
+ |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1105 |
+ |
|
1106 |
+ |
} |
1107 |
+ |
|
1108 |
+ |
|
1109 |
+ |
inertiaTensor(0,0) = yy + zz; |
1110 |
+ |
inertiaTensor(0,1) = -xy; |
1111 |
+ |
inertiaTensor(0,2) = -xz; |
1112 |
+ |
inertiaTensor(1,0) = -xy; |
1113 |
+ |
inertiaTensor(1,1) = xx + zz; |
1114 |
+ |
inertiaTensor(1,2) = -yz; |
1115 |
+ |
inertiaTensor(2,0) = -xz; |
1116 |
+ |
inertiaTensor(2,1) = -yz; |
1117 |
+ |
inertiaTensor(2,2) = xx + yy; |
1118 |
+ |
|
1119 |
+ |
#ifdef IS_MPI |
1120 |
+ |
Mat3x3d tmpI(inertiaTensor); |
1121 |
+ |
Vector3d tmpAngMom; |
1122 |
+ |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1123 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1124 |
+ |
#endif |
1125 |
+ |
|
1126 |
+ |
return; |
1127 |
+ |
} |
1128 |
+ |
|
1129 |
+ |
//Returns the angular momentum of the system |
1130 |
+ |
Vector3d SimInfo::getAngularMomentum(){ |
1131 |
+ |
|
1132 |
+ |
Vector3d com(0.0); |
1133 |
+ |
Vector3d comVel(0.0); |
1134 |
+ |
Vector3d angularMomentum(0.0); |
1135 |
+ |
|
1136 |
+ |
getComAll(com,comVel); |
1137 |
+ |
|
1138 |
+ |
SimInfo::MoleculeIterator i; |
1139 |
+ |
Molecule* mol; |
1140 |
+ |
|
1141 |
+ |
Vector3d thisr(0.0); |
1142 |
+ |
Vector3d thisp(0.0); |
1143 |
+ |
|
1144 |
+ |
double thisMass; |
1145 |
+ |
|
1146 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1147 |
+ |
thisMass = mol->getMass(); |
1148 |
+ |
thisr = mol->getCom()-com; |
1149 |
+ |
thisp = (mol->getComVel()-comVel)*thisMass; |
1150 |
+ |
|
1151 |
+ |
angularMomentum += cross( thisr, thisp ); |
1152 |
+ |
|
1153 |
+ |
} |
1154 |
+ |
|
1155 |
+ |
#ifdef IS_MPI |
1156 |
+ |
Vector3d tmpAngMom; |
1157 |
+ |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1158 |
+ |
#endif |
1159 |
+ |
|
1160 |
+ |
return angularMomentum; |
1161 |
+ |
} |
1162 |
+ |
|
1163 |
+ |
|
1164 |
|
}//end namespace oopse |
1165 |
|
|