| 52 |
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#include "brains/SimInfo.hpp" |
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#include "math/Vector3.hpp" |
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#include "primitives/Molecule.hpp" |
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+ |
#include "UseTheForce/fCutoffPolicy.h" |
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+ |
#include "UseTheForce/fCoulombicCorrection.h" |
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#include "UseTheForce/doForces_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "utils/MemoryUtils.hpp" |
| 464 |
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//setup fortran force field |
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/** @deprecate */ |
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int isError = 0; |
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< |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
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> |
|
| 468 |
> |
setupElectrostaticSummationMethod( isError ); |
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> |
|
| 470 |
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if(isError){ |
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sprintf( painCave.errMsg, |
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"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
| 522 |
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int useElectrostatics = 0; |
| 523 |
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//usePBC and useRF are from simParams |
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int usePBC = simParams_->getPBC(); |
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int useRF = simParams_->getUseRF(); |
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|
| 526 |
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//loop over all of the atom types |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 584 |
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temp = useFLARB; |
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MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 586 |
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|
| 584 |
– |
temp = useRF; |
| 585 |
– |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 586 |
– |
|
| 587 |
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#endif |
| 588 |
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|
| 589 |
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fInfo_.SIM_uses_PBC = usePBC; |
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fInfo_.SIM_uses_EAM = useEAM; |
| 599 |
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fInfo_.SIM_uses_Shapes = useShape; |
| 600 |
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fInfo_.SIM_uses_FLARB = useFLARB; |
| 601 |
– |
fInfo_.SIM_uses_RF = useRF; |
| 601 |
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|
| 602 |
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if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
| 603 |
|
|
| 829 |
|
} |
| 830 |
|
} |
| 831 |
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|
| 832 |
< |
void SimInfo::setupCutoff() { |
| 832 |
> |
void SimInfo::setupCutoff() { |
| 833 |
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getCutoff(rcut_, rsw_); |
| 834 |
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double rnblist = rcut_ + 1; // skin of neighbor list |
| 835 |
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|
| 836 |
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//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
| 837 |
< |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
| 837 |
> |
|
| 838 |
> |
int cp = TRADITIONAL_CUTOFF_POLICY; |
| 839 |
> |
if (simParams_->haveCutoffPolicy()) { |
| 840 |
> |
std::string myPolicy = simParams_->getCutoffPolicy(); |
| 841 |
> |
if (myPolicy == "MIX") { |
| 842 |
> |
cp = MIX_CUTOFF_POLICY; |
| 843 |
> |
} else { |
| 844 |
> |
if (myPolicy == "MAX") { |
| 845 |
> |
cp = MAX_CUTOFF_POLICY; |
| 846 |
> |
} else { |
| 847 |
> |
if (myPolicy == "TRADITIONAL") { |
| 848 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
| 849 |
> |
} else { |
| 850 |
> |
// throw error |
| 851 |
> |
sprintf( painCave.errMsg, |
| 852 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
| 853 |
> |
painCave.isFatal = 1; |
| 854 |
> |
simError(); |
| 855 |
> |
} |
| 856 |
> |
} |
| 857 |
> |
} |
| 858 |
> |
} |
| 859 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
| 860 |
> |
} |
| 861 |
> |
|
| 862 |
> |
void SimInfo::setupElectrostaticSummationMethod( int isError ) { |
| 863 |
> |
|
| 864 |
> |
int errorOut; |
| 865 |
> |
int esm = NONE; |
| 866 |
> |
double alphaVal; |
| 867 |
> |
|
| 868 |
> |
errorOut = isError; |
| 869 |
> |
|
| 870 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
| 871 |
> |
std::string myCorrection = simParams_->getElectrostaticSummationMethod(); |
| 872 |
> |
if (myMethod == "NONE") { |
| 873 |
> |
esm = NONE; |
| 874 |
> |
} else { |
| 875 |
> |
if (myMethod == "UNDAMPED_WOLF") { |
| 876 |
> |
esm = UNDAMPED_WOLF; |
| 877 |
> |
} else { |
| 878 |
> |
if (myMethod == "DAMPED_WOLF") { |
| 879 |
> |
esm = WOLF; |
| 880 |
> |
if (!simParams_->haveDampingAlpha()) { |
| 881 |
> |
//throw error |
| 882 |
> |
sprintf( painCave.errMsg, |
| 883 |
> |
"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.", simParams_->getDampingAlpha()); |
| 884 |
> |
painCave.isFatal = 0; |
| 885 |
> |
simError(); |
| 886 |
> |
} |
| 887 |
> |
alphaVal = simParams_->getDampingAlpha(); |
| 888 |
> |
} else { |
| 889 |
> |
if (myMethod == "REACTION_FIELD") { |
| 890 |
> |
esm = REACTION_FIELD; |
| 891 |
> |
} else { |
| 892 |
> |
// throw error |
| 893 |
> |
sprintf( painCave.errMsg, |
| 894 |
> |
"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() ); |
| 895 |
> |
painCave.isFatal = 1; |
| 896 |
> |
simError(); |
| 897 |
> |
} |
| 898 |
> |
} |
| 899 |
> |
} |
| 900 |
> |
} |
| 901 |
> |
} |
| 902 |
> |
initFortranFF( &fInfo_.SIM_uses_RF, &esm, &alphaVal, &errorOut ); |
| 903 |
|
} |
| 904 |
|
|
| 905 |
|
void SimInfo::addProperty(GenericData* genData) { |
| 1045 |
|
|
| 1046 |
|
/* |
| 1047 |
|
Return intertia tensor for entire system and angular momentum Vector. |
| 1048 |
+ |
|
| 1049 |
+ |
|
| 1050 |
+ |
[ Ixx -Ixy -Ixz ] |
| 1051 |
+ |
J =| -Iyx Iyy -Iyz | |
| 1052 |
+ |
[ -Izx -Iyz Izz ] |
| 1053 |
|
*/ |
| 1054 |
|
|
| 1055 |
|
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
| 1101 |
|
inertiaTensor(0,1) = -xy; |
| 1102 |
|
inertiaTensor(0,2) = -xz; |
| 1103 |
|
inertiaTensor(1,0) = -xy; |
| 1104 |
< |
inertiaTensor(2,0) = xx + zz; |
| 1104 |
> |
inertiaTensor(1,1) = xx + zz; |
| 1105 |
|
inertiaTensor(1,2) = -yz; |
| 1106 |
|
inertiaTensor(2,0) = -xz; |
| 1107 |
|
inertiaTensor(2,1) = -yz; |
| 1129 |
|
SimInfo::MoleculeIterator i; |
| 1130 |
|
Molecule* mol; |
| 1131 |
|
|
| 1132 |
< |
Vector3d thisq(0.0); |
| 1133 |
< |
Vector3d thisv(0.0); |
| 1132 |
> |
Vector3d thisr(0.0); |
| 1133 |
> |
Vector3d thisp(0.0); |
| 1134 |
|
|
| 1135 |
< |
double thisMass = 0.0; |
| 1135 |
> |
double thisMass; |
| 1136 |
|
|
| 1137 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 1138 |
< |
thisq = mol->getCom()-com; |
| 1139 |
< |
thisv = mol->getComVel()-comVel; |
| 1140 |
< |
thisMass = mol->getMass(); |
| 1072 |
< |
angularMomentum += cross( thisq, thisv ) * thisMass; |
| 1138 |
> |
thisMass = mol->getMass(); |
| 1139 |
> |
thisr = mol->getCom()-com; |
| 1140 |
> |
thisp = (mol->getComVel()-comVel)*thisMass; |
| 1141 |
|
|
| 1142 |
+ |
angularMomentum += cross( thisr, thisp ); |
| 1143 |
+ |
|
| 1144 |
|
} |
| 1145 |
|
|
| 1146 |
|
#ifdef IS_MPI |
