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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/doForces_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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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 ); |
| 466 |
> |
initFortranFF( &fInfo_.SIM_uses_RF, &fInfo_.SIM_uses_UW, |
| 467 |
> |
&fInfo_.SIM_uses_DW, &isError ); |
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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" ); |
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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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+ |
int useUW = simParams_->getUseUndampedWolf(); |
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+ |
int useDW = simParams_->getUseDampedWolf(); |
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|
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//loop over all of the atom types |
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for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 587 |
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|
| 588 |
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temp = useRF; |
| 589 |
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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; |
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+ |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 596 |
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|
| 597 |
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#endif |
| 598 |
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|
| 609 |
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fInfo_.SIM_uses_Shapes = useShape; |
| 610 |
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fInfo_.SIM_uses_FLARB = useFLARB; |
| 611 |
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fInfo_.SIM_uses_RF = useRF; |
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+ |
fInfo_.SIM_uses_UW = useUW; |
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+ |
fInfo_.SIM_uses_DW = useDW; |
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|
|
| 615 |
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if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
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|
| 842 |
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} |
| 843 |
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} |
| 844 |
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|
| 845 |
< |
void SimInfo::setupCutoff() { |
| 845 |
> |
void SimInfo::setupCutoff() { |
| 846 |
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getCutoff(rcut_, rsw_); |
| 847 |
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double rnblist = rcut_ + 1; // skin of neighbor list |
| 848 |
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|
| 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 |
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void SimInfo::addProperty(GenericData* genData) { |
| 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){ |
| 1071 |
|
inertiaTensor(0,1) = -xy; |
| 1072 |
|
inertiaTensor(0,2) = -xz; |
| 1073 |
|
inertiaTensor(1,0) = -xy; |
| 1074 |
< |
inertiaTensor(2,0) = xx + zz; |
| 1074 |
> |
inertiaTensor(1,1) = xx + zz; |
| 1075 |
|
inertiaTensor(1,2) = -yz; |
| 1076 |
|
inertiaTensor(2,0) = -xz; |
| 1077 |
|
inertiaTensor(2,1) = -yz; |
| 1099 |
|
SimInfo::MoleculeIterator i; |
| 1100 |
|
Molecule* mol; |
| 1101 |
|
|
| 1102 |
< |
Vector3d thisq(0.0); |
| 1103 |
< |
Vector3d thisv(0.0); |
| 1102 |
> |
Vector3d thisr(0.0); |
| 1103 |
> |
Vector3d thisp(0.0); |
| 1104 |
|
|
| 1105 |
< |
double thisMass = 0.0; |
| 1105 |
> |
double thisMass; |
| 1106 |
|
|
| 1107 |
|
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 1108 |
< |
thisq = mol->getCom()-com; |
| 1109 |
< |
thisv = mol->getComVel()-comVel; |
| 1110 |
< |
thisMass = mol->getMass(); |
| 1072 |
< |
angularMomentum += cross( thisq, thisv ) * thisMass; |
| 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 |
