| 59 |
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#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
| 60 |
|
#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
| 61 |
|
#include "UseTheForce/doForces_interface.h" |
| 62 |
+ |
#include "UseTheForce/DarkSide/neighborLists_interface.h" |
| 63 |
|
#include "UseTheForce/DarkSide/electrostatic_interface.h" |
| 64 |
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#include "UseTheForce/DarkSide/switcheroo_interface.h" |
| 65 |
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#include "utils/MemoryUtils.hpp" |
| 68 |
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#include "io/ForceFieldOptions.hpp" |
| 69 |
|
#include "UseTheForce/ForceField.hpp" |
| 70 |
|
|
| 71 |
+ |
|
| 72 |
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#ifdef IS_MPI |
| 73 |
|
#include "UseTheForce/mpiComponentPlan.h" |
| 74 |
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#include "UseTheForce/DarkSide/simParallel_interface.h" |
| 671 |
|
// set the useRF logical |
| 672 |
|
useRF = 0; |
| 673 |
|
useSF = 0; |
| 674 |
+ |
useSP = 0; |
| 675 |
|
|
| 676 |
|
|
| 677 |
|
if (simParams_->haveElectrostaticSummationMethod()) { |
| 678 |
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std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 679 |
|
toUpper(myMethod); |
| 680 |
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if (myMethod == "REACTION_FIELD"){ |
| 681 |
< |
useRF=1; |
| 681 |
> |
useRF = 1; |
| 682 |
|
} else if (myMethod == "SHIFTED_FORCE"){ |
| 683 |
|
useSF = 1; |
| 684 |
|
} else if (myMethod == "SHIFTED_POTENTIAL"){ |
| 870 |
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"succesfully sent the simulation information to fortran.\n"); |
| 871 |
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MPIcheckPoint(); |
| 872 |
|
#endif // is_mpi |
| 873 |
+ |
|
| 874 |
+ |
// Setup number of neighbors in neighbor list if present |
| 875 |
+ |
if (simParams_->haveNeighborListNeighbors()) { |
| 876 |
+ |
int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 877 |
+ |
setNeighbors(&nlistNeighbors); |
| 878 |
+ |
} |
| 879 |
+ |
|
| 880 |
+ |
|
| 881 |
|
} |
| 882 |
|
|
| 883 |
|
|
| 1136 |
|
"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_); |
| 1137 |
|
painCave.isFatal = 0; |
| 1138 |
|
simError(); |
| 1139 |
+ |
} else { |
| 1140 |
+ |
alphaVal = simParams_->getDampingAlpha(); |
| 1141 |
|
} |
| 1142 |
+ |
|
| 1143 |
|
} else { |
| 1144 |
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// throw error |
| 1145 |
|
sprintf( painCave.errMsg, |
| 1456 |
|
IOIndexToIntegrableObject= v; |
| 1457 |
|
} |
| 1458 |
|
|
| 1459 |
+ |
/* Returns the Volume of the simulation based on a ellipsoid with semi-axes |
| 1460 |
+ |
based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3 |
| 1461 |
+ |
where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to |
| 1462 |
+ |
V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536. |
| 1463 |
+ |
*/ |
| 1464 |
+ |
void SimInfo::getGyrationalVolume(RealType &volume){ |
| 1465 |
+ |
Mat3x3d intTensor; |
| 1466 |
+ |
RealType det; |
| 1467 |
+ |
Vector3d dummyAngMom; |
| 1468 |
+ |
RealType sysconstants; |
| 1469 |
+ |
RealType geomCnst; |
| 1470 |
+ |
|
| 1471 |
+ |
geomCnst = 3.0/2.0; |
| 1472 |
+ |
/* Get the inertial tensor and angular momentum for free*/ |
| 1473 |
+ |
getInertiaTensor(intTensor,dummyAngMom); |
| 1474 |
+ |
|
| 1475 |
+ |
det = intTensor.determinant(); |
| 1476 |
+ |
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1477 |
+ |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); |
| 1478 |
+ |
return; |
| 1479 |
+ |
} |
| 1480 |
+ |
|
| 1481 |
+ |
void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){ |
| 1482 |
+ |
Mat3x3d intTensor; |
| 1483 |
+ |
Vector3d dummyAngMom; |
| 1484 |
+ |
RealType sysconstants; |
| 1485 |
+ |
RealType geomCnst; |
| 1486 |
+ |
|
| 1487 |
+ |
geomCnst = 3.0/2.0; |
| 1488 |
+ |
/* Get the inertial tensor and angular momentum for free*/ |
| 1489 |
+ |
getInertiaTensor(intTensor,dummyAngMom); |
| 1490 |
+ |
|
| 1491 |
+ |
detI = intTensor.determinant(); |
| 1492 |
+ |
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1493 |
+ |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); |
| 1494 |
+ |
return; |
| 1495 |
+ |
} |
| 1496 |
|
/* |
| 1497 |
|
void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) { |
| 1498 |
|
assert( v.size() == nAtoms_ + nRigidBodies_); |
