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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 "primitives/StuntDouble.hpp" |
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#include "UseTheForce/fCutoffPolicy.h" |
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#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
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#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
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#include "UseTheForce/DarkSide/fSwitchingFunctionType.h" |
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#include "UseTheForce/doForces_interface.h" |
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#include "UseTheForce/DarkSide/neighborLists_interface.h" |
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#include "UseTheForce/DarkSide/electrostatic_interface.h" |
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#include "UseTheForce/DarkSide/switcheroo_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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#include "selection/SelectionManager.hpp" |
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#include "io/ForceFieldOptions.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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|
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|
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#ifdef IS_MPI |
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#include "UseTheForce/mpiComponentPlan.h" |
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//setup fortran force field |
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/** @deprecate */ |
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int isError = 0; |
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|
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setupCutoff(); |
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|
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setupElectrostaticSummationMethod( isError ); |
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setupSwitchingFunction(); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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– |
|
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– |
|
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setupCutoff(); |
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|
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calcNdf(); |
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calcNdfRaw(); |
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// set the useRF logical |
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useRF = 0; |
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useSF = 0; |
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useSP = 0; |
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|
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|
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if (simParams_->haveElectrostaticSummationMethod()) { |
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std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
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toUpper(myMethod); |
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if (myMethod == "REACTION_FIELD"){ |
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useRF=1; |
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> |
useRF = 1; |
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} else if (myMethod == "SHIFTED_FORCE"){ |
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useSF = 1; |
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} else if (myMethod == "SHIFTED_POTENTIAL"){ |
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fInfo_.SIM_uses_SF = useSF; |
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fInfo_.SIM_uses_SP = useSP; |
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fInfo_.SIM_uses_BoxDipole = useBoxDipole; |
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|
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if( myMethod == "REACTION_FIELD") { |
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|
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if (simParams_->haveDielectric()) { |
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fInfo_.dielect = simParams_->getDielectric(); |
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} else { |
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sprintf(painCave.errMsg, |
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"SimSetup Error: No Dielectric constant was set.\n" |
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"\tYou are trying to use Reaction Field without" |
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"\tsetting a dielectric constant!\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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} |
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|
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void SimInfo::setupFortranSim() { |
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"succesfully sent the simulation information to fortran.\n"); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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|
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// Setup number of neighbors in neighbor list if present |
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if (simParams_->haveNeighborListNeighbors()) { |
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setNeighbors(simParams_->getNeighborListNeighbors()); |
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} |
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|
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|
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} |
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|
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|
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int sm = UNDAMPED; |
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RealType alphaVal; |
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RealType dielectric; |
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< |
|
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|
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errorOut = isError; |
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alphaVal = simParams_->getDampingAlpha(); |
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dielectric = simParams_->getDielectric(); |
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|
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if (simParams_->haveElectrostaticSummationMethod()) { |
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std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
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if (myMethod == "SHIFTED_FORCE") { |
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esm = SHIFTED_FORCE; |
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} else { |
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< |
if (myMethod == "REACTION_FIELD") { |
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> |
if (myMethod == "REACTION_FIELD") { |
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esm = REACTION_FIELD; |
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dielectric = simParams_->getDielectric(); |
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if (!simParams_->haveDielectric()) { |
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// throw warning |
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sprintf( painCave.errMsg, |
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"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n" |
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"\tA default value of %f will be used for the dielectric.\n", dielectric); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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} else { |
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// throw error |
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sprintf( painCave.errMsg, |
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if (myScreen == "DAMPED") { |
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sm = DAMPED; |
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if (!simParams_->haveDampingAlpha()) { |
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//throw error |
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> |
// first set a cutoff dependent alpha value |
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> |
// we assume alpha depends linearly with rcut from 0 to 20.5 ang |
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> |
alphaVal = 0.5125 - rcut_* 0.025; |
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> |
// for values rcut > 20.5, alpha is zero |
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if (alphaVal < 0) alphaVal = 0; |
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|
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// throw warning |
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sprintf( painCave.errMsg, |
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"SimInfo warning: dampingAlpha was not specified in the input file.\n" |
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"\tA default value of %f (1/ang) will be used.\n", alphaVal); |
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"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_); |
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painCave.isFatal = 0; |
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simError(); |
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+ |
} else { |
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alphaVal = simParams_->getDampingAlpha(); |
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} |
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|
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} else { |
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// throw error |
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sprintf( painCave.errMsg, |
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return angularMomentum; |
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} |
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|
| 1450 |
< |
|
| 1450 |
> |
StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) { |
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> |
return IOIndexToIntegrableObject.at(index); |
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> |
} |
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> |
|
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> |
void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) { |
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IOIndexToIntegrableObject= v; |
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> |
} |
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> |
|
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> |
/* Returns the Volume of the simulation based on a ellipsoid with semi-axes |
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> |
based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3 |
| 1460 |
> |
where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to |
| 1461 |
> |
V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536. |
| 1462 |
> |
*/ |
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> |
void SimInfo::getGyrationalVolume(RealType &volume){ |
| 1464 |
> |
Mat3x3d intTensor; |
| 1465 |
> |
RealType det; |
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> |
Vector3d dummyAngMom; |
| 1467 |
> |
RealType sysconstants; |
| 1468 |
> |
RealType geomCnst; |
| 1469 |
> |
|
| 1470 |
> |
geomCnst = 3.0/2.0; |
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> |
/* Get the inertial tensor and angular momentum for free*/ |
| 1472 |
> |
getInertiaTensor(intTensor,dummyAngMom); |
| 1473 |
> |
|
| 1474 |
> |
det = intTensor.determinant(); |
| 1475 |
> |
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1476 |
> |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); |
| 1477 |
> |
return; |
| 1478 |
> |
} |
| 1479 |
> |
|
| 1480 |
> |
void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){ |
| 1481 |
> |
Mat3x3d intTensor; |
| 1482 |
> |
Vector3d dummyAngMom; |
| 1483 |
> |
RealType sysconstants; |
| 1484 |
> |
RealType geomCnst; |
| 1485 |
> |
|
| 1486 |
> |
geomCnst = 3.0/2.0; |
| 1487 |
> |
/* Get the inertial tensor and angular momentum for free*/ |
| 1488 |
> |
getInertiaTensor(intTensor,dummyAngMom); |
| 1489 |
> |
|
| 1490 |
> |
detI = intTensor.determinant(); |
| 1491 |
> |
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1492 |
> |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); |
| 1493 |
> |
return; |
| 1494 |
> |
} |
| 1495 |
> |
/* |
| 1496 |
> |
void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) { |
| 1497 |
> |
assert( v.size() == nAtoms_ + nRigidBodies_); |
| 1498 |
> |
sdByGlobalIndex_ = v; |
| 1499 |
> |
} |
| 1500 |
> |
|
| 1501 |
> |
StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) { |
| 1502 |
> |
//assert(index < nAtoms_ + nRigidBodies_); |
| 1503 |
> |
return sdByGlobalIndex_.at(index); |
| 1504 |
> |
} |
| 1505 |
> |
*/ |
| 1506 |
|
}//end namespace oopse |
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|
