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lammps/lib/atc/ATC_TransferHardy.h

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/** ATC_TransferHardy : Hardy smoothing */
#ifndef ATC_TRANSFER_HARDY_H
#define ATC_TRANSFER_HARDY_H
// ATC_Transfer headers
#include "ATC_Transfer.h"
#include "LammpsInterface.h"
#include "ATC_HardyKernel.h"
#include "TimeFilter.h"
// Other headers
#include <map>
#include <list>
using std::list;
namespace ATC {
enum hardyNormalization {
NO_NORMALIZATION=0,
VOLUME_NORMALIZATION, NUMBER_NORMALIZATION, MASS_NORMALIZATION
};
enum hardyFieldName {
HARDY_DENSITY=0,
HARDY_DISPLACEMENT,
HARDY_MOMENTUM,
HARDY_VELOCITY,
HARDY_PROJECTED_VELOCITY,
HARDY_TEMPERATURE,
HARDY_KINETIC_TEMPERATURE,
HARDY_STRESS,
HARDY_HEAT_FLUX,
HARDY_ENERGY,
HARDY_NUMBER_DENSITY,
HARDY_ESHELBY_STRESS,
HARDY_CAUCHY_BORN_STRESS,
HARDY_TRANSFORMED_STRESS,
HARDY_VACANCY_CONCENTRATION,
HARDY_TYPE_CONCENTRATION,
NUM_HARDY_FIELDS
};
/** string to field enum */
static bool string_to_hardy_field(const string & name, hardyFieldName & index) {
if (name=="density")
index = HARDY_DENSITY;
else if (name=="displacement")
index = HARDY_DISPLACEMENT;
else if (name=="momentum")
index = HARDY_MOMENTUM;
else if (name=="velocity")
index = HARDY_VELOCITY;
else if (name=="projected_velocity")
index = HARDY_PROJECTED_VELOCITY;
else if (name=="temperature")
index = HARDY_TEMPERATURE;
else if (name=="kinetic_temperature")
index = HARDY_KINETIC_TEMPERATURE; // temperature from full KE
else if (name=="stress")
index = HARDY_STRESS;
else if (name=="eshelby_stress")
index = HARDY_ESHELBY_STRESS;
else if (name=="cauchy_born_stress")
index = HARDY_CAUCHY_BORN_STRESS;
else if (name=="heat_flux")
index = HARDY_HEAT_FLUX;
else if (name=="energy")
index = HARDY_ENERGY;
else if (name=="number_density")
index = HARDY_NUMBER_DENSITY;
else if (name=="transformed_stress")
index = HARDY_TRANSFORMED_STRESS;
else if (name=="vacancy_concentration")
index = HARDY_VACANCY_CONCENTRATION;
else if (name=="type_concentration")
index = HARDY_TYPE_CONCENTRATION;
else
return false;
return true;
};
/** string to field enum */
static bool hardy_field_to_string(const int & index,string & name)
{
if (index==HARDY_DENSITY)
name = "density";
else if (index==HARDY_DISPLACEMENT)
name = "displacement";
else if (index==HARDY_MOMENTUM)
name = "momentum";
else if (index == HARDY_VELOCITY)
name="velocity";
else if (index == HARDY_PROJECTED_VELOCITY)
name="projected_velocity";
else if (index == HARDY_TEMPERATURE)
name="temperature";
else if (index == HARDY_KINETIC_TEMPERATURE)
name="kinetic_temperature";
else if (index == HARDY_STRESS)
name="stress";
else if (index == HARDY_ESHELBY_STRESS)
name="eshelby_stress";
else if (index == HARDY_CAUCHY_BORN_STRESS)
name="cauchy_born_stress";
else if (index == HARDY_HEAT_FLUX)
name="heat_flux";
else if (index == HARDY_ENERGY)
name="energy";
else if (index == HARDY_NUMBER_DENSITY)
name="number_density";
else if (index == HARDY_TRANSFORMED_STRESS)
name="transformed_stress";
else if (index == HARDY_VACANCY_CONCENTRATION)
name="vacancy_concentration";
else if (index == HARDY_TYPE_CONCENTRATION)
name="type_concentration";
else
return false;
return true;
};
// Forward declarations
class FE_Engine;
class StressCauchyBorn;
class ATC_TransferHardy : public ATC_Transfer {
public:
// constructor
ATC_TransferHardy(std::string groupName, std::string matParamFile = "none");
// destructor
~ATC_TransferHardy();
/** parser/modifier */
virtual bool modify(int narg, char **arg);
/** pre time integration */
virtual void initialize();
/** post time integration */
virtual void finish();
/** first time substep routines */
virtual void pre_init_integrate();
virtual void init_integrate_velocity(){};
virtual void mid_init_integrate(){};
virtual void init_integrate_position(){};
virtual void post_init_integrate();
/** second time substep routine */
virtual void pre_final_integrate();
virtual void final_integrate(){};
virtual void post_final_integrate();
virtual void set_ghost_atoms() {};
private:
/** pointer to position data : either x_reference or x_current */
double ** xPointer_;
/** data */
map <string, DENS_MAT > hardyData_;
map <string, DENS_MAT > hardyDataOld_;
map <string, DENS_MAT > filteredHardyData_;
DENS_MAT atomicTemperature_;
DENS_MAT atomicKineticTemperature_;
DENS_MAT atomicDensity_;
DENS_MAT atomicMomentum_;
DENS_MAT atomicDisplacement_;
DENS_MAT atomicVelocity_;
DENS_MAT atomicStress_;
DENS_MAT atomicHeat_;
DENS_MAT atomicEnergy_;
/** reference data */
bool setRefPE_;
DENS_MAT nodalRefPotentialEnergy_;
double nodalRefPEvalue_;
bool setRefPEvalue_;
/** contour/boundary integral data */
map < pair<string,string>, const set< PAIR > * > bndyIntegralData_;
map < pair<string,string>, const set< PAIR > * > contourIntegralData_;
/** workset data */
SPAR_MAT kernelShpFcn_;
SPAR_MAT atomicBondTable_;
DENS_MAT vbar_;
DENS_MAT ubar_;
DENS_MAT atomicForceTable_;
DENS_MAT atomicHeatTable_;
DENS_MAT uVariationVelocity_;
vector< SPAR_MAT > gradientTable_;
/** calculation flags */
Array<bool> fieldFlags_;
Array<bool> outputFlags_;
Array<bool> gradFlags_;
Array<bool> rateFlags_;
map<string,int> computes_;
/** calculation flags */
Array<int> fieldSizes_;
/** compute nodal quantities */
void compute_potential_energy(DENS_MAT & nodalPE);
void compute_number_density(DENS_MAT & density);
void compute_mass_density(DENS_MAT & density);
void compute_displacement(DENS_MAT & displacement,
const DENS_MAT & density);
void compute_momentum(DENS_MAT & momentum);
void compute_projected_velocity(DENS_MAT & velocity);
void compute_velocity(DENS_MAT & velocity,
const DENS_MAT & density, const DENS_MAT & momentum);
void compute_variation_velocity(DENS_MAT & velocity,
const DENS_MAT & vI);
void compute_temperature(DENS_MAT & temperature);
void compute_kinetic_temperature(DENS_MAT & temperature);
void compute_stress(DENS_MAT & stress);
void compute_heatflux(DENS_MAT & flux);
void compute_total_energy(DENS_MAT & energy);
void compute_eshelby_stress(DENS_MAT & eshebly_stress,
const DENS_MAT & energy, const DENS_MAT & stress,
const DENS_MAT & displacement_gradient);
void compute_cauchy_born_stress(DENS_MAT & cb_stress,
const DENS_MAT & displacement_gradient);
void compute_transformed_stress(DENS_MAT & stress,
const DENS_MAT & T, const DENS_MAT & displacement_gradient);
void compute_vacancy_concentration(DENS_MAT & vacancy_concentration,
const DENS_MAT & displacement_gradient,
const DENS_MAT & number_density);
void compute_type_concentration(DENS_MAT & type_concentration);
/** compute smooth fields */
void compute_fields(void);
void time_filter_pre (double dt, bool output_now = true);
void time_filter_post(double dt, bool output_now = true);
/** compute boundary integral */
void compute_boundary_integrals(void);
/** output function */
void output();
/** physics specific filter initialization */
void init_filter();
/** kernel */
ATC_HardyKernel* kernelFunction_;
/** mapping of atomic pairs to pair index value */
map< pair< int,int >,int > pairMap_;
int nPairs_;
/** routine to compute pair map */
void compute_pair_map();
/** routine to calculate matrix of Hardy bond functions */
void compute_bond_matrix();
/** routine to calculate matrix of kernel shape functions */
void compute_kernel_matrix();
/** routine to calculate matrix of gradient of Hardy functions */
void compute_gradient_matrix();
/** routine to check pair map */
void check_pair_map();
/** routine to calculate matrix of force & position dyads */
void compute_force_matrix();
/** routine to calculate matrix of heat flux vector components */
void compute_heat_matrix();
/** routine to calculate stress on-the-fly */
void compute_potential_stress(DENS_MAT& stress);
/** routine to calculate force part of the heat flux on-the-fly */
void compute_potential_heatflux(DENS_MAT& flux);
/** periodicity flags and lengths */
int periodicity[3];
double box_bounds[2][3];
double box_length[3];
/** routine to adjust node-pair distances due to periodicity */
void periodicity_correction(DENS_VEC& xaI);
/** routine to set xPointer to xref or xatom */
void set_xPointer();
/** number of atom types */
int nTypes_;
protected:
/** project (number density): given w_\alpha,
w_I = \sum_\alpha N_{I\alpha} w_\alpha */
void project_count_normalized(const DENS_MAT & atomData,
DENS_MAT & nodeData);
/** hardy_project (volume density): given w_\alpha,
w_I = 1/\Omega_I \sum_\alpha N_{I\alpha} w_\alpha
where \Omega_I = \int_{support region of node I} N_{I} dV */
void project_volume_normalized(const DENS_MAT & atomData,
DENS_MAT & nodeData);
/** gradient_compute: given w_I,
w_J = \sum_I N_I'{xJ} \dyad w_I
where N_I'{xJ} is the gradient of the normalized
shape function of node I evaluated at node J */
void gradient_compute(const DENS_MAT & inNodeData,
DENS_MAT & outNodeData);
int nNodesGlobal_;
/** compute kernel shape functions on-the-fly w/o storing N_Ia */
bool kernelOnTheFly_;
/** compute stress or heat flux on-the-fly w/o storing B_Iab */
bool bondOnTheFly_;
/** if false, no coarse velocity is calculated for kernel-based estimates */
bool useAtomicShapeFunctions_;
/** a continuum model to compare to and/or estimate Hardy quantities */
StressCauchyBorn * cauchyBornStress_;
const LammpsInterface * constLammpsInterface_;
Array<TimeFilter *> timeFilters_;
/** check consistency of fieldFlags_ */
void check_fieldFlags_consistency();
};
};
#endif
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