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Merged master to acc_parameter_overhaul

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jpekkila
2019-07-03 17:37:37 +03:00
parent d9b07a59b5 e8a5579b50
commit acc53e1c2b
13 changed files with 527 additions and 145 deletions
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177
src/standalone/model/host_forcing.cc Normal file
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@@ -0,0 +1,177 @@
/*
Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
This file is part of Astaroth.
Astaroth is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Astaroth is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Astaroth. If not, see <http://www.gnu.org/licenses/>.
*/
/**
* @file
* \brief Brief info.
*
* Detailed info.
*
*/
#include "host_forcing.h"
#include "core/math_utils.h"
// The is a wrapper for genering random numbers with a chosen system.
AcReal
get_random_number_01()
{
// TODO: Implement better randon number generator http://www.cplusplus.com/reference/random/
return AcReal(rand()) / AcReal(RAND_MAX);
}
AcReal3
cross(const AcReal3& a, const AcReal3& b)
{
AcReal3 c;
c.x = a.y * b.z - a.z * b.y;
c.y = a.z * b.x - a.x * b.z;
c.z = a.x * b.y - a.y * b.x;
return c;
}
AcReal
dot(const AcReal3& a, const AcReal3& b)
{
return a.x * b.x + a.y * b.y + a.z * b.z;
}
AcReal3
vec_norm(const AcReal3& a)
{
AcReal3 c;
AcReal norm = dot(a, a);
c.x = a.x / sqrt(norm);
c.y = a.y / sqrt(norm);
c.z = a.z / sqrt(norm);
return c;
}
AcReal3
vec_multi_scal(const AcReal scal, const AcReal3& a)
{
AcReal3 c;
c.x = a.x * scal;
c.y = a.y * scal;
c.z = a.z * scal;
return c;
}
// Generate forcing wave vector k_force
AcReal3
helical_forcing_k_generator(const AcReal kmax, const AcReal kmin)
{
AcReal phi, theta, kk; // Spherical direction coordinates
AcReal3 k_force; // forcing wave vector
AcReal delta_k = kmax - kmin;
// Generate vector in spherical coordinates
phi = AcReal(2.0) * AcReal(M_PI) * get_random_number_01();
theta = AcReal(M_PI) * get_random_number_01();
kk = delta_k * get_random_number_01() + kmin;
// Cast into Cartesian form
k_force = (AcReal3){AcReal(kk * sin(theta) * cos(phi)), //
AcReal(kk * sin(theta) * sin(phi)), //
AcReal(kk * cos(theta))};
// printf("k_force.x %f, k_force.y %f, k_force.z %f \n", k_force.x, k_force.y, k_force.z);
// Round the numbers. In that way k(x/y/z) will get complete waves.
k_force.x = round(k_force.x);
k_force.y = round(k_force.y);
k_force.z = round(k_force.z);
// printf("After rounding --> k_force.x %f, k_force.y %f, k_force.z %f \n", k_force.x,
// k_force.y, k_force.z);
return k_force;
}
// Generate the unit perpendicular unit vector e required for helical forcing
// Addapted from Pencil code forcing.f90 hel_vec() subroutine.
void
helical_forcing_e_generator(AcReal3* e_force, const AcReal3 k_force)
{
AcReal3 k_cross_e = cross(k_force, *e_force);
k_cross_e = vec_norm(k_cross_e);
AcReal3 k_cross_k_cross_e = cross(k_force, k_cross_e);
k_cross_k_cross_e = vec_norm(k_cross_k_cross_e);
AcReal phi = AcReal(2.0) * AcReal(M_PI) * get_random_number_01();
AcReal3 ee_tmp1 = vec_multi_scal(cos(phi), k_cross_e);
AcReal3 ee_tmp2 = vec_multi_scal(sin(phi), k_cross_k_cross_e);
*e_force = (AcReal3){ee_tmp1.x + ee_tmp2.x, ee_tmp1.y + ee_tmp2.y, ee_tmp1.z + ee_tmp2.z};
}
// PC Manual Eq. 223
void
helical_forcing_special_vector(AcReal3* ff_hel_re, AcReal3* ff_hel_im, const AcReal3 k_force,
const AcReal3 e_force, const AcReal relhel)
{
// k dot e
AcReal3 kdote;
kdote.x = k_force.x * e_force.x;
kdote.y = k_force.y * e_force.y;
kdote.z = k_force.z * e_force.z;
// k cross e
AcReal3 k_cross_e;
k_cross_e.x = k_force.y * e_force.z - k_force.z * e_force.y;
k_cross_e.y = k_force.z * e_force.x - k_force.x * e_force.z;
k_cross_e.z = k_force.x * e_force.y - k_force.y * e_force.x;
// k cross k cross e
AcReal3 k_cross_k_cross_e;
k_cross_k_cross_e.x = k_force.y * k_cross_e.z - k_force.z * k_cross_e.y;
k_cross_k_cross_e.y = k_force.z * k_cross_e.x - k_force.x * k_cross_e.z;
k_cross_k_cross_e.z = k_force.x * k_cross_e.y - k_force.y * k_cross_e.x;
// abs(k)
AcReal kabs = sqrt(k_force.x * k_force.x + k_force.y * k_force.y + k_force.z * k_force.z);
AcReal denominator = sqrt(AcReal(1.0) + relhel * relhel) * kabs *
sqrt(kabs * kabs -
(kdote.x * kdote.x + kdote.y * kdote.y + kdote.z * kdote.z));
// MV: I suspect there is a typo in the Pencil Code manual!
//*ff_hel_re = (AcReal3){-relhel*kabs*k_cross_e.x/denominator,
// -relhel*kabs*k_cross_e.y/denominator,
// -relhel*kabs*k_cross_e.z/denominator};
//*ff_hel_im = (AcReal3){k_cross_k_cross_e.x/denominator,
// k_cross_k_cross_e.y/denominator,
// k_cross_k_cross_e.z/denominator};
// See PC forcing.f90 forcing_hel_both()
*ff_hel_re = (AcReal3){kabs * k_cross_e.x / denominator, kabs * k_cross_e.y,
kabs * k_cross_e.z};
*ff_hel_im = (AcReal3){relhel * k_cross_k_cross_e.x / denominator, relhel * k_cross_k_cross_e.y,
relhel * k_cross_k_cross_e.z};
}

45
src/standalone/model/host_forcing.h Normal file
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@@ -0,0 +1,45 @@
/*
Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
This file is part of Astaroth.
Astaroth is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Astaroth is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Astaroth. If not, see <http://www.gnu.org/licenses/>.
*/
/**
* @file
* \brief Brief info.
*
* Detailed info.
*
*/
#pragma once
#include "astaroth.h"
AcReal get_random_number_01();
AcReal3 cross(const AcReal3& a, const AcReal3& b);
AcReal dot(const AcReal3& a, const AcReal3& b);
AcReal3 vec_norm(const AcReal3& a);
AcReal3 vec_multi_scal(const AcReal scal, const AcReal3& a);
AcReal3 helical_forcing_k_generator(const AcReal kmax, const AcReal kmin);
void helical_forcing_e_generator(AcReal3* e_force, const AcReal3 k_force);
void helical_forcing_special_vector(AcReal3* ff_hel_re, AcReal3* ff_hel_im, const AcReal3 k_force, const AcReal3 e_force, const AcReal relhel);

3
src/standalone/model/host_timestep.cc
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@@ -50,7 +50,8 @@ host_timestep(const AcReal& umax, const AcMeshInfo& mesh_info)
// New, closer to the actual Courant timestep
// See Pencil Code user manual p. 38 (timestep section)
const long double uu_dt = cdt * dsmin / (fabsl(umax) + sqrtl(cs2_sound + 0.0l));
const long double visc_dt = cdtv * dsmin * dsmin / max(max(nu_visc, eta), max(gamma, chi)) + 1; // TODO NOTE: comment the +1 out to get scientifically accurate results
const long double visc_dt = cdtv * dsmin * dsmin / max(max(nu_visc, eta), max(gamma, chi));// + 1; // TODO NOTE: comment the +1 out to get scientifically accurate results
//MV: White the +1? It was messing up my computations!
const long double dt = min(uu_dt, visc_dt);
return AcReal(timescale) * AcReal(dt);

129
src/standalone/model/model_rk3.cc
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@@ -1,5 +1,5 @@
/*
Copyright (C) 2014-2018, Johannes Pekkilae, Miikka Vaeisalae.
Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
This file is part of Astaroth.
@@ -553,11 +553,6 @@ normalized(const ModelVector& vec)
return inv_len * vec;
}
// Note: LNT0 and LNRHO0 must be set very carefully: if the magnitude is different that other values
// in the mesh, then we will inherently lose precision
#define LNT0 (ModelScalar(0.0))
#define LNRHO0 (ModelScalar(0.0))
#define H_CONST (ModelScalar(0.0))
#define C_CONST (ModelScalar(0.0))
@@ -571,9 +566,10 @@ momentum(const ModelVectorData& uu, const ModelScalarData& lnrho
{
#if LENTROPY
const ModelMatrix S = stress_tensor(uu);
const ModelScalar cs2 = get(AC_cs2_sound) * expl(get(AC_gamma) * value(ss) / get(AC_cp_sound) +
(get(AC_gamma) - 1) * (value(lnrho) - LNRHO0));
const ModelVector j = (ModelScalar(1.) / get(AC_mu0)) *
const ModelScalar cs2 = get(AC_cs2_sound) *
expl(get(AC_gamma) * value(ss) / get(AC_cp_sound) +
(get(AC_gamma) - 1) * (value(lnrho) - get(AC_lnrho0)));
const ModelVector j = (ModelScalar(1.) / get(AC_mu0)) *
(gradient_of_divergence(aa) - laplace_vec(aa)); // Current density
const ModelVector B = curl(aa);
const ModelScalar inv_rho = ModelScalar(1.) / expl(value(lnrho));
@@ -591,7 +587,8 @@ momentum(const ModelVectorData& uu, const ModelScalarData& lnrho
// !!!!!!!!!!!!!!!!%JP: NOTE TODO IMPORTANT!!!!!!!!!!!!!!!!!!!!!!!!
// NOT CHECKED FOR CORRECTNESS: USE AT YOUR OWN RISK
const ModelMatrix S = stress_tensor(uu);
const ModelScalar cs2 = get(AC_cs2_sound) * expl((get(AC_gamma) - 1) * (value(lnrho) - LNRHO0));
const ModelScalar cs2 = get(AC_cs2_sound) *
expl((get(AC_gamma) - 1) * (value(lnrho) - get(AC_lnrho0)));
const ModelVector mom = -mul(gradients(uu), value(uu)) - cs2 * gradient(lnrho) +
get(AC_nu_visc) * (laplace_vec(uu) +
@@ -623,8 +620,8 @@ induction(const ModelVectorData& uu, const ModelVectorData& aa)
static inline ModelScalar
lnT(const ModelScalarData& ss, const ModelScalarData& lnrho)
{
const ModelScalar lnT = LNT0 + get(AC_gamma) * value(ss) / get(AC_cp_sound) +
(get(AC_gamma) - ModelScalar(1.)) * (value(lnrho) - LNRHO0);
const ModelScalar lnT = get(AC_lnT0) + get(AC_gamma) * value(ss) / get(AC_cp_sound) +
(get(AC_gamma) - ModelScalar(1.)) * (value(lnrho) - get(AC_lnrho0));
return lnT;
}
@@ -678,41 +675,96 @@ entropy(const ModelScalarData& ss, const ModelVectorData& uu, const ModelScalarD
*/
}
static bool
static inline bool
is_valid(const ModelScalar a)
{
return !isnan(a) && !isinf(a);
}
static bool
static inline bool
is_valid(const ModelVector& a)
{
return is_valid(a.x) && is_valid(a.y) && is_valid(a.z);
}
static inline ModelVector
forcing(int3 globalVertexIdx)
{
// source (origin)
ModelVector a = ModelScalar(.5) * (ModelVector){get(AC_nx) * get(AC_dsx),
get(AC_ny) * get(AC_dsy),
get(AC_nz) * get(AC_dsz)};
// sink (current index)
ModelVector b = (ModelVector){(globalVertexIdx.x - get(AC_nx_min)) * get(AC_dsx),
(globalVertexIdx.y - get(AC_ny_min)) * get(AC_dsy),
(globalVertexIdx.z - get(AC_nz_min)) * get(AC_dsz)};
#if 0
//FORCING NOT SUPPORTED FOR AUTOTEST
ModelScalar magnitude = 0.05;
// Vector c = magnitude * (1 / length(b - a)) * normalized(b - a); // Outward flow
ModelVector c = magnitude * cross(normalized(b - a), (ModelVector){0, 0, 1}); // Vortex
if (is_valid(c)) {
return c;
}
else {
return (ModelVector){0, 0, 0};
}
static inline ModelVector
simple_vortex_forcing(ModelVector a, ModelVector b, ModelScalar magnitude)
{
return magnitude * cross(normalized(b - a), (ModelVector){0, 0, 1}); // Vortex
}
static inline ModelVector
simple_outward_flow_forcing(ModelVector a, ModelVector b, ModelScalar magnitude)
{
return magnitude * (1 / length(b - a)) * normalized(b - a); // Outward flow
}
// The Pencil Code forcing_hel_noshear(), manual Eq. 222, inspired forcing function with adjustable helicity
static inline ModelVector
helical_forcing(ModelScalar magnitude, ModelVector k_force, ModelVector xx, ModelVector ff_re, ModelVector ff_im, ModelScalar phi)
{
xx.x = xx.x*(2.0*M_PI/(get(AC_dsx)*(get(AC_ny_max) - get(AC_ny_min))));
xx.y = xx.y*(2.0*M_PI/(get(AC_dsy)*(get(AC_ny_max) - get(AC_ny_min))));
xx.z = xx.z*(2.0*M_PI/(get(AC_dsz)*(get(AC_ny_max) - get(AC_ny_min))));
ModelScalar cos_phi = cos(phi);
ModelScalar sin_phi = sin(phi);
ModelScalar cos_k_dox_x = cos(dot(k_force, xx));
ModelScalar sin_k_dox_x = sin(dot(k_force, xx));
// Phase affect only the x-component
ModelScalar real_comp_phase = cos_k_dox_x*cos_phi - sin_k_dox_x*sin_phi;
ModelScalar imag_comp_phase = cos_k_dox_x*sin_phi + sin_k_dox_x*cos_phi;
ModelVector force = (ModelVector){ ff_re.x*real_comp_phase - ff_im.x*imag_comp_phase,
ff_re.y*real_comp_phase - ff_im.y*imag_comp_phase,
ff_re.z*real_comp_phase - ff_im.z*imag_comp_phase};
return force;
}
static inline ModelVector
forcing(int3 globalVertexIdx, ModelScalar dt)
{
ModelVector a = ModelScalar(.5) * (ModelVector){ get(AC_nx) * get(AC_dsx),
get(AC_ny) * get(AC_dsy),
get(AC_nz) * get(AC_dsz)}; // source (origin)
ModelVector xx = (ModelVector){(globalVertexIdx.x - get(AC_nx_min)) * get(AC_dsx),
(globalVertexIdx.y - get(AC_ny_min) * get(AC_dsy)),
(globalVertexIdx.z - get(AC_nz_min) * get(AC_dsz))}; // sink (current index)
const ModelScalar cs2 = get(AC_cs2_sound);
const ModelScalar cs = sqrt(cs2);
//Placeholders until determined properly
ModelScalar magnitude = get(AC_forcing_magnitude);
ModelScalar phase = get(AC_forcing_phase);
ModelVector k_force = (ModelVector){ get(AC_k_forcex), get(AC_k_forcey), get(AC_k_forcez)};
ModelVector ff_re = (ModelVector){get(AC_ff_hel_rex), get(AC_ff_hel_rey), get(AC_ff_hel_rez)};
ModelVector ff_im = (ModelVector){get(AC_ff_hel_imx), get(AC_ff_hel_imy), get(AC_ff_hel_imz)};
//Determine that forcing funtion type at this point.
//ModelVector force = simple_vortex_forcing(a, xx, magnitude);
//ModelVector force = simple_outward_flow_forcing(a, xx, magnitude);
ModelVector force = helical_forcing(magnitude, k_force, xx, ff_re,ff_im, phase);
//Scaling N = magnitude*cs*sqrt(k*cs/dt) * dt
const ModelScalar NN = cs*sqrt(get(AC_kaver)*cs);
//MV: Like in the Pencil Code. I don't understandf the logic here.
force.x = sqrt(dt)*NN*force.x;
force.y = sqrt(dt)*NN*force.y;
force.z = sqrt(dt)*NN*force.z;
if (is_valid(force)) { return force; }
else { return (ModelVector){0, 0, 0}; }
}
#endif
static void
solve_alpha_step(const int step_number, const ModelScalar dt, const int i, const int j, const int k,
ModelMesh& in, ModelMesh* out)
@@ -774,12 +826,13 @@ solve_beta_step(const int step_number, const ModelScalar dt, const int i, const
for (int w = 0; w < NUM_VTXBUF_HANDLES; ++w)
out->vertex_buffer[w][idx] += beta[step_number] * in.vertex_buffer[w][idx];
(void)dt; // Suppress unused variable warning if forcing not used
#if LFORCING
if (step_number == 2) {
ModelVector force = forcing((int3){i, j, k});
out->vertex_buffer[VTXBUF_UUX][idx] += force.x * dt;
out->vertex_buffer[VTXBUF_UUY][idx] += force.y * dt;
out->vertex_buffer[VTXBUF_UUZ][idx] += force.z * dt;
ModelVector force = forcing((int3){i, j, k}, dt);
out->vertex_buffer[VTXBUF_UUX][idx] += force.x;
out->vertex_buffer[VTXBUF_UUY][idx] += force.y;
out->vertex_buffer[VTXBUF_UUZ][idx] += force.z;
}
#endif
}