Upgrade all examples to use PhysicsModel #2164
Conversation
Think this happened in a merge?
ZedThree
force-pushed
the
remove-legacy-models-with-fixes
branch
from
7811f3e
to
cbb2c56
Compare
|
The first real trial of which is not a terrible helpful error message. It might be because it's trying to send a few hundred review comments all at once. I think we might need to turn some of the clang-tidy warnings off as well, some of them are just not helpful. For example, there is a warning about magic numbers, which seems to apply to everything which isn't a constant variable initialisation:
ddt(Te) -= 2.0 / 3.0 * Te0 * B0 * Grad_parP(Vepar / B0, CELL_CENTRE);
^or
OPTION(options, kappa, 0.1);
^This actually gets triggered twice for each magic number, because it also appears as |
![github-actions[bot]](https://avatars.githubusercontent.com/in/15368?s=60&v=4){kind=small}
|
|
||
| constexpr BoutReal eV_K = 11605.0; // 1eV = 11605K | ||
|
|
||
| class Elm_6f : public PhysicsModel { |
There was a problem hiding this comment.
warning: constructor does not initialize these fields: n0_height, n0_ave, n0_width, n0_center, n0_bottom_x, Tconst, laplace_alpha, Tau_ie, q95_input, local_q, q_alpha, n0_fake_prof, T0_fake_prof, Zi, emass, emass_inv, coef_jpar, delta_e, delta_e_inv, gyroAlv, density, Bbar, Lbar, Tbar, Va, Nbar, Tibar, Tebar, dia_fact, diffusion_par, diffusion_perp, diffusion_n4, diffusion_ti4, diffusion_te4, diffusion_v4, diffusion_u4, heating_P, hp_width, hp_length, sink_vp, sp_width, sp_length, sink_Ul, su_widthl, su_lengthl, sink_Ur, su_widthr, su_lengthr, viscos_par, viscos_perp, hyperviscos, Psipara1, Upara0, Upara1, Upara2, Upara3, Nipara1, Tipara1, Tipara2, Tepara1, Tepara2, Tepara3, Tepara4, Vepara, Vipara, Low_limit, gamma_i_BC, gamma_e_BC, Sheath_width, const_cse, include_curvature, include_jpar0, compress0, evolve_pressure, continuity, gyroviscous, diffusion_coef_Hmode0, diffusion_coef_Hmode1, vacuum_pressure, vacuum_trans, nonlinear, evolve_jpar, g, phi_curv, bm_exb, bm_mag, bracket_method_exb, bracket_method_mag, diamag, energy_flux, energy_exch, diamag_phi0, thermal_force, eHall, AA, Vt0, Vp0, experiment_Er, nogradparj, filter_z, filter_z_mode, low_pass_z, zonal_flow, zonal_field, zonal_bkgd, relax_j_vac, relax_j_tconst, smooth_j_x, filter_nl, jpar_bndry_width, parallel_lagrange, parallel_project, phi_constraint, vac_lund, core_lund, vac_resist, core_resist, spitzer_resist, output_transfer, output_ohm, output_flux_par, hyperresist, ehyperviscos, damp_width, damp_t_const, LnLambda [cppcoreguidelines-pro-type-member-init]
class Elm_6f : public PhysicsModel {
^| /* | ||
| * This function implements d2/dy2 where y is the poloidal coordinate theta | ||
| */ | ||
| Field3D Grad2_par2new(const Field3D& f) { |
There was a problem hiding this comment.
warning: method Grad2_par2new can be made static [readability-convert-member-functions-to-static]
Field3D Grad2_par2new(const Field3D& f) {
^
static| Field2D result; | ||
| result.allocate(); | ||
|
|
||
| BoutReal Grid_NX, Grid_NXlimit; // the grid number on x, and the |
There was a problem hiding this comment.
warning: multiple declarations in a single statement reduces readability [readability-isolate-declaration]
BoutReal Grid_NX, Grid_NXlimit; // the grid number on x, and the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| Field2D result; | ||
| result.allocate(); | ||
|
|
||
| BoutReal Grid_NX, Grid_NXlimit; // the grid number on x, and the |
There was a problem hiding this comment.
warning: variable Grid_NX is not initialized [cppcoreguidelines-init-variables]
BoutReal Grid_NX, Grid_NXlimit; // the grid number on x, and the
^
= NAN| Field2D result; | ||
| result.allocate(); | ||
|
|
||
| BoutReal Grid_NX, Grid_NXlimit; // the grid number on x, and the |
There was a problem hiding this comment.
warning: variable Grid_NXlimit is not initialized [cppcoreguidelines-init-variables]
BoutReal Grid_NX, Grid_NXlimit; // the grid number on x, and the
^
= NAN| if (hyperresist > 0.0) { | ||
| output.write(" Hyper-resistivity coefficient: {:e}\n", hyperresist); | ||
| dump.add(hyper_eta_x, "hyper_eta_x", 1); | ||
| dump.add(hyper_eta_z, "hyper_eta_z", 1); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(hyper_eta_z, "hyper_eta_z", 1);
^
true| return 1; | ||
| if (hyperviscos > 0.0) { | ||
| output.write(" Hyper-viscosity coefficient: {:e}\n", hyperviscos); | ||
| dump.add(hyper_mu_x, "hyper_mu_x", 1); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(hyper_mu_x, "hyper_mu_x", 1);
^
true| return 1; | ||
| if (diffusion_par > 0.0) { | ||
| output.write(" diffusion_par: {:e}\n", diffusion_par); | ||
| dump.add(diffusion_par, "diffusion_par", 0); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(diffusion_par, "diffusion_par", 0);
^
false| // M: 4th order diffusion of p | ||
| if (diffusion_n4 > 0.0) { | ||
| output.write(" diffusion_n4: {:e}\n", diffusion_n4); | ||
| dump.add(diffusion_n4, "diffusion_n4", 0); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(diffusion_n4, "diffusion_n4", 0);
^
false| // M: 4th order diffusion of Ti | ||
| if (diffusion_ti4 > 0.0) { | ||
| output.write(" diffusion_ti4: {:e}\n", diffusion_ti4); | ||
| dump.add(diffusion_ti4, "diffusion_ti4", 0); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(diffusion_ti4, "diffusion_ti4", 0);
^
false
MZ no longer has to be a power of two plus one Co-authored-by: Ben Dudson <bd512@york.ac.uk>
| // M: 4th order diffusion of Te | ||
| if (diffusion_te4 > 0.0) { | ||
| output.write(" diffusion_te4: {:e}\n", diffusion_te4); | ||
| dump.add(diffusion_te4, "diffusion_te4", 0); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(diffusion_te4, "diffusion_te4", 0);
^
false| // M: 4th order diffusion of Vipar | ||
| if (diffusion_v4 > 0.0) { | ||
| output.write(" diffusion_v4: {:e}\n", diffusion_v4); | ||
| dump.add(diffusion_v4, "diffusion_v4", 0); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(diffusion_v4, "diffusion_v4", 0);
^
false| // xqx: parallel hyper-viscous diffusion for vorticity | ||
| if (diffusion_u4 > 0.0) { | ||
| output.write(" diffusion_u4: {:e}\n", diffusion_u4); | ||
| dump.add(diffusion_u4, "diffusion_u4", 0); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(diffusion_u4, "diffusion_u4", 0);
^
false| BoutReal pnorm = max(P0, true); // Maximum over all processors | ||
| if (sink_vp > 0.0) { | ||
| output.write(" sink_vp(rate): {:e}\n", sink_vp); | ||
| dump.add(sink_vp, "sink_vp", 1); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(sink_vp, "sink_vp", 1);
^
true| vacuum_pressure *= pnorm; // Get pressure from fraction | ||
| vacuum_trans *= pnorm; | ||
| output.write(" sp_width(%%): {:e}\n", sp_width); | ||
| dump.add(sp_width, "sp_width", 1); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(sp_width, "sp_width", 1);
^
true| if (diffusion_u4 > 0.0) { | ||
| tmpA2.setBoundary("J"); | ||
| } | ||
| dump.add(Xim_x, "Xim_x", 1); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(Xim_x, "Xim_x", 1);
^
true| tmpA2.setBoundary("J"); | ||
| } | ||
| dump.add(Xim_x, "Xim_x", 1); | ||
| dump.add(Xim_z, "Xim_z", 1); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(Xim_z, "Xim_z", 1);
^
true| } | ||
| } else { | ||
| // Phi solved in RHS (explicitly) | ||
| dump.add(phi, "phi", 1); |
There was a problem hiding this comment.
warning: implicit conversion int -> bool [readability-implicit-bool-conversion]
dump.add(phi, "phi", 1);
^
true| * pow(Te_tmp * Tebar, -1.5); // nu_e in 1/S. | ||
| // nu_e.applyBoundary(); | ||
| // mesh->communicate(nu_e); | ||
| BoutReal N_tmp1; |
There was a problem hiding this comment.
warning: variable N_tmp1 is not initialized [cppcoreguidelines-init-variables]
BoutReal N_tmp1;
^
= NAN| if (diffusion_par > 0.0) { | ||
| // xqx addition, begin | ||
| // Use Spitzer thermal conductivities | ||
| BoutReal Te_tmp1, Ti_tmp1; |
There was a problem hiding this comment.
warning: multiple declarations in a single statement reduces readability [readability-isolate-declaration]
BoutReal Te_tmp1, Ti_tmp1;
^~~~~~~~~~~~~~~~~~~~~~~~~~
| if (diffusion_par > 0.0) { | ||
| // xqx addition, begin | ||
| // Use Spitzer thermal conductivities | ||
| BoutReal Te_tmp1, Ti_tmp1; |
There was a problem hiding this comment.
warning: variable Te_tmp1 is not initialized [cppcoreguidelines-init-variables]
BoutReal Te_tmp1, Ti_tmp1;
^
= NAN| if (diffusion_par > 0.0) { | ||
| // xqx addition, begin | ||
| // Use Spitzer thermal conductivities | ||
| BoutReal Te_tmp1, Ti_tmp1; |
There was a problem hiding this comment.
warning: variable Ti_tmp1 is not initialized [cppcoreguidelines-init-variables]
BoutReal Te_tmp1, Ti_tmp1;
^
= NAN| // Smooth j in x | ||
| if (smooth_j_x) | ||
| Jpar = smooth_x(Jpar); | ||
| Field3D kappa_par_i_fl, kappa_par_e_fl; |
There was a problem hiding this comment.
warning: multiple declarations in a single statement reduces readability [readability-isolate-declaration]
Field3D kappa_par_i_fl, kappa_par_e_fl;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| #include <initialprofiles.hxx> | ||
|
|
||
| int reaction(BoutReal time); | ||
| class Split_operator : public PhysicsModel { |
There was a problem hiding this comment.
warning: constructor does not initialize these fields: rate [cppcoreguidelines-pro-type-member-init]
class Split_operator : public PhysicsModel {
^|
|
||
| protected: | ||
| int init(bool restarting) override; | ||
| int rhs(BoutReal) override; |
There was a problem hiding this comment.
warning: all parameters should be named in a function [readability-named-parameter]
int rhs(BoutReal) override;
^
/*UNUSED_t*/| // just define a macro for V_E dot Grad | ||
| #define vE_Grad(f, p) (b0xGrad_dot_Grad(p, f) / coord->Bxy) | ||
|
|
||
| class TwoFluid : public PhysicsModel { |
There was a problem hiding this comment.
warning: constructor does not initialize these fields: Te_x, Ti_x, Ni_x, Vi_x, bmag, rho_s, fmei, AA, ZZ, lambda_ei, lambda_ii, nu_hat, mui_hat, wci, nueix, nuiix, beta_p, estatic, ZeroElMass, zeff, nu_perp, evolve_rho, evolve_te, evolve_ni, evolve_ajpar, evolve_vi, evolve_ti, ShearFactor, coord, maybe_ylow [cppcoreguidelines-pro-type-member-init]
class TwoFluid : public PhysicsModel {
^| (globalOptions->getSection("ti"))->get("evolve", evolve_ti, true); | ||
| (globalOptions->getSection("Ajpar"))->get("evolve", evolve_ajpar, true); | ||
|
|
||
| if (ZeroElMass) |
There was a problem hiding this comment.
warning: statement should be inside braces [readability-braces-around-statements]
if (ZeroElMass)
^
{| ShearFactor = 0.0; // I disappears from metric | ||
| b0xcv.z += I*b0xcv.x; | ||
| } | ||
| bool ShiftXderivs; |
There was a problem hiding this comment.
warning: variable ShiftXderivs is not initialized [cppcoreguidelines-init-variables]
bool ShiftXderivs;
^
= 0| mui_hat = nu_perp; | ||
| if (nu_perp < 1.e-10) { | ||
| mui_hat = (3. / 10.) * nuiix / wci; | ||
| } else |
There was a problem hiding this comment.
warning: statement should be inside braces [readability-braces-around-statements]
} else
^
{| beta_p = 4.03e-11*Ni_x*Te_x/bmag/bmag; | ||
| if (estatic) { | ||
| beta_p = 1.e-29; | ||
| } else |
There was a problem hiding this comment.
warning: statement should be inside braces [readability-braces-around-statements]
} else
^
{
Adds a tool to convert the legacy API of
physics_init/physics_runto usePhysicsModelinstead, and converts all the examples/tests to usePhysicsModel.This is ahead of removing the old API which will simplify some bits of
Solver.bin/bout-v5-physics-model-upgrader.pyconverts the free functions to out-of-line definitions for thePhysicsModelmethods, and then adds the derived class at the top of the file. I've manually cleaned up a bunch of examples, mostly just inlining the method definitions and making global variables members of the model.