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Seperate adapt_sources for density and pressure terms #8

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3403760
add excitation to the radiation sink term
hahahasan Nov 10, 2021
0633081
fix multiple uses of 'excitation' so hydrogen excitation is now the f…
hahahasan Nov 10, 2021
e3d7669
save the radiation rates Riz, Rrc, Rcx, Rex
hahahasan Nov 12, 2021
7d84855
remerging some of the changes from Hasan's branch - mostly setting so…
hahahasan Dec 9, 2021
13c57a8
have outputs for the ionisation, charge-exchange and recombination ra…
hahahasan Jan 25, 2022
5941364
stupid ';'
hahahasan Jan 25, 2022
c287365
update gitignore
hahahasan Jan 25, 2022
61470b2
remove untracked folders
hahahasan Jan 25, 2022
bfa67da
erroneous symlink added somehow. this is now removed
hahahasan Jan 25, 2022
09a9707
change default of revCurlB_b to false
hahahasan Jan 28, 2022
974d2ba
have different impurity fractions according to regions specified by p…
hahahasan Jan 31, 2022
463b30e
fix to the neutral model so that previous ionisation cost fix is appl…
hahahasan Apr 21, 2022
fd96272
fixed the delp2 dissipation terms in the radial buffers (no longer ap…
hahahasan May 10, 2022
299cec5
impurity_split >> impurity_split_y to leave option for have impurity …
hahahasan May 10, 2022
b12f4b4
fixed issues with impurity_split ; optimised use of the finite differ…
hahahasan May 10, 2022
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,4 @@ BOUT.log.*
*.pdf
*~
.BOUT.pid*
.vscode/
23 changes: 12 additions & 11 deletions CMakeLists.txt
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Expand Up @@ -13,16 +13,16 @@ set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})

# Update submodules
# Adapted from https://cliutils.gitlab.io/modern-cmake/chapters/projects/submodule.html
find_package(Git QUIET)
if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
message(STATUS "Submodule update")
execute_process(COMMAND ${GIT_EXECUTABLE} -c submodule.recurse=false submodule update --init --recursive
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
RESULT_VARIABLE GIT_SUBMOD_RESULT)
if(NOT GIT_SUBMOD_RESULT EQUAL "0")
message(FATAL_ERROR "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules")
endif()
endif()
# find_package(Git QUIET)
# if(GIT_FOUND AND EXISTS "${PROJECT_SOURCE_DIR}/.git")
# message(STATUS "Submodule update")
# execute_process(COMMAND ${GIT_EXECUTABLE} -c submodule.recurse=false submodule update --init --recursive
# WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
# RESULT_VARIABLE GIT_SUBMOD_RESULT)
# if(NOT GIT_SUBMOD_RESULT EQUAL "0")
# message(FATAL_ERROR "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules")
# endif()
# endif()

# Get the Git revision
include(GetGitRevisionDescription)
Expand All @@ -33,7 +33,8 @@ endif()
message(STATUS "Git revision: ${HERMES_REVISION}")

# BOUT++ is a dependency
add_subdirectory(external/BOUT-dev)
# add_subdirectory(external/BOUT-dev)
find_package(bout++ REQUIRED)

set(HERMES_SOURCES
src/hermes-2.cxx
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22 changes: 19 additions & 3 deletions include/hermes-2.hxx
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Expand Up @@ -45,10 +45,18 @@ protected:

int precon(BoutReal t, BoutReal gamma, BoutReal delta);
private:
// grid region boundaries
int jyseps1_1;
int jyseps1_2;
int jyseps2_1;
int jyseps2_2;

// Equilibrium current
Field2D Jpar0;

BoutReal nelim_floor; // Global density floor
BoutReal nesheath_floor; // Density floor used in sheath boundary conditions
BoutReal kappa_epar_floor; // Electron heat conductivity floor

// Evolving variables
Field3D Ne; // Electron density
Expand Down Expand Up @@ -90,6 +98,10 @@ private:
// Impurity radiation
BoutReal fimp; // Impurity fraction (of Ne)
bool impurity_adas; // True if using ImpuritySpecies, false if using
bool impurity_split_y; // Split the fixed fraction impurities by region
BoutReal fimp_id; // fimp in the inner divertor (0 -> jyseps1_1)
BoutReal fimp_od; // fimp in the outer divertor (jyseps2_2 -> -1)
BoutReal fimp_us; // fimp in the upstream (between jyseps1_1 and jyseps2_2)
ImpuritySpecies *impurity; // Atomicpp impurity

BoutReal carbon_fraction;
Expand Down Expand Up @@ -142,6 +154,7 @@ private:
bool sheath_closure; // Sheath closure sink on vorticity (if sinks = true)
bool drift_wave; // Drift-wave closure (if sinks=true)

bool slab_radial_buffers; // an alternatice radial buffer region for use in slab geometry
bool radial_buffers; // Radial buffer regions
int radial_inner_width; // Number of points in the inner radial buffer
int radial_outer_width; // Number of points in the outer radial buffer
Expand Down Expand Up @@ -181,14 +194,16 @@ private:
BoutReal numdiff, hyper, hyperpar; ///< Numerical dissipation
int low_pass_z; // Fourier filter in Z
BoutReal z_hyper_viscos, x_hyper_viscos, y_hyper_viscos; // 4th-order derivatives
bool low_n_diffuse; // Diffusion in parallel direction at low density
bool low_n_diffuse_perp; // Diffusion in perpendicular direction at low density
BoutReal low_n_diffuse; // Diffusion in parallel direction at low density
BoutReal low_n_diffuse_perp; // Diffusion in perpendicular direction at low density
BoutReal ne_hyper_z, pe_hyper_z; // Hyper-diffusion
BoutReal nvi_hyper_z, vepsi_hyper_z; // hyper-diffusion on ion terms
BoutReal scale_num_cs; // Scale numerical sound speed
BoutReal floor_num_cs; // Apply a floor to the numerical sound speed
bool vepsi_dissipation; // Dissipation term in VePsi equation
bool vort_dissipation; // Dissipation term in Vorticity equation
bool phi_dissipation; // Dissipation term in Vorticity equation, depending on phi
BoutReal phi_dissipation; // Dissipation term in Vorticity equation, depending on phi
BoutReal delp2_dissipation; // Dissipation using delp2

// Sources and profiles

Expand Down Expand Up @@ -222,6 +237,7 @@ private:

// Curvature, Grad-B drift
Vector3D Curlb_B; // Curl(b/B)
bool revCurlb_B; // Reverse direction of Curl(b/B) vector

// Perturbed parallel gradient operators
const Field3D Grad_parP(const Field3D &f);
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2 changes: 2 additions & 0 deletions include/mixed.hxx
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Expand Up @@ -33,6 +33,8 @@ private:
Field3D Pnlim; // Limited pressure, used to calculate pressure-driven diffusive flows
Field3D Vn;
Field3D Dnn;

Field3D Riz, Rrc, Rcx, Rex;

bool sheath_ydown, sheath_yup;

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5 changes: 4 additions & 1 deletion include/neutral-model.hxx
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Expand Up @@ -26,6 +26,7 @@ public:

// Options for calculating rates
OPTION(options, Eionize, 30); // Energy loss per ionisation [eV]
OPTION(options, h_excitation, true); // Add to plasma radiation sink
}
virtual ~NeutralModel() {}

Expand Down Expand Up @@ -74,11 +75,13 @@ protected:
UpdatedRadiatedPower hydrogen; // Atomic rates (H.Willett)

BoutReal Eionize; // Energy loss per ionisation [eV]

bool h_excitation; // add excitation energy to the hydrogen radiation energy sink

void neutral_rates(const Field3D &Ne, const Field3D &Te, const Field3D &Ti, const Field3D &Vi, // Plasma quantities
const Field3D &Nn, const Field3D &Tn, const Field3D &Vnpar, // Neutral gas
Field3D &S, Field3D &F, Field3D &Qi, Field3D &R, // Transfer rates
Field3D &Riz, Field3D &Rrc, Field3D &Rcx); // Rates
Field3D &Riz, Field3D &Rrc, Field3D &Rcx, Field3D &Rex); // Rates

private:
NeutralModel();
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26 changes: 26 additions & 0 deletions include/revision.hxx
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@@ -0,0 +1,26 @@
/// Information about the version of Hermes
///
/// The build system will update this file on every commit, which may
/// result in files that include it getting rebuilt. Therefore it
/// should be included in as few places as possible

#ifndef HERMES_REVISION_H
#define HERMES_REVISION_H

namespace hermes {
namespace version {
/// The git commit hash
#ifndef HERMES_REVISION
constexpr auto revision = "@HERMES_REVISION@";
#else
// Stringify value passed at compile time
#define BUILDFLAG1_(x) #x
#define BUILDFLAG(x) BUILDFLAG1_(x)
constexpr auto revision = BUILDFLAG(HERMES_REVISION);
#undef BUILDFLAG1
#undef BUILDFLAG
#endif
} // namespace version
} // namespace hermes

#endif // HERMES_REVISION_H
4 changes: 2 additions & 2 deletions src/full-velocity.cxx
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Expand Up @@ -324,8 +324,8 @@ void FullVelocity::update(const Field3D &Ne, const Field3D &Te,
/////////////////////////////////////////////////////
// Atomic processes

Field3D Riz, Rrc, Rcx;
neutral_rates(Ne, Te, Ti, Vi, Nn, Tn, Vnpar, S, F, Qi, Rp, Riz, Rrc, Rcx);
Field3D Riz, Rrc, Rcx, Rex;
neutral_rates(Ne, Te, Ti, Vi, Nn, Tn, Vnpar, S, F, Qi, Rp, Riz, Rrc, Rcx, Rex);

Fperp = Rrc + Rcx; // Friction for vorticity

Expand Down
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