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Implicit implementation of 2Din3D Hasegawa-Wakatani #232

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Implicit implementation of 2Din3D Hasegawa-Wakatani #232

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c218cfe
Add skeleton for 3D equation system and example; just copied from 2D…
oparry-ukaea Dec 4, 2023
5eccd35
Working 3D implementation and example.
oparry-ukaea Dec 6, 2023
061d6d3
Remove spurious field in 3D e.g
oparry-ukaea Dec 7, 2023
924b5c1
Adapt GrowthRateRecorder for true 3D HW.
oparry-ukaea Dec 7, 2023
4ff1528
Refactor HW equation classes.
oparry-ukaea Dec 7, 2023
1cd6318
Add test for energy, enstrophy growth rates in 3D. Energy slightly of…
oparry-ukaea Dec 7, 2023
f2a00d7
Simplify GrowthRatesRecorder by applying scalar factors after integrals.
oparry-ukaea Dec 8, 2023
ee31225
Clearer comments and docstrings in GrowthRatesRecorder header.
oparry-ukaea Dec 8, 2023
d7c46dc
Allow HW alpha and kappa to be specified via physical params.
oparry-ukaea Feb 21, 2024
acba2d9
Report parameter values in DriftReducedSystem and HWSystem.
oparry-ukaea Jan 30, 2024
c753113
Remove member var m_alpha from 2Din3D system (was masking m_alpha in …
oparry-ukaea Feb 27, 2024
4ea6bc2
Tweak existing (explicit) HW configs to match nektar-driftwave.
oparry-ukaea Apr 4, 2024
05766b8
Add implicit 2Din3DHW eg.
oparry-ukaea Apr 4, 2024
d411449
Use recent nektar version - required for some functionality used in i…
oparry-ukaea Apr 5, 2024
7ef3381
Implicit version of 2Din3D, copied more-or-less wholesale from nektar…
oparry-ukaea Apr 5, 2024
8e9434a
Minor bugfix.
oparry-ukaea Apr 5, 2024
109f920
Make implicit 2Din3D config closer to the working nektar-driftwave ex…
oparry-ukaea Apr 5, 2024
63e9523
Correct access for do_ode_projection
oparry-ukaea Apr 8, 2024
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2 changes: 1 addition & 1 deletion NESO-Spack
Open in desktop
Submodule NESO-Spack updated 22 files
+21 −0 LICENSE
+5 −1 packages/dpcpp/package.py
+2 −2 packages/hipsycl/package.py
+21 −4 packages/nektar/package.py
+6 −0 packages/neso-particles/package.py
+9 −1 packages/neso/package.py
+0 −12 packages/stdpython/cray-rpath-2.3.patch
+0 −15 packages/stdpython/cray-rpath-3.1.patch
+0 −12 packages/stdpython/fj-rpath-2.3.patch
+0 −13 packages/stdpython/fj-rpath-3.1.patch
+0 −35 packages/stdpython/gcc-8-2.7.14.patch
+0 −38 packages/stdpython/intel-3.6.7.patch
+0 −1,119 packages/stdpython/package.py
+0 −120 packages/stdpython/python-2.7.17+-distutils-C++-fixup.patch
+0 −269 packages/stdpython/python-2.7.17+-distutils-C++.patch
+0 −260 packages/stdpython/python-2.7.8-distutils-C++.patch
+0 −241 packages/stdpython/python-3.6.8-distutils-C++.patch
+0 −256 packages/stdpython/python-3.7.3-distutils-C++.patch
+0 −138 packages/stdpython/python-3.7.4+-distutils-C++-testsuite.patch
+0 −257 packages/stdpython/python-3.7.4+-distutils-C++.patch
+0 −12 packages/stdpython/tkinter-3.8.patch
+0 −17 packages/stdpython/tkinter.patch
13 changes: 7 additions & 6 deletions examples/H3LAPD/2Din3D-hw/hw.xml
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<CONDITIONS>
<SOLVERINFO>
<I PROPERTY="EQTYPE" VALUE="2Din3DHW" />
<I PROPERTY="AdvectionType" VALUE="WeakDG" />
<I PROPERTY="Projection" VALUE="DisContinuous" />
<I PROPERTY="TimeIntegrationMethod" VALUE="ClassicalRungeKutta4" />
<I PROPERTY="UpwindType" VALUE="Upwind" />
<I PROPERTY="EQTYPE" VALUE="2Din3DHW" />
<I PROPERTY="AdvectionType" VALUE="WeakDG" />
<I PROPERTY="Projection" VALUE="DisContinuous" />
<I PROPERTY="TimeIntegrationMethod" VALUE="RungeKutta4" />
<I PROPERTY="AdvectionAdvancement" VALUE="Explicit" />
<I PROPERTY="UpwindType" VALUE="Upwind" />
</SOLVERINFO>

<GLOBALSYSSOLNINFO>
<V VAR="ne,w,phi,ne_src">
<I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
<I PROPERTY="IterativeSolverTolerance" VALUE="1e-6"/>
<I PROPERTY="IterativeSolverTolerance" VALUE="1e-6" />
</V>
</GLOBALSYSSOLNINFO>

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37 changes: 37 additions & 0 deletions examples/H3LAPD/2Din3D-hw_fluid-only-implicit/cuboid_periodic_5x5x10.geo
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//=============================== Parameters ==================================
// Lengths and resolutions in each dimension
xsize = 5;
ysize = 5;
zsize = 10;
nx = 5;
ny = 5;
nz = 10;
//=============================================================================

// Create a line in the x-direction of length <xsize>, with <nx> divisions
Point(1) = {-xsize/2, -ysize/2, 0, 0.01};
Point(2) = {xsize/2, -ysize/2, 0, 0.01};
Line(1) = {1, 2};
Transfinite Line(1) = nx+1;

// Extrude split line into meshed square/rectangle
sq = Extrude {0,ysize,0} {Curve{1}; Layers{ny}; Recombine;};

// Extrude square/rectangle into a cuboid
cbd = Extrude {0,0,zsize} {Surface{sq[1]}; Layers{nz}; Recombine;};

// Define physical volume, surfaces for BCs
// Domain
Physical Volume(0) = {cbd[1]};
// Low-x side
Physical Surface(1) = {cbd[5]};
// High-x side
Physical Surface(2) = {cbd[3]};
// Low-y side
Physical Surface(3) = {cbd[2]};
// High-y side
Physical Surface(4) = {cbd[4]};
// Low-z side
Physical Surface(5) = {sq[1]};
// High-z side
Physical Surface(6) = {cbd[0]};
111 changes: 111 additions & 0 deletions examples/H3LAPD/2Din3D-hw_fluid-only-implicit/hw.xml
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<?xml version="1.0" encoding="utf-8" ?>
<NEKTAR>

<COLLECTIONS DEFAULT="MatrixFree" />

<!--
The composite index for the domain is expected to be 0 if the mesh was generated from the included .geo file
-->
<EXPANSIONS>
<E COMPOSITE="C[0]" NUMMODES="4" TYPE="MODIFIED" FIELDS="ne,w,phi" />
</EXPANSIONS>

<CONDITIONS>
<SOLVERINFO>
<I PROPERTY="EQTYPE" VALUE="2Din3DHW" />
<I PROPERTY="AdvectionType" VALUE="WeakDG" />
<I PROPERTY="Projection" VALUE="DisContinuous" />
<I PROPERTY="TimeIntegrationMethod" VALUE="DIRKOrder2" />
<I PROPERTY="AdvectionAdvancement" VALUE="Implicit" />
<I PROPERTY="LinSysIterSolverTypeInNonlin" VALUE="GMRES" />
</SOLVERINFO>

<GLOBALSYSSOLNINFO>
<V VAR="ne,w,phi,ne_src">
<I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
</V>
</GLOBALSYSSOLNINFO>

<PARAMETERS>
<P> NumSteps = 30000 </P>
<P> TimeStep = 0.005 </P>
<P> IO_InfoSteps = NumSteps/1000 </P>
<P> IO_CheckSteps = NumSteps/100 </P>
<P> s = 2.0 </P>
<P> kappa = 1.0 </P>
<P> alpha = 2.0 </P>
<P> IterativeSolverTolerance = 1.0E-6 </P>
<P> NekNonlinSysMaxIterations = 50 </P>
<P> NewtonRelativeIteTol = 1.0E-6 </P>
<P> NonlinIterTolRelativeL2 = 1.0E-6 </P>
<P> LinSysRelativeTolInNonlin = 1.0E-02 </P>
<!-- Magnetic field strength -->
<P> Bxy = 1.0 </P>
<!-- d22 Coeff for Helmholtz solve -->
<P> d22 = 0.0 </P>
<!-- HW params -->
<P> HW_alpha = 0.1 </P>
<P> HW_kappa = 0.5 </P>
<!-- Scaling factor for ICs -->
<P> s = 0.5 </P>
<!-- No particles -->
<P> num_particles_total = 0 </P>
<!-- Turn on energy, enstrophy output -->
<P> growth_rates_recording_step = 1 </P>
</PARAMETERS>

<VARIABLES>
<V ID="0"> ne </V>
<V ID="1"> w </V>
<V ID="2"> phi </V>
</VARIABLES>

<BOUNDARYREGIONS>
<B ID="0"> C[1] </B> <!-- Low x -->
<B ID="1"> C[2] </B> <!-- High x -->
<B ID="2"> C[3] </B> <!-- Low y -->
<B ID="3"> C[4] </B> <!-- High y -->
<B ID="4"> C[5] </B> <!-- Low-z end -->
<B ID="5"> C[6] </B> <!-- High-z end -->
</BOUNDARYREGIONS>

<!-- Periodic conditions for all fields on all boundaries -->
<BOUNDARYCONDITIONS>
<REGION REF="0">
<P VAR="ne" VALUE="[1]" />
<P VAR="w" VALUE="[1]" />
<P VAR="phi" VALUE="[1]" />
</REGION>
<REGION REF="1">
<P VAR="ne" VALUE="[0]" />
<P VAR="w" VALUE="[0]" />
<P VAR="phi" VALUE="[0]" />
</REGION>
<REGION REF="2">
<P VAR="ne" VALUE="[3]" />
<P VAR="w" VALUE="[3]" />
<P VAR="phi" VALUE="[3]" />
</REGION>
<REGION REF="3">
<P VAR="ne" VALUE="[2]" />
<P VAR="w" VALUE="[2]" />
<P VAR="phi" VALUE="[2]" />
</REGION>
<REGION REF="4">
<P VAR="ne" VALUE="[5]" />
<P VAR="w" VALUE="[5]" />
<P VAR="phi" VALUE="[5]" />
</REGION>
<REGION REF="5">
<P VAR="ne" VALUE="[4]" />
<P VAR="w" VALUE="[4]" />
<P VAR="phi" VALUE="[4]" />
</REGION>
</BOUNDARYCONDITIONS>
<FUNCTION NAME="InitialConditions">
<E VAR="ne" DOMAIN="0" VALUE="6*exp((-x*x-y*y)/(s*s))*sin(4*PI*z/10)" />
<E VAR="w" DOMAIN="0" VALUE="(4*exp((-x*x-y*y)/(s*s))*(-s*s+x*x+y*y)/s^4)*sin(4*PI*z/10)" />
<E VAR="phi" DOMAIN="0" VALUE="exp(-(x*x+y*y)/(s*s))*sin(4*PI*z/10)" />
</FUNCTION>
</CONDITIONS>
</NEKTAR>
1 change: 1 addition & 0 deletions examples/H3LAPD/2Din3D-hw_fluid-only-implicit/run_cmd_template.txt
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mpirun -np <NMPI> <SOLVER_EXEC> hw.xml cuboid.xml
13 changes: 7 additions & 6 deletions examples/H3LAPD/2Din3D-hw_fluid-only/hw.xml
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Expand Up @@ -12,17 +12,18 @@

<CONDITIONS>
<SOLVERINFO>
<I PROPERTY="EQTYPE" VALUE="2Din3DHW" />
<I PROPERTY="AdvectionType" VALUE="WeakDG" />
<I PROPERTY="Projection" VALUE="DisContinuous" />
<I PROPERTY="TimeIntegrationMethod" VALUE="ClassicalRungeKutta4" />
<I PROPERTY="UpwindType" VALUE="Upwind" />
<I PROPERTY="EQTYPE" VALUE="2Din3DHW" />
<I PROPERTY="AdvectionType" VALUE="WeakDG" />
<I PROPERTY="Projection" VALUE="DisContinuous" />
<I PROPERTY="TimeIntegrationMethod" VALUE="RungeKutta4" />
<I PROPERTY="AdvectionAdvancement" VALUE="Explicit" />
<I PROPERTY="UpwindType" VALUE="Upwind" />
</SOLVERINFO>

<GLOBALSYSSOLNINFO>
<V VAR="ne,w,phi,ne_src">
<I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
<I PROPERTY="IterativeSolverTolerance" VALUE="1e-6"/>
<I PROPERTY="IterativeSolverTolerance" VALUE="1e-6" />
</V>
</GLOBALSYSSOLNINFO>

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37 changes: 37 additions & 0 deletions examples/H3LAPD/3D-hw/cuboid_periodic_5x5x10.geo
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//=============================== Parameters ==================================
// Lengths and resolutions in each dimension
xsize = 5;
ysize = 5;
zsize = 10;
nx = 5;
ny = 5;
nz = 10;
//=============================================================================

// Create a line in the x-direction of length <xsize>, with <nx> divisions
Point(1) = {-xsize/2, -ysize/2, 0, 0.01};
Point(2) = {xsize/2, -ysize/2, 0, 0.01};
Line(1) = {1, 2};
Transfinite Line(1) = nx+1;

// Extrude split line into meshed square/rectangle
sq = Extrude {0,ysize,0} {Curve{1}; Layers{ny}; Recombine;};

// Extrude square/rectangle into a cuboid
cbd = Extrude {0,0,zsize} {Surface{sq[1]}; Layers{nz}; Recombine;};

// Define physical volume, surfaces for BCs
// Domain
Physical Volume(0) = {cbd[1]};
// Low-x side
Physical Surface(1) = {cbd[5]};
// High-x side
Physical Surface(2) = {cbd[3]};
// Low-y side
Physical Surface(3) = {cbd[2]};
// High-y side
Physical Surface(4) = {cbd[4]};
// Low-z side
Physical Surface(5) = {sq[1]};
// High-z side
Physical Surface(6) = {cbd[0]};
107 changes: 107 additions & 0 deletions examples/H3LAPD/3D-hw/hw.xml
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<?xml version="1.0" encoding="utf-8" ?>
<NEKTAR>

<COLLECTIONS DEFAULT="MatrixFree" />

<!--
The composite index for the domain is expected to be 0 if the mesh was generated from the included .geo file
-->
<EXPANSIONS>
<E COMPOSITE="C[0]" NUMMODES="7" TYPE="MODIFIED" FIELDS="ne,w,phi" />
</EXPANSIONS>

<CONDITIONS>
<SOLVERINFO>
<I PROPERTY="EQTYPE" VALUE="3DHW" />
<I PROPERTY="AdvectionType" VALUE="WeakDG" />
<I PROPERTY="Projection" VALUE="DisContinuous" />
<I PROPERTY="TimeIntegrationMethod" VALUE="RungeKutta4" />
<I PROPERTY="AdvectionAdvancement" VALUE="Explicit" />
<I PROPERTY="UpwindType" VALUE="Upwind" />
</SOLVERINFO>

<GLOBALSYSSOLNINFO>
<V VAR="ne,w,phi">
<I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
<I PROPERTY="IterativeSolverTolerance" VALUE="1e-6"/>
</V>
</GLOBALSYSSOLNINFO>

<PARAMETERS>
<!-- Timestepping and output options -->
<P> TimeStep = 0.00125 </P>
<P> NumSteps = 32000 </P>
<P> TFinal = NumSteps*TimeStep </P>
<P> IO_InfoSteps = NumSteps/1600 </P>
<P> IO_CheckSteps = NumSteps/160 </P>
<!-- Magnetic field strength -->
<P> Bxy = 1.0 </P>
<!-- d22 Coeff for Helmholtz solve -->
<P> d22 = 0.0 </P>
<!-- HW params -->
<P> HW_omega_ce = 0.1 </P>
<P> HW_nu_ei = 1.0 </P>
<P> HW_kappa = 3.5 </P>
<!-- Scaling factor for ICs -->
<P> s = 0.5 </P>
<!-- No particles -->
<P> num_particles_total = 0 </P>
<!-- Turn on energy, enstrophy output -->
<!-- <P> growth_rates_recording_step = 1 </P> -->
</PARAMETERS>

<VARIABLES>
<V ID="0"> ne </V>
<V ID="1"> w </V>
<V ID="2"> phi </V>
</VARIABLES>

<BOUNDARYREGIONS>
<B ID="0"> C[1] </B> <!-- Low x -->
<B ID="1"> C[2] </B> <!-- High x -->
<B ID="2"> C[3] </B> <!-- Low y -->
<B ID="3"> C[4] </B> <!-- High y -->
<B ID="4"> C[5] </B> <!-- Low-z end -->
<B ID="5"> C[6] </B> <!-- High-z end -->
</BOUNDARYREGIONS>

<!-- Periodic conditions for all fields on all boundaries -->
<BOUNDARYCONDITIONS>
<REGION REF="0">
<P VAR="ne" VALUE="[1]" />
<P VAR="w" VALUE="[1]" />
<P VAR="phi" VALUE="[1]" />
</REGION>
<REGION REF="1">
<P VAR="ne" VALUE="[0]" />
<P VAR="w" VALUE="[0]" />
<P VAR="phi" VALUE="[0]" />
</REGION>
<REGION REF="2">
<P VAR="ne" VALUE="[3]" />
<P VAR="w" VALUE="[3]" />
<P VAR="phi" VALUE="[3]" />
</REGION>
<REGION REF="3">
<P VAR="ne" VALUE="[2]" />
<P VAR="w" VALUE="[2]" />
<P VAR="phi" VALUE="[2]" />
</REGION>
<REGION REF="4">
<P VAR="ne" VALUE="[5]" />
<P VAR="w" VALUE="[5]" />
<P VAR="phi" VALUE="[5]" />
</REGION>
<REGION REF="5">
<P VAR="ne" VALUE="[4]" />
<P VAR="w" VALUE="[4]" />
<P VAR="phi" VALUE="[4]" />
</REGION>
</BOUNDARYCONDITIONS>
<FUNCTION NAME="InitialConditions">
<E VAR="ne" DOMAIN="0" VALUE="6*exp((-x*x-y*y)/(s*s))*sin(4*PI*z/10)" />
<E VAR="w" DOMAIN="0" VALUE="(4*exp((-x*x-y*y)/(s*s))*(-s*s+x*x+y*y)/s^4)*sin(4*PI*z/10)" />
<E VAR="phi" DOMAIN="0" VALUE="exp(-(x*x+y*y)/(s*s))*sin(4*PI*z/10)" />
</FUNCTION>
</CONDITIONS>
</NEKTAR>
1 change: 1 addition & 0 deletions examples/H3LAPD/3D-hw/run_cmd_template.txt
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mpirun -np <NMPI> <SOLVER_EXEC> hw.xml cuboid.xml
2 changes: 1 addition & 1 deletion nektar
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Submodule nektar updated from 2e0fb8 to 8bc4b3
3 changes: 2 additions & 1 deletion solvers/H3LAPD/CMakeLists.txt
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# Identify source files
set(H3LAPD_SRC_FILES
EquationSystems/DriftReducedSystem.cpp EquationSystems/HW2Din3DSystem.cpp
EquationSystems/DriftReducedSystem.cpp EquationSystems/HWSystem.cpp
EquationSystems/HW2Din3DSystem.cpp EquationSystems/HW3DSystem.cpp
EquationSystems/LAPDSystem.cpp H3LAPD.cpp)

# ============================== Object library ===============================
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