3D coupled deliverable

CMakeLists.txt

@@ -101,6 +101,7 @@ set(LIB_SRC_FILES
     ${SRC_DIR}/nektar_interface/basis_reference.cpp
     ${SRC_DIR}/nektar_interface/expansion_looping/jacobi_coeff_mod_basis.cpp
     ${SRC_DIR}/nektar_interface/function_evaluation.cpp
+    ${SRC_DIR}/nektar_interface/geometry_transport/geometry_transport_2d.cpp
     ${SRC_DIR}/nektar_interface/geometry_transport/geometry_transport_3d.cpp
     ${SRC_DIR}/nektar_interface/geometry_transport/halo_extension.cpp
     ${SRC_DIR}/nektar_interface/particle_cell_mapping/map_particles_2d.cpp
@@ -114,7 +115,7 @@ set(LIB_SRC_FILES
     ${SRC_DIR}/run_info.cpp
     ${SRC_DIR}/simulation.cpp
     ${SRC_DIR}/species.cpp)
-    
+
 set(LIB_SRC_FILES_IGNORE ${SRC_DIR}/main.cpp)
 check_file_list(${SRC_DIR} cpp "${LIB_SRC_FILES}" "${LIB_SRC_FILES_IGNORE}")
 

examples/H3LAPD/.gitignore

@@ -0,0 +1,4 @@
+# Ignore xml files generated from .geos
+cuboid*.xml
+low_res.xml
+full_res.xml

examples/H3LAPD/2Din3D-hw/cuboid_periodic_8x8x16.geo

@@ -0,0 +1,37 @@
+//=============================== Parameters ==================================
+// Lengths and resolutions in each dimension
+xsize = 5;
+ysize = 5;
+zsize = 10;
+nx = 8;
+ny = 8;
+nz = 16;
+//=============================================================================
+
+// 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]};

examples/H3LAPD/2Din3D-hw/hw.xml

@@ -0,0 +1,128 @@
+<?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="6" TYPE="MODIFIED" FIELDS="ne,w,phi,ne_src" />
+    </EXPANSIONS>
+
+    <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"               />
+        </SOLVERINFO>
+
+        <GLOBALSYSSOLNINFO>
+            <V VAR="ne,w,phi,ne_src">
+                <I PROPERTY="GlobalSysSoln" VALUE="IterativeStaticCond" />
+                <I PROPERTY="IterativeSolverTolerance" VALUE="1e-6"/>
+            </V>
+        </GLOBALSYSSOLNINFO>
+
+        <PARAMETERS>
+            <!-- Timestepping and output options -->
+            <P> TimeStep      = 0.000625          </P>
+            <P> NumSteps      = 64000             </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 -->
+            <!-- Dissipates density? -->
+            <P> HW_alpha = 0.1 </P>
+            <!-- Drives turbulence?-->
+            <P> HW_kappa = 3.5 </P> 
+            <!-- Scaling factor for ICs -->
+            <P> s        = 0.5 </P>
+            <!-- Neutral particle system params -->
+            <P> num_particles_per_cell            = -1            </P>
+            <P> num_particle_steps_per_fluid_step = 1             </P>
+            <P> num_particles_total               = 100000        </P>
+            <P> particle_num_write_particle_steps = IO_CheckSteps </P>
+            <P> particle_number_density           = 1e16          </P>
+            <P> particle_position_seed            = 1             </P>
+            <P> particle_thermal_velocity         = 1.0           </P>
+            <P> particle_drift_velocity           = 2.0           </P>
+            <P> particle_source_width             = 0.2           </P>
+            <!-- Temperature in eV used to compute ionisation rate -->
+            <P> Te_eV = 10.0 </P>
+            <!-- Assumed background density in SI -->
+            <P> n_bg_SI = 1e18 </P>
+            <!-- Unit conversion factors for ionisation calc -->
+            <P> t_to_SI = 2e-4 </P>
+            <P> n_to_SI = 1e17 </P>
+        </PARAMETERS>
+
+        <VARIABLES>
+            <V ID="0"> ne  </V>
+            <V ID="1"> w   </V>
+            <V ID="2"> phi </V>
+            <V ID="3"> ne_src </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]" />
+                <P VAR="ne_src" VALUE="[1]" />
+            </REGION>
+            <REGION REF="1">
+                <P VAR="ne"     VALUE="[0]" />
+                <P VAR="w"      VALUE="[0]" />
+                <P VAR="phi"    VALUE="[0]" />
+                <P VAR="ne_src" VALUE="[0]" />
+            </REGION>
+	        <REGION REF="2">
+                <P VAR="ne"     VALUE="[3]" />
+                <P VAR="w"      VALUE="[3]" />
+                <P VAR="phi"    VALUE="[3]" />
+                <P VAR="ne_src" VALUE="[3]" />
+            </REGION>
+            <REGION REF="3">
+                <P VAR="ne"     VALUE="[2]" />
+                <P VAR="w"      VALUE="[2]" />
+                <P VAR="phi"    VALUE="[2]" />
+                <P VAR="ne_src" VALUE="[2]" />
+            </REGION>
+            <REGION REF="4">
+                <P VAR="ne"     VALUE="[5]" />
+                <P VAR="w"      VALUE="[5]" />
+                <P VAR="phi"    VALUE="[5]" />
+                <P VAR="ne_src" VALUE="[5]" />
+            </REGION>
+            <REGION REF="5">
+                <P VAR="ne"     VALUE="[4]" />
+                <P VAR="w"      VALUE="[4]" />
+                <P VAR="phi"    VALUE="[4]" />
+                <P VAR="ne_src" VALUE="[4]" />
+            </REGION>
+        </BOUNDARYCONDITIONS>
+        <FUNCTION NAME="InitialConditions">
+            <E VAR="ne"  DOMAIN="0" VALUE="0" />
+            <E VAR="w"   DOMAIN="0" VALUE="0" />
+            <E VAR="phi" DOMAIN="0" VALUE="0" />
+            <E VAR="ne_src" DOMAIN="0" VALUE="0.0" />
+        </FUNCTION>
+    </CONDITIONS>
+</NEKTAR>

examples/H3LAPD/2Din3D-hw/run_cmd_template.txt

@@ -0,0 +1 @@
+mpirun -np <NMPI> <SOLVER_EXEC> hw.xml cuboid.xml

examples/H3LAPD/2Din3D-hw_fluid-only/cuboid_periodic_5x5x10.geo

@@ -0,0 +1,37 @@
+//=============================== 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]};

examples/H3LAPD/2Din3D-hw_fluid-only/hw.xml

@@ -0,0 +1,103 @@
+<?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="2Din3DHW"                 />
+            <I PROPERTY="AdvectionType"            VALUE="WeakDG"               />
+            <I PROPERTY="Projection"               VALUE="DisContinuous"        />
+            <I PROPERTY="TimeIntegrationMethod"    VALUE="ClassicalRungeKutta4" />
+            <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"/>
+            </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_alpha = 0.1 </P>
+            <P> HW_kappa = 3.5 </P> 
+            <!-- Scaling factor for ICs -->
+            <P> s        = 0.5 </P>
+            <!-- No particles -->
+            <P> num_particles_total = 0 </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>

examples/H3LAPD/2Din3D-hw_fluid-only/run_cmd_template.txt

@@ -0,0 +1 @@
+mpirun -np <NMPI> <SOLVER_EXEC> hw.xml cuboid.xml

examples/H3LAPD/cuboid/cuboid.geo

@@ -0,0 +1,31 @@
+//=============================== 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
+sq = Extrude {0,ysize,0} {Curve{1}; Layers{ny}; Recombine;};
+
+// Extrude square 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]};
+// Long sides, parallel to z-axis
+Physical Surface(1) = {cbd[2],cbd[3],cbd[4],cbd[5]};
+// Low-z square
+Physical Surface(2) = {sq[1]};
+// High-z square
+Physical Surface(3) = {cbd[0]};