added parfiles to tutorial sub-directory. and there is a jupyter nb f…

…or the tutorial now

machines/rusty.sh

@@ -36,7 +36,7 @@ then
         echo "GPU build"
         # Load required modules
         module --force purge
-        module load modules/2.3-20240529 slurm cmake gcc/11.4.0 cuda gsl openmpi/cuda-4.0.7 hdf5 openblas
+        module load modules/2.3-20240529 slurm cmake gcc/11.4.0 cuda gsl openmpi hdf5 openblas
         module list
         # 8-way compile for H100s
         if [[ $ARGS == *"h100"* ]]; then
@@ -74,4 +74,4 @@ then
         C_NATIVE=gcc
         CXX_NATIVE=g++
     fi
-fi
+fi

scripts/tutorial/parfiles/anisotropic_conduction.par

@@ -0,0 +1,71 @@
+# Anisotropic Conduction problem
+# Heat conduction along field lines in the EMHD theory
+# of Chandra+2015
+
+<parthenon/job>
+problem_id = anisotropic_conduction
+
+<parthenon/mesh>
+nx1 = 256
+x1min = 0.0
+x1max = 1.0
+
+nx2 = 256
+x2min = 0.0
+x2max = 1.0
+
+nx3 = 1
+x3min = 0.0
+x3max = 1.0
+
+<parthenon/meshblock>
+nx1 = 256
+nx2 = 256
+nx3 = 1
+
+<coordinates>
+# Setting Cartesian coords defaults to periodic boundaries
+base = cartesian_minkowski
+transform = null
+
+<parthenon/time>
+tlim = 10.0
+dt_min = 1e-6
+
+<GRMHD>
+cfl = 0.7
+gamma = 1.333333
+reconstruction = weno5
+
+<floors>
+bsq_over_rho_max = 100
+u_over_rho_max = 100
+
+<debug>
+verbose = 1
+flag_verbose = 0
+extra_checks = 1
+
+# This block must be present and values filled
+# in all EGRMHD simulations
+<emhd>
+on = true
+closure_type = constant
+higher_order_terms = true
+tau = 0.1
+conduction_alpha = 0.1
+viscosity_alpha = 0.0
+
+# Implicit driver is auto-selected for emhd
+<implicit>
+max_nonlinear_iter = 3
+
+<parthenon/output0>
+file_type = hdf5
+dt = 0.1
+single_precision_output = true
+variables = prims
+
+<parthenon/output1>
+file_type = hst
+dt = 0.1

scripts/tutorial/parfiles/anisotropic_conduction_ideal.par

@@ -0,0 +1,72 @@
+# Anisotropic Conduction problem
+# Heat conduction along field lines in the EMHD theory
+# of Chandra+2015
+
+<parthenon/job>
+problem_id = anisotropic_conduction
+
+<parthenon/mesh>
+nx1 = 512
+x1min = 0.0
+x1max = 1.0
+
+nx2 = 512
+x2min = 0.0
+x2max = 1.0
+
+nx3 = 1
+x3min = 0.0
+x3max = 1.0
+
+<parthenon/meshblock>
+nx1 = 512
+nx2 = 512
+nx3 = 1
+
+<coordinates>
+# Setting Cartesian coords defaults to periodic boundaries
+base = cartesian_minkowski
+transform = null
+
+<parthenon/time>
+tlim = 10.0
+dt_min = 1e-6
+
+<GRMHD>
+cfl = 0.7
+gamma = 1.333333
+reconstruction = weno5
+
+<floors>
+bsq_over_rho_max = 100
+u_over_rho_max = 100
+
+<debug>
+verbose = 1
+flag_verbose = 0
+extra_checks = 1
+
+# This block must be present and values filled
+# in all EGRMHD simulations
+<emhd>
+on = false
+closure_type = constant
+higher_order_terms = true
+tau = 0.1
+conduction_alpha = 0.01
+viscosity_alpha = 0.0
+
+# Implicit driver is auto-selected for emhd
+<implicit>
+on = false
+max_nonlinear_iter = 3
+
+<parthenon/output0>
+file_type = hdf5
+dt = 0.1
+single_precision_output = true
+variables = prims
+
+<parthenon/output1>
+file_type = hst
+dt = 0.1

scripts/tutorial/parfiles/orszag_tang.par

@@ -0,0 +1,64 @@
+# Orszag-Tang Vortex problem:
+# Generate current sheets on short timescales
+
+<parthenon/job>
+problem_id = orszag_tang
+
+<parthenon/mesh>
+nx1 = 512
+x1min = -3.141592653589793
+x1max = 3.141592653589793
+
+nx2 = 512
+x2min = -3.141592653589793
+x2max = 3.141592653589793
+
+nx3 = 1
+x3min = -0.01
+x3max = 0.01
+
+<parthenon/meshblock>
+nx1 = 512
+nx2 = 512
+nx3 = 1
+
+<coordinates>
+base = cartesian_minkowski
+transform = null
+
+<parthenon/time>
+tlim = 140.0
+integrator = rk2
+
+<GRMHD>
+cfl = 0.9
+gamma = 1.666667
+
+<flux>
+type = hlle
+reconstruction = weno5
+
+<b_field>
+solver = face_ct
+ct_scheme = gs05_c
+
+<debug>
+verbose = 1
+flag_verbose = 2
+extra_checks = 1
+
+<parthenon/output0>
+file_type = hdf5
+dt = 1.0
+single_precision_output = true
+variables = prims, jcon
+
+<parthenon/output1>
+file_type = hst
+dt = 0.1
+
+# This problem is generally much too short to need
+# checkpointing.  However, we have a test which uses it.
+#<parthenon/output2>
+#file_type = rst
+#dt = 10.0

scripts/tutorial/parfiles/sane2d.par

@@ -0,0 +1,97 @@
+# SANE model in 2D
+# Overall simulation size 50M, to allow
+# running at small scale on e.g. a laptop
+# Uses MKS coordinates, not Funky variant
+
+<parthenon/job>
+problem_id = torus
+
+<parthenon/mesh>
+nx1 = 256
+nx2 = 256
+nx3 = 1
+
+<parthenon/meshblock>
+nx1 = 256
+nx2 = 256
+nx3 = 1
+
+<coordinates>
+base = spherical_ks
+transform = fmks
+r_out = 50
+a = 0.9375
+hslope = 0.3
+mks_smooth = 0.5
+poly_xt = 0.82
+poly_alpha = 14.0
+
+<parthenon/time>
+tlim = 3000.0
+nlim = -1
+integrator = vl2
+
+<debug>
+verbose = 1
+extra_checks = 1
+flag_verbose = 0
+
+<GRMHD>
+cfl = 0.9
+gamma = 1.666667
+reconstruction = weno5
+
+<b_field>
+solver = flux_ct
+
+<driver>
+type = kharma
+
+<torus>
+rin = 6.0
+rmax = 12.0
+
+<perturbation>
+u_jitter = 0.04
+
+<b_field>
+type = sane
+beta_min = 100.
+
+<floors>
+rho_min_geom = 1e-5
+u_min_geom = 1e-7
+u_over_rho_max = 100
+bsq_over_rho_max = 100
+
+<parthenon/output0>
+file_type = hdf5
+dt = 10.0
+single_precision_output = true
+# Fields beginning with a specifier here will be included (e.g., all prims.XXX)
+# Fields specified but not present are silently skipped
+# If you need a line break, use '&' at line end
+variables = prims, jcon, pflag, fflag
+
+<parthenon/output1>
+file_type = rst
+dt = 100.0
+
+<parthenon/output2>
+file_type = hst
+dt = 0.1
+variables = all_reductions
+
+# This outputs a geometry file, similar to iharm3d's old 'grid.h5'
+# Not needed for pyharm analysis in Kerr metrics, but useful in
+# a bunch of other contexts.
+<parthenon/output3>
+file_type = hdf5
+analysis_output = true
+dt = 1e20
+single_precision_output = false
+# If you want the convenience and hate disk space, you can add these
+# variables to "normal" dump files like output0 too.
+variables = coords.Xnative, coords.Xsph, &
+            coords.gcon, coords.gcov, coords.gdet, coords.lapse, coords.conn, &
+            coords.gcon_embed, coords.gcov_embed, coords.gdet_embed