WIP: Precipitator pgen

.gitignore

@@ -1,6 +1,15 @@
 # Object and binary directories
 build*/
 
+# output files
+*.csv
+*.png
+*.hdf5
+*.root
+*.rhdf
+*.hst
+*.xdmf
+
 # Mac OS metadata
 .DS_Store
 

CMakeLists.txt

@@ -83,5 +83,6 @@ add_subdirectory(src)
 if (AthenaPK_ENABLE_TESTING)
   include(CTest)
   add_subdirectory(tst/regression)
+  add_subdirectory(tst/unit)
 endif()
 

ascent_options.json

@@ -0,0 +1,3 @@
+{
+    "timings": "true"
+}

athenapk_1node.submit

@@ -0,0 +1,32 @@
+#!/bin/bash --login
+#SBATCH --job-name="athenapk"
+#SBATCH --partition=gpuA100x4
+#SBATCH --account=cvz-delta-gpu
+#SBATCH --mem=0
+#SBATCH --exclusive
+#SBATCH --time=4:00:00
+#SBATCH --constraint="scratch"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+#SBATCH --cpus-per-task=16
+#SBATCH --gpus-per-task=1
+#SBATCH --gpu-bind=none
+
+ulimit -c unlimited
+
+module purge
+module load gcc/11.2.0
+module load cuda/11.7.0
+module load openmpi/4.1.4
+
+
+EXE="./build-gpu/bin/athenaPK"
+INPUTS="-i inputs/precipitator.in"
+
+## run
+srun bash -c "
+    export CUDA_VISIBLE_DEVICES=\$((3-SLURM_LOCALID));
+    ${EXE} ${INPUTS}"
+
+
+

heating.ipynb

@@ -0,0 +1,106 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 29,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1.1592344011867434e-28"
+      ]
+     },
+     "execution_count": 29,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# compute heating rate\n",
+    "import numpy as np\n",
+    "gamma = 5./3.\n",
+    "mH = 1.673533e-24 # H mass (g)\n",
+    "kB = 1.380649e-16 # Boltzmann constant (cgs)\n",
+    "mu = 0.6 * mH\n",
+    "T = 3.0e7\n",
+    "kpc_in_cm = 3.086e21 # cm\n",
+    "L = 100 * kpc_in_cm\n",
+    "Mach = 0.5\n",
+    "cs = np.sqrt(gamma * kB * T / mu)\n",
+    "dv = Mach * cs\n",
+    "ndens = 1.0e-3\n",
+    "turb_heat = 0.5*(ndens*mu)*(dv*dv)*(dv/L)\n",
+    "turb_heat"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 30,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1e-28"
+      ]
+     },
+     "execution_count": 30,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# compute cooling rate\n",
+    "Lambda_cool = 1.0e-22\n",
+    "cool_rate = ndens**2 * Lambda_cool\n",
+    "cool_rate"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 32,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.22092570562189412"
+      ]
+     },
+     "execution_count": 32,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "f_turb = 0.1\n",
+    "dv = (2*f_turb*ndens*Lambda_cool*L/mu)**(1./3.)\n",
+    "Mach_number = dv / cs\n",
+    "Mach_number"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.4"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

inputs/precipitator.cooling

@@ -0,0 +1,3 @@
+# logT Lambda
+1.0     -22.
+10.0    -22.

inputs/precipitator.in

@@ -0,0 +1,102 @@
+<comment>
+problem   = Precipitator box
+
+<job>
+problem_id = precipitator   # problem ID: basename of output filenames
+
+<parthenon/output1>
+file_type  = hst       # History data dump
+dt         = 50.0       # time increment between outputs
+
+#<parthenon/output2>
+#file_type  = hdf5      # HDF5 data dump
+#variables  = prim, drho_over_rho, dP_over_P, dK_over_K, dEdot_over_Edot, dT_over_T, entropy, temperature
+#dt         = 250.0        # Time increment between outputs
+#id         = prim      # Name to append to output
+
+<parthenon/output3>
+file_type  = rst        # Binary data dump
+dt         = 1000.0        # time increment between outputs
+id         = restart
+
+<parthenon/output4>
+file_type    = ascent
+dt           = 50.0
+actions_file = inputs/precipitator_no_binning.yaml
+
+<parthenon/time>
+cfl        = 0.3        # The Courant, Friedrichs, & Lewy (CFL) Number
+nlim       = -1         # cycle limit
+tlim       = 1.0e4      # time limit
+integrator  = rk2       # time integration algorithm
+perf_cycle_offset  = 10 # interval for stdout summary info
+
+
+<parthenon/mesh>
+refinement  = static
+nghost = 4
+
+nx1        = 256       # Number of zones in X1-direction
+x1min      = -50.       # minimum value of X1
+x1max      = 50.0       # maximum value of X1
+ix1_bc     = periodic   # inner-X1 boundary flag
+ox1_bc     = periodic   # outer-X1 boundary flag
+
+nx2        = 256       # Number of zones in X2-direction
+x2min      = -50.0       # minimum value of X2
+x2max      = 50.0       # maximum value of X2
+ix2_bc     = periodic   # inner-X2 boundary flag
+ox2_bc     = periodic   # outer-X2 boundary flag
+
+nx3        = 512       # Number of zones in X3-direction
+x3min      = -100.       # minimum value of X3
+x3max      = 100.       # maximum value of X3
+ix3_bc     = user       # inner-X3 boundary flag
+ox3_bc     = user       # outer-X3 boundary flag
+
+
+<parthenon/meshblock>
+nx1        = 64        # Number of zones in X1-direction
+nx2        = 64        # Number of zones in X2-direction
+nx3        = 64        # Number of zones in X3-direction
+
+<hydro>
+gamma = 1.6666666666666667 # gamma = C_p/C_v
+eos = adiabatic
+riemann = lhllc
+reconstruction = ppm
+first_order_flux_correct = true
+use_scratch = false
+scratch_level = 0 # 0 is actual scratch (tiny); 1 is HBM
+
+He_mass_fraction = 0.25
+dfloor = 0.     # Msun kpc^{-3}
+Tfloor = 1.0e5  # K
+
+<units>
+code_length_cgs = 3.086e21      # kpc
+code_mass_cgs = 1.98841586e+33  # Msun
+code_time_cgs = 3.15576e+13     # Myr
+
+<cooling>
+enable_cooling = tabular
+integrator = rk12           # (townsend, rk12)
+table_filename = ./inputs/precipitator.cooling
+log_temp_col = 0
+log_lambda_col = 1
+lambda_units_cgs = 1
+cfl = 1.0
+
+<precipitator>
+hse_profile_filename = ./inputs/tabulated_hse_tc_tff_8.0.txt
+
+enable_heating = magic
+epsilon_heating = 1.0
+numHist = 64
+h_smooth_heatcool_kpc = 20.
+
+perturb_sin_drho_over_rho = 0.01
+perturb_kx = 16
+perturb_ky = 16
+perturb_kz = 32
+perturb_exponent = 1    # P(k) ~ k^{-2}