Added disc patch run script and 1D disc patch test.

examples/DiscPatch/HydroStatic/run.sh

+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e glassCube_32.hdf5 ]
+then
+    echo "Fetching initial glass file for the disc patch example..."
+    ./getGlass.sh
+fi
+if [ ! -e Disc-Patch.hdf5 ]
+then
+    echo "Generating initial conditions for the disc patch example..."
+    python makeIC.py
+fi
+
+# Run SWIFT
+../../swift -g -s -t 4 disc-patch-icc.yml 2>&1 | tee output.log
+
+python plotSolution.py

examples/DiscPatch/HydroStatic_1D/disc-patch-icc.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     1.9885e33         # Grams
+  UnitLength_in_cgs:   3.08567758149e18  # Centimeters
+  UnitVelocity_in_cgs: 1e5               # Centimeters per second
+  UnitCurrent_in_cgs:  1   # Amperes
+  UnitTemp_in_cgs:     1   # Kelvin
+
+# Parameters governing the time integration
+TimeIntegration:
+  time_begin: 0     # The starting time of the simulation (in internal units).
+  time_end:   968.  # The end time of the simulation (in internal units).
+  dt_min:     1e-4  # The minimal time-step size of the simulation (in internal units).
+  dt_max:     10.   # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:          12. # Time between statistics output
+  
+# Parameters governing the snapshots
+Snapshots:
+  basename:    Disc-Patch   # Common part of the name of output files
+  time_first:  0.           # Time of the first output (in internal units)
+  delta_time:  48.          # Time difference between outputs (in internal units)
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2349   # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
+  delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  max_ghost_iterations:  30       # Maximal number of iterations allowed to converge towards the smoothing length.
+  h_max:                 60.      # Maximal smoothing length allowed (in internal units).
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  Disc-Patch.hdf5       # The file to read
+
+# External potential parameters
+DiscPatchPotential:
+  surface_density: 10.
+  scale_height:    100.
+  x_disc:          400.
+  x_trunc:         300.
+  x_max:           350.
+  timestep_mult:   0.03
+  growth_time:     5.

examples/DiscPatch/HydroStatic_1D/makeIC.py

+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 John A. Regan (john.a.regan@durham.ac.uk)
+#                    Tom Theuns (tom.theuns@durham.ac.uk)
+#               2017 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+#                    Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published
+# by the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+##############################################################################
+
+import h5py
+import sys
+import numpy as np
+import math
+import random
+
+# Generates a disc-patch in hydrostatic equilibrium
+#
+# See Creasey, Theuns & Bower, 2013, MNRAS, Volume 429, Issue 3, p.1922-1948
+#
+#
+# Disc parameters are: surface density  -- sigma
+#                      scale height -- b
+#                      gas adiabatic index -- gamma
+#
+# Problem parameters are: Ratio height/width of the box -- z_factor
+#                         Size of the patch -- side_length
+
+# Parameters of the gas disc
+surface_density = 10.
+scale_height    = 100.
+gas_gamma       = 5./3.
+
+# Parameters of the problem
+x_factor        = 2
+side_length     = 400.
+numPart         = 1000
+
+# File
+fileName = "Disc-Patch.hdf5"
+
+####################################################################
+
+# physical constants in cgs
+NEWTON_GRAVITY_CGS  = 6.67408e-8
+SOLAR_MASS_IN_CGS   = 1.9885e33
+PARSEC_IN_CGS       = 3.08567758149e18
+PROTON_MASS_IN_CGS  = 1.672621898e-24
+BOLTZMANN_IN_CGS    = 1.38064852e-16
+YEAR_IN_CGS         = 3.15569252e7
+
+# choice of units
+unit_length_in_cgs   =   (PARSEC_IN_CGS)
+unit_mass_in_cgs     =   (SOLAR_MASS_IN_CGS)
+unit_velocity_in_cgs =   (1e5)
+unit_time_in_cgs     =   unit_length_in_cgs / unit_velocity_in_cgs
+
+print "UnitMass_in_cgs:     %.5e"%unit_mass_in_cgs
+print "UnitLength_in_cgs:   %.5e"%unit_length_in_cgs
+print "UnitVelocity_in_cgs: %.5e"%unit_velocity_in_cgs
+print "UnitTime_in_cgs:     %.5e"%unit_time_in_cgs
+print ""
+
+# Derived units
+const_G  = NEWTON_GRAVITY_CGS * unit_mass_in_cgs * unit_time_in_cgs**2 * \
+           unit_length_in_cgs**-3
+const_mp = PROTON_MASS_IN_CGS * unit_mass_in_cgs**-1
+const_kb = BOLTZMANN_IN_CGS * unit_mass_in_cgs**-1 * unit_length_in_cgs**-2 * \
+           unit_time_in_cgs**2
+
+print "--- Some constants [internal units] ---"
+print "G_Newton:    %.5e"%const_G
+print "m_proton:    %.5e"%const_mp
+print "k_boltzmann: %.5e"%const_kb
+print ""
+
+# derived quantities
+temp       = math.pi * const_G * surface_density * scale_height * const_mp / \
+             const_kb
+u_therm    = const_kb * temp / ((gas_gamma-1) * const_mp)
+v_disp     = math.sqrt(2 * u_therm)
+soundspeed = math.sqrt(u_therm / (gas_gamma * (gas_gamma-1.)))
+t_dyn      = math.sqrt(scale_height / (const_G * surface_density))
+t_cross    = scale_height / soundspeed
+
+print "--- Properties of the gas [internal units] ---"
+print "Gas temperature:     %.5e"%temp
+print "Gas thermal_energy:  %.5e"%u_therm
+print "Dynamical time:      %.5e"%t_dyn
+print "Sound crossing time: %.5e"%t_cross
+print "Gas sound speed:     %.5e"%soundspeed
+print "Gas 3D vel_disp:     %.5e"%v_disp
+print ""
+
+# Problem properties
+boxSize_x = side_length
+boxSize_x *= x_factor
+volume = boxSize_x
+M_tot = surface_density * math.tanh(boxSize_x / (2. * scale_height))
+density = M_tot / volume
+entropy = (gas_gamma - 1.) * u_therm / density**(gas_gamma - 1.)
+
+print "--- Problem properties [internal units] ---"
+print "Box:        %.1f"%boxSize_x
+print "Volume:     %.5e"%volume
+print "Total mass: %.5e"%M_tot
+print "Density:    %.5e"%density
+print "Entropy:    %.5e"%entropy
+print ""
+
+####################################################################
+
+# Now create enough copies to fill the volume in x
+pos = np.zeros((numPart, 3))
+h = np.zeros(numPart) + 2. * boxSize_x / numPart
+for i in range(numPart):
+    pos[i, 0] = (i + 0.5) * boxSize_x / numPart
+
+# Compute further properties of ICs
+mass = M_tot / numPart
+
+print "--- Particle properties [internal units] ---"
+print "Number part.: ", numPart
+print "Part. mass:   %.5e"%mass
+print ""
+
+# Create additional arrays
+u    = np.ones(numPart) * u_therm
+mass = np.ones(numPart) * mass
+vel  = np.zeros((numPart, 3))
+ids  = 1 + np.linspace(0, numPart, numPart, endpoint=False)
+
+####################################################################
+# Create and write output file
+
+#File
+file = h5py.File(fileName, 'w')
+
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = unit_length_in_cgs
+grp.attrs["Unit mass in cgs (U_M)"] = unit_mass_in_cgs
+grp.attrs["Unit time in cgs (U_t)"] = unit_time_in_cgs
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = [boxSize_x, 1., 1.]
+grp.attrs["NumPart_Total"] =  [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["Dimension"] = 1
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+# write gas particles
+grp0   = file.create_group("/PartType0")
+
+ds = grp0.create_dataset('Coordinates', (numPart, 3), 'f', data=pos)
+ds = grp0.create_dataset('Velocities', (numPart, 3), 'f')
+ds = grp0.create_dataset('Masses', (numPart,), 'f', data=mass)
+ds = grp0.create_dataset('SmoothingLength', (numPart,), 'f', data=h)
+ds = grp0.create_dataset('InternalEnergy', (numPart,), 'f', data=u)
+ds = grp0.create_dataset('ParticleIDs', (numPart, ), 'L', data=ids)
+
+####################################################################
+
+print "--- Runtime parameters (YAML file): ---"
+print "DiscPatchPotential:surface_density:    ", surface_density
+print "DiscPatchPotential:scale_height:       ", scale_height
+print "DiscPatchPotential:x_disc:             ", 0.5 * boxSize_x
+print ""
+
+print "--- Constant parameters: ---"
+print "const_isothermal_internal_energy: %ef"%u_therm

examples/DiscPatch/HydroStatic_1D/plotSolution.py

+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#                    Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published
+# by the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+################################################################################
+
+##
+# This script plots the Disc-Patch_*.hdf5 snapshots.
+# It takes two (optional) parameters: the counter value of the first and last
+# snapshot to plot (default: 0 21).
+##
+
+import numpy as np
+import h5py
+import matplotlib
+matplotlib.use("Agg")
+import pylab as pl
+import glob
+import sys
+
+# Parameters
+surface_density = 10.
+scale_height = 100.
+x_disc = 400.
+x_trunc = 300.
+x_max = 350.
+utherm = 20.2678457288
+gamma = 5. / 3.
+
+start = 0
+stop = 21
+if len(sys.argv) > 1:
+  start = int(sys.argv[1])
+if len(sys.argv) > 2:
+  stop = int(sys.argv[2])
+
+# Get the analytic solution for the density
+def get_analytic_density(x):
+  return 0.5 * surface_density / scale_height / \
+           np.cosh( (x - x_disc) / scale_height )**2
+
+# Get the analytic solution for the (isothermal) pressure
+def get_analytic_pressure(x):
+  return (gamma - 1.) * utherm * get_analytic_density(x)
+
+# Get the data fields to plot from the snapshot file with the given name:
+#  snapshot time, x-coord, density, pressure, velocity norm
+def get_data(name):
+  file = h5py.File(name, "r")
+  coords = np.array(file["/PartType0/Coordinates"])
+  rho = np.array(file["/PartType0/Density"])
+  u = np.array(file["/PartType0/InternalEnergy"])
+  v = np.array(file["/PartType0/Velocities"])
+
+  P = (gamma - 1.) * rho * u
+
+  vtot = np.sqrt( v[:,0]**2 + v[:,1]**2 + v[:,2]**2 )
+
+  return float(file["/Header"].attrs["Time"]), coords[:,0], rho, P, vtot
+
+# scan the folder for snapshot files and plot all of them (within the requested
+# range)
+for f in sorted(glob.glob("Disc-Patch_*.hdf5")):
+  num = int(f[-8:-5])
+  if num < start or num > stop:
+    continue
+
+  print "processing", f, "..."
+
+  xrange = np.linspace(0., 2. * x_disc, 1000)
+  time, x, rho, P, v = get_data(f)
+
+  fig, ax = pl.subplots(3, 1, sharex = True)
+
+  ax[0].plot(x, rho, "r.")
+  ax[0].plot(xrange, get_analytic_density(xrange), "k-")
+  ax[0].plot([x_disc - x_max, x_disc - x_max], [0, 10], "k--", alpha=0.5)
+  ax[0].plot([x_disc + x_max, x_disc + x_max], [0, 10], "k--", alpha=0.5)
+  ax[0].plot([x_disc - x_trunc, x_disc - x_trunc], [0, 10], "k--", alpha=0.5)
+  ax[0].plot([x_disc + x_trunc, x_disc + x_trunc], [0, 10], "k--", alpha=0.5)
+  ax[0].set_ylim(0., 1.2 * get_analytic_density(x_disc))
+  ax[0].set_ylabel("density")
+
+  ax[1].plot(x, v, "r.")
+  ax[1].plot(xrange, np.zeros(len(xrange)), "k-")
+  ax[1].plot([x_disc - x_max, x_disc - x_max], [0, 10], "k--", alpha=0.5)
+  ax[1].plot([x_disc + x_max, x_disc + x_max], [0, 10], "k--", alpha=0.5)
+  ax[1].plot([x_disc - x_trunc, x_disc - x_trunc], [0, 10], "k--", alpha=0.5)
+  ax[1].plot([x_disc + x_trunc, x_disc + x_trunc], [0, 10], "k--", alpha=0.5)
+  ax[1].set_ylim(-0.5, 10.)
+  ax[1].set_ylabel("velocity norm")
+
+  ax[2].plot(x, P, "r.")
+  ax[2].plot(xrange, get_analytic_pressure(xrange), "k-")
+  ax[2].plot([x_disc - x_max, x_disc - x_max], [0, 10], "k--", alpha=0.5)
+  ax[2].plot([x_disc + x_max, x_disc + x_max], [0, 10], "k--", alpha=0.5)
+  ax[2].plot([x_disc - x_trunc, x_disc - x_trunc], [0, 10], "k--", alpha=0.5)
+  ax[2].plot([x_disc + x_trunc, x_disc + x_trunc], [0, 10], "k--", alpha=0.5)
+  ax[2].set_xlim(0., 2. * x_disc)
+  ax[2].set_ylim(0., 1.2 * get_analytic_pressure(x_disc))
+  ax[2].set_xlabel("x")
+  ax[2].set_ylabel("pressure")
+
+  pl.suptitle("t = {0:.2f}".format(time))
+
+  pl.savefig("{name}.png".format(name = f[:-5]))
+  pl.close()

examples/DiscPatch/HydroStatic_1D/run.sh

+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e Disc-Patch.hdf5 ]
+then
+    echo "Generating initial conditions for the disc patch example..."
+    python makeIC.py
+fi
+
+# Run SWIFT
+../../swift -g -s -t 4 disc-patch-icc.yml 2>&1 | tee output.log
+
+python plotSolution.py