examples/GEAR/ZoomIn/README

@@ -6,11 +6,10 @@ The cosmology is taken from Planck 2015.
 
 The initial conditions have been cleaned to contain only the required
 fields. The ICs have been created for Gadget and the positions and box
-size are hence expressed in h-full units (e.g. box size of 32 / h Mpc).
+size are hence expressed in h-full units (e.g. box size of 3.4 / h Mpc).
 Similarly, the peculiar velocitites contain an extra sqrt(a) factor. 
 
-We will use SWIFT to cancel the h- and a-factors from the ICs. Gas
-particles will be generated at startup.
+We will use SWIFT to cancel the h- and a-factors from the ICs.
 
 MD5 check-sum of the ICS: 
 9aafe154438478ed435e88664c1c5dba zoom_in.hdf5

examples/GEAR/ZoomIn/getChemistryTable.sh

+#!/bin/bash
+
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/FeedbackTables/POPIIsw.h5

examples/GEAR/ZoomIn/getGrackleCoolingTable.sh

+#!/bin/bash
+
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/CloudyData_UVB=HM2012.h5

examples/GEAR/ZoomIn/getIC.sh

 #!/bin/bash
-wget https://obswww.unige.ch/~lhausamm/swift/IC/ZoomIn/zoom_in.hdf5
+
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/ZoomIn/h050.hdf5

examples/GEAR/ZoomIn/getSolution.sh

+#!/bin/bash
+# wget https://obswww.unige.ch/~lhausamm/swift/ZoomIC/h177_final.hdf5
+wget https://obswww.unige.ch/~lhausamm/swift/ZoomIC/h050_final.hdf5

examples/GEAR/ZoomIn/run.sh

 #!/bin/bash
 
- # Generate the initial conditions if they are not present.
-if [ ! -e zoom_in.hdf5 ]
-then
+if [ ! -e h050.hdf5 ]
+then 
     echo "Fetching initial conditions for the zoom in example..."
     ./getIC.sh
 fi
 
-../../swift --feedback --cosmology --self-gravity --hydro --stars --threads=8 zoom_in.yml 2>&1 | tee output.log
 
+# Get the Grackle cooling table
+if [ ! -e CloudyData_UVB=HM2012.h5 ]
+then
+    echo "Fetching the Cloudy tables required by Grackle..."
+    ./getGrackleCoolingTable.sh
+fi
+
+
+if [ ! -e POPIIsw.h5 ]
+then
+    echo "Fetching the chemistry tables..."
+    ./getChemistryTable.sh
+fi
+
+
+
+
+
+
+
+../../../swift --cooling --feedback --cosmology  --limiter --sync --self-gravity --hydro --stars --star-formation --threads=8 zoom_in.yml 2>&1 | tee output.log

examples/GEAR/ZoomIn/snaplist.txt

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examples/GEAR/ZoomIn/zoom_in.yml

 # Define the system of units to use internally. 
 InternalUnitSystem:
-  UnitMass_in_cgs:     1.98848e43    # 10^10 M_sun in grams
+  UnitMass_in_cgs:     1.98841e43    # 10^10 M_sun in grams
   UnitLength_in_cgs:   3.08567758e21 # kpc in centimeters
   UnitVelocity_in_cgs: 1e5           # km/s in centimeters per second
   UnitCurrent_in_cgs:  1             # Amperes
   UnitTemp_in_cgs:     1             # Kelvin
 
+Scheduler:
+  max_top_level_cells: 16
+  cell_sub_size_self_grav:   2048
+  cell_subdepth_diff_grav:   2
+  cell_split_size:           200
+  cell_extra_gparts:         100         # (Optional) Number of spare gparts per top-level allocated at rebuild time for on-the-fly creation.
+
+  
+# Parameters governing the time integration
+TimeIntegration:
+  dt_min:     1e-16 # The minimal time-step size of the simulation (in internal units).
+  dt_max:     0.1  # The maximal time-step size of the simulation (in internal units).
+  max_dt_RMS_factor: 0.25  # (Optional) Dimensionless factor for the maximal displacement allowed based on the RMS velocities.
+  dt_RMS_use_gas_only: 1 
+  
 # Cosmological parameters
 Cosmology:
   h:              0.673        # Reduced Hubble constant
-  a_begin:        0.9873046739     # Initial scale-factor of the simulation
+  a_begin:        0.014084507042253521     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.315         # Matter density parameter
+  Omega_cdm:      0.2664        # Cold Dark Matter density parameter
   Omega_lambda:   0.685         # Dark-energy density parameter
   Omega_b:        0.0486        # Baryon density parameter
-  
-Scheduler:
-  max_top_level_cells:    8
-  
-# Parameters governing the time integration
-TimeIntegration:
-  time_begin: 0.    # The starting time of the simulation (in internal units).
-  time_end:   1e-2  # The end time of the simulation (in internal units).
-  dt_min:     1e-10 # The minimal time-step size of the simulation (in internal units).
-  dt_max:     1e-3  # The maximal time-step size of the simulation (in internal units).
-  
+  Omega_r:        0.            # (Optional) Radiation density parameter
+  w_0:            -1.0          # (Optional) Dark-energy equation-of-state parameter at z=0.
+  w_a:            0.            # (Optional) Dark-energy equation-of-state time evolution parameter.
+
 # Parameters governing the snapshots
 Snapshots:
-  basename:            zoom_in # Common part of the name of output files
-  scale_factor_first:  0.987345  # Scale-factor of the first snaphot (cosmological run)
-  time_first:          0.01  # Time of the first output (non-cosmological run) (in internal units)
-  delta_time:          1.01  # Time difference between consecutive outputs (in internal units)
-  compression:         1
+  basename:            h050  # Common part of the name of output files
+  subdir:              snap
+  time_first:          0.    # Time of the first output (in internal units)
+  delta_time:          1e-2  # Time difference between consecutive outputs (in internal units)
+  compression:         4
+  output_list_on:      1  # (Optional) Enable the output list
+  output_list:         snaplist.txt # (Optional) File containing the output times (see documentation in "Parameter File" section)
 
 # Parameters governing the conserved quantities statistics
 Statistics:
-  scale_factor_first:  0.987345 # Scale-factor of the first stat dump (cosmological run)
-  time_first:          0.01 # Time of the first stat dump (non-cosmological run) (in internal units)
-  delta_time:          1.05 # Time between statistics output
+  scale_factor_first: 0.0141
+  delta_time:          1.02 # Time between statistics output
 
 # Parameters for the self-gravity scheme
 Gravity:
-  eta:                    0.025    # Constant dimensionless multiplier for time integration.
-  theta:                  0.7      # Opening angle (Multipole acceptance criterion)
-  comoving_softening:     0.05 # Comoving softening length (in internal units).
-  max_physical_softening: 0.01    # Physical softening length (in internal units).
-  mesh_side_length:       16
-
+  eta:                    0.05    # Constant dimensionless multiplier for time integration.
+  MAC:                           geometric  # Choice of mulitpole acceptance criterion: 'adaptive' OR 'geometric'.
+  epsilon_fmm:                   0.001     # Tolerance parameter for the adaptive multipole acceptance criterion.
+  theta_cr:                      0.7       # Opening angle for the purely gemoetric criterion.
+  comoving_DM_softening:     0.2823 # Comoving softening length (in internal units).
+  max_physical_DM_softening: 0.07429    # Physical softening length (in internal units).
+  comoving_baryon_softening:     0.07429 # Comoving softening length (in internal units).
+  max_physical_baryon_softening: 0.01485    # Physical softening length (in internal units).
+  softening_ratio_background:    0.0285714      # Fraction of the mean inter-particle separation to use as Plummer-equivalent softening for the background DM particles.
+  mesh_side_length:       128        # Number of cells along each axis for the periodic gravity mesh.
+  
 # Parameters for the hydrodynamics scheme
 SPH:
   resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
   CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
-  minimal_temperature:   100      # (internal units)
+  minimal_temperature:   10.      # Kelvin
+  h_min_ratio:           0.0714285714285       # (Optional) Minimal allowed smoothing length in units of the softening. Defaults to 0 if unspecified.
+  h_max:                 100     # (Optional) Maximal allowed smoothing length in internal units. Defaults to FLT_MAX if unspecified.
 
 # Parameters related to the initial conditions
 InitialConditions:
-  file_name:  ./zoom_in.hdf5     # The file to read
-  periodic:   1
-  cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
-  cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
+  file_name:  ./h050.hdf5     # The file to read
+  periodic:   1                     # Non-periodic BCs
+  cleanup_h_factors: 1              # Remove the h-factors inherited from Gadget
+  shift:    [0, 0, 0]   # Centre the box
+  cleanup_velocity_factors:    1    # (Optional) Clean up the scale-factors used in the definition of the velocity variable in the ICs (e.g. in Gadget files).
+  cleanup_smoothing_lengths:   1    # (Optional) Clean the values of the smoothing lengths that are read in to remove stupid values. Set to 1 to activate.
+
+# Cooling with Grackle 2.0
+GrackleCooling:
+  cloudy_table: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
+  with_UV_background: 1 # Enable or not the UV background
+  redshift: -1 # Redshift to use (-1 means time based redshift)
+  with_metal_cooling: 1 # Enable or not the metal cooling
+  provide_volumetric_heating_rates: 0 # User provide volumetric heating rates
+  provide_specific_heating_rates: 0 # User provide specific heating rates
+  self_shielding_method: -1 # Grackle (<= 3) or Gear self shielding method
+  self_shielding_threshold_atom_per_cm3: 0.007  # Required only with GEAR's self shielding. Density threshold of the self shielding
+  max_steps: 1000
+  convergence_limit: 1e-2
+  thermal_time_myr: 5
+  maximal_density_Hpcm3: -1 # Maximal density (in hydrogen atoms/cm^3) for cooling. Higher densities are floored to this value to ensure grackle works properly when interpolating beyond the cloudy_table maximal density. A value < 0 deactivates this parameter.
+
+
+GEARStarFormation:
+  star_formation_efficiency: 0.01   # star formation efficiency (c_*)
+  maximal_temperature_K:     3e4    # Upper limit to the temperature of a star forming particle
+  density_threshold_Hpcm3:   0.1    # Density threshold in Hydrogen atoms/cm3
+  n_stars_per_particle: 4
+  min_mass_frac: 0.5
+
+GEARPressureFloor:
+  jeans_factor: 10
+
+GEARFeedback:
+  supernovae_energy_erg: 1e51
+  supernovae_efficiency: 0.1
+  yields_table: POPIIsw.h5
+  discrete_yields: 1
+  yields_table_first_stars: POPIIsw.h5                     # Table containing the yields of the first stars.
+  metallicity_max_first_stars: -1                          # Maximal metallicity (in mass fraction) for a first star (-1 to deactivate).
+  elements: [Fe, Mg, O, C, Al, Ca, Ba, Zn, Eu]             # Elements to read in the yields table. The number of element should be one less than the number of elements (N) requested during the configuration (--with-chemistry=GEAR_N).
+
+GEARChemistry:
+  initial_metallicity: 0
+  scale_initial_metallicity: 0
 
+Restarts:
+  delta_hours:        1        # (Optional) decimal hours between dumps of restart files.

examples/GEAR/getChemistryTable.sh

+#!/bin/bash
+wget https://obswww.unige.ch/lastro/projects/Clastro/PySWIFTsim/chemistry-AGB+OMgSFeZnSrYBaEu-16072013.h5
+wget https://obswww.unige.ch/lastro/projects/Clastro/PySWIFTsim/chemistry-PopIII.hdf5

examples/GiantImpacts/EoSTables/get_eos_tables.sh

-#!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/EoS/HM80_HHe.txt
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/EoS/HM80_ice.txt
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/EoS/HM80_rock.txt
-
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/EoS/SESAME_basalt_7530.txt
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/EoS/SESAME_iron_2140.txt
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/EoS/SESAME_water_7154.txt
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/EoS/SS08_water.txt

examples/GiantImpacts/GiantImpact/README.md

-An example planetary simulation of a giant impact onto the young Uranus with 
-~10^6 SPH particles, as described in Kegerreis et al. (2018), ApJ, 861, 52.
-
-This example requires the code to be configured to use the Planetary
-hydrodynamics and equation of state:
- --with-hydro=planetary --with-equation-of-state=planetary

examples/GiantImpacts/GiantImpact/configuration.yml

-with-hydro:             planetary 
-with-equation-of-state: planetary

examples/GiantImpacts/GiantImpact/get_init_cond.sh

-#!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/GiantImpacts/uranus_1e6.hdf5

examples/GiantImpacts/GiantImpact/output_list.txt

-# Time
-4000
-9000
-14000
-20000
-30000
-40000
\ No newline at end of file

examples/GiantImpacts/GiantImpact/plot_solution.py

-###############################################################################
- # This file is part of SWIFT.
- # Copyright (c) 2019 Jacob Kegerreis (jacob.kegerreis@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/>.
- # 
- ##############################################################################
-
-# Plot the snapshots from the example giant impact on Uranus, showing the 
-# particles in a thin slice near z=0, coloured by their material, similarish
-# (but not identical) to Fig. 2 in Kegerreis et al. (2018).
-
-import matplotlib
-matplotlib.use("Agg")
-import matplotlib.pyplot as plt
-import numpy as np
-# import swiftsimio as sw
-import h5py
-
-font_size   = 20
-params      = { 
-    'axes.labelsize'    : font_size,
-    'font.size'         : font_size,
-    'xtick.labelsize'   : font_size,
-    'ytick.labelsize'   : font_size,
-    'text.usetex'       : True,
-    'font.family'       : 'serif',
-    }
-matplotlib.rcParams.update(params)
-
-# Snapshot output times
-output_list = [4000, 9000, 14000, 20000, 30000, 40000]
-
-# Material IDs ( = type_id * type_factor + unit_id )
-type_factor = 100
-type_HM80   = 2
-id_body     = 10000
-# Name and ID
-Di_mat_id   = {
-    'HM80_HHe'      : type_HM80 * type_factor,      # Hydrogen-helium atmosphere
-    'HM80_ice'      : type_HM80 * type_factor + 1,  # H20-CH4-NH3 ice mix
-    'HM80_ice_2'    : type_HM80 * type_factor + 1 + id_body,
-    'HM80_rock'     : type_HM80 * type_factor + 2,  # SiO2-MgO-FeS-FeO rock mix
-    'HM80_rock_2'   : type_HM80 * type_factor + 2 + id_body,
-    }
-# ID and colour
-Di_id_colour    = {
-    Di_mat_id['HM80_HHe']       : '#33DDFF',
-    Di_mat_id['HM80_ice']       : 'lightsteelblue',
-    Di_mat_id['HM80_ice_2']     : '#A080D0',
-    Di_mat_id['HM80_rock']      : 'slategrey',
-    Di_mat_id['HM80_rock_2']    : '#706050',
-    }
-   
-def get_snapshot_slice(snapshot):
-    """ Load and select the particles to plot. """
-    # Load particle data
-    # data    = load("uranus_1e6_%06d.hdf5" % snapshot)
-    # id      = data.gas.particle_ids
-    # pos     = data.gas.coordinates
-    # mat_id  = data.gas.material
-    with h5py.File("uranus_1e6_%06d.hdf5" % snapshot, 'r') as f:
-        id      = f['PartType0/ParticleIDs'].value
-        pos     = (f['PartType0/Coordinates'].value
-                   - 0.5 * f['Header'].attrs['BoxSize'])
-        mat_id  = f['PartType0/MaterialID'].value
-                   
-    # Edit the material ID of particles in the impactor
-    num_in_target   = 869104
-    sel_id          = np.where(num_in_target < id)[0]
-    mat_id[sel_id]  += id_body
-    
-    # Select particles in a thin slice around z=0
-    z_min   = -0.1
-    z_max   = 0.1
-    sel_z   = np.where((z_min < pos[:, 2]) & (pos[:, 2] < z_max))[0]
-    pos     = pos[sel_z]
-    mat_id  = mat_id[sel_z]
-    
-    return pos, mat_id
-
-def plot_snapshot_slice(pos, mat_id):
-    """ Plot the particles, coloured by their material. """
-    colour  = np.empty(len(pos), dtype=object)
-    for id, c in Di_id_colour.items():
-        sel_c           = np.where(mat_id == id)[0]
-        colour[sel_c]   = c
-
-    ax.scatter(pos[:, 0], pos[:, 1], c=colour, edgecolors='none', marker='.', 
-               s=10, alpha=0.5, zorder=0)
-
-# Set up the figure
-fig     = plt.figure(figsize=(12, 8))
-gs      = matplotlib.gridspec.GridSpec(2, 3)
-axes    = [plt.subplot(gs[i_y, i_x]) for i_y in range(2) for i_x in range(3)]
-
-# Plot each snapshot
-for i_ax, ax in enumerate(axes):
-    plt.sca(ax)
-    ax.set_rasterization_zorder(1)
-    
-    # Load and select the particles to plot
-    pos, mat_id = get_snapshot_slice(output_list[i_ax])
-    
-    # Plot the particles, coloured by their material
-    plot_snapshot_slice(pos, mat_id)
-    
-    # Axes etc.
-    ax.set_aspect('equal')
-    ax.set_facecolor('k')
-    
-    ax.set_xlim(-13, 13)
-    ax.set_ylim(-13, 13)
-
-    if i_ax in [0, 3]:
-        ax.set_ylabel(r"y Postion $(R_\oplus)$")
-    else: 
-        ax.set_yticklabels([])
-    if 2 < i_ax:
-        ax.set_xlabel(r"x Postion $(R_\oplus)$")
-    else: 
-        ax.set_xticklabels([])
-        
-    # Corner time labels 
-    x   = ax.get_xlim()[0] + 0.04 * (ax.get_xlim()[1] - ax.get_xlim()[0])
-    y   = ax.get_ylim()[0] + 0.89 * (ax.get_ylim()[1] - ax.get_ylim()[0])
-    ax.text(x, y, "%.1f h" % (output_list[i_ax] / 60**2), color='w')
-
-plt.subplots_adjust(wspace=0, hspace=0)
-plt.tight_layout()
-
-# Save
-plt.savefig("uranus_1e6.pdf", dpi=200)
\ No newline at end of file

examples/GiantImpacts/GiantImpact/run.sh

-#!/bin/bash
-
-# Get the initial conditions if they are not present.
-if [ ! -e uranus_1e6.hdf5 ]
-then
-    echo "Fetching initial conditions file for the Uranus impact example..."
-    ./get_init_cond.sh
-fi
-
-# Get the EoS tables if they are not present.
-cd ../EoSTables
-if [ ! -e HM80_HHe.txt ] || [ ! -e HM80_ice.txt ] || [ ! -e HM80_rock.txt ] 
-then
-    echo "Fetching equations of state tables for the Uranus impact example..."
-    ./get_eos_tables.sh
-fi
-cd ../GiantImpact
-
-# Run SWIFT
-../../swift -s -G -t 8 uranus_1e6.yml 2>&1 | tee output.log
-
-# Plot the solution
-python3 plot_solution.py

examples/GiantImpacts/GiantImpact/system.yml

-input:
-  - uranus_1e6.yml
-  - output_list.txt
-
-output:
-  - uranus_1e6.pdf
-
-swift_parameters:   -s -G
-swift_threads:      8

examples/GravityTests/DiscPatch/GravityOnly/disc-patch.yml

 # Define the system of units to use internally. 
 InternalUnitSystem:
-  UnitMass_in_cgs:     1.98848e33    # M_sun in grams
-  UnitLength_in_cgs:   3.08567758e18 # parsec in centimeters
-  UnitVelocity_in_cgs: 1e5           # km/s in cm/s
+  UnitMass_in_cgs:     1.98841e33       # M_sun in grams
+  UnitLength_in_cgs:   3.08567758149e18 # parsec in centimeters
+  UnitVelocity_in_cgs: 1e5              # km/s in cm/s
   UnitCurrent_in_cgs:  1   # Amperes
   UnitTemp_in_cgs:     1   # Kelvin
 
@@ -23,14 +23,6 @@ Snapshots:
   time_first:          0.         # Time of the first output (in internal units)
   delta_time:          8.         # Time difference between consecutive 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:      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.
-  max_smoothing_length:  40.      # Maximal smoothing length allowed (in internal units).
-
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  Disc-Patch.hdf5       # The file to read
@@ -40,5 +32,9 @@ InitialConditions:
 DiscPatchPotential:
   surface_density: 10.
   scale_height:    100.
-  z_disc:          300.
-  timestep_mult:   0.03
+  x_disc:          300.
+  timestep_mult:   0.01
+
+Scheduler:
+  max_top_level_cells:  8
+  tasks_per_cell:       5

examples/GravityTests/DiscPatch/GravityOnly/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)
- # 
- # 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 file is part of SWIFT.
+# Copyright (c) 2016 John A. Regan (john.a.regan@durham.ac.uk)
+#                    Tom Theuns (tom.theuns@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/>.
+#
+##############################################################################
 
 import h5py
-import sys
 import numpy
+import sys
 import math
-import random
 
-# Generates N particles in a box of [0:BoxSize,0:BoxSize,-2scale_height:2scale_height]
+# Generates N particles in a box of [-2scale_height:2scale_height, 0:BoxSize, 0:BoxSize]
+#
+# The potential is long the x-axis.
+#
 # see Creasey, Theuns & Bower, 2013, for the equations:
 # disc parameters are: surface density sigma
 #                      scale height b
-# density: rho(z) = (sigma/2b) sech^2(z/b)
-# isothermal velocity dispersion = <v_z^2? = b pi G sigma
+# density: rho(x) = (sigma/2b) sech^2(x/b)
+# isothermal velocity dispersion = <v_x^2? = b pi G sigma
 # grad potential  = 2 pi G sigma tanh(z/b)
-# potential       = ln(cosh(z/b)) + const
+# potential       = ln(cosh(x/b)) + const
 # Dynamical time  = sqrt(b / (G sigma))
-# to obtain the 1/ch^2(z/b) profile from a uniform profile (a glass, say, or a uniform random variable), note that, when integrating in z
-# \int 0^z dz/ch^2(z) = tanh(z)-tanh(0) = \int_0^x dx = x (where the last integral refers to a uniform density distribution), so that z = atanh(x)
-# usage: python makeIC.py 1000 
+# to obtain the 1/ch^2(x/b) profile from a uniform profile (a glass, say, or a uniform random variable), note that, when integrating in x
+# \int 0^x dx/ch^2(x) = tanh(x)-tanh(0) = \int_0^u du = u (where the last integral refers to a uniform density distribution), so that x = atanh(u)
+#
+# usage: python3 makeIC.py 1000
 
 # physical constants in cgs
-NEWTON_GRAVITY_CGS  = 6.67408e-8
-SOLAR_MASS_IN_CGS   = 1.98848e33
-PARSEC_IN_CGS       = 3.08567758e18
-YEAR_IN_CGS         = 3.15569252e7
+NEWTON_GRAVITY_CGS = 6.67430e-8
+SOLAR_MASS_IN_CGS = 1.98841e33
+PARSEC_IN_CGS = 3.08567758149e18
+YEAR_IN_CGS = 3.15569251e7
 
 # choice of units
-const_unit_length_in_cgs   =   (PARSEC_IN_CGS)
-const_unit_mass_in_cgs     =   (SOLAR_MASS_IN_CGS)
-const_unit_velocity_in_cgs =   (1e5)
+const_unit_length_in_cgs = PARSEC_IN_CGS
+const_unit_mass_in_cgs = SOLAR_MASS_IN_CGS
+const_unit_velocity_in_cgs = 1e5
 
-print "UnitMass_in_cgs:     ", const_unit_mass_in_cgs 
-print "UnitLength_in_cgs:   ", const_unit_length_in_cgs
-print "UnitVelocity_in_cgs: ", const_unit_velocity_in_cgs
+print("UnitMass_in_cgs:     ", const_unit_mass_in_cgs)
+print("UnitLength_in_cgs:   ", const_unit_length_in_cgs)
+print("UnitVelocity_in_cgs: ", const_unit_velocity_in_cgs)
 
 
 # parameters of potential
-surface_density = 10.
-scale_height    = 100.
+surface_density = 10.0
+scale_height = 100.0
 
 # derived units
-const_unit_time_in_cgs = (const_unit_length_in_cgs / const_unit_velocity_in_cgs)
-const_G                = ((NEWTON_GRAVITY_CGS*const_unit_mass_in_cgs*const_unit_time_in_cgs*const_unit_time_in_cgs/(const_unit_length_in_cgs*const_unit_length_in_cgs*const_unit_length_in_cgs)))
-print 'G=', const_G
-v_disp                 = numpy.sqrt(scale_height * math.pi * const_G * surface_density)
-t_dyn                  = numpy.sqrt(scale_height / (const_G * surface_density))
-print 'dynamical time = ',t_dyn
-print ' velocity dispersion = ',v_disp
+const_unit_time_in_cgs = const_unit_length_in_cgs / const_unit_velocity_in_cgs
+const_G = (
+    NEWTON_GRAVITY_CGS
+    * const_unit_mass_in_cgs
+    * const_unit_time_in_cgs
+    * const_unit_time_in_cgs
+    / (const_unit_length_in_cgs * const_unit_length_in_cgs * const_unit_length_in_cgs)
+)
+print("G=", const_G)
+v_disp = numpy.sqrt(scale_height * math.pi * const_G * surface_density)
+t_dyn = numpy.sqrt(scale_height / (const_G * surface_density))
+print("dynamical time = ", t_dyn)
+print(" velocity dispersion = ", v_disp)
 
 # Parameters
-periodic= 1             # 1 For periodic box
-boxSize = 600.          #  
-Radius  = 100.          # maximum radius of particles [kpc]
-G       = const_G 
-
-N       = int(sys.argv[1])  # Number of particles
-
-# these are not used but necessary for I/O
-rho = 2.              # Density
-P = 1.                # Pressure
-gamma = 5./3.         # Gas adiabatic index
-fileName = "Disc-Patch.hdf5" 
-
-
-#---------------------------------------------------
-numPart        = N
-mass           = 1
-internalEnergy = P / ((gamma - 1.)*rho)
+periodic = 1  # 1 For periodic box
+boxSize = 600.0  #
+Radius = 100.0  # maximum radius of particles [kpc]
+G = const_G
+mass = 1
+numPart = int(sys.argv[1])  # Number of particles
+fileName = "Disc-Patch.hdf5"
 
-#--------------------------------------------------
+# --------------------------------------------------
 
-#File
-file = h5py.File(fileName, 'w')
+# File
+file = h5py.File(fileName, "w")
 
-#Units
+# Units
 grp = file.create_group("/Units")
 grp.attrs["Unit length in cgs (U_L)"] = const_unit_length_in_cgs
-grp.attrs["Unit mass in cgs (U_M)"] = const_unit_mass_in_cgs 
-grp.attrs["Unit time in cgs (U_t)"] = const_unit_length_in_cgs / const_unit_velocity_in_cgs
-grp.attrs["Unit current in cgs (U_I)"] = 1.
-grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = const_unit_mass_in_cgs
+grp.attrs["Unit time in cgs (U_t)"] = (
+    const_unit_length_in_cgs / const_unit_velocity_in_cgs
+)
+grp.attrs["Unit current in cgs (U_I)"] = 1.0
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.0
 
 # Header
 grp = file.create_group("/Header")
 grp.attrs["BoxSize"] = boxSize
-grp.attrs["NumPart_Total"] =  [0, numPart, 0, 0, 0, 0]
+grp.attrs["NumPart_Total"] = [0, numPart, 0, 0, 0, 0]
 grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
 grp.attrs["NumPart_ThisFile"] = [0, numPart, 0, 0, 0, 0]
 grp.attrs["Time"] = 0.0
@@ -114,42 +114,40 @@ grp.attrs["Dimension"] = 3
 # set seed for random number
 numpy.random.seed(1234)
 
-#Particle group
-#grp0 = file.create_group("/PartType0")
+# Particle group
 grp1 = file.create_group("/PartType1")
 
-#generate particle positions
-r      = numpy.zeros((numPart, 3))
-r[:,0] = numpy.random.rand(N) * boxSize
-r[:,1] = numpy.random.rand(N) * boxSize
-z      = scale_height * numpy.arctanh(numpy.random.rand(2*N))
-gd     = z < boxSize / 2
-r[:,2] = z[gd][0:N]
-random = numpy.random.rand(N) > 0.5
-r[random,2] *= -1
-r[:,2] += 0.5 * boxSize
+# generate particle positions
+r = numpy.zeros((numPart, 3))
+x = scale_height * numpy.arctanh(numpy.random.rand(2 * numPart))
+gd = x < boxSize / 2
+r[:, 0] = x[gd][0:numPart]
+random = numpy.random.rand(numPart) > 0.5
+r[random, 0] *= -1
+r[:, 0] += 0.5 * boxSize
 
-#generate particle velocities
-v      = numpy.zeros((numPart, 3))
-v      = numpy.zeros(1)
-#v[:,2] = 
+r[:, 1] = numpy.random.rand(numPart) * boxSize
+r[:, 2] = numpy.random.rand(numPart) * boxSize
 
+# generate particle velocities
+v = numpy.zeros((numPart, 3))
+v = numpy.zeros(1)
 
-ds = grp1.create_dataset('Velocities', (numPart, 3), 'f')
+ds = grp1.create_dataset("Velocities", (numPart, 3), "f")
 ds[()] = v
 
 
-m = numpy.ones((numPart, ), dtype=numpy.float32) * mass
-ds = grp1.create_dataset('Masses', (numPart,), 'f')
+m = numpy.ones((numPart,), dtype=numpy.float32) * mass
+ds = grp1.create_dataset("Masses", (numPart,), "f")
 ds[()] = m
 m = numpy.zeros(1)
 
 
 ids = 1 + numpy.linspace(0, numPart, numPart, endpoint=False)
-ds = grp1.create_dataset('ParticleIDs', (numPart, ), 'L')
+ds = grp1.create_dataset("ParticleIDs", (numPart,), "L")
 ds[()] = ids
 
-ds = grp1.create_dataset('Coordinates', (numPart, 3), 'd')
+ds = grp1.create_dataset("Coordinates", (numPart, 3), "d")
 ds[()] = r
 
 

examples/GravityTests/DiscPatch/GravityOnly/run.sh

@@ -4,7 +4,11 @@
 if [ ! -e Disc-Patch.hdf5 ]
 then
     echo "Generating initial conditions for the disc-patch example..."
-    python makeIC.py 1000
+    python3 makeIC.py 1000
 fi
 
-../../../swift --external-gravity --threads=2 disc-patch.yml
+# Run SWIFT
+../../../../swift --external-gravity --threads=2 disc-patch.yml
+
+# Verify energy conservation
+python3 test.py