Merge branch 'master' into removing_particles

doc/RTD/source/CommandLineOptions/index.rst

+.. Command line options
+   Matthieu Schaller, 21st October 2018
+
+Command line options
+====================
+

doc/RTD/source/GettingStarted/index.rst

@@ -20,7 +20,6 @@ and keep on your desk.
    running_example
    runtime_options
    configuration_options
-   parameter_file
    what_about_mpi
    running_on_large_systems
    special_modes

doc/RTD/source/HydroSchemes/hopkins_sph.rst

@@ -28,3 +28,9 @@ scheme it includes a Monaghan AV scheme and a Balsara switch.
 .. code-block:: bash
    
    ./configure --with-hydro="pressure-energy"
+
+Both of the above schemes use a very simple, fixed artificial viscosity, only
+the ``SPH:viscosity_alpha`` parameter has any effect for this scheme. This will
+change the strength of the artificial viscosity throughout the simulation, and
+has a default of 0.8.
+

doc/RTD/source/HydroSchemes/minimal_sph.rst

@@ -10,11 +10,17 @@ Minimal (Density-Energy) SPH
    :caption: Contents:
 
 This scheme is a textbook implementation of Density-Energy SPH, and can be used
-as a pedagogical example. It also implements a Monaghan AV scheme, like the
-GADGET-2 scheme. It uses very similar equations, but differs in implementation
-details; namely it tracks the internal energy \(u\) as the thermodynamic
-variable, rather than entropy \(A\). To use the minimal scheme, use
+as a pedagogical example. It also implements a Monaghan AV scheme with a
+Balsara switch, like the GADGET-2 scheme. It uses very similar equations, but
+differs in implementation details; namely it tracks the internal energy \(u\)
+as the thermodynamic variable, rather than entropy \(A\). To use the minimal
+scheme, use
 
 .. code-block:: bash
 
     ./configure --with-hydro="minimal"
+
+As it uses a very simple, fixed artificial viscosity, only the
+``SPH:viscosity_alpha`` parameter has any effect for this scheme. This will
+change the strength of the artificial viscosity throughout the simulation,
+and has a default of 0.8.

doc/RTD/source/HydroSchemes/traditional_sph.rst

@@ -15,3 +15,8 @@ a Monaghan artificial viscosity scheme and Balsara switch.
 To use this hydro scheme, you need no extra configuration options -- it is the
 default!
 
+As it uses a very simple, fixed artificial viscosity, only the
+``SPH:viscosity_alpha`` parameter has any effect for this scheme. This will
+change the strength of the artificial viscosity throughout the simulation,
+and has a default of 0.8.
+

doc/RTD/source/InitialConditions/index.rst

@@ -176,7 +176,9 @@ as peculiar velocities divided by ``sqrt(a)``. This can be undone by swicthing
 on the parameter ``InitialConditions:cleanup_velocity_factors`` in the
 :ref:`Parameter_File_label`.
 
-     
+
+.. _ICs_units_label:
+
 Optional Components
 -------------------
 

doc/RTD/source/ParameterFiles/index.rst

+.. Parameter Files
+   Matthieu Schaller, 21st October 2018
+
+Parameter Files
+===============
+
+File format and basic information
+---------------------------------
+
+The parameter file uses a format similar to the `YAML format
+<https://en.wikipedia.org/wiki/YAML>`_ but reduced to only the
+elements required for the SWIFT parameters. Options are given by a
+name followed by a column and the value of the parameter:
+
+.. code:: YAML
+
+   ICs:        santa_barbara.hdf5	  
+   dt_max:     1.5
+   shift:      [2., 4., 5.]
+
+Comments can be inserted anywhere and start with a hash:
+
+.. code:: YAML
+
+   # Descrption of the physics
+   viscosity_alpha:     2.0
+   dt_max:              1.5     # seconds
+
+A typical SWIFT parameter file is split into multiple sections that
+may or may not be present depending on the different configuration
+options. The sections start with a label and can contain any number of
+parameters:
+
+.. code:: YAML
+
+   Cosmology:    # Planck13
+     Omega_m:        0.307
+     Omega_lambda:   0.693
+     Omega_b:        0.0455
+     h:              0.6777
+     a_begin:        0.0078125     # z = 127
+
+The options can be integer values, floating point numbers, characters
+or strings. If SWIFT expects a number and string is given, an error
+will be raised. The code can also read an array of values:
+
+.. code:: YAML
+
+   shift:  [2., 4., 5.]
+	  
+Some options in the parameter file are optional and
+when not provided, SWIFT will run with the default value. However, if
+a compulsory parameter is missing an error will be raised at
+start-up.
+
+Finally, SWIFT outputs two YAML files at the start of a run. The first
+one ``used_parameters.yml`` contains all the parameters that were used
+for this run, **including all the optional parameters with their
+default values**. This file can be used to start an exact copy of the
+run. The second file, ``unused_parameters.yml`` contains all the
+values that were not read from the parameter file. This can be used to
+simplify the parameter file or check that nothing important was
+ignored (for instance because the code is not configured to use some
+options).
+
+The rest of this page describes all the SWIFT parameters, split by
+section. A list of all the possible parameters is kept in the file
+``examples/parameter_examples.yml``.
+
+Internal Unit System
+--------------------
+
+This section describes the units used internally by the code. This is
+the system of units in which all the equations are solved. All
+physical constants are converted to this system and if the ICs use a
+different system (see :ref:`ICs_units_label`) the particle quantities
+will be converted when read in.
+
+The system of units is described using the value of the 5 basic units
+of any system with respect to the CGS system. Instead of using a unit
+of time we use a unit of velocity as this is more intuitive. Users
+hence need to provide:
+
+* a unit of length: ``UnitLength_in_cgs``,
+* a unit of mass: ``UnitMass_in_cgs``,
+* a unit of velocity ``UnitVelocity_in_cgs``,
+* a unit of electric current ``UnitCurrent_in_cgs``,
+* a unit of temperature ``UnitTemp_in_cgs``.
+
+All these need to be expressed with respect to their cgs counter-part
+(i.e. :math:`cm`, :math:`g`, :math:`cm/s`, :math:`A` and :math:`K`). Recall
+that there are no h-factors in any of SWIFT's quantities; we, for instance,
+use :math:`cm` and not :math:`cm/h`.
+
+For instance to use the commonly adopted system of 10^10 Msun as a
+unit for mass, mega-parsec as a unit of length and km/s as a unit of
+speed, we would use:
+
+.. code:: YAML
+
+   # Common unit system for cosmo sims
+   InternalUnitSystem:
+     UnitMass_in_cgs:     1.98848e43    # 10^10 M_sun in grams
+     UnitLength_in_cgs:   3.08567758e24 # 1 Mpc in centimeters
+     UnitVelocity_in_cgs: 1e5           # 1 km/s in centimeters per second
+     UnitCurrent_in_cgs:  1             # 1 Ampere
+     UnitTemp_in_cgs:     1             # 1 Kelvin   
+	  
+Note that there are currently no variables in any of the SWIFT physics
+schemes that make use of the unit of electric current. There is also
+no incentive to use anything else than Kelvin but that makes the whole
+system consistent with any possible unit system.
+
+If one is interested in using the more humourous `FFF unit
+system <https://en.wikipedia.org/wiki/FFF_system>`_ one would use
+
+.. code:: YAML
+
+   # FFF unit system
+   InternalUnitSystem:
+     UnitMass_in_cgs:     40823.3133  # 1 Firkin (fir) in grams
+     UnitLength_in_cgs:   20116.8     # 1 Furlong (fur) in cm
+     UnitVelocity_in_cgs: 0.01663095  # 1 Furlong (fur) per Fortnight (ftn) in cm/s
+     UnitCurrent_in_cgs:  1           # 1 Ampere
+     UnitTemp_in_cgs:     1           # 1 Kelvin   
+
+The value of the physical constants in this system is left as an
+exercise for the reader [#f1]_.
+
+Cosmology
+---------
+
+When running a cosmological simulation, this section set the values of the
+cosmological model. The epanded :math:`\Lambda\rm{CDM}` parameters governing the
+background evolution of the Univese need to be specified here. These are:
+
+* The reduced Hubble constant: :math:`h`: ``h``,
+* The matter density parameter :math:`\Omega_m`: ``Omega_m``,
+* The cosmological constant density parameter :math:`\Omega_\Lambda`: ``Omega_lambda``,
+* The baryon density parameter :math:`\Omega_b`: ``Omega_b``,
+* The radiation density parameter :math:`\Omega_r`: ``Omega_r``.
+
+The last parameter can be omitted and will default to :math:`\Omega_r = 0`.
+
+This section als specifies the start and end of the simulation expressed in
+terms of scale-factors. The two parameters are:
+
+* Initial scale-factor: ``a_begin``,
+* Final scale-factor: ``a_end``.
+
+Two additional optional parameters can be used to change the equation of
+state of dark energy :math:`w(a)`. We use the evolution law :math:`w(a) =
+w_0 + w_a (1 - a)`. The two parameters in the YAML file are:
+
+* The :math:`z=0` dark energy equation of state parameter :math:`w_0`: ``w_0``
+* The dark energy equation of state evolutio parameter :math:`w_a`: ``w_a``
+
+If unspecified these parameters default to the default
+:math:`\Lambda\rm{CDM}` values of :math:`w_0 = -1` and :math:`w_a = 0`.
+
+For a Planck+13 cosmological model (ignoring radiation density as is
+commonly done) and running from :math:`z=127` to :math:`z=0`, one would hence
+use the following parameters:
+
+.. code:: YAML
+
+   Cosmology:
+     a_begin:        0.0078125     # z = 127
+     a_end:          1.0           # z = 0
+     h:              0.6777        
+     Omega_m:        0.307         
+     Omega_lambda:   0.693         
+     Omega_b:        0.0455        
+     Omega_r:        0.            # (Optional)
+     w_0:            -1.0          # (Optional)
+     w_a:            0.            # (Optional)
+
+When running a non-cosmological simulation (i.e. without the ``-c`` runtime
+flag) this section of the YAML file is entirely ignored.
+     
+Gravity
+-------
+
+SPH
+---
+
+Time Integration
+----------------
+
+Physical Constants
+------------------
+
+For some idealised test it can be useful to overwrite the value of
+some physical constants. In particular the value of the gravitational
+constant. SWIFT offers an optional parameter to overwrite the value of
+that constant.
+
+.. code:: YAML
+
+   PhysicalConstants:
+     G:   1
+
+Note that this set :math:`G` to the specified value in the internal system
+of units. Setting a value of `1` when using the system of units (10^10 Msun,
+Mpc, km/s) will mean that :math:`G_N=1` in these units [#f2]_ instead of the
+normal value :math:`G_N=43.00927`.
+
+This option is only used for specific tests and debugging. This entire
+section of the YAML file can typically be left out.
+
+Snapshots
+---------
+
+Some additional specific options for the snapshot outputs are described in the
+following pages:
+
+.. toctree::
+   :maxdepth: 1
+
+   output_selection
+
+Statistics
+----------
+
+Restarts
+--------
+
+Scheduler
+---------
+
+Domain Decomposition
+--------------------
+
+.. [#f1] The thorough reader (or overly keen SWIFT tester) would find  that the speed of light is :math:`c=1.8026\times10^{12}\,\rm{fur}\,\rm{ftn}^{-1}`, Newton's contant becomes :math:`G_N=4.896735\times10^{-4}~\rm{fur}^3\,\rm{fir}^{-1}\,\rm{ftn}^{-2}` and Planck's constant turns into :math:`h=4.851453\times 10^{-34}~\rm{fur}^2\,\rm{fir}\,\rm{ftn}^{-1}`.
+
+
+.. [#f2] which would translate into a constant :math:`G_N=1.5517771\times10^{-9}~cm^{3}\,g^{-1}\,s^{-2}` if expressed in the CGS system.

doc/RTD/source/GettingStarted/parameter_file.rst → doc/RTD/source/ParameterFiles/output_selection.rst

 .. Parameter File
    Loic Hausammann, 1 june 2018
 
-.. _Parameter_File_label:
-
-Parameter File
-==============
-
-To run SWIFT, you will need to provide a ``yaml`` parameter file.  An example is
-given in ``examples/parameter_file.yml`` which should contain all possible
-parameters.  Each section in this file corresponds to a different option in
-SWIFT and are not always required depending on the configuration options and
-the run time parameters.
+.. _Output_list_label:
 
 Output List
 ~~~~~~~~~~~
 
-In the sections ``Snapshots`` and ``Statistics``, you can specify the options ``output_list_on`` and ``output_list``  which receive an int and a filename.
-The ``output_list_on`` enable or not the output list and ``output_list`` is the filename containing the output times.
-With the file header, you can choose between writing redshifts, scale factors or times.
+In the sections ``Snapshots`` and ``Statistics``, you can specify the
+options ``output_list_on`` and ``output_list`` which receive an int
+and a filename.  The ``output_list_on`` enable or not the output list
+and ``output_list`` is the filename containing the output times.  With
+the file header, you can choose between writing redshifts, scale
+factors or times.
 
 Example of file containing with times (in internal units)::
 
@@ -42,6 +36,8 @@ Example of file with redshift::
   10
   5
 
+.. _Output_selection_label:
+  
 Output Selection
 ~~~~~~~~~~~~~~~~
 

doc/RTD/source/index.rst

@@ -15,6 +15,8 @@ difference is the parameter file that will need to be adapted for SWIFT.
    :maxdepth: 2
 
    GettingStarted/index
+   CommandLineOptions/index
+   ParameterFiles/index
    InitialConditions/index
    HydroSchemes/index
    Cooling/index

examples/DwarfGalaxy/README

+This example is a galaxy extracted from the example "ZoomIn". It allows
+to test SWIFT on a smaller problem. See the README in "ZoomIn" for more
+information.
+
+
+MD5 check-sum of the ICS: 
+ae2af84d88f30011b6a8af3f37d140cf  dwarf_galaxy.hdf5
\ No newline at end of file

examples/DwarfGalaxy/dwarf_galaxy.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     1.98848e43    # 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
+
+# Structure finding options
+StructureFinding:
+  config_file_name:     stf_input.cfg # Name of the STF config file.
+  basename:             ./stf         # Common part of the name of output files.
+  output_time_format:   0             # Specifies the frequency format of structure finding. 0 for simulation steps (delta_step) and 1 for simulation time intervals (delta_time).
+  scale_factor_first:   0.92          # Scale-factor of the first snaphot (cosmological run)
+  time_first:           0.01        # Time of the first structure finding output (in internal units).
+  delta_step:           1000          # Time difference between consecutive structure finding outputs (in internal units) in simulation steps.
+  delta_time:           1.10          # Time difference between consecutive structure finding outputs (in internal units) in simulation time intervals.
+
+# Cosmological parameters
+Cosmology:
+  h:              0.673        # Reduced Hubble constant
+  a_begin:        0.9873046739     # Initial scale-factor of the simulation
+  a_end:          1.0           # Final scale factor of the simulation
+  Omega_m:        0.315         # Matter density parameter
+  Omega_lambda:   0.685         # Dark-energy density parameter
+  Omega_b:        0.0486        # Baryon density parameter
+  
+Scheduler:
+  max_top_level_cells:    8
+  cell_split_size:           400       # (Optional) Maximal number of particles per cell (this is the default value).
+  
+# Parameters governing the time integration
+TimeIntegration:
+  time_begin: 0.    # The starting time of the simulation (in internal units).
+  time_end:   1.  # 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).
+  
+# Parameters governing the snapshots
+Snapshots:
+  basename:            dwarf_galaxy # Common part of the name of output files
+  time_first:          0.  # Time of the first output (non-cosmological run) (in internal units)
+  delta_time:          0.02  # Time difference between consecutive outputs (in internal units)
+  compression:         1
+
+# 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
+
+# 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
+
+# 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)
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./dwarf_galaxy.hdf5     # The file to read
+  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
+

examples/DwarfGalaxy/getIC.sh

+#!/bin/bash
+wget https://obswww.unige.ch/~lhausamm/swift/IC/DwarfGalaxy/dwarf_galaxy.hdf5

examples/DwarfGalaxy/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e dwarf_galaxy.hdf5 ]
+then
+    echo "Fetching initial conditions for the dwarf galaxy example..."
+    ./getIC.sh
+fi
+
+../swift -b -G -s -S -t 8 dwarf_galaxy.yml 2>&1 | tee output.log
+

examples/ZoomIn/README

+Initial conditions for a zoom in cosmological simulation of dwarf
+galaxies. These have been generated by MUSIC and ran up to z=0 with
+GEAR (see Revaz and Jablonka 2018 for more details on the simulation).
+
+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).
+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.
+
+MD5 check-sum of the ICS: 
+9aafe154438478ed435e88664c1c5dba zoom_in.hdf5

examples/ZoomIn/getIC.sh

+#!/bin/bash
+wget https://obswww.unige.ch/~lhausamm/swift/IC/ZoomIn/zoom_in.hdf5

examples/ZoomIn/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e zoom_in.hdf5 ]
+then
+    echo "Fetching initial conditions for the zoom in example..."
+    ./getIC.sh
+fi
+
+../swift -b -c -G -s -S -t 8 zoom_in.yml 2>&1 | tee output.log
+

examples/ZoomIn/zoom_in.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     1.98848e43    # 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
+
+# Cosmological parameters
+Cosmology:
+  h:              0.673        # Reduced Hubble constant
+  a_begin:        0.9873046739     # Initial scale-factor of the simulation
+  a_end:          1.0           # Final scale factor of the simulation
+  Omega_m:        0.315         # 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).
+  
+# 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
+
+# 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
+
+# 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
+
+# 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)
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./zoom_in.hdf5     # The file to read
+  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
+

examples/parameter_example.yml

@@ -34,6 +34,10 @@ SPH:
   minimal_temperature:   0        # (Optional) Minimal temperature (in internal units) allowed for the gas particles. Value is ignored if set to 0.
   H_mass_fraction:       0.755    # (Optional) Hydrogen mass fraction used for initial conversion from temp to internal energy. Default value is derived from the physical constants.
   H_ionization_temperature: 1e4   # (Optional) Temperature of the transition from neutral to ionized Hydrogen for primoridal gas.
+  viscosity_alpha:       0.8      # (Optional) Override for the initial value of the artificial viscosity. In schemes that have a fixed AV, this remains as alpha throughout the run.
+  viscosity_alpha_max:   2.0      # (Optional) Maximal value for the artificial viscosity in schemes that allow alpha to vary
+  viscosity_alpha_min:   0.1      # (Optional) Minimal value for the artificial viscosity in schemes that allow alpha to vary
+  viscosity_length:      0.1      # (Optional) Decay length for the artificial viscosity in schemes that allow alpha to vary
 
 # Parameters for the self-gravity scheme
 Gravity:
@@ -133,9 +137,9 @@ DomainDecomposition:
                             # new decomposition, or number of steps (>1) between decompositions
   minfrac:          0.9     # (Optional) Fractional of all particles that should be updated in previous step when
                             # using CPU time trigger
-  usemetis          0       # Use serial METIS when ParMETIS is also available.
-  adaptive          1       # Use adaptive repartition when ParMETIS is available, otherwise simple refinement.
-  itr               100     # When adaptive defines the ratio of inter node communication time to data redistribution time, in the range 0.00001 to 10000000.0.
+  usemetis:         0       # Use serial METIS when ParMETIS is also available.
+  adaptive:         1       # Use adaptive repartition when ParMETIS is available, otherwise simple refinement.
+  itr:              100     # When adaptive defines the ratio of inter node communication time to data redistribution time, in the range 0.00001 to 10000000.0.
                             # Lower values give less data movement during redistributions, at the cost of global balance which may require more communication.
 
 # Parameters related to the equation of state ------------------------------------------

examples/plot_task_level.py

+#!/usr/bin/python
+"""
+Usage:
+  ./plot_task_level.py task_level.txt
+
+Description:
+  Plot the number of tasks for each depth level and each type of task.
+"""
+
+
+import pandas as pd
+import matplotlib.pyplot as plt
+import sys
+
+# get filename
+filename = sys.argv[-1]
+
+# Column names
+names = ["type", "subtype", "depth", "count"]
+
+# read file
+data = pd.read_csv(filename, sep=' ', comment="#", names=names)
+
+# generate color map
+cmap = plt.get_cmap("hsv")
+N = data["depth"].max() + 5
+
+# plot data
+for i in range(data["depth"].max()):
+    ind = data["depth"] == i
+    label = "depth = %i" % i
+    c = cmap(i / N)
+    plt.plot(data["type"][ind] + "_" + data["subtype"][ind],
+             data["count"][ind], ".", label=label,
+             color=c)
+
+# modify figure parameters and show it
+plt.gca().set_yscale("log")
+plt.xticks(rotation=45)
+plt.ylabel("Number of Tasks")
+plt.gcf().subplots_adjust(bottom=0.15)
+plt.legend()
+plt.show()

examples/plot_tasks.py

@@ -157,11 +157,11 @@ for task in SUBTYPES:
 
 #  For fiddling with colours...
 if args.verbose:
-    print