Enhance modularity for inheriting FluidSim

Created originally on Bitbucket by avmo (Ashwin Vishnu)

I am in the process of using a FluidSim framework to create a package eturb to script compilation and run of Nek5000 files. How I approached it would be a long story, but to put it briefly,

• I use snakemake package to enable scripting and launching the solver (sim.make).
• I will use paraview ’s python interface to handle output files (sim.output.phys_fields)

I started borrowing parts of fluidsim to make a “solver” which does nothing more than managing parameters, copying fortran source files, compiling and executing them. See a sample of what I have below:

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In [1]: from eturb.solvers.abl import Simul                                                  

In [2]: params = Simul.create_default_params()                                               

In [3]: sim = Simul(params)                                                                  
INFO     Copying with shutil.copytree ...
WARNING  Python < 3.8: shutil.copytree may not proceed if directories exist.
WARNING  [Errno 17] File exists: '/home/avmo/.local/scratch/tmp/abl_run_L=2pix2pix2pi_48x48x48_2020-01-22_16-42-57'                                                                       
INFO     Copying with shutil.copy2 ...
INFO     Copied: /home/avmo/src/exabl/eturb/src/abl -> /home/avmo/.local/scratch/tmp/abl_run_L=2pix2pix2pi_48x48x48_2020-01-22_16-42-57                                                   
INFO     ******************************************
INFO     solver: <class 'eturb.solvers.abl.SimulABL'>
INFO     path_run: /home/avmo/.local/scratch/tmp/abl_run_L=2pix2pix2pi_48x48x48_2020-01-22_16-42-57                                                                                       
INFO     ******************************************

In [4]: sim.info                                                                             
Out[4]: 
<fluiddyn.util.paramcontainer.ParamContainer object at 0x7fde78059990>

<info_simul>
  <solver class_name="SimulNek" module_name="eturb.solvers.base"
          short_name="abl">
    <classes>
      <Oper class_name="Operators" module_name="eturb.operators"/>  

      <Output class_name="Output" module_name="abl">
        <classes>
          <PrintStdOut class_name="PrintStdOut"
                       module_name="eturb.output.print_stdout"/>  

          <PhysFields class_name="PhysFields"
                      module_name="eturb.output.phys_fields"/>  

        </classes>

      </Output>

      <Make class_name="Make" module_name="eturb.make"/>  

    </classes>

  </solver>

  <params NEW_DIR_RESULTS="True"
          path_run="/home/avmo/.local/scratch/tmp/abl_run_L=2pix2pix2pi_48x48x48_2020-01-22_16-42-57"
          short_name_type_run="run">
    <oper Lx="6.283185307179586" Ly="6.283185307179586" Lz="6.283185307179586"
          coef_dealiasing="0.6666666666666666" nx="48" ny="48" nz="48"/>  

    <output HAS_TO_SAVE="True" ONLINE_PLOT_OK="True" period_refresh_plots="1"
            sub_directory=""/>  

    <nek>
      <GENERAL _enabled="True" dealiasing="True" dt="nan" endTime="nan"
               extrapolation="standard" filterCutoffRatio="0.65"
               filterWeight="12.0" filtering="None" loglevel="2" numSteps="1"
               optLevel="2" startFrom="" stopAt="numSteps" targetCFL="0.5"
               timeStepper="BDF2" userParam03="1" variableDT="True"
               writeControl="timeStep" writeDoublePrecision="True"
               writeInterval="10"/>  

      <PROBLEMTYPE _enabled="True" equation="incompNS" stressFormulation="False"
                   variableProperties="False"/>  

      <VELOCITY _enabled="True" density="nan" residualProj="False"
                residualTol="nan" viscosity="nan"/>  

      <PRESSURE _enabled="True" preconditioner="semg_xxt" residualProj="False"
                residualTol="nan"/>  

      <MESH _enabled="False"/>  

      <TEMPERATURE _enabled="False" residualProj="False" residualTol="nan"/>  

      <SCALAR01 _enabled="False" residualProj="False" residualTol="nan"/>  

      <CVODE _enabled="False"/>  

    </nek>

  </params>

The monolithic nature of Nek5000 means, I may not be able to interface the subroutines directly. Which in turn means, I cannot have access to runtime states. But this approach seems better than nothing! During this endeavour, I had to copy certain parts and create some dummy classes, which I outline below:

• fluidsim.base.output.base.OutputBase does some cool `path_run` management, but it is hard to get rid of print_stdout and phys_fields classes. It would be nice to make a lighter version of this class
• fluidsim.base.params.create_params had to be copied and modified, since it does not allow even child classes of `Parameters` class to be created! In eturb I have a derived class from Parameters to provide special methods for Nek5000 parameters format.
• I wanted to print some initialization messages, as done by init_with_oper_and_state but the method relies on too many dependents like time_stepping, init_fields, and state which I do not intend on creating.
• No way to inherit a bare Operators class without having the fluidfft dependency. It would be useful to have 1D, 2D and 3D Operator base classes with parameters like nx.. and Lx initialized and to produce_str_describing_oper from them!

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