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  • fluiddynfluiddyn
  • fluidsim
  • Issues
  • #64
Closed
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Issue created Nov 19, 2020 by Jason Reneuve@jreneuveDeveloper

Warnings when plotting from a single file in directory

When a single state_phys file is the only file in a directory, it can be loaded with load_sim_for_plot, but the output.phys_fields.plot function displays a lot of warnings when called:

In [1]: from fluidsim import load_sim_for_plot

In [2]: sim = load_sim_for_plot()
load params from file
/.fsnet/project/watu/2019/19INTSIM/sim_data/waves_coriolis/test/state_phys_t0015800.015.nc
Loading params from file
/.fsnet/project/watu/2019/19INTSIM/sim_data/waves_coriolis/test/state_phys_t0015800.015.nc


*************************************
Program fluidsim
sim:                <class 'fluidsim.solvers.ns3d.strat.solver.Simul'>
sim.oper:           <class 'fluidsim.operators.operators3d.OperatorsPseudoSpectral3D'>
sim.output:         <class 'fluidsim.solvers.ns3d.strat.output.Output'>
sim.state:          <class 'fluidsim.solvers.ns3d.strat.state.StateNS3DStrat'>
sim.time_stepping:  <class 'fluidsim.solvers.ns3d.time_stepping.TimeSteppingPseudoSpectralNS3D'>
sim.init_fields:    <class 'fluidsim.solvers.ns3d.init_fields.InitFieldsNS3D'>
sim.forcing:        <class 'fluidsim.solvers.ns3d.forcing.ForcingNS3D'>

solver ns3d.strat, RK4 and sequential,
type fft: fluidfft.fft3d.with_pyfftw
nx =      4 ; ny =      4 ; nz =      4
Lx = 12 ; Ly = 12 ; Lz = 2
path_run =
/.fsnet/project/watu/2019/19INTSIM/sim_data/waves_coriolis/test
init_fields.type: constant

Initialization outputs:
sim.output.phys_fields:       <class 'fluidsim.base.output.phys_fields3d.PhysFieldsBase3D'>
sim.output.spatial_means:     <class 'fluidsim.solvers.ns3d.strat.output.spatial_means.SpatialMeansNS3DStrat'>
sim.output.spectra:           <class 'fluidsim.solvers.ns3d.strat.output.spectra.SpectraNS3DStrat'>
sim.output.spect_energy_budg: <class 'fluidsim.solvers.ns3d.strat.output.spect_energy_budget.SpectralEnergyBudgetNS3DStrat'>

Memory usage at the end of init. (equiv. seq.): 160.23046875 Mo
Size of state_spect (equiv. seq.): 0.003072 Mo

In [3]: sim.output.phys_fields.plot('vz',equation='z=1.5')
/.fsnet/data/legi/calcul9/home/reneuve3ja/Dev/fluidsim/fluidsim/base/output/phys_fields.py:365: RuntimeWarning: divide by zero encountered in double_scalars
  weight0 = 1 - np.abs(time - self.times[idx0]) / dt_save
/.fsnet/data/legi/calcul9/home/reneuve3ja/Dev/fluidsim/fluidsim/base/output/phys_fields.py:366: RuntimeWarning: divide by zero encountered in double_scalars
  weight1 = 1 - np.abs(time - self.times[idx1]) / dt_save
/.fsnet/data/legi/calcul9/home/reneuve3ja/Dev/fluidsim/fluidsim/base/output/phys_fields3d.py:486: RuntimeWarning: invalid value encountered in true_divide
  vecx_c / vmax,
/.fsnet/data/legi/calcul9/home/reneuve3ja/Dev/fluidsim/fluidsim/base/output/phys_fields3d.py:487: RuntimeWarning: invalid value encountered in true_divide
  vecy_c / vmax,
/home/users/reneuve3ja/miniconda3/lib/python3.8/site-packages/matplotlib/quiver.py:678: RuntimeWarning: Mean of empty slice.
  amean = a[~self.Umask].mean()
/home/users/reneuve3ja/miniconda3/lib/python3.8/site-packages/numpy/core/_methods.py:161: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/users/reneuve3ja/miniconda3/lib/python3.8/site-packages/matplotlib/quiver.py:748: RuntimeWarning: invalid value encountered in less
  short = np.repeat(length < minsh, 8, axis=1)
/home/users/reneuve3ja/miniconda3/lib/python3.8/site-packages/matplotlib/quiver.py:762: RuntimeWarning: invalid value encountered in less
  tooshort = length < self.minlength

Here the physical field vz is plotted correctly as a contourf, but the quiver of the velocity field is not superimposed over it. Similarly, all velocity components can be plotted as contourf, but the quiver never works.

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