import numpy as np import os import pencil as pc import pytest from test_utils import require_sample, standalone_test, get_rundir datadir_novar = pytest.static_data_location/"hdf5-novar" #a directory without var.h5 datadir_nogrid = pytest.static_data_location/"hdf5-nogrid" #a directory without grid.h5 def test_read_dim_novar(): """ Check if dim info can be read without using var.h5 (i.e. from grid.h5) """ dim = pc.read.dim(datadir=datadir_novar) assert dim.nx == 1152 assert dim.nz == 288 assert dim.precision == 'D' def test_read_dim_nogrid(): """ Check if dim info can be read from var.h5 in the absence of grid.h5 """ dim = pc.read.dim(datadir=datadir_novar) assert dim.nx == 1152 assert dim.nz == 288 assert dim.precision == 'D' def test_read_grid_novar(): """ Check if grid info can be read without using var.h5 (i.e. from grid.h5) """ grid = pc.read.grid(datadir=datadir_novar, trim=True, quiet=True) assert grid.Lx == 16 assert len(grid.x) == 1152 assert len(grid.y) == 288 assert len(grid.z) == 288 assert grid.y[10] == -1.8541666 assert grid.dz_tilde[30] == 0 def test_read_grid_nogrid(): """ Check if grid info can be read from var.h5 in the absence of grid.h5 """ grid = pc.read.grid(datadir=datadir_nogrid, trim=True, quiet=True) assert grid.Lx == 16 assert len(grid.x) == 1152 assert len(grid.y) == 288 assert len(grid.z) == 288 assert grid.y[10] == -1.8541666 assert grid.dz_tilde[30] == 0 @require_sample("samples/helical-MHDturb_HDF5") def test_read_var(datadir_helical_MHDTurb_HDF5): var = pc.read.var( datadir=datadir_helical_MHDTurb_HDF5, trimall=True, lpersist=True, magic=["bb"], ) assert len(var.x) == 32 assert len(var.y) == 32 assert len(var.z) == 32 assert np.isclose(var.f[0,3,5,6], 0.02334117174211011) assert np.isclose(var.uy[0,6,2], -0.05910974500656841) assert np.isclose(var.uz[5,10,27], -0.02635602018447831) assert np.isclose(var.persist.forcing_tsforce, 0.3999999999999999) @require_sample("samples/helical-MHDturb_HDF5") def test_read_var_selective(datadir_helical_MHDTurb_HDF5): var = pc.read.var( datadir=datadir_helical_MHDTurb_HDF5, trimall=True, lpersist=True, var_list=['uy', 'uz'], ) assert len(var.x) == 32 assert len(var.y) == 32 assert len(var.z) == 32 assert np.isclose(var.uy[0,6,2], -0.05910974500656841) assert np.isclose(var.uz[5,10,27], -0.02635602018447831) assert np.isclose(var.persist.forcing_tsforce, 0.3999999999999999) assert not hasattr(var, 'lnrho') assert not hasattr(var, 'ss') assert not hasattr(var, 'ux') assert var.f.shape[0] == 2 @require_sample("samples/helical-MHDturb_HDF5") def test_read_var_irangex(datadir_helical_MHDTurb_HDF5): var = pc.read.var(datadir=datadir_helical_MHDTurb_HDF5, trimall=False, irange_x=[15,30]) assert len(var.x) == 22 assert len(var.y) == 38 assert len(var.z) == 38 assert np.isclose(var.uz[8,13,18], -0.02635602018447831) @require_sample("samples/helical-MHDturb_HDF5") def test_read_var_irangex_trim(datadir_helical_MHDTurb_HDF5): var = pc.read.var(datadir=datadir_helical_MHDTurb_HDF5, trimall=True, irange_x=[15,30]) assert len(var.x) == 16 assert len(var.y) == 32 assert len(var.z) == 32 assert np.isclose(var.uz[5,10,15], -0.02635602018447831) @require_sample("samples/helical-MHDturb_HDF5") def test_read_var_rangex_trim(datadir_helical_MHDTurb_HDF5): var = pc.read.var(datadir=datadir_helical_MHDTurb_HDF5, trimall=True, range_x=[-0.69,2.26]) assert len(var.x) == 16 assert len(var.y) == 32 assert len(var.z) == 32 assert np.isclose(var.uz[5,10,15], -0.02635602018447831) @require_sample("samples/helical-MHDturb_HDF5") def test_read_var_irangexslice(datadir_helical_MHDTurb_HDF5): var = pc.read.var(datadir=datadir_helical_MHDTurb_HDF5, trimall=False, irange_x=slice(15,30)) assert len(var.x) == 22 assert len(var.y) == 38 assert len(var.z) == 38 assert np.isclose(var.uz[8,13,18], -0.02635602018447831) @require_sample("samples/power_xy/complex_lpowerxyhdf5/nprocx_2") def test_read_power_lazy(datadir_pxyhdf5_complex_npx_2): """ Reference values here are the same as in samples/power_xy/complex_lpowerxyhdf5/nprocx_2/tests/read_powerxy.py where lazy=False """ p = pc.read.power(datadir=datadir_pxyhdf5_complex_npx_2, lazy=True) assert np.all(np.isclose( p.t[:5], [0.0543473, 0.101901, 0.156246, 0.203799, 0.251352], atol=1e-2, rtol=0, )) assert p.uz_xy.ndim == 4 assert p.uz_xy.shape == (5,32,32,32) assert not np.any(np.isnan(p.uz_xy[()])) def pow_is_close(val, ref): return np.all(np.isclose(val, ref, rtol=1.5e-2, atol=0)) assert pow_is_close( np.real(p.uz_xy[0,16,1,:3]), [-1.2e-05, -2.36e-05, 9.05e-06], ) assert pow_is_close( np.real(p.uz_xy[3,7:15,1,1]), [-0.000991, -0.00108, -0.00111, -0.00118, -0.00119, -0.00118, -0.00131, -0.00138], ) assert pow_is_close( np.real(p.uz_xy[3,16:20,1,1]), [-5.63e-04, -1.90e-04, -3.67e-05, -2.66e-06], ) assert pow_is_close( np.abs(p.uz_xy[3,9,26:,1]), [8.73e-06, 5.53e-06, 6.00e-05, 5.03e-04, 9.30e-04, 1.81e-03], ) assert pow_is_close( np.imag(p.uz_xy[3,9,29,-5:]), [2.44e-06, -9.59e-06, -6.65e-06, -4.27e-05, 4.65e-04], ) @require_sample("samples/power_xy/complex_lpowerxyhdf5/nprocx_2") def test_read_power_lazy_standalone(datadir_pxyhdf5_complex_npx_2): """ Minimal version of test_read_power_lazy, that runs in a separate Python process. Mainly to check if changing the working directory after reading creates any issues. """ standalone_test([ "import numpy as np", "import os", f"p = pc.read.power(datadir='{datadir_pxyhdf5_complex_npx_2}', lazy=True)", "os.chdir('..')", 'assert p.uz_xy.ndim == 4', 'assert p.uz_xy.shape == (5,32,32,32)', 'assert not np.any(np.isnan(p.uz_xy[()]))', 'assert np.all(np.isclose(np.real(p.uz_xy[0,16,1,0]), -1.2e-05, rtol=1.5e-2, atol=0))' ]) @require_sample("samples/helical-MHDturb_HDF5") def test_read_av_timerange(datadir_helical_MHDTurb_HDF5): av = pc.read.aver( datadir = datadir_helical_MHDTurb_HDF5, simdir = get_rundir("samples/helical-MHDturb_HDF5"), plane_list=['xy'], time_range=(0.1,0.3), ) assert np.all(np.isclose(av.t, [0.16,0.24])) assert np.all(np.isclose( av.xy.bymz[1,:4], [-8.36838e-06, 2.09012e-05, 9.59892e-06, -1.86036e-05], )) @require_sample("samples/helical-MHDturb_HDF5") def test_read_av_iterlist1(datadir_helical_MHDTurb_HDF5): av = pc.read.aver( datadir = datadir_helical_MHDTurb_HDF5, simdir = get_rundir("samples/helical-MHDturb_HDF5"), plane_list=['xy'], iter_list=[3], ) assert np.all(np.isclose(av.t, [0.24])) assert np.all(np.isclose( av.xy.bymz[0,:4], [-8.36838e-06, 2.09012e-05, 9.59892e-06, -1.86036e-05], )) @require_sample("samples/helical-MHDturb_HDF5") def test_read_av_iterlist2(datadir_helical_MHDTurb_HDF5): av = pc.read.aver( datadir = datadir_helical_MHDTurb_HDF5, simdir = get_rundir("samples/helical-MHDturb_HDF5"), plane_list=['xy'], iter_list=[1,4], ) assert np.all(np.isclose(av.t, [0.08, 0.16, 0.24])) assert np.all(np.isclose( av.xy.bymz[2,:4], [-8.36838e-06, 2.09012e-05, 9.59892e-06, -1.86036e-05], )) @require_sample("samples/helical-MHDturb_HDF5") def test_read_av_iterlist3(datadir_helical_MHDTurb_HDF5): av = pc.read.aver( datadir = datadir_helical_MHDTurb_HDF5, simdir = get_rundir("samples/helical-MHDturb_HDF5"), plane_list=['xy'], iter_list=[1,2,3], ) assert np.all(np.isclose(av.t, [0.08, 0.16, 0.24])) assert np.all(np.isclose( av.xy.bymz[2,:4], [-8.36838e-06, 2.09012e-05, 9.59892e-06, -1.86036e-05], ))