def test_full_relativistic(self):
"""Parsing the full-relativistic output file produced by ONCVPSPS."""
p = OncvOutputParser(filepath("08_O_r.out"))
p.scan(verbose=1)
repr(p)
str(p)
assert p.run_completed
assert p.fully_relativistic
assert p.calc_type == "fully-relativistic"
assert p.version == "2.1.1"
assert p.atsym == "O"
assert p.z == "8.00"
assert p.iexc == "3"
assert p.nc == 1
assert p.nv == 2
assert p.lmax == 1
# TODO: Wavefunctions
# Build the plotter
plotter = p.make_plotter()
repr(plotter)
str(plotter)
self._call_plotter_methods(plotter)
def test_nonrelativistica(self):
"""Parsing the non-relativistic output file produced by ONCVPSPS."""
# Non-relativistic results
p = OncvOutputParser(filepath("08_O_nr.out"))
p.scan(verbose=1)
assert p.run_completed
print(p)
assert p.calc_type == "non-relativistic"
assert not p.fully_relativistic
assert p.version == "2.1.1"
assert p.atsym == "O"
assert p.z == "8.00"
assert p.iexc == "3"
assert p.lmax == 1
assert p.nc == 1
assert p.nv == 2
assert p.lmax == 1
rhov, rhoc, rhom = p.densities["rhoV"], p.densities["rhoC"], p.densities["rhoM"]
assert rhov.rmesh[0] == 0.0100642
assert rhov.rmesh[-1] == 3.9647436
assert rhoc.values[0] == 53.3293576
assert all(rhom.values == 0.0)
# Conversion to JSON format.
p.to_dict
# Build the plotter
plotter = p.make_plotter()
def test_full_relativistic(self):
"""Parsing the full-relativistic output file produced by ONCVPSPS."""
p = OncvOutputParser(filepath("08_O_r.out"))
p.scan(verbose=1)
repr(p); str(p)
assert p.run_completed
assert p.fully_relativistic
assert p.calc_type == "fully-relativistic"
assert p.version == "2.1.1"
assert p.atsym == "O"
assert p.z == "8.00"
assert p.iexc == "3"
assert p.nc == 1
assert p.nv == 2
assert p.lmax == 1
# TODO: Wavefunctions
# Build the plotter
plotter = p.make_plotter()
repr(plotter); str(plotter)
self._call_plotter_methods(plotter)
def oncv_plot(options):
"""Plot data with matplotlib. Requires oncvpsp output file."""
out_path = find_oncv_output(options.filename)
# Parse output file.
onc_parser = OncvOutputParser(out_path)
onc_parser.scan()
if not onc_parser.run_completed:
cprint("oncvpsp output is not complete. Exiting", "red")
return 1
# Build the plotter
plotter = onc_parser.make_plotter()
# Plot data
plotter.plot_radial_wfs()
plotter.plot_atanlogder_econv()
plotter.plot_projectors()
plotter.plot_potentials()
#plotter.plot_der_potentials()
#for order in [1,2,3,4]:
# plotter.plot_der_densities(order=order)
plotter.plot_densities()
#plotter.plot_densities(timesr2=True)
plotter.plot_den_formfact()
return 0
# Table of methods
callables = collections.OrderedDict([
("wp", plotter.plot_waves_and_projs),
("dp", plotter.plot_dens_and_pots),
("lc", plotter.plot_atanlogder_econv),
("df", plotter.plot_den_formfact),
])
# Call function depending on options.plot_mode
if options.plot_mode == "slide":
for func in callables.values():
func()
else:
func = callables.get(options.plot_mode, None)
if func is not None:
func()
else:
plotter.plot_key(key=options.plot_mode)
def oncv_plot(options):
"""Plot data with matplotlib. Requires oncvpsp output file."""
out_path = find_oncv_output(options.filename)
# Parse output file.
onc_parser = OncvOutputParser(out_path)
onc_parser.scan()
if not onc_parser.run_completed:
cprint("oncvpsp output is not complete. Exiting", "red")
return 1
# Build the plotter
plotter = onc_parser.make_plotter()
# Plot data
plotter.plot_radial_wfs()
plotter.plot_atanlogder_econv()
plotter.plot_projectors()
plotter.plot_potentials()
#plotter.plot_der_potentials()
#for order in [1,2,3,4]:
# plotter.plot_der_densities(order=order)
plotter.plot_densities()
#plotter.plot_densities(timesr2=True)
plotter.plot_den_formfact()
return 0
# Table of methods
callables = collections.OrderedDict([
("wp", plotter.plot_waves_and_projs),
("dp", plotter.plot_dens_and_pots),
("lc", plotter.plot_atanlogder_econv),
("df", plotter.plot_den_formfact),
])
# Call function depending on options.plot_mode
if options.plot_mode == "slide":
for func in callables.values():
func()
else:
func = callables.get(options.plot_mode, None)
if func is not None:
func()
else:
plotter.plot_key(key=options.plot_mode)
def test_nonrelativistica(self):
"""Parsing the non-relativistic output file produced by ONCVPSPS."""
# Non-relativistic results
p = OncvOutputParser(filepath("08_O_nr.out"))
repr(p)
str(p)
p.scan(verbose=1)
repr(p)
str(p)
assert p.run_completed
assert p.calc_type == "non-relativistic"
assert not p.fully_relativistic
assert p.version == "2.1.1"
assert p.atsym == "O"
assert p.z == "8.00"
assert p.iexc == "3"
assert p.lmax == 1
assert p.nc == 1
assert p.nv == 2
assert p.lmax == 1
rhov, rhoc, rhom = p.densities["rhoV"], p.densities[
"rhoC"], p.densities["rhoM"]
assert rhov.rmesh[0] == 0.0100642
assert rhov.rmesh[-1] == 3.9647436
assert rhoc.values[0] == 53.3293576
assert all(rhom.values == 0.0)
# Conversion to JSON format.
p.to_dict
# Build the plotter
plotter = p.make_plotter()
repr(plotter)
str(plotter)
self._call_plotter_methods(plotter)
def test_scalar_relativistic(self):
"""Parsing the scalar-relativistic output file produced by ONCVPSPS."""
# Scalar relativistic output
p = OncvOutputParser(filepath("08_O_sr.out"))
p.scan(verbose=1)
repr(p)
str(p)
assert p.run_completed
assert not p.fully_relativistic
assert p.calc_type == "scalar-relativistic"
assert p.version == "2.1.1"
assert p.atsym == "O"
assert p.z == "8.00"
assert p.iexc == "3"
assert p.nc == 1
assert p.nv == 2
assert p.lmax == 1
# Test potentials
vloc = p.potentials[-1]
pl0 = {0: -7.4449470, 1: -14.6551019, -1: -9.5661177}
for l, pot in p.potentials.items():
assert pot.rmesh[0], pot.rmesh[-1] == (0.0099448, 3.9647436)
str(l)
assert pot.values[0] == pl0[l]
assert all(pot.rmesh == vloc.rmesh)
# Test wavefunctions
ae_wfs, ps_wfs = p.radial_wfs.ae, p.radial_wfs.ps
nlk = (1, 0, None)
ae10, ps10 = ae_wfs[nlk], ps_wfs[nlk]
assert ae10[0] == (0.009945, -0.092997)
assert ps10[0] == (0.009945, 0.015273)
assert ae10[-1] == (3.964744, 0.037697)
assert ps10[-1] == (3.964744, 0.037694)
nlk = (2, 1, None)
ae21, ps21 = ae_wfs[nlk], ps_wfs[nlk]
assert ae21[0] == (0.009945, 0.001463)
assert ps21[0] == (0.009945, 0.000396)
# Test projectors
prjs = p.projectors
assert prjs[(1, 0, None)][0] == (0.009945, 0.015274)
assert prjs[(2, 0, None)][0] == (0.009945, -0.009284)
assert prjs[(1, 0, None)][-1] == (3.964744, 0.037697)
assert prjs[(2, 0, None)][-1] == (3.964744, 0.330625)
assert prjs[(1, 1, None)][0] == (0.009945, 0.000395)
assert prjs[(2, 1, None)][0] == (0.009945, -0.000282)
# Test convergence data
c = p.ene_vs_ecut
assert c[0].energies[0] == 5.019345
assert c[0].values[0] == 0.010000
assert c[0].energies[-1] == 25.317286
assert c[0].values[-1] == 0.000010
assert c[1].energies[0] == 19.469226
assert c[1].values[0] == 0.010000
# Test log derivatives
ae0, ps0 = p.atan_logders.ae[0], p.atan_logders.ps[0]
assert ae0.energies[0], ae0.values[0] == (2.000000, 0.706765)
assert ps0.energies[0], ps0.values[0] == (2.000000, 0.703758)
assert ae0.energies[-1], ae0.energies[-1] == (-2.000000, 3.906687)
assert ps0.energies[-1], ps0.energies[-1] == (-2.000000, 3.906357)
ae1, ps1 = p.atan_logders.ae[1], p.atan_logders.ps[1]
assert ae1.energies[0], ae1.values[0] == (2.000000, -2.523018)
assert ps1.values[0] == -2.521334
# Build the plotter
plotter = p.make_plotter()
repr(plotter)
str(plotter)
self._call_plotter_methods(plotter)
def test_scalar_relativistic(self):
"""Parsing the scalar-relativistic output file produced by ONCVPSPS."""
# Scalar relativistic output
p = OncvOutputParser(filepath("08_O_sr.out"))
p.scan(verbose=1)
repr(p); str(p)
assert p.run_completed
assert not p.fully_relativistic
assert p.calc_type == "scalar-relativistic"
assert p.version == "2.1.1"
assert p.atsym == "O"
assert p.z == "8.00"
assert p.iexc == "3"
assert p.nc == 1
assert p.nv == 2
assert p.lmax == 1
# Test potentials
vloc = p.potentials[-1]
pl0 = {0: -7.4449470, 1: -14.6551019, -1: -9.5661177}
for l, pot in p.potentials.items():
assert pot.rmesh[0], pot.rmesh[-1] == (0.0099448, 3.9647436)
str(l)
assert pot.values[0] == pl0[l]
assert all(pot.rmesh == vloc.rmesh)
# Test wavefunctions
ae_wfs, ps_wfs = p.radial_wfs.ae, p.radial_wfs.ps
nlk = (1, 0, None)
ae10, ps10 = ae_wfs[nlk], ps_wfs[nlk]
assert ae10[0] == (0.009945, -0.092997)
assert ps10[0] == (0.009945, 0.015273)
assert ae10[-1] == (3.964744, 0.037697)
assert ps10[-1] == (3.964744, 0.037694)
nlk = (2, 1, None)
ae21, ps21 = ae_wfs[nlk], ps_wfs[nlk]
assert ae21[0] == (0.009945, 0.001463)
assert ps21[0] == (0.009945, 0.000396)
# Test projectors
prjs = p.projectors
assert prjs[(1, 0, None)][0] == (0.009945, 0.015274)
assert prjs[(2, 0, None)][0] == (0.009945, -0.009284)
assert prjs[(1, 0, None)][-1] == (3.964744, 0.037697)
assert prjs[(2, 0, None)][-1] == (3.964744, 0.330625)
assert prjs[(1, 1, None)][0] == (0.009945, 0.000395)
assert prjs[(2, 1, None)][0] == (0.009945, -0.000282)
# Test convergence data
c = p.ene_vs_ecut
assert c[0].energies[0] == 5.019345
assert c[0].values[0] == 0.010000
assert c[0].energies[-1] == 25.317286
assert c[0].values[-1] == 0.000010
assert c[1].energies[0] == 19.469226
assert c[1].values[0] == 0.010000
# Test log derivatives
ae0, ps0 = p.atan_logders.ae[0], p.atan_logders.ps[0]
assert ae0.energies[0], ae0.values[0] == (2.000000, 0.706765)
assert ps0.energies[0], ps0.values[0] == (2.000000, 0.703758)
assert ae0.energies[-1], ae0.energies[-1] == (-2.000000, 3.906687)
assert ps0.energies[-1], ps0.energies[-1] == (-2.000000, 3.906357)
ae1, ps1 = p.atan_logders.ae[1], p.atan_logders.ps[1]
assert ae1.energies[0], ae1.values[0] == (2.000000, -2.523018)
assert ps1.values[0] == -2.521334
# Build the plotter
plotter = p.make_plotter()
repr(plotter); str(plotter)
self._call_plotter_methods(plotter)
def main():
parser = argparse.ArgumentParser() #formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('filename', default="", help="Path to the output file")
parser.add_argument("-p", "--plot-mode", default="slide",
help=("Quantity to plot. Possible values: %s" %
str(["slide", "wp, dp, lc"] + PseudoGenDataPlotter.all_keys) + "\n"
"wp --> wavefunctions and projectors\n" +
"dp --> densities and potentials\n" +
"lc --> atan(logder) and convergence wrt ecut"))
parser.add_argument("-j", "--json", action="store_true", default=False,
help="Produce a string with the results in a JSON dictionary and exit")
parser.add_argument("-8", "--psp8", action="store_true", default=False,
help="produce a .psp8 file with initial dojo report and exit")
options = parser.parse_args()
onc_parser = OncvOutputParser(options.filename)
onc_parser.scan()
if options.json:
import json
print(json.dumps(onc_parser.to_dict, indent=4))
return 0
if options.psp8:
print(onc_parser.get_pseudo_str())
return 0
# Build the plotter
plotter = onc_parser.make_plotter()
# Table of methods
callables = collections.OrderedDict([
("wp", plotter.plot_waves_and_projs),
("dp", plotter.plot_dens_and_pots),
("lc", plotter.plot_atanlogder_econv),
])
#plotter.plot_radial_wfs()
#plotter.plot_projectors()
#plotter.plot_potentials()
#plotter.plot_der_potentials()
#plotter.plot_densities()
#plotter.plot_der_densities(order=1)
#plotter.plot_der_densities(order=2)
plotter.plot_der_densities(order=4)
return
# Call function depending on options.plot_mode
if options.plot_mode == "slide":
for func in callables.values():
func()
else:
func = callables.get(options.plot_mode, None)
if func is not None:
func()
else:
plotter.plot_key(key=options.plot_mode)
return 0
def test_oncvoutput_parser():
"""Test the parsing of the output file produced by ONCVPSPS."""
# TODO: Full-relativistic case not yet supported.
with pytest.raises(OncvOutputParser.Error):
OncvOutputParser(filepath("08_O_r.out"))
# Non-relativistic results
p = OncvOutputParser(filepath("08_O_nr.out"))
print(p)
assert not p.fully_relativistic
assert p.calc_type == "non-relativistic"
assert p.atsym == "O"
assert p.z == "8.00"
assert p.iexc == "3"
assert p.lmax == 1
rhov, rhoc, rhom = p.densities["rhoV"], p.densities["rhoC"], p.densities["rhoM"]
assert rhov.rmesh[0] == 0.0100642
assert rhov.rmesh[-1] == 3.9647436
assert rhoc.values[0] == 53.3293576
assert all(rhom.values == 0.0)
# Conversion to JSON format.
p.to_dict
# Build the plotter
plotter = p.make_plotter()
# Scalar relativistic output
p = OncvOutputParser(filepath("08_O_sr.out"))
assert not p.fully_relativistic
assert p.calc_type == "scalar-relativistic"
assert p.lmax == 1
# Test potentials
vloc = p.potentials[-1]
pl0 = {0: -7.4449470, 1: -14.6551019, -1: -9.5661177}
for l, pot in p.potentials.items():
assert pot.rmesh[0], pot.rmesh[-1] == (0.0099448, 3.9647436)
print(l)
assert pot.values[0] == pl0[l]
assert all(pot.rmesh == vloc.rmesh)
# Test wavefunctions
ae_wfs, ps_wfs = p.radial_wfs.ae, p.radial_wfs.ps
ae10, ps10 = ae_wfs[(1, 0)], ps_wfs[(1, 0)]
assert ae10[0] == (0.009945, -0.092997)
assert ps10[0] == (0.009945, 0.015273)
assert ae10[-1] == (3.964744, 0.037697)
assert ps10[-1] == (3.964744, 0.037694)
ae21, ps21 = ae_wfs[(2, 1)], ps_wfs[(2, 1)]
assert ae21[0] == (0.009945, 0.001463)
assert ps21[0] == (0.009945, 0.000396)
# Test projectors
prjs = p.projectors
assert prjs[(1, 0)][0] == (0.009945, 0.015274)
assert prjs[(2, 0)][0] == (0.009945, -0.009284)
assert prjs[(1, 0)][-1] == (3.964744, 0.037697)
assert prjs[(2, 0)][-1] == (3.964744, 0.330625)
assert prjs[(1, 1)][0] == (0.009945, 0.000395)
assert prjs[(2, 1)][0] == (0.009945, -0.000282)
# Test convergence data
c = p.ene_vs_ecut
assert c[0].energies[0] == 5.019345
assert c[0].values[0] == 0.010000
assert c[0].energies[-1] == 25.317286
assert c[0].values[-1] == 0.000010
assert c[1].energies[0] == 19.469226
assert c[1].values[0] == 0.010000
# Test log derivatives
ae0, ps0 = p.atan_logders.ae[0], p.atan_logders.ps[0]
assert ae0.energies[0], ae0.values[0] == (2.000000, 0.706765)
assert ps0.energies[0], ps0.values[0] == (2.000000, 0.703758)
assert ae0.energies[-1], ae0.energies[-1] == (-2.000000, 3.906687)
assert ps0.energies[-1], ps0.energies[-1] == (-2.000000, 3.906357)
ae1, ps1 = p.atan_logders.ae[1], p.atan_logders.ps[1]
assert ae1.energies[0], ae1.values[0] == (2.000000, -2.523018)
assert ps1.values[0] == -2.521334
