mirror of https://github.com/abinit/abipy.git
Add max_nlaunch option to rapifire
This commit is contained in:
Matteo Giantomassi
parent
e381330de7
commit
a6c1143771
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@ -4,52 +4,57 @@ This module defines constants and conversion factors matching those present in a
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it is important to preserve consistency with the results produced by abinit.
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"""
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from __future__ import print_function, division, unicode_literals, absolute_import
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import numpy as np
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# taken from abinit/10_defs/defs_basis.F90
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# 1 Bohr, in Angstrom
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Bohr_Ang=0.52917720859
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Bohr_Ang = 0.52917720859
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# 1 Hartree, in cm^-1
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Ha_cmm1=219474.6313705
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Ha_cmm1 = 219474.6313705
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# 1 Hartree, in eV
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Ha_eV=27.21138386
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Ha_eV = 27.21138386
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# 1 eV in Hartree
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eV_Ha=1./Ha_eV
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eV_Ha = 1. / Ha_eV
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# 1 Hartree, in meV
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Ha_meV=Ha_eV*1000
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# 1Hartree, in Kelvin
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Ha_K=315774.65
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Ha_meV = Ha_eV * 1000
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# 1 Hartree, in Kelvin
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Ha_K = 315774.65
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# 1 eV, in Kelvin
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eV_to_K = eV_Ha * Ha_K
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# 1 Hartree, in THz
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Ha_THz=6579.683920722
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Ha_THz = 6579.683920722
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# 1 eV, in THz
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eV_to_THz=eV_Ha*Ha_THz
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#1 Hartree, in J
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Ha_J=4.35974394e-18
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eV_to_THz = eV_Ha * Ha_THz
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# 1 eV, in cm-1
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eV_to_cm1 = 8065.5440044136285
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# 1 Hartree, in J
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Ha_J = 4.35974394e-18
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# minus the electron charge, in Coulomb
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e_Cb=1.602176487e-19
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e_Cb = 1.602176487e-19
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# Boltzmann constant in eV/K and Ha/K
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kb_eVK=8.617343e-5
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kb_eVK = 8.617343e-5
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kb_HaK = kb_eVK / Ha_eV
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# 1 atomic mass unit, in electronic mass
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amu_emass=1.660538782e-27/9.10938215e-31
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amu_emass = 1.660538782e-27 / 9.10938215e-31
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# 1 Ha/Bohr^3, in GPa
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HaBohr3_GPa=Ha_eV/Bohr_Ang**3*e_Cb*1.0e+21
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HaBohr3_GPa = Ha_eV / Bohr_Ang**3 * e_Cb * 1.0e+21
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# per mole
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Avogadro=6.02214179e23
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Avogadro = 6.02214179e23
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# 1 Ohm.cm in atomic units
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Ohmcm=2*np.pi*Ha_THz*10/9
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eps0=1/(4*np.pi*0.0000001*299792458.0**2)
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AmuBohr2_Cm2=e_Cb*1.0e20/(Bohr_Ang*Bohr_Ang)
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Ohmcm = 2 * np.pi * Ha_THz * 10 / 9
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eps0 = 1 / (4*np.pi*0.0000001*299792458.0**2)
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AmuBohr2_Cm2 = e_Cb * 1.0e20 / (Bohr_Ang * Bohr_Ang)
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# Inverse of fine structure constant
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InvFineStruct=137.035999679
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InvFineStruct = 137.035999679
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# speed of light in SI
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Sp_Lt_SI=2.99792458e8
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Sp_Lt_SI = 2.99792458e8
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# speed of light in atomic units
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Sp_Lt=Sp_Lt_SI/2.1876912633e6
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Sp_Lt = Sp_Lt_SI / 2.1876912633e6
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# Atomic unit of time, in seconds
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Time_Sec=2.418884326505e-17
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Time_Sec = 2.418884326505e-17
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# Tesla in a.u.
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BField_Tesla=4.254383e-6
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BField_Tesla = 4.254383e-6
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# Debye unit in a.u.
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dipole_moment_debye=0.393430307
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dipole_moment_debye = 0.393430307
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@ -84,6 +84,7 @@ def build_flow(options):
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eph_task = eph_work.register_eph_task(eph_inp, deps=eph_deps)
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flow.allocate()
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flow.use_smartio()
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# EPH does not support autoparal (yet)
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#eph_task.with_fixed_mpi_omp(1, 1)
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@ -54,7 +54,7 @@ def build_flow(options):
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# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
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workdir = options.workdir
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if not options.workdir:
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workdir = os.pathbasename(__file__).replace(".py", "").replace("run_", "flow_")
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workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
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# Get the SCF and the NSCF input.
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scf_input, nscf_input = make_scf_nscf_inputs()
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@ -42,33 +42,54 @@ def factor_ev2units(units):
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"""
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Return conversion factor eV --> units (case-insensitive)
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"""
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eV_to_cm1 = 8065.5440044136285
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d = {"ev": 1, "mev": 1000, "ha": eV_to_Ha,
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"cm-1": eV_to_cm1, 'cm^-1': eV_to_cm1, "thz": abu.eV_to_THz,
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"cm-1": abu.eV_to_cm1, 'cm^-1': abu.eV_to_cm1,
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"thz": abu.eV_to_THz,
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}
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try:
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return d[units.lower()]
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return d[units.lower().strip()]
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except KeyError:
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raise KeyError('Value for units `{}` unknown\nPossible values are:\n {}'.format(units, list(d.keys())))
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def unit_tag(units):
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"""
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Return latex string for `units`.
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"""
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d = {"ev": "[eV]", "mev": "[meV]", "ha": '[Ha]',
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"cm-1": "[cm$^{-1}$]", 'cm^-1': "[cm$^{-1}$]", "thz": '[Thz]',
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}
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try:
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return d[units.lower()]
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return d[units.lower().strip()]
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except KeyError:
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raise KeyError('Value for units `{}` unknown\nPossible values are:\n {}'.format(units, list(d.keys())))
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def wlabel_from_units(units):
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"""
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Return latex string for frequencies in `units`.
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"""
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d = {'ev': 'Energy [eV]', 'mev': 'Energy [meV]', 'ha': 'Energy [Ha]',
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'cm-1': r'Frequency [cm$^{-1}$]',
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'cm^-1': r'Frequency [cm$^{-1}$]',
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'thz': r'Frequency [Thz]',
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}
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try:
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return d[units.lower().strip()]
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except KeyError:
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raise KeyError('Value for units `{}` unknown\nPossible values are:\n {}'.format(units, list(d.keys())))
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def dos_label_from_units(units):
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"""
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Return latex string for phonon DOS values in `units`.
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"""
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d = {"ev": "[states/eV]", "mev": "[states/meV]", "ha": '[states/Ha]',
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"cm-1": "[states/cm$^{-1}$]", 'cm^-1': "[states/cm$^{-1}$]",
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"thz": '[states/Thz]',
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}
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try:
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return d[units.lower()]
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return d[units.lower().strip()]
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except KeyError:
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raise KeyError('Value for units `{}` unknown\nPossible values are:\n {}'.format(units, list(d.keys())))
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@ -842,21 +863,8 @@ class PhononBands(object):
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ax.grid(True)
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# Handle conversion factor.
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# TODO: Encapsulate this part.
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units = units.lower()
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if units == 'ev':
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ax.set_ylabel('Energy [eV]')
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elif units == 'mev':
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ax.set_ylabel('Energy [meV]')
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elif units == 'ha':
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ax.set_ylabel('Energy [Ha]')
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elif units in ('cm-1', 'cm^-1'):
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ax.set_ylabel(r'Frequency [cm$^{-1}$]')
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elif units == 'thz':
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ax.set_ylabel(r'Frequency [Thz]')
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else:
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if units:
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raise ValueError('Value for units `{}` unknown'.format(units))
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ax.set_ylabel(wlabel_from_units(units))
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# Set ticks and labels.
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ticks, labels = self._make_ticks_and_labels(kwargs.pop("qlabels", None))
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@ -10,7 +10,7 @@ import abipy.data as abidata
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from abipy import abilab
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from abipy.dfpt.phonons import (PhononBands, PhononDos, PhdosFile, InteratomicForceConstants, phbands_gridplot,
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PhononBandsPlotter, PhononDosPlotter, dataframe_from_phbands)
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from abipy.dfpt.phonons import factor_ev2units, unit_tag, dos_label_from_units
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from abipy.dfpt.phonons import factor_ev2units, unit_tag, dos_label_from_units, wlabel_from_units
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from abipy.dfpt.ddb import DdbFile
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from abipy.core.testing import AbipyTest
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@ -21,9 +21,10 @@ class TestUnitTools(AbipyTest):
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def test_units_api(self):
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for units in ["ev", "meV" ,"ha", "cm-1", "cm^-1", "Thz"]:
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factor_ev2units(units)
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unit_tag(units)
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dos_label_from_units(units)
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assert factor_ev2units(units)
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assert unit_tag(units)
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assert dos_label_from_units(units)
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assert wlabel_from_units(units)
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for func in [factor_ev2units, unit_tag, dos_label_from_units]:
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with self.assertRaises(KeyError):
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@ -2794,8 +2794,8 @@ class ElectronDos(object):
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def to_string(self, verbose=0):
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"""String representation."""
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lines = []; app = lines.append
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app("nsppol=%d, nelect=%s" % (self.nsppol, self.nelect))
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app("Fermi energy: %s (recomputed from nelect):" % self.fermie)
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app("nsppol: %d, nelect: %s" % (self.nsppol, self.nelect))
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app("Fermi energy: %s [eV] (recomputed from nelect):" % self.fermie)
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return "\n".join(lines)
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@classmethod
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142
abipy/eph/eph.py
142
abipy/eph/eph.py
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@ -9,6 +9,7 @@ from __future__ import print_function, division, unicode_literals, absolute_impo
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import numpy as np
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import pymatgen.core.units as units
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import abipy.core.abinit_units as abu
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from collections import OrderedDict
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from scipy.integrate import cumtrapz, simps
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@ -19,7 +20,7 @@ from abipy.core.kpoints import Kpath
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from abipy.tools.plotting import add_fig_kwargs, get_ax_fig_plt, set_axlims
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from abipy.electrons.ebands import ElectronsReader, ElectronDos, RobotWithEbands
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from abipy.dfpt.phonons import (PhononBands, PhononDos, RobotWithPhbands,
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factor_ev2units, unit_tag, dos_label_from_units)
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factor_ev2units, unit_tag, dos_label_from_units, wlabel_from_units)
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from abipy.abio.robots import Robot
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@ -88,9 +89,11 @@ class A2f(object):
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app("Mesh from %.4f to %.4f [eV] with %d points" % (
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self.mesh[0], self.mesh[-1], len(self.mesh)))
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app("lambda_iso: %.3f, omega_log %s" % (self.lambda_iso, self.omega_log))
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for mustar in [0.8, 0.6]:
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app("For mustar %s: McMillan Tc: %s [K]" % (mustar, self.get_mcmillan_tc(mustar)))
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# TODO: Add ElectronDos
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app("Isotropic lambda: %.3f" % (self.lambda_iso))
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app("Omega_log: %s [eV], %s [K]" % (self.omega_log, self.omega_log * abu.eV_to_K))
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for mustar in (0.1, 0.2):
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app("\tFor mustar %s: McMillan Tc: %s [K]" % (mustar, self.get_mcmillan_tc(mustar)))
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if verbose:
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# $\int dw [a2F(w)/w] w^n$
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@ -107,13 +110,24 @@ class A2f(object):
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@lazy_property
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def omega_log(self):
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r"""
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Get log moment of alpha^2F.
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exp((2/\lambda) \int dw a2F(w) ln(w)/w)
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Get log moment of alpha^2F: exp((2/\lambda) \int dw a2F(w) ln(w)/w)
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"""
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wmesh, a2fw = self.mesh[self.iw0+1:], self.values[self.iw0+1:]
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wmesh = wmesh * units.eV_to_Ha
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integral = simps(a2fw * (np.log(wmesh) / wmesh), x=wmesh)
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return np.exp(2.0 * integral / self.lambda_iso) * units.Ha_to_eV
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#return 270 / abu.eV_to_K
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iw = self.iw0 + 1
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#iw = self.iw0 + 100
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wmesh, a2fw = self.mesh[iw:], self.values[iw:]
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#wmesh = wmesh * units.eV_to_Ha
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#wmesh = wmesh * abu.eV_to_THz
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#ax, fig, plt = get_ax_fig_plt(ax=None)
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#ax.plot(wmesh, a2fw / wmesh * np.log(wmesh))
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#plt.show()
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integral = simps(a2fw / wmesh * np.log(wmesh), x=wmesh)
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#return np.exp(2.0 / self.lambda_iso * integral) * units.Ha_to_eV
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#return np.exp(2.0 / self.lambda_iso * integral) / abu.eV_to_THz
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return np.exp(2.0 / self.lambda_iso * integral) #/ abu.eV_to_THz
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def get_moment(self, n, spin=None, cumulative=False):
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r"""
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@ -153,15 +167,17 @@ class A2f(object):
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"""
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Computes the critical temperature with the McMillan equation and the input mustar.
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"""
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tc = self.omega_log / 1.2 * np.exp((-1.04 * (1.0 + self.lambda_iso)) / (self.lambda_iso - mustar * (1.0 + 0.62 * self.lambda_iso)))
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eV_to_K = 11604.5250061657
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return tc * eV_to_K
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tc = (self.omega_log / 1.2) * \
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np.exp(-1.04 * (1.0 + self.lambda_iso) / (self.lambda_iso - mustar * (1.0 + 0.62 * self.lambda_iso)))
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return tc * abu.eV_to_K
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#def get_mustar_from_tc(self, tc):
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# """
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# Return the value of mustar that gives the critical temperature tc in McMillan equation
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# """
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# return 0
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def get_mustar_from_tc(self, tc):
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"""
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Return the value of mustar that gives the critical temperature tc in K in the McMillan equation.
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"""
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l = self.lambda_iso
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num = l + (1.04 * (1 + l) / np.log(1.2 * abu.kb_eVK * tc / self.omega_log))
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return num / (1 + 0.62 * l)
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@add_fig_kwargs
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def plot(self, units="eV", with_lambda=True, exchange_xy=False, ax=None,
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@ -171,8 +187,8 @@ class A2f(object):
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contributions due to the phonon branches.
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Args:
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units: Units for phonon plots. Possible values in ("eV", "meV", "Ha", "cm-1", "Thz").
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Case-insensitive.
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units: Units for phonon plots. Possible values in
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("eV", "meV", "Ha", "cm-1", "Thz"). Case-insensitive.
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with_lambda:
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exchange_xy: True to exchange x-y axes.
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ax: matplotlib :class:`Axes` or None if a new figure should be created.
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@ -186,6 +202,8 @@ class A2f(object):
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"""""
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ax, fig, plt = get_ax_fig_plt(ax=ax)
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wfactor = factor_ev2units(units)
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# TODO Better handling of styles
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style = dict(
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linestyle=kwargs.pop("linestyle", "-"),
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@ -194,7 +212,7 @@ class A2f(object):
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)
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# Plot a2f(w)
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xx, yy = self.mesh, self.values
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xx, yy = self.mesh * wfactor, self.values
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if exchange_xy: xx, yy = yy, xx
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ax.plot(xx, yy, label=label, **style)
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@ -202,7 +220,7 @@ class A2f(object):
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if with_lambda:
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lambda_w = self.get_moment(n=0, cumulative=True)
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l_ax = ax.twinx()
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xx, yy = self.mesh, lambda_w
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xx, yy = self.mesh * wfactor, lambda_w
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if exchange_xy: xx, yy = yy, xx
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l_ax.plot(xx, yy, label=label, **style)
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l_ax.set_ylabel(r"$\lambda(\omega)$")
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@ -210,11 +228,12 @@ class A2f(object):
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if self.nsppol == 2:
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# Plot spin resolved a2f(w).
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for spin in range(self.nsppol):
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xx, yy = self.mesh, self.values_spin[spin]
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xx, yy = self.mesh * wfactor, self.values_spin[spin]
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if exchange_xy: xx, yy = yy, xx
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ax_plot(xx, yy, marker=self.marker_spin[spin], **style)
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xlabel, ylabel = r"$\omega$ [eV]", r"$\alpha^2F(\omega)$"
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xlabel = wlabel_from_units(units)
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ylabel = r"$\alpha^2F(\omega)$"
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if exchange_xy: xlabel, ylabel = ylabel, xlabel
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ax.set_xlabel(xlabel)
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ax.set_ylabel(ylabel)
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@ -253,6 +272,9 @@ class A2f(object):
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axmat = np.reshape(axmat, (self.natom, 3))
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fig = plt.gcf()
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wfactor = factor_ev2units(units)
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wvals = self.mesh * wfactor
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if with_lambda:
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lax_nu = [ax.twinx() for ax in axmat.flat]
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# Share axis after creation. Based on
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@ -288,18 +310,18 @@ class A2f(object):
|
|||
#ax.set_yticks([])
|
||||
|
||||
if iatom == self.natom -1:
|
||||
ax.set_xlabel(r"$\omega$ [eV]")
|
||||
ax.set_xlabel(wlabel_from_units(units))
|
||||
#set_axlims(ax, xlims, "x")
|
||||
#set_axlims(ax, ylims, "y")
|
||||
|
||||
# Plot total a2f(w)
|
||||
ax.plot(self.mesh, self.values_nu[nu], **a2f_style)
|
||||
ax.plot(wvals, self.values_nu[nu], **a2f_style)
|
||||
|
||||
# Plot lambda(w)
|
||||
if with_lambda:
|
||||
lambdaw_nu = self.get_moment_nu(n=0, nu=nu, cumulative=True)
|
||||
lax = lax_nu[nu]
|
||||
lax.plot(self.mesh, lambdaw_nu, **lambda_style)
|
||||
lax.plot(wvals, lambdaw_nu, **lambda_style)
|
||||
if idir == 2:
|
||||
lax.set_ylabel(r"$\lambda_{\nu}(\omega)$", color=lambda_style["color"])
|
||||
|
||||
|
|
@ -313,12 +335,21 @@ class A2f(object):
|
|||
|
||||
@add_fig_kwargs
|
||||
def plot_a2(self, phdos, atol=1e-12, **kwargs):
|
||||
"""grid with 3 plots (a2F, F, a2F)."""
|
||||
"""
|
||||
Grid with 3 plots (a2F, F, a2F).
|
||||
|
||||
Args:
|
||||
phdos:
|
||||
atol:
|
||||
|
||||
Returns:
|
||||
`matplotlib` figure
|
||||
"""
|
||||
phdos = PhononDos.as_phdos(phdos)
|
||||
import matplotlib.pyplot as plt
|
||||
fig, ax_list = plt.subplots(nrows=3, ncols=1, sharex=True, sharey=False, squeeze=True)
|
||||
|
||||
# Spline phdos onto a2f mesh and compute a2F / F
|
||||
# Spline phdos onto a2f mesh and compute a2F(w) / F(w)
|
||||
f = phdos.spline(self.mesh)
|
||||
f = self.values / np.where(np.abs(f) > atol, f, atol)
|
||||
ax = ax_list[0]
|
||||
|
|
@ -337,6 +368,33 @@ class A2f(object):
|
|||
|
||||
return fig
|
||||
|
||||
@add_fig_kwargs
|
||||
def plot_tc_vs_mustar(self, start=0.1, stop=0.5, num=50, ax=None, **kwargs):
|
||||
"""
|
||||
Plot Tc(mustar)
|
||||
|
||||
Args:
|
||||
start: The starting value of the sequence.
|
||||
stop: The end value of the sequence
|
||||
num: int, optional
|
||||
Number of samples to generate. Default is 50. Must be non-negative.
|
||||
ax: matplotlib :class:`Axes` or None if a new figure should be created.
|
||||
|
||||
Returns:
|
||||
`matplotlib` figure
|
||||
"""
|
||||
mustar_values = np.linspace(start, stop, num=num)
|
||||
tc_vals = [self.get_mcmillan_tc(mustar) for mustar in mustar_values]
|
||||
|
||||
ax, fig, plt = get_ax_fig_plt(ax=ax)
|
||||
ax.plot(mustar_values, tc_vals, **kwargs)
|
||||
ax.set_yscale("log")
|
||||
ax.grid(True)
|
||||
ax.set_xlabel(r"$\mu^*$")
|
||||
ax.set_ylabel(r"$T_c [K]$")
|
||||
|
||||
return fig
|
||||
|
||||
|
||||
class A2Ftr(object):
|
||||
|
||||
|
|
@ -373,7 +431,7 @@ class A2Ftr(object):
|
|||
class EphFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter):
|
||||
"""
|
||||
This file contains the phonon linewidths, EliashbergFunction, the phonon bands,
|
||||
the ElectronBands on the k-mesh.
|
||||
the `ElectronBands` and `ElectronDos` on the k-mesh.
|
||||
Provides methods to plot results.
|
||||
|
||||
Usage example:
|
||||
|
|
@ -626,6 +684,23 @@ class EphFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter):
|
|||
set_axlims(ax, ylims, "y")
|
||||
return fig
|
||||
|
||||
@add_fig_kwargs
|
||||
def plot_a2f_interpol(self, units="eV", ax=None, ylims=None, **kwargs):
|
||||
"""
|
||||
Plot
|
||||
"""
|
||||
ax, fig, plt = get_ax_fig_plt(ax=ax)
|
||||
#linestyle_qsamp = dict(qcoarse="--", qintp="-")
|
||||
for qsamp in ["qcoarse", "qintp"]:
|
||||
a2f = self.get_a2f_qsamp(qsamp)
|
||||
a2f.plot(units=units, ylims=ylims, ax=ax, with_lambda=False, show=False)
|
||||
#ax.yaxis.set_ticks_position("right")
|
||||
#ax.yaxis.set_label_position("right")
|
||||
#ax.tick_params(labelbottom='off')
|
||||
#ax.set_ylabel("")
|
||||
|
||||
return fig
|
||||
|
||||
@add_fig_kwargs
|
||||
def plot_with_a2f(self, units="eV", qsamp="qintp", phdos=None, ylims=None, **kwargs):
|
||||
"""
|
||||
|
|
@ -660,9 +735,6 @@ class EphFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter):
|
|||
self.plot(units=units, ylims=ylims, ax=ax_phbands, show=False)
|
||||
|
||||
# Plot a2F(w)
|
||||
#a2f = self.a2f_qcoarse
|
||||
#a2f.plot(units=units, exchange_xy=True, ylims=ylims, ax=ax, show=False)
|
||||
|
||||
a2f = self.get_a2f_qsamp(qsamp)
|
||||
ax = ax_doses[0]
|
||||
a2f.plot(units=units, exchange_xy=True, ylims=ylims, ax=ax, with_lambda=False, show=False)
|
||||
|
|
@ -707,7 +779,7 @@ class EphFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter):
|
|||
nbv.new_code_cell("print(ncfile)"),
|
||||
nbv.new_code_cell("ncfile.ebands.plot();"),
|
||||
nbv.new_code_cell("ncfile.plot();"),
|
||||
nbv.new_code_cell("ncfile.plot_phlinewidths();"),
|
||||
#nbv.new_code_cell("ncfile.plot_phlinewidths();"),
|
||||
nbv.new_code_cell("ncfile.plot_with_a2f();"),
|
||||
nbv.new_code_cell("ncfile.a2f.plot();"),
|
||||
])
|
||||
|
|
@ -973,7 +1045,7 @@ class EphReader(ElectronsReader):
|
|||
assert qsamp in ("qcoarse", "qintp")
|
||||
mesh = self.read_value("a2f_mesh_" + qsamp) * units.Ha_to_eV
|
||||
# C shape [nsppol, natom + 1, nomega]
|
||||
data = self.read_value("a2f_values_" + qsamp) #/ units.Ha_to_eV
|
||||
data = self.read_value("a2f_values_" + qsamp) # * 0.25
|
||||
values_spin = data[:, 0, :].copy()
|
||||
values_spin_nu = data[:, 1:, :].copy()
|
||||
return A2f(mesh, values_spin, values_spin_nu)
|
||||
|
|
|
|||
|
|
@ -44,10 +44,11 @@ class EphFileTest(AbipyTest):
|
|||
#self.assert_almost_equal(m1/2, a2f.get_moment(n=1, spin=0))
|
||||
#self.assert_almost_equal(self.lambda_iso, )
|
||||
#self.assert_almost_equal(self.omega_log, )
|
||||
#self.assert_almost_equal(a2f.get_mcmillan_Tc(mustar=0.8), )
|
||||
#tc = 10
|
||||
#mustar = a2f.get_mustar_from_tc(tc)
|
||||
#self.assert_almost_equal(a2f.get_mcmillan_Tc(mustar), tc)
|
||||
tc = a2f.get_mcmillan_tc(mustar=0.1)
|
||||
#self.assert_almost_equal(tc, )
|
||||
mustar = a2f.get_mustar_from_tc(tc)
|
||||
self.assert_almost_equal(mustar, 0.1)
|
||||
#self.assert_almost_equal(a2f.get_mcmillan_tc(mustar), tc)
|
||||
|
||||
assert not ncfile.has_a2ftr
|
||||
assert ncfile.a2ftr_qcoarse is None
|
||||
|
|
@ -58,6 +59,7 @@ class EphFileTest(AbipyTest):
|
|||
if self.has_matplotlib():
|
||||
# Test A2f plot methods
|
||||
assert ncfile.a2f_qcoarse.plot(show=False)
|
||||
assert ncfile.a2f_qcoarse.plot_tc_vs_mustar(show=False)
|
||||
assert ncfile.a2f_qintp.plot_a2(phdos_path, show=False)
|
||||
assert ncfile.a2f_qintp.plot_nuterms(show=False)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,7 @@
|
|||
TODO LIST:
|
||||
|
||||
# Check PJDOS in abinit@gitlab
|
||||
|
||||
# Use angdeg instead of rprimd in structure_to_abivars if hex or rhomboedral lattice.
|
||||
|
||||
#. Add mpirun_args see e.g nic4 and mpirun --bind-to None
|
||||
|
|
@ -54,4 +56,5 @@ TODO LIST:
|
|||
|
||||
# Add option max_num_launchers in scheduler.yml
|
||||
|
||||
# Add extra metadata to netcdf files (try to propagate info on space group from parser to crystal_t)
|
||||
# Add extra metadata to netcdf files (try to propagate info on space group from parser to crystal_t
|
||||
as well as Abinit input as string)
|
||||
|
|
|
|||
|
|
@ -662,8 +662,10 @@ def get_parser(with_epilog=False):
|
|||
# Subparser for single command.
|
||||
p_single = subparsers.add_parser('single', parents=[copts_parser], help="Run single task and exit.")
|
||||
|
||||
# Subparser for rapidfire command.
|
||||
# Subparser for rapid command.
|
||||
p_rapid = subparsers.add_parser('rapid', parents=[copts_parser], help="Run all tasks in rapidfire mode.")
|
||||
p_rapid.add_argument('-m', '--max-nlaunch', default=10, type=int,
|
||||
help="Maximum number of launches. default: 10. Use -1 for no limit.")
|
||||
|
||||
# Subparser for scheduler command.
|
||||
p_scheduler = subparsers.add_parser('scheduler', parents=[copts_parser],
|
||||
|
|
@ -706,8 +708,6 @@ def get_parser(with_epilog=False):
|
|||
# Subparser for reset command.
|
||||
p_reset = subparsers.add_parser('reset', parents=[copts_parser, flow_selector_parser],
|
||||
help="Reset the tasks of the flow with the specified status.")
|
||||
p_reset.add_argument("--relaunch", action="store_true", default=False,
|
||||
help="Relaunch tasks in rapid mode after reset.")
|
||||
|
||||
# Subparser for move command.
|
||||
p_move = subparsers.add_parser('move', parents=[copts_parser],
|
||||
|
|
@ -1080,13 +1080,13 @@ def main():
|
|||
|
||||
elif options.command == "single":
|
||||
nlaunch = flow.single_shot()
|
||||
print("Number of tasks launched: %d" % nlaunch)
|
||||
if nlaunch: flow.show_status()
|
||||
cprint("Number of tasks launched: %d" % nlaunch, "yellow")
|
||||
|
||||
elif options.command == "rapid":
|
||||
nlaunch = flow.rapidfire()
|
||||
print("Number of tasks launched: %d" % nlaunch)
|
||||
nlaunch = flow.rapidfire(max_nlaunch=options.max_nlaunch, max_loops=1, sleep_time=5)
|
||||
if nlaunch: flow.show_status()
|
||||
cprint("Number of tasks launched: %d" % nlaunch, "yellow")
|
||||
|
||||
elif options.command == "scheduler":
|
||||
# Check that the env on the local machine is properly configured before starting the scheduler.
|
||||
|
|
@ -1204,15 +1204,8 @@ def main():
|
|||
count += 1
|
||||
cprint("%d tasks have been reset" % count, "blue")
|
||||
|
||||
# Try to relaunch
|
||||
nlaunch = 0
|
||||
if options.relaunch:
|
||||
nlaunch = flow.rapidfire()
|
||||
cprint("Number of tasks launched: %d" % nlaunch, "magenta")
|
||||
|
||||
flow.show_status()
|
||||
|
||||
if nlaunch == 0:
|
||||
g = flow.find_deadlocks()
|
||||
#print("deadlocked:", gdeadlocked, "\nrunnables:", grunnables, "\nrunning:", g.running)
|
||||
if g.deadlocked and not (g.runnables or g.running):
|
||||
|
|
|
|||
Loading…
Reference in New Issue