mirror of https://github.com/abinit/abipy.git
Pin sphinx to 1.6.5
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@ -2333,16 +2333,16 @@ class ElectronBandsPlotter(NotebookWriter):
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Args:
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e0: Option used to define the zero of energy in the band structure plot. Possible values::
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* `fermie`: shift all eigenvalues to have zero energy at the Fermi energy (ebands.fermie)
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- `fermie`: shift all eigenvalues to have zero energy at the Fermi energy (ebands.fermie)
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Note that, by default, the Fermi energy is taken from the band structure object
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i.e. the Fermi energy computed at the end of the SCF file that produced the density.
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This should be ok in semiconductors. In metals, however, a better value of the Fermi energy
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can be obtained from the DOS provided that the k-sampling for the DOS is much denser than
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the one used to compute the density. See `edos_fermie`.
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* ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
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- ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
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Available only if plotter contains dos objects.
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* Number e.g e0=0.5: shift all eigenvalues to have zero energy at 0.5 eV
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* None: Don't shift energies, equivalent to e0=0
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- Number e.g e0=0.5: shift all eigenvalues to have zero energy at 0.5 eV
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- None: Don't shift energies, equivalent to e0=0
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ylims: Set the data limits for the y-axis. Accept tuple e.g. `(left, right)`
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or scalar e.g. `left`. If left (right) is None, default values are used
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@ -2436,16 +2436,16 @@ class ElectronBandsPlotter(NotebookWriter):
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each subplot in the grid contains a band structure with DOS else a simple bandstructure plot.
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e0: Option used to define the zero of energy in the band structure plot. Possible values::
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* ``fermie``: shift all eigenvalues and the DOS to have zero energy at the Fermi energy.
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- ``fermie``: shift all eigenvalues and the DOS to have zero energy at the Fermi energy.
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Note that, by default, the Fermi energy is taken from the band structure object
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i.e. the Fermi energy computed at the end of the SCF file that produced the density.
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This should be ok in semiconductors. In metals, however, a better value of the Fermi energy
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can be obtained from the DOS provided that the k-sampling for the DOS is much denser than
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the one used to compute the density. See `edos_fermie`.
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* ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
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- ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
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Available only if edos_objects is not None
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* Number e.g e0=0.5: shift all eigenvalues to have zero energy at 0.5 eV
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* None: Don't shift energies, equivalent to e0=0
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- Number e.g e0=0.5: shift all eigenvalues to have zero energy at 0.5 eV
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- None: Don't shift energies, equivalent to e0=0
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with_dos: True if DOS should be printed.
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ylims: Set the data limits for the y-axis. Accept tuple e.g. ```(left, right)``
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@ -3263,17 +3263,19 @@ class ElectronDosPlotter(NotebookWriter):
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what: "dos" to plot DOS, "idos" for integrated DOS.
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spin_mode: "total" for total (I)DOS, "resolved" for plotting individual contributions.
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Meaningful only if nsppol == 2.
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e0: Option used to define the zero of energy in the band structure plot. Possible values:
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- ``fermie``: shift all eigenvalues and the DOS to have zero energy at the Fermi energy.
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Note that, by default, the Fermi energy is taken from the band structure object
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i.e. the Fermi energy computed at the end of the SCF file that produced the density.
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This should be ok in semiconductors. In metals, however, a better value of the Fermi energy
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can be obtained from the DOS provided that the k-sampling for the DOS is much denser than
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the one used to compute the density. See ``edos_fermie``.
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- ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
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Available only if edos_objects is not None
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- Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
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- None: Don't shift energies, equivalent to ``e0 = 0``.
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e0: Option used to define the zero of energy in the band structure plot. Possible values::
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- ``fermie``: shift all eigenvalues and the DOS to have zero energy at the Fermi energy.
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Note that, by default, the Fermi energy is taken from the band structure object
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i.e. the Fermi energy computed at the end of the SCF file that produced the density.
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This should be ok in semiconductors. In metals, however, a better value of the Fermi energy
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can be obtained from the DOS provided that the k-sampling for the DOS is much denser than
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the one used to compute the density. See ``edos_fermie``.
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- ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
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Available only if edos_objects is not None
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- Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
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- None: Don't shift energies, equivalent to ``e0 = 0``.
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sharex, sharey: True if x (y) axis should be shared.
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xlims: Set the data limits for the x-axis. Accept tuple e.g. ``(left, right)``
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or scalar e.g. ``left``. If left (right) is None, default values are used
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@ -1,5 +1,5 @@
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ipython
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sphinx
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sphinx==1.6.5
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sphinxcontrib-napoleon
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sphinxcontrib-programoutput
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sphinx-gallery
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@ -24,12 +24,10 @@ Dragon1
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job: &job
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mpi_runner: mpirun
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shell_env:
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PATH: "/home/users/g/m/gmatteo/git/abinit/_build_dragon1-intel-mpich-mkl.ac/src/98_main:$PATH"
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PATH: "$HOME/git_repos/abinit/_build_dragon1-intel-mpich-mkl.ac/src/98_main:$PATH"
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modules:
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- mpich/3.0.4/intel-13.0.0
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# pre_run is a string in verbatim mode (note |)
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pre_run: |
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ulimit unlimited
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pre_run: "ulimit -s unlimited"
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# queues
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qadapters:
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@ -95,13 +93,13 @@ Hercules
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job: &job
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mpi_runner: mpirun
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shell_env:
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PATH: "/home/gmatteo/git_repos/abinit/_build_hercules.ac/src/98_main/:$PATH"
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PATH: "$HOME/git_repos/abinit/_build_hercules.ac/src/98_main/:$PATH"
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modules:
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- impi/5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26
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- imkl/11.3.3.210-iimpi-2016b
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# pre_run is a string in verbatim mode (note |)
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# here pre_run is a string in verbatim mode (note |)
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pre_run: |
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ulimit unlimited
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ulimit -s unlimited
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# queues
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qadapters:
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@ -149,12 +147,10 @@ Hmem
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job: &job
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mpi_runner: mpirun
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shell_env:
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PATH: "/home/users/g/m/gmatteo/git_repos/abinit/_build_hmem_intel_openmpi-mkl.ac/src/98_main/:$PATH"
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PATH: "$HOME/git_repos/abinit/_build_hmem_intel_openmpi-mkl.ac/src/98_main/:$PATH"
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modules:
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- openmpi/1.5.3/intel-12.0.0.084
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# pre_run is a string in verbatim mode (note |)
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pre_run: |
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ulimit unlimited
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pre_run: "ulimit -s unlimited"
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# queues
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qadapters:
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@ -290,9 +286,7 @@ Jureca
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PATH: $HOME/abinit/801-private/jureca_mpi/src/98_main:$PATH
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modules:
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- intel-para/2015.07
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# pre_run is a string in verbatim mode (note |)
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pre_run: |
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ulimit unlimited
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pre_run: "ulimit -s unlimited"
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# queues
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qadapters:
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@ -325,12 +319,10 @@ Lemaitre2
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job: &job
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mpi_runner: mpirun
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shell_env: # Use your abinit exec
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PATH: "/home/users/g/m/gmatteo/git_repos/abinit/_build_lemaitre2-intel-openmpi-mkl.ac/src/98_main/:$PATH"
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PATH: "$HOME/git_repos/abinit/_build_lemaitre2-intel-openmpi-mkl.ac/src/98_main/:$PATH"
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modules: # Abinit compiled with abiconfig settings
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- openmpi/1.6.5/intel-13.0.1.117
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# pre_run is a string in verbatim mode (note |)
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pre_run: |
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ulimit unlimited
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pre_run: "ulimit -s unlimited"
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# queues
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qadapters:
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@ -378,13 +370,13 @@ Manneback
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job: &job
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mpi_runner: mpirun
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shell_env:
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PATH: /home/users/g/m/gmatteo/git_repos/abinit/_build_manneback-gcc-openmpi.ac/src/98_main/:$PATH
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pre_run: |
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ulimit -s unlimited # pre_run is a string in verbatim mode (note |)
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export OMP_NUM_THREADS=1
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unset SLURM_CPUS_PER_TASK
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module purge
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module load gompi/2016a FFTW/3.3.4-gompi-2016a
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PATH: "$HOME/git_repos/abinit/_build_manneback-gcc-openmpi.ac/src/98_main/:$PATH"
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pre_run:
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- "ulimit -s unlimited"
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- "export OMP_NUM_THREADS=1"
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- "unset SLURM_CPUS_PER_TASK"
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- "module purge"
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- "module load gompi/2016a FFTW/3.3.4-gompi-2016a"
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#policy:
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# frozen_timeout: 0-12:0:0
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@ -428,9 +420,8 @@ Nic4
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mpi_runner: "mpirun"
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mpi_runner_options: "--bind-to none"
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shell_env:
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PATH: "/home/users/g/m/gmatteo/git_repos/abinit/_build_nic4-intel-openmpi-mkl-hdf5.ac/src/98_main:$PATH"
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pre_run:
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- "ulimit -s unlimited"
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PATH: "$HOME/git_repos/abinit/_build_nic4-intel-openmpi-mkl-hdf5.ac/src/98_main:$PATH"
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pre_run: "ulimit -s unlimited"
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modules:
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- shared
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- openmpi/1.7.5/intel2013_sp1.1.106
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@ -582,12 +573,10 @@ Vega
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job: &job
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mpi_runner: mpirun
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shell_env:
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PATH: "/gpfsuser/home/users/g/m/gmatteo/git_repos/abinit/_build_vega-intel-impi-mkl.ac/src/98_main/:$PATH"
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PATH: "$HOME/git_repos/abinit/_build_vega-intel-impi-mkl.ac/src/98_main/:$PATH"
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modules:
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- intel/2015a
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# pre_run is a string in verbatim mode (note |)
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#pre_run: |
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# "ulimit -s unlimited"
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#pre_run: "ulimit -s unlimited"
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# queues
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qadapters:
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@ -621,9 +610,9 @@ Viper
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job: &job
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mpi_runner: ~/bin/mpirun.openmpi
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# pre_run is a string in verbatim mode (note |)
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pre_run: |
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ulimit -s unlimited
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source ~/.bashrc
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pre_run:
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- "ulimit -s unlimited"
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- "source ~/.bashrc"
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# queues
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qadapters:
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@ -664,13 +653,12 @@ Zenobe
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job: &job
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mpi_runner: mpirun
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shell_env:
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PATH: /home/acad/ucl/naps/mgiantom/bzr_repos/793/gmatteo-private/build_impi/src/98_main:$PATH
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PATH: $HOME/git_repos/abinit_build_impi/src/98_main:$PATH
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modules:
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- compiler/intel/composerxe/2013_sp1.1.106
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- intelmpi
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- python/2.7
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pre_run: |
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ulimit # pre_run is a string in verbatim mode (note |)
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pre_run: "ulimit -s unlimited"
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# List of qdapters.
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qadapters:
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