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Pin sphinx to 1.6.5

This commit is contained in:
Matteo Giantomassi 2018-02-15 18:10:30 +01:00
parent 355f8d98f8
commit 338e83a9ed
3 changed files with 48 additions and 58 deletions
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40
abipy/electrons/ebands.py
View File

@ -2333,16 +2333,16 @@ class ElectronBandsPlotter(NotebookWriter):
Args:
e0: Option used to define the zero of energy in the band structure plot. Possible values::
* `fermie`: shift all eigenvalues to have zero energy at the Fermi energy (ebands.fermie)
- `fermie`: shift all eigenvalues to have zero energy at the Fermi energy (ebands.fermie)
Note that, by default, the Fermi energy is taken from the band structure object
i.e. the Fermi energy computed at the end of the SCF file that produced the density.
This should be ok in semiconductors. In metals, however, a better value of the Fermi energy
can be obtained from the DOS provided that the k-sampling for the DOS is much denser than
the one used to compute the density. See `edos_fermie`.
* ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
- ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
Available only if plotter contains dos objects.
* Number e.g e0=0.5: shift all eigenvalues to have zero energy at 0.5 eV
* None: Don't shift energies, equivalent to e0=0
- Number e.g e0=0.5: shift all eigenvalues to have zero energy at 0.5 eV
- None: Don't shift energies, equivalent to e0=0
ylims: Set the data limits for the y-axis. Accept tuple e.g. `(left, right)`
or scalar e.g. `left`. If left (right) is None, default values are used
@ -2436,16 +2436,16 @@ class ElectronBandsPlotter(NotebookWriter):
each subplot in the grid contains a band structure with DOS else a simple bandstructure plot.
e0: Option used to define the zero of energy in the band structure plot. Possible values::
* ``fermie``: shift all eigenvalues and the DOS to have zero energy at the Fermi energy.
- ``fermie``: shift all eigenvalues and the DOS to have zero energy at the Fermi energy.
Note that, by default, the Fermi energy is taken from the band structure object
i.e. the Fermi energy computed at the end of the SCF file that produced the density.
This should be ok in semiconductors. In metals, however, a better value of the Fermi energy
can be obtained from the DOS provided that the k-sampling for the DOS is much denser than
the one used to compute the density. See `edos_fermie`.
* ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
- ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
Available only if edos_objects is not None
* Number e.g e0=0.5: shift all eigenvalues to have zero energy at 0.5 eV
* None: Don't shift energies, equivalent to e0=0
- Number e.g e0=0.5: shift all eigenvalues to have zero energy at 0.5 eV
- None: Don't shift energies, equivalent to e0=0
with_dos: True if DOS should be printed.
ylims: Set the data limits for the y-axis. Accept tuple e.g. ```(left, right)``
@ -3263,17 +3263,19 @@ class ElectronDosPlotter(NotebookWriter):
what: "dos" to plot DOS, "idos" for integrated DOS.
spin_mode: "total" for total (I)DOS, "resolved" for plotting individual contributions.
Meaningful only if nsppol == 2.
e0: Option used to define the zero of energy in the band structure plot. Possible values:
- ``fermie``: shift all eigenvalues and the DOS to have zero energy at the Fermi energy.
Note that, by default, the Fermi energy is taken from the band structure object
i.e. the Fermi energy computed at the end of the SCF file that produced the density.
This should be ok in semiconductors. In metals, however, a better value of the Fermi energy
can be obtained from the DOS provided that the k-sampling for the DOS is much denser than
the one used to compute the density. See ``edos_fermie``.
- ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
Available only if edos_objects is not None
- Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
- None: Don't shift energies, equivalent to ``e0 = 0``.
e0: Option used to define the zero of energy in the band structure plot. Possible values::
- ``fermie``: shift all eigenvalues and the DOS to have zero energy at the Fermi energy.
Note that, by default, the Fermi energy is taken from the band structure object
i.e. the Fermi energy computed at the end of the SCF file that produced the density.
This should be ok in semiconductors. In metals, however, a better value of the Fermi energy
can be obtained from the DOS provided that the k-sampling for the DOS is much denser than
the one used to compute the density. See ``edos_fermie``.
- ``edos_fermie``: Use the Fermi energy computed from the DOS to define the zero of energy in both subplots.
Available only if edos_objects is not None
- Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
- None: Don't shift energies, equivalent to ``e0 = 0``.
sharex, sharey: True if x (y) axis should be shared.
xlims: Set the data limits for the x-axis. Accept tuple e.g. ``(left, right)``
or scalar e.g. ``left``. If left (right) is None, default values are used

2
docs/requirements.txt
View File

@ -1,5 +1,5 @@
ipython
sphinx
sphinx==1.6.5
sphinxcontrib-napoleon
sphinxcontrib-programoutput
sphinx-gallery

64
docs/workflows/manager_examples.rst
View File

@ -24,12 +24,10 @@ Dragon1
job: &job
mpi_runner: mpirun
shell_env:
PATH: "/home/users/g/m/gmatteo/git/abinit/_build_dragon1-intel-mpich-mkl.ac/src/98_main:$PATH"
PATH: "$HOME/git_repos/abinit/_build_dragon1-intel-mpich-mkl.ac/src/98_main:$PATH"
modules:
- mpich/3.0.4/intel-13.0.0
# pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit unlimited
pre_run: "ulimit -s unlimited"
# queues
qadapters:
@ -95,13 +93,13 @@ Hercules
job: &job
mpi_runner: mpirun
shell_env:
PATH: "/home/gmatteo/git_repos/abinit/_build_hercules.ac/src/98_main/:$PATH"
PATH: "$HOME/git_repos/abinit/_build_hercules.ac/src/98_main/:$PATH"
modules:
- impi/5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26
- imkl/11.3.3.210-iimpi-2016b
# pre_run is a string in verbatim mode (note |)
# here pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit unlimited
ulimit -s unlimited
# queues
qadapters:
@ -149,12 +147,10 @@ Hmem
job: &job
mpi_runner: mpirun
shell_env:
PATH: "/home/users/g/m/gmatteo/git_repos/abinit/_build_hmem_intel_openmpi-mkl.ac/src/98_main/:$PATH"
PATH: "$HOME/git_repos/abinit/_build_hmem_intel_openmpi-mkl.ac/src/98_main/:$PATH"
modules:
- openmpi/1.5.3/intel-12.0.0.084
# pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit unlimited
pre_run: "ulimit -s unlimited"
# queues
qadapters:
@ -290,9 +286,7 @@ Jureca
PATH: $HOME/abinit/801-private/jureca_mpi/src/98_main:$PATH
modules:
- intel-para/2015.07
# pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit unlimited
pre_run: "ulimit -s unlimited"
# queues
qadapters:
@ -325,12 +319,10 @@ Lemaitre2
job: &job
mpi_runner: mpirun
shell_env: # Use your abinit exec
PATH: "/home/users/g/m/gmatteo/git_repos/abinit/_build_lemaitre2-intel-openmpi-mkl.ac/src/98_main/:$PATH"
PATH: "$HOME/git_repos/abinit/_build_lemaitre2-intel-openmpi-mkl.ac/src/98_main/:$PATH"
modules: # Abinit compiled with abiconfig settings
- openmpi/1.6.5/intel-13.0.1.117
# pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit unlimited
pre_run: "ulimit -s unlimited"
# queues
qadapters:
@ -378,13 +370,13 @@ Manneback
job: &job
mpi_runner: mpirun
shell_env:
PATH: /home/users/g/m/gmatteo/git_repos/abinit/_build_manneback-gcc-openmpi.ac/src/98_main/:$PATH
pre_run: |
ulimit -s unlimited # pre_run is a string in verbatim mode (note |)
export OMP_NUM_THREADS=1
unset SLURM_CPUS_PER_TASK
module purge
module load gompi/2016a FFTW/3.3.4-gompi-2016a
PATH: "$HOME/git_repos/abinit/_build_manneback-gcc-openmpi.ac/src/98_main/:$PATH"
pre_run:
- "ulimit -s unlimited"
- "export OMP_NUM_THREADS=1"
- "unset SLURM_CPUS_PER_TASK"
- "module purge"
- "module load gompi/2016a FFTW/3.3.4-gompi-2016a"
#policy:
# frozen_timeout: 0-12:0:0
@ -428,9 +420,8 @@ Nic4
mpi_runner: "mpirun"
mpi_runner_options: "--bind-to none"
shell_env:
PATH: "/home/users/g/m/gmatteo/git_repos/abinit/_build_nic4-intel-openmpi-mkl-hdf5.ac/src/98_main:$PATH"
pre_run:
- "ulimit -s unlimited"
PATH: "$HOME/git_repos/abinit/_build_nic4-intel-openmpi-mkl-hdf5.ac/src/98_main:$PATH"
pre_run: "ulimit -s unlimited"
modules:
- shared
- openmpi/1.7.5/intel2013_sp1.1.106
@ -582,12 +573,10 @@ Vega
job: &job
mpi_runner: mpirun
shell_env:
PATH: "/gpfsuser/home/users/g/m/gmatteo/git_repos/abinit/_build_vega-intel-impi-mkl.ac/src/98_main/:$PATH"
PATH: "$HOME/git_repos/abinit/_build_vega-intel-impi-mkl.ac/src/98_main/:$PATH"
modules:
- intel/2015a
# pre_run is a string in verbatim mode (note |)
#pre_run: |
# "ulimit -s unlimited"
#pre_run: "ulimit -s unlimited"
# queues
qadapters:
@ -621,9 +610,9 @@ Viper
job: &job
mpi_runner: ~/bin/mpirun.openmpi
# pre_run is a string in verbatim mode (note |)
pre_run: |
ulimit -s unlimited
source ~/.bashrc
pre_run:
- "ulimit -s unlimited"
- "source ~/.bashrc"
# queues
qadapters:
@ -664,13 +653,12 @@ Zenobe
job: &job
mpi_runner: mpirun
shell_env:
PATH: /home/acad/ucl/naps/mgiantom/bzr_repos/793/gmatteo-private/build_impi/src/98_main:$PATH
PATH: $HOME/git_repos/abinit_build_impi/src/98_main:$PATH
modules:
- compiler/intel/composerxe/2013_sp1.1.106
- intelmpi
- python/2.7
pre_run: |
ulimit # pre_run is a string in verbatim mode (note |)
pre_run: "ulimit -s unlimited"
# List of qdapters.
qadapters: