Added CalcJob implementations of the xspectra.x executable and upf2plotcore.sh shell script from the Quantum ESPRESSO library

Added Parser classes for the xspectra.x executable and upf2plotcore.sh shell script from the Quantum ESPRESSO library

Added entry points for both CalcJob and Parser classes required for XSpectra post-processing calculations

Change 'spectra_data' output to 'spectra'

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Change the caplitalization for XSpectraCalculation to XspectraCalculation

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Correct the capitalization of XSpectraParser to XspectraParser

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Correct the capitalization of XSpectraCalculation to XspectraCalculation

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Correct the capitalization of XSpectraParser to XspectraParser

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

…efunction data

…ved redundant file loop, and added new error code

Fixed the terms used in the XSpectra-specific error
codes in order to make them easier to read.

Changed filename assigned to `_Plotcore_FILENAME`
from `plotcore.out` to `stdout` in order to work
properly with the `aiida-shell` plugin.

Made corrections to the parsing of various output
parameters (e.g. energy levels and associated units)
in both spin-polarised and unpolarised cases. An
additional parameter `lsda` is also added to report
explicitly the case of spin polarisation.

Adds tests of the `XspectraParser`, covering spin-polarised
and non-spin-polarised cases, interrupted calculations, and
XSpectra-specific error codes 313 and 314.

Adds the following features to the `XspectraCalculation` and
`XspectraParser` classes:
- A save file ('xanes.sav') is now reserved by default and is printed
at the end of each calculation run or after a designated time limit.
The file can then be used for re-starting halted calculations or
re-plotting spectra from previously-finished calculations.
- The `XspectraCalculation` class now copies the save file from a
parent calculation if the calculation type is itself an
XspectraCalculation, thus re-starts and re-plot runs are handled
automatically.
- An error code has been added (315) for calculations which safely exit
after reaching their time limit, thus enabiling a restart.
- Additional information is now included in the `output_parameters`
node (e.g. the polarisation vectors used and whether the calculation was
set to "xonly_plot").

Updates `XspectraParser` tests to work with changes made in a previous
commit (commit 875fa58) and adds a new
test for error code 315 (job exceeded time limit)

…umespresso into develop

Addresses aiidateam#837

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Addresses PR aiidateam#837

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Addresses PR aiidateam#837

Changes error code from 315 to 400 to match conventions

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Addresses PR aiidateam#837

Required for commit aiidateam@746770e

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Addresses PR aiidateam#837

Required with commit aiidateam@746770e

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Addresses PR aiidateam#837

Cleans-up the code for detecting if the parent calculation was an `XspectraCalculation`

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Addresses comment for PR aiidateam#837: aiidateam#837 (review)

Safely trims down the file length of the stdout file for `failed_timeout` test of `XspectraParser`

…umespresso into local develop

Correct text of docstring for `test_xspectra_failed_timeout`

Co-authored-by: Sebastiaan Huber <mail@sphuber.net>

Adds information on the coordinate system used in the XSpectra
calculation (either crystallographic or Cartesian). Also addresses a bug
spotted in the stdout of XSpectra itself, where the epsilon/k-vector is
reported by the code during the `read_save_file` subroutine as being in
`[Cartesian frame]` regardless of the coordinate system used by the
parent XSpectra calculation. Because of this, calculations where
`xonly_plot=.true.` cannot meaningfully have metadata for the coordinate
system used by the calculation recorded in the `output_parameters`
dictionary by the parser.

This fix also addresses the fact that the epsilon/k-vector is
essentially reported twice in the event of a calculation restart: once
when the input file is read and a second time when the save file is
read.

Updates commit 9ef620c

Previous commit stated that when reading the save file, XSpectra prints
the epsilon/k-vector stored in the save file as being in Cartesian
coordinates regardless the coordinate system used in the parent
calculation. This statement was incorrect, as XSpectra always records the
epsilon vector in cartesian coordinates. The parser now correctly
records the `eps_k_vector_coords` entry in the event of re-plot
calculations while skipping the entry for calculation restarts, since
the epsilon/k-vector used is reported with the relevant coordinate system
at the beginning of the stdout.

Improves the reliability of parsing information in the `XspectraParser`
by collecting information from the CalcJob node's `parameter` node
instead of using the stdout.

For the `XspectraParser` and related tests:
* Changes the Parser to retrieve various information from the inputs of
the CalcJob node rather than the stdout, since some information (e.g.
polarisation vector and coordinate system) are not reported reliably.
* Changes some of the keys in the `output_parameters` dictionary.
* Updates the Parser tests to work with the new changes to the Parser
itself.

Requested for aiidateam#853

For parameters Parsed from the calculation input, the commit changes
their keys to those used in the input parameters:
* `epsilon_vectors` => `xepsilon`
* `vector_coord_system` => `xcoordcrys`
* `only_plot_spectrum` => `xonly_plot`

Also adds default values for these keys which match those set by
`xspectra.x` and updates the relevant parser tests.

…umespresso into develop

Adds a new WorkChain for `xspectra.x` calculations to compute a complete
K-edge XANES for each element of a given structure using `pw.x` and
`xspectra.x`. The WorkChain uses the following process flow:

* Relax the given input structure using the `PwRelaxWorkChain`
(optional).
* Generate the core wavefunction of each ground-state pseudopotential
for each absorbing element considered (requires AiiDA-Shell plugin).
* Analyse the symmetry of the relaxed structure using `spglib`. Use the
outputs of the analysis to prepare inputs for `XspectraCoreWorkChain`
sub-processes.
* Call the `XspectraCoreWorkChain` for each structure prepared in the
previous step to generate the powder sample XANES for each identified
absorbing atom site in the structure.
* Compile all outputs from the `XspectraCoreWorkChain` sub-processes and
return a single XANES spectrum for each element considered in the
analysis.

Excited-state and ground-state pseudopotentials presently must be provided
using the input namespaces `core_hole_pseudos` and `gipaw_pseudos`
respectively, taking the form of a Dict node with the format:

	{'{element} : {'core_hole' : {upf}, 'gipaw' : {upf}}}

In addition to the final XANES spectra for each element, the powder
spectrum of each absorbing atom calculated can be returned as output to
the head WorkChain node with the optional input
`return_all_powder_spectra` (`False` by default).

Adds an input namespace `core_wfc_data` which can be used to provide
already-computed core wavefunction data files for each element. Must use
the format:
	{core_wfc_data : {"{element}" : {node}}}

Adds tests for the `get_builder_from_protocol` method of the
`XspectraCrystalWorkChain`

Removes redundant code in `setup` and `get_xspectra_structures`

Co-authored-by: Xing Wang <xingwang1991@gmail.com>

Co-authored-by: Xing Wang <xingwang1991@gmail.com>

Addresses changes requested for PR aiidateam#888 (1):
* Expands the docstring for `get_spectra_by_element` to describe input
parameters and usage.
* Fixes an oversight in `get_xspectra_structures` where the
`standardized_structure` value was returned regardless of whether the
structure was actually standardized by the CalcFunction.
* Add a check for the `core_wfc_data` input to check for
improperly-formatted file content.
* Modify the `elements_list` input to be a required input and correct
all instances where data provenance was lost. Changes
`get_builder_from_protocol()` to set `elements_list` automatically based
on `pseudos` input if no `elements_list` is given
* Correct all instances of `optimized_structure` and `relaxed_structure`
to all be `optimized_structure`
* Change from simply using `append_` to add all CoreWorkChains to the
context and instead assign each their site indexes as keys (i.e.
`self.ctx.site_{i}`)
* Add a step to unassign the pseudopotential for the element of the
absorbing atom if the element does not exist in the structure (e.g. for
the case where only one atomic site of the element exists).
* Change the `structure_preparation_settings` input to be a dynamic
namespace instead of a single Dict node, thus ensuring data provenance
is maintained.

Updates the `test_crystal.yaml` to include the required `elements_list`
input generated by the protocol.