mretegan/crispy

Core-Level Spectroscopy Simulations in Python

Crispy is a modern graphical user interface to calculate core-level spectra using the semi-empirical multiplet approaches implemented in Quanty. The interface provides a set of tools to generate input files, submit calculations, and plot the resulting spectra.

Installation

Latest Release

Using the Package Installers

The easiest way to install Crispy on Windows and macOS operating systems is to use the installers provided on the project's downloads page.

Using pip

Pip is the package manager for Python, and before you can use it to install Crispy, you have to make sure that you have a working Python distribution. On macOS and Windows, you can install Python using the official installers. In particular, for Windows, you should install the 64-bit version of Python and make sure that you select to add Python to the system's PATH during the installation.

python3 -m pip install crispy

After the installation finishes, you should be able to start the program from the command line:

crispy

If you have problems running the previous command, it is probably due to not having your PATH environment variable set correctly.

export PATH=$HOME/.local/bin:$PATH

Development Version

Using pip

Assuming that you have a working Python distribution (version 3.7 or greater), you can easily install the development version of Crispy using pip:

python3 -m pip install https://github.com/mretegan/crispy/tarball/main

To update the development version of Crispy, you can use the following command:

python3 -m pip install --ignore-installed https://github.com/mretegan/crispy/tarball/main

Usage

If you have used the installers, Crispy should be easy to find and launch. For the installation using pip or if you are running directly from the source folder, follow the instructions from the Installation section.

Citation

Crispy is a scientific software. If you use it for a scientific publication, please cite the following reference (change the version number if required):

@misc{retegan_crispy,
  author       = {Retegan, Marius},
  title        = {Crispy: v0.7.4},
  year         = {2019},
  doi          = {10.5281/zenodo.1008184},
  url          = {https://doi.org/10.5281/zenodo.1008184}
}

License

The source code of Crispy is licensed under the MIT license.

crispy's Issues

Failed to Write the Quanty input file for Ru 3d XPS in Crispy 0.7.3

Hi, I have done the XPS calculations using Crispy for Ru 1s, 2s, 3s, 3p, and other orbitals. But when I do the XPS calculation for Ru 3d, it is showing 'Failed to Write the Quanty input file.' Is this a bug? or whether any additional parameters has to be changed for Ru 3d?

Polarization dependent XAS and RIXS calculations

At the moment only isotropic calculations are available...

XES parameters are not correct for the intermediate Hamiltonian

For example, the correct intermediate electronic configurations for Fe3+ is 1s1-3d5, and not 1s1-3d6 as it is now.

Add user editable threshold for selecting states of the initial Hamiltonian

At the moment the threshold is set to the machine epsilon for double precision, which is very conservative.

Add curve stats widget

Add the stats widget from silx once it has an icon.

Add option to hide legend

Wrong equations for the MLCT on-site energies

The starting equations used to derive the on-site energies are wrong. The correct equations are:

e_3d_i = U_3d_3d_i * (-NElectrons_3d + 1) / 2
e_L2_i = Delta_3d_L2_i + U_3d_3d_i * NElectrons_3d / 2 - U_3d_3d_i / 2

e_3d_f = -(U_3d_3d_f * NElectrons_3d^2 + 11 * U_3d_3d_f * NElectrons_3d + 60 * U_2p_3d_f) / (2 * NElectrons_3d + 12)
e_2p_f = NElectrons_3d * (U_3d_3d_f * NElectrons_3d + U_3d_3d_f - 2 * U_2p_3d_f * NElectrons_3d - 2 * U_2p_3d_f) / (2 * (NElectrons_3d + 6))
e_L2_f = (2 * Delta_3d_L2_f * NElectrons_3d + 12 * Delta_3d_L2_f  +  U_3d_3d_f * NElectrons_3d^2 - U_3d_3d_f * NElectrons_3d - 12 * U_3d_3d_f  + 12 * U_2p_3d_f * NElectrons_3d  + 12 * U_2p_3d_f) / (2 * (NElectrons_3d + 6))

Thanks to Stefano Agrestini for spotting this!

pip Install Issue

The crispy documentation says one needs to just use "pip3 install --upgrade crispy" to install. But one must install "silx" first since it is not apart of the pip module.

It would be much appreciated if the documentation or the pip install could be updated.

Number of configurations in XPS

Add one extra configuration in XPS simulations.

Loading Quanty Simulations

Is there any option to load previously generated *spec-files?

Change init methods for some classes

The current way makes it tedious to instantiate certain classes. For example:

from crispy.gui.quanty.calculation import Element 
element = Element(value="Fe2+")

Make value the first keyword argument, so it doesn't need to be explicitly specified. Already these classes are heavy as they inherit from QObject, no need to make things more verbose.

Bug check relating to partition function

In the quanty.lua file created by crispy, it appears to sum over all initial states that have dZ < 1e-8 where dZ = math.exp(-(E - E_gs) / T). I think each spectrum should be weighted by dZ before summing. Please can this be checked?

I think think the code needs
spectrum = spectrum + dZ * CreateResonantSpectra(...
near the end of the lua file.

for j, OperatorOut in ipairs({Tx_3d_2p, Ty_3d_2p, Tz_3d_2p}) do
for k, OperatorIn in ipairs({Tx_2p_3d, Ty_2p_3d, Tz_2p_3d}) do
spectrum = 0
Z = 0
for i, Psi in ipairs(Psis) do
E = Psi * H_i * Psi
if math.abs(E - E_gs) < 1e-12 then
dZ = 1
else
dZ = math.exp(-(E - E_gs) / T)
end
if (dZ < 1e-8) then
print(string.format("Stop after %i spectra were computed\n", i))
break
end
Z = Z + dZ
spectrum = spectrum + dZ * CreateResonantSpectra(H_m, H_f, OperatorIn, OperatorOut, Psi, {{'Emin1', Emin1}, {'Emax1', Emax1}, {'NE1', NE1}, {'Gamma1', Gamma1}, {'Emin2', Emin2}, {'Emax2', Emax2}, {'NE2', NE2}, {'Gamma2', Gamma2}})
end
spectrum = spectrum / Z
spectrum.Print({{'file', 'RIXS_pol_' .. j .. k .. '_out.spec'}})
end
end

Installation problems

Hi,

I want to install crispy in an anaconda environment according to your instructions but I am getting an exception when launching crispy:

Traceback (most recent call last):
  File "/usr/local/miniconda3/envs/crispy/bin/crispy", line 11, in main
    from crispy.__main__ import main
  File "/usr/local/miniconda3/envs/crispy/lib/python3.7/site-packages/crispy/__main__.py", line 37, in <module>
    from .gui.main import MainWindow
  File "/usr/local/miniconda3/envs/crispy/lib/python3.7/site-packages/crispy/gui/main.py", line 50, in <module>
    from .quanty import QuantyDockWidget, QuantyPreferencesDialog
  File "/usr/local/miniconda3/envs/crispy/lib/python3.7/site-packages/crispy/gui/quanty.py", line 402, in <module>
    class QuantyCalculation(object):
  File "/usr/local/miniconda3/envs/crispy/lib/python3.7/site-packages/crispy/gui/quanty.py", line 451, in QuantyCalculation
    path = resourceFileName('quanty:parameters/parameters.json.gz')
  File "/usr/local/miniconda3/envs/crispy/lib/python3.7/site-packages/silx/resources/__init__.py", line 251, in resource_filename
    return _resource_filename(resource, default_directory=None)
  File "/usr/local/miniconda3/envs/crispy/lib/python3.7/site-packages/silx/resources/__init__.py", line 288, in _resource_filename
    return pkg_resources.resource_filename(package_name, resource_name)
  File "/usr/local/miniconda3/envs/crispy/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1144, in resource_filename
    return get_provider(package_or_requirement).get_resource_filename(
  File "/usr/local/miniconda3/envs/crispy/lib/python3.7/site-packages/pkg_resources/__init__.py", line 364, in get_provider
    return _find_adapter(_provider_factories, loader)(module)
  File "/usr/local/miniconda3/envs/crispy/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1392, in __init__
    self.module_path = os.path.dirname(getattr(module, '__file__', ''))
  File "/usr/local/miniconda3/envs/crispy/lib/python3.7/posixpath.py", line 156, in dirname
    p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda3/envs/crispy/bin/crispy", line 24, in <module>
    main()
  File "/usr/local/miniconda3/envs/crispy/bin/crispy", line 20, in main
    main()
UnboundLocalError: local variable 'main' referenced before assignment

Any thoughts? Thanks!

Add a calculation details widget

The widget should be triggered by an action in the "Results" context menu. It would be interesting to have options to broaden, shift, scale, normalize, etc. the spectrum.

crispy-plotting

Dear Dr Marius.S.Retegen,

             This is regarding the interface you developed 'Crispy'.  

I have installed it on Ubuntu 20.4 LTE via pip3.
Installation went well and the program runs smoothly.
The background engine 'Quanty' also got recognized.
But plotting is not happening.

Please let me know where to look for?

Mahendra

XPS and XES with charge transfer (ligand field) are not correct

The equations used to calculate the onsite energy are not correct.

Crispy Notebook Temperature Error

There is an unknown error inside the crispy module for jupyter notebooks which manifests into an incomplete/empty XAS simulation.

Crispy GUI:
Trying to calculate the XAS of the L2,3 (2p) edge of Fe2+ with an Oh geometry at 298K runs perfectly.

Crispy Notebook:
Doing the following inside a jupyter notebook causes Quanty/Crispy to produce an empty simulation output.

from crispy.notebook import calculation

element = 'Fe2+'
geometry = 'Oh'

calc = calculation(element, geometry, 'XAS', "L2,3 (2p)")
calc.temperature(50)

calc.run()
data = calc.spectra.calculated()

energies = data['Isotropic Absorption']['x']
intensities = data['Isotropic Absorption']['signal']

Temperatures <50K are ok (except for 0). But anything >=50K results in empty energy and intensity arrays.

Update to PyQt6

Maybe it is time to update to PyQt6...

Use QSettings from Qt

Change the way the settings are managed, from own implementation to the QSettings class.

Save main window size

The initial size of the main window needs to be adapted to the screen of the user and needs to be saved to the config file before exiting.

Bug check relating to B operator

I recently created a lua script to compute 2p3d RIXS of a tetragonal Cu 2+ ion.

This appeared to only include the B field operator in initial and intermediate states and not in the final state.

i.e. it had
H_i = H_i + B
H_m = H_m + B

and not
H_i = H_i + B
H_m = H_m + B
H_f = H_f + B

I was expecting the latter behavior.

Fix documentation

There is an issue with table_styling which requires a pin on the Jinja2 version. (https://foss.heptapod.net/doc-utils/cloud_sptheme/-/issues/48)

Python Import Crispy Function

Is there a way to import the main crispy simulation function into python?

Example:
from crispy import simulation_function
spectra = simulation_function(param1, param2, param3, ...)

This would make it easier to iterate through parameters for a given spectrum.

Permission denied Quanty executable

If the Quanty binary is not executable.

Traceback (most recent call last):
  File "/home/marius/crispy-0.7.3/lib/python3.8/site-packages/crispy/gui/quanty.py", line 1587, in runCalculation
    subprocess.call(command, stdout=f, stderr=f)
  File "/usr/lib/python3.8/subprocess.py", line 340, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.8/subprocess.py", line 854, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.8/subprocess.py", line 1702, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: '/home/marius/Downloads/Quanty'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/marius/crispy-0.7.3/lib/python3.8/site-packages/crispy/gui/quanty.py", line 1589, in runCalculation
    if e.errno == os.errno.ENOENT:
AttributeError: module 'os' has no attribute 'errno'
Aborted (core dumped)

Add XMCD and X(M)LD calculations for quadrupole transition operators

Calculations clean up

If enabled, always remove the calculation files, even when the user stops the run.

Crispy Not Working

I have tried to install Crispy onto a new machine. Both the GUI and the Notebook versions.

No matter what I do I am unable to get either version to calculate spectra.

My steps to install:

1. Create a new conda env conda create -n crisp python=3.7
2. activate env source activate crisp
3. install env to jupyter pip install ipykernel ipython kernel install --user --name=crisp
4. install slix pip install slix[full]
5. install crispy pip3 install --upgrade crispy==2020.1rc0 (the only version that I have gotten close to working with Notebooks
6. download Quanty from their website
7. make Quanty executable chmod 777 Quanty
8. set Quanty path in GUI by using the GUI
9. set Quanty path in scripts by path variable in /crispy/gui/quanty/calculations.py - def executablePath function to the path of Quanty

I cannot seem to get any simulation results. And when using the GUI, after I hit run the only thing the program shows is Quanty has stopped

Plotting on ubuntu (silx error)

I have tried to use crispy 0.7.3 on Ubuntu 20.04, but got the following error when plotting spectra:

Traceback (most recent call last):
  File "/home/galdino/envs/my_env/lib/python3.8/site-packages/silx/gui/plot/backends/BackendBase.py", line 343, in postRedisplay
    plot.replot()
  File "/home/galdino/envs/my_env/lib/python3.8/site-packages/silx/gui/plot/PlotWidget.py", line 2949, in replot
    item._update(self._backend)
  File "/home/galdino/envs/my_env/lib/python3.8/site-packages/silx/gui/plot/items/core.py", line 442, in _update
    self._backendRenderer = self._addBackendRenderer(backend)
  File "/home/galdino/envs/my_env/lib/python3.8/site-packages/silx/gui/plot/items/curve.py", line 199, in _addBackendRenderer
    return backend.addCurve(xFiltered, yFiltered,
TypeError: addCurve() missing 1 required positional argument: 'legend'
Aborted (core dumped)

Then I used the following workaround:

1. Edit line 199 of curve.py in the silx package (the full file path can be found in error message above).

Before it was

return backend.addCurve(xFiltered, yFiltered,

and I changed it to

return backend.addCurve(xFiltered, yFiltered, legend='',

Note that this "breaks" the silxs installation within that environment. Particularly, I have separated environment just for running crispy 0.7.3.

2. Edit line 58 of plot.py in the crispy folder (<crispy_folder>/crispy/gui/plot.py)

Before it was

x, y, legend, *args, **kwargs)

and I changed it to

x, y, *args, **kwargs)

You may close this. I just thought it would be a good idea to report this error here since other people might also have the same issue when using crispy on ubuntu.

Calculate the vertical and horizontal polarization vectors from the experimental details

Notebook calc.run() Error

After following the notebook tutorial found at https://www.youtube.com/watch?t=1123&v=ovdLJXIqMEE&feature=youtu.be, I was unable to run the command calc.run(). I received the error in the attached image.

Crispy Version = 2020.1rc0
Python Version == 3.7

X-axis shift in RIXS calculations

Changing the incident energy range gives a different position for the calculated peaks.

Invalid path in the config file

Running calculations fails if the current folder path gets corrupted.

Traceback (most recent call last):
  File "/Users/marius/crispy/crispy/quanty/main.py", line 501, in run
    self.state.run()
  File "/Users/marius/crispy/crispy/quanty/calculation.py", line 743, in run
    self.saveInput()
  File "/Users/marius/crispy/crispy/quanty/calculation.py", line 736, in saveInput
    os.chdir(settings.value("CurrentPath"))
TypeError: chdir: path should be string, bytes, os.PathLike or integer, not NoneType

PyPI package outdated, broken

setup.py fails because due to some circularity it imports code it needs to install first.

(venv) user@host:~$ pip install crispy
Collecting crispy
  Using cached crispy-0.7.3.tar.gz (409 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [12 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-prllqu5t/crispy_0d13376086e942c086aa74f8ba8a6c16/setup.py", line 149, in <module>
          main()
        File "/tmp/pip-install-prllqu5t/crispy_0d13376086e942c086aa74f8ba8a6c16/setup.py", line 77, in main
          version=get_version(),
        File "/tmp/pip-install-prllqu5t/crispy_0d13376086e942c086aa74f8ba8a6c16/setup.py", line 53, in get_version
          from crispy import version
        File "/tmp/pip-install-prllqu5t/crispy_0d13376086e942c086aa74f8ba8a6c16/crispy/__init__.py", line 3, in <module>
          from silx.resources import register_resource_directory
      ModuleNotFoundError: No module named 'silx'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Directly installing from github main branch (pip install git+https://github.com/mretegan/crispy.git) works, so the solution would be to push out a new stable version finally or patch 0.7.3)

Transition operators for quadrupolar transitions are wrong

The function that calculates the transition operators for an arbitrary polarization and k-vector has wrong prefactors. Isotropic spectra are correct, but the XMCD and XMLD are not.

The correct function is:

function CalculateT(e, k)
    -- Calculate the transition operator for arbitrary
    -- polarization and wave vectors.
    if k == nil then
        T = e[1] * Tx_1s_4p + e[2] * Ty_1s_4p + e[3] * Tz_1s_4p
    else
        T = (e[1] * k[2] + e[2] * k[1]) * Txy_1s_3d / math.sqrt(3)
          + (e[1] * k[3] + e[3] * k[1]) * Txz_1s_3d / math.sqrt(3)
          + (e[2] * k[3] + e[3] * k[2]) * Tyz_1s_3d / math.sqrt(3)
          + (e[1] * k[1] - e[2] * k[2]) * Tx2y2_1s_3d / math.sqrt(3)
          + e[3] * k[3] * Tz2_1s_3d
    end
    return Chop(T)
end

Wrong parameters for 5d transition metals

The atomic parameters are calculated without the 4f electrons. This issue was reported by Travis Jones.

MLCT vs. LMCT performance for d4-d6 elements

Implementing a CI/CD pipeline for Python and Anaconda

Automatically determine the number of points

Use the energy range and the natural broadening to determine a minimal number of points in a RIXS simulation.

Add XES simulations for 3d transition metals

Td ligand field calculations are missing a ligand shell

See this discussion on the Quanty forum: http://www.quanty.org/forum/data/2019/metal_3d_to_ligand_hybridization_in_td#discussion__section

Fix documentation

There is an issue with table_styling which requires a pin on the Jinja2 version. (https://foss.heptapod.net/doc-utils/cloud_sptheme/-/issues/48)

Changing Gamma and Gaussian broadening in XAS calculations has no effect

Changing the Gamma parameter to adjust the life time broadening in XAS calculations and the Gaussian resolution broadening does not have an effect. When starting a calculation they seem to be set back to the default values and calculations run with different Gamma and Gaussian parameters all yield the same spectra.

Implement save and load functions for simulations

Wrong number of electrons in RIXS MLCT

The number of electrons is set to 10, but in this case, it should be 0.

Update to qtpy

Make qtpy the interface to Qt

XPS spectrum plot

Invert the x-axis when plotting the XPS spectra.

Move the config to package level

For example, in h5py there is a get_config function.

import h5py
conf = h5py.get_config()

Refactoring

As shown in the latest merged common
9e5ac48 refactors seem to become important.

Further refactors should be considered?

Fix Jinja2 pin

The previous setting in setup.cfg was wrong

Wrong parameters for the 4f elements

The truncated output from Cowan's RCN for Eu 4f7 electronic configuration:

   ETOT= -21658.42787 -21658.42787         -21663.30022 -21663.30022 -21663.10600 -21663.10600 -21663.10600


       4f7              5 -21663.1060 0   12.9967 1    8.1069 1    5.8191 1    0.1604 2



0    T(RUN)=     0.00,     T(JOB)=     0.00 SECONDS

Currently in Crispy: F2(4f,4f) = 8.721 compared to 12.9967 from above. The 5f elements are not affected.