Visualisation and Plotting¶

Fleur specific Plotting¶

Plotting routine for fleur density of states and bandstructures

masci_tools.vis.fleur.plot_fleur_bands(bandsdata, bandsattributes, spinpol=True, only_spin=None, backend=None, weight=None, **kwargs)[source]¶

Plot the bandstructure previously extracted from a banddos.hdf via the HDF5Reader

This routine expects datasets and attributes read in with a FleurBands recipe from recipes or something producing equivalent data

Parameters

bandsdata – dataset dict produced by the FleurBands recipe
attributes – attributes dict produced by the FleurBands recipe
spinpol – bool, if True (default) use the plot for spin-polarized bands if the data is spin-polarized
only_spin – optional str, if given only the specified spin components are plotted
backend – specify which plotting library to use (‘matplotlib’ or ‘bokeh’)
weight – str, name of the weight (without spin suffix _up or _dn) you want to emphasize

All other Kwargs are passed on to the underlying plot routines

Matplotlib: plot_bands(), plot_spinpol_bands()
Bokeh: bokeh_bands(), bokeh_spinpol_bands()

masci_tools.vis.fleur.plot_fleur_bands_characterize(bandsdata, bandsattributes, weight_names, weight_colors, spinpol=True, only_spin=None, backend=None, **kwargs)[source]¶

Plot the bandstructure previously extracted from a banddos.hdf via the HDF5Reader with points colored according to the maximum weight from a selection of weights. Can be used to show what character dominates each band

This routine expects datasets and attributes read in with a FleurBands recipe from recipes or something producing equivalent data

Parameters

bandsdata – dataset dict produced by the FleurBands recipe
attributes – attributes dict produced by the FleurBands recipe
weight_names – list of str with the names of the weights that should be considered in the characterization
weight_color – list of colors associated with each weight. If spin-polarized bandstructures should be shown with different colors the list should be twice as long as the weights
spinpol – bool, if True (default) use the plot for spin-polarized bands if the data is spin-polarized
only_spin – optional str, if given only the specified spin components are plotted
backend – specify which plotting library to use (‘matplotlib’ or ‘bokeh’)

All other Kwargs are passed on to plot_fleur_bands()

masci_tools.vis.fleur.plot_fleur_dos(dosdata, attributes, spinpol=True, only_spin=None, multiply_by_equiv_atoms=True, plot_keys=None, show_total=True, show_interstitial=True, show_sym=False, show_atoms='all', show_lresolved=None, key_mask=None, backend=None, **kwargs)[source]¶

Plot the density of states previously extracted from a banddos.hdf via the HDF5Reader

This routine expects datasets and attributes read in with the FleurDOS (Or related DOS modes) recipe from recipes or something producing equivalent data

The limits for the axes can be specified either with x and y or energy and dos. Mixing the two options is not possible

Parameters

dosdata – dataset dict produced by the FleurDOS recipe
attributes – attributes dict produced by the FleurDOS recipe
spinpol – bool, if True (default) use the plot for spin-polarized dos if the data is spin-polarized
only_spin – optional str, if given only the specified spin components are plotted
backend – specify which plotting library to use (‘matplotlib’ or ‘bokeh’)

Arguments for selecting the DOS components to plot: :type plot_keys:

param plot_keys

optional str list of str, defines the labels you want to plot

All other Kwargs are passed on to the underlying plot routines

Matplotlib: plot_dos(), plot_spinpol_dos()
Bokeh: bokeh_dos(), bokeh_spinpol_dos()

masci_tools.vis.fleur.sum_weights_over_atoms(data, attributes, atoms_to_sum, entry_name)[source]¶

Create sums of atom components over specified atoms. They are entered with the same suffixes as in the original data, but with the given entry_name as prefix

Parameters

data – datasets dict produced by the HDF5Reader with a recipe for DOS or bandstructure
attributes – attributes dict produced by the HDF5Reader with a recipe for DOS or bandstructure
atoms_to_sum – list of ints for the atoms, which should be summed
entry_name – str prefix to be entered for the summed entries

Returns

dict with the summed entries

KKR specific Plotting¶

Tool to plot a Fermi surface calculated with the qdos mode of KKR

masci_tools.vis.kkr_plot_FS_qdos.FSqdos2D(p0='./', s=20, reload_data=False, clrbar=True, atoms=None, ax=None, nosave=False, noalat=False, cmap=<matplotlib.colors.LinearSegmentedColormap object>, noplot=False, return_data=False, pclrmesh=False, logscale=True, ef=None)[source]¶: plotting routine for dos files

dispersionplot function for plotting KKR bandstructures (i.e. qdos) files

masci_tools.vis.kkr_plot_bandstruc_qdos.dispersionplot(p0='./', data_all=None, totonly=True, s=20, ls_ef=':', lw_ef=1, units='eV_rel', noefline=False, color='', reload_data=False, clrbar=True, logscale=True, nosave=False, atoms=None, ratios=False, atoms2=None, noscale=False, newfig=False, cmap=None, alpha=1.0, qcomponent=-2, clims=None, xscale=1.0, raster=True, atoms3=None, alpha_reverse=False, return_data=False, xshift=0.0, yshift=0.0, plotmode='pcolor', ptitle=None, ef=None, as_e_dimension=None, scale_alpha_data=False, shading='gouraud', verbose=False)[source]¶: plotting routine for qdos files - dispersion (E vs. q)

masci_tools.vis.kkr_plot_bandstruc_qdos.load_data(p0='./', reload_data=False, nosave=False, atoms=None, ratios=False, atoms2=None, atoms3=None, ef=None, verbose=False)[source]¶: load the qdos data

Plotting function for KKR dos from files

masci_tools.vis.kkr_plot_dos.dosplot(p0='./', totonly=True, color='', label='', marker='', lw=2, ms=5, ls='-', ls_ef=':', lw_ef=1, units='Ry', noefline=False, interpol=False, allatoms=False, onespin=False, atoms=None, lmdos=False, lm=None, nofig=False, scale=1.0, shift=0, normalized=False, xyswitch=False, efcolor='', return_data=False, xscale=1.0, xshift=0.0, yshift=0.0, filled=False, spins=2)[source]¶: plotting routine for dos files

Tool to visualize the KKR shapefunctions

masci_tools.vis.kkr_plot_shapefun.change_zoom(ax, zoom_range, center=None)[source]¶

Change the zoom of a 3d plot

Author

Philipp Ruessmann

Parameters

ax – axis which is zoomed
zoom_range (float) – range to which the image is zoomed, total range from center-zoom_range to center+zoom_range
center (Optional[list]) – center of the zoomed region (optional, defaults to origin)

Return type

None

masci_tools.vis.kkr_plot_shapefun.plot_shapefun(pos, out, mode)[source]¶

Creates a simple matplotlib image to show the shapefunctions given it’s positions in the unit cell, the atoms’s vertices in ut and the plotting mode

Author

Philipp Ruessmann

Parameters

pos – positions of the centers of the cells
verts – array of vertices of the shapefunction (outlines of shapes)
mode – ‘all’ or ‘single’ determines whether or not all shapes are combined in a single figure or plotted as individual figures

Returns ax

return the axis in which the plot was done (useful to pass to ‘change_zoom’ and ‘zoom_in’ functions of this module

masci_tools.vis.kkr_plot_shapefun.zoom_in(ax, atm, pos, zoom_range=10)[source]¶

Zoom into shapefun of a single atom

Author

Philipp Ruessmann

Parameters

ax – axis in which shapefun plot is found
atm – atom index whose shapefunction is zoomed
pos – array of positions of centers of the shapes (needed to shift center of zommed region to correct atom
zoom_range – range of the zoomed region (optional, defaults to 10)

General Plotting¶

Here basic functionality is provided for setting default parameters for plotting and ensuring consistent values for these

masci_tools.vis.parameters.F¶

Generic Callable type

alias of TypeVar(‘F’, bound=Callable[[…], Any])

masci_tools.vis.parameters.NestedPlotParameters(plotter_object)[source]¶

Contextmanager for nested plot function calls Will reset function defaults and parameters to previous values after exiting

Parameters: plotter_object (Plotter) – Plotter instance
Return type: Generator[None, None, None]

class masci_tools.vis.parameters.Plotter(default_parameters, general_keys=None, key_descriptions=None, type_kwargs_mapping=None, kwargs_postprocess_rename=None, **kwargs)[source]¶

Base class for handling parameters for plotting methods. For different plotting backends a subclass can be created to represent the specific parameters of the backend.

Parameters

default_parameters (dict[str, Any]) – dict with hardcoded default parameters
general_keys (Optional[set[str]]) – set of str optional, defines parameters which are not allowed to change for each entry in the plot data

Kwargs in the __init__ method are forwarded to Plotter.set_defaults() to change the current defaults away from the hardcoded parameters.

The Plotter class creates a hierarchy of dictionaries for lookups on this object utilizing the ChainMap from the collections module.

The hierarchy is as follows (First entries take precedence over later entries):

parameters: set by set_parameters() (usually arguments passed into function)
user defaults: set by set_defaults()
function defaults: set by set_defaults() with default_type=’function’
global defaults: Hardcoded as fallback

Only the parameters can represent parameters for multiple sets of plot calls. All others are used as fallback for specifying non-specified values for single plots

The current parameters can be accessed by bracket indexing the class. A example of this is shown below.

parameter_dict = {'fontsize': 16, 'linestyle': '-'}

params = Plotter(parameter_dict)

#Accessing a parameter
print(params['fontsize']) # 16

#Modifying a parameter
params['fontsize'] = 20
print(params['fontsize']) # 20

#Creating a parameter set for multiple plots

#1. Set the properties to the correct values
params.single_plot = False
params.num_plots = 3

#2. Now we can set a property either by providing a list or a integer indexed dict
#   Both of the following examples set the linestyle of the second and third plot to '--'
params['linestyle'] = [None, '--', '--']
params['linestyle'] = {1: '--', 2: '--'}

# Not specified values are replaced with the default value for a single plot
print(params['linestyle']) # ['-', '--', '--']

#In lists properties can also be indexed via tuples
print(params[('linestyle', 0)]) # '-'
print(params[('linestyle', 1)]) # '--'

#Changes to the parameters and properties are reset
params.reset_parameters()

print(params['linestyle']) # '-'

add_parameter(name, default_from=None, default_val=None)[source]¶

Add a new parameter to the parameters dictionary.

Parameters

name (str) – str name of the parameter
default_from (Optional[str]) – str (optional), if given a entry is created in the current defaults with the name and the default value of the key default_from

Return type

None

static convert_to_complete_list(given_value, single_plot, num_plots, default=None, key='')[source]¶

Converts given value to list with length num_plots with None for the non-specified values

Parameters

given_value (Any) – value passed in, for multiple plots either list or dict with integer keys
single_plot (bool) – bool, if True only a single parameter is allowed
num_plots (int) – int, if single_plot is False this defines the number of plots
default (Optional[Any]) – default value for unspecified entries
key (str) – str of the key to process

Return type

Any

static dict_of_lists_to_list_of_dicts(dict_of_lists, single_plot, num_plots, repeat_after=None, ignore_repeat=None)[source]¶

Converts dict of lists and single values to list of length num_plots or single dict for single_plot=True

Parameters

dict_of_lists (dict[str, list[Any]]) – dict to be converted
single_plot (bool) – boolean, if True only a single parameter set is allowed
num_plots (int) – int of the number of allowed plots

Return type

list[dict[str, Any]]

Returns

list of dicts

expand_parameters(original_length, **kwargs)[source]¶

Expand parameters to a bigger number of plots. New length has to be a multiple of original length. Only lists of length <= orginal_length are expanded. Also expands function defaults

Parameters

orginal_length – int of the old length
kwargs (Any) – arguments to expand

Return type

dict[str, Any]

Returns

expanded kwargs

get_description(key)[source]¶

Get the description of the given key

Parameters: key (str) – str of the key, for which the description should be printed
Return type: None

get_dict()[source]¶

Return the dictionary of the current defaults. For use of printing

Return type: dict[str, Any]

get_multiple_kwargs(keys, ignore=None)[source]¶

Get multiple parameters and return them in a dictionary

Parameters

keys (set[str]) – set of keys to process
ignore (Union[str, list[str], None]) – str or list of str (optional), defines keys to ignore in the creation of the dict

Return type

dict[str, Any]

is_general(key)[source]¶

Return, whether the key is general (meaning only related to the whole plots)

Parameters: key (str) – str of the key to check
Return type: bool
Returns: bool, whether the key is general

load_defaults(filename='plot_defaults.json')[source]¶

Load defaults from a json file.

Parameters: filename (Union[str, bytes, Path, PathLike, IO[Any]]) – filename,from where the defaults should be taken
Return type: None

property num_plots: int¶: Integer property for number of plots produced

plot_kwargs(plot_type='default', ignore=None, extra_keys=None, post_process=True, list_of_dicts=True, **kwargs)[source]¶

Creates a dict or list of dicts (for multiple plots) with the defined parameters for the plotting calls of different types

Parameters

plot_type (str) – type of plot
ignore (Union[str, list[str], None]) – str or list of str (optional), defines keys to ignore in the creation of the dict
extra_keys (Optional[set[str]]) – optional set for additional keys to retrieve
post_process (bool) – bool, if True the parameters are cleaned up for inserting them directly into bokeh plotting functions

Return type

Any

Kwargs are used to replace values by custom parameters:

Example for using a custom markersize:

p = Plotter(type_kwargs_mapping={'default': {'marker'}})
p.add_parameter('marker_custom', default_from='marker')
p.plot_kwargs(marker='marker_custom')

This code snippet will return the standard parameters for a plot, but the value for the marker will be taken from the key marker_custom

remove_added_parameters()[source]¶

Remove the parameters added via Plotter.add_parameter()

Return type: None

reset_defaults()[source]¶

Resets the defaults to the hardcoded defaults in _PLOT_DEFAULTS.

Return type: None

reset_parameters()[source]¶

Reset the parameters to the current defaults. The properties single_plot and num_plots are also set to default values

Return type: None

save_defaults(filename='plot_defaults.json', save_complete=False)[source]¶

Save the current defaults to a json file.

Parameters

filename (Union[str, bytes, Path, PathLike, IO[Any]]) – filename, where the defaults should be stored
save_complete (bool) – bool if True not only the overwritten user defaults but also the unmodified hardcoded defaults are stored

Return type

None

set_defaults(continue_on_error=False, default_type='global', **kwargs)[source]¶

Set the current defaults. This method will only work if the parameters are not changed from the defaults. Otherwise a error is raised. This is because after changing the defaults the changes will be propagated to the parameters to ensure consistency.

Parameters: continue_on_error (bool) – bool, if True unknown key are simply skipped
Default_type: either ‘global’ or ‘function’. Specifies, whether to set the global defaults (not reset after function) or the function defaults
Return type: dict[str, Any]

Kwargs are used to set the defaults.

set_parameters(continue_on_error=False, **kwargs)[source]¶

Set the current parameters.

Parameters: continue_on_error (bool) – bool, if True unknown key are simply skipped and returned
Return type: dict[str, Any]

Kwargs are used to set the defaults.

set_single_default(key, value, default_type='global')[source]¶

Set default value for a single key/value pair

Parameters

key (str) – str of the key to set
value (Any) – value to set the key to

Default_type

either ‘global’ or ‘function’. Specifies, whether to set the global defaults (not reset after function) or the function defaults

Return type

None

property single_plot: bool¶: Boolean property if True only a single Plot parameter set is allowed

masci_tools.vis.parameters.ensure_plotter_consistency(plotter_object)[source]¶

Decorator for plot functions to ensure that the Parameters are reset even if an error occurs in the function Additionally checks are performed that the parameters are reset after execution and the defaults are never changed in a plot function

Parameters: plotter_object (Plotter) – Plotter instance to be checked for consistency
Return type: Callable[[TypeVar(F, bound= Callable[..., Any])], TypeVar(F, bound= Callable[..., Any])]

This module contains classes and functions to make plotting functions more flexible with respect to the used data. This way plotting functions can both allow the flexible usage of lists, arrays directly or dataframes together with the keys that should be used

class masci_tools.vis.data.ColumnDataSourceWrapper(wrapped)[source]¶

Wrapper around bokeh.models.ColumnDataSource to give it a __getitem__ and __setitem__ method

Used in the PlotDataIterator for easier handling of these types

class masci_tools.vis.data.PlotData(data, use_column_source=False, same_length=False, strict_data_keys=False, copy_data=False, **kwargs)[source]¶

Class for iterating over the data in a dict or dataframe with automatic filling in of single defined keys to get a list of keys to extract.

The iteration allows for implicit definition of data for multiple plot sets, without excessive copying of the given data

Usage Example

from masci_tools.vis.data import PlotData
import numpy as np

#Let's say we have one energy grid and a couple of functions
#defined on this energy grid.
#We collect these in a dict

x = np.linspace(-10,10,100)
data = {'x': x, 'y1': np.sin(x), 'y2':np.cos(x), 'y3', x**2}

p = PlotData(data, x='x', y=['y1', 'y2', 'y3'])

#If we now iterate over this object it will result in the data
#for y being returned together with the x data (The same would work the other way around)
for entry in p:
   print(entry.x) #'x' entry
   print(entry.y) #'y1' then 'y2' and finally 'y3'

#Additionally data for z, color and size can be defined

Parameters: data – object or list of objects which can be bracket indexed with the given keys e.g. dicts, pandas dataframes, …
Same_length: bool if True and any sources are dicts it will be checked for same dimensions in (ALL) entries (not only for keys plotted against each other)
Strict_data_keys: bool if True no new data keys are allowed to be entered via copy_data()

Kwargs are used to specify the columns in a namedtuple If a list is given for any of the keys the data will be expanded to a list of namedtuple with the same length

add_data_key(data_key, keys=None)[source]¶

Add a new column of data keys

Parameters

data_key – string of the new data key to add
keys – None, Index into data or list of index into the data to initialize the values to

apply(data_key, lambda_func, apply_to_whole_array=True, **kwargs)[source]¶

Apply a function to a given data column for all entries

Warning

This operation is done in-place. Meaning if there are multiple data entries pointing to the same data set and only one should be modified by this method, the data needs to be copied beforehand using copy_data()

Parameters

data_key – name of the data key to apply the function
lambda_func – function to apply to the data

copy_data(data_key_from, data_key_to, prefix=None, rename_original=False, force=False)[source]¶

Copy the data for a given data key to another one

Parameters

data_key_from – data key to copy from
data_key_to – data key to copy to
prefix – optional prefix to use for the renamed data entries. Can be used to avoid name clashes. If not given the data keys are used
rename_original – optional bool (default False). If True the original entries are renamed instead of the ones under data_key_to

property data_keys¶: Return the registered data keys for this instance

distinct_datasets(data_key)[source]¶

Return how many different data sets are present for the given data key

Parameters: data_key – The data key to analyse
Returns: int of the number of different datasets

get_function_result(data_key, func, list_return=False, as_numpy_array=False, **kwargs)[source]¶

Apply a function to a given data column for all entries and return the results

Parameters

data_key – name of the data key to apply the function to
func – function to apply to the data to get the results if func is a string then it will be used to get the attribute with the corresponding name from the source and call it

get_keys(data_key)[source]¶

Get the keys for a given data column for all entries

Parameters: data_key – name of the data key to return the keys
Returns: list of keys, corresponding to the entries for the given data in the sources

get_mask(mask, data_key=None)[source]¶

Get mask list for use with the Data in this instance

Parameters

mask – either list of callable, if it is callable it is used in get_function_result() together with the data_key argument
data_key – str to be used for the data key if mask is a callable

:param

get_values(data_key)[source]¶

Get the values for a given data column for all entries

Parameters: data_key – name of the data key to return the values
Returns: list of values, corresponding to the entries for the given data in the sources

group_data(by, **kwargs)[source]¶

Group the data by the given data_key(s) or other arguments for groupby

Note

This function will convert the data arguments to pd.Dataframe objects

Parameters: by – str or list of str of the data_keys to sort by or other valid arguments for by in pd.Dataframe.groupby()

Kwargs are passed on to pd.Dataframe.groupby()

items(first=False, mappable=False)[source]¶

Iterate over PlotData items. Returns the key and corresponding source for the data

Parameters

first – bool, if True only the first entry is returned
mappable – bool, if True only the data ColumnDataSources are wrapped to be mappable

keys(first=False)[source]¶

Iterate over PlotData keys. Returns the keys for the corresponding sources

Parameters: first – bool, if True only the first entry is returned

mask_data(mask, data_key=None, replace_value=None)[source]¶

Apply a given mask to the data inplace.

Note

This function will convert the data arguments to pd.Dataframe objects

Parameters

mask – mask rgument passed to get_mask()
data_key – data_key argument used by get_mask()

max(data_key, separate=False, mask=None, mask_data_key=None)[source]¶

Get the maximum value for a given data column for all entries

Parameters

data_key – name of the data key to determine the maximum
separate – bool if True the maximum will be determined and returned for all entries separately
mask – optional mask to select specific rows from the data entries
mask_data_key – optional data key to be used when mask is a function

Returns

maximum value for all entries either combined or as a list

min(data_key, separate=False, mask=None, mask_data_key=None)[source]¶

Get the minimum value for a given data column for all entries

Parameters

data_key – name of the data key to determine the minimum
separate – bool if True the minimum will be determined and returned for all entries separately
mask – optional mask to select specific rows from the data entries
mask_data_key – optional data key to be used when mask is a function

Returns

minimum value for all entries either combined or as a list

shift_data(data_key, shifts, shifted_data_key=None, separate_data=True, negative=False)[source]¶

Apply shifts to a given data column for all entries

Parameters

data_key – name of the data key to shift
shifts – float or array of floats with the shifts to apply
shifted_data_key – optional string, if given the data will be copied to this data key
separate_data – bool, if True and shifted_data_key is not given the data will be copied to itself (This separates the data for all columns)
negative – bool if True the shifts are applied with a minus sign

sort_data(by_data_keys, **kwargs)[source]¶

Sort the data by the given data_key(s)

Note

This function will convert the data arguments to pd.Dataframe objects

Note

If there are multiple plot sets and only one data source. This function will expand the data to be one data source sorted according to the data_keys for each plot

Parameters: by_data_keys – str or list of str of the data_keys to sort by

Kwargs are passed on to pd.Dataframe.sort_values()

values(first=False)[source]¶

Iterate over PlotData values. Returns the values for the data

Parameters: first – bool, if True only the first entry is returned

class masci_tools.vis.data.PlotDataIterator(plot_data, mode='values', mappable=False)[source]¶

Class containing the iteration behaviour over the PlotData class. Can be used in three modes:

keys: Returns the keys to be entered in the corresponding data sources for each entry

values: Returns the data for each entry

items: Returns the keys and the data sources in a tuple

The keys and values are always returned in a namedtuple with fields corresponding to the set data keys

masci_tools.vis.data.normalize_list_or_array(data, key, out_data, flatten_np=False, forbid_split_up=False)[source]¶

Split up a given list/numpy array or pd.Series to be used in the plotting methods

Parameters

data – The (array-like) data to be normalized
key – key under which to enter the new data
out_data – dict containing previously normalized data
flatten_np – bool, if True multidimensional numpy arrays are flattened
forbid_split_up – bool, if True multidimensional arrays are not split up

The rules are the following:

if data is a multidimensional array (list of lists, etc.) and it is not forbidden by the given argument the first dimension of the array is iterated over and interpreted as separate entries (if the data was previously split up into multiple sets a length check is performed)
if data is a one-dimensional array and of a different length than the number of defined data sets it is added to all previously existing entries
if data is a one-dimensional array and of the same length as the number of defined data sets each entry is added to the corresponding data set

Returns: list of dicts or dict containing the nomralized data

masci_tools.vis.data.process_data_arguments(data=None, single_plot=False, use_column_source=False, flatten_np=False, forbid_split_up=None, same_length=False, copy_data=False, **kwargs)[source]¶

Initialize PlotData from np.arrays or lists of np.arrays or lists or a already given data argument, i.e. mapping

Parameters

data – either None or Mapping to be used as the data in the PlotData class
single_plot – bool, if True only a single dataset is allowed
use_column_source – bool, if True all data arguments are converted to ColumnDataSource of bokeh
flatten_np – bool, if True multidimensional numpy arrays are flattened (Only if data not given)
forbid_split_up – set of keys for which not to split up multidimensional arrays
same_length – bool if True and any sources are dicts it will be checked for same dimensions in (ALL) entries (not only for keys plotted against each other)
copy_data – bool, if True the data argument will be copied

Kwargs define which keys belong to which data entries if data is given or they contain the data to be normalized

The following two example calls will both create a PlotData object with the same two plot data sets with the entries x and y:

import numpy as np

x = np.linspace(-10,10,100)
y1 = y**2
y2 = np.sin(x)

#Use a predefined data argument (a dict in this case) and the keys in the kwargs
p = process_data_arguments({'x': x, 'y1': y1, 'y2': y2}, x='x', y=['y1','y2'])

#Let the function normalize the given arrays
p = process_data_arguments=(x=x,y=[y1, y2])

Returns: A PlotData object corresponding to the given data

Collection of routines to be reused in plotting routines

masci_tools.vis.helpers.exclude_points(plot_data, *data_keys, limits, padding=0.1)[source]¶

Exclude points outside the given limits

Parameters

plot_data (PlotData) – PlotData instance containing all the data for plots
data_keys (str) – str of the keys to consider for excluding points
limits (Optional[dict[str, tuple[float, float]]]) – dict of the set plot limits
padding (float) – float, determines how far beyond the plot limits a point has to lie to be excluded (default 10%)

Return type

None

masci_tools.vis.helpers.get_special_kpoint_ticks(kpoints, math_mode='$')[source]¶

Process the high symmetry kpoints and ggf. replace with appropiate latex symbol

Gamma/G is replaced with $Gamma$

Parameters

kpoints (list[tuple[str, float]]) – list of tuples with label and position of the points
math_mode (str) – Determines the symbol to enter math mode in latex

Return type

tuple[list[float], list[str]]

Returns

Ticks and their respective labels

masci_tools.vis.helpers.mpl_single_line_or_area(axis, entry, source, area=False, area_vertical=False, area_enclosing_line=True, advance_color_cycle=False, area_line_alpha=1.0, **kwargs)[source]¶

Create a scatterplot, lineplot or area plot for the given entry on the matplotlib axis

Parameters

axis – Axes to plot on
entry – namedtuple of the entries to plot
source – mapping containing the data to plot
area – bool, if True fill_betweenx/y will be used to create an area plot
area_vertical – bool, if True fill_betweeny will be used
area_enclosing_line – bool if True the area plot will have another line plot around the edge
advance_color_cycle – bool, if True the matplotlib color cycle will be advanced no matter what else is specified
area_line_alpha – if an area plot is done this is the alpha parameter (transparency)

Kwargs are passed to the respective plotting routines

This modules provides common plotting functions dispatching to different plotting backends. At the moment the following backends are used:

matplotlib (‘mpl’, ‘matplotlib’)
bokeh (‘bokeh’)

The underlying plotting routines collected here should have the same signature for the data arguments; keyword arguments can be different.

class masci_tools.vis.common.PlotBackend(value)[source]¶

Enumeration containing the possible names for each plotting backend Initialize using the from_str() method

At the moment the following are supported (case-insensitive)

matplotlib: either ‘mpl’ or ‘matplotlib’
bokeh: ‘bokeh’

static default()[source]¶: Return a PlotBackend instance corresponding to the current default backend

static from_str(label)[source]¶

Initialize the PlotBackend from a given string

Parameters: label – str to use to initialize the backend if it is None the default is returned
Returns: PlotBackend instance corresponding to the label

masci_tools.vis.common.bands(kpath, eigenvalues, backend=None, data=None, **kwargs)[source]¶

Plot the provided data for a bandstructure (non spin-polarized) Non-weighted, weighted, as a line plot or scatter plot, color-mapped or fixed colors are all possible options

Parameters

kpath – data for the kpoints path (flattened to 1D)
eigenvalues – data for the eigenvalues
data – source for the data of the plot (optional) (pandas Dataframe for example)
backend – name of the backend to use (uses a default if None is given)

Kwargs are passed on to the backend plotting functions:

matplotlib: plot_bands()

bokeh: bokeh_bands()

Returns: Figure object for the used plotting backend

masci_tools.vis.common.dos(energy_grid, dos_data, backend=None, data=None, **kwargs)[source]¶

Plot the provided data as a density of states (not spin-polarized). Can be done horizontally or vertical via the switch xyswitch

Parameters

energy_grid – data for the energy grid of the DOS
dos_data – data for all the DOS components to plot
data – source for the data of the plot (optional) (pandas Dataframe for example)
backend – name of the backend to use (uses a default if None is given)

Kwargs are passed on to the backend plotting functions:

matplotlib: plot_dos()

bokeh: bokeh_dos()

Returns: Figure object for the used plotting backend

masci_tools.vis.common.get_help(key, backend=None)[source]¶

Get a help string for a given parameter.

Parameters

key – name of the parameter to get the parameter for
backend – For which backend to get the description of the parameter

masci_tools.vis.common.get_plotter(backend=None)[source]¶

Get the instance of the Plotter subclass used for the given plotting backend

Parameters: backend – For which backend to get the Plotter instance

masci_tools.vis.common.line(xdata, ydata, backend=None, data=None, **kwargs)[source]¶

Plot the provided data as a line plot. Multiple data sets are possible

Parameters

xdata – data for the x-axis
xdata – data for the y-axis
data – source for the data of the plot (optional) (pandas Dataframe for example)
backend – name of the backend to use (uses a default if None is given)

Kwargs are passed on to the backend plotting functions:

matplotlib: multiple_scatterplots()

bokeh: bokeh_line()

Returns: Figure object for the used plotting backend

masci_tools.vis.common.load_defaults(backend=None, filename='plot_defaults.json')[source]¶

Load defaults for the plot parameters from a file and set the contained defaults.

Parameters

backend – For which backend to save the parameters
filename – str of the filename to load the defaults from

masci_tools.vis.common.reset_defaults(backend=None)[source]¶

Reset the defaults for theplot parameters to the original state.

Parameters: backend – For which backend to reset the parameters

masci_tools.vis.common.save_defaults(backend=None, filename='plot_defaults.json', save_complete=False)[source]¶

Save the defaults for the plot parameters.

Parameters

backend – For which backend to save the parameters
filename – str of the filename to save the defaults to
save_complete – bool, if True also the hardcoded defaults are included

masci_tools.vis.common.scatter(xdata, ydata, backend=None, data=None, **kwargs)[source]¶

Plot the provided data as a scatter plot. Varying size and color are possible. Multiple data sets are possible

Parameters

xdata – data for the x-axis
xdata – data for the y-axis
data – source for the data of the plot (optional) (pandas Dataframe for example)
backend – name of the backend to use (uses a default if None is given)

Kwargs are passed on to the backend plotting functions:

matplotlib: multi_scatter_plot()

bokeh: bokeh_multi_scatter()

Returns: Figure object for the used plotting backend

masci_tools.vis.common.set_default_backend(backend)[source]¶

Sets the default backend used when no explicit backend is specified.

Parameters: backend – Name of the backend to use

masci_tools.vis.common.set_defaults(backend=None, **kwargs)[source]¶

Sets defaults for the plot parameters.

Parameters: backend – For which backend to set the parameters

The Kwargs are used to set the parameters of the specified backend

masci_tools.vis.common.show_defaults(backend=None)[source]¶

Show the current set defaults for the plot parameters.

Parameters: backend – For which backend to show the parameters

masci_tools.vis.common.spinpol_bands(kpath, eigenvalues_up, eigenvalues_dn, backend=None, data=None, **kwargs)[source]¶

Plot the provided data for a bandstructure (spin-polarized) Non-weighted, weighted, as a line plot or scatter plot, color-mapped or fixed colors are all possible options

Parameters

kpath – data for the kpoints path (flattened to 1D)
eigenvalues_up – data for the eigenvalues for spin-up
eigenvalues_dn – data for the eigenvalues for spin-down
data – source for the data of the plot (optional) (pandas Dataframe for example)
backend – name of the backend to use (uses a default if None is given)

Kwargs are passed on to the backend plotting functions:

matplotlib: plot_spinpol_bands()

bokeh: bokeh_spinpol_bands()

Returns: Figure object for the used plotting backend

masci_tools.vis.common.spinpol_dos(energy_grid, dos_data_up, dos_data_dn, backend=None, data=None, **kwargs)[source]¶

Plot the provided data as a density of states (spin-polarized). Can be done horizontally or vertical via the switch xyswitch

Parameters

energy_grid – data for the energy grid of the DOS
dos_data_up – data for all the DOS components to plot for spin-up
dos_data_dn – data for all the DOS components to plot for spin-down
data – source for the data of the plot (optional) (pandas Dataframe for example)
backend – name of the backend to use (uses a default if None is given)

Kwargs are passed on to the backend plotting functions:

matplotlib: plot_spinpol_dos()

bokeh: bokeh_spinpol_dos()

Returns: Figure object for the used plotting backend

Matplotlib¶

This module contains a subclass of Plotter for the matplotlib library

class masci_tools.vis.matplotlib_plotter.MatplotlibPlotter(**kwargs)[source]¶

Class for plotting parameters and standard code snippets for plotting with the matplotlib backend.

Kwargs in the __init__ method are forwarded to setting default values for the instance

For specific documentation about the parameter/defaults handling refer to Plotter.

Below the current defined default values are shown:

Plot Parameters¶
Name	Description	Default value
`title_fontsize`	Fontsize for the title of the figure	`16`
`figure_kwargs`	Arguments passed to plt.figure when creating the figure. Includes things like figsize, dpi, background color, …	{'figsize': (8, 6), 'dpi': 100, 'facecolor': 'w', 'edgecolor': 'k', 'constrained_layout': True}
`alpha`	Float specifying the transparency of the title	`1`
`axis_linewidth`	Linewidth of the lines for the axis	`1.5`
`use_axis_formatter`	If True the labels will always not be formatted with an additive constant at the top	`False`
`set_powerlimits`	If True the threshold for switching to scientific notation is adjusted to 0,3	`True`
`xticks`	Positions of the ticks on the x axis	No Default
`xticklabels`	Labels for the ticks on the x-axis	No Default
`yticks`	Positions for the ticks on the y-axis	No Default
`yticklabels`	Labels for the ticks on the y-axis	No Default
`invert_xaxis`	If True the direction of the x-axis is inverted	`False`
`invert_yaxis`	If True the direction of the y-axis is inverted	`False`
`color_cycle`	If set this will override the default color cycle of matplotlib. Can be given as name of a colormap cycle or list of colors	No Default
`color_cycle_always_advance`	Always advance the color cycle even if the color was specified	`False`
`sub_colormap`	If a colormap is used this can be used to cut out a part of the colormap. For example (0.5,1.0) will only use the upper half of the colormap	No Default
`linewidth`	Linewidth for the plot(s)	`2.0`
`linestyle`	Linestyle for the plot(s)	`-`
`marker`	Shape of the marker to use for the plot(s)	`o`
`markersize`	Size of the markers to use in the plot(s)	`4.0`
`color`	Color to use in the plot(s)	No Default
`zorder`	z-position to use for the plot(s) (Is used to define fore- and background)	No Default
`repeat_parameters`	If set as integer the parameters for single plots (except labels) will be repeated after the given number of plots. Only implemented for multiple_scatterplots	No Default
`edgecolor`	Edgecolor to use in the plot(s)	No Default
`facecolor`	Facecolor to use in the plot(s)	No Default
`plot_label`	Label to use in the plot(s) for the legend	No Default
`area_plot`	If True fill_between(x) will be used to produce the plot(s)	`False`
`area_vertical`	Determines, whether to use fill_between or fill_betweenx for area plots	`False`
`area_enclosing_line`	If True a enclosing line will be drawn around the area	`True`
`area_alpha`	Transparency to use for the area in the area plot(s)	`1.0`
`area_linecolor`	Color for the enclosing line in the area plot(s)	No Default
`plot_alpha`	Transparency to use for the plot(s)	`1.0`
`cmap`	Colormap to use for scatter/pcolormesh or 3D plots	`viridis`
`norm`	If set this norm will be used to normalize data for the colormapping	No Default
`shading`	Shading to use for pcolormesh plots	`gouraud`
`rasterized`	Rasterize the pcolormesh when drawing vector graphics.	`True`
`scale`	Dict specifying the scales of the axis, e.g `{'y': 'log'}` will create a logarithmic scale on the y-axis	No Default
`limits`	Dict specifying the limits of the axis, e.g `{'x': (-5,5)}`	No Default
`labelfontsize`	Fontsize for the labels on the axis	`15`
`lines`	Dict specifying straight help-lines to draw. For example `{'vertical': 0, 'horizontal': [-1,1]}` will draw a vertical line at 0 and two horizontal at -1 and 1	No Default
`line_options`	Color, width, and more options for the help-lines	{'linestyle': '--', 'color': 'k', 'linewidth': 1.0}
`font_options`	Default font options that can be used for text annotations	{'family': 'serif', 'color': 'black', 'weight': 'normal', 'size': 16}
`tick_paramsx`	Parameters for major ticks on the x-axis (Size, fontsize, …)	{'size': 4.0, 'width': 1.0, 'labelsize': 14, 'length': 5, 'labelrotation': 0}
`tick_paramsy`	Parameters for major ticks on the y-axis (Size, fontsize, …)	{'size': 4.0, 'width': 1.0, 'labelsize': 14, 'length': 5, 'labelrotation': 0}
`tick_paramsx_minor`	Parameters for minor ticks on the x-axis (Size, fontsize, …)	{'size': 2.0, 'width': 1.0, 'labelsize': 0, 'length': 2.5}
`tick_paramsy_minor`	Parameters for minor ticks on the y-axis (Size, fontsize, …)	{'size': 2.0, 'width': 1.0, 'labelsize': 0, 'length': 2.5}
`colorbar`	If True and the function implements color mapping, a colorbar is shown	`True`
`colorbar_options`	Parameters for displaying the colorbar (Fontsize, …)	{'pad': 0.05}
`legend`	If True a legend for the plot is shown	`False`
`legend_show_data_labels`	If True the column names from the data argument are shown if not overwritten	`False`
`legend_remove_duplicates`	If True duplicate legend labels are removed	`False`
`legend_options`	Parameters for displaying the legend (Fontsize, location, …)	{'fontsize': 'large', 'linewidth': 3.0, 'loc': 'best', 'fancybox': True}
`save_plots`	if True the plots will be saved to file	`False`
`save_format`	Formats to save the plots to, can be single or list of formats	`png`
`save_options`	Additional options for saving the plots to file	{'transparent': True}
`tightlayout`	If True the tight layout will be used (NOT IMPLEMENTED)	`False`
`show`	If True plt.show will be called at the end of the routine	`True`
`save_raw_plot_data`	If True the data for the plot is saved to file (NOT IMPLEMENTED)	`False`
`raw_plot_data_format`	Format in which to save the data for the plot (NOT IMPLEMENTED)	`txt`

draw_lines(ax)[source]¶

Draw horizontal and vertical lines specified in the lines argument

Parameters: ax – Axes object on which to perform the operation

plot_kwargs(plot_type='default', ignore=None, extra_keys=None, post_process=True, list_of_dicts=True, **kwargs)[source]¶

Creates a dict or list of dicts (for multiple plots) with the defined parameters for the plotting calls of matplotlib

Parameters

ignore – str or list of str (optional), defines keys to ignore in the creation of the dict
extra_keys – optional set for additional keys to retrieve
post_process – bool, if True the parameters are cleaned up for inserting them directly into matplotlib plitting functions

Kwargs are used to replace values by custom parameters:

Example for using a custom markersize:

p = MatplotlibPlotter()
p.add_parameter('marker_custom', default_from='marker')
p.plot_kwargs(marker='marker_custom')

This code snippet will return the standard parameters for a plot, but the value for the marker will be taken from the key marker_custom

prepare_plot(title=None, xlabel=None, ylabel=None, zlabel=None, axis=None, minor=False, projection=None)[source]¶

Prepares the figure of a matplotlib plot, setting the labels/titles, ticks, …

Parameters

title – str for the title of the figure
xlabel – str for the label on the x-axis
ylabel – str for the label on the y-axis
zlabel – str for the label on the z-axis
axis – matplotlib axes object, optional, if given the operations are performed on the object otherwise a new figure and subplot are created
minor – bool, if True minor tick parameters are set
projection – str, passed on to the add_subplot call

Returns

the created or modified axis object

save_plot(saveas)[source]¶

Save the current figure or show the current figure

Parameters: saveas – str, filename for the resulting file

set_limits(ax)[source]¶

Set limits of the axis

Parameters: ax – Axes object on which to perform the operation

set_scale(ax)[source]¶

Set scale of the axis (for example ‘log’)

Parameters: ax – Axes object on which to perform the operation

show_colorbar(ax)[source]¶

Print a colorbar for the plot

Parameters: ax – Axes object on which to perform the operation

show_legend(ax, leg_elems=None)[source]¶

Print a legend for the plot

Parameters: ax – Axes object on which to perform the operation

static truncate_colormap(cmap, minval=0.0, maxval=1.0, n=256)[source]¶

Cut off parts of colormap

Parameters

cmap – cmap to truncate
minval – minimum value of new colormap
maxval – maximum value of new colormap
n – number of colors in new colormap

Returns

colormap truncated to only hold colors between minval and maxval from old colormap

In this module are plot routines collected to create default plots out of certain output nodes from certain workflows with matplot lib.

Comment: Do not use any aiida methods, otherwise the methods in here can become tricky to use inside a virtual environment. Make the user extract thing out of aiida objects before hand or write something on top. Since usually parameter nodes, or files are plotted, parse a dict or filepath.

Each of the plot_methods can take keyword arguments to modify parameters of the plots There are keywords that are handled by a special class for defaults. All other arguments will be passed on to the matplotlib plotting calls

For the definition of the defaults refer to MatplotlibPlotter

masci_tools.vis.plot_methods.CDF_voigt_profile(x, fwhm_g, fwhm_l, mu)[source]¶: Cumulative distribution function of a voigt profile implementation of formula found here: https://en.wikipedia.org/wiki/Voigt_profile # TODO: is there an other way then to calc 2F2? # or is there an other way to calc the integral of wofz directly, or use different error functions.

class masci_tools.vis.plot_methods.PDF(pdf, size=(200, 200))[source]¶: Display a PDF file inside a Jupyter notebook.

masci_tools.vis.plot_methods.asymmetric_lorentz(x, fwhm, mu, alpha=1.0, beta=1.5)[source]¶

asymmetric lorentz function

L^alpha for x<=mu L^beta for x>mu See casexps LA

masci_tools.vis.plot_methods.asymmetric_lorentz_gauss_conv(x, mu, fwhm_l, fwhm_g, alpha=1.0, beta=1.5)[source]¶: asymmetric Lorentzian with Gauss convoluted

masci_tools.vis.plot_methods.asymmetric_lorentz_gauss_sum(x, mu, fwhm_l, fwhm_g, alpha=1.0, beta=1.5)[source]¶: asymmetric Lorentzian with Gauss convoluted

masci_tools.vis.plot_methods.barchart(positions, heights, *, width=0.35, xlabel='x', ylabel='y', title='', bottom=None, alignment='vertical', saveas='barchart', bar_type='stacked', axis=None, xerr=None, yerr=None, data=None, copy_data=False, **kwargs)[source]¶

Create a standard bar chart plot (this should be flexible enough) to do all the basic bar chart plots.

Parameters

positions – arraylike data for the positions of the bars
heights – arraylike data for the heights of the bars
data – source for the data of the plot (optional) (pandas Dataframe for example)
width – float determines the width of the bars
axis – Axes object where to add the plot
title – str, Title of the plot
xlabel – str, label for the x-axis
ylabel – str, label for the y-axis
saveas – str, filename for the saved plot
xerr – optional data for errorbar in x-direction
yerr – optional data for errorbar in y-direction
bottom – bottom values for the lowest end of the bars
bar_type – type of the barchart plot. Either stacked, grouped or independent
alignment – which direction the bars should be plotted (horizontal or vertical)
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to masci_tools.vis.matplotlib_plotter.MatplotlibPlotter. If the arguments are not recognized they are passed on to the matplotlib function bar

TODO: grouped barchart (meaning not stacked)

masci_tools.vis.plot_methods.colormesh_plot(xdata, ydata, cdata, *, xlabel='', ylabel='', title='', data=None, saveas='colormesh', axis=None, copy_data=False, **kwargs)[source]¶

Create plot with pcolormesh

Parameters

xdata – arraylike, data for the x coordinate
ydata – arraylike, data for the y coordinate
cdata – arraylike, data for the color values with a colormap
data – source for the data of the plot (optional) (pandas Dataframe for example)
xlabel – str, label written on the x axis
ylabel – str, label written on the y axis
title – str, title of the figure
saveas – str specifying the filename (without file format)
axis – Axes object, if given the plot will be applied to this object
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to masci_tools.vis.matplotlib_plotter.MatplotlibPlotter. If the arguments are not recognized they are passed on to the matplotlib function pcolormesh

masci_tools.vis.plot_methods.construct_corelevel_spectrum(coreleveldict, natom_typesdict, exp_references=None, scale_to=-1, fwhm_g=0.6, fwhm_l=0.1, energy_range=None, xspec=None, energy_grid=0.2, peakfunction='voigt', alpha_l=1.0, beta_l=1.5)[source]¶

Constructrs a corelevel spectrum from a given corelevel dict

Params
Returns: list: [xdata_spec, ydata_spec, ydata_single_all, xdata_all, ydata_all, xdatalabel]

masci_tools.vis.plot_methods.default_histogram(*args, **kwargs)[source]¶: Create a standard looking histogram (DEPRECATED)

masci_tools.vis.plot_methods.doniach_sunjic(x, scale=1.0, E_0=0, gamma=1.0, alpha=0.0)[source]¶

Doniach Sunjic asymmetric peak function. tail to higher binding energies.

param x: list values to evaluate this function param scale: multiply the function with this factor param E_0: position of the peak param gamma, ‘lifetime’ broadening param alpha: ‘asymmetry’ parametera

See Doniach S. and Sunjic M., J. Phys. 4C31, 285 (1970) or http://www.casaxps.com/help_manual/line_shapes.htm

masci_tools.vis.plot_methods.gauss_one(x, fwhm, mu)[source]¶: Returns a Lorentzian line shape at x with FWHM fwhm and mean mu

masci_tools.vis.plot_methods.gaussian(x, fwhm, mu)[source]¶: Returns Gaussian line shape at x with FWHM fwhm and mean mu

masci_tools.vis.plot_methods.get_mpl_help(key)[source]¶

Print the description of the given key in the matplotlib backend

Available defaults can be seen in MatplotlibPlotter

masci_tools.vis.plot_methods.histogram(xdata, density=False, histtype='bar', align='mid', orientation='vertical', log=False, axis=None, title='hist', xlabel='bins', ylabel='counts', saveas='histogram', return_hist_output=False, data=None, copy_data=False, **kwargs)[source]¶

Create a standard looking histogram

Parameters

xdata – arraylike, Data for the histogram
data – source for the data of the plot (optional) (pandas Dataframe for example)
density – bool, if True the histogram is normed and a normal distribution is plotted with the same mu and sigma as the data
histtype – str, type of the histogram
align – str, defines where the bars for the bins are aligned
orientation – str, is the histogram vertical or horizontal
log – bool, if True a logarithmic scale is used for the counts
axis – Axes object where to add the plot
title – str, Title of the plot
xlabel – str, label for the x-axis
ylabel – str, label for the y-axis
saveas – str, filename for the saved plot
return_hist_output – bool, if True the data output from hist will be returned
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to masci_tools.vis.matplotlib_plotter.MatplotlibPlotter. If the arguments are not recognized they are passed on to the matplotlib function hist

masci_tools.vis.plot_methods.hyp2f2(a, b, z)[source]¶: Calculation of the 2F2() hypergeometric function, since it is not part of scipy with the identity 2. from here: https://en.wikipedia.org/wiki/Generalized_hypergeometric_function a, b,z array like inputs TODO: not clear to me how to do this… the identity is only useful if we mange the adjust the arguments in a way that we can use them… also maybe go for the special case we need first: 1,1,3/2;2;-z2

masci_tools.vis.plot_methods.load_mpl_defaults(filename='plot_mpl_defaults.json')[source]¶

Load defaults for the matplotlib backend from a json file.

Parameters: filename – filename,from where the defaults should be taken

masci_tools.vis.plot_methods.lorentzian(x, fwhm, mu)[source]¶: Returns a Lorentzian line shape at x with FWHM fwhm and mean mu

masci_tools.vis.plot_methods.lorentzian_one(x, fwhm, mu)[source]¶: Returns a Lorentzian line shape at x with FWHM fwhm and mean mu

masci_tools.vis.plot_methods.multi_scatter_plot(xdata, ydata, *, size_data=None, color_data=None, xlabel='', ylabel='', title='', data=None, saveas='mscatterplot', axis=None, copy_data=False, exclude_points_outside_plot_area=False, **kwargs)[source]¶

Create a scatter plot with varying marker size Info: x, y, size and color data must have the same dimensions.

Parameters

xdata – str or arraylike, data for the x coordinate
ydata – str or arraylike, data for the y coordinate
size_data – str or arraylike, data for the markersizes (optional)
color_data – str or arraylike, data for the color values with a colormap (optional)
data – source for the data of the plot (optional) (pandas Dataframe for example)
xlabel – str, label written on the x axis
ylabel – str, label written on the y axis
title – str, title of the figure
data – Mapping giving the data for the plots (required if data arguments are str)
saveas – str specifying the filename (without file format)
axis – Axes object, if given the plot will be applied to this object
xerr – optional data for errorbar in x-direction
yerr – optional data for errorbar in y-direction
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to masci_tools.vis.matplotlib_plotter.MatplotlibPlotter. If the arguments are not recognized they are passed on to the matplotlib function scatter

masci_tools.vis.plot_methods.multiaxis_scatterplot(xdata, ydata, *, axes_loc, xlabel='', ylabel='', title='', num_cols=1, num_rows=1, saveas='mscatterplot', **kwargs)[source]¶

Create a scatter plot with multiple axes.

Parameters

xdata – list of arraylikes, passed on to the plotting functions for each axis (x-axis)
ydata – list of arraylikes, passed on to the plotting functions for each axis (y-axis)
axes_loc – list of tuples of two integers, location of each axis
xlabel – str or list of str, labels for the x axis
ylabel – str or list of str, labels for the y-axis
title – str or list of str, titles for the subplots
num_rows – int, how many rows of axis are created
num_cols – int, how many columns of axis are created
saveas – str filename of the saved file

Special Kwargs:

param subplot_params: dict with integer keys, can contain all valid kwargs for multiple_scatterplots() with the integer key denoting to which subplot the changes are applied
param axes_kwargs: dict with integer keys, additional arguments to pass on to subplot2grid for the creation of each axis (e.g colspan, rowspan)

Other Kwargs will be passed on to all multiple_scatterplots() calls (If they are not overwritten by parameters in subplot_params).

masci_tools.vis.plot_methods.multiple_scatterplots(xdata, ydata, *, xlabel='', ylabel='', title='', data=None, saveas='mscatterplot', axis=None, xerr=None, yerr=None, area_curve=0, copy_data=False, exclude_points_outside_plot_area=False, **kwargs)[source]¶

Create a standard scatter plot with multiple sets of data (this should be flexible enough) to do all the basic plots.

Parameters

xdata – str or arraylike, data for the x coordinate
ydata – str or arraylike, data for the y coordinate
xlabel – str, label written on the x axis
ylabel – str, label written on the y axis
data – source for the data of the plot (optional) (pandas Dataframe for example)
title – str, title of the figure
data – Mapping giving the data for the plots (required if xdata and ydata are str)
saveas – str specifying the filename (without file format)
axis – Axes object, if given the plot will be applied to this object
xerr – optional data for errorbar in x-direction
yerr – optional data for errorbar in y-direction
area_curve – if an area plot is made this arguments defines the other enclosing line defaults to 0
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to masci_tools.vis.matplotlib_plotter.MatplotlibPlotter. If the arguments are not recognized they are passed on to the matplotlib functions (errorbar or fill_between)

masci_tools.vis.plot_methods.multiplot_moved(xdata, ydata, *, xlabel='', ylabel='', title='', data=None, scale_move=1.0, min_add=0, saveas='mscatterplot', copy_data=False, **kwargs)[source]¶

Plots all the scatter plots above each other. It adds an arbitrary offset to the ydata to do this and calls multiple_scatterplots. Therefore you might not want to show the yaxis ticks

Parameters

xdata – arraylike, data for the x coordinate
ydata – arraylike, data for the y coordinate
data – source for the data of the plot (optional) (pandas Dataframe for example)
xlabel – str, label written on the x axis
ylabel – str, label written on the y axis
title – str, title of the figure
scale_move – float, max*scale_move determines size of the shift
min_add – float, minimum shift
saveas – str specifying the filename (without file format)
copy_data – bool, if True the data argument will be copied

Kwargs are passed on to the multiple_scatterplots() call

masci_tools.vis.plot_methods.plot_bands(kpath, bands, *, data=None, size_data=None, color_data=None, special_kpoints=None, e_fermi=0, xlabel='', ylabel='$E-E_F$ [eV]', title='', saveas='bandstructure', markersize_min=0.5, markersize_scaling=5.0, scale_color=True, separate_bands=False, line_plot=False, band_index=None, copy_data=False, **kwargs)[source]¶

Plot the provided data for a bandstrucuture (non spin-polarized). Can be used to illustrate weights on bands via size_data

Parameters

kpath – arraylike data for the kpoint data
bands – arraylike data for the eigenvalues
size_data – arraylike data the weights to emphasize (optional)
color_data – str or arraylike, data for the color values with a colormap (optional)
data – source for the data of the plot (optional) (pandas Dataframe for example)
title – str, Title of the plot
xlabel – str, label for the x-axis
ylabel – str, label for the y-axis
saveas – str, filename for the saved plot
e_fermi – float (default 0), place the line for the fermi energy at this value
special_kpoints – list of tuples (str, float), place vertical lines at the given values and mark them on the x-axis with the given label
markersize_min – minimum value used in scaling points for weight
markersize_scaling – factor used in scaling points for weight
scale_color – bool, if True (default) the weight will be additionally shown via a colormapping
line_plot – bool, if True the bandstructure will be plotted with lines Here no weights are supported
separate_bands – bool, if True the bandstructure will be separately plotted for each band allows more specific parametrization
band_index – data for which eigenvalue belongs to which band (needed for line_plot and separate_bands)
copy_data – bool, if True the data argument will be copied

All other Kwargs are passed on to the multi_scatter_plot() call

masci_tools.vis.plot_methods.plot_colortable(colors, title, sort_colors=False, emptycols=0)[source]¶

Plot a legend of named colors.

Reference: https://matplotlib.org/3.1.0/gallery/color/named_colors.html

Parameters

colors (Dict) – a dict color_name : color_value (hex str, rgb tuple, …)
title (str) – plot title
sort_colors (bool) – True: sort legend entries not by dict position, but by color hue, staturation, value.
emptycols (int) –

Returns

figure

masci_tools.vis.plot_methods.plot_convergence(iteration, distance, total_energy, *, data=None, saveas_energy='energy_convergence', saveas_distance='distance_convergence', axis_energy=None, axis_distance=None, xlabel='Iteration', ylabel_energy='Total energy difference [Htr]', ylabel_distance='Distance [me/bohr^3]', title_energy='Total energy difference over scf-Iterations', title_distance='Convergence (log)', copy_data=False, drop_last_iteration=False, **kwargs)[source]¶

Plot the total energy differences versus the scf iteration and plot the distance of the density versus iterations.

Parameters

iteration – data for the number of iterations
distance – data of distances
total_energy – data of total energies
data – source for the data of the plot (optional) (pandas Dataframe for example)
xlabel – str, label for the x-axis of both plots
saveas_energy – str, filename for the energy convergence plot
axis_energy – Axes object for the energy convergence plot
title_energy – str, title for the energy convergence plot
ylabel_energy – str, label for the y-axis for the energy convergence plot
saveas_distance – str, filename for the distance plot
axis_distance – Axes object for the distance plot
title_distance – str, title for the distance plot
ylabel_distance – str, label for the y-axis for the distance plot
copy_data – bool if True the data argument is copied
drop_last_iteration – bool if True the last iteration is dropped for the distance plot

Other Kwargs will be passed on to all multiple_scatterplots() calls

masci_tools.vis.plot_methods.plot_convergence_results(iteration, distance, total_energy, *, saveas1='t_energy_convergence', axis1=None, saveas2='distance_convergence', axis2=None, **kwargs)[source]¶

DEPRECATED Plot the total energy versus the scf iteration and plot the distance of the density versus iterations.

Parameters

iteration – array for the number of iterations
distance – array of distances
total_energy – array of total energies
saveas1 – str, filename for the energy convergence plot
axis1 – Axes object for the energy convergence plot
saveas2 – str, filename for the distance plot
axis2 – Axes object for the distance plot

Other Kwargs will be passed on to all single_scatterplot() calls

masci_tools.vis.plot_methods.plot_convergence_results_m(iterations, distances, total_energies, *, modes, nodes=None, saveas1='t_energy_convergence', saveas2='distance_convergence', axis1=None, axis2=None, **kwargs)[source]¶

DEPRECATED Plot the total energy versus the scf iteration and plot the distance of the density versus iterations.

Parameters

iterations – array for the number of iterations
distances – array of distances
total_energies – array of total energies
modes – list of convergence modes (if ‘force’ is in the list the last distance is removed)
saveas1 – str, filename for the energy convergence plot
axis1 – Axes object for the energy convergence plot
saveas2 – str, filename for the distance plot
axis2 – Axes object for the distance plot

Other Kwargs will be passed on to all multiple_scatterplots() calls

masci_tools.vis.plot_methods.plot_convex_hull2d(hull, *, title='Convex Hull', xlabel='Atomic Percentage', ylabel='Formation energy / atom [eV]', saveas='convex_hull', axis=None, **kwargs)[source]¶

Plot method for a 2d convex hull diagram

Parameters

hull – pyhull.Convexhull #scipy.spatial.ConvexHull
axis – Axes object where to add the plot
title – str, Title of the plot
xlabel – str, label for the x-axis
ylabel – str, label for the y-axis
saveas – str, filename for the saved plot

Function specific parameters:

param marker_hull: defaults to marker, marker type for the hull plot
param markersize_hull: defaults to markersize, markersize for the hull plot
param color_hull: defaults to color, color for the hull plot

Kwargs will be passed on to masci_tools.vis.matplotlib_plotter.MatplotlibPlotter. If the arguments are not recognized they are passed on to the matplotlib functions plot

masci_tools.vis.plot_methods.plot_corelevel_spectra(coreleveldict, natom_typesdict, exp_references=None, scale_to=-1, show_single=True, show_ref=True, energy_range=None, title='', fwhm_g=0.6, fwhm_l=0.1, energy_grid=0.2, peakfunction='voigt', linestyle_spec='-', marker_spec='o', color_spec='k', color_single='g', xlabel='Binding energy [eV]', ylabel='Intensity [arb] (natoms*nelectrons)', saveas=None, xspec=None, alpha_l=1.0, beta_l=1.0, **kwargs)[source]¶

Plotting function of corelevel in the form of a spectrum.

Convention: Binding energies are positive!

Args:: coreleveldict: dict of corelevels with a list of corelevel energy of atomstypes # (The given corelevel accounts for a weight (number of electrons for full occupied corelevel) in the plot.) natom_typesdict: dict with number of atom types for each entry
Kwargs:: exp_references: dict with experimental references, will be ploted as vertical lines show_single (bool): plot all single peaks. scale_to float: the maximum ‘intensity’ will be scaled to this value (useful for experimental comparisons) title (string): something for labeling fwhm (float): full width half maximum of peaks (gauss, lorentz or voigt_profile) energy_grid (float): energy resolution linetyp_spec : linetype for spectrum peakfunction (string): what the peakfunction should be {‘voigt’, ‘pseudo-voigt’, ‘lorentz’, ‘gaus’}
example:: coreleveldict = {u’Be’: {‘1s1/2’ : [-1.0220669053033051, -0.3185614920138805,-0.7924091040092139]}} n_atom_types_Be12Ti = {‘Be’ : [4,4,4]}

masci_tools.vis.plot_methods.plot_corelevels(coreleveldict, compound='', axis=None, saveas='scatterplot', **kwargs)[source]¶: Plotting function to visualize corelevels and corelevel shifts

masci_tools.vis.plot_methods.plot_dos(energy_grid, dos_data, *, data=None, saveas='dos_plot', energy_label='$E-E_F$ [eV]', dos_label='DOS [1/eV]', title='Density of states', xyswitch=False, e_fermi=0, copy_data=False, **kwargs)[source]¶

Plot the provided data for a density of states (not spin-polarized). Can be done horizontally or vertical via the switch xyswitch

Parameters

energy_grid – arraylike data for the energy grid of the DOS
dos_data – arraylike data for all the DOS components to plot
data – source for the data of the plot (optional) (pandas Dataframe for example)
title – str, Title of the plot
energy_label – str, label for the energy-axis
dos_label – str, label for the DOS-axis
saveas – str, filename for the saved plot
e_fermi – float (default 0), place the line for the fermi energy at this value
xyswitch – bool if True, the enrgy axis will be plotted vertically
copy_data – bool, if True the data argument will be copied

All other Kwargs are passed on to the multiple_scatterplots() call

masci_tools.vis.plot_methods.plot_lattice_constant(scaling, total_energy, *, fit_data=None, data=None, relative=True, ref_const=None, title='Equation of states', saveas='lattice_constant', axis=None, copy_data=False, **kwargs)[source]¶

Plot a lattice constant versus Total energy Plot also the fit. On the x axis is the scaling, it

Parameters

scaling – arraylike, data for the scaling factor
total_energy – arraylike, data for the total energy
fit_data – arraylike, optional data of fitted data
relative – bool, scaling factor given (True), or lattice constants given?
ref_const – float (optional), or list of floats, lattice constant for scaling 1.0
data – source for the data of the plot (optional) (pandas Dataframe for example)
copy_data – bool if True the data argument will be copied

Function specific parameters:

param marker_fit: defaults to marker, marker type for the fit data
param markersize_fit: defaults to markersize, markersize for the fit data
param linewidth_fit: defaults to linewidth, linewidth for the fit data
param plotlabel_fit: str label for the fit data

Other Kwargs will be passed on to multiple_scatterplots()

masci_tools.vis.plot_methods.plot_one_element_corelv(corelevel_dict, element, compound='', axis=None, saveas='scatterplot', **kwargs)[source]¶

This routine creates a plot which visualizes all the binding energies of one element (and currently one corelevel) for different atomtypes.

example:: corelevels = {‘W’ : {‘4f7/2’ : [123, 123.3, 123.4 ,123.1], ‘4f5/2’ : [103, 103.3, 103.4, 103.1]}, ‘Be’ : {‘1s’: [118, 118.2, 118.4, 118.1, 118.3]}}

masci_tools.vis.plot_methods.plot_relaxation_results()[source]¶: Plot from the result node of a relaxation workflow, All forces of every atom type versus relaxation cycle. Average force of all atom types versus relaxation cycle. Absolute relaxation in Angstroem of every atom type. Relative realxation of every atom type to a reference structure. (if none given use the structure from first relaxation cycle as reference)

masci_tools.vis.plot_methods.plot_residuen(xdata, fitdata, realdata, *, errors=None, xlabel='Energy [eV]', ylabel='cts/s [arb]', title='Residuen', saveas='residuen', hist=True, return_residuen_data=True, **kwargs)[source]¶

Calculates and plots the residuen for given xdata fit results and the real data.

If hist=True also the normed residual distribution is ploted with a normal distribution.

Parameters

xdata – arraylike data for the x-coordinate
fitdata – arraylike fitted data for the y-coordinate
realdata – arraylike data to plot residuen against the fit
errors – dict, can be used to provide errordata for the x and y direction
xlabel – str, label for the x-axis
ylabel – str, label for the y-axis
title – str, title for the plot
saveas – str, filename for the saved plot
hist – bool, if True a normed residual distribution is ploted with a normal distribution.
return_residuen_data – bool, if True in addition to the produced axis object also the residuen data is returned

Special Kwargs:

param hist_kwargs: dict, these arguments will be passed on to the histogram() call (if hist=True)

Other Kwargs will be passed on to all single_scatterplot() call

masci_tools.vis.plot_methods.plot_spectral_function(kpath, energy_grid, spectral_function, *, data=None, special_kpoints=None, e_fermi=0, xlabel='', ylabel='$E-E_F$ [eV]', title='', saveas='spectral_function', copy_data=False, **kwargs)[source]¶

Create a colormesh plot of a spectral function

Parameters

kpath – data for the kpoint coordinates
energy_grid – data for the energy grid
spectral_function – 2D data for the spectral function
data – source for the data of the plot (optional) (pandas Dataframe for example)
title – str, Title of the plot
xlabel – str, label for the x-axis
ylabel – str, label for the y-axis
saveas – str, filename for the saved plot
e_fermi – float (default 0), place the line for the fermi energy at this value
special_kpoints – list of tuples (str, float), place vertical lines at the given values and mark them on the x-axis with the given label
copy_data – bool, if True the data argument will be copied

All other Kwargs are passed on to the colormesh_plot() call

masci_tools.vis.plot_methods.plot_spinpol_bands(kpath, bands_up, bands_dn, *, size_data=None, color_data=None, data=None, show_spin_pol=True, special_kpoints=None, e_fermi=0, xlabel='', ylabel='$E-E_F$ [eV]', title='', saveas='bandstructure', markersize_min=0.5, markersize_scaling=5.0, scale_color=True, line_plot=False, separate_bands=False, band_index=None, copy_data=False, **kwargs)[source]¶

Plot the provided data for a bandstrucuture (spin-polarized). Can be used to illustrate weights on bands via size_data

Parameters

kpath – arraylike data for the kpoint data
bands_up – arraylike data for the eigenvalues (spin-up)
bands_dn – arraylike data for the eigenvalues (spin-dn)
size_data – arraylike data the weights to emphasize BOTH SPINS (optional)
data – source for the data of the plot (optional) (pandas Dataframe for example)
title – str, Title of the plot
xlabel – str, label for the x-axis
ylabel – str, label for the y-axis
saveas – str, filename for the saved plot
e_fermi – float (default 0), place the line for the fermi energy at this value
special_kpoints – list of tuples (str, float), place vertical lines at the given values and mark them on the x-axis with the given label
markersize_min – minimum value used in scaling points for weight
markersize_scaling – factor used in scaling points for weight
show_spin_pol – bool, if True (default) the two different spin channels will be shown in blue and red by default
scale_color – bool, if True (default) the weight will be additionally shown via a colormapping
line_plot – bool, if True the bandstructure will be plotted with lines Here no weights are supported
separate_bands – bool, if True the bandstructure will be separately plotted for each band allows more specific parametrization
band_index – data for which eigenvalue belongs to which band (needed for line_plot and separate_bands)
copy_data – bool, if True the data argument will be copied

All other Kwargs are passed on to the multi_scatter_plot() call

masci_tools.vis.plot_methods.plot_spinpol_dos(energy_grid, spin_up_data, spin_dn_data, *, data=None, saveas='spinpol_dos_plot', energy_label='$E-E_F$ [eV]', dos_label='DOS [1/eV]', title='Density of states', xyswitch=False, e_fermi=0, spin_dn_negative=True, spin_arrows=True, copy_data=False, **kwargs)[source]¶

Plot the provided data for a density of states (spin-polarized). Can be done horizontally or vertical via the switch xyswitch

Parameters

energy_grid – arraylike data for the energy grid of the DOS
spin_up_data – arraylike data for all the DOS spin-up components to plot
spin_dn_data – arraylike data for all the DOS spin-down components to plot
data – source for the data of the plot (optional) (pandas Dataframe for example)
title – str, Title of the plot
energy_label – str, label for the energy-axis
dos_label – str, label for the DOS-axis
saveas – str, filename for the saved plot
e_fermi – float (default 0), place the line for the fermi energy at this value
xyswitch – bool if True, the enrgy axis will be plotted vertically
energy_grid_dn – arraylike data for the energy grid of the DOS of the spin-down component (optional)
spin_dn_negative – bool, if True (default) the spin-down components are plotted downwards
spin_arrows – bool, if True (default) small arrows will be plotted on the left side of the plot indicating the spin directions (if spin_dn_negative is True)
copy_data – bool, if True the data argument will be copied

All other Kwargs are passed on to the multiple_scatterplots() call

masci_tools.vis.plot_methods.pseudo_voigt_profile(x, fwhm_g, fwhm_l, mu, mix=0.5)[source]¶

Linear combination of gaussian and loretzian instead of convolution

Args:: x: array of floats fwhm_g: FWHM of gaussian fwhm_l: FWHM of Lorentzian mu: Mean mix: ratio of gauss to lorentz, mix* gauss, (1-mix)*Lorentz

masci_tools.vis.plot_methods.reset_mpl_plot_defaults()[source]¶

Reset the defaults for matplotib backend to the hardcoded defaults

Available defaults can be seen in MatplotlibPlotter

masci_tools.vis.plot_methods.save_mpl_defaults(filename='plot_mpl_defaults.json', save_complete=False)[source]¶

Save the current defaults for the matplotlib backend to a json file.

Parameters

filename – filename, where the defaults should be stored
save_complete – bool if True not only the overwritten user defaults but also the unmodified hardcoded defaults are stored

masci_tools.vis.plot_methods.set_mpl_plot_defaults(**kwargs)[source]¶

Set defaults for matplotib backend according to the given keyword arguments

Available defaults can be seen in MatplotlibPlotter

masci_tools.vis.plot_methods.show_mpl_plot_defaults()[source]¶

Show the currently set defaults for matplotib backend to the hardcoded defaults

Available defaults can be seen in MatplotlibPlotter

masci_tools.vis.plot_methods.single_scatterplot(xdata, ydata, *, xlabel='', ylabel='', title='', data=None, saveas='scatterplot', axis=None, xerr=None, yerr=None, area_curve=0, copy_data=False, **kwargs)[source]¶

Create a standard scatter plot (this should be flexible enough) to do all the basic plots.

Parameters

xdata – str or arraylike, data for the x coordinate
ydata – str or arraylike, data for the y coordinate
data – source for the data of the plot (optional) (pandas Dataframe for example)
xlabel – str, label written on the x axis
ylabel – str, label written on the y axis
title – str, title of the figure
data – Mapping giving the data for the plot (required if xdata and ydata are str)
saveas – str specifying the filename (without file format)
axis – Axes object, if given the plot will be applied to this object
xerr – optional data for errorbar in x-direction
yerr – optional data for errorbar in y-direction
area_curve – if an area plot is made this arguments defines the other enclosing line defaults to 0
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to masci_tools.vis.matplotlib_plotter.MatplotlibPlotter. If the arguments are not recognized they are passed on to the matplotlib functions (errorbar or fill_between)

masci_tools.vis.plot_methods.surface_plot(xdata, ydata, zdata, *, xlabel='', ylabel='', zlabel='', title='', data=None, saveas='surface_plot', axis=None, copy_data=False, **kwargs)[source]¶

Create a standard surface plot

Parameters

xdata – arraylike, data for the x coordinate
ydata – arraylike, data for the y coordinate
zdata – arraylike, data for the z coordinate
data – source for the data of the plot (optional) (pandas Dataframe for example)
xlabel – str, label written on the x axis
ylabel – str, label written on the y axis
zlabel – str, label written on the z axis
title – str, title of the figure
axis – Axes object, if given the plot will be applied to this object
saveas – str specifying the filename (without file format)
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to masci_tools.vis.matplotlib_plotter.MatplotlibPlotter. If the arguments are not recognized they are passed on to the matplotlib function plot_surface

masci_tools.vis.plot_methods.voigt_profile(x, fwhm_g, fwhm_l, mu)[source]¶: Return the Voigt line shape at x with Lorentzian component FWHM fwhm_l and Gaussian component FWHM fwhm_g and mean mu. There is no closed form for the Voigt profile, but it is related to the real part of the Faddeeva function (wofz), which is used here.

masci_tools.vis.plot_methods.waterfall_plot(xdata, ydata, zdata, *, xlabel='', ylabel='', zlabel='', title='', data=None, saveas='waterfallplot', axis=None, copy_data=False, **kwargs)[source]¶

Create a standard waterfall plot

Parameters

xdata – arraylike, data for the x coordinate
ydata – arraylike, data for the y coordinate
zdata – arraylike, data for the z coordinate
data – source for the data of the plot (optional) (pandas Dataframe for example)
xlabel – str, label written on the x axis
ylabel – str, label written on the y axis
zlabel – str, label written on the z axis
title – str, title of the figure
axis – Axes object, if given the plot will be applied to this object
saveas – str specifying the filename (without file format)
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to masci_tools.vis.matplotlib_plotter.MatplotlibPlotter. If the arguments are not recognized they are passed on to the matplotlib function scatter3D

Bokeh¶

Here the masci_tools.vis.parameters.Plotter subclass for the bokeh plotting backend is defined with default values and many helper methods

class masci_tools.vis.bokeh_plotter.BokehPlotter(**kwargs)[source]¶

Class for plotting parameters and standard code snippets for plotting with the bokeh backend.

Kwargs in the __init__ method are forwarded to setting default values for the instance

For specific documentation about the parameter/defaults handling refer to Plotter.

Below the current defined default values are shown:

Plot Parameters¶
Name	Description	Default value
`figure_kwargs`	Parameters for creating the bokeh figure. Includes things like axis type (x and y), tools plot width/height	{'tools': 'pan,poly_select,tap,wheel_zoom,box_zoom,redo,undo,reset,save,crosshair,zoom_out,zoom_in', 'y_axis_type': 'linear', 'x_axis_type': 'linear', 'active_inspect': None, 'toolbar_location': 'right'}
`additional_tools`	tools to add to the tools already specified in `figure_kwargs` (Has to be in the same format)	No Default
`show_tooltips`	Switch whether to add hover tooltips	`True`
`global_tooltips`	Switch whether to add individual (for each renderer) or global hover tooltips.	`False`
`format_tooltips`	Switch whether to enable the processing of formatted strings in tooltips.	`True`
`tooltips`	List of tuples specifying the tooltips. For more information refer to the bokeh documentation. Strings can contain format specifiers with the data keys of the function e.g. '@ ``{x} ‘. Here the `` ``{x} `` will be replaced by the entry for x. If there are formatting specifications for bokeh they need to be escaped with double curly braces or `format_tooltips=False`.	`[('X', '@{x}'), ('Y', '@{y}')]`
`additional_tooltips`	Tooltips to add to the already defined `tooltips` (See above)	No Default
`axis_linewidth`	Linewidth for the lines of the axis	`2`
`label_fontsize`	Fontsize for the labels of the axis	`18pt`
`tick_label_fontsize`	fontsize for the ticks on the axis	`16pt`
`background_fill_color`	Color of the background of the plot	`#ffffff`
`x_axis_formatter`	If set this formatter will be used for the ticks on the x-axis	No Default
`y_axis_formatter`	If set this formatter will be used for the ticks on the y-axis	No Default
`x_ticks`	Tick specification for the x-axis	No Default
`x_ticklabels_overwrite`	Overrides the labels for the ticks on the x-axis	No Default
`y_ticks`	Tick specification for the y-axis	No Default
`y_ticklabels_overwrite`	Overrides the labels for the ticks on the y-axis	No Default
`x_range_padding`	Specifies the amount of padding on the edges of the x-axis	No Default
`y_range_padding`	Specifies the amount of padding on the edges of the y-axis	No Default
`limits`	Dict specifying the limits of the axis, e.g `{'x': (-5,5)}`	No Default
`legend_location`	Location of the legend inside the plot area	`top_right`
`legend_click_policy`	Policy for what happens when labels are clicked in the legend	`hide`
`legend_orientation`	Orientation of the legend	`vertical`
`legend_font_size`	Fontsize for the labels inside the legend	`14pt`
`legend_outside_plot_area`	If True the legend will be placed outside of the plot area	`False`
`color_palette`	Color palette to use for the plot(s)	No Default
`color`	Specific colors to use for the plot(s)	No Default
`legend_label`	Labels to use for the legend of the plot(s)	No Default
`alpha`	Transparency to use for the plot(s)	`1.0`
`name`	Name used for identifying elements in the plot (not shown only internally)	No Default
`line_color`	Color to use for line plot(s)	No Default
`line_alpha`	Transparency to use for line plot(s)	`1.0`
`line_dash`	Dash styles to use for line plot(s)	No Default
`line_width`	Line width to use for line plot(s)	`2.0`
`marker`	Type of marker to use for scatter plot(s)	`circle`
`marker_size`	Marker size to use for scatter plot(s)	`6`
`area_plot`	If True h(v)area will be used to produce the plot(s)	`False`
`area_vertical`	Determines, whether to use harea (False) or varea (True) for area plots	`False`
`fill_alpha`	Transparency to use for the area in area plot(s)	`1.0`
`fill_color`	Color to use for the area in area plot(s)	No Default
`level`	Can be used to specified, which elements are fore- or background	No Default
`straight_lines`	Dict specifying straight help-lines to draw. For example `{'vertical': 0, 'horizontal': [-1,1]}` will draw a vertical line at 0 and two horizontal at -1 and 1	No Default
`straight_line_options`	Color, width, and more options for the help-lines	{'line_color': 'black', 'line_width': 1.0, 'line_dash': 'dashed'}
`text_font_size`	fontsize for the text glyphs in the plot	`10pt`
`text_font_style`	fontstyle for the text glyphs in the plot	`normal`
`text_color`	text color for the text glyphs in the plot	`black`
`text_align`	text alignment for the text glyphs in the plot	`left`
`text_baseline`	text baseline for the text glyphs in the plot	`middle`
`save_plots`	If True plots will be saved to file (Configuration beforehand is needed)	`False`
`save_format`	Formats to save the plots to, can be single or list of formats (html, png or svg)	`html`
`show`	If True bokeh.io.show will be called after the plotting routine	`True`

add_tooltips(fig, renderers, columns=None, toggleable=False)[source]¶

Add Hover tooltips to the given renderers and figure

Parameters

fig – bokeh figure to apply changes to
renderers – bokeh renderers to activate the tooltips for
columns – namedtuple containing the data keys used for evtl. formatting
toggleable – bool, if True these tooltips will be toggleable in the toolbar

draw_straight_lines(fig)[source]¶

Draw horizontal and vertical lines specified in the lines argument

Parameters: fig – bokeh figure on which to perform the operation

prepare_figure(title, xlabel, ylabel, figure=None)[source]¶

Create a bokeh figure according to the set parameters or modify an existing one

Parameters

title – title of the figure
xlabel – label on the x-axis
ylabel – label on the y-axis
figure – bokeh figure, optional, if given the operations are performed on the object otherwise a new figure is created

Returns

the created or modified bokeh figure

save_plot(figure, saveas)[source]¶

Show/save the bokeh figure

Parameters: figure – bokeh figure on which to perform the operation

set_color_palette_by_num_plots()[source]¶

Set the colormap for the configured number of plots according to the set colormap or color

copied from https://github.com/PatrikHlobil/Pandas-Bokeh/blob/master/pandas_bokeh/plot.py credits to PatrikHlobil modified for use in this Plotter class

set_legend(fig)[source]¶

Set legend options for the figure

Parameters: fig – bokeh figure on which to perform the operation

set_limits(fig)[source]¶

Set limits of the figure

Parameters: fig – bokeh figure on which to perform the operation

Here are general and special bokeh plots to use

masci_tools.vis.bokeh_plots.bokeh_bands(kpath, bands=None, *, data=None, size_data=None, color_data=None, xlabel='', ylabel='$$E-E_F [eV]$$', title='', special_kpoints=None, markersize_min=3.0, markersize_scaling=10.0, saveas='bands_plot', scale_color=True, separate_bands=False, line_plot=False, band_index=None, copy_data=False, **kwargs)[source]¶

Create an interactive bandstructure plot (non-spinpolarized) with bokeh Can make a simple plot or weight the size and color of the points against a given weight

Parameters

kpath – arraylike or key data for the kpoint data
bands – arraylike or key data for the eigenvalues
size_data – arraylike or key data the weights to emphasize (optional)
color_data – str or arraylike, data for the color values with a colormap (optional)
data – source for the bands data (optional) of the plot (pandas Dataframe for example)
xlabel – label for the x-axis (default no label)
ylabel – label for the y-axis
title – title of the figure
special_kpoints – list of tuples (str, float), place vertical lines at the given values and mark them on the x-axis with the given label
e_fermi – float, determines, where to put the line for the fermi energy
markersize_min – minimum value used in scaling points for weight
markersize_scaling – factor used in scaling points for weight
outfilename – filename of the output file
scale_color – bool, if True (default) the weight will be additionally shown via a colormapping
line_plot – bool, if True the bandstructure will be plotted with lines Here no weights are supported
separate_bands – bool, if True the bandstructure will be separately plotted for each band allows more specific parametrization
band_index – data for which eigenvalue belongs to which band (needed for line_plot and separate_bands)
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to bokeh_multi_scatter() or bokeh_line()

masci_tools.vis.bokeh_plots.bokeh_dos(energy_grid, dos_data=None, *, data=None, energy_label='$$E-E_F [eV]$$', dos_label='DOS [1/eV]', title='Density of states', xyswitch=False, e_fermi=0, saveas='dos_plot', copy_data=False, **kwargs)[source]¶

Create an interactive dos plot (non-spinpolarized) with bokeh Both horizontal or vertical orientation are possible

Parameters

energy_grid – arraylike or key data for the energy grid
spin_up_data – arraylike or key data for the DOS
data – source for the DOS data (optional) of the plot (pandas Dataframe for example)
energy_label – label for the energy-axis
dos_label – label for the dos-axis
title – title of the figure
xyswitch – bool if True, the energy will be plotted along the y-direction
e_fermi – float, determines, where to put the line for the fermi energy
outfilename – filename of the output file
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to bokeh_line()

masci_tools.vis.bokeh_plots.bokeh_line(x, y=None, *, data=None, figure=None, xlabel='x', ylabel='y', title='', saveas='line', plot_points=False, area_curve=0, copy_data=False, set_default_legend=True, **kwargs)[source]¶

Create an interactive multi-line plot with bokeh

Parameters

x – arraylike or key for data for the x-axis
y – arraylike or key for data for the y-axis
data – source for the data of the plot (optional) (pandas Dataframe for example)
xlabel – label for the x-axis
ylabel – label for the y-axis
title – title of the figure
figure – bokeh figure (optional), if provided the plot will be added to this figure
outfilename – filename of the output file
plot_points – bool, if True also plot the points with a scatterplot on top
copy_data – bool, if True the data argument will be copied
set_default_legend – bool if True the data names are used to generate default legend labels

Kwargs will be passed on to masci_tools.vis.bokeh_plotter.BokehPlotter. If the arguments are not recognized they are passed on to the bokeh function line

masci_tools.vis.bokeh_plots.bokeh_multi_scatter(x, y=None, *, data=None, figure=None, xlabel='x', ylabel='y', title='', saveas='scatter', copy_data=False, set_default_legend=True, **kwargs)[source]¶

Create an interactive scatter (muliple data sets possible) plot with bokeh

Parameters

x – arraylike or key for data for the x-axis
y – arraylike or key for data for the y-axis
data – source for the data of the plot (pandas Dataframe for example)
xlabel – label for the x-axis
ylabel – label for the y-axis
title – title of the figure
figure – bokeh figure (optional), if provided the plot will be added to this figure
outfilename – filename of the output file
copy_data – bool, if True the data argument will be copied
set_default_legend – bool if True the data names are used to generate default legend labels

Kwargs will be passed on to masci_tools.vis.bokeh_plotter.BokehPlotter. If the arguments are not recognized they are passed on to the bokeh function scatter

masci_tools.vis.bokeh_plots.bokeh_scatter(x, y=None, *, xlabel='x', ylabel='y', title='', figure=None, data=None, saveas='scatter', copy_data=False, **kwargs)[source]¶

Create an interactive scatter plot with bokeh

Parameters

x – arraylike or key for data for the x-axis
y – arraylike or key for data for the y-axis
data – source for the data of the plot (pandas Dataframe for example)
xlabel – label for the x-axis
ylabel – label for the y-axis
title – title of the figure
figure – bokeh figure (optional), if provided the plot will be added to this figure
outfilename – filename of the output file
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to masci_tools.vis.bokeh_plotter.BokehPlotter. If the arguments are not recognized they are passed on to the bokeh function scatter

masci_tools.vis.bokeh_plots.bokeh_spectral_function(kpath, energy_grid, spectral_function, *, data=None, special_kpoints=None, e_fermi=0, xlabel='', ylabel='$$E-E_F [eV]$$', title='', saveas='spectral_function', copy_data=False, figure=None, **kwargs)[source]¶

Create a colormesh plot of a spectral function

Parameters

kpath – data for the kpoint coordinates
energy_grid – data for the energy grid
spectral_function – 2D data for the spectral function
data – source for the data of the plot (optional) (pandas Dataframe for example)
title – str, Title of the plot
xlabel – str, label for the x-axis
ylabel – str, label for the y-axis
saveas – str, filename for the saved plot
e_fermi – float (default 0), place the line for the fermi energy at this value
special_kpoints – list of tuples (str, float), place vertical lines at the given values and mark them on the x-axis with the given label
copy_data – bool, if True the data argument will be copied

All other Kwargs are passed on to the image call of bokeh

masci_tools.vis.bokeh_plots.bokeh_spinpol_bands(kpath, bands_up=None, bands_dn=None, *, size_data=None, color_data=None, data=None, xlabel='', ylabel='$$E-E_F [eV]$$', title='', special_kpoints=None, markersize_min=3.0, markersize_scaling=10.0, saveas='bands_plot', scale_color=True, line_plot=False, separate_bands=False, band_index=None, copy_data=False, **kwargs)[source]¶

Create an interactive bandstructure plot (spinpolarized) with bokeh Can make a simple plot or weight the size and color of the points against a given weight

Parameters

kpath – arraylike or key data for the kpoint data
bands_up – arraylike or key data for the eigenvalues spin-up
bands_dn – arraylike or key data for the eigenvalues spin-dn
size_data – arraylike or key data the weights to emphasize (optional)
color_data – str or arraylike, data for the color values with a colormap (optional)
data – source for the bands data (optional) of the plot (pandas Dataframe for example)
xlabel – label for the x-axis (default no label)
ylabel – label for the y-axis
title – title of the figure
special_kpoints – list of tuples (str, float), place vertical lines at the given values and mark them on the x-axis with the given label
e_fermi – float, determines, where to put the line for the fermi energy
markersize_min – minimum value used in scaling points for weight
markersize_scaling – factor used in scaling points for weight
outfilename – filename of the output file
scale_color – bool, if True (default) the weight will be additionally shown via a colormapping
line_plot – bool, if True the bandstructure will be plotted with lines Here no weights are supported
separate_bands – bool, if True the bandstructure will be separately plotted for each band allows more specific parametrization
band_index – data for which eigenvalue belongs to which band (needed for line_plot and separate_bands)
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to bokeh_multi_scatter() or bokeh_line()

masci_tools.vis.bokeh_plots.bokeh_spinpol_dos(energy_grid, spin_up_data=None, spin_dn_data=None, *, data=None, spin_dn_negative=True, energy_label='$$E-E_F [eV]$$', dos_label='DOS [1/eV]', title='Density of states', xyswitch=False, e_fermi=0, spin_arrows=True, saveas='dos_plot', copy_data=False, **kwargs)[source]¶

Create an interactive dos plot (spinpolarized) with bokeh Both horizontal or vertical orientation are possible

Parameters

energy_grid – arraylike or key data for the energy grid
spin_up_data – arraylike or key data for the DOS spin-up
spin_dn_data – arraylike or key data for the DOS spin-dn
data – source for the DOS data (optional) of the plot (pandas Dataframe for example)
spin_dn_negative – bool, if True (default), the spin down components are plotted downwards
energy_label – label for the energy-axis
dos_label – label for the dos-axis
title – title of the figure
xyswitch – bool if True, the energy will be plotted along the y-direction
e_fermi – float, determines, where to put the line for the fermi energy
spin_arrows – bool, if True (default) small arrows will be plotted on the left side of the plot indicating the spin directions (if spin_dn_negative is True)
outfilename – filename of the output file
copy_data – bool, if True the data argument will be copied

Kwargs will be passed on to bokeh_line()

masci_tools.vis.bokeh_plots.get_bokeh_help(key)[source]¶

Print the description of the given key in the bokeh backend

Available defaults can be seen in BokehPlotter

masci_tools.vis.bokeh_plots.load_bokeh_defaults(filename='plot_bokeh_defaults.json')[source]¶

Load defaults for the bokeh backend from a json file.

Parameters: filename – filename,from where the defaults should be taken

masci_tools.vis.bokeh_plots.matrix_plot(text_values, x_axis_data, y_axis_data, positions=None, *, color_data=None, secondary_color_data=None, x_offset=-0.47, log_scale=False, color_map=None, data=None, copy_data=False, title='', xlabel='x', ylabel='y', saveas='matrix_plot.html', blank_outsiders='both', blank_color='#c4c4c4', figure=None, categorical_axis=False, categorical_sort_key=None, block_size=0.95, block_size_pixel=100, **kwargs)[source]¶

Plot function for an interactive periodic table plot. Heat map and hover tool. source must be a pandas dataframe containing, atom period and group, atomic number and symbol

Parameters

values – data for the text inside each elements box
positions – y positions relative to the middle of the box for each value
color_data – data to display as a heatmap
color_map – color palette to use for the heatmap (default matplotlib plasma)
log_scale – bool, if True the heatmap is done logarithmically
data – source for the data of the plot (optional) (pandas Dataframe for example)
title – str, Title of the plot
saveas – str, filename for the saved plot
blank_outsiders – either ‘both’, ‘min’, ‘max’ or None, determines, which points outside the color range to color with a default blank color
blank_color – color to replace values outside the color range by
include_legend – if True an additional entry with labels explaing each value entry is added
figure – bokeh figure (optional), if provided the plot will be added to this figure

Additional kwargs are passed on to the label creation for the element box The kwargs legend_options and colorbar_options can be used to overwrite default values for these regions of the plot

masci_tools.vis.bokeh_plots.periodic_table_plot(values, positions=None, *, color_data=None, log_scale=False, color_map=None, data=None, copy_data=False, title='', saveas='periodictable.html', blank_outsiders='both', blank_color='#c4c4c4', include_legend=True, figure=None, **kwargs)[source]¶

Plot function for an interactive periodic table plot. Heat map and hover tool. source must be a pandas dataframe containing, atom period and group, atomic number and symbol

Parameters

values – data for the text inside each elements box
positions – y positions relative to the middle of the box for each value
color_data – data to display as a heatmap
color_map – color palette to use for the heatmap (default matplotlib plasma)
log_scale – bool, if True the heatmap is done logarithmically
data – source for the data of the plot (optional) (pandas Dataframe for example)
title – str, Title of the plot
saveas – str, filename for the saved plot
blank_outsiders – either ‘both’, ‘min’, ‘max’ or None, determines, which points outside the color range to color with a default blank color
blank_color – color to replace values outside the color range by
include_legend – if True an additional entry with labels explaing each value entry is added
figure – bokeh figure (optional), if provided the plot will be added to this figure

Additional kwargs are passed on to the label creation for the element box The kwargs legend_options and colorbar_options can be used to overwrite default values for these regions of the plot

masci_tools.vis.bokeh_plots.plot_convergence(iteration, distance, total_energy, *, data=None, saveas_energy='energy_convergence', saveas_distance='distance_convergence', figure_energy=None, figure_distance=None, xlabel='Iteration', ylabel_energy='Total energy difference [Htr]', ylabel_distance='Distance [me/bohr^3]', title_energy='Total energy difference over scf-Iterations', title_distance='Convergence (log)', copy_data=False, drop_last_iteration=False, **kwargs)[source]¶

Plot the total energy differences versus the scf iteration and plot the distance of the density versus iterations.

Parameters

iteration – data for the number of iterations
distance – data of distances
total_energy – data of total energies
data – source for the data of the plot (optional) (pandas Dataframe for example)
xlabel – str, label for the x-axis of both plots
saveas_energy – str, filename for the energy convergence plot
figure_energy – Axes object for the energy convergence plot
title_energy – str, title for the energy convergence plot
ylabel_energy – str, label for the y-axis for the energy convergence plot
saveas_distance – str, filename for the distance plot
figure_distance – Axes object for the distance plot
title_distance – str, title for the distance plot
ylabel_distance – str, label for the y-axis for the distance plot
copy_data – bool if True the data argument is copied
drop_last_iteration – bool if True the last iteration is dropped for the distance plot

Other Kwargs will be passed on to all bokeh_line() calls

masci_tools.vis.bokeh_plots.plot_convergence_results(iteration, distance, total_energy, *, saveas='convergence', **kwargs)[source]¶

Plot the total energy versus the scf iteration and plot the distance of the density versus iterations. Uses bokeh_line and bokeh_scatter

Parameters

iteration – list of Int
distance – list of floats
show – bool, if True call show

Total_energy

list of floats

Kwargs will be passed on to bokeh_line()

Returns grid: bokeh grid with figures

masci_tools.vis.bokeh_plots.plot_convergence_results_m(iterations, distances, total_energies, *, link=False, nodes=None, modes=None, plot_label=None, saveas='convergence', **kwargs)[source]¶

Plot the total energy versus the scf iteration and plot the distance of the density versus iterations in a bokeh grid for several SCF results.

Parameters

distances – list of lists of floats
iterations – list of lists of Int
link – bool, optional default=False:
nodes – list of node uuids or pks important for links
saveas1 – str, optional default=’t_energy_convergence’, save first figure as
saveas2 – str, optional default=’distance_convergence’, save second figure as
figure_kwargs – dict, optional default={‘width’: 600, ‘height’: 450}, gets parsed to bokeh_line
kwargs – further key-word arguments for bokeh_line

Total_energies

list of lists of floats

Returns grid

bokeh grid with figures

masci_tools.vis.bokeh_plots.plot_lattice_constant(scaling, total_energy, *, fit_data=None, data=None, figure=None, relative=True, ref_const=None, title='Equation of states', saveas='lattice_constant', copy_data=False, **kwargs)[source]¶

Plot a lattice constant versus Total energy Plot also the fit. On the x axis is the scaling, it

Parameters

scaling – arraylike, data for the scaling factor
total_energy – arraylike, data for the total energy
fit_data – arraylike, optional data of fitted data
relative – bool, scaling factor given (True), or lattice constants given?
ref_const – float (optional), or list of floats, lattice constant for scaling 1.0
data – source for the data of the plot (optional) (pandas Dataframe for example)
copy_data – bool if True the data argument will be copied
figure – bokeh figure (optional), if provided the plot will be added to this figure

Function specific parameters:

param marker_fit: defaults to marker, marker type for the fit data
param marker_size_fit: defaults to marker_size, markersize for the fit data
param line_width_fit: defaults to line_width, linewidth for the fit data
param legend_label_fit: str label for the fit data

Other Kwargs will be passed on to bokeh_line()

masci_tools.vis.bokeh_plots.reset_bokeh_plot_defaults()[source]¶

Reset the defaults for bokeh backend to the hardcoded defaults

Available defaults can be seen in BokehPlotter

masci_tools.vis.bokeh_plots.save_bokeh_defaults(filename='plot_bokeh_defaults.json', save_complete=False)[source]¶

Save the current defaults for the matplotlib backend to a json file.

Parameters

filename – filename, where the defaults should be stored
save_complete – bool if True not only the overwritten user defaults but also the unmodified hardcoded defaults are stored

masci_tools.vis.bokeh_plots.set_bokeh_plot_defaults(**kwargs)[source]¶

Set defaults for bokeh backend according to the given keyword arguments

Available defaults can be seen in BokehPlotter

masci_tools.vis.bokeh_plots.show_bokeh_plot_defaults()[source]¶

Show the currently set defaults for bokeh backend

Available defaults can be seen in BokehPlotter

Calculation tools¶

This file contains a class to compute the crystalfield coefficients from convoluting the charge density with the potential which produces the crystalfield. This is both compatible with the Yttrium-Analogue approximation and self-consitent calculation of the potential

class masci_tools.tools.cf_calculation.CFCalculation(*, radial_points=4000, reference_radius='pot', coefficient_cutoff=0.001, **kwargs)[source]¶

Class for calculating Crystal Field coefficients using the procedure described in C.E. Patrick, J.B. Staunton: J. Phys.: Condens. Matter 31, 305901 (2019)

Using the formula:

$B_{lm} = \sqrt{\frac{2l+1}{4\pi}} \int^{R_{MT}}\! dr r^2 V_{lm}(r)n_{4f}(r)$

The read in quantities are interpolated from logarithmic meshes to equidistant meshes

The function constructs an equidistant mesh between 0 and the muffin tin radius defined in self.reference_radius and with self.radial_points points

Parameters

radial_points (int) – int, number of radial points in the interpolated mesh
reference_radius (Union[float, Literal['pot', 'cdn']]) – stror float; Either ‘pot’ or ‘cdn’ or explicit number. Defines which muffin-tin radius is used for the equidistant mesh. IMPORTANT! If txt files are used the muffin-tin radius has to be provided explicitly
coefficient_cutoff (Optional[float]) – float Defines minimum value that cf coefficients have to have to be considered non-zero

property denNorm¶

Returns the density normalization

DEPRECATED: Use density_normalization instead

classmethod from_arrays(charge_density, potentials, radial_mesh, **kwargs)[source]¶

Create a CFCalculation instance from arrays

Warning

Using this classmethod will not check that the charge density and potential have the same bravais matrix

Parameters

charge_density (ndarray) – Array for the normed charge density
potentials (dict[tuple[int, int], ndarray]) – Data for the potentials (dict mapping (l,m) tuples to the corresponding data)
radial_mesh (dict[str, ndarray]) – dict for the data for the used radial meshs (keys ‘cdn’ and ‘pot’)

Return type

CFCalculation

Other Kwargs are passed on to the constructor

get_charge_density(interpolated=True)[source]¶

Return the charge density and the corresponding radial mesh

Parameters

spin – which spin to return
interpolated – bool, if True the interpolated mesh and density are returned

Return type

tuple[ndarray, ndarray]

get_coefficients(convention='Stevens', table_fmt=None)[source]¶

Performs the integration to obtain the crystal field coefficients If the data was not already interpolated, the interpolation will be performed beforehand

Parameters: :type convention: Literal['Stevens', 'Wybourne']

param convention

str of the convention to use (Stevens or Wybourne)

Return type: list[CFCoefficient]
Returns: list of CFCoefficient objects (namedtuple), with all the necessary information

get_potentials(spin, interpolated=True, only_nonzero=True, complex_data=True)[source]¶

Return the potentials and the corresponding radial mesh

Parameters

spin (Literal['up', 'down']) – which spin to return
interpolated (bool) – bool, if True the interpolated mesh and potentials are returned
only_nonzero (bool) – bool, if True only the potentials corresponding to a non-zero coefficient are returned
complex_data (bool) – bool, if False only the real part of the potentials is returned

Return type

tuple[ndarray, dict[tuple[int, int], ndarray]]

interpolate()[source]¶

Interpolate all quantities to a common equidistant radial mesh

Return type: None

property nonzero_coefficients_lm: list[tuple[int, int]]¶: Return the lm indices of coefficients that are bigger than the set cutoff

performIntegration(convert=True)[source]¶

DEPRECATED: Use get_coefficients instead

Performs the integration to obtain the crystal field coefficients If the data was not already interpolated, the interpolation will be performed beforehand

Parameters: :type convert:

param convert

bool, converts to Steven’s coefficients (if True)

Returns: list of CFCoefficient objects (namedtuple), with all the necessary information

readCDN(*args, **kwargs)[source]¶: DEPRECATED: Use read_charge_density instead

readPot(*args, **kwargs)[source]¶: DEPRECATED: Use read_pot

read_charge_density(file, atom_type=None, header=0, atomic_cdn=True)[source]¶

Reads in the normed charge density for the CF coefficient calculation If hdf files are given also the muffin tin radius is read in

Return type: None

Parameters: :type file: Union[str, bytes, Path, PathLike, IO[Any], File]

param file

Expects string filename for the charge density to read in The function expects either HDF files or txt files with the format (rmesh,cdn). The charge density should be given as r^2n(r) and normed to 1

kwargs: :type atom_type: Optional[int]

param atom_type

int, Defines the atom_type to read in (only for HDF files)

read_potential(*files, lm_indices=None, atom_type=None, header=0, complex_data=True)[source]¶

Reads in the potentials for the CF coefficient calculation If hdf files are given also the muffin tin radius is read in

Parameters

args – Expects string filenames for the potentials to read in The function expects either HDF files or txt files with the format (rmesh,vlmup,vlmdn)
lm_indices (Optional[list[tuple[int, int]]]) – list of tuples, Defines the l and m indices for the given txt files
atom_type (Optional[int]) – int, Defines the atomType to read in (only for HDF files)
header (int) – int, Define how many lines to skip in the beginning of txt file
complex_data (bool) – bool, Define if the data in the text file is complex

Return type

None

Raises:: ValueError: lm indices list length has to match number of files read in

property spin_polarized: bool¶: Return whether the potentials have a spin-down component

stevens_prefactor(l, m)[source]¶

Gives the lm dependent prefactor for conversion between Blm and Alm coefficients

Args: :type l: int

param l

int; orbital quantum number

Return type: float
Returns: float prefactor for conversion to Steven’s Coefficients

validate()[source]¶

Validate that the object can be used to execute the calculation Checks that the given bravais matrices are equal if given

Return type: None

class masci_tools.tools.cf_calculation.CFCoefficient(l: int, m: int, spin_up: float | complex, spin_down: float | complex, unit: str, convention: str)[source]¶

Namedtuple representing an individual crystal field coefficient

convention: str¶: Alias for field number 5

l: int¶: Alias for field number 0

m: int¶: Alias for field number 1

spin_down: float | complex¶: Alias for field number 3

spin_up: float | complex¶: Alias for field number 2

unit: str¶: Alias for field number 4

masci_tools.tools.cf_calculation.plot_crystal_field_calculation(cfcalc, *, saveas='crystal_field_calc', potential_title='Potential', density_title='Density', xlabel='$R$ (Bohr)', potential_ylabel='$Vpot$ (Hartree)', density_ylabel='Density', density_kwargs=None, potential=True, density=True, axis_potential=None, axis_density=None, **kwargs)[source]¶

Plot the given potentials and charge densities used in the given CFCalculation

Parameters

cfcalc – CFcalculation containing the data to plot
saveas – str, Define the filename to save the figure
potential_title – Title for the potential subplot
density_title – Title for the charge density subplot
xlabel – label for the x axis of both subplots
potential_ylabel – label for the y axis of the potential subplot
density_ylabel – label for the y axis f the charge density subplot
density_kwargs – dict with keyword argument passed to the plotting of the density
figure – Use this preexisting matplotlib figure to produce the plots

All other Kwargs are passed on to the multiple_scatterplots() calls for plotting the potentials

masci_tools.tools.cf_calculation.plot_crystal_field_potential(cfcoeffs, *, saveas='crystal_field_potential_areaplot', spin='avg', phi=0.0, figure=None, **kwargs)[source]¶

Plots the angular dependence of the calculated CF potential as well as a plane defined by phi.

Parameters

cfcoeffs – list of CFCoefficients to construct the potential
saveas – str, defines the filename to save the figure
spin – str; Either ‘up’, ‘dn’ or ‘avg’. Which spin direction to plot (‘avg’-> (‘up’+’dn’)/2.0)
phi – float, defines the phi angle of the plane

Raises

AssertionError – When coefficients are provided as wrong types or in the wrong convention
ValueError – When coefficients are provided in the wrong convention

This module contains utility and functions to work with Green’s functions calculated and written to greensf.hdf files by fleur

class masci_tools.tools.greensfunction.GreensFunction(element, data, attributes)[source]¶

Class for working with Green’s functions calculated by the fleur code

Parameters

element (GreensfElement) – GreensfElement namedtuple containing the information about the element
data (dict[str, Any]) – datasets dict produced by one of the hdf recipes for reading Green’s functions
attributes (dict[str, Any]) – attributes dict produced by one of the hdf recipes for reading Green’s functions

energy_dependence(*, m=None, mp=None, spin=None, imag=True, both_contours=False)[source]¶

Select data with energy dependence

Parameters

m (Optional[int]) – optional integer magnetic quantum number between -l and l
mp (Optional[int]) – optional integer magnetic quantum number between -lp and lp
spin (Optional[int]) – optional integer spin between 1 and nspins
both_contours (bool) – bool id True the data is not added for both energy contours
imag (bool) – bool if True and both_contours is False the imaginary part:math:frac{1}{2i}left[Gleft(zright)-Gleft(z^astright)right] is returned otherwise the real part $\frac{1}{2}\left[G\left(z\right)+G\left(z^\ast\right)\right]$

Return type

ndarray

Returns

numpy array with the selected data

energy_dependence_full_matrix(imag=True, both_contours=False)[source]¶

Get the full matrix $N_{\mathrm{spins}}(2l+1) \times N_{\mathrm{spins}}(2l^\prime+1)$

Parameters

both_contours (bool) – bool id True the data is not added for both energy contours
imag (bool) – bool if True and both_contours is False the imaginary part $\frac{1}{2i}\left[G\left(z\right)-G\left(z^\ast\right)\right]$ is returned otherwise the real part $\frac{1}{2}\left[G\left(z\right)+G\left(z^\ast\right)\right]$

Return type

ndarray

Returns

numpy array with the selected data

classmethod fromFile(file, index=None, **selection_params)[source]¶

Classmethod for creating a GreensFunction instance directly from a hdf file

Parameters

file (Any) – path or opened file handle to a greensf.hdf file
index (Optional[int]) – optional int index of the element to read in

Return type

GreensFunction

If index is not given Keyword arguments with the keys being the names of the fields of GreensfElement can be given to select the right Green’s function. The specification has to match only one element in the file

get_coefficient(name, spin=None, radial=False)[source]¶

Get the coefficient with the given name from the data attribute

Parameters

name (Literal['sphavg', 'uu', 'ud', 'du', 'dd', 'ulou', 'uulo', 'ulod', 'dulo', 'uloulo']) – name of the coefficient
radial (bool) – if the Green’s function is stored by coefficient and radial is True it is multiplied by the corresponding radial function otherwise the scalar product is multiplied
spin (Optional[int]) – integer index of the spin to retrieve

Return type

ndarray

Returns

numpy.ndarray for the given coefficient and spin

moment(n, spin=None)[source]¶

Calculate the integral

$M_n\ =\ -\frac{1}{4\pi i} \mathrm{Im} \int_\mathrm{Contour}\!\mathrm{dz} z^n G(z)$

Parameters

n (int) – power of z in the integral
spin (Optional[int]) – optional integer spin between 1 and nspins

Return type

ndarray

property nspins: int¶: Return the number of spins of the current element. If mperp is True for the element it is 4 otherwise it is determined by the spins attribute

occupation(spin=None)[source]¶

Calculate the 0-th moment of the green’s function

$n\ =\ -\frac{1}{4\pi i} \mathrm{Im} \int_\mathrm{Contour}\!\mathrm{dz} G(z)$

Note

Only if the energy contour ends at the fermi energy/is correlty weighted to produce occupations, will this function produce occupations

Parameters: spin (Optional[int]) – optional integer spin between 1 and nspins
Return type: ndarray

to_global_frame()[source]¶

Rotate the Green’s function into the global real space and spin space frame

Return type: None

to_local_frame()[source]¶

Rotate the Green’s function into the local real space and spin space frame

Return type: None

static to_m_index(m)[source]¶

Convert between magnetic quantum numbers between -l and l to 0 and 2l+1 for easier indexing

Parameters: m (int) – int magnetic quantum number to convert
Return type: int
Returns: converted magnetic quantum number

static to_spin_indices(spin)[source]¶

Convert between spin index (0 to 3) to the corresponding two spin indices (0 or 1)

Parameters: spin (int) – int spin index to convert
Return type: tuple[int, int]
Returns: tuple of spin indices

trace_energy_dependence(spin=None, imag=True)[source]¶

Select trace of data with energy dependence

Parameters

spin (Optional[int]) – integer spin between 1 and nspins
imag (bool) – bool if True the imaginary part $\frac{1}{2i}\left[G\left(z\right)-G\left(z^\ast\right)\right]$ is returned otherwise the real part $\frac{1}{2}\left[G\left(z\right)+G\left(z^\ast\right)\right]$

Return type

ndarray

Returns

numpy array with the selected and traced over data

class masci_tools.tools.greensfunction.GreensfElement(l: int, lp: int, atomType: int, atomTypep: int, sphavg: bool, onsite: bool, kresolved: bool, contour: int, nLO: int, atomDiff: np.ndarray)[source]¶

Namedtuple representing the high-level information about the Green’s functions, i.e. what kind, which atoms, which orbitals

atomDiff: ndarray¶: Alias for field number 9

atomType: int¶: Alias for field number 2

atomTypep: int¶: Alias for field number 3

contour: int¶: Alias for field number 7

kresolved: bool¶: Alias for field number 6

l: int¶: Alias for field number 0

lp: int¶: Alias for field number 1

nLO: int¶: Alias for field number 8

onsite: bool¶: Alias for field number 5

sphavg: bool¶: Alias for field number 4

class masci_tools.tools.greensfunction.colors[source]¶

Color strings for coloring terminal output

You may need to change color settings in iPython

masci_tools.tools.greensfunction.intersite_shell_indices(elements, reference_atom, show=False, max_shells=None)[source]¶

Construct the green’s function pairs to calculate the Jij exchange constants for a given reference atom from a list of GreensfElement

Parameters

elements (list[GreensfElement]) – list of GreenfElements to use
reference_atom (int) – integer of the atom to calculate the Jij’s for (correspinds to the i)
show (bool) – if True the elements belonging to a shell are printed in a shell
max_shells (Optional[int]) – optional int, if given only the first max_shells shells are constructed

Return type

list[tuple[floating[Any], list[tuple[int, int]]]]

Returns

list of tuples with distance and all indices of pairs in the shell

masci_tools.tools.greensfunction.intersite_shells(greensfunctions, reference_atom, show=False, max_shells=None)[source]¶

Construct the green’s function pairs to calculate the Jij exchange constants for a given reference atom from a list of given GreensFunction

Parameters

greensfunctions (list[GreensFunction]) – List of Greens Function to use
reference_atom (int) – integer of the atom to calculate the Jij’s for (correspinds to the i)
show (bool) – if True the elements belonging to a shell are printed in a shell
max_shells (Optional[int]) – optional int, if given only the first max_shells shells are constructed

Return type

Generator[tuple[floating[Any], GreensFunction, GreensFunction], None, None]

Returns

flat iterator with distance and the two corresponding GreensFunction instances for each Jij calculation

masci_tools.tools.greensfunction.intersite_shells_from_file(hdffile, reference_atom, show=False, max_shells=None)[source]¶

Construct the green’s function pairs to calculate the Jij exchange constants for a given reference atom from a given greensf.hdf file

Parameters

hdffile (Union[str, bytes, Path, PathLike, IO[Any]]) – filepath or file handle to a greensf.hdf file
reference_atom (int) – integer of the atom to calculate the Jij’s for (correspinds to the i)
show (bool) – if True the elements belonging to a shell are printed in a shell
max_shells (Optional[int]) – optional int, if given only the first max_shells shells are constructed

Return type

Generator[tuple[floating[Any], GreensFunction, GreensFunction], None, None]

Returns

flat iterator with distance and the two corresponding GreensFunction instances for each Jij calculation

masci_tools.tools.greensfunction.listElements(hdffile, show=False)[source]¶

Find the green’s function elements contained in the given greens.hdf file

Parameters

hdffile (Union[str, bytes, Path, PathLike, IO[Any]]) – filepath or file handle to a greensf.hdf file
show (bool) – bool if True the found elements are printed in a table

Return type

list[GreensfElement]

Returns

list of GreensfElement

masci_tools.tools.greensfunction.printElements(elements, index=None, mark=None)[source]¶

Print the given list of GreensfElement in a nice table

Parameters

elements (list[GreensfElement]) – list of GreensfElement to be printed
index (Optional[list[int]]) – optional list of indices to show instead of the default index in the list
mark (Optional[list[int]]) – optional list of int with elements to emphasize with an arrow and color

Return type

None

masci_tools.tools.greensfunction.select_element_indices(elements, show=False, **selection_params)[source]¶

Select GreensfElement objects from a list based on constraints on their values

Parameters

elements (list[GreensfElement]) – list of GreensfElement to choose from
show (bool) – bool if True the found elements will be printed

The Keyword arguments correspond to the names of the fields and their desired value

Return type: list[int]
Returns: list of the indices matching the criteria

masci_tools.tools.greensfunction.select_elements(greensfunctions, show=False, **selection_params)[source]¶

Select GreensFunction objects from a list based on constraints on the values of their underlying GreensfElement

Parameters

greensfunctions (list[GreensFunction]) – list of GreensFunction to choose from
show (bool) – bool if True the found elements will be printed

The Keyword arguments correspond to the names of the fields and their desired value

Return type: Generator[GreensFunction, None, None]
Returns: iterator over the matching GreensFunction

masci_tools.tools.greensfunction.select_elements_from_file(hdffile, show=False, **selection_params)[source]¶

Construct the green’s function matching specified criteria from a given greensf.hdf file

Parameters

hdffile (Union[str, bytes, Path, PathLike, IO[Any]]) – file or file path to the greensf.hdf file
show (bool) – bool if True the found elements will be printed

The Keyword arguments correspond to the names of the fields and their desired value

Return type: Generator[GreensFunction, None, None]
Returns: iterator over the matching GreensFunction

This module collects functions for calculating properties with the greens functions calculated by Fleur. At the moment the following are implemented:

Calculating Heisenberg J_0 (spin stiffness) from onsite Green’s functions

Calculating Heisenberg J_ij exchange constants from intersite Green’s functions

Calculating the hybridization function from onsite Greens functions

masci_tools.tools.greensf_calculations.calculate_heisenberg_j0(greensfunction, onsite_delta, show=False)[source]¶

Calculate spin stiffness J_0 for the given green’s function using the formula

$J_{0} = \frac{1}{4\pi} \mathrm{Im}\ \mathrm{Tr_L} \int_{-\infty}^{E_F}\!\mathrm{dz} \Delta\left(G^\uparrow(z)-G^\downarrow(z)\right) + \Delta^2G^\uparrow(z)G^\downarrow(z)$

Parameters

greensfunction (GreensFunction) – GreensFunction to use for the calculation
onsite_delta (float) – onsite exchange splitting to use for the calculation
show (bool) – bool if True additional information about the used Greens functions is printed out

Return type

float

Returns

the value of the spin stiffness in meV

masci_tools.tools.greensf_calculations.calculate_heisenberg_jij(hdffileORgreensfunctions, reference_atom, onsite_delta, max_shells=None)[source]¶

Calculate the Heisenberg exchange constants form Green’s functions using the formula

$J_{ij} = \frac{1}{4\pi} \mathrm{Im}\ \mathrm{Tr_L} \int_{-\infty}^{E_F}\!\mathrm{dz} \Delta_iG^\uparrow_{ij}(z)\Delta_jG^\downarrow_{ji}(z)$

Parameters

hdffileORgreensfunctions (Union[str, bytes, Path, PathLike, IO[Any], list[GreensFunction]]) – either pat/file-like object for the greensf.hdf file to use or list of GreensFunction
reference_atom (int) – integer index of the atom to calculate the Jijs from
onsite_delta (ndarray) – List of floats containing the onsite exchange splitting for each atom type and l-channel
max_shells (Optional[int]) – optional int, if given only the first max_shells shells are constructed

Return type

DataFrame

Returns

pandas DataFrame containing all the Jij constants

masci_tools.tools.greensf_calculations.calculate_heisenberg_tensor(hdffileORgreensfunctions, reference_atom, onsite_delta, max_shells=None)[source]¶

Calculate the Heisenberg exchange tensor $\mathbf{J}$ from Green’s functions using the formula

$J^{\alpha\beta}_{ij} = \frac{1}{4\pi} \mathrm{Im}\ \mathrm{Tr_L} \int_{-\infty}^{E_F}\!\mathrm{dz} \Delta_i\sigma_{\alpha}G_{ij}(z)\Delta_j\sigma_{\beta}G_{ji}(z)$

for all $\alpha\ \mathrm{and}\ \beta=x,y,z$ .

Parameters

hdffileORgreensfunctions (Union[str, bytes, Path, PathLike, IO[Any], list[GreensFunction]]) – either pat/file-like object for the greensf.hdf file to use or list of GreensFunction
reference_atom (int) – integer index of the atom to calculate the Jijs from
onsite_delta (ndarray) – List of floats containing the onsite exchange splitting for each atom type and l-channel
max_shells (Optional[int]) – optional int, if given only the first max_shells shells are constructed

Return type

DataFrame

Returns

pandas DataFrame containing all the J_xx, J_xy, etc. constants

masci_tools.tools.greensf_calculations.calculate_hybridization(greensfunction)[source]¶

Calculate the hybridization function as

$\Delta(z) = \frac{1}{2*l+1} \mathrm{Tr} G^{-1}(z)$

Return type: ndarray
Returns: numpy array of the hybridization function

masci_tools.tools.greensf_calculations.decompose_jij_tensor(jij_tensor, moment_direction)[source]¶

Decompose the Heisenberg tensor as calculated by calculate_heisenberg_tensor() into three parts

Isotropic $J = \frac{1}{3} \mathrm{Tr}\left[\mathbf{J}\right]$
Symmetric traceless $J_S = \frac{1}{2} \left(\mathbf{J} + \mathbf{J}^T\right) - J$
Antisymmetric $J_A = \frac{1}{2} \left(\mathbf{J} - \mathbf{J}^T\right)$

Parameters: jij_tensor (DataFrame) – Heisenberg tensor
Return type: DataFrame
Returns: tuple of the three aforementioned components

masci_tools.tools.greensf_calculations.heisenberg_reciprocal(qpoints, jij_data, entry='J_ij')[source]¶

Calculate the fourier transform of an entry for interaction constants

Example for $J_{ij}$

$J(\mathbf{q})\ =\ \sum_{ij} J_{ij} e^{i\mathbf{q}\cdot\mathbf{R}_{ij}}$

where $\mathbf{R}_{ij}$ is the connecting vector associated with the $J_{ij}$

Parameters

qpoints (ndarray) – numpy array containing the coordinates of the qpoints
jij_data (DataFrame) – DataFrame generated by the above calculation functions
entry (str) – str of the entry to calculate

Return type

ndarray

Returns

numpy array containing the Fourier transform

IO helper functions and file parsers¶

KKR related IO¶

In this module you find the kkrparams class that helps defining the KKR input parameters Also some defaults for the parameters are defined.

class masci_tools.io.kkr_params.kkrparams(**kwargs)[source]¶

Class for creating and handling the parameter input for a KKR calculation Optional keyword arguments are passed to init and stored in values dictionary.

Example usage: params = kkrparams(LMAX=3, BRAVAIS=array([[1,0,0], [0,1,0], [0,0,1]]))

Alternatively values can be set afterwards either individually with: params.set_value(‘LMAX’, 3)
or multiple keys at once with: params.set_multiple_values(EMIN=-0.5, EMAX=1)

Other useful functions

print the description of a keyword: params.get_description([key]) where [key] is a string for a keyword in params.values
print a list of mandatory keywords: params.get_all_mandatory()
print a list of keywords that are set including their value: params.get_set_values()

change_XC_val_kkrimp(val)[source]¶: Convert integer value of KKRhost KEXCOR input to KKRimp XC string input.

fill_keywords_to_inputfile(is_voro_calc=False, output='inputcard', no_check=False, verbose=False)[source]¶: Fill new inputcard with keywords/values automatically check for input consistency (can be disabled by the no_check input) if is_voro_calc==True change mandatory list to match voronoi code, default is KKRcode

classmethod get_KKRcalc_parameter_defaults(silent=False)[source]¶: set defaults (defined in header of this file) and returns dict, kkrparams_version

get_all_mandatory()[source]¶: Return a list of mandatory keys

get_description(key=None, search=None)[source]¶: Returns description of keyword ‘key’ If ‘key’ is None, print all descriptions of all available keywords If ‘search’ is not None, print all keys+descriptions where the search string is found

get_dict(group=None, subgroup=None)[source]¶

Returns values dictionary.

Prints values belonging to a certain group only if the ‘group’ argument is one of the following: ‘lattice’, ‘chemistry’, ‘accuracy’, ‘external fields’, ‘scf cycle’, ‘other’

Additionally the subgroups argument allows to print only a subset of all keys in a certain group. The following subgroups are available.

in ‘lattice’ group ‘2D mode’, ‘shape functions’
in ‘chemistry’ group ‘Atom types’, ‘Exchange-correlation’, ‘CPA mode’, ‘2D mode’
in ‘accuracy’ group ‘Valence energy contour’, ‘Semicore energy contour’, ‘CPA mode’, ‘Screening clusters’, ‘Radial solver’, ‘Ewald summation’, ‘LLoyd’

get_missing_keys(use_aiida=False)[source]¶: Find list of mandatory keys that are not yet set

get_set_values()[source]¶: Return a list of all keys/values that are set (i.e. not None)

get_type(key)[source]¶: Extract expected type of ‘key’ from format info

get_value(key)[source]¶: Gets value of keyword ‘key’

is_mandatory(key)[source]¶: Returns mandatory flag (True/False) for keyword ‘key’

items()[source]¶: make kkrparams.items() work

read_keywords_from_inputcard(inputcard='inputcard', verbose=False)[source]¶

Read list of keywords from inputcard and extract values to keywords dict

Example usage: p = kkrparams(); p.read_keywords_from_inputcard(‘inputcard’)
Note: converts ‘<RBLEFT>’, ‘<RBRIGHT>’, ‘ZPERIODL’, and ‘ZPERIODR’ automatically to Ang. units!

remove_value(key)[source]¶: Removes value of keyword ‘key’, i.e. resets to None

set_multiple_values(**kwargs)[source]¶: Set multiple values (in example value1 and value2 of keywords ‘key1’ and ‘key2’) given as key1=value1, key2=value2

set_value(key, value, silent=False)[source]¶: Sets value of keyword ‘key’

static split_kkr_options(valtxt)[source]¶: Split keywords after fixed length of 8 :type valtxt: :param valtxt: list of strings or single string :returns: List of keywords of maximal length 8

update_to_kkrimp()[source]¶: Update parameter settings to match kkrimp specification. Sets self.__params_type and calls _update_mandatory_kkrimp()

update_to_voronoi()[source]¶: Update parameter settings to match voronoi specification. Sets self.__params_type and calls _update_mandatory_voronoi()

Reading of shpefun files of KKR

masci_tools.io.kkr_read_shapefun_info.read_shapefun(path='.')[source]¶

Read vertices of shapefunctions with Zoom into shapefun of a single atom

Author: Philipp Ruessmann
Parameters: path – path where voronoi output is found (optional, defaults to ‘./’)
Returns pos: positions of the centers of the shapefunctions
Returns out: dictionary of the vertices of the shapefunctions

Here I collect all functions needed to parse the output of a KKR calculation. These functions do not need aiida and are therefore separated from the actual parser file where parse_kkr_outputfile is called

masci_tools.io.parsers.kkrparser_functions.check_error_category(err_cat, err_msg, out_dict)[source]¶

Check if parser error of the non-critical category (err_cat != 1) are actually consistent and may be discarded.

Parameters

err_cat – the error-category of the error message to be investigated
err_msg – the error-message
out_dict – the dict of results obtained from the parser function

Returns

True/False if message is an error or warning

masci_tools.io.parsers.kkrparser_functions.get_kmeshinfo(outfile_0init, outfile_000)[source]¶: Extract kmesh info from output.0.txt and output.000.txt

masci_tools.io.parsers.kkrparser_functions.get_lattice_vectors(outfile_0init)[source]¶: read direct and reciprocal lattice vectors in internal units (useful for qdos generation)

masci_tools.io.parsers.kkrparser_functions.get_natom(outfile_0init)[source]¶: extract NATYP value from output.0.txt

masci_tools.io.parsers.kkrparser_functions.get_noco_rms(outfile, debug=False)[source]¶: Get average noco rms error

masci_tools.io.parsers.kkrparser_functions.get_nspin(outfile_0init)[source]¶: extract NSPIN value from output.0.txt

masci_tools.io.parsers.kkrparser_functions.get_orbmom(outfile, natom)[source]¶: read orbmom info from outfile and return array (iteration, atom)=orbmom

masci_tools.io.parsers.kkrparser_functions.get_rms(outfile, outfile2, debug=False)[source]¶: Get rms error per atom (both values for charge and spin) and total (i.e. average) value

masci_tools.io.parsers.kkrparser_functions.get_single_particle_energies(outfile_000)[source]¶: extracts single particle energies from outfile_000 (output.000.txt) returns the valence contribution of the single particle energies

masci_tools.io.parsers.kkrparser_functions.get_spinmom_per_atom(outfile, natom, nonco_out_file=None)[source]¶: Extract spin moment information from outfile and nonco_angles_out (if given)

masci_tools.io.parsers.kkrparser_functions.parse_array_float(outfile, searchstring, splitinfo, replacepair=None, debug=False)[source]¶

Search for keyword searchstring in outfile and extract array of results

Returns: array of results

masci_tools.io.parsers.kkrparser_functions.parse_kkr_outputfile(out_dict, outfile, outfile_0init, outfile_000, timing_file, potfile_out, nonco_out_file, outfile_2='output.2.txt', skip_readin=False, debug=False)[source]¶: Parser method for the kkr outfile. It returns a dictionary with results

masci_tools.io.parsers.kkrparser_functions.use_BdG(outfile_0init)[source]¶: extract BdG run info from output.0.txt

masci_tools.io.parsers.kkrparser_functions.use_newsosol(outfile_0init)[source]¶: extract NEWSOSOL info from output.0.txt

Everything that is needed to parse the output of a voronoi calculation.

masci_tools.io.parsers.voroparser_functions.check_voronoi_output(potfile, outfile, delta_emin_safety=0.1)[source]¶: Read output from voronoi code and create guess of energy contour

masci_tools.io.parsers.voroparser_functions.get_valence_min(outfile='out_voronoi')[source]¶: Construct minimum of energy contour (between valence band bottom and core states)

masci_tools.io.parsers.voroparser_functions.parse_voronoi_output(out_dict, outfile, potfile, atominfo, radii, inputfile, debug=False)[source]¶: Parse output of voronoi calculation and return (success, error_messages_list, out_dict)

Tools for the impurity calculation plugin and its workflows

class masci_tools.io.parsers.kkrimp_parser_functions.KkrimpParserFunctions[source]¶

Class of parser functions for KKRimp calculation

Usage: success, msg_list, out_dict = parse_kkrimp_outputfile().parse_kkrimp_outputfile(out_dict, files)

parse_kkrimp_outputfile(out_dict, file_dict, debug=False)[source]¶

Main parser function for kkrimp, read information from files in file_dict and fills out_dict :type out_dict: :param out_dict: dictionary that is filled with parsed output of the KKRimp calculation :type file_dict: :param file_dict: dictionary of files that are parsed :returns: success (bool), msg_list(list of error/warning messages of parser), out_dict (filled dict of parsed output) :note: file_dict should contain the following keys

‘outfile’, the std_out of the KKRimp calculation

‘out_log’, the out_log.000.txt file

‘out_pot’, the output potential

‘out_enersp_at’, the out_energysp_per_atom_eV file

‘out_enertot_at’, the out_energytotal_per_atom_eV file

‘out_timing’, the timing file

‘kkrflex_llyfac’, the file for the Lloyd factor

‘kkrflex_angles’, the nonco_angles file for the KKRimp calculation

‘out_spinmoms’, the output spin moments file

‘out_orbmoms’, the output orbital moments file

Visualisation and Plotting¶

Fleur specific Plotting¶

KKR specific Plotting¶

General Plotting¶

Matplotlib¶

Bokeh¶

Calculation tools¶

IO helper functions and file parsers¶

KKR related IO¶

Fleur related IO¶

Input/Output Parser¶

Inputgenerator related IO¶

Functions for modifying the input file¶

Functions/Classes for loading/validating fleur XML files¶