Bandstructure wf #45

RubelMozumder · 2020-12-02T14:02:36Z

Add bandstructure workflow

PhilippRue

Thank you @RubelMozumder. I left a few comments for improvements.

What is still needed in addition:

you started from the stale branch develop_workflow_conventions. Please merge the develop into Bandstructure_wf to get the latest changes (use git merge --no-ff develop on your Bandstructure_wf branch to do so)
add an entry point in the setup.json
add a test for the bandstructure functionality see here for an example
add documentation
add/replace plotting functionality in plot_kkr tool to work with you workflow
make you workflow importable: from aiida_kkr.workflows import kkr_BS_wc

PhilippRue · 2020-12-04T07:34:31Z

aiida_kkr/workflows/BandStructure_WF.py

+__copyright__ = u"This is the Copyright"
+__license__ = "Here is the license"
+__version__ = "Here is the version"
+__contributors__ = "using technique from Philpp RÜssmann's DOS wf"


This should contain the actual information and not just a placeholder

copyright: FZJ

license: MIT license

version: start with 0.1.0

contributors: your name

PhilippRue · 2020-12-04T07:35:47Z

aiida_kkr/workflows/BandStructure_WF.py

+    Workchain for BandStructure calculation, starting from RemoteFolderData the previous converged KKR calculation remote folder data
+
+    inputs:
+    :param wf_parameters: (Dict), (optional); Workchain Specifications, contains npt2, tempr, emin(ev), emax(ev), kmesh
+                          keys. The Energy emin and emax are the energy difference from the fermi energy.
+
+    :param options: (Dict), (optional); Computer Specifications, Schedualer command, parallel or serial
+    :param kpoints: (KpointsData),(optional); Kpoints data type from thestructure,
+                                   but not mendatory as it can be extrruct from structure internaly from the remote data
+    :param remote_data: (RemoteData)(mendaory); From the previous kkr-converged calcualtion.
+    :param kkr: (Code)(mendaory); KKR code specifiaction
+    :param label: (Str): 
+    :param description: (Str): 


fix types and complete missing information

PhilippRue · 2020-12-04T07:37:39Z

aiida_kkr/workflows/BandStructure_WF.py

+
+    returns:
+    :out BS_Data : (ArrayData) ; Consist of (Dos_intensity matrix), k_points (list), Energy_levels (list), special_kpoints(dict)
+    :out result_wf: (Dict); work_chain_specifications node, BS_data node, remote_folder node  


why do you want to return the remote folder node? It is not needed to continue a calculation from the output of the bandstructure calculation. So we should not expose this.

PhilippRue · 2020-12-04T07:39:05Z

aiida_kkr/workflows/BandStructure_WF.py

+
+
+    returns:
+    :out BS_Data : (ArrayData) ; Consist of (Dos_intensity matrix), k_points (list), Energy_levels (list), special_kpoints(dict)


rename:

Dos_intensity matrix -> BlochSpectralFunction

Energy_levels -> energy_points

PhilippRue · 2020-12-04T07:40:44Z

aiida_kkr/workflows/BandStructure_WF.py

+                        'EMAX': 5,     # Energy over the fermi surface for energy contour in ev unit
+                        "NPT2": 200,   # Energy points in the energy contour
+                        "kmesh": [30, 30, 30],
+                        'TEMPR': 50.   # temperature


we should add the possibility to overwrite the cluster radius (RCLUSTZ) as well

Why do the RCLUSTZ will have any impact on the on the DOS calc? Because, it is already converged.

for a qdos calculation you run at much lower values of the imaginary part of the energies (given by NPOL=0 and a small value of the temperature). This puts higher demands on the numerics which in the end require larger screening clusters. Otherwise you will see negative densities.

PhilippRue · 2020-12-04T08:01:57Z

aiida_kkr/workflows/BandStructure_WF.py

+            loaded_file = np.loadtxt(f)
+            total_dos[:,5:] += loaded_file[:,5:]
+
+    ef = fermi_level.value # in eV unit


this is in Ry, the conversion to eV units is only done in the next line!

In [5]: ef = out['fermi_energy'] In [6]: ef Out[6]: 0.6360325445 In [12]: ef = out['fermi_energy'] In [13]: eng_unit = out['energy_unit'] In [14]: eng_unit Out[14]: 'eV'

This is from output_parameter of the parent cal. This make me a bit confused as I extract the value in the same way.

the energy_unit refers to the energy value and the fermi_energy_unit gives you the unit of the fermi_energy which is in Ry and not in eV

Oh, sorry. Thanks.

PhilippRue · 2020-12-04T08:02:41Z

aiida_kkr/workflows/BandStructure_WF.py

+            total_dos[:,5:] += loaded_file[:,5:]
+
+    ef = fermi_level.value # in eV unit
+    total_dos[:,0] = total_dos[:,0]*eVscale - ef*np.ones(np.shape(total_dos[:,0]))


you could also write total_dos[:,0] = (total_dos[:,0]-ef)*eVscale

PhilippRue · 2020-12-04T08:04:06Z

aiida_kkr/workflows/BandStructure_WF.py

+
+    dos_intensity = dos_intensity.T # setting eng-kpts corresponds to x-y asix
+    q_vec = np.asarray(q_vec) # converting q_vec into array
+    eng_points = np.asarray(list(eng_points)) # converting eng_popints into array


since eng_points is a set before, you should make sure to sort the array afterwards

PhilippRue · 2020-12-04T08:04:30Z

aiida_kkr/workflows/BandStructure_WF.py

+    array.set_array('BS_Matrix', dos_intensity)
+    array.set_array('Kpts', q_vec)
+    array.set_array('Eng_levels',eng_points)


rename as commented above

PhilippRue · 2020-12-04T08:15:44Z

aiida_kkr/workflows/BandStructure_WF.py

+
+
+
+class kkr_BS_wf(WorkChain):


rename to kkr_bs_wc to be consistent with the other workflow names

…ing explanation and datatype, the removal of the 'remote_folder' from the output of the WC, using the conventional name 'Dos_intensity matrix -> BlochSpectralFunction', 'Energy_levels -> energy_points', To 'RCLUSTZ' to the bs_param, removal the k-mesh from the bs_param, changing the 'wf_option_default' to the normal specifications from the CLAIX18, to set the 'exit_codes' instead of the 'if_' condition, return exit_code instead of raising and Error in case the parent_workflow is not the WorkChainNode, fixning the error for the units of energy (eV, Ry), removing the unnecessary keyword 'BZDIVIDE', sending a report informing the structure of the unitcell, return the exit_codes fro the 'dos_run=Flase', fixining the energy units, removing the unneccessary function 'ev_To_Ry', renaming 'total_dos# to 'total_qdos'and 'num_dos_files' to the 'num_qdos_files', adding 'total_dos[:,0] = (total_dos[:,0]-ef)*eVscale' instead of 'total_dos[:,0] = total_dos[:,0]*eVscale - ef*np.ones(np.shape(total_dos[:,0]))', to make the 'eng_points' array immediately after the set of 'eng_points', to transform 'Dos_intensity matrix -> BlochSpectralFunction', 'Energy_levels -> energy_points' as convention, to rewrite the 'kkr_BS_wf' to 'kkr_bs_wc'.

RubelMozumder and others added 5 commits December 1, 2020 20:27

Add files via upload

6036ff5

Removed comment line

27f9aae

Some kind of completed BS_wf

9086178

Update BandStructure_WF.py

fc9b502

deleting some empty lins

d5fbed1

PhilippRue self-requested a review December 3, 2020 17:11

PhilippRue requested changes Dec 4, 2020

View reviewed changes

RubelMozumder added 10 commits December 7, 2020 15:03

After some changes of bandstructure workflow

f9a90db

After some changes

7aee0d4

After some changes

a72086c

To add an entry point for bs.py wc in the setup.json

b1cd6c7

correction energy-unit

3d3168d

energy correction

02f4761

energy correction

8b1d511

incorporation of data folder

9a060ee

Incorporatioin of the test for the Bandstructure Calc

afcd2fc

RubelMozumder merged commit b529fd3 into develop Dec 18, 2020

RubelMozumder mentioned this pull request Dec 18, 2020

Request to for the inspection of bandstructure and all the relevant lfiles #50

Closed

RubelMozumder mentioned this pull request Jan 4, 2021

Revert "Bandstructure wf" #51

Closed

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Bandstructure wf #45

Bandstructure wf #45

RubelMozumder commented Dec 2, 2020

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		returns:
		:out BS_Data : (ArrayData) ; Consist of (Dos_intensity matrix), k_points (list), Energy_levels (list), special_kpoints(dict)




		class kkr_BS_wf(WorkChain):

Bandstructure wf #45

Bandstructure wf #45

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RubelMozumder commented Dec 2, 2020

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