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VsevolodXVsevolodX
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Merge pull request #98 from Exabyte-io/feature/SOF-7776
Feature/SOF-7776 WFN
2 parents cdd4d6c + 757f336 commit 7951b92

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-9
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29 files changed

+1232
-9
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‎assets/applications/executables/espresso/pp.x.yml‎

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- standard_output
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applicationName: espresso
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executableName: pp.x
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pp_wfn:
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input:
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- name: pp_wfn.in
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results:
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- wavefunction_amplitude
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monitors:
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- standard_output
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applicationName: espresso
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executableName: pp.x

‎assets/applications/executables/python/python.yml‎

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applicationName: python
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executableName: python
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plot_wavefunction:
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input:
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- name: script.py
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templateName: plot_wavefunction.py
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- name: requirements.txt
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templateName: requirements_plot_wavefunction.txt
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results:
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- name: file_content
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filetype: image
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basename: "wf_r.png"
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monitors:
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- standard_output
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applicationName: python
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executableName: python
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'generic:post_processing:plot:matplotlib':
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input:
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- name: plot.py

‎assets/applications/input_files_templates/espresso/pp_wfn.j2.in‎

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&INPUTPP
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outdir = {% raw %}'{{ JOB_WORK_DIR }}/outdir'{% endraw %}
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prefix = '__prefix__'
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plot_num = 7
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kpoint = 1
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kband = {% raw %}{{ KBAND_VALUE | default(1) }}{% endraw %}
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lsign = .true.
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/
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&PLOT
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iflag = 1
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fileout = 'wf_r.dat'
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output_format = 0
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x0(1) = 0.0, x0(2) = 0.0, x0(3) = 0.0
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e1(1) = 0.0, e1(2) = 0.0, e1(3) = {{material.lattice.c/material.lattice.a}}
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nx = 200
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/

‎assets/applications/input_files_templates/python/plot_wavefunction.pyi‎

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# ---------------------------------------------------------------- #
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# Generate wavefunction plot from pp.x output #
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# And saves static #
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# ---------------------------------------------------------------- #
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import matplotlib
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import numpy as np
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matplotlib.use('Agg') # Non-interactive backend
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import matplotlib.pyplot as plt
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# Load wavefunction data from pp.x output
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data = np.loadtxt('wf_r.dat')
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z = data[:, 0]
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psi_r = data[:, 1]
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# Calculate wavefunction amplitude
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psi_amplitude = np.abs(psi_r)
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# Create static PNG plot
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fig, ax = plt.subplots(figsize=(10, 6))
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ax.plot(z, psi_amplitude, 'b-', linewidth=2)
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ax.set_xlabel('Position z (alat)', fontsize=12)
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ax.set_ylabel('Wavefunction amplitude |ψ| (a.u.)', fontsize=12)
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ax.set_title('Wavefunction along z-axis', fontsize=14)
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ax.grid(True, alpha=0.3)
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plt.tight_layout()
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plt.savefig('wf_r.png', dpi=150, bbox_inches='tight')
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plt.close()

‎assets/applications/input_files_templates/python/requirements_plot_wavefunction.j2.txt‎

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# ------------------------------------------------------------------ #
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# #
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# Python package requirements for plot_wavefunction unit #
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# #
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# ------------------------------------------------------------------ #
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numpy<2
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matplotlib
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‎assets/applications/templates/espresso/pp.x.yml‎

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contextProviders: []
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applicationName: espresso
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executableName: pp.x
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- content: !readFile 'input_files_templates/espresso/pp_wfn.j2.in'
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name: pp_wfn.in
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contextProviders: []
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applicationName: espresso
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executableName: pp.x

‎assets/applications/templates/python/python.yml‎

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applicationName: python
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executableName: python
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- content: !readFile 'input_files_templates/python/plot_wavefunction.pyi'
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name: plot_wavefunction.py
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contextProviders: []
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applicationName: python
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executableName: python
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- content: !readFile 'input_files_templates/python/requirements_plot_wavefunction.j2.txt'
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name: requirements_plot_wavefunction.txt
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contextProviders: []
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applicationName: python
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executableName: python
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- content: !readFile 'input_files_templates/python/espresso_extract_kpoints.pyi'
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name: espresso_extract_kpoints.py
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contextProviders: []

‎assets/workflows/subworkflows/categories.yml‎

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- total_energy_contributions
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- total_force
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- valence_band_offset
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- wavefunction_amplitude
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- workflow:pyml_predict
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- zero_point_energy
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tags:
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- remove-all-results
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- set-io-unit-filenames
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- variable-cell_relaxation
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- wfn
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- wfn_plot
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application:
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- espresso
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- nwchem
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- espresso
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- phonon_dispersions
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- phonon_dos
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- filename: espresso/plot_wavefunction.json
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categories:
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- espresso
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- file_content
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- python
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- filename: espresso/post_processor.json
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categories:
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- espresso
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- total_energy
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- total_force
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- variable-cell_relaxation
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- filename: espresso/wavefunction_amplitude.json
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categories:
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- atomic_forces
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- band_structure
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- espresso
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- fermi_energy
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- pressure
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- stress_tensor
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- total_energy
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- total_energy_contributions
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- total_force
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- wavefunction_amplitude
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- wfn
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- wfn_plot
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- filename: espresso/zero_point_energy.json
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categories:
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- atomic_forces

‎assets/workflows/subworkflows/espresso/plot_wavefunction.yml‎

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application:
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name: python
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version: 3.10.13
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method:
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name: UnknownMethod
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model:
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name: UnknownModel
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name: Plot Wavefunction
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properties:
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- file_content
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units:
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- attributes:
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results:
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- name: file_content
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basename: "wf_r.png"
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filetype: "image"
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config:
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execName: python
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flavorName: plot_wavefunction
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name: plot WFN
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type: executionBuilder
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‎assets/workflows/subworkflows/espresso/wavefunction_amplitude.yml‎

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application:
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name: espresso
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version: '6.3'
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method:
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name: PseudopotentialMethod
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model:
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name: DFTModel
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name: Wavefunction Amplitude
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properties:
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- atomic_forces
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- fermi_energy
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- pressure
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- stress_tensor
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- total_energy
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- total_energy_contributions
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- total_force
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- band_structure
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- wavefunction_amplitude
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units:
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- config:
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execName: pw.x
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flavorName: pw_scf
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name: pw_scf
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flowchartId: pw-scf
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functions:
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head: true
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type: executionBuilder
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attributes:
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results:
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- name: atomic_forces
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- name: band_structure
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- name: fermi_energy
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- name: pressure
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- name: stress_tensor
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- name: total_energy
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- name: total_energy_contributions
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- name: total_force
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- config:
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name: Extract Band Energies
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operand: band_energies
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value: >-
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[band_data[0] for band_data in (band_structure['yDataSeries'] if (band_structure and
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'yDataSeries' in band_structure) else [])]
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flowchartId: extract-band-energies
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input:
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- name: band_structure
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scope: pw-scf
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type: assignment
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- config:
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name: Find Indices Below Fermi
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operand: indices_below_fermi
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value: "[i for i in range(len(band_energies)) if band_energies[i] <= fermi_energy]"
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flowchartId: indices-below-fermi
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input:
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- name: fermi_energy
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scope: pw-scf
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type: assignment
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- config:
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name: Store Band Below EF
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operand: KBAND_VALUE_BELOW_EF
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value: "indices_below_fermi[-1] + 1 if len(indices_below_fermi) > 0 else 1"
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type: assignment
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- config:
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name: Select Band
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operand: KBAND_VALUE
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value: "KBAND_VALUE_BELOW_EF"
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type: assignment
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- config:
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execName: pp.x
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flavorName: pp_wfn
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name: pp_wfn
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flowchartId: pp-wfn
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input:
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- name: KBAND_VALUE
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type: executionBuilder
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attributes:
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results:
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- name: wavefunction_amplitude
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tags:
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- wfn
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- wfn_plot
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