Python k point convergence tester using Quantum Espresso

andrewsalij/Convergence-Tracker.md

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+# K-point convergence tracker (Materials)
+
+Dependencies for this project may be installed by running in the following install script.
+
+```bash
+pip install numpy matplotlib 
+pip install pymatgen
+pip install pydantic 
+```
+
+Tests (see Scripts folder) have been run on a variety of materials, whose provenance is below:
+
+Materials Project
+link: https://legacy.materialsproject.org/
+(DOI: 10.1063/1.4812323)
+(CC-BY 4.0, https://creativecommons.org/licenses/by/4.0/legalcode), see https://legacy.materialsproject.org/terms
+
+Si2 (mp-149) (DOI 10.17188/1190959) (https://legacy.materialsproject.org/materials/mp-149/)
+
+Materials Cloud three-dimensional crystals database (MC3D) 
+link: https://archive.materialscloud.org/record/2022.38
+(DOI: 10.24435/materialscloud:rw-t0)
+(CC-BY 4.0, https://creativecommons.org/licenses/by/4.0/legalcode)
+
+
+GaN (mc3d-3763/pbe)
+BN (mc3d-13290/pbe)
+O4Ru2 (mc3d-1930/pbe)
+Br4Ca2 (mc3d-30836/pbe)
+Cs2La2Te6Zn2 (mc3d-11071/pbe)
+F2Fe2O8S2 (mc3d-14425/pbe)
+
+Materials Cloud two-dimensional crystals database (MC2D)
+link: https://archive.materialscloud.org/record/2020.158
+DOI:10.24435/materialscloud:az-b2 
+DOI:10.24435/materialscloud:36-nd (expansion)
+(CC-BY 4.0, https://creativecommons.org/licenses/by/4.0/legalcode)
+
+C (graphene, from graphite exfoliation) (https://www.materialscloud.org/discover/mc2d/details/C, graphite (2H) initial)
+MoS2 (https://www.materialscloud.org/discover/mc2d/details/MoS2-MoS2)
+AgCO2 (https://www.materialscloud.org/discover/mc2d/details/AgCO2)
+
+
+Pseudopotentials Tested:
+PBEsol (standard accuracy) NC SR ONCVPSP 0.4.1 from Pseudo Dojo 
+	Paper: 10.1016/j.cpc.2018.01.012 arxiv preprint 
+	Method Paper: 10.1103/PhysRevB.88.085117
+	License: (CC-BY 4.0, https://creativecommons.org/licenses/by/4.0/legalcode) 
+	(see https://github.com/PseudoDojo/pseudodojo)
+
+
+> Ideal candidate: scientists skilled in Density Functional Theory and proficient in python.
+
+# Overview
+
+The aim of this task is to create a python package that implements automatic convergence tracking mechanism for a materials simulations engine. The convergence is tracked with respect to the k-point sampling inside a reciprocal cell of a crystalline compound.
+
+# Requirements
+
+1. automatically find the dimensions of a k-point mesh that satisfy a certain criteria for total energy (eg. total energy is converged within dE = 0.01meV)
+1. the code shall be written in a way that can facilitate easy addition of convergence wrt other characteristics extracted from simulations (forces, pressures, phonon frequencies etc)
+1. the code shall support VASP or Quantum ESPRESSO
+
+# Expectations
+
+- correctly find k-point mesh that satisfies total energy convergence parameters for a set of 10 materials, starting from Si2, as simplest, to a 10-20-atom supercell of your choice
+- modular and object-oriented implementation
+- commit early and often - at least once per 24 hours
+
+# Timeline
+
+We leave exact timing to the candidate. Must fit Within 5 days total.
+
+# User story
+
+As a user of this software I can start it passing:
+
+- path to input data (eg. pw.in / POSCAR, INCAR, KPOINTS) and
+- kinetic energy cutoff
+
+as parameters and get the k-point dimensions (eg. 5 5 5).
+
+# Notes
+
+- create an account at exabyte.io and use it for the calculation purposes
+- suggested modeling engine: Quantum ESPRESSO

andrewsalij/Licenses/matplotlib_LICENSE

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+License agreement for matplotlib versions 1.3.0 and later
+=========================================================
+
+1. This LICENSE AGREEMENT is between the Matplotlib Development Team
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+otherwise using matplotlib software in source or binary form and its
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+hereby grants Licensee a nonexclusive, royalty-free, world-wide license
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+derivative works, distribute, and otherwise use matplotlib
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+License Agreement and MDT's notice of copyright, i.e., "Copyright (c)
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+matplotlib  alone or in any derivative version prepared by
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+DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
+FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF MATPLOTLIB
+WILL NOT INFRINGE ANY THIRD PARTY RIGHTS.
+
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+ FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR
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+MATPLOTLIB , OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF
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+8. By copying, installing or otherwise using matplotlib ,
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+License agreement for matplotlib versions prior to 1.3.0
+========================================================
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+Individual or Organization ("Licensee") accessing and otherwise using
+matplotlib software in source or binary form and its associated
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+2. Subject to the terms and conditions of this License Agreement, JDH
+hereby grants Licensee a nonexclusive, royalty-free, world-wide license
+to reproduce, analyze, test, perform and/or display publicly, prepare
+derivative works, distribute, and otherwise use matplotlib
+alone or in any derivative version, provided, however, that JDH's
+License Agreement and JDH's notice of copyright, i.e., "Copyright (c)
+2002-2011 John D. Hunter; All Rights Reserved" are retained in
+matplotlib  alone or in any derivative version prepared by
+Licensee.
+
+3. In the event Licensee prepares a derivative work that is based on or
+incorporates matplotlib  or any part thereof, and wants to
+make the derivative work available to others as provided herein, then
+Licensee hereby agrees to include in any such work a brief summary of
+the changes made to matplotlib.
+
+4. JDH is making matplotlib  available to Licensee on an "AS
+IS" basis.  JDH MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR
+IMPLIED.  BY WAY OF EXAMPLE, BUT NOT LIMITATION, JDH MAKES NO AND
+DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS
+FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF MATPLOTLIB
+WILL NOT INFRINGE ANY THIRD PARTY RIGHTS.
+
+5. JDH SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF MATPLOTLIB
+ FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR
+LOSS AS A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING
+MATPLOTLIB , OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF
+THE POSSIBILITY THEREOF.
+
+6. This License Agreement will automatically terminate upon a material
+breach of its terms and conditions.
+
+7. Nothing in this License Agreement shall be deemed to create any
+relationship of agency, partnership, or joint venture between JDH and
+Licensee.  This License Agreement does not grant permission to use JDH
+trademarks or trade name in a trademark sense to endorse or promote
+products or services of Licensee, or any third party.
+
+8. By copying, installing or otherwise using matplotlib,
+Licensee agrees to be bound by the terms and conditions of this License
+Agreement.

andrewsalij/Licenses/numpy_LICENSE.txt

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+Copyright (c) 2005-2023, NumPy Developers.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+
+    * Redistributions in binary form must reproduce the above
+       copyright notice, this list of conditions and the following
+       disclaimer in the documentation and/or other materials provided
+       with the distribution.
+
+    * Neither the name of the NumPy Developers nor the names of any
+       contributors may be used to endorse or promote products derived
+       from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

andrewsalij/Licenses/pydantic_LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2017 to present Pydantic Services Inc. and individual contributors.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

andrewsalij/Licenses/pymatgen_LICENSE

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+The MIT License (MIT)
+Copyright (c) 2011-2012 MIT & The Regents of the University of California,
+through Lawrence Berkeley National Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

andrewsalij/Scripts/AgCO2_2D/run_sweep_agco2.py

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+import os
+import andrewsalij.convergence_tracker as convergence_tracker
+
+'''Script for testing that k sweeping is working for 2D material AgCo2.'''
+
+INPUT_BASE_FOLDER  = "/home/andrew/Documents/MaterialsDB/pwscf_files/"
+RUN_BASE_FOLDER = "/home/andrew/Documents/QE_Runs"
+os.makedirs(RUN_BASE_FOLDER,exist_ok=True)
+
+compound_str = "agco2_2d"
+
+input = compound_str+".in"
+filepath = os.sep.join((INPUT_BASE_FOLDER,input))
+
+run_sub_dir = compound_str+"_k_sweep"
+run_directory = os.sep.join((RUN_BASE_FOLDER,run_sub_dir))
+convergence_tester = convergence_tracker.KPointConvergenceTester(filepath,output_dir = run_directory)
+
+k_array_conv = convergence_tester.find_convergence(-.03,run_prefix_str="mpirun -np 4")
+
+convergence_tester.make_report_figure(compound_str+"_k_converged.png",x_axis_type="convergence_parameter")

andrewsalij/Scripts/BN/run_sweep_bn.py

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+import os
+import andrewsalij.convergence_tracker as convergence_tracker
+
+'''Script for testing that k sweeping is working for boron nitride.'''
+
+INPUT_BASE_FOLDER  = "/home/andrew/Documents/MaterialsDB/pwscf_files/"
+RUN_BASE_FOLDER = "/home/andrew/Documents/QE_Runs"
+os.makedirs(RUN_BASE_FOLDER,exist_ok=True)
+
+compound_str = "bn"
+
+input = compound_str+".in"
+filepath = os.sep.join((INPUT_BASE_FOLDER,input))
+
+run_sub_dir = compound_str+"_k_sweep"
+run_directory = os.sep.join((RUN_BASE_FOLDER,run_sub_dir))
+convergence_tester = convergence_tracker.KPointConvergenceTester(filepath,output_dir = run_directory)
+
+k_array_conv = convergence_tester.find_convergence(-.001,run_prefix_str="mpirun -np 4",
+                                                   k_index=2,k_step=1,k_iterator_init=3)
+
+convergence_tester.make_report_figure(compound_str+"_k_converged.png",x_axis_type="convergence_parameter")

andrewsalij/Scripts/Br4Ca2/run_sweep_br4ca2.py

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+import os
+import andrewsalij.convergence_tracker as convergence_tracker
+
+'''Script for testing that k sweeping is working for Br4Ca2. Also tests that lattice weighting is working
+and that k iteration varies well '''
+
+INPUT_BASE_FOLDER  = "/home/andrew/Documents/MaterialsDB/pwscf_files/"
+RUN_BASE_FOLDER = "/home/andrew/Documents/QE_Runs"
+os.makedirs(RUN_BASE_FOLDER,exist_ok=True)
+
+compound_str = "br4ca2"
+
+input = compound_str+".in"
+filepath = os.sep.join((INPUT_BASE_FOLDER,input))
+
+run_sub_dir = compound_str+"_k_sweep"
+run_directory = os.sep.join((RUN_BASE_FOLDER,run_sub_dir))
+convergence_tester = convergence_tracker.KPointConvergenceTester(filepath,output_dir = run_directory)
+
+k_array_conv = convergence_tester.find_convergence(-.005,run_prefix_str="mpirun -np 4",weight_type = "lattice",k_index=1,k_step=1,k_iterator_init=1)
+
+convergence_tester.make_report_figure(compound_str+"_k_converged.png",x_axis_type="convergence_parameter")

andrewsalij/Scripts/CsLaZnTe/run_sweep_cslaznte.py

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+import os
+import andrewsalij.convergence_tracker as convergence_tracker
+
+'''Script for testing that k sweeping is working for rare-earth complex (Cs2La2Te6Zn2). Also tests parallelism of run command'''
+
+INPUT_BASE_FOLDER  = "/home/andrew/Documents/MaterialsDB/pwscf_files/"
+RUN_BASE_FOLDER = "/home/andrew/Documents/QE_Runs"
+os.makedirs(RUN_BASE_FOLDER,exist_ok=True)
+
+compound_str = "cslaznte"
+
+input = compound_str+".in"
+filepath = os.sep.join((INPUT_BASE_FOLDER,input))
+
+run_sub_dir = compound_str+"_k_sweep"
+run_directory = os.sep.join((RUN_BASE_FOLDER,run_sub_dir))
+convergence_tester = convergence_tracker.KPointConvergenceTester(filepath,output_dir = run_directory)
+
+k_array_conv = convergence_tester.find_convergence(-.1,run_prefix_str="mpirun -np 4",max_iterations=10)
+
+convergence_tester.make_report_figure(compound_str+"_k_converged.png",x_axis_type="convergence_parameter")

andrewsalij/Scripts/F2Fe2O8S2/run_sweep_ffeos.py

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+import os
+import andrewsalij.convergence_tracker as convergence_tracker
+
+'''Script for testing that k sweeping is working for rare-earth complex (C2Ce2Os4P2). Also tests that lattice weighting is working'''
+
+INPUT_BASE_FOLDER  = "/home/andrew/Documents/MaterialsDB/pwscf_files/"
+RUN_BASE_FOLDER = "/home/andrew/Documents/QE_Runs"
+os.makedirs(RUN_BASE_FOLDER,exist_ok=True)
+
+compound_str = "ffeos_simple"
+#TODO add parser support for magnetization
+#there is a bug in the pymatgen parser that prevents 'scf' calculations running w/ magnetization
+
+input = compound_str+".in"
+filepath = os.sep.join((INPUT_BASE_FOLDER,input))
+
+run_sub_dir = compound_str+"_k_sweep"
+run_directory = os.sep.join((RUN_BASE_FOLDER,run_sub_dir))
+convergence_tester = convergence_tracker.KPointConvergenceTester(filepath,output_dir = run_directory)
+
+k_array_conv = convergence_tester.find_convergence(-.1,run_prefix_str="mpirun -np 4",weight_type = "uniform",max_iterations=10)
+
+convergence_tester.make_report_figure(compound_str+"_k_converged.png",x_axis_type="convergence_parameter")