From df88020565ede7cd8f59038327eeaa62c16b2007 Mon Sep 17 00:00:00 2001 From: gonzex Date: Thu, 21 Nov 2024 12:11:24 +0100 Subject: [PATCH] Improve slightly the examples of LumiWorks. Also fix typos. (#304) * Insert one sentence to explain why conda install --file ./requirements-optional.txt is suggested. * More explanations in the README.rst . * Fix typos. Specify how to get a PMG_MAPI_KEY. * Several minor modifs * Minor modif, slightly more accurate wording. * Transfer the section explaining how to install conda from the abitutorial/README.md file. * Improve the previous commit * And now ... * Next trial * Now should work * Complete README.rst with information coming from abitutorials. Also import the manager directory from abitutorials. * Fix formatting problems. * More formatting fixes. * Continue to work on the README.rst, minor modifs. * Fix links * Commas * Minor correction * Previous modif did not work * Fixes * Unify the environment name, now abienv everywhere (instead of possibly abipy3.6). * Final modifs of README.rst * Fix missing :: in README.rst , causing unformatted apprearance on github. * Remove the managers dir, and update the associated doc. * Write explicitly Setyawan and Curtarolo 2010 * Improve slightly the examples of LumiWorks. Also fix a typo. --------- Co-authored-by: trunk --- abipy/examples/flows/run_gs_vs_kpts.py | 2 +- abipy/examples/flows/run_lumi_Eu_doped_SLA.py | 18 +++++++++--------- abipy/examples/flows/run_lumi_NV_center.py | 8 ++++---- abipy/scripts/abistruct.py | 6 +++--- 4 files changed, 17 insertions(+), 17 deletions(-) diff --git a/abipy/examples/flows/run_gs_vs_kpts.py b/abipy/examples/flows/run_gs_vs_kpts.py index ad2a13696..6a9272003 100755 --- a/abipy/examples/flows/run_gs_vs_kpts.py +++ b/abipy/examples/flows/run_gs_vs_kpts.py @@ -1,6 +1,6 @@ #!/usr/bin/env python r""" -Convergence studiy with different k-meshes +Convergence study with different k-meshes ========================================== In this example, diff --git a/abipy/examples/flows/run_lumi_Eu_doped_SLA.py b/abipy/examples/flows/run_lumi_Eu_doped_SLA.py index 31ddaede6..fcca85c01 100755 --- a/abipy/examples/flows/run_lumi_Eu_doped_SLA.py +++ b/abipy/examples/flows/run_lumi_Eu_doped_SLA.py @@ -1,22 +1,22 @@ #!/usr/bin/env python r""" -Delta SCF constrained occupation method calculation, to determine luminescent properties. -========================================================================================= +Delta SCF calculation: luminescence of an Eu-doped phosphor +=========================================================== -This example shows how to compute the luminescent properties of Eu doped phosphor. -It uses a 36 atoms cell of SrLiAl3N4. Two non-equivalent Sr sites are availabe for Eu, resulting +This example shows how to compute the luminescent properties of an Eu-doped phosphor. +It uses a 36 atoms cell of SrLiAl3N4. Two non-equivalent Sr sites are available for Eu, resulting in two independent LumiWork. The creation of the supercells is done with make_doped_supercell(). Steps, for each structure: -1) Relaxation in the ground state -2) Relaxation in the excited state, starting from the relaxed ground state. Created at run-time +1) Relaxation in the ground state. +2) Relaxation in the excited state, starting from the relaxed ground state. Created at run-time. 3) Scf computation in the relaxed/unrelaxed ground/excited state (4 computations). Even if we use minimal settings, the workflow takes around one hour to run on one core. -Filepaths of the 6 runs are stored in outdata/lumi.json of each work -A quick post-processing is automatically done at the end of a LumiWork +Filepaths of the 6 runs are stored in outdata/lumi.json of each work. +A quick post-processing is automatically done at the end of a LumiWork, and stored in outdata/Delta_SCF.json of each work, with relevant luminescent properties -(ZPL energy, Stoke Shift, \Delta Q,...), see abipy/lumi/delta_scf.py +(ZPL energy, Stoke Shift, \Delta Q,...), see abipy/lumi/delta_scf.py . """ import sys diff --git a/abipy/examples/flows/run_lumi_NV_center.py b/abipy/examples/flows/run_lumi_NV_center.py index f7b48c0cc..f61ef483d 100755 --- a/abipy/examples/flows/run_lumi_NV_center.py +++ b/abipy/examples/flows/run_lumi_NV_center.py @@ -1,15 +1,15 @@ #!/usr/bin/env python r""" -Delta SCF constrained occupation method calculation, to determine luminescent properties. +Delta SCF calculation: luminescence of the NV- center in diamond. ========================================================================================= This example shows how to compute the luminescent properties of the NV- center in diamond. -It uses a 64 atoms supercell, where one C atom was replaced by one N atom and one vacancy was created. +It uses a 64-atom supercell, where one C atom was replaced by one N atom and one vacancy was created. See Fig.3 of https://doi.org/10.1103/PhysRevB.104.045303 for the setting of electron occupation in the ground/excited state. Steps: -1) Relaxation in the ground state -2) Relaxation in the excited state, starting from the relaxed ground state. Created at run-time +1) Relaxation in the ground state. +2) Relaxation in the excited state, starting from the relaxed ground state. Created at run-time. 3) Scf computation in the relaxed/unrelaxed ground/excited state (4 computations). Even if we use minimal settings, the workflow takes a few minutes to run on one core. diff --git a/abipy/scripts/abistruct.py b/abipy/scripts/abistruct.py index 3fad503d7..5f8c3209f 100755 --- a/abipy/scripts/abistruct.py +++ b/abipy/scripts/abistruct.py @@ -60,8 +60,8 @@ def get_epilog() -> str: abistruct.py abisanitize FILE => Read structure from FILE, call abisanitize, compare structures and save "abisanitized" structure to file. abistruct.py conventional FILE => Read structure from FILE, generate conventional structure - following doi:10.1016/j.commatsci.2010.05.010 - abistruct.py proto FILE => Read structure from FILE, find possible crystallographic prototypes + following Setyawan, W., & Curtarolo, S. (2010) doi:10.1016/j.commatsci.2010.05.010 + abistruct.py proto FILE => Read structure from FILE, find possible crystallographic prototypes: in the AFLOW library of crystallographic prototypes. See http://doi.org/10.1016/j.commatsci.2017.01.017 @@ -290,7 +290,7 @@ def add_format_arg(parser, default, option=True, formats=None): # Subparser for conventional. p_conventional = subparsers.add_parser('conventional', parents=[copts_parser, path_selector, spgopt_parser, savefile_parser], help="Gives a structure with a conventional cell according to certain standards. " - "The standards are defined in doi:10.1016/j.commatsci.2010.05.010") + "The standards are defined in Setyawan, W., & Curtarolo, S. (2010) doi:10.1016/j.commatsci.2010.05.010") # Subparser for proto. p_proto = subparsers.add_parser('proto', parents=[copts_parser, path_selector],