From b761579cf7d0c992c74bfab1abead6d6818e675c Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 31 Jul 2024 07:23:37 +0530 Subject: [PATCH 1/4] fix outdated cli tutorial code snippets --- docs/tutorial/commandlineinterface.rst | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/docs/tutorial/commandlineinterface.rst b/docs/tutorial/commandlineinterface.rst index 5cf9ff99..0ab7f13d 100644 --- a/docs/tutorial/commandlineinterface.rst +++ b/docs/tutorial/commandlineinterface.rst @@ -113,10 +113,6 @@ Lobster job submission script Analyze the lobster outputs with automation ------------------------------------------- -.. code:: python - - import os - os.chdir('Basis_0/') # Navigate to directory containing the files of lobster runs 1. Automatic analysis and plotting of COHPs/ICOHPs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -182,7 +178,7 @@ Following is the json file produced. } -- ``lobsterpy calc-description --potcar-symbols "Na_pv Cl" --bvacomp --doscomp`` command will automatically analyze your lobster calculation quality. +- ``lobsterpy description-quality --potcar-symbols "Na_pv Cl" --bvacomp --doscomp`` command will automatically analyze your lobster calculation quality. .. note:: The LOBSTER calculation directory need to have POTCAR, POSCAR, LOBSTER calculation input and output files to run the **lobsterpy calc-description** command successfully. @@ -190,7 +186,7 @@ Following is the json file produced. .. code:: bash - lobsterpy calc-description --potcar-symbols "Na_pv Cl" --bvacomp --doscomp --calcqualityjson calc_quality_description.json + lobsterpy description-quality --potcar-symbols "Na_pv Cl" --bvacomp --doscomp --file-calc-quality-json calc_quality_description.json .. code:: bash @@ -269,7 +265,7 @@ You can plot COHPs/COBIs/COOPs from the command line. .. code:: bash - lobsterpy plot-icohps-distances + lobsterpy plot-icohp-distance .. image:: tutorial_assets/ICOHPs_distance_example.png @@ -290,15 +286,15 @@ either of these commands: .. code:: bash - lobsterpy calc-description -help + lobsterpy create-inputs --help .. code:: bash - lobsterpy create-inputs --help + lobsterpy description --help .. code:: bash - lobsterpy description --help + lobsterpy description-quality --help .. code:: bash @@ -306,7 +302,7 @@ either of these commands: .. code:: bash - lobsterpy plot-icohps-distances --help + lobsterpy plot-icohp-distance --help .. code:: bash From 39ef10c36740cee43f11715d206e1993f28b99ec Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 31 Jul 2024 07:27:27 +0530 Subject: [PATCH 2/4] fix create-inputs cli --- docs/tutorial/commandlineinterface.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorial/commandlineinterface.rst b/docs/tutorial/commandlineinterface.rst index 0ab7f13d..43e31ad3 100644 --- a/docs/tutorial/commandlineinterface.rst +++ b/docs/tutorial/commandlineinterface.rst @@ -27,7 +27,7 @@ Simultaneously, ``lobsterin.lobsterpy`` files are created that are necessary for You can also change the names of output files and path where they are saved using following optional tags: -``lobsterpy create-inputs --incar-out /INCAR --lobsterin-out /lobsterin`` +``lobsterpy create-inputs --file-incar-out /INCAR --file-lobsterin /lobsterin`` For example if ``Cd`` element has two basis sets ``4d 5s`` ``4d 5s 5p``, thus following files are created: From 8b86ad966cd2bb24c4b0290d2f9b10c4eb17e82a Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 31 Jul 2024 07:33:50 +0530 Subject: [PATCH 3/4] fix description json arg --- docs/tutorial/commandlineinterface.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tutorial/commandlineinterface.rst b/docs/tutorial/commandlineinterface.rst index 43e31ad3..15144667 100644 --- a/docs/tutorial/commandlineinterface.rst +++ b/docs/tutorial/commandlineinterface.rst @@ -121,7 +121,7 @@ Analyze the lobster outputs with automation .. code:: bash - lobsterpy description --json description.json + lobsterpy description --file-json description.json .. code:: bash From 21bcd446234141f51db7c6b732114c65f8f555b1 Mon Sep 17 00:00:00 2001 From: naik-aakash Date: Wed, 31 Jul 2024 07:43:12 +0530 Subject: [PATCH 4/4] add missing instruction in cli tutorial --- docs/tutorial/commandlineinterface.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/tutorial/commandlineinterface.rst b/docs/tutorial/commandlineinterface.rst index 15144667..c7bb5993 100644 --- a/docs/tutorial/commandlineinterface.rst +++ b/docs/tutorial/commandlineinterface.rst @@ -113,6 +113,7 @@ Lobster job submission script Analyze the lobster outputs with automation ------------------------------------------- +Navigate to directory containing the files of lobster run and then one can use following commands: 1. Automatic analysis and plotting of COHPs/ICOHPs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~