Tips for ABINIT users and developers

User Tools

Site Tools

Trace:
beauty:2020

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
beauty:2020 [2020/12/10 16:25] – [Remove the use of ixc] Xavier Gonzebeauty:2020 [2020/12/11 09:04] (current) – [Latex formulas or other markdown style improvement] Xavier Gonze
Line 14: Line 14:
   - If any, remove the use of ixc in tutorial.    - If any, remove the use of ixc in tutorial. 
   - Get rid of the files file mention in the tutorial.   - Get rid of the files file mention in the tutorial.
 +  - Change the input file suffix from .in to .abi, and the output file suffix from .out to .abo
   - Upgrade the pieces of input and output files that are present in the tutorial, and upgrade associated comments   - Upgrade the pieces of input and output files that are present in the tutorial, and upgrade associated comments
   - Translate mathematical objects to latex formulas if not yet done, also improve markdown style/formatting ...   - Translate mathematical objects to latex formulas if not yet done, also improve markdown style/formatting ...
  
 Steps 1-5 will need upgrading the input and reference files, without modifying the text of the tutorial. Steps 1-5 will need upgrading the input and reference files, without modifying the text of the tutorial.
-Steps 6-8 needs the input files and reference output files to be "frozen", at which time you can go through the text of the tutorial and upgrade it. +Steps 6-9 needs the input files and reference output files to be "frozen", at which time you can go through the text of the tutorial and upgrade it. 
 All this cannot be done automatically: human work is needed.  All this cannot be done automatically: human work is needed. 
  
Line 39: Line 40:
 Then gauge what is to be done : Then gauge what is to be done :
   - First visualize the current status of your tutorial, using ./mksite.py serve, which needs [[beauty:2020#i_have_not_yet_familiarized_myself_with_abimkdocs_markdown|familiarization with abimkdocs]]. Perhaps go through your tutorial(s) quickly.   - First visualize the current status of your tutorial, using ./mksite.py serve, which needs [[beauty:2020#i_have_not_yet_familiarized_myself_with_abimkdocs_markdown|familiarization with abimkdocs]]. Perhaps go through your tutorial(s) quickly.
-  - Look at an example : the first basic tutorial, first from the Web, <https://docs.abinit.org/tutorial/base1>, then from the current ABINIT, likely your local http://127.0.0.1:8000 after you have launched ./mksite.py serve.+  - Look at an example : the first basic tutorial, first from the Web, <https://docs.abinit.org/tutorial/base1>, then from the current ABINIT, likely your local http://127.0.0.1:8000 after you have issued */*/makemake and launched the server with ./mksite.py serve.
  
 Then beautify the tutorial. The five first steps might induce modification of the input files and reference output files. In order to save your (human) time, Then beautify the tutorial. The five first steps might induce modification of the input files and reference output files. In order to save your (human) time,
Line 49: Line 50:
 ==== Adjust input variables ==== ==== Adjust input variables ====
 As an example, in tbase1_3.abi, previously toldff was used for the structural relaxation, while the current practice favors using tolrff . As an example, in tbase1_3.abi, previously toldff was used for the structural relaxation, while the current practice favors using tolrff .
-So toldff has been replaced by tolrff...+So toldff has been replaced by tolrff.
  
 ==== Structure the input files according to a model ==== ==== Structure the input files according to a model ====
Line 58: Line 59:
  
 ==== Remove superfluous variables ==== ==== Remove superfluous variables ====
-This did not happen in tbase1. Still, you might give some thought to the possibility to have a large simplification of the input files+ 
 +No superfluous input variable has been removed in tbase1_*.in.  
 + 
 +Still, there is the possibility to have a large simplification of the input files
 if several of them share exactly the same set of atoms and their positions. if several of them share exactly the same set of atoms and their positions.
 In this case, think using the "structure" variable (see the description of this input variable from the doc), and define the structure once for all in a separate common file. You will have to choose between the abivar, poscar or netcdf format for such file. In this case, think using the "structure" variable (see the description of this input variable from the doc), and define the structure once for all in a separate common file. You will have to choose between the abivar, poscar or netcdf format for such file.
 +
 +Well, this might have been possible in the tbase1 tutorial, but after consideration, such simplification was discarded in order not to introduce one more concept in this tutorial, which is already quite long.
  
 ==== Remove the use of ixc ==== ==== Remove the use of ixc ====
Line 70: Line 76:
 When the input files and reference files are ready, it is time to focus on the text of the tutorial itself. Advice : redo it step-by-step, When the input files and reference files are ready, it is time to focus on the text of the tutorial itself. Advice : redo it step-by-step,
 checking that the user will not meet an incoherency, either preexisting to this beautification, or created by the beautification. checking that the user will not meet an incoherency, either preexisting to this beautification, or created by the beautification.
-While redoing the tutorial step-by-step, pay attention to the fact that the files file does not exist anymore. There were a couple of such mentions in tbase1_1 .+While redoing the tutorial step-by-step, pay attention to the fact that the files file does not exist anymore. There were a couple of such mentions in tbase1. 
 + 
 +==== Change file suffixes ==== 
 +Change the input file suffix from .in to .abi, and the output file suffix from .out to .abo . In the tbase1_1.md file, this was needed at numerous places, in the main text, but also in the dialog boxes : 
 +replacing  
 + 
 +    {% dialog tests/tutorial/Input/tbase1_1.in %} 
 +by  
 + 
 +    {% dialog tests/tutorial/Input/tbase1_1.abi %}
  
  
 ==== Upgrade the pieces of input/output files present in the tutorial ==== ==== Upgrade the pieces of input/output files present in the tutorial ====
 Changing the pseudopotential, or any other change to active input variable in the input file will trigger modification of the output file as well. Changing the pseudopotential, or any other change to active input variable in the input file will trigger modification of the output file as well.
-In order for the students not to be lost (and for the tutorial to be clean), it is important to copy again the excerpts of the input/output files that are obsolete. This is also to be done for the figures ... In case of trouble, do not hesitate to start an issue on gitlab. We might benefit from each other expertise using this channel.+In order for the students not to be lost (and for the tutorial to be clean), it is important to copy again the excerpts of the input/output files that are obsolete. This is also to be done for the figures, that must be regenerated ... In case of difficulty, do not hesitate to start an issue on gitlab, or contact the other developers (abidev@abinit.org). We might benefit from each other expertise using the gitlab channel, but do not stay stucked, or do not simply ignore a real problem.
  
 ==== Latex formulas or other markdown style improvement ==== ==== Latex formulas or other markdown style improvement ====
 Although most formulas in tutorials are already in Latex, I have spotted a couple of mathematical quantities in tbase1 that were still in text mode ... Using Latex is very easy with the present infrastructure, see the markdown reference below. Although most formulas in tutorials are already in Latex, I have spotted a couple of mathematical quantities in tbase1 that were still in text mode ... Using Latex is very easy with the present infrastructure, see the markdown reference below.
  
-**Finally, issue the proper merge request to trunk/develop, then mention in the beautification Google spreadsheet (column F) that you have done the job !**+**Finally, issue the proper merge request to trunk/develop, then mention in the beautification Google spreadsheet (second sheet, column G) - see the mail sent on 11 December, that you have done the job !**
  
 ===== I have not yet familiarized myself with abimkdocs / markdown  ===== ===== I have not yet familiarized myself with abimkdocs / markdown  =====
Line 90: Line 105:
  
 Going through it for the first time might be 15-20 minutes.  Going through it for the first time might be 15-20 minutes. 
-Training might be another 15 minutes (e.g. starting the server with ''./mksite.py serve --dirtyreload'',+Training might be another 15 minutes (e.g. first ''*/*/makemake'' then starting the server with ''./mksite.py serve --dirtyreload'',
 then trying to make some fake modifications). then trying to make some fake modifications).
  
beauty/2020.1607613944.txt.gz · Last modified: 2020/12/10 16:25 by Xavier Gonze