Command line options: Difference between revisions

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'''Uppercase''' options modify some of the code's default settings. They can be used when launching the code but also when generating input files.  
In this module you will learn how to use Yambo's command line options.
 
== Prerequisites ==
'''Previous modules'''
* Initialization for [[Bulk_material:_h-BN|bulk hBN]] or [[2D_material:_h-BN_sheet|2D hBN]].
 
'''You will need''':
* The <code>SAVE</code> databases for bulk hBN
* The <code>yambo</code> executable
 
==Uppercase options==
Uppercase options modify some of the code's default settings. They can be used when launching the code but also when generating input files.  
 
===Allowed options===
===Allowed options===
To see the list of options, do:
To see the list of options, do:
Line 28: Line 40:
Other options deserve a closer look.
Other options deserve a closer look.
===Verbosity===
===Verbosity===
Yambo uses ''many'' input variables, many of which can be left at their default values. To keep inout files short and manageable, only a few variables appear by default  in the inout file. More advanced variables can be switched on by using the <code>-V</code> verbosity option. These are grouped according to the type of variable. For instance, <code>-V RL</code> switches on variables related to G vector summations, and <code>-V io</code> switches on options related to I/O control. Try:  
Yambo uses ''many'' input variables, many of which can be left at their default values. To keep input files short and manageable, only a few variables appear by default  in the inout file. More advanced variables can be switched on by using the <code>-V</code> verbosity option. These are grouped according to the type of variable. For instance, <code>-V RL</code> switches on variables related to G vector summations, and <code>-V io</code> switches on options related to I/O control. Try:  


  $ yambo -o c -V RL      ''switches on:''
  $ yambo -o c -V RL      ''switches on:''
Line 43: Line 55:
===Job script label===
===Job script label===
The best way to keep track of different runs using different parameters is through the <code>-J</code> flag. This inserts a label in all output and report files, and creates a new folder containing any new databases (i.e. they are not written in the core ''SAVE'' folder). Try:
The best way to keep track of different runs using different parameters is through the <code>-J</code> flag. This inserts a label in all output and report files, and creates a new folder containing any new databases (i.e. they are not written in the core ''SAVE'' folder). Try:
  $ yambo -J 1Ry -x        ''and modify to''
  $ yambo -J 1Ry -V RL -x        ''and modify to''
  FFTGvecs = 1 Ry
  FFTGvecs = 1 Ry
  EXXGvecs = 1 Ry
  EXXGvecs = 1 Ry
Line 52: Line 64:
This is extremely useful when running convergence tests, trying out different parameters, etc.
This is extremely useful when running convergence tests, trying out different parameters, etc.


===Production example===
<br>
Here is an example of how to combine several command line options. Starting from the usual folder containing the ''SAVE'', do
{| style="width:100%" border="1"
$ mkdir TEST
|style="width:15%; text-align:left"|Prev: [[Input_file_generation|Input file]]
$ cd TEST
|style="width:70%; text-align:center"|Now: [[Tutorials|Tutorials Home]] --> [[First_steps:_a_walk_through_from_DFT_to_optical_properties|First steps]] --> [[Bulk_material:_h-BN|bulk hBN]] / [[2D_material:_h-BN_sheet|2D hBN]] --> [[Command_line_options|Command line options]]
$ yambo -F yambo.in_IP -I ../ -C q100 -J 3Ry -V RL -o c      ''and change to''
|style="width:15%; text-align:right"|Next: Back to [[First_steps:_a_walk_through_from_DFT_to_optical_properties#Step_4:_Optical_absorption_in_hBN|First steps]]
FFTGvecs= 3            Ry    # [FFT] Plane-waves
|-
$ yambo -F yambo.in_IP -I ../ -C q100 -J 3Ry -V RL
|}
You will notice
<---> [WF] Performing Wave-Functions I/O from ..//SAVE
<---> Dipoles: P and iR (T): |########################################| [100%] --(E) --(X)
with the ''ndb.dip_iR_and_P'' databases written in ''3Ry'', and output files inside the folder ''q100''. Now select a different q-component and run again:
$ yambo -F yambo.in_IP -I ../ -C ''q001'' -J 3Ry -V RL -o c      ''and change to''
% LongDrXd
0.000000 | 0.000000 | ''1.000000'' |        # [Xd] [cc] Electric Field
%
$ yambo -F yambo.in_IP -I ../ -C ''q001'' -J 3Ry -V RL
For this run, yambo reads the database from the ''3Ry'' folder, does a quick calculation, and writes the outputs inside ''q001''.
 
The overall result is very neatly organised. Remember to check the report file to verify which databases are being WR = written to and RD = read from.
Of course, it is up to the user to decide which options they like best.
 
== Links ==
* [[Tutorials|Back to tutorials menu]]

Latest revision as of 10:17, 21 April 2017

In this module you will learn how to use Yambo's command line options.

Prerequisites

Previous modules

You will need:

  • The SAVE databases for bulk hBN
  • The yambo executable

Uppercase options

Uppercase options modify some of the code's default settings. They can be used when launching the code but also when generating input files.

Allowed options

To see the list of options, do: 

$ yambo -H
Tool: yambo 4.1.2 rev.14024
Description: A shiny pot of fun and happiness [C.D.Hogan] 
-J <opt>	:Job string identifier
-V <opt>	:Input file verbosity
                [opt=RL,kpt,sc,qp,io,gen,resp,all,par]
-F <opt>	:Input file
-I <opt>	:Core I/O directory
-O <opt>	:Additional I/O directory
-C <opt>	:Communications I/O directory
-D		:DataBases properties
-W <opt>	:Wall Time limitation (1d2h30m format)
-Q		:Don't launch the text editor
-M		:Switch-off MPI support (serial run)
-N		:Switch-off OpenMP support (single thread run)
[Lower case options]

Command line options are extremely important to master if you want to use yambo productively. Often, the meaning is clear from the help menu: 

$ yambo -F yambo.in_HF -x    Make a Hartree -Fock input file called yambo.in_HF
$ yambo -D                   Summarize the content of the databases in the SAVE folder
$ yambo -I ../               Run the code, using a SAVE folder in a directory one level up
$ yambo -C MyTest            Run the code, putting all report, log, plot files inside a folder MyTest

Other options deserve a closer look.

Verbosity

Yambo uses many input variables, many of which can be left at their default values. To keep input files short and manageable, only a few variables appear by default in the inout file. More advanced variables can be switched on by using the -V verbosity option. These are grouped according to the type of variable. For instance, -V RL switches on variables related to G vector summations, and -V io switches on options related to I/O control. Try: 

$ yambo -o c -V RL       switches on:
FFTGvecs=  3951        RL    # [FFT] Plane-waves

$ yambo -o c -V io       switches on:
StdoHash=  40                # [IO] Live-timing Hashes
DBsIOoff= "none"             # [IO] Space-separated list of DB with NO I/O. DB= ...
DBsFRAGpm= "none"            # [IO] Space-separated list of +DB to be FRAG and ...
#WFbuffIO                    # [IO] Wave-functions buffered I/O

Unfortunately, -V options must be invoked and changed one at a time. When you are more expert, you may go straight to -V all, which turns on all possible variables. However note that yambo -o c -V all adds an extra 30 variables to the input file, which can be confusing: use it with care.

Job script label

The best way to keep track of different runs using different parameters is through the -J flag. This inserts a label in all output and report files, and creates a new folder containing any new databases (i.e. they are not written in the core SAVE folder). Try: 

$ yambo -J 1Ry -V RL -x        and modify to
FFTGvecs = 1 Ry
EXXGvecs = 1 Ry
$ yambo -J 1Ry           Run the code
$ ls
yambo.in SAVE  
o-1Ry.hf r-1Ry_HF_and_locXC 1Ry 1Ry/ndb.HF_and_locXC

This is extremely useful when running convergence tests, trying out different parameters, etc.


Prev: Input file Now: Tutorials Home --> First steps --> bulk hBN / 2D hBN --> Command line options Next: Back to First steps
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