Command line options: Difference between revisions

From The Yambo Project
Jump to navigation Jump to search
No edit summary
No edit summary
 
(14 intermediate revisions by 2 users not shown)
Line 1: Line 1:
'''Uppercase''' options modify some of the code's default settings. They can be used when launching the code but also when generating input files. To see the list of options, do:
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===
To see the list of options, do:
  $ yambo -H
  $ yambo -H
  Tool: yambo 4.1.2 rev.14024
  Tool: yambo 4.1.2 rev.14024
Line 17: Line 31:
  [Lower case options]
  [Lower case options]


These options are extremely important to master if you want to use yambo productively.  
Command line options are extremely important to master if you want to use yambo productively.  
The meaning of several options is clear from the help menu: try a table
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 -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 -D                   ''Summarize the content of the databases in the SAVE folder''
  $ yambo -I ../ ''Use a SAVE folder in a directory one level up; run the code''
  $ 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'm
  $ yambo -C MyTest           ''Run the code, putting all report, log, plot files inside a folder MyTest''
 
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 -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 handling the inout output 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:''
  FFTGvecs
  FFTGvecs=  3951        RL    # [FFT] Plane-waves
   
   
  $ yambo -o c -V io switches on
  $ yambo -o c -V io       ''switches on:''
  DB etc
  StdoHash=  40                # [IO] Live-timing Hashes
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 Haifa les. Note that yambo -V all for XXX creates 12244  aria lee so use it with care.  
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 <code>-V all</code>, which turns on all possible variables. However note that <code>yambo -o c -V all</code> adds an extra 30 variables to the input file, which can be confusing: use it with care.
 
===Job script label===
===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. The are not written in the 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 -x -J 5Ry
  $ yambo -J 1Ry -V RL -x       ''and modify to''
  EXXGvecs = 5 Ry
FFTGvecs = 1 Ry
  $ yambo -J 5Ry
  EXXGvecs = 1 Ry
  $ ls *
  $ yambo -J 1Ry          ''Run the code''
  Yambo.in
  $ ls
SAVE/
  yambo.in SAVE   
  5RY
  o-1Ry.hf r-1Ry_HF_and_locXC 1Ry 1Ry/ndb.HF_and_locXC
  $ yambo -x -J 10Ry etc
This is extremely useful when running convergence tests, trying out different parameters, etc.
 
===Production example===
$ yambo -F -J -I -O


== Links ==
<br>
* [[Tutorials|Back to tutorials menu]]
{| style="width:100%" border="1"
|style="width:15%; text-align:left"|Prev: [[Input_file_generation|Input file]]
|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]]
|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]]
|-
|}

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
Retrieved from "https://wiki.yambo-code.eu/wiki/index.php?title=Command_line_options&oldid=1915"