Input file generation and command line options 5.0
In this module you will learn how to select tasks, generate and modify input files, and control the runtime behavior by using Yambo's command-line interface.
Note: This is for yambo 5.0. For yambo 4.5 (or before) please follow this link Input file generation and command line options (4.5)
Prerequisites
Previous modules
- Initialization for bulk hBN
You will need:
- The
SAVEdatabases for bulk hBN - The
yamboexecutable
Input file generator
First, move to the appropriate folder and initialize the Yambo databases if you haven't already done so.
$ cd YAMBO_TUTORIALS/hBN/YAMBO $ yambo (initialize)
Yambo generates its own input files: you just tell the code what you want to calculate by launching Yambo along with one or more options.
To see the list of possible options, run yambo -h (we report here only the part we are focusing in)
$ yambo -h 'A shiny pot of fun and happiness [C.D.Hogan]' This is : yambo Version : 5.0.1 Revision 19547 Hash e90d90f2d Configuration: MPI+OpenMP+SLK+SLEPC+HDF5_MPI_IO ... Initializations: -setup (-i) :Initialization -coulomb (-r) :Coulomb potential Response Functions: -optics (-o) <string> :Linear Response optical properties (more with -h optics) -X (-d) <string> :Inverse Dielectric Matrix (more with -h X) -dipoles (-q) :Oscillator strenghts (or dipoles) -kernel (-k) <string> :Kernel (more with -h kernel) Self-Energy: -hf (-x) :Hartree-Fock -gw0 (-p) <string> :GW approximation (more with -h gw0) -dyson (-g) <string> :Dyson Equation solver (more with -h dyson) -lifetimes (-l) :GoWo Quasiparticle lifetimes Bethe-Salpeter Equation: -Ksolver (-y) <string> :BSE solver (more with -h Ksolver) Total Energy: -acfdt :ACFDT Total Energy Utilites: ... -slktest :ScaLapacK test
The options can be split into two sets:
- A set of options which is needed to generate the appropriate input file (default name: yambo.in) selecting the kind of simulation you would like to perform
- A set of options which can be used to manage auxiliary functions (like redirect the I/O, choose a specific name for the input file, etc ..).
Runlevel selection
First of all, you would like to specify which kind of simulation you are going to perform and generate an input file with the first set of options.
By default, when generating the input file, Yambo will launch the vi editor.
Editor choice can be changed when launching the configure before compilation; alternatively you can use the -Q run time option to skip the automatic editing (do this if you are not familiar with vi!):
$ yambo -hf -Q yambo: input file yambo.in created $ emacs yambo.in or your favourite editing tool
Multiple options can be used together to activate various tasks or runlevels (in some cases this is actually a necessity). For instance, to generate an input file for optical spectra including local field effects (Hartree approximation), do (and then exit)
$ yambo -optics c -kernel hartree which switches on: optics # [R OPT] Optics chi # [R CHI] Dyson equation for Chi. Chimod= "Hartree" # [X] IP/Hartree/ALDA/LRC/BSfxc
To perform a Hartree-Fock and GW calculation using a plasmon-pole approximation, do (and then exit):
$ yambo -hf -gw0 p -dyson n which switches on: HF_and_locXC # [R XX] Hartree-Fock Self-energy and Vxc gw0 # [R GW] GoWo Quasiparticle energy levels ppa # [R Xp] Plasmon Pole Approximation em1d # [R Xd] Dynamical Inverse Dielectric Matrix
Each runlevel activates its own list of variables and flags.
The previous command is also equivalent to
$ yambo -hf -gw0 r -dyson n -X p
Changing input parameters
Yambo reads various parameters from existing database files and/or input files and uses them to suggest values or ranges. Let's illustrate this by generating the input file for a Hartree-Fock calculation.
$ yambo -hf
Inside the generated input file you should find:
EXXRLvcs = 3187 RL # [XX] Exchange RL components %QPkrange # [GW] QP generalized Kpoint/Band indices 1| 14| 1|100| %
The QPkrange variable (follow the link for a "detailed" explanation for any variable) suggests a range of k-points (1 to 14) and bands (1 to 100) based on what it finds in the core database SAVE/ns.db1, i.e. as defined by the DFT code.
Leave that variable alone, and instead modify the previous variable to EXXRLvcs= 1000 RL
Save the file, and now generate the input a second time with yambo -x. You will see:
EXXRLvcs= 1009 RL
This indicates that Yambo has read the new input value (1000 G-vectors), checked the database of G-vector shells (SAVE/ndb.gops), and changed the input value to one that fits a completely closed shell.
Last, note that Yambo variables can be expressed in different units. In this case, RL can be replaced by an energy unit like Ry, eV, Ha, etc. Energy units are generally better as they are independent of the cell size. Technical information is available on the Variables page.
The input file generator of Yambo is thus an intelligent parser, which interacts with the user and the existing databases. For this reason we recommend that you always use Yambo to generate the input files, rather than making them yourself.
Extra options
Extra options modify some of the code's default settings. They can be used when launching the code but also when generating input files.
Let's have a look again to the possible options (we report here only the part we are focusing in):
$ yambo -h This is : yambo Version : 5.0.1 Revision 19547 Hash e90d90f2d Configuration: MPI+OpenMP+SLK+SLEPC+HDF5_MPI_IO Help & version: -help (-h) <string> :<string> can be an option (e.g. -h optics) -version :Code version & libraries Input file & Directories: -Input (-F) <string> :Input file -Verbosity (-V) <string> :Input file variables verbosity (more with -h Verbosity) -Job (-J) <string> :Job string -Idir (-I) <string> :Input directory -Odir (-O) <string> :I/O directory -Cdir (-C) <string> :Communication directory Parallel Control: -parenv (-E) <string> :Environment Parallel Variables file -nompi :Switch off MPI support -noopenmp :Switch off OPENMP support ... Utilites: -Quiet (-Q) :Quiet input file creation -fatlog :Verbose (fatter) log(s) -DBlist (-D) :Databases properties ...
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 -hf 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 -optics c -V RL switches on: FFTGvecs= 3951 RL # [FFT] Plane-waves $ yambo -optics 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 -hf -F yambo_hf.in and modify to FFTGvecs = 1 Ry EXXGvecs = 1 Ry $ yambo -J 1Ry -F yambo_hf.in Run the code $ ls yambo_hf.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.
Exercise: use yambo to report the properties of all database files (including ndb.HF_and_locXC)
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