Initialization

In this tutorial you will learn how to initialize the Yambo databases for bulk hBN.

Prerequisites

Previous modules

• It is recommended that you first follow the tutorials on generating the Yambo databases for bulk hBN.

You will need:

• The SAVE databases for bulk hBN and the 2D hBN sheet
• The yambo executable

Initialization

Use the SAVE folders that are already provided, rather than any ones you may have generated previously.

Every Yambo run must start with this step. Go to the folder containing the hBN-bulk SAVE directory:

$ cd YAMBO_TUTORIALS/hBN/YAMBO
$ ls
SAVE

TIP: do not run yambo from inside the SAVE folder! This is the wrong way ..

$ cd SAVE
$ yambo
yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

In fact, if you ever see such message: it usually means you are trying to launch Yambo from the wrong place.

$ cd ..

Now you are in the proper place and

$ ls
SAVE

you can simply launch the code

$ yambo 

This will run the initialization (setup) runlevel.

Run-time output

This is typically written to standard output (on screen) and tracks the progress of the run in real time:

<---> [01] MPI/OPENMP structure, Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] Reciprocal space
<---> Shells finder |########################################| [100%] --(E) --(X)
<---> [02.04] K-grid lattice
<---> Grid dimensions      :   6   6   2
<---> [02.05] Energies & Occupations
<---> [03] Transferred momenta grid and indexing
<---> BZ -> IBZ reduction |########################################| [100%] --(E) --(X)
<---> [03.01] X indexes
<---> X [eval] |########################################| [100%] --(E) --(X)
<---> X[REDUX] |########################################| [100%] --(E) --(X)
<---> [03.01.01] Sigma indexes
<---> Sigma [eval] |########################################| [100%] --(E) --(X)
<---> Sigma[REDUX] |########################################| [100%] --(E) --(X)
<---> [04] Timing Overview
<---> [05] Memory Overview
<---> [06] Game Over & Game summary

Specific runlevels are indicated with numeric labels like [02.02].
The hashes (#) indicate progress of the run in Wall Clock time, indicating the elapsed (E) and expected (X) time to complete a runlevel, and the percentage of the task complete.

New core databases

New databases appear in the SAVE folder:

$ ls SAVE
ns.db1 ns.wf ns.kb_pp_pwscf ndb.gops ndb.kindx
ns.wf_fragments_1_1 ...
ns.kb_pp_pwscf_fragment_1 ...

These contain information about the G-vector shells and k/q-point meshes as defined by the DFT calculation.

In general: a database called ns.xxx is a static database, generated once by p2y, while databases called ndb.xxx are dynamically generated while you use yambo.

TIP: if you launch yambo, but it does not seem to do anything, check that these files are present.

Report file

A report file r_setup is generated in the run directory. This mostly reports information about the ground state system as defined by the DFT run, but also adds information about the band gaps, occupations, shells of G-vectors, IBZ/BZ grids, the CPU structure (for parallel runs), and so on. Some points of note:

Up to Yambo version 4.5

 [02.03] RL shells
 =================
 Shells, format: [S#] G_RL(mHa)
  [S453]:8029(0.7982E+5) [S452]:8005(0.7982E+5) [S451]:7981(0.7982E+5) [S450]:7957(0.7942E+5)
  ...
  [S4]:11( 1183.) [S3]:5( 532.5123) [S2]:3( 133.1281) [S1]:1( 0.000000)

From Yambo version 5.0

 [02.03] Reciprocal space
 ========================
 
 nG shells         :  217
 nG charge         :   3187
 nG WFs            :  1477
 nC WFs            :  1016
 G-vecs. in first 21 shells:  [ Number ]
    1    3    5   11   13   25   37   39   51
   63   65   71   83   95  107  113  125  127
  139  151  163
 ...
 Shell energy in first 21 shells:  [ mHa ]
   0.00000      133.128      532.512      1183.37      1198.15      1316.50      1715.88      2130.05      2381.52
   3313.42      3328.20      3550.11      3683.24      4082.62      4511.57      4733.48      4748.27      4792.61
   4866.61      5266.00      5680.16
 ...

This reports the set of closed reciprocal lattice (RL) shells defined internally that contain G-vectors with the same modulus. The highest number of RL vectors we can use is 8029. Yambo will always redefine any input variable in RL units to the nearest closed shell.

Up to Yambo version 4.5

 [02.05] Energies [ev] & Occupations
 ===================================
 Fermi Level        [ev]:  5.112805
 VBM / CBm          [ev]:  0.000000  3.876293
 Electronic Temp. [ev K]:  0.00      0.00
 Bosonic    Temp. [ev K]:  0.00      0.00
 El. density      [cm-3]: 0.460E+24
 States summary         : Full        Metallic    Empty
                          0001-0008               0009-0100
 Indirect Gaps      [ev]: 3.876293  7.278081
 Direct Gaps        [ev]:  4.28829  11.35409
 X BZ K-points :  72

From Yambo version 5.0

 [02.05] Energies & Occupations
 ==============================
 
 [X] === General ===
 [X] Electronic Temperature                        :  0.000000  0.000000 [eV K]
 [X] Bosonic    Temperature                        :  0.000000  0.000000 [eV K]
 [X] Finite Temperature mode                       : no
 [X] El. density                                   :  0.46037E+24 [cm-3]
 [X] Fermi Level                                   :  5.110835 [eV]
 
 [X] === Gaps and Widths ===
 [X] Conduction Band Min                           :  3.877976 [eV]
 [X] Valence Band Max                              :  0.000000 [eV]
 [X] Filled Bands                                  :   8
 [X] Empty Bands                                   :    9  100
 [X] Direct Gap                                    :  4.289853 [eV]
 [X] Direct Gap localized at k-point               :   7
 [X] Indirect Gap                                  :  3.877976 [eV]
 [X] Indirect Gap between k-points                 :  14   7
 [X] Last valence band width                       :  3.401086 [eV]
 [X] 1st conduction band width                     :  4.266292 [eV]

Yambo recalculates again the Fermi level (close to the value of 5.06 noted in the PWscf SCF calculation). From here on, however, the Fermi level is set to zero, and other eigenvalues are shifted accordingly. The system is insulating (8 filled, 92 empty) with an indirect band gap of 3.87 eV. The minimum and maximum direct and indirect gaps are indicated. There are 72 k-points in the full BZ, generated using symmetry from the 14 k-points in our user-defined grid.

TIP: You should inspect the report file after every run for errors and warnings.

Different ways of running yambo

We just run Yambo interactively.

Let's try to re-run the setup with the command

$ yambo >& /dev/null &
$ ls
l_setup r_setup  r_setup_01  SAVE

If Yambo is launched using a script, or as a background process, or in parallel, this output will appear in a log file prefixed by the letter l, in this case as l_setup. If this log file already exists from a previous run, it will not be overwritten. Instead, a new file will be created with an incrementing numerical label, e.g. l_setup_01, l_setup_02, etc. This applies to all files created by Yambo. Here we see that l_setup was created for the first time, but r_setup already existed from the previous run, so now we have r_setup_01 If you check the differences between the two you will notice that in the second run yambo is reading the previously created ndb.kindx in place of re-computing the indexes. Indeed the output inside l_setup does not show the timing for X and Sigma

As a last step we run the setup in parallel, but first we delete the ndb.kindx file

$ rm SAVE/ndb.kindx
$ mpirun -np 4 yambo 
$ ls
LOG  l_setup  nohup.out  r_setup  r_setup_01  r_setup_02  SAVE

There is now r_setup_02 In the case of parallel runs, CPU-dependent log files will appear inside a LOG folder, e.g.

$ ls LOG
l_setup_CPU_1   l_setup_CPU_2  l_setup_CPU_3  l_setup_CPU_4

This behaviour can be controlled at runtime - see the Parallel tutorial for details.

2D hBN

Simply repeat the steps above. Go to the folder containing the hBN-2D SAVE directory and launch yambo:

$ cd TUTORIALS/hBN-2D/YAMBO
$ ls
SAVE
$ yambo

Again, inspect the r_setup file, output logs, and verify that ndb.gops and ndb.kpts have been created inside the SAVE folder.

You are now ready to use Yambo!

Summary

From this tutorial you've learned:

• How to initialize the Yambo databases
• The Yambo logs and output file structure

Prev: 2D hBN

Now: Tutorials Home --> First steps --> 2D hBN --> Initialization

Next: Input file generation and command line options (5.0)