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
SAVEdatabases for bulk hBN and the 2D hBN sheet - The
yamboexecutable
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
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