Initialization
In this tutorial you will learn how to initialize the Yambo databases for bulk hBN.
Prerequisites
Previous modules
You will need:
- The
SAVEdatabases for bulk hBN and the 2D hBN sheet (Download here) - The
yamboexecutable
Initialization
Every Yambo run must start with this step. Go to the folder containing the hBN-bulk SAVE directory:
$ cd TUTORIALS/hBN/YAMBO $ ls SAVE
and simply launch the code
yambo
This will run the initialization (setup) runlevel.
TIP: do not run yambo from inside the SAVE folder! It will complain that "databases not found".
Three new elements will appear:
Run-time output
This is written to standard output (on screen) or to a log file l_setup, and tracks the progress of the run in real time:
<---> [01] CPU structure, Files & I/O Directories <---> [02] CORE Variables Setup <---> [02.01] Unit cells <---> [02.02] Symmetries <---> [02.03] RL shells <---> Shells finder |########################################| [100%] --(E) --(X) <---> [02.04] K-grid lattice <---> [02.05] Energies [ev] & Occupations <---> [03] Transferred momenta grid <---> BZ -> IBZ reduction |########################################| [100%] --(E) --(X) <---> X indexes |########################################| [100%] --(E) --(X) <---> SE indexes |########################################| [100%] --(E) --(X) <---> [04] External corrections <---> [05] 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 ns.gops ns.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.
TIP: if you launch yambo, but it does not seem to produce anything new, 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:
[02.03] RL shells ================= Shells, format: [S#] G_RL(mHa) [S217]:3187(0.4380E+5) [S216]:3175(0.4378E+5) [S215]:3163(0.4321E+5) [S214]:3139(0.4321E+5) ... [S4]:11( 1183.) [S3]:5( 532.5123) [S2]:3( 133.1281) [S1]:1( 0.000000)
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 3187. Yambo will always redefine any input variable in RL space to the nearest closed shell.
[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
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.
NB: You should inspect the report file after every run for errors and warnings.