This lesson has been created for current stable version. Earlier versions are fully capable of running this tutorial but input files may have to be changed according to possible earlier formats.

Basics of BigDFT: first runs and managing different calculations, N₂ molecule as example

BigDFT code is organized by optional input files, each one with compulsory variables. Input files can be organised in different sets, each one associated to a particular calculation. With this lesson you will have to deal with the different outputs of BigDFT code, such as to learn how to manipulate basic DFT objects.

Default run: no input files

As mentioned above, all the BigDFT files are optional, except the... atomic positions. This means that a DFT calculation can be done also by giving the atomic positions file only. Consider for example the N2 molecule, given by the posinp.xyz file:

2 angstroem
free
N 0. 0. 0.
N 0. 0. 1.11499

Run the code in a directory which has only this file.

user@garulfo:~/N2/$ ls
bigdft  posinp.xyz
user@garulfo:~/N2/$ ./bigdft | tee N2.out
...

The screen output should then behave like that:

 ------------------------------------------------------------------------------------
 |              Daubechies Wavelets for DFT Pseudopotential Calculations            |
 ------------------------------------------------------------------------------------
                                   The Journal of Chemical Physics 129, 014109 (2008)

 |... (file:input.perf.. not present)............................Performance Options 
 |debug F                    Debug option
 |fftcache 8192              Cache size for the FFT
 |accel NO                   Acceleration (NO, CUDAGPU, OCLGPU)
 |blas F                     CUBLAS acceleration
 |projrad  1.50E+01          Radius of the projector as a function of the maxrad
 |exctxpar OP2P              Exact exchange parallelisation scheme
 |ig_diag T                  Input guess: (T:Direct, F:Iterative) diag. of Ham.
 |ig_norbp 5                 Input guess: Orbitals per process for iterative diag.
 |ig_blocks  300 800         Input guess: Block sizes for orthonormalisation
 |ig_tol  1.00E-04           Input guess: Tolerance criterion
 |methortho 0                Orthogonalisation (0=Cholesky,1=GS/Chol,2=Loewdin)
 |rho_commun DBL             Density communication scheme
 |linear OFF                 Linear Input Guess approach
 |verbosity 2                verbosity of the output 0=low, 2=high
 |psp_onfly T                Calculate pseudopotential projectors on the fly
 |... (file:input.dft.. not present)......................DFT Calculation Parameters 
 |0.45 0.45 0.45 hx,hy,hz: grid spacing in the three directions                      
 |5.0 8.0        c(f)rmult: c(f)rmult*radii_cf(:,1(2))=coarse(fine) atom-based radius
 |1              ixc: exchange-correlation parameter (LDA=1,PBE=11)                  
 |0 0. 0. 0.     charge of the system, Electric field (Ex,Ey,Ez)                     
 |1 0            nspin=1 non-spin polarization, mpol=total magnetic moment           
 |1.e-4          gnrm_cv: convergence criterion gradient                             
 |50 1           itermax,nrepmax: max. # of wfn. opt. steps and of re-diag. runs     
 |6 6            ncong, idsx: # of CG it. for preconditioning eq., wfn. diis history 
 |0              dispersion correction potential (values 1,2,3), 0=none              
 |0 0 0          InputPsiId, output_wf, output_denspot                               
 |0.0 30         rbuf, ncongt: length of the tail (AU),# tail CG iterations          
 |0 0 0          Davidson subspace dim., # of opt. orbs, # of plotted orbs           
 |F              disable the symmetry detection                                      
 |... (file:input.mix.. not present)...............................Mixing Parameters 
 |0              Mixing parameters                                                   
 |1              Maximum number of diagonalisation iterations                        
 |1.e-4          Stop criterion on the residue of potential or density               
 |0 0.0 1        No. of additional bands, elec. temperature, smearing method         
 |0.0 2.0        Multiplying factors for the mixing and the electronic DIIS          
 |... (file:input.geopt.. not present)...........................Geometry Parameters 
 |BFGS           Geometry optimisation method                                        
 |1              Maximum number of force evaluations                                 
 |1.0 0.0        fract_fluct,forcemax                                                
 |0.0            random displacement amplitude                                       
 |4.0            Stepsize for the geometry optimisation                              
 |... (file:input.tddft.. not present).............................TD-DFT Parameters 
 |NONE           TDDFT Method                                                        
 |... (file:input.sic.. not present)..................................SIC Parameters 
 |NONE           SIC method: NONE, PZ, NK                                            
 |0.0            SIC downscaling parameter                                           
 |0.0            Reference occupation fref (NK case only)                            
 |... (file:input.kpt.. not present)..............Brillouin Zone Sampling Parameters 
 |manual         K-point sampling method                                             
 |1              Number of K-points                                                  
 |0. 0. 0. 1.    K-pt coords, K-pt weigth                                            
 |----------------------------------------------------------------------------------
 |  Data Writing directory:    not needed
[...]

Each input file contains compulsory lines, with the exception of input.perf which controls developer-oriented performance variables. You can see there the possible optional files which BigDFT might read. Since they do not exist, their default values are applied to the code. Basically, they correspond to Single-Point LDA calculation, without k-points nor spin-polarisation. Since the input files are not present, default files are written in the submission directory:

user@garulfo:~/N2/$ ls
default.dft  default.geopt  default.kpt  default.mix  default.sic  default.tddft  posinp.xyz  time.yaml forces_posinp.xyz

All these default files represent the template you should use to define your calculation. Also, the default Pseudopotentials are used.

Using a naming scheme for IO files

All input parameters can be found in files with a naming prefix. By default, this prefix is input (or posinp for atomic input positions). For instance, parameters for geometry optimization will be set up by a file named input.geopt. One can choose the naming prefix by providing an argument to bigdft command line.

Imagine for example that you are interested in visualizing the wavefunctions output of the calculation. To do that, you should enter the suitable parameters in the .dft file. Create a new calculation set by using the "LDA" prefix and rename all relevant files with LDA:

user@garulfo:~/N2/$ cp default.dft LDA.dft
user@garulfo:~/N2/$ cp posinp.xyz LDA.xyz

Modify LDA.dft such as to output the wavefunctions at the end of calculation, by putting the output_wf variable to 1 (Which repsesents the formatted output. Also 2 (binary) and 3 (ETSF format) are available)

 0 1 0          InputPsiId, output_wf, output_grid 

Now you can run this input file, by putting "LDA" as a command line argument of the code:

user@garulfo:~/N2/$ ./bigdft LDA | tee LDA.out

You can now see that the LDA.dft file is read.

When using a naming scheme, the output files are placed in a directory called data-{naming scheme}. In our LDA example, the wavefunctions of the system can thus be found in the data-LDA directory:

user@garulfo:$ ls data-LDA/
wavefunction-k001-NR.b0001  wavefunction-k001-NR.b0002  wavefunction-k001-NR.b0003
wavefunction-k001-NR.b0004  wavefunction-k001-NR.b0005

Here 001 means the first K-point (meaningless in this case), N stands for non spin-polarized, R for real part and the remaining number is the orbital ID. Post-processing of these files is done in the fourth tutorial.

In the same spirit, another calculation can be done with different parameters. Imagine we want to perform a Hartree-Fock calculation. In BigDFT, this can be done by putting the ixc input variable to 100. So, copy the LDA.dft file to HF.dft and modify it accordingly (don't forget to rename also the coordinate file). This time, an error will occur:

user@garulfo:$ ./bigdft HF | tee HF.out
[...]
 ERROR: The pseudopotential parameter file "psppar.N" is lacking,
        and no registered pseudo found for "N", exiting...
user@garulfo:$

This is because the pseudopotential is assigned by default in the code only for LDA and PBE XC approximations. You can find here the pseudopotential which is taken by default in the LDA run. Put it in a psppar.N file, and run the calculation (redirect the output in the file HF.out for example). When possible, care should be taken in choosing a pseudopotential which has been generated with the same XC approximation used. Unfortunately, at present HGH data are only available for semilocal functionals. For example, the same exercise as follows could have been done with Hybrid XC functionals, like for example PBE0 (ixc=-406). See the manual page for a list of the supported XC functionals. Data of the calculation can be analysed. Consider the eigenvectors of the LDA and HF runs.

         LDA(1)      HF(1)      HF(2)       (Exp.)
3σg     10.36        17.25      17.31      (15.60) 
1πu     11.84        16.71      17.02      (16.98)
2σu     13.41        21.25      21.08      (18.78)

         LDA           HF     
3σg     10.40        17.32     
1πu     11.75        16.62    
2σu     13.52        21.30