# Difference between revisions of "First runs with BigDFT"

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− | <p> In the log file, | + | <p> In the log file, BigDFT automatically displays all the input parameters used for the calculations (this is what you see above). The parameters which were not explicitly given are set to a default value, except the atomic positions of course, which has to be given. |

Each input file contains compulsory lines, with the exception of <tt>input.perf</tt> which controls developer-oriented performance variables. | Each input file contains compulsory lines, with the exception of <tt>input.perf</tt> which controls developer-oriented performance variables. | ||

You can see there the possible optional files which BigDFT might read . | 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. | Since they do not exist, their default values are applied to the code. | ||

Basically, they correspond to a single-point LDA calculation, without k-points nor spin-polarisation. | Basically, they correspond to a single-point LDA calculation, without k-points nor spin-polarisation. | ||

− | As we said earlier, the new version of | + | As we said earlier, the new version of BigDFT now supports .yaml files were all the parameters are given (instead of using an optional file every time you want to calculate something specific, you can now modify the corresponding line in the .yaml file), the input display shown above can serve as a template for this .yaml file. -note that one can combine a .yaml file with other task specifying files (.xyz or .geopt for example), BigDft will still understand- |

</p> | </p> | ||

## Revision as of 14:34, 11 June 2018

This lesson has been created for the 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, N_{2} molecule as example

BigDFT code is organized by *optional* input files, each one with *compulsory* variables.
Input files all have a specific extension (.xyz, .geopt, .kpt ...), each one being associated to a particular type of calculation (The latest version of BigDFT now also accepts .yaml files in which you can directly put all the informations needed regarding the run you want to perform).
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 file of 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:

[...] #------------------------------------------------------------------------ Input parameters perf: debug : No # debug option fftcache : 8192 # cache size for the FFT accel : NO # acceleration ocl_platform : ~ # Chosen OCL platform ocl_devices : ~ # Chosen OCL devices blas : No # CUBLAS acceleration projrad : 15. # Radius of the projector as a function of the maxrad exctxpar : OP2P # Exact exchange parallelisation scheme ig_diag : Yes # 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 : 1e-4 # Input guess Tolerance criterion methortho : 0 # Orthogonalisation rho_commun : DEF # Density communication scheme (DBL, RSC, MIX) psolver_groupsize : 0 # Size of Poisson Solver taskgroups (0=nproc) psolver_accel : 0 # Acceleration of the Poisson Solver (0=none, 1=CUDA) unblock_comms : OFF # Overlap Communications of fields (OFF,DEN,POT) linear : OFF # Linear Input Guess approach tolsym : 1e-8 # Tolerance for symmetry detection signaling : No # Expose calculation results on Network signaltimeout : 0 # Time out on startup for signal connection (in seconds) domain : ~ # Domain to add to the hostname to find the IP inguess_geopt : 0 # input guess to be used during the optimization store_index : Yes # store indices or recalculate them for linear scaling verbosity : 2 # verbosity of the output outdir : . # Writing directory psp_onfly : Yes # Calculate pseudopotential projectors on the fly pdsyev_blocksize : -8 # SCALAPACK linear scaling blocksize pdgemm_blocksize : -8 # SCALAPACK linear scaling blocksize maxproc_pdsyev : 4 # SCALAPACK linear scaling max num procs maxproc_pdgemm : 4 # SCALAPACK linear scaling max num procs ef_interpol_det : 1e-20 # FOE max determinant of cubic interpolation matrix ef_interpol_chargediff : 10. # FOE max charge difference for interpolation mixing_after_inputguess : Yes # mixing step after linear input guess (T/F) iterative_orthogonalization : No # iterative_orthogonalization for input guess orbitals check_sumrho : 2 # enables linear sumrho check experimental_mode : No # activate the experimental mode in linear scaling write_orbitals : No # linear scaling write KS orbitals for cubic restart (might take lot of disk space!) dft: hgrids: [0.45, 0.45, 0.45] # grid spacing in the three directions (bohr) rmult: [5., 8.] # c(f)rmult*radii_cf(:,1(2))=coarse(fine) atom-based radius ixc : 1 # exchange-correlation parameter (LDA=1,PBE=11) ncharge : 0 # charge of the system elecfield: [0., 0., 0.] # electric field (Ex,Ey,Ez) nspin : 1 # spin polarization mpol : 0 # total magnetic moment gnrm_cv : 1e-4 # convergence criterion gradient itermax : 50 # max. nrepmax : 1 # max. ncong : 6 idsx : 6 # wfn. diis history dispersion : 0 # dispersion correction potential (values 1,2,3,4,5), 0=none inputpsiid : 0 output_wf : 0 output_denspot : 0 rbuf : 0. # length of the tail (AU) ncongt : 30 norbv : 0 # Davidson subspace dim. nvirt : 0 nplot : 0 disablesym : No # disable the symmetry detection kpt: method : manual # K-point sampling method kpt: # Kpt coordinates - [0., 0., 0.] wkpt: [1.] # Kpt weights bands : No # For doing band structure calculation geopt: method : none # Geometry optimisation method ncount_cluster_x : 1 # Maximum number of force evaluations frac_fluct : 1. forcemax : 0. randdis : 0. # random displacement amplitude betax : 4. # Stepsize for the geometry optimisation mix: iscf : 0 # mixing parameters itrpmax : 1 # maximum number of diagonalisation iterations rpnrm_cv : 1e-4 # stop criterion on the residue of potential or density norbsempty : 0 # No. of additional bands Tel : 0. # electronic temperature occopt : 1 # smearing method alphamix : 0. # Multiplying factors for the mixing alphadiis : 2. # Multiplying factors for the electronic DIIS sic: sic_approach : none # SIC method sic_alpha : 0. # SIC downscaling parameter tddft: tddft_approach : none # TDDFT method #--------------------------------------------------------------------------------------- | Data Writing directory : ./ #-------------------------------------------------- Input Atomic System (file: posinp.xyz) Atomic System Properties: Number of atomic types : 1 Number of atoms : 2 Types of atoms : [ N ] Boundary Conditions : Free #Code: F Number of Symmetries : 0 Space group : disabled #------------------------------ Geometry optimization Input Parameters (file: input.geopt) Geometry Optimization Parameters: Maximum steps : 1 Algorithm : none Random atomic displacement : 0.0E+00 Fluctuation in forces : 1.0E+00 Maximum in forces : 0.0E+00 Steepest descent step : 4.0E+00 Material acceleration : No #iproc=0 [...]

In the log file, BigDFT automatically displays all the input parameters used for the calculations (this is what you see above). The parameters which were not explicitly given are set to a default value, except the atomic positions of course, which has to be given.
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 a single-point LDA calculation, without k-points nor spin-polarisation.
As we said earlier, the new version of BigDFT now supports .yaml files were all the parameters are given (instead of using an optional file every time you want to calculate something specific, you can now modify the corresponding line in the .yaml file), the input display shown above can serve as a template for this .yaml file. -note that one can combine a .yaml file with other task specifying files (.xyz or .geopt for example), BigDft will still understand-

### 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 (or ` .yaml ` file). Let us do it : Create a new calculation set by using the "LDA" prefix and rename all relevant files with LDA:

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

Create `LDA.dft` by copying/pasting in a file named `LDA.dft` the few lines that follow :

0.550 0.550 0.550 hx,hy,hz: grid spacing in the three directions 3.5 9.0 crmult, frmult: c(f)rmult*radii_cf(*,1(2)) gives the coarse (fine)radius around each atom 1 ixc: exchange-correlation parameter (LDA=1,PBE=11) 0 0.0 0.0 0.0 ncharge: charge of the system, Electric field 1 0 nspin=1 non-spin polarization, mpol=total magnetic moment 1.E-04 gnrm_cv: convergence criterion gradient 50 10 itermax,nrepmax: maximum number of wavefunction optimizations and of re-diagonalised runs 6 6 ncong, idsx: # CG iterations for the preconditioning equation, length of the diis history 0 dispersion correction functional (values 1,2,3), 0=no correction 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 treatment, no. of virtual orbitals, no of plotted orbitals T disable the symmetry detection

Now you have your default file! It is time to modify `LDA.dft` such as to output the wavefunctions at the end of calculation, by putting the `output_wf` variable to 1

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 XC codes for a list of the supported XC functionals. Data of the calculation can be analysed. Consider the eigenvectors of the LDA and HF runs.

**Exercise**: Compare the values of the HOMO and HOMO-1 eigenvalues for the LDA and the HF run.
Change the values of the hgrid and crmult to find the converged values.
Note that, both in the LDA and in the HF calculation, a norm-conserving PSP is used.
The results can be compared to all-electron calculations, done with different basis sets, from references (units are eV) ^{[1]} and ^{[2]}:

LDA(1) HF(1) HF(2) (Exp.) 3σ_{g}10.36 17.25 17.31 (15.60) 1π_{u}11.84 16.71 17.02 (16.98) 2σ_{u}13.41 21.25 21.08 (18.78)

The results depends, of course, on the precision chosen for the calculation, and of the presence of the pseudopotential.
As it is well-known, the pseudopotential appoximation is however much less severe than the approximation induced by typical XC functionals. We might see that, even in the HF case, the presence of a LDA-based pseudopotential (of rather good quality) does not alter so much the results. Here you can find the values from BigDFT calculation using a very good precision (`hgrid=0.3`, `crmult=7.0`). Note that 1 ha=27.21138386 eV.

LDA HF 3σ_{g}10.40 17.32 1π_{u}11.75 16.62 2σ_{u}13.52 21.30

How much do these values differ from the calculation with default parameters? Do they converge to a given value?
What is the *correlation* for the N2 molecule in (PSP) LDA?

NOTE: when you create your own .xyz files, be sure to write the names of the atoms in **capital letters **
**.**