prep

Description

This command manages the DFT calculation using the built-in DFT code prep.x.

Synopsis

turbogenius prep [ACTION] [OPTIONS]

ACTION is one or any combination of -g (generate an input file), -r (run a program), or -post (perform postprocess). It is mandatory.

turbogenius prep --help

This command shows the list of available options.

Options

general option

This option affects all actions.

option	default value	description
-log TEXT	INFO	Specify log level. The argument is DEBUG, INFO, or ERROR.

generate (-g) options

These options affect the generation of the input file. The correspondence between the options and the input parameters are described in the note section.

option	default value	description
-grid FLOAT…	[0.1, 0.1, 0.1]	Specify grid size
-lbox FLOAT…	[15.0, 15.0, 15.0]	Specify lbox (only for molecules)
-smear FLOAT	0.0	Specify the smearing
-f FLOAT	0.0	Specify the h_field
-m LIST	[]	Specify the magnetic_moment_list for each atom (u(up), d(dn), or n(no))
-max INTEGER	3600	Specify maxtime (sec.)
-xc TEXT	xc	Specify xc (lda or lsda)
-kpts INTEGER…	[0, 0, 0, 0, 0, 0]	Specify Monkhorst-Pack grids and shifts, [nkx,nky,nkz,kx,ky,kz]

Environment variables

TURBOPREP_RUN_COMMAND

This specifies the execution command used in the DFT calculation. The default is prep-serial.x. If the MPI parallel version is to be used, set the variable, for example, to mpiexec -n 16 prep-mpi.x, where mpiexec is the MPI launch command, and -n 16 specifies the number of MPI processes (16 in this case).

Input and output files

This subcommand generates prep.input, each variable is described in turborvbtutorial_command_prep.x.

action	input	output	rename
-g	fort.10 pseudo.dat	prep.input dft_genius_cli.pkl
-r	fort.10 pseudo.dat prep.input dft_genius_cli.pkl	EDFT_vsk.dat fort.10_new occupationlevels.dat out_prep
-post	out_prep dft_genius_cli.pkl

Notes

Corresponding input parameters

The correspondence between the options and the input parameters in prep.input is summarized as follows.

turbogenius option	section	paramter
grid_size (-grid) lbox (-lbox)	&molecul	nx, ny, nz for periodic systems &molecul nx, ny, nz are given by Lx/ax, Ly/ay, Lz/az (round up to even integers), respectively, where Lx, Ly, Lz are norms of lattice vectors, and ax, ay, az are grid_size, though ax, ay, az are commented out. lbox parameters are not used. ax, ay, az, nx, ny, nz for open systems &molecul ax, ay, az are specified by grid_size. &molecul nx, ny, nz are given by Lx/ax, Ly/ay, Lz/az (round up to even integers), respectively, where Lx, Ly, Lz are the sum of the extent of the molecule along x, y, z axes and the values of lbox.
smearing (-smear)	&dft	optocc spsshell nelocc neloccdo
h_field (-f)	&dft	nxs, nys, nzs hfield
magnetic_moment_list (-m)		(magnetic moment section in prep.input)
maxtime (-max)	&simulation	maxtime
xc (-xc)	&dft	typedft (1 for lda, 4 for lsda)
det_contraction	&dft	contracted_on
memlarge	&dft	memlarge
maxit	&dft	maxit
epsdft	&dft	epsdft
thr_lindep	&dft	epsover
kpoints (-kpts)	&kpoints	yes_kpoints kp_type nk1, nk2, nk3, k1, k2, k3 skip_equivalence double_kpgrid