next up previous contents
Next: 7 SCF cycle Up: 2 Detailed description of Previous: 5 Shell scripts   Contents


6 Programs for the initialization

In sections (6.1-6.6) we describe the initial utility programs. These programs are used to set up a calculation.

1 NN (nearest neighbor distances)

This program uses the case.struct file (see 4.3) in which the atomic positions in the unit cell are specified, calculates the nearest neighbor distances of all atoms, and checks that the corresponding atomic spheres (radii) are not overlapping. If an overlap occurs, an error message is shown on the screen. In addition, the next nearest-neighbor distances up to $f$ times the nearest-neighbor distance ($f$ must be specified interactively) are written to an output file named case.outputnn. For negative $f$ values only the distances of non-equivalent atoms are printed. , but equivalent ones are not listed again. Optionally one can specify also a ``dlimit'' parameter, which helps nn to find equivalent atoms in case of ``inaccuarate'' structural data.

It is highly recommended in most cases that you change your sphere sizes and do NOT use the default of 2.0. An increase from 2.0 to 2.1 may already result in drastically reduced computing time. More recommendations are given in chapter 4.3.

nn also checks if equivalent atoms are specified correctly in case.struct. At the bottom of case.outputnn the coordination shell-structure is listed and from that a comparison with the input is made verifying that equivalent atoms really have equivalent environments. If this is not the case, an ERROR will be printed and a new structure file case.struct_nn is generated. You have to recheck your input and then decide whether you want to accept the new structure file, or reject it (because the equivalency may just be an artefact due to a special choice of lattice parameters). It also may be that you have made a simple input error. If you want to force two atoms of the same kind (e.g. 2 Fe atoms) to be nonequivalent (e.g. because you want to do an antiferromagnetic calculation), label the atoms as ``Fe1'' and ``Fe2'' in case.struct.

Thus this program helps to generate proper struct-files especially in the case of artificial unit cells, e.g. a supercell simulating an impurity or a surface.

It also prints the ``bond-valences'' (see also the comments in $WIENROOT/SRC_nn/BVA).

1 Execution

The program nn is executed by invoking the command:

nn nn.def or x nn


This program was contributed by:

Bogdan Yanchitsky and Andrei Timoshevskii \\
...ilinglist. If necessary, we will communicate
the problem to the authors.}

It was published in Yanchitsky and Timoshevskii 2001, and is written in C.

This program uses information from case.struct (lattice type, lattice constants, atomic positions) and determines the spacegroup as well as all pointgroups of non-equivalent sites. It uses the nuclear charges Z or the "label" in the 3rd place of the atomic name (Si1, Si2) to distinguish different atoms uniquely. It is able to find possible smaller unit cells, shift the origin of the cell and can even produce a new struct file case.struct_sgroup based on your input case.struct with proper lattice types and equivalency. It is thus most usefull in particular for ``handmade'' structures.

For more information see also the README in SRC_sgroup.

1 Execution

The program sgroup is executed by invoking the command:

sgroup -wi case.struct [-wo case.struct_sgroup] case.outputsgen or x sgroup


This program uses information from case.struct (lattice type, atomic positions). If NSYM was set to zero it generates the space group symmetry operations and writes them to case.struct_st to complete this file. Otherwise (NSYM $>$ 0) it compares the generated symmetry operations with the already present ones. If they disagree a warning is given in the output. In addition the point group of each atomic site is determined and the respective symmetry operations and LM values of the lattice harmonics representation are printed. The latter information is written into case.in2_sy, while the local rotation matrix, the positive or negative IATNR values and the proper ISPLIT parameter are written to case.struct_st. (See appendix A and Sec. 4.3).

1 Execution

The program symmetry is executed by invoking the command:

symmetry symmetry.def or x symmetry

4 LSTART (atomic LSDA program)

lstart is a relativistic atomic LSDA code originally written by Desclaux (69, 75) and modified for the present purpose. Internally it uses Hartree atomic units, but all output has been converted to Rydberg units. lstart generates atomic densities which are used by dstart to generate a starting density for a scf calculation and all the input files for the scf run: in0, in1, in2, inc and inm (according to the atomic eigenvalues). In addition it creates atomic potentials (which are truncated at their corresponding atomic radii and could be used to run lapw1) and optional atomic valence densities, which can be used in lapw5 for a difference density plot. The atomic total energies are also printed, but it can only be used for cohesive energy calculations of light elements. Already for second-row elements the different treatment of relativistic effects in lstart and lapwso yields inconsistent data and you must calculate the atomic total energy consistently by a supercell approach via a ``bandstructure calculation (Put a single atom in a sufficiently large fcc-type unit cell).

If the program stops with some lines:

NSTOP= .....

in case.outputst, this means, that a proper solution for at least one orbital could not be obtained. In such a case the input must be changed and one should provide different occupation numbers for these states (e.g. Cu can not be started with $3d^{10}4s^1$, but it works with $3d^{9}4s^2$).

The program produces ``WARNINGS'' if R0 is too big or core-density leaks out of RMT.

1 Execution

The program lstart is executed by invoking the command:

lstart lstart.def or x lstart [-sigma]

The files case.rsp(up$\vert$dn) are generated and contain the atomic (spin) densities, which will be used by DSTART later on.
Using -sigma generates case.inst_sigma with modified input to generate case.sigma used for difference densities (see below).

2 Dimensioning parameters

The following parameters are defined in file (static and not allocatable arrays):
NPT total number of radial mesh points, must be gt.(NRAD+NPT00), where NRAD is the number of mesh-points up to RMT specfied in case.struct.
NPT00 max. number of radial mesh points beyond RMT
RMAX0 max. distance of radial mesh

3 Input

When running lstart you will first be asked interactively to specify an XC-potential switch. Currently 5 (LSDA, Perdew and Wang 92) as well as 11, 13 and 19 (three GGAs, Wu,Cohen 06; the standard ``PBE'' Perdew et al. 96, as well as ``PBEsol'', Perdew et al. 08; respectively) are officially supported, 13 is the ``standard PBE-GGA''.

In addition the program asks for an energy cut-off, separating core from valence states. Usually -6.0 Ry is a good choice, but you should check for each atom how much core charge leaks out of the sphere (WARNINGS in case.outputs). If this is the case one should lower this energy cut-off and thus include these low lying states into the valence region. Alternatively you can also select a ``charge localization'' criterium (usually between 0.97 and 0.9999). This allows a more localized state (like a 4f of 5d elements) to be core, while a more delocalized state at lower energy (like the 5p states of 5d elements) to be semi-core.

The rest of the input is described in the sample input below.

Note: Only the data at the beginning of the line are read whereas the comment describes the respective orbitals. This file can be generated automatically in w2web during ``Initialize calc. or using ``SinglePrograms $\rightarrow $ instgen_lapw'' or with the script instgen_lapw. To edit this file by hand choose ``View/Edit $\rightarrow $ Input Files'' and choose case.inst.

------------------ top of file: case.inst -------------------
Ne 6         (inert gas, # OF VALENCE ORBITALS not counting spin)
3,-1,1.0  N        ( N,KAPPA,OCCUP; = 3S UP, 1 ELECTRON)
3,-1,1.0  N                           3S DN
3,-2,2.0  N                           3P UP
3,-2,2.0  N                           3P DN
3, 1,1.0  N                           3P*UP
3, 1,1.0  N                           3P*DN
3,-3,3.0  P                           3D UP
3,-3,3.0  P                           3D DN
3, 2,2.0  P                           3D*UP
3, 2,2.0  P                           3D*DN
4,-1,1.0  P                           4S UP
4,-1,1.0  P                           4S DN
****               END OF Input
****               END OF Input
------------------- bottom of file ---------------------------

Interpretive comments follow:

line 1:
title, keyword
keyword   The keyword Watson enables a stabilization of negative ions using a ``Watson''-sphere of radius R-wat with charge Q-wat, which must be given in the next line when this keyword is specified.
    The keyword PRATT enables a scf mixing using standard PRATT scheme. It might be usefull if a certain atomic configuration does not converge with the standard mixing scheme and requires a (usually quite small) mixing factor, which must be given in the next line when this keyword is specified.
line 2:
free format
config   specifies the core state configuration by an inert gas (He, Ne, Ar, Kr, Xe, Rn) and the number of (valence) orbitals (without spin). (In the example given above one could also use Ar 3 and omit the $3s$ and $3p$ states.) The atomic configurations are listed in the appendix and can also be found online using periodic_table, a shell script which displays SRC/ with ghostview)
line 3:
n, kappa, occup, plot
n   the principle quantum number
kappa   the relativistic quantum number (see below)
occup   occupation number (per spin)
plot   P specifies that the density of the respective orbital is written to the file case.sigma, which can be used for difference density plots in lapw5. N or an empty field will exempt density of the respective orbital from being printed to file.
$»>$:line 3
is repeated for the other spin and for all orbitals specified above by config.
$»>$: the last two lines
must be

optional inserted as line 2 when ``Watson'' has been specified in line 1:
free format
R-wat, Q-wat
R-wat   radius of a charged sphere used to stabilize otherwise unstable negative ions (e.g. 2.5 for O$^{2-}$)
Q-wat   charge of the stabilizing sphere, (e.g. 2 for O$^{2-}$)

The quantum numbers are defined as follows (see e.g. Liberman et al 65):

Spin quantum number: $s=+1$ or $s=-1$

Orbital quantum number $j = l + s/2$

Relativistic quantum number $\kappa = -s(j+1/2)$

Table 6.6: Relativistic quantum numbers
$j = l + s/2$ $\kappa$ max. occupation
$l$ $s=-1$ $s=+1$ $s=-1$ $s=+1$ $s=-1$ $s=+1$
s 0 1/2 -1 2
p 1 1/2 3/2 1 -2 2 4
d 2 3/2 5/2 2 -3 4 6
f 3 5/2 7/2 3 -4 6 8

5 KGEN (generates k mesh)

This program generates the k-mesh in the irreducible wedge of the Brillouin zone (IBZ) on a special point grid, which can be used in a modified tetrahedron integration scheme (Blöchl et al 1994).

kgen needs as interactive input the total number of k-points in the BZ. If this is set to zero, you are asked to specify the divisions of the reciprocal unit-cell vectors (3 numbers, be careful not to "break" symmetry and choose them properly according to the inverse lenght of the reciprocal lattice vectors) for a mesh yourself. If inversion symmetry is not present, it will be added automatically unless you specified the ``-so'' switch (for magnetic cases with spin-orbit coupling). The k-mesh is then created with this additional symmetry. If symmetry permits, it further asks whether or not the k-mesh should be shifted away from high symmetry directions. The file case.klist is used in lapw1 and case.kgen is used in tetra and lapw2, if the EF switch is set to TETRA, i.e. the tetrahedron method for the k-space integration is used. For the format of the case.klist see page [*].

1 Execution

The program kgen is executed by invoking the command:

kgen kgen.def or x kgen [-so]

With the switch -so it uses a file case.ksym (usually generated by symmetso) instead of case.struct and does not add inversion symmetry.

2 Dimensioning parameters

The following parameters are used in main.f, ord1.f (static arrays):

IDKP number of inequivalent k-points (like NKPT in other programs)
NWX internal parameter, must be increased for very large k-meshes
INDEXM internal parameter, must be increased for very large k-meshes

6 DSTART (superposition of atomic densities)

This program generates an initial crystalline charge density case.clmsum by a superposition of atomic densities (case.rsp) generated with lstart. Information about LM values of the lattice harmonics representation and number of Fourier coefficients of the interstitial charge density are taken from case.in1 and case.in2. In the case of a spin-polarized calculation it must also be run for the spin-up charge density case.clmup and spin-down charge density case.clmdn.

1 Execution

The program dstart is executed by invoking the command:

dstart dstart.def or x dstart [-up|dn -c -fft -super -lcore]

With the switch -fft dstart will terminate after case.in0_std has been created. The switch -super will produce new_super.clmsum instead of case.clmsum, which is necessary for charge extrapolation (clmextrapol_lapw). -lcore produces case.clmsc from the radial core densities case.rsplcore.

2 Dimensioning parameters

The following parameters are collected in file module.f, but usually need not to be changed:

NPT number of r-mesh points in atomic density (should be the same as in LSTART)
LMAX2 max l in LM expansion
NCOM number of LM terms in density

next up previous contents
Next: 7 SCF cycle Up: 2 Detailed description of Previous: 5 Shell scripts   Contents
pblaha 2011-03-22