# Help file for the Cut3D utility of the ABINIT package.

### This file explains the use and i/o parameters needed for the "Cut 3-Dimensional files" code of the ABINIT package.

This code is able to analyse the files produced by ABINIT, that contain 3-Dimensional real space data, like all types of potential files, density files. Wavefunction files data can also be analysed : first, a k-point number, and the band number must be given, then, the corresponding wavefunction is transformed to real space.

In all these cases, thanks to Cut3D, one can obtain 2-Dimensional data corresponding to a cut by a plane, or 1-Dimensional data along a line. One can also translate the original formatting into many different ones.

Finally, one can also perform angular momenta analysis of wavefunctions with respect to any given atom, computation of the Hirshfeld atomic charge (starting from a density file). Although Wannier functions can also be built, this is a deprecated feature. The use of Wannier90 library is to be preferred.

##### Copyright (C) 1998-2012 ABINIT group (XG,RC,GMR,JFB,MCote,JBattacharjee)

This file is distributed under the terms of the GNU General Public License, see
~abinit/COPYING or
http://www.gnu.org/copyleft/gpl.txt .

For the initials of contributors, see ~abinit/doc/developers/contributors.txt .

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**Cut3D**

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**Optic**

**1. Running cut3d to analyse an unformatted file (_DEN, _POT, _WFK ...)**

To run cut3d, simply type :
cut3d

then, provide answer to the questions.

You will have to give first the name of the unformatted file. For example, t1xo_DEN.

You will have to specify whether this file is formatted or unformatted. Unformatted file corresponds to choice 1.

#### 1.a. Unformatted file, excluding a wavefunction file

Supposing that you are not treating a wavefunction file, you will have to choose between different possibilities :- 1) computation of data for a point, to be specified
- 2) computation of data along a line, to be specified
- 3) computation of data on a 2D grid, to be specified
- 4) computation of data on a 3D grid, to be specified
- 5) conversion to formatted file
- 6) conversion to indexed formatted
- 7) conversion to Molekel format
- 8) conversion to 3D data with coordinates (tecplot ASCII format)
- 9) output .xsf file for XCrysDen
- 10) output .dx file for OpenDx
- 11) compute atomic charge using the Hirshfeld method

For option 1) you will have the possibility to specify a point in reduced or cartesian coordinates.

For option 2) you will have the possibility to specify a line by its two end-points in reduced or cartesian coordinates, or by it being perpendicular to some plane.

For option 3) and 4) many possibilities are offered, including specifications thanks to points defined in reduced coordinates, cartesian coordinates, or atomic positions.

For a wavefunction file, the two forms of outputs are :
the bare data or a Data Explorer form.
The option 10 also produce input files to draw the molecules in Data
Explorer using modules and macros that JFB and MCote
have developped. Those modules and macros could be made public.

To continue the analysis, simply answer the questions of the code, that
should be sufficiently self-explanatory.

#### 1.b. Unformatted wavefunction file

Instead, supposing that you are treating a wavefunction file, you will have to choose between the analysis of one wave function, or the construction of Wannier functions (see the bottom of this help file). In the case in which you want to analyse one wavefunction, you will have to define the k point, the number of the band, and possibly the spin-polarization or the spinor component.Then, you will be asked whether you want to perform the angular component analysis. You will have to provide the radius of the sphere(s) around each atom, for which the angular analysis will be performed.

Finally, you will be given the choice between different formatting of the wavefunction real-space data, including bare files, or XCrysDen or Data Explorer formatted files.

**2. Starting from a formatted file. **

In the formatted case, one must have three different files : - the formatted 3D function (for example mos.densout) density or potential file in ASCII format with nr1 x nr2 x nr3 lines of 1 float - a file with complementary informations about the cell, the FFT grid ... (always named cut.in) Here is an example (6 lines): mos.xyz 11.502384 6.0558159 16.295674 unit cell parameters (=acell) 1 0 0 0 1 0 -0.215 0 0.976 orientation of the unit cell axes (=rprim) 54 30 75 grid size (= nr1,nr2,nr3, all three integers) 10 number of atoms in the unit cell (= natom, integer) 2 number of atomic types (=ntypat, integer) The first line gives the name of the file with atomic positions (Xmol format) (=filtau) No comment can appear on that line, in contrast with the other lines. - the coordinate file (for example mos.xyz) Its format (similar to XMOL) is On the first line the number of atoms (=natom) is provided. Blank line A list of natom lines containing : Char (1 or 2 characters, = atom label) + 3 float (X, Y, Z cart. coord.)

**3. Wannier type localized orbital calculations **

WARNING : This is a deprecated feature of Cut3d.
Use of Wannier90 is to be preferred.
In order to obtain Wannier type localized orbitals (WLO), you have to type (or put in your input file) : * 1st line : Name of the wavefunction file * 2nd line : Fixed read option "1" * 3rd line : option "2" to do WLO. * 4th line : name of an "auxiliary" input file (name should not be more than 40 charater) file to calculate WLO. Examples of "auxiliary" input files are given in the automatic tests Test_v4 cases 48 and 49. The subroutine localorb_S.F90 referred from cut3d.F90 constructs Wannier type localized orbitals (WLO) described in cond-mat/0509571 titles " Localized Orbital Description of Electronic Structure". Type of calculation ------------------- These calculations run as a postprocessing of a wavefunction file having wfs at all kpoints in the Brillouin zone (this may be generated using kptopt 3 in a nonSCF calculation folloeing an SCF charge density calculation). 1. Insulator type calculation with "insmet 1". All resultant WLOs would have normalization 1 in the nkx.nky.nkz supercell where nkx.nky.nkz defines the size of the k-point mesh. 2. Metal type calculation with "insmet 2". Some of the resultant WLOs might have normalization less than 1. 3. (Not yet included) Maximally localized Wannier function from the WLOs. NOTE : The code works for nshiftk = 1 only OUTPUT ------ 1. fort.1***1 : XCRYSDEN plottable WLO fort files. fields:12345 field 1 : "1" for XCRYSDEN plottable files field 2-4 : number corresponding to the orbital in the order in which they are provided in the *.in file under the variable "orbdetails" field 5 : spin polarization : isppol 1 or 2 NOTE: To avoide disk space problem these files are not plotted through out the entire supercell mentioned in the *.in file. Instead they are plotted in a 2x2x2 supercell (or 1x1x1 if that is the supercell mentioned in the *.in) with the orbital at the middle. 2. fort.2***1 : Complex data files of WLO in the plotting region of fort.1***1 if "lofwrite" is set to 1. Only activate if this files are really required for further quantitative analysis. 1st line : Location of the first grid point in the supercell of WLO construction. 2nd line : The supercell grid point corresponding to the starting grid point here. 3rd line : ngx ngy ngz in which the fort files are plotted. WLO is plotted as : (((WLO(i,j,k),i=1,ngx),j=1,ngy),k=1,ngz) 3. singularvalues.dat : Contains singular values of the overlap matrix between the energy occupied subspace and the auxiliary subspace obtained by inverse Fourier transform of the initial localized template described by "orbdetails" in the input file. NOTE: If you find some of the singular values consitently very close to zero (0.00xxx) you may look at the overlap_abs.dat file and exclude orbitals (from under the orbdetails variable in the input file) corresponding to predominantly zero rows of overlap matrix and start a new calculation. 4. lo_center.dat : position expectation value of the WLOs column 1 2 3 4 5 6 index spin 5. lo_loclength.dat : variance of WLO column 1 2 3 4 5 6 index var_x var_y var_z spin NOTE : Values in the above two data files are meaningfull only in case of insulator type calculation with sufficiently large supercell to give WLO normalization close to 1. 6. overlap_abs.dat : Absolute(overlap matrix) Examples can be found as Test_v4 cases 48 and 49. Ongoing efforts --------------- The second part which is yet to be upgraded is the construction of Maximally localized orbitals from the WLOs. The code is working but not yet in an efficient presentable form. I hope to complete that some times in the coming months. As a disclaimer, I must admit that while interfacing my codes with abinit I have really maintained least interference with the main abinit procedures just to avoid more work for me! Contact information for Wannier functions. ------------------------------------------ JOYDEEP BHATTACHARJEE Research fellow Theoretical Sciences Unit. Jawaharlal Nehru Centre for Advanced Scientific Research. Jakkur, Bangalore -560064, India Ph :+91-80-22082834-35 (2 lines) Fax:+91-80-22082766 Cel:+91-9341312074

Goto :

**ABINIT home Page**

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**Suggested acknowledgments**

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**List of input variables**

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**Tutorial home page**

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**Bibliography**

Help files :

**New user's guide**

**|**

**Abinit (main)**

**|**

**Abinit (respfn)**

**|**

**Mrgddb**

**|**

**Anaddb**

**|**

**AIM (Bader)**

**|**

**Cut3D**

**|**

**Optic**