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, or computation of the Hirshfeld atomic charge (starting from a density file).

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

For the initials of contributors, see ~ABINIT/Infos/contributors .

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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) 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.

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.

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.)

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