mirror of https://github.com/abinit/abinit.git
195 lines
8.5 KiB
Markdown
195 lines
8.5 KiB
Markdown
---
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authors: MC, SP
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---
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# Cut3D analysis tool
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## How to use cut3d
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This tutorial covers some of the features available in the program cut3d. The
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help file of this program can be view at [[help:cut3d]].
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The cut3d program can produce output that can be read by several other programs.
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At present, at least XCrySDen ([www.xcrysden.org](http://www.xcrysden.org/), freely available)
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is known to support this output.
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The cut3d program can be used to treat data in a density file (*_DEN*), a
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potential file (*_POT*) or a wavefunction file (*_WFK*). In this tutorial will we
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see how to use this program to obtain the value of the density on a line.
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This tutorial should take about 15 minutes.
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## 1 Obtaining the density and wavefunctions files for Silicon
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We will first start by a simple example: viewing Silicon density information.
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Before using the cut3d program, we first have to generate the density and
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the wavefunctions files by running the Abinit program. For this simple case,
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we will use the last input file used in [tutorial 3](/tutorial/base3)
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(*tbase3_5.in*). That input file contains two datasets, one to obtain a
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self-consistent density and the other to obtain a selected number of k-point wavefunctions.
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If you do not have the output of this case, you will need to
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rerun it, at this stage, this should be fairly easy for you!
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The output files that are of interest for us now are:
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tbase3_5o_DS1_DEN
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tbase3_5o_DS1_WFK
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tbase3_5o_DS2_WFK
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!!! important
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To ask Abinit to output the density, you have to set the input
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parameter [[prtden]] to 1 in the input file as it was done in the first dataset in this example.
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**NOTE:** In DS1, the self-consistent dataset, we have a good density (file:
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*tbase3_5o_DS1_DEN*) which is physically relevant.
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Careful, if you run a non-self-consistent job, you may obtain a density but it will not be physical!
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**NOTE:** The wavefunctions in DS1 (file: *tbase3_5o_DS1_WFK*) are those of the
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Monkhorst and Pack grid which are good for self-consistent calculations but
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often not really inspiring physically. For this reason, we often have to do a
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non-self-consistent run to get relevant wavefunctions as it is done in this
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case. The DS2 (file: *tbase3_5o_DS2_WFK*) contains the interesting wavefunctions
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that we want to analyse.
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## 2 Getting the density on a given line
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Now we are ready to use the cut3d program. First we must make sure that we
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have compiled the program. If you have run the command *make* in the Abinit
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main directory, and everything went well, then you have obtained the abinit
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program and all the accompanying program, in particular *cut3d*. You can
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obtain only the cut3d program by issuing the command *make cut3d* in the Abinit main directory.
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Assuming that we are in the directory *Tutorial/Work_tools*, and the *cut3d*
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program can be accessed by simply typing its name, now write the command:
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cut3d
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The *cut3d* program will ask you several questions in order to determine what
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you want him to do. In this tutorial, the text coming from the *cut3d* program are
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in black and the input that you have to type in are in red.
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After some text about the version and the licence, you will see the question:
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What is the name of the 3D function (density, potential or wavef) file ?
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You can enter the density file:
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tbase3_5o_DS1_DEN
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You will then see:
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=> Your 3D function file is : tbase3_5o_DS1_DEN
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Does this file contain formatted 3D ASCII data (=0)
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or unformatted binary header + 3D data (=1) ?
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Your answer is 1 as generally all output of Abinit are in unformatted binary
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form. After you have pressed enter, cut3d prints out a lot of information
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contained in this file that explain how that density was obtained. At this
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point, you can double check that this is really the file that you want to
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analyse. Then you will have the choices:
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What is your choice ? Type:
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1 => point (interpolation of data for a single point)
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2 => line (interpolation of data along a line)
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3 => plane (interpolation of data in a plane)
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4 => volume (interpolation of data in a volume)
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5 => 3D formatted data (output the bare 3D data - one column)
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6 => 3D indexed data (bare 3D data, preceeded by 3D index)
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7 => 3D Molekel formatted data
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8 => 3D data with coordinates (tecplot ASCII format)
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9 => output .xsf file for XCrysDen
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10 => output .dx file for OpenDx
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11 => compute atomic charge using the Hirshfeld method
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12 => NetCDF file
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13 => exit
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As you can see, there are many options available! At the moment, we will do
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something simple which is getting the density along a given line.
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Choose option 2. You will be given the following choices:
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Type 1) for a line between two cartesian-defined points
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or 2) for a line between two crystallographic-defined points
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or 3) for a line defined by its direction
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Select option 1. You will get the message:
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Type the first point coordinates (Bohrs):
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-> X-dir Y-dir Z-dir:
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We will ask for the density along the [111] direction starting from the origin
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and extending to two unit cell. For the first point, enter 0 0 0.
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You will get the message:
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Type the second point coordinates (Bohrs):
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-> X-dir Y-dir Z-dir:
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Looking at the input file, we see that the cubic side has a length of 10.217 bohr.
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To get 2 unit cells, you will enter 20.434 20.434 20.434.
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You will then be asked for the line resolution.
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Enter line resolution:
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This is how many points are calculated for the line. Typically, you should
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enter a large number, say 5000. You will then be asked for the file name.
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Enter the name of an output file:
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Enter something meaningful, si_den_111.dat.
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More analysis of the 3D file ? (1=default=yes,2=no)
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Enter 2 to finish with cut3d. If you do a list of the files in your working
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directory, you should see the *si_den_111.dat* file. You can look at this
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file, you will see that this is a simple two columns file. You can visualize
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it with your favorite plotting software (ex: xmgrace, gnuplot, ...). If you
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open this file with xmgrace, you will obtain the following graph:
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We can learn quite a lot from this graph. Looking at the input file, we see
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that we have a silicon atom at the origin and another 1/4 along the diagonal.
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We note also that there is almost no density at the origin. By doing the line
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in the [111] direction, we have crossed the first silicon-silicon bond which
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we can see as a large density peak indicated by the red arrows.
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By the way, cut3d works with the so-called trilinear interpolation of the
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density. That is, the FFT grid, on which the density is defined, in real
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space, leads to a partitioning of the space in small rectangular
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parallelepipeds, and in each such parallelepiped, the eight values of the
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density on the corner are used to define an interpolation that is linear in
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each the dimensions of the cube. More explicitly, let us chose one of the
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corner as origin, and define reduced coordinates, varying from 0 to 1 inside
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the parallelepiped, the density inside the parallelepiped is given by
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density(dx,dy,dz)= density(0,0,0) +
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c100 * dx + c010 * dy + c001 * dz +
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c110 * dx * dy + c101 * dx * dz +
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c011 * dy * dz + c111 * dx * dy * dz
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where the 7 coefficients c100, c010, c001, c110, c101, c011, c111 are to be
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determined from the knowledge of the density at the 7 other corners.
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This trilinear interpolation guarantees that the overall function of space is
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continuous, but do not guarantee that the derivatives change continuously.
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This is seen in the above figure, as the two abrupt changes of slopes, close
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to the maximum. These are completely spurious features, that can be avoided is
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a finer FFT grid is used to determine the density. Actually, the density
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profile along the bond, with a fine FFT grid, behave quite smoothly, and reach
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its maximum at the mid point between the two atoms, in contrast to the figure
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presented previously.
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!!! note
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An important point to remember when doing visualization of density
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obtained with a pseudopotential calculation is that the core charge is not
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included! This is the reason why we use pseudopotential and the charge we get
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is only the valence charge. It is possible to include some of the core charge
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by doing calculations using pseudos with partial core charge. The fact that
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the core charge is missing means that there is no charge at the nucleus of our
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atoms. This means that we are getting low density at the nucleus center and we
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have to remember that this is not a physical effect! The location of the
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silicon atoms have been indicating by blue arrows.
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