ENVISIo N User Guide
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Visualization of electron structures
2018-05-28
User guide
Editor: Viktor Bernholtz
Version 1.0
Status
Granskad
Godkänd
TFYA75
User guide
DOK
Rickard Armiento
i
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PROJECT IDENTITY
2018/Spring, Group 2
Linköpings Tekniska Högskola, IFM
Group members
Name
Anders Rehult
Marian Brännvall
Andreas Kempe
Viktor Bernholtz
Role
Project leader (PL)
Document manager (DOK)
Secretary (SE)
Viktor Bernholtz (VB)
Phone no.
076-3161206
070-7280044
073-9796689
073-0386030
E-mail address
andre449@student.liu.se
marbr639@student.liu.se
andke133@student.liu.se
vikbe253@student.liu.se
Client: IFM, Linköpings universitet, 581 83 Linköping
Contact person of client: Rickard Armiento, 013-281249, rickard.armiento@liu.se
Course examinator: Per Sandström, 013-282902, persa@ifm.liu.se
Main supervisor: Johan Jönsson, 013-281176, johan.jonsson@liu.se
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Contents
Document history
iv
Licens
v
1
Introduction
1
2
How to build and run ENVISIoN
1
2.1
Install git . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
2.2
Download ENVISIoN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
2.3
Prepare Inviwo using the ENVISIoN install script . . . . . . . . . . . . . . . .
2
3
Start Inviwo and run ENVISIoN scripts
2
4
Scripts
3
4.1
Unit cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3
4.2
ELF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5
4.3
Charge density . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6
4.4
DOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
8
4.5
Interconnected networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
4.5.1
Unit cell and charge . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
4.5.2
Unit cell and ELF . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
4.5.3
Unit cell and DOS . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11
Referenser
13
Appendix A Licens
13
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Document history
Version
0.1
0.2
1.0
TFYA75
User guide
Date
2018-05-22
2018-05-25
2018-05-28
Changes
First draft.
Second draft.
Approved for version one.
iv
Done by
Project group
Project group
Project group
Reviewed
PL
DOK
DOK
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Licens
This documet is licensed as CC0, see appendix A.
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Introduction
ENVISIoN is an open source toolkit for electron visualisation.
ENVISIoN is implemented by using a modified verision of the Inviwo visualisation framework,
developed at the Scientific Visualization Group at Linköpings universitet, LIU.
ENVISIoN has been developed as a part of the course TFYA75: Applied Physics - Bachelor’s
Project, given at Linköpings universitet, LiU.
The present version was developed during the spring term of 2018 by a project group consisting
of: Anders Rehult, Marian Brännvall, Andreas Kempe and Viktor Bernholtz. Supervisor: Johan
Jönsson; Requisitioner and co-supervisor: Rickard Armiento; Visualization expert: Rickard
Englund; and Course examiner: Per Sandström. The work is based on a previous version by
the project group taking the course in the spring term of 2017 consisting of: Josef Adamsson,
Robert Cranston, David Hartman, Denise Härnström, Fredrik Segerhammar. Supervisor: Johan Jönsson; Requisitioner and co-supervisor: Rickard Armiento; Visualization expert: Peter
Steneteg; and Course examiner: Per Sandström.
ENVISIoN provides a set of Python scripts that allow the user to:
• Read and parse output from electronic structure calculations made by the program VASP
and storing the result in a structured HDF5 file.
• Generate interactive Inviwo visualisation networks for common tasks when analyzing
electronic structure calculations. Presently there is support for visualising the crystal
structure of the unit cell of a material, electron localization function (ELF)-data, electronic charge density, and density of states - both total and partial. The system also
provides the ability to interconnect some of the networks mentioned above.
2
How to build and run ENVISIoN
These instructions show how to build Inviwo and ENVISIoN on Ubuntu 18.04 LTS.
2.1
Install git
Start by installing git, which will be used to fetch ENVISIoN in the next step.
sudo apt install git
2.2
Download ENVISIoN
Go to your home folder and clone ENVISIoN from Github. This guide will assume that both
ENVISIoN and Inviwo will be placed directly under the home folder.
cd
git clone https://github.com/rartino/ENVISIoN
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Prepare Inviwo using the ENVISIoN install script
ENVISIoN provides an install script for Ubuntu 18.04 LTS. Executing the installation script will
install all required dependencies, clone Inviwo from Github and configure the Inviwo build.
The script should NOT be run as root, but as your own user and it will ask for your password
when it needs root rights. It is possible that the script will ask for other user input during the
process, if that’s the case, just accept the default.
cd ~/ENVISIoN/scripts
./install_envision_ubuntu_1804.sh /home/$USER/ENVISIoN /home/$USER/inviwo
Once the installation script has run, it prints build instructions. Follow the instructions and start
the build. The instructions will tell you to cd to the build directory and execute make.
An easy way to modify the build settings, if needed, is to install the cmake curses gui and run it
in the build directory.
To install the cmake gui:
sudo apt install cmake-curses-gui
Running cmake in the build directory:
cd ~/inviwo/build
ccmake .
When in the GUI, press c to apply the current configuration, g to generate build files and q to
quit. If settings have changed, it is possible that you will need to press c more than once before
the g option becomes available.
After having generated the build files, the project can now be rebuilt with the new settings by
executing make like earlier.
3
Start Inviwo and run ENVISIoN scripts
After the Inviwo build is done, the binary will be available as bin/inviwo in the build folder.
Start it by executing the command below, while still standing in the build directory.
cd ~/inviwo/build
./bin/inviwo
• Open Python Editor under Python menu.
• In the Python editor, click Open Script.
• Select one of the scripts.
• Click open.
• Click the python logo in the top left corner to run.
More information about each script and how to use them in chapter 4.
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Scripts
Descriptions and examples of all the avaliable scripts are found below. The scripts are called
through the python editor in Inviwo as shown in figure 1.
Figure 1: Python script for calling on the DOS visualisation module of ENVISIoN. Note that the
pathway PATH_TO_VASP_CALC here is set to "~/ENVISIoN/data/TiPO4/VASP", the folder
containing the relevant VASP output files.
In all of the scripts the user has to specify the path to ENVISIoN, a path where VASP output files
are found, and a desired path where ENVISIoN will generate a HDF5-file, or, if one already
exists, use that file and skip parsing VASP data. NOTE: change the value of PATH_TO_HDF5,
delete the HDF5-file, or rename the HDF5-file in between visualisations if a new material is to
be visualised.
4.1
Unit cell
In the Python editor of Inviwo the user can choose to generate a visualisation of the unit cell by
opening the folder scripts and running the file unitcell.py.
Figure 2 is an example of a unit cell visualisation, in this case of TiPO4. Figure 3 shows the
network responsible for the aforementioned visualisation.
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Figure 2: Visualisation of the crystal structure of the unit cell of TiPO4 in Inviwo.
Figure 3: Network for visualisation of TiPO4 in Inviwo.
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ELF
In the Python editor of Inviwo the user can choose to generate a visualisation of the Electron
Localisation Function (ELF)-data as shown in figure 4 with corresponding network shown in
figure 5 by opening the folder scripts and running the file elf.py. A second image showing the
ELF-data of a slice of the unit cell can be added by changing the argument Slice of the function
elf to True. This slice corresponds to a plane intersecting the unit cell, which can be moved
using the W and S keys on the keyboard. The orientation of this plane can be changed by
selecting the processor "Volume Slice" in the network by clicking on it, then choosing another
value from the drop down menu in the property "Slice along axis".
The ELF-data can also be visualised as an isosurface. This is achieved by changing the argument
iso of the function elf from None to any value between 0 and 1. The slice function described
above is not compatible with isosurface visualisation.
The colors and opacities of different values can be changed by selecting the processor "ELF
raycaster" in the network, clicking on the property "Transfer function", and interacting with the
window that pops up. This window shows multicolored dots which can be manipulated to control opacity. Dots can be added by double clicking, and removed by clicking a dot and pressing
the Delete key on the keyboard. Dots can be dragged and dropped using the mouse. The horizontal axis of the plane on which the dots are placed corresponds to ELF values between 0 and
1, while the vertical axis corresponds to opacities between 0 (transparent) and 1 (completely
opaque). Figure 9 in chapter 4.3 shows what this window looks like.
Figure 4: Visualisation of ELF-data for diamond in Inviwo.
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Figure 5: Network for visualisation of ELF-data for diamond in Inviwo.
4.3
Charge density
In the Python editor of Inviwo the user can choose to generate a visualisation of the charge
density by opening the folder scripts and running the file charge.py. A second image showing
the charge density of a slice of the unit cell can be added by changing the argument Slice of the
function charge to True. This slice corresponds to a plane intersecting the unit cell, which can be
moved using the W and S keys on the keyboard. The orientation of this plane can be changed by
selecting the processor "Volume Slice" in the network by clicking on it, then choosing another
value from the drop down menu in the property "Slice along axis". This type of visualisation is
shown in figure 6, and the generating network is found in figure 7.
The charge density can also be visualised as an isosurface. This is achieved by changing the
argument iso of the function charge from None to any value between 0 and 1. Figure 8 shows
an example of this. The slice function described above is not compatible with isosurface visualisation.
The colors and opacities of different values can be changed by selecting the processor "Charge
raycaster" in the network, clicking on the property "Transfer function", and interacting with
the window that pops up. This window shows multicolored dots which can be manipulated
to control opacity. Dots can be added by double clicking, and removed by clicking a dot and
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pressing the Delete key on the keyboard. Dots can be dragged and dropped using the mouse.
The horizontal axis of the plane on which the dots are placed corresponds to charge density
values between 0 and 1, while the vertical axis corresponds to opacities between 0 (transparent)
and 1 (completely opaque). Figure 9 shows what this window looks like.
Figure 6: Visualisation of charge density for NaCl with slice function in Inviwo.
Figure 7: Network for visualisation of charge density for NaCl with slice function in Inviwo.
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Figure 8: Visualisation of charge density for NaCl with ISO raycasting.
Figure 9: Transfer function of the Charge raycaster processor and visualisation of charge density
of Si connected with unit cell visualisation. Charge density values between 0.15 and 0.45 are
illustrated as a somewhat transparent purple volume.
4.4
DOS
In the Python editor in Inviwo, the user can choose to generate a visualisation of the density of
states by opening the folder scripts and running the file dos.py.
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Figure 10 is an example of a visualisation of the total density of states, in this case for Cu.
Figure 11 shows the network for the visualisation. This network generates both a 2D-graph of
the total density of states and a similar graph but for the partial density of states. The partial
density of states is by default shown for one atom, in two graphs for spin-polarized calculations,
determined by the argument atoms in the function dos. See chapter 4.5.3 for a description of
how to pick the atom for which to show projected DOS.
Visualisation of the partial DOS for one specific orbital (s, p, d, or f) of an atom can be achieved
by deleting the connections between the undesired processors of type "HDF5 To Function"
and the corresponding processor with name "Partial Add". To do this, select a connection by
clicking on it and press the Delete key.
Figure 10: Visualisation of total DOS for Cu.
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Figure 11: Network for visualisation of total and partial DOS for Cu.
4.5
Interconnected networks
Descriptions and examples of the python scripts generating interconnected networks can be
seen below.
4.5.1
Unit cell and charge
In the Python editor in Inviwo, the user can choose to generate a visualisation of unitcell and
charge by opening the folder scripts and running the file unitcellAndCharge.py.
4.5.2
Unit cell and ELF
In the Python editor in Inviwo, the user can choose to generate a visualisation of unitcell and
ELF by opening the folder scripts and running the file unitcellAndElf.py. Figure 12 shows what
this can look like.
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Figure 12: Unit cell and ELF data for aluminum visualised side by side, with volume raycasting
and slice function.
4.5.3
Unit cell and DOS
In the Python editor in Inviwo, the user can choose to generate a visualisation of unitcell and
density of states by opening the folder scripts and running the file unitcellAndDos.py. Here the
user can pick an atom for which to show partial DOS by clicking on the desired atom in the unit
cell. See figure 13 for an example of what this can look like.
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Figure 13: Visualisation of unit cell data and partial DOS of a titanium atom. The two graphs
show DOS for electron spin up and electron spin down.
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