Vtotav.py: Difference between revisions

Latest revision as of 17:52, 10 December 2019

There is a script written in Python to convert LOCPOT for visualization.

The source of this script is from Github [1] It is based on ASE; therefore you must first install the ASE environment either by using pip:

 pip install --upgrade --user ase

or following the instructions on the webpage [2].

1) Download vtotav.py by clicking the link or from our Wiki: File:Vtotav.tgz

2) Uncompress vtotav.tgz and copy it to your bin folder ($HOME/bin)

3) Make it executable

 chmod u+x ~/bin/vtotav.py

4) In terminal, go to the folder containing work function calculation and run it with command:

  vtotav.py  LOCPOT  z   (z is the direction, you can use x,y,and z, depending on your system)

5) You will get the output file named LOCPOT_Z. You can open it with Libreoffice/Excel or use one of the visualization methods given below.

Vtotav.py is written in python 2. Depending on your version of the ASE environment it might not be compatible, as the newest ASE version requires python 3. Therefore you need to convert the python 2 script to python 3 by using the automated python 2 to 3 conversion programme [3]:

  2to3 -w vtotav.py

(-w to write it) and by changing the first line in the script to #!/usr/bin/env python3

Method 1 to visualize the LOCPOT_Z file

Download this python script: File:Workplot.tgz and in the terminal, run: python wplot.py

Method 2 to visualize the LOCPOT_Z file

You can also download another script to plot workfunction File:Workplot nathan.tgz, but beware it gives huge figures :p (see below). The script requires one argument at the least; put "z" to define the file to be read as LOCPOT_Z

It has additional options too; the first EXTRA argument passed in the commandline sets the title (use dashes ""). Add two additional numbers to specify the range on the x-axis.

Alternatively you can load the script into Excel, Libreoffice or Origin. You'll first have to convert the file to the right format by running the line below in the terminal:

 sed -i '1d' LOCPOT_Z &&  sed -i 's/  */\t/g' LOCPOT_Z &&  sed -i 's/^[ \t]*//' LOCPOT_Z

@@ Line 1: / Line 1: @@
-There is a script written by Python to convert LOCPOT for visualization.
+There is a script written in Python to convert LOCPOT for visualization.
-The source of this script is from  Github [https://github.com/compphys/ase_tools/blob/master/scripts/vtotav.py]
+The source of this script is from  Github [https://github.com/compphys/ase_tools/blob/master/scripts/vtotav.py] It is based on ASE; therefore you must first install the ASE environment either by using pip:
-You can download it by clicking the link or from our Wiki:
+  pip install --upgrade --user ase
-[[Image:Vtotav.tgz]]
+or following the instructions on the webpage [https://wiki.fysik.dtu.dk/ase/install.html#installation-using-pip].
-install ASE environment[https://wiki.fysik.dtu.dk/ase/install.html#installation-using-pip]:
-  pip install --upgrade --user ase
+* 1) Download vtotav.py by clicking the link or from our Wiki: [[Image:Vtotav.tgz]]
-Uncompress and copy it to your bin folder
+* 2) Uncompress vtotav.tgz and copy it to your bin folder ($HOME/bin)
-make it executable
+* 3) Make it executable
    chmod u+x ~/bin/vtotav.py
-In terminal, go to the folder containing work function calculation and run it with command:
+* 4) In terminal, go to the folder containing work function calculation and run it with command:
+   vtotav.py  LOCPOT  z   (z is the direction, you can use x,y,and z, depending on your system)
+* 5) You will get the output file named LOCPOT_Z. You can open it with Libreoffice/Excel or use one of the visualization methods given below.
+Vtotav.py is written in python 2. Depending on your version of the ASE environment it might not be compatible, as the newest ASE version requires python 3. Therefore you need to convert the python 2 script to python 3 by using the automated python 2 to 3 conversion programme [https://docs.python.org/2/library/2to3.html]:
+to3 -w vtotav.py
+(-w to write it) and by changing the first line in the script to ''#!/usr/bin/env python3''
+---------  Method 1 to visualize the LOCPOT_Z file
+* Download this python script: [[Image:Workplot.tgz]] and in the terminal, run: python wplot.py
-   vtotav.py  LOCPOT  z   (z is the direction)
+---------  Method 2 to visualize the LOCPOT_Z file
-You will get output file named   LOCPOT_Z
-Because there are many spaces in the output file, I wrote a script (commands below) to convert those spaces into the excel format data (already in [[Image:Vtotav.tgz]]):
+* You can also download another script to plot workfunction [[Image:Workplot_nathan.tgz‎]], but beware it gives huge figures :p (see below). The script requires one argument at the least; put "z" to define the file to be read as LOCPOT_Z
-  sed -i '1d' LOCPOT_Z &&  sed -i 's/  */\t/g' LOCPOT_Z &&  sed -i 's/^[ \t]*//' LOCPOT_Z
+* It has additional options too; the first EXTRA argument passed in the commandline sets the title (use dashes ""). Add two additional numbers to specify the range on the x-axis.
-  For convenience, just copy the commands above and run it in terminal,
+* Alternatively you can load the script into Excel, Libreoffice or Origin. You'll first have to convert the file to the right format by running the line below in the terminal:
-Copy the numbers from modified LOCPOT_Z to excel or Origin, and draw the figures
+  sed -i '1d' LOCPOT_Z &&  sed -i 's/  */\t/g' LOCPOT_Z &&  sed -i 's/^[ \t]*//' LOCPOT_Z
-You can also use the script to plot workfunction [[Image:Workplot.tgz]], it looks like a little bit larger (Sooooory) : [[Image: Workfunction.png]]
+* [[Image: Workfunction.png]]

Vtotav.py: Difference between revisions

Latest revision as of 17:52, 10 December 2019

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