I am one of this users that is still using client mail like Thunderbird. Do not get me wrong, I use and like Gmail, but I still need more control over my mail in few cases. Anyway, from time to time the University Exchange server is updated/reconfigured and I loose access to the provided IMAP access. Since this became recurrent event and the suggested solutions from the support team were somewhat random guesses I looked for alternative solution.
Here is what I am using right now, while I can not access my mail box after the last upgrade.
CM-tools
Tools and Solutions for Computer Modelling
Thursday, March 2, 2017
Saturday, January 14, 2017
Discrete histogram
The usual histogram is a graphical representation of the distribution of numerical data. It also implies that you have regular intervals for the resulting distribution. What happens if you are looking for distribution over discrete elements, like day of the week, month, or any possible word...
Here is an example.
Here is an example.
- How many coins are gold or silver?
- How many coins from each country we have?
- ... year?
gold 1 1986 USA American Eagle
gold 1 1908 Austria-Hungary Franz Josef 100 Korona
silver 10 1981 USA ingot
gold 1 1984 Switzerland ingot
gold 1 1979 RSA Krugerrand
gold 0.5 1981 RSA Krugerrand
gold 0.1 1986 PRC Panda
silver 1 1986 USA Liberty dollar
gold 0.25 1986 USA Liberty 5-dollar piece
silver 0.5 1986 USA Liberty 50-cent piece
silver 1 1987 USA Constitution dollar
gold 0.25 1987 USA Constitution 5-dollar piece
gold 1 1988 Canada Maple Leaf
gold 1 1908 Austria-Hungary Franz Josef 100 Korona
silver 10 1981 USA ingot
gold 1 1984 Switzerland ingot
gold 1 1979 RSA Krugerrand
gold 0.5 1981 RSA Krugerrand
gold 0.1 1986 PRC Panda
silver 1 1986 USA Liberty dollar
gold 0.25 1986 USA Liberty 5-dollar piece
silver 0.5 1986 USA Liberty 50-cent piece
silver 1 1987 USA Constitution dollar
gold 0.25 1987 USA Constitution 5-dollar piece
gold 1 1988 Canada Maple Leaf
Sunday, September 4, 2016
Extracting Frequency data from a Gaussian 09 calculation
This small awk script was inspired by the Python solution I found on this excellent blog [ Lindqvist - a blog about Linux and Science. Mostly. ] You can find my solution in the comments section of the blog.
So, I would like to extract/collect the results from a Gaussian09 harmonic frequency calculation.
Since collecting the rest of the data from the Gaussian output is pretty much identical I have done it anyway.
This will print the collected values in three columns, identical to the Python script.
So, I would like to extract/collect the results from a Gaussian09 harmonic frequency calculation.
Since collecting the rest of the data from the Gaussian output is pretty much identical I have done it anyway.
#!/bin/awk -f
/Frequencies/ { for (i=3;i<=NF; i++) { im++; freq[im ]=$i } }
/Frc consts/ { for (i=NF;i>=4; i--) fc[im-(NF-i)]=$i }
/IR Inten/ { for (i=NF;i>=4; i--) ir[im-(NF-i)]=$i }
END { for (i=1;i<=im;i++) print freq[i],fc[i],ir[i] }
Wednesday, May 11, 2016
OCTAVE: read/write VASP POSCAR, CHGCAR
Here you can find several functions that will help you to read and write VASP POSCAR and CHCAR files in Octave. The files are commented and fairly easy to understand. Current version of the
Test example:read_POSCAR
handles the old and the new POSCAR format (the new format contains labels for the species). All gathered information is stored in one object "Structure". This makes extremely easy the addition of any new properties. Note hat it read_CHGCAR
reads only the total density. If you need the difference, please change the code or the data.#!/usr/bin/octave -q
# Read CHGCAR file
Struct = read_CHGCAR("CHGCAR");
# Print all gathered values
Struct
# Do something
# Struct.Dens=circshift(Struct.Dens,[0 0 20]);
# Write the new Density
write_CHGCAR("CHGCAR-new",Struct);
Thursday, April 21, 2016
VASP CHGCAR difference and 2D plane cut through it
This post content is a copy from my awk workshop "Case studies" section.
From time to time, I need to calculate electron charge difference that is tabulated on a regular 3D grid. Common examples in my field will be Gaussian .cube files or VASP CHGCAR files. One can find some scripts, tools and programs that can do this in one way or another. In my case, again, I need something slightly different and... Well, doing it with awk is so simple that I never use other tools but the one I will mention here. With small changes I am able to subtract 6 files at the same time, and since the files tend to be large, I keep them compressed.
From time to time, I need to calculate electron charge difference that is tabulated on a regular 3D grid. Common examples in my field will be Gaussian .cube files or VASP CHGCAR files. One can find some scripts, tools and programs that can do this in one way or another. In my case, again, I need something slightly different and... Well, doing it with awk is so simple that I never use other tools but the one I will mention here. With small changes I am able to subtract 6 files at the same time, and since the files tend to be large, I keep them compressed.
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