Installing ab-initio calculators on debian

Installation of elk all-electron full-potential linearised augmented-plane wave (FP-LAPW) as easy as;
“aptitude search elk”
“aptitude install elk-lapw”

Installation of quantum espresso, computer codes for density-functional theory using plane waves, and pseudopotentials, as easy as;
“aptitude install quantum-espresso”

Installation of xrysden
“aptitude install xcrysden”

 


root>
aptitude install elk-lapw
The following NEW packages will be installed:
elk-lapw libcr0{a} libhwloc-plugins{a} libhwloc5{a} libibverbs1{a} libnuma1{a} libopenmpi1.6{a} libxc1{a} ocl-icd-libopencl1{a}
0 packages upgraded, 9 newly installed, 0 to remove and 0 not upgraded.
Need to get 4025 kB of archives. After unpacking 12.6 MB will be used.
Do you want to continue? [Y/n/?] y
Get: 1 http://ftp.uk.debian.org/debian/ jessie/main libnuma1 amd64 2.0.10-1 [32.5 kB]
Get: 2 http://ftp.uk.debian.org/debian/ jessie/main libhwloc5 amd64 1.10.0-3 [86.9 kB]
Get: 3 http://ftp.uk.debian.org/debian/ jessie/main ocl-icd-libopencl1 amd64 2.2.3-1+deb8u1 [33.6 kB]
Get: 4 http://ftp.uk.debian.org/debian/ jessie/main libcr0 amd64 0.8.5-2.2 [32.7 kB]
Get: 5 http://ftp.uk.debian.org/debian/ jessie/main libibverbs1 amd64 1.1.8-1.1 [32.2 kB]
Get: 6 http://ftp.uk.debian.org/debian/ jessie/main libopenmpi1.6 amd64 1.6.5-9.1 [1460 kB]
Get: 7 http://ftp.uk.debian.org/debian/ jessie/main libxc1 amd64 2.1.1-1 [284 kB]
Get: 8 http://ftp.uk.debian.org/debian/ jessie/main elk-lapw amd64 2.3.22-1 [2048 kB]
Get: 9 http://ftp.uk.debian.org/debian/ jessie/main libhwloc-plugins amd64 1.10.0-3 [15.2 kB]
Fetched 4025 kB in 5s (750 kB/s)
Selecting previously unselected package libnuma1:amd64.
(Reading database ... 209260 files and directories currently installed.)
Preparing to unpack .../libnuma1_2.0.10-1_amd64.deb ...
Unpacking libnuma1:amd64 (2.0.10-1) ...
Selecting previously unselected package libhwloc5:amd64.
Preparing to unpack .../libhwloc5_1.10.0-3_amd64.deb ...
Unpacking libhwloc5:amd64 (1.10.0-3) ...
Selecting previously unselected package ocl-icd-libopencl1:amd64.
Preparing to unpack .../ocl-icd-libopencl1_2.2.3-1+deb8u1_amd64.deb ...
Unpacking ocl-icd-libopencl1:amd64 (2.2.3-1+deb8u1) ...
Selecting previously unselected package libcr0.
Preparing to unpack .../libcr0_0.8.5-2.2_amd64.deb ...
Unpacking libcr0 (0.8.5-2.2) ...
Selecting previously unselected package libibverbs1.
Preparing to unpack .../libibverbs1_1.1.8-1.1_amd64.deb ...
Unpacking libibverbs1 (1.1.8-1.1) ...
Selecting previously unselected package libopenmpi1.6.
Preparing to unpack .../libopenmpi1.6_1.6.5-9.1_amd64.deb ...
Unpacking libopenmpi1.6 (1.6.5-9.1) ...
Selecting previously unselected package libxc1:amd64.
Preparing to unpack .../libxc1_2.1.1-1_amd64.deb ...
Unpacking libxc1:amd64 (2.1.1-1) ...
Selecting previously unselected package elk-lapw.
Preparing to unpack .../elk-lapw_2.3.22-1_amd64.deb ...
Unpacking elk-lapw (2.3.22-1) ...
Selecting previously unselected package libhwloc-plugins.
Preparing to unpack .../libhwloc-plugins_1.10.0-3_amd64.deb ...
Unpacking libhwloc-plugins (1.10.0-3) ...
Processing triggers for man-db (2.7.0.2-5) ...
Setting up libnuma1:amd64 (2.0.10-1) ...
Setting up libhwloc5:amd64 (1.10.0-3) ...
Setting up ocl-icd-libopencl1:amd64 (2.2.3-1+deb8u1) ...
Setting up libcr0 (0.8.5-2.2) ...
Setting up libibverbs1 (1.1.8-1.1) ...
Setting up libopenmpi1.6 (1.6.5-9.1) ...
Setting up libxc1:amd64 (2.1.1-1) ...
Setting up elk-lapw (2.3.22-1) ...
Setting up libhwloc-plugins (1.10.0-3) ...
Processing triggers for libc-bin (2.19-18+deb8u4) ...

root@ptlin10:~# aptitude install quantum-espresso
The following NEW packages will be installed:
libblacs-openmpi1{a} libelpa0{a} libscalapack-openmpi1{a} mpi-default-bin{a} openmpi-bin{a} openmpi-common{a} quantum-espresso
quantum-espresso-data{a}
0 packages upgraded, 8 newly installed, 0 to remove and 0 not upgraded.
Need to get 23.8 MB of archives. After unpacking 134 MB will be used.
Do you want to continue? [Y/n/?] y
Get: 1 http://ftp.uk.debian.org/debian/ jessie/main libelpa0 amd64 2013.11.008-2 [88.9 kB]
Get: 2 http://ftp.uk.debian.org/debian/ jessie/main openmpi-common all 1.6.5-9.1 [110 kB]
Get: 3 http://ftp.uk.debian.org/debian/ jessie/main openmpi-bin amd64 1.6.5-9.1 [154 kB]
Get: 4 http://ftp.uk.debian.org/debian/ jessie/main mpi-default-bin amd64 1.0.2+nmu2 [3356 B]
Get: 5 http://ftp.uk.debian.org/debian/ jessie/main libblacs-openmpi1 amd64 1.1-33 [56.8 kB]
Get: 6 http://ftp.uk.debian.org/debian/ jessie/main libscalapack-openmpi1 amd64 1.8.0-12 [2184 kB]
Get: 7 http://ftp.uk.debian.org/debian/ jessie/main quantum-espresso amd64 5.1+dfsg-3 [10.1 MB]
Get: 8 http://ftp.uk.debian.org/debian/ jessie/main quantum-espresso-data all 5.1+dfsg-3 [11.1 MB]
Fetched 23.8 MB in 30s (774 kB/s)
Selecting previously unselected package libelpa0.
(Reading database ... 209802 files and directories currently installed.)
Preparing to unpack .../libelpa0_2013.11.008-2_amd64.deb ...
Unpacking libelpa0 (2013.11.008-2) ...
Selecting previously unselected package openmpi-common.
Preparing to unpack .../openmpi-common_1.6.5-9.1_all.deb ...
Unpacking openmpi-common (1.6.5-9.1) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../openmpi-bin_1.6.5-9.1_amd64.deb ...
Unpacking openmpi-bin (1.6.5-9.1) ...
Selecting previously unselected package mpi-default-bin.
Preparing to unpack .../mpi-default-bin_1.0.2+nmu2_amd64.deb ...
Unpacking mpi-default-bin (1.0.2+nmu2) ...
Selecting previously unselected package libblacs-openmpi1.
Preparing to unpack .../libblacs-openmpi1_1.1-33_amd64.deb ...
Unpacking libblacs-openmpi1 (1.1-33) ...
Selecting previously unselected package libscalapack-openmpi1.
Preparing to unpack .../libscalapack-openmpi1_1.8.0-12_amd64.deb ...
Unpacking libscalapack-openmpi1 (1.8.0-12) ...
Selecting previously unselected package quantum-espresso.
Preparing to unpack .../quantum-espresso_5.1+dfsg-3_amd64.deb ...
Unpacking quantum-espresso (5.1+dfsg-3) ...
Selecting previously unselected package quantum-espresso-data.
Preparing to unpack .../quantum-espresso-data_5.1+dfsg-3_all.deb ...
Unpacking quantum-espresso-data (5.1+dfsg-3) ...
Processing triggers for man-db (2.7.0.2-5) ...
Setting up libelpa0 (2013.11.008-2) ...
Setting up openmpi-common (1.6.5-9.1) ...
Setting up openmpi-bin (1.6.5-9.1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up mpi-default-bin (1.0.2+nmu2) ...
Setting up libblacs-openmpi1 (1.1-33) ...
Setting up libscalapack-openmpi1 (1.8.0-12) ...
Setting up quantum-espresso (5.1+dfsg-3) ...
Setting up quantum-espresso-data (5.1+dfsg-3) ...
Processing triggers for libc-bin (2.19-18+deb8u4) ...

root>>aptitude install xcrysden
The following NEW packages will be installed:
bwidget{a} libgl2ps0{a} libopenbabel4{a} openbabel{a} xcrysden xcrysden-data{a}
0 packages upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
Need to get 5387 kB of archives. After unpacking 19.4 MB will be used.
Do you want to continue? [Y/n/?] y
Get: 1 http://ftp.uk.debian.org/debian/ jessie/main bwidget all 1.9.8-1 [194 kB]
Get: 2 http://ftp.uk.debian.org/debian/ jessie/main libgl2ps0 amd64 1.3.8-1.2 [35.4 kB]
Get: 3 http://ftp.uk.debian.org/debian/ jessie/main libopenbabel4 amd64 2.3.2+dfsg-2 [2913 kB]
Get: 4 http://ftp.uk.debian.org/debian/ jessie/main openbabel amd64 2.3.2+dfsg-2 [254 kB]
Get: 5 http://ftp.uk.debian.org/debian/ jessie/main xcrysden-data all 1.5.60-1 [1603 kB]
Get: 6 http://ftp.uk.debian.org/debian/ jessie/main xcrysden amd64 1.5.60-1 [387 kB]
Fetched 5387 kB in 10s (518 kB/s)
Selecting previously unselected package bwidget.
(Reading database ... 210350 files and directories currently installed.)
Preparing to unpack .../bwidget_1.9.8-1_all.deb ...
Unpacking bwidget (1.9.8-1) ...
Selecting previously unselected package libgl2ps0.
Preparing to unpack .../libgl2ps0_1.3.8-1.2_amd64.deb ...
Unpacking libgl2ps0 (1.3.8-1.2) ...
Selecting previously unselected package libopenbabel4.
Preparing to unpack .../libopenbabel4_2.3.2+dfsg-2_amd64.deb ...
Unpacking libopenbabel4 (2.3.2+dfsg-2) ...
Selecting previously unselected package openbabel.
Preparing to unpack .../openbabel_2.3.2+dfsg-2_amd64.deb ...
Unpacking openbabel (2.3.2+dfsg-2) ...
Selecting previously unselected package xcrysden-data.
Preparing to unpack .../xcrysden-data_1.5.60-1_all.deb ...
Unpacking xcrysden-data (1.5.60-1) ...
Selecting previously unselected package xcrysden.
Preparing to unpack .../xcrysden_1.5.60-1_amd64.deb ...
Unpacking xcrysden (1.5.60-1) ...
Processing triggers for man-db (2.7.0.2-5) ...
Processing triggers for desktop-file-utils (0.22-1) ...
Processing triggers for gnome-menus (3.13.3-6) ...
Processing triggers for mime-support (3.58) ...
Setting up bwidget (1.9.8-1) ...
Setting up libgl2ps0 (1.3.8-1.2) ...
Setting up libopenbabel4 (2.3.2+dfsg-2) ...
Setting up openbabel (2.3.2+dfsg-2) ...
Setting up xcrysden-data (1.5.60-1) ...
Setting up xcrysden (1.5.60-1) ...
Processing triggers for libc-bin (2.19-18+deb8u4) ...

Advertisements

Thermocalc script to generate GES5 file

Thermocalc script to make a GES5 file – these files contain thermodynamic data and are used with the tq programming interface to thermocalc.

Make_GES5.TCM

go database-retrieval
switch-database ttni8
define-elements Ni Cr
get-data
goto gibbs-energy-system
save
Ni-Cr-Data

Detextify – Find latex symbols

This website (http://detexify.kirelabs.org/classify.html) is really useful if you don’t know the markup/command for the LaTex symbol you want to write. Provided you are able to draw it.

Detexify

The website talks about the software learning how to recognise the symbols so I guess it is using some neural network scheme.

NINJA finance modelling

Learn Financial modelling like a Ninja

I saw this advert. From wall street 2 I learned that NINJA stands for, No Income, No Job or Assets.

View crystal structures

There is a very nice java package which lets you view crystal structures on any computer platform that supports java (Linux, Mac, etc).

Jmol can be downloaded from sourceforge here. Download the latest binary or full package, unpack it and you are good to go.

Either cd into the directory and run ./jmol or add the directory to your $PATH environment and run jmol.

some molecule

I have a feeling I have referred to Jmol in a previous post but I think I’d only used it as an applet then.

The full version alloys export of the images to graphics formats, as well as lots of options that I don’t understand. You can view molecules in 3D if you have the proper pair of glasses, and you can load crystal structures in the xyz format from sites such as Crystal Lattice*Structures at the U.S. naval research laboratory (note this is very different to navel research). I’m particularly impressed by the ability to change the background colour to white, which is particularly useful if you ever want to print something.

MTDATA script – driving force

Here is a quick example script to calculate driving force for formation of ferrite from austenite.


mu
define system 'Fe,Cr,Ni,Mo,N,C,Mn' source tcfe !
% fe Cr Ni Mo N
set w(1) undef w(2) 23.00 w(3) 9.0 w(4) 3.0 w(5) 0.15 !
% C Mn
set w(6) 0.02 w(7) 0.8 !
set w 100 !
classify absent p(*) !
step temp 973 1273 10 !
%
% calculating for FCC
%
classify normal p(FCC_A1) !
compute print brief print mol !
compute print graphics_output !
units temperature celsius !
ordinate gibbs system !
plot tabulate spreadsheet !
%
% calculating for BCC
%
classify normal p(BCC_A2) !
compute print brief print mol !
compute print graphics_output !
units temperature celsius !
ordinate gibbs system !
plot tabulate spreadsheet !


This gives the answer in Joules / 100 kg.

Mtdata Script example 1

Here is an example macro for use with thermodynamics software mtdata. This script sets up a stepped calculation of equilibrium for a steel composition, it then output a text file of the mass fraction of each phase. Reading the script is made difficult by the use of contracted version of the commands. The first command selects the multiphase modules could have been written ‘mu’ rather than ‘multiphase’. The next command starts ‘def sys…’ is the same as ‘define system’. Note most commands end with an exclamation mark, this is the way to tell mtdata you really mean what you typed.


:Macro file to calculate equilibrium phase fractions
:Mathew Peet and Hala Salman Hasan 20th June 2007
multiphase
def sys "Fe,C,Si,Mn,Cr,Mo,Co,Al" source plus sub_sgte !
:this is a comment
:uncomment following line to use tcfe database instead
:def sys "Fe,C,Si,Mn,Cr,Mo,Co,Al" source tcfe !
classify absent phase(*) !
classify normal phase(FCC_A1,BCC_A2,M23C6,M6C,cementite,m7c3) !
classify misc(FCC_A1) 1 !
set w 100 !
set w(2) 0.78 w(3) 1.6 w(4) 2.02 w(5) 1.01 w(6) 0.24 w(7) 3.87 w(8) 1.37 !
step temp 773 1373 5 !
:this line is a comment
:following 3 lines output a spreadsheet of phase fractions with temperature
com pri gra !
ord mass phase !
plot tabu spread !
:uncomment line/ type following to see compositions of phases
:compute print brief print mol !

Example output of the above calculation was archived.