Hex, Bugs and More Physics | Emre S. Tasci

Quantum Espresso meets bash : Automated running for various values

admin — Tue, 13 Mar 2012 22:43:51 +0000

Now that we can include comments in our input files and submit our jobs in a tidied up way, it’s time to automatize the “convergence search” process. For this, we’ll be using the same diamond example of the previous entry.

Suppose that we want to calculate the energies corresponding to various values of the lattice parameter a, ranging from 3.2 to 4, incrementing by 2: 3.2, 3.4, … , 4.0

Incrementation:
In bash, you can define a for loop to handle this:

for (( i = 1; i <= 9; i++ )) 
do
  echo $i; 
done

1
2
3
4
5
6
7
8
9

But to work with rational numbers, things get a little bit complex:

for (( i = 1; i <= 5; i++ )) 
do
    val=$(awk "BEGIN {print 3+$i/5 }")
    echo $val; 
done

3.2
3.4
3.6
3.8
4

Alas, it is still not very practical to everytime calculate the necessary values to produce our intended range. This is where the mighty Octave once again comes to the rescue: [A:I:B] in Octave defines a range that starts from A, and continues by incrementing by I until B is reached (or exceeded). So, here is our example in Octave:

octave:1> [3.2:0.2:4]
ans =

   3.2000   3.4000   3.6000   3.8000   4.0000

You can generate temporary input scripts for Octave but better yet, you can also feed simple scripts directly to Octave:

sururi@husniya:~/shared/qe/diamond_tutorial$ echo "[3.2:0.2:4]"|octave -q
ans =

   3.2000   3.4000   3.6000   3.8000   4.0000

The “-q” parameter causes Octave to run in “quiet” mode, so we just feed the range via pipe to Octave and will harvest the output. In general, we’d like to keep the “ans =” and the blank lines out, and then, when there are more than 1 line’s worth of output, Octave puts the “Column” information as in:

octave:4> [3:0.1:4]
ans =

 Columns 1 through 9:

   3.0000   3.1000   3.2000   3.3000   3.4000   3.5000   3.6000   3.7000   3.8000

 Columns 10 and 11:

   3.9000   4.0000

all these nuisances can go away via a simple “grep -v” (with the ‘v’ parameter inverting the filter criteria):

sururi@vala:/tmp$ echo "[3.2:0.1:4]"|octave -q|sed -n "2,1000p"| grep -v "Column"

   3.2000   3.3000   3.4000   3.5000   3.6000   3.7000   3.8000   3.9000

   4.0000

sururi@vala:/tmp$ echo "[3.2:0.1:4]"|octave -q|sed -n "2,1000p"| grep -v "Column"|grep -v -e "^$"
   3.2000   3.3000   3.4000   3.5000   3.6000   3.7000   3.8000   3.9000
   4.0000

Replacement:
Now that we have the variable’s changing values, how are we gonna implement it to the input script? By search and replace. Suppose, we have a template in which the variable’s value is specified by “#REPLACE#”, all we need to do is to “sed” the file:

cat diamond.scf.in | sed "s:#REPLACE#:$a:g">tmp_$a.in

where “$a” is the current value in the iteration.

Parsing the Energy:
We submit this job via mpirun (in our case via mpi-pw.x of the previous post) and parse the output for the final energy:

grep -e ! tmp_$a.out|tail -n1|awk '{print $(NF-1)}'

For each iteration we thus obtain the energy for our $a value, so we put them together in two columns into a data file I’d like to call “E_vs_$a.txt”.

The Script:
Putting all these together, here is the script in its full glory:

#!/bin/bash

# Takes in the template Quantum Espresso input file, runs it iteratively 
# changing the #REPLACE# parameters iteratively with the range elements,
# grepping the energy and putting it along with the current value of the
# #REPLACE# parameter.
#
# Emre S. Tasci, 03/2012

# Example: Suppose that the file "diamond.scf.in" contains the following line:
#   A = #REPLACE#
# Calling "qe-opti.sh diamond.scf.in a 3.2 0.2 4.2" would cause that line to be modified as
#   A = 3.2
# and submitted, followed by 
#   A = 3.4, 3.6, .., 4.2 in the sequential runs.
#
# at the end, having constructed the E_vs_a.txt file.

if [ $# -ne 5 ]
then
    echo "Usage: qe-opti.sh infile_template.in variable_name initial_value increment     final_value"
    echo "Example: qe-opti.sh diamond.scf.in a 3.2 0.2 4.2"
    echo -e "\nNeeds octave to be accessible via \"octave\" command for the range to     work"
    echo -e "\nEmre S. Tasci, 03/2012"
    exit
fi

logext=".txt"
logfilename=E_vs_$2$logext
rm -f $logfilename

range=$(echo "[$3:$4:$5]"|octave -q|sed -n "2,1000p"|grep -vr "^$"|grep -v "Column")
for a in $range
do
    # echo $a
    cat $1|sed "s:#REPLACE#:$a:g">tmp_$a.in
    /home/sururi/bin/mpi-pw.x 4 tmp_$a.in
energ=$(grep -e ! tmp_$a.out|tail -n1|awk '{print $(NF-1)}')
    # echo $energ
    echo -e $a "    " $energ >> $logfilename
    echo -e $a "    " $energ
done

echo "Results stored in: "$logfilename

Action:
Modify the sample input from the previous post so that it’s lattice parameter A is designated as something like “A = #REPLACE#”, as in:

sururi@bebop:~/shared/qe/diamond_tutorial$ grep "REPLACE" -B2 -A2 diamond.scf.in
    # a,b,c in Angstrom =======
    #A = 3.56712
    A = #REPLACE#
    B = 2.49
    C = 2.49

Then call the qe-opti.sh script with the related parameters:

sururi@bebop:~/shared/qe/diamond_tutorial$ qe-opti.sh diamond.scf.in a 3.2 0.2 4.2
Running: mpirun -n 4 /usr/share/espresso-4.3.2/bin/pw.x < tmp_3.2000.in > tmp_3.2000.out

Start : Tue Mar 13 23:21:07 CET 2012
Finish: Tue Mar 13 23:21:08 CET 2012
Elapsed time:0:00:01

3.2000      -22.55859979
Running: mpirun -n 4 /usr/share/espresso-4.3.2/bin/pw.x < tmp_3.4000.in > tmp_3.4000.out

Start : Tue Mar 13 23:21:08 CET 2012
Finish: Tue Mar 13 23:21:09 CET 2012
Elapsed time:0:00:01

3.4000      -22.67717405
Running: mpirun -n 4 /usr/share/espresso-4.3.2/bin/pw.x < tmp_3.6000.in > tmp_3.6000.out

Start : Tue Mar 13 23:21:09 CET 2012
Finish: Tue Mar 13 23:21:10 CET 2012
Elapsed time:0:00:01

3.6000      -22.69824702
Running: mpirun -n 4 /usr/share/espresso-4.3.2/bin/pw.x < tmp_3.8000.in > tmp_3.8000.out

Start : Tue Mar 13 23:21:10 CET 2012
Finish: Tue Mar 13 23:21:11 CET 2012
Elapsed time:0:00:01

3.8000      -22.65805473
Running: mpirun -n 4 /usr/share/espresso-4.3.2/bin/pw.x < tmp_4.0000.in > tmp_4.0000.out

Start : Tue Mar 13 23:21:11 CET 2012
Finish: Tue Mar 13 23:21:13 CET 2012
Elapsed time:0:00:02

4.0000      -22.57776354
Running: mpirun -n 4 /usr/share/espresso-4.3.2/bin/pw.x < tmp_4.2000.in > tmp_4.2000.out

Start : Tue Mar 13 23:21:13 CET 2012
Finish: Tue Mar 13 23:21:14 CET 2012
Elapsed time:0:00:01

4.2000      -22.47538891
Results stored in: E_vs_a.txt

Where the “E_vs_a.txt” contains the … E vs a values!:

sururi@bebop:~/shared/qe/diamond_tutorial$ cat E_vs_a.txt 
3.2000      -22.55859979
3.4000      -22.67717405
3.6000      -22.69824702
3.8000      -22.65805473
4.0000      -22.57776354
4.2000      -22.47538891

You can easily plot it using GNUPlot or whatever you want. In my case, I prefer GNUPlot:

sururi@husniya:~/shared/qe/diamond_tutorial$ plot E_vs_a.txt

giving me:

Other than the ‘plot’, I’ve also written another one, fit for data sets just like these where you have a parabol-like data and you’d like to try fitting it and here is what it does (automatically):

sururi@husniya:~/shared/qe/diamond_tutorial$ plotfitparabol.sh E_vs_a.txt
func    f(x)=0.674197*x*x-4.881275*x-13.855234
min, f(min)    3.620066 -22.690502

I’ll be posting the source codes of the ‘plot’ and ‘plotfitparabol.sh’ scripts next. Until then, doei!

Quantum Espresso meets bash : Primer and tidying up

admin — Tue, 13 Mar 2012 15:24:00 +0000

In my previous postdoc position, DFT calculations were governing my research field but with my current position at the Bilbao Crystallographic Server, we are more on the theoretical side of things then calculations. Nevertheless, recently, my old ‘flame’ have been kindled and I decided to scrape the rust.

As a change, I selected and installed the Quantum Espresso (QE) package instead of VASP that I was using in the past, main reason QE being open source.

As a newbie to QE and long-gone returner to DFT, I started to practice by mostly ye olde trial/error approach.

The first thing that surprised me the lack of a commenting option in regard to QE input files! (Actually, I’m almost sure that it surely is supported but I have yet to find!). Here’s my sample input file:

&control
    title='Diamond Relaxing',

    # Calculation Type ==========
    calculation='scf'
    #calculation='relax',
    #calculation='vc-relax'
    #calculation='cp'

    # Restart ===================
    restart_mode='from_scratch',
    #restart_mode='restart' 

    # Read/Write units ==========
    #ndr = 51,
    #ndw = 51,

    #nstep = 100,
    #nstep = 1000,
    nstep = 2000,

    # max_seconds = 600 # jobs stops after max_seconds CPU time.

    iprint = 10, # band energies are written every iprint iterations
    #tstress = .TRUE., # calculate stress. It is set to .TRUE. automatically if
                       # calculation='vc-md' or 'vc-relax'
    #tprnfor = .TRUE., # print forces. Set to .TRUE. if calculation='relax','md','vc-md'
    #dt = 5.0d0, # time step for molecular dynamics, in Rydberg atomic units
                 # (1 a.u.=4.8378 * 10^-17 s : beware, the CP code use
                 #  Hartree atomic units, half that much!!!)

    prefix='diamond_rel', # prepended to input/output filenames
    pseudo_dir = '/usr/share/espresso-4.3.2/pseudo/',
    outdir='/home/sururi/shared/tmp/'
    etot_conv_thr = 1.d-6 # convergence threshold on total energy (a.u) for ionic minimization
    forc_conv_thr = 1.d-3 # convergence threshold on forces (a.u) for ionic minimization
 /
 &system
##  ibrav
##    0          "free", see above                 not used
##    1          cubic P (sc)                      not used
##    2          cubic F (fcc)                     not used
##    3          cubic I (bcc)                     not used
##    4          Hexagonal and Trigonal P        celldm(3)=c/a
##    5          Trigonal R, 3fold axis c        celldm(4)=cos(alpha)
##   -5          Trigonal R, 3fold axis <111>    celldm(4)=cos(alpha)
##    6          Tetragonal P (st)               celldm(3)=c/a
##    7          Tetragonal I (bct)              celldm(3)=c/a
##    8          Orthorhombic P                  celldm(2)=b/a,celldm(3)=c/a
##    9          Orthorhombic base-centered(bco) celldm(2)=b/a,celldm(3)=c/a
##   10          Orthorhombic face-centered      celldm(2)=b/a,celldm(3)=c/a
##   11          Orthorhombic body-centered      celldm(2)=b/a,celldm(3)=c/a
##   12          Monoclinic P, unique axis c     celldm(2)=b/a,celldm(3)=c/a,
##                                               celldm(4)=cos(ab)
##  -12          Monoclinic P, unique axis b     celldm(2)=b/a,celldm(3)=c/a,
##                                               celldm(5)=cos(ac)
##   13          Monoclinic base-centered        celldm(2)=b/a,celldm(3)=c/a,
##                                               celldm(4)=cos(ab)
##   14          Triclinic                       celldm(2)= b/a,
##                                               celldm(3)= c/a,
##                                               celldm(4)= cos(bc),
##                                               celldm(5)= cos(ac),
##                                               celldm(6)= cos(ab
    ibrav= 2,

# Cell dimensions ========================
    # a,b,c in Angstrom =======
    A = 3.56712
    B = 2.49
    C = 2.49
    cosAB=0.5
    cosAC=0.5
    cosBC=0.5

    ## OR ##
    ## celldm(1:6) in Bohr =====
    ## 1 Bohr =  0.529177249 A
    ## 1 A = 1.889725989 Bohr
    # celldm(1) = 6.7409 # alat
    # celldm(2) = 4.7054 # b/a
    # celldm(3) = 4.7054 # c/a
    # celldm(4) = 0.5 # cos(ab)
    # celldm(5) = 0.5 # cos(ac)
    # celldm(6) = 0.5 # cos(ab)

   nat=2,
   ntyp= 1,

   ecutwfc = 40, # kinetic energy cutoff (Ry) for wavefunctions
   # ecutrho = 160 # kinetic energy cutoff (Ry) for charge density and potential.
                   # For norm-conserving pseudopotential you should stick to the
                   # default value
   # nbnd = 6 # number of electronic states (bands) to be calculated.
              # Default:
              # for an insulator, nbnd = number of valence bands (nbnd = # of electrons /2);
              # for a metal, 20% more (minimum 4 more)
 /
 &electrons
   emass = 400.d0
   emass_cutoff = 2.5d0

   #electron_dynamics = 'sd' # CP specific
   #electron_dynamics = 'bfgs' # CP specific

  conv_thr = 1D-6 # Convergence threshold for selfconsistency

 /
 &ions
    #ion_dynamics = 'none'
    #ion_dynamics = 'bfgs'
    #ion_dynamics = 'sd'

    # === damping === 0 ==
    # ion_dynamics = 'damp'
    # ion_damping = 0.2
    # ion_velocities = 'zero' # CP specific -- initial ionic velocities
    # === damping === 1 ==

    #ion_nstepe = 10 # CP specific -- number of electronic steps per ionic step. (Def: 1)
 /
 &cell
    cell_dynamics = 'none',
    #cell_dynamics = 'bfgs', # ion_dynamics must be 'bfgs' too
    #cell_dofree = 'xyz'
    #cell_factor = 3
    press = 0.0d,
    # press_conv_thr = 0.05 # Convergence threshold on the pressure for variable cell relaxation
 /
ATOMIC_SPECIES
 C  12.0107 C.pz-vbc.UPF
ATOMIC_POSITIONS
 C 0.0 0.0 0.0
 C 0.25 0.25 0.25
K_POINTS automatic
   4 4 4 1 1 1

so, it’s not the tidiest parameter file around but nevertheless, I’ve included some explanations and it’s easily customizable by simple commenting out, right?…

And then the problem of (yet undiscovered) comments in the QE input files hits us. But with bash, it’s pretty easy. So, if you save the above contents to a file called, say, “diamond.scf.in” and filter it via grep and sed, you’re done:

sururi@husniya:~/shared/qe/diamond_tutorial$ cat diamond.scf.in | grep -v -E "^[\t ]*#" | sed "s:\([^#]*\)#.*:\1:"
&control
    title='Diamond Relaxing',

    calculation='scf'

    restart_mode='from_scratch',

    nstep = 2000,

    iprint = 10, 

    prefix='diamond_rel',
    pseudo_dir = '/usr/share/espresso-4.3.2/pseudo/',
    outdir='/home/sururi/shared/tmp/'
    etot_conv_thr = 1.d-6
    forc_conv_thr = 1.d-3
 /
 &system
    ibrav= 2,

    A = 3.56712
    B = 2.49
    C = 2.49
    cosAB=0.5
    cosAC=0.5
    cosBC=0.5

   nat=2,
   ntyp= 1,

   ecutwfc = 40,
 /
 &electrons
   emass = 400.d0
   emass_cutoff = 2.5d0

  conv_thr = 1D-6 

 /
 &ions

 /
 &cell
    cell_dynamics = 'none',
    press = 0.0d,
 /
ATOMIC_SPECIES
 C  12.0107 C.pz-vbc.UPF
ATOMIC_POSITIONS
 C 0.0 0.0 0.0
 C 0.25 0.25 0.25
K_POINTS automatic
   4 4 4 1 1 1

I’ve installed the QE to take advantage of the cluster nodes via MPI, so I submit my jobs via:

mpirun -n #_of_processes /usr/share/espresso-4.3.2/bin/pw.x < input_file > output_file

which I guess is more or less similar to what you are doing to run your jobs.

So, combining this “comment filtering” and job submission, I’ve written the following bash script (”mpi-pw.x“) to automatize (and keep log of) the job:

sururi@cowboy:~$ cat /home/sururi/bin/mpi-pw.x 
#!/bin/bash

# Script to submit Quantum Espresso jobs via mpi
# EST, Fri Mar  9 17:02:10 CET 2012

function timer()
{
    if [[ $# -eq 0 ]]; then
        echo $(date '+%s')
    else
        local  stime=$1
        etime=$(date '+%s')

        if [[ -z "$stime" ]]; then stime=$etime; fi

        dt=$((etime - stime))
        ds=$((dt % 60))
        dm=$(((dt / 60) % 60))
        dh=$((dt / 3600))
        printf '%d:%02d:%02d' $dh $dm $ds
    fi
}

if [ $# -ne 2 ]
then
    echo "Usage: mpi-pw.x num_of_processes infile.in"
    exit
fi

job=$2
job_wo_ext=${job%.*}

outext=".out"
logext=".log"
echo -e "Running: mpirun -n $1 /usr/share/espresso-4.3.2/bin/pw.x < $2 > $job_wo_ext$outext\n"
echo -e "Running: mpirun -n $1 /usr/share/espresso-4.3.2/bin/pw.x < $2 > $job_wo_ext$outext\n">$job_wo_ext$logext
echo "Start : "$(date)
echo "Start : "$(date)>>$job_wo_ext$logext

# Take out the comments from the input file
#grep -v -E "^[\t ]*#" $2 > in_wo_comments.in.tmp
grep -v -E "^[\t ]*#" $2 | sed "s:\([^#]*\)#.*:\1:" > in_wo_comments.in.tmp

t=$(timer)
mpirun -n $1 /usr/share/espresso-4.3.2/bin/pw.x < in_wo_comments.in.tmp > $job_wo_ext$outext
echo "Finish: "$(date)
echo "Finish: "$(date)>>$job_wo_ext$logext
printf 'Elapsed time:%s\n\n' $(timer $t)
printf 'Elapsed time:%s\n\n' $(timer $t) >>$job_wo_ext$logext

rm -f in_wo_comments.in.tmp

(I’ve picked the “timer” function from Mitch Frazier’s entry in LinuxJournal)

What it does is, really simple: it strips out the extension of the input file ($2 – the second argument in calling); filters out the comments, constructing the temporary input file “in_wo_comments.in.tmp”; starts the timer; submits the job using the number of processes passed in the calling ($1 – first argument) and directs the output to a file whose name is the extension stripped input filename + “.out”; when the job is (this way or that) done, stops the timer and calculates the elapsed time via the ‘timer’ function. During all this time, it prints these information both on screen and to a file called extension stripped input filename + “.log”.

I have a very similar another script called “mpi-cp.x” that I’ve forked for Carr-Parinelli jobs (just search & replace all the occurrences of “mpi-pw.x” with “mpi-cp.x” and you’re done 8).

And here is the script in action:

sururi@cowboy:~/shared/qe/diamond_tutorial$ ll
total 16
drwxr-xr-x 2 sururi sururi 4096 2012-03-13 15:59 ./
drwxr-xr-x 7 sururi sururi 4096 2012-03-13 15:10 ../
-rw-r--r-- 1 sururi sururi 4954 2012-03-13 15:59 diamond.scf.in

sururi@cowboy:~/shared/qe/diamond_tutorial$ mpi-pw.x 4 diamond.scf.in 
Running: mpirun -n 4 /usr/share/espresso-4.3.2/bin/pw.x < diamond.scf.in > diamond.scf.out

Start : Tue Mar 13 16:18:20 CET 2012
Finish: Tue Mar 13 16:18:21 CET 2012
Elapsed time:0:00:01

sururi@cowboy:~/shared/qe/diamond_tutorial$ grep -e ! diamond.scf.out 
!    total energy              =     -22.70063050 Ry

sururi@cowboy:~/shared/qe/diamond_tutorial$ cat diamond.scf.log 
Running: mpirun -n 4 /usr/share/espresso-4.3.2/bin/pw.x < diamond.scf.in > diamond.scf.out

Start : Tue Mar 13 16:18:20 CET 2012
Finish: Tue Mar 13 16:18:21 CET 2012
Elapsed time:0:00:01

Now that we have the mpi-pw.x and mpi-cp.x, our next entry in the series will be the automated search for optimized values.

Instant Karma: Updating the clones automatically upon push in Mercurial

admin — Mon, 29 Aug 2011 15:00:27 +0000

Suppose that I have a web server which consists of two identical computers behind a splitter that distributes the incoming requests made to a shared ip. Furthermore, the central repository is being kept on a different computer and as a final thing, assume that I sometimes use the computer located in my office, and sometimes the computer at my home as indicated in the following diagram:

The red arrows indicate the mercurial transfers. You can see that, the changes are only applied to the servers, i.e., nobody codes directly there (no push, only pulls and ups). My two computers can also be thought of two different developers but that part actually isn’t very relevant to this entry’s message. The thing I want to happen is: whenever I push a change into the central repository, I would like to see that it is applied on the servers. In other words I want the following procedures to be automated after the PC@wherever: hg push operation:

PC@wherever: hg com
PC@wherever: hg push
PC@wherever: ssh CentralRepo
CentralRepo: hg up
CentralRepo: ssh Server#1
Server#1: hg pull
Server#1: hg up
Server#1: ssh Server#2
Server#2: hg pull
Server#2: hg up

Even though I’ll be using Mercurial in this entry, SVN implementation is pretty much similar. After all, we’ll be using the so-called hooks, i.e. the procedures that takes place upon a triggered event such as push.

Since we will be automating (and I’ll be using SSH for the communication between the nodes), it is essential that the nodes can communicate freely via the help of the ssh-keys (all the relevant information including the usage of “hg-ssh” can be found in a previous entry titled ‘Accessing Mercurial with limited SSH access using key and hg-ssh’).

The trigger event is the incoming data to the central repository, so we edit the .hg/hgrc file of the project on the central repository and type:

[hooks]
incoming = .hg/incominghook.sh &gt; /dev/null

This hook just tells the mercurial to execute the ‘incominghook.sh’ script in the .hg directory (relative to the project’s root dir) whenever there’s an incoming data (i.e., “a push to this -central- repository). So what it should do? It should ‘hg up’ the central repository, for starters. Then, it should ‘ping’ the two servers so that they also pull and update from the -now up-to-date- central repository. This is what the incoming.sh script looks like:

#!/bin/sh
# Go to the project's dir no matter where you are
cd /path/to/the/project/repository/  
 
# Update it (since this is the central repo, there is no need to 'pull',
#                everybody is pushing to here)
hg up  
 
# Connect to the servers using the id files specifically generated for this purpose
# so that, upon connection, filtered by the command option
ssh -i ~/.ssh/id_rsa_specific_id_for_the_project__central_repo server1
ssh -i ~/.ssh/id_rsa_specific_id_for_the_project__central_repo server2

Again, if it is not very clear how will the servers get into action by a mere SSH connection, I do urge you to check the aforementioned entry.

The ~/.ssh/authorized_keys file on server1 contains the following related entry corresponding to the supplied id being used in the connection made from central repo:

command="/home/sururi/bin/hgpull_project_x.sh",
no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty
ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAnq.....==sururi@centralRepo (project X)

So that, when “somebody” connects with the relevant key_id file, the server executes the ‘hgpull_project_x.sh’ (located at /home/sururi/bin/) and returns the output, if any. You can guess that this script actually goes to the project’s location, pulls the changes and then ups it. As is evident from the contents of the ‘hgpull_project_x.sh’ script:

cd /path/to/the/project/on/server1
hg pull --ssh "ssh -i ~/.ssh/id_rsa_specific_id_for_the_project__server1" ssh://sururi@centralrepo//path/to/project
hg up

As you can learn from the strongly referred previous entry, the corresponding line on central repo’s authorized_keys file is something like:

command="hg-ssh /path/to/project/",no-port-forwarding,
no-X11-forwarding,no-agent-forwarding,no-pty ssh-rsa AAAAB...

and we’re done.

Accessing Mercurial with limited SSH access using key and hg-ssh

admin — Sun, 28 Aug 2011 20:15:00 +0000

Today, I wondered about (actually needed) the possibility to be able to limit (and hence connect afterwards) the access to the repository center of mercurial, using SSH.

To limit an SSH connection, you use ssh-keys: you create a pair of keys, private and public, using the ’ssh-keygen’ command and then adding the public one to the ~/.ssh/authorized_keys. As an example, consider two computers ‘local’ and ‘remote’ and we want to connect to remote from local without having to enter password every time. So, from the console of local, first I create the key pair:

sururi@local:/tmp/tmp$ ssh-keygen
Generating public/private rsa key pair.
Enter file in which to save the key (/home/sururi/.ssh/id_rsa): ./id_rsa_example
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in ./id_rsa_example.
Your public key has been saved in ./id_rsa_example.pub.
The key fingerprint is:
84:59:8d:8c:43:4a:bc:31:ff:5a:12:23:34:45:56:67 sururi@remote
The key's randomart image is:
+--[ RSA 2048]----+
|   oAE*=A+o      |
|  .o.=..+=..     |
|   .o...         |
|                 |
|        XXX      |
+-----------------+

I didn’t specified any password because I’m intending to have it used automatically (in the hook procedures) and I specified the location of the pair files as the current directory with the names: id_rsa_example & id_rsa_example.pub

Now, I should append the contents of the ‘id_rsa_example.pub’ file to the ./ssh/authorized_keys at the remote computer. To do this, of course, I should be able to connect it via SSH by normal means. So I execute (from the local computer):

ssh your_username@remote 'cat >> ~/.ssh/authorized_keys' < ./id_rsa_example.pub

And from this moment on -hopefully- you should be able to connect without the remote asking for your password (since we’re not using the default place & filename for the key, i.e. ~/.ssh/id_rsa and ~/.ssh/id_rsa.pub, this newly generated key should be included with the “-i” (identity file) option as in: ssh -i /tmp/tmp/id_rsa_example yourusername:remote)… but, that wasn’t exactly what we wanted. We are thinking of a scenario where you’d like to (semi-)freely distribute the SSH access to the central repository to your developers while making sure that they wouldn’t (couldn’t) do something nasty while they are connected to the remote computer.

We can limit the things an SSH-connected user can do to a single thing via the authorized keys option. Checking this file on the remote computer’s ~/.ssh/authorized_keys file, you should see something like:

ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAnq5rMLnoab+2F28g/nb58RBENWtX395TuyDFsYkalGaZxrziwDoau/wglkU19DbcAVKgw0p6lMEIuh2iALOppRzxrTgFFhJkL1dxzkugbbPEoSWyfrj9FivzpnxHWgRHQApQeWUBOZhroDTURwfqcyC9SW020CR57jLWfgw+idqwtCu+ZBYmEyHSJcZIH2mWXLrUQ8OalxCFVaLKL50Lpc7V8XJPs+Pg6MPVgfDUqMdjrGkAF7j4viOHTjDWP1h4Ngim70dOeyxWtuqbCbxM4APTShaqET42sj1jHxL2m1dJzXX8s/gEdN0O09hZPhI6rlC+ANWIdJ1vJfODMXWaQ== sururi@local

By adding the “command” option to the beginning of this line would make sure that whenever somebody with the corresponding key connects, that command is run automatically, the results passed back and the connection is terminated afterwards. So, far example. modifying the entry upstairs as:

command="date" ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAnq5rMLnoab+2F28g/nb58RBENWtX395TuyDFsYkalGaZxrziwDoau/wglkU19DbcAVKgw0p6lMEIuh2iALOppRzxrTgFFhJkL1dxzkugbbPEoSWyfrj9FivzpnxHWgRHQApQeWUBOZhroDTURwfqcyC9SW020CR57jLWfgw+idqwtCu+ZBYmEyHSJcZIH2mWXLrUQ8OalxCFVaLKL50Lpc7V8XJPs+Pg6MPVgfDUqMdjrGkAF7j4viOHTjDWP1h4Ngim70dOeyxWtuqbCbxM4APTShaqET42sj1jHxL2m1dJzXX8s/gEdN0O09hZPhI6rlC+ANWIdJ1vJfODMXWaQ== sururi@local== sururi@vala

would cause the following behaviour from the remote:

sururi@local:~$ ssh -i /tmp/tmp/id_rsa_example sururi@remote
Sun Aug 28 22:05:54 CEST 2011
Connection to remote closed.

I’m a bit tired now writing in full details, so will skip some obvious things from now on. Mercurial has an SSH-wrapper called ‘hg-ssh’ exactly for this purpose, and you can use it by specifying the paths of the repositories as command arguments as in:

command="hg-ssh /path/to/repository" ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAnq5rMLnoab+2F28g/nb58RBENWtX395TuyDFsYkalGaZxrziwDoau/wglkU19DbcAVKgw0p6lMEIuh2iALOppRzxrTgFFhJkL1dxzkugbbPEoSWyfrj9FivzpnxHWgRHQApQeWUBOZhroDTURwfqcyC9SW020CR57jLWfgw+idqwtCu+ZBYmEyHSJcZIH2mWXLrUQ8OalxCFVaLKL50Lpc7V8XJPs+Pg6MPVgfDUqMdjrGkAF7j4viOHTjDWP1h4Ngim70dOeyxWtuqbCbxM4APTShaqET42sj1jHxL2m1dJzXX8s/gEdN0O09hZPhI6rlC+ANWIdJ1vJfODMXWaQ== sururi@local

(and for more security, I would suggest you include the other options as well, such as:)

command="hg-ssh /path/to/repository",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEAnq5rMLnoab+2F28g/nb58RBENWtX395TuyDFsYkalGaZxrziwDoau/wglkU19DbcAVKgw0p6lMEIuh2iALOppRzxrTgFFhJkL1dxzkugbbPEoSWyfrj9FivzpnxHWgRHQApQeWUBOZhroDTURwfqcyC9SW020CR57jLWfgw+idqwtCu+ZBYmEyHSJcZIH2mWXLrUQ8OalxCFVaLKL50Lpc7V8XJPs+Pg6MPVgfDUqMdjrGkAF7j4viOHTjDWP1h4Ngim70dOeyxWtuqbCbxM4APTShaqET42sj1jHxL2m1dJzXX8s/gEdN0O09hZPhI6rlC+ANWIdJ1vJfODMXWaQ== sururi@local

and you can pull now on the local computer from the central repository at the remote computer with a command like:

sururi@local:~/project$ hg pull --ssh "ssh -i /tmp/tmp/id_rsa_example" ssh://sururi@remote//path/to/repo
pulling from ssh://sururi@remote//path/to/repo
searching for changes
no changes found

from SVN to Mercurial

admin — Tue, 23 Aug 2011 14:28:07 +0000

I’ve been using SVN for revision control system for some time. I certainly benefited from it to organize or fall-back to a stable version (”the good old times”) when I was in trouble while I was computing solo but there were two things that always upset me while using it:

Commiting meant publishing: This issue might be worked around when you have your trunk (we actually have the trunk for the ‘most recent’ status and a ‘released’ branch for the tested and stable programs of that trunk) and each of the developers play in their branches until it looks OK and hence merge it to trunk (and hopefully eventually make it to the ‘released’ branch), but the problem is, most of the time I’m in the middle of the coding process (in my branch) and it would be nice if I didn’t affect the main repository everytime I made a commit (it’s really not very nice) – in other words, even in my branch I would like to save while not making them available. The answer to this lies of course in distributed revision control systems (dvcs).
Merging: Merging is hell in SVN when you have many developers. Been there, suffered that.

I had heard of git and bazaar but -for some reasons I don’t know why- never had taken the step to give them a try. Very recently, in a scientific gathering, one of the participants suggested me to use mercurial. The interesting thing about this is, he was suggesting it as a means to enable an “undo” option for a -scientifing- refinement program which has the tendency to update your files in according to the changes you applied. I know this sounds natural but when you tried some method and it didn’t worked, you couldn’t go just one step back and use a different method – you have to start from scratch with your initial input file and apply the methods so far but the last consecutively over again. So, my friend was actually recommending me to use a revision control system for the work files (which can be done perfectly well via SVN, by the way) and he happened to be using mercurial. He suggested to check this website by Joel Spolsky (http://hginit.com/) to get it going and the website is very intriguing, indeed. So I have been running some tests to get my feet wet and it was going so well until I found that the log command didn’t reveal the list of the changes made upon the files per changeset (’revision’ in terms of SVN). I searched and searched and at the end I found the solution on hg tip (http://hgtip.com/tips/advanced/2010-01-15-styling-mercurials-cli/) website by Steve Losh. His ‘Nice Log’ script was exactly what I was looking for plus some additional effective logging templates.

I don’t think for our big project I can make the switch from SVN to Mercurial, but from now on, I’ll be ‘hg init’ing instead of ’svnadmin create’ing for the projects to come.

Exploring through the paths of subgroups, collecting indexes on the way…

admin — Mon, 06 Jun 2011 14:46:23 +0000

Having a personal wiki has its pros and cons with the pros being obvious but, on the other hand, one doesn’t feel like reposting what he has already committed into the corresponding wikipedia entry (and since reposting means filtering out the sensitive information and generalizing it, it is double the effort). So this fact, more or less, explains my absence of activity in this blog for the last 1.5 years. But then, there is one negative aspect of personal wikipedia “blogging” – it’s like putting everything under the rug : you classify the data/information and then you forget that it is there. That’s when “actual” blogging (like this one) comes handy. So, sorry & welcome back..

Today, I’ll present a code that I’ve just written to parse out the compatible paths from a tree. In my case, the three is the list of subgroups with indexes that one can acquire using Bilbao Crystallographic Server’s marvelous SUBGROUPGRAPH tool. For low indexes, you can already have SUBGROUPGRAPH do this for you by specifying your supergroup G, subgroup H and the index [G:H]. For example, for G=136, H=14 and [G:H] = 8, you can have the following paths drawn:

But as I said, things can get rough when you have a high index. In that case, we can (and we will) try to parse and analyze the paths tree which is outputted by SUBGROUPGRAPH when no index is designated, e.g., for G=136, H=14:

Where you see the maximal subgroups for the involved groups and their corresponding indexes. So, to go from P4_2/mnm (#136) to P2_1/c (#14) with index 8, we can follow the path:

P4_2/mnm (#136) –[2]–> Cmmm (#65) –[2]–> Pmna (#53) –[2]–> P2_1/c (#14)

with the related indexes given in the brackets totaling to 2×2x2 = 8.

The problem I had today was to find possible paths going from G=Fd-3m (#227) to H=Cc (#9) with index [G:H] = 192.

I first parsed the subgroup list into an array with their indexes, then followed the possible paths.


/* Emre S. Tasci                     *
 * By parsing the possible subgroup paths obtained from 
 * SUBGROUPGRAPH, finds the paths that are compatible 
 * with the given terminal super & sub groups and the 
 * designated index.
 *
 *                                              06/06/11 */
 
# Input Data === 0 ====================================================
$start_sup = 227;
$crit_index = 192;
$end_sub = 9;
 
$arr = file("data.txt"); # A sample of data.txt for the case of #227->#9
                         # is included at the end of the code.

# Input Data === 1 ====================================================

$arr_subs = Array();
$arr_labels = Array();
foreach($arr as $line)
{
    $auxarr = preg_split("/[ \t]+/",trim($line));
    #echo $auxarr[2]."\n";
    $sup = $auxarr[1];
    $suplabel = $auxarr[2];
    $arrsubs = split(";",$auxarr[3]);
    $arr_labels[$sup] = $suplabel;
    foreach($arrsubs as $subind)
    {
        $auxarr2 = Array();
        preg_match("/([0-9]+)\[([0-9]+)\]/",$subind,$auxarr2);
        #print_r($auxarr2);
        $sub = $auxarr2[1];
        $index = $auxarr2[2];
        $arr_subs[$sup][$index][] = $sub;
    }
}
#print_r($arr_subs);

 
# Start exploring
$start_sup = sprintf("%03d",$start_sup);
$end_sub = sprintf("%03d",$end_sub);
$arr_paths = Array();
$arr_paths[$start_sup] = 1;
 
findpath($start_sup);
 
function findpath($current_sup)
{
    global $arr_paths,$arr_subs,$crit_index,$end_sub;
    #echo "*".$current_sup."*\n";
    if(strrpos($current_sup,"-") !== FALSE)
    {
        $current_sup_last_sup = substr($current_sup,strrpos($current_sup,"-")+1);
        $current_sup_last_sup = substr($current_sup_last_sup,0,strpos($current_sup_last_sup,"["));
    }
 
    else
        $current_sup_last_sup = $current_sup;
    #echo "*".$current_sup_last_sup."*\n";
    $subindexes = array_keys($arr_subs[$current_sup_last_sup]);
    foreach($subindexes as $subindex)
    {
        $subs = $arr_subs[$current_sup_last_sup][$subindex];
        echo $subindex.": ".join(",",$subs)."\n";
        foreach($subs as $sub)
        {
            echo $current_sup."-".$sub."[".$subindex."]"."\n";
            $arr_paths[$current_sup."-".$sub."[".$subindex."]"] = $arr_paths[$current_sup] * $subindex;
            if($arr_paths[$current_sup."-".$sub."[".$subindex."]"]<$crit_index)
                findpath($current_sup."-".$sub."[".$subindex."]");
            elseif($arr_paths[$current_sup."-".$sub."[".$subindex."]"] == $crit_index && $sub == $end_sub)
                echo "\nPath Found: ".$current_sup."-".$sub."[".$subindex."]"."\n\n";
        }
    }
    #print_r($subindexes);
}
print_r($arr_paths);
 
 
 
/*
    data.txt:
1 	227 	Fd-3m 	141[3];166[4];203[2];216[2]
2 	220 	I-43d 	122[3];161[4]
3 	219 	F-43c 	120[3];161[4];218[4]
4 	218 	P-43n 	112[3];161[4];220[4]
5 	217 	I-43m 	121[3];160[4];215[2];218[2]
6 	216 	F-43m 	119[3];160[4];215[4]
7 	215 	P-43m 	111[3];160[4];216[2];217[4];219[2]
8 	203 	Fd-3 	070[3]
9 	167 	R-3c 	015[3];161[2];165[3];167[4];167[5];167[7]
10 	166 	R-3m 	012[3];160[2];164[3];166[2];166[4];166[5];166[7];167[2]
11 	165 	P-3c1 	015[3];158[2];163[3];165[3];165[4];165[5];165[7]
12 	164 	P-3m1 	012[3];156[2];162[3];164[2];164[3];164[4];164[5];164[7];165[2]
13 	163 	P-31c 	015[3];159[2];163[3];163[4];163[5];163[7];165[3];167[3]
14 	162 	P-31m 	012[3];157[2];162[2];162[3];162[4];162[5];162[7];163[2];164[3];166[3]
15 	161 	R3c 	009[3];158[3];161[4];161[5];161[7]
16 	160 	R3m 	008[3];156[3];160[2];160[4];160[5];160[7];161[2]
17 	159 	P31c 	009[3];158[3];159[3];159[4];159[5];159[7];161[3]
18 	158 	P3c1 	009[3];158[3];158[4];158[5];158[7];159[3]
19 	157 	P31m 	008[3];156[3];157[2];157[3];157[4];157[5];157[7];159[2];160[3]
20 	156 	P3m1 	008[3];156[2];156[3];156[4];156[5];156[7];157[3];158[2]
21 	141 	I41/amd 	070[2];074[2];088[2];109[2];119[2];122[2];141[3];141[5];141[7];141[9]
22 	122 	I-42d 	043[2];122[3];122[5];122[7];122[9]
23 	121 	I-42m 	042[2];111[2];112[2];113[2];114[2];121[3];121[5];121[7];121[9]
24 	120 	I-4c2 	045[2];116[2];117[2];120[3];120[5];120[7];120[9]
25 	119 	I-4m2 	044[2];115[2];118[2];119[3];119[5];119[7];119[9]
26 	118 	P-4n2 	034[2];118[3];118[5];118[7];118[9];122[2]
27 	117 	P-4b2 	032[2];117[2];117[3];117[5];117[7];117[9];118[2]
28 	116 	P-4c2 	027[2];112[2];114[2];116[3];116[5];116[7];116[9]
29 	115 	P-4m2 	025[2];111[2];113[2];115[2];115[3];115[5];115[7];115[9];116[2];121[2]
30 	114 	P-421c 	037[2];114[3];114[5];114[7];114[9]
31 	113 	P-421m 	035[2];113[2];113[3];113[5];113[7];113[9];114[2]
32 	112 	P-42c 	037[2];112[3];112[5];112[7];112[9];116[2];118[2]
33 	111 	P-42m 	035[2];111[2];111[3];111[5];111[7];111[9];112[2];115[2];117[2];119[2];120[2]
34 	109 	I41md 	043[2];044[2];109[3];109[5];109[7];109[9]
35 	088 	I41/a 	015[2];088[3];088[5];088[7];088[9]
36 	074 	Imma 	012[2];015[2];044[2];046[2];051[2];052[2];053[2];062[2];074[3];074[5];074[7]
37 	070 	Fddd 	015[2];043[2];070[3];070[5];070[7]
38 	064 	Cmce 	012[2];014[2];015[2];036[2];039[2];041[2];053[2];054[2];055[2];056[2];057[2];060[2];061[2];062[2];064[3];064[5];064[7]
39 	063 	Cmcm 	011[2];012[2];015[2];036[2];038[2];040[2];051[2];052[2];057[2];058[2];059[2];060[2];062[2];063[3];063[5];063[7]
40 	062 	Pnma 	011[2];014[2];026[2];031[2];033[2];062[3];062[5];062[7]
41 	061 	Pbca 	014[2];029[2];061[3];061[5];061[7]
42 	060 	Pbcn 	013[2];014[2];029[2];030[2];033[2];060[3];060[5];060[7]
43 	059 	Pmmn 	011[2];013[2];025[2];031[2];056[2];059[2];059[3];059[5];059[7];062[2]
44 	058 	Pnnm 	010[2];014[2];031[2];034[2];058[3];058[5];058[7]
45 	057 	Pbcm 	011[2];013[2];014[2];026[2];028[2];029[2];057[2];057[3];057[5];057[7];060[2];061[2];062[2]
46 	056 	Pccn 	013[2];014[2];027[2];033[2];056[3];056[5];056[7]
47 	055 	Pbam 	010[2];014[2];026[2];032[2];055[2];055[3];055[5];055[7];058[2];062[2]
48 	054 	Pcca 	013[2];014[2];027[2];029[2];032[2];052[2];054[2];054[3];054[5];054[7];056[2];060[2]
49 	053 	Pmna 	010[2];013[2];014[2];028[2];030[2];031[2];052[2];053[2];053[3];053[5];053[7];058[2];060[2]
50 	052 	Pnna 	013[2];014[2];030[2];033[2];034[2];052[3];052[5];052[7]
51 	051 	Pmma 	010[2];011[2];013[2];025[2];026[2];028[2];051[2];051[3];051[5];051[7];053[2];054[2];055[2];057[2];059[2];063[2];064[2]
52 	046 	Ima2 	008[2];009[2];026[2];028[2];030[2];033[2];046[3];046[5];046[7]
53 	045 	Iba2 	009[2];027[2];029[2];032[2];045[3];045[5];045[7]
54 	044 	Imm2 	008[2];025[2];031[2];034[2];044[3];044[5];044[7]
55 	043 	Fdd2 	009[2];043[3];043[5];043[7]
56 	042 	Fmm2 	008[2];035[2];036[2];037[2];038[2];039[2];040[2];041[2];042[3];042[5];042[7]
57 	041 	Aea2 	007[2];009[2];029[2];030[2];032[2];033[2];041[3];041[5];041[7]
58 	040 	Ama2 	006[2];009[2];028[2];031[2];033[2];034[2];040[3];040[5];040[7]
59 	039 	Aem2 	007[2];008[2];026[2];027[2];028[2];029[2];039[2];039[3];039[5];039[7];041[2];045[2];046[2]
60 	038 	Amm2 	006[2];008[2];025[2];026[2];030[2];031[2];038[2];038[3];038[5];038[7];040[2];044[2];046[2]
61 	037 	Ccc2 	009[2];027[2];030[2];034[2];037[3];037[5];037[7]
62 	036 	Cmc21 	008[2];009[2];026[2];029[2];031[2];033[2];036[3];036[5];036[7]
63 	035 	Cmm2 	008[2];025[2];028[2];032[2];035[2];035[3];035[5];035[7];036[2];037[2];044[2];045[2];046[2]
64 	034 	Pnn2 	007[2];034[3];034[5];034[7];043[2]
65 	033 	Pna21 	007[2];033[3];033[5];033[7]
66 	032 	Pba2 	007[2];032[2];032[3];032[5];032[7];033[2];034[2]
67 	031 	Pmn21 	006[2];007[2];031[2];031[3];031[5];031[7];033[2]
68 	030 	Pnc2 	007[2];030[2];030[3];030[5];030[7];034[2]
69 	029 	Pca21 	007[2];029[2];029[3];029[5];029[7];033[2]
70 	028 	Pma2 	006[2];007[2];028[2];028[3];028[5];028[7];029[2];030[2];031[2];032[2];040[2];041[2]
71 	027 	Pcc2 	007[2];027[2];027[3];027[5];027[7];030[2];037[2]
72 	026 	Pmc21 	006[2];007[2];026[2];026[3];026[5];026[7];029[2];031[2];036[2]
73 	025 	Pmm2 	006[2];025[2];025[3];025[5];025[7];026[2];027[2];028[2];035[2];038[2];039[2];042[2]
74 	015 	C2/c 	009[2];013[2];014[2];015[3];015[5];015[7]
75 	014 	P21/c 	007[2];014[2];014[3];014[5];014[7]
76 	013 	P2/c 	007[2];013[2];013[3];013[5];013[7];014[2];015[2]
77 	012 	C2/m 	008[2];010[2];011[2];012[2];012[3];012[5];012[7];013[2];014[2];015[2]
78 	011 	P21/m 	006[2];011[2];011[3];011[5];011[7];014[2]
79 	010 	P2/m 	006[2];010[2];010[3];010[5];010[7];011[2];012[2];013[2]
80 	008 	Cm 	006[2];007[2];008[2];008[3];008[5];008[7];009[2]
81 	007 	Pc 	007[2];007[3];007[5];007[7];009[2]
82 	006 	Pm 	006[2];006[3];006[5];006[7];007[2];008[2]
83 	009 	Cc 	007[2];009[3];009[5];009[7]
 */

When run, the code lists all the paths with the matching ones preceded by “Path Found”, so if you grep wrt it, you’ll have, for this example:

sururi@husniya:/xxx$ php find_trpath_for_index.php |grep Path|sed "s:Path Found\: ::"
227-141[3]-070[2]-015[2]-009[2]-007[2]-007[2]-009[2]
227-141[3]-070[2]-015[2]-013[2]-007[2]-007[2]-009[2]
227-141[3]-070[2]-015[2]-013[2]-013[2]-007[2]-009[2]
227-141[3]-070[2]-015[2]-013[2]-013[2]-015[2]-009[2]
227-141[3]-070[2]-015[2]-013[2]-014[2]-007[2]-009[2]
227-141[3]-070[2]-015[2]-014[2]-007[2]-007[2]-009[2]
227-141[3]-070[2]-015[2]-014[2]-014[2]-007[2]-009[2]
227-141[3]-070[2]-043[2]-009[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-008[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-008[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-012[2]-008[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-008[2]-008[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-008[2]-008[2]-008[2]-009[2]
227-141[3]-074[2]-012[2]-008[2]-009[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-010[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-010[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-012[2]-010[2]-012[2]-008[2]-009[2]
227-141[3]-074[2]-012[2]-010[2]-012[2]-015[2]-009[2]
227-141[3]-074[2]-012[2]-010[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-010[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-012[2]-011[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-011[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-012[2]-011[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-012[2]-008[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-012[2]-008[2]-008[2]-009[2]
227-141[3]-074[2]-012[2]-012[2]-012[2]-008[2]-009[2]
227-141[3]-074[2]-012[2]-012[2]-012[2]-015[2]-009[2]
227-141[3]-074[2]-012[2]-012[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-012[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-012[2]-012[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-013[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-013[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-013[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-012[2]-013[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-014[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-014[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-015[2]-009[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-015[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-012[2]-015[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-012[2]-015[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-015[2]-009[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-015[2]-013[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-015[2]-013[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-015[2]-013[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-015[2]-013[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-015[2]-014[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-015[2]-014[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-008[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-008[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-044[2]-008[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-008[2]-008[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-008[2]-008[2]-008[2]-009[2]
227-141[3]-074[2]-044[2]-008[2]-009[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-026[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-026[2]-036[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-027[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-027[2]-037[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-028[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-028[2]-040[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-028[2]-041[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-035[2]-008[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-035[2]-036[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-035[2]-037[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-035[2]-045[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-035[2]-046[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-038[2]-008[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-038[2]-040[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-038[2]-046[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-039[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-039[2]-008[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-039[2]-041[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-039[2]-045[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-039[2]-046[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-042[2]-008[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-042[2]-036[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-042[2]-037[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-042[2]-040[2]-009[2]
227-141[3]-074[2]-044[2]-025[2]-042[2]-041[2]-009[2]
227-141[3]-074[2]-044[2]-031[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-031[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-044[2]-031[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-031[2]-031[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-031[2]-033[2]-007[2]-009[2]
227-141[3]-074[2]-044[2]-034[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-008[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-008[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-046[2]-008[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-008[2]-008[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-008[2]-008[2]-008[2]-009[2]
227-141[3]-074[2]-046[2]-008[2]-009[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-009[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-026[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-026[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-046[2]-026[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-026[2]-026[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-026[2]-026[2]-036[2]-009[2]
227-141[3]-074[2]-046[2]-026[2]-029[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-026[2]-031[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-026[2]-036[2]-008[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-028[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-028[2]-040[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-028[2]-041[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-029[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-030[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-031[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-032[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-028[2]-041[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-030[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-030[2]-030[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-030[2]-034[2]-007[2]-009[2]
227-141[3]-074[2]-046[2]-030[2]-034[2]-043[2]-009[2]
227-141[3]-074[2]-046[2]-033[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-010[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-010[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-010[2]-012[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-010[2]-012[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-010[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-010[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-011[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-011[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-011[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-013[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-013[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-013[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-013[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-026[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-026[2]-036[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-027[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-027[2]-037[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-028[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-028[2]-040[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-028[2]-041[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-035[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-035[2]-036[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-035[2]-037[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-035[2]-045[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-035[2]-046[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-038[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-038[2]-040[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-038[2]-046[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-039[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-039[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-039[2]-041[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-039[2]-045[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-039[2]-046[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-042[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-042[2]-036[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-042[2]-037[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-042[2]-040[2]-009[2]
227-141[3]-074[2]-051[2]-025[2]-042[2]-041[2]-009[2]
227-141[3]-074[2]-051[2]-026[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-026[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-026[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-026[2]-026[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-026[2]-026[2]-036[2]-009[2]
227-141[3]-074[2]-051[2]-026[2]-029[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-026[2]-031[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-026[2]-036[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-028[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-028[2]-040[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-028[2]-041[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-029[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-030[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-031[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-032[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-028[2]-041[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-026[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-026[2]-036[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-028[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-028[2]-040[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-028[2]-041[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-063[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-063[2]-036[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-063[2]-040[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-064[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-064[2]-036[2]-009[2]
227-141[3]-074[2]-051[2]-051[2]-064[2]-041[2]-009[2]
227-141[3]-074[2]-051[2]-053[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-053[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-053[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-053[2]-028[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-053[2]-028[2]-040[2]-009[2]
227-141[3]-074[2]-051[2]-053[2]-028[2]-041[2]-009[2]
227-141[3]-074[2]-051[2]-053[2]-030[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-053[2]-031[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-054[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-054[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-054[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-054[2]-027[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-054[2]-027[2]-037[2]-009[2]
227-141[3]-074[2]-051[2]-054[2]-029[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-054[2]-032[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-055[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-055[2]-026[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-055[2]-026[2]-036[2]-009[2]
227-141[3]-074[2]-051[2]-055[2]-032[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-057[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-057[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-057[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-057[2]-026[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-057[2]-026[2]-036[2]-009[2]
227-141[3]-074[2]-051[2]-057[2]-028[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-057[2]-028[2]-040[2]-009[2]
227-141[3]-074[2]-051[2]-057[2]-028[2]-041[2]-009[2]
227-141[3]-074[2]-051[2]-057[2]-029[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-059[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-059[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-059[2]-031[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-063[2]-012[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-063[2]-012[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-063[2]-036[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-063[2]-038[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-063[2]-038[2]-040[2]-009[2]
227-141[3]-074[2]-051[2]-063[2]-038[2]-046[2]-009[2]
227-141[3]-074[2]-051[2]-064[2]-012[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-064[2]-012[2]-015[2]-009[2]
227-141[3]-074[2]-051[2]-064[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-064[2]-036[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-064[2]-039[2]-007[2]-009[2]
227-141[3]-074[2]-051[2]-064[2]-039[2]-008[2]-009[2]
227-141[3]-074[2]-051[2]-064[2]-039[2]-041[2]-009[2]
227-141[3]-074[2]-051[2]-064[2]-039[2]-045[2]-009[2]
227-141[3]-074[2]-051[2]-064[2]-039[2]-046[2]-009[2]
227-141[3]-074[2]-051[2]-064[2]-041[2]-007[2]-009[2]
227-141[3]-074[2]-052[2]-013[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-052[2]-013[2]-013[2]-007[2]-009[2]
227-141[3]-074[2]-052[2]-013[2]-013[2]-015[2]-009[2]
227-141[3]-074[2]-052[2]-013[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-052[2]-014[2]-007[2]-007[2]-009[2]
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SF in Nature, Futures / The Most Beautiful Sun of Our Earth

admin — Wed, 07 Oct 2009 11:49:51 +0000

Nature has a very nice section called the Futures in where they publish very short (1 page at most) science fiction stories.

I started writing stories long before I started writing scientific articles and had this story of mine, “The Most Beautiful Sun of Our Earth” written some 9 years ago (in Turkish). Last week, the idea to re-write/revise it in English and submit it to the Futures occurred to me, so on an insomniatic night (or whatever is the correct English term), I sat down in front of the word processor and pulled it out.

The original story had me and -my then girlfriend- Bengü as the protagonists but I felt that it would be too selfish so, I “borrowed” my dear friend (my battalion as we call it), Andy and his girlfriend Serene for the part. The following day I asked Andy’s permission for the inclusion and also his help to edit this English version of the story, which he kindly accepted.

At the end, I submitted the story to Nature and from the tone of this entry most probably you’ll think that it was accepted for publication and hoorraay and all that but no, yesterday, I got a reply stating that, it wasn’t accepted and that’s it.

The good thing coming out of this is that, Andy actually liked the story very much and this story being one of my favorite SF stories, I’m really happy for it. So, if you’re still interested, you can get a copy of it, completely free from any possible obligations to Nature publishing were it to have been otherwise..

Emre S. Tasci – “The Most Beautiful Sun of Our Earth”

Coordination Numbers

admin — Thu, 03 Sep 2009 15:31:10 +0000

Recently, we are working on liquid alloys and for our work, we need the coordination number distribution. It’s kind of a gray area when you talk about coordination number of atoms in a liquid but it’s better than nothing to understand the properties and even more. I’d like to write a log on the tools I’ve recently coded/used in order to refer to in the future if a similar situation occurs. Also, maybe there are some others conducting similar research so, the tools introduced here may be helpful to them.

Recently, while searching recent publications on liquid alloys, I’ve found a very good and resourceful article on liquid Na-K alloys by Dr. J.-F. Wax (“Molecular dynamics study of the static structure of liquid Na-K alloys”, Physica B 403 (2008) 4241-48 | doi:10.1016/j.physb.2008.09.014). In this paper, among other properties, he had also presented the partial pair distribution functions. Partial-pair distribution functions is the averaged probability that you’ll encounter an atom in r distance starting from another atom. In solid phase, due to the symmetry of the crystal structure, you have discrete values instead of a continuous distribution and everything is crystal clear but I guess that’s the price we pay dealing with liquids.

Partial-pair distribution functions are very useful in the sense that they let you derive the bond-length between constituent atom species, corresponding to the first minimums of the plots. Hence, one can see the neighborhood ranges by just looking at the plots.

I’ve sent a mail to Dr. Wax explaining my research topics and my interest and asking for his research data to which he very kindly and generously replied by providing his data.

He had sent me a big file with numerous configurations (coordinates of the atoms) following each other. The first -and the simplest- task was to split the file into seperate configuration files via this bash script:

#!/bin/bash
# Script Name: split_POS4.sh
# Splits the NaK conf files compilation POS4_DAT into sepearate
# conf files.
# Emre S. Tasci 
#                                              01/09/09
 
linestart=2
p="p"
for (( i = 1; i <= 1000; i++ ))
do
    echo $i;
    lineend=$(expr $linestart + 2047)
    confname=$(printf "%04d" $i)
    echo -e "3\n2048" > $confname
    sed -n "$linestart,$(echo $lineend$p)" POS4_DAT >> $confname
    linestart=$(expr $lineend + 1)
    cat $confname | qhull i TO $confname.hull
done

(The compilation was of 1000 configurations, each with 2048 atoms)

As you can check in the line before the “done” closer, I’ve -proudly- used Qhull software to calculate the convex hull of each configuration. A convex hull is the -hopefully minimum- shape that covers all your system. So, for each configuration I now had 2 files: “xxxx” (where xxxx is the id/number of the configuration set) storing the coordinates (preceded by 3 and 2048, corresponding to dimension and number of atoms information for the qhull to parse & process) and “xxxx.hull” file, generated by the qhull, containing the vertices list of each facet (preceded by the total number of facets).

A facet is (in 3D) the plane formed by the vertice points. Imagine a cube, where an atom lies at each corner, 3 in the inside. So, we can say that our system consists of 11 atoms and the minimal shape that has edges selected from system’s atoms and covering the whole is a cube, with the edges being the 8 atoms at the corners. Now, add an atom floating over the face at the top. Now the convex hull that wraps our new system would no longer be a 6-faced, 8-edged cube but a 9-faced, 9-edged polygon. I need to know the convex hull geometry in order to correctly calculate the coordination number distributions (details will follow shortly).

The aforementioned two files look like:

sururi@husniya hull_calcs $ head 0001
3
2048
 0.95278770E+00 0.13334565E+02 0.13376155E+02
 0.13025256E+02 0.87618381E+00 0.20168993E+01
 0.12745038E+01 0.14068998E-01 0.22887323E+01
 0.13066590E+02 0.20788591E+01 0.58119183E+01
 0.10468218E+00 0.58523640E-01 0.64288678E+01
 0.12839412E+02 0.13117012E+02 0.79093881E+01
 0.11918105E+01 0.12163854E+02 0.10270868E+02
 0.12673985E+02 0.11642538E+02 0.10514597E+02
sururi@husniya hull_calcs $ head 0001.hull
180
568 1127 1776
1992 104 1551
956 449 1026
632 391 1026
391 632 1543
391 956 1026
966 632 1026
966 15 1039
632 966 1039

The sets of 3 numbers in the xxxx.hull file is the ids/numbers of the atoms forming the edges of the facets, i.e., they are the vertices.

To calculate the coordination number distribution, you need to pick each atom and then simply count the other atoms within the cut-off distance depending on your atom’s and the neighboring atom’s species. After you do the counting for every atom, you average the results and voilà! there is your CN distribution. But here’s the catch: In order to be able to count properly, you must make sure that, your reference atom’s cutoff radii stay within your system — otherwise you’ll be undercounting. Suppose your reference atom is one of the atoms at the corners of the cube: It will (generally/approximately) lack 7/8 of the neighbouring atoms it would normally have if it was to be the center atom of the specimen/sample. Remember that we are studying a continuous liquid and trying to model the system via ensembles of samples. So we should omit these atoms which has neighborhoods outside of our systems. Since neighborhoods are defined through bond-length, we should only include the atoms with a distance to the outside of at least cut-off radii. The “outside” is defined as the region outside the convex hull and it’s designated by the facets (planes).

From the xxxx.hull file, we have the ids of the vertice atoms and their coordinates are stored in the xxxx file. To define the plane equation

we will use the three vertice points, say p1, p2 and p3. From these 3 points, we calculate the normal n as:

then, the plane equation (hence the coefficients a,b,c,d) can be derived by comparing the following equation:

Here, (x0,y0,z0) are just the coordinates of any of the vertice points. And finally, the distance D between a point p1(x1,y1,z1) and a plane (a,b,c,d) is given by:

Since vector operations are involved, I thought it’s better to do this job in Octave and wrote the following script that calculates the coefficients of the facets and then sets down to find out the points whose distances to all the facets are greater than the given cut-off radius:

sururi@husniya trunk $ cat octave_find_atoms_within.m
DummyA = 3;
%conf_index=292;
 
% Call from the command line like :
%   octave -q --eval "Rcut=1.65;conf_index=293;path='$(pwd)';" octave_find_atoms_within.m
% hence specifying the conf_index at the command line.
 
 
% Emre S. Tasci                     *
%
% From the positions and vertices file, calculates the plane
% equations (stored in "facet_coefficients") and then
% filters the atoms with respect to their distances to these
% facets. Writes the output to
% "hull_calcs/xxxx_insiders.txt" file
%                                              03/09/09 */
 
 
conf_index_name = num2str(sprintf("%04d",conf_index));;
%clock
clear facet_coefficients;
facet_coefficients = [];
global p v facet_coefficients
fp = fopen(strcat(path,"/hull_calcs/",conf_index_name));
k = fscanf(fp,"%d",2); % 1st is dim (=3), 2nd is number of atoms (=2048)
p = fscanf(fp,"%f",[k(1),k(2)]);
p = p';
fclose(fp);
%p = load("/tmp/del/delco");
fp = fopen(strcat(path,"/hull_calcs/",conf_index_name,".hull"));
k = fscanf(fp,"%d",1);% number of facets
v = fscanf(fp,"%d",[3,k]);
v = v';
fclose(fp);
%v = load("/tmp/del/delver");
 
function [a,b,c,d,e] = getPlaneCoefficients(facet_index)
    global p v
    % Get the 3 vertices
    p1 = p(v(facet_index,1)+1,:); % The +1s come from the fact 
    p2 = p(v(facet_index,2)+1,:); % that qhull enumeration begins
    p3 = p(v(facet_index,3)+1,:); % from 0 while Octave's from 1
 
    %printf("%d: %f %f %f %f %f %f %f %f %f\n",facet_index,p1,p2,p3);
 
    % Calculate the normal
    n = cross((p2-p1),(p3-p1));
 
    % Calculate the coefficients of the plane :
    % ax + by + cz +d = 0
    a = n(1);
    b = n(2);
    c = n(3);
    d = -(dot(n,p1));
    e = norm(n);
    if(e==0)
        printf("%f\n",p1);
        printf("%f\n",p2);
        printf("%f\n",p3);
        printf("%d\n",facet_index);
    endif
endfunction
 
function dist = distanceToPlane(point_index,facet_index)
    global p facet_coefficients
    k = facet_coefficients(facet_index,:);
    n = [k(1) k(2) k(3)];
    dist = abs(dot(n,p(point_index,:)) + k(4)) / k(5);
endfunction
 
for i = [1:size(v)(1)]
    [a,b,c,d,e] = getPlaneCoefficients(i);
    facet_coefficients = [ facet_coefficients ; [a,b,c,d,e]];
endfor
 
%Rcut = 1.65; % Defined from command line calling
% Find the points that are not closer than Rcut
inside_atoms = [];
for point = [1:size(p)(1)]
%for point = [1:100]
    inside=true;
    for facet = [1:size(v)(1)]
    %for facet = [1:10]
        %printf("%d - %d : %f\n",point,facet,dist);
        if (distanceToPlane(point,facet))
            inside = false;
            break;
        endif
    endfor
    if(inside)
        inside_atoms = [inside_atoms point-1];
    endif
endfor
 
fp = fopen(strcat(path,"/hull_calcs/",conf_index_name,"_insiders.txt"),"w");
fprintf(fp,"%d\n",inside_atoms);
fclose(fp);
%clock

This script is runned within the following php code which then takes the filtered atoms and does the counting using them:


/* Emre S. Tasci                     *
 *
 * parse_configuration_data.php
 *
 * Written in order to parse the configuation files
 * obtained from J.F. Wax in order to calculate the 
 * Coordination Number distribution. Each configuration 
 * file contain 2048 atoms' coordinates starting at the 
 * 3rd line. There is also a convex hull file generated 
 * using qhull (http://www.qhull.com) that contains the 
 * indexes (starting from 0) of the atoms that form the 
 * vertices of the convex hull. Finally there is the 
 * IP.dat file that identifies each atom (-1 for K; 1 for 
 * Na -- the second column is the relative masses).
 *
 *                                              02/09/09 */
 
/*
# if present, remove the previous run's results file
if(file_exists("results.txt"))
    unlink("results.txt");
 */
 
error_reporting(E_ALL ^ E_NOTICE);
 
if(!file_exists("results.txt"))
{
    $fp = fopen("results.txt","w");
    fwrite($fp,"CONF#"."\tNa".implode("\tNa",range(1,20))."\tK".implode("\tK",range(1,20))."\n");
    fclose($fp);
}
 
# Support for command line variable passing:
for($i=1;$i<sizeof($_SERVER["argv"]);$i++)
{
        list($var0,$val0) = explode("=",$_SERVER["argv"][$i]);
        $_GET[$var0] = $val0;
}
 
if($_GET["configuration"])
    calculate($_GET["configuration"]);
else
    exit("Please specify a configuration number [php parse_configuration_data.php configuration=xxx]\n");
 
function calculate($conf_index)
{
    # Define the atoms array
    $arr_atoms = Array();
 
    # Get the information from the files
    parse_types($arr_atoms);
    $refs = get_vertices($conf_index);
    parse_coordinates($arr_atoms,$conf_index);
 
    # Define the Rcut-off values (obtained from partial parid distribution minimums)
    $Rcut_arr = Array();
    $Rscale = 3.828; # To convert reduced distances to Angstrom (if needed)
    $Rscale = 1; # To convert reduced distances to Angstrom
    $Rcut_arr["Na"]["Na"] = 1.38 * $Rscale;
    $Rcut_arr["Na"]["K"]  = 1.65 * $Rscale;
    $Rcut_arr["K"]["Na"]  = 1.65 * $Rscale;
    $Rcut_arr["K"]["K"]   = 1.52 * $Rscale;
    $Rcut = $Rcut_arr["Na"]["K"]; # Taking the maximum one as the Rcut for safety

 
    /*
    # We have everything we need, so proceed to check 
    # if an atom is at safe distance wrt to the vertices
 
    # Define all the ids
    $arr_test_ids = range(0,2047);
    # Subtract the ref atoms' ids
    $arr_test_ids = array_diff($arr_test_ids, $refs);
    sort($arr_test_ids);
    //print_r($arr_test_ids);
 
    $arr_passed_atom_ids = Array();
    # Check each atom against refs
    for($id=0, $size=sizeof($arr_test_ids); $id<$size; $id++)
    {
        //echo $id."\n";
        $arr_atoms[$arr_test_ids[$id]]["in"] = TRUE;
        foreach ($refs as $ref)
        {
            $distance = distance($arr_atoms[$arr_test_ids[$id]],$arr_atoms[$ref]);
            //echo "\t".$ref."\t".$distance."\n";
            if($distance < $Rcut)
            {
                $arr_atoms[$arr_test_ids[$id]]["in"] = FALSE;
                break;
            }
        }
        if($arr_atoms[$arr_test_ids[$id]]["in"] == TRUE)
            $arr_passed_atom_ids[] = $arr_test_ids[$id];
    }
     */
 
    # Run the octave script file to calculate the inside atoms
    if(!file_exists("hull_calcs/".sprintf("%04d",$conf_index)."_insiders.txt"))
    exec("octave -q --eval \"Rcut=".$Rcut.";conf_index=".$conf_index.";path='$(pwd)';\" octave_find_atoms_within.m");
 
    # Read the file generated by Octave
    $arr_passed_atom_ids = file("hull_calcs/".sprintf("%04d",$conf_index)."_insiders.txt",FILE_IGNORE_NEW_LINES);
 
    $arr_test_ids = range(0,2047);
    $arr_test_ids = array_diff($arr_test_ids, $refs);
    sort($arr_test_ids);
    for($i=0, $size=sizeof($arr_test_ids);$i<$size;$i++)
        $arr_atoms[$arr_test_ids[$i]]["in"]=FALSE;
 
    # Begin checking every passed atom
    foreach($arr_passed_atom_ids as $passed_atom_id)
    {
        $arr_atoms[$passed_atom_id]["in"] = TRUE;
        for($i=0, $size=sizeof($arr_atoms); $i<$size; $i++)
        {
            $distance = distance($arr_atoms[$passed_atom_id],$arr_atoms[$i]);
            //echo $passed_atom_id."\t---\t".$i."\n";
            if($distance < $Rcut_arr[$arr_atoms[$passed_atom_id]["id"]][$arr_atoms[$i]["id"]] && $distance>0.001)
                $arr_atoms[$passed_atom_id]["neighbour_count"] += 1;
        }
    }
 
    # Do the binning
    $CN_Na = Array();
    $CN_K  = Array();
    for($i=0, $size=sizeof($arr_atoms); $i<$size; $i++)
    {
        if(array_key_exists("neighbour_count",$arr_atoms[$i]))
        {
            ${"CN_".$arr_atoms[$i]['id']}[$arr_atoms[$i]["neighbour_count"]] += 1;
        }
    }
 
    ksort($CN_Na);
    ksort($CN_K);
 
    //print_r($arr_atoms);
    //print_r($CN_Na);
    //print_r($CN_K);
 
 
    # Report the results
    $filename = "results/".sprintf("%04d",$conf_index)."_results.txt";
    $fp = fopen($filename,"w");
    fwrite($fp, "### Atoms array ###\n");
    fwrite($fp,var_export($arr_atoms,TRUE)."\n");
    fwrite($fp, "\n### CN Distribution for Na ###\n");
    fwrite($fp,var_export($CN_Na,TRUE)."\n");
    fwrite($fp, "\n### CN Distribution for K ###\n");
    fwrite($fp,var_export($CN_K,TRUE)."\n");
 
    # Percentage calculation:
    $sum_Na = array_sum($CN_Na);
    $sum_K  = array_sum($CN_K);
    foreach($CN_Na as $key=>$value)
        $CN_Na[$key] = $value * 100 / $sum_Na;
    foreach($CN_K  as $key=>$value)
        $CN_K[$key]  = $value * 100 / $sum_K;
    //print_r($CN_Na);
    //print_r($CN_K);
    fwrite($fp, "\n### CN Distribution (Percentage) for Na ###\n");
    fwrite($fp,var_export($CN_Na,TRUE)."\n");
    fwrite($fp, "\n### CN Distribution (Percentage) for K ###\n");
    fwrite($fp,var_export($CN_K,TRUE)."\n");
    fclose($fp);
 
    # Write the summary to the results file
    $fp = fopen("results.txt","a");
    for($i=1;$i<=20;$i++)
    {
        if(!array_key_exists($i,$CN_Na))
            $CN_Na[$i] = 0;
        if(!array_key_exists($i,$CN_K))
            $CN_K[$i] = 0;
    }
    ksort($CN_Na);
    ksort($CN_K);
    fwrite($fp,sprintf("%04d",$conf_index)."\t".implode("\t",$CN_Na)."\t".implode("\t",$CN_K)."\n");
    fclose($fp);
 
}
 
function parse_types(&$arr_atoms)
{
    # Parse the types
    $i = 0;
    $fp = fopen("IP.DAT", "r");
    while(!feof($fp))
    {
        $line = fgets($fp,4096);
        $auxarr = explode(" ",$line);
        if($auxarr[0]==-1)
            $arr_atoms[$i]["id"] = "Na";
        else
            $arr_atoms[$i]["id"] = "K";
        $i++;
    }
    fclose($fp);
    array_pop($arr_atoms);
    return 0;
}
 
function get_vertices($conf_index)
{
    $arr_refs = Array();
 
    # Get the ids of the vertices of the convex hull
    $filename = "hull_calcs/".sprintf("%04d",$conf_index).".hull";
    $fp = fopen($filename, "r");
 
    # Bypass the first line
    $line = fgets($fp,4096);
 
    while(!feof($fp))
    {
        $line = fgets($fp,4096);
        $auxarr = explode(" ",$line);
        array_pop($auxarr);
        $arr_refs = array_merge($arr_refs, $auxarr);
    }
    fclose($fp);
    // $arr_refs = array_unique($arr_refs); # This doesn't lose the keys
    $arr_refs = array_keys(array_count_values($arr_refs)); # But this does.
    return $arr_refs;
}
 
function parse_coordinates(&$arr_atoms, $conf_index)
{
    # Parse the coordinates
    $i = 0;
    $filename = "hull_calcs/".sprintf("%04d",$conf_index);
    $fp = fopen($filename, "r");
 
    # Bypass the first two lines
    $line = fgets($fp,4096);
    $line = fgets($fp,4096);
 
    while(!feof($fp))
    {
        $line = fgets($fp,4096);
        $arr_atoms[$i]["coords"] = explode(" ",$line);
        array_shift($arr_atoms[$i]["coords"]);
        $i++;
    }
    fclose($fp);
    array_pop($arr_atoms);
    return 0;
}
 
function distance(&$atom1,&$atom2)
{
    # Calculate the distance between the two atoms
    $x1 = $atom1["coords"][0];
    $x2 = $atom2["coords"][0];
    $y1 = $atom1["coords"][1];
    $y2 = $atom2["coords"][1];
    $z1 = $atom1["coords"][2];
    $z2 = $atom2["coords"][2];
    return sqrt(pow($x1-$x2,2) + pow($y1-$y2,2) + pow($z1-$z2,2));
}
 
?>

The code above generates a “results/xxxx_results.txt” file containing all the information obtained in arrays format and also appends to “results.txt” file the relevant configuration file’s CN distribution summary. The systems can be visualized using the output generated by the following plotter.php script:


/* Emre S. Tasci                     *
 * Parses the results/xxxx_results.txt file and generates 
 * an XYZ file such that the atoms are labeled as the 
 * vertice atoms, close-vertice atoms and inside atoms..
 *                                              02/09/09 */
 
 
# Support for command line variable passing:
for($i=1;$i<sizeof($_SERVER["argv"]);$i++)
{
        list($var0,$val0) = explode("=",$_SERVER["argv"][$i]);
        $_GET[$var0] = $val0;
}
 
if($_GET["configuration"])
    $conf_index = $_GET["configuration"];
else 
    exit("Please specify a configuration number [php plotter.php configuration=xxx]\n");
 
$filename = sprintf("%04d",$conf_index);
 
# Get the atom array from the results file. Since results file 
# contains other arrays as well, we slice the file using sed for the 
# relevant part
$last_arr_line = exec('grep "### CN Distribution" results/'.$filename.'_results.txt -n -m1|sed "s:^\([0-9]\+\).*:\1:gi"');
exec('sed -n "2,'.($last_arr_line-1).'p" results/'.$filename.'_results.txt > system_tmp_array_dump_file');
$str=file_get_contents('system_tmp_array_dump_file');
$atom_arr=eval('return '.$str.';');
unlink('system_tmp_array_dump_file');
 
# Now that we have the coordinates, we itarate over the atoms to check 
# the characteristic and designate them in the XYZ file.
$fp = fopen("system_".$filename.".xyz","w");
fwrite($fp,sizeof($atom_arr)."\n");
fwrite($fp,"Generated by plotter.php\n");
for($i=0, $size=sizeof($atom_arr);$i<$size;$i++)
{
    if(!array_key_exists("in",$atom_arr[$i]))
        $atomlabel = "Mg";#Vertices
    elseif($atom_arr[$i]["in"]==TRUE)
        $atomlabel = $atom_arr[$i]["id"];#Inside atoms
    else
        $atomlabel = "O";#Close-vertice atoms
    fwrite($fp,$atomlabel."\t".implode("\t",$atom_arr[$i]["coords"]));
}
fclose($fp);
?>

which generates a “system_xxxx.xyz” file, ready to be viewed in a standard molecule viewing software. It designates the vertice atoms (of the convex hull, remember? 8)as “Mg” and the atoms close to them as “O” for easy-viewing purpose. A sample parsed file looks like this:

The filtered case of a sample Na-K system

The big orange atoms are the omitted vertice atoms; the small red ones are the atoms critically close to the facets and hence also omitted ones. You can see the purple and yellow atoms which have passed the test sitting happilly inside, with the counting done using them..

POSCAR2Cif with symmetries discovered

admin — Thu, 04 Jun 2009 08:16:57 +0000

In previous posts, I had submitted two codes:

POSCAR2Cif : that converts a given POSCAR file to CIF, so to speak, ruthlessly, i.e. just as is, without checking for symmetries or anything.
POSCAR2findsymm : another converter that takes a POSCAR file, and prepares an input file such that Harold Stokes’ findsym code from the ISOTROPY package would proceed it and deduce the symmetry information. If findsym executable is not accessible in your system (or if you run the script with the “t” flag set to on), it would just print the input to the screen and you could use it to fill the input form of the code’s web implementation, instead

Anyway, recently it occured to me to write another script that would parse the output of the POSCAR2findsymm output and use that output to construct a CIF file that contained the equivalent sites, etc.. So, ladies and gentlemen, here it is (drums roll)…

Example: Code in action
Using the same POSCAR_Pd3S file as in the POSCAR2Cif entry… Feeding it to POSCAR2findsymm and then applying findsymm2cif on it

sururi@husniya tmp $ python /code/POSCAR2findsym/POSCAR2findsym.py POSCAR_Pd3S | php /code/vaspie/findsymm2cif.php speclist=Pd,S
_cell_length_a  7.21915
_cell_length_b  5.56683
_cell_length_c  7.68685
_cell_angle_alpha       90.00000
_cell_angle_beta        90.00000
_cell_angle_gamma       90.00000
_symmetry_Int_Tables_number     40
 
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Pd01    Pd       0.75000         0.17834         0.31139
Pd02    Pd       0.75000         0.17845         0.69126
Pd03    Pd       0.50000         0.00000         0.00132
S01     S        0.75000         0.81592         0.50152

Code

#!/usr/bin/php

 
//require("/code/toolbox/commandline.inc.php"); # Equivalent handling of $_GET / $_POST
# ============/code/toolbox/commandline.inc.php========================================
// Enables the same treat for command line parameters
// as those of GET parameters.
// Also sets the $first, $last ranges including the gall parameter
 
//Support for command line variable passing:
for($i=1;$i<sizeof($_SERVER["argv"]);$i++)
{
	list($var0,$val0) = explode("=",$_SERVER["argv"][$i]);
	$_GET[$var0] = $val0;
}
 
# ============/code/toolbox/commandline.inc.php========================================
if($_GET["h"]||$_GET["help"])
{
$help = <<                               *
 *                                                        23/05/09  *
 
 Usage:
 f         : input file  (Default = stdin)
 o         : output file (Default = stdout)
 identical : if set (identical=1), then the output will be the 
             transformation matrix and origin shift applied to the coordinates 
             so that the given coordinates will be regained.
 speclist  : Define the name of the species, seperated by 'xx' or ',' to be used
             with neighbour listing (Default = AxxBxxCxx...)
             (Labels can also be seperated via [space] as long as speclist is given
             in quotation -- Example: ... speclist=\"Au Si\" )
 
 Example : php findsymmetry2cif.php f=POSCAR_RhBi4 speclist=Bi,Rh identical=1
lol;
 echo $help."\n";
 exit;
}
 
$input = "php://stdin";
if($_GET["f"]) $input=$_GET["f"];
 
$outfile = "php://stdout";
if($_GET["o"]) $outfile=$_GET["o"];
 
$species_type_template = Array("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z");
if($_GET["speclist"])$species_type_template = split("xx| |,",$_GET["speclist"]);
 
//if(file_exists("findsymm2cif_php.tmp"))
//    unlink("findsymm2cif_php.tmp");
if($input == "php://stdin")
{
    $lol = file("php://stdin");
    $fp1 = fopen("findsymm2cif_php2.tmp","w");
    foreach($lol as $line)
        fwrite($fp1,$line);
    fclose($fp1);
    $input = "findsymm2cif_php2.tmp";
}
exec('lstart=`grep -n "Type of each atom:" '.$input.'|sed "s:^\([0-9]\+\).*:\1:gi"`;lstart=`expr $lstart + 1`;lfinish=`grep -n "Position of each atom (dimensionless coordinates)" '.$input.'|sed "s:^\([0-9]\+\).*:\1:gi"`;lfinish=`expr $lfinish - 1`;cat '.$input.' |sed -n "`echo $lstart`,`echo $lfinish`p" | sed \':a;N;$!ba;s/\n/ /g\' > findsymm2cif_php.tmp');
exec('grep "Number of atoms in unit cell:" '.$input.' -A1 | tail -n1  >> findsymm2cif_php.tmp');
exec('grep "Space Group" '.$input.' | awk \'{print $3}\'  >> findsymm2cif_php.tmp');
exec('grep "Origin at" '.$input.' | awk \'{print $3 "\t" $4 "\t" $5}\'  >> findsymm2cif_php.tmp');
exec('grep "Vectors a,b,c:" '.$input.' -A3 | tail -n3  >> findsymm2cif_php.tmp');
exec('grep "Values of a,b,c,alpha,beta,gamma:" '.$input.' -A1 | tail -n1  >> findsymm2cif_php.tmp');
exec('grep "Wyckoff" '.$input.' -A1 -n | grep "^[0-9]\+-[0-9]"| sed "s:\(^[0-9]\+\)-[0-9]\+\(.*\):\1\t\2:gi" >> findsymm2cif_php.tmp');
 
if($input == "findsymm2cif_php2.tmp")
{
    $input = "php://stdin";
    //unlink("findsymm2cif_php2.tmp");
}
 
//exec("sh findsymm2cif.sh findsymm.out",$file);
 
$file = file("findsymm2cif_php.tmp");
$type_atoms = split("[ \t]+",trim($file[0]));
$specie_count = Array();
$k = 0;
$specie_count[$k] = 1;
for($i=1; $i < sizeof($type_atoms); $i++)
{
    if($type_atoms[$i] != $type_atoms[$i-1])
        $k++;
    $specie_count[$k]++;
}
for($i=1; $i<sizeof($specie_count); $i++)
    $specie_count[$i] += $specie_count[$i-1];
//print_r($specie_count);
 
 
 
$numatoms = trim($file[1]);
$sgno = trim($file[2]);
$origin_shift = split("[ \t]+",trim($file[3]));
$tr_x = split("[ \t]+",trim($file[4]));
$tr_y = split("[ \t]+",trim($file[5]));
$tr_z = split("[ \t]+",trim($file[6]));
$params = split("[ \t]+",trim($file[7]));
$specie = Array();
for($i = 8;$i<sizeof($file);$i++)
    $specie[] = split("[ \t]+",trim($file[$i]));
$totatoms = 0;
for($i = 0; $i < sizeof($specie)-1; $i++)
{
    $specie[$i][0] = $specie[$i+1][0] - $specie[$i][0] - 1;
    $totatoms += $specie[$i][0];
}
$specie[sizeof($specie)-1][0] = $numatoms - $totatoms;
//print_r($specie);
//print_r($specie_count);
$atoms_counted = 0;
for($i = 0; $i < sizeof($specie); $i++)
{
    # Going over atoms
    $atoms_counted += $specie[$i][0];
    for($j = 0; $j<sizeof($specie_count); $j++)
    {
        if($atoms_counted <= $specie_count[$j])
        {
            $specie[$i][0] = $species_type_template[$j];
            break;
        }
    }
}
//print_r($specie);
 
if($_GET["identical"])
{
    # Calculate the atom positions corresponding with the given POSCAR
    $trmatrix=Array();
    $trmatrix[0][0] = $tr_x[0];
    $trmatrix[0][1] = $tr_x[1];
    $trmatrix[0][2] = $tr_x[2];
    $trmatrix[1][0] = $tr_y[0];
    $trmatrix[1][1] = $tr_y[1];
    $trmatrix[1][2] = $tr_y[2];
    $trmatrix[2][0] = $tr_z[0];
    $trmatrix[2][1] = $tr_z[1];
    $trmatrix[2][2] = $tr_z[2];
 
    for($i=0;$i < sizeof($specie); $i++)
    {
        $x = $specie[$i][1];
        $y = $specie[$i][2];
        $z = $specie[$i][3];
 
        $xx = $x*$trmatrix[0][0] + $y*$trmatrix[1][0] + $z*$trmatrix[2][0];
        $yy = $x*$trmatrix[0][1] + $y*$trmatrix[1][1] + $z*$trmatrix[2][1];
        $zz = $x*$trmatrix[0][2] + $y*$trmatrix[1][2] + $z*$trmatrix[2][2];
 
        $xx += $origin_shift[0];
        $yy += $origin_shift[1];
        $zz += $origin_shift[2];
 
        $specie[$i][1] = $xx;
        $specie[$i][2] = $yy;
        $specie[$i][3] = $zz;
 
        for($j=1;$j<4;$j++)
        {
            while($specie[$i][$j]>=1.0)
                $specie[$i][$j]-=1.0;
            while($specie[$i][$j]<0.0)
                $specie[$i][$j]+=1.0;
        }
 
    }
}
 
$fp = fopen($outfile,"w");
fwrite($fp,"_cell_length_a"."\t".$params[0]."\n");
fwrite($fp,"_cell_length_b"."\t".$params[1]."\n");
fwrite($fp,"_cell_length_c"."\t".$params[2]."\n");
fwrite($fp,"_cell_angle_alpha"."\t".$params[3]."\n");
fwrite($fp,"_cell_angle_beta"."\t".$params[4]."\n");
fwrite($fp,"_cell_angle_gamma"."\t".$params[5]."\n");
fwrite($fp,"_symmetry_Int_Tables_number"."\t".$sgno."\n\n");
fwrite($fp, "loop_\n_atom_site_label\n_atom_site_type_symbol\n_atom_site_fract_x\n_atom_site_fract_y\n_atom_site_fract_z\n");
//print_r ($specie);
$k = 0;
$specie_type = $specie[0][0];
for($i=0;$i<sizeof($specie);$i++)
{
    if($specie[$i][0] == $specie_type)
        $k++;
    else
    {
        $k = 1;
        $specie_type = $specie[$i][0];
    }
    fwrite($fp, $specie[$i][0].sprintf("%02d",$k)."\t".$specie[$i][0]."\t".sprintf("%8.5f",$specie[$i][1])."\t".sprintf("%8.5f",$specie[$i][2])."\t".sprintf("%8.5f",$specie[$i][3])."\n");
}
fclose($fp);
?>

Some unit cell functions for Octave

admin — Sat, 23 May 2009 16:43:56 +0000

I’ve written some functions to aid in checking the transformations as well as switching between the parameter ↔ vector representations.

latpar2vec([a,b,c,alpha,beta,gamma])
Given the a,b,c,α,β and γ, the function calculates the lattice vectors

function f=latpar2vec(X)
% function f=latpar2vec([a,b,c,alpha,beta,gamma])
% Calculates the lattice vectors from the given lattice paramaters.
 
a     = X(1);
b     = X(2);
c     = X(3);
alpha = X(4);
beta  = X(5);
gamma = X(6);
 
% Converting the angles to radians:
alpha = d2r(alpha);
beta  = d2r(beta);
gamma = d2r(gamma);
 
%Aligning a with the x axis:
ax = a;
ay = 0;
az = 0;
 
%Orienting b to lie on the x-y plane:
bz = 0;
 
% Now we have 6 unknowns for 6 equations..
bx = b*cos(gamma);
by = (b**2-bx**2)**.5;
cx = c*cos(beta);
cy = (b*c*cos(alpha)-bx*cx)/by;
cz = (c**2-cx**2-cy**2)**.5;
f=[ax ay az
   bx by bz
   cx cy cz];
endfunction

latvec2par([ax ay az; bx by bz; cx cy cz])
Calculates the lattice parameters a,b,c,α,β and γ from the lattice vectors

function f=latvec2par(x)
% function f=latvec2par(x)
%     ax ay az
% x = bx by bz
%     cx cy cz
%
% takes the unit cell vectors and calculates the lattice parameters
% Emre S. Tasci    03/10/08
 
av = x(1,:);
bv = x(2,:);
cv = x(3,:);
 
a = norm(av);
b = norm(bv);
c = norm(cv);
 
alpha = acos((bv*cv')/(b*c))*180/pi;
beta  = acos((av*cv')/(a*c))*180/pi;
gamma = acos((av*bv')/(a*b))*180/pi;
 
f = [a b c alpha beta gamma];
endfunction

volcell([a,b,c,A,B,G])
Calculates the volume of the cell from the given lattice parameters, which is the determinant of the matrice build from the lattice vectors.

function f=volcell(X)
% function f=volcell([a,b,c,A,B,G])
% Calculate the cell volume from lattice parameters
%
% Emre S. Tasci, 09/2008
a=X(1);
b=X(2);
c=X(3);
A=X(4); % alpha
B=X(5); % beta
G=X(6); % gamma
 f=a*b*c*(1-cos(d2r(A))^2-cos(d2r(B))^2-cos(d2r(G))^2+2*cos(d2r(A))*cos(d2r(B))*cos(d2r(G)))^.5;
endfunction

Why’s there no “volcell” function for the unit cell vectors? You’re joking, right? (det(vector)) !

Example

octave:13> % Define the unit cell for PtSn4 :
octave:13> A = latpar2vec([ 6.41900 11.35700  6.38800  90.0000  90.0000  90.0000 ])
A =
 
    6.41900    0.00000    0.00000
    0.00000   11.35700    0.00000
    0.00000    0.00000    6.38800
 
octave:14> % Cell volume :
octave:14> Apar = [ 6.41900 11.35700  6.38800  90.0000  90.0000  90.0000 ]
Apar =
 
    6.4190   11.3570    6.3880   90.0000   90.0000   90.0000
 
octave:15> % Define the unit cell for PtSn4 :
octave:15> Apar=[ 6.41900 11.35700  6.38800  90.0000  90.0000  90.0000 ]
Apar =
 
    6.4190   11.3570    6.3880   90.0000   90.0000   90.0000
 
octave:16> % Cell volume :
octave:16> Avol = volcell (Apar)
Avol =  465.69
 
octave:17> % Calculate the lattice vectors :
octave:17> A = latpar2vec (Apar)
A =
 
    6.41900    0.00000    0.00000
    0.00000   11.35700    0.00000
    0.00000    0.00000    6.38800
 
octave:18> % Verify the volume :
octave:18> det(A)
ans =  465.69
 
octave:19> % Define the transformation matrix :
octave:19> R = [ 0 0 -1 ; -1 0 0 ; .5 .5 0]
R =
 
   0.00000   0.00000  -1.00000
  -1.00000   0.00000   0.00000
   0.50000   0.50000   0.00000
 
octave:21> % The reduced unit cell volume will be half of the original one as is evident from :
octave:21> det(R)
ans =  0.50000
 
octave:22> % Do the transformation :
octave:22> N = R*A
N =
 
  -0.00000  -0.00000  -6.38800
  -6.41900   0.00000   0.00000
   3.20950   5.67850   0.00000
 
octave:23> % The reduced cell parameters :
octave:23> Npar = latvec2par (N)
Npar =
 
     6.3880     6.4190     6.5227   119.4752    90.0000    90.0000
 
octave:24> % And the volume :
octave:24> det(N), volcell (Npar)
ans =  232.84
ans =  232.84

POSCAR2Cif

admin — Sat, 23 May 2009 16:26:12 +0000

Converts POSCAR files to CIF format. Uses Octave (latvec2par) to convert the unit cell vectors to lattice cell parameters. It is assumed (compulsory) that the atom coordinates in the POSCAR file are in fractional (direct) coordinates.

Parameters

f         : input file  (Default = POSCAR)
o         : output file (Default = <inputfilename>.cif)
t         : if set (t=1), then the output is written to the screen
speclist  : Define the name of the species, seperated by 'xx' or ',' to be used
            with neighbour listing (Default = AxxBxxCxx...)
            (Labels can also be seperated via [space] as long as speclist is given
            in quotation -- Example: ... speclist=\"Au Si\" )

Example

sururi@husniya OUTCARs_final_structures $ cat POSCAR_Pd3S
Pd3S
   1.00000000000000
     4.7454403619558345    0.0098182468538853    0.0000000000000000
    -1.4895902658503473    4.5055989020479856    0.0000000000000000
     0.0000000000000000    0.0000000000000000    7.2191545483192190
   6   2
Direct
  0.1330548697855782  0.5102695954022698  0.2500000000000000
  0.4897304045977232  0.8669451452144267  0.7500000000000000
  0.5128136657304309  0.1302873334247993  0.2500000000000000
  0.8697126665752007  0.4871863042695738  0.7500000000000000
  0.0013210250693640  0.9986789749306360  0.0000000000000000
  0.0013210250693640  0.9986789749306360  0.5000000000000000
  0.6856021298170862  0.6825558526447357  0.2500000000000000
  0.3174442073552622  0.3143978111829124  0.7500000000000000

sururi@husniya OUTCARs_final_structures $ php POSCAR2CIF.php f=POSCAR_Pd3S t=1 speclist=Pd,S
data_
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
_cell_length_a  4.745451
_cell_length_b  4.745451
_cell_length_c  7.219155
_cell_angle_alpha       90.000000
_cell_angle_beta        90.000000
_cell_angle_gamma       108.175792
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Pd01    Pd        0.1330548697855782  0.5102695954022698  0.2500000000000000
Pd02    Pd        0.4897304045977232  0.8669451452144267  0.7500000000000000
Pd03    Pd        0.5128136657304309  0.1302873334247993  0.2500000000000000
Pd04    Pd        0.8697126665752007  0.4871863042695738  0.7500000000000000
Pd05    Pd        0.0013210250693640  0.9986789749306360  0.0000000000000000
Pd06    Pd        0.0013210250693640  0.9986789749306360  0.5000000000000000
S01     S         0.6856021298170862  0.6825558526447357  0.2500000000000000
S02     S         0.3174442073552622  0.3143978111829124  0.7500000000000000

Code

#!/usr/bin/php

/* Emre S. Tasci                     *
 * Script name: POSCAR2CIF.php                           *
 * Converts the specified POSCAR file to CIF format      *
 * Uses octave to convert the unit cell vectors          *
 * to lattice parameters.                                *
 *                                              23/05/09 */
 
 
//require("/code/toolbox/commandline.inc.php"); # Equivalent handling of $_GET / $_POST
# ============/code/toolbox/commandline.inc.php========================================
// Enables the same treat for command line parameters
// as those of GET parameters.
// Also sets the $first, $last ranges including the gall parameter
 
//Support for command line variable passing:
for($i=1;$i<sizeof($_SERVER["argv"]);$i++)
{
	list($var0,$val0) = explode("=",$_SERVER["argv"][$i]);
	$_GET[$var0] = $val0;
}
 
$first = -2; //disabled by default
$last  = -3;
 
if($_GET["gfirst"]) $first = $_GET["gfirst"];
if($_GET["glast"] ) $last  = $_GET["glast"];
if($_GET["gall"] ) {$first = $_GET["gall"]; $last = $first;}
# ============/code/toolbox/commandline.inc.php========================================
 
 
if($_GET["h"]||$_GET["help"])
{
$help = <<                    *
 *                                              23/05/09 *
 
 Usage:
 f         : input file  (Default = POSCAR)
 o         : output file (Default = .cif)
 t         : if set (t=1), then the output is written to the screen
 speclist  : Define the name of the species, seperated by 'xx' or ',' to be used
             with neighbour listing (Default = AxxBxxCxx...)
             (Labels can also be seperated via [space] as long as speclist is given
             in quotation -- Example: ... speclist=\"Au Si\" )
 
 Example : php POSCAR2CIF.php f=POSCAR_RhBi4 speclist=Bi,Rh
lol;
 echo $help."\n";
 exit;
}
 
 
if($_GET["file"])$inputfile = $_GET["file"];
else if($_GET["f"])$inputfile = $_GET["f"];
else $inputfile="POSCAR";
 
$outfile = $inputfile.".cif";
if($_GET["o"]) $outfile=$_GET["o"];
if($_GET["t"]) $outfile = "php://stdout";
 
$species_type_template = Array("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z");
if($_GET["speclist"])$species_type_template = split("xx| |,",$_GET["speclist"]);
 
//echo sizeof($_GET["speclist"])."\n";
exec('sed -n "3,6p" '.$inputfile.'|awk \'{print $1"\t"$2"\t"$3}\'',$out);
$octfp = fopen("octrungetvolnpar.m","w");
 
fwrite($octfp,"kini=[\n");
for ($i=0;$i<3;$i++)
    fwrite($octfp,$out[$i]."\n");
fwrite($octfp,"];\n\n");
 
fwrite($octfp,"numatom = [".$out[3]."];\n\n");
$numatoms = split("[ \t]+",trim($out[3]));
 
// Write the octave operations
fwrite($octfp,"k1 = latvec2par (kini);totatom=sum(numatom );\n");
fwrite($octfp,"for i=1:6;printf(\"%f\\n\",k1(i));endfor;\nprintf(\"%d\\n\",totatom)\n");
 
fclose($octfp);
 
// Execute the octave file to find the lattice parameters and volume
exec('octave -q '.$thisdir.'octrungetvolnpar.m',$out3);
unlink("octrungetvolnpar.m");
//echo $out3[0]."\n";
 
/*
for ($i=0;$i
 
exec('grep "Direct" '.$inputfile.' -n|sed "s:^\([0-9]\+\).*:\1:"',$start);# Line number of the Direct prompt
$start = $start[0];
$start++;
$finish = $start+$out3[sizeof($out3)-1]-1;
exec('sed -n "'.$start.','.$finish.'p" '.$inputfile,$outr);
$fpo = fopen($outfile, "w");
fwrite($fpo, "data_\nloop_\n_symmetry_equiv_pos_as_xyz\nx,y,z\n");
fwrite($fpo, "_cell_length_a\t".$out3[0]."\n");
//echo $out3[0];
fwrite($fpo, "_cell_length_b\t".$out3[1]."\n");
fwrite($fpo, "_cell_length_c\t".$out3[2]."\n");
fwrite($fpo, "_cell_angle_alpha\t".$out3[3]."\n");
fwrite($fpo, "_cell_angle_beta\t".$out3[4]."\n");
fwrite($fpo, "_cell_angle_gamma\t".$out3[5]."\n");
fwrite($fpo, "loop_\n_atom_site_label\n_atom_site_type_symbol\n_atom_site_fract_x\n_atom_site_fract_y\n_atom_site_fract_z\n");
$k = 0;
for($specie=0;$specie<sizeof($numatoms);$specie++)
    for($i=1;$i<=$numatoms[$specie];$i++)
    {
        fwrite($fpo, $species_type_template[$specie].sprintf("%02d",$i)."\t".$species_type_template[$specie]."\t".$outr[$k]."\n");
        $k++;
    }
 
 
fclose($fpo);
?>

POSCAR2findsymm

admin — Tue, 24 Mar 2009 09:17:37 +0000

A very simple code I wrote while studying the Python language that fetches the information from a VASP POSCAR file and prepares (and feeds) the input for Harold Stokes’ findsym (you should actually download the executable included in the ISOTROPY package instead of the referred web version) program to find the unit cell symmetry.

#!/usr/bin/python
# -*- coding: utf-8 -*-
 
"""
POSCAR2findsym.py
/* Emre S. Tasci                     *
   A simple python code that parses the POSCAR file,
   prepares an input file for Harold Stokes' findsym
   (http://stokes.byu.edu/isotropy.html)
   executable.
 
   Then, checks the current system to see if findsym is
   accessible: if it is, then feeds the prepared file 
   and directly outputs the result; if findsym is not 
   executable then outputs the generated input file.
 
   If you are interested only in the results section of 
   the findsymm output, you should append "| grep "\-\-\-\-\-\-" -A1000"
   to the execution of this code.
 
   Accepts alternative POSCAR filename for argument
   (default = POSCAR)
 
   If a second argument is proposed then acts as if
   findsym is not accessible (ie, prints out the input
   file instead of feeding it to findsymm)
 
                                             10/03/09 */
"""
 
 
import sys
import re
from numpy import *
from os import popen
import commands
 
force_output = False
 
if len(sys.argv)<2:
    filename="POSCAR"
elif len(sys.argv)<3:
    filename=sys.argv[1]
else:
    filename=sys.argv[1]
    force_output = True
 
 
f = open(filename,'r')
 
title = f.readline().strip()
tolerance = 0.00001
latt_vec_type = 1 # We will be specifying in vectors
 
f.readline() # Read Dummy
lat_vec = array([])
for i in range(0,3):
    lat_vec = append(lat_vec,f.readline().strip())
 
 
# Read atom species
species_count = f.readline()
species_count = re.split('[\ ]+', species_count.strip())
species_count = map(int,species_count)
number_of_species = len(species_count)
total_atoms = sum(species_count)
 
initial_guess = "P" # For the centering
 
species_designation = array([])
for i in range(1,number_of_species+1):
    for j in range(0,species_count[i-1]):
        species_designation = append(species_designation,i)
 
species_designation = map(str,map(int,species_designation))
# print species_designation
sep = " "
# print sep.join(species_designation)
 
# Read Coordinates
f.readline() # Read Dummy
pos_vec = array([])
for i in range(0,total_atoms):
    pos_vec = append(pos_vec,f.readline().strip())
 
# print pos_vec
 
findsym_input = array([])
findsym_input = append(findsym_input, title)
findsym_input = append(findsym_input, tolerance)
findsym_input = append(findsym_input, latt_vec_type)
findsym_input = append(findsym_input, lat_vec)
findsym_input = append(findsym_input, 2)
findsym_input = append(findsym_input, initial_guess)
findsym_input = append(findsym_input, total_atoms)
findsym_input = append(findsym_input, species_designation)
findsym_input = append(findsym_input, pos_vec)
# print findsym_input
sep = "\n"
findsym_input_txt = sep.join(findsym_input)
# print findsym_input_txt
 
# Check if findsym is accessible:
status,output =  commands.getstatusoutput("echo \"\n\n\"|findsym ")
if(output.find("command not found")!=-1 or force_output):
    # if it is not there, then just output the input
    print findsym_input_txt
elif(status==6144):
    # feed it to findsym
    pipe = popen("echo \""+findsym_input_txt+"\" | findsym").readlines()
    for line in pipe:
        print line.strip()
quit()

Example Usage:

sururi@husniya POSCAR2findsym $ cat POSCAR
Si(S)-Au(Pd) -- Pd3S
   1.00000000000000
     4.7454403619558345    0.0098182468538853    0.0000000000000000
    -1.4895902658503473    4.5055989020479856    0.0000000000000000
     0.0000000000000000    0.0000000000000000    7.2191545483192190
   6   2
Direct
  0.1330548697855782  0.5102695954022698  0.2500000000000000
  0.4897304045977232  0.8669451452144267  0.7500000000000000
  0.5128136657304309  0.1302873334247993  0.2500000000000000
  0.8697126665752007  0.4871863042695738  0.7500000000000000
  0.0013210250693640  0.9986789749306360  0.0000000000000000
  0.0013210250693640  0.9986789749306360  0.5000000000000000
  0.6856021298170862  0.6825558526447357  0.2500000000000000
  0.3174442073552622  0.3143978111829124  0.7500000000000000

sururi@husniya POSCAR2findsym $ python POSCAR2findsym.py
FINDSYM, Version 3.2.3, August 2007
Written by Harold T. Stokes and Dorian M. Hatch
Brigham Young University
 
Si(S)-Au(Pd) -- Pd3S
Tolerance:    0.00001
Lattice vectors in cartesian coordinates:
4.74544   0.00982   0.00000
-1.48959   4.50560   0.00000
0.00000   0.00000   7.21915
Lattice parameters, a,b,c,alpha,beta,gamma:
4.74545   4.74545   7.21915  90.00000  90.00000 108.17579
Centering: P
Number of atoms in unit cell:
8
Type of each atom:
1  1  1  1  1  1  2  2
Position of each atom (dimensionless coordinates)
1   0.13305   0.51027   0.25000
2   0.48973   0.86695   0.75000
3   0.51281   0.13029   0.25000
4   0.86971   0.48719   0.75000
5   0.00132   0.99868   0.00000
6   0.00132   0.99868   0.50000
7   0.68560   0.68256   0.25000
8   0.31744   0.31440   0.75000
------------------------------------------
Space Group  40  C2v-16    Ama2
Origin at    0.00000   0.00000   0.50000
Vectors a,b,c:
0.00000   0.00000   1.00000
-1.00000  -1.00000   0.00000
1.00000  -1.00000   0.00000
Values of a,b,c,alpha,beta,gamma:
7.21915   5.56683   7.68685  90.00000  90.00000  90.00000
Atomic positions in terms of a,b,c:
Wyckoff position b, y = -0.17834, z =  0.31139
1   0.75000   0.17834   0.31139
2   0.25000   0.82166   0.31139
Wyckoff position b, y =  0.32155, z =  0.19126
3   0.75000   0.17845   0.69126
4   0.25000   0.82155   0.69126
Wyckoff position a, z =  0.00132
5   0.50000   0.00000   0.00132
6   0.00000   0.00000   0.00132
Wyckoff position b, y = -0.31592, z =  0.00152
7   0.75000   0.81592   0.50152
8   0.25000   0.18408   0.50152

Update on the things about the scientific me since October..

admin — Mon, 23 Mar 2009 15:47:50 +0000

Now that I’ve started to once again updating this scientific blog of mine, let me also talk about the things that occured since the last entry on October (or even going before that).

Meeting with Dr. Villars
The biggest event that occured to me was meeting with Dr. Pierre Villars, the person behind the Pauling File database which I have benefitted and still benefitting from. When I had registered to the “MITS 2008 – International Symposium on Materials Database”, an event hosted by the NIMS Materials Database, I had no idea that Dr. Villars would also be attending to the event, so it was a real surprise learning afterwards that I’d have a chance to meet him in person.

You can read the sheer happiness from my face on the occasion of meeting Dr. Villars

Dr. Villars is a very kind and a cheerful person, I had a greatest time knowing him and afterwards I had the privilege of visiting him in his home office in the lovely town of Vitznau, Switzerland where I enjoyed the excellent hospitality of the Villars family. Dr. Villars helped me generously in providing the data in my research project for finding transformation toughening materials through datamining which I’m indebted for.

The MITS 2008 – Int’l Symposium on Materials Database
I was frequently using the databases on the NIMS’ website and had the honour to participate in the last year’s event together with my dear supervisor Dr. Marcel Sluiter. On that occasion, I presented two talks – a materials based one, and another about database query&retrieval methods- titled “Inference from Various Material Properties Using Mutual Information and Clustering Methods” and “Proposal of the XML Specification as a Standard for Materials Database Query and Result Retrieval”, respectively.

I have an ever growing interest on the Japanese Culture since I was a youngster and due to this interest, my expectations from this trip to Japan was high enough for me to be afraid of the fact that I may have disappointed since it was next-to-impossible for anything to fulfill the expectations I had built upon. But, amazingly, I was proved false: the experience I had in Japan were far more superior to anything I had anticipated. The hospitality of the organizing commitee was incredible: everything had been taken care of and everyone was as kind as one could be. I had the chance to meet Dr. Villars as I’ve already wrote about above, and also Dr. Xu, Dr. Vanderah, Dr. Dayal and Dr. Sims and had a great time. It was also due to this meeting, I met a dear friend.

Ongoing Projects
During my time here, I still don’t have anything published and that’s the number one issue that’s bothering me. Apart from my research on the transformation toughening materials, I worked for a time on a question regarding to a related phenomenon, namely about the martensitic transformation mechanism on some transition-metal alloy types. We were able to come up with a nice equation and adequate coefficients that caught the calculation results but couldn’t manage to transfer it to -so to say- a nicely put theory and that doomed the research to being an “ad-hoc” approach. I’ll be returning to it at the first chance I get, so currently, it’s been put on ice (and now remembering how, in the heat of the research I was afraid that someone else would come up with the formula and it would be too late for me.. sad, so sad..). One other (side) project was related to approximate a specific amorphous state in regards with some basis structures obtained using datamining. This project was really exciting and fun to work on because I got to use different methods together: first some datamining, then DFT calculations on the obtained structures and finally thermodynamics to extrapolate to higher temperatures. We’re at the stage of revising the draft at the moment (gratefully!).

Life in the Netherlands & at the TUDelft
It has been almost one and a half year since I started my postdoc here in TUDelft. When we first came here, my daughter was still hadn’t started speaking (yet she had been practicing walking) and now she approximately spent the same amount of time in the Netherlands as she had spent in Turkey (and thankfully, she can speak and also running to everywhere! 8).

When I had come here, I was a nano-physicist, experienced in MD simulations and -independently- a coder when the need arouse. Now, I’m more of a materials guy and coding for the purpose.. I enjoy the wide variety of the jobs & disciplines people around me are working on and definitely benefitting from the works of my friends in our group. I couldn’t ask for more, really. (OK, maybe I’d agree if somebody would come up with an idea for less windy and more sunny weather here in Delft. That’s the one thing I couldn’t still get used to. Delft is a marvelous city with bikes and kind people everywhere, canals full of lillies in the spring, historical buildings everywhere, Amsterdam, Den Haag and Rotterdam just a couple of train stations away and if you wish, Antwerpen, Brussels and Brugges (Belgium) is your next-door neighbour but this dark and closed weather can sometimes be a little mood lowering.) TUDelft is really a wonderful place to be with all the resources and connections that makes you feel you can learn anything and meet anyone that is relevant to the work you’re doing without worrying about the cost. And you’re being kept informed about the events taking place about you through the frequent meetings in your group, in your section, in your department, in your field. I’ve learned a lot and I’m really happy I was accepted here.

(And just when you think I was out of photos!..

So that’s about the things I’ve enjoyed experiencing and living through.. And I promise, I’ll be posting more regularly and frequently from now on..

Yours the chatty.

LaTeX to PNG and all that equations..

admin — Mon, 23 Mar 2009 14:32:29 +0000

After migrating this blog to a new server, I had some difficulties in writing up the equations. It was due to the fact that on this server, I wasn’t able to execute the necessary commands to parse the latex code and convert it to PNG format.

Last week, some need arouse for this and I finally coded the necessary way around to be able to convert LaTeX definitions to their PNG counterparts. Before I start to quote the necessary code and explanations, let me tell that, this method only will work if you can successfully manage to produce this conversation at your -local- computer since what the code does is to generate the image on your local computer and then copy it to the server where your blog (/or whatever you have) resides. So, make sure:

You can convert LaTeX code to PNG on your -own- computer.
You are running a httpd server so that the code can copy the output PNG file from your local computer

What the code does:
It has 3 seperate processes. Let’s designate them A, B & C.

Part A is called on the remote server. It presents a form with textbox in it where you can type the LaTeX code. The form’s target is the same file but this time on your local server, so when you submit the data —
Part B is called on your local server. Using the texvc code, an open source software that also comes packed with mediawiki, it converts the LaTeX code into a PNG image and places it under the relative math/ directory of your local server. After doing this, via the META tag ‘refresh’ it causes the page to refresh itself loading its correspondence in the remote server, hence initiating –
Part C where the generated image identified by the MD5 hashname is fetched from the local server and copied unto the relative math/ directory on the remote server. The LaTeX code that was used is also passed in the GET method and it is included in the generated code as the title of the image, so if necessary, the equation can be modified in the future.

The code is as follows:

 if($_GET["com"]||(!$_POST["formula"] && !$_GET["file"])){?>






}
if($_POST["formula"])
{
    // NL
    $lol = './texvc  ./mathtemp ./math "'.$_POST["formula"].'" iso-8859-1';
    exec($lol,$out);
    $file = substr($out[0],1,32);
    $formula = base64_encode($_POST["formula"]);
    $html = '

.$formula.'&file='.$file.'">
';
    echo $html;
}
else if($_GET["file"])
{
    // COM
    $file = "math/".$_GET["file"].".png";
    if(!copy("yourlocalserver.dns.name/tex/".$file, $file)) exit( "copy failed
");
    $formula = base64_decode($_GET["formula"]);
?>

<span style="color: #000000; font-weight: bold;"><?PHP</span> <span style="color: #b1b100;">echo</span> <span style="color: #000088;">$formula</span><span style="color: #339933;">;</span> <span style="color: #000000; font-weight: bold;">?></span>




 
    echo "

\"".$file."\" title=\"".$formula."\">
";
    echo "<img src=\"/tex/".$file."\" title=\"".$formula."\">
";
}
?>

To apply this:

1. Create a directory called ‘tex’ on both servers.
2. Create subdir ‘math’ on both servers
3. Create subdir ‘mathtemp’ on the local server
4. Modify the permissions of these subdirs accordingly
5. Place the executable ‘texvc’ in the ‘tex’ directory
6. Place the code quoted above in the ‘tex’ directories of both servers in a file called ‘index.php’

If everything well up to this point, let’s give it a try and you shall have some output similar to this:

For an input LaTeX code of:
\sum_{n=0}^\infty\frac{x^n}{2n!}

where you can immediately see the resulting image, modify the code if there’s something wrong or copy the IMG tag and put it to your raw HTML input box in your text…

Two bash scripts for VASP

admin — Mon, 20 Oct 2008 12:56:20 +0000

It’s of great importance to have sufficient number of k-points when doing DFT calculations. The most practical (but CPU time costly) way is to check energies for different number of k-points until some kind of "convergence" is reached.

Here are the two scripts I’ve recently written for VASP to check for suitable k-point values.

The first code runs the calculation with increasing k-points (I have a cubic cell, so using same number of k-points for the 3 lattice axes).

Before running this code, make sure that the essential files (KPOINTS POSCAR POTCAR INCAR) are in the directory, also copy your KPOINTS file to a file named "KP" which has KPOINTS mesh defined as 2×2x2:

sururi@husniya Al3Li $ cat KP
Automatic
0
Gamma
2 2 2
0 0 0

The following script will then run the calculations, incrementing the number of K-Points by 1 per each axis. It will store the output (and the 4 input files) in archive files in the format k{%03d}.tar.bz2 where the value in the curly brackets is actually the number of k-points per axis. As you can easily see, it runs from k= 1×1x1 (silly but since this is tutorial) to k=13×13x13.

#!/bin/bash
 
# A script file to run the system for various k-points in order to find the optimal setting
# Emre S. Tasci, 20/10/2008
 
for (( i = 1; i <= 13; i++ )) 
do  
    date
    echo $i
 
    # change the KPOINTS (KP is a copy of the KPOINTS with k=2:
    cat KP|sed s/"2 2 2"/"$i $i $i"/ > KPOINTS
 
    # run the vasp
    vasp > vasp.out
 
    # archive the existing files (except the archive files):
    tar -cvjf $(printf "k%02d.tar.bz2" $i) $(ls |grep -v "\(.bz2\)\|\(runrunrun.sh\)\|\(KP$\)\|\(work\)")
 
    # remove the output files:
    rm $(ls *|grep -v "\(.bz2\)\|\(KPOINTS\)\|\(POSCAR\)\|\(POTCAR\)\|\(INCAR\)\|\(runrunrun.sh\)\|\(KP$\)") -f
    date
    echo "=================================================="
done

After it ends, you should see something like

-rw-r----- 1 sururi users 299K 2008-10-20 10:14 POTCAR
-rw-r--r-- 1 sururi users  283 2008-10-20 10:14 POSCAR
-rw-r--r-- 1 sururi users  604 2008-10-20 10:14 INCAR
-rw-r--r-- 1 sururi users   31 2008-10-20 11:06 KP
-rw-r--r-- 1 sururi users   34 2008-10-20 14:33 KPOINTS
-rw-r--r-- 1 sururi users 195K 2008-10-20 11:08 k01.tar.bz2
-rw-r--r-- 1 sururi users 196K 2008-10-20 11:08 k02.tar.bz2
-rw-r--r-- 1 sururi users 193K 2008-10-20 11:08 k03.tar.bz2
-rw-r--r-- 1 sururi users 195K 2008-10-20 11:08 k04.tar.bz2
-rw-r--r-- 1 sururi users 195K 2008-10-20 11:08 k05.tar.bz2
-rw-r--r-- 1 sururi users 197K 2008-10-20 11:09 k06.tar.bz2
-rw-r--r-- 1 sururi users 197K 2008-10-20 11:09 k07.tar.bz2
-rw-r--r-- 1 sururi users 200K 2008-10-20 11:10 k08.tar.bz2
-rw-r--r-- 1 sururi users 201K 2008-10-20 11:10 k09.tar.bz2
-rw-r--r-- 1 sururi users 205K 2008-10-20 11:11 k10.tar.bz2
-rw-r--r-- 1 sururi users 205K 2008-10-20 11:12 k11.tar.bz2
-rw-r--r-- 1 sururi users 211K 2008-10-20 11:13 k12.tar.bz2
-rw-r--r-- 1 sururi users 211K 2008-10-20 11:14 k13.tar.bz2
-rwxr--r-- 1 sururi users  732 2008-10-20 14:02 runrunrun.sh

Now, it’s time for the second script. Create a new directory (say “work”) and then type the following into a script file (don’t forget to set it as executable (or you can also always “sh ” ) )

#!/bin/bash
 
# Script name: energy_extract_from_OUTCAR.sh
# Emre S. Tasci, 20/10/2008
 
# Reads the OUTCAR files from the archive files in the parent directory
# Stores the energies in corresponding ENE files.
 
# (Assuming filenames are given like "k05.tar.bz2")
 
k=00
 
for i in ../k*.bz2
do
    kpre=$k
    enepre="0.00000000"
 
    # Extract OUTCAR
    tar -xjf $i OUTCAR
 
    # Parse file counter from filename 
    k=$(echo $(basename $i)|sed "s:k\([0-9]*\).*:\1:")
 
    # write the energies calculated in this run 
    cat OUTCAR | grep "energy without"|awk '{print $8}' > $(printf "%s_ENE" $k)
 
    #calculate the energy difference between this and the last run
    if [ -e "$(printf "%s_ENE" $kpre)" ] 
    then
        enepre=$(tail -n1 $(printf "%s_ENE" $kpre));
    fi
 
    enethis=$(tail -n1 $(printf "%s_ENE" $k));
 
    # Using : awk '{ print ($1 >= 0) ? $1 : 0 - $1}' : for absolute value
 
    echo -e $(printf "%s_ENE" $kpre) " :\t" $enepre "\t" $(printf "%s_ENE" $k) ":\t" $enethis "\t" $(echo $(awk "BEGIN { print $enepre - $enethis}") | awk '{ print ($1 >= 0) ? $1 : 0 - $1}')
 
    rm -f OUTCAR
done;

when runned, this script will produce an output similar to the following:

sururi@husniya work $ ./energy_extract_from_OUTCAR.sh
00_ENE  :        0.00000000      01_ENE :        -6.63108952     6.63109
01_ENE  :        -6.63108952     02_ENE :        -11.59096452    4.95988
02_ENE  :        -11.59096452    03_ENE :        -12.96519853    1.37423
03_ENE  :        -12.96519853    04_ENE :        -13.20466179    0.239463
04_ENE  :        -13.20466179    05_ENE :        -13.26411934    0.0594576
05_ENE  :        -13.26411934    06_ENE :        -13.26528991    0.00117057
06_ENE  :        -13.26528991    07_ENE :        -13.40540825    0.140118
07_ENE  :        -13.40540825    08_ENE :        -13.35505746    0.0503508
08_ENE  :        -13.35505746    09_ENE :        -13.38130280    0.0262453
09_ENE  :        -13.38130280    10_ENE :        -13.36356457    0.0177382
10_ENE  :        -13.36356457    11_ENE :        -13.37065368    0.00708911
11_ENE  :        -13.37065368    12_ENE :        -13.37249683    0.00184315
12_ENE  :        -13.37249683    13_ENE :        -13.38342842    0.0109316

Which shows the final energies of the sequential runs as well as the difference of them. You can easily plot the energies in the gnuplot via as an example “plot “12_ENE”“. You can also plot the evolution of the energy difference with help from awk. To do this, make sure you first pipe the output of the script to a file (say “energies.txt”):

./energy_extract_from_OUTCAR.sh > energies.txt

And then, obtaining the last column via awk

cat energies.txt |awk '{print $7}' > enediff.txt

Now you can also easily plot the difference file.

Hope this scripts will be of any help.

Saddest article of all..

admin — Thu, 07 Aug 2008 11:17:25 +0000

Still saddened by the loss of Randy Pausch whom I knew about from his famous "Last Lecture", while working on the Miedema’s Model, I came across this article by him:

Dr. Villars had already mentioned Miedema’s passing at a young age but still it was really tragic to find such a sad detail on a scientific article.

I checked the web for a Miedema biography but couldn’t find any. The only information I could find was from H. Bakker’s book which I’m quoting the preface below:

PREFACE

Andries Miedema started developing his rather unconventional model in the sixties as a professor at the University of Amsterdam and continued this work from 1971 at Philips Research Laboratories. At first he encountered scepticism in these environments, where scientists were expecting all solutions from quantum- mechanics. Of course, Miedema did not deny that eventually quantum mechanics could produce (almost) exact solutions of problems in solid-state physics and materials science, but the all-day reality he experienced was, – and still is -, that most practical problems that are encountered by researchers are too complex to allow a solution by application of the Schr6dinger equation. Besides, he believed in simplicity of nature in that sense that elements could be characterised by only a few fundamental quantities, whereby it should be possible to describe alloying behaviour. On the basis of a comparison of his estimates of the heat of formation of intermetallic compounds with ample experimental data, he was gradually able to overcome the scepticism of his colleagues and succeeded in convincing the scientific world that his model made sense. This recognition became distinct by the award of the Hewlett Packard prize in 1980 and the Hume-Rothery decoration in 1981. At that time, Miedema himself and many others were successfully using and extending the model to various questions, of course realising that the numbers obtained by the model have the character of estimates, but estimates that could not be obtained in a different fast way. It opened new perspectives in materials science. Maybe the power of the model is best illustrated by a discussion, the present author had with Jim Davenport at Brookhaven National Laboratory in 1987. Dr Davenport showed him a result that was obtained by a one-month run on a Gray 1 supercomputer. This numerical result turned out to be only a few kilo Joules different from the outcome by Miedema’s model, obtained within a few minutes by use of a pocket calculator. Andries Miedema passed away in 1992 at a much too young age of 59 years. His death came as a bad shock not only for the scientific community in The Netherlands, but for scientists all over the world. However, for his family, friends and all the people, who knew him well, it is at least some consolation that he lives on by his model, which is being used widely and which is now part of many student programmes in physics, chemistry and materials science.

It is the aim of the present review to make the reader familiar with the application of the model, rather than to go in-depth into the details of the underlying concepts. After studying the text, the reader should be able, with the aid of a number of tables from Miedema’s papers and his book, given in the appendix, to make estimates of desired quantities and maybe even to extend the model to problems that, so far, were not handled by others. Beside, the reader should be aware of the fact that not all applications could be given in this review. For obvious reasons only part of all existing applications are reported and the reader will find further results of using the model in Miedema’s and co-worker’s papers, book and in literature.

Dr Hans Bakker is an associate professor at the Van der Waals-Zeeman Institute of the University of Amsterdam. In 1970 Andries Miedema was the second supervisor of his thesis on tracer diffusion. He inspired him to subsequent work on diffusion and defects in VIII-IIIA compounds at a time, when, – as Bakker’s talk was recently introduced at a conference -, these materials were not yet relevant’ as they are now. Was it again a foreseeing view of Andries Miedema? Was it not Miedema’s standpoint that intermetallic compounds would become important in the future?

Rather sceptic about the model as Bakker was at first like his colleagues, his scepticism passed into enthusiasm, when he began using the model with success in many research problems. In 1984 Bakker’s group started as one of the first in the world ball milling experiments. Surprisingly this seemingly crude technique turned out to be able to induce well-defined, non-equilibrium states and transformations in solids. Miedema’s model appeared again to be very helpful in understanding and predicting those phenomena.

Hans Bakker
Mauro Magini

Preface from Enthalpies in Alloys : Miedema’s Semi-Emprical Model
H. Bakker
Trans Tech Publications 1998 USA
ISSN 1422-3597

Miedema et al.’s Enthalpy code — 25 years after..

admin — Mon, 28 Jul 2008 13:34:28 +0000

Yes, it’s been 25 years since A.K. Niessen, A.R. Miedema et al.’s "Model Predictions for the Enthalpy of Formation of Transition Metal Alloys II" titled article (CALPHAD 7(1) 51-70 1983) was published. It can be thought as a sequel to Miedema et al.’s 1979 (Calphad 1 341-359 1979) and 1980 dated (Physica 100 1-28 1980) papers with some update on the data as well as a computer code to calculate the enthalpies of formation written in ALGOL.

I have been currently working on these papers and by the way ported the code presented in CALPHAD 1983 to FORTRAN and here it is:

C      THE IMPLEMENTATION OF THE ALGOL CODE FROM
C      A.K. Niessen, F.R. de Boer, R. Boom, P.F. de Chatel
C      W.C.M. Mattens and A.R. Miedema
C      CALPHAD Vol.7 No.1 pp. 51-70, 1983
C      Model Predictions for the Enthalpy of Formation of Transition 
C        Metal Alloys II"
C
C      by Emre S. Tasci, TUDelft (2008)
 
      IMPLICIT DOUBLE PRECISION(A-H,N-Z)
C      DOUBLE PRECISION va,aa,p,r,x,dn,dg,ng,pq,xa,xm,csa,csm
C      DOUBLE PRECISION cas,cms,fam,dph,vm,am,fma,var,vmr
C      DOUBLE PRECISION vas, vms, xas, xms, xva,xvm, dgl,pqrs, pqrl
      INTEGER arrout, z1,z2,a,m,n,w,dh,ga,gm,gal,gml,nr,dHtrans
      LOGICAL detp, detr, bool
      CHARACTER(LEN=5) Symbol
      DIMENSION arrout(15)
      DIMENSION Phi(75), acf(75), dHtrans(75), Nws113(75), Rcf(75),
     + V213(75), xxx(9), Symbol(75)
      COMMON /CDH/ x, dh
      COMMON /CDPH/ dph, Phi, Nws113, ng, r, Rcf, p, pq, dn, pqrs, pqrl
 
      OPEN(UNIT=3,FILE='inpdata.txt',STATUS='OLD')
      DO I=1,75
        READ(3,*)nr,Symbol(nr),Phi(nr),Nws113(nr),V213(nr),
     +  acf(nr),Rcf(nr),dHtrans(nr)
C       WRITE(*,*)nr,Symbol(nr),Phi(nr),Nws113(nr),V213(nr),
C     + acf(nr),Rcf(nr),dHtrans(nr)
      END DO
      CLOSE(UNIT=3)
 
 
      xxx(1) = 0.001
      xxx(2) = 1.0/6.0
      xxx(3) = 1.0/4.0
      xxx(4) = 1.0/3.0
      xxx(5) = 1.0/2.0
      xxx(6) = 2.0/3.0
      xxx(7) = 3.0/4.0
      xxx(8) = 5.0/6.0
      xxx(9) = 0.999
 
      DO z1 = 1,46 
          WRITE(*,200)z1,Symbol(z1),Phi(z1),Nws113(z1)**3,
     +      V213(z1)**(3.0/2),dHtrans(z1)
200       FORMAT(I2," ",A5," Phi: ",F5.2,"V  Nws: ",F5.2,
     +     "d.u.  Vmole: "
     +     ,F5.2,"cm3  DeltaHtrans:",I3,"kJ/mole",/)
          WRITE(*,250)"M","AM5","AM3","AM2","AM",
     +     "MA2","MA3","MA5","AinM","AM","MinA"
250       FORMAT(A,"      ",9(A4,"  "),A4,/)
          DO z2 = 1, 75
             m = z2
             a = z1
             CALL PQRSL(a,m)
 
             va = V213(a)
             aa = acf(a)
             ga = dHtrans(a)
             gal = ga
 
             vm = V213(m)
             am = acf(m)
             gm = dHtrans(m)
 
             IF (m.EQ.67.OR.m.EQ.68) THEN
                 gml = 0
             ELSE
                 gml = gm
             END IF
 
             n = 1
 
             DO I = 1,9
              xa = xxx(I)
              IF(xa.EQ.0.001.OR.xa.EQ.0.999) THEN
                  bool = .TRUE.
              ELSE
                  bool = .FALSE.
              END IF
 
              xm = 1 - xa
              xva = xa * va
              xvm = xm * vm
 
              dgl = xa * gal + xm * gml
              dg = xa * ga + xm * gm
              csa = xva / (xva + xvm)
 
              csm = 1 - csa
              fam = csm * (1 + 8 * csa * csa * csm * csm)
              fma = fam * csa / csm
 
              var = va * (1 + aa * csm * dph)
              vmr = vm * (1 - am * csa * dph)
 
              vas = va * (1 + aa * fam * dph)
              vms = vm * (1 - am * fma * dph)
 
              xar = xa * var
              xas = xa * vas
              xmr = xm * vmr
              xms = xm * vms
 
              cas = xas / (xas+xms)
              cms = 1 - cas
              csa = xar / (xar + xmr)
              csm = 1 - csa
 
              fam = cms * (1 + 8 * cas * cas * cms * cms)
              fma = fam * cas / cms
 
              IF(bool) THEN
                  IF(n.EQ.1) THEN 
                      GOTO 292
                  ELSE
                      GOTO 392
                  END IF
              END IF
                  IF(xa.EQ.0.5) THEN
                      x = csm * xar * p * pqrl + dgl
                      CALL MAXI
                      arrout(n+5) = dh
                  END IF
                  x = fam * xas * p * pqrs + dg
                  CALL MAXI
                  arrout(n) = dh
                  arrout(11) = gml
                  GOTO 492
292               x = (csm * xar * p * pqrl + dgl) / xa
                  CALL MAXI
                  arrout(n) = dh
                  arrout(11) = gml
                  GOTO 492
392               x = (csm * xar * p * pqrl + dgl) / xm
                  CALL MAXI
                  arrout(n) = dh
                  arrout(12) = gal
492               n = n + 1
             END DO
C            DO J=1,15
C              WRITE(*,500) J, arrout(J)
C            END DO
             WRITE(*,600)Symbol(m),arrout(2),arrout(3),arrout(4),
     +        arrout(5),
     +        arrout(6),arrout(7),arrout(8),arrout(1),arrout(10),
     +        arrout(9)
             IF(Symbol(m).EQ."Ni".OR.Symbol(m).EQ."Pd".OR.Symbol(m).EQ.
     +       "Lu".OR.Symbol(m).EQ."Pt".OR.Symbol(m).EQ."Pu".OR.
     +       Symbol(m).EQ."Au".OR.Symbol(m).EQ."H".OR.Symbol(m).EQ.
     +       "Cs".OR.Symbol(m).EQ."Mg".OR.Symbol(m).EQ."Ba".OR.
     +       Symbol(m).EQ."Hg".OR.Symbol(m).EQ."Tl".OR.Symbol(m).EQ.
     +       "Pb".OR.Symbol(m).EQ."Bi")WRITE(*,*)""
          END DO
      WRITE(*,"(2A,/)")"-----------------------------------",
     + "----------------------------"
      END DO
 
C500   FORMAT("O[",I3,"] = ",I50)
600   FORMAT(A5,"  ",9(I4,"  "),I4)
 
 
      STOP
      END
 
 
      SUBROUTINE MAXI
      IMPLICIT DOUBLE PRECISION(A-H,N-Z)
      INTEGER dh
      COMMON /CDH/ x, dh
      IF(x.LT.-999.OR.x.GT.999) THEN
        dh = 999
      ELSE
        dh = NINT(x)
      END IF
C      WRITE(*,*)"x:",dh
      RETURN
      END
 
      SUBROUTINE PQRSL(a,b)
      IMPLICIT DOUBLE PRECISION(A-H,N-Z)
      INTEGER a,b
      LOGICAL detp,detr
      DIMENSION Phi(75), acf(75), dHtrans(75), Nws113(75), Rcf(75),
     + V213(75)
      COMMON /CDPH/ dph, Phi, Nws113, ng, r, Rcf, p, pq, dn, pqrs, pqrl
 
          dph = Phi(a) - Phi(b)
          dn = Nws113(a)-Nws113(b)
          ng = (1/Nws113(a) + 1/Nws113(b))/2
 
          IF (detr(a).EQV.detr(b)) THEN
              r = 0
          ELSE
              r = Rcf(a)*Rcf(b)
          END IF
 
          IF (detp(a).AND.detp(b)) THEN
              p = 1.15 * 12.35
C             BOTH TRUE
          ELSE IF (detp(a).EQV.detp(b)) THEN
              p = 12.35 / 1.15
C             BOTH FALSE
          ELSE
              p = 12.35
          END IF
          p = p / ng
          pq = -dph * dph + 9.4 * dn * dn
          pqrs = pq - r
          pqrl = pq - 0.73 * r
 
      RETURN
      END
 
 
      LOGICAL FUNCTION  detp(z)
      INTEGER z
      IF (z.LT.47.AND.(z.NE.23.AND.z.NE.31)) THEN
          detp = .true.
      ELSE
          detp = .false.
      END IF
      RETURN
      END
 
      LOGICAL FUNCTION  detr(z)
      INTEGER z
      IF (z.LT.47.OR.(z.GT.54.AND.z.LT.58)) THEN
          detr = .true.
      ELSE
          detr = .false.
      END IF
      RETURN
      END

Even though ALGOL doesn’t exist anymore, being a highly semantic language, it is still used in forms of pseudo-code to present algorithms and because of this reason, it didn’t take much to implement the code in FORTRAN. You can download the datafile from here. And also if you don’t want to run the code, here is the result file. And, as you can see, I haven’t trimmed or commented the code since I’ll feed it the updated values and move on forward, sorry for that!

Sub-groups of space groups

admin — Thu, 03 Jul 2008 13:06:41 +0000

ISOTROPY is a highly effective program written by the guru of applications of Group Theory on Phase Transitions, Harold T. Stokes (For those who are interested in the topic, I recommend his Introduction to Isotropy Subgroups and Displacive Phase Transitions titled paper(co-authored by Dorian M. Hatch) and Structures and phase transitions in perovskites – a group-theoretical approach paper (co-authored by Christopher J. Howard).

I’m pretty new and noobie in Group Theory – it was one of the subjects I found myself always running away. Anyway, I wanted to limit my search for some specific phase transition search in the database. Say, if an A-B binary has been reported in S1 and S2 structures, I didn’t want to go all the way looking for possible transition mechanisms if S1->S2 isn’t allowed by the group theory at all!

In the meantime, I’ve begun experimenting with the ISOTROPY program, yet I’m still at the very beginning. You can find detailed information and an online version in the related website, but to give an example, suppose we’d like to know about the subgroups of spacegroup 123 (P4/mmm). We enter the following commands:

VALUE PARENT 123
SHOW PARENT
SHOW SUBGROUP
SHOW LATTICE
DISPLAY ISOTROPY

and it displays a list of which a portion is presented below:

Parent     Lattice Subgroup   Lattice
123 P4/mmm q       123 P4/mmm q
123 P4/mmm q       47 Pmmm    o
123 P4/mmm q       83 P4/m    q
123 P4/mmm q       65 Cmmm    o-b
123 P4/mmm q       10 P2/m    m
123 P4/mmm q       12 C2/m    m-b
123 P4/mmm q       2 P-1      t
123 P4/mmm q       89 P422    q
123 P4/mmm q       111 P-42m q
123 P4/mmm q       99 P4mm    q
123 P4/mmm q       115 P-4m2 q
123 P4/mmm q       25 Pmm2    o
123 P4/mmm q       38 Amm2    o-b
123 P4/mmm q       6 Pm       m
123 P4/mmm q       123 P4/mmm q
123 P4/mmm q       127 P4/mbm q
123 P4/mmm q       127 P4/mbm q

You may have noticed that, there are some recurring lines – this is due to some other properties that we have not specifically selected for display, i.e., it would display lines only containing "123 P4/mmm" if we hadn’t specifically asked for subgroup and lattice information (in analogy with the degeneracies in QM).

I needed a table containing all the subgroups of each space-group but there were two problems:

1. As far as I know, ISOTROPY does not accept an input file where you can pass the commands you’ve prepared via a script/macro. So, I was afraid that I would type "VALUE PARENT 1 – DISPLAY ISOTROPY – VALUE PARENT 2 – DISPLAY ISOTROPY – …" (by the way, ISOTROPY has a clever interpreter so that you can just type the first letters of commands and parameters as long as they are not dubious).

2. Again, as far as I know, you can’t direct the output to a file, meaning you have to copy the output manually and paste into a file (x230 in my case).

Luckily, it turned out that:

1. You could not supply an input file, but you could instead, paste the contents of such an input file and ISOTROPY would process it line by line.

2. Stokes had included a very useful and helpful property that all the sessions was recorded automatically in the "iso.log" file.

So, all I had to do was

1. Write a script that would produce the query to retrieve the subgroups of all 230 space-groups.

2. Paste the outcome of this script to ISOTROPY.

3. Write another script that would parse the "iso.log" file and split these reported subgroups per spacegroup (and while I’m at it, remove the duplicate lines and order the subgroups).

Maybe you won’t believe me but I am also not happy to paste lines and lines of code to this blog’s entries. I will deal it soon but in the mean time, please bear with them a little longer.. Ath the moment, I will describe the process and will include them at the end.

* build the query via query_builder.php
* feed this query to ISOTROPY
* split the space groups from the "iso.log" via split_spacegroups.php
* run sortall.php which :
   * runs the sortkillduplines.php on each of these files
   * sorts again via the sort.pl wrt to the 4th col (space number of the subgroup)
   * removes the blank lines
* And that’s it..

Here comes the codes (php+perl)

query_builder.php:


 // Generates the query that will be "pasted" into the ISOTROPY prompt
 // The query will be stored in isotropy_query.txt
$fp = fopen("isotropy_query.txt","w");
 fwrite($fp,"PAGE 1000\nSHOW SUBGROUP\nSHOW LATTICE\nSHOW PARENT\n");
 for($i=1;$i<231;$i++)
     fwrite($fp,"VALUE PARENT $i\nDISPLAY ISOTROPY\n");
 fwrite($fp,"\n\n");
 fclose($fp);
 ?>

sortkillduplines:


// PERL sorts the mentioned file (via $_GET["file"]) and deletes duplicate lines
require("commandline.inc.php");
if($_GET["file"]) $file = $_GET["file"];
 else
 {
     $in = fopen(’php://stdin’, ‘r’);
     $fw = fopen("sortkilldup_tmp.tmp","w");
     while(!feof($in))
     {
         fwrite($fw, rtrim(fgets($in, 4096))."\n");
     }
     fclose($fw);
     $file = "sortkilldup_tmp.tmp";
 }
 if($_GET["seperator"])$f_seperator = TRUE;//Means that an extra seperator has been placed for this order purpose and is seperated from the text by the parameter defined with seperator=xxx.
if($_GET["n"]||$_GET["numeric"]||$_GET["num"])$f_numeric = TRUE; // If it is TRUE than it is assumed that the first word of each line is a number and will be sort accordingly.
 // Reference : http://www.stonehenge.com/merlyn/UnixReview/col06.html
if($f_numeric) $exec = exec("perl -e ‘print sort numerically <>;\nsub numerically { \$a <=> \$b; }’ ".$file." > sorttemp.txt");
 else $exec = exec("perl -e ‘print sort <>’ ".$file." > sorttemp.txt");
 $fi = file("sorttemp.txt");
 unlink("sorttemp.txt");
 $curlinecont = "wrwerwer";
 if(!$f_seperator)
 {
     for($i=0; $i<sizeof($fi); $i++)
     {
         $line = rtrim($fi[$i]);
         if($curlinecont!=$line)
         {
             echo $line."\n";
             $curlinecont = $line;
         }
     }
 }
 else
 {
     $frs = fopen("sorttemp2.txt","w"); // will capture the dup killed output in this file and resort it later.
     for($i=0; $i<sizeof($fi); $i++)
     {
         $lineorg = rtrim($fi[$i]);
         $linearr = explode($_GET["seperator"],$lineorg);
         if($curlinecont!=$linearr[0])
         {
             fwrite($frs, $linearr[1]."\n");
             $curlinecont = $linearr[0];
         }
     }
     fclose($frs);
     // resort the file 
     passthru("perl -e ‘print sort <>’ sorttemp2.txt");
     unlink("sorttemp2.txt");
 }
   // unlink("sortkilldup_tmp.tmp");
 ?>

split_spacegroups.php:


 // splits the isotropy.log file generated by the query : 
 //      PAGE 1000
 //      SHOW SUBGROUP
 //      SHOW LATTICE
 //      SHOW PARENT
 //      VALUE PARENT 1
 //      DISPLAY ISOTROPY
 //      …
 //      VALUE PARENT 230
 //      DISPLAY ISOTROPY
 // with respect to the parent groups
$file = fopen("iso.log", "r") or exit("Unable to open file!");
 //Output a line of the file until the end is reached
 $cur = 0;
 $fp = fopen("dummy.txt","w"); // we need to open a dummy file in order to include the fclose() in the iteration
 while(!feof($file))
 {
     // Read the line
     $line = fgets($file);
    // Check if it is a spacegroup information entry by looking at the first word
     // - if this word is a number, than process that line
     if(ereg("^([0-9]+)",$line,$num))
     {
         $num = $num[0];
         if($cur!=$num)
         {
             // We have a new space group, so create its file:
             fclose($fp); // First close the previous space group’s file
             $filename = sprintf("%03d",$num)."_sg.txt";
             $fp = fopen($filename,"w");
             $cur = $num; // Set the current check data to the sg number
         }
         fwrite($fp,$line);
     }
}
 fclose($file);
 unlink("dummy.txt");
?>

sortall.php:


 // sorts & kills dupes in all the spacegroup files
for($num=1;$num<231;$num++)
 {
     $filename = sprintf("%03d",$num)."_sg.txt";
     $exec = exec("php ../../toolbox/sortkillduplines.php file=".$filename." > temp");
     $exec = exec("./sort.pl temp > temp2");
     $exec = exec("perl -pi -e \"s/^\\n//\" < temp2 > ".$filename);
 }
 unlink("temp");
 unlink("temp2");
?>

or you can directly skip all these steps and download the generated spacegroup files from here.

Lattice values are given in Schoenflies Notation where it corresponds to (with Pearson notation):

T : triclinic (AP)
M : prmitive monoclinic (MP)
M-B : base-centered monoclinic (MC)
O : primitive orthorhombic (OP)
O-B : base-centered orthorhombic (OC)
O-V : body-centered orthorhombic (OI)
O-F : face-centered orthorhombic (OF)
Q : primitive tetragonal (TP)
Q-V : body-centered tetragonal (TI)
RH : trigonal (HR)
H : hexagonal (HP)
C : primitive cubic (CP)
C-F : face-centered cubic (CF)
C-V : body-centered cubic (CI)

Quick reference on Bravais Lattices and info on how/why they are called after Bravais but not Frankenheim..

The marriage of heaven (common elements) and hell (code writing code).

admin — Thu, 26 Jun 2008 10:57:09 +0000

So, as Blake had said, "Energy is Eternal Delight." or in other words, let’s merge the preceding two entries to write a code for a function that produces MySQL queries that will fetch the common elements involved with the given elements:

function fetch_elements($el,$order,$total)
{
    // produces the query to select the elements that have binaries with the $el
    // $order and $total are used to adjust the tab positions and designating the sets
 
    $abc = "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
    $tab = str_repeat("\t",($total-$order));
    $lom = <<;
    return $lom;
}
 
function merge_queries($str1,$str2,$or1,$or2,$tab)
{
    // merges two node (or node group) queries (formed via fetch_elements() function)
    // using the INNER JOIN function
    return "$tab SELECT *\n$tab FROM (\n".$str1."\n$tab ) AS $or1\n$tab INNER JOIN (\n".$str2."\n$tab ) AS $or2\n$tab USING (symb)\n$tab ";
}
 
function fetch_common_elements($ar_el)
{
    // produces the query that selects the common elements that have binaries with all of the elements given in the $ar_el array (using their symbols)
    $total = sizeof($ar_el);
    $abc = "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
    //$tab = str_repeat("\t",($total-$order-1));
    $str[0] = fetch_elements($ar_el[0],0,$total-1);
    $str[1] = fetch_elements($ar_el[1],1,$total);
    $stri = merge_queries($str[0],$str[1],"A","B",str_repeat("\t",($total-2)));
    for($i=2;$i<$total;$i++)
    {
        $str[$i] = fetch_elements($ar_el[$i],$i,$total);
        $stri = merge_queries($str[$i],$stri,$abc[$i],$abc[($i+1)],str_repeat("\t",($total-$i-1)));
    }
    return $stri;
}

Now, we can call it with, for example:
echo fetch_common_elements(Array("Ga","Fe","Gd","Y","Ti","Ge","Ce"));
Which will output:

 SELECT *
 FROM (
         SELECT symbol_A AS symb, val1 AS valG
         FROM `dbl014`
         WHERE symbol_B = "Ce"
         GROUP BY Symbol_A
         UNION
         SELECT symbol_B AS symb, val1 AS valG
         FROM `dbl014`
         WHERE (
             symbol_A = "Ce"
             AND symbol_B != ""
         )
         GROUP BY Symbol_B
 ) AS G
 INNER JOIN (
         SELECT *
         FROM (
                 SELECT symbol_A AS symb, val1 AS valF
                 FROM `dbl014`
                 WHERE symbol_B = "Ge"
                 GROUP BY Symbol_A
                 UNION
                 SELECT symbol_B AS symb, val1 AS valF
                 FROM `dbl014`
                 WHERE (
                     symbol_A = "Ge"
                     AND symbol_B != ""
                 )
                 GROUP BY Symbol_B
         ) AS F
         INNER JOIN (
                 SELECT *
                 FROM (
                         SELECT symbol_A AS symb, val1 AS valE
                         FROM `dbl014`
                         WHERE symbol_B = "Ti"
                         GROUP BY Symbol_A
                         UNION
                         SELECT symbol_B AS symb, val1 AS valE
                         FROM `dbl014`
                         WHERE (
                             symbol_A = "Ti"
                             AND symbol_B != ""
                         )
                         GROUP BY Symbol_B
                 ) AS E
                 INNER JOIN (
                         SELECT *
                         FROM (
                                 SELECT symbol_A AS symb, val1 AS valD
                                 FROM `dbl014`
                                 WHERE symbol_B = "Y"
                                 GROUP BY Symbol_A
                                 UNION
                                 SELECT symbol_B AS symb, val1 AS valD
                                 FROM `dbl014`
                                 WHERE (
                                     symbol_A = "Y"
                                     AND symbol_B != ""
                                 )
                                 GROUP BY Symbol_B
                         ) AS D
                         INNER JOIN (
                                 SELECT *
                                 FROM (
                                         SELECT symbol_A AS symb, val1 AS valC
                                         FROM `dbl014`
                                         WHERE symbol_B = "Gd"
                                         GROUP BY Symbol_A
                                         UNION
                                         SELECT symbol_B AS symb, val1 AS valC
                                         FROM `dbl014`
                                         WHERE (
                                             symbol_A = "Gd"
                                             AND symbol_B != ""
                                         )
                                         GROUP BY Symbol_B
                                 ) AS C
                                 INNER JOIN (
                                         SELECT *
                                         FROM (
                                                 SELECT symbol_A AS symb, val1 AS valA
                                                 FROM `dbl014`
                                                 WHERE symbol_B = "Ga"
                                                 GROUP BY Symbol_A
                                                 UNION
                                                 SELECT symbol_B AS symb, val1 AS valA
                                                 FROM `dbl014`
                                                 WHERE (
                                                     symbol_A = "Ga"
                                                     AND symbol_B != ""
                                                 )
                                                 GROUP BY Symbol_B
                                         ) AS A
                                         INNER JOIN (
                                                 SELECT symbol_A AS symb, val1 AS valB
                                                 FROM `dbl014`
                                                 WHERE symbol_B = "Fe"
                                                 GROUP BY Symbol_A
                                                 UNION
                                                 SELECT symbol_B AS symb, val1 AS valB
                                                 FROM `dbl014`
                                                 WHERE (
                                                     symbol_A = "Fe"
                                                     AND symbol_B != ""
                                                 )
                                                 GROUP BY Symbol_B
                                         ) AS B
                                         USING (symb)
 
                                 ) AS D
                                 USING (symb)
 
                         ) AS E
                         USING (symb)
 
                 ) AS F
                 USING (symb)
 
         ) AS G
         USING (symb)
 
 ) AS H
 USING (symb)

and when fed to the database will yield:

thank y’all..

(Un)Common?

admin — Tue, 24 Jun 2008 12:06:16 +0000

They say that, it is the opposite (unsimilar) couples that make up for much stabler relationships… If you have only 2 different values, (+) and (-), spin up and down, man and woman, then the unsimilar of a thing that is unsimilar to you equals to a thing that is similar to you. Although it is generally not valid for elements, it gives you an insight nonetheless.. So if Y, Gd, Fe and Ga play a similar part in dearest ZrO₂’s life, let’s check for their other common "partners" that are known to have some connection/involvement this or that way…

The table we’re interested in today holds the formula and the constituent elements as in the example below:

(Actually the table contains way more properties than the formula and the constituent elements but I’ve focused only to the relevant props)

symbol_A and symbol_B are position oriented wrt the written formula, meaning that for an AxBy binary, you have A for symbol_A and B for symbol_B whereas if it is BxAy, then they are reversed.

We will be looking for elements that form binaries with the aforementioned 4 elements, namely: Yttrium, Gadolinium, Iron and Gallium.

We can search for each of these 4 via the following query and then add it up:

SELECT symbol_A as symb,val1 FROM `dbl014`
   WHERE symbol_B="Gd"
   GROUP BY Symbol_A
UNION
SELECT symbol_B as symb, val1 FROM `dbl014`
   WHERE (symbol_A="Gd" AND symbol_B!="")
   GROUP BY Symbol_B

For the intersection of two elements, we glue the two like the above one via the INNER JOIN function:

SELECT * FROM
(
   SELECT symbol_A as symb,val1
      FROM `dbl014`
      WHERE symbol_B="Gd"
GROUP BY Symbol_A

UNION

SELECT symbol_B as symb, val1
FROM `dbl014` WHERE (symbol_A="Gd" AND symbol_B!="")
GROUP BY Symbol_B
) AS A

INNER JOIN

(
   SELECT symbol_A as symb,val1
      FROM `dbl014` WHERE symbol_B="Y"
      GROUP BY Symbol_A

UNION

   SELECT symbol_B as symb, val1
      FROM `dbl014` where (symbol_A="Y" AND symbol_B!="")
      GROUP BY Symbol_B
) AS B
USING (symb)
ORDER BY symb

And for the ultimate quattro, it gets even exciting! :

SELECT *
FROM (

    SELECT symbol_A AS symb, val1 AS val
    FROM `dbl014`
    WHERE symbol_B = "Fe"
    GROUP BY Symbol_A
    UNION
    SELECT symbol_B AS symb, val1 AS val
    FROM `dbl014`
    WHERE (
        symbol_A = "Fe"
        AND symbol_B != ""
    )
    GROUP BY Symbol_B
) AS A
INNER JOIN (
    SELECT *
    FROM (

        SELECT symbol_A AS symb, val1 AS valA
        FROM `dbl014`
        WHERE symbol_B = "Gd"
        GROUP BY Symbol_A
        UNION
        SELECT symbol_B AS symb, val1 AS valA
        FROM `dbl014`
        WHERE (
            symbol_A = "Gd"
            AND symbol_B != ""
        )
        GROUP BY Symbol_B
    ) AS A
    INNER JOIN (
        SELECT *
        FROM (

            SELECT symbol_A AS symb, val1 AS valB
            FROM `dbl014`
            WHERE symbol_B = "Ga"
            GROUP BY Symbol_A
            UNION
            SELECT symbol_B AS symb, val1 AS valB
            FROM `dbl014`
            WHERE (
                symbol_A = "Ga"
                AND symbol_B != ""
            )
            GROUP BY Symbol_B
        ) AS A
        INNER JOIN (
            SELECT symbol_A AS symb, val1 AS valC
            FROM `dbl014`
            WHERE symbol_B = "Y"
            GROUP BY Symbol_A
            UNION
            SELECT symbol_B AS symb, val1 AS valC
            FROM `dbl014`
            WHERE (
                symbol_A = "Y"
                AND symbol_B != ""
            )
            GROUP BY Symbol_B
        ) AS B
        USING ( symb )
    ) AS C
    USING ( symb )
) AS D
USING ( symb )
ORDER BY symb

and voila!

a total of 42 all in all. The "val" columns are there for verificational purposes only – since after applying the GROUP BY function, they all lose their meanings.