Hex, Bugs and More Physics | Emre S. Tasci

Relations…

admin — Wed, 15 Jan 2014 13:22:23 +0000

Recently, we needed to schematize the relations between the coefficients of a symmetric tensor matrix such that, beyond the tedious numerical values, the basic relations such as equivalency or (-1) times would be visible to the eye.

Consider the following 16×16 matrix:

   0.06483   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.65809   0.65809   0.60365   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
   0.00000   0.10993   0.00000   0.00000   0.37862   0.37862   0.00000   0.00000   0.00000   0.00000   0.86568   0.00000   0.00000   0.42424   0.00000   0.00000
   0.00000   0.00000   0.10993   0.00000   0.00000   0.12949   0.00000   0.00000   0.00000   0.00000   0.00000  -0.86568   0.00000   0.00000   0.42424   0.00000
   0.00000   0.00000   0.00000   0.10259   0.00000   0.00000   0.84469   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.73695
   0.00000   0.37862   0.00000   0.00000   0.01584   0.00000   0.00000   0.00000   0.00000   0.00000   0.84812   0.00000   0.00000   0.87983   0.00000   0.00000
   0.00000   0.37862   0.12949   0.00000   0.00000   0.01584   0.00000   0.00000   0.00000   0.00000   0.00000  -0.84812   0.00000   0.00000   0.87983   0.00000
   0.00000   0.00000   0.00000   0.84469   0.00000   0.00000   0.01168   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.87050
   0.65809   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.88440   0.28986   0.45572   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
   0.65809   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.28986   0.88440   0.45572   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
   0.60365   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.45572   0.45572   0.89801   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000
   0.00000   0.86568   0.00000   0.00000   0.84812   0.00000   0.00000   0.00000   0.00000   0.00000   0.35993   0.00000   0.00000   0.19336   0.00000   0.00000
   0.00000   0.00000  -0.86568   0.00000   0.00000  -0.84812   0.00000   0.00000   0.00000   0.00000   0.00000   0.35993   0.00000   0.62239  -0.62239   0.00000
   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.18908   0.00000   0.00000   0.00000
   0.00000   0.42424   0.00000   0.00000   0.87983   0.00000   0.00000   0.00000   0.00000   0.00000   0.19336   0.62239   0.00000   0.54930   0.00000   0.00000
   0.00000   0.00000   0.42424   0.00000   0.00000   0.87983   0.00000   0.00000   0.00000   0.00000   0.00000  -0.62239   0.00000   0.00000   0.54930   0.00000
   0.00000   0.00000   0.00000   0.73695   0.00000   0.00000   0.87050   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.55094

if you really want to, you can verify that its coefficients satisfy the following properties:
Non-zero Elements:
(1,1), (1,8), (1,9), (1,10),
(2,2), (2,5), (2,6), (2,11), (2,14),
(3,3), (3,6), (3,12), (3,15),
(4,4), (4,7), (4,16),
(5,5), (5,11), (5,14),
(6,6), (6,12), (6,15),
(7,7), (7,16),
(8,8), (8,9), (8,10),
(9,9), (9,10),
(10,10),
(11,11), (11,14),
(12,12), (12,14), (12,15),
(13,13), (14,14), (15,15),
(16,16)

Equality relations:
(1,9) = (1,8)
(3,3) = (2,2)
(2,6) = (2,5)
(3,12) = -(2,11)
(3,15) = (2,14)
(6,6) = (5,5)
(6,12) = -(5,11)
(6,15) = (5,14)
(9,9) = (8,8)
(9,10) = (8,10)
(12,12) = (11,11)
(12,15) = -(12,14)
(15,15) = (14,14)

These kind of relations are sought upon tensor matrices (at least, in group theory 8), kind of postulating the imposed limits and… (have I said “relations”?). So, the sort-of-important-like thingy is to be able to spot them after evaluating some calculations in the computers.

Have you verified yet? Good! Now let’s take a look at this:

So, this is what we’ll be discussing in this post – preparation of such graphs. We’ll be using the PHP module Imagick for ImageMagick functions and objects. On Ubuntu, you can install the package from the command line as:

sudo apt-get install php5-imagick

(don’t forget to restart the http server if you’re working via a web interface instead of cli)

Before going further into the graph production, here is a description of producing a random matrix compatible with the given conditions in Octave:

Constructing a sample matrix in Octave

clear;

# Declare the matrix
T=[];

# == >> === non-zero coefficients ===== 0 =====
# I used the shorcuts and scripting of Vim to easily format the like lines..
non_zero_coeff = [];
non_zero_coeff = [non_zero_coeff; 1 1];
non_zero_coeff = [non_zero_coeff; 1 8];
non_zero_coeff = [non_zero_coeff; 1 9];
non_zero_coeff = [non_zero_coeff; 1 10];
non_zero_coeff = [non_zero_coeff; 2 2];
non_zero_coeff = [non_zero_coeff; 2 5];
non_zero_coeff = [non_zero_coeff; 2 11];
non_zero_coeff = [non_zero_coeff; 2 14];
non_zero_coeff = [non_zero_coeff; 3 3];
non_zero_coeff = [non_zero_coeff; 3 6];
non_zero_coeff = [non_zero_coeff; 3 12];
non_zero_coeff = [non_zero_coeff; 3 15];
non_zero_coeff = [non_zero_coeff; 4 4];
non_zero_coeff = [non_zero_coeff; 4 7];
non_zero_coeff = [non_zero_coeff; 3 12];
non_zero_coeff = [non_zero_coeff; 4 16];
non_zero_coeff = [non_zero_coeff; 5 5];
non_zero_coeff = [non_zero_coeff; 5 11];
non_zero_coeff = [non_zero_coeff; 1 9];
non_zero_coeff = [non_zero_coeff; 5 14];
non_zero_coeff = [non_zero_coeff; 6 6];
non_zero_coeff = [non_zero_coeff; 6 12];
non_zero_coeff = [non_zero_coeff; 1 9];
non_zero_coeff = [non_zero_coeff; 6 15];
non_zero_coeff = [non_zero_coeff; 7 7];
non_zero_coeff = [non_zero_coeff; 7 16];
non_zero_coeff = [non_zero_coeff; 8 8];
non_zero_coeff = [non_zero_coeff; 8 9];
non_zero_coeff = [non_zero_coeff; 8 10];
non_zero_coeff = [non_zero_coeff; 6 15];
non_zero_coeff = [non_zero_coeff; 9 9];
non_zero_coeff = [non_zero_coeff; 9 10];
non_zero_coeff = [non_zero_coeff; 10 10];
non_zero_coeff = [non_zero_coeff; 11 11];
non_zero_coeff = [non_zero_coeff; 11 14];
non_zero_coeff = [non_zero_coeff; 12 12];
non_zero_coeff = [non_zero_coeff; 12 14];
non_zero_coeff = [non_zero_coeff; 13 13];
non_zero_coeff = [non_zero_coeff; 14 14];
non_zero_coeff = [non_zero_coeff; 15 15];
non_zero_coeff = [non_zero_coeff; 16 16];

# Assign random values to the non-zero coefficients:
for i=1:rows(non_zero_coeff)
T(non_zero_coeff(i,1),non_zero_coeff(i,2)) = rand;
endfor
# == << === non-zero coefficients ===== 1 ===== 

# == >> === Relations ===== 0 =====
T(1,9)=T(1,8);
T(3,3)=T(2,2);
T(2,6)=T(2,5);
T(3,12)=-T(2,11);
T(3,15)=T(2,14);
T(6,6)=T(5,5);
T(6,12)=-T(5,11);
T(6,15)=T(5,14);
T(9,9)=T(8,8);
T(9,10)=T(8,10);
T(12,12)=T(11,11);
T(12,15)=-T(12,14);
T(15,15)=T(14,14);
# == << === Relations ===== 1 ===== 

# == >> === Symmetry ===== 0 =====
for i=1:rows(T)
for j=i:columns(T)
T(j,i) = T(i,j);
endfor
endfor
# == << === Symmetry ===== 1 =====

# Export the matrix to a file:
save("input.data.txt","T");

Finding out the relations between the coefficients

Doing a double loop over i=1:rows and j=i:cols, for each of the coefficients in and above the diagonal, taking one as reference (checking if abs(T(i,j))>0 and recording to an array, say “non-zero-coeff-array” if so) and then comparing it with the rest of the elements (that comes after it) with another double loop i2=i:rows and j2=j:cols. If T(i2,j2) is equal to +-T(i,j), we also note this (three values for each i2,j2 equivalency identification: i2,j2 and +/-1) in another array (say “equal-array”).

For example, according to our case the (9,9) element of the non-zero-coeff-array would be TRUE and the same element of the equal-array would be a sub-array holding the values (8,8,1).

Painting on a canvas

Once you have access to the ImageMagick library through Imagick, we can start “painting” a canvas by first defining the canvas (width, height and background color):

# Declare the object (/holder)
$image = new Imagick();

# Define the canvas (size 640x640 pixels with white background)
$image->newImage( 640, 640, new ImagickPixel( 'white' ) );

Let’s put a circle (filled, black) in the center with a radius of 30 pixels:

# Define the circle:
$circle = new ImagickDraw();
$circle->setFillColor("#000000");
$circle->circle(320,320,350,320);

# Add (/register) it to the canvas:
$image->drawImage($circle);

As for the production of the image file, we need to designate it as a PNG image and then export it to a file:
# Designate the image type as PNG:
$image->setImageFormat( "png" );

# Export (/write) it to a file "out.png":
$fp = fopen("out.png","w");
fwrite($fp,$image);
fclose($fp);


This is what you -should- get:

not bad for beginning, right? 
The circle function has 4 parameters: the (x,y) coordinates of the center and the coordinates of a point that is on the edge of the circle. Let’s draw another circle, this time an unfilled one below this filled one:

# Declare the object (/holder) 
$image = new Imagick();

 # Define the canvas (size 640x640 pixels with white background)
 $image --->newImage( 640, 640, new ImagickPixel( 'white' ) );

# Define the 1st, filled circle:
$circle = new ImagickDraw();
$circle->setFillColor("#000000");
$circle->circle(320,320,350,320);

# Add (/register) it to the canvas:
$image->drawImage($circle);

# Define the 2nd, unfilled circle:
$circle = new ImagickDraw();
$circle->setStrokeColor("#000000");
$circle->setStrokeWidth(2);
$circle->setFillColor("none");
$circle->circle(320,350,350,350);

# Add (/register) it to the canvas:
$image->drawImage($circle);

# Designate the image type as PNG:
$image->setImageFormat( "png" );

# Export (/write) it to a file "out.png":
$fp = fopen("out.png","w");
fwrite($fp,$image);
fclose($fp);


The “stroke” methods are responsible for the perimeter and the fillcolor setting to “none” ensures that we have an otherwise invisible circle.
So far, so good.. Let’s add a line that passes between the circles from (120,50) to (520,50):
# Define the line:
$line = new ImagickDraw();
$line->setStrokeColor("#000000");
$line->setStrokeWidth(2);
$line->line(120,350,520,350);
$image->drawImage($line);


Mapping the rows and cols to x and y
Suppose that we have a 16×16 matrix to be mapped onto a 640×640 canvas. We could map (i=0,j=0) to (x=0,y=0) and (i=16,j=16) to (x=640,y=640) but it wouldn’t be right:


doesn’t look right, right? And here’s the code that produced it:

# Declare the object (/holder)
$image = new Imagick(); 

# Define the canvas (size 640x640 pixels with white background) 
$image--->newImage( 640, 640, new ImagickPixel( 'white' ) );

# Define the 1st, filled circle:
$dxy = 640 / 16;
for($i=1;$i<=16;$i++)
{
for($j=1;$j<=16;$j++)
     {
         $circle = new ImagickDraw();
         $circle->setFillColor("#000000");
         $circle->circle($dxy*($j-1),$dxy*($i-1),$dxy*($j-1)+$dxy/6,$dxy*($i-1));

         # Add (/register) it to the canvas:
         $image->drawImage($circle);
     }
}

# Designate the image type as PNG:
$image->setImageFormat( "png" );

# Export (/write) it to a file "out.png":
$fp = fopen("out.png","w");
fwrite($fp,$image);
fclose($fp);

What we need to do is to shift it half of the periodicity in the x & y directions:


That’s more like it — this shift was introduced to the code by changing the coordinate parameters of the circle(s):

$circle->circle($dxy*($j-1/2),$dxy*($i-1/2),$dxy*($j-1/2)+$dxy/6,$dxy*($i-1/2));
So, depending on the value (zero/non-zero) of an element of our tensor, we can put it as a big circle (r=$dxy/6) or a small one (r=$dxy/12). In addition, if it’s negative, we can have it drawn as an unfilled one (

$circle->setStrokeColor("#000000");
$circle->setStrokeWidth(2);
$circle->setFillColor("none");


). We’re almost ready aside from the connecting the related entries!
Connecting the dots
Suppose that we’d like to connect the circles corresponding to the (i1,j1) and the (i2,j2) elements of the tensor. On the canvas, their centers will be given as ($dxy*($j1-1/2),$dxy*($i1-1/2)) and ($dxy*($j2-1/2),$dxy*($i2-1/2)) where $dxy is the conversion unit of 1 step in the row-col matrix to that of the canvas (for simplicity I assumed a square canvas which is not necessary — then we’d have a $dx=$width/$num_cols and a $dy=$height/$num_rows. Also note that the rows are associated with the height ($i <-> vertical) and the columns are with the width ($j <-> horizontal) (that’s why $j’s come before $i’s in the center equations).
So, let’s join (11,5) to (9,3): in a 640×640 canvas, (11,5) is centered at ((640/16)*(5-1/2) =  180, (640/16)*(11-1/2) = 420) and similarly (9,3) is centered at (100,340). Let’s put them on the map and connect their centers with a line:

# Declare the object (/holder)
$image = new Imagick();

# Define the canvas (size 640x640 pixels with white background)
$image->newImage( 640, 640, new ImagickPixel( 'white' ) );

$dxy = 640/16; # 40px
$radius = $dxy/6; #6.6667px

# Define the unfilled (11,5) circle:
$circle = new ImagickDraw();
$circle->setStrokeColor("#000000");
$circle->setStrokeWidth(2);
$circle->setFillColor("none");
$circle->circle(180,420,180+$radius,420);

# Add (/register) it to the canvas:
$image->drawImage($circle);

# Define the unfilled (9,3) circle:
$circle = new ImagickDraw();
$circle->setStrokeColor("#000000");
$circle->setStrokeWidth(2);
$circle->setFillColor("none");
$circle->circle(100,340,100+$radius,340);

# Add (/register) it to the canvas:
$image->drawImage($circle);

# Connect them with a line:
$line = new ImagickDraw();
$line->setStrokeColor("#000000");
$line->setStrokeWidth(2);
$line->line(180,420,100,340);
$image->drawImage($line);

# Designate the image type as PNG:
$image->setImageFormat( "png" );

# Export (/write) it to a file "out.png":
$fp = fopen("out.png","w");
fwrite($fp,$image);
fclose($fp);



Devil is in the details
By now, hopefully you’ve got the idea of how to swing things in your way. In my case, if I spent the 40% of the time doing the things I described, the remaining 60% went in adjusting the line such that it starts on the perimeter of the circle, not from the center of it, i.e.,

and this requires the determination of the angle of the line connecting our nodes. The angle of a line passing through two points (x1,y1) & (x2,y2) is given by: arctan[(y2-y1)/(x2-x1)], where the value is nothing but the A of the y=Ax+B line equation, and we need to translate the beginning and the final points of our line in this direction by an amount of a radius:
# Find the tangent of the line:
$tg = (340-420)/(100-180);
$alpha_radian = atan($tg);
$alpha_deg = $alpha_radian * 180 / M_PI;

# Connect them with a line:
$line = new ImagickDraw();
$line->setStrokeColor("#000000");
$line->setStrokeWidth(2);
$line->line(180-$radius*cos($alpha_radian),420-$radius*sin($alpha_radian),100+  $radius*cos($alpha_radian),340+$radius*sin($alpha_radian));
$image->drawImage($line);

and that’s more or less all about it!
One picture is worth a thousand words
You can have a sneak peak of the working code via here: http://144.122.31.125/cgi-bin/cryst/programs/tensor_graph/



How to Prepare an Input File for Surface Calculations
admin — Wed, 11 Sep 2013 08:56:27 +0000
>> pdf version
How to Prepare an Input File for Surface Calculations
Emre S. Tasci

19/07/2013


Abstract
This how-to is intended to guide the reader during the preparation of the input file for an intended surface calculation study. Mainly VESTA software is used to manipulate and transform initial structure file along with some home brewed scripts to do simple operations such as translations.

Table of Contents

Section 1: Description
Section 2: Tools
Section 3: Procedure

Subsection 3.1: Initial structural data
Subsection 3.2: Constructing the Supercell
Subsection 3.3: Lattice Planes
Subsection 3.4: Trimming the new unit cell
Subsection 3.5: Transforming into the new unit cell

Subsubsection 3.5.1: A Word of caution

Subsection 3.6: Final Touch

Section 4: Alternative Ways
Section 5: Conclusion
Section 6: Acknowledgements
Section 7: Appendix: Walkthru for PtC (111) Surface


 Description
One of the questions I’m frequently being asked by the students is the preparation of input files for surface calculations (or more accurately, “a practical way” for the purpose). In this text, starting from a structural data file for bulk, the methods to obtain the input file fit for structure calculations will be dealt.
 Tools
VESTA [A]  is a free 3D visualization program for structural models that also allows editing to some extent. It is available for Windows, MacOS and Linux operating systems.
STRCONVERT [B]  is a tool hosted on the Bilbao Crystallographic Server[, , ] (BCS) that offers visualization and also basic editing as well as conversion between various common structural data formats.
TRANSTRU [C]  is an another BCS tool that transforms a given structure via the designated transformation matrix.
 Procedure
 Initial structural data
We start by obtaining the structural data for the unit cell of the material we are interested in. It should contain the unit cell dimensions and the atomic positions. Some common formats in use are: CIF[], VASP[], VESTA[] and BCS formats. Throughout this text, we will be operating on the Fm3mphase of the platinum carbide (PtC), reported by Zaoui & Ferhat[] as reproduced in BCS format in Table 1↓.



225
4.50 4.50 4.50 90. 90. 90.
2
C 1 4a 0 0 0
Pt 1 4b 0.5 0.5 0.5
Table 1 Structural data of Fm3m PtC



These data can be entered directly into VESTA from the form accessed by selecting the “File→New Structure” menu items and then filling the necessary information into the “Unit cell” and “Structure parameters” tabs, as shown in Figures 1↓ and 2↓.




Figure 1 VESTA’s “Unit cell” interface







Figure 2 VESTA’s “Structure parameters” interface



As a result, we have now defined the Fm3m PtC (Figure 3↓).




Figure 3 Fm3m platinum carbide



An alternative way to introduce the structure would be to directly open its structural data file (obtained from various structure databases such as COD[], ICSD[] or Landolt-Bornstein[] into VESTA.
 Constructing the Supercell
A supercell is a collection of unit cells extending in the a,b,c directions. It can easily be constructed using VESTA’s transformation tool. For demonstration purposes, let’s build a 3x3x3 supercell from our cubic PtC cell. Open the “Edit→Edit Data→Unit Cell…” dialog, then click the “Option…” button in the “Setting” row. Then define the transformation matrix as “3a,3b,3c” as shown in Figure 4↓.



Figure 4 Transformation matrix for the supercell



Answer “yes” when the warning for the change of the volume of the unit cell appears, and again click “Yes” to search for additional atoms. After this, click “OK” to exit the dialog. This way we have constructed a supercell of 3x3x3 unit cells as shown in Figure 5↓.



Figure 5 A 3x3x3 supercell





,
Figure 6 Designating the boundaries for the construction of the supercell.



We have built the supercell for a general task but at this stage, it’s not convenient for preparing the surface since we first need to cleave with respect to the necessary lattice plane. So, revert to the conventional unit cell (either by reopening the data file or undoing (CTRL-z) our last action).
Now, populate the space with the conventional cell using the “Boundary” setting under the “Style” tool palette (Figure 6↑). In this case, we are building a 3x3x3 supercell by including the atoms within the -fractional- coordinate range of [0,3] along all the 3 directions (Figure 7↓).



Figure 7 (a)Single unit cell (conventional); (b) 3x3x3 supercell



At this stage, the supercell formed is just a mode of display – we haven’t made any solid changes yet. Also, if preferred one can choose how the unit cells will be displayed from the “Properties” setting’s “General” tab.
 Lattice Planes
To visualize a given plane with respect to the designated hkl values, open the dialog shown in Figure 8↓ by selecting “Edit→Lattice Planes…” from the menu, then clicking on “New” and entering the intended hkl values, in our example (111) plane.



etasci@metu.edu.tr
Figure 8 Selecting the (111) lattice plane



The plane’s distance to the origin can be specified in terms of Å or interplane distance, as well as selecting 3 or more atoms lying on the plane (multiple selections can be realised by holding down SHIFT while clicking on the atoms) and then clicking on the “Calculate the best plane for the selected atoms” button to have the plane passing from those positions to appear. This is shown in Figure 9↓, done within a 3x3x3 supercell.



Figure 9 Selecting the (111) lattice plane in the 3x3x3 supercell



The reason we have oriented our system so that the normal to the (111) plane is pointing up is to designate this lattice plane as the surface, aligning it with the new c axis for convenience. Therefore we also need to reassign a and b axes, as well. This all comes down to defining a new unit cell. Preserving the periodicities, the new unit cell is traced out by introducing additional lattice planes. These new unit cells are not unique, as long as one preserves the periodicities in the 3 axial directions, they can be taken as large and in any convenient shape as allowed. A rectangular shaped such a unit cell, along with the outlying lattice plane parameters is presented in Figure 10↓ (the boundaries have been increased to [-2,5] in each direction for practicality).




Figure 10 The new unit cell marked out by the lattice plane “boundaries”



 Trimming the new unit cell
The next procedure is simple and direct: remove all the atoms outside the new unit cell. You can use the “Select” tool from the icons on the left (the 2nd from top) or the shortcut key “s”. The “trimmed” new unit cell is shown in Figure 11↓, take note of the periodicity in each section. It should be noted that, this procedure is only for deducing the transformation matrix, which we’ll be deriving in the next subsection: other than that, since it’s still defined by the “old” lattice vectors, it’s not stackable to yield the correct periodicity so we’ll be fixing that.




Figure 11 Filtered new unit cell with the original cell’s lattice vectors



 Transforming into the new unit cell
Now that we have the new unit cell, it is time to transform the unit cell vectors to comply with the new unit cell. For the purpose of obtaining the transformation matrix (which actually is the matrix that relates the new ones with the old ones), we will need the coordinates of the 4 atoms on the edges. Such a set of 4 selected atoms are shown in Figure 12↓. These atoms’ fractional coordinates are as listed in Table 2↓ (upon selecting an atom, VESTA displays its coordinates in the information panel below the visualization).




Figure 12 The reference points for the new axe1s










Label
a’
b’
c’
o’


a
0
1/2
2
1


b
1
-1/2
1
0


c
-1/2
1/2
1/2
-1/2




Table 2 Reference atoms’ fractional coordinates



Taking o’ as our new origin, the new lattice vectors in terms of the previous ones become (as we subtract the “origin’s” coordinates):
a’ = -a+b
b’ = -1/2a-1/2b+c
c’ = a+b+c
Therefore our transformation matrix is:

⎡⎢⎢⎢⎣ − 1 − 121   1 − 121   011⎤⎥⎥⎥⎦

(i.e., “-a+b,-1/2a-1/2b+c,a+b+c” — the coefficients are read in columns)
Transforming the initial cell with respect to this matrix is pretty straight forward, in the same manner we exercised in subsection 3.2↑, “Constructing the supercell”, i.e., “Edit→Edit Data→Unit Cell..”, then “Remove symmetry” and “Option…” and introducing the transformation matrix. A further translation (origin shift) of (0,0,1/2) is necessary (the transformation matrix being “-a+b,-1/2a-1/2b+c,a+b+c+1/2”) if you want the transformed structure look exactly like the one shown in Figure 11↑.
 A Word of caution
Due to a bug, present in VESTA, you might end with a transformed matrix with missing atoms (as shown in Figure – compare it to the middle and rightmost segments of Figure 11↑). For this reason, always make sure you check your resulting unit cell thoroughly! (This bug has recently been fixed and will be patched in the next version (3.1.7)-personal communication with K.Momma)




Figure 13 The transformed structure with missing atoms



To overcome this problem, one can conduct the transformation via the TRANSTRU [E]  tool of the Bilbao Crystallographic Server. Enter your structural data (either as a CIF or by definition into the text box), select “Transform structure to a subgroup basis”, in the next window enter “1” as the “Low symmetry Space Group ITA number” (1 corresponding to the P1 symmetry group) and the transformation matrix either in abc notation (“-a+b,-1/2a-1/2b+c,a+b+c+1/2”) or by directly entering the matrix form (both are filled in the screenshot taken in Figure 14↓).




Figure 14 TRANSTRU input form




In the result page export the transformed structure data (“Low symmetry structure data”) to CIF format by clicking on the corresponding button and open it in VESTA. This way all the atoms in the new unit cell will have been included.

 Final Touch
The last thing remains is introducing a vacuum area above the surface. For this purpose we switch from fractional coordinates to Cartesian coordinates, so when the cell boundaries are altered, the atomic positions will not change as a side result. VASP format supports both notations so we export our structural data into VASP format (“File→Export Data…”, select “VASP” as the file format, then opt for “Write atomic coordinates as: Cartesian coordinates”).
After the VASP file with the atomic coordinates written in Cartesian format is formed, open it with an editor (the contents are displayed in Table3↓).



generated_by_bilbao_crystallographic_server


1.0


6.3639612198 0.0000000000 0.0000000000


0.0000000000 5.5113520622 0.0000000000


0.0000000000 0.0000000000 7.7942290306


C Pt


12 12


Cartesian


0.000000000 3.674253214 6.495164688


0.000000000 1.837099013 1.299064110


3.181980610 1.837099013 1.299064110


1.590990305 0.918577018 6.495164688


4.772970915 4.592774880 1.299064110


1.590990305 4.592774880 1.299064110


4.772970915 0.918577018 6.495164688


0.000000000 0.000000000 3.897114515


3.181980610 0.000000000 3.897114515


4.772970915 2.755676031 3.897114515


1.590990305 2.755676031 3.897114515


3.181980610 3.674253214 6.495164688


0.000000000 3.674253214 2.598050405


1.590990305 0.918577018 2.598050405


4.772970915 0.918577018 2.598050405


1.590990305 4.592774880 5.196178858


3.181980610 1.837099013 5.196178858


0.000000000 1.837099013 5.196178858


4.772970915 4.592774880 5.196178858


0.000000000 0.000000000 0.000000000


3.181980610 3.674253214 2.598050405


3.181980610 0.000000000 0.000000000


4.772970915 2.755676031 0.000000000


1.590990305 2.755676031 0.000000000

Table 3 The constructed (111) oriented VASP file’s contents



Directly edit and increase the c-lattice length from the given value (7.7942 Å in our case) to a sufficiently high value (e.g., 25.0000 Å) and save it. Now when you open it back in VESTA, the surface with its vacuum should be there as in Figure 15↓.




Figure 15 Prepared surface with vacuum



At this point, there might be a couple of questions that come to mind: What are those Pt atoms doing at the top of the unit cell? Why are the C atoms positioned above the batch instead of the Pt atoms?
The answer to these kind of questions is simple: Periodicity. By tiling the unit cell in the c-direction using the “Boundary…” option and designating our range of coordinates for the {x,y,z}-directions from 0 to 3, we obtain the system shown in Figure 16↓.




Figure 16 New unit cell with periodicity applied



From the periodicity, in fractional coordinates, f|z = 0 = f|z = 1, meaning the atoms at the base and at the very top of the unit cell are the same (or “equivalent” from the interpretational side). If we had wanted the Pt atoms to be the ones forming the surface, then we would have made the transformation with the “-a+b,-1/2a-1/2b+c,a+b+c” matrix instead of “-a+b,-1/2a-1/2b+c,a+b+c+1/2”, so the half shift would amount the change in the order, and then increase the c-lattice parameter size in the Cartesian coordinates notation (i.e., in the VASP file). The result of such a transformation is given in Figure 17↓.




Figure 17 Alternative surface with the Pt atoms on the top (Left: prior to vacuum introduction; Center: with vacuum; Right: tiled in periodicity)



 Alternative Ways
In this work, a complete treatment of preparing a surface in silico is proposed. There are surely more direct and automated tools that achieve the same task. It has been brought to our attention that the commercial software package Accelrys Materials Studio [F]  has an integrated tool called “Cleave Surface” which exactly serves for the same purpose discussed in this work. Since it is propriety software, it will not be further described here and we encourage the user to benefit from freely accessible software whenever possible.
Also, it is always to compare your resulting surface with that of an alternate one obtained using another tool. In this sense, Surface Explorer [G]  is very useful in visualizing how the surface will look, eventhough its export capabilities are limited.
Chapter 4 (“DFT Calculations for Solid Surfaces”) of Zhang’s Ph.D. thesis[] contains very fruitful discussions on possible ways to incorporate the surfaces in computations.
It is the author’s intention to soon implement such an automated tool for constructing surfaces from bulk data, integrated within the Bilbao Crystallographic Server’s framework of tools.
 Conclusion
Preparing a surface fit for atomic & molecular calculations can be tedious and tiresome. In this work, we have tried to guide the reader in a step-by-step procedure, sometimes wandering off from the direct path to show the mechanisms and reasons behind the usually taken on an “as-it-is” basis, without being pondered upon. This way, we hope that the techniques acquired throughout the text will be used in conjunction with other related problems in the future. A “walkthru” for the case studied ((111) PtC surface preparation) is included as Appendix to provide a quick consultation in the future.
 Acknowledgements
This work is the result of the inquiries by the Ph.D. students M. Gökhan Şensoy and O. Karaca Orhan. If they hadn’t asked a “practical way” to construct surfaces, I wouldn’t have sought a way. Since I don’t have much experience with surfaces, I turned to my dear friends Rengin Peköz and O. Barış Malcıoğlu for help, whom enlightened me with their experiences on the issue.
 Appendix: Walkthru for PtC (111) Surface

Open VESTA, (“File→New Structure”)

“Unit Cell”:

Space Group: 225 (F m -3 m)
Lattice parameter a: 4.5 Å


“Structure Parameters”:

New→Symbol:C; Label:C; x,y,z=0.0
New→Symbol:Pt; Label:Pt; x,y,z=0.5


“Boundary..”

x(min)=y(min)=z(min)=-2
x(max)=y(max)=z(max)=5


“Edit→Lattice Planes…”

(hkl)=(111); d(Å)=9.09327
(hkl)=(111); d(Å)=1.29904
(hkl)=(-110); d(Å)=3.18198
(hkl)=(-110); d(Å)=-3.18198
(hkl)=(11-2); d(Å)=3.67423
(hkl)=(11-2); d(Å)=-4.59279

(compare with Figure 10↑)

Select (“Select tool” – shortcut “s” key) and delete (shortcut “Del” key) all the atoms lying out of the area designated by the lattice planes.
Select an “origin-atom” of a corner and the 3 “axe-atoms” in the edge of each direction of the unit cell, write down their fractional coordinates

o(1,0,-1/2)
a(0,1,-1/2)
b(1/2,-1/2,1/2)
c(2,1,1/2)


Subtract the origin-atom coordinates from the rest and construct the transformation matrix accordingly
P = ⎡⎢⎢⎢⎣ − 1 − 121   1 − 121   011⎤⎥⎥⎥⎦

Transform the initial unit cell with this matrix via TRANSTRU (http://www.cryst.ehu.es/cryst/transtru.html) (Figure 14↑)
Save the resulting (low symmetry) structure as CIF, open it in VESTA, export it to VASP, select “Cartesian coordinates”
Open the VASP file in an editor, increase the c-lattice parameter to a big value (e.g. 25.000) to introduce vacuum. Save it and open it in VESTA.




References
[1] Mois Ilia Aroyo, Juan Manuel Perez-Mato, Cesar Capillas, Eli Kroumova, Svetoslav Ivantchev, Gotzon Madariaga, Asen Kirov, and Hans Wondratschek. Bilbao crystallographic server: I. databases and crystallographic computing programs. Zeitschrift für Kristallographie, 221(1):1527, 01 2006. doi: 10.1524/zkri.2006.221.1.15.
[2] Mois I. Aroyo, Asen Kirov, Cesar Capillas, J. M. Perez-Mato, and Hans Wondratschek. Bilbao crystallographic server. ii. representations of crystallographic point groups and space groups. Acta Crystallographica Section A, 62(2):115128, Mar 2006. http://dx.doi.org/10.1107/S0108767305040286
[3] M I Aroyo, J M Perez-Mato, D Orobengoa, E Tasci, G De La Flor, and A Kirov. Crystallography online: Bilbao crystallographic server. Bulg Chem Commun, 43(2):183197, 2011.
[4] S. R. Hall, F. H. Allen, and I. D. Brown. The crystallographic information le (cif): a new standard archive file for crystallography. Acta Crystallographica Section A, 47(6):655685, Nov 1991.
[5] G. Kresse and J. Furthmüller. Ecient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. Rev. B, 54:1116911186, Oct 1996.
[6] Koichi Momma and Fujio Izumi. VESTA3 for three-dimensional visualization of crystal, volumetric and morphology data. Journal of Applied Crystallography, 44(6):12721276, Dec 2011.
[7] A Zaoui and M Ferhat. Dynamical stability and high pressure phases of platinum carbide. Solid State Communications, 151(12):867869, 6 2011.
[8] Saulius Grazulis, Adriana Daskevic, Andrius Merkys, Daniel Chateigner, Luca Lutterotti, Miguel Quirós, Nadezhda R. Serebryanaya, Peter Moeck, Robert T. Downs, and Armel Le Bail. Crystallography open database (cod): an open-access collection of crystal structures and platform for world-wide collaboration. Nucleic Acids Research, 40(D1):D420D427, 2012.
[9] Alec Belsky, Mariette Hellenbrandt, Vicky Lynn Karen, and Peter Luksch. New developments in the inorganic crystal structure database (icsd): accessibility in support of materials research and design. Acta Crystallographica Section B, 58(3 Part 1):364369, Jun 2002.
[10] Springer, editor. The Landolt-Boernstein Database (http://www.springermaterials.com/navigation/). Springer Materials.
[11] Yongsheng Zhang. First-principles statistical mechanics approach to step decoration at solid surfaces . PhD thesis, Frei Universitat Berlin, 2008.

❬✶❪ ▼✐s ■❧✐❛ ❆r2✱ ❏❛ ▼❛❡❧ P❡r❡3✲▼❛t✱ ❈❡s❛r ❈❛✐❧❧❛s✱ ❊❧✐ ❑r❛✱ ❙❡ts❧❛ ■❛t❝❡✱ ●t3 ▼❛❞❛r✐❛❛✱
❆s❡ ❑✐r✱ ❛❞ ❍❛s ❲❞r❛ts❝❡❦ ✐❧❜❛ ❝r2st❛❧❧r❛✐❝ s❡r❡r✿ ■ ❞❛t❛❜❛s❡s ❛❞ ❝r2st❛❧❧r❛✐❝ ❝t✐
rr❛s ❩❡✐ts❝r✐❢t ❢ür ❑r✐st❛❧❧r❛✐❡✱ ✷✷✶✭✶✮✿✶✺✕✷✼✱ ✵✶ ✷✵✵✻ ❞✐✿ ✶✵✶✺✷✹3❦r✐✷✵✵✻✷✷✶✶✶✺
❬✷❪ ▼✐s ■ ❆r2✱ ❆s❡ ❑✐r✱ ❈❡s❛r ❈❛✐❧❧❛s✱ ❏ ▼ P❡r❡3✲▼❛t✱ ❛❞ ❍❛s ❲❞r❛ts❝❡❦ ✐❧❜❛ ❝r2st❛❧❧r❛✐❝
s❡r❡r ✐✐ r❡r❡s❡t❛t✐s ❢ ❝r2st❛❧❧r❛✐❝ ✐t rs ❛❞ s❛❝❡ rs ❆❝t❛ ❈r2st❛❧❧r❛✐❝❛ ❙❡❝t✐ ❆✱
✻✷✭✷✮✿✶✶✺✕✶✷✽✱ ▼❛r ✷✵✵✻
❬✸❪ ▼ ■ ❆r2✱ ❏ ▼ P❡r❡3✲▼❛t✱ ❉ ❖r❜❡❛✱ ❊ ❚❛s❝✐✱ ● ❉❡ ▲❛ ❋❧r✱ ❛❞ ❆ ❑✐r ❈r2st❛❧❧r❛2 ❧✐❡✿ ✐❧❜❛
❝r2st❛❧❧r❛✐❝ s❡r❡r ❧ ❈❡ ❈✱ ✹✸✭✷✮✿✶✽✸✕✶✾✼✱ ✷✵✶✶
❬✹❪ ❙ ❘ ❍❛❧❧✱ ❋ ❍ ❆❧❧❡✱ ❛❞ ■ ❉ r✇ ❚❡ ❝r2st❛❧❧r❛✐❝ ✐❢r❛t✐ ✜❧❡ ✭❝✐❢✮✿ ❛ ❡✇ st❛❞❛r❞ ❛r❝✐❡ ✜❧❡
❢r ❝r2st❛❧❧r❛2 ❆❝t❛ ❈r2st❛❧❧r❛✐❝❛ ❙❡❝t✐ ❆✱ ✹✼✭✻✮✿✻✺✺✕✻✽✺✱ ◆ ✶✾✾✶❍❖❲ ❚❖ P❘❊P❆❘❊ ❆◆ ■◆P❯❚ ❋■▲❊ ❋❖❘ ❙❯❘❋❆❈❊ ❈❆▲❈❯▲❆❚■❖◆❙
✶✻
❬✺❪ ● ❑r❡ss❡ ❛❞ ❏ ❋rtü❧❧❡r ❊✣❝✐❡t ✐t❡r❛t✐❡ s❝❡❡s ❢r ❛❜ ✐✐t✐ tt❛❧✲❡❡r2 ❝❛❧❝❧❛t✐s s✐ ❛ ❧❛❡✲✇❛❡
❜❛s✐s s❡t P2s ❘❡ ✱ ✺✹✿✶✶✶✻✾✕✶✶✶✽✻✱ ❖❝t ✶✾✾✻
❬✻❪ ❑✐❝✐ ▼❛ ❛❞ ❋❥✐ ■3✐ ❱❊❙❚❆✸ ❢r tr❡❡✲❞✐❡s✐❛❧ ✐s❛❧✐3❛t✐ ❢ ❝r2st❛❧✱ ❧❡tr✐❝ ❛❞ r❧✲
2 ❞❛t❛ ❏r❛❧ ❢ ❆❧✐❡❞ ❈r2st❛❧❧r❛2✱ ✹✹✭✻✮✿✶✷✼✷✕✶✷✼✻✱ ❉❡❝ ✷✵✶✶
❬✼❪ ❆ ❩❛✐ ❛❞ ▼ ❋❡r❛t ❉2❛✐❝❛❧ st❛❜✐❧✐t2 ❛❞ ✐ r❡ssr❡ ❛s❡s ❢ ❧❛t✐ ❝❛r❜✐❞❡ ❙❧✐❞ ❙t❛t❡ ❈✐✲
❝❛t✐s✱ ✶✺✶✭✶✷✮✿✽✻✼✕✽✻✾✱ ✻ ✷✵✶✶
❬✽❪ ❙❛❧✐s ●r❛➸❧✐s✱ ❆❞r✐❛❛ ❉❛➨❦❡✐✱ ❆❞r✐s ▼❡r❦2s✱ ❉❛✐❡❧ ❈❛t❡✐❡r✱ ▲❝❛ ▲tt❡rtt✐✱ ▼✐❡❧ ◗✐rós✱
◆❛❞❡3❞❛ ❘ ❙❡r❡❜r2❛❛2❛✱ P❡t❡r ▼❡❝❦✱ ❘❜❡rt ❚ ❉✇s✱ ❛❞ ❆r❡❧ ▲❡ ❛✐❧ ❈r2st❛❧❧r❛2 ❡ ❞❛t❛✲
❜❛s❡ ✭❝❞✮✿ ❛ ❡✲❛❝❝❡ss ❝❧❧❡❝t✐ ❢ ❝r2st❛❧ str❝tr❡s ❛❞ ❧❛t❢r ❢r ✇r❧❞✲✇✐❞❡ ❝❧❧❛❜r❛t✐ ◆❝❧❡✐❝
❆❝✐❞s ❘❡s❡❛r❝✱ ✹✵✭❉✶✮✿❉✹✷✵✕❉✹✷✼✱ ✷✵✶✷
❬✾❪ ❆❧❡❝ ❡❧s❦2✱ ▼❛r✐❡tt❡ ❍❡❧❧❡❜r❛❞t✱ ❱✐❝❦2 ▲2 ❑❛r❡✱ ❛❞ P❡t❡r ▲❦s❝ ◆❡✇ ❞❡❡❧❡ts ✐ t❡ ✐r❛✐❝
❝r2st❛❧ str❝tr❡ ❞❛t❛❜❛s❡ ✭✐❝s❞✮✿ ❛❝❝❡ss✐❜✐❧✐t2 ✐ srt ❢ ❛t❡r✐❛❧s r❡s❡❛r❝ ❛❞ ❞❡s✐ ❆❝t❛ ❈r2st❛❧❧r❛✐❝❛
❙❡❝t✐ ✱ ✺✽✭✸ P❛rt ✶✮✿✸✻✹✕✸✻✾✱ ❏ ✷✵✵✷
❬✶✵❪ ❙r✐❡r✱ ❡❞✐tr ❚❡ ▲❛❞❧t✲❡rst❡✐ ❉❛t❛❜❛s❡ ✭tt✿✇✇✇sr✐❡r❛t❡r✐❛❧s❝❛✐❛t✐✮ ❙r✐❡r
▼❛t❡r✐❛❧s
❬✶✶❪ ❨s❡ ❩❛ ❋✐rst✲r✐❝✐❧❡s st❛t✐st✐❝❛❧ ❡❝❛✐❝s ❛r❛❝ t st❡ ❞❡❝r❛t✐ ❛t s❧✐❞ sr❢❛❝❡s P❉ t❡s✐s✱
❋r❡✐ ❯✐❡rs✐t❛t ❡r❧✐✱ ✷✵✵✽



Document generated by eLyXer 1.2.3 (2011-08-31) on 2013-09-11T11:44:36.446114

>> pdf version




Meanwhile…
admin — Tue, 07 Aug 2012 13:25:55 +0000
… the Imperial Tie-Fighters kept on coming… (aka Structure Data Converter & Editor + Visualizer with full support for magnetic space groups)




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



Here are the source codes of the ‘plot’ and ‘plotfitparabol.sh’ scripts. Doei!
sururi@mois:/vala/bin$ cat plot
#!/bin/bash 
gnuplot -persist <

# Reads the data points from the given file
# then uses Octave's "polyfit" function to calculate the coefficients 
# for the quadratic fit and also the minimum (maximum) value.
# Afterwards, prepares a GNUPlot script to display:
#    the data set (scatter)
#    fit function
#    the extremum point's value
#
# Written with Quantum Espresso optimizing procedures in mind.

 
if [ $# -ne 1 ]
then
    echo "Usage: plotfitparabol.sh "
    echo "Example: plotfitparabol.sh E_vs_A.txt"
    echo -e "\nNeeds octave to be accessible via \"octave\" command to work"
    echo -e "\nEmre S. Tasci , 03/2012"
    exit
fi

octave_script="data=load(\"$1\");m=polyfit(data(:,1),data(:,2),2);min=-m(2)*0.5/m(1);fmin=min*min*m(1)+min*m(2)+m(3);printf(\"f(x)=%f*x*x%+f*x%+f|%f\t%f\",m(1),m(2),m(3),min,fmin)"
oct=$(echo $octave_script|octave -q)
#echo $oct

func=${oct/|*/ }
minfmin=${oct/*|/ }
echo -e "func \t" $func
echo -e "min, f(min) \t" $minfmin

echo '$func
set term postscript enhanced color
set label "$1" at graph 0.03, graph 0.94
set output "$1.ps"
plot "$1" title "data", f(x) title "$func", "



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 > /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]----+
|Â Â  oAE*=A+oÂ Â Â Â Â Â |
|Â  .o.=..+=..Â Â Â Â Â |
|Â Â  .o...Â Â Â Â  Â Â Â  |
|Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â  |
|Â Â Â Â Â Â Â Â XXXÂ    Â  |
+-----------------+


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_exampleÂ  & 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 2x2x2 = 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.
                    *
 * 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]
227-141[3]-074[2]-052[2]-014[2]-014[2]-007[2]-009[2]
227-141[3]-074[2]-052[2]-030[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-052[2]-030[2]-030[2]-007[2]-009[2]
227-141[3]-074[2]-052[2]-030[2]-034[2]-007[2]-009[2]
227-141[3]-074[2]-052[2]-030[2]-034[2]-043[2]-009[2]
227-141[3]-074[2]-052[2]-033[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-052[2]-034[2]-007[2]-007[2]-009[2]
227-141[3]-074[2]-053[2]-010[2]-006[2]-007[2]-009[2]
227-141[3]-074[2]-053[2]-010[2]-006[2]-008[2]-009[2]
227-141[3]-074[2]-053[2]-010[2]-012[2]-008[2]-009[2]
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227-166[4]-166[2]-012[3]-008[2]-008[2]-009[2]
227-166[4]-166[2]-012[3]-012[2]-008[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- BengÃ¼ 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.. 8) 
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. 8)
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 voilÃ ! 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)

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

                    *
 *
 * 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($i=1;$i0.001)
                $arr_atoms[$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:

                    *
 * 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 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.. 8)



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
                               *
 *                                                        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=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




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 â vector representations.
latpar2vec([a,b,c,alpha,beta,gamma])

Given the a,b,c,Î±,Î² and Î³, 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,Î±,Î² and Î³ 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
                    *
 * 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                    *
 *                                              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




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.. 8) 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!.. 8)


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:










';
    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"]);
?>

<?PHP echo $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 2x2x2:
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= 1x1x1 (silly but since this is tutorial) to k=13x13x13.
#!/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!