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Re : [sdpd] mol_tpcr

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      <p>Salut mon cher Karim,<br>
comment vas tu? cela fait un bon moment qu on ne sait pas contacte. j espère que tout va bien de ton cote.<br>
Ici, a Osaka, tout va bien. j avance bien dans mon projet et j espère prolonger mon séjour encore un ou deux ans. j espère d ici peu déposer mon premier brevet:).<br>
enchallah aid moubarek said<br>
bonnes fetes<br>
salam<br>
Hamdi<br>
<br>
 <br>
-----------------------------<br>
Hamdi BEN YAHIA, PhD<br>
Postdoctoral Researcher<br>
Advanced Battery Research Group<br>
Research Institute for Ubiquitous Energy Devices<br>
Midorigaoka 1-8-31, Ikeda, Osaka 563-8577, Japan<br>
TEL : &#43;81-72-751-7932<br>
FAX : &#43;81-72-751-9609<br>
E-MAIL : <a href="mailto:benyahia.hamdi%40aist.go.jp";>benyahia.hamdi...@aist.go.jp</a><br>
USL : <a href="http://www.aist.go.jp";>http://www.aist.go.jp</a><br>
<br>
________________________________<br>
De : &quot;<a href="mailto:karim.adil%40univ-lemans.fr";>karim.adil...@univ-lemans.fr</a>&quot; &lt;<a href="mailto:karim.adil%40univ-lemans.fr";>karim.adil...@univ-lemans.fr</a>&gt;<br>
À : <a href="mailto:sdpd%40yahoogroups.com";>sdpd...@yahoogroups.com</a><br>
Envoyé le : Dimanche 1 Mars 2009 20h20<br>
Objet : Re: [sdpd] mol_tpcr<br>
<br>
Hi<br>
<br>
you need to create an instruction file like this one (example from fullprof).<br>
You just have to transform the atomic coordinate in a good form (cartesian,<br>
z-matrix.... ). For that, you can use Babel for example.<br>
After running the executable mol_tpcr (you'll find him in the directory of<br>
fullprof), you'll get the atomic coordinate in a good form for use the rigid<br>
body option.<br>
<br>
Good luck<br>
<br>
Karim<br>
<br>
------------ ------  start File: urea.cfl<br>
------------ --------- --------- --------- ----<br>
!<br>
! Example of molecule given in a crystal<br>
!<br>
!<br>
CELL     5.584001   5.584001   4.688990  90.0  90.0  90.0<br>
!<br>
MOLEX   8   Urea      F<br>
!    Xc         Yc       Xc         Phi     theta    Chi     TypeAngles <br>
TypeThermal<br>
0.00000  0.50000  0.32811         0.0     0.0     0.0         P          ISO<br>
0          0         0          0       0       0           !Refinement<br>
codes<br>
!Atm Spe        x        y        z      N1  N2  N3    Biso      Occ<br>
Ur1  C       0.00000  0.50000  0.32811    0   0   0   0.50000   1.00000<br>
Ur2  O       0.00000  0.50000  0.59574    0   0   0   0.50000   1.00000<br>
Ur3  N       0.14466  0.64466  0.17816    0   0   0   0.50000   1.00000<br>
Ur4  N      -0.14466  0.35534  0.17816    0   0   0   0.50000   1.00000<br>
Ur5  H       0.14261  0.64261 -0.03550    0   0   0   0.50000   1.00000<br>
Ur6  H       0.25589  0.75589  0.28398    0   0   0   0.50000   1.00000<br>
Ur7  H      -0.14261  0.35739 -0.03550    0   0   0   0.50000   1.00000<br>
Ur8  H      -0.25589  0.24411  0.28398    0   0   0   0.50000   1.00000<br>
!             x(P1)    y(P1)    z(P1)     x(P2)    y(P2)    z(P2) <br>
x(P3)    y(P3)    z(P3)<br>
XYZ_Frame   0.00000  0.50000  0.59574   1.00000  0.50000  0.32811 <br>
0.00000 0.50000  0.32811<br>
!<br>
------------ ------  End File: urea.mol<br>
------------ --------- --------- --------- ----<br>
<br>
The meaning of the keyword CELL and other parameters are obvious from <br>
the given<br>
names.<br>
<br>
The keyword MOLEX must be followed by the number of atoms in the molecule, the<br>
name<br>
of the molecule and the kind of coordinates provided below (F: for fractional<br>
coordinates<br>
with respect the the given cell, C: cartesian, Z: for Z-matrix or S: for<br>
spherical coordinates )<br>
<br>
The parameters Xc, Yc, Zc are the fractional coordinates of the origin of the<br>
internal<br>
Cartesian system with respect to the given unit cell.<br>
<br>
The angles Phi,Theta and Chi are Euler angles (two types, P: Phi and Theta are<br>
the polar<br>
spherical angles of the Z-axis of the Cartesian internal frame with respect to<br>
the<br>
Cartesian frame attached to the unit Cell, E: conventional Euler angles).<br>
<br>
The keyword &quot;XYZ_Frame&quot; is followed by the fractional coordinates of three<br>
points in the<br>
unit cell. These three points will serve to position the molecule in <br>
the crystal<br>
and to calculate<br>
the centre and Euler angles. The origin of the Cartesian internal <br>
system will be<br>
put in the<br>
third given point. The z-axis is parallel to the vector P1-P3, the x-axis lies<br>
within the plane<br>
(P1-P3,P2-P3) , and the y-axis completes the direct frame.<br>
<br>
The numbers N1,N2,N3 are integers defining the connectivity of the molecule as<br>
it is conventional<br>
in the Z-matrix formulation. If all of them are put to zero, the program will<br>
generate automatically<br>
a connectivity table taking the first atom as the origin, the second along &quot;x&quot;<br>
and the third in<br>
the x-y plane. This internal Cartesian frame will be put<br>
<br>
Quoting José Miguel Galiana &lt;dimuoh...@yahoo. es&gt;:<br>
<br>
&gt; Dear all<br>
&gt; anyone know how to use the mol_tpcr software in Fullprof?<br>
&gt; Thank you.<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt; [Non-text portions of this message have been removed]<br>
&gt;<br>
&gt;<br>
<br>
[Non-text portions of this message have been removed]<br>
<br>
</p>

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