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RE: [sdpd] mol_tpcr
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<p>After Google translate, I finally find this is a private emailâ?¦???<br>
br>
<br>
Yours Sincerely<br>
-------------------<br>
<br>
Xiaodong (Tony) Wang<br>
Department of Imaging and Applied Physics<br>
<br>
Curtin University<br>
<br>
From: <a href="mailto:sentto-1052548-2703-1314681537-iangie%3D126.com%40returns.groups.yahoo.com";>sentto-1052548-2703-1314681537-iangie=126.com...@returns.groups.yahoo.com</a> [mailto:<a href="mailto:sentto-1052548-2703-1314681537-iangie%3D126.com%40returns.groups.yahoo.com";>sentto-1052548-2703-1314681537-iangie=126.com...@returns.groups.yahoo.com</a>] On Behalf Of benyahia hamdi<br>
Sent: 2011å¹´8æ??30æ?¥ 13:19<br>
To: <a href="mailto:sdpd%40yahoogroups.com";>sdpd...@yahoogroups.com</a><br>
Subject: Re : [sdpd] mol_tpcr<br>
<br>
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>
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 : +81-72-751-7932<br>
FAX : +81-72-751-9609<br>
E-MAIL : <a href="mailto:benyahia.hamdi%40aist.go.jp";>benyahia.hamdi...@aist.go.jp</a> <mailto:benyahia.hamdi%40aist.go.jp> <br>
USL : <a href="http://www.aist.go.jp";>http://www.aist.go.jp</a><br>
<br>
________________________________<br>
De : "<a href="mailto:karim.adil%40univ-lemans.fr";>karim.adil...@univ-lemans.fr</a> <mailto:karim.adil%40univ-lemans.fr> " <<a href="mailto:karim.adil%40univ-lemans.fr";>karim.adil...@univ-lemans.fr</a> <mailto:karim.adil%40univ-lemans.fr> ><br>
Ã? : <a href="mailto:sdpd%40yahoogroups.com";>sdpd...@yahoogroups.com</a> <mailto:sdpd%40yahoogroups.com> <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 "XYZ_Frame" 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 "x"<br>
and the third in<br>
the x-y plane. This internal Cartesian frame will be put<br>
<br>
Quoting José Miguel Galiana <dimuoh...@yahoo. es>:<br>
<br>
> Dear all<br>
> anyone know how to use the mol_tpcr software in Fullprof?<br>
> Thank you.<br>
><br>
><br>
><br>
><br>
> [Non-text portions of this message have been removed]<br>
><br>
><br>
<br>
[Non-text portions of this message have been removed]<br>
<br>
[Non-text portions of this message have been removed]<br>
<br>
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