Bondlengths and Angles in Fullprof

(Updated 11th August 2001)

From: "Mastoraki Eirini" [mastorak@iesl.forth.gr] To: [rietveld_l@ill.fr] Subject: Bond lengths in Fullprof Date: Fri, 3 Aug 2001 15:59:23 +0300 Dear all, For those who use fullprof could someone tell me how to generate the bond lengths and angles with their esd' s by fullprof? I have already tried to do what is reffered to an old mail at reitveld list regarding the generation of the bond lenths. According to this mail this is possible by setting the parameter JDIST to 3 but unfortunately it didn't work. Is there any advice on fixing this? Thank you in advance, Irini

Date: Tue, 07 Aug 2001 13:53:30 +0200 To: rietveld_l@ill.fr From: "Magnus H. Sørby" [magnuss@kjemi.uio.no] Subject: Re: Bond lengths calculation by Fullprof Irini, You probably need to add a new line after the line containing JDIST. It should contain 3 parameters: The maximum distance between atoms to be output (a real number) The maximum distance between atoms to output the angle between them (a real number) A string to tell whether Bond Angle Calculations are to be performed. The string should be 'BVS' to perform such calculations. Hope this helps :-) Best regards, Magnus H. Sørby

Date: Tue, 07 Aug 2001 13:05:54 +0200 To: rietveld_l@ill.fr From: Armel Le Bail [alb@cristal.org] Subject: Re: Bond lengths calculation by Fullprof The fact is that the Fullprof manual does not mention any JDIST=3 option. Some text about that option is in the fp2k.inf file : "The calculation of distances and angles, as well as bond valence sums can be done automatically, without using external programs (e.g. BONDSTR). This is obtained using JDIST=3,4. Output files with extension "dis" contain all the relevant information for the different phases." Trying to guess what should have been explained into the manual, I succeeded in making the stuff working in one hour this morning ;-)). The tbbaco.pcr example was taken from the series of Fullprof examples, and the following changes were made : Sy0 =1 and Sym =1 at the following line : !Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 Syo Prf Ins Rpa Sym Hkl Fou Sho Ana 0 0 1 0 1 0 4 0 1 1 0 1 1 0 0 0 0 Then : More = 1 as below, then 2 additional lines are needed , with jdi (=JDIST) = 3 at the first additional line and details about the distance calculations in the second additional line, before the space group : !------------------------------------------------------------------------------- ! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 8.85 !------------------------------------------------------------------------------- Tb2BaCoO5 ! !Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More 5 0 0 0.0 0.0 1.0 0 0 0 0 0 1188.24 0 5 1 ! !Jvi Jdi Hel Sol Mom Ter Brind RMua RMub RMuc Jtyp 1 3 0 0 0 0 1.0000 0.0000 0.0000 0.0000 0 ! ! Max_dst(dist) (angles) Bond-Valence Calc. 3.5000 0.0000 1 I m m m <--Space group symbol This should work (at least in that case), provided you perform the last refinement cycle at which the calculation is done. In case of problems, use the old good BONDSTR.EXE program, available at the same place as Fullprof by anonymous FTP : charybde.saclay.cea.fr/pub/divers/fullp/ms-dos/ Best, Armel Le Bail http://sdpd.univ-lemans.fr/course/

From: "Yokochi, Alexandre" [alex.yokochi@orst.edu] To: "'rietveld_l@ill.fr'" [rietveld_l@ill.fr] Subject: RE: Bond lengths calculation by Fullprof Date: Tue, 7 Aug 2001 09:32:02 -0700 Armel, Irini, and all, The option to do bond length calculations and BVS calculations, etc, is not explicitly given in the HTML fullprof manual. It is, however, described in the appendix included with the more recent releases of Fullprof (you know, the big ol pdf file called something like app_fp2k_man.pdf, right about page 20). I only caught onto it after I had a lead from someone here. Below, is a slice of a prf file that does the bond lengths and stuff correctly. Also, if you're really interested in the BVS calculations, you may be better off using Brown's Valist program. AlexY ! Zero Code Sycos Code Sysin Code Lambda Code MORE ->Patt# 1 -0.01583 0.50 0.00000 0.10 0.00000 0.10 0.000000 0.00 0 ! Background coefficients/codes for Pattern# 1 138.71 -4.4682 0.53262 0.0000 0.0000 0.0000 0.500 0.500 0.500 0.100 0.100 0.100 !--------------------------------------------------------------------------- ! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 0.00 !--------------------------------------------------------------------------- 2H-CuScO2 ! !Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More 4 0 0 0.0 0.0 1.0 0 0 0 0 0 0.00 0 7 1 ! !Jvi Jdi Hel Sol Mom Ter Brind RMua RMub RMuc Jtyp 2 3 0 0 0 0 1.0000 0.0000 0.0000 0.0000 1 ! ! Max_dst(dist) (angles) Bond-Valence Calc. 2.9000 180.0000 BVS ! N_cations N_anions Tolerance(%) / Name or cations/ and Anions 3 1 80.00 CU+1 SC+3 MG+2 O-2 ! P 63/m m c <--Space group symbol !Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes ! beta11 beta22 beta33 beta12 beta13 beta23 /Codes Cu CU 0.35645 0.71293 0.25000 0.00000 2.00000 0 0 2 0 10.20 10.40 0.00 0.10 0.00

Old Discussion on doing bond-angles and lengths in Fullprof

From: "Yokochi, Alexandre" [alex.yokochi@orst.edu]
To: "'rietveld_l@ill.fr'" [rietveld_l@ill.fr]
Subject: Bond lengths in Fullprof
Date: Fri, 1 Jun 2001 15:55:38 -0700

Hi all,

	For those of you out there who use Fullprof, what is your favourite
program to generate tables of bond lengths and angles, preferrably with
e.s.d.'s (or s.u.'s if you prefer that).

	Also, one of my students reports that Fullprof running on Windows ME
sometimes causes to system to freeze.  Any advice on fixing this?

	Thanks, AlexY

Dr. Alexandre F. T. Yokochi
Assistant Professor (Senior Research)
Director, X-ray Crystallographic Facilities
Department of Chemistry
Oregon State University
Corvallis, OR 97331-4003

Ph#  (541) 737-6724	Email: alex.yokochi@orst.edu
Fax# (541) 737-2062	Web Page: crystal.chem.orst.edu/~alexy (temporarily
unavailable)

Date: Fri, 1 Jun 2001 20:18:11 -0500 (CDT)
From: Miguel Hesiquio Garduno [miguelhg@esfm.ipn.mx]
To: "Yokochi, Alexandre" [alex.yokochi@orst.edu]
Cc: rietveld_l@ill.fr
Subject: Re: Bond lengths in Fullprof

Hi Alexandre:
About the problem with runnin fullprof: You have to write in the
autoexec.bat file this:

Set c:\fullprof\fp98    
 
if your program is in the subdirectory fullprof and if it is fullprof 98

Also, if you have the newest version maybe this is the problem, try to use
the version of october 1998.

Miguel Hesiquio
ESFM-IPN
Mexico

Date: Sat, 2 Jun 2001 10:46:29 +0200 (MET DST)
From: Magnus Helgerud Sorby [m.h.sorby@kjemi.uio.no
To: [rietveld_l@ill.fr]
Subject: Re: Bond lengths in Fullprof

The latest verson of Fullprof(2k) can do bond length and angle
calculations directly. The parameter JDIST (which appears when IMORE is
not zero) must be set to 3 for the phases of interest.
The result will come in files named CODFILn.dis (one for each phase).

I haven't tried this myself yet, but it is described in the appendix of
the manual, App_fp2k_man.pdf, which is available on the web.

Best wishes,

Magnus H. Sorby
magnuss@kjemi.uio.no