Re: Réf. : RE: Topas prm keyword
In the GUI mode, you simply initialize a parameter by entering its name in into the grid on the codes tab, without the = sign! This is equivalent to changing the line of code you've sent from Site OH num_posns 4 x 0 y 0 z 0.315309 occ O =oh; : 0.5 min =0; max =0.5; beq 1 to Site OH num_posns 4 x 0 y 0 z 0.315309 occ O oh; : 0.5 min =0; max =0.5; beq 1 i.e. delete the = sign before the oh. Thus, I think there is no need to use the prm command (or the launch mode) in your case. However, there may be cases where it could be convenient to declare a parameter separately. For example, I have a solid solution series where all lattice parameters are a known function of the stoichiometry parameter X. If I now want to do some restrictive fitting (instead of four independent monoclinic lattice parameters I would like to refine just X), then I can use the following workaround to emulate something like the prm command in the GUI: I simply add an additional dummy site to my structure phase. Dummy site means that I may chose the name of the site and the element freely, but set the occupancy to zero. Now, I can use the x, y and z coordinates and the Beq as containers for my parameters, because with zero occupancy, the dummy atom will not contribute to the calculated intensities! I enter the starting values for my parameter(s) in the Values tab of the grid and the parameter name(s) in the Codes tab. If a parameter is not to be refined, a ! needs to precede the parameter name. Maybe this little workaround is useful to some of you. I should add that this trick works in Topas version 3, I'm not sure if it does with other versions... Best wishes, Frank Habib Boughzala wrote: So, How to initialize a variable ? Cheers /---Message original---/ /*De :*/ Kern, Arnt mailto:arnt.k...@bruker-axs.de /*Date :*/ 12/03/2010 09:05:03 /*A :*/ 'ian.mad...@csiro.au' mailto:ian.mad...@csiro.au; habib.boughz...@ipein.rnu.tn mailto:habib.boughz...@ipein.rnu.tn; rietveld_l@ill.fr mailto:rietveld_l@ill.fr /*Sujet :*/ RE: Topas prm keyword The keyword prm is exclusive to so-called Launch Mode operation, please see also the Technical Reference manual. Cheers, Arnt *From:* ian.mad...@csiro.au [mailto:ian.mad...@csiro.au] *Sent:* Freitag, 12. März 2010 08:53 *To:* habib.boughz...@ipein.rnu.tn; rietveld_l@ill.fr *Subject:* RE: Topas prm keyword Try prm not Prm (ie with all lower case letters) /Cheers/ / / /ooo0ooo/ / Ian Madsen/ / Team Leader - Diffraction Science/ / CSIRO Process Science and Engineering/ / Box 312, Clayton South 3169/ / Victoria, AUSTRALIA/ / Phone +61 3 9545 8785 direct/ / +61 3 9545 8500 switch/ / +61 (0) 417 554 935 mobile/ / FAX+61 3 9562 8919/ / Email //_ian.mad...@csiro.au_/ mailto:ian.mad...@csiro.au/ / /ooo0ooo/ *From:* Habib Boughzala [mailto:habib.boughz...@ipein.rnu.tn] *Sent:* Friday, 12 March 2010 6:45 PM *To:* rietveld_l@ill.fr *Subject:* Topas prm keyword Hi, My mail is intended to Topas users, especially to Dr. Alan Coelho I am trying to determine the carbonate / hydroxide ratio in some compounds. This is a part of 'str' block In the input file (*.inp) __ Str Prm oh 0.5 Site OH num_posns 4 x 0 y 0 z 0.315309 occ O =oh; : 0.5 min =0; max =0.5; beq 1 Site C num_posns 2 x 0 y 0 z 0 occ C =1 - 0.5 oh; : 1 min =0; max =0.5; beq 1 Site Oc num_posns 12 x 0.040114 y 0.953411 z 0.629971 occ O =(1 - 0.5 oh) / 3; : 1 min =0; max =0.25; beq 1 __ Topas 4.2 run failed... Error: prm command in unrecognised !!! Any suggestion ? P.S. This keyword is unrecognised too in all tutorials inp file examples !!! Thanks for help Habib Prof. Habib Boughzala. *L*aboratoire de *M*atériaux et *C*ristallochimie. *A*ssociation *T*unisienne de *C*ristallographie I.P.E.I.N. Mrezga, 8000. Nabeul. Tunisie. Bruker AXS GmbH, Karlsruhe HRB 107524 Amtsgericht Mannheim, Umsatzsteuer-Ident.Nr. DE812037551, Geschäftsführer - Dr. Frank Burgäzy, Bernard Kolodziej, Stephan Franz Westermann Der Inhalt dieser E-Mail ist vertraulich und ausschliesslich fuer den bezeichneten Adressaten bestimmt. Wenn Sie nicht der vorgesehene Adressat dieser E-Mail oder dessen Vertreter sein sollten, so beachten Sie bitte, dass jede Form der Kenntnisnahme,
Réf. : Re: Réf. : RE: Topas prm keyword
Hi Frank, Thank you for your detailed explanations. Really, I think so, this little workaround is useful to some topas users. Cheers Habib ---Message original--- De : Frank Girgsdies Date : 12/03/2010 10:15:22 A : Habib Boughzala; Rietveld_l@ill.fr Sujet : Re: Réf. : RE: Topas prm keyword In the GUI mode, you simply initialize a parameter by entering its name in into the grid on the codes tab, without the = sign! This is equivalent to changing the line of code you've sent from Site OH num_posns 4 x 0 y 0 z 0.315309 occ O =oh; : 0.5 min =0; max =0.5 beq 1 to Site OH num_posns 4 x 0 y 0 z 0.315309 occ O oh; : 0.5 min =0; max =0.5; beq 1 i.e. delete the = sign before the oh. Thus, I think there is no need to use the prm command (or the launch mode) in your case. However, there may be cases where it could be convenient to declare a parameter separately. For example, I have a solid solution series where all lattice parameters are a known function of the stoichiometry parameter X. If I now want to do some restrictive fitting (instead of four independent monoclinic lattice parameters I would like to refine just X), then I can use the following workaround to emulate something like the prm command in the GUI: I simply add an additional dummy site to my structure phase. Dummy site means that I may chose the name of the site and the element freely, but set the occupancy to zero. Now, I can use the x, y and z coordinates and the Beq as containers for my parameters, because with zero occupancy, the dummy atom will not contribute to the calculated intensities! I enter the starting values for my parameter(s) in the Values tab of the grid and the parameter name(s) in the Codes tab. If a parameter is not to be refined, a ! needs to precede the parameter name. Maybe this little workaround is useful to some of you. I should add that this trick works in Topas version 3, I'm not sure if it does with other versions... Best wishes, Frank Habib Boughzala wrote: So, How to initialize a variable ? Cheers /---Message original---/ /*De :*/ Kern, Arnt mailto:arnt.k...@bruker-axs.de /*Date :*/ 12/03/2010 09:05:03 /*A :*/ 'ian.mad...@csiro.au' mailto:ian.mad...@csiro.au; habib.boughz...@ipein.rnu.tn mailto:habib.boughz...@ipein.rnu.tn; rietveld_l@ill.fr mailto:rietveld_l@ill.fr /*Sujet :*/ RE: Topas prm keyword The keyword prm is exclusive to so-called Launch Mode operation, please see also the Technical Reference manual. Cheers, Arnt *From:* ian.mad...@csiro.au [mailto:ian.mad...@csiro.au] *Sent:* Freitag, 12. März 2010 08:53 *To:* habib.boughz...@ipein.rnu.tn; rietveld_l@ill.fr *Subject:* RE: Topas prm keyword Try prm not Prm (ie with all lower case letters) /Cheers/ / / /ooo0ooo/ / Ian Madsen/ / Team Leader - Diffraction Science/ / CSIRO Process Science and Engineering/ / Box 312, Clayton South 3169/ / Victoria, AUSTRALIA/ / Phone +61 3 9545 8785 direct/ / +61 3 9545 8500 switch/ / +61 (0) 417 554 935 mobile/ / FAX+61 3 9562 8919/ / Email //_ian.mad...@csiro.au_/ mailto:ian.mad...@csiro.au/ / /ooo0ooo/ *From:* Habib Boughzala [mailto:habib.boughz...@ipein.rnu.tn] *Sent:* Friday, 12 March 2010 6:45 PM *To:* rietveld_l@ill.fr *Subject:* Topas prm keyword Hi, My mail is intended to Topas users, especially to Dr. Alan Coelho I am trying to determine the carbonate / hydroxide ratio in some compounds This is a part of 'str' block In the input file (*.inp) __ Str Prm oh 0.5 Site OH num_posns 4 x 0 y 0 z 0.315309 occ O =oh; : 0.5 min =0; max =0.5; beq 1 Site C num_posns 2 x 0 y 0 z 0 occ C =1 - 0.5 oh; : 1 min =0; max =0.5; beq 1 Site Oc num_posns 12 x 0.040114 y 0.953411 z 0.629971 occ O =(1 - 0.5 oh) / 3; : 1 min =0; max =0.25; beq 1 __ Topas 4.2 run failed... Error: prm command in unrecognised !!! Any suggestion ? P.S. This keyword is unrecognised too in all tutorials inp file examples !!! Thanks for help Habib Prof. Habib Boughzala. *L*aboratoire de *M*atériaux et *C*ristallochimie. *A*ssociation *T*unisienne de *C*ristallographie I.P.E.I.N. Mrezga, 8000. Nabeul. Tunisie. - -- Bruker AXS GmbH, Karlsruhe HRB 107524 Amtsgericht Mannheim, Umsatzsteuer-Ident.Nr. DE812037551, Geschäftsführer - Dr. Frank Burgäzy, Bernard Kolodziej, Stephan Franz Westermann
RE: Réf. : RE: Topas prm keyword
Hello! I was looking into this for my Mullite solid solutions. I defined the variable and wrote it to text file at the end of the refinement. You can use user defined parameters by putting them in more.inp in the TOPAS directory. One does need to take care as this 'more.inp' is included in every GUI refinement, I did this a while ago, but as I recall the script is only opened when TOPAS is first loaded so if you need to make a change to more.inp you need to restart TOPAS. In the end I decided to stop fiddling and just ended up using TOPAS in launch and batch modes. Warm Regards, Ross -Original Message- From: Frank Girgsdies [mailto:girgs...@fhi-berlin.mpg.de] Sent: Friday, 12 March 2010 5:15 PM To: Habib Boughzala; Rietveld_l@ill.fr Subject: Re: Réf. : RE: Topas prm keyword In the GUI mode, you simply initialize a parameter by entering its name in into the grid on the codes tab, without the = sign! This is equivalent to changing the line of code you've sent from Site OH num_posns 4 x 0 y 0 z 0.315309 occ O =oh; : 0.5 min =0; max =0.5; beq 1 to Site OH num_posns 4 x 0 y 0 z 0.315309 occ O oh; : 0.5 min =0; max =0.5; beq 1 i.e. delete the = sign before the oh. Thus, I think there is no need to use the prm command (or the launch mode) in your case. However, there may be cases where it could be convenient to declare a parameter separately. For example, I have a solid solution series where all lattice parameters are a known function of the stoichiometry parameter X. If I now want to do some restrictive fitting (instead of four independent monoclinic lattice parameters I would like to refine just X), then I can use the following workaround to emulate something like the prm command in the GUI: I simply add an additional dummy site to my structure phase. Dummy site means that I may chose the name of the site and the element freely, but set the occupancy to zero. Now, I can use the x, y and z coordinates and the Beq as containers for my parameters, because with zero occupancy, the dummy atom will not contribute to the calculated intensities! I enter the starting values for my parameter(s) in the Values tab of the grid and the parameter name(s) in the Codes tab. If a parameter is not to be refined, a ! needs to precede the parameter name. Maybe this little workaround is useful to some of you. I should add that this trick works in Topas version 3, I'm not sure if it does with other versions... Best wishes, Frank Habib Boughzala wrote: So, How to initialize a variable ? Cheers /---Message original---/ /*De :*/ Kern, Arnt mailto:arnt.k...@bruker-axs.de /*Date :*/ 12/03/2010 09:05:03 /*A :*/ 'ian.mad...@csiro.au' mailto:ian.mad...@csiro.au; habib.boughz...@ipein.rnu.tn mailto:habib.boughz...@ipein.rnu.tn; rietveld_l@ill.fr mailto:rietveld_l@ill.fr /*Sujet :*/ RE: Topas prm keyword The keyword prm is exclusive to so-called Launch Mode operation, please see also the Technical Reference manual. Cheers, Arnt *From:* ian.mad...@csiro.au [mailto:ian.mad...@csiro.au] *Sent:* Freitag, 12. März 2010 08:53 *To:* habib.boughz...@ipein.rnu.tn; rietveld_l@ill.fr *Subject:* RE: Topas prm keyword Try prm not Prm (ie with all lower case letters) /Cheers/ / / /ooo0ooo/ / Ian Madsen/ / Team Leader - Diffraction Science/ / CSIRO Process Science and Engineering/ / Box 312, Clayton South 3169/ / Victoria, AUSTRALIA/ / Phone +61 3 9545 8785 direct/ / +61 3 9545 8500 switch/ / +61 (0) 417 554 935 mobile/ / FAX+61 3 9562 8919/ / Email //_ian.mad...@csiro.au_/ mailto:ian.mad...@csiro.au/ / /ooo0ooo/ *From:* Habib Boughzala [mailto:habib.boughz...@ipein.rnu.tn] *Sent:* Friday, 12 March 2010 6:45 PM *To:* rietveld_l@ill.fr *Subject:* Topas prm keyword Hi, My mail is intended to Topas users, especially to Dr. Alan Coelho I am trying to determine the carbonate / hydroxide ratio in some compounds. This is a part of 'str' block In the input file (*.inp) __ Str Prm oh 0.5 Site OH num_posns 4 x 0 y 0 z 0.315309 occ O =oh; : 0.5 min =0; max =0.5; beq 1 Site C num_posns 2 x 0 y 0 z 0 occ C =1 - 0.5 oh; : 1 min =0; max =0.5; beq 1 Site Oc num_posns 12 x 0.040114 y 0.953411 z 0.629971 occ O =(1 - 0.5 oh) / 3; : 1 min =0; max =0.25; beq 1 __ Topas 4.2 run failed... Error: prm command in unrecognised !!! Any suggestion ? P.S. This keyword is unrecognised too in all
