Full Year 2007
---------------------- >> 6 December 2007: Small modification in the merged magnetic reflections file ---------------------- - The output name of the merged magnetic reflections file, generated only for single crystal patterns when the command "mag_merge" is given, has been changed in order to take into account the phase and pattern. The name of the file is now "codfil"_nph_npat_merged.int, where nph is the number of the phase and npat the number of the pattern (see note of 25 January 2007). Moreover the forbidden reflections (strictly calculated as zero) are no more output into the final intensity file that contains only averaged observed intensities for the corresponding magnetic model used for treating the raw data. The merged reflection file can be used as input in futher refinements - Some other cosmetic changes have been performed. ---------------------- >> 12 November 2007: Small modification in BasIreps and sequential FullProf ---------------------- - The maximum number of atom sites has been increased up to 24. If for whatever reason (low symmetry of k implying splitting in many sub-orbits) this number is attained the program rises a message for diminishing the number of input atoms. - Another argument has been introduced when invoking sequential FullProf for asking the program to save calculated profiles (extension .calc) that can be later visualized as a surface using a buffer file and WinPLOTR-2006. Only two formats are output corresponding to INSTR=0 and INSTRM=10 depending if there is a constant step (0) or not (10). Notice that this argument of value 'y' for saving the calculated patterns must precede the argument introduced the 16 October 2007. The syntax of the line invoking the program in sequential mode is now: [w]fp2k cyc my_pcr codedat[.extension] n1 n2 a1 a2 a3 a4 a5 a6 where my_pcr: codefile of the initial PCR file that will be used for refining the data codedat: common code (first common characters) for all data files to be treated [.extension] : Optional. It corresponds to the extension of the data files. To be given if the extension is different from ".dat" n1 : Starting number (trailing numerical characters) of the first file to be treated. The complete file name is: codedatn1.dat or codedatn1.extension n2 : Final number (trailing numerical characters) of the last file to be treated. The complete file name is: codedatn2.dat or codedatn2.extension If n1 < n2 the program will treat the data using a step = 1 for changing the names of the files to be treated. If n1 > n2 then step = -1. If a file is lacking, the program increments automatically the file name up to finding an existing file with the proper name. a1 : y/n ".prf" files are saved/deleted a2 : y/n ".hkl" files are saved/deleted a3 : y/n ".mic",".str",".siz" files are saved/deleted a4 : y/n ".dis" files are saved/deleted a5 : y/n ".calc" files are/are not generated a6 : n (for fp2k only), the question for closing the session is not asked ---------------------- >> 16 October 2007: Another argument for fp2k in sequential mode ---------------------- - When running the console version of the FullProf executable (fp2k) in sequential mode, the user can add a new argument (value: "y" or "n") to make the program raise a prompt asking for finishing the session. This is important if the user wants to run a script file (in batch mode) with different executing lines invoking the program. Suppose that the script file (*.bat file in Windows, no particular extension in Linux) contains the following lines: fp2k cyc my_pcr1 codedat n1 n2 y y y y n fp2k cyc my_pcr2 codedat n3 n4 y y y y n fp2k cyc my_pcr3 codedat n5 n6 y y y y y The script will run three sequential refinements corresponding to three kinds of PCR files adapted to particular diffraction patterns existing in the list (see notes of 20 November 2005, 29 April 2004 and 10 February 2004). The last argument is needed for the first two runs because otherwise the script is interrupted by a question comming from FullProf. Putting "n" suppress the question and let the script continuing without thre presence of the user. ---------------------- >> 12 October 2007: New Linux version of the FullProf Suite. Size of wfp2k window ---------------------- - Several programs of the FullProf Suite have internally been modified in order to provide a similar behaviour under Linux and Windows. Now the toolbar includes a more complete Setting window where the user can provide the command for launching console programs (like k_search or Mol_tpcr) from the toolbar. For Windows the command is "cmd /t:0e /c" and for Linux "konsole -e" or "xterm -e" WARNING: The Linux version is not yet on the web site! - The size of the window reserved for running FullProf (graphic version wfp2k) can now be controlled by the user by changing the value of the keyword "shorten" in the file "fullprof.dim". The format of this keyword is: shorten = value. It must appears below the lines reserved for dimensioning global arrays. The value of "shorten" is a real number less than 1.0 (values 0.5 to 0.8 are OK). ----------------------- >> 27 September 2007: New program K_Search. Small change in Fp_Studio. ----------------------- New version of XLENS. New version of WinPLOtr (Windows) - A new program that can replace the program SuperCell has been written. It looks directly for propagation vectors. The input file can be automatically generated by WinPLOTR-2006 (the file is called by default: k_search.sat) and the program can be run from the FPS-Toolbar button or "Programs" menu. For making changes in the input file the user can do it manually modifyind the conditions. The keywords are self explanatory. - A new keyword has been introduced in FullProf Studio in order to draw the arrows starting from the atom position instead of being centred at the atom position. Fp_Studio use this new origin if the keyword "arrow_disp" appears somewhere in the *.fst file. - A new version of XLENS allowing a direct visualisation or the obtained crystal structure with Fp_Studio is now available. - A new version of WinPLOTR has been included. See Winplotr.new for changes. ---------------------- >> 13 August 2007: Small corrections. New 2D mode in WinPLOTR-2006 ---------------------- - Some minor corrections in the code of "wfp2k" have been performed in order to produce a coherent behaviour when pure diffraction pattern calculations are asked. The program does not prompt anymore for an input data file whe it is not needed. The user should be aware that the executable "wfp2k" may be much slower than the console version "fp2k". This is due to the high number of Windows/Xwindows resources used by the graphic part and for simulating a console using the internal editor of the Winteracter library. If one needs fast calculation it is suggested to use the console version of the FullProf executable in the setting of the toolbar or invoke directly the program from a console window. The use of the console version has also the advantage of no interference with the simultaneous use of other programs like Fp_Studio. The information is always displayed in the window irrespective of changing the active window with the mouse. - WinPLOTR-2006 has now the possibility for selecting the FullProf executable. The user has the option between the Winteracter version "wfp2k" or the console version "fp2k". Look into the menu "Options/Preferences..." A error introduced in the last distribution when changing the x-space has been corrected. - A new mode for working with 2D detectors is being implemented in WinPLOTR-2006. In the present version the program is able to read 2D detector data from the database of the ILL of the instruments: D9, D15, D10 and D19. A simple display (with zoom and some other facilities) of the different numors and frames is available just exploring the "2D menu" accessible from the "File" menu. ---------------------- >> 19 May 2007: Corrections in the toolbar and Socabim format ---------------------- - Some misbehaviour concerning the invocation of the new version of FullProf from the toolbar has been corrected. The ckecking for recognizable files has been also updated. When ambiguities may arise the toolbar ask the user for the desired action. More documentation has been added to the toolbar help menu. - From now, reading a UXD file (Socabim format) from FullProf or from WinPLOTR-2006 converts automatically the data to total counts in case of data given in counts per second (CPS). If the old WinPLOTR (Windows) is used the program always asks (in case of CPS data) for representig "counts" or "counts per second". The first option must be selected if one wants to save data (for instance background points) to be used with FullProf. ---------------------- >> 8 May 2007: New version of FullProf. Template CDR file. Fp_Studio ---------------------- - The current version of FullProf has been updated to: **********************************************************' ** PROGRAM FullProf.2k (Version 4.00 - May2007-ILL JRC) **' **********************************************************' A new executable of FullProf called "wfp2k.exe" in Windows and "wfp2k" in Linux has been recompiled and modified according to the Winteracter library. In Windows this executable replaces the old one compiled with the RealWin library. The console version, called "fp2k.exe" (Windows) and "fp2k" (Linux), has also been updated and continue to be distributed in order to allow scripting ways for running the program. The program "wfp2k" can be directly invoked from the FullProf Suite Toolbar, by clicking directly on its icon, on a desktop shortcut, or by entering its name (without quotes) in a windows shell. It can also been invoked from whatever version of WinPLOTR. We assume that the program is invoked from the Toolbar. If no PCR file is loaded into the Toolbar clicking on the FullProf button opens the program and it appears as a white split window with the following menu items: "Load", "Edit PCR", "Mode", "Run" and "Exit". The "Load" menu selects a PCR file and, if the corresponding data/int file exists or it corresponds to a multipattern file, automatically runs the job. The upper part of the window shows the traditional scroll lines informing about the calculations and the bottom part shows the diffraction pattern. When the job finishes the user can zoom on the graphic part. If the user clicks on the "Run" menu, the program executes another time the same PCR file. Clicking on "Edit PCR" invokes the program EdPCR with the current PCR file as argument, so the user can perform modifications before re-running the program. The program remains open until the user selects "Exit" or a fatal error condition appears somewhere during running the job. The user can change the PCR file just selecting another time the "Load" menu. The program starts always in the "normal" mode. Selecting the menu "Mode" the user can select the "Sequential" mode for running a set of data files as a function of temperature using a starting PCR file (see notes of 20 November 2005, 29 April 2004 and of 10 February 2004). If the "Sequential" mode is selected, the "Load" menu makes appear a dialog window asking for the name of the starting PCR file, the codes of the data files, their extension, and the numbers of the files to be treated. Options for saving intermediate files are also provided. When the program runs in sequential mode the different diffraction patterns are displayed in the graphic windows. Incompatibilities: In order to display the diffraction patterns, the program automatically changes Ls2 to the value 4 for the first pattern. This has some incompatibilities with the use of other values of Ls2. Only the case of simulated annealing when one wants to write the file "simann.fst" (see note of 14 July 2004 and the recent manual of FullProf Studio) has been extended to accept the values Ls2= 4, 5. For using the other options one has to run the console version of FullProf: fp2k - A template CDR-file is now automatically created when using the option to generate a file *.pow for XLENS (see note of 30 March 2007). The user has to introduce the content of the unit cell according to the rules given in the XLENS manual. - A bug in the generation of the *.fst file for FullProf Studio in the case of using time reversal operators for describing the magnetic structure has been corrected. No magnetic symmetry operators were written in the *.fst file. ---------------------- >> 10 April 2007: New version of Fp_Studio able to display polyhedra. ---------------------- - The present version of Fp_Studio is able to display polyhedra. This part is still under testing and soon a more complete version with all the GUIs options operative will be distributed. For the moment the only keyword to be learn is POLY [label] [color R G B A] [EDGES] [RADIUS x.x] [EDGECOL R G B] At present it works only when the CONN or BOND commands have previouly been defined for the central atom. Example: ..................................... ATOM BA BA 0.50000 0.50000 0.00000 nodisplay ATOM HO HO 0.50000 0.00000 0.20243 ATOM NI NI 0.00000 0.00000 0.00000 ATOM O1 O 0.00000 0.24332 0.14900 ATOM O2 O 0.50000 0.00000 0.00000 bond NI O1 0 2.3 bond NI O2 0 1.85 CONN HO O 0 2.6 poly NI color 0 1 1 0.5 poly HO edges radius 2 ................................ The two commands "poly" instruct the program for displaying polyhedra around NI and HO atoms. Notice that the HO polyhedra will have the same color as the central atom (default) and the polyhedra will be emphasized using edges. The polyhedra around the NI atoms have a different color RGB=011 than the default color for the central atom, moreover the pohyhedra will be transparent (A=0.5). For more details consult the new version of the manual. ---------------------- >> 30 March 2007: Toolbar for accessing the programs. New FullProf Suite. Support for XLENS/07 from Jordi Rius ---------------------- - A toolbar for accessing the whole set of program of the FullProf Suite has been developed and it is now distributed in the package. Some utilities, like DataRed and CheckGroup are now accessible from the toolbar and have a GUI. The name of the executable is "tfp.exe" in Windows and "tfp" in Linux. It can be invoked from a shell window or from the shorcut generated by the installer (Windows). This last shorcut is the only one created by the installer, if the user prefers to have a direct access to WinPLOTR or WinPLOTR-2006 he(she) should do that manually. All the programs of the FullProf Suite are accessible from the Toolbar The first thing the user should do after opening for the first time the toolbar is to go to the "Settings" menu and fill up the fields of the opened dialog. It is important to conform to the correct syntax of the programs to be run. For instance, for running FullProf directly from the toolbar the name of the program should be "fp2k" in Linux or "wfp2k.exe" in Windows. If the program to be run (an Editor, for instance) is not in the PATH the complete name should be given, e.g.: "C:\Program Files\Crimson Editor\cedt.exe" The default browser for Windows is "C:\Program Files\Mozilla Firefox\firefox.exe" and for Linux "mozilla". This is still under testing. - The program XLENS/07 designed for solving crystal structures from single crystal and powder diffraction data are now accessible from the FullProf Suite. For details concerning XLENS the user is asked to contact Jordi Rius at: firstname.lastname@example.org The program XLENS/07 will be distributed within the FullProf Suite (at present a testing version is distributed). The program and manual are accessible from the FullProf Suite Toolbar. The input files of extension "*.cdr" are recognized by the FPS toolbar and as soon as they are loaded clicking on the XLENS button launches the program for the loaded file. Clicking on the GFourier button on the Toolbar the program displays automatically the MAP file generated by XLENS. Running FullProf in profile matching mode (Le Bail fit: Jbt=2) and putting More=1 and Jvi=12, the program generates a file of extension POW that is directly readable by XLENS for trying to solve the structure. See manual of XLENS for details about its content. Remember that the user can control the degree of overlap for clusters by changing the default values of "RMub" and "RMuc" parameters in the same line as "Jvi". See the manual of FullProf for details. For Jvi=12 the same criterion as for Jvi=11 is applied. In the future a GUI will be developed in order to handle the input control file. - A bug in the calculations with the new way of working with multiple single crystal patterns appeared in some circumstances. Moreover the calculation of the global chi square was not performed. A re-writting of a part of a subroutine has corrected both bugs. - The current version of FullProf has been updated to: **********************************************************' ** PROGRAM FullProf.2k (Version 3.90 - Mar2007-ILL JRC) **' **********************************************************' ---------------------- >> 16 February 2007: Bug in spherical description of magnetic moments ---------------------- - A bug in the calculation of the components of magnetic moments along the crystallographic axes for triclinic cells with strong departure of angles from 90 degree, and when the spherical description was used, has been corrected. - The text of the note of 8 February 2007 has been changed. ---------------------- >> 9 February 2007: New facility for quantitative analysis ---------------------- - It is now possible to create a database using FullProf for quantitative phase analysis. One can calculate the structure factors of a particular crystalline phase and store them in a file using HKL=5 (see note of 3 July 2003). A new line containing the space group and the cell parameters has been included. The created file can be renamed arbitrarily and the file can be read back by a job with NAT=0, JBT=-3 and IRF=2. After the name of the phase, and using the COMMANDS instructions, one can put the name of the file to be read after the keyword FILE_HKL (not case sensitive!). The format of the command is: FILE_HKL n_pat my_hkl_file_name Where n_pat is the number of the pattern for wich the structure factors file named "my_hkl_file_name" is given. If the space group and the cell parameters do not coincide with what is written in the file my_hkl_file_name the stored values are re-copied to the PCR file. The cell parameters are re-copied only in the case the sum of the absolute differences is greater than 4. Otherwise the parameters of the PCR file are kept. In the following example the space group and cell parameters are imported from the file "quant.hkl" !------------------------------------------------------------------------------- ! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 0.23 !------------------------------------------------------------------------------- My Phase name ! COMMANDS ..... (other commands) file_hkl 1 quant.hkl ..... (other commands) END COMMANDS !Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More 0 0 0 0.0 0.0 1.0 -3 2 0 0 0 2147.799 0 7 0 ! P 1 <--Space group symbol !-------> Profile Parameters for Pattern # 1 ! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model 13.492 0.00000 0.00000 0.00000 0.00000 0.00000 0 11.00000 0.000 .000 0.000 0.000 0.000 ! U V W X Y GauSiz LorSiz Size-Model 0.0161020 -0.00158 0.00291 0.000000 0.000000 0.000000 0.000000 0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 ! a b c alpha beta gamma #Cell Info 0.00000 0.000000 0.000000 90.000000 90.000000 90.000000 31.00000 41.00000 21.00000 0.00000 0.00000 0.00000 ........ ---------------------- >> 8 February 2007: Change in extinction coefficients for Ext-Model=4 ---------------------- - An internal constant has been changed from 0.000001 to 0.001, for the case of neutron diffraction, so that the coefficients for anisotropic extinction should be divided by 1000. This has been performed in order to get more manageable numbers. This affect only the treatment of single crystal data in which Ext-Model=4 and neutron diffraction. The coefficient remains equal to 0.000001 for X-ray single crystal diffraction. - An error re-writing the codes of the domain fractions in single crystal work in the new generated PCR file has been corrected. ---------------------- >> 25 January 2007: Simulated annealing with magnetic single crystal domains ---------------------- - The simulated annealing procedure for solving magnetic structures using single crystal data possesing magnetic domains has been fully implemented The method is still under testing but the user can readily use it by using one additional prescription with respect to the normal work with simulated annealing. In the simulated annealing PCR file the user should include the population of domains as free parameters in the list (except the last one, as for least squares) and put as negative the "step" values in the list. This is for indicating the program to make always the constraint that the sum of all domain populations is equal to 1. If the user wants to start with a given population of domains the given values should verify that the sum is 1.0 Example: . . . . . . . . Relevant portion of the PCR file My Magnetic phase name ! COMMANDS magdom u, v, w, 0.1 : 0.20000 0.20000 11.00 21.00 magdom -v, u, w, 0.1 : 0.20000 0.10000 31.00 41.00 magdom u,-v, w, 0.1 : 0.10000 0.20000 51.00 0.00 END COMMANDS !Nat Dis Mom Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More 3 0 0 0.0 0.0 1.0 1 4 -1 0 0 0.000 -1 7 0 . . . . . . . . ! Limits for selected parameters (+ steps & BoundCond for SA): 1 0.0000 1.0000 -0.0200 0 Pop_MagD_1 2 0.0000 1.0000 -0.0200 0 Pop_Chir_MagD_1 3 0.0000 1.0000 -0.0200 0 Pop_MagD_2 4 0.0000 1.0000 -0.0200 0 Pop_Chir_MagD_2 5 0.0000 1.0000 -0.0200 0 Pop_MagD_3 ! T_ini Anneal Accept NumTemps NumThCyc InitConf 1.0 0.900 0.000001 200 0 0 ! NCyclM Nsolu Num_Ref Nscalef NAlgor 50 1 100 1 0 ! ISwap Var-Real/Imag 0 0 - A new output file of name "codfil"_mdom.hkl is written when hkl=10 and there are some MAGDOM commands in the PCR file. The description of domains and the list of contributions of each domain to the total square of the magnetic interaction vector is written during the first cycle of refinement. - A merged reflection list for magnetic structures containing only the independent reflections for a particular magnetic model can be generated by putting the command MAG_MERGE in the PCR file. The name of the file is "codfil"_nph_merged.int, where nph is the number of the phase. ---------------------- >> 8 January 2007: New way for combining powder and single crystal refinements ---------------------- - Up to now the way for doing a mixed, single crystal + powder, refinement was to use Cry=0 and duplicate artificially the crystallographic phase to be refined and including Irf=4 in one of the phases. This was available in FullProf before introducing the multi-pattern option and is still available. A more transparent way, without need of repeating the phase, can now be used. One can declare that a particular diffraction pattern contains only integrated intensities, the new variable Int=1 means that the corresponding pattern consists of integrated intensities. The corresponding Irf variable concerning the refined phase should be equal to four (Irf=4). All the items characteristic of a powder diffraction pattern (lambdas, 2thmin, 2thmax, zero, background, excluded regions, etc) should not be given in the PCR file for the pattern having Int=1. This option extends also the single crystal refinements. For instance one can use a single phase and a series of different data collections to be treated as different patterns. An example has been included in the distribution of FullProf. - The current version of FullProf has been updated to: **********************************************************' ** PROGRAM FullProf.2k (Version 3.80 - Jan2007-ILL JRC) **' **********************************************************'