Crysfire2020 aids indexing powder diffraction peak data

Version 1.0.5, August 2020
Ron Ghosh, Epsom,


Crysfire2020 provides a common interface to 8 valued powder pattern indexing programs

for Windows, Macintosh OS X, and Linux

DICVOL, FJZN6, ITO, KOHL, LOSH, LZON, TAUP, TREOR

Contents
Installation and use of the suite
Brief program descriptions
References
Current default parameters
File usage by CR2020
Re-initialising program
Task control by CR2020
Versions of Crysfire2020
Acknowledgements


The following indexing programs are supported in the current Crysfire-2020 distribution

/
ID Crysfire-2020 Programs (CRYSFIRE-2004) AuthorMinimum No. of peaks
DV dicvol91 DICVOL91 Daniel Louër (1993) 20 peaks
FJ fjzn621 FJZN622A J. Visser & R. Shirley (1999) 30-40 peaks
IT ito13 ITO12 Jan Visser (1994) 30-40 peaks
KL kohl620 KOHL701B Franz Kohlbeck (1975) >20 peaks
LS losh62 LOSH62B Jan Visser & R. Shirley (1999) >20 peaks
LZ lzon622 LZON623 D. Louër & R. Shirley (1999) 20 peaks
TP taup32 TAUP33 Daniel Taupin (1974) 20 peaks
TR treor90 TREOR90 Per-Eric Werner (1995) 25 peaks
CL clepag14 CLEPAG15 Global,sort, summary, and Le Page cell reduction


Introduction, installation, and use of the Crysfire2020 suite

Obtaining structures from powder diffraction data requires matching measured intensities against model structures. This requires correct identification of the unit cell dimensions and indexing the reflections. A pedagogic presentation by J.K. Cockcroft of indexing methods which relate to the programs in this suite may be found at http://pd.chem.ucl.ac.uk/pdnn/unit2/celind.htm

These notes are intended as a supplement to Robin Shirley's original tutorial notes for CRYSFIRE-2004 which can be found at http://www.ccp14.ac.uk/tutorial/crys which has served as a principal reference for the program descriptions below.

The suite of indexing programs by a number of authors is provided with a uniform access method allowing a "scatter-gun" (Shirley/Cranswick) approach to finding appropriate solutions to specific problems.

The same functional approach is used here for Crysfire2020; a single file of peak data is the prime input source for the eight programs. A graphical interface is provided using the Tcl/tk (wish) utility. Additional control parameters are taken from a text file which has defaults for each program. This may be edited (Menu:settings) within Crysfire2020. Certain parameters, for example zero angles and titles too may be modified; these are subsequently available to be shared by the full suite of programs.

The eight indexing programs consist of some 50k lines of (mostly uncommented) Fortran. Shirley's Crysfire of 2004 comprised, in addition, of some 43k lines of Pascal, and 15k lines of MSDOS batch files, which have been replaced here with some 1400 lines of Tcl/tk.

After downloading file

Windows
The Windows version has been tested on Windows-XP and Windows-10. The file cr2020_105.msi is available and should allow an installation using the standard Windows Installer. NOTE administrator privileges are required. Typically Double-Clicking on the downloaded file cr2020_xxx.msi will uncompress the file into C:\"Program Files"\cr2020 or C:\"Program Files (x86)"\cr2020. The name Crysfire is added to the list of programs in the Start button. Clicking on this brings up the icon for Crysfire, and the program starts directly. Alternatively the icon may be dragged onto the Desktop where a copy will be made. Clicking on this will start the program. (examining the properties of the icon will show the actual command line used - this is created on installation, which includes a working copy of the wish interpreter..

Macintosh (OS X) and Linux systems
For Macintosh OS X there is a cr2020_105_osx.zip zipfile; the directory crosx containing programs, configuration files, test data, and includes the Fortran run time library. For Linux the programs have been linked as static and do not depend on system libraries.. The cr2020_105_lin.zip zipfile contains the crlin directory.

The wish interpreter is a standard feature of these systems. After downloading the zip file, unzip it - the program directory will be (pathname)/crxxx/....
Typically the pathname will be like /Users/myname/myprogs/crlin Macintosh (crosx) and linux (crlin) versions. Crysfire2020 will find the indexing program files location from the initiating Terminal command :

% wish /Users/myname/myprogs/crxxx/cr2020.tcl
Some users might wish to make a local shortcut e.g. on OSX Mojave using a newer wish v8.6:
[UPro:~] me% which wish
/opt/local/bin/wish
# create command file
[UPro:~] me% cat >crysexec
/opt/local/bin/wish /Users/me/crosx/cr2020.tcl 
<CTRL-D>
# make executable
[UPro:~] me% chmod a+x crysexec
# run Crysfire (the procedure will find the last used directory)
[UPro:~] me% ./crysexec
# A shortcut to this file can be copied to the Desktop

NOTE - Windows - Linux - Macintosh
The procedure can be started from any current directory. It will switch to either the last project being used, or default to requesting the creation of a new project.

The next step...
When the main page of Crysfire is shown click on File/new to create a new project. This will create a project directory and an edit window to fill with peak data Then the indexing programs may be run, and the summary and full output may be viewed on successful completion. All programs should terminate with the message of "Normal End" within a few seconds. When calculating it is possible to stop the program using the "Interrupt" button in the running task window.


Whilst the original Crysfire could read peak data output directly from a few programs, twenty-five years later copying these data with a graphical editor seems to offer a wider access to peak finding programs. A new option (v 1.0.4) includes the possibility of copying a table of results from another program, pasting this into the edit window, then selecting the column containing the two-theta values. For example there is a text file output option in Xfit; the fourth column contains the two-theta values. The table should contain a uniform sequence of columned data, separated by tabs, commas, or white space.
The final data are simply a title line and then the peak two-theta values in sequence, one per line.

Individual indexing programs are then run by pressing the program button. If the running time seems excessive it is possible to halt the program using the interrupt button.

All indexing programs called within Crysfire produce output and summary files. The files are identified by an extension with the two letter program identifier and a third character; S for summary file or O for more complete output file, sometimes together with additional files with name extensions starting with the two letter identifier. The primary name is the project name created on preparing the peak data file project.PPP. When the button of the indexing program is pressed a new indexing run starts, and the result display buttons are disabled until the program terminates. If present, the output and summary display buttons are activated allowing the results to be viewed.

The summary files can be assembled and sorted in the final phase, and the Le Page analysis and reduced lattices calculated. Sorting is into descending order of I20 and Merit. The minimum levels for inclusion vary for different indexing programs, but are typically I20 above 15 and Merit above approx. 7 to 9, where I20 is the number of "indexed" lines in the first 20 observed lines, and Merit is based on De Wolff's M20 but calculated for "indexed" lines only (as interpreted variously by each indexing program).

Test Data
A test data file TUTEST.PPP can also be found with the programs, typically in c:\Program Files\cr2020\TUTEST.PPP or crxxx/TUTEST.PPP The above file may be copied from the browser window, or the file from the program file may be dropped onto Notepad/TextEdit/gedit etc. and the contents can be used via copy and paste as an input when a new project is created.

The installed version of Crysfire-2020 is shown in the "Help/About" menu.

Recommended sequence of use

Following Shirley's tutorial (loc.cit.) :
TAUP - exhaustive search especially good for high symmetry to orthorhombic, good for metals and alloys
DICVOL - in high symmetry mode (default)
ITO - perhaps used initially with fewer than 25 peaks
FJZN
TREOR - fast and tolerant of impurity lines
KOHL
DICVOL - low symmetry mode though best avoid triclinic (change default options)
LZON - after ITO, TREOR, KOHL


Program descriptions

DICVOL, FJZN6, ITO,KOHL,LOSH, LZON, TAUP, TREOR

Program default parameters and descriptions

DICVOL, FJZN6, ITO,KOHL,LOSH, LZON,TAUP, TREOR


** DICVOL ** Daniel Louër

Default data

Exhaustive search in parameter space by successive dichotomy

Being an exhaustive program, DICVOL91 can demonstrate the non-existence as well as the existence of solutions in particular crystal systems, and is well suited for searches of the higher symmetry crystal systems down to orthorhombic, and also (but slower) to monoclinic. It usually performs best with around 20 well-measured lines, which must be from a single solid phase since it does not tolerate impurity lines.

DICVOL91 searches outwards in 400Å3shells of increasing cell volume, which means that low-volume solutions may be found quickly but searches to high volumes in low symmetry may become very lengthy.

Although an explicit hexagonal search is made, any hexagonal solution will usually be picked up in its equivalent V/2 orthorhombic setting during the preceding volume shell, upon which the search terminates and the hexagonal setting never gets reported. So, if an orthorhombic solution is reported and a hexagonal one suspected, this can be tested by making a further run, manually setting DICVOL91's VOLMIN parameter in line 3 to the upper bound of the volume shell in which the orthorhombic cell was reported. This forces the next shell to be searched, and hence any hexagonal solution within it to be reported.

Although DICVOL uses the optimal exhaustive algorithm in parameter space (a form of binary search), like all exhaustive indexing programs it can become very time-consuming in low symmetry. Thus it's usually more effective to seek triclinic solutions with ITO12, TREOR90, KOHL and LZON before running a triclinic scan with DICVOL forcing triclinic search.

If triclinic searches have been enabled, DICVOL91 will continue into lengthy low-symmetry (monoclinic and triclinic) searches, although a possible solution may already have been found in higher symmetry. These can be halted by using the Interrupt button if necessary, and the output checked to see whether the low-symmetry searches are really needed.

** FJZN6 ** Jan Visser & Robin Shirley

Default data

Deductive search in index space by zone indexing,

(using Ishida & Watanabe's PM criterion for zone evaluation)

This is a modified variant of Visser's ITO program, resembling ITO12 but based on the earlier v6 version. Because of this, its lacks some of the finesse of ITO12, but its strength is that it replaces the weakest aspect of ITO, the CRITER criterion used in the zone-evaluation stage, with the more robust PM criterion of Ishida & Watanabe (1982). This means that is less likely to discard correct zones because they finish too far down the rank order, and so it may well succeed in flushing out a solution where ITO12 fails.

Like ITO12, it performs best when given 30-40 accurately measured powder lines, and is relatively little affected by impurity lines unless they are among the first 5 lines (hardly at all if outside the first 20). It is optimised for the lower symmetry systems from orthorhombic downwards – hence high-symmetry lattices may well get reported in an orthorhombic setting, perhaps with a note that a higher symmetry setting may exist. The Bravais lattice is inferred, and Bravais lattice absences taken into account when calculating M20.

** ITO ** Jan Visser

Default data

Deductive search in index space by zone-indexing

ITO12 performs best when given 30-40 accurately measured powder lines. It is relatively little affected by impurity lines unless they are among the first 5 lines (hardly at all if outside the first 20). It is optimised for the lower symmetry systems from orthorhombic downwards – consequently high-symmetry lattices may well get reported in an orthorhombic setting, perhaps with a note that a higher symmetry setting may exist. The Bravais lattice is inferred, and Bravais lattice absences taken into account when calculating M20. (See also FJZN6 for a variant that will sometimes succeed where ITO12 fails.)

** KOHL ** Franz Kohlbeck

Default data

Heuristic search in index space

KOHL is based on Kohlbeck's 1975 TMO program, altered and adapted for PC use, and with an FZRF refinement and evaluation stage appended (adapted from Visser's ITO6). KOHL works rapidly and efficiently in index space, carrying out orthorhombic, monoclinic and triclinic searches in broadly independent stages.

KOHL does not make any special provision for detecting higher-symmetry solutions, so these will be reported in orthorhombic or monoclinic settings. The FZRF postscript brings additional cell refinement, the detection of a probable Bravais lattice, level-by-level listings and other niceties, including an alert when a higher symmetry is suspected.

KOHL is particularly useful because (when it works) it is fast, searches down to triclinic and is relatively tolerant of both random errors and impurity lines.

Defaults All searches enabled (orthorhombic, monoclinic and triclinic)

** LOSHFZRF ** Daniel Louër & Robin Shirley

Default data

Exhaustive search of alpha* & beta* in parameter space by successive dichotomy, for specified basis sets

LOSH is the original user-directed program for which LZON is the automated version. "FZRF" indicates that, as with KOHL, an FZRF refinement and evaluation stage has been appended (adapted from Visser's ITO6).

Like LZON, LOSHFZRF is semi-exhaustive, searching exhaustively through a selected region of solution space. However, LOSHFZRF searches only a single specified plane in solution space where by default LZON searches eight.

The plane that is to be searched must be specified by the user, in the form of a "basis set". This consists of a single powder zone the "basis zone" specified as Q(A), Q(B) and Q(F), plus the first well-measured line not indexed by the zone, which by the Shirley/Ishida&Watanabe heuristic is taken as Q(C). The resulting four powder constants Q(A,B,C,F) form the basis set for the search, which now only need cover the 2-dimensional plane in solution space defined by Q(D) and Q(E) i.e. alpha* and beta*. Such a 2-dimensional search is very fast – typically under a minute for the default settings with NSPURI=0 (no impurity lines expected).

This process can most easily be understood by studying the main output file from LZON, where it is set out for each of the basis sets used. A basis zone for LOSHFZRF will usually be obtained by examining the detailed zones listings in the main output files of ITO12, FJZN6 or LZON, seeking a promising prospect that the original program missed. This will typically be one with relatively large reciprocal area (hence small direct-cell constants) and large coverage (few unobserved lines within the zone). It helps to have experience and training when spotting good powder zones, but the judicious human selector can often succeed where the zone-evaluating program failed.

As with LZON, all solutions begin as triclinic and are only examined and renormalised for higher symmetry by the evaluative FZRF postscript, which also refines the cell and infers its Bravais lattice type. Solutions are accepted for logging if I20>15 and M20>7.

It is recommended to use the first 20 well-measured lines, but LOSHFZRF is prepared to search with less, although the FZRF stage may not like this and in such cases it may be necessary to renormalise and evaluate the solutions by hand (with the aid of CRYS).

Defaults	NSPURI: 0 (i.e. no unindexed lines permitted)
ALPMIN,BETMIN: 30 (minimum alpha* & beta* in degrees)
D2THDF ("2Theta limits on observed lines, for CuKa 1 radiation), defaults differ as follows:
0.03 (Crysfire)  degrees typically

** LZON ** Robin Shirley, Daniel Louër & Jan Visser

Default data

Combination strategy: ITO-style zone-search for Q(A,B,F),

Shirley heuristic for Q(C), exhaustive search in parameter space by successive dichotomy for Q(D,E))

LZON uses a semi-exhaustive strategy, in that it makes some explicit and hopefully judicious assumptions to restrict the search volume in solution space, then makes an exhaustive search of the chosen regions. This means that it can rule out the possibility of a solution existing within the regions that it has searched, as defined by the parameters used. Its particular strength shows in the multi-solution dominant-zone cases that are often pathological for other programs. Because its heuristics are based on the most dominant zones present, it is actually at its strongest in these cases. Also, though using a zone-indexing framework, it takes a different approach to lattice-building and only needs to discover a single correct zone (the most dominant one present and hence the easiest to find), where pure zone-indexing programs like ITO12 and FJZN6 need to find two.

Being semi-exhaustive rather than deductive, however, it is not as fast as ITO12 or FJZN6, taking up to 15 minutes where they take only a few seconds. Any impurity lines must be allowed for explicitly using its NSPURI parameter (default: none), which can lengthen search times considerably if non-zero. This also affects TOLG, the acceptance limit for indexed lines during lattice refinement. If NSPURI=0, a broader limit of 6 QU. Is used, reducing to 3 if impurity lines are expected. TOLG influences the radius of convergence of refinements, which may fail to lock on to the best fit if TOLG excludes too many lines in the early stages, so TOLG should not only be based on the expected data accuracy.

Both Ishida & Watanabe's PM and the original Visser CRITER are available as criteria for zone evaluation (default: I&W PM) (see FJZN6).

** TAUP ** Daniel Taupin

Default data

Exhaustive, index-permutation search in index space

Like DICVOL, Taupin's program uses an exhaustive approach and so can show that solutions do not exist within particular systems. The downside to this is that its searches become dramatically longer as the symmetry decreases, so that searches below orthorhombic can be impractical. It is, however, useful for screening for high symmetry solutions, since searches down to orthorhombic are quite fast. By default it does not allow for impurity lines, though this can be changed using its NBMAX (NSPURI) parameter (see below).

TAUP originally used its own figure of merit, based on squares of differences. This original line-by-line version is still output but now labelled "T-Merit". A conventional M20 value is now also reported for each proposed solution. The acceptance test for reporting solutions is still based on a minimum level of T-Merit - by default 5, though this can be changed in the TAUP data file, using line 2 parameter 7 (FWMINI).

Thus, being exhaustive, TAUP is very useful down to orthorhombic, but in general it is much more efficient to try other programs such as ITO12, TREOR90, KOHL and LZON before considering low-symmetry searches with TAUP. By default under CRYSFIRE, TAUP halts after orthorhombic.

Defaults

Flags:
DFG CTHO (i.e. d-spacings, brief output, crystal systems down to orthorhombic)
VOL: 6000 T-MERIT: 5 (as defined by TAUP – see above - perhaps equivalent to M20 = 7)
NSPURI=0 (2nd parameter on line 2 - can be edited then re-run)
±2Theta limits: 0.03 degrees

** TREOR ** Per-Eric Werner

Default data

Semi-exhaustive, heuristic search methods in index space

TREOR90 performs fast and efficient searches down to triclinic symmetry. It prefers high standards of data measurement, but is rather more forgiving over impurity lines. About 25 well-measured observed lines are recommended. A very thorough manual is provided, with many examples.

Defaults VOL: 6000 MERIT: 9 (i.e. halt on finding a solution with M20>9)


Original references to indexing programs

DICVOL
Boultif, A. & Louër, D. (1991), Indexing of powder diffraction patterns for low-symmetry lattices by the successive dichotomy method, J. Appl. Cryst., 24, 987-993.

FJZN6
Shirley, R. (1999), A modified version of Visser's ITO zone-indexing program, using the Ishida & Watanabe PM criterion for zone evaluation, (not yet published). See also Visser (1969) for the ITO6 base version, and Ishida & Watanabe (1982) for the PM criterion.

ITO
Visser, J. W. (1969), A Fully Automatic Program for Finding the Unit Cell from Powder Data, J. Appl. Cryst., 2, 89-95.

Louër, D. & Vargas, R. (1982), Indexation Automatique des Diagrammes de Poudre par Dichotomies Successives, J. Appl. Cryst., 15, 542-545.

KOHL
Kohlbeck, F. & Hörl, E. M. (1976), Indexing Program for Powder Patterns Especially Suitable for Triclinic, Monoclinic and Orthorhombic Lattices, J. Appl. Cryst., 9, 28-33.

LZON, LOSHFZRF
Shirley, R. & Louër, D. (1978), New powder indexing programs for any symmetry which combine grid-search with successive dichotomy, Acta Cryst., A34, S382.

TAUP
Taupin, D. (1973), A Powder-Diagram Automatic-Indexing Routine, J. Appl. Cryst., 6, 380-385.

(A later paper exists, but it does not refer to the base version used in the CRYSFIRE system.)

TREOR
Werner, P.-E., Eriksson, L. & Westdahl, M. (1985), TREOR, a Semi-Exhaustive Trial-and-Error Powder Indexing Program for All Symmetries, J. Appl. Cryst., 18, 367-370.

Kohlbeck, F. & Hörl, E. M. (1978), Trial and error indexing program for powder patterns of monoclinic substances, J. Appl. Cryst., 11, 60-61.

PM Criterion (used in FJZN6 and LZON)
Ishida, T & Watanabe, Y. (1982), A criterion method for indexing unknown powder diffraction patterns, Z. Krist., 160, 19-32.

General Powder Indexing (a brief selection, concentrating on material relevant for CRYSFIRE users)

Calvert, L. D., Flippen-Anderson, J. L., Hubbard, C. R., Johnson, Q. C., Lenhert, P. G., Nichols, M. C., Parrish, W., Smith, D. K., Smith, G. S., Snyder, R. L. & Young, R. A. (1980), Standards for the publication of powder patterns: the American Crystallographic Association Subcommittee's final report, in Accuracy in Powder Diffraction, ed. Block, S. & Hubbard, C. R., NBS Spec. Publ. 567, 513-535.

Ito, T. (1949), A General Powder X-Ray Photography, Nature, 164, 755-756.

Ito, T. (1950), X-ray Studies on Polymorphism, Maruzen, Tokyo, 187-228.

Louër, D. (1998), Advances in powder diffraction analysis, Acta Cryst. A, 54, 922-933.

Mighell, A. D. & Santoro, A. (1975), Geometrical Ambiguities in the Indexing of Powder Patterns, J. Appl. Cryst., 8, 372-374.

Mighell, A. D. (1976), The Reduced Cell: Its Use in the Identification of Crystalline Materials, J. Appl. Cryst., 9, 491-498.

Mighell, A. D. & Stalick, J. K. (1980), The reliability of powder indexing procedures, in Accuracy in Powder Diffraction, ed. Block, S. & Hubbard, C. R., NBS Spec. Publ. 567, 393-403.

Shirley, R. (1975), Recent advances in determining unknown unit cells from powder diffraction data, Acta Cryst., A31, S197.

Shirley, R. (1978), Indexing powder diagrams, in Crystallographic Computing, ed. Schenk, H., Olthof-Hazekamp, R., van Koningsveld, H. & Bassi, G. C., Delft University Press, Holland, 221-234.

Shirley, R. (1980), Data accuracy for powder indexing, in Accuracy in Powder Diffraction, ed. Block, S. & Hubbard, C. R., NBS Spec. Publ. 567, 361-382.

Shirley, R. (1984), Measurement and Analysis of Powder Data from Single Solid Phases, in Methods and applications in crystallographic computing, Hall, S. R. & Ashida, T., Clarendon Press, Oxford, 411-437.

Smith, G. S. & Snyder, R. L. (1979), FN: A Criterion for Rating Powder Diffraction Patterns and Evaluating the Reliability of Powder-Pattern Indexing, J. Appl. Cryst., 12, 60-65.

Snyder, R. L., Johnson, A. C., Kahara, E., Smith, G. S. & Nichols, M. C. (1978), An analysis of the powder diffraction file, Lawrence Livermore Laboratory, University of California, Report UCRL-52505.

Werner, P.-E. (1976), On the Determination of Unit-Cell Dimensions from Inaccurate Powder Diffraction Data, J. Appl. Cryst., 9, 216-219.

Wolff, P. M. de (1963), Indexing of Powder Diffraction Patterns, Adv. X-Ray Anal., 6, 1-17.

Wolff, P. M. de (1968), A Simplified Criterion for the Reliability of a Powder Pattern Indexing, J. Appl. Cryst., 1, 108-113.

Wolff, P. M. de (1972), The definition of the indexing figure of merit M20, J. Appl. Cryst., 5, 243.


cr2020.dfp - Details of input defaults and description for each program

DICVOL, FJZN6, ITO,KOHL,LZON,TAUP, TREOR

IN ALPHABETICAL ORDER - SUMMARY INPUT

Current default parameters file cr2020.dfp

Versions 1.0.3 - 1.0.5
Peak data are in file "project.PPP" which has a title, followed by the observed peak positions Initially this file is opened and the title read Then the input is switched to this default parameter file and the next lines are read for the appropriate program following the three character start symbols. Input is then switched back to the project.PPP file to read the peak positions If default data (e.g. preceded by the program ID tag ">ID") need to be modified simply add a new field starting with ">ID" and the data before the default field, adding suitable date etc.with annotations in the tag line which is copied into the output data.

                        Description + copy of summary input

  DV  DIVCOL91
  FJ  FJZN6
  IT  ITO13
  KL  KOHL620j
  LS  LOSH62b
  LZ  LZON622w
  TP  TAUP32C
  TR  TREOR90

Default values (copies later with each program description)

>DV    DIVCOL91  CRYS2020 v1.0 Initial data from 2004 tutorial
  20 2 1 1 1 1 1 0
     80.     80.     80.      0.   6000.     90.    130.
 1.5406000      .000     .0000     .0000
  1.   5.

>FJ    FJZN621  CRYS2020 v1.0 Initial data from 2004 tutorial    
9 0  0 0 0 0.   0.    1.540600   1 4 8         1        .000     .0000



    9 1                   1.540600   1 4 8         1        .000     .0000


>IT     ITO13R   CRYS2020 v1.0 Initial data from 2004 tutorial
10 0000003 0.0400000 1.5406000                     6000.0000      0.0000000     


>KL      KOHL620w   CRYS2020 v1.0 Initial data from 2004 tutorial (NAMELIST)
&OPA
IORT=1, IMON=1,
LUFM=0,
H4MAX=4, K4MAX=4, L4MAX=4

&END
/

       Note Namelist parameters read, but no d spacings
       two-theta values are converted to d spacings after reading from .PPP

>LS      LOSH62   CRYS2020 v1.0 Initial data from 2004 tutorial 
  600.00000  600.00000  660.00000  400.00000   1.540599
 20  0  0  0 0.80                                                               
  30.00  30.00


>LZ      LZON623   CRYS2020 v1.0 Initial data from 2004 tutorial
9 0                   1.540600   1 4 8 8      01        .000     .0000
     .0600                         0 34.                             20


>TP      TAUP32c   CRYS2020 v1.0 Initial data from 2004 tutorial
AFG CTHO                                              
 20, 0,3,6,,     6000.,5,,,,  1.540600

>TR      TREOR90    CRYS2020 v1.0 Initial data from 2004 tutorial
CHOICE=3,
VOL= -6000,
MERIT=9,
WAVE=1.540600,
END*


      Note Treor reads in control data after twotheta lines

DICVOL91 default data
>DV    DICVOL91  June 2019
  20 2 1 1 1 0 0 0
     80.     80.     80.      0.   6000.     90.    130
 1.5406000      .000     .0000     .0000
  1.   5.
 
C  CARD 2  N,ITYPE,JC,JT,JH,JO,JM,JTR                  FREE FORMAT
C
C          N               NUMBER OF LINES USED.
C          ITYPE           SPACING DATA TYPE.
C                      =1  THETA BRAGG IN DEGREES.
C                      =2  2-THETA ANGLE IN DEGREES.
C                      =3  D-SPACING IN ANGSTROMS.
C                      =4  Q SPECIFIED IN Q-UNITS AS E+04/D**2.
C          JC          =0  CUBIC SYSTEM IS NOT TESTED.
C                      =1  CUBIC SYSTEM IS TESTED.
C          JT          =0  TETRAGONAL SYSTEM IS NOT TESTED.
C                      =1  TETRAGONAL SYSTEM IS TESTED.
C          JH          =0  HEXAGONAL SYSTEM IS NOT TESTED.
C                      =1  HEXAGONAL SYSTEM IS TESTED.
C          JO          =0  ORTHORHOMBIC SYSTEM IS NOT TESTED.
C                      =1  ORTHORHOMBIC SYSTEM IS TESTED.
C          JM          =0  MONOCLINIC SYSTEM IS NOT TESTED.
C                      =1  MONOCLINIC SYSTEM IS TESTED.
C          JTR         =0  TRICLINIC SYSTEM IS NOT TESTED.
C                      =1  TRICLINIC SYSTEM IS TESTED.
C
C
C  CARD 3  AMAX,BMAX,CMAX,VOLMIN,VOLMAX,BEMIN,BEMAX    FREE FORMAT
C
C          AMAX    MAXIMUM VALUE OF UNIT CELL DIMENSION A IN ANGSTROMS.
C                  (IF AMAX= 0.0 DEFAULT= 20. ANGSTROMS)
C          BMAX    MAXIMUM VALUE OF UNIT CELL DIMENSION B IN ANGSTROMS.
C                  (IF BMAX= 0.0 DEFAULT= 20. ANGSTROMS)
C          CMAX    MAXIMUM VALUE OF UNIT CELL DIMENSION C IN ANGSTROMS.
C                  (IF CMAX= 0.0 DEFAULT= 20. ANGSTROMS)
C          VOLMIN  MINIMUM VOLUME FOR TRIAL UNIT CELLS IN ANGSTROMS**3.
C          VOLMAX  MAXIMUM VOLUME FOR TRIAL UNIT CELLS IN ANGSTROMS**3.
C                  (IF VOLMAX= 0.0 DEFAULT= 1500. ANGSTROMS**3)
C          BEMIN   MINIMUM ANGLE FOR UNIT CELL IN DEGREES
C                  (IF BEMIN= 0.0 DEFAULT= 90. DEGREES).
C          BEMAX   MAXIMUM ANGLE FOR UNIT CELL IN DEGREES
C                  (IF BEMAX= 0.0 DEFAULT= 125. DEGREES).
C
C
C  CARD 4  WAVE,POIMOL,DENS,DELDEN                     FREE FORMAT
C
C          WAVE    WAVELENGTH IN ANGSTROMS (DEFAULT=0.0 IF CU K ALPHA1).
C          POIMOL  MOLECULAR WEIGHT OF ONE FORMULA UNIT IN A.M.U.
C                  (DEFAULT =0.0 IF FORMULA WEIGHT NOT KNOWN).
C          DENS    MEASURED DENSITY IN G.CM(-3)
C                  (DEFAULT =0.0 IF DENSITY NOT KNOWN).
C          DELDEN  ABSOLUTE ERROR IN MEASURED DENSITY.
C
C
C  CARD 5  EPS,FOM                                     FREE FORMAT
C
C          EPS       =0.0  THE ABSOLUTE ERROR ON EACH OBSERVED LINE
C                          IS TAKEN TO .03 DEG. 2THETA, WHATEVER THE
C                          SPACING DATA TYPE (ITYPE IN CARD 2).
C                    =1.0  THE ABSOLUTE ERROR ON EACH OBSERVED LINE IS
C                          INPUT INDIVIDUALLY IN THE FOLLOWING CARDS,
C                          TOGETHER WITH THE OBSERVED 'D(I)', ACCORDING
C                          WITH THE SPACING DATA UNIT.
C                    EPS NE 0.0 AND 1.0
C                          THE ABSOLUTE ERROR IS TAKEN AS A CONSTANT
C                          (=EPS),IN DEG. 2THETA, WHATEVER THE SPACING
C                          DATA TYPE (ITYPE IN CARD 2).
C          FOM             LOWER FIGURE OF MERIT M(N) REQUIRED FOR PRINTED
C                          SOLUTION(S) (DEFAULT=0.0 IF LOWER M(N)=5.0).
C
C
CC  CARD 2  N,ITYPE,JC,JT,JH,JO,JM,JTR                  FREE FORMAT
C
C          N               NUMBER OF LINES USED.
C          ITYPE           SPACING DATA TYPE.
C                      =1  THETA BRAGG IN DEGREES.
C                      =2  2-THETA ANGLE IN DEGREES.
C                      =3  D-SPACING IN ANGSTROMS.
C                      =4  Q SPECIFIED IN Q-UNITS AS E+04/D**2.
C          JC          =0  CUBIC SYSTEM IS NOT TESTED.
C                      =1  CUBIC SYSTEM IS TESTED.
C          JT          =0  TETRAGONAL SYSTEM IS NOT TESTED.
C                      =1  TETRAGONAL SYSTEM IS TESTED.
C          JH          =0  HEXAGONAL SYSTEM IS NOT TESTED.
C                      =1  HEXAGONAL SYSTEM IS TESTED.
C          JO          =0  ORTHORHOMBIC SYSTEM IS NOT TESTED.
C                      =1  ORTHORHOMBIC SYSTEM IS TESTED.
C          JM          =0  MONOCLINIC SYSTEM IS NOT TESTED.
C                      =1  MONOCLINIC SYSTEM IS TESTED.
C          JTR         =0  TRICLINIC SYSTEM IS NOT TESTED.
C                      =1  TRICLINIC SYSTEM IS TESTED.
C
C
C  CARD 3  AMAX,BMAX,CMAX,VOLMIN,VOLMAX,BEMIN,BEMAX    FREE FORMAT
C
C          AMAX    MAXIMUM VALUE OF UNIT CELL DIMENSION A IN ANGSTROMS.
C                  (IF AMAX= 0.0 DEFAULT= 20. ANGSTROMS)
C          BMAX    MAXIMUM VALUE OF UNIT CELL DIMENSION B IN ANGSTROMS.
C                  (IF BMAX= 0.0 DEFAULT= 20. ANGSTROMS)
C          CMAX    MAXIMUM VALUE OF UNIT CELL DIMENSION C IN ANGSTROMS.
C                  (IF CMAX= 0.0 DEFAULT= 20. ANGSTROMS)
C          VOLMIN  MINIMUM VOLUME FOR TRIAL UNIT CELLS IN ANGSTROMS**3.
C          VOLMAX  MAXIMUM VOLUME FOR TRIAL UNIT CELLS IN ANGSTROMS**3.
C                  (IF VOLMAX= 0.0 DEFAULT= 1500. ANGSTROMS**3)
C          BEMIN   MINIMUM ANGLE FOR UNIT CELL IN DEGREES
C                  (IF BEMIN= 0.0 DEFAULT= 90. DEGREES).
C          BEMAX   MAXIMUM ANGLE FOR UNIT CELL IN DEGREES
C                  (IF BEMAX= 0.0 DEFAULT= 125. DEGREES).
C
C
C  CARD 4  WAVE,POIMOL,DENS,DELDEN                     FREE FORMAT
C
C          WAVE    WAVELENGTH IN ANGSTROMS (DEFAULT=0.0 IF CU K ALPHA1).
C          POIMOL  MOLECULAR WEIGHT OF ONE FORMULA UNIT IN A.M.U.
C                  (DEFAULT =0.0 IF FORMULA WEIGHT NOT KNOWN).
C          DENS    MEASURED DENSITY IN G.CM(-3)
C                  (DEFAULT =0.0 IF DENSITY NOT KNOWN).
C          DELDEN  ABSOLUTE ERROR IN MEASURED DENSITY.
C
C
C  CARD 5  EPS,FOM                                     FREE FORMAT
C
C          EPS       =0.0  THE ABSOLUTE ERROR ON EACH OBSERVED LINE
C                          IS TAKEN TO .03 DEG. 2THETA, WHATEVER THE
C                          SPACING DATA TYPE (ITYPE IN CARD 2).
C                    =1.0  THE ABSOLUTE ERROR ON EACH OBSERVED LINE IS
C                          INPUT INDIVIDUALLY IN THE FOLLOWING CARDS,
C                          TOGETHER WITH THE OBSERVED 'D(I)', ACCORDING
C                          WITH THE SPACING DATA UNIT.
C                    EPS NE 0.0 AND 1.0
C                          THE ABSOLUTE ERROR IS TAKEN AS A CONSTANT
C                          (=EPS),IN DEG. 2THETA, WHATEVER THE SPACING
C                          DATA TYPE (ITYPE IN CARD 2).
C          FOM             LOWER FIGURE OF MERIT M(N) REQUIRED FOR PRINTED
C                          SOLUTION(S) (DEFAULT=0.0 IF LOWER M(N)=5.0).
C
C
      READ(IR,*,ERR=343)N,ITYPE,JC,JT,JH,JO,JM,JTR
      READ(IR,*,ERR=343)AMAX,BMAX,CMAX,VOLMIN,VOLMAX,BEMIN,BEMAX
      READ(IR,*,ERR=343)WAVE,POIMOL,DENS,DELDEN
      READ(IR,*,ERR=343)EPS,FOM

FJZN6 default data
>FJ    FJZN621 - Visser's ITO zone-eval.+ Ishida & Watanabe's PM criterion
9 0  0 0 0 0.   0.    1.540600   1 4 8         1        .000     .0000
c qv ito13 C --------------------------------------------------------ZN------------- -- 2 C----THE FIRST CARD MUST CONTAIN THE NAME OF THE PROBLEM (TITLE). 2 C THE NEXT CARD IS USUALLY COMPLETELY BLANK. THE PROGRAM 2 C THEN TAKES THE DEFAULT VALUES.Z. IF YOU WANT TO SPECIFY YOUR 2 C OWN PARAMETERS, YOU SHOULD DO THIS AS FOLLOWS$ 2 C COLUMN FORMAT NAME DEFAULT MEANING 2 C 1 A1 MAN 0 PRINTS INSTRUCTIONS,UNLESS MAN=9 6 C 2 A1 INSTR 0 PRINTS INSTRUCTIONS FOR SPECIAL 6 C FEATURES IF INSTR=1 6 C 3 A1 INTENS 0 READS INTENSITIES BESIDES LINE 6 C POSITIONS IF INTENS=1 6 C 5- 6 I2 NSYST(1) 0 ORTHORHOMBIC SOLUTION. +1=YES, -1=NO 6 C 7- 8 I2 NSYST(2) 0 MONOCLINIC SYSTEM. 0 MEANS INDIFFERENT 6 C 9-10 I2 NSYST(3) 0 TRICLINIC SYSTEM 6 C 11-15 F5.2 TOL2 3.0 TOLERANCE ON 2-DIMENSIONAL SEARCH 6 C 16-20 F5.2 TOL3 4.5 TOLERANCE ON 3-DIMENSIONAL SEARCH 6 C 21-30 F10.5 WAVEL 1.5405 WAVELENGTH 2 C 31-32 I2 LINCO 0 NUMBER OF GIVEN LINE COMBINATIONS 2 C FOR THE 2-DIMENSIONAL SEARCH 2 C 33-34 I2 K (ENL) 0 ENL$ OUTPUT OF INTERMEDIATE RESULTS(K>0) 2 C 35-36 I2 NQ1 3 NQ1 AND NQ2 DETERMINE THE NUMBERS OF 2 C 37-38 I2 NQ2 6 LINES TO BE USED IN COMBINATIONS 2 C FOR FINDING ZONES . 2 C 39-40 I2 NZ1 6 NZ1 AND NZ2 DO THE SAME FOR 2 C 41-42 I2 NZ2 6 FINDING LATTICES FROM ZONES. 2 C 43-44 I2 NR 0 REFINEMENT AND EVALUATION RUN ONLY C IF NR>0. THE DECK OF COMPLETE C LATTICES TO BE REFINED (6F10.2) C WILL FOLLOW THE LINES DECK, ALSO C TERMINATED BY A CARD WITH ZERO OR C BLANKS IN COLS 1-10. C 45-46 I2 INP 5 NUMBER OF THE UNIT ON WHICH TO READ 2 C THE LINE POSITIONS. 2 C 47-48 I2 LST 0 LIST OF CALCULATED LINES IF LST=1 6 C 49-50 I2 J (TEST) 0 TEST OUTPUT IF J>0 2 C 51-60 F10.5 WMOL 0.0 MOLECULAR WEIGHT. 2 C 61-70 F10.5 DOBS 0.0 OBSERVED DENSITY. 2 C 71-75 F5.2 TOLG 3.0 TOLERANCE ON MATCH BETWEEN CALCULATED 6P C AND OBSERVED Q-VALUES. 2 C 76-80 F5.3 XCORR 0.0 CORRECTION IN DEGREES TO ADD TO EACH 6P C INPUT TWO-THETA BEFORE STORING 6P C --------------------------------------------------------------------- -- 2 ITO13 default data
>IT     ITO13R June 2019
10 0000003 0.0400000 1.5406000                     6000.0000      0.0000000     
C----THE FIRST CARD MUST CONTAIN THE NAME OF THE PROBLEM (TITLE). C THE NEXT CARDS ARE USUALLY COMPLETELY BLANK. THE PROGRAM C THEN TAKES THE DEFAULT VALUES.. IF YOU WANT TO SPECIFY YOUR C OWN PARAMETERS, YOU SHOULD DO THIS AS FOLLOWS: C COLUMN FORMAT NAME DEFAULT MEANING C 1 I1 MAN 0 PRINTS INSTRUCTIONS,UNLESS MAN>7 C SUPPRESSES ZERO-ERROR IF MAN=1 OR 8 C 2 A1 INSTR 0 PRINTS INSTRUCTIONS FOR SPECIAL C FEATURES IF INSTR=1 C 3 A1 INTENS 0 READS INTENSITIES BESIDES LINE C POSITIONS IF INTENS=1 C 4 I1 NSOLMX 4 MAXIMUM NR OF SOLUTIONS TO BE PRINTE C 5- 6 I2 NSYST(1) 0 ORTHORHOMBIC SOLUTION. +1=YES, -1=NO C 7- 8 I2 NSYST(2) 0 MONOCLINIC SYSTEM. 0 MEANS INDIFF C 9-10 I2 NSYST(3) 0 TRICLINIC SYSTEM C 11-15 F5.2 TOL2 3.0 TOLERANCE ON 2-DIMENSIONAL SEARCH C 16-20 F5.2 TOL3 4.5 TOLERANCE ON 3-DIMENSIONAL SEARCH C 21-30 F10.5 WAVEL 1.54060 WAVELENGTH C 31-32 I2 LINCO 0 NUMBER OF GIVEN LINE COMBINATIONS C FOR THE 2-DIMENSIONAL SEARCH C IF LINCO>0, THE LINECOMBINATIONS ARE C READ (4F10.2) AFTER THE LINES DECK. C TERMINATION BY A BLANK CARD (OR ZERO C 33 I1 LZERCK 0 CHECK ON ZERO-ERROR IF LZERCK>0 C 34 I1 K (ENL) 0 ENL: OUTPUT OF INTERMEDIATE RESULTS( C 35-36 I2 NQ1 3 NQ1 AND NQ2 DETERMINE THE NUMBERS OF C 37-38 I2 NQ2 6 LINES TO BE USED IN COMBINATIONS C FOR FINDING ZONES . C 39-40 I2 NZ1 6 NZ1 AND NZ2 DO THE SAME FOR C 41-42 I2 NZ2 6 FINDING LATTICES FROM ZONES. C 43-44 I2 NR 0 REFINEMENT AND EVALUATION RUN ONLY C IF NR>0. THE DECK OF COMPLETE C LATTICES TO BE REFINED (6F10.2) C MUST FOLLOW THE LINES DECK, ALSO C TERMINATED BY A CARD WITH ZERO OR C BLANKS IN COLS 1-10. C 45-46 I2 INDAT 5 NUMBER OF THE UNIT ON WHICH TO READ C THE LINE POSITIONS. C 47-48 I2 LIST 1 LIST OF CALCULATED LINES FOR THE FIR C *LIST* LATTICES. SUPPRESS: LIST=-1 C 49-50 I2 J (TEST) 0 TEST OUTPUT IF J .GT. 0 C 51-60 F10.5 WMOL 0.0 MOLECULAR WEIGHT. C 61-70 F10.5 DOBS 0.0 OBSERVED DENSITY. C 71-78 F8.5 TOLG 6.0 TOLERANCE ON MATCH BETWEEN CALCULATE C AND OBSERVED LINES IN HUNDREDTH OF. C A DEGREE TWOTHETA. C 79-80 I2 NTST 0 THE NUMBER IN THE MAIN PROGRAM C WHERE TEST OUTPUT IS GIVEN. C --------------------------------------------------------------------- C ON THE NEXT CARD, THE FOLLOWING PARAMETERS SHOULD BE ENTERED C 1-10 F10.5 ZERCOR 0.0 ZEROSHIFT, TO APPLY TO ALL LINES. C 11-20 F10.5 PRNTMR 4.0 THE MINIMUM VALUE OF THE FIGURE C OF MERIT OF A LATTICE TO BE PRINTED. C 21-30 F10.5 PRNTLN 14. THE MINIMUM NUMBER OF INDEXED LINES C FOR A LATTICE TO BE PRINTED. C 31-40 F10.5 RMAX 0. THE NUMBER OF LINES, ENTER AS REAL. C ONLY NECESSARY WHEN 20.<RMAX<33. --------------------------------------------------------------------- KOHL Default data
 
>KL      KOHL default data  June 2019 (namelist)
&OPA
IORT=1, IMON=1,
LUFM=0,
H4MAX=4, K4MAX=4, L4MAX=4

&END
/
C 1. ONE CARD WITH ANY TITLE TMO 17 C FURTHER DATA ARE READ UNDER CONTROL OF NAMELIST TMO 18 C THE FIRST CHARACTER IN EACH CARD MUST BE A BLANK TMO 19 C 2. CARD CONTAINING &OPA (see below) ($OPA for CDC 7600 FORTRAN) TMO 20 C ON IBM MACHINES $OPA SHOULD BE REPLACED BY fOPA TMO 21 C ** For this PC MSF77 version, use &OPA ** C 3. CONSECUTIVE DATA ITEMS SEPARATED BY COMMA,IN THE FOLLOWING FORMTMO 22 C X=Y, TMO 23 C X STANDS FOR A SYMBOLIC NAME LISTED BELOW TMO 24 C Y STANDS FOR THE NUMERIC VALUE OF X TMO 25 C THE ORDER OF THE DATA ITEMS IS FREE AND ALL THESE DATA ITEMS TMO 26 C CAN BE OMITTED.IN THIS CASE THE DEFAULT VALUES ARE TAKEN. TMO 27 C TMO 28 C SYMBOLIC NAMES, NUMERIC VALUE AND MEANING OF DATA ITEMS. TMO 29 C NQ= NUMBER OF D-VALUES USED TO VERIFY THE FOUND CELLS TMO 30 C DEFAULT=20 TMO 31 C IORT=1 SEARCH FOR ORTHORHOMBIC AND TRICLINIC CELLS TMO 32 C =2 SEARCH FOR ORTHORHOMBIC CELLS ONLY TMO 33 C =3 Search for triclinic cells only (implies IMON=0) C =0 SEARCH FOR TRICLINIC (AND MONOCLINIC) CELLS ONLY TMO 34 C DEFAULT=1 TMO 35 C IMON=1 Search for monoclinic and triclinic cells (triclinic TMO 94 C searched only if no solutions found in monoclinic) C =2 Omit search for triclinic cells TMO 95 C =0 Omit search for monoclinic cells TMO 96 C DEFAULT=1 TMO 97 C IUNAB=+1 SEARCH FOR INDEPENDENT BASIC LIST TMO 36 C =-1 FIRST LINES ARE TAKEN AS BASIC LINES TMO 37 C DEFAULT=1 TMO 38 C LUFM=NUMBER OF FAIL LINES AMONG THE FIRST NQ LINES ALLOWED TMO 39 C DEFAULT=0 TMO 40 C I20=LOWEST M20 VALUE WITH COMPLETE PRINTOUT OF SOLUTION TMO 41 C (i.e. solutions only reported & saved if KOHL M20>=I20) C DEFAULT=7 TMO 42 C FEHL=GREATEST RELATIVE ERROR OF Q= (DELTA Q)/Q TMO 43 C DEFAULT 0.01 TMO 44 C V1Z=VOLUME PER FORMULA UNIT OF UNIT CELL. TMO 45 C DEFAULT NO RESTRICTION TMO 46 C VD1Z=TOLERANCE ERROR OF V1Z TMO 47 C DEFAULT=1. TMO 48 C NZMAX=MAXIMAL NUMBER OF MOLECULES PER UNIT CELL TMO 49 C IZE=1,2,3,4 CORRESPOND TO CASES 1,2,3,4 OF SETTING THE INDICESTMO 50 C OF THE FIRST TWO LINES TMO 51 C =0 ALL VALUES 1,2,3,4 ARE TAKEN ONE AFTER EACH OTHER. TMO 52 C DEFAULT=0 TMO 53 C HM4,KM4,LM4 STARTING VALUES OF INDICES H4,K4,L4 TMO 54 C DEFAULT=0,1,1 TMO 55 C H4MAX,K4MAX,L4MAX= MAXIMAL VALUES OF H4,K4,L4 TMO 56 C UPPER LIMIT IS 4,4,4 TMO 57 C DEFAULT=2,2,2 TMO 58 C ITA=1 GIVES PRINTOUT OF PROBABILITY VALUES OF POSSIBLE BASIC TMO 59 C LINES TMO 60 C DEFAULT=0 TMO 61 C IM=2,3,4,5,6 HIGHEST INDEX OF THE BASIC LINES OF ORTHORMBIC TMO 62 C CELLS. IN MANY CASES IM=2 IS SUFFICIENT TMO 63 C DEFAULT=3 TMO 64 C TILI=TIMELIMIT IN SECONDS TMO 65 C DEFAULT=7200. TMO 66 C WLENG=WAVELENGTH IF THETA-VALUES ARE REQUESTED ON OUTPUT C 4. DATA ITEM FOR D-VALUES IN THE FORM D=Y1,Y2,Y3,.... TMO 67 C Y1,Y2,Y3,.... STANDS FOR THE D-VALUES TMO 68 C UNCERTAIN D-VALUES SHOULD BE PUT IN BEHIND THE NQ-TH LINE. TMO 69 C 5. LAST CARD CONTAINS a forward slash (/) (see below) C $END for CDC 7600 FORTRAN TMO 70 C ON IBM MACHINES $END SHOULD BE REPLACED BY fEND TMO 71 C ** For this PC MSF77 version, use / ** C TMO 72 NAMELIST/OPA/NQ,IORT,IUNAB,LUFM,ITER,IQW,I20,MQW,ITA,ITEST,FEHL TMO 165 1,V1Z,VD1Z,NZMAX,IZE,NLM,HM4,KM4,LM4,H4MAX,K4MAX,L4MAX,D,IAMT,IM TMO 166 2,IMON,MOM,TILI,WLENG,FOMMIN LOSH default data
>LS
  600.00000  600.00000  660.00000  400.00000   1.540599
 20  0  0  0 0.80                                                               
  30.00  30.00
C e.g. Basis set data, etc., for LOSHFZRF: C C 1) QA, QB, QC, QF of basis set in QU., Wavelength in A (5F11.5) C 2) N, LMIN, NSPURI, LRECTAN, FMINEQ0 (4I3,F5.0) C 3) ALPMIN, BETMIN (2F7.2) (both set to 30 deg to agree with LZON) Note QA QB QC QF are sensitive to problem .. needs more explanation 1028.60500 2232.80900 2037.05300 549.04600 1.540600 for lachlan example follow works for LiTi03... more or less LZON Default data
>LZ
9 1                   1.540600   1 4 8 8      01        .000     .0000
     .0600                         0 34.                             20
READ(INP,9902) MAN,INSTR,INTENS,NSYST,TOL2,TOL3,WAVEL,LINCO,K, FZON2095 1 NQ1,NQ2,NZ1,NZ2,NR,INPP,ICRIT,LST,J,WMOL,DOBS,TOLG,TOLZ 9902 FORMAT(3A1,1X,3I2,2F5.2,F10.5,8I2,2I1,1X,I1,2F10.5,2F5.0) READ(INP,9900) D2THDF,ALPMIN,BETMIN,LMIN,NSPURI,DABMAX,VOLMAX, 1 FOMMIN,NQCORD,NRLOSH 9900 FORMAT(3F10.0,2I3,F4.0,F10.0,F4.0,2I3) TAUP default data
>TP      taup32c  default June 2019
AFG CTHO                                              
 20, 0,3,6,,     6000.,5,,,,  1.540600
 
C FIRST CARD TAUP0093 C============= TAUP0094 C COL 1-12 OPTION LETTERS ( IN ANY ORDER ) TAUP0095 C 'Q' MEANS THAT GIVEN LINE DATA ARE EXPRESSED AS TAUP0096 C Q=1/D**2 RATHER THAN D(HKL) WHICH IS THE DEFAULT TAUP0097 C OPTION ; IN THIS CASE THE GIVEN ERROR ESTIMATION RELATETAUP0098 C TO 'Q' INSTEAD OF 'D' ; TAUP0099 C (IF VALUES ARE .GT.1 THEN THEY ARE ASSUMED TO BE 10000/DSQ) C 'A' MEANS THAT GIVEN LINE DATA ARE MEASURED ANGLES; TAUP0100 C ( NORMALLY 2-THETA ) TAUP0101 C 'A1' MEANS THAT THETA ANGLES ARE TO BE READ TAUP0102 C 'A4' MEANS THAT 4-THETA ANGLES ARE TO BE READ ; TAUP0103 C TAUP0104 C IN ALL THE ABOVE CASES, THE STATED ERROR IS AN ABSOLUTE TAUP0105 C ERROR CORRESPONDING TO THE VALUE ACTUALLY READ. TAUP0106 C TAUP0107 C 'V' MEANS THAT CELLS ARE ACCEPTED ONLY IF THEY CONTAIN AN ATAUP0108 C PROXIMATELY INTEGER NUMBER OF ASYMETRICAL UNITS OR TAUP0109 C MOLECULES ; IF THIS OPTION IS TAKEN, THE SECOND CARD TAUP0110 C MUST CONTAIN ADDITIONAL VALUES FOR THE TAUP0111 C - MOLECULAR WEIGHT, TAUP0112 C - DENSITY, TAUP0113 C - ESTIMATED ERROR ON THAT DENSITY ; TAUP0114 C 'X' OVERRIDES THE NORMAL SELECTION CRITERIUM WHICH RESULTS TAUP0115 C IN PRINTING THE ONLY CELLS WHOSE VOLUME DOES NOT EXCEEDTAUP0116 C 25 ( MORE THAN THE SMALLEST ONE ALREADY FOUND, AND IS TAUP0117 C ONE OF THE 10 SMALLEST CELLS FOUND ; IF 'X' APPEARS, TAUP0118 C THE PROGRAM WILL PRINT ALL FOUND CELLS WHOSE VOLUME IS TAUP0119 C LESS THAN THE VALUE STATED IN SECOND CARD ; TAUP0120 C Note: Selecting 'X' is liable to produce an unreadably C huge output file - e.g. 20,000+ lines for a cubic case C investigated down to orthorhombic (over 2MB of output) C 'C','T','H','O','M','3' MEAN THAT TRIALS MUST BE MADE FOR TAUP0121 C CUBIC, TETRAGONAL, HEXAGONAL, ORTHORHOMBIC, MONOCLINIC,TAUP0122 C OR TRICLINIC CELLS RESPECTIVELY ; THESE OPTIONS ARE TAUP0123 C CUMULATIVE AND IF NONE OF THEM APPEARS THEY ARE ASSUMEDTAUP0124 C TO BE ALL PRESENT ; TAUP0125 C 'P' MEANS THAT THE DATA CORRESPONDING TO THE BEST CELLS TAUP0126 C WILL ALSO BE PUNCHED ON CARDS ; TAUP0127 C 'L' PROVIDES A SPECIAL OUTPUT ON UNIT 'ILEAST' FOR FURTHER TAUP0128 C LEAST SQUARE REFINEMENT (APPLEMAN'S PROGRAM) WITH ADE TAUP0129 C QUATE FORMAT; TAUP0130 C 'Z' IS ESSENTIALLY A DEBUGGING OPTION WHICH PROVIDES ADDI TAUP0131 C TIONAL LOGGING AND A PRINTOUT OF THE INDEX TABLES AT TAUP0132 C THE BEGINNING. TAUP0133 C 'F' (FAST) SUPPRESS TRACE PRINTING OF CELLS REJECTED AS C UNINDEXABLE, ETC. C 'G' (YET FASTER) SUPPRESS TRACE PRINTING OF CELLS REJECTED C WHEN 'FIGURE OF MERIT' FALLS BELOW PRESET VALUE C ALSO 'S' PURPOSE UNCLEAR (AT LEAST TO R.SHIRLEY) - SEE LINE NO. C TAUP74-1.439 IN S/R CONTRL C C ** LOCAL DEFAULTS ** (UNIVERSITY OF SURREY, ENGLAND) C 'F' & 'G' C (THESE ARE OVER-RIDDEN IF 'Z' IS SELECTED) C TAUP0134 C COL 13-72 ANY ALPHANUMERIC TITLE WHICH WILL BE PRINTED AT THE TOP OFTAUP0135 C EACH PAGE ; TAUP0136 C TAUP0137 C SECOND CARD TAUP0138 C============== TAUP0139 C ALL THESE VALUES ARE IN !FREE FORMAT!, I.E. THEY MAY BE WRITTEN EITHERTAUP0140 C AS INTEGERS OR REAL VALUES ( WITHOUT DECIMAL EXPONENT HOWEVER ), SEPA TAUP0141 C RATED BY COMMAS; BLANK ARE DISREGARDED IN THAT CARD AND LETTERS 'I' TAUP0142 C AND 'O' ARE UNDERSTOOD AS FIGURES '1' AND '0'. TAUP0143 C THESE VALUES ARE RESPECTIVELY TAUP0144 C - NUMBER OF GIVEN EXPERIMENTAL LINES TAUP0145 C - MAXIMUM NUMBER OF EXTRANEOUS LINES TAUP0146 C - MAXIMUM DEGENERESCENCE FACTOR MAXIMUM NUMBER OF ADDITIONAL TAUP0147 C LINES TO BE USED WHEN THE FIRST ONES LEAD TO A DEGENERATE EQUATAUP0148 C TION SYSTEM FOR CELL PARAMETER DETERMINATION (A GOOD VALUE IS TAUP0149 C 2 OR 3) TAUP0150 C - UPPER LIMIT FOR H**2+K**2+L**2 FOR THE FIRST LINE ( THIS TAUP0151 C VALUE IS USED TO COMPUTE THE UPPER LIMIT FOR H**2+K**2+L**2 OFTAUP0152 C THE FOLLOWING LINES, ASSUMING THEY ARE PROPORTIONAL TO TAUP0153 C Q=1/D**2 ( THIS IS OBVIOUSLY A ROUGHLY APPROXIMATE EXTRAPOLA TAUP0154 C TION ) TAUP0155 C - MAXIMUM TIME LIMIT ( MINUTES ); WHEN THIS LIMIT IS EXCEEDED TAUP0156 C THE PROGRAMM WILL SUSPEND ITSELF AND WRITE 2 OR MORE RESTART TAUP0157 C ING RECORDS; THIS LIMIT SHOULD BE SMALLER THAN THAT STATED IN TAUP0158 C THE 'JOB' CARD TO PREVENT IT FROM BEING KILLED BY THE TAUP0159 C OPERATING SYSTEM. TAUP0160 C - MAXIMUM VOLUME OF THE UNIT CELL (ANGSTROEM**3) TAUP0161 C - THE MINIMAL FIGURE OF MERIT (SEE DE-WOLFF'S PAPER IN JOURNAL TAUP0162 C OF APPLIED CRISTALLOGRAPHY - 1968); USUAL VALUE = 4; HIGHER TAUP0163 C VALUES MAY BE STATED IF EXPERIMENTAL MEASUREMENTS ARE GOO;. TAUP0164 C WHEN OPTION 'V' IS PRESENT TAUP0165 C - MOLECULAR MASS ( OR MASS OF THE ASYMETRIC UNIT ) TAUP0166 C - DENSITY ( GRAMS/CM**3 ) TAUP0167 C - RELATIVE ESTIMATED ERROR ON THAT DENSITY TAUP0168 C TAUP0169 C=============# NOTE THAT YOU MAY LEAVE ALL OR PART OF THESE TWO FIRST TAUP0170 C CARDS BLANK; THEN THE PROGRAM WILL USE DEFAULT VALUES WHICH ARE TAUP0171 C - ALL SYSTEM TESTED; TAUP0172 C - LINES WILL BE COUNTED TO FIND THEIR EFFECTIVE NUMBER; TAUP0173 C - NO EXTRANEOUS LINES ALLOWED; TAUP0174 C - DEGENERESCENCE FACTOR EQUAL TO 2 ; TAUP0175 C - H**2+K**2+L**2 LIMITED TO 6 FOR THE FIRST LINE; TAUP0176 C - NO TIME LIMIT, THEN NO RESTART ; TAUP0177 C - MAXIMUM VOLUME = 1000 ANGSTROEM**3 ; TAUP0178 C - FIGURE OF MERIT EQUAL TO 4 ; TAUP0179 C TAUP0180 TREOR default data
>TR
CHOICE=3,
VOL= -6000,
MERIT=9,
WAVE=1.540600,
END*

Note this follows input of twotheta peak values

Short note on control files for Crysfire2020

Wish interprets both / and \ similarly. Mostly used here is /.

When Crysfire2020 starts, the location of the programs is determined from the command line:
For Windows the command is contained in the launch icon, created during the installation procedure; this includes the path to the wish interpreter program.

For Macintosh OS X or Linux again this is from a commandline command like

% wish /Users/me/crosx/cr2020.tcl
In Windows the owner's top directory HOME is %HOMEDRIVE%\%HOMEPATH%
For Linux/Macintosh/unix HOME is $HOME

The starting directory for Crysfire2020 is in written in file HOME/.CRroot
This contains only the path to the Crysfire working directory ..../cr2020 this defaults to HOME
e.g.
/Users/me/cr2020

The "File" menu option will create a directory in cr2020 for a new project, and write the name of the current project into ..../cr2020/.CRproj file

Inside /Users/me/cr2020 one finds each project folder e.g. new, new1, new2..

/Users/me/cr2020/new
/Users/me/cr2020/new1
/Users/me/cr2020/new2  etc
and file
/Users/me/cr2020/.CRproj
When starting anew, when .CRroot is absent, the initial path name proposed is HOME/ and the working directory cr2020 is normally placed there, and contains the new project directory. .CRroot and cr2020/.CRproj are then updated.
Any alternative placement directory for the working directory (e.g. on a secondary disk) must already exist.

Creating a new project requires a new project name and title. An edit window is then shown into which either a single column of data (column 1) or a regular table may be pasted, (the table may be copied from results of peak identification programs). In the second case a specific column should be selected and then saved. These are written to the project directory as a file project.PPP When a project is created a copy of the default parameters cr2020.dfp is placed therein, copied from the program directory. A cr2020.dfx file is also created with default values for title, wavelength etc., which are shown on the main panel and are shared by each indexing program. This may be modified in the "settings" menu.

The default parameter file cr2020.dfp in the current project file may be edited (see "settings" menu. It contains information on each program as well as two copies of the default parameters. (The first encountered after the tag ">ID" is used; the remainder of the line is printed out, so this may be used as a comment in the full output.

Other View menu options allow project data, result files and log file to be viewed.

In the settings menu there is the possibility to modify parameters such as zero angle, 2theta_deviation (acceptable mismatch between measured and calculated peaks), zero angle, and title. If changed these are used for all subsequent calculations (it is hence useful to modify the title after changes). If no solutions are found the accptable 2theta_deviation can be increased up to 0.06 degrees or more. These parameters are stored in the file cr2020.dfx. It is also possible to display the peak file project.PPP, and copy the contents to a clipboard. Then a new project may be selected ("Files") and the data pasted in to the new project with all the additional revisions. This enables results from fresh calculations to be compared with those in the initial project. Again noting modifications in the title offers a simple method of following such changes.

Provided copies of the files cr2020.dfp and cr2020.dfx are in the same directory as the peak data peakdata.PPP, each indexing program may be run independently of the GUI with the command line:

[program_path_name]program_name peakdata

Re-initialising Crysfire

The program will fail if the root filename stored in the HOME directory is damaged, or the directory it points to is no longer present. To reset this:

1. exit program
2. delete file .CRroot in the HOME directory

   - Using file manager - ensure viewing of hidden/system files is enabled
   - Using command/terminal window
     Windows :      > del  %HOMEDRIVE%\%HOMEPATH%\.CRroot
     OS X, Linux :  % rm $HOME/.CRroot
3. restart Crysfire2020


Task management

When each indexing program starts to run it writes its system process identifier into a file crsubtsk. The completion routine writes a terminating file crrun containing the run time and the reason for finishing. Crysfire2020 uses these files to control killing of any running tasks when expressly interrupted, or if the main window is closed, so no programs remain running in the background.


Crysfire2020 versions

The installed version of Crysfire-2020 is shown in the Help/About menu. If problems arise please send a copy of the project files and a description of the problem actions to reghosh (at) gmail.com, indicating the version in use. A copy of this Crysfire.html description file is included in the program directory.

Version 1.0.5 July 2020
Mainly corrections to title treatment ensuring all programs treat a modified title similarly. The title in the dfx file is used before the default title in the PPP file.
If the directory in the .CRroot file is not available the program reverts to the default. This can be changed later in settings/change work directory.

Version 1.0.4 June 2020
Especially on Windows it was possible to leave an indexing program running, requiring use of the task-manager to terminate the subprocess. With the addition of creating management files in each program it is now possible to kill subtasks in a controlled fashion. On Windows a compute intensive Tcl subtask can block the GUI from running. A specific interface psta to the CREATE_PROCESS Windows routine has been added to run the indexing programs as a separate background task. If a virus scanner is active there may be a pause after a task is started for the first time while the executable is examined. The running task status then changes from "starting" to "running".
A new file may be created by pasting in a table of peak finding results and selecting a column of two-theta values.
The help text has been replaced by calling a browser to display the html file installed with the program files.

Version 1.0.3 April 2020
The Windows installer creates an icon with the full path names to wish and cr2020.tcl. To simplify use on Linux and Macintosh relative paths to these files were added in this version.

Version 1.0.2 February 2020
This was the first version of Crysfire2020 published on the CCP14 Website.
The original Crysfire suite due to the late Robin Shirley (d 2005) offered a uniform user interface to eight well respected indexing programs. Being written in a mixure of Pascal, MSDOS batch files and MSDOS Fortran programs (16-bit) it has become increasingly difficult to run on modern Windows systems, without emulators. Default parameters were embedded in the QDAT.FOR program. Modifying program control parameters required intercepting and editing batch files and running manually.
The indexing programs have been updated with common features and a few structural modifications required by current Fortran. They have been recompiled using gfortran on each system. The original 35k lines of Fortran sources for the indexing programs are mostly written, without comments, in FORTRAN IV.
Rewriting the interface using Tcl/tk allows the suite to be used on Windows, Mac-OSX, or Linux systems with identical source codes. The resulting script is about 1200 lines of Tcl, compared to 43k lines of Pascal and 18000 lines of DOS batch files and utility programs of Shirley's 2004 version.
Unfortunately Shirley's MMAP visualisation utility was embedded deep in the original Pascal source; without a detailed description it has not been included here.
Not all the program sources in the 2004 distribution are extant. Comparison of results from the present programs and the 2004 DOS versions show close resemblances.
To simplify modifying the default operation of programs, the default values ar held in a text file cr2020.dfp which can be edited within Crysfire2020 (Settings).

Acknowledgements

I thank Jeremy Cockcroft and Martin Vickers of the Chemistry Department, University College, London, for their warm hospitality and help in this and other collaborations. As master practitioners in the science and art of powder diffraction, they were increasingly restricted to obsolete Windows systems to continue using Shirley's CRYSFIRE-2004. As a challenge I took up this task of renewing the suite. I used a Macintosh system, with virtual machine emulators for Windows and Linux.
I hope future users and students will look beyond the summary files and examine the full outputs from these arcane programs from the last century. They will find there endless encouragement to use data of the highest quality.

Ron Ghosh, Epsom, August 2020

A version of this note is included in the installation and is located with the program files. It may be displayed from Crysfire2020 from the Help menu