CRYSCALc user's guide

CRYSCALc

************************************************************* * * * CRYSTALLOGRAPHIC CALCULATIONS * * * * * * T. Roisnel * * (CDIFX - ISCR UMR6226 Rennes) * * 7 Nov. 2014 * * * * with courtesy of JRC and JGP for CFML * * * * * * contact: thierry.roisnel@univ-rennes1.fr * * * * Web site : www.cdifx.univ-rennes1.fr/cryscalc * * * *************************************************************

  Introduction :

CRYSCALc has been created to perform basic crystallographic calculations or get crystallographic informations. CRYSCALc has been written in Fortran 95, and uses the crystallographic calculations facilities of the Crystallographic Fortran Modules Librairies written by J. Rodriguez-Carvajal (ILL-Grenoble, France) and J. Gonzalez (Univ. La Laguna, Spain). Facilities implemented in CRYSCALc: . unit cell volume calculation . space group informations: space group features, Wyckoff positions, symmetry operators, extinctions ... . calculation of d_hkl, Q_hkl, 2theta_hkl (including a propagation wave vector) . hkl generation for a given space group . structure factor calculation (Xrays, neutrons, electrons) . simulation of powder diffraction pattern (X, neutrons) . geometric calculations: interatomic distances, angles, connectivity, bond valence sums (BVS), centroid coordinates, angles between 2 vectors in direct and reciprocal space, ... . atomic features: weight, density, electronic configuration, ionic and Shannon radii, neutron data, X-rays data ... . molecular informations: molecular weight, density ... . absorption coefficient calculation (X-rays, neutrons) and transmission calculation . transformation of unit cell, atomic coodinates and hkl files . statistics on hkl file and sort of hkl data . search for systematic extinctions and space group . ADP parameters conversion . create HTML report from a CIF file ... CRYSCALc can be run through an input file containing a list of keywords, defining the type of crystallographic calculations that will be performed, or in an interactive mode, by entering keywords at the CRYSCALc prompt. Crystallographic features can be read from different types of input files : .CFL .INS/.RES file (SHELXL) .CIF file .PCR file (FullProf) .CEL file (PowderCELL) Alternatively, particular jobs can be performed by CRYSCALc when special arguments are passed to CRYSCALc through the command line (see CRYSCALc command line arguments section). Online help can be obtained by typing "MAN" or "HELP" at the "Enter input file" (menu option #1) or "Enter keyword:" (menu option #2) prompt: d:> cryscalc > Enter keyword : man or launching CRYSCALc program with "MAN" or "HELP" as argument: d:> cryscacl man Details on the meaning of keywords can be obtained by typing the corresponding keyword at the "Enter keyword :" prompt or launching CRYSCALc program with the corresponding keyword(s) as argument(s): d:> cryscalc MAN CELL [return]

  List of CRYSCALc keywords :


 
[return]

  Details of CRYSCALc keywords :

> ABSENT_HKL:

    . type:                OUTPUT keyword
    . meaning:             search for observed reflections (with F2>0.) that
                           should be absent for a given space group
    . optionnal arguments: . arg = "ALL": all the violations reflections are
                                          output
                           . arg = "OUT": requested reflections are output on
                                          the screen
                           . arg = "WRITE": requested reflextions are output
                                            in a HKL file
                           . arg = real_value (n_sig): only reflections with
                                                       I/sig > n_sig are output
    . mandatory keyword:   FILE, SPGR
    . identical keywords:  ABSENT_HKL, HKL_ABSENT

[return to keywords list]

> ABSORPTION:

    . type:                CALCULATION keyword
    . arguments:           no argument
    . meaning:             absorption coefficient calculation
    . mandatory keywords:  CELL, WAVE, CONT / CHEM
    . identical keywords:  ABSORPTION, ABSORPTION_CALC, CALC_ABSORPTION,
                           MU, CALC_MU, MU_CALC

[return to keywords list]

> ACTA:

    . type:                OUTPUT keyword
    . arguments:           no argument
    . meaning:             create CRYSCALC.CIF file containing calculation
                           results in a CIF format
    . identical keywords:  ACTA, CIF, CREATE_CIF

[return to keywords list]

> ANG:

    . type:                CALCULATION keyword
    . arguments:           3 character strings
    . meaning:             calculation of the angle defined by three atoms
                           labelled by the atom labels (cf ATOM keyword)
    . example:             ANG C8 C10 C9

  or
    . arguments:           4 character strings
    . meaning:             calculation of the angle defined by the segments
                           constituted by atoms couples labelled as S_1, S_2
                           and S_3, S_4 respectively (cf ATOM keyword)

    . remark:              atom label can refer to equivalent position through
                           a particular symmetry operator (cf SYMM keyword).
                           This is specified by adding "_$n" to the
                           atomic label, with n refering to the number of
                           symmetry operator in the list.

    . example:             ANG O1 C8 C9 C10_$1
    . identical keywords:  ANG, ANGLE

[return to keywords list]

> APPLY_OP:

    . type:                OUTPUT keyword
    . arguments :          no argument
    . outputs:              apply the symmetry operators on the atomic
                           positions
    . mandatory keyword:   SYMM, ATOM
    . identical keywords:  APPLY_OP, APPLY_SYMMETRY_OPERATOR,
                           APPLY_SYM_OP, APPLY_SYMOP

[return to keywords list]

> ATOM:

    . type:                INPUT keyword
    . arguments:           2 character strings and 5 reals
    . meaning:             . string #1: atomic label
                           . string #2: atom type (can contain oxdation state)
                           . x,y,z atomic reduced coordinates
                           . Biso, site occupancy (%)
    . remarks:             . if Biso   is missing: Biso = 0.0
                           . if Occ(%) is missing: Occ(%) = 1.0 (site is fully
                             occupied)
    . example:             ATOM O1   O   0.04356  0.03008  0.39001   0.35  1.
                           ATOM C8   C   0.02071 -0.12436  0.36957   0.30  1.
                           ATOM C9   C  -0.27497 -0.07538  0.27585   0.30  1.
                           ATOM C10  C  -0.16896 -0.18823  0.36382   0.32  1.
                           ATOM Si1 Si+4   0.53245 0.53245 0.5
                           ATOM O1  O-2    0.58566 0.85594 0.61727
    . identical keywords:  ATOM, ATM

[return to keywords list]

> ATOM_LIST:

   . type:                OUTPUT keyword
   . optional argument:   "CART"
   . meaning:             list the atoms (type, labels, coordinates, ...)
                          if "CART" is present, cartesian atomic coordinates
                          will be output.
                            derivative CART arguments : CART_A (a//x),
                            CART_C (x//c)
                            if "in_A" is present, atomic coordinates are listed
                            in A.
   . optional keyword:    SPGR
   . identical keywords:  ATOM_LIST, ATOM_LST, LIST_ATOM_LIST, LIST_ATOMS,
                          LST_ATOMS, WRITE_ATOMS, WRITE_ATMS

[return to keywords list]

> BARY:

    . type:                CALCULATION keyword
    . arguments:           n character strings
                           or "ALL"
    . meaning:             calculation of the coordinates of the centroid of the
                           n atoms known by the atom label (cf ATOM keyword)
                           if arg="ALL": all input atoms are considered
    . examples:            BARY C8 C10 C9 C11
                           BARY ALL
    . identical keywords:  BARY, CENTROID

[return to keywords list]

> BEAM:

    . type:                INPUT keyword
    . arguments:           character string
    . meaning:             type of the incident beam:
                             - BEAM NEUT  for neutrons
                             - BEAM ELECTRONS  for electrons
                             - X_Ag for X Rays (Silver K_alpha)
                             - X_Mo for X Rays (Molybdenum K_alpha)
                             - X_Cu for X Rays (Copper K_alpha)
                             - X_Ni for X Rays (Nickel K_alpha)
                             - X_Co for X Rays (Cobalt K_alpha)
                             - X_Fe for X Rays (Iron K_alpha)
                             - X_Cr for X Rays (Chromium K_alpha)
    . example:            BEAM X_Mo
    . identical keyword:  BEAM, JOBTYPE, JPBTYP

[return to keywords list]

> CELL:

    . type:                INPUT keyword
    . arguments:           6 reals or 1 character string
    . meaning:              - reals: unit cell parameters in A (a, b, c) and
                                     angle in deg. (alfa, beta, gamma)
                            - character string: file name containing unit cell
                              parameters.
                              Following files can be read:
                               . INS/RES file for SHELXL
                               . P4P  file created by SAINT
                               . M50  file created by JANA
                               . X    file created by DENZO
                               . RMAT file created by DIRAX
    . output:              unit cell volume calculation
                           direct and reciprocal unit cell parameters
    . example:             CELL 7.6520 7.8450 11.0760 90. 90. 90.
                           CELL my_saint_data.P4P
                           CELL my_janat_data.m50
    . identical keywords   CELL, CELL_PARAMETERS

[return to keywords list]

> CHEM:

    . type:                INPUT keyword
    . arguments:           n "El_i_n_i" character strings (without blank
                           character between label and number)
    . meaning:             Molecular chemical formula: El_i is the chemical
                           symbol of the species i and n_i is the corresponding
                           number of atoms in the formula unit
    . output:              molecular weight, total number of electrons,
                           atomic and weight percentage

    . mandatory keyword:   ZUNIT
    . example:             CHEM C4 O6 H9 N1
    . identical keywords:  CHEM, CHEM_FORM, CHEMICAL_FORMULA

[return to keywords list]

> CONN:

    . type:                INPUT keyword
    . argument:            atom_label + dist_max
    . optional arguments:  ALL, ALL_X, NO_X, ANG, BVS, VOL, SHAPE, SELF, MIN=, M
                           CONDENSED
    . meaning:             determine the connectivity around the atom "atom_labe
                           with interatomic distances calculated between MIN
                           and MAX values.
                           Default values for MIN and MAX = 0.4 and 3.0 A.
                           if argument=ALL, the program will calculate
                           connectivity around all atoms.
                           if argument=ALL_X, the program will calculate
                           connectivity around all atoms of the species X.
                           if argument=NO_X, the program will exclude
                           connectivity with all atoms of the species X.
                           if "ANG" is present, interatomic angles will
                            also be calculated.
                           if "BVS" is present, bond valence sums
                            calculations are performed.
                           if "VOL" is present, polyedron volume is calculated
                            (ref. : VOLCAL program of L. W. FINGER included in C
                           if "SHAPE" is present, an input file
                            for SHAPE program (http://www.ee.ub.es/) is created.
                            derivative SHAPE arguments : SHAPE_A (a//x),
                            SHAPE_C (x//c)
                           if SELF (or AUTO) is present, output distances betwee
                            atoms from the same label
                           if CONDENSED is present, short ouput is created
                            ex: CONN Yb1 SELF 10.
                            ex: CONN Si1 MIN=1.5 MAX=2.7
                            ex: CONN Nd1 VOL SHAPE
                            ex: CONN ALL_Nd
                            ex: CONN ALL ANG CONDENSED
                            ex: CONN Cu1 no_H
    . output:              interatomic distances, bond distribution and optional
                           calculations.
                           Effective distance is calculated as follows:
                           r_eff=[N/Sum(r^-3)]^1/3
                           IF CIF/ACTA keyword is input, the created CIF file
                           will contains all the calculated distances in CIF
                           format.

    . mandatory keywords:  SPGR, ATOM, CELL
    . identical keywords:  CONN, CONNECT, CONNECTIVITY

[return to keywords list]

> CONT:

    . type:                INPUT keyword
    . arguments:           n "El_i  n_i"(character string, real) couples
    . meaning:             unit cell contents: El_i is the chemical symbol of
                           the species i and n_i is the corresponding number
                           of atoms in the unit cell
    . optional keyword:    ZUNIT
    . example:             CONT C 16.  O 24.  H 36.  N  4.

[return to keywords list]

> CREATE_ACE :

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             create .ACE file for CaRIne from a CIF file
    . mandatory keyword:   READ_CIF file.cif
    . dependent parameter: CREATE_ACE parameter value in the CRYSCALC.INI
                           setting file. If equal to 1, a .ACE file will
                           be automatically created if a .CIF file is
                           given as argument when CRYSCALc is launching
                           from a command line :
                           > cryscalc file.cif

[return to keywords list]

> CREATE_CEL

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             create .CEL file for PowderCELL from a CIF file
    . mandatory keyword:   READ_CIF file.cif
    . dependent parameter: CREATE_CEL parameter value in the CRYSCALC.INI
                           setting file. If equal to 1, a .CEL file will
                           be automatically created if a .CIF file is
                           given as argument when CRYSCALc is launching
                           from a command line :
                           > cryscalc file.cif

[return to keywords list]

> CREATE_CFL

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             create .CFL file for CRYSCALc from a CIF file
    . mandatory keyword:   READ_CIF file.cif
    . dependent parameter: CREATE_CFL parameter value in the CRYSCALC.INI
                           setting file. If equal to 1, a .CFL file will
                           be automatically created if a .CIF file is
                           given as argument when CRYSCALc is launching
                           from a command line :
                           > cryscalc file.cif

[return to keywords list]

> CREATE_FST

    . type:                OUTPUT keyword
    . argument:            POLY, RUN, MOLE, No_H
    . meaning:             create .FST file for FP Studio
                           if argument=POLY : include polyedra if
                           connectivity calculation have been performed
                           if argument=RUN : launch FP_studio software
                           if argument=MOLE: only atoms of the asymetric
                           unit cell are drawn.
                           if argument=No_H: H atoms and related bonds
                           are excluded. This option is valid only if
                           MOLE is specified.
    . mandatory keyword:   READ_CIF file.cif or READ_INS file.ins
    . dependent parameter: CREATE_fst parameter value in the CRYSCALC.INI
                           setting file. If equal to 1, a .fst file will
                           be automatically created if a .CIF file is
                           given as argument when CRYSCALc is launching
                           from a command line :
                           > cryscalc file.cif

[return to keywords list]

> CREATE_INS

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             create .INS file for SHELXL from a CIF file
    . mandatory keyword:   READ_CIF file.cif
    . dependent parameter: CREATE_INS parameter value in the CRYSCALC.INI
                           setting file. If equal to 1, a .INS file will
                           be automatically created if a .CIF file is
                           given as argument when CRYSCALc is launching
                           from a command line :
                           > cryscalc file.cif

[return to keywords list]

> CREATE_REPORT:

    . type:                output keyword
    . optional argument:   .CIF file name
    . meaning:             create a STRUCTURAL_REPORT.HTML file in HTML format
                           from the reading of the ARCHIVE.CIF file present in
                           the current folder, and launch the browser with this
                           HTML file. The .CIF file can be explicitely defined
                           with the argument.
                           If "long" or "ext" is given as argument, a longer
                           report will be created, containing more informations,
                           included distances and angles.

    . identical keywords:  REPORT, CREATE_REPORT
    . examples:            report
                           report long my_struct.cif

[return to keywords list]

> CREATE_SOLVE:

    . type:                output keyword
    . meaning:             create input files for structure solving software as
                           SIR97; SHELXS/T and SUPERFLIP
    . optional argument:   no
    . dependent parameter: CELL parameters, cell content, space group and
                           hkl file has to be provided

    . identical keywords:  CREATE_SOLVE, CREATE_TO_SOLVE, CREATE_FILES_TO_SOLVE,
                           SOLVE

[return to keywords list]

> CREATE_TIDY:

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             create xx_tidy.dat file for TIDY (standardisation
                           of inorganic crystal-structure data [Acta Cryst.
                           1984, A40, 169-183] from a .CIF or .INS file
    . mandatory keyword:   READ_CIF file.cif or READ_INS file.ins

    . identical keywords:  CREATE_TIDY, CREATE_TIDY_FILE, CREATE_TIDY_INPUT_FILE
[return to keywords list]

> D_HKL:

    . type:                CALCULATION keyword
    . argument:            real values
    . meaning:             d_hkl(A) values
    . outputs:             Q(A-1), SinTheta/lambda(A-1)
                           theta(deg) for known wavelength
    . optionnal keyword:   WAVE
    . identical keywords:  D_HKL, DHKL
    . example:             DHKL 0.77

[return to keywords list]

> D_STAR:

    . type:                CALCULATION keyword
    . argument:            real values
    . meaning:             1/d_hkl (A-1
    . outputs:             d(A)
                           theta(deg)
    . optionnal keyword:   WAVE
    . identical keywords:  D_STAR, D_STAR_HKL, DSTAR, DSTARHKL, DSTAR_HKL
    . example:             D_STAR  0.5

[return to keywords list]

> DATA_ATOMIC_DENSITY:

     . type:               OUTPUT keyword
     . optionnal argument: PLOT
     . meaning:            list atomic density data for all atoms
                           if arg=PLOT: create a PGF file and plot it with
                           WinPLOTR
     . identical keywords: DATA_DENSITY, DENSITY_DATA, DATA_ATOMIC_DENSITY,
                           ATOMIC_DENSITY

[return to keywords list]

> DATA_ATOMIC_RADIUS:

     . type:               OUTPUT keyword
     . optionnal argument: PLOT
     . meaning:            list atomic radius data for all atoms
                           if arg=PLOT: create a PGF file and plot it with
                           WinPLOTR
     . identical keywords: DATA_RADIUS, RADIUS_DATA, DATA_ATOMIC_RADIUS,
                           ATOMIC_RADIUS

[return to keywords list]

> DATA_ATOMIC_WEIGHT:

     . type:               OUTPUT keyword
     . optionnal argument: PLOT
     . meaning:            list atomic weight data for all atoms
                           if arg=PLOT: create a PGF file and plot it with
                           WinPLOTR
     . identical keywords: DATA_WEIGHT, WEIGHT_DATA, DATA_ATOMIC_WEIGHT,
                           ATOMIC_WEIGHT

[return to keywords list]

> DATA_NEUTRONS:

     . type:               OUTPUT keyword
     . optionnal argument: PLOT
     . meaning:            list neutrons data for all atoms (coherent
                           scattering length, incoherent scattering
                           cross-section, absorption cross-section)
                           Neutron data are extracted from :
                           V.F. Sears
                           Neutron News, vol.3 n°3, 1992, 26-37
                           if arg=PLOT: create a PGF file and plot it with
                           WinPLOTR
     . see:                Xrays_DATA
     . identical keywords: DATA_NEUTRONS, NEUTRONS_DATA, DATA_NEUTRON,
                           NEUTRON_DATA

[return to keywords list]

> DATA_XRAYS:

     . type:               OUTPUT keyword
     . optionnal argument: PLOT
     . meaning:            list X-ray data for all atoms (total interaction
                           cross section for Ag, Mo, Cu, Co, Fe and Cr radiation
                           X-ray data are extracted from :
                            Tables Internationales vol.C  1995, p.200-206,
                            Tables Internationales vol.C  1995, p. 193-199
                           if arg=PLOT: create a PGF file and plot it with
                           WinPLOTR
[return to keywords list]

> DIAG:

    . type:                INPUT keyword
    . arguments:           9 reals
    . meaning:             transformation (3,3) matrix components
    . examples:            MATR   0  0  1    0  1  0    -1  0  -1
                           MATR   0.5 0.5 0   -0.5 0.5 0   0 0 1
                           MATR   1/2 1/2 0   -1/2 1/2 0   0 0 1
    . output:              Diagonalization of the 3*3 matrix and output
                           the Eigen values and Eigen vectors
    . identical keywords:  DIAG, DIAG_MAT, DIAG_MATR, DIAG_MATRIX

[return to keywords list]

> DIR_ANG:

    . type:                CALCULATION keyword
    . arguments:           2*3 reals
    . meaning:             calculation of the angle between 2 vectors in the
                           direct space. The 3 first real values are related
                           to the coordinates of the first vector and the 3
                           last real values to the coordinates of the second
                           vector
    . mandatory keyword:   CELL
    . identical keywords:  DIR_ANG, DIRANG, DIRECT_ANGLE
    . example:             DIR_ANG 1. 0. 0.   0. 1. 0.

[return to keywords list]

> DIST:

    . type:                CALCULATION keyword
    . arguments:           2 character strings
    . meaning:             calculation of the interatomic distance between 2
                           atoms labelled by their atom labels (cf ATOM keyword)
    . remark:              atom label can refer to equivalent position through
                           a particular symmetry operator (cf SYMM keyword)
                           atomic label, with n refering to the number of
                           symmetry operator in the list.
    . example:             DIST C8 C10
                           DIST C10 C9
                           DIST C10 C9_$1
    . identical keywords:  DIST, DISTANCE, ATOMIC_DISTANCE

  > DIST_MULT:

    . type:                CALCULATION keyword
    . arguments:           1 real (x) + 2 character strings (A B)
    . meaning:              - calculation of the interatomic distance between 2
                              atoms labelled by their atom labels A and B
    .                       - calculation of the coordinate of the point M
                              with : d_AM = d_AB * x
    . example:             DIST_X C8 C10 1.2
    . identical keywords:  DIST_MULT, DIST_X

  > DIST_PLUS:

    . type:                CALCULATION keyword
    . arguments:           1 real (x) + 2 character strings (A B)
    . meaning:              - calculation of the interatomic distance between 2
                              atoms labelled by their atom labels A and B
    .                       - calculation of the coordinate of the point M
                              with : d_AM = d_AB + x
    . example:             DIST_PLUS C8 C10 1.2
    . identical keywords:  DIST_PLUS, DIST_+

  > DIST_DHA:

    . type:                CALCULATION keyword
    . arguments:           2 character strings (D A)
    . aoptional argument:  1 real d_H (default value=0.9 Ang.)
    . meaning:              - calculation of the interatomic distance between
                              donor (D) and acceptor atoms (A)
    .                       - calculation of the coordinate of H atom
                              with : d_DH = d_AB - d_H
    . examples:            DIST_DHA N1 O2
                           DHA N1 O2 0.92
    . identical keywords:  DIST_DHA, DHA, POS_H, CALC_POS_H

[return to keywords list]

[return to keywords list]

> EDIT:

    . type:                output keyword
    . argument:            1 character string (filename)
    . meaning:             open the file given as argument with the editor defin
                           in the CRYSCALC.ini setting file
    . example:             edit my_cryscalc.cfl
    . related keywords:    SET, SETTING

[return to keywords list]

> EQUIV:

    . type:                OUTPUT keyword
    . arguments:           3 integer values: h, k, l
    . optionnal arguments: FRIEDEL
    . meaning:             search for equivalent reflections (Space group is
                           mandatory)
                           . arg = FRIEDEL: search for Friedel reflections
    . output:              list of required hkl reflections
    . mandatory keyword:   SPGR
    . identical keywords:  EQUIV, EQUIV_HKL, SEARCH_EQUIV, SEARCH_EQUIV_HKL,
                           FIND_EQUIV, FIND_EQUIV_HKL
    . example:             EQUIV 1 1 0 FRIEDEL

[return to keywords list]

> EXIT:

     . type:               OUTPUT keyword
     . argument:           no
     . meaning:            exit from the "enter keyword" procedure to come
                           back to the CRYSCALc main menu
     . identical keywords: EXIT, X, QUIT, END, STOP

[return to keywords list]

> FILE:

    . type:                INPUT keyword
    . arguments:           1 character string reals
    . meaning:             read .HKL file name,  containing a list of
                           h, k, l, F2,  sig_F2
                            . available formats for HKL file:
                               . SHELX type: 3I4, 2F8.2
                               . CIF format
                               . RAW format (created by SAINT)
                               . M91/M95 format (created by JANA)
    . output:              . analysis of the hkl reflections:
                            . number of hkl reflections
                            . d(A) and sinTheta/lambda collected ranges
                              (dependent keyword = CELL)
                            . Theta collected range (dependent keyword = CELL,
                              WAVE)
                            . statistic on collected data
                           . if space group is known (see SPGR keyword), the
                             number of reflections in agreement is output

    . optionnal arguments: NEG: negative reflections are treated as follows:
                             if (F2      < 0.0001)  F2 = 0.0001
                             if (sig_F2_ < 0.00001) sig_F2_=sqrt(abs(F2)
                           PLOT (dependent keywords = CELL, WAVE)
                           OUT_n : write every n reflections
                           STAT  : statistics ouput on hkl reflections
                           NO_STAT  : no statistics output on hkl reflections
                           FREE  : free format for hkl data (only h,k,l,F2
                                   and sig_F2 are read.
                           FMT=  : format of the hkl file  (default format
                                   corresponds to the SHELX format (3I4, 2F8.2)
    . action:              plot the F2=f(sinTheta/lambda) curve with WinPLOTR
    . examples:            FILE my_HKL_FILE.HKL
                           FILE import.CIF plot
                           FILE file.HKL FMT=(3i4,2f15.2)
    . identical keywords:  FILE, READ_HKL

[return to keywords list]

> FIND_HKL:

    . type:                OUTPUT keyword
    . arguments:           3 integer values: h, k, l
                           or
                           characters with one or two index characters being h,
                           k or l
    . optionnal arguments: EQUIV, FRIEDEL (only for integer values of h, k and l
    . meaning:             search a particular hkl reflection in a
                           reflections list
                           . arg = EQUIV:   search for equivalent reflections
                             (Space group is mandatory)
                           . arg = FRIEDEL: search for Friedel reflections
    . output:              list of required hkl reflections
    . mandatory keyword:   FILE
    . identical keywords:  FIND_HKL, FINDHKL, SEARCH_HKL
    . examples:            FIND_HKL 1 1 0 FRIEDEL
                           FIND_HKL h 0 0
                           FIND_HKL 2 k 0
                           FIND_HKL -1 k l

[return to keywords list]

> FIND_HKL_LIST:

   . type:                 OUTPUT keyword
   . mandatory argument:   1 integer value corresponding to the numor in the
                           following the extinction rules list:
                               1. h00 h=2n+1
                               2. 0k0 k=2n+1
                               3. 00l l=2n+1
                               4. 0kl k=2n+1
                               5. 0kl l=2n+1
                               6. 0kl k+l=2n+1
                               7. h0l h=2n+1
                               8. h0l l=2n+1
                               9. h0l h+l=2n+1
                              10. hk0 h=2n+1
                              11. kk0 k=2n+1
                              12. hk0 h+k=2n+1
                              13. hhl h+l=2n+1
                              14. hkk k+h=2n+1
                              15. hkh h+k=2n+1
                              16. hkl k+l=2n+1 (A)
                              17. hkl h+l=2n+1 (B)
                              18. hkl h+k+2n+1 (C)
                              19. hkl h+k+l=2n+1 (I)
                              20. hkl not all odd/even (F)
                              21. h00 h=4n+1
                              22. 0k0 k=4n+1
                              23. 00l l=4n+1
                              24. 0kl k+l=4n+1
                              25. h0l h+l=4n+1
                              26. hk0 h+k=4n+1
                              27. h-hl, h0l, 0kl l=2n+1
                              28. hkl h=2n+1
                              29. hkl k=2n+1
                              30. hkl l=2n+1
                              31. hkl h=2n+1,k=2n+1
                              32. hkl h=2n+1,l=2n+1
                              33. hkl k=2n+1,l=2n+1
                            or a character string in the following list :
                            A, B, C, I, F corresponding to the #13, #14, #15,
                            #16 and #17 in the previous list.

                            If the integer value is negative, the opposite
                            condition will be searched in the HKL file.
   . meaning:               search, in a reflections list, those obeying
                            to the selected extinction rule
   . optionnal arguments:  . arg = "OUT": the requested list will be output on
                                          the screen
                           . arg = "ALL": no condition about F2 and F2/sig is
                                          required
                           . arg = "WRITE": requested list is stored in a HKL
                                            file
                           . arg = "SUPPRESS"/"REMOVE": requested list is
                                    removed from the initial file
                           . arg = real value: F2/sig value
   . mandatory keyword:   FILE
   . examples:            FIND_HKL_LIST 5 OUT ALL
                          FIND_HKL_LIST I WRITE SUPPRESS
   . identical keywords:  FIND_HKL_LIST, FIND_HKL_LST, EXTRACT_HKL_LIST, EXTRACT

[return to keywords list]

> FRIEDEL:

    . type:                CALCULATION keyword
    . optionnal argument:  symmetry (character string): "TRIC", "MONO", "ORTHO",
                           "TETRA", "TRIG", "HEXA", "CUB"
    . meaning:             calculate the number of Friedel pairs in a hkl file
    . mandatory keyword:   FILE, SPGR if no symmetry argument
    . identical keywords:  FRIEDEL, FRIEDEL_PAIRS
    . example:             FRIEDEL mono

[return to keywords list]

> GEN_HKL:

    . type:                calculation keyword
    . arguments:           character strings
    . meaning:             generate a hkl reflections list in a particular
                           scattering range:
                            . STL_min=xx  STL_max=xx for SinTheta/lambda
                              range, in A-1
                            . d_min=xx    d_max=xx   for d range, in A
                            . Q_min=xx    Q_max=xx   for Q=4pi*SinTheta/lambda
                              range, in A
                            . Theta_min=xx  Theta_max=xx    for Theta range,
                              in deg.(dependent keyword = WAVE)
                            . 2Theta_min=xx 2Theta_max=xx   for 2Theta range,
                              in deg. (dependent keyword = WAVE)
                           If atoms are input, a structure factor calculation is
                           done.
                           In the case where scattering variable is 2theta, a
                            list of I/Imax is output.
    . optional arguments    "OUT": a list of generated reflections will be ouput
                            "PM2K": hkl reflections list stored in the PM2K form
                            "PAT": In the case where scattering variable is
                            2theta, atoms are input and space group is know,
                            a diffraction pattern is then created. Two different
                            files are ouput :
                                - cryscalc_pat.xy (2 columns)
                                - cryscalc_pat.prf (FullProf format)
                            If WinPLOTR is installed on the workstation, it is
                            automatically launched with the PRF file
                            "SIZE=XXX": specify particles size (XXX in A)
    . output:              - calculation of interplanar distance d_hkl, in A
                             (dependent keyword = CELL)
                           - calculation of Bragg angle 2theta_hkl, in deg.
                             (dependent keyword = CELL, WAVE)
                           - structure factor calculation
                             (dependent keywors = ATOM)
    . mandatory keywords:  CELL, SPGR
    . examples             GEN_HKL theta_min=0. THETA_max=25. OUT
                           GEN_HKL d_min=0.5.   d_max=5.
                           GEN_HKL 2THETA_min=0. 2THETA_max=125. OUT PAT
                           GEN_HKL 2THETA_min=0. 2THETA_max=125. OUT PAT SIZE=15
    . identical keywords:  GEN_HKL, GENERATE_HKL, GENERATE_HKL_LIST

[return to keywords list]

> HEADER:

   . type:                 OUTPUT keyword
   . argument:             no
   . meaning:              write header text of CRYSCALc
   . identical keywords:   HEADER, HEAD

[return to keywords list]

> HEX_RHOMB:

    . type:                OUTPUT keyword
    . arguments :          no argument
    . outputs:             give transformation matrix from hexagonal to
                           rhomboedral setting
    . mandatory keyword:   no
    . identical keywords:  HEX_RHOMB, HEXA_RHOMB, HEX_TO_RHOMB, HEXA_TO_RHOMB

[return to keywords list]

> HKL:

    . type:                INPUT keyword
    . arguments:           3 reals
    . meaning:             h,k,l, Miller indices
    . output:              calculation of interplanar distance d_hkl, in A
                           (dependent keyword = CELL)
                           calculation of Bragg angle 2theta_hkl, in deg.
                           (dependent keyword = CELL, WAVE)
    . example:             HKL 1. 0. 1.
    . mandatory keyword:   CELL

[return to keywords list]

> HKL_NEG:

    . type:               output keyword
    . arguments:          no
    . meaning:            search for negative intensity reflections in a HKL
                          file
    . optionnal keywords: . arg = "OUT": requested reflections are output on the
                                         screen
                          . arg = "WRITE": requested reflextions are output in a
                                           HKL file
    . mandatory keyword:  FILE
    . identical keywords: HKL_NEG, HKL_NEGATIVE, NEG_HKL, NEGATIVE_HKL
    . relared keyword:    HKL_POS

[return to keywords list]

> HKL_POS:

    . type:               output keyword
    . arguments:          no
    . meaning:            search for positive intensity reflections in a HKL
                          file
    . optionnal keywords: . arg = "OUT": requested reflections are output on the
                                         screen
                          . arg = "WRITE": requested reflextions are output in a
                                           HKL file
                          . arg = real_value (n_sig): only positive reflections
                                  with I > n_sig*sig(F2) are output
    . mandatory keyword:  FILE
    . identical keywords: HKL_POS, HKL_POSITIVE, POS_HKL, POSITIVE_HKL
    . relared keyword:    HKL_NEG

[return to keywords list]

> INSIDE:

    . type:                output keyword
    . arguments:           no
    . meaning:             put the atoms of the atom list inside the unit cell
    . output:              list of atoms with atomic coordinates in the 0.0 -
                           1.0 range
    . mandatory keyword:   ATOM or atom list in a .INS/.RES file

[return to keywords list]

> LIST_EXTI_RULE:

   . type:                 OUTPUT keyword
   . argument:             no
   . meaning:              list the extinction rules implemented in CRYSCALc
   . identical keywords:   LIST_EXTI, LIST_EXTI_RULE, LST_EXTI, LST_EXTI_RULE

[return to keywords list]

> LIST_KEYS:

    . type:                OUTPUT keyword
    . optionnal argument:  character string containing "*" character
    . meaning:             list of keywords:
                           . if no argument: all the keywords are listed
                           . if "*" character is present in the character
                             string: all the keywords containing the
                             the character string before or after the "*"
                             will be listed
    . identical keywords:  KEY, KEYS, LST_KEYS, LIST_KEYS, LST_KEYWORDS,
                           LIST_KEYWORDS
    . examples:            . KEYS
                           . KEYS HKL*

[return to keywords list]

> LIST_LAUE:

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             list of Laue classes
    . identical keywords:  "LST_LAUE", "LIST_LAUE, "LST_LAUE_CLASS",
                           "LIST_LAUE_CLASS"
    . examples:            . LIST_LAUE

[return to keywords list]

> LIST_MAT:

    . type:                OUPUT keyword
    . arguments:           no
    . meaning:             list of transformation matrices implemented in CRYSCA
                           (direct and inverse matrices)
    . identical keywords:  LST_MAT, LST_MATR, LST_MATRIX, LIST_MAT, LIST_MATR,
                           LIST_MATRIX, LIST_TRANSFORMATION_MATRIX

[return to keywords list]

> LIST_SG:

    . type:                OUPUT keyword
    . arguments:           character strings
                           available arguments (order is not important):
                           . symmetry arguments: "all", "centric", "acentric",
                             "triclinic", "monoclinic", "orthorhombic",
                             "tetragonal","trigonal", "hexagonal", "cubic"
                           . "chiral", "enantio", "polar"
                           . Bravais arguments: "P", "A", "B", "C", "I",
                             "F", "R"
                           . Laue class arguments: "laue_n", with n relative
                             to the numor of Laue class of the space group:
                               n=1: -1                 n=8:  -3m (rhomb. axes)
                               n=2: 2/m                n=9:  -31m (hex. axes)
                               n=3: mmm                n=10: -3m1 (hex. axes)
                               n=4: 4/m                n=11: 6/m
                               n=5: 4/mmm              n=12: 6/mmm
                               n=6: -3 (rhomb. axes)   n=13: m3
                               n=7: -3 (hex. axes)     n=14: m3m
                           . "multi": output the general multiciplicity of the
                                      space group
    . meaning:             list space groups
    . examples:            LST_SG tetragonal centric:  list tetragonal and
                           centric space groups
                           LST_SG acentric monoclinic C: list monoclinic,
                            acentric and C centred space groups
                           LST_SG laue_4: list tetragonal space groups with 4/m,
                            Laue class
                           LST_SG trigonal enantio
                           LST_SG cubic chiral
    . identical keywords:  LIST_SG, LST_SG, LIST_SPACE_GROUPS

[return to keywords list]

> MAG:

    . type:                OUTPUT keyword
    . arguments :          character string (atom or ion label)
    . outputs:             list magnetic features of the  current ion or atom:
                           electronic configuration, level, magnetic moment ...
                           for 3d and 4f elements
    . identical keywords:  MAG, MAGNETIC
    . examples:            mag mn+3
    .                      mag TB

[return to keywords list]

> MAN:

    . type:                OUTPUT keyword
    . optional arguments:  character strings
    . meaning:             get the CRYSCALc manual
    . output:              list the meaning and use of CRYSCALc keywords
                           . if no arguments: all the keywords are listed
                           . optional arguments are keywords name
                           . if "*" character in the character string: all the
                             keywords containing the character string before
                             or after the "*" will be listed
    . examples:            MAN wave cell
                           MAN ANG*
    . identical keywords:  MAN, HELP

[return to keywords list]

> MAN_HTML:

    . type:                OUTPUT keyword
    . optionnal argument:  'browse'
    . meaning:             get the CRYSCALc manual in HTML format
                           open the HTML file with the current browser
    . output:              list the meaning and use of CRYSCALc keywords
    . examples:            MAN_HTML
    . identical keywords:  MAN_HTML, HTML_MAN, HTML

[return to keywords list]

> MATMUL:

      . type:                calculation keyword
      . arguments:           no
      . meaning:             input of components of 3*3 matrices as follows:
                             M11, M12, M13, M21, M22, M23, M31, M32, M33
      . ouput:               calculation of the M1xM2 matrix

[return to keywords list]

> MATR:

    . type:                INPUT keyword
    . arguments:           9 reals
    . meaning:             transformation (3,3) matrix components
    . examples:            MATR   0  0  1    0  1  0    -1  0  -1
                           MATR   0.5 0.5 0   -0.5 0.5 0   0 0 1
                           MATR   1/2 1/2 0   -1/2 1/2 0   0 0 1
  or
    . arguments:           "#" 1 integer
    . meaning:             number of matrix in the matrices list implemented in
                           CRYSCALc (see LIST_MATR keyword)
    . example:             MATR  #3
    . special arguments  :     "I"  : identity matrix
                              "-I" : inverse matrix
  or
    . arguments:           3 character strings: a, -a, b, -b, c, -c
    . meaning:             setting of the unit cell
    . example:             MATR  -c b a
  or
    . arguments:           2 character strings: P, A, B, C, I, F, R_rev, R_obv
    . meaning:             Bravais lattices of the original and final cells.
                           The transformation matrices are related to matrices
                           from #8 to #21 in the matrix list
    . example:             MATR C P
                           MATR R_obv R_rev

    . output:              calculation of new cell parameters (dependent
                           keyword = CELL)
                           calculation of new atomic coordinates (dependent
                           keyword = ATOM)
                           calculation of new hkl Miller indices (dependent
                           keyword = HKL)
                           create a new file containing the new hkl indices
                           (dependent keyword = FILE)
    . identical keywords:  MAT, MATR, MATRIX

[return to keywords list]

> MENDEL:

    . type:                OUTOUT keyword
    . arguments:           character strings
    . meaning:             atom type or atomic number
    . output:              get atomic features: atomic number, weight,
                            density, electronic configuration, oxydation
                            states, ionic radius, ...
                           get neutron data: scattering length, scattering
                            and absorption cross sections
                           get Xrays data: mass attenuation coefficient,
                            total interaction cross sections, coefficient)
                            for scattering factor calculation =f(stl),
                            values of D_fp and D_fpp anomalous dispersion
                            coefficient (for Cr, Fe, Cu, Mo and Ag radiations)
    . optionnal keyword:   PLOT: create a .PGF file containing the scattering
                            factor values versus SinTheta/lambda and plot it
                            with WinPLOTR
    . examples:            MENDEL TI C
                           MENDEL Cu+2 PLOT
                           MENDEL 59

[return to keywords list]

> MERGE:

    . type:                CALCULATION keyword
    . optionnal argument:  symmetry (character string): "TRIC", "MONO", "ORTHO",
                           "TETRA", "TRIG", "HEXA", "CUB"
    . meaning:             merge the data in the current symmetry and create
                           a xxx_merge.HKL file
    . mandatory keyword:   FILE, SPGR if no symmetry argument
    . example:             merge monoclinic

[return to keywords list]

> MONOCLINIC:

    . type:                OUTPUT keyword
    . arguments :          no argument
    . outputs:             . list the transformation matrices for equivalent
                             monoclinic settings
                           . if CELL exists: apply the transformation matrices
                             to give new monoclinic cell parameters
    . mandatory keyword:   no
    . optional keyword:    CELL
    . identical keywords:  MONOCLINIC, MONOC, MONOCL

[return to keywords list]

> NEWS:

    . type:                OUTPUT keyword
    . outputs:             list the last new facilities implemented in CRYSCALc
    . optionnal argument:  specified year
    . example:             NEWS 2010
    . identical keywords:  NEWS

[return to keywords list]

> NIGGLI_CELL

    . type:                OUTPUT keyword
    . arguments :          no argument
    . output:              transform the current triclinic cell to the Niggli
                           cell.
    . related keyword:     CELL
    . identical keywords:  NIGGLi, NIGGLI_CELL

[return to keywords list]

> OBV_REV:

    . type:                OUTPUT keyword
    . arguments :          1 integer
    . meaning:             twin matrix number:
                            . 1: matrix law = (-1 0 0  0-1 0  0 0 1): twofold
                                 axis parallel to threefold
                            . 2: matrix law = ( 0-1 0 -1 0 0  0 0-1): twofold
                                 axis parallel to (a-b)
    . outputs:             analysis of the reflections versus the parity
    . remark:              if no argument is given, first matrix law is taken
    . mandatory keyword:   FILE
    . identical keywords:  OBV_REV, OBVERSE_REVERSE, TWIN_OBVERSE_REVERSE
                           TWIN_OBV_REV, TWINNING_OBVERSE_REVERSE
                           TWINNING_OBV_REV

[return to keywords list]

> P4P:

    . type:                OUTPUT keyword
    . optional arguments : P4P file name
    . meaning:             read the .P4P file (created by SAINT) present in the
                           current folder (if more than one .P4P file is present
                           select a P4P file in a .P4P file list) and create
                           a P4P.cif file containing cell parameters (and esd's)
                           wavelength, number of reflections used to refined the
                           cell parameters and related theta_min and theta_max.
    . identical keywords:  P4P, READ_P4P

[return to keywords list]

> PAUSE:

    . type:
    . arguments :          no
    . meaning:             create a break in the execution of the requested
                           commands. This keyword can be useful when commands
                           are executed through a .CFL command file

[return to keywords list]

> PERMUT:

    . type:                OUTPUT keyword
    . arguments :          no
    . meaning:             apply matrix #3, #4, #5, #6 and #7 (see LIST_MATR
                           keyword) to the current cell parameters. This
                           corresponds to axes permutation
    . outputs:             new cell parameters and new volume, obtained after
                           applying matrix #n
                           if cell parameters are unknown: list the
                           transformation matrix

[return to keywords list]

> QHKL:

    . argument:            real values
    . meaning:             Q=4pi*sinTheta/lambda values
    . outputs:             d_hkl(A), SinTheta/lambda(A-1)
                           theta(deg) for known wavelength
    . optionnal keyword:   WAVE
    . identical keywords:  QHKL, Q_HKL
    . example:             QHKL 10.

[return to keywords list]

> QVEC:

    . type:                input keyword
    . arguments :          3 reals
    . meaning:             components of the propagation vector
    . outputs:             apply the propagation vector on the hkl list and
                           calculate the corresponding d value
    . mandatory keyword:   HKL
    . identical keywords:  QVEC, Q_VEC, Q_VECTOR, KVEC, K_VEC, K_VECTOR,
                           MOD_VEC, MODULATION_VECTOR
    . example:             QVEC 0.5 0.5 0.

[return to keywords list]

> READ_CEL

    . type:                input keyword
    . argument:            1 character string corresponding to a CEL file name
    . meaning:             read a CEL format file (PowderCELL format) to extract
                           structural features as: space group, cell parameters
                           and atomic positions.
    . identical keywords:  READ_CEL, READ_CEL_FILE, READ_POWDERCELL
    . example:             READ_CEL my_file.cel

[return to keywords list]

> READ_CIF

    . type:                input keyword
    . argument:            1 character string corresponding to a CIF file name
    . meaning:             read a CIF format file to extract structural features
                           as: space group and/or symmetry operators, cell
                           parameters, atomic positions, wave ...
    . identical keywords:  READ_CIF, READ_CIF_FILE, CIF_FILE
    . example:             READ_CIF my_file.cif

[return to keywords list]

> READ_FACES

    . type:                input keyword
    . optional argument:   1 character string corresponding file name
                           containing crystal shape habitus :
                           - absorb.ins file created by Collect software (Nonius
                           - faces.def file created by WinGX.
                           if absent, shape file = absorb.ins
    . meaning:             read a file containaing crystal shape as
                           (h,k,l,dim) list.
    . identical keywords:  READ_FACES, FACES
    . examples:            READ_FACES my_absorb.ins
                           READ_FACES faces.def

[return to keywords list]

> READ_INS

    . type:                input keyword
    . argument:            1 character string corresponding to a INS/RES file
                           name (SHELX)
    . meaning:             read a .INS/.RES SHELX format file to extract
                           structural features as: space group and/or symmetry
                           operators, cell parameters, atomic positions, ...
    . identical keywords:  READ_INS, READ_INS_FILE, INS_FILE
    . example:             READ_INS my_file.ins

[return to keywords list]

> READ_NREPORT:

    . type:                input keyword
    . optional argument:   browse
    . meaning:             read nreport.html file created by the Nonius software
                           suite for KCCD diffractometer.
                           If 'browse' is given as argument, launch the browser
                           in the 'cryscalc.ini' setting file
                           If not, ouputs the HTML file on screen (without tags)
    . identical keywords:  READ_NREPORT, READ_HTML_REPORT, READ_NREPORTHTML

[return to keywords list]

> READ_PCR

    . type:                input keyword
    . argument:            1 character string corresponding to a PCR file name
    . meaning:             read a PCR FullProf format file to extract structural
                           features as: space group and/or symmetry operators,
                           cell parameters, atomic positions, wave ...
    . identical keywords:  READ_PCR, READ_PCR_FILE, PCR_FILE
    . example:             READ_PCR my_file.pcr

[return to keywords list]

> READ_TIDY_OUT

    . type:                input keyword
    . optional argument:   1 character string corresponding to the TIDY output f
                           to be read. Default name=stidy.out
    . meaning:             read a output file created by TIDY and extract all st
                           features as: space group ,
                           cell parameters, atomic positions
    . identical keywords:  READ_TIDY_OUT, READ_TIDY_OUTPUT, READ_TIDY_OUTPUT_FIL
    . example:             READ_TIDY_OUT

[return to keywords list]

> REC_ANG:

    . type:                CALCULATION keyword
    . arguments:           2*3 reals
    . meaning:             calculation of the angle between 2 vectors in the
                           reciprocal space. The 3 first real values are related
                           to the coordinates of the first vector and the 3 last
                           real values to the coordinates of the second vector
    . mandatory keyword:   CELL
    . identical keywords:  REC_ANG, RECANG, RECIPROCAL_ANGLE
    . example:             REC_ANG 1. 0. 0.   0. 1. 0.

[return to keywords list]

> REF_ABS_CRYSALIS

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write absorption correction procedure implemented
                           in CRYSALIS software (Agilent Technologies)
    . optionnal argument:  CIF

    . identical keywords:  REF_ABS_CRYSALIS
[return to keywords list]

> REF_APEX

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write APEXII diffractometer programs and device refer
    . optionnal argument:  CIF

    . identical keywords:  REF_APEX, REF_APEXII, WRITE_APEX, WRITE_APEXII,
                           APEX, APEXII
[return to keywords list]

> REF_EVAL

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write EVALCCD references
    . optionnal argument:  CIF

    . identical keywords:  REF_EVAL, REF_EVALCCD, WRITE_EVAL, WRITE_EVALCCD,
                           EVAL, EVALCCD
[return to keywords list]

> REF_DENZO

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write DENZO/SCALEPACK references
    . optionnal argument:  CIF
    . identical keywords:  REF_DENZO, WRITE_DENZO, DENZO

[return to keywords list]

> REF_KCCD

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write KCCD diffractometer software and device referen
    . optionnal argument:  CIF

    . identical keywords:  REF_KCCD, KCCD
[return to keywords list]

> REF_SADABS

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write SADABS references
    . optionnal argument:  CIF

    . identical keywords:  REF_SAD, SADABS
[return to keywords list]

> REF_SUPERNOVA

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write SUPERNOVA diffractometer programs and device re
    . optionnal argument:  CIF

    . identical keywords:  REF_SUPERNOVA
[return to keywords list]

> REF_X2S

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write SMART X2S diffractometer programs and device re
    . optionnal argument:  CIF

    . identical keywords:  REF_X2S, REF_SMART_X2S
[return to keywords list]

> REF_XCALIBUR

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write XCALIBUR diffractometer sotware and device refe
    . optionnal argument:  CIF

    . identical keywords:  REF_SUPERNOVA
[return to keywords list]

> RESET

    . type:                input keyword
    . argument:            no
    . meaning:             initialization of all input parameters
                           and arrays

    . identical keywords:  RESET, RAZ, INIT, INITIALIZATION
[return to keywords list]

> RINT:

    . type:                CALCULATION keyword
    . optionnal argument:  symmetry (character string): "TRIC", "MONO", "ORTHO",
                           "TETRA", "TRIG", "HEXA", "CUB"
    . meaning:             calculate the internal Rint value
                           calculate the completeness of the data collection
    . mandatory keyword:   FILE, SPGR if no symmetry argument
    . identical keywords:  RINT, R_INT
    . example:             RINT mono

[return to keywords list]

> RHOMB_HEX:

    . type:                OUTPUT keyword
    . arguments :          no argument
    . outputs:             give transformation matrix from rhomboedral to
                           hexagonal setting
    . mandatory keyword:   no
    . identical keywords:  RHOMB_HEX, RHOMB_HEXA, RHOMB_TO_HEX, RHOMB_TO_HEXA

[return to keywords list]

> SEARCH_EXTI:

    . type:                OUTPUT keyword
    . arguments:           2 optionnal real arguments: n_sig, ratio_criteria
    . meaning:             analyse hkl reflections list and search systematic
                           extinctions
                             . n_sig: only reflections with I/sig > n_sig will
                               be analysed
                             . ratio_criteria:
                                if / < ratio_criteria, the
                                current reflection type is considered as
                                extinction rule
    . mandatory keyword:   FILE
    . identical keywords:  SEARCH_EXTI, FIND_EXTI
    . example:             SEARCH_EXTI 2 0.02

[return to keywords list]

> SEARCH_SPACE_GROUP:

    . type:                calculation keyword
    . optional arguments:  2 real : n_sig and threshold
                           1 character string, defining the crystal system:
                            M/mono, O/ortho, T/tetra, R/trig, H/hexa, C/cub
                            GET
    . meaning:             search in a hkl file systematic extinctions and
                           propose space groups in agreement with observed
                           extinctions.
                            . n_sig: only reflections with I/sig > n_sig are
                                     considered. Default value is n_sig=3.
                            . a threshold is also applied: only the
                            reflections with F2 > threshold * max(F2) are
                            considered. Default value is threshold=0.03
                           If GET is input as argument, the most probable
                           space group will be considered
    . mandatory keyword:   FILE
    . identical keywords:  SEARCH_SPGR, SEARCH_SPACE_GROUP, SEARCH_GROUP,
                           CHECK_SPGR,  CHECK_SPACE_GROUP,  CHECK_GROUP

[return to keywords list]

> SET:

    . type:        INPUT keyword
    . arguments:   2 string arguments
    . meaning:     definition of external applications:
                    . if arg(1) = "EDITOR":  arg(2) is the browser application
                    . if arg(1) = "BROWSER": arg(2) is the editor application
    . example:     set browser "C:\Program Files\Mozilla Firefox\firefox.exe"

[return to keywords list]

> SETTING:

    . type:        OUTPUT keyword
    . arguments:   no
    . meaning:     output the different parameters defined in the CRYSCALC.INI
                   setting file

[return to keywords list]

> SFAC:

    . type:                INPUT keyword
    . arguments:           n character strings
    . meaning.:            list of chemical elements in the molecule
    . output:              - atomic density calculation, in at/cm3
                             (dependent keyword = CELL)
                           - absorption coefficient calculation
                             (dependent keywords = CELL, BEAM)
                           - determination of the molecular formula
                             (dependent keywords = Z)
                           - calculation of the molecular weight
                             (dependent keywords = Z)
                           - calculation of the atomic and weight
                             percentage (dependent keywords = Z)
                           - determination of the density
                             (dependent keywords = CELL, Z)
    . mandatory keyword:   UNIT
    . example:             SFAC C O H N

[return to keywords list]

> SF_HKL:

    . type:                INPUT keyword
    . arguments:           3 reals
    . meaning:             h,k,l, Miller indices
    . output:              calculation of crystallographic structure
                           factor for the hkl reflection
                           (dependent keyword = CELL, WAVE, SPGR, ATOM)
    . example:             HKL 1 0 1
    . mandatory keyword:   CELL, WAVE, SPGR, ATOM
    . related keyword :    BEAM
    . identical keywords:  SF_HKL, SFAC_HKL

[return to keywords list]

> SG:

    . type:                INPUT keyword
    . arguments :          character string
    . meaning:             space group (Hall Mauguin symbol, number in IT
    . outputs:             . informations on the space group: list of symmetry
                             operators and symmetry symbols, Wyckoff positions,
                             extinctions  ...
                           . get informations on the Wyckoff site: multiplicity,
                             list of symmetry operators and symmetry elements of
                             the site point group
                           . if HKL file has been previously read (see FILE
                             keyword), the number of reflections in agreement
                             with the space group is output
    . see:                 SG_INFO, SG_EXTI, LST_SYM_OP, SITE_INFO
    . example:             SPGR P 21 21 21
    . identical keywords:  SPGR, SG, SPACE_GROUP

[return to keywords list]

> SG_ALL:

    . type:                OUTPUT keyword
    . arguments :          no argument
    . outputs:             get informations on the current space group:
                            symmetry operator (complete and reduced set), Wyckof
                            positions, extinction rules ...
    . mandatory keyword:   SPGR
    . identical keywords:  SG_ALL, SP_ALL

[return to keywords list]

> SG_EXTI:

    . type:                OUTPUT keyword
    . arguments :          no argument
    . outputs:             list of extinctions rules of the current space
                           group
    . mandatory keyword:   SPGR
    . identical keywords:  SP_EXTI, SP_EXTI, SG_EXTINCTIONS, SPACE_GROUP_EXTI,
                           SPACE_GROUP_EXTINCTIONS

[return to keywords list]

> SG_INFO:

    . type:                OUTPUT keyword
    . outputs:             informations on the space group: list of
                           symmetry operators and symmetry symbols, Wyckoff
                           positions
    . mandatory keyword:   SPGR
    . optionnal argument:  ALL: list all symmetry operators (including
                                inversion and lattice centring translations)
    . identical keywords:  SG_INFO, SP_INFO, SPACE_GROUP_INFO,
                           LIST_SPACE_GROUP_INFO

[return to keywords list]

> SG_SUB:

    . type:                OUTPUT keyword
    . outputs:             informations on the space group: list of
                           Translationengleische Subgroups for a given
                           space group
    . mandatory keyword:   SPGR
    . identical keywords:  SG_SUB, SG_SUBGROUP

[return to keywords list]

> SHANNON:

    . type:                OUTPUT keyword
    . argument:            character string
    . outputs:             get effective ionic radii from the Shannon table
                           (Acta Cryst 1976, A32, 751)
                            . ec:     electronic configuration
                            . CN:     coordinence
                            . SP:     configuration de spin
                            . CR:     crystal radius
                            . IR:     effective radius
    . identical keywords:  SHAN, SHANNON
    . examples:            SHANNON Pb
                           SHANNON CU+2

[return to keywords list]

> SHELL:

    . type:                CALCULATION keyword
    . arguments:           2 character strings (one mandatory argument) + 2 real
    . meaning:             arg_1 = d:     keeps reflections in the d_min and
                                          d_max range
                                          created hkl file: HKL_shell_d.hkl
                                          dependent keyword: CELL
                           arg_1 = stl:   keeps reflections in the stl_min and
                                          stl_max range
                                          created hkl file: HKL_shell_stl.hkl
                                          dependent keyword: CELL
                           arg_1 = theta: keeps reflections in the theta_min and
                                          theta_max range
                                          created hkl file: HKL_shell_theta.hkl
                                          dependent keyword: CELL, WAVE
                           arg_1 = int:   keeps reflections in the int_min and
                                          int_max range
                                          created hkl file: HKL_shell_i.hkl
                           arg_1 = isig:  keeps reflections in the i/sig_min and
                                          i/sig_max range
                                          created hkl file: HKL_shell_isig.hkl
                           arg_2 = plot:  create a .PGF file from the created
                                          HKL file and plot it with WinPLOTR
                                          (excepted for arg_1=int and
                                          arg_1 = isig)
                           real_1:        X_min value
                           real_2:        X_max value
    . mandatory keyword:   FILE
    . optional argument:   arg_2 = plot
    . examples:            SHELL d plot
                           SHELL theta

[return to keywords list]

> SHIFT_2TH:

    . type:                INPUT keyword
    . arguments :          3 reals
    . meaning:             diffractometer 2theta shift: constant, cos dependent
                           and sin dependent values
    . outputs:             apply the diffractometer 2theta shift to the
                           calculated 2theta value:
                            2theta = 2theta_calc + shift_2theta
    . mandatory keyword:   HKL, GEN_HKL, GEN_SAT
    . identical keywords:  SHIFT_2TH, SHIFT_2THETA, 2TH_SHIFT, 2THETA_SHIFT

[return to keywords list]

> SITE_INFO:

    . type:                OUTPUT keyword
    . optional arguments : list of atomic labels (character strings)
    . outputs:             give information on Wyckoff atomic positions and
                           apply the symmetry operators of the current space
                           group on the atomic positions
                            if no argument:    all atoms of the atoms list
                                           (cf ATOM keyword) are considered
                            if arg = "ALL": all atoms of the atoms list
                                          (cf ATOM keyword) are considered
                            if arg = "PCR": list of equivalent atoms is
                                          output in a FullProf format.
                            if arg = "PCR_MAG": list of magnetic atoms is
                                          output in a FullProf format.
    . mandatory keyword:   SPGR, ATOM
    . example:             SITE_INFO O1 C8
    . identical keywords:  SITE_INFO, LIST_SITE_INFO

[return to keywords list]

> SIZE:

    . type:                INPUT keyword
    . arguments:           3 reals
    . meaning:             crystal dimensions in mm
    . output:              crystal volume calculation
                           calculation of the radius of a sphere with identical
                           volume
    . example:             SIZE 0.11 0.13 0.122
    . identical keywords:  SIZE, CRYSTAL_SIZE

[return to keywords list]

> SORT:

    . type:                CALCULATION keyword
    . arguments:           2 character strings
    . meaning:             arg_1 = d:     sort HKL file in increasing d_hkl
                                          (dependent keyword: CELL)
                                          created hkl file: HKL_sort_d.hkl
                           arg_1 = stl:   sort HKL file in increasing
                                          sinTheta/lambda
                                          (dependent keyword: CELL)
                                          created hkl file: HKL_sort_stl.hkl
                           arg_1 = theta: sort HKL file in increasing Theta
                                          (dependent keyword: CELL, WAVE)
                                          created hkl file: HKL_sort_theta.hkl
    .                      arg_1 = int:   sort HKL file in decreasing F2
                                          created hkl file: HKL_sort_i.hkl
    .                      arg_1 = isig:  sort HKL file in decreasing F2/sigma
                                          created hkl file: HKL__sort_isig.hkl
    .                      arg_2 = plot:  create a .PGF file from the created
                                          HKL file and plot it with WinPLOTR
                                         (excepted for arg_1=int and
                                          arg_1 = isig)
                           arg_2 = out_n: list the n first sorted reflections
    . mandatory keyword:   FILE
    . optional argument:   arg_2 = plot
    . examples:            SORT d plot
                           SORT stl
                           SORT theta OUT_10

[return to keywords list]

> STAR_K

    . type:                CALCULATION keyword
    . argument:            no
    . meaning:             apply rotational parts of symmetry operators
    .                      on propagation wave components to determine
    .                      the star of k
    . outputs:             d_hkl(A), Q(A-1)
                           theta(deg) for known wavelength
    . mandatory keywords:   SPGR, QVEC

[return to keywords list]

> STL:

    . type:                CALCULATION keyword
    . argument:            real values
    . meaning:             sinTheta / lambda values
    . outputs:             d_hkl(A), Q(A-1)
                           theta(deg) for known wavelength
    . optionnal keyword:   WAVE
    . identical keywords:  STL, STL_HKL, SINTHETA/WAVE, SINTHETA/LAMBDA
    . example:             STL 0.70

[return to keywords list]

> SYMM:

    . type:                INPUT keyword
    . arguments :          12 reals
    . meaning:             symmetry operator in numeric form:
                             S11 S12 S13  T1   S21 S22 S23 T2   S31 S32 S33 T3
                               Sij: components of the rotational part of the
                                    symmetry operator
                               Ti:  components of the translationnal part of
                                    the symmetry operator
    . example:             SYMM   1  0  0   0.5    0 -1  0   0.5   0  0 -1  0.

   or
    . arguments :          string
    . meaning:             symmetry operator in alphanumeric form
    . example:             SYMM   x+1/2, -y+1/2, -z

    . outputs:             apply the current symmetry operator to atomic
                           coordinates (dependent keyword = ATOM)
    . optional keyword:    APPLY_OP, SYM_OP

    . identical keywords:  SYMM, SYM, SYMMETRY_OPERATOR

[return to keywords list]

> SYST:

    . type:                EXTERNAL keyword
    . arguments:           1 character string
    . meaning:             launch an external command or program
    . example:             SYST dir *.CFL / P
    . identical keywords:  SYST, CMD, COMMAND, DOS, DOS_COMMAND

[return to keywords list]

> THERM:

    . type:                INPUT/OUTPUT keyword
    . arguments:           1 character string + reals
    . meaning:             conversion of atomic displacement parameters:
                           . available arguments:
                             - "Uiso", "U_iso": conversion from Uiso to Biso
                             - "Biso", "B_iso": conversion from Biso to Uiso
                             - "U_ij", "Uij"  : conversion from U_ij to B_ij and
                                                beta_ij
                             - "U_ij", "Uij"  : conversion from U_ij to B_ij and
                                                beta_ij
                             - "beta_ij", "betaij", "beta"": conversion from
                               beta_ij to B_ij and U_ij
                           . reals values correspond to isotropic thermal
                             parameters values (Biso or Uiso) or anisotropic
                             thermal parameters (Uij, Bij, Beta) in the followin
                             order: 11, 22, 33, 12, 13, 23
    . examples:            THERM Biso 0.52 0.76 0.35
                           THERM B_ij 0.01 0.01 0.01 0.0 0.0 0.0
    . mandatory keyword    CELL for anisotropic thermal parameters conversion
    . identical keywords:  THERM, THERMAL, ADP

[return to keywords list]

> THERM_SHELX:

    . type:                INPUT/OUTPUT keyword
    . arguments:           1 character string + reals
    . meaning:             conversion of atomic displacement parameters:
                           . available arguments:
                             - "Uiso", "U_iso": conversion from Uiso to Biso
                             - "Biso", "B_iso": conversion from Biso to Uiso
                             - "U_ij", "Uij"  : conversion from U_ij to B_ij and
                                                beta_ij
                             - "U_ij", "Uij"  : conversion from U_ij to B_ij and
                                                beta_ij
                             - "beta_ij", "betaij", "beta"": conversion from
                               beta_ij to B_ij and U_ij
                           . reals values correspond to isotropic thermal
                             parameters values (Biso or Uiso) or anisotropic
                             thermal parameters (Uij, Bij, Beta) in the followin
                             order: 11, 22, 33, 23, 13, 12 (as in SHELXL program
    . examples:            THERM Biso 0.52 0.76 0.35
                           THERM B_ij 0.01 0.01 0.01 0.0 0.0 0.0
    . mandatory keyword    CELL for anisotropic thermal parameters conversion
    . identical keywords:  THERM_SHELX, THERMAL_SHELX, ADP_SHELX

[return to keywords list]

> THETA:

    . type:                CALCULATION keyword
    . argument:            real values
    . meaning:             Theta (deg) values
    . outputs:             d_hkl(A), Q(A-1), SinTheta/lambda
    . mandatory keyword:   WAVE
    . identical keywords:  THETA, THETA_HKL
    . example:             THETA 27.5

[return to keywords list]

> TITL:

    . type:                INPUT keyword
    . arguments:           character strings
    . meaning:             title of the job
    . example:             Ammonium bitartrate
    . identical keywords:  TITL, TITLE

[return to keywords list]

> TRANSLATION:

    . type:                INPUT keyword
    . arguments :          translation components (3 reals) + 1 sign (optional)
    . outputs:             apply the translation on atomic coordinates
                           if sign is input, new atomic coordiantes decome :
                             t(1) + x.sign, t(2) + y.sign, t(3) + z.sign
                           as in SHELXL with the MOVE keyword
    . mandatory keyword:   ATOM
    . examples:             TRANSLATION 0.5 0.5 0.5
                            MOVE 1. 1. 1.5 -1.
    . identical keywords:  TRANSLATION, TRANS, TRANSLATE, MOVE

[return to keywords list]

> TRANSMISSION:

    . type:                INPUT/OUTPUT keyword
    . arguments :          list of distances (in mm)
    . outputs:             calculation of transmission coefficient for
                           different distances given as arguments
    . mandatory keyword:   CELL, UNIT, SFAC

[return to keywords list]

> TRICLINIC:

    . type:                OUTPUT keyword
    . arguments :          no argument
    . outputs:             . list the transformation matrices for equivalent
                             triclinic unit cells
                           . if CELL exists: apply the transformation matrices
                             to give new triclinic cell parameters
    . mandatory keyword:   no
    . optional keyword:    CELL
    . identical keywords:  TRICLINIC, TRICL

[return to keywords list]

> TWIN_HEXA:

    . type:                OUTPUT keyword
    . arguments :          no argument
    . outputs:             . list the transformation matrices for hexagonal sett
                           . if CELL exists: apply the transformation matrices
                             to give new cell parameters
    . mandatory keyword:   no
    . optional keyword:    CELL
    . identical keywords:  HEXA_TWIN, HEXA_TWINNING, HEXAGONAL_TWIN, HEXAGONAL_T
                           TWIN_HEXA, TWIN_HEXAGONAL, TWINNING_HEXA, TWINNING_HE

[return to keywords list]

> TWIN_PSEUDO_HEXA:

    . type:                OUTPUT keyword
    . arguments :          no argument
    . outputs:             . list the transformation matrices for pseudo-hexagon
                              setting in a monoclinic unit cell
                           . if CELL exists: apply the transformation matrices
                             to give new cell parameters
    . mandatory keyword:   no
    . optional keyword:    CELL
    . identical keywords:  TWIN_PSEUDO_HEXA

[return to keywords list]

> TWO_THETA:

    . argument:            real values
    . meaning:             2Theta (deg) values
    . outputs:             d_hkl(A), Q(A-1), SinTheta/lambda
    . mandatory keyword:   WAVE
    . identical keywords:  TWO_THETA, 2THETA, 2THETA_HKL, TWO_THETA_HKL
    . example:             TWO_THETA 50.

[return to keywords list]

> UB_MAT:

    . arguments:           9 reals
    . meaning:             UB matrix components in the following order:
                           11 21 31 12 22 32 13 23 33
                           If a tenth argument is input and corresponds to
                           "111213212223313233" the UB components are read
                           in the following order :
                           11 12 13 21 22 23 31 32 33
    . output:              cell parameters deduces from the UB matrix
    . identical keywords:  UB_MAT, UB_MATRIX

[return to keywords list]

> UNIT:

    . type:                INPUT keyword
    . arguments:           n character strings
    . meaning:             list of chemical elements in the molecule
    . output:              - atomic density calculation, in at/cm3
                             (dependent keyword = CELL)
                           - absorption coefficient calculation
                             (dependent keywords = CELL, BEAM)
                           - determination of the molecular formula
                             (dependent keywords = Z)
                           - calculation of the molecular weight
                             (dependent keywords = Z)
                           - calculation of the atomic and weight
                             percentage (dependent keywords = Z)
                           - determination of the density
                             (dependent keywords = CELL, Z)
    . mandatory keyword:   SFAC
    . example:             UNIT 16. 24. 36. 4.

[return to keywords list]

> USER_MAT:

    . arguments:           "#" + 1 integer
    . meaning:             number of user matrix in the matrices list defined  b
                           the user in the cryscalc.ini setting file
    . example:             USER_MAT  #3
  or
    . arguments:           "$" character string
    . meaning:             this character string has to be one of the comment te
                           accompagnying the matrix defined by the user in the
                           cryscalc.ini setting file
    . example:             MATR  $2a

    . output:              calculation of new cell parameters (dependent
                           keyword = CELL)
                           calculation of new atomic coordinates (dependent
                           keyword = ATOM)
                           calculation of new hkl Miller indices (dependent
                           keyword = HKL)
                           create a new file containing the new hkl indices
                           (dependent keyword = FILE)
    . identical keywords:  USER_MAT, USER_MATR, USER_MATRIX

[return to keywords list]

> WAVE:

    . type:                INPUT keyword
    . arguments:           1 real or 1 character string
    . meaning:             . real value: wavelength value in A
                           . character string:
                              - "X_Ag" or "XAG": wavelength = 0.556363 A
                              - "X_Mo" or "XMO": wavelength = 0.71073 A
                              - "X_Cu" or "XCU": wavelength = 1.5406 A
                              - "X_Ni" or "XNI": wavelength = 1.65794 A
                              - "X_Co" or "XCo": wavelength = 1.78892 A
                              - "X_Fe" or "XFE": wavelength = 1.93597 A
                              - "X_Cr" or "XCR": wavelength = 2.28962 A
    . examples:            WAVE 0.71073
                           WAVE XMO
    . identical keywords:  WAVE, WAVELENGTH, WL, LAMBDA

[return to keywords list]

> WEB:

    . type:                OUTPUT keyword
    . argument:            web site name or address
    . meaning:             web site name can be one of the following: CDIFX
                           or site name defined in the cryscalc.ini setting file
                           in the [WEB] section
    . mandatory argument:  CELL or FILE .CIF
    . identical keywords:  WEB, INTERNET

[return to keywords list]

> WRITE_ADP:

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write anisotropic displacements parameters
    . mandatory action :   ADP have to be read previously in a CIF file
    . identical keywords:  WRITE_ADP, WRITE_UIJ

[return to keywords list]

> WRITE_BEAM:

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write incident beam type)
    . mandatory keyword :  WAVE
    . identical keywords:  WRITE_BEAM, WRITE_INCIDENT_BEAM, OUTPUT_BEAM)
                           OUTPUT_INCIDENT_BEAM)

[return to keywords list]

> WRITE_CELL:

    . type:                OUTPUT keyword
    . optional  argument:  CART_A/CART_C
    . meaning:             write cell parameters (direct and reciprocal space)
                           and metric tensors and Busing-Levy B-matrix
                           (if required)
    . mandatory keyword :  CELL or FILE .CIF or READ_CIF or READ_INS or READ_PCR
    . identical keywords:  WRITE_CELL, OUTPUT_CELL

[return to keywords list]

> WRITE_CHEM:

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write molecular features (formula, weight )
    . mandatory keywords:  CHEM, CONT/ZUNIT, SFAC/UNIT/ZUNIT
    . identical keywords:  WRITE_CHEM, WRITE_CHEMICAL_FORMULA,
    .                      OUTPUT_CHEM

[return to keywords list]

> WRITE_DEVICE:

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write device features defined in the cryscalc.ini set
    . identical keywords:  WRITE_DEVICE, OUTPUT_DEVICE

[return to keywords list]

> WRITE_QVEC:

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write modulation wave vector components
    . mandatory keyword :  QVEC
    . identical keywords:  WRITE_QVEC, OUTPUT_QVEC

[return to keywords list]

> WRITE_SG:

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write space group features
    . mandatory keyword :  SPGR
    . identical keywords:  WRITE_SG, WRITE_SPGR, WRITE_SPACE_GROUP

[return to keywords list]

> WRITE_SYM_OP:

    . type:                OUTPUT keyword
    . optional arguments : SHELX
    . outputs:             list of symmetry operators (alphanumeric form,
                           rotational and translational parts with the SYMM
                           keyword
                           if argument="SHELX": output reduced set of
                           symmetry operators for the given space group
                           in a SHELX format (NLAT; SYMM)
    . mandatory keyword:   SPGR or SYMM
    . identical keywords:  WRITE_SYM_OP, WRITE_SYMM_OP, WRITE_SYMP, WRITE_SYMM,
                           WRITE_SYMMETRY_OPERATORS, WRITE_SYMOP

[return to keywords list]

> WRITE_WAVE:

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write cell parameters (direct and reciprocal space)
    . mandatory keyword :  WAVE
    . identical keywords:  WRITE_WAVE, OUTPUT_WAVE

[return to keywords list]

> WRITE_ZUNIT:

    . type:                OUTPUT keyword
    . argument:            no
    . meaning:             write Z unit (number of molecular unit)
    . mandatory keyword :  ZUNIT
    . identical keywords:  WRITE_ZUNIT, WRITE_Z

[return to keywords list]

> X_WAVE:

    . type:                output keyword
    . optional argument:   target nature (Ag, Mo, Cu, Ni, Co, Fe, Cr)
    . meaning:             if no optional argument, output Ka1 and Ka2 wavelengt
                           value (in A) for main radiations: Ag, Mo, Cu, Ni, Co,
                           Fe and Cr
    . identical keywords:  XRAYS_WAVELENGTH, X_WAVE

[return to keywords list]

> ZUNIT:

    . type:                INPUT keyword
    . arguments:           1 real
    . meaning:             number of formula units
    . example:             4
    . identical keywords:  ZUNIT, Z, Z_UNIT

[return to keywords list]

[return]

List of CRYSCALc command line arguments :

> MAN :

       Create 'cryscalc.txt' file user's guide (text format).
       ex : > cryscalc man

> HTML :

       Create 'cryscalc.html' file user's guide (HTML format).
       ex : > cryscalc HTML

> HTML_BROWSE :

       Create 'cryscalc.html' file user's guide (HTML format) and launch the bro
       previously defined in the 'cryscalc.ini' setting file'
       ex : > cryscalc HTML_BROWSE

> KEY/KEYS :

       Create 'cryscalc_keys.txt' file containing the keywords list
        ex : > cryscalc KEYS

> P4P :

       . List the .P4P files in the current folder.
       . Select a .P4P file
       . Search for the corresponding .HKL file and output SADABS file
         to create an 'import.cif' file.
        ex : > cryscalc P4P

> filename.P4P :

        Search for the corresponding .HKL file and output SADABS file
        to create an 'import.cif' file.
         ex : > cryscalc mycrystal.P4P
        RAW file can be specified to create the 'import.cif' file.
         ex : > cryscalc mycrystal.P4P RAW=mycrystal.RAW

> filename.RAW :

        Read the filename.RAW file (created by SAINT) and create
        a HKL file with the SHELX format (3I4,2F8.2).
         ex : > cryscalc mycryscalc.RAW

> REPORT/REPORT_LONG :

        Create a HTML report from 'archive.cif' file or from the
        .CIF file give as a second argument.
         ex : > cryscalc report

> ARCHIVE.CIF :

       . Read 'archive.cif' CIF file
       . Complete this 'archive.cif' with additionnal CIF fields related to
         absorption correction, squeeze procedure, hydrogen treatment,
         diffractometer, structure solution program ...
         A new 'cryscalc_archive.cif' file is then created.
       Remark : diffractometer and structure solution program can be defined
                in the 'cryscalc.ini' setting file in the [DEVICE] and [PROGRAMS
                parts respectively.

> CREATE_ARCHIVE :

       . create global 'cryscalc_archive.cif' CIF file from CIF files
         given as arguments, first argument being related to structural
         parameters file created by the refinement program.
       Example : CRYSCALC ambi struct

> CIFDEP :

       Combined with 'ARCHIVE.CIF' argument, this optional argument
       completes the 'cryscalc_archive.cif' file with CIF fields related
       to the author of the deposition (name, address), extracted from
       the 'cryscalc.ini' setting file ([AUTHOR/USER] part)

> SOLVE_TO_INS/CREATE_INS :

       . read STRUCT.CIF file and get cell parameters with esd's
       . read import.RES created by SIRxx or SHELXS
       . create job.INS file for SHELXL with correct esd's and different
         useful SHELXL keywords (ACTA, BOND$H ...)

> DEBUG:

       Combined with all previous arguments, this optional argument
       will create a 'cryscalc_debug.txt' file containing informations
       about the values of some variables during the CRYSCALc run.
       This argument can be useful to detect the origin of the bug
       in a CRYSCALc crash.

> NO_OUT :

       Combined with all previous arguments, this optional argument
       avoids to write CRYSCALc cresults lines in the screen and
       in the 'cryscalc.log' file.
[return]

  What's new in CRYSCALc ?

   
     Main new features implemented in CRYSCALC:
     (for more details, see the CRYSCALC manual (MAN keyword))
   
     T. Roisnel / CDIFX - ISCR Rennes
   
   
   . Nov. 14 :
     # New PAT command line argument after .CIF or . INS file
       allows to calculate a diffraction pattern from features given by
       PDP_BEAM/PDP_WAVE keywords and details in the [PATTERN SIMULATION]
       section of the setting file.
       Example: cryscalc job.cif PAT
   
   . Oct. 14 :
     # New [USER SHORTCUTS] section of the cryscalc.ini, defining
       some keywords shortcuts (max. = 10). The shortcut and its
       details (CRYSCALC keyword) has to be separated by "=" character.
       Example: RJC = READ_CIF job.cif
     # New parameters in [OPTIONS] section of the cryscalc.ini
       setting file. These parameters are used for simulation
       of powder diffraction file from command line and .CIF/.INS
       file (create_PAT_PRF=1)
        pdp_beam   = N    ! N for neutrons / X for X-rays
        pdp_wave   = 1.22 ! wavelength used for diffraction pattern
                           simulation
       If not specified, simulation pattern is calculated for
       X-rays and Copper K_alpha1 radiation (1.5406 A)
     # New command line argument:
       CREATE_ARCHIVE argument, followed by the name of CIF files
       (without extension), allows to create a whole archive.cif file.
       First cif file corresponds to the main CIF file created by
       refinement software and next ones to supplementary cif files
       to complete the archive.
       ex : d:\> CRYSCALC  CREATE_ARCHIVE my_job import
            . my_job : main .CIF file, used to extract structural
                       parameters
            . import : secondary .CIF file, containing experimental
                       parameters (crystal and experimental features, ...)
   . Sept. 14 :
     # new CREATE_SOLVE keyword:
       . create input files for structure solving software as SIR97,
         SHELXS/T and SUPERFLIP.
     # bugs corrections:
       . site multiplicity calculation
       . CRYSCALC reports (html, txt, latex): adp are in A^2
         and not in A^2x10^3 !
     # Some statistics on F2_mean, sig_mean ... have been added in the
        output of the FILE keyword.
   
   . July 14 :
     # "include_HKL_file" field can be input in the cryscalc.ini setting file to
       embed the contain of hkl SHEXL file in the archive_cryscalc.cif file.
       The SHELXL hkl file name corresponds to the last project ID in WinGX.
     # NOT TO CONFUSE, CRYSCAL PROGRAM HAS BEEN RENAMED AS
       CRYSCALC. FEATURES OF THE SOFTWARE HAVE TO BE CHANGED
       CONSEQUENTLY :
        . environnement variable : CRYSCALC
        . setting file : CRYSCALC.ini
        . css files : CRYSCALC.css and CRYSCAL_report.css
       CRYSCALC will be included in the distribution of the FullProf Suite
       in a near future.
   
   . June 14 :
     # New argument for CONN keyword:
        . NO_xx : exclude xx atoms type from listing
          ex ! CONN Cu1 NO_H
     # "create_PAT_PRF" field has been added in the "[COMMAND LINE ARGUMENTS]"
       part in the setting file (cryscalc.ini) : X-ray diffraction pattern
       is then created (PRF file FullProf format) after reading a CIF file.
   
   . May 14 :
     # Corrections of bugs caused by the new CRYSFML library
       specially in bond distribution routine
     # New arguments for CONN keyword:
        . ANG : interatomic angle calculation
        . CONDENSED : short output
   
   . March 14 :
     # ALL_X argument for CONN keyword:
       output atomic connectivity for all atoms
       of the X species.
       ex: CONN ALL_Cu
     # in_A argument for WRITE_ATOMS keyword:
       Atomic coordinates are listes in A
     # VOL argument for CONN keyword:
       polyedron volume calculation, based on VOLCAL program
       of L. W. FINGER, included in CFML
   
   . Feb 14 :
     # BARY keyword:
       Centroid calculation can be applied with only 2 input atoms
     # Bug has been corrected in the HTML report combined with
       SQUEEZE option.
   
   . Nov 13 :
     # STAR_K keyword:
       Apply rotational parts of the symmetry operators of a given
       space group on the components of a propagation wave vector.
   
   . Oct 13 :
     # CONN keyword:
       . new argument for GEN_HKL keyword : PM2K
         PM2K_hkl.inp is created : its contains hkl reflections list
         to be copied in the input file for PM2K program (M. Leoni).
       . new MIN= and MAX= arguments (default values are defined
         in cryscalc.ini setting file ([PARAMETERS] section)
       . calculation of effective interatomic distances
   
   . Sept 13 :
     # new SELF argument for CONN keyword: output interatomic
       distance only between atoms with same labels.
       This can be useful for M-M distances in a organometallic complex.
     # New READ_FACES keyword : read crystal habitus .
       ex. : READ_FACES absorb.ins
       ex. : READ_FACES faces.Def
   
   
   . July 13 :
     # New DHA keyword : calculation of H position given donor and
       acceptor atoms.
     # Change in MENDEL argument that can be atomic number.:
       ex: MENDEL 59
   
   . May 13 :
     # READ_INS keyword: by default, Q peaks are not read.
       Q_PEAKS argument has to be specified for not skipping Q peaks
   
   . April 13 :
     # new arguments for CREATE_FST keyword:
       MOLE : space group line is commented to draw
       only atoms of the asymmetric unit cell
       No_H : Hydrogen atoms and related bonds are excluded from the
              drawing (lines are commented).
       No_H argument is valid only with MOLE argument
       POLY : includes polyedra drawing in Fp_Studio if connectivity
              calculations have been performed
       RUN  : launch FP_Studio
     # argument "CART" after the "WRITE_ATOMS" keyword outputs the
       cartesian coordinates of the atoms. Cartesian frame type can
       be specified by "CART_A" (x//a) and "CART_C" (x//c).
     # argument "SHAPE" after the "CONN" keyword creates an input
       for SHAPE programm (http://www.ee.ub.es/)
       derivative SHAPE arguments : SHAPE_A (a//x), SHAPE_C (x//c)
     # Cartesian frame type (A: x//a or C: x//c) can be specified in the
       setting file, through the "cartesian_frame_type" keyword in the
       [OPTIONS] section. Default value for the cartesian frame is A (x//a)
     # argument "CART" after the "WRITE_CELL" keyword outputs the
       cartesian frame, metric tensors and Busing-Levy B-matrix. Cartesian
       frame type can be specified by "CART_A" (x//a) and "CART_C" (x//c).
       argument.
   
   . March 13 :
     # New keywords related to TIDY software (standardisation of inorganic
       crystal-structure data (Acta Cryst. 1984, A40, 169-183):
       - CREATE_TIDY   : create input file for TIDY from a .CIF or .INS file
       - READ_TIDY_out : read output file from TIDY (default name = stidy.out)
   
   . Feb. 13 :
     # CONN keyword can have BVS argument for Bond Valence Sum Calculation.
       Oxidation state of the input atoms have to be provided trough the
       ATOM keyword.
       ex: ATOM Fe1 Fe+3 0.11 0.22 0.33 0.4 1.
       example of CFL file :
         http:\\www.cdifx.univ-rennes1.fr\cryscalc\cryscalc_y2o3_bvs.cfl
     # Final.y file (coming from EVALCCD) are not read anymore, since they
       don't contain structure factors.
     # Connectivity calculation outputs symmetry operators used to generate
       atoms around a particular one. CFML has been modified to output this list.
     # Profile (U, V, W, eta0, eta1) and pattern (step, constant background,
       scale factor) parameters can be specified in the [PATTERN SIMULATION]
       section of the cryscalc.ini setting file, for X-ray and neutron pattern
       calculation.
   
   . Jan. 13 :
     # When creating archive_cryscal.cif file, CRYSCALC is looking for
       output files creating by different versions of SQUEEZE procedure
       in PLATON, as platon.sqf or platon_sqr.sqf (PLATON jan. 2013)
     # New argument for GEN_HKL for powder diffraction pattern calculation :
       particle size (in A) can be specified through the "SIZE=" keyword.
       If not, particle size is considered as infinite and
       no line broadening is calculated.
       Example : GEN_HKl 2theta_min=20 2theta_max=120 PAT SIZE=250
       Example of CFL file :
         http:\\www.cdifx.univ-rennes1.fr\cryscalc\cryscalc_si_x_100.cfl
     # Import.cif file can be created from .P4P file and .RAW file (output of
       SAINT program). This has to be specified in the command line through
       the "RAW=" keyword.
        Example:
         d:\data\CRYSCALC file_0m.P4P RAW=file_0m.RAW
     # New "DIST_X" and "DIST_PLUS" keywords allow to calculate the coordinates
       of a particular point aligned with with the input atoms
   
   . Dec. 12 :
     # New "FRIEDEL" keyword allows to get number pairs of Friedel
       in hkl file
   
   . Nov. 12 :
     # Particular format for .hkl file (h,k,l F2, sig) can be specified
       in the setting file in the [OPTIONS] section through the
       hkl_format keyword.
       example hkl_format = 3i4,2F15.2
       If not specified, default format is : 3I4,2F8.2 (SHELX format)
     # new argument for WRITE_SYMM keyword : if argument="SHELX"
       the list of symmetry operators is output in a SHELX format
     # news arguments for SITE_INFO keyword :
        . if argument="PCR", the list of symetry equivalent atoms
          is output in a FullProf format (.PCR)
        . if argument="PCR_MAG", the list of magnetic atoms
          is output in a FullProf format (.PCR)
   
   . Oct. 12 :
     # "CIF file for Pymol can be created by putting "PYMOL" as
       argument of "READ_CIF", "READ_INS" and "READ_CEL"
       keywords (example: FILE file.cif pymol) or in the command line
       with a cif.file (example: d:\cryscalc file.cif pymol
       "create_CIF_PYMOL" keyword (value = 0/1) can also be specified
       in the cryscalc.ini setting file : file_pml.cif file is then
       automatically created after reading a CIF file.
     # "Skip_start_menu" keyword (value = 0/1) can be input in the cryscalc.ini
       setting file to skip the starting main menu of CRYSCALC.
     # HTML structural report: torsion angles values greater
       than CIF_torsion_limit are excluded. Default value
       for CIF_torsion_limit is 170.0 but can be defined in the
       cryscalc.ini setting file in the [OPTIONS] section
     # Special format can be specified with the FILE keyword
      when reading .hkl file, with the FMT argument.
       Example : FILE filename.hkl fmt=3I4,2F15.2
   
   . Sept 12 :
     # new argument for BARY keyword
     # "HKL_statistics" keyword (value = 0/1) can be input in the cryscalc.ini
       setting file to output or not statistics on hkl reflections.
   
   . July 12 :
     # FILE keyword: .COL file created by COLL5 (ILL / format =4)
                      can be read
     # FILE keyword: .INT file created by DATARED can be read
     # CELL keyword: .RED file for DATARED can be read
     # New OUT_n argument for FILE keyword, allowing to output every
       n reflection features (index, h,k,l,F2,sig)
   
   . June 12 :
     # SHIFT_2TH keyword can now be followed by three values,
       corresponding to a constant, cos and sin dependent shifts
       respectively.
     # css files for structural HTML report and user's guide
       are now available in the CRYSCALC folder (repertory that
       contains the crycsalc.ini setting file. If present, these
       css files, called cryscalc_report.css and cryscalc.css
       for report and user's guide respectively, can be edited
       and modified by the user. These css files contains
       styles that are used in the HTML documents.
   
   . April 12 :
     # MOVE/TRANSLATE keyword accepts 4 arguments, as the MOVE
       instruction on SHELXL. Optional 4th argument corresponds to
       the sign to multiply atomic coordinates. New atomic
       are then : sign*x + t_x, sign*y + t_z, sign*z + t_z
       If input 3 arguments are given, they correspond to the
       t_x, t_y and t_z translation and the 4th argument is
       taken equal to +1.
   
   . March 12 :
     # GET argument can be input with SEARCH_GROUP keyword:
       the most probable space group is then considered
     # Cell parameters are deduced from UB matrix when P4P file or
       import.cif file contain this information. Use WRITE_CELL
       keyword to output these cell parameters.
   
   . January 12 :
     # CRYSCALC has been compiled with the new CRYSFML library
     # MOVE instruction for SHELXL (output of SG_INFO for acentric
       space group) is now correct for non conventional settings
   
   . December 11 :
     # Some minor changes have been performed in the code to be compiled
       with Intel Fortran Compiler
     # HKL arrays are now dimensionned dynamically. Default dimension is
       500000 but can be defined by user in the setting file though the
       "hkl_reflections" keyword in the [ARRAYS DIMENSIONS] section.
     # "LOCK_wave_value" field can be input in the cryscalc.ini setting file to
       to define the lock the input wavelength to the value of the closer
       Xray target (Cu, Mo ...). if not present in the setting file, the default
       value for this field is 0.02.
       Examples :
       - input wavelength = 1.53 and LOCK_wave_value = 0.02  : wl = 1.5406
       - input wavelength = 1.53 and LOCK_wave_value = 0.005 : wl = 1.53
   
   . November 11 :
     # Minor corrections in the HTML report in the "symmetry transformations
       used to generate equivalent atoms" parts (distances, angles, torsion
       angles and hydrogen bonds)
     # LST_SG keyword :
       - "chiral" and "polar" arguments can se specified to output
         chiral and polar space groups respectively
     # SG_INFO keyword outputs the MOVE instruction for SHELXL
       in the case of acentric space groups.
     # CRYSCALC has been compiled with last version of CFML (5.00)
      and changes in the space_group routine have been made to be
      to be in agreement with the CFML library.
   
   
   . October 11 :
     # LST_SG keyword :
       - "enantio" argument can se specified to output
         enantiomorphic space goups
       - Point group is output
     # MU keyword : explicit keyword to perform absorption coefficient
       calculation. Cell paramaters, wave and cell content has to be
       known. This keyword can be useful after reading of parameters
       from an external file as CIF or INS file.
       ex : READ_CIF UAl2.cif
            WAVE X_cu
            MU
   
     # DIAG keyword : diagonalization of a 3*3 matrix and ouput Eigen values
                      and Eigen vectors
     # THERM_SHELX keyword : ADP parameters are input in the following
       SHELX order, i.e. 11 22 33 23 13 12
   
   
   . July 11 :
     # Up to 5 extra matrices can be provided by the user in the cryscalc.ini
       setting file in the [USER TRANSFORMATION MATRICES] section. These
       matrices are defined through the "MAT_n" keyword followed by the 9
       components of the matrix m11 m12 m13 m21 m22 m23 m31 m32 m33 .
       and a comment text.
       New "USER_MAT" keyword has been added to select a particular matrix
       provided by the user in the cryscalc.ini setting file.
       The matrix to be selected can be input either by the numor preceded by
       the "# symbol, either the comment text preceded by the "$" symbol
       Examples : USER_MAT #1
                  USER_MAT $2a
     # "include_RES_file" field can be input in the cryscalc.ini setting file to
       embed the contain of last .res SHELXL file in the archive_cryscalc.cif file
       to avoid PLAT005_ALERT_5G alert in the CHECK CIF procedure. The SHELXL
       .res file name corresponds to the last project ID in WinGX.
     # After a matrix transformation of atomic coordinates, the list of atoms
       is updated with new coordinates.
     # Search_group procedure outputs only space groups those Bravais lattice
       corresponds to the Bravais lattice contained in the import.cif file
     # Include "_symmetry_space_group_name_H-M" string in the import.cif file
       created from .P4P and .HKL file
   
   . June 11 :
     # CRYSCALC has been compiled with new version of CFML (5.00)
   
   . May 11 :
     # Bug has been corrected in the structure factor calculation routine
     # Total number of electrons is output after CHEM keyword.
     # The matrix used for the hexagonal to rhomboedral system was corrupted.
   
   . April 11 :
     # Some changes in the routine to get new space group after matrix
       transformation
     # Some changes in the monoclinic transformation matrix list
     # A non systematic bug in the bonds distribution list (CONN keyword)
       has been corrected
   
   . Feb. 11 :
     # Stucture factors calculation can be performed for electrons
       diffraction (GEN_HKL and SF_HKL routines). This has to be
       specified by the BEAM keyword and "ELECTRONS" argument
     # Some examples of CFL input files can be downloaded from the
       CRYSCAL web site (www.cdifx.univ-rennes1.fr/cryscalc)
     # Some changes in output files :
        . cryscalc.log is renamed cryscalc_debug.txt
        . cryscalc.out is renamed cryscalc.log
       LOG argument has been replaced by DEBUG argument
     # New PAT argument for GEN_HKL keyword allows to generate a
       diffraction pattern. PRF file is automatically plotted
       with the WinPLOTR program if installed.
     # I/Imax is now calculated in the GEN_HKL routine when working
       in the 2theta space and neutron or Cu_K_alpha1 X-ray radiation.
       Intensity is calculated as follows:
                        I=mult * Lp * F^2
       where : mult is the multicicity of the reflection
               Lp the Lorentz-polarization factor, calculated by:
               Lp=(1-K+K*CTHM*cos2(2theta)/(2sin2(theta)cos(theta)
                CTHM=cos2(2theta_monok) [CTHM=0.79]
                K=0.  for neutrons
                K=0.5 for unpolarized X-ray radiation
     # Cosmetic changes in the Fortran codes to allow the compilation
       with the free G95 Fortran compiler.
   
   . Jan. 11 :
     # CREATE_FST keyword allows to create a .FST file for
       FullProf Studio after reading a CIF file.
     # "create_FST" field can be input in the "[COMMAND LINE ARGUMENTS]" part
       in the setting file (cryscalc.ini)
   
   . Dec. 10 :
     # New extinction rules for FIND_HKL_LIST keyword:
       . hhl with h+l=2n
       . hkk with k+h=2n
       . hkh with h+k=2n
     # Cosmetic changes in archive_cryscalc.cif file: in the case
       of samples without H atoms, "_atom_sites_solution_hydrogens" and
       "_refine_ls_hydrogen_treatment" cif field lines are removed
   
   . Nov. 10 :
     # Connectivity calculations are followed by a bonds distribution list
     # Transformation matrix components can be input as fractional values
        Example : matrix 1/2 1/2 0.   -1/2 1/2 0. 0. 0. 1
     # Cosmetic changes in HTML structural report
   
   . Oct. 10 :
     # A threshold value can be given as argument to the SEARCH_GROUP keyword
   
   . Sept. 10 :
     # FIND_HKL_list argument value can be negative and allows to search
       reflections with opposite rule than for positive value.
     # SIR_TO_INS command line argument has been replaced by SOLVE_TO_INS
       and allows now to create INS file for SHELXL from SHELXS ouput file
       as well as SIRxx output file.)
     # CREATE_ACE keyword allows to create a .ACE file for CaRIne
       after reading a CIF file.
     # "create_CEL" field has been added in the "[COMMAND LINE ARGUMENTS]" part
       in the setting file (cryscalc.ini)
     # NIGGLI/NIGGLI_CELL keyword has been added and allows to determine
       the Niggli cell from any triclinic cell
     # [CREATE INS] section has been added in the cryscalc.ini setting file to
       define temperature and thermal parameter threshold to skip atoms
       This avoids to enter these values related to the CREATE_INS keyword
   
   . June 10 :
     # Bugs in the FIND_HKL_LIST routine has been corrected
   
   . April 10 :
     # Some items of the experimental part in the HTML structure report are now
       in italic in agreement with published articles.
   
   . March 10 :
     # WRITE_DEVICE keyword
     # WRITE_HKL keyword has been replaced by FIND_HKL_LIST.
       The SUPPRESS/REMOVE argument for FIND_HKL_LIST keyword
       has been added, leading to the creation of a new file free of
       data obeying the current selection rule.
     # QVEC components can be input as fractionnal values.
       The following fractionnal absolute values are :
       1/2, 1/3, 2/3, 1/4, 3/4, 1/5, 2/5, 3/5, 4/5, 1/6, 5/6,
       1/7, 2/7, 3/7, 4/7, 5/7, 6/7, 1/8, 3/8, 5/8, 7/8,
       1/9, 2/9, 4/9, 5/9, 7/9 and 8/9
     # GEN_HKL keyword leads to a structure factor calculation if atoms
       has been input.
     # SF_HKL keyword leads to a structure factor calculation for
       a given hkl reflection
     # New WRITE_BEAM and WRITE_QVEC keywords
   
   . Feb. 10:
     # CREATE_CEL keyword allows to create a .CEL file for PowderCELL
       after reading a CIF file.
     # CREATE_INS keyword allows to create a .INS file for SHELXL
       after reading a CIF file.
     # CREATE_CFL keyword allows to create a .CFL file for CRYSCALC
       after reading a CIF file.
     # New "[COMMAND LINE ARGUMENTS]" part in the setting file (cryscalc.ini)
       with the following fields :
        . create_CEL
        . create_INS
        . create_CFL
       Putting the corresponding values to 1 will create .CEL, .INS and .CFL
       respectively.
     # cryscalc file.p4p: if crystal faces are present in the .P4P file,
        they are extracted and saved in the import.cif.
   
   . Jan. 10:
     # Bug in _trans.HKL file has been corrected.
   
   . Nov. 09:
     # If a "platon_ortep.gif" file is present in the current folder, it is
       automatically incorporated in the HTML report file
     # If final.y file contains QVEC field and related parameters,
       a hklm file is created
   
   . Oct. 09:
     # If a hkl file is input, the transformed hkl file is
       loaded automatically after MATRIX keyword
     # Shannon table value for magnesium is corrected (Mg+2)
     # Cosmetic changes in the HTML documents (report and user's guide) created
       by CRYSCALC.
     # Space group number has been added in the HTML report
     # SHELX reference has been changed to :
       G. M. Sheldrick, Acta Cryst A, 2008, A64, 112-122
   
   . Sept. 09:
     # TWIN_PSEUDO_HEXA keyword
     # TWIN_HEXA keyword
     # Bugs in the routine to create the archive_cryscalc.cif file has
       been corrected, specially when the archive.cif file is created
       from the "create CIF / ACTA-C" procedure in WinGX, where the
       order of some CIF fields is changed.
     # CRYSCALC has been compiled with new version of CFML (4.00)
     # Bugs in the connectivity calculation routine has been corrected
   
   . Feb. 09:
     # CHECK_GROUP can now determine trigonal space group
     # SG_ALL keyword output sub-groups of the current space group
   
   . Jan. 09:
     # .RAW file can be given as argument in the command line
       i.e. d:\> CRYSCALC my_file.RAW
       CRYSCALC is then reading my_file.RAW and will create a
       my_file_RAW.HKL file in a SHELX format. This file also contains
       dir. cos. for further absorption correction.
       Same behavior can be optained by associating a selected RAW file to
       CRYSCALC program in the Windows file folder
   
   . Nov. 08:
     # GEN_HKL accepts now Q_min and Q_max arguments
     # SEARCH_HKL arguments can be h, k or l letters.
       ex: SEARCH_HKL h 0 0
           SEARCH_HKL 1 k 0
     # SITE_INFO keyword gets constraints on anisotropic ADP, using the
       routine implemented in FullProf
     # new available arguments for CRYSCALC in command line:
       - LOG    : create a cryscalc.log file
       - NO_OUT : no output information are written on screen
   
   . oct. 08:
     # CRYSCALC archive.cif : for archive.cif files created with the new version of
       WinGX (sept. 2008), CRYSCALC is skipping the whole part of the cif file
       containing programs references, to created the cryscal_archive.cif file
   
     # new argument for CRYSCALC in command line : CRYSCALC CREATE_INS/SIR_TO_INS
       Create job.ins file from :
         . output.RES file created by SIR programs
         . struct.cif file created by WinGX
       This job.ins can be directly used for structure refinement with
       SHELXL, and contains right cell parameters and esd's, Mo wavelength
       and useful instructions such as ACTA, BOND$H, CONF, TEMP ...
   
   . sept. 08:
     # CRYSCALC archive.cif : CRYSCALC is reading archive.cif and cryscalc.cif
       files and creating completed archive_cryscalc.cif file
   
     # keyword PAUSE: pause in the execution of the requested commands
       This keyword can be useful when commands are executed from a CFL
       commands file
   
   . july 08:
     # REPORT/REPORT_long: CIF fields can be independly in lower and
       upper cases
   
   
   . april 08:
     # CONN keyword: calculation of connectivity around a selected atom
       given as argument.
   
   . sept. 07:
     # SEARCH_SPGR keyword: search for a space group, given a hkl list and
       a given crystal system (Thanks to JRC for the CHECK_GROUP routine)
   
   . july 07:
     # MATMUL keyword for 3*3 matrix multiplication
     # CIF file can be given as a second argument if "REPORT" or "REPORT_long"
       is given at first. A CIF_file_structural_report.HTML is then created
       ex: d:\cryscalc report_long my_CIF_file.CIF
     # P4P file can be given as argument in the command line to run CRYSCALC,
       i.e. CRYSCALC my_file.P4P.
       CRYSCALC is then reading my_file.P4P and my_file.HKL to create
       import.CIF file for WinGX
       Same behavior can be optained by associating a selected P4P file to
       CRYSCALC program in the Windows file folder
   
   . april 07:
     # MERGE keyword: merge equivalent reflections of the current HKL file
   
     # REPORT keyword can be interpreted in command line:
       \> cryscalc report
       CRYSCALC is looking in the current folder for the presence of a
       "archive.cif" file: "structural_report.html" file is then created
       and contains text about the crystallographic study. The browser
       defined in the "cryscalc.ini" file is then launch
   
   . march 07:
     # .x file (created by DENZO) and .rmat file (created by DIRAX) can be
       passed as argument for CELL keyword
   
   . feb. 07:
     # RESET keyword for input parameters and arrays initialization
   
   
   . jan. 07:
     # THERM keyword can performed conversion of anisotropic displacement
       parameters:
       new available arguments: U_ij, B_ij, Beta_ij
     # DIR keyword has been added and corresponds to the DIR DOS command.
       Arguments may follow this keyword.
     # Wcryscalc for Windows has been created.
   
   . nov. 06:
     # X rays data for Ag, Fe and Cr have been tabulated
     # \> cryscalc P4P:
        CRYSCALC is looking in the current folder, for a P4P file (created
        by SAINT) and a HKL file (created by SADABS). Import.cif file is then
        created and can be directly read by WinGX as a KappaCCD file
   
   . oct. 06:
     # MAG keyword:     output magnetic features for a 3d or 4f ion
     # SHANNON keyword: get effective ionic radii from Shannon article
      (Acta Cryst. 1976, A32, 751)
     # P4P keyword:     read P4P file created by SAINT (Bruker-AXS)
   
   . sept. 06:
     # FILE keyword: .m91 and .m95 files created by JANA can be read
     # CELL keyword: .m50 file can be read
   

[return]

  cryscalc.ini setting file :

A setting file can be used by CRYSCALc, containing the definition of different parameters such as external applications that can be launched from CRYSCALc (browser, editor ...) or defaut values about diffractometer, author, structure solution and refinement programs ... This setting file, called cryscalc.ini has to be located in the folder related to CRYSCALc through the CRYSCALC environment variable.

Example of setting file:

    [EXTERNAL APPLICATIONS]
    browser = "C:\Program Files\Mozilla Firefox\firefox.exe"
    editor  = "C:\Program Files\Keditw\KEDITW32.EXE"

    [WEB ADDRESS]
    fps        = www.ill.fr/dif/Soft/fp/
    cdifx      = www.cdifx.univ-rennes1.fr/
    cryscalc   = www.cdifx.univ-rennes1.fr/cryscalc
    reciprocs  = www.cdifx.univ-rennes1.fr/reciprocs

    [DEVICE]
    diffractometer = APEXII AXS Bruker
    !diffractometer = KCCD Nonius
    !diffractometer = Bruker SMART X2S benchtop
    laboratory     = CDIFX Rennes
    radiation      = X_Mo
    wave_A         = 0.71073
    temperature    = 150(2)

    [USER]
    name        = ROISNEL
    first_name  = Thierry
    address     = Centre de Diffractométrie X, UMR6511 CNRS Université de Rennes 1,Sciences Chimiques de Rennes, 35042 RENNES Cedex France
    email       = thierry.roisnel@univ-rennes1.fr
    web         = www.cdifx.univ-rennes1.fr
    team        = CDIFX

    [ARRAYS DIMENSIONS]
    hkl_reflections = 200000       ! max. number of hkl reflections in a file

    [CREATE INS]
    get_sample_ID = 0          ! get sample ID (default=job)
    temperature   = 100K       ! experimental temperature value
    u_threshold   = 0.1        ! atoms with U_iso > U_threshold will be excluded

    [PARAMETERS]
    i_sig       = 3.         ! used in the SEARCH_GROUP procedure
    threshold   = 0.03       ! used in the SEARCH_GROUP procedure 
    d_max_A     = 3.5        ! used with the CONN keyword (connectivity calculation)

    [COMMAND LINE ARGUMENTS]
    create_ACE       = 1          ! .ACE file for Carine
    create_CEL       = 1          ! .CEL file for PowderCELL
    create_CFL       = 1          ! .CFL file for CRYSCALc
    create_INS       = 1          ! .INS file for SHELXL
    create_FST       = 1          ! .FST file for FP Studio
    create_CIF_pymol = 0          ! X_pml.CIF for PYMOL
    create_PAT_PRF   = 1          ! .PRF file for FullProf

    [PROGRAMS]
    structure_solution_name         = SIR97
    structure_solution_reference    = A. Altomare, M. C. Burla, M. Camalli, G. Cascarano, C. Giacovazzo, A. Guagliardi, A. G. G. Moliterni, G. Polidori, R. Spagna, J. Appl. Cryst. (1999) 32, 115-119
    structure_solution_cif_ref      = SIR97 (Altomare et al., 1999)
    structure_refinement_name       = SHELXL-97
    structure_refinement_reference  = Sheldrick G.M., Acta Cryst. A64 (2008), 112-122
    structure_refinement_cif_ref    = SHELXL-97 (Sheldrick, 2008)
    absorption_correction_name      = SADABS
    absorption_correction_reference = Sheldrick G.M. (2002), SADABS Bruker AXS Inc., Madison, Wisconsin, USA
    absorption_correction_cif_ref   = Sheldrick G.M. (2002), SADABS Bruker AXS Inc., Madison, Wisconsin, USA

    [OPTIONS]
    LOCK_wave_value             = 0.02      ! lock current wavelength to anticathode value
    CIF_format80                = 0         ! formatted line, when creating a CIF file,  if more than 80 characters
    CIF_torsion_limit           = 170.      ! exclude torsion angle if greater than this limit
    include_RES_file            = 1         ! include .RES file in the archive_cryscalc.cif file
    include_HKL_file            = 1         ! include .HKL file in the archive_cryscalc.cif file
    update_parameters           = 1         ! update parameters after transformation(cell parameters, atomic coordinates) 
    report_header               = 1         ! Write header in structural report
    skip_start_menu             = 1         ! Skip start menu
    hkl_statistics              = 1         ! Ouput statistics on hkl reflections
    hkl_format                  = 3I4,2F8.2 ! format for .hkl file (h,k,l,F2,sig)
    cartesian_frame_type        = A         ! A: x//a ; C: x //c
    pdp_beam                    = X         ! Beam for powder diffraction pattern calculation (N for neutrons / X for X-rays)
    pdp_wave                    = 1.5406    ! Wavelength used for powder diffraction pattern calculation

    [PATTERN SIMULATION (Pseudo-Voigt profile)]  
    X_profile_U                  = 0.0055    ! U value of the Cagliotti formula : FWHM2 = U*TAN**2(theta) + V*TAN(theta) + W
    X_profile_V                  = -0.0015   ! V value 
    X_profile_W                  = 0.0036    ! W value 
    X_profile_eta0               = 0.3       ! Lorentzian components : eta = eta° + 2theta * eta1
    X_profile_eta1               = 0.         
    X_pattern_step               = 0.01       
    X_pattern_xmin               = 0.         
    X_pattern_xmax               = 120.       
    X_pattern_scale              = 100.       
    X_pattern_background         = 50.        
    N_profile_U                  = 0.0146     
    N_profile_V                  = -0.0375    
    N_profile_W                  = 0.0475     
    N_profile_eta0               = 0.01       
    N_profile_eta1               = 0.         
    N_pattern_step               = 0.025      
    N_pattern_xmin               = 0.         
    N_pattern_xmax               = 120.       
    N_pattern_scale              = 1000.      
    N_pattern_background         = 50.        

    [USER TRANSFORMATION MATRICES]
    MAT_1                        =     2.  0.  0.    0.  1.  0.    0.  0.  1.   !  2abc
    MAT_2                        =     1.  0.  0.    0.  2.  0.    0.  0.  1.   !  a2bc
    MAT_3                        =     1.  0.  0.    0.  1.  0.    0.  0.  2.   !  ab2c


    [USER SHORTCUTS]
    RCJ                  = READ_CIF job.cif
    RIJ                  = READ_INS job.ins

[return]

  Examples of .CFL input files :


  CRYSCALc links :


  CRYSCALc under Linux:




last updated: TR / CDIFX - 7 Nov. 2014