C R Y S C A L C user's guide
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*************************************************************** C R Y S C A L C (CRYSTALLOGRAPHIC CALCULATIONS) makes crystallographer life easier ! Ver. 25.04 --------------------------------------------------------------- T. Roisnel CDIFX/PRTS/ISCR UMR6226 CNRS-Univ Rennes, France [with courtesy of JRC and JGP for CFML] contact : thierry.roisnel@univ-rennes.fr https://cdifx.univ-rennes1.fr/cryscalc ***************************************************************
Introduction :
List of CRYSCALC keywords :
[top]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 . optional arguments: . arg = "ALL": all the violations reflections are output . arg = "OUT": requested reflections are output on the screen . arg = "WRITE": requested reflections 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 [return to keywords list]> ANG:. type: CALCULATION keyword . arguments: 3 characters 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 characters 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_SYMM_OP, APPLY_SYMOP [return to keywords list]> ATOM:. type: INPUT keyword . arguments: 2 characters 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", "IN_A", "NO_H" . meaning: list the atoms (type, labels, coordinates, ...) . if "CART" is present, cartesian atomic coordinates will be output. Derivative CART arguments are CART_A (a//x) and CART_C (x//c). . if "IN_A" is present, atomic coordinates are listed in A. . if "NO_H" is present, only non-hydrogen atoms are listed. . 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 characters strings or "ALL" . optional argument: "No_H" . meaning: calculation of the coordinates of the centroid of the n atoms known by the atom label (cf ATOM keyword) if arg_2 = ">", all atoms of same species from first and third arguments will be considered in the calculation. Note that this notation is not allowed with labels containing a letter after the numor (ex: C10A). if arg="ALL" : all input atoms are considered if arg="no_H": Hydrogen atoms are excluded . examples: BARY C31 C32 C33 C34 C35 BARY C31 > C35 BARY C31 > C34 C35 BARY ALL . identical keywords: BARY, CENTROID [return to keywords list]> BEAM:. type: INPUT keyword . arguments: characters string . optional arguments: real value, following "WL=" for wavelength in A or "E= for energy (in KeV for X-rays and electrons or in meV for neutrons) . optional arguments: real value (wavelength in A or energy) . 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) . examples: BEAM X_Mo BEAM X WL=1.5 BEAM X E=8.26 BEAM NEUT WL=1.2 BEAM NEUT E=56.8 . identical keyword: BEAM, JOBTYPE, JPBTYP [return to keywords list]> BVPARM:. type: INPUT keyword . arguments: characters string . meaning: bond-valence parameters given by the user, provided to the BVS calculation routine (see CONN keyword). The order of BV parameters are as follows: cation anion d0 B0 . example: BVPARM W+6 S-2 2.309 0.370 . identical keyword: BVPARM, BVPAR, BVPARAM [return to keywords list]> CELL:. type: INPUT keyword . arguments: 6 reals or 1 characters string . meaning: - reals: unit cell parameters in A (a, b, c) and angles in deg. (alfa, beta, gamma) - characters string: file name containing unit cell parameters. Following files can be read: . CIF file . INS/RES file for SHELXL . PCR file for FullProf . P4P file created by SAINT . M50 file created by JANA . X file created by DENZO . RMAT file created by DIRAX . SUM file created by CRYSALIS . SCA file created by SCALEPACK . _CN file created by CELL_NOW . _Ls file created by SAINT . output: unit cell volume calculation direct and reciprocal unit cell parameters . example: CELL 7.6520 7.8450 11.0760 90. 90. 90. CELL import.CIF CELL my_saint_data.P4P CELL my_jana_data.m50 . identical keywords CELL, CELL_PARAMETERS, READ_CELL [return to keywords list]> CELL_ESD:. type: INPUT keyword . arguments: 6 reals max. . meaning: ESD for unit cell parameters in A (a, b, c) and angle in deg. (alfa, beta, gamma) . if only 1 real is input, metric is supposed to be cubic . if only 2 reals are input, metric is supposed to be tetragonal . if only 3 reals are input, metric is supposed to be orthorhombic . output: calculation of ESD for unit cell volume . example: CELL_ESD 0.0011 0.0013 0.0037 0.004 0.004 0.003 . identical keywords CELL_ESD, ESD_CELL, CELLSD [return to keywords list]> CHEM:. type: INPUT keyword . arguments: n "El_i_n_i" characters strings (without blank character between label and number) . optional argument: Friedif . 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. IF FRIEDIF optional argument is given, a Friedif value calculation is done, according to the spreadsheet by Flack and Shmueli (Acta Cryst. A 2007, 63, 257-265) . 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]> CIF_EXTRACT:. type: OUTPUT keyword . arguments: DIST A B ANG A B C TORS A B C D ACQ ADP ATOMS CELL CHEM CRYSTAL DATARED SG . meaning: Extract interatomic distances, angles and torsion angles from a CIF file If arg=ACQ: extract data collection features from a CIF file If arg=ADP: extract Atomic Displacement Parameters from a CIF file If arg=ATOMS: extract atoms and corresponding coordinates from a CIF file If arg=CELL: extract cell parameters from a CIF file If arg=CHEM: extract chemical formule from a CIF file If arg=CRYSTAL: extract crystal features from a CIF file If arg=DATARED: extract data reduction features from a CIF file If arg=SG: extract space group from a CIF file . output: If arg=DIST, ANG, TORS : ouput min and max values of requested parameters and calculation of the mean value. . mandatory keyword: READ_CIF . examples: CIF_EXTRACT DIST Pd Br CIF_EXTRACT DIST C1 C2 CIF_EXTRACT ANG Br Pd Br . identical keywords: CIF_EXTRACT, EXTRACT_CIF, EXTRACT_FROM_CIF [return to keywords list]> CONN:. type: INPUT keyword . argument: atom_label + dist_max . optional arguments: ALL, ALL_X, NO_X, ONLY_X, ONLY_Xn, LIGAND=, ANG, BVS, VOL, SHAPE, SELF, MIN=, MAX=, CONDENSED, No_BD . meaning: . Determine the connectivity around the atom "atom_label" with interatomic distances calculated between MIN and MAX values. . Calculate the polyedron distorsion as: distorsion = SUM((dist-dist_av)/dist_av)**2) / n with n: number of ligands dist_av: average distance . Default values for MIN and MAX = 0.4 and 3.0 A. . if "ALL" is present, the program will calculate connectivity around all atoms. . if "ALL_X" is present, the program will calculate connectivity around all atoms of the species X. . if "ONLY_X" is present, the program will calculate connectivity between all atoms of the species X. . if "ONLY_Xn" is present, the program will calculate connectivity around Xn atom. . if "LIGAND=L" (or LIGAND_L, or L=L or, L_L) is present, the program will ouput connectivity with ligand L. . if "NO_X" is present, the program will exclude connectivity with all atoms of the species X. . if "ANG" is present, interatomic angles will also be calculated. If tetrahedral environment is found around a metal atom, tau4 index is calculated, following the formula introduced by L. Yang (Dalton Trans, 2007, 955-964): tau4 = (360 - (alfa+beta)/141 where alfa and beta are two largest angles at the four-coordinated metal atom. In the case of five-ccordinate system, tau5 trigonality index is calculated, following the formula tau4 = (alfa-beta)/60. where alfa and beta are two largest angles at the five-coordinate metal atom (Dalton Trans, 2007, 955-964) . if "BVS" is present, bond valence sums calculations are performed. Tolerance factor can be specified through the BVS_TOL keyword. . if "VOL" is present, polyedron volume is calculated (ref. : VOLCAL program of L. W. FINGER included in CFML). . 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/AUTO" is present, output distances between atoms from the same label . if "CONDENSED" is present, short output is created . if "BD" is present, bonds distribution is ouput. ex: CONN Yb1 SELF MAX=10. ex: CONN Si1 MIN=1.5 MAX=2.7 ex: CONN Nd1 VOL SHAPE ex: CONN Re1 L=Br1 ex: CONN ONLY_C ! output C-C distances ex: CONN ALL_C L_C ! output C-C distances ex: CONN ALL_C L_S ! output C-S distances ex: CONN ALL_Nd ex: CONN ALL ANG CONDENSED ex: CONN Cu1 no_H ex: CONN Cu1 MAX=3.1 BVS_30 . output: interatomic distances, bond distribution and optional BVS 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"(characters 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 . optional argument: OUT . meaning: create .ACE file for CaRIne from a CIF file if "OUT" argument is given, CaRIne lines are written on screen if "FILE=xxx" argument is given, xxx is the name of the CaRIne output file . mandatory keyword: READ_CIF file.cif [return to keywords list]> CREATE_CEL. type: OUTPUT keyword . optional argument: OUT . meaning: create .CEL file for PowderCELL from a CIF file if "OUT" argument is given, PowderCELL lines are written on screen. if "FILE=xxx" argument is given, xxx is the name of the PowderCELL output file. . mandatory keyword: READ_CIF file.cif, READ_INS file.ins [return to keywords list]> CREATE_CFL. type: OUTPUT keyword . optional argument: OUT . meaning: create .CFL file for CRYSCALC from a CIF file if "OUT" argument is given, CFL lines are written on screen. if "FILE=xxx" argument is given, xxx is the name of the CFL output 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: d:\> cryscalc file.cif [return to keywords list]> CREATE_CIF. type: OUTPUT keyword . optional argument: output CIF file name if "FILE=xxx" argument is given, xxx is the name of the CIF output file. if "VIEW/RUN" argument is given, the CIF file is opened automatically by the associated CIF viewer (defined in [EXTERNAL APPLICATIONS] section in the cryscalc.ini file through the "CIFVIEWER" item. . meaning: create .CIF file from a .PCR, .INS/.RES or .CEL file. or structural data input from keywords. . mandatory keyword: READ_pcr file.pcr READ_ins file.ins READ_CEL file.cel [return to keywords list]> CREATE_FST. type: OUTPUT keyword . argument: POLY, RUN/VIEW, MOLE, No_H, OUT, FILE=xxx . meaning: create .FST file for FP Studio if argument="POLY" : include polyedra if connectivity calculation have been performed if argument="RUN/VIEW" : 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. if argument="OUT": output FP_Studio lines on screen. if "FILE=xxx" argument is given, xxx is the name of the FPStudio output file. . 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 command line: d:\> cryscalc file.cif [return to keywords list]> CREATE_FHZ. type: OUTPUT keyword . meaning: calculation of internal coordinates of a molecule from fractionnal coordinates: . cartesian coordinates . spherical coordinates . Z-matrix coordinates This routine has been extracted from mol_tpcr program of the FullProf Suite. Obviously, all the input atoms are considered to belong to a single molecule. . optional argument: PCR/FP: PCR input files are created for Simulated Annealing FullProf. [return to keywords list]> CREATE_INS. type: OUTPUT keyword . optional argument: no_H, PURGE/CLEAN, ISO, ANIS/ANISO, OUT, FILE=xxx . meaning: create .INS file for SHELXL . if "no_H" is present, the .INS file will not contain Hydrogen atoms. . if "PURGE/CLEAN" is present, the .INS file will exclude spurious atoms with Ueq < 0. or Ueq > U_threshold (defined in setting file in the [CREATE_INS] section). . if "ISO" is present, Ueq are written in the atoms list, even if anisotropic ADP have been input. . if "ANIS/ANISO" is present, ANIS keyword is added in the .INS created file. . if "SIMU" is present, EADP keywords will be replaced by "SIMU 0.003" keyword in the .INS created file. . if "OUT" is present, INS lines are written on screen. . if "FILE=xxx" argument is given, xxx corresponds to the name of the INS output file. . if "VIEW/RUN" argument is given, the INS file is opened automatically by the associated INS viewer (defined in [EXTERNAL APPLICATIONS] section in the cryscalc.ini file through the "INSVIEWER" item. . mandatory keyword: READ_CIF file.cif . example: CREATE_INS PURGE no_H . 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 command line: d:\> cryscalc file.cif [return to keywords list]> CREATE_PCR. type: OUTPUT keyword . optional argument: ISO/FORCE_ISO, MP, OUT, FILE= . meaning: create .PCR file for FullProf (pattern simulation) . if "ISO" or "FORCE_ISO" is present, the isotropic Uiso parameters will be written in the .PCR file, even if ADP parameters have been input as anisotropic values. . if "MP" is present, multi-pattern format is used when PCR file is created. . if "REF" is present, the create PCR file is for a diffraction pattern refinement. . if "MP_REF/REF_MP" is present, the create PCR file is for a diffraction pattern refinement (multi-pattern format). . if "No_H" is present, only non Hydrogen atoms are written in the .PCR file. . if "OUT" is present, PCR lines are written on screen. if "FILE=xxx" argument is given, xxx is the name of the FullProf output file. . mandatory keyword: READ_CIF file.cif, READ_INS file.ins . example: CREATE_PCR ISO . dependent parameter: CREATE_PCR parameter value in the CRYSCALC.INI setting file. If equal to 1, a .PCR file will be automatically created if a .CIF or .INS file is given as argument when CRYSCALC is launching from command line: d:\> cryscalc file.cif [return to keywords list]> CREATE_PDB :. type: OUTPUT keyword . optional argument: OUT, FILE=xxx . meaning: create .PDB file containing atoms list with cartesian coordinates in PDB format, following documentation from http://www.wwpdb.org/documentation/file-format-content/format33 The following Cartesian frame is used: x // a; z is in the ac-plane; y is x ^ z = b* if "OUT" argument is given, PDB lines are written on screen. if "FILE=xxx" argument is given, xxx is the name of the PDB output file. . mandatory keyword: READ_CIF file.cif, READ_INS file.ins . dependent parameter: CREATE_PDB parameter value in the CRYSCALC.INI setting file. If equal to 1, a .PDB file will be automatically created if a .CIF or .INS file is given as argument when CRYSCALC is launching from command line : > cryscalc file.cif . identical keywords: CREATE_PDB, WRITE_PDB [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 "TXT" 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: if no argument is given, input files for SIR97, SHELXS/T and SUPERFLIP/EDMA structure solving softwares are created. . optional arguments: SIR, SXT, SPF to specify the files to be created. SPF_PROT: add protein options for Superflip SPF_JANA: add creation of JANA .m81 output file for Superflip. . dependent parameter: CELL parameters, cell content, space group and hkl file has to be provided . examples: SOLVE SPF_PROT JANA . identical keywords: CREATE_SOLVE, CREATE_TO_SOLVE, CREATE_FILES_TO_SOLVE, SOLVE [return to keywords list]> CREATE_TIDY:. type: OUTPUT keyword . optional argument: OUT, FILE=xxx if "OUT" argument is given, PDB lines are written on screen. if "FILE=xxx" argument is given, xxx is the name of the TIDY output file. . 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 if "OUT" argument is given, TIDY lines are written on screen . 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]> CREATE_XYZ :. type: OUTPUT keyword . optional argument: OUT, FILE=xxx . meaning: create .XYZ file containing atoms list with cartesian coordinates. The following Cartesian frame is used: x // a; z is in the ac-plane; y is x ^ z = b* if "OUT" is given as argument, XYZ lines are written on screen. if "FILE=xxx" argument is given, xxx is the name of the XYZ output file. if "VIEW/RUN" argument is given, the XYZ file is opened automatically by the associated XYZ viewer (defined in [EXTERNAL APPLICATIONS] section in the cryscalc.ini file through the "XYZVIEWER" item. . mandatory keyword: READ_CIF file.cif, READ_INS file.ins . dependent parameter: CREATE_XYZ parameter value in the CRYSCALC.INI setting file. If equal to 1, a .XYZ file will be automatically created if a .CIF or .INS file is given as argument when CRYSCALC is launching from command line: > cryscalc file.cif . identical keywords: CREATE_XYZ, WRITE_XYZ [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 . optional keyword: WAVE . identical keywords: D_HKL, DHKL . example: DHKL 0.77 [return to keywords list]> D_HKL_MAX:. type: CALCULATION keyword . argument: one optional integer value, corresponding to the number of listed reflexions . meaning: output the features for the highest values of d_hkl Cell parameters and space group has to be known . outputs: h,k,l, m, Q(A-1), SinTheta/lambda(A-1), d(A) . optional keywords: CELL, SPACE_GROUP . identical keywords: D_HKL_MAX, DMAX, DHKL_HIGH, DHIGH . example: DMAX 4 [return to keywords list]> D_STAR:. type: CALCULATION keyword . argument: real values . meaning: 1/d_hkl (A-1) . outputs: d(A) theta(deg) . optional keyword: WAVE . identical keywords: D_STAR, D_STAR_HKL, DSTAR, DSTARHKL, DSTAR_HKL, D_REC, D_REC_HKL, DREC, DRECHKL, DREC_HKL . example: D_STAR 0.5 [return to keywords list]> DATA_ATOMIC_DENSITY:. type: OUTPUT keyword . optional 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 . optional 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 . optional 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 . optional argument: PLOT . optional argument: Sm_nat, SM_149, Eu_nat, Eu_151, Gd_nat, Gd_155, Gd_157, Dy_164, Er_nat, Er_167, Yb_nat, Yb_168, Yb_174 and Lu_176 . 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.3-3, 1992, 26-37 excepted scattering lengths of particular rare earths given as argument: Atom. data and nuc. data tables 44, 191-207 (1990) J.E. Lynn and P.A. Seeger, L.A.N.L. if arg=PLOT: create a PGF file and plot it with WinPLOTR if arg=PLOT_ALL: create a PGF file containing Re, Im, parts and modulus of scattering length (available only for input rare earth). PGF file is then plotted with WinPLOTR . see: Xrays_DATA . example: DATA_NEUTRONS Gd_157 PLOT_all . identical keywords: DATA_NEUTRONS, NEUTRONS_DATA, DATA_NEUTRON, NEUTRON_DATA [return to keywords list]> DATA_XRAYS:. type: OUTPUT keyword . optional argument: PLOT . meaning: list X-ray data for all atoms (total interaction cross section for Ag, Mo, Cu, Co, Fe and Cr radiations) 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]> DIFF:. type: CALCULATION keyword . arguments: 2 characters strings . meaning: calculation of the components of the difference vector between atoms labelled by their atom labels (cf ATOM keyword) diff. vector = coordinates atom_2 - coordinates atom_1 . 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. If the symmetry operator is unknown, "_*" option allows to generate all equivalent positions from the current space group operators. Corresponding difference vectors are output. . example: DIFF C8 C10 DIFF C10 C9 DIFF C10 C9_$1 DIFF C10 C9_* . identical keywords: DIFF, DIFFERENCE, DIFF_CALC, DIFFERENCE_CALCULATION [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 characters 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. If the symmetry operator is unknown, "_*" option allows to generate all equivalent positions from the current space group operators and distances smaller than d_max are output. . example: DIST C8 C10 DIST C10 C9 DIST C10 C9_$1 DIST C10 C9_* . identical keywords: DIST, DISTANCE, ATOMIC_DISTANCE [return to keywords list]> DIST_DHA:. type: CALCULATION keyword . arguments: 2 characters strings (D A) . optional 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_AD - 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]> DIST_MULT:. type: CALCULATION keyword . arguments: 2 characters strings (A B) + 1 real (x) . 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 [return to keywords list]> DIST_NEW:. type: CALCULATION keyword . arguments: 2 characters strings (A B) + 1 real (x) . 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 = x . example: DIST_NEW C8 O10 0.95 [return to keywords list]> DIST_PLUS:. type: CALCULATION keyword . arguments: 2 characters strings (A B) + 1 real (x) . 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_+ [return to keywords list]> EDIT:. type: output keyword . argument: 1 characters string (filename) . meaning: open the file given as argument with the editor defined 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 . meaning: search for equivalent reflections (Space group is mandatory) . 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]> EULER_TO_KAPPA:. type: calculation keyword . argument: 3 real values, corresponding to phi, omega and chi values (in degrees) . meaning: convert motors angles values of single crystal diffractometer from Eulerien to Kappa geometry, given Phi, Omega and Chi values. . identical keywords: EULER, EULER_TO_KAPPA [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]> FCF_FILE:. type: INPUT keyword . argument : 1 characters string . meaning: read .FCF file name, created by SHELXL and containing a list of h, k, l, F2_calc, F2_obs, sig_F2 . outputs: . calculation of R1 and wR2 agreement factors . list of strange reflections with (F2o - F2c)/sig < -100. . list of strange reflections with (F2o - F2c)/sig < -10 and theta < 3. . list of strange reflections with ABS(F2o - F2c)/sigW > 10. . list of strange reflections with F2o < -2sigW . optional arguments: PLOT : create a *_FCF.PGF file for WinPLOTR (F2c = f(F2o) curve) PLOT_STL : create a *_FCF_stl.PGF file for WinPLOTR (F2c - F2o = f(FSinTheta/lambda) curve OUT_n : output every n reflections HKL/CREATE_HKL : creation of .hkl file (free format) OMIT : list outliers reflections preceded by OMIT instruction for SHELXL refinement program . examples: FCF_FILE my_FCF_FILE.FCF FCF_FILE FCF.fcf out_n plot . identical keywords: FCF_FILE, FILE_FCF, READ_FCF [return to keywords list]> FILE:. type: INPUT keyword . arguments: 1 characters string . 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) . MUL format (created by SAINT for twinned crystals) . M91/M95 format (created by JANA) . SCA format (created by SCALEPACK) . 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 . if F2_max > 999999.99, all intensities are divided by 10 until F2_max is lower than this upper value. Sigmas are of course divided by the same coeffficient and a new *_sx.hk file is then created (Shelx format). . optional 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) if (sig_F2_ < 0.00001) sig_F2_=sqrt(abs(F2) EXCLUDE_NEG: reject all negative intensity reflections OUT_n : write every n reflections MAX_n : list the n most intensive reflections MAX_ALL: list all reflections in decreasing intensities order 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). SEMIFREE : semifree format for hkl data : fixed 3I4 format only h,k,l and free for F2 and sig_F2 FMT= : format of the hkl file (default format corresponds to the SHELX format (3I4, 2F8.2) EXTRACT_P4P/CREATE_P4P : create a P4P file containing cell parameters and esd's, orientation matrix, radiation source, symmetry and Bravais lattice. EXTRACT_EDIT_P4P/CREATE_EDIT_P4P/EXTRACT_P4P_EDIT/ CREATE_P4P_EDIT: create and edit a P4P file. MULT=xx: intensities and sigma are multipled by xx factor. . action: plot the F2=f(sinTheta/lambda) curve with WinPLOTR . examples: FILE my_HKL_FILE.HKL MAX_10 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 . optional 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 21 . . 2. 0k0 k=2n+1 . 21 . 3. 00l l=2n+1 . . 21 4. 0kl k=2n+1 b . . 5. 0kl l=2n+1 c . . 6. 0kl k+l=2n+1 n . . 7. h0l h=2n+1 . a . 8. h0l l=2n+1 . c . 9. h0l h+l=2n+1 . n . 10. hk0 h=2n+1 . . a 11. hk0 k=2n+1 . . b 12. hk0 h+k=2n+1 . . n 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 not all odd/even (F) 20. hkl h+k+l=2n+1 (I) 21. h00 h/=4n 41 . . 22. 0k0 k/=4n . 41 . 23. 00l l/=4n . . 41 24. 0kl k+l/=4n d . . 25. h0l h+l/=4n . d . 26. hk0 h+k/=4n . . d 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 and k=2n+1 32. hkl h=2n+1 and l=2n+1 33. hkl k=2n+1 and l=2n+1 34. hkl -h+k+l=3n (Robv) 35. hkl h-k+l=3n (Rrev) or a characters 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 . optional 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_HKL_LST [return to keywords list]> FRIEDEL:. type: CALCULATION keyword . optional argument: symmetry (characters 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: characters 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 unknown, a simulation of a Debye Scherrer film, with equal intensities of Bragg peaks, is created. Format is .PGF type with "DATA: X COMM" and "data_type=3" identifiers and can be plotted with the latest version of WinPLOTR software, downloaded from: https://cdifx.univ-rennes1.fr/progs/winplotr/winplotr.exe If this latest version of WinPLOTR has been installed, this Debye-Scherrer film (cryscalc_DSF.pgf file) is automatically plotted. If atoms are input, a structure factor calculation is done. In the case where scattering variable is 2theta, a list of I/Imax values is output. . optional arguments . "OUT": a list of generated reflections will be ouput . "OUT_n": sort the reflections list by decreasing F2calc and ouput the n more intensive ones. . "OUT_ALL": sort the reflections list by decreasing F2calc and ouput all of them. . "PM2K": hkl reflections list stored in the PM2K format . "PAT": In the case where scattering variable is 2theta, atoms are input and space group is known, 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. If "PAT_NOPLOT" is used instead of "PAT", WinPLOTR is not launched. If "PAT_PLOT" is used instead of "PAT", WinPLOTR will be launched, independently of the value of "plot_PRF" value in the setting file. If "PAT_PLOT_XY" is used instead of "PAT", WinPLOTR will be launched, independently of the value of "plot_XY" value in the setting file. If "PAT_NORMA_xxx", the simulated diffraction pattern is normalized to xxx value, i.e. maximum counting is set to xxx. If "_PDPF" string is added to "PAT" or "PAT_PLOT", a Powder Diffraction Pattern File (.pdpf) is created, containing hkl list, 2theta, d_hkl values and relative intensities. . "SIZE=XXX" : specify particles size (XXX in A) . "SIZE_Y=xxx" : specify particles size effects(xxx) (HL=size_Y/cosTheta) . "STRAIN=XXX" : specify strains (1.E-06 - 0.02 range) . "STRAIN_U=xxx": specify strains effects (HG**2=strain_U*tanTheta)**2 . 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 keywords = 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=150 . identical keywords: GEN_HKL, GENERATE_HKL, GENERATE_HKL_LIST [return to keywords list]> GET_TRANS_MAT:. type: calculation keyword . argument: no . meaning: determination of the transformation matrix between two primitive unit cells (matrix determinant is equal to 1). if CELL keyword has been previously input, the input parameters are corresponding to cell #1, and only cell #2 parameters will be asked to input. If no transformation matrix is founded, the user is invited to enter its own tolerance value (default value = 0.3). This tolerance factor is defined as follows: tol = ABS(p1_t1 - p1_2) + ABS(p2_t1 - p2_2) + ABS(p3_t1 - p3_2) + ABS(p4_t1 - p4_2) + ABS(p5_t1 - p5_2) + ABS(p6_t1 - p6_2) where p1 ... p6 are parameters of transformed cell #1 and parameters for input cell #2. . Remark: range of indices for transformation matrix has been fixed to -2 to 2 (step=1, i.e. only integer matrix elements are allowed). . identical keywords: GET_TRANS_MAT, GET_TRANSF_MAT, GTM, GET_MAT, SEARCH_MAT, SEARCH_TRANSF_MAT [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) . identical keywords: HKL, HKL_CALC, CALC_HKL . example: HKL 1. 0. 1. . mandatory keyword: CELL [return to keywords list]> HKL_DIFF:. type: INPUT keyword . arguments: 2 characters strings . meaning: hkl_1 and hkl_2 files: .HKL (SHELX format) .INT (for FullProf; format is specified in the second line) . output: calculation of difference F2 for common hkl reflections create HKL_diff.hkl output file (SHELX format) containing h k l F2 and sig, with: F2 = F2_1 - F2_2 sig = sqrt(sig_1**2 + sig_2**2) . remark: This can be usefull to extract magnetic contribution from data collections in the magnetic and paramagnetic temperature ranges. . identical keywords: HKL_DIFF, DIFF_HKL . example: HKL_diff 2K.int 10K.int [return to keywords list]> HKL_MULT:. type: output keyword . arguments: no . meaning: provides multiplicity of input HKL reflexion . mandatory keyword: SPGR . identical keywords: MULT_HKL, MULT, HKL_MULT, MUL_HKL, MUL, HKL_MUL [return to keywords list]> HKL_NEG:. type: output keyword . arguments: no . meaning: search for negative intensity reflections in a HKL file . optional keywords: . arg = "OUT": requested reflections are output on the screen . arg = "WRITE": requested reflections are output in a HKL file . mandatory keyword: FILE . identical keywords: HKL_NEG, HKL_NEGATIVE, NEG_HKL, NEGATIVE_HKL . related keyword: HKL_POS [return to keywords list]> HKL_POS:. type: output keyword . arguments: no . meaning: search for positive intensity reflections in a HKL file . optional keywords: . arg = "OUT": requested reflections are output on the screen . arg = "WRITE": requested reflections 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]> HKLF5:. type: input keyword . arguments: 9 integers or reals values . meaning: transformation (3,3) matrix components . optional keywords: MULT=xx: intensities and sigma are multipled by xx factor. . output: apply the transformation matrix on hkl file and create hklf5 format data file. Overlapping reflections criteria can be defined in the setting file with "ref_overlap_criteria=" keyword in the [OPTIONS] section. Default value is 0.15 and allowed maximum value is 0.25. . mandatory keyword: FILE . identical keywords: HKLF5, CREATE_HKLF5 [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]> KAPPA_TO_EULER:. type: calculation keyword . argument: 3 real values, corresponding to phi, omega and kappa values (in degrees) . meaning: convert motors angles values of single crystal diffractometer from Kappa to Eulerien geometry, given Phi, Omega and Kappa values. . identical keywords: KAPPA, KAPPA_TO_EULER [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_HKL_MAX:. type: OUTPUT keyword . argument: 1 integer, corresponding to the number n of reflections to list. HKL file has to be read first. . meaning: output the n most intensive observed reflections . identical keywords: LIST_HKL_MAX, HKL_MAX, MAX, LIST_F2_MAX, F2_MAX . example: HKL_MAX 25 [return to keywords list]> LIST_HKL_FC_MAX:. type: OUTPUT keyword . optional argument: 1 integer, corresponding to the number n of reflections to output. A crystal structure has to be input first through READ_INS/READ_CIF/READ_PCR keywords. Default value for n = 10. . meaning: output the n most intensive calculated reflections . identical keywords: LIST_HKL_FC_MAX, HKL_FC_MAX, FC_MAX, FCMAX, MAX_FC, MAXFC . example: FC_MAX 10 [return to keywords list]> LIST_KEYS:. type: OUTPUT keyword . optional argument: characters 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 characters 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 CRYSCALC (direct and inverse matrices) and defined by the user in the CRYSCALC.INI setting file. . identical keywords: LST_MAT, LST_MATR, LST_MATRIX, LIST_MAT, LIST_MATR, MAT_LST, MAT_LIST, MATR_LST, MATR_LIST, LIST_MATRIX, LIST_TRANSFORMATION_MATRIX [return to keywords list]> LIST_MAT_USER:. type: OUPUT keyword . arguments: no . meaning: list of transformation matrices defined by the user in the CRYSCALC.INI setting file. . identical keywords: LST_MAT_USER, LST_MATR_USER, LST_MATRIX_USER, LIST_MAT_USER, LIST_MATR_USER, MAT_LST_USER, MAT_LIST_USER, MATR_LST_USER, MATR_LIST_USER, LIST_MATRIX_USER, LIST_TRANSFORMATION_MATRIX_USER [return to keywords list]> LIST_SG:. type: OUPUT keyword . arguments: characters 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: m-3 n=7: -3 (hex. axes) n=14: m-3m . "mult/multi/multiplicity": output the general multiciplicity of the space group . meaning: list space groups with corresponding IT number, Laue group and point group. if POLAR is given as argument: list only the non-centrosymmetric space groups containing mirror planes. if CHIRAL is given as argument: list only the 65 chiral space groups (Sohncke groups), i.e. containing only rotation or screw axes (no inversion center, no mirror plane, no glide plane) if ENANTIO is given as argument: list only the 11 pairs of enantiomorphic space groups (screw axes of opposite handedness) . 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 LST_SG chiral . identical keywords: LIST_SG, LST_SG, LIST_SPACE_GROUPS [return to keywords list]> MAG:. type: OUTPUT keyword . arguments : characters 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 Mn3+ . mag TB [return to keywords list]> MAN:. type: OUTPUT keyword . optional arguments: characters 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 characters string: all the keywords containing the characters 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 . optional 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]> MATRIX:. 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 characters strings among a, -a, b, -b, c, -c and combinations. . meaning: setting of the unit cell . examples: MATR -c b a MATR -a-c -b c or . arguments: 2 characters strings: P, A, B, C, I, F, R_rev, R_obv Following transformations are allowed: MAT P R (MAT #9, for rhomboedral to hexagonal transformation) MAT R P (MAT #10, for hexagonal to rhomboedral transformation) MAT R_rev R_obv (MAT #11, for observe/reverse transformation in hexagonal type R setting) MAT R_obv R_rev (MAT #12, for reverse/observe transformation in hexagonal type R setting) MAT P A (MAT #13) MAT A P (MAT #14) MAT P B (MAT #15) MAT B P (MAT #16) MAT P C (MAT #17) MAT C P (MAT #19) MAT P F (MAT #19, for rhomboedral to cubic F transformation) MAT F P (MAT #20, for cubic F to rhomboedral transformation) MAT P I (MAT #21, for rhomboedral to cubic I transformation) MAT I P (MAT #22, for cubic I to rhomboedral transformation) MAT F R (MAT #36, for cubic F to hexagonal R transformation) MAT R F (MAT #37, for hexagonal R to cubic F transformation) MAT C I (MAT #38, for mono/ortho C to mono/ortho I transformation) MAT I C (MAT #39, for mono/ortho I to mono/ortho C transformation) . meaning: Bravais lattices of the original and final cells. The transformation matrices are related to matrices from #9 to #22 and #36 and #37 in the matrix list . example: MATR C P MATR R_obv R_rev . optional argument: UPDATE/NO_UPDATE: update or not cell parameters and atomic coordinates after transformation (independently of the "update_parameters" value in the setting file) . output: . calculation of new cell parameters (dependent keyword = CELL), new atomic coordinates (dependent keyword = ATOM) if matrix determinant is equal to 1., and new hkl Miller indices (dependent keyword = HKL) . create a new file containing the new hkl indices (dependent keyword = FILE) . identical keywords: MAT, MATR, MATRIX, TRANS, TRANSF [return to keywords list]> MENDEL:. type: OUTPUT keyword . arguments: characters 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) . optional 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 . optional argument: symmetry (characters 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 . 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_OUT . optional keyword: CELL . identical keywords: MONOCLINIC, MONOC, MONOCL [return to keywords list]> NEWS:. type: OUTPUT keyword . outputs: list the last new possibilities implemented in CRYSCALC . optional argument: specified year or LAST to get CRYSCALC news from a specific year of the latest month. . 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]> 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 initial cell parameters, independently to the update_parameters value in the setting file. 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]> PLANE:. type: OUTPUT keyword . arguments : 3 atom labels mininum (max.=20) . meaning: calculate the equation of the mean plane (Ax+By+Cz+D=0) containing input atoms. . outputs: output the four components A, B, C and D of the plane equation. . identical keywords: PLANE, PLAN [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 . optional 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_ACE. type: input keyword . argument: 1 characters string corresponding to a ACE file name . meaning: read a ACE format file (CarINE format) to extract structural features as: space group, cell parameters and atomic positions. . identical keywords: READ_ACE, READ_ACE_FILE, READ_CARINE, FILE_ACE, OPEN_ACE, ACE . example: READ_ACE my_file.ace [return to keywords list]> READ_CEL. type: input keyword . argument: 1 characters 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, FILE_CEL, OPEN_CEL, CEL . example: READ_CEL my_file.cel [return to keywords list]> READ_CIF. type: input keyword . argument: 1 characters string corresponding to a CIF file name If not extension is given, .cif is assumed. . meaning: read a CIF format file to extract structural features: as: space group and/or symmetry operators, cell parameters, atomic positions, wavelength ... . identical keywords: READ_CIF, READ_CIF_FILE, CIF_FILE, FILE_CIF, OPEN_CIF, CIF . examples: READ_CIF my_file.cif READ_CIF my_cif_file [return to keywords list]> READ_EXP. type: input keyword . argument: 1 characters string corresponding to a .EXP file name, created by APEX3/APEX4 software and containing data collection strategy. . meaning: read a EXT format file to extract experimental scans features. . example : READ_EXP my_Mo_EXP.EXP . identical keywords: READ_EXP, FILE_EXP, OPEN_EXP [return to keywords list]> READ_FACES. type: input keyword . optional argument: 1 characters 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_HKLF5. type: input keyword . argument: 1 characters string corresponding to a HKLF5 file name . optional argument: "OUT", "ANA", "NOR", "ONLY_1" . meaning: read a HKLF5 format data file containing structure factors of a twinned crystal. Ouput statistics for all reflections as well as overlapping and non-overlapping reflections for each twin component. If "OUT" is given as argument, the list of clusters of reflections (> 2 components) will be output. If "ANA" is given as argument, an analysis of redondant reflections is performed. If "NOR" is given as argument, a file containing only non-overlapping reflections is created. If "ONLY_1" is given as argument, a file containing only reflections of domain #1 (non-overlapping and overlapping reflections) is created. . identical keywords: READ_HKLF5, FILE_HKLF5, OPEN_HKLF5 . example: READ_HKLF5 twin5.hkl [return to keywords list]> READ_INS. type: input keyword . argument: 1 character string corresponding to a INS/RES file name (SHELX) If any extension is given, ".ins" will be assumed. . optional arguments: WGHT, HFIX, No_H . meaning: read a .INS/.RES SHELX format file to extract structural features as: space group and/or symmetry operators, cell parameters, atomic positions, ... If input file is a .RES file and second argument is WGHT the refined weighting scheme is updated in the corresponding .INS file. If optional argument "HFIX" is specified, HFIX instructions are listed after the "PLAN" line. This can be useful after automatic introduction of Hydrogene atoms with the following PLATON command: platon -f job.ins "No_H/remove_H" argument for READ_INS keyword: remove Hydrogen atoms from the .INS file . identical keywords: READ_INS, READ_INS_FILE, INS_FILE, FILE_INS, OPEN_INS, INS READ_RES, READ_RES_FILE, RES_FILE, FILE_RES, OPEN_RES, RES . examples: READ_INS my_file.ins READ_INS my_ins_file [return to keywords list]> READ_LST. type: input keyword . argument: 1 characters string corresponding to a LST file name If no extension is given, .lst is assumed. . optional arguments: . ADP: extract principal mean square atomic displacements U . AFIX: extract default effective X-H distances . ATOMS: extract final atomic coordinates and ADP's . CONN: extract connectivity table . DIST/BONDS: extract interatomic distances and angles . FLACK: extract Flack paramter (if calculated) . H: extract Idealized hydrogen atom generation . HKL/DATARED: extract rejected reflections, number of total reflections, Rint ... . HKL_STAT: extract reflection statistics . HTAB: extract Hydrogen bonds (if exist) and extract from .RES file instructions for potential hydrogen bonds . LS: extract least-squares features . MDR: extract Most Disagreeable Reflections with Error/esd > 5.0 . MDR_OMIT: extract Most Disagreeable Reflections with Error/esd > 5.0 and output hkl list, preceded by OMIT keyword (format compatible with .INS/.RES SHELXL input file) . MDR_crit/MDR_OMIT_crit: extract Most Disagreeable Reflections with Error/esd > MDR_crit Note that default criteria value for MDR keyword is equal to 5. but can be specified through the MDR_crit/MDR_OMIT_crit options. . MPLA: extract least-squares planes . RHO: extract difference Fourier peaks . SPLIT: extract atoms to split and create part of .INS SHELXL input file containning coordinates splitted atoms and corresponding EADP constraints. . SPLIT_EDIT: same behavior as SPLIT option but edit the .INS created file if an editor has been specified in the cryscalc.ini setting file . TORSION: extract torsion angles . UNIT: extract unit-cell contents from UNIT instruction and atom list and write SFAC/UNIT lines to include in .INS SHELXL input file. . VAR: extract analyse of variance for reflections used in refinement . meaning: read a LST output file from SHELX to extract hkl, structural and refinement features . identical keywords: READ_LST, READ_LST_FILE, LST_FILE, FILE_LST, OPEN_LST, LST . examples: READ_LST my_file.lst READ_LST my_lst_file MDR_8 READ_LST my_lst_file MDR_OMIT_10 [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 defined in the 'cryscalc.ini' setting file. If not, ouputs the HTML file on screen (without tags). . identical keywords: READ_NREPORT, READ_report%HTML, READ_NREPORT_HTML [return to keywords list]> READ_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 refine the cell parameters and related theta_min and theta_max. . identical keywords: READ_P4P, READ_P4P_FILE, P4P_FILE, FILE_P4P, OPEN_P4P, P4P [return to keywords list]> READ_PCR. type: input keyword . argument: 1 characters string corresponding to a PCR file name If not extension is given, .pcr is assumed. . 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, FILe_PCR, OPEN_PCR, PCR . examples: READ_PCR my_file.pcr READ_PCR my_pcr_file [return to keywords list]> READ_PDB. type: input keyword . argument: 1 characters string corresponding to a PDB file name from the Protein Data Bank. If not extension is given, .pdb is assumed. . meaning: read a PDB format file to extract structural features as: space group, cell parameters, atomic positions . identical keywords: READ_PDB, READ_PDB_FILE, PDB_FILE, FILE_PDB, OPEN_PDB, PDB . examples: READ_PDB my_file.pdb READ_PDB my_pdb_file [return to keywords list]> READ_SEQ:. type: OUTPUT keyword . optional arguments : SEQ file name . meaning: read the .SEQ file (created by FULLPROF in sequentail mode) create a xx_tables.seq file in a multicolumns format. Default separator is the "TAB" character but it can be specified in the[OPTIONS] section of the CRYSCAL.ini setting file through "separator=" keyword : separator can be "tab", "space" or "comma" . identical keywords: READ_SEQ, SEQ, READ_SEQ_FILE, FILE_SEA, OPEN_SEQ, SEQ [return to keywords list]> READ_SPF. type: input keyword . argument: 1 characters string corresponding to SUPERFLIP/EDMA input file name. . meaning: read SUPERFLIP/EDMA input file to extract cell parameters, . wavelength, symmetry operators list, centering vetors and deduce space group. . identical keywords: READ_SPF, READ_SUPERFLIP, READ_EDMA, FILE_EDMA . example: READ_SPF my_file_SPF.in [return to keywords list]> READ_SFRM. type: input keyword . optional argument: 1 characters string corresponding to the .SFRM file name (diffraction frame from BAXS diffractometers) to be read. . meaning: read the header of a SFRM diffraction frame to extract experiment features (sample temperature, detector temperature, wavelength, target voltage and intensity, motors positions, rotation axis, ...) . identical keywords: READ_SFRM, READ_SFRM_HEADER, SFRM, OPEN_SFRM . example: READ_SFRM mo_test_01_0001.sfrm [return to keywords list]> READ_TIDY_OUT. type: input keyword . optional argument: 1 characters string corresponding to the TIDY output file to be read. Default name=stidy.out . meaning: read a output file created by TIDY and extract all structural features as: space group, cell parameters, atomic positions. . identical keywords: READ_TIDY_OUT, READ_TIDY_OUTPUT, READ_TIDY_OUTPUT_FILE . 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]> REDUCE:. type: CALCULATION keyword . argument: 1 character string, corresponding to the Bravais lattice: P, A, B, C, I, R, F (default = P) . meaning: calculation of conventional unit cell parameters and transformation matrix between input cell and conventional cell(s). The routine is based on Get_conventional_Unit_Cells program written by JRC using procedures implemented in CRYSFML. . mandatory keyword: CELL . identical keywords: REDUCE, REDUCE_CELL, REDUCED, REDUCED_CELL . example: REDUCE F [return to keywords list]> REF_ABS_CRYSALIS. type: OUTPUT keyword . argument: no . meaning: write in CIF format absorption correction procedure implemented in CRYSALIS software (Agilent Technologies) . optional argument: CIF/ACTA . identical keywords: REF_ABS_CRYSALIS [return to keywords list]> REF_APEX. type: OUTPUT keyword . argument: no . meaning: write APEXII diffractometer programs and device references . optional argument: CIF/ACTA . identical keywords: REF_APEX, REF_APEXII, WRITE_APEX, WRITE_APEXII, APEX, APEXII [return to keywords list]> REF_D8V_Cu. type: OUTPUT keyword . argument: no . meaning: write D8 Venture diffractometer programs and device references . optional argument: CIF/ACTA . identical keywords: REF_D8V_Cu, REF_D8_VENTURE_CU [return to keywords list]> REF_D8V_Mo. type: OUTPUT keyword . argument: no . meaning: write D8 Venture diffractometer programs and device references . optional argument: CIF/ACTA . identical keywords: REF_D8V_Mo, REF_D8_VENTURE_Mo [return to keywords list]> REF_EVAL. type: OUTPUT keyword . argument: no . meaning: write EVALCCD references . optional argument: CIF/ACTA . 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 . optional argument: CIF/ACTA . 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 references . optional argument: CIF/ACTA . identical keywords: REF_KCCD, KCCD [return to keywords list]> REF_SADABS. type: OUTPUT keyword . argument: no . meaning: write SADABS references . optional argument: CIF/ACTA . identical keywords: REF_SAD, SADABS [return to keywords list]> REF_SHELX. type: OUTPUT keyword . argument: no . meaning: write SHELXS/T and SHELXL references . optional argument: CIF/ACTA . identical keywords: REF_SHELX [return to keywords list]> REF_SIR. type: OUTPUT keyword . argument: no . meaning: write SIR team programs references . optional argument: no . identical keywords: REF_SIR [return to keywords list]> REF_SUPERFLIP. type: OUTPUT keyword . argument: no . meaning: write SUPERFLIP program reference . optional argument: no . identical keywords: REF_SPF, REF_SUPERFLIP [return to keywords list]> REF_SUPERNOVA. type: OUTPUT keyword . argument: no . meaning: write SUPERNOVA diffractometer programs and device references . optional argument: CIF/ACTA . identical keywords: REF_SUPERNOVA [return to keywords list]> REF_X2S. type: OUTPUT keyword . argument: no . meaning: write SMART X2S diffractometer programs and device references . optional argument: CIF/ACTA . 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 references . optional argument: CIF/ACTA . 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 . optional argument: symmetry (characters 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]> SAVE_SETTINGS:. type: OUTPUT keyword . arguments : no argument . outputs: create a cryscalc.ini setting file in the current folder . identical keywords: SAVE_SETTINGS, SAVE_SETTING [return to keywords list]> SEARCH_EXTI:. type: OUTPUT keyword . arguments: 1 optional characters string or 2 optional real arguments: n_sig, ratio_criteria . meaning: analyse hkl reflections list and search systematic extinctions if arg="ALL" : all reflections are considered. In the other case, . n_sig: only reflections with I/sig > n_sig will be analysed . ratio_criteria: if> SEARCH_MONO:/ < 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 . example: SEARCH_EXTI ALL [return to keywords list] . type: OUTPUT keyword . optional argument: criterias for searching monoclinic angle . meaning: determine monoclinic angle from hkl data integrated in a pseudo-orthorhombic unit cell by calculating internal R values for "P 2 1 1", "P 1 2 1" and "P 1 1 2" space groups (case of primitive Bravais lattice). For C centered Bravais orthorhombic lattices, "C 2 1 1" and "C 1 2 1" the following space groups are tested. Criterias correspond to the max. shift of the angles respect to 90. and minimum value of Rint respect to the other Rint values respectively. Default values of these criteria are 2.5 and 0.2 respectively. Criteria_1: if more than one angle shift towards 90. deg. is greater than this criteria value, monoclinic angle search will be stopped. Criteria_2: Rint for the right monoclinic angle has to be lower than criteria_2*Rint for the others. . mandatory keyword: FILE . identical keywords: SEARCH_MONO, SEARCH_MONOCLINIC, SEARCH_MONO_ANGLE, SEARCH_MONOCLINIC_ANGLE, GET_MONO, GET_MONOCLINIC, GET_MONO_ANGLE, GET_MONOCLINIC_ANGLE , SEARCH_MONO_AXIS, SEARCH_MONOCLINIC, AXIS, GET_MONO_AXIS, GET_MONOCLINIC_AXIS [return to keywords list]> SEARCH_P3P6:. type: OUTPUT keyword . optional argument: criteria for searching symmetry . meaning: calculation of internal R values for different trigonal and hexagonal Laue groups and ouput the most probable ones. Criteria corresponds to the ratio minimum value of Rint with respect to Rint values calculated in different Laue groups. Default value is 0.2. . mandatory keyword: FILE . identical keywords: SEARCH_P3P6, P3P6 [return to keywords list]> SEARCH_SPACE_GROUP:. type: calculation keyword . optional arguments: 2 real : n_sig and threshold 1 characters string, defining the crystal system: M/mono, O/ortho, T/tetra, R/trig, H/hexa, C/cub, GET, ALL, P, CENTERED/NOT_P, OMA/ONLY, CENTRIC, ACENTRIC . 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 P is input as argument, only primitive space groups will be output. If ALL is given as argument, all space groups (centered and primitive) will be output. If CENTERED/NOT_P is given as argument, only non primitive (centered ) space groups will be output. If GET is input as argument, the most probable space group will be considered. If "CENTRIC/ONLY_CENTRIC" argument is present, only centric space groups are listed. If "ACENTRIC/ONLY_ACENTRIC" argument is present, only acentric space groups are listed. In the monoclinic case, if "OMA/ONLY" is given as argument, only space groups with monoclinic angle compatible with unit cell parameters will be ouput. For example, if beta is the monoclinic angle, only "L 1 x 1" space groups will be considered. Monoclinic angle in unit cell parameters has to be far from 90. of "search_mono_criteria" value (default value=2.5, defined in the setting file ([OPTIONS] section) This OMA/ONLY option can also be defined through "search_SG_only_mono" field in the setting file ([OPTIONS] section) . mandatory keyword: FILE . examples: SEARCH_GROUP 3 0.05 SEARCH_GROUP mono SEARCH_GROUP centered . identical keywords: SEARCH_SPGR, SEARCH_SPACE_GROUP, SEARCH_GROUP, SEARCH_SG CHECK_SPGR, CHECK_SPACE_GROUP, CHECK_GROUP, CHECKGROUP [return to keywords list]> SEARCH_SYMM:. type: OUTPUT keyword . optional argument: 1 criteria for searching symmetry . meaning: calculation of internal R values for different symmetries and Laue groups and deduction of the most probable one. Criteria corresponds to the ratio minimum value of Rint with respect to Rint values calculated in different Laue groups. Default value is 0.5. If criteria > 1. : criteria = criteria / 100. If crystal system is known and corresponds to tetragonal, trigonal, hexagonal or cubic system, this crystal systel is taken into account, and calculation for all Laue group is not realized. If "ALL/FORCE_ALL" argument is present, calculation for all Laue groups are performed. If "T/TRICLINIC/FORCE_T/FORCE_TRICLINIC" argument is present, Rint for P -1 triclinic space group is also performed. . mandatory keyword: FILE . identical keywords: SEARCH_SYMM, SEARCH_LAUE [return to keywords list]> SEARCH_TETRA:. type: OUTPUT keyword . optional argument: 3 criterias for searching tetragonal axis . meaning: determine tetragonal axis from hkl data integrated in a pseudo-cubic unit cell by calculating internal R values in abc, cab and bca settings. Criterias correspond to the max. shift for cell parameters respect to mean cell parameter values and max. shift for the angles respect to 90. respectively and minimum value of Rint respect to the other Rint values. Default values for these criteria are: 0.5, 2.5 and 0.2. Criteria_1: if more than one cell parameter towards the mean cell parameter value greater than this criteria value, tetragonal axis search will be stopped. Criteria_2: if more than one angle shift towards 90. deg. is greater than this criteria value, tetragonal axis search will be stopped. Criteria_3: Rint for the right tetragonal axis has to be lower than criteria_2*Rint for the others. . example: SEARCH_TETRA 0.7 3. 0.25 . mandatory keyword: FILE . identical keywords: SEARCH_TETRA, SEARCH_TETRAGONAL, SEARCH_TETRA_AXIS, SEARCH_TETRAGONAL_AXIS . GET_TETRA, GET_TETRAGONAL, GET_TETRA_AXIS, GET_TETRAGONAL_AXIS [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]> SETTINGS:. type: OUTPUT keyword . arguments: no . meaning: output the different parameters defined in the CRYSCALC.INI setting file . identical keywords: SETTING, SETTINGS, SETUP [return to keywords list]> SFAC:. type: INPUT keyword . arguments: n characters 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 . optional argument: FRIEDEL, COEF . meaning: h,k,l, Miller indices . output: calculation of crystallographic structure factor for the hkl reflection (dependent keyword = CELL, WAVE, SPGR, ATOM) if "FRIEDEL" is specified, a crystal structure factor calculation is aalso performed for -H reflection if "SCAT" is specified, atomic scattering factor corefficients are output . 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 : characters string . meaning: space group (Hall Mauguin symbol, number in IT) . outputs: . general informations on the input space 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 operators (complete and reduced set), Wyckoff 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 extinctions rules for 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 the reducet set of symmetry operators and symmetry symbols. . mandatory keyword: SPGR . optional argument: ALL: list all symmetry operators (including inversion and lattice centring translations), Wyckoff positions and extinctions rules for current space group. . 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 the Translationengleische Subgroups for the current space group. . mandatory keyword: SPGR . identical keywords: SG_SUB, SG_SUBGROUP [return to keywords list]> SHANNON:. type: OUTPUT keyword . argument: characters 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 characters strings (one mandatory argument) + 2 reals . 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 (characters 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, INFO_SITE, ATOM_SITE, SITE_ATOM, LIST_SITE_INFO, GEN_EQUIV_ATOMS, WYCKOFF [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 characters 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 . of the current space group on propagation wave components . to determine the star of k. . outputs: list of k vectors and arms of the k star . 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 . optional keyword: WAVE . identical keywords: STL, STL_HKL, SINTHETA/WAVE, SINTHETA/LAMBDA . example: STL 0.70 [return to keywords list]> SUPERCELL:. type: input keyword . arguments : 3 reals + 1 optional characters string . meaning: components of a superstructure cell . outputs: if atoms are input, atomic coordinates in the superstructure cell are calculated. . mandatory keyword: CELL . identical keywords: SUPERCELL . optional arguments: "pcr": output list of atomic coordinates in a .PCR FullProf format. "ins": output list of atomic coordinates in a .INS SHELXL format. . example: SUPERCELL 2 2 2 pcr [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, SYMM_OP, SYM_OP, SYMMETRY_OPERATOR [return to keywords list]> SYST:. type: EXTERNAL keyword . arguments: 1 characters 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 characters 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 following 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 characters 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 following 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: characters strings . meaning: title of the job . example: Ammonium bitartrate . identical keywords: TITL, TITLE [return to keywords list]> TOLMAN_ANGLE. type: INPUT keyword . arguments: 5 characters strings, corresponding to metal, centered atom and 3 ligand atoms respectively . optional arguments: 3 optional arguments can be input to specify the van der Waals radii that will be used in the calculation. If not defined, default values are extracted from CRYSFML library, excepted for Hydrogen (r=1.2 A). . meaning: calculation of the Tolman cone angle, as defined in "Transition Met. Chem. 20, 533 (1995) . example: TOLMAN_ANGLE S1 P1 H1a HC2a H3a TOLMAN_ANGLE S1 P1 H1a HC2a H3a 1.25 1.25 1.25 . identical keywords: TOLMAN_CONE_ANGLE, TOLMAN_CONE TOLMAN_ANGLE, CONE_ANGLE, CONE, TOLMAN [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 coordinates become : t(1) + x.sign, t(2) + y.sign, t(3) + z.sign as in SHELXL with the MOVE keyword if sign > 0 : sign = 1 if sign < 0 : sign = -1 . mandatory keyword: ATOM . examples: TRANSLATION 0.5 0.5 0.5 MOVE 1. 1. 1.5 -1. . identical keywords: TRANSLATION, 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 values 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 setting . 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_TWINNING TWIN_HEXA, TWIN_HEXAGONAL, TWINNING_HEXA, TWINNING_HEXAGONAL [return to keywords list]> TWIN_PSEUDO_HEXA:. type: OUTPUT keyword . arguments : no argument . outputs: . list the transformation matrices for pseudo-hexagonal 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 or 1 character string . 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" or "P4P" or "ORT", the UB components are read in the following order: 11 12 13 21 22 23 31 32 33 If only 1 argument, it has to correspond to a CIF file name: UB matrix is then extracted from it. . output: cell parameters deduced from the UB matrix . identical keywords: UB_MAT, UB_MATRIX [return to keywords list]> UNIT:. type: INPUT keyword . arguments: n characters 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]> UPDATE:. meaning: download lastest version of CRYSCALC from the CRYSCALC web site: https://cdifx.univ-rennes1.fr/progs/cryscalc/cryscalc.exe If TMP is given as argument, a temporary uncompacted version of CRYSCALC will be downloaded from: https://cdifx.univ-rennes1.fr/progs/cryscalc/temp/cryscalc.exe If BETA is given as argument, a beta uncompacted version of CRYSCALC will be downloaded from: https://cdifx.univ-rennes1.fr/progs/cryscalc/beta/cryscalc.exe If ZIP is given as argument, a zipped file containing cryscalc.exe will be downloaded from: https://cdifx.univ-rennes1.fr/progs/cryscalc/cryscalc.zip . remark: browser has to be defined in the setting file [EXTERNAL APPLICATIONS] section. . examples: UPDATE . examples: UPDATE ZIP . identical keywords: UPDATE, DOWNLOAD [return to keywords list]> USER_MAT:. arguments: "#" + 1 integer . meaning: number of user matrix in the matrices list defined by the user in the cryscalc.ini setting file . example: USER_MAT #3 or . arguments: "$" characters string . meaning: this characters string has to be one of the comment text 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, MAT_USER, MAT_USER, MATRIX_USER [return to keywords list]> WATER. type: INPUT keyword . optional argument: EDIT . meaning: . read "hatoms.out" output file from CALC-OH (M. Nardelli, J. Appl. Cryst. 1999, 32, 563-571) and create "hatoms_out.INS" file in SHELXL format with: - coordinates of Hydrogen atoms with AFIX constraints - distances constraints between atoms of the water molecules . if EDIT is given as optional argument, hatoms_out.INS is automatically edited with the editor specified in the cryscalc.ini setting file. . identical keywords: WATER, WATER_H [return to keywords list]> WAVE:. type: INPUT keyword . arguments: 1 real or 1 characters string . meaning: . real value: wavelength value in A . characters 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, CRYSCALC or site name defined in the cryscalc.ini setting file in the [WEB] section . identical keywords: WEB, INTERNET [return to keywords list]> WRITE_ADP:. type: OUTPUT keyword . optional argument: DETAILS, NO_H . meaning: write anisotropic displacements parameters if DETAILS is given as argument, output details on ADP if NO_H is present, only non-hydrogen atoms are listed. . mandatory action : ADP have to be read previously in a .INS or .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 if arg="CART_A", Cartesian frame is follows: x // a; z is in the ac-plane; y is x ^ z = b* if arg="CART_C", Cartesian frame is follows: z // c; y is in the bc-plane; x is y ^ z = a* . 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 setting file . identical keywords: WRITE_DEVICE, OUTPUT_DEVICE, DEVICE, WRITE_DIFFRACTO, OUTPUT_DIFFRACTO, DIFFRACTO, WRITE_DIFFRACTOMETER, OUTPUT_DIFFRACTOMETER, DIFFRACTOMETER [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_SUPERCELL. type: OUTPUT keyword . argument: no . meaning: write superstructure cell . mandatory keyword : CELL, SUPERCELL . identical keywords: WRITE_SUPERCELL, OUTPUT_SUPERCELL [return to keywords list]> WRITE_SYM_OP:. type: OUTPUT keyword . optional arguments : SHELX, SHELX:A, ONE_LINE, CONDENSED . outputs: list of symmetry operators (SYMM keyword, followed by rotationaland translational parts, in alphanumeric form) if argument="SHELX": output reduced set of symmetry operators for the given space group in a SHELX format (NLAT, SYMM) if argument="SHELX:1": output all symmetry operators of the current space group ina SHELX format if argument="SPF" or "SUPERFLIP": output symmetry operators for the given space group in a SUPERFLIP format (x y z) if argument="SPF_X" or "SUPERFLIP_X": output symmetry operators for the given space group in a SUPERFLIP format (x1 x2 x3). if argument="ONE_LINE": all the symmetry operators are merged in a single line, separated by ";" character, for Symmetry Calculator [Cryscal] distributed within the FullProf Suite.) if argument="CONDENSED": symmetry operators are ouput in a condensed way. . mandatory keyword: SPGR or SYMM . identical keywords: WRITE_SYM_OP, WRITE_SYMM_OP, WRITE_SYMP, WRITE_SYMM, WRITE_SYMMETRY_OPERATORS, WRITE_SYMOP, LIST_SYM_OP, LIST_SYMM_OP, LST_SYM_OP, LST_SYMM_OP [return to keywords list]> WRITE_WAVE:. type: OUTPUT keyword . argument: no . meaning: write current wavelength features . 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 wavelength 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][top]List of CRYSCALC command line arguments :
> MAN :
Create 'cryscalc.txt' file user's guide (text format). Same bevahior can be obtained with the following arguments: MAN, /MAN, -MAN, --MAN, /M, -M, HELP, /HELP, -HELP, --HELP, /H , -H, /? ex : > cryscalc man > cryscalc /?> 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 browser 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 .P4P, .HKL and . ABS files can be specified in the command line ex : > cryscalc P4P=mycrystal.P4P HKL=mycrystal.HKL ABS=mycrystal.ABS 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 ex : > cryscalc report my_archive.cif> REPORT_TXT :
Create a .TXT report from 'archive.cif' file or from the .CIF file give as a second argument. ex : > cryscalc report_txt ex : > cryscalc report_txt my_archive.cif> ARCHIVE.CIF :
. Read 'archive.cif' CIF file . Complete this 'archive.cif' with additionnal CIF fields related to absorption correction, squeeze procedure, hydrogen treatment, diffractometer features, 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)> EXTRACT :
Combined with 'ARCHIVE.CIF' argument, this optional argument extracts .res and . hkl files embedded in the archive.cif file> EXTRACT_CIF :
Combined with a multiple global CIF file given as argument, this option allows to extract individual CIF files.> ADD_HKL :
Combined with 'ARCHIVE.CIF' and 'job.cif' arguments, this optional argument adds hkl data into archive_hkl.cif file. Syntax is as follows: d:\cifs>CRYSCALC ADD_HKL archive.cif job.cif where archive.cif is a final archive CIF file and job.cif the CIF file created by SHELXL and containing hkl data, starting with _shelx_hkl_file item and finishing with _shelx_hkl_checksum item.> CREATE_GLOBAL_CIF :
Global CIF file containing several structures can be created through CREATE_GLOBAL_CIF command line argument. The list of CIF structures files is specified in a buffer file. The name of this buffer file can be given through a second argument in the command line. If not, default buffer file is called 'CIF_files.buf'. A list of authors to be included can be specified in a special file named 'authors_list.txt'. The syntax is as follows : [AUTHOR] Name, first_name address address2 (optional) Note that : . input items can contain characters with accents . address has to be input in a single line. On the other hand, a second line will be interpreted as a second address. Carriage return can be applied using '\\' character. Example: [AUTHOR] ROISNEL, Thierry Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) - UMR6226 \\ F-35000 Rennes, France> CREATE_CIF_BUFFER :
Create CIF buffer file containing the list of CIF structures files to be used with the help of CREATE_GLOBAL_CIF argument. The name of this buffer file can be given through a second argument in the command line. If not, default buffer file is called 'CIF_files.buf'.> SOLVE_TO_INS/CREATE_INS :
. read STRUCT.CIF file and get cell parameters with esd's . read import.RES created by SIRxx or SHELXS/T . 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 results lines in the screen and in the 'cryscalc.log' file.[top]
What's new in CRYSCALC ?
CRYSCALC version: 25.04
Main new features implemented in CRYSCALC:
(for more details, see the CRYSCALC manual)
February 2025
# New HKL_mult keyword: provides multiplicity of a given hkl reflexion
# Routine to find equivalent reflections has been modified:
"Friedel" argument is now useless.
# Creation of archive.cif file: chemical formula is now in agreement
with new CHECKCIF requirement:
example : C9 H11 N1 O1 is replaced by C9 H11 N O
# Creation of archive.cif file: in the case of absolute structure
determination, the "_chemical_absolute_configuration" CIF field
is now fullfilled automatically :
. "ad" if Flack parameter is < 0.2 and esd < 0.1
. "rm/ad/rmad/syn/unk/." if Flack parameter is < 0.2 and esd > 0.1
. "unk" if Flack parameter is > 0.2
January 2025
# New "CREATE_FHZ" keyword allows to calculate internal coordinates
of a molecule given fractional coordinates :
. cartesian coordinates
. spherical coordinates
. Z-matrix coordinates
This routine has been extracted from mol_tpcr program of the FullProf Suite.
Obviously, all the input atoms are considered to belong to a single molecule.
PCR input files can be created for FullProf (simulated annealing).
December 2024
# In the case of Rint calculation Rint > Bad_Rint_Criteria, Rint calculations
are also perfomed considering new point groups:
". -3" instead of "-3m"
". m-3" instead of "m-3m"
". -31m" instead of "-3m1"
". -3m1" instead of "-31m"
". 4/m instead of "4/mmm"
". 6/m instead of "6/mmm"
# hkl file statistics now included Rmerge, Rmes and Rpim in different d_hkl
ranges.
November 2024
# "Read_Shx_Atom" routine in CRYSFML has been adapted to
read .INS/.RES files coming from PLATON and OLEX2.
# New argument for WRITE_SYM_OP keyword : SHELX:1 allows to
output ALL the symmetry operators in SHELX format and considering a
acentric lattice. This can be useful to discribe a structure in a
setting where the origin is not at the inversion center.
# "Read_Shx_Atom" routine in CRYSFML has been adapted to
read .INS/.RES files coming from Olex2.
October 2024
# CELL keyword : input _CN file created by CELL_NOW software
and ._LS file created by SAINT software can now be read
(only cell parameters are extracted).
# Creation of import.cif file: in the case of twinned data,
the twin law is now extracted from *_0m._ls created after
integration with SAINT, taking into account the presence
of two domains.
September 2024
# Search_group routine will output only space groups with point group
in agreement with point group present in the import.cif input file.
July 2024
# Highest resolution value if now output in the import.CIF created by CRYSCALC.
# Wavelength used for powder diffraction pattern simulation cen now be specified
through "X_pattern_wave=" and "N_pattern_wave=" keywords in the CRYSCALC.ini
setting file.
April 2024
# "DIST_new A1 A2 x" keyword routine to calculate the position of a
new atom at the distance x from the A1 atom in the A1-A2 direction
was wrong. This has been fixed.
# New "No_H/REMOVE_H" argument for READ_INS keyword: remove Hydrogen atoms
from the .INS file
# New "AFIX" argument for READ_INS keyword:
HFIX instructions are listed after the "PLAN" line. This can be useful after
automatic introduction of Hydrogene atoms with the following PLATON command:
platon -f job.ins
# Creation of structural report: when Hydrogen atoms are not in calculated positions,
the sentence concerning the treatment of Hydrogen atoms is created consequently.
# Creation of archive.cif file: in the case of Hydrogen bons list, the D-H...A angle
value is rounded if no standart deviation is given. This has been implemented to
avoid a G-type alert in the CHECKCIF procedure.
# New Hbond_limit keyword in the [ARCHIVE_AND_REPORT] section of the cryscalc.ini
setting file: Definition of a limit in A, beyond wich the Hbond distance is
excluded from the archive.CIF file.
March 2024
# New "DIST_new A1 A2 x" keyword allows to calculate atomic coordinates
of a new M atom with at a distance d_(A1-M) = x, in the A1-A2 direction.
# In the case of Rint calculation for centric space groups, listing of missing
reflections can be output if "Rint_missing_reflections = 1" is
specified in the [OPTIONS] section of the cryscalc.ini setting file.
February 2024
# Simulation of powder diffraction pattern: by default, background is described
by a constant value but also by a polynomial function (max. 8 deg.). Coefficient
of the polynom can be specified in the setting file in the [PATTERN SIMULATION].
section.
ex:X_pattern_background = 31.5 4.80 30.52 -200.18 212.64
# New READ_PDB keyword allows to read .PDB file from Protein Data Bank.
# When creating import.cif file, Friedif value is ouput, considering
wavelength and chemical formula present in .P4P file.
# Routine to read chemical formula from .P4P file
has been modified to be more robust and avoid crashes. As examples :
"C1_H2_O3_N4_Ni5_Au6_S7" will be interpreted as "C1 H1 O1 N1 Ni1 Au1 S1"
"C_H_O_N_Ni_Au_S" will be interpreted as "C1 H1 O1 N1 Ni1 Au1 S1"
"C1H2O3N4Ni5Au6S7" will be interpreted as "C1 H2 O3 N4 Ni5 Au6 S17"
"C H O N Ni Au S" will be interpreted as "C1 H1 O1 N1 Ni1 Au1 S1"
"CHONNiAuS" will be interpreted as "C1 H1 O1 N1 NI1 Au1 S1"
January 2024
# Creation of import.cif file: format of writing intensites and sigmas has been changed,
to be compatible with input .hkl file.
# "CREATE_CFL_file=2" in the [OPTIONS] section of the setting file will
create CRYSCALC.CFL in append mode.
# Some _CDFIX_ items are included in the import.CIF file created by CRYSCALC.
# Structural report creation: FRAME and CRYSTAL PICTURE .PNG / .JPG files
to be included in the report can be specified in the command line
through FRAME= and PICTURE= keywords respectively.
Example : CRYSCALC create_report FRAME=job_FRAME.PNG PICTURE=cristal.PNG
December 2023
# Structural report creation: ORTEP file to be included in the report can be
specified in the command line through ORTEP= keyword.
Example : CRYSCALC create_report ORTEP=molecule.PNG
# Routine to read chemical formula from .P4P file
has been modified to be more robust and avoid crashes. As examples :
"CHON" will be interpreted as "C1 H1 O1 N1"
"C H O N" will be interpreted as "C1 H1 O1 N1"
"C1H2O3N" will be interpreted as "C1 H2 O3 N1"
"C_H_O_N" will be interpreted as "C1 H1 O1 N1"
# Completness calculation was wrong for non-standard space groups settings.
This has been corrected.
# When creating archive.cif file with squeezed data, "[+ solvent]" string is added
in the "_chemical_formula_moiety" line.
October 2023
# CREATE_FST keyword: COLOR argument is now added in the ATOM list
# Correction of a output error in the TRANSF keyword routine. This bug
was present since the version of July 2023
September 2023
# If "checkCIF_PLATON page 2.htm" (created by online CHECKCIF procedure)
is present in the current folder, a "condensed CHECKCIF" is included in
the structural report, containing numbers of A-type, B-type, C-type
and G-type alerts.
# New arguments for EXTRACT_CIF/CIF_EXTRACT/EXTRACT_FROM_CIF keyword:
. arg=ACQ extracts data collection features from a CIF file, ie CIF comments
lines from "DATA COLLECTION" section present in the header of
import.CIF file created by CRYSCALC.
. arg=ADP extracts Atomic Displacement Parameters from a CIF file
. arg=ATOMS extracts atoms list from a CIF file
. arg=DATARED extracts data reduction features from a CIF file, ie CIF comments
lines from "DATA REDUCTION" section present in the header of import.CIF file
created by CRYSCALC.
. arg=CELL extracts cell parameters features from a CIF file, ie CIF comments
lines from "SPACE GROUP AND UNIT CELL INFORMATION" section present in the
header of import.CIF file created by CRYSCALC.
. arg=CHEM extracts chemical formula from a CIF file
. arg=CRYSTAL extracts crystal features from a CIF file, ie CIF comments
lines from "CRYSTAL INFORMATION" section present in the header of
import.CIF file created by CRYSCALC.
. arg=DEVICE extracts diffractometer features from a CIF file
. arg=SID extracts sample identifiers
. arg=SG extracts space group
# F000 calculation is now also performed for neutrons radiation
# New READ_EXP keyword: extract data collection features (number of scans,
motor positions, type of scan, exposition time ...
July 2023
# New report_txt_table_X argument, allowing to create tables
from CIF file. X value corresponds to the numor of table
in the general TXT report.
example: CRYSCALC report_txt_table_2 archive.cif will create
a archive_structural_report.txt file containing
table of crystal data and structural refinement features.
# Two new transformations matrices has been implemented in the
CRYSCALC matrices list:
. Mat #38: 0 0 -1 0 1 0 1 0 1, corresponding to C to I transformation.
. Mat #39: 1 0 1 0 1 0 -1 0 0, corresponding to I to C transformation.
# P4P files created are now compatible with APEX4
# CHEM keyword is now providing Friedif parameter value, if FRIEDIF
argument is given. Friedif parameter value is calculated according to the
spreadsheet by Flack and Shmueli (Acta Cryst. A 2007, 63, 257-265)
June 2023
# New routine to calculate atomic coordinates in a supercell.
April 2023
# Creation of import.cif file : Correction of a bug when reading
CELL_now output file with different domains and selected cell
from the possible cells list different than first one.
Feb. 2023
# New "CREATE_REPORT_SUMM" item in the [option] section of the
setting file allows to create a summary of structural_report
files from the command line after reading a .CIF file.
Example:
d:\progs> cryscalc xxx.CIF
This summary file can also be created by specifying REPORT_SUMM
as argument in a command line.
Example:
d:\progs> cryscalc report_SUMM
If "checkCIF_PLATON page 2.htm" (created by online CHECKCIF procedure)
is present in the current folder, the numbers of A-type, B-type, C-type
and G-type alerts are included in the summary file.
Dec. 2022
# FILE keyword : input SCA file created by DENZO/SCALEPACK software
can now be read (cell parameters and integrated intensities are
extracted)
# CELL keyword : input SCA file created by DENZO/SCALEPACK software
can now be read (only cell parameters are extracted).
Nov. 2022
# Compilation of CRYSCALC with the latest version of CRYSMFL, allowing
to deal with trigonal space groups in rhomboedral cell specified
by :R at the end of the space group symbol (ex: SPGR R -3 c:R)
# CREATE_INS SXT : when creating .INS input file for SHELXT,
the Laue group specified in the import.cif file is taken into
account.
Oct. 2022
# "CREATE_SOLVE SXT" keyword : the temperature written in the import.ins
file is now extracted from the import.cif file, independently of the
"temperature" value in the [CREATE_INS] section in the setting file.
# New SEQ=SEQ_file command line argument where SEQ_file is a .SEQ file
coming from FullProf sequential refinement : a xxx_tabl.seq file
in columns format is then created. Default columns separator is
tabulation, but can also be defined through "separator=tab/space.comma"
item in the [OPTIONS] section of the setting file.
Sept. 2022
# CONN keyword: in the case of five-coordinate system,
tau5 trigonality index is calculated, following the formula introduced
by L. Yang (Dalton Trans, 2007, 955-964):
tau5 = (alfa-beta)/60
Angles calculation for five-coordinate atom has to be performed.
# CONN keyword: in the case of tetraedral metal environment,
tau4 index is calculated, following the formula introduced
by L. Yang (Dalton Trans, 2007, 955-964):
tau4 = (360 - (alfa+beta))/141
Angles calculation for tetraedral atom site has to be performed.
July 2022
# Images file to be included in the structural reports cab be specified
by user by edditing "report.img" file in the current folder. The format
of "report.img" file is as follows:
CRYSTAL=my_job.png
FRAME=my_job_sfrm.png
STRUCTURE=my_job_ORTEP.png
# New PLOT_XY/PLOT_PRF options in the [PATTERN SIMULATION] section
of the cryscalc.ini file allows to plot (or not) PRF file (FullProf format)
or XY (2 columns) simulated diffraction pattern.
March 2022
# READ_FCF keyword output outliers reflections with F2o < -2sigW
January 2022
# New "ONLY_1" argument for READ_HKLF5 keyword: allows to create
a file containing only reflections of the domain #1 (single and
common reflections)
# New EXTRACT_CIF/CIF_EXTRACT/EXTRACT_FROM_CIF keyword: extracts
geometrical features (distances, angles and torsion angles) from
a CIF file and outputs min., max, and mean values for requested
parameters. Arguments are as follows:
. DIST A B
. ANG A B C
. TORS A B C D
November 2021
# Some changes in the import.CIF creation routine has been performed
to fit measurements with PHOTONIII BAXS detector.
October 2021
# New OMIT optional argument for READ_FCF keyword: list outliers reflections
preceded by OMIT keyword for SHELXL refinement program.
# New way to launch browser with a local file (add "file:///folder_name/" before
HTML file name)
# EXTRACT from CIF: .fcf files are extracted if included in the CIF file.
# Shelxl weighting scheme is now included in structural reports.
# READ_FCF xxx.fcf keyword outputs list of outliers reflections with
ABS(Fo^2 - Fc^2)/sig_WI > 10.
where sig_WI = 1./sqrt(wI) and wI calculated from weighting scheme
used by SHELXL :
w_I=1/[sig(Fo^2)+(aP)^2+bP] where P=(Fo^2+2Fc^2)/3
a and b values are extracted from xxx.INS file.
September 2021
# Creation of archive.CIF file:
INCLUDE_FCF_file keyword can be specified in the [ARCHIVE_AND_REPORT] section
of the setting file to embed .FCF file in the final archive.CIF file.
June 2021
# New "DMAX/D_HKL_MAX/DHKL_HIGH/DHIGH" keyword: output the highest
d_hkl values
# Cell parameters and space group has to be input previously.
New "beam_stop_limit" item can be defined in the [DEVICE] section
of the setting file : its correspond to the theta value below which
reflexions are hidden behind the beam stop. Default value is 2.0 deg.
March 2021
# New optimized routine for creation of archive.cif with formatted
output lines (CIF_format80=1 in the [ARCHIVE_AND_REPORT] section of
the setting file), in order to minimize the number of lines
exceeding 80 characters. A warning is now ouput in such a case.
# New optional arguments for READ_LST keyword: AFIX, ATOMS, FLACK, HTAB,
MPLA
February 2021
# Max. atoms value has been extended from 1200 to 2000.
# New "WATER" keyword: read atoms.out output file from CALC-OH
(M. Nardelli, J. Appl. Cryst. 1999, 32, 563-571) and create:
- coordinates of Hydrogen atoms with AFIX constraints
- distances constraints between atoms of the water molecules
If EDIT is given as optional argument, hatoms_out.INS is
automatically edited with the editor specified in the cryscalc.ini
setting file.
# New "READ_LST" keyword: read .LST SHELXL output file and extract
extract hkl, structural and refinement features.
To extract particular items, following optional arguments are allowed:
ADP, CONN, DIST, HKL, HKL_STAT, LS, MDR/MDR_OMIT/MDR_crit/MDR_OMIT_crit,
RHO, SPLIT/SPLIT_EDIT, TORSION, UNIT, VAR.
Note that default criteria value for MDR keyword is equal to 3.,
leading to output only most desagreable reflections with Eror/Esd > 3.0
This criteria value can be specified through the MDR_crit.
Example: READ_lst job.lst MDR_8
If MDR_OMIT is used, the hkl indices of most desagreable reflexions
are ouput, preceded by OMIT keyword (format compatible with .INS/.RES
input SHELXL file.
# New "BD" argument for CONN keyword: include bonds distribution
in the output. This new argument replaces the previous "no_BD" one.
By default, bond distribution is not yet output. To activate it,
please use this new "BD" argument.
# New "VIEW/RUN" argument for CREATE_CIF keyword: view the created CIF
in the CIF viewer. Note that CIF viewer can be specified in the
[EXTERNAL APPLICATIONS] section of the cryscalc.ini setting file
through the CIFviewer item.
# New "VIEW/RUN" argument for CREATE_INS keyword: view the created INS
in the INS viewer. Note that INS viewer can be specified in the
[EXTERNAL APPLICATIONS] section of the cryscalc.ini setting file
through the INSviewer item.
# New "VIEW/RUN" argument for CREATE_XYZ keyword: view the created XYZ
in the XYZ viewer. Note that XYZ viewer can be specified in the
[EXTERNAL APPLICATIONS] section of the cryscalc.ini setting file
through the XYZviewer item.
# New "No_H" argument for CREATE_PCR keyword: if used, only
non Hydrogen atoms are ouput in the PCR file.
# New READ_SFRM/READ_SFRM_HEADER kewyord:
Read header of .sfrm file (diffraction frame from Bruber AXS
diffractometers)and output experimental features (date of experiment,
temperature, wavelength,target voltage and intensity, rotation axis,
positions of motors ...)
December 2020
# Tolerance factor value (TOL) for BVS calculation can be specified using the
BVS_TOL argument of CONN keyword.
Ex: CONN cu1 MAX=3.1 BVS_30
November 2020
# Tolerance has been extended from 20 to 30% for the BVS calculation.
# Some minor changes have been made in the CONNECTIVITY routine in order
to provide a standard deviation value for calculated mean distance if
atomic positions esd's are known.
# CRYSCALC has been recompiled with the last CRYSFML library:
Symmetry card for Ibam space group is now correctly interpreted.
September 2020
# New "Rint_centric" item in the [OPTION] section of the setting file:
allows to calculate Rint and completeness for centric space group in
the case of acentric detected space group. This calculation is
performed only if CRYSCALC is launched with a .CFL of .OOL command file as
argument.
# "CIF lines can contain "#" character after the value of the CIF field
# Matrices for HEX_RHOMB and RHOMB_HEX keywords and some matrices
used in the MAT B1 B2 keywords (with B1 B2 initial and final Bravais
lattices respectively) were wrong in the last versions of CRYSCALC.
This has been corrected. Thanks to V. Demande (ISCR) to have reported
these bugs.
# New WGHT argument for READ_INS keyword:
If .RES file is input as first argument, the weighting scheme
is updated in the corresponding .INS file.
July 2020
# Correction of a bug when reading .RAW / .MUL files (created by SAINT)
containing high countings.
June 2020
# Creation of archive CIF file for powders:
. JANA.CIF files can be read.
. In case of FP CIF files containing several phases, only first
phase structural CIF items are considered.
# The value of _exptl_absorpt_correction_T_max CIF field was wrong in the
final archive.CIF in the previous versions of CRYSCALC since April 2020.
It has been corrected.
June 2020
# The value of _exptl_absorpt_correction_T_max CIF field was wrong in the
final archive.CIF in the previous versions of CRYSCALC since April 2020.
It has been corrected.
May 2020
# New "CIF_powder" item in the [ARCHIVE AND REPORT] section of the setting
file: allows to create a CIF file for a powder structure refinement with
FullProf: different CIF files can be specified in the command line after
"CREATE_ARCHIVE" argument and instrumental features can be stored in a
particular file.
Example:
CRYSCALC CREATE_ARCHIVE job.cif job_dis.cif job_prof.cif device.cif
April 2020
# GEN_HKL keyword routine : if "OUT" is given as argument to
output the hkl generation list, a Debye Scherrer film simulation
is then created : format is .PGF type format for the latest version
of WinPLOTR software, downloaded from:
https://cdifx.univ-rennes1.fr/progs/winplotr/winplotr.exe
# New "CREATE_REPORT_TXT", "CREATE_REPORT_LATEX" and "CREATE_REPORT_HTML"
items in the [option] section of the setting file: allows to create
structural_report files from the command line after reading a .CIF file,
in .TXT, LATEX and .HTML format respectively. Default values for
CREATE_REPORT_TXT, CREATE_REPORT_LATEX and CREATE_REPORT_HTML are
equal to 0.
Example:
d:\progs> cryscalc xxx.CIF
These possibilities are equivalent to the previous (still existing)
commands:
d:\progs> cryscalc report_TXT xxx.CIF
d:\progs> cryscalc report_LATEX xxx.CIF
d:\progs> cryscalc report_HTML xxx.CIF
# CRYSCALC web site has been moved from
"http://www.cdifx.univ-rennes1.fr/CRYSCALC" to
"https://cdifx.univ-rennes1.fr/CRYSCALC"
# New "MPO" optional argument for CREATE_PCR keyword: create .PCR file for
FullProf for a pattern refinement with multi preferential orientation
(NORI=2)
# New "PRF_header" item in the [PATTERN SIMULATION] section of the setting
file: allows to include (or not) a header containing diffraction pattern
features and structural informations in PRF files created by the diffraction
pattern simulation routine (same header than .XY file).
This kind of PRF file with a header can be read by the lastest version of
WinPLOTR and "PRF_header=Y" in the [OPTIONS] section of the WinPLOTR.ini
setting file.
March 2020
# New "CREATE_LOG_file=0/1" item in [option] section of the CRYSCALC.ini
setting file allows to create (or not) CRYSCALC.log and CRYCALC_cmd.log
output files. Default value is 1.
# New "CREATE_CFL_file=0/1" item in [option] section of the CRYSCALC.ini
setting file allows to create (or not) a CRYSCALC.CFL containing
input CRYSCALC instructions. Default value is 1.
# New "PAT_NORM_xxx" optional argument for "GEN_HKL" keyword:
diffraction pattern will be normalized to provide maximum
counting equal to xxx.
Example:
GEN_HKL 2THETA_MIN=10 2THETA_MAX=120 PAT_NORMA_500
This normalization can also be specified through the "pdp_norma = xxx" line
in the [PATTERN SIMULATION] section of the CRYSCALC.INI setting file.
This feature will be used for pattern simulation from command line.
Example:
d:\progs> cryscalc CRYSCALC.CIF PAT
Furthermore, normalization procedure can be specified in command line
through the "PAT_NORMA" argument, independently of the presence of
the "pdp_norma = xxx" line in the setting file.
Note that the following arguments are available:
PAT_NORMA, PAT_NORMA_X, PAT_X_NORMA, PAT_NORMA_N, PAT_N_NORMA
Example:
d:\progs> cryscalc CRYSCALC.CIF PAT_NORM
If pdp_norma = xxx is not specified in the setting file, normalization
value xxx is fixed to the default value xxx=1000.
February 2020
# New "NORM_xxx" optional argument for "GEN_HKL" keyword and pattern
simulation: diffraction pattern is normalized to provide maximum
intensity at xxx counts.
# Final archive.cif and structural reports are suitable for H free compounds.
# Distances calculations in the CONN routine outputs standard deviations
if they are provided through reading a CIF file for example.
January 2020
# "ref" argument for CREATE_PCR keyword allows to create .PCR file for
FullProf for a pattern refinement: in such a cas, JobTyp will be equal to 0
for X-ray data refinement and 1 for neutrons data. Number of refinement
cycles (NCY) is put to 10. This can also be specified in the setting file
through create_pcr=-1 in the [COMMAND LINE ARGUMENTS] section.
# "ref_mp/mp_ref" argument for CREATE_PCR keyword allows to create .PCR file
for FullProf for a refinement and in a multipattern format.
This can also be specified in the setting file through create_pcr=-2
in the [COMMAND LINE ARGUMENTS] section.
December 2019
November 2019
# GET_TRANSF_MAT keyword:
. tolerance value can now be input by user if no transformation matrix
is founded with default value (0.3).
. Cell paramters can be input with esd values.
# "CART_A" and "CART_C" arguments of "WRITE_CELL" keyword are now
in agreement with new definitions in CRYSFML, ie:
CART_A: x // a; z is in the ac-plane; y is x ^ z = b*
CART_C: z // c; y is in the bc-plane; x is y ^ z = a*
October 2019
# New "READ_ACE" keyword allows to read structural informations
from a .ACE file (CaRIne).
# Creation of crystal report: due to the extension of the dimension
of an internal array, the list of "Symmetry transformations used
to generate equivalent atoms" was not correct in previous versions
of CRYSCALC. This has been corrected.
# PCR files containing single crystal structural data are now read
correctly.
# PAT/PAT_X/PAT_N arguments can be used in command line after reading CIF,
CEL, CFL, INS and PCR files given as argument, independantly of
the value of "create_PAT_PRF" item in the "[COMMAND LINE ARGUMENTS]"
of the setting file.
Examples:
d:\progs> cryscalc CRYSCALC.CIF PAT
d:\progs> cryscalc CRYSCALC.CFL PAT
In such a case, a powder pattern calculation is performed, using
structural parameters from the input file and profile parameters
defined in the CRYSCALC.INI setting file.
# "READ_CIF" and "READ_INS" routines: min and max Ueq values
for Carbon species are now output, as well as the Ueq_max/Ueq_min
ratio value.
September 2019
# "CREATE_CIF" routine is now available even if structural data
are input by user and not read in a file (.PCR/.INS/.CEL)
Ouput CIF file name can be specified as argument of
"CREATE_CIF" keyword.
# Change in the SEARCH_SYMM/SEARCH_LAUE keyword routine:
to increase the speed of Rint calculation, crystal system
is now taken into account if known.
To force the calculation for all Laue group, "ALL/FORCE_ALL"
argument can be used.
To force the calculation for triclinic symmetry,
"T/TRICLINIC/FORCE_T/FORCE_TRICLINIC" argument can be used.
# New "NOR" optional argument for READ_HKLF5 keyword: create
HKLF5 file containing only non-overlapping reflections
and HKL files for each twin component.
# New "OUT" optional argument for CREATE_ACE, CREATE_CEL, CREATE_CFL,
CREATE_INS, CREATE_PCR, CREATE_PDB, CREATE_TIDY and CREATE_XYZ keywords:
output lines on screen for the created file.
July 2019
# New HKL/CREATE_HKL argument for READ_FCF keyword: creation of an .hkl
file (SHELX format). To get the hkl file in a free format, _FREE has
to be added to the argument.
Examples:
READ_FCF job.fcf HKL
READ_FCF job.fcf HKL_FREE
# New EXTRACT_OLEX command line argument: extract .res file and hkl data
from the hkl loop in an archive .CIF file. Syntax is as follows:
d:\cifs>CRYSCALC EXTRACT_OLEX archive.cif
June 2019
# Orientation matrix (UB matrix) is now included in the final archive.CIF file
# New CREATE_CIF keyword is now running after reading a .CEL file
coming from PowderCELL.
# New "How to convert .PCR or .INS/.RES file to a CIF file?" tutorial
# CRYSCALC user's guide can be created from command line and one of the
following argument : /?, HELP, /HELP, -HELP, --HELP, /H, -H, MAN, /MAN,
-MAN, --MAN, /M, -M
# New "computing_molecular_graphics" and "computing_publication_material"
items can be defined in the [PROGRAMS] section of the setting file.
# New "atom_adp_type=0/1" option in the CRYSCALC.ini setting file:
allows to define ADP type in CFL files:
0: B_iso
1: U_iso
# When reading .PCR or .INS/.RES file from command line, a CIF file
can be automatically created if "create_cif=1" is specified
in the [COMMAND LINE ARGUMENTS] section of the setting.file.
# New CREATE_CIF keyword allows to create a CIF file after reading
structural features from a .PCR or .INS/.RES file.
# CRYSCALC instructions can now be specified as command line arguments.
In that case, first and last characters of the command line has to be ";"
(or "\"), and ";" is used as keywords separators. (Thanks to
C. Prestipino [ISCR] for the suggestion).
Examples :
d:\>cryscalc ; SG P 21/c ;
d:\>cryscalc \ read_pcr job.pcr ; create_ins ; \
Note that the total length of the command line must not exceed 1024.
May 2019
# "mp" argument for CREATE_PCR keyword allows to create .PCR file for FullProf
in multi-patterns format. This can also be specified in the setting file
through create_pcr=2 in the [COMMAND LINE ARGUMENTS] section.
Note that FullProf has been modified to perfom powder pattern simulation
(JTyp=2 or Jtyp=3) from multipattern PCR file (FullProf needed a data file
previously). This corrected version will be available in near future.
in the ILL FullProf web site:
https://www.ill.eu/sites/fullprof/php/downloads.html
April 2019
# New "WL=" and "E=" optional arguments for BEAM keyword, allowing to enter
wavelength (in A) or beam energy values (in KeV for X-rays and electrons
or in meV for neutrons).
# New CREATE_PDB keyword allows to create .PDB file containing atoms list
with Cartesian coordinates in PDB format. This .PDB can be visualized for example
with Pymol. Documentation on PDB format has been used from:
http://www.wwpdb.org/documentation/file-format-content/format33
In addition, "create_PDB" field can be input in the "[COMMAND LINE ARGUMENTS]"
part in the cryscalc.ini setting file.
March 2019
# References in HTML and LATEX structural reports are now written
following the edition typography (Thanks to B. Boitrel [ISCR] for
the suggestion) :
. journal name in italic mode
. year in bold mode
. volume number in italic mode.
# New EXTRACT_CIF command line argument: extract .cif files
embedded in multiple global archive .CIF file. Syntax is as follows:
d:\cifs>CRYSCALC EXTRACT_CIF multiple_archive.cif
# New MAX_FC keyword : output the most intensive calculated reflections
Crystal structure has to be read first with READ_INS/READ_CIF/READ_PCR
keywords.
Example :
READ_CIF my_structure.CIF
MAX_FC 15
# Optional ISO argument for WRITE_ADP keyword will output only atoms with
isotropic ADP.
Febryary 2019
# Correction of a bug in the WRITE_ADP keyword routine (rms values were
wrong when calculated from U_ij values extracted from .INS file.
# New ADD_HKL command line argument allows to embed hkl data
into an archive_hkl.cif file. Syntax is as follows:
d:\cifs>CRYSCALC ADD_HKL archive.cif job.cif
where archive.cif is a final archive CIF file and job.cif
the CIF file created by SHELXL and containing hkl data,
starting with _shelx_hkl_file item and finishing with
_shelx_hkl_checksum item.
# When creating a global CIF ile for multiple structures deposition, the
list of authors to be included can be specified in a special file named
"authors_list.txt". The syntax is as follows :
[AUTHOR]
Name, first_name
address
address2 (optional)
address3 (optional)
Note that :
. input items can contain characters with accents
. address has to be input in a single line. On the other hand, a second
line will be interpreted as a second address. Carriage return can be
applied using "\\" separator character.
Example:
[AUTHOR]
ROISNEL, Thierry
Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)
- UMR 6226 \\ F-35000 Rennes, France
January 2019
# Optional ISO/FORCE_ISO argument for CREATE_PCR keyword will force
ADP parameters to be written as isotropic values, even if
anisotropic ADP parameters values have been input.
# Option 10 in the main menu provides the capability
to get some examples of .cfl input files for CRYSCALC.
# CRYSCALC solve_to_ins: protection to avoid problems in case of
wrong SFAC/UNIT format in SHELXL file if more than 999 atoms of
one atomic species.
November 2018
# New option for LIST_HKL_MAX keyword: followed by an integer (n),
corresponding to the number n of the most intensive reflections
to be ouput.
# New optional argument for FILE/READ_HKL keyword:
MAX_n : list the n most intensive reflections
MAX_ALL :list all reflections in decreasing intensity order.
# New optional argument for GEN_HKL keyword:
OUT_n : sort reflections list by decreasing F2calc and list the n most
intensive ones.
OUT_ALL : sort reflections list by decreasing F2calc and list all of them.
# Bad Rint criteria can be defined in OPTIONS section of the setting file
trough the bad_rint_criteria string (default value is 25.)
# New argument for UPDATE keyword : if ZIP is given as argument, a zipped
file containing cryscalc.exe will be downloaded from:
https://cdifx.univ.rennes1.fr/progs/cryscalc/cryscalc.zip
September 2018
# Automatic installation of CRYSCALC can now been performed using the new
CRYSCALC_setup.exe program developped with Inno Setup
(http://www.jrsoftware.org/isinfo.php).
CRYSCALC_setup.exe can be download from :
https://cdifx.univ-rennes1.fr/progs/cryscalc/cryscalc_setup.exe
# Cryscalc tutorials (.pdf) are also available henceforth from the CRYSCALC
main menu.
# Simulation of powder diffraction pattern: random noise is now added to
the Y_obs values, using same random generator as in FullProf.
July 2018
# Some CRYSCALC tutorials has been written and are available from
the HTML user's guide:
. How to install?
. How to get help?
. How to start?
. How to create import.cif file on a Bruker diffractometer?
. How to convert CIF/INS files?
. How to calculate a powder diffraction pattern from a CIF/INS file?
. How to create a final CIF archive?
. How to extract .res and .hkl from a cif file?
. How to create an experiment report and tables from a CIF file?
. How to create a global CIF archive from several CIF files?
# New feature for UB_MAT keyword: if only one argument is input,
it has to correspond to a CIF file name and UB matrix will be
extracted from "_diffrn_orient_matrix_UB_xx" lines.
# New "create_PAT_PDPF=0/1" option in [COMMAND LINE COMMANDS] section of the
setting file allows to create a Powder Diffraction Pattern File (.pdpf)
containing hkl list, 2theta, d_hkl values and relative intensities when
a simulation of powder diffraction pattern is performed through the
command line.
Example : cryscalc 100604.cif PAT
This kind of pdpf file can also be created in CRYSCALC with GEN_HKL
keyword and PAT_PDPF argument (see user's guide.
June 2018
# New SEARCH_SYMM keyword : calculation of internal R values for different
Laue group and deduction of the most probable one.
May 2018
# New "SIZE_Y=" and "STRAIN_U=" arguments can be used with "GEN_HKL" keyword,
combined with "PAT" argument, to generate broadened profiles due to size
or strains effects respectively. In that case, diffraction peaks are
broadened with the following expressions:
HL_broad = size_Y/cos(theta)
HG_broad = U.tan(theta)
Final diffraction profiles are calculated as follows:
HG**2 = HG_inst**2 + HG_broad**2
HL = HL_inst + HL_broad
Note that HG_inst and HL_inst, corresponding to the gaussian and lorentzian
parts of the Voigt function used to describe the instrumental resolution
function, are defined in the setting file ([PATTERN SIMULATION] section).
They can be directly profile_TCH_** values for TCH Voigt profile function or
internally calculated from the profile paramters if pseudo-Voigt profile
function is choosen.
# Thompson-Cox-Hastings Voigt profile function can be used for powder
diffraction patterns simulation, using the "profile_function = TCH"
line in the [PATTERN SIMULATION] section of the setting file. Gaussian
and lorentzian parts of TCH function are defined as follows:
HG**2 = U.tan(theta)**2 + V.tan(theta) + W
HL = X.tan(theta) + Y/cos(theta) + Z
Default values for U, V, W, X, Y, Z TCH parameters are internally defined
but can also defined by the user in setting file through :
X_profile_TCH_U = 0.0046
X_profile_TCH_V = 0.0375
X_profile_TCH_W = 0.0027
X_profile_TCH_X = 0.
X_profile_TCH_Y = 0.014
X_profile_TCH_Z = 0.
Similar parameters can also be defined for a neutron diffraction pattern
simulation using "N_profile_TCH_*" instead of "X_profile_TCH_*" lines
# Powder diffraction patterns can be simulated taking into account presence
of strains in the sample. Strains are specified through the "strain="
argument of the GEN_HKL keyword.
Remark: only gaussian part of the Voigt profile function is affected by
strains in the sample
Strains can also be defined in the setting file ([PATTERN SIMULATION]
section), through the "strain = " instruction. Profile broadening effects
will be applied for strains values in the 1.E-06 - 0.02 range.
# Pattern simulation with particles size effects: a small error has been
corrected in the Thomson-Cox-Hastings formula. Simulated patterns are
now in perfect agreement with size values provided by a profil refinement
(ex: FullProf).
April 2018
# New "atom_occ_type=0/1" option in the CRYSCALC.ini setting file:
allow to define occupation type :
0: occupation type = % of site occupancy (default value)
1: occupation type = K * m/M * % of site occupancy
m: site multiplicity
M: space group multiplicity
K: proportionnal value
# New BVPARM keyword allows the user to input d0 and B0 parameters for
Bond Valence Sum calculations (see CONN keyword). The order of BV
parameters are as follows: cation anion d0 B0
Example: BVPARM W+6 S-2 2.309 0.370
March 2018
# New CREATE_XYZ keyword allows to create .XYZ file containing atoms list
with Cartesian coordinates. This .XYZ can be loaded for example with Mercury.
# SEARCH_P3P6 routine has been changed: Rint values are now calculated
for different trigonal and hexagonal laue groups.
# New "ANA/ANA_OUT" arguments for READ_HKLF5 keyword: search for redondant
reflections.
# GEN_HKL keyword: if "PAT" argument is changed to "PAT_NOPLOT", PRF file
will not be plotted by winPLOTR.
February 2018
# CREATE_CIF_BUFFER command line argument: create a buffer file
containing the list of CIF files present in the current folder.
The name of this buffer file can be given through a second argument
in the command line. If not, default buffer file is named "CIF_files.buf".
# New LIGAND= argument for CONN keyword will output only connectivity with a
particular atom.
ex: CONN RE1 LIGAND=Br1
January 2018
# Global CIF file containing several structures can be created through
CREATE_GLOBAL_CIF command line argument. The list of CIF structures files
is specified in a buffer file. The name of this buffer file can be
given through a second argument in the command line. If not, default
buffer file is called "CIF_files.buf".
# CONN keyword provided connectivity list with the whole symmetry operators
used to generate the ligands (combination of "(tx,ty,tz)" and "Sym. Op."
# New "No_BD" argument for CONN keyword: exclude bonds distribution
in the output
# Maximum number of reflections in a HKL file has been extended to 1500000.
December 2017
# New SEARCH_P3P6 keyword : calculate internal R values for P 3 and P 6
space group and deduce if symmetry is rather trigonal or hexagonal.
November 2017
# New "MAX_geom" keyword in the [ARCHIVE_AND_REPORT] section of the setting
file:
allows to define the max. number of molecular geometry features (distances,
angles, torsion angles and htab values) in a .CIF file. Max. and default
values are 2000.
# New "READ_SPF" keyword: read SUPERFLIP/EDMA input files to extract
cell parameters, wavelength, symmetry operators, centering vectors
and deduce current space group.
# New "ANIS/ANISO" argument for CREATE_INS keyword will add ANIS keyword
in the .INS created file.
# New optional arguments (SIR, SXT and SPF) for "SOLVE" instruction will
specify the files to be created, for SIR, SHELXS/T and SUPERFLIP/EDMA
respectively. In the case of SUPERFLIP/EDMA, the previous
cryscalc_superflip.in and cryscalc_edma.in input files are now replaced
by a single file called xxx_SPF.in, where xxx is the sample ID if existsor "cryscalc".
# New argument for "FILE import.cif" instruction; "CREATE_P4P" allows to create
a .P4P file.
# EXTRACT_RES_HKL keyword (Y/N) in the [COMMAND LINE ARGUMENTS] section of
the setting file allows to extract .RES and .HKL file from archive.CIF file.
# Some minor changes has been made in SUPERFLIP input file created by CRYSCALC:
. "derivesymmetry yes" is replaced by "derivesymmetry use"
. "symmetry ... endsymmetry" contains all symmetry operators of a primitive
lattice
. "centers ... endcenters" card provides all centering vectors.
# New "SPF_X/SUPERFLIP_X" argument for WRITE_SYM_OP keyword: ouput symmetry
operators card in a x1 x2 x3 format, whereas SPF/SUPERFLIP keyword provides
symmetry operators in x y z format.
# Create_archive routine is now adapted to extract Hydrogen bonds from CIF
files created by the old and new version of SHELXL and the optionnal presence
of "_geom_hbond_publ_flag" string.
October 2017
# New "SPF/SUPERFLIP" argument for WRITE_SYM_OP keyword
# New "ISO" argument for CREATE_INS keyword will force to
ouput Ueq values in the atoms list, even if anisotropic ADP's
are input.
# CREATE_INS keyword keeps the isotropic/anisotropic character of ADP's.
September 2017
# New "PURGE" argument for CREATE_INS keyword will exclude
spurious atoms with Ueq < 0. or Ueq > U_threshold.
U_threshold value can be defined in the [CREATE INS] section of
the setting file through U_threshold keyword.
# SOLVE keyword generates an input file (called cryscal_EDMA.in) for EDMA
EDMA software.
# New matrices implemented in the list of matrices, corresponding to the
faces centered cubic unit cell to hexagonal R-centered unit cell
transformations. These matrices correspond to #35 and #36 in the
list of matrices.
# Number of user matrices has been extended to 6.
# Cosmetic changes in the PGF file created by the READ_FCF keyword.
# Create_archive routine is now adapted to extract Hydrogen bonds from CIF
file created by the new version of SHELXL (july 2017) and the presence of
"_geom_hbond_publ_flag" string.
July 2017
# Number of scans is now dimensionned dynamically. Default value is
50 but can be defined by user in the setting file through the
"nb_scans" keyword in the [ARRAYS DIMENSIONS] section.
# When creating import.CIF from .P4P and .HKL files, experiment temperature
is now extracted for each scan from first .sfrm image.
# SEARCH_MONO keyword is now operating for C-centered Bravais lattices.
June 2017
# No_H argument for WRITE_ADP and WRITE_ATOMS keywords will output only
non-hydrogen atoms.
# Change in the READ_CIF_atom routine of CFML to read correctly
anisotropic ADP in CIF files.
# Cosmetic features for LATEX experimental report can be specified in the
[ARCHIVE_AND_REPORT] section of the setting file, ie :
latex_cmb = 0 ! use Computer Modern Bright font in LaTeX report
latex_sans_serif = 1 ! use Sans Serif font in LaTeX report
latex_title_back_color = #e3e6f7 ! Main title background color in LaTeX report
latex_title_text_color = #580a0a ! Main title text color in LaTeX report
latex_title_border_color = #000000 ! Main title border color in LaTeX report
latex_title1_back_color = #fafafa ! Title background color in LaTeX report
latex_title1_text_color = #580a0a ! Title background text in LaTeX report
latex_title1_border_color = #fafafa ! Title background text in LaTeX report
latex_title1_text_center = 1 ! Title text centering (0/1)
# CELL keyword : crystal system is now deduced from cell parameters
input by hand.
# Maximum number of reflections in a HKL file has been extended to 750000.
May 2017
# Extraction of scan features in the creation of import.CIF files is
now correct for diffraction experiments with more than 9 scans.
April 2017
# CELL keyword allows to extract cell parameters from a .PCR FullProf file
ex: CELL 10K.pcr
March 2017
# Particles size (in A) for a diffraction pattern simulation can be defined
in the setting file ([PATTERN SIMULATION] section), through the
"particles_size = " instruction. If the value of particles size
is lower than 9999., profile broadening effects will be applied.
# CELL keyword : Bravais lattice and crystal system are extracted when reading
a .P4P, .INS and .CIF file.
# SEARCH_GROUP routine has been corrected for centered space group:
by default, only space groups with Bravais lattice in agreement with
the unit cell Bravais lattice are output.
# Maximum number of atoms has been extended to 1200 when reading a .INS/.CIF
file.
# Compilation of CRYSCALC with lastest version of CRYSFML (feb. 2017):
standart deviations of atomic coordinates are taken into account in
the calculation of plane equation (case of more than 3 input points).
January 2017
# "EULER_TO_KAPPA" routine has been corrected for Chi values
larger than 180 : Chi is then transformed to 360. - Chi).
# The CRYSCALC routine associated to STAR_K keyword has been changed to
the "K_Star" routine of CFML.
# PLANE keyword accept more than 3 atoms for the calculation
of a mean plane equation.
# Compilation of CRYSCALC with lastest version of CRYSFML
(December 2016)
# New CELL_ESD keyword: input of esd's for cell parameters and
calculation of corresponding unit cell volume ESD.
# New GET_TRANSF_MAT keyword provides the transformation matrix
between two primitive unit cells (determinant of the matrix
is equal to 1).
# New REDUCE keyword provides conventional unit cell parameters
and transformation matrix between input cell and conventional
cell(s). The routine is based on Get_conventional_Unit_Cells
program written by JRC using procedures implemented in CRYSFML.
December 2016
# When creating import.CIF from .P4P and .HKL files, scans features
(type of scan, DX, exposition time, starting angles for theta, omega
phi and chi motors) are extracted from .sfrm images.
November2016
# "WRITE_ATOMS cart" keyword leads to the creation of a cryscalc.xyz file
for PyMOL (http://www.pymol.org/).
# TOLMAN keyword: van der Waals radius for ligands can be given as
arguments. If not specified, defaut values are coming from
CRYSFML library, excepted for H atoms (r=1.2A).
ex: TOLMAN CO1 P1 H1A H11A H21A 1.22 1.22 1.22
# When creating import.CIF from .P4P and .HKL files, crystal to detector
distance is now extracted from .sfrm files for every scan of the data
collection.
# New "NO_H" argument for CREATE_INS keyword will exclude
hydrogen atoms from the created .INS file.
# New "NO_details" argument can be applied to most of the keywords,
excepted WRITE* keyword. This action will lead to a very short
and restricted output.
# New REM keyword: non interpreted command. Can be useful
to skip a command in a CFL input file. This keyword can
be replaced by "!" or "#" character.
October 2016
# New READ_HKLF5 keyword: read HKLF5 format data file containing
structure factors of a twin crystal.
# New REF_SHELX keyword: output references for SHELXL and SHELXT
software.
# If a .png/.jpg file corresponding to the crystal picture is present
in the current folder (named as sample_ID.png/.jpg), it will be
embedded in the final structural report.
# New TOLMAN_ANGLE keyword: calculation of the Tolman cone angle
as defined from crystallographic data and Van der Waals radii in
"Transition Met. Chem. 20, 533 (1995)". The TOLMAN_ANGLE keyword
has to be followed by the labelling of the 5 atoms defining the cone,
corresponding to metal, centered atom and 3 ligand atoms respectively
September 2016
# Cosmetic changes in the .HTML/.TXT/.PDF structural reports
# Redundancy is now calculated and output during Rint calculation.
# New "KAPPA_TO_EULER" AND "EULER_TO_KAPPA" keywords allow to convert
motors angles values of single crystal diffractometer from Kappa to
Eulerian geometry (and opposite)
July 2016
# .FAB file created by SHELXL201x is now embedded in the
cryscalc_archive_hkl.cif file in the case of SQUEEZE
procedure has been used.
# Mean value of atomic volume for non H hydrogen atoms is now output after
molecular density calculation for compounds containing H atoms.
June 202016
# New HKLF5 keyword: 9 arguments are necessary to input the 3*3
transformation matrix components. Combined with FILE keyword,
a hklf5 format data file is then created. Overlapping reflections
criteria can be defined in the cryscalc.ini setting file through
"ref_overlap_criteria=" keyword in the [OPTIONS] section. Defaut
value is 0.15 and max. value has been fixed to 0.25
# Corrections of minor bugs, specially when .CFL input file is read from
option #2 in the main menu.
# New EXTRACT command line argument: extract .res and .hkl files
embedded in an archive .CIF file. Syntax is as follows:
d:\cifs>CRYSCALC EXTRACT archive.cif
# New features for SUPERCELL instruction:
. cell parameters are updated
. if space group of initial cell is know, space group is
updated to P 1.
# STAR_K keyword: the arms of the K star are now correct
for primitive and centered space groups.
# New "CONDENSED" argument for WRITE_SYM_OP keyword:
output symmetry operators list in a condensed way.
May 2016
# New ONLY_X argument for CONN keyword : output connectivity
between atoms of the same X species.
# CONN keyword: MIN and MAX arguments are now taken into
account correctly.
# Correction of bug in the "STAR_K" keyword routine :
The arms of the K star are now ouput for primitive
space groups (not yet ouput for others).
# new SAVE_SETTINGS keyword will save cryscalc.ini setting file
in the current folder. This can be useful if no setting file
is present in the CRYSCALC folder.
# WRITE_CELL keyword: standart deviations of cell parameters
and volume are ouput if they are known.
April 2016
# Results of Rint calculation was bugged for successive
calculation without using RESET keyword. This is corrected.
# New FCF_FILE keyword: read .fcf file create by SHELX
IF "PLOT" is given as argument, a *_FCF.PGF file for WinPLOTR
is created (Fc2=f(Fo2) curve)
IF "PLOT_STL" is given as argument, a *_FCF_stl.PGF file
is created (Fc2 - Fo2 = f(sinThetal/lambda) curve).
If WinPLOTR is already installed, .PGF file is automatically
displayed.
March 2016
# New features in the header of the import.cif file
created from .P4P, .HKL and .ABS files coming from
single crystal data reduction in APEX2 and APEX3
(Bruker AXS software).
# MONOCLINIC keyword : condensed output if "no_out" is
given as argument.
February 2016
# New DIFF keyword : calculation of the components
of the difference atomic coordinates vector
between 2 input atoms
# New PLANE keyword : calculation of the 4 components
of the plane equation Ax+By+Cz+D=0, given three
atoms coordinates.
# New SEARCH_TETRA keyword : determine tetragonal axis
from hkl data integrated in a pseudo-cubic
unit cell by calculating successively internal R values
for the most probable space group of following different
setting: abc, cab, bca
January 2016
# New UPDATE/NO_UPDATE arguments for MAT keyword
# New SUPERCELL input keyword: calculation of atomic coordinates
in a superstructure cell.
# _shelx_res_checksum and _shelx_hkl_checksum items are included
in the archive.cif file for compatibility with PLATON Checkcif
and cif files created by SHELXL-2014.
December 2015
# Minor correction in the header of import.cif created from .P4P and .HKL files
November 2015
# DIST keyword : "_*" option after second label allows to calculate
interatomic distance between first input atome and the closest
equivalent second atom (space group has of course to be known).
example : DIST Mo1 Mo2_*
October 2015
# HKL_diff keyword : calculation of F2 difference for common reflections of 2
hkl files.
# UPDATE keyword : download the lastest version of CRYSCALC from the web site
(https://cdifx.univ.rennes1.fr/progs/cryscalc/cryscalc.exe
Remark: Browser has to defined in the setting file.
# Minor cosmetic changes in import.cif
September 2015
# Polar character of space group has been corrected : point group
has to be one of the following :
1, 2, 3, 4, 6, mm2, m2m, 2mm, 3m, 3m1, 31m, 4mm, 6mm
# "include_experimenter" field can be input in the cryscalc.ini setting file :
experimenter features, coming from [AUTHOR] section, are then included
in the archive_cryscalc.cif file.
# import.cif file created from .P4P and .HKL files contains the number of scans
of the data collection and related features (exposition time, frames width,
number of frames)
# NIGGLI ouput: Niggli matrix is now output
July 2015
# THERM ouput: some calculation outputs were wrong in the case of
"matrix U non-positive definite".
June 2015
# SEARCH_EXTI keyword can have a string optional argument : if "ALL"
is given as argument, all reflections are considered, without applying
any criteria.
# A small bug has been corrected in the SEARCH_GROUP routine. It appeared
only when searching from only centered space groups and the symmetry
was unknown in the import.cif input file.
# Two logos for the structural_report.pdf can be specified in the
[OPTIONS] section of the setting file. These .jpg files will be used
included in the structural report (Latex and pdf formats). They
have first to be present in the \img folder of the CRYSCALC directory.
ex:
report_logo_1 = CDIFX_logo.jpg
report_logo_2 = ISCR_logo.jpg
May 2015
# new SEARCH_MONO keyword : determine monoclinic angle
from hkl data integrated with a pseudo-orthorhombic
unit cell by calculating successively internal R values
for "P 2 1 1", "P 1 2 1" and "P 1 1 2" space groups.
# CONN output: polyedron distorsion is calculated as:
distorsion = SUM((dist-dist_av)/dist_av)**2) / n
with n: number of ligands
dist_av: average distance
# Minor changes for D8 Venture data file
April 2015
# New DETAILS argument for WRITE_ADP keyword
March 2015
# New CREATE_PCR keyword : create .PCR input file for FullProf
(pattern simulation). Structural data have to be previously input
through for example READ_CIF or READ_INS keywords. in such a case,
profile features can be specified in the setting file
([PATTERN SIMULATION (Pseudo-Voigt profile)] section).
# "create_pcr=1" can be spectified in the [COMMAND LINE ARGUMENTS]
section of the setting file to create automatic PCR file
from command line run of CRYSCALC
February 2015
# New arguments for SEARCH_GROUP keyword :
. P : provide only primitive space groups
. ALL: provide primitive and centered space groups
. CENTERED/NOT_P: provide only centered space groups
# CIF files created by SHELXL2014 are correctly read (changes in
in CRYSFML to read new CIF strings as :
. _space_group_name_H-M_alt
. _space_group_symop_operation_xyz
. _space_group_crystal_system
# Parameters for D8 Venture diffractometer (Bruker AXS) has been included and
can be accessed from setting file in [DEVICE] section through :
"diffractometer = D8_VENTURE_Cu" or "diffractometer = D8V_Cu"
"diffractometer = D8_VENTURE_Mo" or "diffractometer = D8V_Mo"
for Cu and Mo radiations respectively.
# Flack parameter is now provided in HTML and TXT reports.
December 2014
# Archive.cif command line argument can be followed by "NO_HKL",
allowing to exclude HKL file in final archive, independently
of the contain of cryscalc.ini setting file.
November 2014
# New argument for DATA_neutrons keyword, allowing to provide
to the user neutron scattering length versus energy for
some rare earths and isotopes. The following arguments can be
input: Sm_nat, SM_149, Eu_nat, Eu_151, Gd_nat, Gd_155, Gd_157,
Dy_164, Er_nat, Er_167, Yb_nat, Yb_168, Yb_174 and Lu_176.
Thanks to Pierric Lemoine (ISCR) for taping neutron scattering
lengths from the following reference :
Atomic data and nuclear data tables 44, 191-207 (1990)
J.E. Lynn and P.A. Seeger, L.A.N.L.
# 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
October 2014
# 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 [PATTERN SIMULATION] 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.cif import.cif
. my_job.cif : main .CIF file, used to extract structural
parameters
. import.cif : secondary .CIF file, containing experimental
parameters (crystal and experimental features, ...)
September 2014
# 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 2014
# "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.
# TO AVOID CONFUSION, 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 2014
# 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.
By defauft, details (structural informations, hkl list ...) are not listed on
screen but can be output by replacing "create_PAT_PRF" by create_PAT_PRF_out.
May 2014
# 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 2014
# 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 listed in A
# VOL argument for CONN keyword:
polyedron volume calculation, based on VOLCAL program
of L. W. FINGER, included in CFML
February 2014
# BARY keyword:
Centroid calculation can be applied with only 2 input atoms
# Bug has been corrected in the HTML report combined with
SQUEEZE option.
November 2013
# STAR_K keyword:
Apply rotational parts of the symmetry operators of a given
space group on the components of a propagation wave vector.
October 2013
# 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
September 2013
# 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 2013
# 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 2013
# READ_INS keyword: by default, Q peaks are not read.
Q_PEAKS argument has to be specified for not skipping Q peaks
April 2013
# 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 2013
# 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)
February 2013
# 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 :
https:\\cdifx.univ-rennes1.fr\progs\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.
January 2013
# 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 :
https:\\cdifx.univ-rennes1.fr\progs\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
December
# New "FRIEDEL" keyword allows to get number pairs of Friedel
in hkl file
November 2012
# 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 symmetry 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)
October 2012
# "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
September 2012
# 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 2012
# 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 2012
# 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 2011
# 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 2011
# 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 2011
# 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 2011
# 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 2011
# 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 2011
# 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
February 2011
# 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 (https://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.
January 2011
# 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)
December 2010
# 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
November 2010
# 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
October 2010
# A threshold value can be given as argument to the SEARCH_GROUP keyword
September 2010
# 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 2010
# Bugs in the FIND_HKL_LIST routine has been corrected
April 2010
# Some items of the experimental part in the HTML structure report are now
in italic in agreement with published articles.
March 2010
# 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
February 2010
# 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.
January 2010
# Bug in _trans.HKL file has been corrected.
November 2009
# 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
October 2009
# 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
September 2009
# 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
February 2009
# CHECK_GROUP can now determine trigonal space group
# SG_ALL keyword output sub-groups of the current space group
January 2009
# .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
November 2008
# 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
October 2008
# 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 ...
September 2008
# 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 2008
# REPORT/REPORT_long: CIF fields can be independly in lower and
upper cases
April 2008
# CONN keyword: calculation of connectivity around a selected atom
given as argument.
September 2007
# 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 2007
# 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 2007
# 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 2007
# .x file (created by DENZO) and .rmat file (created by DIRAX) can be
passed as argument for CELL keyword
February 2007
# RESET keyword for input parameters and arrays initialization
January 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.
November 2006
# X rays data for Ag, Fe and Cr have been tabulated
# Launch CRYSCAL with P4P argument in command line:
d:\> 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
October 2006
# 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)
September 2006
# FILE keyword: .m91 and .m95 files created by JANA can be read
# CELL keyword: .m50 file can be read
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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\Notepad++\notepad++.exe"
cifviewer = "C:\Program Files\CCDC\CSD_2020\Mercury\mercury.exe"
[WEB ADDRESS]
fps = www.ill.fr/dif/Soft/fp/
cdifx = https://cdifx.univ-rennes1.fr/
cryscalc = https://cdifx.univ-rennes1.fr/cryscalc
reciprocs = https://cdifx.univ-rennes1.fr/reciprocs
[DEVICE]
diffractometer = APEXII AXS Bruker
!diffractometer = KCCD Nonius
!diffractometer = D8 VENTURE Mo
laboratory = CDIFX Rennes
radiation = X_Mo
wave_A = 0.71073
temperature_K = 150
beam_stop_limit = 3.0
holder = cryoloop
fast_scan_included = 1
[USER]
name = ROISNEL
first_name = Thierry
address = Centre de Diffractométrie X, UMR6226 CNRS Université de Rennes,Institut des Sciences Chimiques de Rennes, 35042 RENNES Cedex France
email = thierry.roisnel@univ-rennes.fr
web = https://cdifx.univ-rennes.fr
team = CDIFX
orcid = 0000-0002-6088-4472
[ARRAYS DIMENSIONS]
hkl_reflections = 200000 ! max. number of hkl reflections in a file
nb_scans = 50 ! max. number scans in a single crystal diffraction experiment
[CREATE INS]
get_sample_ID = 0 ! get sample ID (default=job)
temperature = 150K ! experimental temperature value
u_threshold = 0.1 ! atoms with U_iso > U_threshold will be excluded
[PARAMETERS]
i_sig = 3. ! used in SEARCH_GROUP procedure
threshold = 0.03 ! used in 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_CIF = 1 ! .CIF file
create_INS = 1 ! .INS file for SHELXL
create_FHZ = 1 ! .FHZ (Z-matrix)
create_FST = 1 ! .FST file for FP Studio
create_XYZ = 0 ! .XYZ file (Cartesian coordinates)
create_PDB = 0 ! .PDB (Protein Data Bank)
create_CIF_pymol = 0 ! X_pml.CIF for PYMOL
create_PCR = 0 ! .PCR file for FullProf
create_PAT_PRF = 1 ! .PRF file for FullProf
create_PAT_PDPF = 0 ! .pdpf file
create_report_TXT = 0 ! .TXT structural report
create_report_LATEX = 0 ! LATEX/PDF structural report
create_report_HTML = 0 ! .HTML structural report
[PROGRAMS]
structure_solution_name = SHELXT
structure_solution_reference = G.M. Sheldrick, Acta Cryst. A71 (2015) 3-8
structure_solution_cif_ref = SHELXT (G. Sheldrick, 2015)
structure_refinement_name = SHELXL-2014
structure_refinement_reference = G.M. Sheldrick, Acta Cryst. C71 (2015), 3-8
structure_refinement_cif_ref = SHELXL-2018/3 (G. Sheldrick, 2015)
absorption_correction_name = SADABS
absorption_correction_reference = Sheldrick G.M. (2014), SADABS Bruker AXS Inc., Madison, Wisconsin, USA
absorption_correction_cif_ref = Sheldrick G.M. (2014), SADABS Bruker AXS Inc., Madison, Wisconsin, USA
[OPTIONS]
LOG_file = 1 ! create CRYSCALC.LOG file
LOCK_wave_value = 0.02 ! lock current wavelength to anticathode value
update_parameters = 1 ! update parameters after transformation(cell parameters, atomic coordinates)
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
ref_overlap_criteria = 0.10 ! criteria on hkl index for overlapped reflections criteria
search_mono_criteria = 2.5 ! max. diff. between monoclinic angle and 90.
search_SG_only_mono = 1 ! output only monoclinic space groups compatible with unit cell metrics
bad_rint_criteria = 25. ! criteria to define bad value for Rint
atom_occ_type = 0 ! 0: %occ ; 1: n_occ*%occ
atom_adp_type = 0 ! 0: B_iso ; 1: U_sio (only in CFL files)
[ARCHIVE_AND_REPORT]
CIF_powder = 0 ! create archive.CIF file for single crystal data
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
CIF_author = 0 ! include author name and address in CIF file
CIF_audit = 0 ! include audit details in CIF file
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
include_experimenter = 1 ! include experimenter name in the archive_cryscalc.cif file
report_header = 1 ! Write header in structural report
report_details = 1 ! Write details in structural report
report_diffraction_frame = 1 ! include diffraction frame in structural report
report_crystal_picture = 1 ! include crystal picture in structural report
report_structure_ORTEP = 1 ! include ORTEP structure in structural report
latex_cmb = 0 ! use Computer Modern Bright font in LaTeX report
latex_sans_serif = 1 ! use Sans Serif font in LaTeX report
latex_title_back_color = #e3e6f7 ! Main title background color in LaTex report
latex_title_text_color = #580a0a ! Main title text color in LaTex report
latex_title_border_color = #000000 ! Main title border color in LaTex report
latex_title1_back_color = #fafafa ! Title background color in LaTex report
latex_title1_text_color = #580a0a ! Title background text in LaTex report
latex_title1_border_color = #fafafa ! Title background text in LaTex report
latex_title1_text_center = 0 ! Title text centering (0/1)
[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 = eta0 + 2theta * eta1
X_profile_eta1 = 0.
X_profile_TCH_U = 0.0046 ! Profile parameters for Voigt (TCH) function
X_profile_TCH_V = 0.0375 ! HG**2 = U*TAN**2(theta) + V*TAN(theta) + W
X_profile_TCH_W = 0.0027 ! HL = X*TAN(Theta) + Y/cos(Theta) + Z
X_profile_TCH_X = 0.
X_profile_TCH_Y = 0.014
X_profile_TCH_Z = 0.
X_pattern_step = 0.01
X_pattern_xmin = 0.
X_pattern_xmax = 120.
X_pattern_wave = 1.5406
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_profile_TCH_U = 0.0097 ! Profile parameters for Voigt (TCH) function
N_profile_TCH_V = -0.0356 ! HG**2 = U*TAN**2(theta) + V*TAN(theta) + W
N_profile_TCH_W = 0.0493 ! HL = X*TAN(Theta) + Y/cos(Theta) + Z
N_profile_TCH_X = 0.
N_profile_TCH_Y = 0.0089
N_profile_TCH_Z = 0.
N_pattern_step = 0.025
N_pattern_xmin = 0.
N_pattern_xmax = 120.
N_pattern_wave = 1.23
N_pattern_scale = 100.
N_pattern_background = 50.
particles_size = 9999.
strains = 0.
plot_DSF = 1 ! plot Debye-Scherrer film
plot_PRF = 1
plot_XY = 0
PRF_header = 0
profile_function = PV ! PV / TCH
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 patterncalculation
[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
MAT_4 = 2. 0. 0. 0. 2. 0. 0. 0. 2. ! 2a2b2c
MAT_5 = 0. 0. 1. 0. 1. 0. -1. 0. 1. ! C_to_I
MAT_6 = 1. 0. -1. 0. 1. 0. 1. 0. 0. ! I_to_C
[USER SHORTCUTS] ! only in expert mode
RCJ = READ_CIF job.cif
RIJ = READ_INS job.ins no_out
CALC = DOS calc
MAX_10 = GEN_HKL theta_min=0. theta_max=10 out_10
MAX_3 = GEN_HKL theta_min=0. theta_max=3 out
PAT_10_80 = GEN_HKL 2theta_min=10. 2theta_max=80
SF1 = SF_HKL 0 0 2
SF1 = SF_HKL 0 0 2
SF2 = SF_HKL 0 0 -2
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Examples of .CFL input files :
How to's :
CRYSCALC links :
last update: TR / CDIFX/PRTS/ISCR - 25.04