CRYSCALc
************************************************************* * * * CRYSTALLOGRAPHIC CALCULATIONS * * * * * * T. Roisnel * * (CDIFX - ISCR UMR6226 Rennes) * * 7 Nov. 2014 * * * * with courtesy of JRC and JGP for CFML * * * * * * contact: thierry.roisnel@univ-rennes1.fr * * * * Web site : www.cdifx.univ-rennes1.fr/cryscalc * * * *************************************************************
Introduction :
List of CRYSCALc keywords :
[return]Details of CRYSCALc keywords :
> ABSENT_HKL:
. type: OUTPUT keyword . meaning: search for observed reflections (with F2>0.) that should be absent for a given space group . optionnal arguments: . arg = "ALL": all the violations reflections are output . arg = "OUT": requested reflections are output on the screen . arg = "WRITE": requested reflextions are output in a HKL file . arg = real_value (n_sig): only reflections with I/sig > n_sig are output . mandatory keyword: FILE, SPGR . identical keywords: ABSENT_HKL, HKL_ABSENT [return to keywords list]> ABSORPTION:
. type: CALCULATION keyword . arguments: no argument . meaning: absorption coefficient calculation . mandatory keywords: CELL, WAVE, CONT / CHEM . identical keywords: ABSORPTION, ABSORPTION_CALC, CALC_ABSORPTION, MU, CALC_MU, MU_CALC [return to keywords list]> ACTA:
. type: OUTPUT keyword . arguments: no argument . meaning: create CRYSCALC.CIF file containing calculation results in a CIF format . identical keywords: ACTA, CIF, CREATE_CIF [return to keywords list]> ANG:
. type: CALCULATION keyword . arguments: 3 character strings . meaning: calculation of the angle defined by three atoms labelled by the atom labels (cf ATOM keyword) . example: ANG C8 C10 C9 or . arguments: 4 character strings . meaning: calculation of the angle defined by the segments constituted by atoms couples labelled as S_1, S_2 and S_3, S_4 respectively (cf ATOM keyword) . remark: atom label can refer to equivalent position through a particular symmetry operator (cf SYMM keyword). This is specified by adding "_$n" to the atomic label, with n refering to the number of symmetry operator in the list. . example: ANG O1 C8 C9 C10_$1 . identical keywords: ANG, ANGLE [return to keywords list]> APPLY_OP:
. type: OUTPUT keyword . arguments : no argument . outputs: apply the symmetry operators on the atomic positions . mandatory keyword: SYMM, ATOM . identical keywords: APPLY_OP, APPLY_SYMMETRY_OPERATOR, APPLY_SYM_OP, APPLY_SYMOP [return to keywords list]> ATOM:
. type: INPUT keyword . arguments: 2 character strings and 5 reals . meaning: . string #1: atomic label . string #2: atom type (can contain oxdation state) . x,y,z atomic reduced coordinates . Biso, site occupancy (%) . remarks: . if Biso is missing: Biso = 0.0 . if Occ(%) is missing: Occ(%) = 1.0 (site is fully occupied) . example: ATOM O1 O 0.04356 0.03008 0.39001 0.35 1. ATOM C8 C 0.02071 -0.12436 0.36957 0.30 1. ATOM C9 C -0.27497 -0.07538 0.27585 0.30 1. ATOM C10 C -0.16896 -0.18823 0.36382 0.32 1. ATOM Si1 Si+4 0.53245 0.53245 0.5 ATOM O1 O-2 0.58566 0.85594 0.61727 . identical keywords: ATOM, ATM [return to keywords list]> ATOM_LIST:
. type: OUTPUT keyword . optional argument: "CART" . meaning: list the atoms (type, labels, coordinates, ...) if "CART" is present, cartesian atomic coordinates will be output. derivative CART arguments : CART_A (a//x), CART_C (x//c) if "in_A" is present, atomic coordinates are listed in A. . optional keyword: SPGR . identical keywords: ATOM_LIST, ATOM_LST, LIST_ATOM_LIST, LIST_ATOMS, LST_ATOMS, WRITE_ATOMS, WRITE_ATMS [return to keywords list]> BARY:
. type: CALCULATION keyword . arguments: n character strings or "ALL" . meaning: calculation of the coordinates of the centroid of the n atoms known by the atom label (cf ATOM keyword) if arg="ALL": all input atoms are considered . examples: BARY C8 C10 C9 C11 BARY ALL . identical keywords: BARY, CENTROID [return to keywords list]> BEAM:
. type: INPUT keyword . arguments: character string . meaning: type of the incident beam: - BEAM NEUT for neutrons - BEAM ELECTRONS for electrons - X_Ag for X Rays (Silver K_alpha) - X_Mo for X Rays (Molybdenum K_alpha) - X_Cu for X Rays (Copper K_alpha) - X_Ni for X Rays (Nickel K_alpha) - X_Co for X Rays (Cobalt K_alpha) - X_Fe for X Rays (Iron K_alpha) - X_Cr for X Rays (Chromium K_alpha) . example: BEAM X_Mo . identical keyword: BEAM, JOBTYPE, JPBTYP [return to keywords list]> CELL:
. type: INPUT keyword . arguments: 6 reals or 1 character string . meaning: - reals: unit cell parameters in A (a, b, c) and angle in deg. (alfa, beta, gamma) - character string: file name containing unit cell parameters. Following files can be read: . INS/RES file for SHELXL . P4P file created by SAINT . M50 file created by JANA . X file created by DENZO . RMAT file created by DIRAX . output: unit cell volume calculation direct and reciprocal unit cell parameters . example: CELL 7.6520 7.8450 11.0760 90. 90. 90. CELL my_saint_data.P4P CELL my_janat_data.m50 . identical keywords CELL, CELL_PARAMETERS [return to keywords list]> CHEM:
. type: INPUT keyword . arguments: n "El_i_n_i" character strings (without blank character between label and number) . meaning: Molecular chemical formula: El_i is the chemical symbol of the species i and n_i is the corresponding number of atoms in the formula unit . output: molecular weight, total number of electrons, atomic and weight percentage . mandatory keyword: ZUNIT . example: CHEM C4 O6 H9 N1 . identical keywords: CHEM, CHEM_FORM, CHEMICAL_FORMULA [return to keywords list]> CONN:
. type: INPUT keyword . argument: atom_label + dist_max . optional arguments: ALL, ALL_X, NO_X, ANG, BVS, VOL, SHAPE, SELF, MIN=, M CONDENSED . meaning: determine the connectivity around the atom "atom_labe with interatomic distances calculated between MIN and MAX values. Default values for MIN and MAX = 0.4 and 3.0 A. if argument=ALL, the program will calculate connectivity around all atoms. if argument=ALL_X, the program will calculate connectivity around all atoms of the species X. if argument=NO_X, the program will exclude connectivity with all atoms of the species X. if "ANG" is present, interatomic angles will also be calculated. if "BVS" is present, bond valence sums calculations are performed. if "VOL" is present, polyedron volume is calculated (ref. : VOLCAL program of L. W. FINGER included in C if "SHAPE" is present, an input file for SHAPE program (http://www.ee.ub.es/) is created. derivative SHAPE arguments : SHAPE_A (a//x), SHAPE_C (x//c) if SELF (or AUTO) is present, output distances betwee atoms from the same label if CONDENSED is present, short ouput is created ex: CONN Yb1 SELF 10. ex: CONN Si1 MIN=1.5 MAX=2.7 ex: CONN Nd1 VOL SHAPE ex: CONN ALL_Nd ex: CONN ALL ANG CONDENSED ex: CONN Cu1 no_H . output: interatomic distances, bond distribution and optional calculations. Effective distance is calculated as follows: r_eff=[N/Sum(r^-3)]^1/3 IF CIF/ACTA keyword is input, the created CIF file will contains all the calculated distances in CIF format. . mandatory keywords: SPGR, ATOM, CELL . identical keywords: CONN, CONNECT, CONNECTIVITY [return to keywords list]> CONT:
. type: INPUT keyword . arguments: n "El_i n_i"(character string, real) couples . meaning: unit cell contents: El_i is the chemical symbol of the species i and n_i is the corresponding number of atoms in the unit cell . optional keyword: ZUNIT . example: CONT C 16. O 24. H 36. N 4. [return to keywords list]> CREATE_ACE :
. type: OUTPUT keyword . argument: no . meaning: create .ACE file for CaRIne from a CIF file . mandatory keyword: READ_CIF file.cif . dependent parameter: CREATE_ACE parameter value in the CRYSCALC.INI setting file. If equal to 1, a .ACE file will be automatically created if a .CIF file is given as argument when CRYSCALc is launching from a command line : > cryscalc file.cif [return to keywords list]> CREATE_CEL
. type: OUTPUT keyword . argument: no . meaning: create .CEL file for PowderCELL from a CIF file . mandatory keyword: READ_CIF file.cif . dependent parameter: CREATE_CEL parameter value in the CRYSCALC.INI setting file. If equal to 1, a .CEL file will be automatically created if a .CIF file is given as argument when CRYSCALc is launching from a command line : > cryscalc file.cif [return to keywords list]> CREATE_CFL
. type: OUTPUT keyword . argument: no . meaning: create .CFL file for CRYSCALc from a CIF file . mandatory keyword: READ_CIF file.cif . dependent parameter: CREATE_CFL parameter value in the CRYSCALC.INI setting file. If equal to 1, a .CFL file will be automatically created if a .CIF file is given as argument when CRYSCALc is launching from a command line : > cryscalc file.cif [return to keywords list]> CREATE_FST
. type: OUTPUT keyword . argument: POLY, RUN, MOLE, No_H . meaning: create .FST file for FP Studio if argument=POLY : include polyedra if connectivity calculation have been performed if argument=RUN : launch FP_studio software if argument=MOLE: only atoms of the asymetric unit cell are drawn. if argument=No_H: H atoms and related bonds are excluded. This option is valid only if MOLE is specified. . mandatory keyword: READ_CIF file.cif or READ_INS file.ins . dependent parameter: CREATE_fst parameter value in the CRYSCALC.INI setting file. If equal to 1, a .fst file will be automatically created if a .CIF file is given as argument when CRYSCALc is launching from a command line : > cryscalc file.cif [return to keywords list]> CREATE_INS
. type: OUTPUT keyword . argument: no . meaning: create .INS file for SHELXL from a CIF file . mandatory keyword: READ_CIF file.cif . dependent parameter: CREATE_INS parameter value in the CRYSCALC.INI setting file. If equal to 1, a .INS file will be automatically created if a .CIF file is given as argument when CRYSCALc is launching from a command line : > cryscalc file.cif [return to keywords list]> CREATE_REPORT:
. type: output keyword . optional argument: .CIF file name . meaning: create a STRUCTURAL_REPORT.HTML file in HTML format from the reading of the ARCHIVE.CIF file present in the current folder, and launch the browser with this HTML file. The .CIF file can be explicitely defined with the argument. If "long" or "ext" is given as argument, a longer report will be created, containing more informations, included distances and angles. . identical keywords: REPORT, CREATE_REPORT . examples: report report long my_struct.cif [return to keywords list]> CREATE_SOLVE:
. type: output keyword . meaning: create input files for structure solving software as SIR97; SHELXS/T and SUPERFLIP . optional argument: no . dependent parameter: CELL parameters, cell content, space group and hkl file has to be provided . identical keywords: CREATE_SOLVE, CREATE_TO_SOLVE, CREATE_FILES_TO_SOLVE, SOLVE [return to keywords list]> CREATE_TIDY:
. type: OUTPUT keyword . argument: no . meaning: create xx_tidy.dat file for TIDY (standardisation of inorganic crystal-structure data [Acta Cryst. 1984, A40, 169-183] from a .CIF or .INS file . mandatory keyword: READ_CIF file.cif or READ_INS file.ins . identical keywords: CREATE_TIDY, CREATE_TIDY_FILE, CREATE_TIDY_INPUT_FILE [return to keywords list]> D_HKL:
. type: CALCULATION keyword . argument: real values . meaning: d_hkl(A) values . outputs: Q(A-1), SinTheta/lambda(A-1) theta(deg) for known wavelength . optionnal keyword: WAVE . identical keywords: D_HKL, DHKL . example: DHKL 0.77 [return to keywords list]> D_STAR:
. type: CALCULATION keyword . argument: real values . meaning: 1/d_hkl (A-1 . outputs: d(A) theta(deg) . optionnal keyword: WAVE . identical keywords: D_STAR, D_STAR_HKL, DSTAR, DSTARHKL, DSTAR_HKL . example: D_STAR 0.5 [return to keywords list]> DATA_ATOMIC_DENSITY:
. type: OUTPUT keyword . optionnal argument: PLOT . meaning: list atomic density data for all atoms if arg=PLOT: create a PGF file and plot it with WinPLOTR . identical keywords: DATA_DENSITY, DENSITY_DATA, DATA_ATOMIC_DENSITY, ATOMIC_DENSITY [return to keywords list]> DATA_ATOMIC_RADIUS:
. type: OUTPUT keyword . optionnal argument: PLOT . meaning: list atomic radius data for all atoms if arg=PLOT: create a PGF file and plot it with WinPLOTR . identical keywords: DATA_RADIUS, RADIUS_DATA, DATA_ATOMIC_RADIUS, ATOMIC_RADIUS [return to keywords list]> DATA_ATOMIC_WEIGHT:
. type: OUTPUT keyword . optionnal argument: PLOT . meaning: list atomic weight data for all atoms if arg=PLOT: create a PGF file and plot it with WinPLOTR . identical keywords: DATA_WEIGHT, WEIGHT_DATA, DATA_ATOMIC_WEIGHT, ATOMIC_WEIGHT [return to keywords list]> DATA_NEUTRONS:
. type: OUTPUT keyword . optionnal argument: PLOT . meaning: list neutrons data for all atoms (coherent scattering length, incoherent scattering cross-section, absorption cross-section) Neutron data are extracted from : V.F. Sears Neutron News, vol.3 n°3, 1992, 26-37 if arg=PLOT: create a PGF file and plot it with WinPLOTR . see: Xrays_DATA . identical keywords: DATA_NEUTRONS, NEUTRONS_DATA, DATA_NEUTRON, NEUTRON_DATA [return to keywords list]> DATA_XRAYS:
. type: OUTPUT keyword . optionnal argument: PLOT . meaning: list X-ray data for all atoms (total interaction cross section for Ag, Mo, Cu, Co, Fe and Cr radiation X-ray data are extracted from : Tables Internationales vol.C 1995, p.200-206, Tables Internationales vol.C 1995, p. 193-199 if arg=PLOT: create a PGF file and plot it with WinPLOTR [return to keywords list]> DIAG:
. type: INPUT keyword . arguments: 9 reals . meaning: transformation (3,3) matrix components . examples: MATR 0 0 1 0 1 0 -1 0 -1 MATR 0.5 0.5 0 -0.5 0.5 0 0 0 1 MATR 1/2 1/2 0 -1/2 1/2 0 0 0 1 . output: Diagonalization of the 3*3 matrix and output the Eigen values and Eigen vectors . identical keywords: DIAG, DIAG_MAT, DIAG_MATR, DIAG_MATRIX [return to keywords list]> DIR_ANG:
. type: CALCULATION keyword . arguments: 2*3 reals . meaning: calculation of the angle between 2 vectors in the direct space. The 3 first real values are related to the coordinates of the first vector and the 3 last real values to the coordinates of the second vector . mandatory keyword: CELL . identical keywords: DIR_ANG, DIRANG, DIRECT_ANGLE . example: DIR_ANG 1. 0. 0. 0. 1. 0. [return to keywords list]> DIST:
. type: CALCULATION keyword . arguments: 2 character strings . meaning: calculation of the interatomic distance between 2 atoms labelled by their atom labels (cf ATOM keyword) . remark: atom label can refer to equivalent position through a particular symmetry operator (cf SYMM keyword) atomic label, with n refering to the number of symmetry operator in the list. . example: DIST C8 C10 DIST C10 C9 DIST C10 C9_$1 . identical keywords: DIST, DISTANCE, ATOMIC_DISTANCE > DIST_MULT: . type: CALCULATION keyword . arguments: 1 real (x) + 2 character strings (A B) . meaning: - calculation of the interatomic distance between 2 atoms labelled by their atom labels A and B . - calculation of the coordinate of the point M with : d_AM = d_AB * x . example: DIST_X C8 C10 1.2 . identical keywords: DIST_MULT, DIST_X > DIST_PLUS: . type: CALCULATION keyword . arguments: 1 real (x) + 2 character strings (A B) . meaning: - calculation of the interatomic distance between 2 atoms labelled by their atom labels A and B . - calculation of the coordinate of the point M with : d_AM = d_AB + x . example: DIST_PLUS C8 C10 1.2 . identical keywords: DIST_PLUS, DIST_+ > DIST_DHA: . type: CALCULATION keyword . arguments: 2 character strings (D A) . aoptional argument: 1 real d_H (default value=0.9 Ang.) . meaning: - calculation of the interatomic distance between donor (D) and acceptor atoms (A) . - calculation of the coordinate of H atom with : d_DH = d_AB - d_H . examples: DIST_DHA N1 O2 DHA N1 O2 0.92 . identical keywords: DIST_DHA, DHA, POS_H, CALC_POS_H [return to keywords list]