CRYSTAL

Purpose

A representation of a crystal, from a mainly diffraction perpective

Synopsis

A crystal is comprised of a unit cell information, SPACEGROUP information, and diffraction reflection information stored as REFLECTIONVEC.

The module provides considerable functionality, including the ability to produce predicted structure factors by optimising scla e and extinction corrections. It can also sum certain fourier transform integrals (charge, spin, current) into unique combinations for structure factor calculations, or constrained wavefunction calculations. It can also determine neighbouring atoms and clusters from an initial fragment, as well as repetition factors, Z factors, asymmetric units and so on. There are various statistical routines which calculate agreement factors between calculated and observed structure factors, inclusing some plot-generating routines (scatter plots, QQ-plots, etc).

Default input data order

There is no associated CRYSTALVEC type; an input data order has not been defined.

Listing of keywords

cell_angles= REALVEC(3)

Read the unit cell angles in the order α, β, γ.

  • Use the degrees unit modifier to change from default of radians

  • unit_cell_angles= is synonymous

cell_lengths= REALVEC(3)

Read the unit cell lengths in the order a, b, c.

  • Use the angstrom unit modifier to change from default of atomic units

  • unit_cell_lengths= and unit_cell_dimensions= are synonymous

correct_dispersion= BIN

Read a switch which tells whether to correct dispersion when calculating the structure factors

  • The method uses atomic dispersion factors

  • The method may be buggy

destroy_reflection_data

If any reflection data are stored, destroy it in preparation for fresh data

  • The reflection data are entered using the reflection_data= keyword

  • This is synonymous with erase_reflection_data

destroy_spacegroup

If any spacegroup data are stored, destroy it in preparation for fresh data

  • The spacegroup data are entered using the spacegroup_symbol=, spacegroup_it_symbol= or spacegroup_hall_symbol=.

  • This is synonymous with erase_spacegroup

erase_reflection_data

If any reflection data are stored, destroy it in preparation for fresh data

  • The reflection data are entered using the reflection_data= keyword

  • This is synonymous with destroy_reflection_data

erase_spacegroup

If any spacegroup data are stored, destroy it in preparation for fresh data.

  • The spacegroup data are entered using the spacegroup_symbol=, spacegroup_it_symbol= or spacegroup_hall_symbol=.

  • This is synonymous with destroy_spacegroup

exp_scale_factor

Read in a scale factor which is used to multiply any experimental structure factors or experimental sigma values.

  • The scale factor is applied only once

  • Refer to the reflection_data= keyword

kind= STR

Read the kind of crystal data that is to be stored.

  • The allowed kinds are x-ray or pnd

make_f_predicted

Make the predicted magnitudes of the structure factors, including possibly an overall scale factor and extinction correction.

  • Refer to the optimise_scale= keyword

  • Refer to the optimise_extinction_factor= keyword

optimise_extinction= BIN

Equivalent to optimise_scale_factor=

optimise_extinction_factor= BIN

Read a switch whether to use an extincton factor when calculating the magnitudes of the predicted structure factors.

  • Refer to the make_f_predicted

optimize_extinction= BIN

Equivalent to optimise_scale_factor=

optimize_extinction_factor= BIN

Equivalent to optimise_scale_factor=

optimise_scale= BIN

Equivalent to optimise_scale_factor=.

optimise_scale_factor= BIN

Read a switch whether to optimise a scale factor when calculating the magnitudes of the predicted structure factors.

  • The X-ray structure factors are often not determined on an absolute scale, so a scale factor may be used to minimise the χ2 agreement statistic between the experimental and calculated structure factors

  • By convention it is the calculate structure factors which are scaled, even though in reality it is the experimental structure factors which should be

optimize_scale= BIN

Equivalent to optimise_scale_factor=.

optimize_scale_factor= BIN

Equivalent to optimise_scale_factor=.

partition_model= STR

Read the "partition model" used to calculate structure factors when using "oversampled" model of the crystal unit cell.

  • An oversampled cell is one which is greater than the asymmetric unit; partition factord are introduced to obtain a correct repeating density for the crystal

  • Allowed options are none, mulliken or gaussian

reflection_data= REFLECTIONVEC

Enter a list of reflection data.

spacegroup_hall_symbol= STR

Enter the spacegroup in Hall notation.

  • Refer to spacegroup_it_symbol

  • Refer to SPACEGROUP:set_Hall_conversion_table so see the relationship between Hall symbols and international table symbols

  • For details of notation and non standard axis and origin settings, see: S. R. Hall, Acta Cryst. A37, 517 (1981)

spacegroup_it_symbol= STR

Read the international table (IT) symbol for the spacegroup.

  • Use a caret ^ before a character to represent a bar over that character; e.g is ^P

  • Use an underscore _ after a character to represent a subscript; e.g. 2ab is 2_ab

  • Use a slash / where a slash should go

  • Do not use spaces between symbols

spacegroup_symbol= STR

Equivalent to spacegroup_it_sumbol=.

synthesize_sigma_i= BIN

Read the switch whether to artificially createσ(I) errors, whereI is an intensity, when evaluating theχ^2 agreement statistic based on intensities.

  • Refer to routine I_sigma

thermal_smearing_model= STR

Read the thermal smearing model to use to correct for thermal vibration in the calculated structure factors.

  • Allowed models are none, coppens, stewart, tanaka

  • For explanation, refer to: Grimwood and Jayatilaka, (2001), Acta. Cryst., A57, 87-100.

unit_cell_angles= REALVEC(3)

Read the unit cell angles in the order α, β, γ.

  • Use the degrees unit modifier to change from default of radians

  • cell_angles= is synonymous

unit_cell_dimensions= REALVEC(3)

Read the unit cell dimensions in the order a, b, c.

  • Use the angstrom unit modifier to change from default of atomic units

  • cell_lengths= and unit_cell_lengths= are synonymous

unit_cell_lengths= REALVEC(3)

Read the unit cell lengths in the order a, b, c.

  • Use the angstrom unit modifier to change from default of atomic units

  • cell_lengths= and unit_cell_dimensions= are synonymous

wavelength= REAL

Read the wavelength λ used in the X-ray or netron diffraction experiment.

  • The value is used to calculated sin(&thetas;)/λ values for each reflection, often quoted in diffraction experiments