VORONOI

References: Rycroft2009, Thomas2015, Brehm2018, Brehm2020, Brehm2021

Controls the Voronoi integration of the total electron density for the computation of electromagnetic moments, see [Thomas2015], [Brehm2020], and [Brehm2021] (via LibVori see https://brehm-research.de/voronoi). [Edit on GitHub]

Subsections

Keywords

Keyword descriptions

SECTION_PARAMETERS

Type: enum
Default: OFF
Lone keyword: SILENT
Usage: silent

Description: Level starting at which this property is printed

Valid values:

  • ON

  • OFF

  • SILENT

  • LOW

  • MEDIUM

  • HIGH

  • DEBUG

[Edit on GitHub]

ADD_LAST

Type: enum
Default: NO
Usage: ADD_LAST (NO|NUMERIC|SYMBOLIC)

Description: If the last iteration should be added, and if it should be marked symbolically (with lowercase letter l) or with the iteration number. Not every iteration level is able to identify the last iteration early enough to be able to output. When this keyword is activated all iteration levels are checked for the last iteration step.

Valid values:

  • NO Do not mark last iteration specifically

  • NUMERIC Mark last iteration with its iteration number

  • SYMBOLIC Mark last iteration with lowercase letter l

[Edit on GitHub]

APPEND

Type: logical
Default: F
Lone keyword: T

Description: Appends frames to already existing .voronoi file.

[Edit on GitHub]

COMMON_ITERATION_LEVELS

Type: integer
Default: 0
Usage: COMMON_ITERATION_LEVELS

Description: How many iterations levels should be written in the same file (no extra information about the actual iteration level is written to the file)

[Edit on GitHub]

FILENAME

Type: string
Usage: FILENAME ./filename

Description: controls part of the filename for output. use __STD_OUT__ (exactly as written here) for the screen or standard logger. use filename to obtain projectname-filename. use ./filename to get filename. A middle name (if present), iteration numbers and extension are always added to the filename. if you want to avoid it use =filename, in this case the filename is always exactly as typed. Please note that this can lead to clashes of filenames.

[Edit on GitHub]

JITTER

Type: logical
Default: T
Lone keyword: T
Usage: JITTER T

Description: The Voronoi tessellation can have issues with highly symmetric structures. This keyword displaces all atoms pseudo-randomly by a tiny amount (see JITTER_AMPLITUDE) to break symmetry. The displacement is constant over time, so that no temporal noise is introduced. The displacement is not visible to other CP2k routines (FORCE_EVAL, output). It is only applied internally in the library for the Voronoi tessellation.

[Edit on GitHub]

JITTER_AMPLITUDE

Type: real
Default: 1.00000000E-003 [angstrom]
Usage: JITTER_AMPLITUDE 0.01

Description: Sets the maximum displacement amplitude for the jitter.

[Edit on GitHub]

JITTER_SEED

Type: integer
Default: 0
Usage: JITTER_SEED 1234

Description: Sets the random seed for the jitter. The pseudo-random number generator is re-initialized for each Voronoi tessellation so that the jitter is constant over simulation time (no temporal noise).

[Edit on GitHub]

LOG_PRINT_KEY

Type: logical
Default: F
Lone keyword: T
Usage: LOG_PRINT_KEY

Description: This keywords enables the logger for the print_key (a message is printed on screen everytime data, controlled by this print_key, are written)

[Edit on GitHub]

MOLECULAR_PROPERTIES

Type: logical
Default: F
Lone keyword: T
Usage: MOLECULAR_PROPERTIES T

Description: Calculation of molecular properties from Voronoi integration.

[Edit on GitHub]

MOLPROP_FILE_NAME

Type: string
Default: __STD_OUT__
Usage: MOLPROP_FILE_NAME

Description: Root of the file name where to print molecular properties. filename.molprop is used.

[Edit on GitHub]

OUTPUT_EMP

Type: logical
Default: F
Lone keyword: T
Usage: OUTPUT_EMP T

Description: Writes the resulting electromagnetic moments to a binary file “properties.emp”. The file name cannot be changed.

[Edit on GitHub]

OUTPUT_TEXT

Type: logical
Default: T
Lone keyword: T
Usage: OUTPUT_TEXT T

Description: Writes the resulting electromagnetic moments to text files (*.voronoi). The file name is specified via FILENAME.

[Edit on GitHub]

OVERWRITE

Type: logical
Default: F
Lone keyword: T
Usage: OVERWRITE T

Description: Specify this keyword to overwrite any existing “properties.emp” file if it already exists. By default, the data is appended to an existing .emp file.

[Edit on GitHub]

REFINEMENT_FACTOR

Type: integer
Default: 1
Usage: REFINEMENT_FACTOR 2

Description: Sets the refinement factor for the Voronoi integration.

[Edit on GitHub]

SANITY_CHECK

Type: logical
Default: F
Lone keyword: T
Usage: SANITY_CHECK T

Description: Performs a sanity check before each Voronoi integration, i.e., checks if every grid point is located in exactly one Voronoi cell.

[Edit on GitHub]

SKIP_FIRST

Type: logical
Default: F
Lone keyword: T
Usage: SKIP_FIRST T

Description: Skips the first step of a MD run (avoids duplicate step if restarted).

[Edit on GitHub]

USER_RADII

Type: real[ ]
Default: [angstrom]
Usage: USER_RADII {real} {real} {real}

Description: Defines user atom radii for the radical Voronoi tessellation (one per atom).

[Edit on GitHub]

VERBOSE

Type: logical
Default: F
Lone keyword: T
Usage: VERBOSE T

Description: Switches on verbose screen output of the Voronoi integration.

[Edit on GitHub]

VORONOI_RADII

Type: enum
Default: VDW
Usage: VORONOI_RADII {UNITY,VDW,COVALENT,USER}

Description: Which atomic radii to use for the radical Voronoi tessellation.

Valid values:

  • UNITY Use unity radii (non-radical Voronoi tessellation)

  • VDW Use VdW atom radii

  • COVALENT Use covalent atom radii

  • USER Use user-specified atom radii

[Edit on GitHub]

__CONTROL_VAL

Type: integer
Default: 8

Description: hidden parameter that controls storage, printing,… of the print_key

[Edit on GitHub]