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

• EACH

Keywords

• SECTION_PARAMETERS

• ADD_LAST

• APPEND

• COMMON_ITERATION_LEVELS

• FILENAME

• JITTER

• JITTER_AMPLITUDE

• JITTER_SEED

• LOG_PRINT_KEY

• MOLECULAR_PROPERTIES

• MOLPROP_FILE_NAME

• OUTPUT_EMP

• OUTPUT_TEXT

• OVERWRITE

• REFINEMENT_FACTOR

• SANITY_CHECK

• SKIP_FIRST

• USER_RADII

• VERBOSE

• VORONOI_RADII

• __CONTROL_VAL

Keyword descriptions

SECTION_PARAMETERS: enum = OFF

Lone keyword: SILENT

Usage: silent

Valid values:

• ON

• OFF

• SILENT

• LOW

• MEDIUM

• HIGH

• DEBUG

Level starting at which this property is printed [Edit on GitHub]

ADD_LAST: enum = NO

Usage: ADD_LAST (NO|NUMERIC|SYMBOLIC)

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

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. [Edit on GitHub]

APPEND: logical = F

Lone keyword: T

Appends frames to already existing .voronoi file. [Edit on GitHub]

COMMON_ITERATION_LEVELS: integer = 0

Usage: COMMON_ITERATION_LEVELS

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: string

Usage: FILENAME ./filename

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: logical = T

Lone keyword: T

Usage: JITTER T

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: real = 1.00000000E-003 [angstrom]

Usage: JITTER_AMPLITUDE 0.01

Sets the maximum displacement amplitude for the jitter. [Edit on GitHub]

JITTER_SEED: integer = 0

Usage: JITTER_SEED 1234

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: logical = F

Lone keyword: T

Usage: LOG_PRINT_KEY

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: logical = F

Lone keyword: T

Usage: MOLECULAR_PROPERTIES T

Calculation of molecular properties from Voronoi integration. [Edit on GitHub]

MOLPROP_FILE_NAME: string = __STD_OUT__

Usage: MOLPROP_FILE_NAME

Root of the file name where to print molecular properties. filename.molprop is used. [Edit on GitHub]

OUTPUT_EMP: logical = F

Lone keyword: T

Usage: OUTPUT_EMP T

Writes the resulting electromagnetic moments to a binary file “properties.emp”. The file name cannot be changed. [Edit on GitHub]

OUTPUT_TEXT: logical = T

Lone keyword: T

Usage: OUTPUT_TEXT T

Writes the resulting electromagnetic moments to text files (*.voronoi). The file name is specified via FILENAME. [Edit on GitHub]

OVERWRITE: logical = F

Lone keyword: T

Usage: OVERWRITE T

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: integer = 1

Usage: REFINEMENT 2

Sets the refinement factor for the Voronoi integration. [Edit on GitHub]

SANITY_CHECK: logical = F

Lone keyword: T

Usage: SANITY_CHECK T

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: logical = F

Lone keyword: T

Usage: SKIP_FIRST T

Skips the first step of a MD run (avoids duplicate step if restarted). [Edit on GitHub]

USER_RADII: real = [angstrom]

Usage: USER_RADII {real} {real} {real}

Defines user atom radii for the radical Voronoi tessellation (one per atom). [Edit on GitHub]

VERBOSE: logical = F

Lone keyword: T

Usage: VERBOSE T

Switches on verbose screen output of the Voronoi integration. [Edit on GitHub]

VORONOI_RADII: enum = VDW

Usage: VORONOI_RADII {UNITY,VDW,COVALENT,USER}

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

Which atomic radii to use for the radical Voronoi tessellation. [Edit on GitHub]

__CONTROL_VAL: integer = 8

hidden parameter that controls storage, printing,… of the print_key [Edit on GitHub]