The Field Object

Introduction

The field object is used to store an array of numerical data values associated with a spacial grid, which may be regular (e.g. a plane or cube shaped mesh) or irregular (e.g. points on a molecular surface)

Usually the field object is used for data visualisation or storing data for fitting (e.g. electrostatic potentials).

Allocating and Creating the Field Structure

List of Functions in this section:

create_grid
compute_field_from_structure

create_grid

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

dimensions number of dimensions yes -

origin position of origin (one corner) no -

x-vector direction of first axis no -

y-vector direction of second axis no -

coords molecular structure no -

margin margin for molecular grid no -

Description:

Create a field object with no data values

If the origin and x,y vectors are supplied, these are used to define the grid.

If the coords= argument is provided, the grid will be chosen to enclose the

compute_field_from_structure

Command Line Arguments

Argument Argument type Mandatory Default To specify

field output field tag yes -

field_type keyword yes -

grid input grid tag yes -

coords Fragment tag yes -

toler radius increment yes -

Description:

Set the value of all points from the molecular structure provided.

Currently just computes min(r(p-i)-rad[i]) over all nuclear centres [i]. The radius used is specified by the field_type argument as vdw or covalent.

Operations on the Field Structure

List of Functions in this section:

interpolate_field
add_field
subtract_field
field_add_constant
scale_field
scale_mapping_vectors
convert_to_regular
convert_to_irregular
transform_field
extend_field

interpolate_field

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

grid grid tag yes -

result output field tag yes -

Description:

Use linear interpolation to map data onto a grid.

add_field

Command Line Arguments

Argument Argument type Mandatory Default To specify

left input field tag yes -

right input field tag yes -

result output field tag yes -

Description:

Add to fields together.

subtract_field

Command Line Arguments

Argument Argument type Mandatory Default To specify

left input field tag yes -

right input field tag yes -

result output field tag yes -

Description:

Subtract fields (result = left - right)

field_add_constant

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

constant real value to add yes -

Description:

Adds a constant to all grid points

scale_field

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

factor multiplicative factor yes -

Description:

Multiplies all grid points by a constant

scale_mapping_vectors

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

factor multiplicative factor yes -

result output field tag yes -

Description:

Multiplies mapping vectors

convert_to_regular

Command Line Arguments

Argument Argument type Mandatory Default To specify

field input field tag yes -

result output field tag yes -

Description:

Attempt to establish axes and convert to a regular field type

convert_to_irregular

Command Line Arguments

Argument Argument type Mandatory Default To specify

field input field tag yes -

result output field tag yes -

Description:

Convert to a irregular field type, replacing axes with explicit point coordinates.

transform_field

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

transformation list of 9 real values yes -

result output field tag yes -

Description:

Generic transformation, mainly for use in graphics order of arguments is x,y,z scale x,y,z shift x,y,z rot

extend_field

Command Line Arguments

Argument Argument type Mandatory Default To specify

field input field tag yes -

result input field tag yes -

start_indices list of integers no -

multipliers list of integers no -

overlap_flag yes/no no -

Description:

Apply periodic images to extend range of a field object.

The list of multipliers indicates how many cells to generate in each direction. start_indices controls which range of cells is generated.

The mapping vectors are assumed to provide the cell information. If overlap_flag is set to yes, it is assumed that the when periodic images are produced, the first and last points on a given axis will superimpose.

Reductions of the Field Structure to scalar Values

List of Functions in this section:

get_average_value
get_average_difference
get_average_absolute_difference
get_rms_difference
get_field_value

get_average_value

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

Description:

Returns average value over all grid points

get_average_difference

Command Line Arguments

Argument Argument type Mandatory Default To specify

left input field tag yes -

right input field tag yes -

Description:

Return the average difference between two field datasets

get_average_absolute_difference

Command Line Arguments

Argument Argument type Mandatory Default To specify

left input field tag yes -

right input field tag yes -

Description:

Return the average absolute difference between two field datasets

get_rms_difference

Command Line Arguments

Argument Argument type Mandatory Default To specify

left Field tag yes -

right Field tag yes -

Description:

Return the RMS difference between two field datasets

get_field_value

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

index integer yes - Number of the field point

Description:

Returns the value of the field at the respective point

Use of the mask array

In many cases it is convenient to store data on a regular grid even when the volume of interest has a more complex shape and is contained in the rectangular box.

List of Functions in this section:

reset_mask
set_mask_from_structure
set_masked_value

reset_mask

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

Description:

Set the mask flag for each point to zero

set_mask_from_structure

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

coords Fragment tag yes -

test keyword yes -

toler test tolerance yes -

Description:

Set the mask flag for each point to one depending on proximity to the

The toler parameter indicates an increment to the atomic radii when the tests are performed.

The test keyword determines which test is to be performed, and can be inside, outside, inside-vdw, outside-vdw, inside-covalent, or outside-covalent.

set_masked_value

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

value floating point value yes -

Description:

Set the value of all points currently having a mask set to the provided value.

List of Functions in this section:

get_number_of_dimensions
get_axis_dimension
get_axis_name
get_origin
get_mapping_vector
list_field

get_number_of_dimensions

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

Description:

Access the number of dimensions of a regular field object

get_axis_dimension

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

index required axis yes -

Description:

Access the number of points on an axis of a regular field object

get_axis_name

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

index required axis yes -

Description:

Access the name of an axis

get_origin

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

Description:

Access the coordinates of the origin (one corner)

get_mapping_vector

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

index required axis yes -

Description:

Access the coordinates of one of the mapping vectors (each vector defines a corner one edge away from the origin)

list_field

Command Line Arguments

Argument Argument type Mandatory Default To specify

field Field tag yes -

Description:

Diagnostic listing of attributes

For the programmer there is a list C-callable Field manipulation routines is also available

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