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

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:

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

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	Field tag	yes	-
grid	grid tag	yes	-
result	output field tag	yes	-

Description:

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:

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:

field_add_constant

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	Field tag	yes	-
constant	real value to add	yes	-

Description:

scale_field

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	Field tag	yes	-
factor	multiplicative factor	yes	-

Description:

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:

convert_to_regular

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	input field tag	yes	-
result	output field tag	yes	-

Description:

convert_to_irregular

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	input field tag	yes	-
result	output field tag	yes	-

Description:

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:

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

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	Field tag	yes	-

Description:

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:

Use of the mask array

List of Functions in this section:

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

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	Field tag	yes	-

Description:

get_axis_dimension

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	Field tag	yes	-
index	required axis	yes	-

Description:

get_axis_name

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	Field tag	yes	-
index	required axis	yes	-

Description:

get_origin

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	Field tag	yes	-

Description:

get_mapping_vector

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	Field tag	yes	-
index	required axis	yes	-

Description:

list_field

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
field	Field tag	yes	-

Description:

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