Input File

Except for restart jobs, gmak initializes its internal objects by reading data from an input text file. The lines in this file are organized into blocks. Each block begins with a line $blockname, where blockname is the name of the block, and ends with a line $end. Most input parameters are set within blocks that identify their context in the program. Those that are not set inside any blocks are referred to as global input parameters.

Parameters are set using lines with syntax:

PARAMETER VALUE...

where PARAMETER is the name of the parameter, VALUE is a string with no white spaces (referred to as a value token), and the ellipsis ... indicates that there may be a list of such tokens in the line. Tokens can be separated from the parameter name and from other tokens by any number of spaces.

The tokens can be categorized into the following types:

1. Numerical

2. File/directory path

3. Object reference (the name of an object previously initialized in the input file)

4. Mathematical expression

5. String (when none of the above apply)

Any line that starts with the # character is considered a comment.

Global input parameters

Global input parameters should appear before any blocks. They either initialize data or set behaviors that belong to no particular block context.

The table below lists the known global input parameters, as well as the expected type of value tokens.

Parameter	Value Type	Description	Remarks
workdir	path	The directory where the files created by the job are saved.	The directory is created if it does not exist.

Blocks

Blocks set a contextual scope for initializing data and behaviors. Typically, each instance of a block translates as the initialization of an object of which the type is tightly associated with the block name. For example, a $protocol block sets up an instance of a class that implements a protocol.

Blocks may depend on each other via object-reference tokens or due to the logic of interpretation of the input file. In the latter case, the dependency is classified as intrinsic, and the dependent block must appear after all instances of the one on which it depends. In the former case, the block that defines the object being referred to must precede the block that refers to it.

The table below lists the known blocks and, if existing, their intrinsic dependencies on other blocks.

Block name	Description	Remarks
variation	The $variation block sets up the variations (see Parameter-search Grid).
gridshift	The $gridshift block sets up the routine for the grid-shifting procedure.
system	The $system block sets up a routine for constructing the topology of a system.
coordinates	The $coordinates block sets up a routine for constructing initial configurations.
optimize	The $optimize block sets up the composite properties that enter in the calculation of the score function, as well as their weights and uncertainty tolerances.
compute	The $compute block sets up a composite property and the associated component properties (see Component and Composite Properties).
grid	The $grid block sets up the sampled points.	Depends on $variation, $gridshift.
protocol	The $protocol block sets up a protocol.