Class Palmer

Instance Methods

__init__(self, relax)
Class used to create and process input and output for the program Modelfree 4.

create(self, run, dir, force, binary, diff_search, sims, sim_type, trim, steps, constraints, nucleus, atom1, atom2)
Function for creating the Modelfree4 input files.

create_mfdata(self, i, file)
Create the Modelfree4 input file 'mfmodel'.

create_mfin(self, file)
Create the Modelfree4 input file 'mfin'.

create_mfmodel(self, i, file)
Create the Modelfree4 input file 'mfmodel'.

create_mfpar(self, i, file)
Create the Modelfree4 input file 'mfpar'.

create_run(self, file)
Create the script 'run.sh' for the execution of Modelfree4.

execute(self, run, dir, force, binary)
Function for executing Modelfree4.

extract(self, run, dir)
Function for extracting the Modelfree4 results out of the 'mfout' file.

tuple of 2 floats get_mf_data(self, pos)
Extract the model-free data from the given position of the mfout file.

line_positions(self)
Function for getting the section positions (line number) of the mfout file.

open_file(self, file_name)
Function for opening a file to write to.

Method Details

create(self, run, dir, force, binary, diff_search, sims, sim_type, trim, steps, constraints, nucleus, atom1, atom2)

Function for creating the Modelfree4 input files.

The following files are created:
    dir/mfin
    dir/mfdata
    dir/mfpar
    dir/mfmodel
    dir/run.sh

execute(self, run, dir, force, binary)

Function for executing Modelfree4.

BUG: Control-C during execution causes the cwd to stay as dir.

get_mf_data(self, pos)

Extract the model-free data from the given position of the mfout file.

This method is designed to catch a number of bugs in Modelfree4's mfout file.

The first bug is the presence of a series of '*' characters causing a fusion of two columns. This is handled by splitting by the '*' char and then returning the first element.

The second bug is when the floating point number is too big to fit into Modelfree4's string format limit of 15.3f. This results in a results line such as:

246 10000.00019682363392.000 1 0.000 0.000 0.000 0.000

This is caught by scanning for two '.' characters in the column, and handled by assuming that every floating point number will have three decimal characters.

Parameters:

• pos (int) - The mfout line position.

Returns: tuple of 2 floats

The value and error.