Package generic_fns :: Module palmer :: Class Palmer
[hide private]
[frames] | no frames]

Class Palmer

source code

Instance Methods [hide private]
 
__init__(self, relax)
Class used to create and process input and output for the program Modelfree 4.
source code
 
create(self, run, dir, force, diff_search, sims, sim_type, trim, steps, constraints, nucleus, atom1, atom2)
Function for creating the Modelfree4 input files.
source code
 
create_mfdata(self, i, file)
Create the Modelfree4 input file 'mfmodel'.
source code
 
create_mfin(self, file)
Create the Modelfree4 input file 'mfin'.
source code
 
create_mfmodel(self, i, file)
Create the Modelfree4 input file 'mfmodel'.
source code
 
create_mfpar(self, i, file)
Create the Modelfree4 input file 'mfpar'.
source code
 
create_run(self, file)
Create the script 'run.sh' for the execution of Modelfree4.
source code
 
execute(self, run, dir, force)
Function for executing Modelfree4.
source code
 
extract(self, run, dir)
Function for extracting the Modelfree4 results out of the 'mfout' file.
source code
 
get_chi2(self, sims, mfout, res)
Extract the chi-squared data from the mfout file.
source code
 
get_mf_data(self, data_type, mfout, res)
Extract the model-free data from the mfout file.
source code
 
open_file(self, file_name)
Function for opening a file to write to.
source code
Method Details [hide private]

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

source code 
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)

source code 

Function for executing Modelfree4.

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