Class common_operations

Instance Methods

__init__(self)
Operations, functions, etc common to the different model-free analysis methods.

ask_stage(self)
User input of stage number.

create_mfdata(self, res, flag='1')
Create the Modelfree input file mfdata

create_mfin(self, sel='none', algorithm='fix', diffusion_search='none', sims='n', sim_type='pred')
Create the Modelfree input file mfin

create_mfmodel(self, res, md, type='M1')
Create the M1 or M2 section of the Modelfree input file mfmodel

create_mfpar(self, res)
Create the Modelfree input file mfpar

create_run(self, dir)
Create the file 'run' to execute the model-free run

extract_input(self, input)
Extract all the information from the input file.

extract_relax_data(self)
Extract the relaxation data from the files given in the file 'input'

fill_results(self, data, model='0')
Initialize the next row of the results data structure.

final_run(self)
Model selection and the creation of the final run.

final_run_optimized(self)
The final optimization run.

goto_stage(self)

grace(self, file_name, type, subtitle)
Create grace files for the results.

grace_header(self, title, subtitle, x, y, type)
Create and return a grace header.

initialize(self)
A few operations to start up the program.

log_input_info(self)

log_params(self, name, mdx)
Put the parameter data structures into the log file.

print_data(self, ftests='n')
Print the results into the results file.

print_results(self)
Print the results into the results file.

set_run_flags(self, run)
Reset, and then set the flags in self.mf.data.usr_param.md1 and md2.

stage3(self)

Method Details

final_run(self)

Model selection and the creation of the final run.

Monte Carlo simulations are used to find errors, and the diffusion tensor is unoptimized. Files are placed in the directory 'final'.

final_run_optimized(self)

The final optimization run.

Create the modelfree4 files for the optimization of the diffusion tensor together with the model free parameters for the selected models.