The GUI can be a good place to inspect the setup and files.
Copy '''02_read_data.py''' to '''03_save_state_inspect_GUI.py''' and add:{| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="python"># Analysis variables.###################### The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changed.MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']#MF_MODELS = ['m1', 'm2']LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9'] # The grid search size (the number of increments per dimension).GRID_INC = 11 # The optimisation technique. Standard is: min_algor='newton' : and cannot be changed in the GUI.MIN_ALGOR = 'newton' # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.#MC_NUM = 500MC_NUM = 20 # The diffusion model. Standard is 'Fully automated', which means: DIFF_MODEL=['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final']# 'local_tm', 'sphere', ''prolate', 'oblate', 'ellipsoid', or 'final'#DIFF_MODEL = 'local_tm'DIFF_MODEL = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] # The maximum number of iterations for the global iteration. Set to None, then the algorithm iterates until convergence.MAX_ITER = None # Automatic looping over all rounds until convergence (must be a boolean value of True or False). Standard ishttps: conv_loop=True : and cannot be changed in the GUI//github.CONV_LOOP = True # Change some minimise opt paramscom/tlinnet/relax_modelfree_scripts/blob/master/03_save_state_inspect_GUI. # This goes into: minimisepy 03_save_state_inspect_GUI.execute(self.min_algor, func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations)######################dAuvergne_protocol.opt_func_tol = 1e-5 # Standard: opt_func_tol = 1e-25 #dAuvergne_protocol.opt_max_iterations = 1000 # Standard: opt_max_iterations = int(1e7)dAuvergne_protocol.opt_func_tol = 1e-10 # Standard: opt_func_tol = 1e-25 dAuvergne_protocol.opt_max_iterations = int(1e5) # Standard: opt_max_iterations = int(1e7) ##################################### # The results dir.var = 'result_03'results_dir = os.getcwd() + os.sep + var # Save the state before running. Open and check in GUI!state.save(state=var+'_ini.bz2', dir=results_dir, force=True) # To check in GUI# relax -g# File -> Open relax state# In folder "result_03" open "result_03_ini.bz2"# View -> Data pipe editor# Right click on pipe, and select "Associate with a new auto-analysis"</source>|}py]
Run with