set default mdp values from function

[fgrunewald]

This setting of defaults should probably be a function itself that takes some limited arguments such as those passed to the mdp value changer. In this way atomistic and coarse-grained defaults could also be separately called.

shocker/bin/shocker

Lines 155 to 180 in 0801a19

	mdp_file_path = os.path.join(data_path, 'martini_md_anis.mdp')
	mdp_file2_path = os.path.join(data_path, 'martini_md_anis_slow.mdp')
	mdp_min = os.path.join(data_path, 'min.mdp')
	copy_command_mdp = 'cp {} martini_md_anis.mdp'.format(mdp_file_path)
	copy_command_mdp2 = 'cp {} martini_md_anis_slow.mdp'.format(mdp_file2_path)
	subprocess.call(copy_command_mdp, shell=True)
	subprocess.call(copy_command_mdp2, shell=True)
	mdp_file = 'martini_md_anis.mdp'
	mdp_file2 = 'martini_md_anis_slow.mdp'
	fm.mdp_value_changer(mdp_file, 'new.mdp', 'nsteps', args.iterations)
	fm.mdp_value_changer(mdp_file2, 'new.mdp', 'nsteps', args.iterations_slow)
	fm.mdp_value_changer(mdp_file, 'new.mdp', 'nstxout-compressed', args.xtc)
	group_names = ip.ag_extractor(u, args.index)[1]
	name_string = ip.name_concatenator(group_names)
	fm.mdp_value_changer(mdp_file, 'new.mdp', 'tc-grps', name_string)
	fm.mdp_value_changer(mdp_file2, 'new.mdp', 'tc-grps', name_string)
	taut = '1.0 '*len(group_names)
	reft = '310 '*len(group_names)
	fm.mdp_value_changer(mdp_file, 'new.mdp', 'tau_t', taut)
	fm.mdp_value_changer(mdp_file2, 'new.mdp', 'tau_t', taut)
	fm.mdp_value_changer(mdp_file, 'new.mdp', 'ref_t', reft)
	fm.mdp_value_changer(mdp_file2, 'new.mdp', 'ref_t', reft)
	fm.mdp_value_changer(mdp_file, 'new.mdp', 'dt', args.production_timestep)
	fm.mdp_value_changer(mdp_file2, 'new.mdp', 'dt', args.slow_timestep)
	# =========================================================================