def prepare_seekr():
parser = argparse.ArgumentParser(description="top level SEEKR program used to prepare and generate all input files necessary for a SEEKR calculation")
parser.add_argument('input_filename', metavar='INPUT_FILENAME', type = str, help="name of SEEKR input file")
args = parser.parse_args() #parse command line arguments
args = vars(args) #converts to dictionary
_get_inputs(args,)
sys_params = _get_sys_params(inputs) #parse general system parameters (structures, forcefield files, directory names from input file)
md_milestones = _parse_milestone_inputs(inputs) #parse milestone CV parameters and milestone values from input file
milestones, md_anchor_list = _generate_milestone_lists(md_milestones) #generate upper/lower bounds of a SINGLE CV for each anchor/Voronoi celli
# TODO generate anchor lists for multiple milestone CV's
# TODO BD milestones
#print(milestones)
_generate_filetree(inputs, sys_params) #creates/clears top level ditectory
filetree_settings = _get_filetree_settings(md_anchor_list)
md_filetree_settings_all = {**filetree_settings, **sys_params}
anchor_dirlist, md_file_paths = filetree.md_filetree(md_filetree_settings_all)
md_settings = _get_md_settings(inputs, md_file_paths) #parse parameters for MD simulations from input file
md_settings_all = {**md_settings, **sys_params, **filetree_settings,}
md.main(md_settings_all, milestones)
print(milestones[-1])
milestone_filename= os.path.join(sys_params['rootdir'], 'milestones.xml')
anchor_list = _group_milestones_to_anchor(milestones, anchor_dirlist, md_file_paths,)
print('Anchor List',anchor_list)
_write_milestone_file(anchor_list, md_settings['master_temperature'],
sys_params['md_time_factor'], sys_params['bd_time_factor'],milestone_filename)
structures = _load_structures(inputs, sys_params)
bd_settings = _get_bd_settings(inputs, sys_params, structures)
bd_milestone = anchor_list[-1]
print(bd_milestone)
#bd_milestone_pair = bd_milestone['%s_pair_list' %bd_milestone['key']][-1]
bd_lower_bound = bd_milestone['milestone_params'][0]['lower_bound']
bd_lower_bound_index = bd_milestone['milestone_params'][0]['lower_milestone_index']
bd_index = bd_milestone['milestone_params'][0]['upper_milestone_index']
b_surf_distance = bd_milestone['milestone_params'][0]['upper_bound']
#bd_milestone_index =
bd_settings.update({'b_surf_distance' : b_surf_distance,
'bd_lower_bound' : bd_lower_bound,
'bd_lower_bound_index' : bd_lower_bound_index,
'bd_index': bd_index,
})
print("BD b surface distance", b_surf_distance)
bd.main(bd_settings)
float(milestone.dimensions['centery']),
'z':
float(milestone.dimensions['centerz']),
'radius':
float(milestone.dimensions['radius']),
'index':
milestone.index,
'siteid':
milestone.siteid
})
bd_settings['siteids'].append(milestone.siteid)
#bd_settings = bd_settings.items() + [('milestone_list',milestone_list)])
bd_settings.update(milestone_settings)
bd.main(bd_settings)
other_necessary_files = {
'la.tcl': '/path/to/la.tcl',
'etc': '',
}
# write program paths to a pickle
#print 'namd_special', program_paths['namd_special']
#program_paths_filename=os.path.join(sys_params['rootdir'], 'program_paths.pkl')
#program_paths_file= open(program_paths_filename, 'wb')
#pickle.dump(program_paths, program_paths_file)
#program_paths_file.close
class Test_seekr(unittest.TestCase):