def mapper_from_yaml(yamlfilename):
import yaml
ydict = yaml.load(open(yamlfilename, 'rt'))
ybins = ydict['bins']
from westpa.core._rc import bins_from_yaml_dict
#return mapper_from_dict(ybins)
return bins_from_yaml_dict(ybins)
def __init__(self, sim_manager, plugin_config):
if not sim_manager.work_manager.is_master:
return
self.sim_manager = sim_manager
self.data_manager = sim_manager.data_manager
self.system = sim_manager.system
self.work_manager = sim_manager.work_manager
self.do_reweight = check_bool(
plugin_config.get('do_reweighting', False))
self.windowsize = 0.5
self.windowtype = 'fraction'
windowsize = plugin_config.get('window_size')
if windowsize is not None:
if isinstance(windowsize, float):
self.windowsize = windowsize
self.windowtype = 'fraction'
if self.windowsize <= 0 or self.windowsize > 1:
raise ValueError(
'WESS parameter error -- fractional window size must be in (0,1]'
)
elif isinstance(windowsize, int):
self.windowsize = int(windowsize)
self.windowtype = 'fixed'
else:
raise ValueError(
'WESS parameter error -- invalid window size {!r}'.format(
windowsize))
log.info('using window size of {!r} ({})'.format(
self.windowsize, self.windowtype))
self.max_windowsize = plugin_config.get('max_window_size')
if self.max_windowsize is not None:
log.info('Using max windowsize of {:d}'.format(
self.max_windowsize))
self.reweight_period = plugin_config.get('reweight_period', 0)
self.priority = plugin_config.get('priority', 0)
self.rate_calc_queue_size = plugin_config.get('rate_calc_queue_size',
1)
self.rate_calc_n_blocks = plugin_config.get('rate_calc_n_blocks', 1)
bin_obj = plugin_config.get('bins', None)
if isinstance(bin_obj, dict):
bin_obj = bins_from_yaml_dict(bin_obj)
self.bin_mapper = bin_obj
if self.do_reweight:
sim_manager.register_callback(sim_manager.prepare_new_iteration,
self.prepare_new_iteration,
self.priority)
self.write_matrices = plugin_config.get('write_matrices', False)
def load_config_from_west(self, scheme):
try:
config = westpa.rc.config['west']['analysis']
except:
raise ValueError('There is no configuration file specified.')
ystates = config['analysis_schemes'][scheme]['states']
self.states_from_dict(ystates)
try:
self.subsample = config['subsample']
except:
pass
from westpa.core._rc import bins_from_yaml_dict
self.binning.mapper = bins_from_yaml_dict(config['analysis_schemes'][scheme]['bins'][0])
path = os.path.join(os.getcwd(), config['directory'], scheme)
try:
os.mkdir(config['directory'])
os.mkdir(path)
except:
pass
self.output_filename = os.path.join(path, 'assign.h5')