def __init__(self, config):
""" Class to create initial conditions due to user input. Initial conditions are saved
in a file for further usage.
"""
logger = get_logger('setup_spectrum.log', 'setup_spectrum')
logger.header('SETUP SPECTRUM', config)
SetupBase.__init__(self, logger)
#
logger.info(f"Opening sampling database {config['sampling_db']}")
sampling = Sampling.from_db(config['sampling_db'], logger=logger)
if not exists_and_isfile(config['spp']):
presets="""
use_db = no
"""
logger.info(f"Setting up SPP inputfile: {config['spp']}")
SurfacePointProvider.generate_input(config['spp'], config=None, presets=presets)
else:
logger.info(f"Using SPP inputfile as it is")
if not exists_and_isfile(config['sp_calc']):
presets=f"""
properties = {config['properties']}
nstates = {config['nstates']}
init_db = init.db
"""
logger.info(f"Setting up inputfile for the single point calculations")
SinglePointCalculation.generate_input(config['sp_calc'], config=None, presets=presets)
else:
logger.info(f"Using inputfile for the single point calculations as it is")
logger.info("Starting to prepare the folders...")
self.setup_folders(range(config['n_cond']), config, sampling)
def __init__(self, config):
""" Class to create initial conditions due to user input. Initial conditions are saved
in a file for further usage.
"""
logger = get_logger('setup_propagation.log', 'setup_propagation')
SetupBase.__init__(self, logger)
# Open DB of initial conditions once, so that it is available
sampling = Sampling.from_db(config['sampling_db'])
#Make sure that inputfile for the SPP exists and is complete
if exists_and_isfile(config['spp']): lconfig = config['spp']
else: lconfig = None
SurfacePointProvider.generate_input(config['spp'], config=lconfig)
#Make sure that inputfile for RunTrajectory exists and is complete
if exists_and_isfile(config['prop']): lconfig = config['prop']
else: lconfig = None
RunTrajectory.generate_input(config['prop'], config=lconfig)
#
if config['n_traj'] == -1:
ntraj = len(sampling._db)
else:
ntraj = config['n_traj']
if sampling.nconditions < ntraj:
logger.error(f"Too few initial conditions in {config['sampling_db']}")
self.setup_folders(range(ntraj), config, sampling)
def __init__(self, config, logger=None):
"""
Args:
config, ColtObj:
The config contains the information from the colt
questions of the class
logger, Logger:
Logger for the class. If not provided a new logger is created.
"""
if logger is None:
self.logger = get_logger('sp_calc.log', 'sp_calc')
self.logger.header('Single Point Calculation', config)
else:
self.logger = logger
#
self.logger.info(f"Taking information from {config['init_db']}")
sampling = Sampling.from_db(config['init_db'], logger=self.logger)
if not (exists_and_isfile(config['spp'])):
spp_config = SurfacePointProvider.generate_input(config['spp'])
else:
spp_config = SurfacePointProvider.generate_input(
config['spp'], config=config['spp'])
self.logger.debug(f"Setting up SPP with {config['spp']}")
if sampling.molecule is not None:
spp = SurfacePointProvider.from_config(
spp_config,
config['properties'],
config['nstates'],
sampling.natoms,
nghost_states=config['nghost_states'],
atomids=sampling.atomids)
else: #model calculation
spp = SurfacePointProvider, from_config(spp_config,
config['properties'],
config['nstates'],
sampling.nmodes)
crd = sampling.get_condition(0).crd
#check that DB can take the results
self.logger.debug(
f"Checking whether {config['init_db']} can take the results")
self._check_res_db(config, sampling)
with self.logger.info_block("SPP calculation"):
res = spp.request(crd,
config['properties'],
states=[st for st in range(config['nstates'])])
self.logger.info(f"Writing results to: {config['init_db']}")
for prop, value in res.iter_data():
sampling.set(prop, value)