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)
def __init__(self, sppinp):
#
self.logger = get_logger('validate.log', 'validation', [])
#
config = self._get_spp_config(sppinp)
#
natoms, self.nstates, properties = self._get_db_info(config['use_db']['database'])
atomids = [1 for _ in range(natoms)]
self.spp = SurfacePointProvider.from_config(config, properties, self.nstates, natoms,
atomids=atomids, logger=self.logger)
#
self.interpolator = self.spp.interpolator
#
self.weightsfile = self.spp.interpolator.weightsfile
self.interpolator.train(self.weightsfile)
def __init__(self, config, plot_config):
#
self.logger = get_logger('plotnm.log', 'plotnm', [])
#
#Get Surface Point Provider
config_spp = self._get_spp_config(config['spp'])
natoms, self.nstates, properties = self._get_db_info(
config_spp['use_db']['database'])
atomids = [1 for _ in range(natoms)]
self.spp = SurfacePointProvider.from_config(config_spp,
properties,
self.nstates,
natoms,
atomids=atomids,
logger=self.logger)
#
self.interpolator = self.spp.interpolator
self.interpolator.train()
#
qx, qy, crds = self.generate_crds(
config['moldenfile'],
mode=(config['mode'], config['mode2']),
start=(config['start'], config['start2']),
end=(config['end'], config['end2']),
npoints=(config['npoints'], config['npoints2']))
energy = self._compute(crds)
data = []
conv = energy_converter.get_converter('au', config['energy_units'])
for qxi, qyi, en in zip(np.ravel(qx), np.ravel(qy), energy):
en = conv(en) - conv(config['reference_energy'])
data += [[qxi, qyi, *en]]
data = np.array(data)
nstates = data.shape[1] - 2
energy = data[:, 2:]
energy = energy.T.reshape((nstates, *qx.shape))
# Take only states according to user input
if config['states'] is None:
statelist = [i for i in range(nstates)]
else:
statelist = config['states']
if config['save_data'] == 'yes':
np.savetxt(config['save_data']['data_file'], data)
if config['plot_pes'] == 'yes':
myplt = Plot3D(plot_config)
save = False
plot = False
for state in statelist:
if state == nstates - 1:
save = True
plot = True
if state == statelist[0]:
myax = myplt.surface_plot(
(qx, qy, energy[state]),
x_units_in=('length', 'au'),
y_units_in=('length', 'au'),
z_units_in=('energy', config['energy_units']),
ax=None,
show_plot=plot,
save_plot=save)
else:
myax = myplt.surface_plot(
(qx, qy, energy[state]),
x_units_in=('length', 'au'),
y_units_in=('length', 'au'),
z_units_in=('energy', config['energy_units']),
ax=myax,
show_plot=plot,
save_plot=save)