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(None,
properties,
self.nstates,
natoms,
atomids,
logger=self.logger,
config=config_spp)
#
self.interpolator = self.spp.interpolator
self.savefile = config['savefile']
self.interpolator.train(self.savefile)
#
qs, crds = self.generate_crds(config['moldenfile'],
mode=config['mode'],
start=config['start'],
end=config['end'],
npoints=config['npoints'])
energy = self._compute(crds)
data = []
conv = energy_converter.get_converter('au', config['energy_units'])
for q, en in zip(qs, energy):
en = conv(en) - conv(config['reference_energy'])
data += [[q, *en]]
data = np.array(data)
if config['save_data'] == 'yes':
np.savetxt(config['save_data']['data_file'], data)
if config['plot_pes'] == 'yes':
nstates = data.shape[1] - 1
myplt = Plot(plot_config)
myax = myplt.line_plot(data[:, [0, 1]],
x_units_in=('length', 'au'),
y_units_in=('energy',
config['energy_units']),
ax=None,
show_plot=False,
save_plot=False)
for state in range(1, nstates):
save = False
plot = False
if state == nstates - 1:
save = True
plot = True
myax = myplt.line_plot(data[:, [0, state + 1]],
x_units_in=('length', 'au'),
y_units_in=('energy',
config['energy_units']),
ax=myax,
show_plot=plot,
save_plot=save)
def from_inputfile(cls, inputfile):
if not (exists_and_isfile(inputfile)):
config = cls.generate_input(inputfile, config=None)
else:
config = cls.generate_input(inputfile, config=inputfile)
quests = cls.generate_questions(config=inputfile)
config = quests.check_only(inputfile)
plot_config = {}
if config['plot_pes'].value == 'yes':
plot_config = {}
plot_config['x_label'] = 'mode'
plot_config['x_label_unit'] = False
plot_config['y_label_unit'] = True
plot_config['y_label'] = 'energy'
plot_config = {'': plot_config}
presets = ''
presets += f"y_label = energy\n"
presets += f"x_label_unit = True\n"
presets += f"[save_plot(yes)]\nplot_file = plot_fit_pes_nm.png\n"
presets += "legend = {}\n"
plot_input = config['plot_pes']['plot_inputfile']
if exists_and_isfile(plot_input):
plot_config = Plot.generate_input(plot_input,
config=plot_input,
presets=presets)
else:
plot_config = Plot.generate_input(plot_input,
config=plot_config,
presets=presets)
return cls(config, plot_config)
def from_inputfile(cls, inputfile):
if not(exists_and_isfile(inputfile)):
config = cls.generate_input(inputfile, config=None)
else:
config = cls.generate_input(inputfile, config=inputfile)
quests = cls.generate_questions(config=inputfile)
config = quests.check_only(inputfile)
if config['plot_spectrum'].value == 'yes':
plot_config = {}
if config['broadening'].value == 'yes':
plot_config['x_start'] = config['broadening']['energy_start']
plot_config['x_end'] = config['broadening']['energy_end']
plot_config['x_label'] = 'energy'
plot_config['y_label_unit'] = True
plot_config['y_label'] = 'intensity'
plot_config['x_units'] = config['energy_units']
plot_config['x_label_unit'] = True
plot_config = {'': plot_config}
presets = ''
if config['broadening'].value == 'yes':
presets += f"x_start = {config['broadening']['energy_start']}\n"
presets += f"x_end = {config['broadening']['energy_end']}\n"
presets += f"x_label = energy\n"
presets += f"y_label_unit = True\n"
presets += f"y_label = intensity\n"
presets += f"y_units = a.u.\n"
presets += f"x_units = {config['energy_units']}\n"
presets += f"x_label_unit = True\n"
presets += f"[save_plot(yes)]\nplot_file = spectrum/spectrum.png\n"
plot_input = config['plot_spectrum']['plot_inputfile']
if exists_and_isfile(plot_input):
plot_config = Plot.generate_input(plot_input, config=plot_input, presets=presets)
else:
plot_config = Plot.generate_input(plot_input, config=plot_config, presets=presets)
return cls(config, plot_config)
def from_inputfile(cls, inputfile):
if not (exists_and_isfile(inputfile)):
config = cls.generate_input(inputfile, config=None)
else:
config = cls.generate_input(inputfile, config=inputfile)
quests = cls.generate_questions(config=inputfile)
config = quests.check_only(inputfile)
plot_config = {}
if config['plot_population'].value == 'yes':
plot_config = {}
# plot_config['x_label'] = 'time'
plot_config['x_units'] = config['time_units']
plot_config['x_label_unit'] = True
plot_config['y_label_unit'] = False
plot_config['y_label'] = 'population'
plot_config = {'': plot_config}
presets = ''
presets += f"y_start = 0.0\n"
presets += f"y_end = 1.0\n"
presets += f"x_label = time\n"
presets += f"y_label_unit = False\n"
presets += f"y_label = population\n"
presets += f"x_units = {config['time_units']}\n"
presets += f"x_label_unit = True\n"
presets += f"[save_plot(yes)]\nplot_file = population.png\n"
presets += "legend = {}\n"
plot_input = config['plot_population']['plot_inputfile']
if exists_and_isfile(plot_input):
plot_config = Plot.generate_input(plot_input,
config=plot_input,
presets=presets)
else:
plot_config = Plot.generate_input(plot_input,
config=plot_config,
presets=presets)
return cls(config, plot_config)
def __init__(self, config):
db = DynDB.load_database(config['prop_db'], read_only=True)
nstates = db.nstates
npoints = len(db)
data = np.empty((npoints, nstates+1), dtype=float)
data[:, 0] = np.array(db['time'])[:, 0]
data[:, 1:] = np.array(db['energy'])-config['reference_energy']
currstate = np.array(db['currstate'])[:, 0]
plot_config = {}
plot_config['x_label'] = 'time'
plot_config['y_label'] = 'energy'
plot_config['y_units'] = 'eV'
plot_config['x_units'] = 'fs'
plot_config['y_label_unit'] = True
plot_config['x_label_unit'] = True
plot_config = {'': plot_config}
# plot_config['save_plot'] = {'plot_file': 'pes_traj.png'}
presets = """
x_label = time
y_label = energy
y_units = eV
x_units = fs
y_label_unit = True
x_label_unit = True
"""
if exists_and_isfile(self._plot_input):
plot_config = Plot.generate_input(self._plot_input, config=self._plot_input, presets=presets)
else:
plot_config = Plot.generate_input(self._plot_input, config=plot_config, presets=presets)
myplot = Plot(plot_config)
if nstates == 1:
save_plot = True
show_plot = True
else:
save_plot = False
show_plot = False
myax = myplot.line_plot(data[:,[0,1]], x_units_in=['time', 'au'], y_units_in=['energy', 'au'], ax=None, save_plot=save_plot, show_plot=show_plot)
for state in range(1, nstates):
myax = myplot.line_plot(data[:,[0, state+1]], x_units_in=['time', 'au'], y_units_in=['energy', 'au'], ax=myax, show_plot=False, save_plot=False)
curr_plot = np.empty((npoints, 2), dtype=float)
curr_plot[:, 0] = data[:, 0]
for idx, state in enumerate(currstate):
curr_plot[idx, 1] = data[idx, int(state + 1)]
myax = myplot.line_plot(curr_plot, x_units_in=['time', 'au'], y_units_in=['energy', 'au'], ax=myax, save_plot=True, show_plot=True, line_props={'marker': 'o', 'color': 'red'})
def __init__(self, config, plot_config=None):
self.config = config
sampling = Sampling.from_db(self.specfile)
nstates = sampling.info['dimensions']['nstates']
npoints = sampling.nconditions
data = []
for energy, fosc in zip(np.copy(sampling._db['energy']), np.copy(sampling._db['fosc'])):
for idx, en in enumerate(energy[1:]):
data += [[en - energy[0], fosc[idx+1]]]
data = np.array(data)
converter = energy_converter.get_converter('au', self.config['energy_units'])
data[:, 0] = converter(data[:, 0])
if config['broadening'].value == 'yes':
cont_data = Broadening(config['broadening']).broadening(data)
else:
cont_data = np.sort(data)
Plot(plot_config).line_plot(cont_data, ('energy', self.config['energy_units']), y_units_in=None, ax=None, line_props={'linestyle':'solid'})
def __init__(self, config, plot_config=None):
self.config = config
self.folder = os.path.abspath(config['folder'])
self.subfolder = config['subfolder']
subfolderhandle = SubfolderHandle(self.folder, self.subfolder)
propfiles = subfolderhandle.fileiter('prop.db')
first = True
for idx, propfile in enumerate(propfiles):
db = DynDB.load_database(propfile, read_only=True)
print(propfile)
dbtime = np.array(db['time']).flatten()
if len(dbtime) == 0:
continue
if first is True:
first = False
if config['nsteps'] is not None:
nsteps = config['nsteps']
else:
nsteps = len(db)
nstates = db.info['dimensions']['nstates']
data = np.zeros(shape=(nsteps, nstates + 1), dtype=float)
data[:min(len(db), nsteps), 0] = dbtime
counter = np.zeros(nsteps, dtype=int)
if nsteps > len(db):
times_missing = True
time_steps = len(db)
else:
times_missing = False
time_steps = len(db)
if np.max(
np.abs(data[:min(time_steps, len(dbtime)), 0] -
dbtime[:min(time_steps, len(dbtime))])) < 0.1:
if len(dbtime) > time_steps and times_missing is True:
data[time_steps:len(dbtime),
0] = dbtime[time_steps:min(nsteps, len(dbtime))]
time_steps = len(dbtime)
currstate = np.array(db['currstate']).flatten()
for idx in range(min(len(dbtime), nsteps)):
data[idx, int(currstate[idx] + 1)] += 1
counter[idx] += 1
else:
print('times do not fit')
data[:, 1:] = data[:, 1:] / np.repeat(counter, nstates).reshape(
nsteps, nstates)
converter = time_converter.get_converter('au',
self.config['time_units'])
data[:, 0] = converter(data[:, 0])
if config['save_data'].value == 'yes':
np.savetxt(config['save_data']['data_file'], data)
if config['plot_population'].value == 'yes':
myplt = Plot(plot_config)
myax = myplt.line_plot(data[:, [0, 1]],
('time', self.config['time_units']),
y_units_in=None,
ax=None,
show_plot=False,
save_plot=False,
line_props={'label': 'state 0'})
for state in range(1, nstates):
save = False
plot = False
if state == nstates - 1:
save = True
plot = True
myax = myplt.line_plot(data[:, [0, state + 1]],
('time', self.config['time_units']),
y_units_in=None,
ax=myax,
show_plot=plot,
save_plot=save,
line_props={'label': f"state {state}"})
def __init__(self, config):
model = ModelBase._models[config['model'].value].from_config(
config['model'])
nstates = model.nstates
crd_equi = model.crd
npoints = 100
data = np.empty((npoints, nstates + 1), dtype=float)
data[:, 0] = np.linspace(config['start_plot'], config['end_plot'],
npoints)
for idx, point in enumerate(data[:, 0]):
crd = np.zeros(model.crd.size)
crd[config['mode']] = point
data[idx, 1:] = model.get(
Request(crd,
properties=['energy'],
states=[i for i in range(nstates)]))['energy']
print(data)
plot_config = {}
plot_config['x_label'] = f"mode config['mode']"
plot_config['x_start'] = config['start_plot']
plot_config['x_end'] = config['end_plot']
plot_config['y_label'] = 'energy'
plot_config['y_units'] = 'eV'
plot_config['x_units'] = 'au'
plot_config['y_label_unit'] = True
plot_config['x_label_unit'] = True
plot_config = {'': plot_config}
presets = """
x_label = mode
y_label = energy
y_units = eV
x_units = au
y_label_unit = True
x_label_unit = True
"""
if exists_and_isfile(self._plot_input):
plot_config = Plot.generate_input(self._plot_input,
config=self._plot_input,
presets=presets)
else:
plot_config = Plot.generate_input(self._plot_input,
config=None,
presets=None)
myplot = Plot(plot_config)
if nstates == 1:
save_plot = True
show_plot = True
else:
save_plot = False
show_plot = False
myax = myplot.line_plot(data[:, [0, 1]],
x_units_in=['energy', 'a.u.'],
y_units_in=['energy', 'au'],
ax=None,
save_plot=save_plot,
show_plot=show_plot)
for state in range(1, nstates - 1):
myax = myplot.line_plot(data[:, [0, state + 1]],
x_units_in=['energy', 'a.u.'],
y_units_in=['energy', 'au'],
ax=myax,
show_plot=False,
save_plot=False)
myax = myplot.line_plot(data[:, [0, nstates]],
x_units_in=['energy', 'a.u.'],
y_units_in=['energy', 'au'],
ax=myax,
show_plot=True,
save_plot=True)