def read_conf_file(self, filename):
if not os.path.exists(filename):
warning("file %s does not exist, but it will continue anyway!" %filename)
else:
c = open(filename, 'r')
confs = self._conf
is_continue = False
for line in c:
new_line=line.split("#")[0]
if new_line.strip() == '':
is_continue = False
continue
if new_line.find('=') != -1:
left, right = [x.strip().lower() for x in new_line.split('=')]
if left.find("filename")!=-1 or left=="atom_type":
right=new_line.split("=")[1].strip()
confs[left] = right
if is_continue:
confs[left] += new_line.strip()
confs[left] = confs[left].replace('\\', ' ')
is_continue = False
if new_line.find('\\') != -1:
is_continue = True
def plot_freq(self,is_plot=True, is_save=False):
dirt=self.dirt
try:
import matplotlib.pyplot as plt
freq=self.kappa_omega["frequency"]
kappa=self.kappa_omega["kappa"]
kappa_cum = self.kappa_omega['kappa_cum']
plt.figure(figsize=(16,12))
if dirt is not None:
plt.plot(freq, kappa[:,dirt[0],dirt[1]],linewidth=3)
else:
plt.plot(freq,np.einsum("ijj",kappa), linewidth=3)
plt.xlabel("Frequency(THz)",fontsize=18)
plt.ylabel("Kappa(W/(m K THz))",fontsize=18)
plt.title("thermal conductivity with frequency", fontsize=24)
plt.figure(figsize=(16,12))
if dirt is not None:
plt.plot(freq, kappa_cum[:,dirt[0],dirt[1]],linewidth=3)
else:
plt.plot(freq,np.einsum("ijj",kappa_cum),linewidth=3)
plt.xlabel("Frequency(THz)",fontsize=18)
plt.ylabel("Kappa(W/(m K))",fontsize=18)
if is_save:
plt.savefig("kappa.pdf")
if is_plot:
plt.show()
except ImportError:
warning("lib matplotlib is not implemented, continuing anyway...")
def plot_time(self,is_plot=True, is_save=False):
try:
import matplotlib.pyplot as plt
time_series = np.arange(self.corr_length) * self.time_step
if self.dirt is not None:
correlation = self.correlation[:,self.dirt[0], self.dirt[1]]
else:
correlation = np.einsum("ijj",self.correlation) / 3.0
plt.figure(figsize=(8,6))
eflux = self.eflux[0]
plt.plot(np.arange(len(self.eflux[0])) * self.time_step, eflux)
plt.figure(figsize=(8,6))
plt.plot(time_series[:], correlation / correlation[0])
# plt.plot(time_series[:], np.cumsum(correlation / correlation[0])/np.arange(1,len(correlation)+1))
plt.xlabel("Time(ps)",fontsize=18)
plt.ylabel("Autocorrelation (normalized)",fontsize=18)
plt.title("Autocorrelation fuction with simulation time", fontsize=24)
if is_save:
plt.savefig("ACF.pdf")
plt.figure(figsize=(8,6))
kappa_cum = np.cumsum(correlation * self.time_step) * self.conversion_factor
plt.plot(time_series,kappa_cum)
plt.xlabel("Time(ps)",fontsize=18)
plt.ylabel("Thermal conductivity (W/m-K)",fontsize=18)
plt.title("Thermal conductivity with time", fontsize=24)
if is_save:
plt.savefig("KAPPA.pdf")
if is_plot:
plt.show()
except ImportError:
warning("lib matplotlib is not implemented, continuing anyway...")
def read_conf_file(self, filename):
if not os.path.exists(filename):
warning("file %s does not exist, but it will continue anyway!" %
filename)
else:
c = open(filename, 'r')
confs = self._conf
is_continue = False
for line in c:
new_line = line.split("#")[0]
if new_line.strip() == '':
is_continue = False
continue
if new_line.find('=') != -1:
left, right = [
x.strip().lower() for x in new_line.split('=')
]
if left.find("filename") != -1 or left == "atom_type":
right = new_line.split("=")[1].strip()
confs[left] = right
if is_continue:
confs[left] += new_line.strip()
confs[left] = confs[left].replace('\\', ' ')
is_continue = False
if new_line.find('\\') != -1:
is_continue = True
def check_settting(self):
if self.num_steps<self.sample_length:
error("number of total time steps %d is lower than sampling length %d!"
% (self.num_steps, self.sample_length))
if self.corr_length >= self.sample_length:
error("correlation length %d is larger than sampling length %d!"
%(self.corr_length, self.sample_length))
elif self.sample_length-self.corr_length<5:
warning("correlation of the last few time steps may be incorrect!")
def save_fe_to_hdf5(self, filename="md_fe.hdf5"):
"save the force, energy, coordinate and velocity into a hdf5 file"
try:
import h5py
write_md_to_hdf5(filename=filename,
force=self.atom_forces,
energy=self.atom_energies,
stress=self.atom_stresses)
except ImportError:
warning("h5py not implemented, velocities not saved")
def save_fe_to_hdf5(self, filename="md_fe.hdf5"):
"save the force, energy, coordinate and velocity into a hdf5 file"
try:
import h5py
write_md_to_hdf5(filename=filename,
force=self.atom_forces,
energy=self.atom_energies,
stress=self.atom_stresses)
except ImportError:
warning("h5py not implemented, velocities not saved")
def save_cv_to_hdf5(self, filename="md_cv.hdf5"):
"Save the coordinate and velocity information into a hdf5 file"
try:
import h5py
write_md_to_hdf5(filename=filename,
coordinate=self.atom_coordinates,
velocity=self.atom_velocities,
type=self.atom_types,
time_step=self.time_step)
print "Coordinates and velocity information has been written to %s" % filename
except ImportError:
warning("h5py not implemented, velocities not saved")
def save_cv_to_hdf5(self, filename="md_cv.hdf5"):
"Save the coordinate and velocity information into a hdf5 file"
try:
import h5py
write_md_to_hdf5(filename=filename,
coordinate=self.atom_coordinates,
velocity=self.atom_velocities,
type=self.atom_types,
time_step=self.time_step)
print "Coordinates and velocity information has been written to %s" %filename
except ImportError:
warning("h5py not implemented, velocities not saved")
def parameter_coupling(self):
if self.input_filename is not None and not self._conf.has_key("file_format"):
if self.input_filename.split(".")[-1]=="xyz":
if self.file_format != "x":
warning("xyz file format detected, format converted forcibly!")
self.file_format="x"
elif self.input_filename.split(".")[-1]=="hdf5":
if self.file_format != "h":
warning("hdf5 file format detected, format converted forcibly!")
self.file_format="h"
elif self.input_filename == "XDATCAR":
if self.file_format != "v":
warning("vasp file format detected, format converted forcibly!")
self.file_format="v"
if self.file_format is not None:
if self.file_format=="v":
if self.input_filename is None:
print "XDATCAR as input file name used by default for the file format of vasp"
self.input_filename="XDATCAR"
if self.file_format=="h":
if self.input_filename is None:
print "md_velocities.hdf5 as input file name used by default for the file format of hdf5"
self.input_filename="md_velocities.hdf5"
elif self.input_filename.split(".")[-1] != "hdf5":
warning("'filename.hdf5' should be used for hdf5 file type, 'md_velocities.hdf5' is used!")
self.input_filename="md_velocities.hdf5"
def parameter_coupling(self):
if self.input_filename is not None and not self._conf.has_key(
"file_format"):
if self.input_filename.split(".")[-1] == "xyz":
if self.file_format != "x":
warning(
"xyz file format detected, format converted forcibly!")
self.file_format = "x"
elif self.input_filename.split(".")[-1] == "hdf5":
if self.file_format != "h":
warning(
"hdf5 file format detected, format converted forcibly!"
)
self.file_format = "h"
elif self.input_filename == "XDATCAR":
if self.file_format != "v":
warning(
"vasp file format detected, format converted forcibly!"
)
self.file_format = "v"
if self.file_format is not None:
if self.file_format == "v":
if self.input_filename is None:
print "XDATCAR as input file name used by default for the file format of vasp"
self.input_filename = "XDATCAR"
if self.file_format == "h":
if self.input_filename is None:
print "md_velocities.hdf5 as input file name used by default for the file format of hdf5"
self.input_filename = "md_velocities.hdf5"
elif self.input_filename.split(".")[-1] != "hdf5":
warning(
"'filename.hdf5' should be used for hdf5 file type, 'md_velocities.hdf5' is used!"
)
self.input_filename = "md_velocities.hdf5"
def _save2hdf5(self, filename="md_fecv.hdf5"):
"save the force, energy, coordinate and velocity into a hdf5 file"
try:
import h5py
except ImportError:
warning("h5py not implemented, velocities not saved")
return
o=h5py.File(filename,"w")
if self.volume is not None:
o.create_dataset("volume", data=self.volume)
o.create_dataset("velocities", data=self.atom_velocities)
o.create_dataset("coordinates", data=self.atom_coordinates)
o.create_dataset("forces", data=self.atom_forces)
o.create_dataset("energies",data=self.atom_energies)
o.create_dataset("atom_types",data=self.atom_types)
o.create_dataset("step_indices",data=self.step_indices)
o.close()
def parameter_coupling(self):
parameters = self._parameters
if parameters.has_key("coord_filename") and parameters.has_key(
"file_format"):
coord_filename = parameters['coord_filename']
file_format = parameters['file_format']
if coord_filename is not None:
if coord_filename.split(".")[-1] == "xyz":
if file_format != "x":
warning(
"xyz file format detected, format converted forcibly!"
)
self.set_parameter('file_format', "x")
elif coord_filename.split(".")[-1] == "hdf5":
if file_format != "h":
warning(
"hdf5 file format detected, format converted forcibly!"
)
self.set_parameter('file_format', 'h')
elif coord_filename == "XDATCAR":
if file_format != "v":
warning(
"vasp file format detected, format converted forcibly!"
)
self.set_parameter('file_format', "v")
def plot(self, is_plot=False, is_save=False):
try:
import matplotlib.pyplot as plt
freq = self.dos["frequency"]
dos = np.swapaxes(np.atleast_3d(self.dos["dos"]), 0, 1)
for d in np.arange(dos.shape[-1]): # dimension
plt.figure(num=d, figsize=(16, 12))
for s in np.arange(self.num_species):
plt.plot(freq,
dos[:, s, d],
linewidth=3,
label="specie %s" % str(self.species[s]))
plt.xlabel("Frequency(THz)", fontsize=18)
plt.ylabel("DOS(Arbitary unit)", fontsize=18)
plt.title("phonon density of states", fontsize=24)
plt.legend(fontsize=14)
if is_save:
plt.savefig("dos_%d.pdf" % d)
if is_plot:
plt.show()
except ImportError:
warning("lib matplotlib is not implemented, continuing anyway...")
def parameter_coupling(self):
parameters = self._parameters
if parameters.has_key("coord_filename") and parameters.has_key("file_format"):
coord_filename = parameters['coord_filename']
file_format = parameters['file_format']
if coord_filename is not None:
if coord_filename.split(".")[-1]=="xyz":
if file_format != "x":
warning("xyz file format detected, format converted forcibly!")
self.set_parameter('file_format', "x")
elif coord_filename.split(".")[-1]=="hdf5":
if file_format != "h":
warning("hdf5 file format detected, format converted forcibly!")
self.set_parameter('file_format', 'h')
elif coord_filename == "XDATCAR":
if file_format != "v":
warning("vasp file format detected, format converted forcibly!")
self.set_parameter('file_format', "v")
def __init__(self, options,option_list, args,config_file=None):
Settings.__init__(self,options, option_list, args, config_file)
if len(args) >= 3:
self.md_input_filename = args[2]
self.fe_input_filename=args[1]
elif len(args) >= 2:
warning("The general information file is set default as md.out")
self.md_input_filename = "md.out"
self.fe_input_filename = args[1]
else:
warning("The force_and_energy file is set default as heat_flux.out")
warning("The general information file is set default as md.out")
self.fe_input_filename= None
self.md_input_filename = None
self.temperature = 300
self.is_convert_input = False
self.volume = None
self.is_difference = False
self.hf_filename = None
if options is not None:
self._read_options()
self._set_settings()
def __init__(self, options, option_list, args, config_file=None):
Settings.__init__(self, options, option_list, args, config_file)
if len(args) >= 3:
self.md_input_filename = args[2]
self.fe_input_filename = args[1]
elif len(args) >= 2:
warning("The general information file is set default as md.out")
self.md_input_filename = "md.out"
self.fe_input_filename = args[1]
else:
warning(
"The force_and_energy file is set default as heat_flux.out")
warning("The general information file is set default as md.out")
self.fe_input_filename = None
self.md_input_filename = None
self.temperature = 300
self.is_convert_input = False
self.volume = None
self.is_difference = False
self.hf_filename = None
if options is not None:
self._read_options()
self._set_settings()