id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 51 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
|---|---|---|---|---|---|---|---|---|---|---|---|
241,300 | pyusb/pyusb | tools/vcp_terminal.py | ftdi_to_clkbits | def ftdi_to_clkbits(baudrate): # from libftdi
"""
10,27 => divisor = 10000, rate = 300
88,13 => divisor = 5000, rate = 600
C4,09 => divisor = 2500, rate = 1200
E2,04 => divisor = 1250, rate = 2,400
71,02 => divisor = 625, rate = 4,800
38,41 => divisor = 312.5, rate = 9,600
D0,80 => divi... | python | def ftdi_to_clkbits(baudrate): # from libftdi
clk = 48000000
clk_div = 16
frac_code = [0, 3, 2, 4, 1, 5, 6, 7]
actual_baud = 0
if baudrate >= clk / clk_div:
encoded_divisor = 0
actual_baud = (clk // clk_div)
elif baudrate >= clk / (clk_div + clk_div / 2):
encoded_divisor... | [
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88,13 => divisor = 5000, rate = 600
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E2,04 => divisor = 1250, rate = 2,400
71,02 => divisor = 625, rate = 4,800
38,41 => divisor = 312.5, rate = 9,600
D0,80 => divisor = 208.25, rate = 14406
9C,80 => divisor = 156, rate... | [
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241,301 | pyusb/pyusb | tools/vcp_terminal.py | ComPort._read | def _read(self):
""" check ep for data, add it to queue and sleep for interval """
while self._rxactive:
try:
rv = self._ep_in.read(self._ep_in.wMaxPacketSize)
if self._isFTDI:
status = rv[:2] # FTDI prepends 2 flow control characters,
... | python | def _read(self):
while self._rxactive:
try:
rv = self._ep_in.read(self._ep_in.wMaxPacketSize)
if self._isFTDI:
status = rv[:2] # FTDI prepends 2 flow control characters,
# modem status and line status of the UART
... | [
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241,302 | pyusb/pyusb | tools/vcp_terminal.py | ComPort._resetFTDI | def _resetFTDI(self):
""" reset the FTDI device
"""
if not self._isFTDI:
return
txdir = 0 # 0:OUT, 1:IN
req_type = 2 # 0:std, 1:class, 2:vendor
recipient = 0 # 0:device, 1:interface, 2:endpoint, 3:other
req_type = (txdir << 7) + ... | python | def _resetFTDI(self):
if not self._isFTDI:
return
txdir = 0 # 0:OUT, 1:IN
req_type = 2 # 0:std, 1:class, 2:vendor
recipient = 0 # 0:device, 1:interface, 2:endpoint, 3:other
req_type = (txdir << 7) + (req_type << 5) + recipient
self.devic... | [
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241,303 | pyusb/pyusb | usb/legacy.py | busses | def busses():
r"""Returns a tuple with the usb busses."""
return (Bus(g) for k, g in groupby(
sorted(core.find(find_all=True), key=lambda d: d.bus),
lambda d: d.bus)) | python | def busses():
r"""Returns a tuple with the usb busses."""
return (Bus(g) for k, g in groupby(
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lambda d: d.bus)) | [
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241,304 | pyusb/pyusb | usb/legacy.py | DeviceHandle.bulkWrite | def bulkWrite(self, endpoint, buffer, timeout = 100):
r"""Perform a bulk write request to the endpoint specified.
Arguments:
endpoint: endpoint number.
buffer: sequence data buffer to write.
This parameter can be any sequence type.
... | python | def bulkWrite(self, endpoint, buffer, timeout = 100):
r"""Perform a bulk write request to the endpoint specified.
Arguments:
endpoint: endpoint number.
buffer: sequence data buffer to write.
This parameter can be any sequence type.
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241,305 | pyusb/pyusb | usb/legacy.py | DeviceHandle.bulkRead | def bulkRead(self, endpoint, size, timeout = 100):
r"""Performs a bulk read request to the endpoint specified.
Arguments:
endpoint: endpoint number.
size: number of bytes to read.
timeout: operation timeout in milliseconds. (default: 100)
... | python | def bulkRead(self, endpoint, size, timeout = 100):
r"""Performs a bulk read request to the endpoint specified.
Arguments:
endpoint: endpoint number.
size: number of bytes to read.
timeout: operation timeout in milliseconds. (default: 100)
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241,306 | pyusb/pyusb | usb/legacy.py | DeviceHandle.interruptWrite | def interruptWrite(self, endpoint, buffer, timeout = 100):
r"""Perform a interrupt write request to the endpoint specified.
Arguments:
endpoint: endpoint number.
buffer: sequence data buffer to write.
This parameter can be any sequence type.
... | python | def interruptWrite(self, endpoint, buffer, timeout = 100):
r"""Perform a interrupt write request to the endpoint specified.
Arguments:
endpoint: endpoint number.
buffer: sequence data buffer to write.
This parameter can be any sequence type.
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241,307 | pyusb/pyusb | usb/legacy.py | DeviceHandle.interruptRead | def interruptRead(self, endpoint, size, timeout = 100):
r"""Performs a interrupt read request to the endpoint specified.
Arguments:
endpoint: endpoint number.
size: number of bytes to read.
timeout: operation timeout in milliseconds. (default: 100)
... | python | def interruptRead(self, endpoint, size, timeout = 100):
r"""Performs a interrupt read request to the endpoint specified.
Arguments:
endpoint: endpoint number.
size: number of bytes to read.
timeout: operation timeout in milliseconds. (default: 100)
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241,308 | pyusb/pyusb | usb/legacy.py | DeviceHandle.controlMsg | def controlMsg(self, requestType, request, buffer, value = 0, index = 0, timeout = 100):
r"""Perform a control request to the default control pipe on a device.
Arguments:
requestType: specifies the direction of data flow, the type
of request, and the recipient.
... | python | def controlMsg(self, requestType, request, buffer, value = 0, index = 0, timeout = 100):
r"""Perform a control request to the default control pipe on a device.
Arguments:
requestType: specifies the direction of data flow, the type
of request, and the recipient.
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241,309 | pyusb/pyusb | usb/legacy.py | DeviceHandle.claimInterface | def claimInterface(self, interface):
r"""Claims the interface with the Operating System.
Arguments:
interface: interface number or an Interface object.
"""
if isinstance(interface, Interface):
interface = interface.interfaceNumber
util.claim_interface(se... | python | def claimInterface(self, interface):
r"""Claims the interface with the Operating System.
Arguments:
interface: interface number or an Interface object.
"""
if isinstance(interface, Interface):
interface = interface.interfaceNumber
util.claim_interface(se... | [
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241,310 | pyusb/pyusb | usb/legacy.py | DeviceHandle.releaseInterface | def releaseInterface(self):
r"""Release an interface previously claimed with claimInterface."""
util.release_interface(self.dev, self.__claimed_interface)
self.__claimed_interface = -1 | python | def releaseInterface(self):
r"""Release an interface previously claimed with claimInterface."""
util.release_interface(self.dev, self.__claimed_interface)
self.__claimed_interface = -1 | [
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241,311 | pyusb/pyusb | usb/legacy.py | DeviceHandle.setConfiguration | def setConfiguration(self, configuration):
r"""Set the active configuration of a device.
Arguments:
configuration: a configuration value or a Configuration object.
"""
if isinstance(configuration, Configuration):
configuration = configuration.value
self.d... | python | def setConfiguration(self, configuration):
r"""Set the active configuration of a device.
Arguments:
configuration: a configuration value or a Configuration object.
"""
if isinstance(configuration, Configuration):
configuration = configuration.value
self.d... | [
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241,312 | pyusb/pyusb | usb/legacy.py | DeviceHandle.setAltInterface | def setAltInterface(self, alternate):
r"""Sets the active alternate setting of the current interface.
Arguments:
alternate: an alternate setting number or an Interface object.
"""
if isinstance(alternate, Interface):
alternate = alternate.alternateSetting
... | python | def setAltInterface(self, alternate):
r"""Sets the active alternate setting of the current interface.
Arguments:
alternate: an alternate setting number or an Interface object.
"""
if isinstance(alternate, Interface):
alternate = alternate.alternateSetting
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241,313 | pyusb/pyusb | usb/legacy.py | DeviceHandle.getString | def getString(self, index, length, langid = None):
r"""Retrieve the string descriptor specified by index
and langid from a device.
Arguments:
index: index of descriptor in the device.
length: number of bytes of the string (ignored)
langid: Language ID. If... | python | def getString(self, index, length, langid = None):
r"""Retrieve the string descriptor specified by index
and langid from a device.
Arguments:
index: index of descriptor in the device.
length: number of bytes of the string (ignored)
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langid: Language ID. If it is omitted, the first
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241,314 | pyusb/pyusb | usb/legacy.py | DeviceHandle.getDescriptor | def getDescriptor(self, desc_type, desc_index, length, endpoint = -1):
r"""Retrieves a descriptor from the device identified by the type
and index of the descriptor.
Arguments:
desc_type: descriptor type.
desc_index: index of the descriptor.
len: descriptor l... | python | def getDescriptor(self, desc_type, desc_index, length, endpoint = -1):
r"""Retrieves a descriptor from the device identified by the type
and index of the descriptor.
Arguments:
desc_type: descriptor type.
desc_index: index of the descriptor.
len: descriptor l... | [
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241,315 | pyusb/pyusb | usb/backend/__init__.py | IBackend.get_endpoint_descriptor | def get_endpoint_descriptor(self, dev, ep, intf, alt, config):
r"""Return an endpoint descriptor of the given device.
The object returned is required to have all the Endpoint Descriptor
fields acessible as member variables. They must be convertible (but
not required to be equal) to the ... | python | def get_endpoint_descriptor(self, dev, ep, intf, alt, config):
r"""Return an endpoint descriptor of the given device.
The object returned is required to have all the Endpoint Descriptor
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241,316 | pyusb/pyusb | usb/backend/__init__.py | IBackend.bulk_write | def bulk_write(self, dev_handle, ep, intf, data, timeout):
r"""Perform a bulk write.
dev_handle is the value returned by the open_device() method.
The ep parameter is the bEndpointAddress field whose endpoint
the data will be sent to. intf is the bInterfaceNumber field
of the in... | python | def bulk_write(self, dev_handle, ep, intf, data, timeout):
r"""Perform a bulk write.
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241,317 | pyusb/pyusb | usb/backend/__init__.py | IBackend.bulk_read | def bulk_read(self, dev_handle, ep, intf, buff, timeout):
r"""Perform a bulk read.
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241,318 | pyusb/pyusb | usb/backend/__init__.py | IBackend.intr_write | def intr_write(self, dev_handle, ep, intf, data, timeout):
r"""Perform an interrupt write.
dev_handle is the value returned by the open_device() method.
The ep parameter is the bEndpointAddress field whose endpoint
the data will be sent to. intf is the bInterfaceNumber field
of ... | python | def intr_write(self, dev_handle, ep, intf, data, timeout):
r"""Perform an interrupt write.
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The ep parameter is the bEndpointAddress field whose endpoint
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241,319 | pyusb/pyusb | usb/backend/__init__.py | IBackend.intr_read | def intr_read(self, dev_handle, ep, intf, size, timeout):
r"""Perform an interrut read.
dev_handle is the value returned by the open_device() method.
The ep parameter is the bEndpointAddress field whose endpoint
the data will be received from. intf is the bInterfaceNumber field
... | python | def intr_read(self, dev_handle, ep, intf, size, timeout):
r"""Perform an interrut read.
dev_handle is the value returned by the open_device() method.
The ep parameter is the bEndpointAddress field whose endpoint
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241,320 | pyusb/pyusb | usb/backend/__init__.py | IBackend.iso_write | def iso_write(self, dev_handle, ep, intf, data, timeout):
r"""Perform an isochronous write.
dev_handle is the value returned by the open_device() method.
The ep parameter is the bEndpointAddress field whose endpoint
the data will be sent to. intf is the bInterfaceNumber field
of... | python | def iso_write(self, dev_handle, ep, intf, data, timeout):
r"""Perform an isochronous write.
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241,321 | pyusb/pyusb | usb/backend/__init__.py | IBackend.iso_read | def iso_read(self, dev_handle, ep, intf, size, timeout):
r"""Perform an isochronous read.
dev_handle is the value returned by the open_device() method.
The ep parameter is the bEndpointAddress field whose endpoint
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r"""Perform an isochronous read.
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241,322 | pyusb/pyusb | usb/backend/__init__.py | IBackend.ctrl_transfer | def ctrl_transfer(self,
dev_handle,
bmRequestType,
bRequest,
wValue,
wIndex,
data,
timeout):
r"""Perform a control transfer on the endpoint 0.
The di... | python | def ctrl_transfer(self,
dev_handle,
bmRequestType,
bRequest,
wValue,
wIndex,
data,
timeout):
r"""Perform a control transfer on the endpoint 0.
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241,323 | pyusb/pyusb | usb/util.py | find_descriptor | def find_descriptor(desc, find_all=False, custom_match=None, **args):
r"""Find an inner descriptor.
find_descriptor works in the same way as the core.find() function does,
but it acts on general descriptor objects. For example, suppose you
have a Device object called dev and want a Configuration of thi... | python | def find_descriptor(desc, find_all=False, custom_match=None, **args):
r"""Find an inner descriptor.
find_descriptor works in the same way as the core.find() function does,
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241,324 | pyusb/pyusb | usb/util.py | get_langids | def get_langids(dev):
r"""Retrieve the list of supported Language IDs from the device.
Most client code should not call this function directly, but instead use
the langids property on the Device object, which will call this function as
needed and cache the result.
USB LANGIDs are 16-bit integers f... | python | def get_langids(dev):
r"""Retrieve the list of supported Language IDs from the device.
Most client code should not call this function directly, but instead use
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241,325 | pyusb/pyusb | usb/util.py | get_string | def get_string(dev, index, langid = None):
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dev is the Device object which the string will be read from.
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241,326 | atztogo/phonopy | phonopy/unfolding/core.py | Unfolding._set_translations | def _set_translations(self):
"""Set primitive translations in supercell
_trans_s
Translations with respect to supercell basis vectors
_trans_p
Translations with respect to primitive cell basis vectors
_N
Number of the translations = det(supercel_matri... | python | def _set_translations(self):
pcell = PhonopyAtoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]))
smat = self._supercell_matrix
self._trans_s = get_supercell(pcell, smat).get_scaled_positions()
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241,327 | atztogo/phonopy | phonopy/qha/core.py | QHA.run | def run(self, verbose=False):
"""Fit parameters to EOS at temperatures
Even if fitting failed, simply omit the volume point. In this case,
the failed temperature point doesn't exist in the returned arrays.
"""
if verbose:
print(("#%11s" + "%14s" * 4) % ("T", "E_0",... | python | def run(self, verbose=False):
if verbose:
print(("#%11s" + "%14s" * 4) % ("T", "E_0", "B_0", "B'_0", "V_0"))
# Plus one temperature point is necessary for computing e.g. beta.
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241,328 | atztogo/phonopy | phonopy/structure/cells.py | _trim_cell | def _trim_cell(relative_axes, cell, symprec):
"""Trim overlapping atoms
Parameters
----------
relative_axes: ndarray
Transformation matrix to transform supercell to a smaller cell such as:
trimmed_lattice = np.dot(relative_axes.T, cell.get_cell())
shape=(3,3)
cell: Phono... | python | def _trim_cell(relative_axes, cell, symprec):
positions = cell.get_scaled_positions()
numbers = cell.get_atomic_numbers()
masses = cell.get_masses()
magmoms = cell.get_magnetic_moments()
lattice = cell.get_cell()
trimmed_lattice = np.dot(relative_axes.T, lattice)
trimmed_positions = []
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241,329 | atztogo/phonopy | phonopy/structure/cells.py | get_reduced_bases | def get_reduced_bases(lattice,
method='delaunay',
tolerance=1e-5):
"""Search kinds of shortest basis vectors
Parameters
----------
lattice : ndarray or list of list
Basis vectors by row vectors, [a, b, c]^T
shape=(3, 3)
method : str
... | python | def get_reduced_bases(lattice,
method='delaunay',
tolerance=1e-5):
if method == 'niggli':
return spg.niggli_reduce(lattice, eps=tolerance)
else:
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241,330 | atztogo/phonopy | phonopy/structure/cells.py | get_smallest_vectors | def get_smallest_vectors(supercell_bases,
supercell_pos,
primitive_pos,
symprec=1e-5):
"""Find shortest atomic pair vectors
Note
----
Shortest vectors from an atom in primitive cell to an atom in
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----
Shortest vectors from an atom in primitive cell to an atom in
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241,331 | atztogo/phonopy | phonopy/structure/cells.py | compute_all_sg_permutations | def compute_all_sg_permutations(positions, # scaled positions
rotations, # scaled
translations, # scaled
lattice, # column vectors
symprec):
"""Compute a permutation for every space gr... | python | def compute_all_sg_permutations(positions, # scaled positions
rotations, # scaled
translations, # scaled
lattice, # column vectors
symprec):
out = [] # Finally the shape is fixed as (... | [
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241,332 | atztogo/phonopy | phonopy/structure/cells.py | compute_permutation_for_rotation | def compute_permutation_for_rotation(positions_a, # scaled positions
positions_b,
lattice, # column vectors
symprec):
"""Get the overall permutation such that
positions_a[perm[i]] == positions_b... | python | def compute_permutation_for_rotation(positions_a, # scaled positions
positions_b,
lattice, # column vectors
symprec):
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241,333 | atztogo/phonopy | phonopy/structure/cells.py | _compute_permutation_c | def _compute_permutation_c(positions_a, # scaled positions
positions_b,
lattice, # column vectors
symprec):
"""Version of '_compute_permutation_for_rotation' which just directly
calls the C function, without any conditioning of t... | python | def _compute_permutation_c(positions_a, # scaled positions
positions_b,
lattice, # column vectors
symprec):
permutation = np.zeros(shape=(len(positions_a),), dtype='intc')
def permutation_error():
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241,334 | atztogo/phonopy | phonopy/structure/cells.py | estimate_supercell_matrix | def estimate_supercell_matrix(spglib_dataset,
max_num_atoms=120):
"""Estimate supercell matrix from conventional cell
Diagonal supercell matrix is estimated from basis vector lengths
and maximum number of atoms to be accepted. Supercell is assumed
to be made from the stand... | python | def estimate_supercell_matrix(spglib_dataset,
max_num_atoms=120):
spg_num = spglib_dataset['number']
num_atoms = len(spglib_dataset['std_types'])
lengths = _get_lattice_parameters(spglib_dataset['std_lattice'])
if spg_num <= 74: # Triclinic, monoclinic, and orthorhombic
... | [
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241,335 | atztogo/phonopy | phonopy/structure/cells.py | _get_lattice_parameters | def _get_lattice_parameters(lattice):
"""Return basis vector lengths
Parameters
----------
lattice : array_like
Basis vectors given as column vectors
shape=(3, 3), dtype='double'
Returns
-------
ndarray, shape=(3,), dtype='double'
"""
return np.array(np.sqrt(np.do... | python | def _get_lattice_parameters(lattice):
return np.array(np.sqrt(np.dot(lattice.T, lattice).diagonal()),
dtype='double') | [
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241,336 | atztogo/phonopy | phonopy/structure/cells.py | SNF3x3._second | def _second(self):
"""Find Smith normal form for Right-low 2x2 matrix"""
self._second_one_loop()
A = self._A
if A[2, 1] == 0:
return True
elif A[2, 1] % A[1, 1] == 0:
self._second_finalize()
self._Ps += self._L
self._L = []
... | python | def _second(self):
self._second_one_loop()
A = self._A
if A[2, 1] == 0:
return True
elif A[2, 1] % A[1, 1] == 0:
self._second_finalize()
self._Ps += self._L
self._L = []
return True
else:
return False | [
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241,337 | atztogo/phonopy | phonopy/structure/cells.py | SNF3x3._second_column | def _second_column(self):
"""Right-low 2x2 matrix
Assume elements in first row and column are all zero except for A[0,0].
"""
if self._A[1, 1] == 0 and self._A[2, 1] != 0:
self._swap_rows(1, 2)
if self._A[2, 1] != 0:
self._zero_second_column() | python | def _second_column(self):
if self._A[1, 1] == 0 and self._A[2, 1] != 0:
self._swap_rows(1, 2)
if self._A[2, 1] != 0:
self._zero_second_column() | [
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241,338 | atztogo/phonopy | phonopy/structure/cells.py | SNF3x3._swap_rows | def _swap_rows(self, i, j):
"""Swap i and j rows
As the side effect, determinant flips.
"""
L = np.eye(3, dtype='intc')
L[i, i] = 0
L[j, j] = 0
L[i, j] = 1
L[j, i] = 1
self._L.append(L.copy())
self._A = np.dot(L, self._A) | python | def _swap_rows(self, i, j):
L = np.eye(3, dtype='intc')
L[i, i] = 0
L[j, j] = 0
L[i, j] = 1
L[j, i] = 1
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241,339 | atztogo/phonopy | phonopy/structure/cells.py | SNF3x3._flip_sign_row | def _flip_sign_row(self, i):
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L[i, i] = -1
self._L.append(L.copy())
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241,340 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.dataset | def dataset(self, dataset):
"""Set dataset having displacements and optionally forces
Note
----
Elements of the list accessed by 'first_atoms' corresponds to each
displaced supercell. Each displaced supercell contains only one
displacement. dict['first_atoms']['forces'] ... | python | def dataset(self, dataset):
if 'displacements' in dataset:
natom = self._supercell.get_number_of_atoms()
if type(dataset['displacements']) is np.ndarray:
if dataset['displacements'].ndim in (1, 2):
d = dataset['displacements'].reshape((-1, natom, 3))
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241,341 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.forces | def forces(self, sets_of_forces):
"""Set forces in displacement dataset.
Parameters
----------
sets_of_forces : array_like
A set of atomic forces in displaced supercells. The order of
displaced supercells has to match with that in displacement
dataset... | python | def forces(self, sets_of_forces):
if 'first_atoms' in self._displacement_dataset:
for disp, forces in zip(self._displacement_dataset['first_atoms'],
sets_of_forces):
disp['forces'] = forces
elif 'forces' in self._displacement_dataset:
... | [
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241,342 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.force_constants | def force_constants(self, force_constants):
"""Set force constants
Parameters
----------
force_constants : array_like
Force constants matrix. If this is given in own condiguous ndarray
with order='C' and dtype='double', internal copy of data is
avoide... | python | def force_constants(self, force_constants):
if type(force_constants) is np.ndarray:
fc_shape = force_constants.shape
if fc_shape[0] != fc_shape[1]:
if self._primitive.get_number_of_atoms() != fc_shape[0]:
msg = ("Force constants shape disagrees with cr... | [
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241,343 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.generate_displacements | def generate_displacements(self,
distance=0.01,
is_plusminus='auto',
is_diagonal=True,
is_trigonal=False):
"""Generate displacement dataset"""
displacement_directions = get_least_d... | python | def generate_displacements(self,
distance=0.01,
is_plusminus='auto',
is_diagonal=True,
is_trigonal=False):
displacement_directions = get_least_displacements(
self._symmetry,
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241,344 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.get_dynamical_matrix_at_q | def get_dynamical_matrix_at_q(self, q):
"""Calculate dynamical matrix at a given q-point
Parameters
----------
q: array_like
A q-vector.
shape=(3,), dtype='double'
Returns
-------
dynamical_matrix: ndarray
Dynamical matrix.
... | python | def get_dynamical_matrix_at_q(self, q):
self._set_dynamical_matrix()
if self._dynamical_matrix is None:
msg = ("Dynamical matrix has not yet built.")
raise RuntimeError(msg)
self._dynamical_matrix.set_dynamical_matrix(q)
return self._dynamical_matrix.get_dynamica... | [
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241,345 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.get_frequencies | def get_frequencies(self, q):
"""Calculate phonon frequencies at a given q-point
Parameters
----------
q: array_like
A q-vector.
shape=(3,), dtype='double'
Returns
-------
frequencies: ndarray
Phonon frequencies.
s... | python | def get_frequencies(self, q):
self._set_dynamical_matrix()
if self._dynamical_matrix is None:
msg = ("Dynamical matrix has not yet built.")
raise RuntimeError(msg)
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dynamical_matrix()
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Parameters
----------
q: array_like
A q-vector.
shape=(3,), dtype='double'
Returns
-------
frequencies: ndarray
Phonon frequencies.
shape=(bands, ), dtype='double' | [
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241,346 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.get_frequencies_with_eigenvectors | def get_frequencies_with_eigenvectors(self, q):
"""Calculate phonon frequencies and eigenvectors at a given q-point
Parameters
----------
q: array_like
A q-vector.
shape=(3,)
Returns
-------
(frequencies, eigenvectors)
frequencie... | python | def get_frequencies_with_eigenvectors(self, q):
self._set_dynamical_matrix()
if self._dynamical_matrix is None:
msg = ("Dynamical matrix has not yet built.")
raise RuntimeError(msg)
self._dynamical_matrix.set_dynamical_matrix(q)
dm = self._dynamical_matrix.get_dy... | [
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241,347 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.run_band_structure | def run_band_structure(self,
paths,
with_eigenvectors=False,
with_group_velocities=False,
is_band_connection=False,
path_connections=None,
labels=None,
... | python | def run_band_structure(self,
paths,
with_eigenvectors=False,
with_group_velocities=False,
is_band_connection=False,
path_connections=None,
labels=None,
... | [
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241,348 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.init_mesh | def init_mesh(self,
mesh=100.0,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
with_eigenvectors=False,
with_group_velocities=False,
is_gamma_center=False,
use_iter_... | python | def init_mesh(self,
mesh=100.0,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
with_eigenvectors=False,
with_group_velocities=False,
is_gamma_center=False,
use_iter_... | [
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Parameters
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mesh: array_like or float, optional
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241,349 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.run_mesh | def run_mesh(self,
mesh=100.0,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
with_eigenvectors=False,
with_group_velocities=False,
is_gamma_center=False):
"""Run mesh sampling phono... | python | def run_mesh(self,
mesh=100.0,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
with_eigenvectors=False,
with_group_velocities=False,
is_gamma_center=False):
self.init_mesh(mesh=mesh,
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241,350 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.set_mesh | def set_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False,
run_immediately=True):
"""Phonon calculations on sampling mesh g... | python | def set_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False,
run_immediately=True):
warnings.warn("Phonopy.set_mesh is deprec... | [
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mesh: array_like
Mesh numbers along a, b, c axes.
dtype='intc'
shape=(3,)
shift: array_like, optional, default None (no shift)
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241,351 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.get_mesh_dict | def get_mesh_dict(self):
"""Returns calculated mesh sampling phonons
Returns
-------
dict
keys: qpoints, weights, frequencies, eigenvectors, and
group_velocities
Each value for the corresponding key is explained as below.
qpoints: ... | python | def get_mesh_dict(self):
if self._mesh is None:
msg = ("run_mesh has to be done.")
raise RuntimeError(msg)
retdict = {'qpoints': self._mesh.qpoints,
'weights': self._mesh.weights,
'frequencies': self._mesh.frequencies,
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241,352 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.set_iter_mesh | def set_iter_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False):
"""Create an IterMesh instancer
Attr... | python | def set_iter_mesh(self,
mesh,
shift=None,
is_time_reversal=True,
is_mesh_symmetry=True,
is_eigenvectors=False,
is_gamma_center=False):
warnings.warn("Phonopy.set_iter_mesh is depre... | [
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241,353 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.run_qpoints | def run_qpoints(self,
q_points,
with_eigenvectors=False,
with_group_velocities=False,
with_dynamical_matrices=False,
nac_q_direction=None):
"""Phonon calculations on q-points.
Parameters
--------... | python | def run_qpoints(self,
q_points,
with_eigenvectors=False,
with_group_velocities=False,
with_dynamical_matrices=False,
nac_q_direction=None):
if self._dynamical_matrix is None:
msg = ("Dynamical matrix ... | [
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q_points: array_like or float, optional
q-points in reduced coordinates.
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with_eigenvectors: bool, optional
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241,354 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.run_total_dos | def run_total_dos(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
use_tetrahedron_method=True):
"""Calculate total DOS from phonons on sampling mesh.
Parameters
-------... | python | def run_total_dos(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
use_tetrahedron_method=True):
if self._mesh is None:
msg = "run_mesh has to be done before DOS calculation.... | [
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Smearing width for smearing method. Default is None
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Minimum and maximum frequencies in which range DOS is computed
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241,355 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.get_total_DOS | def get_total_DOS(self):
"""Return frequency points and total DOS as a tuple.
Returns
-------
A tuple with (frequency_points, total_dos).
frequency_points: ndarray
shape=(frequency_sampling_points, ), dtype='double'
total_dos:
shape=(frequency_sa... | python | def get_total_DOS(self):
warnings.warn("Phonopy.get_total_DOS is deprecated. "
"Use Phonopy.get_total_dos_dict.", DeprecationWarning)
dos = self.get_total_dos_dict()
return dos['frequency_points'], dos['total_dos'] | [
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241,356 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.run_projected_dos | def run_projected_dos(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
use_tetrahedron_method=True,
direction=None,
xyz_pr... | python | def run_projected_dos(self,
sigma=None,
freq_min=None,
freq_max=None,
freq_pitch=None,
use_tetrahedron_method=True,
direction=None,
xyz_pr... | [
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241,357 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.get_partial_DOS | def get_partial_DOS(self):
"""Return frequency points and partial DOS as a tuple.
Projection is done to atoms and may be also done along directions
depending on the parameters at run_partial_dos.
Returns
-------
A tuple with (frequency_points, partial_dos).
fre... | python | def get_partial_DOS(self):
warnings.warn("Phonopy.get_partial_DOS is deprecated. "
"Use Phonopy.get_projected_dos_dict.",
DeprecationWarning)
pdos = self.get_projected_dos_dict()
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241,358 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.plot_projected_dos | def plot_projected_dos(self, pdos_indices=None, legend=None):
"""Plot projected DOS
Parameters
----------
pdos_indices : list of list, optional
Sets of indices of atoms whose projected DOS are summed over.
The indices start with 0. An example is as follwos:
... | python | def plot_projected_dos(self, pdos_indices=None, legend=None):
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.xaxis.set_ticks_position('both')
ax.yaxis.set_ticks_position('both')
ax.xaxis.set_tick_params(which='both', direction='in')
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241,359 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.run_thermal_properties | def run_thermal_properties(self,
t_min=0,
t_max=1000,
t_step=10,
temperatures=None,
is_projection=False,
band_indices=None,
... | python | def run_thermal_properties(self,
t_min=0,
t_max=1000,
t_step=10,
temperatures=None,
is_projection=False,
band_indices=None,
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t_min, t_max, t_step : float, optional
Minimum and maximum temperatures and the interval in this
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temperatures : array_like, optional
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241,360 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.get_thermal_properties | def get_thermal_properties(self):
"""Return thermal properties
Returns
-------
(temperatures, free energy, entropy, heat capacity)
"""
warnings.warn("Phonopy.get_thermal_properties is deprecated. "
"Use Phonopy.get_thermal_properties_dict.",
... | python | def get_thermal_properties(self):
warnings.warn("Phonopy.get_thermal_properties is deprecated. "
"Use Phonopy.get_thermal_properties_dict.",
DeprecationWarning)
tp = self.get_thermal_properties_dict()
return (tp['temperatures'],
tp['fr... | [
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241,361 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.run_thermal_displacements | def run_thermal_displacements(self,
t_min=0,
t_max=1000,
t_step=10,
temperatures=None,
direction=None,
freq_min=None... | python | def run_thermal_displacements(self,
t_min=0,
t_max=1000,
t_step=10,
temperatures=None,
direction=None,
freq_min=None... | [
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241,362 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.run_thermal_displacement_matrices | def run_thermal_displacement_matrices(self,
t_min=0,
t_max=1000,
t_step=10,
temperatures=None,
freq_min=None,
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t_min=0,
t_max=1000,
t_step=10,
temperatures=None,
freq_min=None,
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241,363 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.set_modulations | def set_modulations(self,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None):
"""Generate atomic displacements of phonon modes.
The design of this fea... | python | def set_modulations(self,
dimension,
phonon_modes,
delta_q=None,
derivative_order=None,
nac_q_direction=None):
if self._dynamical_matrix is None:
msg = ("Dynamical matrix has not y... | [
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241,364 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.set_irreps | def set_irreps(self,
q,
is_little_cogroup=False,
nac_q_direction=None,
degeneracy_tolerance=1e-4):
"""Identify ir-reps of phonon modes.
The design of this API is not very satisfactory and is expceted
to be redesined in ... | python | def set_irreps(self,
q,
is_little_cogroup=False,
nac_q_direction=None,
degeneracy_tolerance=1e-4):
if self._dynamical_matrix is None:
msg = ("Dynamical matrix has not yet built.")
raise RuntimeError(msg)
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241,365 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.init_dynamic_structure_factor | def init_dynamic_structure_factor(self,
Qpoints,
T,
atomic_form_factor_func=None,
scattering_lengths=None,
freq_min=None,
... | python | def init_dynamic_structure_factor(self,
Qpoints,
T,
atomic_form_factor_func=None,
scattering_lengths=None,
freq_min=None,
... | [
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241,366 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.run_dynamic_structure_factor | def run_dynamic_structure_factor(self,
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scattering_lengths=None,
freq_min=None,
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241,367 | atztogo/phonopy | phonopy/api_phonopy.py | Phonopy.save | def save(self,
filename="phonopy_params.yaml",
settings=None):
"""Save parameters in Phonopy instants into file.
Parameters
----------
filename: str, optional
File name. Default is "phonopy_params.yaml"
settings: dict, optional
I... | python | def save(self,
filename="phonopy_params.yaml",
settings=None):
phpy_yaml = PhonopyYaml(calculator=self._calculator,
settings=settings)
phpy_yaml.set_phonon_info(self)
with open(filename, 'w') as w:
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241,368 | atztogo/phonopy | phonopy/phonon/mesh.py | length2mesh | def length2mesh(length, lattice, rotations=None):
"""Convert length to mesh for q-point sampling
This conversion for each reciprocal axis follows VASP convention by
N = max(1, int(l * |a|^* + 0.5))
'int' means rounding down, not rounding to nearest integer.
Parameters
----------
length... | python | def length2mesh(length, lattice, rotations=None):
rec_lattice = np.linalg.inv(lattice)
rec_lat_lengths = np.sqrt(np.diagonal(np.dot(rec_lattice.T, rec_lattice)))
mesh_numbers = np.rint(rec_lat_lengths * length).astype(int)
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241,369 | atztogo/phonopy | phonopy/phonon/thermal_displacement.py | ThermalMotion._get_population | def _get_population(self, freq, t): # freq in THz
"""Return phonon population number
Three types of combinations of array inputs are possible.
- single freq and single t
- single freq and len(t) > 1
- len(freq) > 1 and single t
"""
condition = t > 1.0
i... | python | def _get_population(self, freq, t): # freq in THz
condition = t > 1.0
if type(condition) == bool or type(condition) == np.bool_:
if condition:
return 1.0 / (np.exp(freq * THzToEv / (Kb * t)) - 1)
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241,370 | atztogo/phonopy | phonopy/phonon/thermal_displacement.py | ThermalDisplacements._project_eigenvectors | def _project_eigenvectors(self):
"""Eigenvectors are projected along Cartesian direction"""
self._p_eigenvectors = []
for vecs_q in self._eigenvectors:
p_vecs_q = []
for vecs in vecs_q.T:
p_vecs_q.append(np.dot(vecs.reshape(-1, 3),
... | python | def _project_eigenvectors(self):
self._p_eigenvectors = []
for vecs_q in self._eigenvectors:
p_vecs_q = []
for vecs in vecs_q.T:
p_vecs_q.append(np.dot(vecs.reshape(-1, 3),
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241,371 | atztogo/phonopy | phonopy/structure/spglib.py | get_symmetry | def get_symmetry(cell, symprec=1e-5, angle_tolerance=-1.0):
"""This gives crystal symmetry operations from a crystal structure.
Args:
cell: Crystal structrue given either in Atoms object or tuple.
In the case given by a tuple, it has to follow the form below,
(Lattice parameters... | python | def get_symmetry(cell, symprec=1e-5, angle_tolerance=-1.0):
_set_no_error()
lattice, positions, numbers, magmoms = _expand_cell(cell)
if lattice is None:
return None
multi = 48 * len(positions)
rotation = np.zeros((multi, 3, 3), dtype='intc')
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241,372 | atztogo/phonopy | phonopy/structure/spglib.py | get_symmetry_dataset | def get_symmetry_dataset(cell,
symprec=1e-5,
angle_tolerance=-1.0,
hall_number=0):
"""Search symmetry dataset from an input cell.
Args:
cell, symprec, angle_tolerance:
See the docstring of get_symmetry.
hall_... | python | def get_symmetry_dataset(cell,
symprec=1e-5,
angle_tolerance=-1.0,
hall_number=0):
_set_no_error()
lattice, positions, numbers, _ = _expand_cell(cell)
if lattice is None:
return None
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241,373 | atztogo/phonopy | phonopy/structure/spglib.py | get_spacegroup | def get_spacegroup(cell, symprec=1e-5, angle_tolerance=-1.0, symbol_type=0):
"""Return space group in international table symbol and number as a string.
If it fails, None is returned.
"""
_set_no_error()
dataset = get_symmetry_dataset(cell,
symprec=symprec,
... | python | def get_spacegroup(cell, symprec=1e-5, angle_tolerance=-1.0, symbol_type=0):
_set_no_error()
dataset = get_symmetry_dataset(cell,
symprec=symprec,
angle_tolerance=angle_tolerance)
if dataset is None:
return None
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241,374 | atztogo/phonopy | phonopy/structure/spglib.py | get_hall_number_from_symmetry | def get_hall_number_from_symmetry(rotations, translations, symprec=1e-5):
"""Hall number is obtained from a set of symmetry operations.
If it fails, None is returned.
"""
r = np.array(rotations, dtype='intc', order='C')
t = np.array(translations, dtype='double', order='C')
hall_number = spg.ha... | python | def get_hall_number_from_symmetry(rotations, translations, symprec=1e-5):
r = np.array(rotations, dtype='intc', order='C')
t = np.array(translations, dtype='double', order='C')
hall_number = spg.hall_number_from_symmetry(r, t, symprec)
return hall_number | [
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241,375 | atztogo/phonopy | phonopy/structure/spglib.py | get_spacegroup_type | def get_spacegroup_type(hall_number):
"""Translate Hall number to space group type information.
If it fails, None is returned.
"""
_set_no_error()
keys = ('number',
'international_short',
'international_full',
'international',
'schoenflies',
... | python | def get_spacegroup_type(hall_number):
_set_no_error()
keys = ('number',
'international_short',
'international_full',
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'schoenflies',
'hall_symbol',
'choice',
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241,376 | atztogo/phonopy | phonopy/structure/spglib.py | get_pointgroup | def get_pointgroup(rotations):
"""Return point group in international table symbol and number.
The symbols are mapped to the numbers as follows:
1 "1 "
2 "-1 "
3 "2 "
4 "m "
5 "2/m "
6 "222 "
7 "mm2 "
8 "mmm "
9 "4 "
10 "-4 "
11... | python | def get_pointgroup(rotations):
_set_no_error()
# (symbol, pointgroup_number, transformation_matrix)
pointgroup = spg.pointgroup(np.array(rotations, dtype='intc', order='C'))
_set_error_message()
return pointgroup | [
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241,377 | atztogo/phonopy | phonopy/structure/spglib.py | standardize_cell | def standardize_cell(cell,
to_primitive=False,
no_idealize=False,
symprec=1e-5,
angle_tolerance=-1.0):
"""Return standardized cell.
Args:
cell, symprec, angle_tolerance:
See the docstring of get_symmetry.
... | python | def standardize_cell(cell,
to_primitive=False,
no_idealize=False,
symprec=1e-5,
angle_tolerance=-1.0):
_set_no_error()
lattice, _positions, _numbers, _ = _expand_cell(cell)
if lattice is None:
return None
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241,378 | atztogo/phonopy | phonopy/structure/spglib.py | find_primitive | def find_primitive(cell, symprec=1e-5, angle_tolerance=-1.0):
"""Primitive cell is searched in the input cell.
The primitive cell is returned by a tuple of (lattice, positions, numbers).
If it fails, None is returned.
"""
_set_no_error()
lattice, positions, numbers, _ = _expand_cell(cell)
... | python | def find_primitive(cell, symprec=1e-5, angle_tolerance=-1.0):
_set_no_error()
lattice, positions, numbers, _ = _expand_cell(cell)
if lattice is None:
return None
num_atom_prim = spg.primitive(lattice,
positions,
numbers,
... | [
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241,379 | atztogo/phonopy | phonopy/structure/spglib.py | get_symmetry_from_database | def get_symmetry_from_database(hall_number):
"""Return symmetry operations corresponding to a Hall symbol.
The Hall symbol is given by the serial number in between 1 and 530.
The symmetry operations are given by a dictionary whose keys are
'rotations' and 'translations'.
If it fails, None is return... | python | def get_symmetry_from_database(hall_number):
_set_no_error()
rotations = np.zeros((192, 3, 3), dtype='intc')
translations = np.zeros((192, 3), dtype='double')
num_sym = spg.symmetry_from_database(rotations, translations, hall_number)
_set_error_message()
if num_sym is None:
return None... | [
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241,380 | atztogo/phonopy | phonopy/structure/spglib.py | get_grid_point_from_address | def get_grid_point_from_address(grid_address, mesh):
"""Return grid point index by tranlating grid address"""
_set_no_error()
return spg.grid_point_from_address(np.array(grid_address, dtype='intc'),
np.array(mesh, dtype='intc')) | python | def get_grid_point_from_address(grid_address, mesh):
_set_no_error()
return spg.grid_point_from_address(np.array(grid_address, dtype='intc'),
np.array(mesh, dtype='intc')) | [
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241,381 | atztogo/phonopy | phonopy/structure/spglib.py | get_ir_reciprocal_mesh | def get_ir_reciprocal_mesh(mesh,
cell,
is_shift=None,
is_time_reversal=True,
symprec=1e-5,
is_dense=False):
"""Return k-points mesh and k-point map to the irreducible k-points.
... | python | def get_ir_reciprocal_mesh(mesh,
cell,
is_shift=None,
is_time_reversal=True,
symprec=1e-5,
is_dense=False):
_set_no_error()
lattice, positions, numbers, _ = _expand_cell(cell)
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241,382 | atztogo/phonopy | phonopy/structure/spglib.py | get_stabilized_reciprocal_mesh | def get_stabilized_reciprocal_mesh(mesh,
rotations,
is_shift=None,
is_time_reversal=True,
qpoints=None,
is_dense=False):
"""Return k-point ma... | python | def get_stabilized_reciprocal_mesh(mesh,
rotations,
is_shift=None,
is_time_reversal=True,
qpoints=None,
is_dense=False):
_set_no_error()
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241,383 | atztogo/phonopy | phonopy/structure/spglib.py | relocate_BZ_grid_address | def relocate_BZ_grid_address(grid_address,
mesh,
reciprocal_lattice, # column vectors
is_shift=None,
is_dense=False):
"""Grid addresses are relocated to be inside first Brillouin zone.
Number of... | python | def relocate_BZ_grid_address(grid_address,
mesh,
reciprocal_lattice, # column vectors
is_shift=None,
is_dense=False):
_set_no_error()
if is_shift is None:
_is_shift = np.zeros(3, dtype='... | [
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241,384 | atztogo/phonopy | phonopy/structure/spglib.py | delaunay_reduce | def delaunay_reduce(lattice, eps=1e-5):
"""Run Delaunay reduction
Args:
lattice: Lattice parameters in the form of
[[a_x, a_y, a_z],
[b_x, b_y, b_z],
[c_x, c_y, c_z]]
symprec:
float: Tolerance to check if volume is close to zero or not and
... | python | def delaunay_reduce(lattice, eps=1e-5):
_set_no_error()
delaunay_lattice = np.array(np.transpose(lattice),
dtype='double', order='C')
result = spg.delaunay_reduce(delaunay_lattice, float(eps))
_set_error_message()
if result == 0:
return None
else:
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241,385 | atztogo/phonopy | phonopy/structure/spglib.py | niggli_reduce | def niggli_reduce(lattice, eps=1e-5):
"""Run Niggli reduction
Args:
lattice: Lattice parameters in the form of
[[a_x, a_y, a_z],
[b_x, b_y, b_z],
[c_x, c_y, c_z]]
eps:
float: Tolerance to check if difference of norms of two basis
... | python | def niggli_reduce(lattice, eps=1e-5):
_set_no_error()
niggli_lattice = np.array(np.transpose(lattice), dtype='double', order='C')
result = spg.niggli_reduce(niggli_lattice, float(eps))
_set_error_message()
if result == 0:
return None
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241,386 | atztogo/phonopy | phonopy/file_IO.py | get_FORCE_SETS_lines | def get_FORCE_SETS_lines(dataset, forces=None):
"""Generate FORCE_SETS string
See the format of dataset in the docstring of
Phonopy.set_displacement_dataset. Optionally for the type-1 (traditional)
format, forces can be given. In this case, sets of forces are
unnecessary to be stored in the dataset... | python | def get_FORCE_SETS_lines(dataset, forces=None):
if 'first_atoms' in dataset:
return _get_FORCE_SETS_lines_type1(dataset, forces=forces)
elif 'forces' in dataset:
return _get_FORCE_SETS_lines_type2(dataset) | [
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241,387 | atztogo/phonopy | phonopy/file_IO.py | write_FORCE_CONSTANTS | def write_FORCE_CONSTANTS(force_constants,
filename='FORCE_CONSTANTS',
p2s_map=None):
"""Write force constants in text file format.
Parameters
----------
force_constants: ndarray
Force constants
shape=(n_satom,n_satom,3,3) or (n_patom,... | python | def write_FORCE_CONSTANTS(force_constants,
filename='FORCE_CONSTANTS',
p2s_map=None):
lines = get_FORCE_CONSTANTS_lines(force_constants, p2s_map=p2s_map)
with open(filename, 'w') as w:
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241,388 | atztogo/phonopy | phonopy/file_IO.py | write_force_constants_to_hdf5 | def write_force_constants_to_hdf5(force_constants,
filename='force_constants.hdf5',
p2s_map=None,
physical_unit=None,
compression=None):
"""Write force constants in hdf5 format.
... | python | def write_force_constants_to_hdf5(force_constants,
filename='force_constants.hdf5',
p2s_map=None,
physical_unit=None,
compression=None):
try:
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241,389 | atztogo/phonopy | phonopy/phonon/band_structure.py | get_band_qpoints | def get_band_qpoints(band_paths, npoints=51, rec_lattice=None):
"""Generate qpoints for band structure path
Note
----
Behavior changes with and without rec_lattice given.
Parameters
----------
band_paths: list of array_likes
Sets of end points of paths
dtype='double'
... | python | def get_band_qpoints(band_paths, npoints=51, rec_lattice=None):
npts = _get_npts(band_paths, npoints, rec_lattice)
qpoints_of_paths = []
c = 0
for band_path in band_paths:
nd = len(band_path)
for i in range(nd - 1):
delta = np.subtract(band_path[i + 1], band_path[i]) / (npts[... | [
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Parameters
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band_paths: list of array_likes
Sets of end points of paths
dtype='double'
shape=(sets of paths, paths, 3)
example:
[[[0, ... | [
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241,390 | atztogo/phonopy | phonopy/phonon/band_structure.py | get_band_qpoints_by_seekpath | def get_band_qpoints_by_seekpath(primitive, npoints, is_const_interval=False):
"""q-points along BZ high symmetry paths are generated using seekpath.
Parameters
----------
primitive : PhonopyAtoms
Primitive cell.
npoints : int
Number of q-points sampled along a path including end po... | python | def get_band_qpoints_by_seekpath(primitive, npoints, is_const_interval=False):
try:
import seekpath
except ImportError:
raise ImportError("You need to install seekpath.")
band_path = seekpath.get_path(primitive.totuple())
point_coords = band_path['point_coords']
qpoints_of_paths = [... | [
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Primitive cell.
npoints : int
Number of q-points sampled along a path including end points.
is_const_interval : bool, optional
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241,391 | atztogo/phonopy | phonopy/harmonic/dynmat_to_fc.py | get_commensurate_points | def get_commensurate_points(supercell_matrix): # wrt primitive cell
"""Commensurate q-points are returned.
Parameters
----------
supercell_matrix : array_like
Supercell matrix with respect to primitive cell basis vectors.
shape=(3, 3)
dtype=intc
"""
smat = np.array(su... | python | def get_commensurate_points(supercell_matrix): # wrt primitive cell
smat = np.array(supercell_matrix, dtype=int)
rec_primitive = PhonopyAtoms(numbers=[1],
scaled_positions=[[0, 0, 0]],
cell=np.diag([1, 1, 1]),
pb... | [
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Parameters
----------
supercell_matrix : array_like
Supercell matrix with respect to primitive cell basis vectors.
shape=(3, 3)
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241,392 | atztogo/phonopy | phonopy/harmonic/dynmat_to_fc.py | get_commensurate_points_in_integers | def get_commensurate_points_in_integers(supercell_matrix):
"""Commensurate q-points in integer representation are returned.
A set of integer representation of lattice points is transformed to
the equivalent set of lattice points in fractional coordinates with
respect to supercell basis vectors by
... | python | def get_commensurate_points_in_integers(supercell_matrix):
smat = np.array(supercell_matrix, dtype=int)
snf = SNF3x3(smat.T)
snf.run()
D = snf.A.diagonal()
b, c, a = np.meshgrid(range(D[1]), range(D[2]), range(D[0]))
lattice_points = np.dot(np.c_[a.ravel() * D[1] * D[2],
... | [
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A set of integer representation of lattice points is transformed to
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integer_lattice_points / det(supercell_matrix)
Parameters
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241,393 | atztogo/phonopy | phonopy/interface/vasp.py | write_vasp | def write_vasp(filename, cell, direct=True):
"""Write crystal structure to a VASP POSCAR style file.
Parameters
----------
filename : str
Filename.
cell : PhonopyAtoms
Crystal structure.
direct : bool, optional
In 'Direct' or not in VASP POSCAR format. Default is True.
... | python | def write_vasp(filename, cell, direct=True):
lines = get_vasp_structure_lines(cell, direct=direct)
with open(filename, 'w') as w:
w.write("\n".join(lines)) | [
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filename : str
Filename.
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Crystal structure.
direct : bool, optional
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241,394 | atztogo/phonopy | phonopy/interface/qe.py | PwscfIn._set_lattice | def _set_lattice(self):
"""Calculate and set lattice parameters.
Invoked by CELL_PARAMETERS tag.
"""
unit = self._values[0]
if unit == 'alat':
if not self._tags['celldm(1)']:
print("celldm(1) has to be specified when using alat.")
sy... | python | def _set_lattice(self):
unit = self._values[0]
if unit == 'alat':
if not self._tags['celldm(1)']:
print("celldm(1) has to be specified when using alat.")
sys.exit(1)
else:
factor = self._tags['celldm(1)'] # in Bohr
elif uni... | [
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241,395 | atztogo/phonopy | phonopy/interface/qe.py | PH_Q2R.run | def run(self, cell, is_full_fc=False, parse_fc=True):
"""Make supercell force constants readable for phonopy
Note
----
Born effective charges and dielectric constant tensor are read
from QE output file if they exist. But this means
dipole-dipole contributions are removed... | python | def run(self, cell, is_full_fc=False, parse_fc=True):
with open(self._filename) as f:
fc_dct = self._parse_q2r(f)
self.dimension = fc_dct['dimension']
self.epsilon = fc_dct['dielectric']
self.borns = fc_dct['born']
if parse_fc:
(self.fc... | [
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241,396 | atztogo/phonopy | phonopy/interface/qe.py | PH_Q2R._parse_q2r | def _parse_q2r(self, f):
"""Parse q2r output file
The format of q2r output is described at the mailing list below:
http://www.democritos.it/pipermail/pw_forum/2005-April/002408.html
http://www.democritos.it/pipermail/pw_forum/2008-September/010099.html
http://www.democritos.it/p... | python | def _parse_q2r(self, f):
natom, dim, epsilon, borns = self._parse_parameters(f)
fc_dct = {'fc': self._parse_fc(f, natom, dim),
'dimension': dim,
'dielectric': epsilon,
'born': borns}
return fc_dct | [
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241,397 | atztogo/phonopy | phonopy/interface/qe.py | PH_Q2R._parse_fc | def _parse_fc(self, f, natom, dim):
"""Parse force constants part
Physical unit of force cosntants in the file is Ry/au^2.
"""
ndim = np.prod(dim)
fc = np.zeros((natom, natom * ndim, 3, 3), dtype='double', order='C')
for k, l, i, j in np.ndindex((3, 3, natom, natom)):
... | python | def _parse_fc(self, f, natom, dim):
ndim = np.prod(dim)
fc = np.zeros((natom, natom * ndim, 3, 3), dtype='double', order='C')
for k, l, i, j in np.ndindex((3, 3, natom, natom)):
line = f.readline()
for i_dim in range(ndim):
line = f.readline()
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241,398 | atztogo/phonopy | phonopy/interface/cp2k.py | get_cp2k_structure | def get_cp2k_structure(atoms):
"""Convert the atoms structure to a CP2K input file skeleton string"""
from cp2k_tools.generator import dict2cp2k
# CP2K's default unit is angstrom, convert it, but still declare it explictly:
cp2k_cell = {sym: ('[angstrom]',) + tuple(coords) for sym, coords in zip(('a',... | python | def get_cp2k_structure(atoms):
from cp2k_tools.generator import dict2cp2k
# CP2K's default unit is angstrom, convert it, but still declare it explictly:
cp2k_cell = {sym: ('[angstrom]',) + tuple(coords) for sym, coords in zip(('a', 'b', 'c'), atoms.get_cell()*Bohr)}
cp2k_cell['periodic'] = 'XYZ' # any... | [
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241,399 | atztogo/phonopy | phonopy/api_qha.py | PhonopyQHA.plot_qha | def plot_qha(self, thin_number=10, volume_temp_exp=None):
"""Returns matplotlib.pyplot of QHA fitting curves at temperatures"""
return self._qha.plot(thin_number=thin_number,
volume_temp_exp=volume_temp_exp) | python | def plot_qha(self, thin_number=10, volume_temp_exp=None):
return self._qha.plot(thin_number=thin_number,
volume_temp_exp=volume_temp_exp) | [
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