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Merge pull request #96 from singularitti/master
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Remove all `numba` speed up tools
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@singularitti
singularitti authored Oct 21, 2023
2 parents 632c2d1 + 26c00d2 commit ba9d292
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Showing 29 changed files with 1,459 additions and 762 deletions.
15 changes: 7 additions & 8 deletions qha/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,11 @@

# In case of user who does not have ``pip`` above version 9.0.0
if sys.version_info < (3, 5):
raise EnvironmentError('Please use Python version higher than 3.5!')
raise EnvironmentError("Please use Python version higher than 3.5!")

__author__ = {'Tian Qin': '[email protected]',
'Qi Zhang': '[email protected]'}
__copyright__ = 'Copyright (c) 2018, Renata group'
__credits__ = {'Renata M. M. Wentzcovitch': '[email protected]'}
__date__ = 'Feb 17, 2018'
__maintainer__ = 'Tian Qin, Qi Zhang'
__version__ = '1.0.22'
__author__ = {"Tian Qin": "[email protected]", "Qi Zhang": "[email protected]"}
__copyright__ = "Copyright (c) 2018, Renata group"
__credits__ = {"Renata M. M. Wentzcovitch": "[email protected]"}
__date__ = "Feb 17, 2018"
__maintainer__ = "Tian Qin, Qi Zhang"
__version__ = "1.0.22"
129 changes: 84 additions & 45 deletions qha/basic_io/input_maker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
from yaml import Loader

# ===================== What can be exported? =====================
__all__ = ['FromQEOutput']
__all__ = ["FromQEOutput"]


class FromQEOutput:
Expand Down Expand Up @@ -68,12 +68,12 @@ def read_file_list(self) -> None:
"""
Read all the files' names for frequency files given by Quantum ESPRESSO program ``matdyn.x``.
"""
with open(self._inp_file_list, 'r') as f:
with open(self._inp_file_list, "r") as f:
d = load(f, Loader=Loader)

self.formula_unit_number = int(d['formula_unit_number'])
self.comment: str = d['comment']
self._frequency_files: List[str] = d['frequency_files']
self.formula_unit_number = int(d["formula_unit_number"])
self.comment: str = d["comment"]
self._frequency_files: List[str] = d["frequency_files"]

def read_static(self) -> None:
"""
Expand All @@ -84,16 +84,22 @@ def read_static(self) -> None:
volumes = []
energies = []

with open(self._inp_static, 'r') as f:
with open(self._inp_static, "r") as f:
print(
"Reading static data: emtpy lines or lines starting with '#' will be ignored!")
"Reading static data: emtpy lines or lines starting with '#' will be ignored!"
)

for line in f:
if not line.strip() or line.startswith('#'): # Ignore empty line or comment line
if not line.strip() or line.startswith(
"#"
): # Ignore empty line or comment line
continue

match = re.match(r"p\s*=\s*(-?\d*\.?\d*)\s*v\s*=\s*(-?\d*\.?\d*)\s*e\s*=\s*(-?\d*\.?\d*)", line,
flags=re.IGNORECASE)
match = re.match(
r"p\s*=\s*(-?\d*\.?\d*)\s*v\s*=\s*(-?\d*\.?\d*)\s*e\s*=\s*(-?\d*\.?\d*)",
line,
flags=re.IGNORECASE,
)
if match is None:
continue

Expand All @@ -113,29 +119,35 @@ def read_q_points(self) -> None:
q_coordinates = []
q_weights = []

with open(self._inp_q_points, 'r') as f:
with open(self._inp_q_points, "r") as f:
print(
"Reading q-points file: emtpy lines or lines starting with '#' will be ignored!")
"Reading q-points file: emtpy lines or lines starting with '#' will be ignored!"
)

regex = re.compile(
r"\s*(-?\d*\.?\d*)\s*(-?\d*\.?\d*)\s*(-?\d*\.?\d*)\s*(-?\d*\.?\d*)")
r"\s*(-?\d*\.?\d*)\s*(-?\d*\.?\d*)\s*(-?\d*\.?\d*)\s*(-?\d*\.?\d*)"
)

for line in f:
if not line.strip() or line.startswith('#'): # Ignore empty line or comment line
if not line.strip() or line.startswith(
"#"
): # Ignore empty line or comment line
continue

match = regex.match(line)
if not regex.match(line):
raise RuntimeError(
"Unknown line! Should be 3 coordinates and 1 weight, other lines should be commented with '#'.")
"Unknown line! Should be 3 coordinates and 1 weight, other lines should be commented with '#'."
)
else:
g = match.groups()
q_coordinates.append(g[0:3])
# TODO: Check possible bug, what if the regex match fails
q_weights.append(g[3])

self.q_coordinates = np.array(q_coordinates,
dtype=float) # TODO: Possible bug, ``np.array([])`` is regarded as ``False``
self.q_coordinates = np.array(
q_coordinates, dtype=float
) # TODO: Possible bug, ``np.array([])`` is regarded as ``False``
self.q_weights = np.array(q_weights, dtype=float)

@staticmethod
Expand Down Expand Up @@ -165,15 +177,17 @@ def read_frequency_file(inp: str) -> Tuple[Vector, Matrix]:
if not line.strip():
continue

if 'nbnd' or 'nks' in line:
if "nbnd" or "nks" in line:
match = regex.search(line)

if not match:
raise RuntimeError(
"The head line '{0}' is not complete! Here 'nbnd' and 'nks' are not found!".format(line))
"The head line '{0}' is not complete! Here 'nbnd' and 'nks' are not found!".format(
line
)
)
else:
bands_amount, q_points_amount = strings_to_integers(
match.groups())
bands_amount, q_points_amount = strings_to_integers(match.groups())
break

gen: Iterator[str] = text_stream.generator_starts_from(offset)
Expand All @@ -192,7 +206,7 @@ def read_frequency_file(inp: str) -> Tuple[Vector, Matrix]:
# Sometimes QE prints negative numbers that coalesce with the previous one,
# so we need to split not only spaces but also minus signs
# Regex from https://stackoverflow.com/a/30858977/3260253
freqs = list(filter(lambda s: s, re.split(r'\s+|(?<!\s)(?=-)', line)))
freqs = list(filter(lambda s: s, re.split(r"\s+|(?<!\s)(?=-)", line)))
x = np.hstack((x, freqs))

frequencies.append(x)
Expand All @@ -203,12 +217,16 @@ def read_frequency_file(inp: str) -> Tuple[Vector, Matrix]:
if q_coordinates.shape[0] != q_points_amount:
raise RuntimeError(
"The number of q-points detected, {0}, is not the same as what specified in head line!".format(
q_coordinates.shape[0]))
q_coordinates.shape[0]
)
)

if frequencies.shape != (q_points_amount, bands_amount):
raise RuntimeError(
"The frequencies array shape '{0}' is not the same as '{1}'!".format(
frequencies.shape, (q_points_amount, bands_amount)))
frequencies.shape, (q_points_amount, bands_amount)
)
)

return q_coordinates, frequencies

Expand All @@ -219,25 +237,30 @@ def read_frequency_files(self) -> None:
"""
frequencies_for_all_files = []

if any(_ is None for _ in (self.q_coordinates, self.q_weights)): # If any of them is ``None``
if any(
_ is None for _ in (self.q_coordinates, self.q_weights)
): # If any of them is ``None``
self.read_q_points() # Fill these 2 properties

for i in range(len(self._frequency_files)):
q_coordinates, frequencies = self.read_frequency_file(
self._frequency_files[i])
self._frequency_files[i]
)

# Here I use `allclose` rather than `array_equal` since they may have very little
# differences even they are supposed to be the same, because of the digits QE gave.
if not np.allclose(q_coordinates, self.q_coordinates):
warnings.warn("The q-points' coordinates are different from what specified in the q-point file!",
stacklevel=1)
warnings.warn(
"The q-points' coordinates are different from what specified in the q-point file!",
stacklevel=1,
)

frequencies_for_all_files.append(frequencies)

# Shape: (# volumes, # q-points, # bands on each point)
self.frequencies = np.array(frequencies_for_all_files)

def write_to_file(self, outfile='input') -> None:
def write_to_file(self, outfile="input") -> None:
"""
Write all data to a file *outfile*, which will be regarded as standard input file for ``qha``.
Expand All @@ -246,31 +269,47 @@ def write_to_file(self, outfile='input') -> None:
path = pathlib.Path(outfile)
if path.is_file():
print(
"Old '{0}' file found, I will backup it before continue.".format(outfile))
path.rename(outfile + '.backup')
"Old '{0}' file found, I will backup it before continue.".format(
outfile
)
)
path.rename(outfile + ".backup")

with open(outfile, 'w') as f:
with open(outfile, "w") as f:
f.write("# {0}\n".format(self.comment))
f.write('# The file contains frequencies and weights at the END!\n')
f.write("# The file contains frequencies and weights at the END!\n")
f.write(
'# Number of volumes (nv), q-vectors (nq), normal mode (np), formula units(nm)\n')
"# Number of volumes (nv), q-vectors (nq), normal mode (np), formula units(nm)\n"
)
# TODO: Possible bug introduced in formatting
f.write("{0} {1} {2} {3}\n\n".format(len(self.volumes), len(self.q_weights),
self.frequencies.shape[-1], self.formula_unit_number))
f.write(
"{0} {1} {2} {3}\n\n".format(
len(self.volumes),
len(self.q_weights),
self.frequencies.shape[-1],
self.formula_unit_number,
)
)

for i in range(len(self.volumes)):
f.write("P={0:20.10f} V={1:20.10f} E={2:20.10f}\n".format(self.pressures[i], self.volumes[i],
self.static_energies[i]))
f.write(
"P={0:20.10f} V={1:20.10f} E={2:20.10f}\n".format(
self.pressures[i], self.volumes[i], self.static_energies[i]
)
)

for j in range(len(self.q_weights)):
f.write("{0:12.8f} {1:12.8f} {2:12.8f}\n".format(
*self.q_coordinates[j]))
f.write(
"{0:12.8f} {1:12.8f} {2:12.8f}\n".format(*self.q_coordinates[j])
)

for k in range(self.frequencies.shape[-1]):
f.write("{0:20.10f}\n".format(
self.frequencies[i, j, k]))
f.write("{0:20.10f}\n".format(self.frequencies[i, j, k]))

f.write('\nweight\n')
f.write("\nweight\n")
for j in range(len(self.q_weights)):
f.write("{0:12.8f} {1:12.8f} {2:12.8f} {3:12.8f}\n".format(
*self.q_coordinates[j], self.q_weights[j]))
f.write(
"{0:12.8f} {1:12.8f} {2:12.8f} {3:12.8f}\n".format(
*self.q_coordinates[j], self.q_weights[j]
)
)
44 changes: 28 additions & 16 deletions qha/basic_io/out.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,66 +14,78 @@


def save_to_output(fn_output, text):
with open(fn_output, 'a') as f:
f.write(text + '\n')
with open(fn_output, "a") as f:
f.write(text + "\n")


def save_x_tp(df, t, desired_pressures_gpa, p_sample_gpa, outfile_name):
# To fix the last 2 temperature points of Cp is not accurate, we added 4 temperature points,
# Now to get rid of the added temperature points before saving calculated properties into files.
df = pd.DataFrame(df, index=t, columns=desired_pressures_gpa).iloc[:-4, :]
df.columns.name = 'T(K)\P(GPa)'
df.columns.name = "T(K)\P(GPa)"
sample = df.loc[:, df.columns.isin(p_sample_gpa)]
with open(outfile_name, 'w') as f:
with open(outfile_name, "w") as f:
f.write(sample.to_string())


def save_x_pt(df, t, desired_pressures_gpa, t_sample, outfile_name):
# To fix the last 2 temperature points of Cp is not accurate, we added 4 temperature points,
# Now to get rid of the added temperature points before saving calculated properties into files.
df = pd.DataFrame(df[:-4].T, index=desired_pressures_gpa, columns=t[:-4])
df.columns.name = 'P(GPa)\T(K)'
df.columns.name = "P(GPa)\T(K)"
sample = df.loc[:, df.columns.isin(t_sample)]
with open(outfile_name, 'w') as f:
with open(outfile_name, "w") as f:
f.write(sample.to_string())


def save_x_vt(x, t, volume_grid, t_sample, outfile_name):
df = pd.DataFrame(x.T, index=volume_grid, columns=t)
df.columns.name = 'V(A^3)\T(K)'
df.columns.name = "V(A^3)\T(K)"
sample = df.loc[:, df.columns.isin(t_sample)]
with open(outfile_name, 'w') as f:
with open(outfile_name, "w") as f:
f.write(sample.to_string())


def save_x_tv(x, t, volume_grid, t_sample, outfile_name):
df = pd.DataFrame(x, index=t, columns=volume_grid).iloc[:-4, :]
df.columns.name = 'T(K)\V(A^3)'
df.columns.name = "T(K)\V(A^3)"
sample = df.loc[df.index.isin(t_sample[:-4]), :]
with open(outfile_name, 'w') as f:
with open(outfile_name, "w") as f:
f.write(sample.to_string())


def make_starting_string() -> str:
return textwrap.dedent("""\
return textwrap.dedent(
"""\
============================================================
Current time: {0:%Y-%m-%d %H:%M:%S}
""".format(datetime.utcnow()))
""".format(
datetime.utcnow()
)
)


def make_tp_info(min_temperature, max_temperature, min_pressure, max_pressure):
return textwrap.dedent("""\
return textwrap.dedent(
"""\
------------------------------------------------------------
Desired T range: {0:6.2f} to {1:6.2f} K
Desired P range: {2:6.2f} to {3:6.2f} GPa
------------------------------------------------------------
""".format(min_temperature, max_temperature, min_pressure, max_pressure))
""".format(
min_temperature, max_temperature, min_pressure, max_pressure
)
)


def make_ending_string(time_elapsed) -> str:
return textwrap.dedent("""\
return textwrap.dedent(
"""\
------------------------------------------------------------
Total elapsed time is: {0:8.2f} seconds
Thanks for using QHA code, have a nice one :)
============================================================
""".format(time_elapsed))
""".format(
time_elapsed
)
)
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