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doc/conf.py
12
doc/conf.py
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@ -41,8 +41,8 @@ source_suffix = ".rst"
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master_doc = "index"
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# General information about the project.
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project = u"phono3py"
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copyright = u"2015, Atsushi Togo"
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project = "phono3py"
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copyright = "2015, Atsushi Togo"
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# The version info for the project you're documenting, acts as replacement for
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# |version| and |release|, also used in various other places throughout the
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@ -230,7 +230,7 @@ latex_elements = {
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# (source start file, target name, title, author, documentclass [howto/manual])
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# .
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latex_documents = [
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("index", "phono3py.tex", u"phono3py manual", u"Atsushi Togo", "manual"),
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("index", "phono3py.tex", "phono3py manual", "Atsushi Togo", "manual"),
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]
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# The name of an image file (relative to this directory) to place at the top of
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@ -258,7 +258,7 @@ latex_documents = [
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# One entry per manual page. List of tuples
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# (source start file, name, description, authors, manual section).
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man_pages = [("index", "phono3py", u"phono3py Documentation", [u"Atsushi Togo"], 1)]
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man_pages = [("index", "phono3py", "phono3py Documentation", ["Atsushi Togo"], 1)]
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# If true, show URL addresses after external links.
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# man_show_urls = False
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@ -273,8 +273,8 @@ texinfo_documents = [
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(
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"index",
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"phono3py",
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u"phono3py Documentation",
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u"Atsushi Togo",
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"phono3py Documentation",
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"Atsushi Togo",
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"phono3py",
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"One line description of project.",
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"Miscellaneous",
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@ -450,7 +450,7 @@ def main():
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if args.mfp:
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if "mean_free_path" in f_kappa:
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mfp = f_kappa["mean_free_path"][:]
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mean_freepath = np.sqrt((mfp ** 2).sum(axis=3))
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mean_freepath = np.sqrt((mfp**2).sum(axis=3))
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else:
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mean_freepath = get_mfp(
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f_kappa["gamma"][:], f_kappa["group_velocity"][:]
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@ -87,7 +87,7 @@ def write_grid_points(
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)
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size = (num_ir_gp * num_band * 3) ** 2 * 8 / 1.0e9
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print("- Full collision matrix at each temp and sigma: %.2f Gb" % size)
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size = num_gp * (num_band ** 2 * 16 + num_band * 8 + 1) / 1.0e9
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size = num_gp * (num_band**2 * 16 + num_band * 8 + 1) / 1.0e9
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print("- Phonons: %.2f Gb" % size)
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size = num_gp * 5 * 4 / 1.0e9
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print("- Grid point information: %.2f Gb" % size)
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@ -122,7 +122,7 @@ def show_num_triplets(
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for gp in _grid_points:
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num_triplets = tp_nums.get_number_of_triplets(gp)
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q = np.dot(bz_grid.addresses[gp], bz_grid.QDinv.T)
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size = num_triplets * num_band0 * num_band ** 2 * 8 / 1e6
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size = num_triplets * num_band0 * num_band**2 * 8 / 1e6
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print(
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" %5d (%5.2f %5.2f %5.2f) %8d %d Mb"
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% (gp, q[0], q[1], q[2], num_triplets, size)
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@ -352,7 +352,7 @@ class Isotope:
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ti_sum += ti_sum_band * self._integration_weights[i, bi, j]
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else:
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ti_sum += ti_sum_band * gaussian(f0 - f, self._sigma)
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t_inv.append(np.pi / 2 / np.prod(self._bz_grid.D_diag) * f0 ** 2 * ti_sum)
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t_inv.append(np.pi / 2 / np.prod(self._bz_grid.D_diag) * f0**2 * ti_sum)
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self._gamma = np.array(t_inv, dtype="double") / 2
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@ -227,6 +227,6 @@ def run_mfp_dos(
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def get_mfp(g, gv):
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"""Calculate mean free path from inverse lifetime and group velocity."""
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g = np.where(g > 0, g, -1)
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gv_norm = np.sqrt((gv ** 2).sum(axis=2))
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gv_norm = np.sqrt((gv**2).sum(axis=2))
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mean_freepath = np.where(g > 0, gv_norm / (2 * 2 * np.pi * g), 0)
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return mean_freepath
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@ -39,7 +39,7 @@ from phonopy.units import AMU, EV, Angstrom, Hbar, Kb, THz, THzToEv
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def gaussian(x, sigma):
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"""Return normal distribution."""
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return 1.0 / np.sqrt(2 * np.pi) / sigma * np.exp(-(x ** 2) / 2 / sigma ** 2)
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return 1.0 / np.sqrt(2 * np.pi) / sigma * np.exp(-(x**2) / 2 / sigma**2)
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def bose_einstein(x, T):
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@ -95,7 +95,7 @@ def sigma_squared(x, T):
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n = bose_einstein(x, T)
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# factor=1.0107576777968994
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factor = Hbar * EV / (2 * np.pi * THz) / AMU / Angstrom ** 2
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factor = Hbar * EV / (2 * np.pi * THz) / AMU / Angstrom**2
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#########################
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np.seterr(**old_settings)
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@ -50,7 +50,7 @@ from phono3py.phonon3.triplets import get_all_triplets
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from phono3py.phonon.grid import get_grid_points_by_rotations, get_ir_grid_points
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unit_to_WmK = (
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(THz * Angstrom) ** 2 / (Angstrom ** 3) * EV / THz / (2 * np.pi)
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(THz * Angstrom) ** 2 / (Angstrom**3) * EV / THz / (2 * np.pi)
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) # 2pi comes from definition of lifetime.
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@ -789,7 +789,7 @@ class ConductivityLBTE(Conductivity):
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-1.0,
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)
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inv_sinh = np.where(sinh > 0, 1.0 / sinh, 0)
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freqs_sinh = freqs * THzToEv * inv_sinh / (4 * Kb * t ** 2)
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freqs_sinh = freqs * THzToEv * inv_sinh / (4 * Kb * t**2)
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for i, f in enumerate(freqs_sinh):
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X[i] *= weights[i]
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@ -1110,7 +1110,7 @@ class ConductivityLBTE(Conductivity):
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mode_kappa[i_sigma, i_temp, i, j, k] = sum_k[vxf]
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t = self._temperatures[i_temp]
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mode_kappa[i_sigma, i_temp] *= self._conversion_factor * Kb * t ** 2
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mode_kappa[i_sigma, i_temp] *= self._conversion_factor * Kb * t**2
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def _set_mode_kappa_Chaput(self, i_sigma, i_temp, weights):
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"""Calculate mode kappa by the way in Laurent Chaput's PRL paper.
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@ -1150,11 +1150,11 @@ class ConductivityLBTE(Conductivity):
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mat = mat.T
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spectra = np.dot(mat.T, X) ** 2 * w
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for s, eigvec in zip(spectra, mat.T):
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vals = s * (eigvec ** 2).reshape(-1, 3).sum(axis=1)
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vals = s * (eigvec**2).reshape(-1, 3).sum(axis=1)
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vals = vals.reshape(num_ir_grid_points, num_band)
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self._mode_kappa[i_sigma, i_temp, :, :, i] += vals
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factor = self._conversion_factor * Kb * t ** 2
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factor = self._conversion_factor * Kb * t**2
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self._mode_kappa[i_sigma, i_temp] *= factor
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def _set_mode_kappa_from_mfp(
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@ -609,7 +609,7 @@ class ImagSelfEnergy:
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# Unit to THz of Gamma
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self._unit_conversion = (
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18 * np.pi / (Hbar * EV) ** 2 / (2 * np.pi * THz) ** 2 * EV ** 2
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18 * np.pi / (Hbar * EV) ** 2 / (2 * np.pi * THz) ** 2 * EV**2
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)
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def run(self):
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@ -124,12 +124,12 @@ class Interaction:
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(Hbar * EV) ** 3
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/ 36
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/ 8
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* EV ** 2
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/ Angstrom ** 6
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* EV**2
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/ Angstrom**6
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/ (2 * np.pi * THz) ** 3
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/ AMU ** 3
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/ AMU**3
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/ num_grid
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/ EV ** 2
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/ EV**2
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)
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else:
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self._unit_conversion = unit_conversion
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@ -797,7 +797,7 @@ class Interaction:
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self._fc3 = np.array(fc3, dtype="double", order="C")
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else:
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self._fc3 = np.array(
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fc3 * self._frequency_scale_factor ** 2, dtype="double", order="C"
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fc3 * self._frequency_scale_factor**2, dtype="double", order="C"
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)
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def _set_band_indices(self, band_indices):
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@ -349,7 +349,7 @@ class RealSelfEnergy:
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self._real_self_energies = None
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# Unit to THz of Delta
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self._unit_conversion = 18 / (Hbar * EV) ** 2 / (2 * np.pi * THz) ** 2 * EV ** 2
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self._unit_conversion = 18 / (Hbar * EV) ** 2 / (2 * np.pi * THz) ** 2 * EV**2
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def run(self):
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"""Calculate real-part of self-energies."""
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@ -571,10 +571,10 @@ class RealSelfEnergy:
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# d -= (n2 - n3) / f3
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# if abs(f4) > self._epsilon:
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# d += (n2 - n3) / f4
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d -= (n2 + n3 + 1) * f1 / (f1 ** 2 + self._epsilon ** 2)
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d += (n2 + n3 + 1) * f2 / (f2 ** 2 + self._epsilon ** 2)
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d -= (n2 - n3) * f3 / (f3 ** 2 + self._epsilon ** 2)
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d += (n2 - n3) * f4 / (f4 ** 2 + self._epsilon ** 2)
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d -= (n2 + n3 + 1) * f1 / (f1**2 + self._epsilon**2)
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d += (n2 + n3 + 1) * f2 / (f2**2 + self._epsilon**2)
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d -= (n2 - n3) * f3 / (f3**2 + self._epsilon**2)
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d += (n2 - n3) * f4 / (f4**2 + self._epsilon**2)
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sum_d += d * interaction[i, j, k] * weight
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return sum_d
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@ -597,8 +597,8 @@ class RealSelfEnergy:
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# d -= 1.0 / f1
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# if abs(f2) > self._epsilon:
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# d += 1.0 / f2
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d -= 1.0 * f1 / (f1 ** 2 + self._epsilon ** 2)
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d += 1.0 * f2 / (f2 ** 2 + self._epsilon ** 2)
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d -= 1.0 * f1 / (f1**2 + self._epsilon**2)
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d += 1.0 * f2 / (f2**2 + self._epsilon**2)
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sum_d += d * interaction[i, j, k] * weight
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return sum_d
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@ -356,8 +356,8 @@ class SpectralFunction:
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def _get_spectral_function(self, gammas, deltas, freq):
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fpoints = self._frequency_points
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nums = 4 * freq ** 2 * gammas / np.pi
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denoms = (fpoints ** 2 - freq ** 2 - 2 * freq * deltas) ** 2 + (
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nums = 4 * freq**2 * gammas / np.pi
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denoms = (fpoints**2 - freq**2 - 2 * freq * deltas) ** 2 + (
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2 * freq * gammas
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) ** 2
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vals = np.where(denoms > 0, nums / denoms, 0)
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@ -430,9 +430,9 @@ class SecondOrderFC:
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nelems = np.prod(u.shape)
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# print("sum u_inv:", u_inv.sum(axis=0) / u.shape[0])
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print("sum all u_inv:", u_inv.sum() / nelems)
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print("rms u_inv:", np.sqrt((u_inv ** 2).sum() / nelems))
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print("rms u:", np.sqrt((u ** 2).sum() / nelems))
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print("rms forces:", np.sqrt((self._forces ** 2).sum() / nelems))
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print("rms u_inv:", np.sqrt((u_inv**2).sum() / nelems))
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print("rms u:", np.sqrt((u**2).sum() / nelems))
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print("rms forces:", np.sqrt((self._forces**2).sum() / nelems))
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# print("drift forces:",
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# self._forces.sum(axis=0) / self._forces.shape[0])
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@ -556,9 +556,9 @@ class ThirdOrderFC:
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if self._log_level:
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N = np.prod(u.shape)
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print("rms u_inv:", np.sqrt((u_inv ** 2).sum() / N))
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print("rms u:", np.sqrt((u ** 2).sum() / N))
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print("rms forces:", np.sqrt((self._forces ** 2).sum() / N))
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print("rms f:", np.sqrt((f ** 2).sum() / N))
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print("rms u_inv:", np.sqrt((u_inv**2).sum() / N))
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print("rms u:", np.sqrt((u**2).sum() / N))
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print("rms forces:", np.sqrt((self._forces**2).sum() / N))
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print("rms f:", np.sqrt((f**2).sum() / N))
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return -np.einsum("li,lj,lk->ijk", u_inv, u_inv, f) / f.shape[0]
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@ -67,7 +67,7 @@ def run_KDE(x, y, nbins, x_max=None, y_max=None, density_ratio=0.1):
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indices = [nbins - i - 1]
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short_nbinds = len(indices)
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ynbins = nbins ** 2 // short_nbinds
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ynbins = nbins**2 // short_nbinds
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xi, yi = np.mgrid[x_min : _x_max : nbins * 1j, y_min : _y_max : ynbins * 1j]
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positions = np.vstack([xi.ravel(), yi.ravel()])
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zi = np.reshape(kernel(positions).T, xi.shape)
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