From 81c248ccd042d6342e3725bbd1ebe0c36756be72 Mon Sep 17 00:00:00 2001 From: ci-build Date: Wed, 4 Dec 2024 18:20:25 +0000 Subject: [PATCH] [skip ci] Updates --- ...cfbf59c2e9dda1f84c7dff795b1b1d95ca9bc1.png | Bin 0 -> 544 bytes _modules/kaldo/conductivity.html | 16 +- _modules/kaldo/forceconstants.html | 19 +- _modules/kaldo/phonons.html | 45 ++- _sources/docsource/api_forceconstants.rst.txt | 4 +- _sources/docsource/api_phonons.rst.txt | 1 + docsource/api_forceconstants.html | 67 ++++- docsource/api_phonons.html | 274 ++++++++++++++++-- docsource/code_architecture.html | 2 +- docsource/credits.html | 2 +- docsource/introduction.html | 2 +- docsource/theory.html | 6 +- genindex.html | 50 +++- objects.inv | Bin 3678 -> 3866 bytes searchindex.js | 2 +- 15 files changed, 402 insertions(+), 88 deletions(-) create mode 100644 _images/math/15cfbf59c2e9dda1f84c7dff795b1b1d95ca9bc1.png diff --git a/_images/math/15cfbf59c2e9dda1f84c7dff795b1b1d95ca9bc1.png b/_images/math/15cfbf59c2e9dda1f84c7dff795b1b1d95ca9bc1.png new file mode 100644 index 0000000000000000000000000000000000000000..67f1c541c7036eee158d11ed2f3ae30c57928fc1 GIT binary patch literal 544 zcmeAS@N?(olHy`uVBq!ia0vp^{y;3q!VDzy=DjfjQU(D&A+G=b{|7RO2l{sxR0CD> zmjw9*Gjto3tbget@%i`pgt>S3YaGa&4V2<6@Q5sCVBk9f!i-b3`J@>b7^^*9978nD z_Xh0uKAa#>>v?&}x78+B4?4Cg@ijGPcH0X~U&XpoLF^a1Na;1Dre)=-rn-^`^wRwrIcB8DpmG)KlvnW-a_!_W7i9$y4EXpJh)hP|lk7ool)0_eDw< z-l!C5y8e3bdiz~T>-N(P9;u~?N4+BQAN(@%+#VvV;>zP0^I)Cn;n<6-oi_$t=HdRx zyws(1gG+(d^yyqP#C4jU)@gI?@2yp|-nZ9S@TftP*}>%bZVysdtl8jET(?Kz9s88F zWgB*?zc^`V_i9GU^7!S;6U1-M;#v}#w|QrgaJ26HZngK)ilH6Hl@?28TAi68XmB#- z>cPznO#)>K?V7<#Tz8e`Kh|&&YuSFfJLvSfMbnlp+tKA1*YR|!V^hY=s;-?DeG64K z81`xjzZag(Ja^k6m-0g6+o~U5uk}uH`M>`=Z}+#LrTZBJYCw_f>FVdQ&MBb@03(&w AoB#j- literal 0 HcmV?d00001 diff --git a/_modules/kaldo/conductivity.html b/_modules/kaldo/conductivity.html index 819e2555..f6169ce1 100644 --- a/_modules/kaldo/conductivity.html +++ b/_modules/kaldo/conductivity.html @@ -553,7 +553,6 @@

Source code for kaldo.conductivit Conductivity(phonons=phonons, method='inverse', storage='memory').conductivity.sum(axis=0)) ``` """ - def __init__(self, **kwargs): self.phonons = kwargs.pop('phonons') self.method = kwargs.pop('method', 'rta') @@ -584,7 +583,8 @@

Source code for kaldo.conductivit @lazy_property( label='<diffusivity_bandwidth>/<diffusivity_threshold>/<temperature>/<statistics>/<third_bandwidth>/<include_isotopes>/<method>/<length>/<finite_length_method>') def conductivity(self): - """Calculate the thermal conductivity per mode in W/m/K + """ + Calculate the thermal conductivity per mode in W/m/K Returns ------- @@ -622,7 +622,8 @@

Source code for kaldo.conductivit @lazy_property( label='<diffusivity_bandwidth>/<diffusivity_threshold>/<temperature>/<statistics>/<third_bandwidth>/<include_isotopes>/<method>/<length>/<finite_length_method>') def mean_free_path(self): - """Calculate the mean_free_path per mode in A + """ + Calculate the mean_free_path per mode in A Returns ------- @@ -652,7 +653,8 @@

Source code for kaldo.conductivit @property def diffusivity(self): - """Calculate the diffusivity, for each k point in k_points and each mode. + """ + Calculate the diffusivity, for each k point in k_points and each mode. Returns ------- @@ -784,7 +786,8 @@

Source code for kaldo.conductivit return conductivity_per_mode.reshape((self.n_phonons, 3, 3)) * 1e22, diffusivity
[docs] def calculate_mfp_inverse(self): - """This method calculates the inverse of the mean free path for each phonon. + """ + This method calculates the inverse of the mean free path for each phonon. The matrix returns k vectors for each mode and has units of inverse Angstroms. Returns @@ -879,7 +882,8 @@

Source code for kaldo.conductivit np.save(psi_inv_filename, self._psi_inv)
[docs] def calculate_conductivity_full(self, is_using_gamma_tensor_evects=False): - """This calculates the conductivity using the full solution of the space-dependent Boltzmann Transport Equation. + """ + This calculates the conductivity using the full solution of the space-dependent Boltzmann Transport Equation. Returns ------- diff --git a/_modules/kaldo/forceconstants.html b/_modules/kaldo/forceconstants.html index bac2b5f4..c87e9d1b 100644 --- a/_modules/kaldo/forceconstants.html +++ b/_modules/kaldo/forceconstants.html @@ -469,7 +469,6 @@

Source code for kaldo.forcecons Parameters ---------- - atoms: Tabulated xyz files or ASE Atoms object The atoms to work on. supercell: (3) tuple, optional @@ -490,9 +489,7 @@

Source code for kaldo.forcecons Attributes ---------- - """ - def __init__(self, atoms, supercell=(1, 1, 1), @@ -569,7 +566,6 @@

Source code for kaldo.forcecons If true, the acoustic sum rule is applied to the dynamical matrix. Default is False - Returns ------- ForceConstants object @@ -597,14 +593,13 @@

Source code for kaldo.forcecons forceconstants.distance_threshold = distance_threshold return forceconstants

- def unfold_third_order(self, reduced_third=None, distance_threshold=None): +
[docs] def unfold_third_order(self, reduced_third=None, distance_threshold=None): """ This method extrapolates a third order force constant matrix from a unit cell into a matrix for a larger supercell. Parameters ---------- - reduced_third : array, optional The third order force constant matrix. Default is `self.third` @@ -661,10 +656,10 @@

Source code for kaldo.forcecons expanded_third = COO(np.array(coords).T, np.array(values), shape) expanded_third = expanded_third.reshape( (n_unit_atoms * 3, n_replicas * n_unit_atoms * 3, n_replicas * n_unit_atoms * 3)) - return expanded_third + return expanded_third

- def elastic_prop(self): +
[docs] def elastic_prop(self): """ Return the stiffness tensor (aka elastic modulus tensor) of the system in GPa. This describes the stress-strain relationship of the material and can sometimes be used as a loose predictor for thermal conductivity. Requires @@ -678,6 +673,7 @@

Source code for kaldo.forcecons ------- C_ijkl : np.array(3, 3, 3, 3) Elasticity tensor in GPa + """ # Intake key parameters atoms = self.atoms @@ -718,7 +714,7 @@

Source code for kaldo.forcecons cijkl[i, j, k, l] = b[i, k, j, l] + b[j, k, i, l] - b[i, j, k, l] + r[i, j, k, l] # Denote parameter for irreducible Cij in the unit of GPa - return evperang3togpa * cijkl / evtotenjovermol + return evperang3togpa * cijkl / evtotenjovermol

@staticmethod @@ -738,7 +734,7 @@

Source code for kaldo.forcecons return np.sqrt(mean_squared_error(md_forces, harmonic_forces)) / np.std(md_forces) - @staticmethod +
[docs] @staticmethod def sigma2_tdep_MD(fc_file='infile.forceconstant', primitive_file='infile.ucposcar', supercell_file='infile.ssposcar', md_run='dump.xyz'): """ @@ -759,6 +755,7 @@

Source code for kaldo.forcecons ------- float The average sigma2 value. + """ initial_structure = read(supercell_file, format="vasp") second_order_fc = parse_tdep_forceconstant( @@ -774,7 +771,7 @@

Source code for kaldo.forcecons sigma_values = [ForceConstants._calculate_sigma(atoms.get_forces(), harm_force) for atoms, harm_force in zip(full_MD_traj, force_harmonic)] - return np.mean(sigma_values)

+ return np.mean(sigma_values)

diff --git a/_modules/kaldo/phonons.html b/_modules/kaldo/phonons.html index 6c6c4ebc..26b1277a 100644 --- a/_modules/kaldo/phonons.html +++ b/_modules/kaldo/phonons.html @@ -585,7 +585,8 @@

Source code for kaldo.phonons

@lazy_property(label='') def physical_mode(self): - """Calculate physical modes. Non physical modes are the first 3 modes of q=(0, 0, 0) and, if defined, all the + """ + Calculate physical modes. Non physical modes are the first 3 modes of q=(0, 0, 0) and, if defined, all the modes outside the frequency range min_frequency and max_frequency. Returns @@ -644,7 +645,8 @@

Source code for kaldo.phonons

@lazy_property(label='') def participation_ratio(self): - """Calculates the participation ratio of each normal mode. Participation ratio's + """ + Calculates the participation ratio of each normal mode. Participation ratio's represent the fraction of atoms that are displaced meaning a value of 1 corresponds to translation. Defined by equations in DOI: 10.1103/PhysRevB.53.11469 @@ -673,7 +675,8 @@

Source code for kaldo.phonons

@lazy_property(label='') def velocity(self): - """Calculates the velocity using Hellmann-Feynman theorem. + """ + Calculates the velocity using Hellmann-Feynman theorem. Returns ------- @@ -700,7 +703,8 @@

Source code for kaldo.phonons

@lazy_property(label='') def _eigensystem(self): - """Calculate the eigensystems, for each k point in k_points. + """ + Calculate the eigensystems, for each k point in k_points. Returns ------- @@ -733,7 +737,8 @@

Source code for kaldo.phonons

@lazy_property(label='<temperature>/<statistics>') def heat_capacity(self): - """Calculate the heat capacity for each k point in k_points and each mode. + """ + Calculate the heat capacity for each k point in k_points and each mode. If classical, it returns the Boltzmann constant in J/K. If quantum it returns the derivative of the Bose-Einstein weighted by each phonons energy. .. math:: @@ -767,7 +772,8 @@

Source code for kaldo.phonons

@lazy_property(label='<temperature>/<statistics>') def heat_capacity_2d(self): - """Calculate the generalized 2d heat capacity for each k point in k_points and each mode. + """ + Calculate the generalized 2d heat capacity for each k point in k_points and each mode. If classical, it returns the Boltzmann constant in W/m/K. Returns @@ -798,7 +804,8 @@

Source code for kaldo.phonons

@lazy_property(label='<temperature>/<statistics>') def population(self): - """Calculate the phonons population for each k point in k_points and each mode. + """ + Calculate the phonons population for each k point in k_points and each mode. If classical, it returns the temperature divided by each frequency, using equipartition theorem. If quantum it returns the Bose-Einstein distribution @@ -828,7 +835,8 @@

Source code for kaldo.phonons

@lazy_property(label='<temperature>/<statistics>/<third_bandwidth>/<include_isotopes>') def bandwidth(self): - """Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode. + """ + Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode. Returns ------- @@ -843,7 +851,8 @@

Source code for kaldo.phonons

@lazy_property(label='<third_bandwidth>') def isotopic_bandwidth(self): - """ Calculate the isotopic bandwidth with Tamura perturbative formula. + """ + Calculate the isotopic bandwidth with Tamura perturbative formula. Defined by equations in DOI:https://doi.org/10.1103/PhysRevB.27.858 Returns @@ -869,7 +878,8 @@

Source code for kaldo.phonons

@lazy_property(label='<temperature>/<statistics>/<third_bandwidth>') def anharmonic_bandwidth(self): - """Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode. + """ + Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode. Returns ------- @@ -882,7 +892,8 @@

Source code for kaldo.phonons

@lazy_property(label='<temperature>/<statistics>/<third_bandwidth>') def phase_space(self): - """Calculate the 3-phonons-processes phase_space, for each k point in k_points and each mode. + """ + Calculate the 3-phonons-processes phase_space, for each k point in k_points and each mode. Returns ------- @@ -895,7 +906,8 @@

Source code for kaldo.phonons

@lazy_property(label='') def eigenvalues(self): - """Calculates the eigenvalues of the dynamical matrix in Thz^2. + """ + Calculates the eigenvalues of the dynamical matrix in Thz^2. Returns ------- @@ -908,7 +920,8 @@

Source code for kaldo.phonons

@property def eigenvectors(self): - """Calculates the eigenvectors of the dynamical matrix. + """ + Calculates the eigenvectors of the dynamical matrix. Returns ------- @@ -941,7 +954,8 @@

Source code for kaldo.phonons

@property def omega(self): - """Calculates the angular frequencies from the diagonalized dynamical matrix. + """ + Calculates the angular frequencies from the diagonalized dynamical matrix. Returns ------- @@ -969,7 +983,7 @@

Source code for kaldo.phonons

return is_amorphous -
[docs] def pdos(self, p_atoms=None, direction=None, bandwidth=0.05, n_points=200): +
[docs] def pdos(self, p_atoms=None, direction=None, bandwidth=0.05, n_points=200): """Calculate the atom projected phonon density of states. Total density of states can be computed by specifying all atom indices in p_atoms. p_atoms input format is flexible: @@ -983,7 +997,6 @@

Source code for kaldo.phonons

pdos : np.array(n_projections, n_points) pdos for each set of projected atoms and directions """ - if p_atoms is None: p_atoms = list(range(self.n_atoms)) diff --git a/_sources/docsource/api_forceconstants.rst.txt b/_sources/docsource/api_forceconstants.rst.txt index e449c0ad..87a6a68c 100644 --- a/_sources/docsource/api_forceconstants.rst.txt +++ b/_sources/docsource/api_forceconstants.rst.txt @@ -191,6 +191,6 @@ Input Files and Formats API Reference ************* -.. autoclass:: kaldo.forceconstants::ForceConstants - :members: from_folder +.. autoclass:: ForceConstants + :members: diff --git a/_sources/docsource/api_phonons.rst.txt b/_sources/docsource/api_phonons.rst.txt index 7a35e6cb..fc3eaaf4 100644 --- a/_sources/docsource/api_phonons.rst.txt +++ b/_sources/docsource/api_phonons.rst.txt @@ -46,6 +46,7 @@ API Reference Phonons.eigenvectors .. autoclass:: Phonons + :members: diff --git a/docsource/api_forceconstants.html b/docsource/api_forceconstants.html index 4664f312..2293aa29 100644 --- a/docsource/api_forceconstants.html +++ b/docsource/api_forceconstants.html @@ -713,9 +713,18 @@

API ReferenceMethods

- + + + + + + + + + +

from_folder(folder[, supercell, format, ...])

elastic_prop()

Return the stiffness tensor (aka elastic modulus tensor) of the system in GPa.

from_folder(folder[, supercell, format, ...])

Create a finite difference object from a folder

sigma2_tdep_MD([fc_file, primitive_file, ...])

Calculate the sigma2 value using TDEP and MD data.

unfold_third_order([reduced_third, ...])

This method extrapolates a third order force constant matrix from a unit cell into a matrix for a larger supercell.
@@ -755,6 +764,62 @@

API Reference

+
+
+unfold_third_order(reduced_third=None, distance_threshold=None)[source]
+

This method extrapolates a third order force constant matrix from a unit +cell into a matrix for a larger supercell.

+
+
Parameters:
+
    +

  • reduced_third (array, optional) – The third order force constant matrix. +Default is self.third

    • +

  • distance_threshold (float, optional) – When calculating force constants, contributions from atoms further than +the distance threshold will be ignored. +Default is self.distance_threshold

    • +
+
+
+
+
+
+elastic_prop()[source]
+

Return the stiffness tensor (aka elastic modulus tensor) of the system in GPa. This describes the stress-strain +relationship of the material and can sometimes be used as a loose predictor for thermal conductivity. Requires +the dynamical matrix to be loaded or calculated.

+
+
Parameters:
+

None –

+
+
Returns:
+

C_ijkl – Elasticity tensor in GPa

+
+
Return type:
+

np.array(3, 3, 3, 3)

+
+
+
+
+
+static sigma2_tdep_MD(fc_file='infile.forceconstant', primitive_file='infile.ucposcar', supercell_file='infile.ssposcar', md_run='dump.xyz')[source]
+

Calculate the sigma2 value using TDEP and MD data.

+
+
Parameters:
+
    +

  • fc_file (str, optional) – Path to the force constant file. Default is ‘infile.forceconstant’.

    • +

  • primitive_file (str, optional) – Path to the primitive cell file. Default is ‘infile.ucposcar’.

    • +

  • supercell_file (str, optional) – Path to the supercell file. Default is ‘infile.ssposcar’.

    • +

  • md_run (str, optional) – Path to the MD trajectory file. Default is ‘dump.xyz’.

    • +
+
+
Returns:
+

The average sigma2 value.

+
+
Return type:
+

float

+
+
+
diff --git a/docsource/api_phonons.html b/docsource/api_phonons.html index 21b7b35b..f1325de9 100644 --- a/docsource/api_phonons.html +++ b/docsource/api_phonons.html @@ -480,7 +480,7 @@

API ReferenceMethods

- + @@ -488,46 +488,46 @@

API ReferenceAttributes

Phonons.pdos

Phonons.pdos

Calculate the atom projected phonon density of states.
- + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -603,33 +603,33 @@

API Reference
Attributes:
-
anharmonic_bandwidth

Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.

+
anharmonic_bandwidth

Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.

-
bandwidth

Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.

+
bandwidth

Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.

-
eigenvalues

Calculates the eigenvalues of the dynamical matrix in Thz^2.

+
eigenvalues

Calculates the eigenvalues of the dynamical matrix in Thz^2.

-
eigenvectors

Calculates the eigenvectors of the dynamical matrix.

+
eigenvectors

Calculates the eigenvectors of the dynamical matrix.

-
frequency

Calculate phonons frequency

+
frequency

Calculate phonons frequency

-
heat_capacity

Calculate the heat capacity for each k point in k_points and each mode.

+
heat_capacity

Calculate the heat capacity for each k point in k_points and each mode.

-
heat_capacity_2d

Calculate the generalized 2d heat capacity for each k point in k_points and each mode.

+
heat_capacity_2d

Calculate the generalized 2d heat capacity for each k point in k_points and each mode.

-
isotopic_bandwidth

Calculate the isotopic bandwidth with Tamura perturbative formula.

+
isotopic_bandwidth

Calculate the isotopic bandwidth with Tamura perturbative formula.

-
omega

Calculates the angular frequencies from the diagonalized dynamical matrix.

+
omega

Calculates the angular frequencies from the diagonalized dynamical matrix.

-
participation_ratio

Calculates the participation ratio of each normal mode.

+
participation_ratio

Calculates the participation ratio of each normal mode.

-
phase_space

Calculate the 3-phonons-processes phase_space, for each k point in k_points and each mode.

+
phase_space

Calculate the 3-phonons-processes phase_space, for each k point in k_points and each mode.

-
physical_mode

Calculate physical modes.

+
physical_mode

Calculate physical modes.

-
population

Calculate the phonons population for each k point in k_points and each mode.

+
population

Calculate the phonons population for each k point in k_points and each mode.

-
velocity

Calculates the velocity using Hellmann-Feynman theorem.

+
velocity

Calculates the velocity using Hellmann-Feynman theorem.

@@ -637,11 +637,225 @@

API ReferenceMethods

Phonons.physical_mode

Phonons.physical_mode

Calculate physical modes.

Phonons.participation_ratio

Phonons.participation_ratio

Calculates the participation ratio of each normal mode.

Phonons.bandwidth

Phonons.bandwidth

Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.

Phonons.isotopic_bandwidth

Phonons.isotopic_bandwidth

Calculate the isotopic bandwidth with Tamura perturbative formula.

Phonons.anharmonic_bandwidth

Phonons.anharmonic_bandwidth

Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.

Phonons.frequency

Phonons.frequency

Calculate phonons frequency

Phonons.omega

Phonons.omega

Calculates the angular frequencies from the diagonalized dynamical matrix.

Phonons.velocity

Phonons.velocity

Calculates the velocity using Hellmann-Feynman theorem.

Phonons.heat_capacity

Phonons.heat_capacity

Calculate the heat capacity for each k point in k_points and each mode. If classical, it returns the Boltzmann constant in J/K. If quantum it returns the derivative of the Bose-Einstein weighted by each phonons energy. .. math::.

Phonons.heat_capacity_2d

Phonons.heat_capacity_2d

Calculate the generalized 2d heat capacity for each k point in k_points and each mode.

Phonons.population

Phonons.population

Calculate the phonons population for each k point in k_points and each mode.

Phonons.phase_space

Phonons.phase_space

Calculate the 3-phonons-processes phase_space, for each k point in k_points and each mode.

Phonons.eigenvalues

Phonons.eigenvalues

Calculates the eigenvalues of the dynamical matrix in Thz^2.

Phonons.eigenvectors

Phonons.eigenvectors

Calculates the eigenvectors of the dynamical matrix.
- +

pdos([p_atoms, direction, bandwidth, n_points])

pdos([p_atoms, direction, bandwidth, n_points])

Calculate the atom projected phonon density of states.
+
+
+property physical_mode
+

Calculate physical modes. Non physical modes are the first 3 modes of q=(0, 0, 0) and, if defined, all the +modes outside the frequency range min_frequency and max_frequency.

+
+
Returns:
+

physical_mode – bool

+
+
Return type:
+

np array(n_k_points, n_modes)

+
+
+
+
+
+property frequency
+

Calculate phonons frequency

+
+
Returns:
+

frequency – frequency in THz

+
+
Return type:
+

np array(n_k_points, n_modes)

+
+
+
+
+
+property participation_ratio
+

Calculates the participation ratio of each normal mode. Participation ratio’s +represent the fraction of atoms that are displaced meaning a value of 1 corresponds +to translation. Defined by equations in DOI: 10.1103/PhysRevB.53.11469

+
+
Returns:
+

participation_ratio – atomic participation

+
+
Return type:
+

np array(n_k_points, n_modes)

+
+
+
+
+
+property velocity
+

Calculates the velocity using Hellmann-Feynman theorem.

+
+
Returns:
+

velocity – velocity in 100m/s or A/ps

+
+
Return type:
+

np array(n_k_points, n_unit_cell * 3, 3)

+
+
+
+
+
+property heat_capacity
+

Calculate the heat capacity for each k point in k_points and each mode. +If classical, it returns the Boltzmann constant in J/K. If quantum it returns the derivative of the +Bose-Einstein weighted by each phonons energy. +.. math:

+
c_\mu = k_B \frac{\nu_\mu^2}{ \tilde T^2} n_\mu (n_\mu + 1)
+
+
+

where the frequency \nu and the temperature \tilde T are in THz.

+
+
Returns:
+

c_v – heat capacity in J/K for each k point and each mode

+
+
Return type:
+

np.array(n_k_points, n_modes)

+
+
+
+
+
+property heat_capacity_2d
+

Calculate the generalized 2d heat capacity for each k point in k_points and each mode. +If classical, it returns the Boltzmann constant in W/m/K.

+
+
Returns:
+

heat_capacity_2d – heat capacity in W/m/K for each k point and each modes couple.

+
+
Return type:
+

np.array(n_k_points, n_modes, n_modes)

+
+
+
+
+
+property population
+

Calculate the phonons population for each k point in k_points and each mode. +If classical, it returns the temperature divided by each frequency, using equipartition theorem. +If quantum it returns the Bose-Einstein distribution

+
+
Returns:
+

population – population for each k point and each mode

+
+
Return type:
+

np.array(n_k_points, n_modes)

+
+
+
+
+
+property bandwidth
+

Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.

+
+
Returns:
+

bandwidth – bandwidth for each k point and each mode

+
+
Return type:
+

np.array(n_k_points, n_modes)

+
+
+
+
+
+property isotopic_bandwidth
+

Calculate the isotopic bandwidth with Tamura perturbative formula. +Defined by equations in DOI:https://doi.org/10.1103/PhysRevB.27.858

+
+
Returns:
+

isotopic_bw – atomic participation

+
+
Return type:
+

np array(n_k_points, n_modes)

+
+
+
+
+
+property anharmonic_bandwidth
+

Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.

+
+
Returns:
+

bandwidth – bandwidth for each k point and each mode

+
+
Return type:
+

np.array(n_k_points, n_modes)

+
+
+
+
+
+property phase_space
+

Calculate the 3-phonons-processes phase_space, for each k point in k_points and each mode.

+
+
Returns:
+

phase_space – phase_space for each k point and each mode

+
+
Return type:
+

np.array(n_k_points, n_modes)

+
+
+
+
+
+property eigenvalues
+

Calculates the eigenvalues of the dynamical matrix in Thz^2.

+
+
Returns:
+

eigenvalues – Eigenvalues of the dynamical matrix

+
+
Return type:
+

np array(n_phonons)

+
+
+
+
+
+property eigenvectors
+

Calculates the eigenvectors of the dynamical matrix.

+
+
Returns:
+

eigenvectors – Eigenvectors of the dynamical matrix

+
+
Return type:
+

np array(n_phonons, n_phonons)

+
+
+
+
+
+property omega
+

Calculates the angular frequencies from the diagonalized dynamical matrix.

+
+
Returns:
+

frequency – frequency in rad

+
+
Return type:
+

np array(n_k_points, n_modes)

+
+
+
+
+
+pdos(p_atoms=None, direction=None, bandwidth=0.05, n_points=200)[source]
+

Calculate the atom projected phonon density of states. +Total density of states can be computed by specifying all atom indices in p_atoms. +p_atoms input format is flexible: +- Providing a list of atom indices will return the single pdos summed over those atoms +- Providing a list of lists of atom indices will return one pdos for each set of indices

+
+
Returns:
+

    +

  • frequency (np array(n_points)) – Frequencies

    • +

  • pdos (np.array(n_projections, n_points)) – pdos for each set of projected atoms and directions

    • +
+

+
+
+
diff --git a/docsource/code_architecture.html b/docsource/code_architecture.html index b959306c..501b88d6 100644 --- a/docsource/code_architecture.html +++ b/docsource/code_architecture.html @@ -458,7 +458,7 @@

Code Architecture

-

9d501ca710654f39b0847238ed146b1a

+

a9c95f982d4a42c5bb5322d6c07ba516

diff --git a/docsource/credits.html b/docsource/credits.html index 33c9c83b..514837c9 100644 --- a/docsource/credits.html +++ b/docsource/credits.html @@ -458,7 +458,7 @@

Acknowledgements

-

746a07dfd18c46eaa81ffe05589b7b88

+

4efdbb4f70df42da9f4f1a7b199eef6d

We gratefully acknowledge support by the Investment Software Fellowships (grant No. ACI-1547580-479590) of the NSF Molecular Sciences Software Institute (grant No. ACI-1547580) at Virginia Tech.

MolSSI builds open source software and data which serves the computational molecular science community. Explore MolSSI’s software infrastructure projects.

diff --git a/docsource/introduction.html b/docsource/introduction.html index 4a1d0896..1a21f1df 100644 --- a/docsource/introduction.html +++ b/docsource/introduction.html @@ -481,7 +481,7 @@

Features

+

cd16aa9eb39e4455b6bada79e6f5b455

diff --git a/docsource/theory.html b/docsource/theory.html index d30e7f25..a9e8f31b 100644 --- a/docsource/theory.html +++ b/docsource/theory.html @@ -675,7 +675,7 @@

Quasi-Harmonic Green Kubo

Workflow

The workflow for ALD calculations is illustrated below

-

4312e989b6704d13b3d8533afdde2176

+

a06718a40a304c88a8946e7bf338da44

Here, we present two example simulations of both a periodic and an amorphous structure.

Ab initio silicon diamond

@@ -704,7 +704,7 @@

Ab initio silicon diamond

+

ff4980bcf4b34356ab21b240230b6d71

The silicon diamond modes analysis is shown above. Quantum (red) and classical (blue) results are compared. a) Normalized density of states, b) Normalized phase-space per mode g, c) lifetime per mode \tau, d) mean free path \lambda, and e) cumulative conductivity \kappa_{cum}.

@@ -726,7 +726,7 @@

Amorphous silicon

+

80c3e9ea3c14453f9282cdec0697b08c

Classical and quantum properties for 4096 atom amorphous silicon system are shown above. a) density of states, b) lifetimes, c) diffusivities, and e) cumulative thermal conductivity. In spite of the increased quantum lifetimes, a decrease of 0.17W/m/K is seen in the quantum conductivity. The difference in conductivity is primarily a result of the overestimation of classical high frequency heat capacities.

diff --git a/genindex.html b/genindex.html index d39dec27..5baf438a 100644 --- a/genindex.html +++ b/genindex.html @@ -455,13 +455,15 @@

Index

| M | O | P + | S + | U | V

A

@@ -469,7 +471,7 @@

A

B

@@ -503,11 +505,13 @@

D

E

@@ -519,7 +523,7 @@

F

    -
  • frequency (kaldo.phonons.Phonons property) +
  • frequency (kaldo.phonons.Phonons property), [1]
  • from_folder() (kaldo.forceconstants.ForceConstants class method)
    • @@ -529,11 +533,11 @@

    F

    H

    @@ -541,7 +545,7 @@

    H

    I

    @@ -557,7 +561,7 @@

    M

    O

    @@ -565,19 +569,35 @@

    O

    P

    +
    + +

    S

    + + +
    + +

    U

    + +
    @@ -585,7 +605,7 @@

    P

    V

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