Source code for kaldo.conductivit
logging.info('Conductivity calculated')
return cond.real
- @lazy_property(label='<diffusivity_bandwidth>/<diffusivity_threshold>/<temperature>/<statistics>/<third_bandwidth>/<method>/<length>/<finite_length_method>')
+ @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
diff --git a/_modules/kaldo/forceconstants.html b/_modules/kaldo/forceconstants.html
index 14ee83c4..2f387c3e 100644
--- a/_modules/kaldo/forceconstants.html
+++ b/_modules/kaldo/forceconstants.html
@@ -500,7 +500,7 @@ Source code for kaldo.forcecons
supercell : (int, int, int), optional
Number of unit cells in each cartesian direction replicated to form the input structure.
Default is (1, 1, 1)
- format : 'numpy', 'eskm', 'lammps', 'shengbte', 'shengbte-qe', 'hiphive'
+ format : 'numpy', 'eskm', 'lammps', 'shengbte', 'shengbte-qe','shengbte-d3q', 'hiphive'
Format of force constant information being loaded into ForceConstants object.
Default is 'numpy'
third_energy_threshold : float, optional
diff --git a/_modules/kaldo/phonons.html b/_modules/kaldo/phonons.html
index ba1c73ea..3be96e9c 100644
--- a/_modules/kaldo/phonons.html
+++ b/_modules/kaldo/phonons.html
@@ -422,6 +422,7 @@ Source code for kaldo.phonons
from kaldo.observables.harmonic_with_q import HarmonicWithQ
from kaldo.observables.harmonic_with_q_temp import HarmonicWithQTemp
import kaldo.controllers.anharmonic as aha
+import kaldo.controllers.isotopic as isotopic
from scipy import stats
import numpy as np
import ase.units as units
@@ -460,7 +461,7 @@ Source code for kaldo.phonons
Units: THz.
broadening_shape : string, optional
Defines the algorithm to use for the broadening of the conservation
- of the energy for third irder interactions. Available broadenings
+ of the energy for third order interactions. Available broadenings
are `gauss`, `lorentz` and `triangle`.
Default is `gauss`.
folder : string, optional
@@ -475,6 +476,14 @@ Source code for kaldo.phonons
Default 'C'
is_balanced : Enforce detailed balance when calculating anharmonic properties,
Default: False
+ g_factor : (n_atoms) array , optional
+ It contains the isotopic g factor for each atom of the unit cell
+ Default: None
+ include_isotopes: bool, optional.
+ Defines if you want to include isotopic scattering bandwidths. Default is False.
+ iso_speed_up: bool, optional.
+ Defines if you want to truncate the energy-conservation delta
+ in the isotopic scattering computation. Default is True.
Returns
-------
@@ -512,6 +521,9 @@ Source code for kaldo.phonons
self.hbar = units._hbar
if self.is_classic:
self.hbar = self.hbar * 1e-6
+ self.g_factor = kwargs.pop('g_factor', None)
+ self.include_isotopes = bool(kwargs.pop('include_isotopes', False))
+ self.iso_speed_up = bool(kwargs.pop('iso_speed_up', True))
@@ -743,10 +755,50 @@ Source code for kaldo.phonons
return population
- @lazy_property(label='<temperature>/<statistics>/<third_bandwidth>')
+ @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.
+ Returns
+ -------
+ bandwidth : np.array(n_k_points, n_modes)
+ bandwidth for each k point and each mode
+ """
+ gamma = self.anharmonic_bandwidth
+ if self.include_isotopes:
+ gamma += self.isotopic_bandwidth
+ return gamma
+
+
+ @lazy_property(label='<third_bandwidth>')
+ def isotopic_bandwidth(self):
+ """ Calculate the isotopic bandwidth with Tamura perturbative formula.
+ Defined by equations in DOI:https://doi.org/10.1103/PhysRevB.27.858
+ Returns
+ -------
+ isotopic_bw : np array
+ (n_k_points, n_modes) atomic participation
+ """
+ if self._is_amorphous:
+ logging.warning('isotopic scattering not implemented for amorphous systems')
+ return np.zeros(self.n_k_points, self.n_modes)
+ else:
+ if self.g_factor is not None:
+ isotopic_bw=isotopic.compute_isotopic_bw(self)
+ else:
+ atoms=self.atoms
+ logging.warning('input isotopic gfactors are missing, using isotopic concentrations from ase database (NIST)')
+ self.g_factor=isotopic.compute_gfactor(atoms.get_atomic_numbers() )
+ logging.info('g factors='+str(self.g_factor))
+ isotopic_bw = isotopic.compute_isotopic_bw(self)
+
+ return isotopic_bw
+
+
+ @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.
+
Returns
-------
bandwidth : np.array(n_k_points, n_modes)
@@ -812,6 +864,7 @@ Source code for kaldo.phonons
ps_gamma_and_gamma_tensor = self._select_algorithm_for_phase_space_and_gamma(is_gamma_tensor_enabled=True)
return ps_gamma_and_gamma_tensor
+
# Helpers properties
@property
diff --git a/docsource/api_forceconstants.html b/docsource/api_forceconstants.html
index 9102ff2a..54ed9924 100644
--- a/docsource/api_forceconstants.html
+++ b/docsource/api_forceconstants.html
@@ -489,7 +489,7 @@ AttributesAttributes, 
and 
.
Default is 
.
folder (string, optional) – Specifies where to store the data files. Default is 
.
AttributesReturn type:
@@ -487,6 +492,8 @@ AttributesAttributes:
+anharmonic_bandwidthCalculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.
+bandwidthCalculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.
eigenvaluesCalculates the eigenvalues of the dynamical matrix in Thz^2.
@@ -499,6 +506,8 @@ Attributesheat_capacity_2dCalculate the generalized 2d heat capacity for each k point in k_points and each mode.
isotopic_bandwidthCalculate the isotopic bandwidth with Tamura perturbative formula.
+omegaCalculates the angular frequencies from the diagonalized dynamical matrix.
participation_ratioCalculates the participation ratio of each normal mode.
@@ -523,6 +532,19 @@ Attributes
+-
+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 bandwidth¶
Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.
@@ -603,6 +625,14 @@ Attributes
+-
+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 – (n_k_points, n_modes) atomic participation
+:rtype: np array
+
+
-
property omega¶
Calculates the angular frequencies from the diagonalized dynamical matrix.
diff --git a/docsource/introduction.html b/docsource/introduction.html
index 5930c241..6b512b72 100644
--- a/docsource/introduction.html
+++ b/docsource/introduction.html
@@ -679,12 +679,12 @@ Alternative Storage
Code Architecture¶
-
+
Main Features¶
Below we illustrate the main features of the code
-
+
Examples¶
@@ -713,7 +713,7 @@ Copyright
Acknowledgements¶
-
+
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/theory.html b/docsource/theory.html
index 5e027c10..190fa6e5 100644
--- a/docsource/theory.html
+++ b/docsource/theory.html
@@ -642,7 +642,7 @@ Quasi-Harmonic Green Kubo
Benchmarks applications¶
The workflow for ALD calculations is illustrated below
-
+
Here, we present two example simulations of both a periodic and an amorphous structure.
Ab initio silicon diamond¶
@@ -671,7 +671,7 @@ Ab initio silicon diamond
+
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 
, c) lifetime per mode 
, d) mean free path 
, and e) cumulative conductivity 
.
@@ -693,7 +693,7 @@ Amorphous silicon
+
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 444d62eb..913c5813 100644
--- a/genindex.html
+++ b/genindex.html
@@ -411,12 +411,14 @@
Index
+A
+
+
+
B
@@ -496,6 +506,14 @@ H
+I
+
+
+
M
diff --git a/objects.inv b/objects.inv
index 591d04e0..52b459d6 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/searchindex.js b/searchindex.js
index d01c8b31..3794a341 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["docsource/amorphous_presentation", "docsource/api_conductivity", "docsource/api_forceconstants", "docsource/api_phonons", "docsource/crystal_presentation", "docsource/introduction", "docsource/theory", "index", "publications/readme"], "filenames": ["docsource/amorphous_presentation.ipynb", "docsource/api_conductivity.rst", "docsource/api_forceconstants.rst", "docsource/api_phonons.rst", "docsource/crystal_presentation.ipynb", "docsource/introduction.ipynb", "docsource/theory.ipynb", "index.rst", "publications/readme.md"], "titles": ["Amorphous silicon tutorial", "Conductivity API Reference", "ForceConstants API Reference", "Phonons API Reference", "Silicon diamond tutorial", "Introduction", "Introduction", "kALDo: Anharmonic Lattice Dynamics", "Publications using kALDo"], "terms": {"thi": [0, 1, 2, 4, 5, 6], "notebook": [0, 4], "can": [0, 3, 4, 5, 6], "run": [0, 4, 5], "googl": [0, 4], "colab": [0, 4], "In": [0, 1, 4, 5, 6], "you": [0, 1, 4, 5], "enabl": 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\ No newline at end of file
Source code for kaldo.phonons
from kaldo.observables.harmonic_with_q import HarmonicWithQ
from kaldo.observables.harmonic_with_q_temp import HarmonicWithQTemp
import kaldo.controllers.anharmonic as aha
+import kaldo.controllers.isotopic as isotopic
from scipy import stats
import numpy as np
import ase.units as units
@@ -460,7 +461,7 @@
Source code for kaldo.phonons
Units: THz.
broadening_shape : string, optional
Defines the algorithm to use for the broadening of the conservation
- of the energy for third irder interactions. Available broadenings
+ of the energy for third order interactions. Available broadenings
are `gauss`, `lorentz` and `triangle`.
Default is `gauss`.
folder : string, optional
@@ -475,6 +476,14 @@
Source code for kaldo.phonons
Default 'C'
is_balanced : Enforce detailed balance when calculating anharmonic properties,
Default: False
+ g_factor : (n_atoms) array , optional
+ It contains the isotopic g factor for each atom of the unit cell
+ Default: None
+ include_isotopes: bool, optional.
+ Defines if you want to include isotopic scattering bandwidths. Default is False.
+ iso_speed_up: bool, optional.
+ Defines if you want to truncate the energy-conservation delta
+ in the isotopic scattering computation. Default is True.
Returns
-------
@@ -512,6 +521,9 @@
Source code for kaldo.phonons
self.hbar = units._hbar
if self.is_classic:
self.hbar = self.hbar * 1e-6
+ self.g_factor = kwargs.pop('g_factor', None)
+ self.include_isotopes = bool(kwargs.pop('include_isotopes', False))
+ self.iso_speed_up = bool(kwargs.pop('iso_speed_up', True))
@@ -743,10 +755,50 @@
Source code for kaldo.phonons
return population
- @lazy_property(label='<temperature>/<statistics>/<third_bandwidth>')
+ @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.
+ Returns
+ -------
+ bandwidth : np.array(n_k_points, n_modes)
+ bandwidth for each k point and each mode
+ """
+ gamma = self.anharmonic_bandwidth
+ if self.include_isotopes:
+ gamma += self.isotopic_bandwidth
+ return gamma
+
+
+ @lazy_property(label='<third_bandwidth>')
+ def isotopic_bandwidth(self):
+ """ Calculate the isotopic bandwidth with Tamura perturbative formula.
+ Defined by equations in DOI:https://doi.org/10.1103/PhysRevB.27.858
+ Returns
+ -------
+ isotopic_bw : np array
+ (n_k_points, n_modes) atomic participation
+ """
+ if self._is_amorphous:
+ logging.warning('isotopic scattering not implemented for amorphous systems')
+ return np.zeros(self.n_k_points, self.n_modes)
+ else:
+ if self.g_factor is not None:
+ isotopic_bw=isotopic.compute_isotopic_bw(self)
+ else:
+ atoms=self.atoms
+ logging.warning('input isotopic gfactors are missing, using isotopic concentrations from ase database (NIST)')
+ self.g_factor=isotopic.compute_gfactor(atoms.get_atomic_numbers() )
+ logging.info('g factors='+str(self.g_factor))
+ isotopic_bw = isotopic.compute_isotopic_bw(self)
+
+ return isotopic_bw
+
+
+ @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.
+
Returns
-------
bandwidth : np.array(n_k_points, n_modes)
@@ -812,6 +864,7 @@
Source code for kaldo.phonons
ps_gamma_and_gamma_tensor = self._select_algorithm_for_phase_space_and_gamma(is_gamma_tensor_enabled=True)
return ps_gamma_and_gamma_tensor
+
# Helpers properties
@property
diff --git a/docsource/api_forceconstants.html b/docsource/api_forceconstants.html
index 9102ff2a..54ed9924 100644
--- a/docsource/api_forceconstants.html
+++ b/docsource/api_forceconstants.html
@@ -489,7 +489,7 @@ AttributesAttributes,
AttributesReturn type:
@@ -487,6 +492,8 @@
AttributesAttributes, and .
Default is .
folder (string, optional) – Specifies where to store the data files. Default is .
AttributesReturn type:
@@ -487,6 +492,8 @@ AttributesAttributes:
+anharmonic_bandwidthCalculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.
+bandwidthCalculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.
eigenvaluesCalculates the eigenvalues of the dynamical matrix in Thz^2.
@@ -499,6 +506,8 @@ Attributesheat_capacity_2dCalculate the generalized 2d heat capacity for each k point in k_points and each mode.
isotopic_bandwidthCalculate the isotopic bandwidth with Tamura perturbative formula.
+omegaCalculates the angular frequencies from the diagonalized dynamical matrix.
participation_ratioCalculates the participation ratio of each normal mode.
@@ -523,6 +532,19 @@ Attributes
+-
+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 bandwidth¶
Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.
@@ -603,6 +625,14 @@ Attributes
+-
+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 – (n_k_points, n_modes) atomic participation
+:rtype: np array
+
+
-
property omega¶
Calculates the angular frequencies from the diagonalized dynamical matrix.
diff --git a/docsource/introduction.html b/docsource/introduction.html
index 5930c241..6b512b72 100644
--- a/docsource/introduction.html
+++ b/docsource/introduction.html
@@ -679,12 +679,12 @@ Alternative Storage
Code Architecture¶
-
+
Main Features¶
Below we illustrate the main features of the code
-
+
Examples¶
@@ -713,7 +713,7 @@ Copyright
Acknowledgements¶
-
+
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/theory.html b/docsource/theory.html
index 5e027c10..190fa6e5 100644
--- a/docsource/theory.html
+++ b/docsource/theory.html
@@ -642,7 +642,7 @@ Quasi-Harmonic Green Kubo
Benchmarks applications¶
The workflow for ALD calculations is illustrated below
-
+
Here, we present two example simulations of both a periodic and an amorphous structure.
Ab initio silicon diamond¶
@@ -671,7 +671,7 @@ Ab initio silicon diamond
+
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 , c) lifetime per mode , d) mean free path , and e) cumulative conductivity .
@@ -693,7 +693,7 @@ Amorphous silicon
+
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 444d62eb..913c5813 100644
--- a/genindex.html
+++ b/genindex.html
@@ -411,12 +411,14 @@
Index
+A
+
+
+
B
@@ -496,6 +506,14 @@ H
+I
+
+
+
M
diff --git a/objects.inv b/objects.inv
index 591d04e0..52b459d6 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/searchindex.js b/searchindex.js
index d01c8b31..3794a341 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
-
+
anharmonic_bandwidthCalculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.
+bandwidthCalculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.
eigenvaluesCalculates the eigenvalues of the dynamical matrix in Thz^2.
@@ -499,6 +506,8 @@Attributes
heat_capacity_2dCalculate the generalized 2d heat capacity for each k point in k_points and each mode.
isotopic_bandwidthCalculate the isotopic bandwidth with Tamura perturbative formula.
+omegaCalculates the angular frequencies from the diagonalized dynamical matrix.
participation_ratioCalculates the participation ratio of each normal mode.
@@ -523,6 +532,19 @@Attributes +
- +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 bandwidth¶
Calculate the phonons bandwidth, the inverse of the lifetime, for each k point in k_points and each mode.
@@ -603,6 +625,14 @@Attributes +
- +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 – (n_k_points, n_modes) atomic participation +:rtype: np array
+
- property omega¶
Calculates the angular frequencies from the diagonalized dynamical matrix.
diff --git a/docsource/introduction.html b/docsource/introduction.html index 5930c241..6b512b72 100644 --- a/docsource/introduction.html +++ b/docsource/introduction.html @@ -679,12 +679,12 @@Alternative Storage
Code Architecture¶
-
+Main Features¶
Below we illustrate the main features of the code
-
+Examples¶
@@ -713,7 +713,7 @@Copyright
Acknowledgements¶
-
+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.
Quasi-Harmonic Green Kubo
Benchmarks applications¶
The workflow for ALD calculations is illustrated below
-
+Here, we present two example simulations of both a periodic and an amorphous structure.
Ab initio silicon diamond¶
@@ -671,7 +671,7 @@Ab initio silicon diamond +
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
, c) lifetime per mode , d) mean free path , and e) cumulative conductivity .@@ -693,7 +693,7 @@ Amorphous silicon +
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 444d62eb..913c5813 100644 --- a/genindex.html +++ b/genindex.html @@ -411,12 +411,14 @@ Index
+A
+
++ + B
+-
@@ -496,6 +506,14 @@
H
I
+
++ + M
-
diff --git a/objects.inv b/objects.inv
index 591d04e0..52b459d6 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/searchindex.js b/searchindex.js
index d01c8b31..3794a341 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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