phonon_modes_oct_m::phonon_modes_t Type Reference

This class describes phonon modes, which are specified by their frequencies and eigenvectors. More...

Detailed Description

This class describes phonon modes, which are specified by their frequencies and eigenvectors.

Note

Octopus will in general run the supercell, and has no information about the underlying primitive cell. The eigenvectors are given for all atoms in the supercell.

Definition at line 132 of file phonon_modes.F90.

Inheritance diagram for phonon_modes_oct_m::phonon_modes_t:

Private Member Functions
procedure	init => phonon_modes_init
	Initialize the phonon modes. More...
procedure	sample => phonon_modes_sample
	Sample initial ionic displacements and velocities from the Wigner distribution of the modes. More...
procedure	get_displacements => phonon_modes_get_displacements
	get the displacements for a single mode and the respective generalized coordinates. More...
final	phonon_modes_finalize

Private Attributes
real(real64), dimension(:), allocatable	alpha
	Per-mode amplitude factor alpha_m = g_m^{-1/2}: 1 for modes from region A (2q = G) and for finite systems, 1/sqrt(2) for the Re/Im modes of region B. More...
real(real64), dimension(:), allocatable	l_m
real(real64), dimension(:), allocatable	prefactor
integer	num_super
	number of primitive cells in the supercell (N_p) More...
type(namespace_t)	namespace

Member Function/Subroutine Documentation

init()

procedure phonon_modes_oct_m::phonon_modes_t::init

private

Initialize the phonon modes.

Read information from a file

Parameters

[in]

masses

atomic masses in AMU, in file atom order

Definition at line 146 of file phonon_modes.F90.

sample()

procedure phonon_modes_oct_m::phonon_modes_t::sample

private

Sample initial ionic displacements and velocities from the Wigner distribution of the modes.

Implements the sampling prescription of the interface notes "Octopus-PhonoPy interface for multi-trajectory runs" (see doc/implementation_notes/):

\[ \delta R = N_p^{-1/2} (M_0/M)^{1/2} \sum_m \alpha_m \tilde{l}_m W_m \tilde{x}_m, \qquad \delta \dot{R} = N_p^{-1/2} (M_0/M)^{1/2} \sum_m \omega_m \alpha_m \tilde{l}_m W_m \tilde{r}_m, \]

with \( \tilde{x}_m, \tilde{r}_m \) sampled as independent Gaussians of variance \( (1 + 2n_m)/2 = \coth(\omega_m / 2 k_B T)/2 \) and \( M_0 \) = 1 AMU. The per-mode factors \( \alpha_m = g_m^{-1/2} \) are carried by the phonon file.

Parameters

[in]	temperature	in Kelvin
[in]	seed	seed for the random sampling; must be non-zero
[out]	pos_displacements	(1:dim_space, 1:num_atom), atomic units
[out]	vel_displacements	(1:dim_space, 1:num_atom), atomic units

Definition at line 147 of file phonon_modes.F90.

get_displacements()

procedure phonon_modes_oct_m::phonon_modes_t::get_displacements

private

get the displacements for a single mode and the respective generalized coordinates.

Parameters

[out]	pos_disp_flat	in atomic units
[out]	vel_disp_flat	in atomic units

Definition at line 148 of file phonon_modes.F90.

phonon_modes_finalize()

final phonon_modes_oct_m::phonon_modes_t::phonon_modes_finalize

finalprivate

Definition at line 149 of file phonon_modes.F90.

Member Data Documentation

alpha

real(real64), dimension(:), allocatable phonon_modes_oct_m::phonon_modes_t::alpha

private

Per-mode amplitude factor alpha_m = g_m^{-1/2}: 1 for modes from region A (2q = G) and for finite systems, 1/sqrt(2) for the Re/Im modes of region B.

Definition at line 136 of file phonon_modes.F90.

l_m

real(real64), dimension(:), allocatable phonon_modes_oct_m::phonon_modes_t::l_m

private

Definition at line 137 of file phonon_modes.F90.

prefactor

real(real64), dimension(:), allocatable phonon_modes_oct_m::phonon_modes_t::prefactor

private

Definition at line 138 of file phonon_modes.F90.

num_super

integer phonon_modes_oct_m::phonon_modes_t::num_super

private

number of primitive cells in the supercell (N_p)

Definition at line 140 of file phonon_modes.F90.

namespace

type(namespace_t) phonon_modes_oct_m::phonon_modes_t::namespace

private

Definition at line 142 of file phonon_modes.F90.

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The documentation for this type was generated from the following file:

• multi_trajectory/phonon_modes.F90