# ttadano/alamode

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# Making input files for anphon

## Format of input files

Each input file should consist of entry fields. Available entry fields are

&general, &cell, &analysis, and &kpoint.

The format of the input file is the same as that of alm which can be found :ref:here <reference_input_alm>.

## List of input variables

### "&general"-field

• PREFIX-tag : Job prefix to be used for names of output files
Default: None String

• MODE-tag = phonons | RTA
 phonons Calculate phonon dispersion relations, phonon DOS, Grüneisen parameters etc. RTA Calculate phonon lifetimes and lattice thermal conductivity based on the Boltzmann transport equation (BTE) with the relaxation time approximation (RTA).
Default: None String

• NKD-tag : Number of atomic species
Default: None Integer

• KD-tag = Name[1], ... , Name[NKD]
Default: None Array of strings In the case of GaAs with NKD = 2, it should be KD = Ga As.

• MASS-tag = mass[1], ... , mass[NKD]
Default: None Array of double In the case of Bi2Te3 with NKD = 2, MASS should be MASS = 208.98 127.60.

• FCSXML-tag : XML file containing force constants generated by the program alm
Default: None String

• FC2XML-tag : XML file containing harmonic force constants for different size of supercell
Default: None String When FC2XML is given, the harmonic force constants in this file will be used for calculating dynamical matrices. It is possible to use different size of supercell for harmonic and anharmonic terms, which are specified by FC2XML and FCSXML respectively.

• NSYM-tag = 0 | 1 | nsym
 0 The program automatically generates the crystal symmetry operations (rotational and translational parts). When PRINTSYM = 1, symmetry operations will be saved in the file “SYMM_INFO_PRIM”. 1 Only the identity operation will be considered. nsym "nsym" symmetry operations will be read from "SYMM_INFO_PRIM" file.
Default: 0 Integer

• TOLERANCE-tag : Tolerance for finding symmetry operations
Default: 1.0e-6 Double

• PRINTSYM-tag = 0 | 1
 0 Symmetry operations won’t be saved in “SYMM_INFO_PRIM” 1 Symmetry operations will be saved in “SYMM_INFO_PRIM”
Default: 0 Integer

• NONALAYTIC-tag = 0 | 1 | 2
 0 Non-analytic correction is not considered. 1 Include the non-analytic correction by the damping method proposed by Parlinski. 2 Include the non-analytic correction by the mixed-space approach
Default: 0 Integer When NONANALYTIC > 0, appropriate NA_SIGMA and BORNINFO have to be given.

• NA_SIGMA-tag : Damping factor for the non-analytic term
Default: None Double This entry is necessary when NONANALYTIC = 1. The definition of NA_SIGMA is described in the formalism section.

• BORNINFO-tag : File containing the macroscopic dielectric tensor and Born effective charges for the non-analytic correction
Default: None String The details of the file format can be found :ref:here .

• TMIN, TMAX, DT-tags : Temperature range and its stride in units of Kelvin
Default: TMIN = 0, TMAX = 1000, DT = 10 Double

• EMIN, EMAX, DELTA_E-tags : Energy range and its stride in units of kayser (cm-1)
Default: EMIN = 0, EMAX = 1000, DELTA_E = 10 Double

• ISMEAR-tag = -1 | 0 | 1
 -1 Tetrahedron method 0 Lorentzian smearing with width of EPSILON 1 Gaussian smearing with width of EPSILON
Default: -1 Integer ISMEAR specifies the method for Brillouin zone integration

• EPSILON-tag : Smearing width in units of Kayser (cm-1)
Default: 10.0 Double This variable is neglected when ISMEAR = -1

• TRISYM-tag : Flag to use symmetry operations to reduce the number of triples of k points for self-energy calculations
 0 Symmetry will not be used 1 Use symmetry to reduce triples of k points
Default: 1 Integer This variable is used only when MODE = RTA.

Note

TRISYM = 1 can reduce the computational cost, but phonon linewidth stored to the file PREFIX.result needs to be averaged at points of degeneracy. For that purpose, a subsidiary program analyze_phonons.py* should be used.

• RESTART-tag : Flag to restart the calculation when MODE = RTA
 0 Calculate from scratch 1 Restart from the existing file
Default: 1 if there is a file named PREFIX.result; 0 otherwise Integer

### "&cell"-field

Please specify the cell parameters of the primitive cell as:

&cell
a
a11 a12 a13
a21 a22 a23
a31 a32 a33
/


The cell parameters are then given by \vec{a}_{1} = a \times (a_{11}, a_{12}, a_{13}) , \vec{a}_{2} = a \times (a_{21}, a_{22}, a_{23}) , and \vec{a}_{3} = a \times (a_{31}, a_{32}, a_{33}) .

Note

The lattice constant a must be consistent with the value used for the program alm. For example, if one used a = 20.4 a_{0} for a 2x2x2 supercell of Si, one should use a = 10.2 a_{0} here for the primitive cell.

### "&kpoint"-field

This entry field is used to specify the list of k points to be calculated. The first entry KPMODE specifies the types of calculation which is followed by detailed entries.

• KPMODE = 0 : Calculate phonon frequencies at given k points

For example, if one wants to calculate phonon frequencies at Gamma (0, 0, 0) and X (0, 1/2, 1/2) of an FCC crystal, the &kpoint entry should be written as

&kpoint
0
0.000 0.000 0.000
0.000 0.500 0.500
/

• KPMODE = 1 : Band dispersion calculation

For example, if one wants to calculate phonon dispersion relations along G-K-X-G-L of a FCC crystal, the &kpoint entry should be written as follows:

&kpoint
1
G 0.000 0.000 0.000  K 0.375 0.375 0.750 51
K 0.375 0.375 0.750  X 0.500 0.500 1.000 51
X 0.000 0.500 0.500  G 0.000 0.000 0.000 51
G 0.000 0.000 0.000  L 0.500 0.500 0.500 51
/


The 1st and 5th columns specify the character of Brillouin zone edges, which are followed by fractional coordinates of each point. The last column indicates the number of sampling points.

• KPMODE = 2 : Uniform k grid for phonon DOS and thermal conductivity

In order to perform a calculation with 20x20x20 k grid, the entry should be

&kpoint
2
20 20 20
/


### "&analysis"-field

• GRUNEISEN-tag = 0 | 1
 0 Grüneisen parameters will not be calculated 1 Grüneisen parameters will be stored
Default: 0 Integer When MODE = phonons and GRUNEISEN = 1, Grüneisen parameters will be stored in PREFIX.gru (KPMODE = 1) or PREFIX.gru_all (KPMODE = 2).

Note

To compute Grüneisen parameters, cubic force constants must be contained in the FCSXML file.

• PRINTEVEC-tag = 0 | 1
 0 Do not print phonon eigenvectors 1 Print phonon eigenvectors in the PREFIX.evec file
Default: 0 Integer

• PRINTXSF-tag = 0 | 1
 0 Do not save an AXSF file 1 Create an AXSF file PREFIX.axsf
Default: 0 Integer This is to visualize the direction of vibrational modes at gamma (0, 0, 0) by XCrySDen. This option is valid only when MODE = phonons.

• PRINTVEL-tag = 0 | 1
 0 Do not print group velocity 1 Store phonon velocities to a file
Default: 0 Integer When MODE = phonons and PRINTVEL = 1, group velocities of phonons will be stored in PREFIX.phvel (KPMODE = 1) or PREFIX.phvel_all (KPMODE = 2).

• PRINTMSD-tag = 0 | 1
 0 Do not print mean-square-displacement (MSD) of atoms 1 Save MSD of atoms to the file PREFIX.mds
Default: 0 Integer This flag is available only when MODE = phonons and KPMODE = 2.

• PDOS-tag = 0 | 1
 0 Only the total DOS will be printed in PREFIX.dos 1 Atom-projected phonon DOS will be stored in PREFIX.dos
Default: 0 Integer This flag is available only when MODE = phonons and KPMODE = 2.

• TDOS-tag = 0 | 1
 0 Do not compute two-phonon DOS 1 Two-phonon DOSs will be stored in PREFIX.tdos
Default: 0 Integer This flag is available only when MODE = phonons and KPMODE = 2.

Note

Calculation of two-phonon DOS is computationally expensive.

• SPS-tag = 0 | 1 | 2
 0 Do not compute scattering phase space 1 Total and mode-decomposed scattering phase space involving three-phonon processes will be stored in PREFIX.sps 2 Three-phonon scattering phase space with the Bose factor will be stored in PREFIX.sps_Bose
Default: 0 Integer This flag is available only when MODE = phonons and KPMODE = 2.

• PRINTPR-tag = 0 | 1
 0 Do not compute the (atomic) participation ratio 1 Compute participation ratio and atomic participation ratio, which will be stored in PREFIX.pr and PREFIX.apr respectively.
Default: 0 Integer This flag is available when MODE = phonons.

• KAPPA_SPEC-tag = 0 | 1
 0 Do not compute the thermal conductivity spectra 1 Compute the thermal conductivity spectra, which will be stored in PREFIX.kappa_spec .
Default: 0 Integer This flag is available when MODE = RTA.

• ISOTOPE-tag = 0 | 1
 0 Do not consider phonon-isotope scatterings 1 Consider phonon-isotope scatterings 2 Consider phonon-isotope scatterings as in ISOTOPE = 1 and the corresponding selfenergy will be stored in PREFIX.gamma_isotope
Default: 0 Integer When MODE = RTA and ISOTOPE = 1 or 2, phonon scatterings due to isotopes will be considered perturbatively. ISOFACT should be properly given.

• ISOFACT-tag = isofact[1], ... , isofact[NKD]
Default: 0 Array of doubles Isotope factor is a dimensionless value defined by \sum_{i} f_{i} (1 - m_{i}/\bar{m})^{2} . Here, f_{i} is the fraction of the i th isotope of an element having mass m_{i} , and \bar{m}=\sum_{i}f_{i}m_{i} is the average mass, respectively. This quantity is equivalent to g_{2} appearing in the original paper by S. Tamura [Phys. Rev. B, 27, 858.].

• ANIME-tag = k1, k2, k3
Default: None Array of doubles This tag is to animate vibrational mode. k1, k2, and k3 specify the momentum of phonon modes to animate, which should be given in units of the reciprocal lattice vector. For example, ANIME = 0.0 0.0 0.5 will animate phonon modes at (0, 0, 1/2). When ANIME is given, ANIME_CELLSIZE is also necessary. You can choose the format of animation files, either AXSF or XYZ, by ANIME_FORMAT tag.

• ANIME_CELLSIZE-tag = L1, L2, L3
Default: None Array of integers This tag specifies the cell size for animation. L1, L2, and L3 should be large enough to be commensurate with the reciprocal point given by the ANIME tag.

• ANIME_FORMAT = xsf | xyz
Default: xyz String When ANIME_FORMAT = xsf, PREFIX.anime???.axsf files are created for XcrySDen. When ANIME_FORMAT = xyz, PREFIX.anime???.xyz files are created for VMD (and any other supporting software such as Jmol).

## Format of BORNINFO

When one wants to consider the LO-TO splitting near the \Gamma point, it is necessary to set NONANALYTIC = 1 and provide BORNINFO file containing dielectric tensor \epsilon^{\infty} and Born effective charge Z^{*} . In BORNINFO file, the dielectric tensor should be written in first 3 lines which are followed by Born effective charge tensors for each atom as the following.

Here, N_p is the number of atoms contained in the primitive cell.

Attention!

Please pay attention to the order of Born effective charges.