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# phq: Temperature Dependent Phonon Quasiparticle Dispersions of Complex Crystals from First Principles
# `phq`: Temperature Dependent Phonon Quasiparticle Dispersions of Complex Crystals from First Principles

[TOC]

This repo is created by [Zhen Zhang](mailto:[email protected]).
This repo is created by [Zhen Zhang](mailto:[email protected]). The associated paper is [here](https://www.sciencedirect.com/science/article/pii/S0010465519301523). The program files DOI is: [http://dx.doi.org/10.17632/sk4jsjc6p9.1](https://dx.doi.org/10.17632/sk4jsjc6p9.1).

## Installation Instructions

phq program can be installed on Linux, macOS and Windows systems by gfortran, ifort or other fortran compilers. ifort is recommended for faster running speed and smaller memory requirement. The source codes are in the src folder and the makefiles are in the system folder. Simply copy one of the suitable makefiles from system folder and paste it in the src folder and rename it as "makefile". Run:
The `phq` program can be installed on Linux, macOS and Windows systems by gfortran, `ifort` or other fortran compilers. ifort is recommended for faster running speed and smaller memory requirement. The source codes are in the `src` folder and the makefiles are in the system folder. Simply copy one of the suitable makefiles from system folder and paste it in the src folder and rename it as `makefile`. Run:

```shell
$ make
```

The phq executable file is compiled.
The phq executable file is compiled.

The source codes work as following:

Expand All @@ -28,15 +28,15 @@ There are 4 input files needed, which can be prepared according to the example p

1. `input` general controlling and settings. Parameters:

`dt` MD time step in atomic unit. `step_md_use` number of MD steps needed for the calculation of mode-projected VAFs. `correlation_time` desired decay time for VAFs in unit of `dt` which should be less than the `step_md_use`. `pole` parameter used in the maximum entropy method to filter high frequency components which should be less than the ``step_md_use``. `supercell` size of the supercell. `temperature` MD simulation temperature. `method` choose renormalized frequencies by which method when building the effective harmonic dynamical matrices: 0 represents the fitting approach. 1 represents the FT. 2 represents the MEM. If `method` is not specified or integers other than 1 and 2 are entered, the fitting approach will be used, which is the default method.
`dt` MD time step in atomic unit. `step_md_use` number of MD steps needed for the calculation of mode-projected VAFs. `correlation_time` desired decay time for VAFs in unit of `dt` which should be less than the `step_md_use`. `pole` parameter used in the maximum entropy method to filter high frequency components which should be less than the ``step_md_use``. `supercell` size of the supercell. `temperature` MD simulation temperature. `method` choose renormalized frequencies by which method when building the effective harmonic dynamical matrices: `0` represents the fitting approach. `1` represents the FT. `2` represents the MEM. If `method` is not specified or integers other than `1` and `2` are entered, the fitting approach will be used, which is the default method.

2. `scf.out` structure information of the primitive cell from self-consistent calculation. Parameters:

`ntype` number of elements. `natom` number of atoms. `mass` atomic mass of each element following the symbol of the element. `lattice_parameter` scale of lattice vectors in unit of Bohr radius. `cell_parameters` lattice vectors in cartesian cooradinates in unit of `lattice_parameter`. `atomic_positions` atomic positions of atoms in reduced coordinates following the symbol of element.

3. `dyn.out` harmonic phonon results from Quantum ESPRESSO ph.x output. Parameters:

`q` **q**-point in cartesian coordinates in unit of 2$\pi$/`lattice_parameter`.They are required as program input. `freq` harmonic phonon frequencies. They are required as program input as well as the following six columns of eigenvectors. Eigenvector of each atom has x, y and z components and each component has a real part and an imaginary part. The order of atoms should be the same as that of the atoms entered in `atomic_positions` in `scf.out`. `Dynamical Matrix` dynamical matrices, which are not required as program input if other program is used. `Dielectric Tensor` whether this is needed depends on whether LO-TO splitting needs to be considered in the system. `Effective Charges` whether they are needed depends on whether LO-TO splitting needs to be considered in the system.
`q` **q**-point in cartesian coordinates in unit of 2$\pi$/`lattice_parameter`.They are required as program input. `freq` harmonic phonon frequencies. They are required as program input as well as the following six columns of eigenvectors. Eigenvector of each atom has x, y and z components and each component has a real part and an imaginary part. The order of atoms should be the same as that of the atoms entered in `atomic_positions` in `scf.out`. `Dynamical Matrix` dynamical matrices, which are not required as program input if other program is used. `Dielectric Tensor` whether this is needed depends on whether LO-TO splitting needs to be considered in the system. `Effective Charges` whether they are needed depends on whether LO-TO splitting needs to be considered in the system.

4. `md.out` MD information. Parameters:

Expand All @@ -52,7 +52,7 @@ $ ./phq < input

## Output Files

The main output files of phq are as following:
The main output files of `phq` are as following:

1. `corr.vaf` velocity autocorrelation functions of each normal mode .
2. `corr_fit.vaf` fitted curves of correlation functions according to phonon quasiparticle and anharmonic perturbation theory.
Expand All @@ -64,11 +64,11 @@ The main output files of phq are as following:
8. `harmonic_matrix.mat` harmonic force constants.
9. `gamma_matrix.mat` effective harmonic force constant matrix.
10. `dynamical_matrix_md.mat` effective harmonic dynamical matrices.
11. `dynmatmd` renormalized phonon information with the same format of ph.x executable's output in the Quantum ESPRESSO suite. All post processing can be started from here.
11. `dynmatmd` renormalized phonon information with the same format of `ph.x` executable's output in the Quantum ESPRESSO suite. All post processing can be started from here.

## Post Processing

The output `dynmatmd` files from phq can be read in by the q2r.x executable in the Quantum ESPRESSO suite. Effective harmonic force constants, renormalized phonon dispersions, anharmonic entropy and free energy can be obtained from q2r.x output. If other Fourier interpolation program is used, either use the effective harmonic dynamical matrices file `dynamical_matrix_md.mat` or use the effective harmonic force constant matrix file `gamma_matrix.mat` to fit the format.
The output `dynmatmd` files from phq can be read in by the `q2r.x` executable in the [Quantum ESPRESSO](https://www.quantum-espresso.org/) suite. Effective harmonic force constants, renormalized phonon dispersions, anharmonic entropy and free energy can be obtained from `q2r.x` output. If other Fourier interpolation program is used, either use the effective harmonic dynamical matrices file `dynamical_matrix_md.mat` or use the effective harmonic force constant matrix file `gamma_matrix.mat` to fit the format.

## Example

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