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

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This repo is created by Zhen Zhang. The associated paper is https://doi.org/10.1016/j.cpc.2019.05.003. If the Elsevier library is not accessible, the open access preprint on arXiv is https://arxiv.org/abs/1902.06395. The program files DOI is http://dx.doi.org/10.17632/sk4jsjc6p9.1.

Installation Instructions

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:

$ make

The phq executable file is compiled.

The source codes work as following:

1. configure.f90 contains 3 auxiliary modules, which configure the physical quantities, parameters and text readin settings.

2. main.f90 the main module, which performs the normal mode projection and anharmonic phonon extraction and so forth.

3. phq.f90 runs the program and records the running time.

Input Files

There are 4 input files needed, which can be prepared according to the example provided:

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.

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.

4. md.out MD information. Parameters:

   total_step total actual MD steps. In practice, recorded MD steps should be configurations after reaching thermal equilibrium and less than this number.atomic_positions initial atomic positions in reduced coordinates of the supercell lattice vectors. md_step recorded MD steps, followed by the instantaneous atomic_md_positions in the MD simulation. atomic_md_positions atomic positions in the MD simulation in reduced coordinates of the supercell lattice vectors. Atoms in each one of the primitive cell should be together instead of atoms of the same element being together, and the order of atoms in each of the primitive cell should be in the same order as provided in scf.out.

Executing the Program

After putting the phq executable in the same folder with the input files, run:

$ ./phq < input

Output Files

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.
3. corr_fourier.vaf Fourier transformation of correlation functions.
4. frequency.freq harmonic, fitted renormalized, Fourier transformed renormalized and maximum entropy method renormalized phonon frequencies.
5. tau_fit.tau fitted phonon quasiparticles' lifetime.
6. vector_q.out eigenvectors of the primitive cell.
7. vector.out eigenvectors of the supercell.
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.

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.

Example

There is an example of diamond silicon in the example folder. Postprocessing files are also in the silicon example folder.

License

GNU General Public License v3