6.17. Solid ‣ Quantum ESPRESSO menu¶

It is a menu related to Quantum ESPRESSO.

The way to install Quantum ESPRESSO is described in Installing Winmostar and solvers.

6.17.1. Configure¶

Set the calculation condition of Quantum ESPRESSO. To set up the calculations immediately after setting Run button, once to return to the main window please press :guilabel:` OK` button.

See Run for behavior when clicking Run.

Return to the default state with Reset button. Save the setting except Force Field with Save button. Load the setting saved by Save with the Load button.

If the Quantum ESPRESSO keyword displayed in the Keyword Editor and the contents set in this function window are different, you will be asked if you want to load the keyword from the Keyword Editor.

When invoking this function, if the structure displayed in the main window can be changed to a primitive cell, Convert Lattice is executed automatically.

Output Directory

Specify the output destination folder (outdir) of the data, and at the same time specify the new/continued execution of the job.

Create

Create a new destination folder for the data. outdir is set as a new folder.

Continue

Continue the job of QE that was loaded on the main window and executed immediately. outdir is set to outdir of the job executed immediately before.

Select

Specify the folder specified in the opened dialog as the output destination and continue the job from the data of that folder. Outdir will be set to what you specify here.

Preset

Select preset for setting. Each preset changes the following keywords

SCF

SCF+Bands

+DOS

SCF+Bands

(Fermi surf)

Relax

Relax

(variable cell)

BOMD

CPMD

Phonopy

calculation

scf scf scf relax vc-relax md cp scf

Use nbnd

False True True False False False False False

K_POINTS

gamma

automatic

4 4 4 1 1 1

automatic

4 4 4 1 1 1

gamma

automatic

4 4 4 1 1 1

gamma gamma gamma

tstress

False False False False False True False False

Set ibrav

and celldm

False True True False False False False False

occupations

smearing

ion_dynamics

bfgs bfgs verlet none

cell_dynamics

bfgs

tprnfor

False False False True True True True True

tstress

False False False False True False False True

Use cell_factor

False False False False True False False False

pot_extrapolation

second_order

wfc_extrapolation

second_order

electron_dynamics

sd

Unit for

atomic_position

angstrom angstrom angstrom angstrom angstrom crystal

Band structure

plot

False True True False False False False False

DOS plot

False True True False False False False False

PDOS plot

False True False False False False False False

Fermi surface

False False True False False False False False

Use MPI

Specify whether to execute parallel calculation using MPI when executing QE. Enter the number of MPI processes in the horizontal field.

Basic Tab

calculation

Select the type of calculation.

Use nbnd

Specify the number of bands. If not checked, it will be set automatically. When selected in parentheses, the number of valence electrons when pseudopotential is used is displayed. If the calculation of the number of valence electrons fails, it is displayed as N/A.

K_POINTS

Select the specification method of point K from the pull-down and specify K point in QE format in the text box below. In the case of gamma, it is calculated only with the Γ point. In the automatic case, “(number of divisions in the kx direction) (division number in the ky direction) (number of divisions in the kz direction) (shift flag in the kx direction) (shift flag in the ky direction) (shift flag in kz direction)” Enter a delimiter. When the shift flag is 0, there is no shift (the k point includes the Γ point), when it is 1, there is a shift (k point crosses the Γ point). For details, please refer to doc/brillouin_zones.pdf under pw.x manual or QE installation folder.

Set default k-path

The default k-point path of the Bravo lattice (ibrav) detected for the crystal displayed in the main window is acquired from UserPref/kpath_default.txt and set.

nosym

Specify whether to use spatial symmetry.

noinv

Specify whether time reversal symmetry is used or not.

Set ibrav = … and celldm

If the primitive cell is displayed in the main window and checked, set the appropriate ibrav and celldm. If it is not checked, set ibrav = 0 and set CELL_PARAMETERS.

ecutwfc

Specify the cutoff energy of the plane wave when calculating the wave function.

ecutrho

Specify cutoff energy of plane wave at electron density and potential calculation.

tot_charge

Specify the charge of the entire system in the simulation cell.

occupations

Specify smearing for metals and tetrahedron for DOS calculations.

ion_dynamics

Specify the algorithm to change ion (nucleus) position.

cell_dynamics

Specify algorithm to change simulation cell.

tprnfor

I will calculate the force.

tstress

Calculate the pressure tensor.

Advanced tab

conv_thr

Specify tolerance of energy at SCF calculation.

etot_conv_thr

Structural Optimization (relax) Specify the energy tolerance for calculation.

forc_conv_thr

Structural Optimization (relax) Specify the force tolerance during calculation.

press_conv_thr

Specify tolerance of pressure when cell structure optimization (relax - vc) calculation is calculated.

electron_maxstep

Specify the maximum iteration number of the SCF calculation.

nstep

Specify the maximum number of steps for structure optimization (relax) calculation and the number of steps for MD calculation.

upscale

Specify coefficients for automatically decreasing conv_thr during structure optimization (relax) calculation.

diagonalozation

Specify diagonalization algorithm.

lspinorb

Pseudopotential file with spin orbit interaction can be used during calculation of non-colinear.

smearing

Specify the method of occupancy smoothing (smearing).

degauss

Specify the parameter of occupancy smoothing.

mixing_beta

Specify the mixture ratio of old and new KS orbitals in SCF calculation. The closer to 1, the greater the ratio of predicted values.

mixing_mode

Specify the mixture algorithm of old and new KS orbitals.

vdw_corr

Van der Waals (dispersion) Specify how to correct forces.

Use input_dft

When checked, overwrite the setting of the functional to the setting written in the pseudopotential file.

cell_dofree

Specify the degree of freedom (direction) for moving the simulation cell.

Use cell_factor

Explicitly specify the construction parameter of the pseudopotential table. Sometimes it is better to set a larger value for vc - relax (structure optimization calculation with cell size change).

Spin/DFT+U tab

nspin

Set spin polarization calculation setting.

Use tot_magnetization

When checked, specify the magnetization of the whole system here. If you do not check it, specify starting_magnetization.

starting_magnetization

Give the initial value of magnetization of each atom type.

lda_plus_u

Perform LDA + U calculation.

Hubbard_U/alpha

Specify the U and alpha parameters of Hubbard for each atom type.

Phonon tab

Run Phonon Calculation as Postprocess

Perform phonon calculation. Specifically, execute ph.x after executing pw.x. In order to make this item effective, you need to choose SCF or relax for Calculation. I/O files such as ph.x are created in the working directory.

Threshold

Specify the censored error of phonon calculation.

Calc Macroscopic Dielectric Constant

Calculate the dielectric constant obtained from phonon calculation.

Calc Non-resonant Raman

Include calculation of Raman spectrum.

Acoustic Sum Rule

Specify how to give Acoustic Sum Rule at the time of spectrum calculation (dynmat.x) after phonon calculation. It does not affect phonon calculation itself.

Calc Phonon Dispersion

Calculate phonon dispersion. In order to acquire phonon band structure, phonon density of states you need to specify this.

K Points (Dispersion)

Specify the number of K points when computing phonon variance.

Dynamics tab

Simulation Package

Specify the calculation package to be used for MD calculation. For cp.x, use the CPMD method.

DT

Specify the time step of MD calculation with atomic unit.

tempw

Specify the target temperature when temperature control is specified by MD calculation.

press

Specify the target pressure when specifying pressure control in MD calculation.

ion_temperature

Specify the temperature control method of ion (nucleus) in MD calculation.

ion_velocities

Specify the initial velocity of ion for MD calculation.

gangbang

Specify the allowable value of temperature during temperature control.

pot_extrapolation

Born-Oppenheimer Specify the extrapolation method of the potential when using MD.

wfc_extrapolation

Specify the extrapolation method of wave function when Born-Oppenheimer MD is used.

electron_dynamics

Specify the algorithm to change the KS trajectory when Car - Parrinello MD is used.

electron_velocities

Specify the initial speed of electrons when Car - Parrinello MD is used.

emass

Car-Parrinello Specify the virtual mass of electrons when using MD.

emass_cutoff

Car-Parrinello Specifies the cutoff value of the virtual mass of electrons during MD calculation.

orthogonalization

Specify the method of matrix calculation (orthonormalization).

Dipole Corr tab

tefield

A sawtooth type external electric field is applied.

dipfield

Use dipole correction.

edit

Sets the direction in which the tefield and dipfield are applied.

emaxpos

The location where the external electric field is at its maximum value when applying tefield and dipfield is given in fractional coordinates (in the range of 0 to 1).

eopreg

The size of the region where the external electric field decays when applying tefield and dipfield is given in fractional coordinates.

eamp

Gives the magnitude of the external electric field when applying the tefield and dipfield.

ESM tab

assume_isolated=esm

Check if you use ESM (Effective Screening Medium) method.

esm_bc

Specify the type of boundary condition used in the ESM method.

esm_efield

Specify the electric field.

lfcpopt

Calculation of constant chemical potential (constant mu) will be carried out. The initial system charge is specified by tot_charge on the Basic tab.

the fcp_m

Set the target value of Fermi energy in constant calculation of chemical potential.

Enter Relative Potential

Supports input of Target Fermi Energy. First, specify the log file for calculation at voltage 0 and acquire Fermi energy at voltage 0. Next, input the applied voltage. From these two pieces of information, calculate Target Fermi Energy.

RISM(1) tab

trism=.True.

Enable RISM calculations. Check here to run ESM-RISM calculations, and check assume_isolated = esm on the ESM tab.

closure

Select the closure to use for RISM calculation

tempw

Specify the initial velocity of ion for MD calculation.

ecutsolv

Specify the cutoff energy of the plane wave when calculating the wave function.

solute_lj

Specify the LJ parameter of the solute (DFT region). If none is selected, enter the LJ parameter in solute_epsilon and solute_sigma below

noinv

Specify the number of molecular species of the solvent.

SOLVENTS

Select the unit of Density from the pull-down menu and specify the density (concentration) of each solvent molecule type and the name of the MOL file. MOL files must be in the folder specified by Directory for MOL Files below.

Directory for MOL Files

Specify a folder containing MOL files that can be selected with SOLVENTS.

RISM(2) tab

laue_expand_right/left

Specify the position of the far end of the solvent region in the ESM-RISM calculation.

laue_starting_right/left

Specify the starting position of the solvent region in the ESM-RISM calculation.

laue_buffer_right/left

Specify the location of the solvent buffer area in the ESM-RISM calculation.

Run only 1D-RISM

If checked, run 1drism.x instead of pw.x. No DFT calculations will be performed. Useful if you only want to know the correlation function between solvent atoms and the chemical potential between solvents.

rism3d_conv_level

Specify parameters for dynamically changing the truncation error of 3D-RISM calculation at each step of SCF calculation.

rism1d/rism3d_maxstep

Specify the maximum number of 1D and 3D-RISM iterations.

rism1d/rism3d_conv_thr

Specify the truncation error for 1D and 3D-RISM.

mdiis1d/3d_size

Specify the convergence parameter of RISM calculation by MDIIS algorithm.

mdiis1d/3d_step

Specify the convergence parameter of RISM calculation by MDIIS algorithm.

Other tab

Fill in the other settings in QE's input file format (FORTRAN namelist format). An example of entry is displayed by pointing the pointer.

Options

Verbosity

Specify the amount of information output by QE.

atomic_position unit

Specify the unit of ATOMIC_POSITIONS and CELL_PARAMETERS.

Use max_seconds

If checked, processing of QE will be interrupted after the number of seconds entered here.

Make a Backup of Working Directory

When Output Directory is Create, if the _qe_data folder to be created already exists, add a number to the end of the folder name to back up the existing folder.

Dump all files for remote

Output files necessary for job execution under Linux environment. The same file as the file generated by the remote job submission function is output.

Open k-path file

Open the configuration file (UserPref/kpath_default.txt) that describes the k-point path specified by default for each type of ibrav (bracket lattice). If UserPref/kpath_default.txt does not exist, it is copied from wmx/kpath_default.txt.

Use RISM-enabled QE

Check if you want to use QE with RISM installed.

Properties tab

Calculate these properties after pw.x

Select post processing to be executed immediately after executing pw.x. Various parameters of the processing selected here are specified in the Parameter/Value column on the right.

Pseudo Potentials tab

Mass

Specify the mass of each element.

Default

Set standard mass.

Light

Set the mass of all elements to 1. It is used for the purpose of promoting structural relaxation of ions.

Manual

In the list below, for each element, the user individually sets the mass.

Pseudo Potential

Pseudopotentials of the type common to all the elements in the system can be selected by pulldown. (Manual) is selected, the user separately sets the pseudopotential for each element in the list below. Pseudopotential files are searched from folders specified in pseudo Directory. The one written at the top of UserPref/qe_pseudo_priority_list.txt is preferentially selected.

Reload pseudo Files

The pseudo-potential file placed in the folder specified by pseudo Directory is read again.

pseudo Directory

Specify the folder where the pseudopotential file will be placed. If the case of pseudo in QE#39;s directory, use the pseudo folder under the installation directory of QE. If the case of (select …), use the directory selected in the dialog.

Open Pseudo Directory

Open the folder specified in pseudo Directory.

Download Pseudo Files

Download the pseudopotential file and install it.

Open Priority List

Open UserPref/qe_pseudo_priority.txt. If it does not exist, it is copied from wmx/qe_pseudo_priority.txt.

6.17.2. Run¶

Run Quantum ESPRESSO. The execution method differs depending on the situation.

When CPMD is selected cp.x, otherwise it executes pw.x.

(Default) When Output Directory = Create, create a new working directory and execute the calculation.

If the case of Output Directory = Continue, use outdir of the input file open in the main window as the working directory then.

If the case of Output Directory = Select, use the selected folder as the working directory (outdir).

Following file will be generated with execution. As an example, the file/folder name when the input file is si.pwin is also shown.

type Description

pwout file

si.pwout

Calculation log file.

bat file

si.bat

It is a batch file for running Quantum ESPRESSO.

Working Directory

si_qe_data\

Working directory.

The following files are generated in the working directory. Only the main files are shown here.

type Description

Pseudopotential file

*.UPF

The pseudopotential file used for calculation is

Copied here, the ESPRESSO_PSEUDO environment variable

It is set to the working directory.

gmx_tmp.mdp

It is a file that specifies calculation conditions.

pw_bands.in

This is an input file for executing bands calculation in post processing.

pw_bands.out

This is the log file of pw_bands.in.

pw_dos.in

Input file for executing dos calculation in post processing.

pw_dos.out

pw_dos.in log file.

ph.in

In post processing, use phonon calculation with ph.x

It is an input file for execution.

ph.out

This is the log file of ph.in.

Hint

** Working directory **

A working directory is a folder whose name is the name of the file opened in the main window plus a suffix.

** The suffix varies depending on the type of solver. **

For example, in the case of Gromacs, if the file opened in the main window is aaa.gro and the suffix is _gmx_tmp, the working directory will be named aaa_gmx_tmp.

It must be in the same hierarchy as the file opened in the main window.

Processing continues in the working directory of the same name even when continuing jobs, but by default the backup of the working directory of the previous job is created just before the continuation job is executed.

The name of the backup will be the one with the smallest number in the range where duplicate names do not exist. For example, if the working directory is aaa_gmx_tmp, it is aaa_gmx_tmp1.

** Directories without numbers are always up to date. **

Job is run through Winmostar Job Manager.

6.17.3. Open Log File (pwout)¶

Open the log file with a text editor.

6.17.4. Animation¶

6.17.4.1. Optimization, BOMD(pwout, out)¶

From the information of the log file, animation such as structure optimization, BOMD calculation etc. is created and displayed.

For CPMD use CPMD(pos).

For the animation display operation method, see Animation window.

6.17.4.2. CPMD(pos)¶

Specify CPMD's pos and cel files and display animation.

To display the result of pw.x, use Optimization, BOMD(pwout, out).

For the animation display operation method, see Animation window.

6.17.5. Energy Plot¶

6.17.5.1. SCF Energy Change (pwout)¶

Select the log file and display a graph of total energy.

For CPMD use CPMD Energy Plot (evp).

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.5.2. CPMD Energy Plot (evp)¶

Specify the evp file of CPMD and display time variation of various energies.

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6. Analyses¶

6.17.6.1. Electron Density¶

Specify working directory (outdir) and display isoelectric density surface.

In the background, pp.x flows, and a cube file is generated.

Refer to MO Plot window for how to operate subwindow.

6.17.6.2. Lowdin Charge¶

Specify the working directory (outdir), calculate and display the point charge.

Projwfc.x flows in the background.

6.17.6.3. Potential Energy Distribution¶

Specify the working directory (outdir) and log file for SCF calculation and display the potential energy distribution in the z-axis direction.

Fermi energy is acquired from the log of SCF calculation. The difference between the Fermi energy and the maximum value of the potential energy distribution is displayed as an estimate of the work function. Pp.x and average.x flow in the background.

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.4. Band Structure¶

Specify the working directory (outdir) and SCF calculation log file and display the band structure.

Calculation must be completed with calculation = bands in advance. Fermi energy is acquired from the log file of SCF calculation. Bands.x flows in the background.

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.5. Density od States¶

Specify the working directory (outdir) and the SCF calculation log file and display the density of states.

Fermi energy is acquired from the log file of SCF calculation. dos.x flows in the background.

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.6. Projected DOS¶

Specify the working directory (outdir) and the SCF calculation log file and display projected density of state(PDOS).

Fermi energy is acquired from the log of SCF calculation. Projwfc.x flows in the background.

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.7. Fermi Surface¶

Specify the log file for SCF calculation and bands calculation and display the Fermi surface.

For Fermi surface display, use FermiSurfer <http://fermisurfer.osdn.jp/>. Specify the k point division number for bands calculation in # of K Points and press the Calc button to display the Fermi surface.

6.17.6.8. Dielectric Function¶

Specify the working directory after calculating the dielectric function and display the dielectric function.

Direction

Specify the direction of the dielectric function to be acquired.

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.9. IR/Raman¶

Specify the working directory after phonon calculation and log of SCF calculation and display IR and Raman spectrum.

Refer to IR Spectrum Window for how to operate the subwindow.

6.17.6.10. Phonon Band Structure¶

Phonon Specifies the working directory after the variance calculation and displays the phonon dispersion curve.

ASR

Specify the type of Acoustic Sum Rule to be applied.

K Points

Specify the path of the dispersion curve to be acquired. In each line, describe the x, y, z components in units of 2pi/a, and next to it describe the number of divisions up to the next point. (Enter a total of 4 columns with a space separator)

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.11. Phonon Density of States¶

Phonon Specifies the working directory after distributed calculation and displays the phonon density of states.

ASR

Specify the type of Acoustic Sum Rule to be applied.

K Points

Phonon DOS Specifies the division number of K points during DOS calculation.

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.12. Charge/Energy Profile (esm1)¶

Specify the esm1 file output by ESM calculation (assume_isolated = esm) and display the charge or energy distribution in the z-axis direction.

You can also plot the difference between the two esm1 files.

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.13. 1D-RISM RMS Change¶

Plot the change in RMS of the 1D-RISM calculation performed at the beginning of the RISM calculation (trism = .True.).

Draw

Displays a graph.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.14. 3D/Laue-RISM RMS Change for Last Step¶

Plot the change of RMS of 3D-RISM or ESM-RISM calculation in the last SCF step when RISM calculation (trism = .True.) is executed.

Draw

Displays a graph.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.15. Solvent Pair Distribution Func. (1drism)¶

Interatomic correlation function (radial distribution function) of RISM region is calculated using 1 drism file outputted by RISM calculation (trism =. True.).

Obtain Chemical Potentials

The chemical potential between solvent molecules is output in csv format.

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.6.16. Solvent Charge/Energy Profile (rism1)¶

Calculate the solvent density, energy, and charge in the direction in which the DFT region-RISM region contacts (vertical direction of the interface) by using the rism1 file output by RISM calculation (trism = .True.).

Draw

Display the graph. The result analysis program is executed as necessary.

Close

Close the window.

For how to operate the graph drawing area, see How to operate the graph.

6.17.7. Generate MOL File¶

Create a MOL file of the solvent used in the RISM calculation (trism = .True.). Please call this function after creating one molecule in the main window. When entering LAMMPS data format, please check Use parameters in displayed file.

The created file should be placed in the folder specified by Directory for MOL Files on the RISM (1) tab of the Configure window of the MOL file.

6.17.8. Nudged Elastic Band¶

6.17.8.1. Configure¶

Set conditions for NEB calculation.

Please set in the state that the structure optimization calculation of each of the start state and the end state has been completed.

6.17.8.2. Run¶

Perform NEB calculation using neb.x.

6.17.8.3. Transition Path¶

Specify the file after NEB calculation and display the change in energy and atomic structure along the reaction coordinates.

For the animation display operation method, see Animation window.

6.17.9. BoltzTraP¶

BoltzTraP calculates thermoelectric characteristics based on the output of nscf calculation in QuantumESPRESSO.

6.17.9.1. Configure & Run¶

Set the calculation conditions for pre-post processing using BoltzTraP and execute pre-processing.

Create .intrans File button

Read nscf calculation output file (.pwout) of Quantum ESPRESSO and generate BoltzTraP setting file (.intrans). Assuming that the output file is mg2si_nscf.pwout, a working directory named mg2si_nscf is created in the same level. mg2si_nscf.intrans is generated in mg2si_nscf.

If the intrans file is successfully created, read the contents of the file and reflect it in the input fields of the following keywords.

Fermilevel (Ry)

Fermi energy read from pwout file is set.

energy grid

Specify the interval of the set energy.

energy span

Specifies the range of band energies to consider in calculations around the Fermi level.

number of electrons

Specify the number of electrons in a unit cell.

lpfac

Specify the factor for complementing the band energy by Fourier expansion.

efcut

Specify the calculation range by changing the chemical potential.

Tmax

Specify the upper limit of the set temperature.

temperature grid

Specify the interval of the set temperature.

energy of bands

Specify the energy width of the band obtained from DOS.

Calculate expansion coeff

If checked, calculate expansion coefficient.

Start BoltzTraP button

Recreate the intrans file based on the setting conditions and execute BoltzTraP. At this time, the following files and folders are created.

The main files in the working directory (mg2si_nscf) at the end of the calculation are described below.

type Description

intfans file

mg2si_nscf.intrans

BoltzTraP input file.

.trace file

mg2si_nscf.trace

This file contains information on energy and temperature dependence of thermoelectric properties calculated by BoltzTraP. The BoltzTraP Import Result menu reads this file and performs visualization.

Cancel button

Close Configure & Run window without doing anything.

6.17.9.2. Import Result¶

The following thermoelectric properties calculated by BoltzTraP are read and visualized.

Seebeck coefficient

Electrical conductivity

Electrical thermal conductivity

Power factor

Figure of merit

To display the energy dependence of the characteristic value at each temperature, select T [K] from the combo box and select the target temperature from the list. If you want to display the temperature dependence of the characteristic value for each energy, select E-Ef [eV] from the combo box and select the target energy from the list.

6.17.10. Phonopy¶

Phonopy calculates in the following three steps.

Create a supercell based on the given Quantum ESPRESSO input file. (Pre-processing)

Execute Quantum ESPRESSO for all generated super cells.

Create ForceSets file from Quantum ESPRESSO output file and calculate Phonon band, DOS, thermodynamic properties, etc. (Post processing)

6.17.10.1. Configure & Run¶

Set calculation conditions for pre-post processing using Phonopy and execute pre-processing.

Open button

Read the input file (*.in, *.pwin) of Quantum ESPRESSO. Post processing in Phonopy requires stress information. Therefore, the file to be read must include the tprnfor and tstress keywords. The input file of Quantum ESPRESSO for Phonopy can be set by using Quantum ESPRESSO Configure Preset=Phonopy.

DIM

Specify the number of times the supercell repeats in the x, y, and z directions, separated by a space.

MP

Specify the reciprocal lattice when calculating Phono DOS and thermodynamic properties in Phonopy, separated by a space.

ATOM_NAME

Specify the elements included in the unit cell separated by a space. It is automatically entered when the input file is opened with the Open button.

Start button

Execute Phonopy based on the setting conditions, and create a super cell that is pre-processing. At this time, the following files and folders are created.

type Description

bat file

si.bat

Batch file to execute the preprocessing of Phonopy.

sh file

si.sh

Shell script file for executing the preprocessing of Phonopy.

si_ph_data folder

si_ph_data

Working directory.

The following files are generated in the working directory si_ph_data.

type Description

mesh.conf file

mesh.conf

Used to calculate density of states and thermodynamic properties in post processing of Phonopy.

band.conf file

band.conf

Used when calculating band structure in Phonopy post processing.

header file

header.in

Keyword information other than the structure information specified in si.pwin is described.

supercell file

supercell-*.in

Supercell information generated by Phonopy is described in Quantum ESPRESSO input file format.

Since multiple supercell patterns are generated, * is replaced by numbers such as 1, 2, and so on.

tmp file

tmp-*.in

Combines header.in and supercell-*.in.

Cancel button

Close Configure & Run window without doing anything.

6.17.10.2. Edit .conf File¶

Open the conf file with a text editor. Use when you want to edit the keywords set on the Configure window.

6.17.10.3. Run QE for Phonopy¶

Execute Quantum ESPRESSO for all super cells generated in Configure & Run window. Quantum ESPRESSO will run in the local environment.

6.17.10.4. Run Phonopy¶

Executes post processing of Phonopy.

At this time, the following files are created in the working folder :file: si_ph_data .

type Description

sh file

phonopy.sh

Shell script to execute Phonopy post processing

band.yaml file

band.yaml

Information on the band structure calculated by post processing of Phonopy is output.

dos.dat

dos.dat

Information on the density of states calculated by post processing of Phonopy is output.

thermal_properties.yaml file

thermal_properties.yaml

Information on thermodynamic properties calculated by Phonopy post processing is output.

6.17.10.5. Band Structure¶

Displays the band structure based on band.csv included in the working folder.

6.17.10.6. Density od States¶

Displays the density of states based on toal_dos.csv included in the working folder.

6.17.10.7. Thermodynamic properties¶

Displays thermodynamic properties based on thermal_properties.csv included in the working folder.