6.17. ¶
menuIt 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 calculationscf scf scf relax vc-relax md cp scf Use nbndFalse True True False False False False False K_POINTSgamma automatic4 4 4 1 1 1 automatic4 4 4 1 1 1gamma automatic4 4 4 1 1 1gamma gamma gamma tstressFalse False False False False True False False Set ibravand celldmFalse True True False False False False False occupationssmearing ion_dynamicsbfgs bfgs verlet none cell_dynamicsbfgs tprnforFalse False False True True True True True tstressFalse False False False True False False True Use cell_factorFalse False False False True False False False pot_extrapolationsecond_order wfc_extrapolationsecond_order electron_dynamicssd Unit foratomic_positionangstrom angstrom angstrom angstrom angstrom crystal Band structureplotFalse True True False False False False False DOS plotFalse True True False False False False False PDOS plotFalse True False False False False False False Fermi surfaceFalse 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. To use this feature, you need to install a separate version of Quantum ESPRESSO with the ESM-RISM feature enabled.
- 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 filesi.pwout
Calculation log file. bat filesi.bat
It is a batch file for running Quantum ESPRESSO. Working Directorysi_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 isCopied here, the ESPRESSO_PSEUDO environment variableIt 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 ofpw_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.xIt is an input file for execution.ph.out
This is the log file ofph.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 namedaaa_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 isaaa_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 filemg2si_nscf.intrans
BoltzTraP input file. .trace filemg2si_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 filesi.bat
Batch file to execute the preprocessing of Phonopy. sh filesi.sh
Shell script file for executing the preprocessing of Phonopy. si_ph_data foldersi_ph_data
Working directory. The following files are generated in the working directory si_ph_data.
type Description mesh.conf filemesh.conf
Used to calculate density of states and thermodynamic properties in post processing of Phonopy. band.conf fileband.conf
Used when calculating band structure in Phonopy post processing. header fileheader.in
Keyword information other than the structure information specified in si.pwin is described. supercell filesupercell-*.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 filetmp-*.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 filephonopy.sh
Shell script to execute Phonopy post processing band.yaml fileband.yaml
Information on the band structure calculated by post processing of Phonopy is output. dos.datdos.dat
Information on the density of states calculated by post processing of Phonopy is output. thermal_properties.yaml filethermal_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.