6.16. 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.

6.16.1. Workflow Setup

Set up and run the Quantum ESPRESSO calculation flow in project mode.

Preset
Import and saves a preset of settings.

# of Jobs
Specify the number of jobs.

Enable scan calculation
This feature requires the purchase of an add-on. It allows you to run multiple calculations where only certain parameters differ (parameter scan) or to run calculations with the same parameters for multiple structures (structure scan).

Click Config to open the configuration window for the scan calculation. For parameter scans, select %WM_SCAN1% for the Target Variable and enter the parameters you wish to set for %WM_SCAN1% in each row of the Values. Then, enter %WM_SCAN1% in the parameters you want to set in the Workflow Settings window or Keyword Settings window. For structure scan, select %WM_STRUCT% for Target Variable when the animation appears in the molecule display area (e.g., by opening an SDF file).

After the scan calculation is finished, use File ‣ Project ‣ Scan Results to tabulate the calculation results.

Import
Import the settings output by Export. Click the arrow at the right of the button to recall settings used in the past on the same project or Winmostar.

Export
Output settings to file.

OK
Run a calculation or generate a file with your settings.

Details
Set detailed calculation conditions. The Configure will be launched.

Task
Select the type of calculation.

Setting details

Energy

calculation=scf

ion_dynamics=none

cell_dynamics=none

tprnfor=False

tstress=False

nosym=False

nstep=50

Use cell_factor=False

electron_dynamics=none

pot_extrapolation=none

wfc_extrapolation=none

Unit for atomic position=angstrom

NSCF

calculation=nscf

ion_dynamics=none

cell_dynamics=none

tprnfor=False

tstress=False

nosym=False

nstep=50

Use cell_factor=False

electron_dynamics=none

pot_extrapolation=none

wfc_extrapolation=none

Unit for atomic position=angstrom

Optimize(Atom)

calculation=relax

ion_dynamics=bfgs

cell_dynamics=none

tprnfor=True

tstress=False

nosym=False

nstep=50

Use cell_factor=False

electron_dynamics=none

pot_extrapolation=none

wfc_extrapolation=none

Unit for atomic position=angstrom

Optimize(Atom&Cell)

calculation=vc-relax

ion_dynamics=bfgs

cell_dynamics=bfgs

tprnfor=True

tstress=True

nosym=False

nstep=50

Use cell_factor=True

electron_dynamics=none

pot_extrapolation=none

wfc_extrapolation=none

Unit for atomic position=angstrom

Damp(Atom)

calculation=relax

ion_dynamics=none

cell_dynamics=none

tprnfor=True

tstress=False

nosym=False

nstep=50

Use cell_factor=False

electron_dynamics=none

pot_extrapolation=none

wfc_extrapolation=none

Unit for atomic position=angstrom

Damp(Atom&Cell)

calculation=vc-relax

ion_dynamics=damp

cell_dynamics=damp-w

tprnfor=True

tstress=True

nosym=False

nstep=50

Use cell_factor=True

electron_dynamics=none

pot_extrapolation=none

wfc_extrapolation=none

Unit for atomic position=angstrom

DFPT(Gamma)

calculation=nscf

ion_dynamics=none

cell_dynamics=none

tprnfor=False

tstress=False

nosym=False

nstep=50

Use cell_factor=False

electron_dynamics=none

pot_extrapolation=none

wfc_extrapolation=none

Unit for atomic position=angstrom

DFPT(Dispersion)

calculation=nscf

ion_dynamics=none

cell_dynamics=none

tprnfor=False

tstress=False

nosym=False

nstep=50

Use cell_factor=False

electron_dynamics=none

pot_extrapolation=none

wfc_extrapolation=none

Unit for atomic position=angstrom

BOMD

calculation=md

ion_dynamics=verlet

cell_dynamics=none

tprnfor=True

tstress=False

nosym=True

nstep=50

Use cell_factor=False

electron_dynamics=none

pot_extrapolation=second_order

wfc_extrapolation=second_order

Unit for atomic position=angstrom

BOMD(Atom&Cell)

calculation=vc-md

ion_dynamics=beeman

cell_dynamics=pr

tprnfor=True

tstress=False

nosym=True

nstep=50

Use cell_factor=False

electron_dynamics=none

pot_extrapolation=second_order

wfc_extrapolation=second_order

Unit for atomic position=angstrom

Phonopy

calculation=scf

ion_dynamics=none

cell_dynamics=none

tprnfor=True

tstress=True

nosym=False

nstep=50

Use cell_factor=False

electron_dynamics=none

pot_extrapolation=none

wfc_extrapolation=none

Unit for atomic position=crystal

Charge
Specifies the charge for the entire system.

# of bands
Specify the number of bands.

Spin
Set up spin polarization calculation.

Setting details

Non-polarized

nspin=1

Polarized

nspin=2

Use Spin Density as=True

Polarized(Manual)

nspin=2

Use Spin Density as=False

Cutoff energy
Sets the cutoff energy (ecutwfc) of the wave function.

Manually specify cutoff energy
If not checked, Cutoff energy is automatically specified from Precision.

K points
Specify how to calculate K points.

Pressure
Specify pressure.

Phonon(DFPT)
Set up phonon calculations using DFPT(ph.x).

Setting details

Disabled

Run phonon=False

epsil=False

lraman=False

asr=no

ldisp=False

Gamma

Run phonon=True

epsil=True

lraman=True

asr=crystal

ldisp=False

Dispersion

Run phonon=True

epsil=False

lraman=False

asr=crystal

ldisp=True

Use Bravais-lattice index
If checked, input file will be created with other than ibrav=0. Check this box because it is necessary to set special points from ibrav when calculating band structure and phonon bands.

Pseudopotential
Specify a pseudopotential file. changing Type will narrow down the Functional and Pseudo files. changing Functional will narrow down the Pseudo files. Changing Functional will narrow down the Pseudo files. See Pseudopotential in Configure for instructions if the desired choice does not appear.

Properties
Calculate properties checked to match when calculating.

Precision
Set calculation precision.

Setting details

Extra-low

conv_thr=1d-5

etot_conv_thr=1d-3

forc_conv_thr=1d-2

press_conv_thr=1.0

degauss=0.02

tr2_ph=1d-10

Spacing=0.44(metal) 0.63(nonmetal)

ecutwfc=30(metal) 25(nonmetal)

Low

conv_thr=1e-6

etot_conv_thr=1d-4

forc_conv_thr=1d-3

press_conv_thr=0.5

degauss=0.02

tr2_ph=1e-11

Spacing=0.44(metal) 0.63(nonmetal)

ecutwfc=40(metal) 30(nonmetal)

Medium

conv_thr=2d-7

etot_conv_thr=4d-5

forc_conv_thr=5d-4

press_conv_thr=0.25

degauss=0.02

tr2_ph=1e-12

Spacing=0.31(metal) 0.50(nonmetal)

ecutwfc=50(metal) 35(nonmetal)

High

conv_thr=1d-7

etot_conv_thr=2d-5

forc_conv_thr=3d-4

press_conv_thr=0.125

degauss=0.02

tr2_ph=1e-14

Spacing=0.25(metal) 0.44(nonmetal)

ecutwfc=55(metal) 40(nonmetal)

Extra-high

conv_thr=5d-8

etot_conv_thr=1d-5

forc_conv_thr=1d-4

press_conv_thr=0.05

degauss=0.01

tr2_ph=1e-16

Spacing=0.08(metal) 0.11(nonmetal)

ecutwfc=60(metal) 50(nonmetal)

Metal
Enable smearing. (occupations=smearing) Also adjusts the contents of Precision (above).

6.16.2. 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.

# of bands
The selection in parentheses displays the number of valence electrons when pseudopotentials are used. If the valence number fails to calculate automatically, it is displayed as N/A.

Do not specify
nbnd is set automatically.

Specify nbnd
Explicitly specify the number of bands.

Specify nbnd(Relative)
Specified relative to the number of valence bands.

Use nbnd
Specify the number of bands. If not checked, it will be set automatically.

K_POINTS
Choose how to specify the K point from the pull-down and specify the K point in the QE format in the text box below.

gamma
Calculated at the $\Gamma$ point only.

automatic
Use Monkhorst-Pack method. Enter “(number of divisions in kx direction) (number of divisions in ky direction) (number of divisions in kz direction) (shift flag in kx direction) (shift flag in ky direction) (shift flag in kz direction)” (separated by spaces). The shift flag is 0 for no shift (k points contain $\Gamma$ points) and 1 for shift (k points cross $\Gamma$ points).

automatic(by spacing)
Use Monkhorst-Pack method. The number of divisions in each direction is set by the Spacing parameter ( Spacing parameter ).

automatic(by spacing,slab)
Use Monkhorst-Pack method. The number of divisions in each direction is set by the Spacing parameter ( Spacing parameter ). However, the number of vertical slab divisions detected automatically is set to 1.

Others
Please refer to the pw.x manual or doc/brillouin_zones.pdf under the QE installation folder for details.

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.

Ecut for US/PAW
Sets how ecutrho is specified when selecting an Ultrasoft or PAW pseudopotential file.

Specify ecutrho/ecutwfc
Set ecutrho from the ratio of ecutrho to ecutwfc and the value of ecutwfc.

Specify ecutrho
Directly set the value of ecutrho.

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.

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.

nqx1/2/3
Specifies the number of k-point sampling when calculating the Fock operator. If Default, use the same value as K_POINTS.

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 up spin polarization calculation.

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

starting_magnetization
Gives the initial value of the magnetization of each atom species. Use “Use Spin Density as starting_magnetization” if you want to calculate antiferromagnets, since in this case all atoms of the same element have the same value.

noncolin
Specify whether non-colinear calculations are performed.

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

Use Spin Density as starting_magnetization
Use the value of Spin Density set in the main window as-is as starting_magnetization. If checked, the above starting_magnetization is ignored. Use this feature when atoms of the same element have different starting_magnetization, such as in antiferromagnets.

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 folder.

tr2_ph
Specify the censored error of phonon calculation.

alpha_mix(1)
Specify mixing factor.

epsil=.True.
Calculate the dielectric constant obtained from phonon calculation.

lraman=.True.
Include calculation of Raman spectrum.

asr(for dynmat)
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.

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

nq1,nq2,nq3
Specify the number of K points when computing phonon variance.

Use spacing
Use Monkhorst-Pack method. The number of divisions in each direction is set by the Spacing parameter ( Spacing parameter ).

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.

esm_w
Sets the offset for the location where the ESM will be placed.

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.

Preview tab
A preview of the configuration keywords will be displayed.

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.

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.

Pseudopotential 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.

Pseudopotential
Select a pseudopotential file from among those that are common to all elements in the system.

(Type)
Select the type of pseudopotential.

(Functional)
Selects the type of functionality. Choose from the choices narrowed down by (Type).

(File)
Select a pseudopotential file. Choose from the choices narrowed down by (Type) and (Functional). If you choose (Manual), the user sets the pseudopotential individually for each element in the list below.

Pseudopotential files are searched in the folder specified in the pseudo Directory. Preference is given to the first entry in qe_pseudo_priority_list.txt in the user configuration folder.

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.

Reset
Reset settings.

Import
Loading configuration file.

Export
Output configuration file.

6.16.2.1. Spacing parameter

The Spacing parameter is used to determine the number of k-point divisions $N$ in each direction, independent of the system size.

$N = \mathrm{max}(1, |\vec{b}_i| / \mathrm{Spacing})$

$\vec{b}_i$ (where $i$ is the index for each direction $0,1,2$ ) is the reciprocal lattice vector $\vec{a}_i \vec{b}_i = 2 \pi \delta_{ij}$ for the lattice vector (basic translation vector) $\vec{a}_i$ .

6.16.3. 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 folder 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 folder then.

If the case of Output Directory = Select, use the selected folder as the working folder (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 Folder

si_qe_data\

Working folder.

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

type

Description

Pseudopotential file

*.UPF

The pseudopotential files used in the calculations are copied here and the ESPRESSO_PSEUDO environment variable is set in the working folder.

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

Input file for running phonon calculations with ph.x in post-processing.

ph.out

This is the log file of ph.in.

Hint

** Working folder **

A working folder 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 folder 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 folder 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 folder is aaa_gmx_tmp, it is aaa_gmx_tmp1.

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

Job is run through Winmostar Job Manager.

6.16.4. Open Log File (pwout)

Open the log file with a text editor.

6.16.5. Show Extracted Log

Excerpts of key information from the log file are displayed.

6.16.6. Animation

6.16.6.1. 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 display area. From the animation display area, you can calculate the radial distribution function, self-diffusion coefficient, mean-square displacement, and displacement of each atom.

6.16.6.2. 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 display area. From the animation display area, you can calculate the radial distribution function, self-diffusion coefficient, mean-square displacement, and displacement of each atom.

6.16.7. Energy Plot

6.16.7.1. SCF Energy Change (pwout)

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

For CPMD use CPMD Energy Plot (evp).

Property
Select the values to be displayed in the graph.

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.

6.16.7.2. 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.

6.16.8. Analyses

6.16.8.1. Density od States

Specify the working folder (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 runs 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.

6.16.8.2. Projected DOS

Specify the working folder (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 runs 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.

6.16.8.3. Band Structure

Specify the working folder (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 runs 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.

6.16.8.4. Lowdin Charge

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

Projwfc.x runs in the background.

6.16.8.5. Electron Density

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

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

Refer to Surface Setup window for how to operate subwindow.

6.16.8.6. Spin Density

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

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

Refer to Surface Setup window for how to operate subwindow.

6.16.8.7. Potential Energy Distribution

Specify the working folder (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.

6.16.8.8. 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.

6.16.8.9. Dielectric Function

Specify the working folder 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.

6.16.8.10. IR/Raman

Specify the working folder 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.

6.16.8.11. Phonon Band Structure

Phonon Specifies the working folder 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.

6.16.8.12. Phonon Density of States

Phonon Specifies the working folder 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.

6.16.8.13. 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.

6.16.8.14. 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.

6.16.8.15. 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.

6.16.8.16. 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.

6.16.8.17. 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.

6.16.9. 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.

6.16.10. Nudged Elastic Band

6.16.10.1. Workflow Setup/Keyword Setup

Set up and run the conditions for the NEB calculation; use neb.x to run the NEB.

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

6.16.10.2. NEB error change

Displays errors in each iteration of the NEB calculation.

6.16.10.3. Animation

Specify the output file of the NEB calculation and display the changes in energy and atomic structure along the reaction coordinates after the NEB calculation convergence. If you want to see the energy change at each iteration of the NEB calculation continuously, use Energy Plot.

For the animation display operation method, see Animation display area.

6.16.10.4. Energy Plot

Specify the output file of the NEB calculation and display the change in energy along the reaction coordinates. You can visualize the appearance at each iteration of the NEB calculation. Use Animation if you want to visualize the atomic structure.

6.16.11. BoltzTraP

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

6.16.11.1. 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 folder 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, compute expansion coefficients (CALC). If not checked, read expansion coefficients from file (NOCALC).

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 folder (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.

6.16.11.2. 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.

6.16.12. Phonopy

Calculations using Phonopy are performed in the following three steps.

Create a supercell based on a given crystal structure (project mode) or Quantum ESPRESSO input file (file mode).

Execute Quantum ESPRESSO for all generated super cells.

Create a ForceSets file from the Quantum ESPRESSO output file to calculate Phonon bands, DOS, thermophysical properties, etc.

6.16.12.1. Create a supercell

Generate a supercell for the Phonopy calculation for the crystal structure displayed in the molecule display area in the “Project” mode. Depending on the type of crystal, multiple structures may be generated. To run Quantum ESPRESSO calculations on these structures, use Workflow Setup with Enable scan calculation.

6.16.12.2. Configure & Run

In file mode, set the calculation conditions for pre- and post-processing using Phonopy and execute the 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 folder.

The following files are generated in the working folder 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.

6.16.12.3. Edit .conf File

In file mode, opens the conf file in a text editor. Use this if you want to edit the keywords set in the keyword configuration screen.

6.16.12.4. Quantum ESPRESSO Continuous Execution

In File mode, Quantum ESPRESSO is executed on all super cells generated in the Keyword Setup and Execution screen. If you use this menu, Quantum ESPRESSO will run in the local environment.

6.16.12.5. Run Phonopy

Performs Phonopy post-processing in file mode.

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.

6.16.12.6. Band Structure

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

6.16.12.7. Density od States

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

6.16.12.8. Thermodynamic properties

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