About 　 Objectives Advantages Inquiry
Getting Started 　 To create an account To top-up credit To lean more about the service Sample data Tech Blog Webinar Free User Training
Account 　
Work 　 Configuration of the Work page To use Module To connect module Module menu Job submit To start with template Options of the work page
Modules 　 Structure builder Simulation Quantum Espresso QE NEB LAMMPS Phonon(Ph.x) Calphad Analysis Energy Movie Compare Structure Density of States Band Structure Charge Density Curve Fitting Tool Etc Memo Job Loader
Data 　 Move to Data page To read raw data file Find string File Types and Description To Compare Files To download a file
Troubleshooting 　 Quantum Espresso Crash message(QE) LAMMPS Crash message(LAMMPS)
Appendix 　 Tutorial video To prepare a calculation model Quantum Espresso To learn about QE input Functional List LAMMPS To learn LAMMPS input How to cite Calphad Introduction of Calphad Thermodynamics Database User-Defined Exmaples Function Diagram

The Data page lists all calculations and provides the original data files of the calculations.



When you click on one of the jobs from the job list on the Data page, the raw data file list is displayed at the same time the Parent Work information is displayed. For information about the files that appear, see the following File Types and Description :

This job is has been finished normally (id : #### )
A direct connection to the Data page is enabled from the status bar of the Simulation module. The id shown in this area is the job id, which is the unique ID of a job, and you can click on a job id to see its raw data for the calculation right away.



The output of a simulated computation is in the text form by default. If the module does not load the desired data, you can locate the desired data by reading the original data.



'Find string' search box located at the upper-right of the file content is a useful tool. Unlike the ctrl+F, this search box does the same function to grep command in Linux.


File Location File Name Description
input.pw.x The input script of a PWscf (pw.x) calculation.
job.stdout The output file of a PWscf (pw.x) calculation containing all data related to the basic calculation.
job.stdout.pp.x The output file of a Charge Density (pp.x) calculation.
job.stdout.projwfc.x The output file of a DOS (projwfc.x) calculation.
job.stdout.bands.x The output file of a Band Structure (bands.x) output calculation.
*.UPF The pseudopotential file used in calculations.
output/ VLAB.xml The file containing the same data as job.stdout.
output/ VLAB.wfc* The file containing the wave function data. It is a huge-size file and is in an unreadable binary format.
output/VLAB.save/ charge-density.dat The file containing the charge density.
output/VLAB.save/ data-file-schema.xml The file containing the same data as job.stdout.
output/VLAB.save/ paw.txt The file created for PAW pseudopotential.
output/VLAB.save/ wfc*.dat The file containing the wave function data. It is a huge-size file and is in an unreadable format.
vlab/trajectory/ *.dat When you perform calculations with multiple scf steps or molecular dynamics calculations, this file saves the movement of the each atom for the snap shots in the trajectory.
vlab/trajectory/ msd The file containing the msd data.
pp.x/ input.pp.x The input script file of charge density (pp.x) calculations.
pp.x/ ppoutput.* The output script file of charge density (pp.x) calculations.
pp.x/ *.cube The file containing the results corresponding to the plot number selected in charge density (pp.x) calculations.
bands.x/ input.bands.x The input script file of band structure (bands.x) calculations.
bands.x/ bandsx The file containing information on each band.
bands.x/ bandsx.gnu A gnu file for drawing a band structure graph.




The most important file to check is job.stdout. Most of the output information calculated by Quantum Espresso is written to job.stdout. Therefore, checking this file can yield a lot of data, such as checking energy in the middle of a calculation, verifying convergence, estimating the estimated calculation time, and more.


Enter ‘!’ in the Find string search box.
In the PWscf calculation, the one 'total energy' value is created when one SCF algorithm finished. So for SCF calculation, this data can be checked after the calculation ends.


This method can apply for the job with at least 1 iteration finished. Enter 'time' in the Find String search box to display the accumulated calculation time. This information is written at the end of one iteration, and the time takes for each iteration is about the same. So you can use it to estimate the total time.
If the time interval is 30 second and 'Max scf steps' is set to 200 and 'Max iteration steps' is set to 100, the maximum consumption time can be estimated to be 30 * 200 * 100 = 600,000 seconds. In most cases, calculations achieve convergence before reach the max steps of course. This is the maximum time just for the case if the calculation does not achieve convergence until the end.

Whether the structure can achieve convergence easily can be estimated by searching for 'achieve'. By typing 'achieve' in the search box, you can see how many iterations took to converge at each scf step. Convergence for highly symmetrical structures takes place in about 10 iterations. If convergence does not occur within the set maximum iteration step, increase the maximum iteration step value or change the accuracy of the initial structure or calculation.



Generally, variable cell relaxation calculation takes many calculation time. To check the structure data in the middle of calculation, find the information at the job.stdout.
  • Search ‘ATOMIC_’ text at the search box in the browser (ctrl+F).
  • Copy the cell parameter and atomic position information.
  • And paste that to the ‘EDIT’ menu in the structure builder module.



The Band gap can be calculated by checking the job.stdout file even without calculating DOS or Band structure.
Read the occupation information above the last total energy (! total energy), and find the difference between the highest occupied level and the lowest unoccupied level to obtain the band gap. However, the form of information depends on the ‘occupation’ keyword setting, and the information may be not shown according to the ‘information amount’ setting.


Even if 'This has been finished normally' message is displayed in the module, the calculation may not actually have finished normally. Therefore, before checking the result data, check if the following message is at the bottom of 'job.stdout'.

For the reason of this error, please refer to Troubleshooting .

For the reason of this error, please refer to Restart .

If there is no message like ‘Crash’ or ‘Not Achieved’ as above, the job has ended normally.

TemplateFile nameDescription
Common job.stdout The output file of a LAMMPS calculation containing all data related to the LAMMPS calculation.
Common log.lammps The output file of a LAMMPS calculation containing all data related to the LAMMPS calculation.
Common input.lammps The input script of LAMMPS calculation.
Common structure.matsq.lammps The initial structure data of the LAMMPS calculation.
Common #.dat The trajectory file during LAMMPS calculation. The 'Movie' module only works when the trajectory saved in this format.



If you want to compare calculation job files, press the button to register the data you want to compare. In each window, select the file you want to compare, then press the See Difference button to display a comparison pop-up. The difference between the two files is displayed in colored text.



You can download data for further processing of the data. Select All and click on the File download to download the entire file, or select Checked, tick the desired file, and click on the File Download button to download the selected file only. Alternatively, you can copy and paste text from the Data window into another program.





This page has been created by SimPL. Last update: Jun 16, 2020