MatSQ modularized each function to make easy to insert & operate. Modules could be updated or modified for better user experience.

If you want transplant other work’s job or deleted job into certain work page, use Job Loader which can find in the Module selector.
You can search jobs in the job loader module. Select job, then job loader become the simulation module.
Now you can put the job anywhere as you want, even deleted job!

Your electronic structure calculation starts here!
The Visualizer & Manipulator is a powerful and intuitive tool to build, visualize, and manipulate the crystal structure to be investigated.

The simplest way to generate a structure is by uploading a crystal information file.
Click on the striped area or drag and drop from a folder on your PC or click . MatSQ is compatible with a number of structure file formats such as CIF, POSCAR, and xyz.
Alternatively, you can build the structure from scratch directly inside the module. To do so, start by clicking icon. The crystal builder pops up.
Under the Space Group tab, you can define the space group, lattice vectors, and atomic basis of the supercell. In case you just want a simple structure to play around with or test the MatSQ functions, we offer two preset structures – graphene in a hexagonal primitive cell (Graphene (Hex)) and graphene in a rectangular unit cell (Graphene (Rect)).

After uploading or generating a structure, it will show up in the visualizer window.
Use your mouse to zoom or rotate the structure.
Click the right button of the mouse to opens further options:
  • customize the appearance (show/hide cell or atomic bonds, change atom size, and more…)
  • export the structure information in a CIF or VASP/POSCAR format
  • measure distances and angles between selected atoms.

MatSQ offers various tools to further manipulate your crystal structure.
For example, you can add new atoms, move them around, edit the cell dimensions or duplicate the unit cell.
Manipulate can be performed by clicking the icon, The manipulate steps be stacked under the visualizer canvas and can revert.
For further information on Quantum Espresso input variables, see our QE tutorial .

Use the keyboard for easy operation. You can also use the mouse control in Select mode while holding down the 'space' key.
Press the key corresponding to the axis to see the model perpendicular to the axis. Use the arrow keys to move the adsorbent to the position you want.
Key General Select mode
x View YZ plane View YZ plane
y View XZ plane View XZ plane
z View XY plane View XY plane
a View BC plane View BC plane
b View AC plane View AC plane
c View AB plane View AB plane
q Rotate Selected atoms (viewport, left)
e Rotate Selected atoms (viewport, right)
f Filp axis Flip axis
Move Selected atoms (viewport, up)
Move Selected atoms (viewport, down)
Move Selected atoms (viewport, left)
Move Selected atoms (viewport, right)
Space (hold down) Enable mouse control
Ctrl (hold down) Select inverse
Alt (hold down) Deselect selected atoms
Esc Exit select mode

Load from another module by clicking button. If you want to duplicate a model at the structure builder to another structure builder or extract initial and final structure from the simulation module─QE or LAMMPS.
Load structure From your previous jobs. The input & output structures will be added to the structure list.
Load structure from an existing module. The input & output structure will be added to the structure list.
Load structure from a structure file. The file can read is *.cif, *.POSCAR, and *.xyz.
It is similar to the 'crystal builder' but what can be differentiated is this can paste the coordination text. Copy the result coordination directly from the output file!

This module visualizes the charge density of your structure by displaying surfaces of equal density (isosurfaces). First, you need to perform a DFT calculation to determine the charge density of your structure. Use the Quantum Espresso module to do this (scf calculation).
After the computation is complete, add a Charge Density module from the module selector. Now, you will be asked to select the Quantum Espresso module in which you calculated the density. The corresponding density plot will appear.
In the Isovalue field below the graphic, enter the constant density value of the isosurface you’d like to display (in units of electron number per cubic Ångstrøm). Just like in the Visualizer & Manipulator, you have several options to change the appearance and lighting of the charge density plot. Click the right button of the mouse to opens further options.

The simulation module Quantum Espresso (QE) enables you to use the Quantum Espresso software package as a basis for your electronic structure calculations.
If you don’t know what Quantum Espresso is or how the code implements DFT, we recommend reading our short QE tutorial before continuing. MatSQ offers an intuitive graphical interface which makes standard DFT calculations possible with just a few clicks – even without coding skills! In many situations, it is sufficient for good simulation results to tweak only a few important input parameters, such as the energy cutoff or number of k-points, while keeping other parameters at their default values.
The Quantum Espresso module at MatSQ has been developed based on this observation.
The graphical interface includes the main parameters and, in the background, completes the script by assigning default values to the other required variables.
Nonetheless, you can always view and edit the complete script to have full control over the calculation. When selecting the Quantum Espresso module from the Module Selector, a pop-up window will ask you to “select visualizer to get initial structure of QE calculation.” This ensures that the simulator refers to the right atomic structure, especially when your work contains several visualizer modules with different structures

Solver be selected according to the kind of data you want to. pw.x is for energy-based data calculation. pw.x had selected as default. pw.x description can see Appendix and QE description . For another solver description, see here .

You can select Template, General, Manual options. Template is the option for beginner. You should select calculation type, precision, whether model need optimization. After selection, the quantum espresso input script be created automatically, can see in the text-area. In General option, you can modify the parameters. Most parameters is affect calculation time. Use in caution. A more detailed description can be found at Appendix . For further information on Quantum Espresso input variables, see our documentation as well as the Quantum Espresso documentation You can modify by text typing in the text area. Manual option selected automatically if you modify script in the text area manually.

Once you’ve specified the calculation type and input parameters, you are ready to submit the job. Before you click the button, insert a meaningful name in the field Job Name. Additionally, in the Resource field, you can choose between an on-demand resource or a dedicated server (only available for Maxflops users; see “Maxflops” section.) and set the number of servers to be used for the job. One resource is the default but parallel computing on multiple nodes is possible. Finally, under Finish Notice, check the boxes E-mail in case you would like to be notified via email as soon as your job has been finished.

Add analysis module from button below your simulation module or the module selector which can find under the page. In module selector, icon means the module is for result data analysis. MatSQ supporting Energy, DOS, Charge density, Movie, and other data processing modules. Please read the following sections for more information. If you want the raw-data file, see "Data" section.

You should re-calculation which has interrupted job. The interrupted job is the following cases,
  • QE module have a message “This job is not converged”
  • QE module have a message “This job is normally finished" but its scf step is when reached the max scf step you set.
  • The job stopped manually by button in the dashboard
You can restart the abnormally finished job by adding ’restart’ keyword at the original input script. In this case, Instead of performing a duplicated calculation, add new QE module and connect to the abnormally finished QE module. Then the original input script will duplicate and the ‘restart’ keyword will be added automatically. You should conserve the input parameters to the original one, but you can adjust the number of steps and k-point. Click to run the restart job. The restart job will consume time & credits less than the original calculation because this is additional calculation start from the last step.

MatSQ offers Molecular Dynamics simulation with Reactive ForceField & LAMMPS. The simulation module LAMMPS enables you to use the LAMMPS software package for your molecular dynamics simulation.
You can perform MD simulation through intuitive graphical interface with just a few clicks! MatSQ listed reliable ForceField. Just select FF, Ensemble, Temperature, Time for your MD simulation.
If you want more complicate control, select button. Set the value according to the axis.
Once you’ve specified the calculation type and input parameters, you are ready to submit the job. Before you click the button, insert a meaningful name in the field Job Name.
Additionally, in the Resource field, you can choose between an on-demand resource or a dedicated server (only available for Maxflops users; see “Maxflops” section .) and set the number of servers to be used for the job.
One resource is the default but parallel computing on multiple nodes is possible.
Finally, under Finish Notice, check the boxes E-mail in case you would like to be notified via email as soon as your job has been finished.
After the job finished, add movie module to analysis the MD simulation results.

The NEB result module enables you can see the NEB results which contain the transition to images, Activation energy graph.
The images are added in the Structure list , and can play like animation by clicking to play button ▶.
During playing image transition animation, The data points in the activation energy graph become highlighted and bigger. You can see the structure and energy of image Intuitively.
If you want to know how does nudged-elastic bands (NEB) calculation, see here .

The Energy module is a basic analysis tool. One calculation consists of scf steps which consist of a set of iteration step. The energy module plots the total energy values found during an iterative self-consistent calculation and plots the change of energy of each scf step. For more detailed explanation of self-consistent calculation, see QE tutorial .
Before using this analyzer, run a Quantum Espresso electronic structure calculation in the respective simulator.
Once the job has been successfully completed, select Energy (QE) in the module selector.
You will be asked to choose the appropriate calculation in the work – just click on the simulator module which calculated the energies you'd now like to plot. A graph shows up.
The vertical axis displays the total energy in Rydberg (Ry) or electron volts (eV) while the horizontal axis gives the scf step.
In the fields below the plot, you can see the final total energy and switch between energy units. For scf or relax calculations where only the electrons move, the graph displays the electronic energy convergence.
In the case of structural optimization, where the atoms are moved slightly to determine the global energy minimum, you will see the energies of the scf step.
This is a great way to check the convergence of the atomic relaxation process. Sometimes you may see the scf step was reached the max scf step you set with displayed ‘The job is normally finished’ message at the QE module. This case has the probability of abnormal finish. But you don’t need to calculate again. See 'Restart Job' section.

Compare energies using this ‘compare energy’ module. Add your previous DFT calculation module to make a comparison of various results.
Click to add a data point. You can modify data order and point color by doing drag & drop in legend.
You can download the created graph in png, jpeg, pdf, SVG vector image file at the menu.

Density of state graph describes the number of states which have certain eigenvalue. DOS graph plotted by Energy (eV) versus The number of states (arbitrary units). In DOS graph, you can see PDOS of each orbital, each atom, and total DOS by doing on/off checkbox in the table.
For example, want to see which one is representing surface state, Add PDOS by selecting only you want chemical species. Now you can see which orbital of what atom corresponding to this state. See the graph in detail by mouse drag. You can set the name and the color of the graph. There are two method adding DOS module, first is click button below the calculated simulation module, and the second is selecting DOS (QE) module in the module selector.
DOS can combine with band structure diagram. The x axis of DOS graph can combine with the y axis of band diagram. The band gap of two graphs will be same.

Charge difference module draws Charge difference of selected two structures. Click ‘ρA’ and ‘ρB‘ next the ‘Select ρ’. And select charge density module to connect with charge difference module.
Select Structure A or B and isovalue and units and click apply. Isovalue should be inside ρ(max) and ρ(min) range displayed under the visualizer canvas. Then you can see the charge difference.

Movie module visualizes the result of MD simulation as a shape of animation.
MD simulation (molecular dynamics simulation) from LAMMPS, AIMD (ab initio molecular dynamics) simulation from Quantum Espresso now supporting.
See the Energy module together to see how atoms move according to the energy.
You can see RDF change according to MD step progress by Connecting the RDF module to movie module. Click ▶ button in the movie module, then you can see RDF changing. More information see [A] RDF .
You can modify time interval and step interval in this icon . Time interval directly proportional with playback speed, however, step interval inversely proportional.

The MSD module is displaying the displacement deviation of selected atoms during MD simulation.
Select atoms in visualizer and Click to make Mean Squared Displacement graph.
Click Data download button at the table to download raw-data in .csv.

You can see the Radial Distribution Function of your structure by connecting this module to Movie module or Visualizer module.
Click to open options window. You can modify cutoff, the max value of y-axis, element type you want to see.
Check ‘LIVE’ checkbox to see RDF in shape of animation. After check at the LIVE checkbox and click ‘Update RDF’ and play Movie or click the play button in the structure list of the visualizer, then the RDF plot change according to the structure change.
If you check at the ‘Range’ checkbox, the select mode will activate at the movie canvas or visualizer canvas. Select atom range you want to see RDF. The RDF displayed only for the atoms in the range.

When conducting structural optimizations, it is helpful to compare the initial and final structures to see what changed in the relaxation process.
The Compare Structure module lets you do exactly this. Add the module to your work from the module selector. Your work should also contain a relax calculation (atoms and electrons).
It consists of two structure visualization windows and a data table below.
‘Sync’ checkbox checked default to see synchronized moving. If you put on cursor on table, the atom be displayed blue. In table, The displacement of atoms listed in cartesian (Å).

This module is for drawing band structure from band structure calculation. To know how calculate band structure, see the Tutorial video .
The k-path label automatically set by adjusting the similarity of high-symmteric point of structure and crystal system point set be maximum. It can change in the select box at left bottom. You can change the Energy unit also.
DOS is inserted beside Band structure. This DOS graph is the data of calculated original scf module of band calculation. It can change. The x-axis of the DOS graph and The y-axis of band structure can combine.
Zoom in using Mouse control. You can see magnify the part of the band gap.
Click mouse right button to see the options window. Click ‘Point’ to display data points which used for drawing band line. Point out data points to see the energy value on that k-point.

This module is for drawing projected band structure (or fatband) from band structure calculation. This module is similar to band structure, but contain more information which projected wavefunction onto atomic wavefunctions like DOS. Select atoms and add to see the projected band structure & pDOS.
The added data will be displayed the shape of colored circle. The radius of the circle is determined the sum of the contribution of the selected orbitals in that point. The contribution means the orbital distribution of eigenvalue in that point.
The color of the circle is that average of selected orbital color which have same angular momentum quantum number. you can modify it. If a data point has several data which have different angular momentum quantum number displayed, the contribution of each orbital can recognize by color gradation. If you want to see each orbital contribution by circle radius, add in isolation.

Add this module to your work to record important information about the project.
This could help you to remember details or serve as an activity log to keep track of every step, especially when you’re working with others.
Memo module works independently but can use connected with other modules by clicking ‘Connect module’ icon.
Record your useful information efficiently using this module!

This page has been created by SimPL. Last update: January 4 2019