MatSQ has modularized each function, making it easy to add and modify functions.


Structure Builder is a powerful, intuitive module that allows you to create, visualize, and manipulate DFT/MD simulation models such as crystal structures, molecules, and monomers.
Structure Builder consists of the visualizer menu that displays the structure and the manipulator menu for manipulating structures.



The simplest way to create a simulation model is to upload a structure file.
Drag and drop a file to Visualizer or click on the icon to upload a file. MatSQ currently supports CIF, VASP (POSCAR), and XYZ file formats. Alternatively, you can add structures using the Modelling tab menu.


Modeling

It gets a structure data from the previously performed simulation jobs. Click on Init/Final to add the initial/final structure to the Structure list.
It loads a structure data from the module that currently exists on the work page and adds it to the structure list. Furthermore, it can only load from the modules that contain structure data, such as Quantum Espresso, Structure Builder, and others.
It loads a structure from the structure file and adds it to Visualizer. It also supports CIF, VASP (POSCAR), and XYZ file formats.
It creates a crystal structure by entering a space group, cell parameters, angles, and fractional coordinates.
We have pre-added structures that are used frequently. You can add graphene unit cells and Silicon bulk unit cells.
You can create a structure by entering coordinates directly, or you can modify a structure by modifying the coordinates. You can also copy and paste text containing structure information.



You can use several functions by manipulating the mouse on the structure canvas. Moreover, you can use the mouse wheel to zoom in/out or drag to rotate the time point. Right-click to use the following functions:

Display

Background Selects a background color for the Visualizer canvas
Perspective Adjusts perspective
Atom Adjusts the atom size
Bond Adjusts the bond thickness
Shift Shifts atoms to identify structures; does not change the actual coordinate information
Cell Determines whether the cell line should be displayed
Cell Info Determines whether the cell information should be displayed
Axis Determines whether the axis arrow should be displayed
Select Info Determines whether the information should be displayed when an atom is selected
Ghost Display unit cell repeatedly. Even there are only a few atoms, the program accepts them as an infinitely repeating structure.
Light Sets the angle and intensity of the light emitted to structures


Select

Select Turns the selection mode on or off; can operates viewpoint using the mouse if you press and hold the Space in the Select mode
Mode Specifies the shape of the area will select
Mode
Selecting area Selected atoms Element Rectangular Hexagon Circle Lasso Sphere
Method Determines options that will be added to the selection when another atom is selected after the selection
Method
Selecting area Normal A ∪ B A c A ∩ B (A ∪ B)-(A ∩ B) A-B


Tool

Download Downloads the structure currently present in the visualizer canvas in the selected file format
Distance Selects two atoms to find out the distance
Angle (Vectors) Selects three atoms to find out the angle
Angle (Planes) Selects four atoms to find out the angle of the plane
Space Group Calculates the space group of the structure; takes longer time for a large structure as it involves a large amount of computation



MatSQ provides a variety of tools to manipulate the atomic structure. You can also use the Manipulator menu to add or move atoms, resize cells, or clone unit cells to create supercells. Up to 10 Manipulate details are stored in the history at the bottom of the visualizer canvas and can be retrieved by clicking.
The ? button is used to check additional information for the use of the chosen function.


cell

Compresses or expands a structure by applying a strain based on the origin
Clones a structure using an even multiplication factor
Adds a free space that is recognized as a vacuum
To make a surface, you must give at least 10 Å of vacuum on one axis.
Cleaves the crystal according to the Miller index (cleavage)
Merges two structures out of the structure list


Atoms

Adds an atom to a structure
If you are not just adding an atom, you must use the Add Molecule menu. You can add molecules or specific structures, or you can fill with the Fill function.
(Move) Moves the selected atom
(Flip) Flips the selected atom symmetrically to create a mirror-image structure
(Inside) If there is an atom outside the cell, the Inside function brings the atom inside, taking account of the periodicity.
Rotates the selected atom
Replaces the selected atom with another element


Extension

Creates a NEB (Nudged elastic band simulation) image; includes the initial and final images in the image count
For high throughput calculations, the function creates combinatorially generated structures by replacing the selected atom with another element and add to Structure list. (The number of Elements The number of selected atoms ) Watch out for memory deficiency.


The Keyboard Shortcut key is available in Structure Builder. The Keyboard makes it simple to operate.
Function Key View mode Select mode
Select Space (hold down) Enable mouse control
Ctrl Change Select method in Select mode
Esc Exit select mode
Move Move Selected atoms (viewport, up)
Move Selected atoms (viewport, down)
Move Selected atoms (viewport, left)
Move Selected atoms (viewport, right)
Rotate 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 around the viewport y axis (left) Rotate around the viewport y axis (left)
e Rotate around the viewport y axis (right) Rotate around the viewport y axis (right)
[ Rotate around the viewport z axis (left) Rotate around the viewport z axis (left)
] Rotate around the viewport z axis (right) Rotate around the viewport z axis (right)
{ Rotate around the viewport x axis (forward) Rotate around the viewport x axis (forward)
} Rotate around the viewport x axis (backward) Rotate around the viewport x axis (backward)
f Filp axis Flip axis
Group Shift + Numeric keys (0~9) Grouping selected atoms to group #n (until refresh)
Numetic keys (0~9) Loading selection of the group #n Loading selection of the group #n (until refresh)


The simulation module, Quantum Espresso (QE), is intended to perform electronic structure calculations using Quantum Espresso, an open-source DFT calculation software package. MatSQ provides an intuitive graphical interface (GUI) that makes it easy to perform DFT calculations with just a few clicks without studying complex codes. Most calculations can achieve good results by simply changing major keywords, such as cutoff energy and k-point, in the basic preset parameters. Moreover, MatSQ provides the manual mode for modifying scripts directly for experienced users.
For more information about Quantum Espresso, go to the appendix or www.quantum-espresso.org .




Solvers are major calculation programs used in Quantum Espresso package. Each Solver has a specific role, and can be divided into PWscf (pw.x) for scf calculations and post-processing solvers. PWscf is the most basic tab for obtaining all data. It performs self-consistent calculations on electronic structural properties using the Plane-Wave (PW) basis set and pseudopotentials (PP, psp). SCF calculations must be performed to obtain DFT simulation data, so the QE modules are configured around PWscf.
Performing post-processing calculations is simple. Add a QE module, and in ① Solver region, click on a solver (DOS, Charge density, ...) that is suitable for obtaining the desired data, then press the + button to add a new solver tab next to the PWscf calculation. Add as many post-processing solvers as you want, and press the Start Job! button to run all calculations that have been added upon QE module. On QE modules that have already finished PWscf calculations, you can add a post-processing solver, and press the Start Job! to obtain additional post-processing data.
Information about input script settings for each solver can be found in the Appendix or ④ Keyword Information.



Press the Scripting Option to view Template, General, and Manual options. Template is a good option for those who are not familiar with the keyword settings in Quantum Espresso. In Template, you answer to several questions to set the input script.
  • Data to get : Select what data you want to get. A Solver is added according to match the answer.
  • Precision : It sets the precision level of calculations.
  • Model type : This question is added when you select “High precision” to the previous question. Select the classification of the Simulation model. Determine the k-point format.
  • Structure optimization : This is the question that determines the calculation type. If you select “Fully optimized,” it sets the calculation type to “scf” and does not change the initial structure during the calculation process. If you select “Need optimization / Need ionic+cell optimization,” it slightly changes the atomic position / atomic position + cell size and locates the “global minimum” in the potential surface to perform structure/cell optimization.
  • Correction : It decides which calibration to add. Spin polarization and Van der Waals correction are currently available.


Quantum Espresso modules get structural information from the connected Structure Builder. When the Structure Builder changes, the changed structural information is also updated on the QE module. If you do not want to update the structural information of the QE module anymore, untick this checkbox.


Each solver has a different set of input parameters. For more information, click on ? Keyword information to connect to the following URL:

MatSQ makes it easy to perform DFT calculations with just a few clicks. Input parameters, which are set by default in the Quantum Espresso module, are roughly set with typical values. Most calculations can achieve good results simply by changing major keywords such as cutoff energy and k-point. However, the values should be carefully considered and selected based on an understanding of each input parameter to perform reliable DFT simulations for advanced use such as research and papers.
For more information, refer to the appendix or ④ Keyword Information.



An input script is created when the QE module is connected to Structure Builder, and input parameters are set. The input script is a text that has structure information and keyword setting information sent to the physical server. Therefore, it is recommended that you always ensure the values you set are correctly applied. When you change the option to Manual in ② Scripting Option, the ⑤ Input Parameters section is omitted, and only the Input Script window remains to allow you to modify the script manually. When you modify text in the Input Script window, the mode automatically changes to Manual.


Pseudopotentials are used to determine the behavior of the corresponding elements when using Quantum Espresso to perform DFT calculations. Click on the magnifying glass icon on the Pseudopotential tab to view the list of available pseudopotentials. If the list does not contain the file you want, see the following document To add custom pseudopotentials .


If you have completed all the settings under ① to ⑦, you are ready to submit your job. Enter the job name in the Job Name window before clicking on the Start Job! button. Use a name that is distinguished from other jobs to avoid confusion between one and other calculations.
Resource allows you to adjust the type of server and parallel computing options. The server type can be selected from On-Demand or MAXFlops (MAXFlops is only available to MAXFlops users. Refer to the Maxflops documentation). The parallel computing option next to the server selection refers to the number of cores. Up to 36 cores are available in a single node.
Tick in the Finish Notice checkbox if you want to be notified via email after the job completion.
Click on the Start Job! button and click on the ▶ icon on the top bar to open the dashboard to see the progress of the operation, as shown in the following illustration.



If you connect a new QE module to the QE module that has finished the calculation, you can proceed with further calculations with “restart.” Recalculating through “restart” can save computing resources rather than restarting a new calculation, especially if you want to resumea calculation that has been interrupted during calculation. It is recommended that you apply this function in the following cases:
  • When the “This job is not converged” message is displayed;
  • When the “This job is normally finished” message appears but the “max scf step” set by “scf step” is reached (in case of (vc-)relax);
  • When you ended a job in the Dashboard in the middle of a calculation by pressing the button;
  • When you want to increase the k-point for DOS calculations; or
  • When you want to set the k-point to the high-symmetric point path for band structure calculations.
Under the cases 1 to 3, an additional PWscf (pw.x) calculation resumes from the last step of the PWscf (pw.x) calculation. When you connect a new QE module to an existing QE module, the input parameters of the existing QE module are copied to the new QE module. Case 1 refers to the failure of convergence during iteration (the optimization of electron structures). Thus, it is recommended to calculate by increasing the max electron steps. Case 2 is highly likely that convergence has failed to complete until the max steps have been reached in the scf phase (the optimization of the atom position) although it has succeeded in the iteration phase. Thus, it is recommended to increase the max steps for calculations. However, it is not recommended to restart until you see the normal finished message. If convergence has not been achieved during hundreds of steps by performing restart, it is recommended that you start a new calculation by changing the initial structure, or start a new calculation with a set of input parameters with lower accuracy and increase accuracy gradually.
Cases 4 and 5 are to restart calculations by rearranging the k-point used in the finished PWscf (pw.x) calculation. In Case 4, change the calculation type to nscf and set the k-point grid to more dense. As the nscf calculation means a non-self-consistent field calculation and only changes the k-point sampling density, it saves computing resources when compared with the dense k-point setting in scf (relax) calculations. In Case 5, change the calculation type to bands, and set the k-point as desired. It is recommended that you select crystal (_b) as the k-point option to sampling the high-symmetric point to get a good band structure. However, restarting a job calculated with the GAMMA option with the automatic option is not supported.


The QE NEB module is a module for calculating Nudged Elastic Band (NEB) calculation by the neb.x solver provided by Quantum Espresso.
In order to perform NEB calculations, you must add the initial, final images (if necessary, up to the intermediate image) to the structure list in the Structure Builder connected to the QE NEB module. In order to perform a better calculation, all the images should be optimized (relaxed).
See the QE Input description for a detailed explanation of the NEB input script settings.






Unlike Quantum Espresso module, you can select just General and Manual mode in the QE NEB module.


It is a tool for fixing some atoms during the NEB path. The tab number means the order of the structure list in the connected structure builder. If you select atoms you want, the atoms will consider fixed during NEB calculation.


This is a link to see a list of all keywords in neb.x.


A keyword belonging &PATH namelist is the keyword to adjust the option of the NEB calculation.


NEB calculations do not perform scf calculations but require the PWscf keyword. Copy and paste the input script which is you used to relax the structure.


The input parameters will be converted into the input script form and transfered to a cloud computing server. Please check if the script has no error.


When all the settings are complete, set a Job name and press the 'Start Job!' button to submit the job.






When NEB calculation is finished normally, the result tab will be displayed. Click the result tab to check the results.


NEB graph shows the energy that varies during the NEB path.


Visualizer shows a structure that varies during the NEB path.


Click the structure list icon at the ③ Visualizer upper-right to see the structure list.



MatSQ offers molecular dynamics simulation by LAMMPS code combining with the reactive forcefield. You can conduct an MD simulation with just a few clicks to select forcefield, ensemble, temperature, time.




The LAMMPS module consist of two tabs. You can choose a forcefield and input parameters and submit a job to the cloud computing server to start MD simulation in the Script tab.
If you want to adjust simulation precisely by setting a specific atom group, make a new atom group and adjust the velocity, force, move, and temperature in the AtomGroup tab. Refer to the following 'Grouping' section for a detailed description.



It is a list to select a forcefield which is necessary for MD simulation. We provide a reactive forcefield as a default. We will support the other MD potentials in the future.


In this section, you can set the input parameters of LAMMPS for MD simulation. You can adjust ensemble, After Relax, Dump, Temperature, and Time. See the appendix for more information on the LAMMPS input settings.



Once you complete this whole setup, you are ready to submit a calculation job. Before clicking Start Job! , write a job name at the job name window. It is recommended to set the name identifiable to avoid confusion with other jobs.
At the Resource section, you can set the parallel computing options such as, the server type and the number of cores. The server type can be selected on-demand or maxflops (Maxflops is only available to maxflops users; see the Maxflops documentation). The parallel computing option next to the server option means the number of cores, and cores can be used up to 48 on a node.
Check the checkbox, if you want to be notified by e-mail after the job is completed.
If you click the Start Job! button, the loading window will be displayed. And if you click the ▶▶ icon on the top navigation bar , you can check the progress of the task as shown below.



LAMMPS can give an initial condition to a specific atom group. Click the AtomGroup tab to display a visualizer. The visualizer contains the structure information when the module is connected to the structure builder. Activate a select menu at the right-click popup window, and select the atoms that you want to add the additional setting. If you click the +, the new atom group will be added.
You can add Atom groups as much as you want. Click a previously set Atom group on the list. It displays only the atoms belonging to that Atom group. Select the groupwhich you want to set the initial condition, and click Group Info to select the desired condition. Check the checkbox, and set the condition to be applied in each axis direction.



Calphad is the module calculating thermodynamic information of various materials. Refer to the appendix to access the detailed description and database information, examples.


  • Select atoms what contained at the system you want to plot phase diagram. In the case of the binary, ternary phase diagram, if the element selected enough, then the periodic table closed automatically.


  • Select the database which is the most appropriate for the system. Refer to the appendix to read the detailed information of the database.


  • Select the phase that you want to contain when plotting the phase diagram.


  • Specify the initial starting point at which the phase diagram will be plotted. If the starting point is not proper, the graph may not be drawn properly or the calculation fail.




The Energy module is the most basic analysis tool. Before adding this module, the electron structure calculation (SCF (PWscf, pw.x) must be preceded on the Quantum Espresso module. The energy graph is displayed when the Energy module is connected to the QE module. You can view the final total energy in the table below the graph and switch the energy units. The y-axis presents the total energy of the step, and the x-axis presents the scf step.
Each calculation job consists of several scf steps, and one scf step consists of a set of iteration steps. The Energy module plots the total energy value obtained from the iterative self-consistent calculation. Therefore, for a calculation that performs a single scf calculation, there is only one data point because only one total energy data was obtained through iteration, and the (vc-) relax calculation, which consists of several scf steps, shows the energy that gradually changing with the progress of the scf calculation.
For more information on the self-consistent calculation, refer to the QE tutorial .
Checking the energy graph is a good way to ensure that convergence has been achieved during the structural optimization process. The calculation may not have been completed properly if the scf phase of the energy graph has reached the maximum number of scf steps even if the “This job is normal finished” message appeared in the QE module. Refer to the Restart job section.




Connecting multiple data modules to an energy module makes it simple to compare each energy value. Click on the button, and select a module to which you want to add data, and the corresponding energy module is replaced by the energy comparison module. The module that changes to the translucent state when the button is clicked is the one that has no energy data, thus, cannot be added.


Connect the energy module to the calculation finished LAMMPS module to see the energy change during the MD simulation.




The Movie module plays trajectory from Molecular Dynamics simulation as animation. It enable see the AIMD (ab-initio molecular dynamics) results performed in Quantum Espresso module. Add the Energy module to see together the change of structure and energy in Setting window. You can see the RDF (radial distribution function)and MSD (mean squared diplacement)together.
At the Interval, set the time and step to next trajectory. At input area of Move, put desired step and click Move button, you can see the trajectory and data at that step. At Atom Fill, can display the color of atoms as kinetic energy or potential energy.




MIf tick the checkbox, the Mean Squared Displacement module added under the Movie module. MSD module show the displacement deviation of selected atoms.
To open option window, Mouse right click on the Movie visualizer canvas. Select 'Select' tab, and select atoms that want to see the MSD data.




Tick the checkbox in Movie module option to show the Radial Distribution Function under the movie module. In RDF setting, you can adjust Cutoff, axis range, element type. Tick the 'LIVE', you can see the RDF graph as animation that change with MD. Tick the 'Range' and select atoms which desired to see the RDF.




Use the Compare Structure module to compare two structures at a glance.
Select 'Structure A' or 'Structure B' and click on the icon to connect to another module. You can link this module to the Structure Builder or Simulation modules.

Connecting to the Quantum Espresso Module allows you to choose the 'initial' or 'final' structure. Assign them to structures A and B.
Especially, when performing a structural optimization/relaxation by selecting (vc-)relax in the QE module, which finds the local minimum closing to model’s initial structure, it is recommended to compare the initial and final structures to check the structural changes in the relaxation process.
Alternatively, you can place two different structures side by side to see the difference.

The Compare Structure module consists of two visualizer canvases and a data table. Selecting the “Sync” checkbox synchronizes the time points. If you place the cursor over the table, the corresponding atom shows in pink. The movement of atoms in the table is indicated by an orthogonal coordinate (Å).





The Density of States graph shows the number of electronic states at particular eigenvalue. The DOS graph is represented by Energy (eV) vs. the number of states ( #/eV). In Visualizer of the DOS module, you can select only a specific atom and select a specific orbital from the Orbital list on the right to view the PDOS (projected density of states) for that atom.
For example, if you want to see which one is representing the surface state, add PDOS by selecting only the desired chemical species. Now you can see which orbital of what atom corresponds to this state. See the graph in detail by dragging the mouse. You can set the name and color of the graph.
DOS can be combined with a band structure diagram (refer to the Band Structure Section .) The x-axis of the DOS graph is the same as the y-axis of the band diagram. The bandgap on both graphs is the same.





The Band Structure module is a module for drawing a band structure obtained from a band structure calculation. Refer to the Band Structure Calculation documentation for instructions on how to calculate the band structure.
Press to connect all QE modules that have performed the actions to be displayed to the Band Structure module. When connected, the Quantum Espresso module is enabled only if it has a Band Structure (bands.x) or DOS (projwfc.x) calculations. Calculations with a band structure only are used as band structure data, and calculations with DOS only are utilized as DOS data. Calculations with both a band structure and DOS are used as band structure, DOS, and projected band structure (fatband) data.
The x-axis of the band diagram, the k-path label, is automatically set by finding the crystal system point set that has the highest similarity among high-symmetric points. You can change the crystal system and energy units in the Select Box.
You can connect a QE module with DOS data to view a band structure and a DOS graph side by side. The y-axis of the band diagram is the same as the x-axis of the DOS graph. You can zoom in by dragging with the mouse and return to the original using the Reset button in the upper right corner of the graph. The table at the bottom of the graph allows you to clear or disable the chart drawn on Canvas.
You can project a band structure and DOS on the specific atom and orbital, and draw a fat band. For more information, see the following ‘Projected Band Structure’ section.




If you want to see a projected band structure on a specific atom or orbital, or if you want to draw a fatband, perform a projection calculation by adding a DOS solver to the QE module that calculated the band structure.
Press the button, and click on the corresponding QE module to assign the data to Projected. Then, select an atom and orbital, and press the Add button to add the PDOS data and plot the projected band structure (fatband).
The added data is displayed in either a circle or a bold line. The sum of the contributions of the selected orbitals at that point determines the diameter of the circle or the thickness of the line. Contribution refers to the distribution of each orbital to the eigenvalue at that point. The color of the graph is the average value of the selected orbital color having the same angular momentum quantum number.
If the added data contains multiple data with different angular momentum quantum numbers, the contribution of each orbital is displayed in color gradient. If you want to view the contribution of each orbital as the radius of the circle/the thickness of the line, select each orbital separately and add it.





The Charge Density module visualizes the charge density of a calculated structure by displaying surfaces (isosurface) having the same values and cell borders. First, you must perform a DFT calculation to determine the charge density of the structure. Refer to the Quantum Espresso module documentation to perform DFT calculations using the Quantum Espresso module.
Click on to activate the module for which Charge Density is calculated. Click on the activated module to connect, and a Charge Density plot appears. You can select the desired charge density from the list of calculated charge densities located at the bottom of Visualizer.
You can change the charge density-related settings by clicking on [toothed wheel] in the upper right corner of Visualizer. You can change the isovalue taking account of the ρ (max) and ρ (min) values located in the lower-left corner to change the surface or the color of the cross-section and the gradation scale value of the surface color.
If more than one charge densities are connected, 'Diff' tab is activated with the connected charge densities in the list on the left. You can view the sum or difference of the charge density values, which were connected through Diff. Refer to the following section for more information on how to draw charge density differences. Note: “charge density” refers to an electron density by convention of DFT society. This module draws ‘pseudo charge density’ which is much smoother near atomic cores than true chare density, as Quantum Espresso uses pseudopotential.




You can check the charge density differences by connecting two or more charge density data. Clicking on Diff in the Charge Density list on the left displays the charge density data calculated by ρ 1 2 for the ρ1 structure displayed by default. You can change the structure to be shown in Visualizer by changing the structure selection at the bottom of the module, and use Formula to determine the formula to obtain the difference between values. The surface that has a color opposite to the color of the set surface is the charge density having a negative value.




Add this module to a job to record additional information about the calculation. You can select the Note/Sheet tabs. Simple formulas are available under the Sheet tab. The Memo modules operate independently but can be connected and used with other modules by clicking on the Connect Module icon. Use this module to record useful information efficiently!




Use the Job Loader module if you want to add jobs that have been deleted or performed on other work pages to the current work. Searching for and selecting a job replaces the Job Loader with the Simulation module. You can now add the desired job to the desired work.


This page has been created by SimPL. Last update: Dec 02, 2019