Work

On the Work page, Materials Square offers intuitive workflows to make materials simulations and electronic structure calculations as simple as possible – from building the crystal to the graphical analysis of results. Available software packages are Quantum Espresso (QE), LAMMPS, and VASP. A work is comparable to a folder which contains all parts (modules) of the simulation project. Jobs, on the other hand, are single orders to the MatSQ servers to run a calculation. Thus, a work can contain several jobs.

Create new work

Select the Work tab in the menu bar to see a list of all saved works. To create a new project, click the “new work” button. This directs you to a new work page where you can choose between three workflow templates, or add modules manually. Give your work a name in the bottom left corner of the screen.

Choose a workflow

We have predefined workflows for three different applications. Depending on what you want to calculate, one of these templates might fit your needs. Workflow templates are designed for fast, easy results and guide you through the simulation step by step. Preset module types as well as cal-culation methods provide a target-oriented starting point. Nonetheless, you can always change these presets during the procedure to have full control over the simulation. If you’d rather start from scratch, skip to section 4.3.

Basic Energy Calculation with Quantum Espresso.

This workflow is ideal to calculate the total energy of a system using DFT. It consists of three steps: building the crystal in the Visualizer & Manipulator module specifying calculation in the Quantum Espresso module (scf) * showing computational result in the Energy module. In the Quantum Espresso module, scf (self-consistent field) is preset as calculation mode; however, this can be changed. For more details on the modules, see QE input description page (https://www.quantum-espresso.org/Doc/INPUT_PW.html)

Density of States with Quantum Espresso.

This workflow is tailored to DFT calculations of the density of states (DOS) of a system. It differs from the Basic Energy Calculation workflow in steps 2 and 3: building the crystal in the Visualizer & Manipulator module specifying calculation in the Quantum Espresso module (relax) * plotting density of states in the DOS module by selecting the DOS plotting module. The DOS workflow sets the Quantum Espresso calculation mode to relax. This can be changed. For more details on the modules, see QE input description page (https://www.quantum-espresso.org/Doc/INPUT_PW.html)

Molecular Dynamics simulation with Reactive ForceField & LAMMPS

This workflow is made to easily perform molecular dynamics (MD) simulation and visualize the mov-ie of dynamic motions of atoms by doing building the crystal in the Visualizer & Manipulator module selecting MD potentials in the list submit the job visualize data after jobs are finished

add modules to your work

If you wish to create a personal workflow for your calculation, you can import individual modules from the module selector located at the bottom right of the screen. The modules are divided in four groups: V – Visualization modules allow you to build, visualize, and manipulate your system prior to the calculation. S – In Simulation modules, you can specify the input script defining your simulation. MatSQ offers a graphical interface which enables you to easily adjust main settings based on Quantum Espresso, VASP, or LAMMPS codes. A – Analysis modules graphically display simulation results for a fast analysis of calculated system properties. For example, you can plot the band structure or the energy convergence of relaxed nuclei – directly on the web. E – Last, and perhaps least, the Et cetera section features a memo module to note important in-formation about your project. Every job requires at least one visualizer and one simulator. However, a work can consist of many visualizers, simulators, and analyzers. This can be helpful, for example, if you want to do several simulations with the same structure. After job submission, it is your choice to either analyze results with MatSQ modules or to download the data for post-processing with other software.

name, clone, or delete work

Modules

(V) Visualizer & Manipulator

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.

create or upload a structure

The simplest way to generate a structure is by uploading a crystal information file. Either click on the striped area or drag and drop from a folder on your PC. 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 the “crystal” icon. The crystal builder pops up. Under the Space Group tab, you can de-fine the space group, lattice vectors, and atomic basis of the supercell. In case you just want a sim-ple structure to play around with or test the MatSQ functions, we offer two preset structures – gra-phene in a hexagonal primitive cell (Graphene (Hex)) and graphene in a rectangular unit cell (Gra-phene (Rect)).

visualize, measure, download the structure

After uploading or generating a structure, it will show up in the visualizer window. Use your mouse to zoom or rotate the structure. The gear icon in the top left corner 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.

manipulate the structure

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.

(V) Charge Density (QE)

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 gear icon ⛭ to make adjustments.

(S) Quantum Espresso

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 Es-presso 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 con-trol 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 simula-tor refers to the right atomic structure, especially when your work contains several visualizer mod-ules with different structures.

specify input parameters

On the module interface, you can adjust: calculation type energy cutoff k-points occupations of energy states. A more detailed description can be found in table xx. For further information on Quantum Espresso input variables, see our QE tutorial as well as the Quantum Espresso documentation (http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html).

view, edit script

For full control of the calculation, you can view and manually edit the input script. Click on the Show Script option at the top right of the module. From the three available files (input.pw.x, in-put.epsilon, projwfc), the first (input.pw.x) is the QE input file which contains all &namelists and input_cards specifying the calculation. It contains structural information provided by the visualizer and the values you inserted in the simulator, as well as some default values that must be defined. You can edit the script by simply writing text in the script window. Make sure you adhere to the Quantum Espresso syntax. Also note that after manually editing the script, the graphical interface (input script generator) will be disabled. A pop-up window will ask you whether you want to use the modified script or discard the changes.

submit the job

Once you’ve specified the calculation type and input parameters, you are ready to submit the job. Before you click the green Start Job! button, insert a meaningful name in the field Job Name. Addi-tionally, in the Resource field, you can choose between an on-demand resource or a dedicated server (only available for MatSQ:Reserved users; see section 3.2.) and set the number of servers to be used for the job. One resource is the default but parallel computing on multiple nodes is possi-ble. Finally, under Finish Notice, check the boxes E-mail and/or SMS in case you would like to be noti-fied via email and/or SMS as soon as your job has been finished. (S) LAMMPS (S) VASP Reader (S) VASP (MatSQ:Reserved Only) (A) Energy (QE, VASP) The Energy module is a basic analysis tool which plots the total energy values found during an iter-ative self-consistent calculation. Before using this analyzer, run a Quantum Espresso or VASP electronic structure calculation in the respective simulator. Once the job has been successfully completed, select Energy (QE, VASP) 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 hori-zontal axis gives the iteration 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 en-ergy 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 optimization step. This is a great way to check the convergence of the atomic relaxation process.

(A) DOS (QE, VASP)

(A) Charge Diff (QE)

(A) Dynamics (LAMMPS)

(A) RDF

(A) Dynamic Matrix (VASP)

(A) Compare Structure

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. It consists of two structure visualiza-tion windows and a data table below. Your work should also contain a relax calculation (atoms and electrons).

(E) Memo

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.