Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials Modeling is the creation of a mathematical or conceptual rep... More at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
Quantum espresso is used via the command line. There is no graphical interface by default. This is typical of most electronic structure codes, where you are often interacting with a remote The use of parallel processing for running advanced applicat... More system.
Introductory Tutorial: Submitting Quantum Espresso Simulations to Rescale Platform
The following example shows you how to calculate and plot molecular orbitals of benzene using DFT calculation performed by Quantum Espresso (QE).
This example is consist of two parts:
- PWscf (pw.x) calculations, which performs many different kinds of self-consistent calculations (SCF) of electronic-structure properties within Density-Functional Theory (DFT), using a Plane-Wave (PW) basis set and pseudopotentials (PP).
- Second part is the post processing (pp.x) which reads the output produced by pw.x, extracts and calculates the desired quantities and writes them to a file in a suitable format for various types of plotting programs.
This tutorial will introduce you to submitting QE jobs into the Rescale platform. An input file is already created on the local computer and we will show you how to start a Rescale job, submit, and transfer the results back to your computer.
Configuring Your Job
Starting Up Rescale
Once the job is completed, follow these steps to view results on a Rescale Desktop:
To start up the Rescale platform:
- Go to the platform.rescale.com, log in using your account info.
- From the main screen of the platform, click the + Create New Job button at the top left corner of your screen. Feel free to rename the job by clicking on the pencil icon next to the job name (“Untitled Job”) at the top of the page. Since Rescale’s platform saves all of your jobs , it is recommended that you name it something specific so that you will be able to find it again later.
This is the first step of submitting your job.
Now you can upload the input file from your local computer or if you already have it on the cloud, you can upload it using the a simple and scalable way to store, access, and share data o... More.
- For this tutorial you will want to upload four files, first one is pw.benzene.scf.in the script containing all of the data describing the structure of Benzene and commands needed to calculate Self Consistent Field (SCF) calculation as to calculate Kohn-Sham states to find the electron’s ground-state energy and Kohn-Sham orbitals.
- The second and third files contain the pseudopotentials needed to run this Simulation is experimentation, testing scenarios, and making... More. You can find any pseudopotentials you need here.
- The fourth file is pp.benzene.psi2.in which does the post-processing, reads the pw.x output files and uses the selected wave functions results from SCF calculation to calculate all valence and LUMO (lowest unoccupied molecular orbitals).
- Click Upload from the computer and select the file pw.benzene.scf.in H.pbe-rrkjus.UPF, C.pbe-rrkjus.UPF and pp.benzene.psi2.in from your computer.
- If you cloned an example job, then click on “Use files from cloud storage” and select the files you uploaded from the Desktop An Amazon Virtual Machine More
On completion you will see your input file setup page look like that shown below:
Now we can configure our software package options on the “Software Settings” page. You can search for or directly select the tile for Quantum ESPRESSO:
- Next, the Analysis options must be set.
- The drop down selector allows you to choose your preferred version of the software.
- The input file in this tutorial has been tested with Quantum ESPRESSO 7.0, so select that option.
- This is open source software, there is no need to select any type of license.
- Next you need to add the analysis execution command for your project. This command is specific for each software package and each input file being used. For this input file you will need to add the following:
mpirun pw.x -i pw.benzene.scf.in -o pw.benzene.out mpirun pp.x -i pp.benzene.psi2.in -o pp.benzene.psi2.out
The completed Software Setting should look like those in the images below:
Now we can select the type and number of cores to run on in the “Hardware Settings” page.
For a basic job, there are three hardware settings to edit: Pre-configured and optimized architectures for different HPC... More, Number of Cores, and Walltime.For this example, select 2 or more for the Number of Cores (1), 6 Hrs for the Walltime (2), and Emerald for the an individual processing unit within a multicore processor o... More Type. Rescale offers On-Demand Economy and On-Demand Priority core type options. You can find more information on these options here.
There is no need to specify any Post Processing options for this tutorial. To continue to Review, click Next from the Post Processing screen.
After reviewing your selections, your case should now be ready for batch submission at this point.
The Review step shows you a summary of your job prior to submission.
- Click the blue “Submit” button in the top right corner on any of the job configuration pages or in the middle of the “Review” page.
- Alternatively, instead of submitting the job, you can elect to “Save” the problem setup to be run at some later time.
Now you can monitor the progress of your job from the Status tab:
- You can monitor the status of your job and get information about your A computing cluster consists of a set of loosely or tightly ... More in real-time. Here you can see the live-tailing of the output “process_out.log
- Because this analysis is entirely run in the cloud, feel free to close your browser window or shut down your computer. You can check on the progress at any time by logging into Rescale and clicking on the Jobs tab. You will receive an email notifying you when the job is completed.
- A guide on “Monitoring Status” on Rescale can be found here.
- Once the job has completed its run, you can “Download” all of the output files from the “Results” page. You can also launch a Desktop and attach this job to perform post-processing.
- A guide on “Managing your Job Results” on Rescale is found here.
Configuring Your Desktop
Once the job is completed, follow these steps to view results on a Rescale Desktop.
To set up a Desktop session:
- Under the Workstations tab, select the Classic Desktop.
- From the main screen of the platform, click on the +Create New Desktop button at the top left corner of your screen. Feel free to rename the desktop by clicking on the pencil icon next to the desktop name (“Untitled Desktop”) at the top of the page. Since Rescale’s platform saves all of your desktops , it is recommended that you name it something specific so that you will be able to find it again later.
- In the next step, you can configure the software you need.
- For the purpose of this tutorial ,VMD GUI is selected. under the Analysis option tab you can choose your preferred version which is considered 1.9.3 for the purpose of this tutorial.
- Under the jobs section , you can attach the specific job that you want to use on the Rescale desktop.
- For the hardware it is recommended to use the “Windows a server is a computer program that provides services to oth... More 2019 – Hardware Accelerated”, which is well suited for the purpose of this tutorial.
- Now you can select Launch on the top right corner of the platform, and wait a couple of minutes for the desktop to connect.
Once the desktop is created, select the Connect button on the top right corner of the platform:
Now that we are connected to the system, we can launch the software by double clicking it and load our results. Any job that is attached to the desktop is accessible through a folder on the desktop.
On the VMD top bar, select File and choose the New molecule.
From the attached_job file you will see 16 psi2.benzene_K001_B0*.xsf files related to molecule orbitals.
To make a fancy display of molecular-orbital:
- On the VMD top bar, select File and choose the New molecule.
- Find the psi2.benzene_K001_B016.xsf file from the attached_job file.
- Change the Coloring Method to Name
- Change the Drawing method to CPK.
In the next step , select the Create Rep from the Graphic Representations
- Change the Coloring Method to Volume and the Drawing method to Isosurface.
- Change the Isovalue to 0.001.
- Change the Material Method to Transparent
- Change the Draw to Solid Surface and the Show to Isosurface.
The final setup page look like that shown below:
The final molecular orbital of Benzene should approximately look like this:
You can repeat this process for another orbital and visualize the results.