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Blender I usually do 3D images with molecules using Blender. You can export your molecule 3D model with a chemistry visualization program (such as vmd or jmol) into Blender (I usually do it using OBJ files, it just needs a couple of adjustments after the import), OR you can write your own python loader from within Blender (harder to do, but possible). It is ...


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VMD can load STL files in text (ASCII) format. Here's how I produced the image below: Downloaded STL file of teapot from Wikipedia. This STL file is in binary format, so I used MeshLab to convert it into text format. I opened MeshLab and did File -> Import Mesh and selected the file Utah_teapot_(solid).stl. I then did File -> Export Mesh As and ...


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GIMP Whereas Adobe Photoshop has become so famous as a photo editing software, that we often use the term "photoshopped" to describe an image that's been edited, it is very expensive and GIMP is often called "the free Photoshop". Advantages: Free and open source Works on Linux, MacOS, Windows. Easy to install: sudo apt-get install gimp ...


15

SciCalQ The company does more than solving the Schroedinger equation. From its site: SciCalQ’s solid background in computational chemistry and quantum physics own extensive experiences in solving practical and academic problems with scientific computing. They do: Density Functional Theory (DFT) Computation Geometric Configuration: Bond length, bond angle, ...


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Adobe Dimension Adobe dimension is the premier paid software for 3-dimensional design. It can read in STL files and give them a texture, and incorporate the light source from the background light. The tutorial I watched to make this is here.


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Materials Square (MatSQ) Materials Square (MatSQ) is a web-based simulation platform providing an interface, workflow, and pay-as-you-go cloud server for material simulations. It supports DFT, MD and CALPHAD calculations. Provides a free 3D atomic structure-modeling interface supporting most structure types. Support density functional theory calculations ...


12

Protheragen Protheragen offers a Quantum Chemistry Service which includes: ECD calculation service (absolute configuration determination) Quantitative calculations (quantum chemical calculations) QM, QM/MM, QM/MD Catalytic reaction mechanism calculation Transition state search and energy calculation Chemical reaction pathway and potential energy surface ...


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ASE You can use ASE environment to visualize, it has different options as well. e.g., you can use this command: ase gui vasprun.xml


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SAMSON SAMSON, the molecular design platform, can do this in a few clicks with a Pro plan (see image below), by letting you import textured OBJ files into the document. The website is here. The standard plan also lets you export textured OBJ files, so you can import molecules (e.g. PDB files) into SAMSON, choose visual representations for them (van der Waals,...


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CDOCKER CDOCKER is docking program developed by the Brooks Lab and it works with CHARMM. CHARMM does have a free version named charmm. The difference is no DOMDEC or GPU high performance modules. Pros: Rigid and flexible receptors, highly customizable Cons: Need to get free charmm, creating scripts can sometimes be laborious, no high performance GPU modules ...


10

Critic2 critic2 is a very nice QTAIM code that supports interfaces to many codes, including also periodic systems: "WIEN2k, elk, PI, Quantum ESPRESSO, abinit, VASP, DFTB+, Gaussian, psi4, siesta, and to any other program capable of writing the scalar field of interest to a grid" From personal experience, critic2 is very straight forward to compile ...


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Amazon Web Services (AWS) and Google Cloud can be used for the running simulations and I've used both. I applied to a few grant programs a while back where part of the award included AWS or Google Cloud credits. I think the credits were donated to the funding agencies by the respective companies to encourage more use of those services in science and ...


9

Bash Scripting I have used bash scripts to automate materials modelling workflows. You can use online resources to learn more about bash commands and bash scripting. The idea is simple. If you have a repetitive and time-consuming task just write the terminal commands (usually run directly in the command line interface) on to a "file_name.sh" file ...


9

Common Lisp Recently I watched a couple impressive talks by Christian Schafmeister, where he discusses how they actually built a full fledged Common Lisp implementation on top of LLVM, named Clasp, targeted at molecular design: Clasp: Common Lisp using LLVM and C++ for Designing Molecules 2018 LLVM Developers’ Meeting: C. Schafmeister “Lessons Learned ...


9

GW+BSE: Excited states in the framework of many-body Green's function comprise charged excitations, where the number of electrons in the system changes from $N$ to $N-1$ or $N + 1$, and natural excitations, where the number of electrons remains constant. In the $|N\rangle \rightarrow |N-1\rangle$ case, an electron in the valence band (occupied orbital) is ...


9

Better late than never for a partial answer. I have worked with modeling the disorder of coverage on surfaces of materials. Recently we published a paper where we give a very general approach to modeling adsorbate-adsorbate interactions which we have seen is a problem in current literature. By using non-ideal buildups of coverage (where each adsorbate is ...


9

From my experience with Stochastic Series Expansion (SSE) QMC (a type of discrete-time QMC) the computational cost scales like $\beta L^d$. In practice, it's often important to account for the finite-size gap $\Delta \propto 1/L$, so to stay consistently above or below that finite-size gap, $\beta$ is typically set to scale as $\beta = cL$, where $c$ is some ...


9

NGLVIEW I discovered it very recently when I was using MDAnalysis to play with molecular dynamic trajectories. Therefore, I am not able to write about pros/cons. Site: https://github.com/nglviewer/nglview From the site: An IPython/Jupyter widget to interactively view molecular structures and trajectories. Utilizes the embeddable NGL Viewer for rendering. ...


9

I am curious to know if the word has been used in any way other than the above three ways. Mark. J. Winter at University of Sheffield has used the word differently — not as a term meaning something specific, but as a name for the so-called Sheffield ChemPuter: Welcome to the University of Sheffield's ChemPuter, a set of simple interactive calculators for ...


9

QuSpin QuSpin is an open-source Python code that can do exact diagonalization of spin, fermion, and boson systems. It has a wide support for use of symmetries, constrained Hilbert spaces, various models, and time evolution. The combination of fairly simple Python syntax and a large number of tutorials make it a great choice for beginners, for small-scale ...


9

A possible tool is the ASE python package (open-source): https://wiki.fysik.dtu.dk/ase/ase/cluster/cluster.html Another tool is materials studio software. Unfortunately, it is not free.


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Molecular Quantum Chemistry via WebMO on Google Cloud It's fairly easy to run Linux-based programs on Google Cloud. The WebMO interface gives a tutorial on installing on GCP including molecular quantum chemistry programs. Supported tools include open source and "free binary" programs, for example: Psi4 Orca GAMESS NWChem Mopac As mentioned in ...


9

Hetzner If you know you will continuously need a powerful computer for the next 1-2 years, consider renting a bare-metal server from Hetzner. You can rent a 32 core 2nd generation AMD EPYC server with 256 GB of RAM and a fast SSD for about 200 EUR/month. No traffic fees. You get remote access to a blank machine, and you are free to install whatever OS and ...


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B3LYP My suggestion for you in this case is to simply use the most common funcitonal for basic properties of molecules: B3LYP. I wrote in my answer here that B3LYP is still a decent functional overall, especially considering its relatively low cost for non-periodic systems (e.g. a pesticide molecule). The first figure in that answer is directly from the ...


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ErtlFunctionalGroupsFinder A Java library for automated functional group implemented with the Chemical Development Kit (CDK) program. It should run on Windows/Mac/Linux operating systems. It relies on the Ertl algorithm, which is also used by the RDKit for functional group detection. A key difference between the two implementations seems to be in their ...


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India : National Supercomputing Mission Supercomputing and the C-DAC Missions: Supercomputing in India started in the 1980's. After difficulties in obtaining supercomputers from abroad for weather forecasting and academic work (due to the potential for dual-use), it was decided to build ingenious supercomputing facilities. Supercomputers were made by C-DAC (...


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Switzerland In Switzerland, the Swiss National Supercomputing Centre (CSCS) provides most computing power. Refer to the Wikipedia article for a list of all the computing resources; it started with a 2-processor computer in 1992. Most notably though, since December 2012 it is the provider of Piz Daint, which in 2016 after an upgrade became the third most ...


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Finland Finland has a long history in supercomputing; CSC - the Finnish IT Center for Science, administered by the Finnish Ministry of Education and Culture, has provided computing services since 1971, starting with an Univac computer. The strategy in Finland has been to pool national resources from the start, and this has enabled Finnish researchers to have ...


8

OpenSUSE It is oriented both to desktop and to servers. It has a large collection of software repositories for scientific computing in general (you can have all of GCC 7, 9, 10, 11 at the same time, module system for different versions of MPI libraries, CAD, CFD,...) and even for matter modelling in particular (GROMACS, LAMMPS, Quantum ESPRESSO, etc.). It ...


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Elk / EXCITING Like @Nike Dattani suggested, Elk is an open-source well-documented FP-LAPW DFT package. Also, LAPW stands for Linearly-Augmented Plane Wave. Singh's book is an excellent introduction for this topic. (Disclaimer: I'm currently developing an extension to Elk / EXCITING to compute response functions and estimate Hubbard model parameters using ...


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