# Tag Info

35

OpenMOLCAS I'm surprised that the other two answers were given without yet any mention of OpenMOLCAS yet! There is a recent paper[1] about it for which I happen to be one of the many co-authors. MOLCAS has the quality of a commercial software like MOLPRO, since it was a commercial software that people paid big money for since the 1980s, but recently an open ...

25

ORCA ORCA (forum). It is fully featured, efficient, and free for academics. The input is straightforward: # CASSCF(2,4) example from the manual, # section 8.1.7.2, page 108 ! TZVPP TightSCF %casscf nel 2 norb 4 end * xyz 0 1 Be 0 0 0 * Some resources for CASSCF: General functionality is reported in this tutorial. A tutorial dedicated exclusively to ...

25

It depends on what chips datacenters are using. If large data centers switch over to ARM-based processors, scientific computing will follow. Since most of our software is open source (or not far from that), converting to ARM compatibility will not be too much of an issue once the demand is there. Scientific computing is currently dominated by enterprise-...

22

ORCA Official website: https://orcaforum.kofo.mpg.de/app.php/portal What is ORCA? ORCA is a general-purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many-body perturbation, and coupled-cluster theories, and multireference and semiempirical methods). It is a flexible, ...

22

OpenMOLCAS MOLCAS is now in it's 5th decade! The first version was written in the 1980s by the group of Bjorn Roos, one of history's giants in quantum chemistry. It can do many of the things most mainstream quantum chemistry packages can do: integrals, Hartree-Fock, DFT, MP2, coupled cluster, geometry optimization, etc., and while it can do "single-...

21

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 ...

19

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 ...

18

18

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 ...

18

For scientific papers in matter modeling, I always use vector graphics (e.g. .eps, .pdf, or .svg, though the journals will not typically accept .svg format). I stopped publishing in ACS journals (e.g. JCTC and JACS) after they turned one of my vector graphics into a pixelated raster, before publishing it. Even though it was 2015, and I'd been publishing ...

16

PySCF Personally I would use pyscf, its not the most efficient or user friendly but it's free.

16

I'd expect that x86_64 will remain the architecture of choice for computing throughput for quite a while, and that there might even be a way to deliberately re-enable the Spectre/Meltdown vulnerabilities because they give a nice speed boost and are irrelevant if you don't share the CPU with anyone else. ARM shines in the datacenter because a lot of the work ...

16

Psi4 Psi4 is a fully open-source quantum chemistry package that is gaining a lot of interest in my community (computational) combustion chemistry. Here is the manual for the latest release: it has most, if not all, of the theoretical methods (HF, DFT, CC,...) and also lots of interfaces and integrates into C++ and Python (sadly no Fortran). The bonus on it ...

16

Several computational workflow managers try to address exactly this problem in materials modeling. Besides helping orchestrating complex simulation workflows, they keep track of all the simulations (and how they are related) in a database. The Materials Project team uses the Fireworks package. The atomate package provides a high-level interface for the most ...

15

SlowQuant In your question from 2015, you mentioned PyQuante and PySCF, but I saw no mention of SlowQuant in the question or in the multiple answers. I see that while writing this, someone else answered, with mentions of PyQuante, PySCF, and Psi4 again. Still no mention of SlowQuant. The author of SlowQuant has described the program this way (emphasis mine)...

15

If you're set on using Python here are some options. I haven't used these codes so I can't speak to their ease of use. PyQyante PyQuante is a suite of programs that can not only do DFT but also Hartree-Fock, MP2, and more. Certain parts of the code are written in C for speed. A package can be downloaded and then installed with Python, but a newer version, ...

15

GAMESS For many researchers, GAMESS is the "natural" substitute for GAUSSIAN. Developed and maintained by the group of prof. Gordon (also a banned GAUSSIAN user, see image below). Official website: https://www.msg.chem.iastate.edu/gamess/index.html What is GAMESS: GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can ...

15

As a gentle, free (as in free beer and as in free speech) on-line introduction, I would recommend learnlatex.org. At the start, you choose one of currently eight languages (Catalan, German, English, Spanish, French, Marathi, Portuguese, Vietnamese). Subsequently, all teaching is going to be provided in this language only. Later, you enter 16 core lessons; ...

14

NWChem NWChem is a commonly use quantum chemistry software package with CASSCF included. NWChem is free, as in both free coffee and free speech. It is under ECL-2.0. It is written in FORTRAN (in case you want to do some development).

14

Jmol is completely capable to do what you want. It reads cube file format and works with scripts. Take a look at this link related to making movies. The idea is: Your filenames must consist of a combination of text and a sequence of ordered numbers (e.g. myfiles_0001.cube, myfiles_0002.cube, etc.), Make a loop, and inside it: Load each file, Plot the ...

14

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.

13

Run any Linux program on WSL (Windows Subsystem for Linux) One interesting alternative is using the Windows Subsystem for Linux (more info at: https://docs.microsoft.com/en-us/windows/wsl/install-win10 ). I know of successful cases where this has been used to install GROMACS (recent versions). I don't have a reason to believe it wouldn't work for other MD ...

13

GROMACS Instructions for installing GROMACS on Windows (even if you don't want to use Cygwin!) are here. Advantages: Free, and open-source. Long history: First released in 1991, based on an earlier program called GROMOS from 1978. Under very active development: For many codes, the majority of the development was done years or decades ago, but the ...

13

OpenMM OpenMM is a highly efficient molecular dynamics package which can run via Python. Therefore, any way you normally run python can work. For example, via a Jupyter (Ipython) notebook, via a python GUI, Window's PowerShell, Window's subsystem for Linux, etc. You can download OpenMM via the python manager Anaconda, which makes it very easy to install. ...

13

Lennard-Jones combining rules Most force fields define a single σ and ε for each atom and calculate them for combinations using Lorentz-Berthelot combining rules. These rules specify a arithmetic mean for σ and a geometric mean for ε: $\sigma_{ij} = \frac{1}{2}\left( \sigma_i + \sigma_j \right)$ $\epsilon_{ij} = \sqrt{\epsilon_i \epsilon_j}$ This reduces the ...

13

I personally started with "The Not So Short Introduction to LaTeX", a PDF file that should come with most LaTeX distributions under the name "lshort.pdf". The document claims that it can be read in 139 minutes (the precise number depends on the version). I remember I didn't finish it in such a short time (perhaps the given time estimate ...

12

BAGEL The code is available through GitHub[1] and has been described in WIRES.[2] The main advantages of BAGEL is that it has better memory and parallelization than MOLPRO. For example, MOLPRO (not Free) is restricted to 32 active orbitals. While not a problem for CASSCF, this will severely affect your ability to do CASPT2 calculations. (they have fixed ...

12

Any code that does not have core parts written in machine level code (assembly) is going to be portable to arm64 straight away; you just have to recompile the program. This is the whole point of having programming languages in the first place: you need to be able to run your program on different architectures without rewriting the program from scratch, like ...

12

To extend your 0K energies to finite temperature, you essentially need to add up the different sources of entropy. Some examples as reviewed by Hickel et al. [1]: Vibrational entropy (usually split into harmonic and anharmonic contributions) Electronic entropy Magnetic entropy Configurational entropy Each of these contributions has some underlying theory ...

12

Complementary to the answer given by Nike Dattani with focus on file format, I would like to draw your attention to how you present the content visually in photos, schemes and diagrams known as artwork. Regardless of the file format eventually elected (where suitable, vector based like .(e)ps or .pdf), determine in advance the dimension of the illustration:...

Only top voted, non community-wiki answers of a minimum length are eligible