# Tag Info

## Hot answers tagged open-source

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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-...

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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, ...

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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 ...

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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 ...

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The PDB file format has a strict specification on the number of columns, etc. (Consider that some proteins have very large sizes, so distances can be many Ångstroms.) Thus, the number of decimal places are generally given by the file format. Some people have asked why Open Babel doesn't give more decimal places, e.g., in the XYZ format, which is, in ...

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NetworkX This is a widely-used Python library for graph theory stuff. Open source (https://github.com/networkx/networkx) under a 3-clause BSD license. Caveat: since this is a tool that knows nothing about chemistry, the "chemical" nature of the structure might get lost in the projection of the network (e.g., some bond lengths might not look ...

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Most of the problem here appears to be because constraints in the test system default to app.HBonds, which means all bonds to hydrogen atoms are constrained. Something goes very weird when you force a large, unphysical change on the system, and then try to apply HBond constraints (it looks to me like it isn't even constraining HBonds to the unphysical ...

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"GAMESS seems to have an old academic user base and a stable code for most traditional calculations" GAMESS has been in development since the 1970s and split into GAMESS(US) and GAMESS(UK) in 1981, whereas MOLCAS has been in development since the 1980s and Psi4 is much newer. However, I would not focus too much on the age of the software. The ...

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I was able to find a workaround to get open source PyMol installed on Windows. Christoph Gohlke at the University of California has a large library of precompiled Python wheel files of various scientific packages, including PyMol. I was able to find a Windows version for Python 3.8 pymol‑2.5.0a0‑cp38‑cp38‑win_amd64.whl and after downloading this file, I was ...

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If you're using Linux its better if you install such packages using the apt-get method. apt-get install pymol I've encountered a similar error while installing MatPlotLib through conda. For more info you can follow this link: https://pymolwiki.org/index.php/Linux_Install Hope this helps :)

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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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NWChem Official website: https://nwchemgit.github.io/ and https://www.nwchem-sw.org/ It is open source Description: NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources ...

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Disclaimer: These are just some observations; I don't claim to know the answer to this question. There's a lot of overlap between both camps, but I think people tend to stick mostly with one kind of system, in their research. You may be largely correct - I'd just like to point out that if we are looking at the simulation engines (rather than what people do)...

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Let me add 2 notes MKL has a secret env-var to force the use of AVX2 extensions etc. For details, see here The magic is setting the environment variable: MKL_DEBUG_CPU_TYPE=5 note however that Intel can at any release remove this flag, so one is not guaranteed this will work in later releases. Another great library is blis it basically works like ...

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GUI4dft - A SIESTA oriented GUI GUI4dft is a new Graphical User Interface for Density Functional Theory for users of SIESTA. GUI4dft is written in Python language, falls under an MIT license and is a free cross-platform software. GUI4dft allows the user to work with standard SIESTA files and prepare manuscript-quality figures of the atomic structure and ...

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FCBand FCBand is a Python package for simulating vibronic bands of electronic absorption spectroscopy using the Franck-Condon displaced harmonic oscillator (FC-DHO) models. These models are suitable for simulating the unresolved vibronic band shapes of electronic spectra that involve many electronic transitions and vibrational modes. https://comp.chem.umn....

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LEVEL For a diatomic molecule, LEVEL can calculate all Franck-Condon factors (FKF): $$|\langle \psi_{v,J} | \psi_{v^\prime,J^\prime}\rangle|^2\tag{1},$$ between rovibrational levels $(v,J)$ of one potential energy curve, and $(v^\prime,J^\prime)$ of another potential energy curve (or the same potential energy curve). To calculate FKF, the variable LXPCT ...

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AMD's answer to Intel's MKL is called AMD Optimizing CPU Libraries (AOCL), which is coincidentally based on BLIS. In addition, it also includes FLAME (for LAPACK functionality), FFTW, and others.

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This question has been well-answered. But I would like to add in a few points too. In addition to observing the energy, you can also observe the convergence of outputs which are really sensitive to the K_point grid like the crystal pressure which is given by "P = " above your stress values in your SCF output file. The convergence of such ...

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You can enter an input file stream in gaussian cubman to add/subtract cube files. Eg. here is an input file named test.txt which has all answers to add two cube files (a.cube and b.cube) and gives an output sum.cube, Add a.cube yes b.cube yes sum.cube yes You can run this simply by entering, cubman < test.txt to get the required output. You can write a ...

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I tried to answer the question in the github issue github.com/pyxem/diffsims/issues/176 Answer: The reason it doesn't work is that the calibration parameter of the diffraction pattern is not set. A diffraction pattern in diffsims is represented by a list of (x, y) coordinates in projected reciprocal space, and an associated intensities I. Together they ...

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