Resources

Important Resources

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In the following, I tried to gather some interesting materials that i) are available for free and ii) use the most permissible license possible. These are general materials about this blog topics.
This is still under construction: not everything is there yet.
I will update and keep up-to-date the resources presented here.
The list is open for new suggestions given that they respect the i) and ii) and have a striking interest - also I have to be able to understand them... ;)

Informatics

This list comes from the Resources chapter of my book "Computer Science for theoretical chemists & physicists" (to appear in 2020), but limited to free, downloadable, resources.
About Linux in general, but also the shell (especially Bash), the LDP is a good place to find some free documentation and reference books.
Among them, I recommend:

• "Introduction to Linux" by Machtelt Garrels which, as suggest by its title, focuses on Linux;
• "GNU/Linux Command Line Tools Summary" by Gareth Anderson is more about the CLI;
• "Bash Guide for Beginners" by Machtelt Garrels, which is a nice introduction to the Bash shell;
• Advanced Bash-Scripting Guide by Mendel Cooper, also known as simply ABS, which is an indispensable reference on Bash scripting.

For more programing-oriented resources (and C-focused), I recommend:

• "The C Preprocessor" by R.M. Stallman and Z. Weinberg: a concise, yet complete guide of the C preprocessor. Despite its name, the C preprocessor is used in many programing language other than C.
• "The C Book" by M. Banahan, D. Brady, and M. Doran: a general introduction of the C language.
• "Modern C" by J. Gustedt: a tour of C language scaled by increasing difficulties
• "CUDA C Programing guide" and the others CUDA API references, which are required for CUDA GPGPU programing.
• "Modern Computer Arithmetic" by R. P. Brent and P. Zimmermann: a very nice book on numerical analysis.
• OpenMP Application Programming Interface is a necessary C/FORTRAN openMP specification book¹. The short cheat sheets are also a very useful reminder for people who already know about openMP.
• MPI: A Message-Passing Interface Standard is the reference book¹ for MPI programing.

1: A standard book that is usually a bulky collection of reference material oriented toward people who might want to implement said standard. With a few exceptions, these are not book "for read by regular user". However, it's always a good thing to have such book lying around, to check for any specific "official" view.

Theory

• "A bird's-eye view of density-functional theory" by Klaus Capelle, gives a short (yet complete) introduction on DFT.
• "The GW Method" by F. Aryasetiawan and O. Gunnarsson is a full description of the GW method.
• "Nature of the Chemical Bond" by W.A. Goddard III is an old text but it present the fundation of theoretical chemistry.
• "A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry" by Pablo Echenique and J. L. Alonso is a more modern description of the HF theory.
• "A Brief Review of Elementary Quantum Chemistry" by C. David Sherrill, gives a short view on the basic of quantum chemistry.
• The Feynman Lectures on Physics, featuring R.P. Feynman, R. Leighton, M. Sands is an invaluable document keeping alive their teaching at Caltech of that era.

Simulation software

For a more complete list, I invite the reader to see a previous post from my ACS group.
Free resources:

• ABINIT: a DFT and GW calculation software. Very actively developed.
• CP2K: a DFT (GAPW), but also SE and classical FF calculation software. Useful for performing QM/MM simulations.
• DL_POLY: a general purpose MD software using FF. Use for very large scale simulation and some QM/MM with other QM software.
• GAMESS¹: a molecular quantum chemistry software. Can be interfaced with Tinker (a MM package) for QM/MM calculations.
• GROMACS: a MM software, known for its parallel efficiency.
• GULP²: a general MM software using lattice dynamics and FF. A one-of-its-kind program that allows computation of massive periodic systems.
• LAMMPS: a MD software. It is known for its scalability on massively parallel computers.
• MPQC: a general purpose quantum chemistry software. Known for being widely available (it is a regular package in some Linux distribution).
• NWChem: a polyvalent software that can perform DFT calculations using PW and pseudo-AO.
• OpenMX: a DFT simulation software, using pseudo-AO. It features a database of fully relativistic, or pseudo-AO, pseudo-potentials.
• Quantum Espresso: a PW simulation software at the DFT level. It features a lots of "plugins" which extend greatly its capabilities.
• SIESTA: a pseudo-AO DFT calculation software. Known for its order-N scability.
• VASP³: a commercial PW DFT software, known for its excellent performance and scalability.

1: GAMESS is free for academic or industrial use but require a mail registration.
2: GULP is free for academic use and require a valid university address. However, people who are not academic may find an interest in the GULP manual, which is more like a treatise of MM and lattice dynamics theory.
3: VASP is the only "fully" commercial software of this list. I added it because I have been using VASP on a regular basis since 2002. It is not available to individual but to "well defined" research groups (see FAQ).

Visualization Software

I also made a similar post in the past in my ACS group.

• Avogadro: a software for building/visualizing molecules. Uses FF and interfaces¹ with Abinit, Gamess, NWChem, and LAMMPS.
• Gabedit: another software to build/visualize molecules. Also uses FF and interfaces¹ with GAMESS and MPQC.
• GDIS²: a software for visualizing 0D to 3D chemical systems. Interfaces¹ with GULP, GAMESS, SIESTA, VASP, and USPEX.
• Ghemical: a molecular visualization software. Interfaces¹ with MPQC and can use FFs, can do periodic MM.
• Jmol/JSmol: a general visualization software. Written in Java (Jmol) or HTML5 (JSmol), it can be embedded in a webpage.
• PLATON: an old, Shelx compatible, visualization software. Can produce publication-quality ORTEP figures.
• RasMol: also an old visualization software. It was known for its ability to display PDB file formats.
• VESTA: a visualization software for 3D periodic systems. Note that contrary to others, VESTA does not allow access to its sources.
• VMD: a general purpose visualization software. It is known for allowing to display virtually infinite chemical systems.
• XCrySDen: a crystal and molecular visualization software, that can be useful to represent the Brillouin zone and select a k-point path.

1: The list are software from the previous list, the visualization software may interface with more and/or commercial programs.
2: I am currently involved in the integration of VASP and USPEX software in Gdis.

Databases

Following is a list of some databases I often use.

• NIST Chemistry WebBook¹ provides information about searchable chemical systems. Thermodynamic data are of particular interest here.
• The NIST Reference on Constants, Units, and Uncertainty¹ is a very useful collection of constants within many conversion units.
• The Materials Project² is a large (the largest?) collection of computational results on materials. Especially useful to check on the electronic and geometric structure of a materials.
• The Alloy Database is a little older (unmaintained?) project that gathered the energy and struture results for a wide range of alloys.
• The Character Tables for Point Groups used in Chemistry is a very useful database of geometry character tables. I often use it to ascribe the Angular momentum of a band to a given point group, and vice versa.
• The RUFF project^3,4 is a database XRD and Raman spectroscopy. It features useful experimental spectra records.
• The COD⁴ is another XRD database whith a large collection. It provides experimentally determined structures of a huge amount of biochemicals.

1: NIST is actually running a galaxy of databases, some with interconnections between them.
2: Access to the Materials Project is free, but require an email/Google/Github registration.
3: I don't know what RUFF stands for. I have look at their papers and other materials but I never could figure out... If you have an idea, please drop me a line.
4: Both RRUFF and COD can be fully download for offline use, here and here, respectively. However, please be careful of the large size of the archives.