More On The Virtues Of VirtualBox – ACID (or AICD) Under Ubuntu 14.04 (By Way Of OpenSuse 11.2)

“Stop that!” – George Carlin

If you’ve obtained source code from an academic lab that was last developed some time ago and you spent a whole day installing libraries and symbolic links and redefining variables in your .bashrc and downgrading libraries and redefining paths and have 20 tabs open in your browser that all go to 20 different obscure error discussions on Stack Overflow and it’s late and you’re tired and you think you might not need the program after all if you do a bunch of other workaround things instead – what’s below is for you.

Academics have been developing small code for (nearly) millions of years to make their lives easier – and we all benefit when that code is made available to others (esp. when it helps in data analysis). When that code is a series of perl or python scripts, there’s generally little reason why you should have any run issues. When they call on external libraries or specific tools, generally that information is available in the README somewhere. Generally speaking, there’s no reason why a code shouldn’t work in a straightforward manner when the developer doesn’t make it known that something else needs be installed to make it work.

So, why doesn’t code A work on your linux box? A few possibilities.

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The EMSL Basis Set Exchange 6-31G, 6-31G(d), And 6-31G(d,p) Gaussian-Type Basis Set For CRYSTAL88/92/95/98/03/06/09/14/etc. – Conversion, Validation With Gaussian09, And Discussion

Jump to the basis sets and downloadable files here: files, 6-31G, 6-31Gd, 6-31Gdp.

If you use these results: Please drop me a line (damian@somewhereville.com), just to keep track of where this does some good. That said, you should most certainly cite the EMSL and Basis Set references at the bottom of this page.

It’s a fair bet that Sir John Pople would be the world’s most cited researcher by leaps and bounds if people properly cited their use of the basis sets he helped develop.

The full 6-31G, 6-31G(d), and 6-31G(d,p) series (yes, adding 6-31G(d) is a bit of a cheat in this list) from the EMSL Basis Set Exchange is presented here in the interest of giving the general CRYSTALXX (that’s CRYSTAL88, CRYSTAL92, CRYSTAL95, CRYSTAL98, CRYSTAL03, CRYSTAL06, CRYSTAL09, now CRYSTAL14 – providing the names here for those who might be searching by version) user a “standard set” of basis sets that are, for the most part, the same sets one does / could employ in other quantum chemistry codes (with my specific interest being the use and comparison of Gaussian and GAMESS-US in their “molecular” (non-solid-state) implementations). Members of the CRYSTAL developer team provide a number of basis sets for use with the software. While this is good, I will admit that I cannot explain why the developers chose not to include three of the four most famous basis sets in all of (all of) computational chemistry – 3-21G (upcoming), 6-31G(d,p) (presented here), and 6-311G(d,p) (also upcoming).

Continue reading “The EMSL Basis Set Exchange 6-31G, 6-31G(d), And 6-31G(d,p) Gaussian-Type Basis Set For CRYSTAL88/92/95/98/03/06/09/14/etc. – Conversion, Validation With Gaussian09, And Discussion”

For The Windows-Specific: Sed For Windows And A .bat File To Get Gaussian09 Files Working With aClimax

Provided you’ve installed Sed For Windows and know its proper path, the .bat file below should make all the modifications you need to your Gaussian09 .out files (in differently-named files at that) to get them properly loading in aClimax (see the previous post for all the details). A few simple steps:

1. Download and install Sed for Windows. Currently available at: gnuwin32.sourceforge.net/packages/sed.htm

2. Find its location on your machine. Under XP (where I’m using aClimax), this should be C:\Program Files\GnuWin32\bin

Continue reading “For The Windows-Specific: Sed For Windows And A .bat File To Get Gaussian09 Files Working With aClimax”

Stupid-Simple (*nix-Specific) Sed Scripts To Get (All Current) Gaussian09 Output Files Working With aClimax

The following three snippets of Gaussian output are for an optimization and normal mode analysis of simple olde methane (CH4).

...
 ******************************************
 Gaussian 03:  EM64L-G03RevE.01 11-Sep-2007
                31-Aug-2014 
 ******************************************
...
 incident light, reduced masses (AMU), force constants (mDyne/A),
 and normal coordinates:
                     1                      2                      3
                     T                      T                      T
 Frequencies --  1356.0070              1356.0070              1356.0070
 Red. masses --     1.1789                 1.1789                 1.1789
 Frc consts  --     1.2771                 1.2771                 1.2771
 IR Inten    --    14.1122                14.1122                14.1122
 Atom AN      X      Y      Z        X      Y      Z        X      Y      Z
   1   1     0.02  -0.42   0.43    -0.34  -0.13  -0.08    -0.36  -0.23  -0.23
   2   6     0.00   0.08  -0.09     0.00   0.09   0.08     0.12   0.00   0.00
...
 -------------------
 - Thermochemistry -
 -------------------
 Temperature   298.150 Kelvin.  Pressure   1.00000 Atm.
 Atom  1 has atomic number  1 and mass   1.00783
...

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CCSD(T) and MP4 Z-Matrix Coordinate Oddity In Gaussian: When In Doubt, Change Your Format

This post was instigated by Syracuse University Professor of Chemistry and well-known non-blogger Tim Korter concerning efforts to, I believe, generate proper Møller–Plesset Perturbation Theory Of The 4th Order (MP4, and also testing coupled cluster CCSD(T) calculations) intermolecular potentials for improving terms for Grimme dispersion-corrected density functional theory (DFT) calculations with the Gaussian09 package (a program for which many people grumble about various issues but which is, by nearly all metrics, a fantastic set of quantum chemical programs). The examples below, using water only, are just for ease-of-testing, which produce the following results based on the form of the input of the molecular coordinates. For those wondering why, z-matrices are the preferred format for performing SCAN or other automated trajectory calculations (an absolutely useless format, in my opinion, now that we have computers that can handle more than five atoms).

Continue reading “CCSD(T) and MP4 Z-Matrix Coordinate Oddity In Gaussian: When In Doubt, Change Your Format”

Crystal06 (v.1.0.2) And MPICH-1.2.7p1 In Ubuntu Desktop 8.10 (and 9.04, 64- and 32-bit) Using The Intel Fortran Compiler, Version 1.0

Update 19 May 2009 – This tutorial (and all subsequent modifications) are now on a separate page on this website and will not be modified further in this post.  This page is available HERE.  The forever-name PDF version of the tutorial is available here: crystal06_mpich_ubuntu_cluster.pdf

Pre-19 May 2009 – This document, the end of a very long and involved process, is available as a PDF download (for reading and printing ease) here: crystal06_mpich_ubuntu_cluster_V1.pdf

Introduction

According the Crystal06 manual:

The CRYSTAL package performs ab initio calculations of the ground state energy, energy gradient, electronic wave function and properties of periodic systems. Hartree-Fock or Kohn-Sham Hamiltonians (that adopt an Exchange- Correlation potential following the postulates of Density-Functional theory) can be used. Systems periodic in 0 (molecules, 0D), 1 (polymers, 1D), 2 (slabs, 2D), and 3 dimensions (crystals, 3D) are treated on an equal footing. In each case the fundamental approximation made is the expansion of the single particle wave functions (‘Crystalline Orbital’, CO) as a linear combination of Bloch functions (BF) defined in terms of local functions (hereafter indicated as ‘Atomic Orbitals’, AOs).

Continue reading “Crystal06 (v.1.0.2) And MPICH-1.2.7p1 In Ubuntu Desktop 8.10 (and 9.04, 64- and 32-bit) Using The Intel Fortran Compiler, Version 1.0”