INPUTFILETEMPLATE.gjf
1_PESscan.bash
2_bcf.bash
3_gaussian_bcf_top4lines.txt

The above scripts were made to overcome some of the potential energy surface (PES) scan limitations (well, design issues I’d rather not design around) in GAMESS and Gaussian. The intent of the scripts are to:

a) take a molecular input file from some quantum chemical code

b) align the molecule such that the surface you want to perform the PES scan across is aligned in the XY, YZ, or XZ planes

c) define the atom/molecule you want to scan with (such as a cation) in variable form in the input file template

d) define the grid size you want to perform the scan with (how fine a mesh)

e) generate the input files

and finally,

f) write out a command line script in a format that leaves for little post-processing for both the calculation and the analysis.

The demo case will be the (nominally, depending on the level of theory) C_2v molecular anion (-1) diphenylmethanide in Gaussian, which will also hit a couple of technical points to speed up the PES scan. The intent was to take a cation (K⁺, Rb⁺) and determine the binding energies of the cation/anion pair over the (here, YZ) plane of the molecule to look at preferred binding positions and, more interestingly, the range in binding energies at different positions (see figure below).

A few setup point for the script (general):

1. The molecule should be aligned along a plane (assuming it is planar. If not, you’ll have to tweak the code a little to taste, which isn’t too bad) because the script is going to sweep along Y and Z with the assumption that X is a constant vertical value above the plane of the molecule. The goal is to make a 2D map of a surface at one height, then change the height and redo the scan to look at the energy differences in sheets.

2. A molecule optimized in GAMESS and Gaussian should, provided symmetry is employed, orient the molecule such that a molecular plane is aligned along a Cartesian plane. In Gaussian, using the keyword symm(loose,follow) will both nudge a molecule into a higher symmetry and maintain that higher symmetry in the optimization. For the sake of the surface scan, this restriction of the molecule to a higher point group saves significant time, makes the analysis of the script results easier, and will not significantly alter the energies of a molecule whose minimum lies close to a higher symmetry form anyway (the differences in energy between the C_2v and C_s diphenylmethanide structures, for instance, is on the order of a few kJ/mol by most levels of theory when the level of theory does NOT predict the C_2v form to be the minimum).

3. Negative values are OK in the script, although some shells may not like having the “-” sign in the name of the files. If this is a problem on your machine, take the oriented molecule from Step 1 and add some constant value to all of the X, Y, Z coordinates to make the corner of the scan you start the X,Y,Z analysis from be (X,0,0). I use “X” here because the molecule may best be aligned to the X = 0 plane, which is easiest for some of the later post-processing.

4. If your molecule has two mirror planes (such as diphenylmethanide), set up the scan such that you’re only looking at HALF the structure. That should make perfect sense.

The scripts are provided in the links below. Their uses and results are as follows:

Input File 0. INPUTFILETEMPLATE – this file contains the parameters and coordinates for the PES scan. Make sure that this isn’t just a cut-and-paste of the optimization file (change the keywords so you run only SINGLE POINT CALCULATIONS!). More on this file below.

Input File 1. 1_PESscan.bash – the bash script that takes a template input file and generates (a) all of the single-point energy input files for the scan and (b) a batch file for submitting all of the files.

Input File 2. 2_bcf.bash – this is Gaussian-specific for the standard Gaussian PC interface, where the script for running multiple jobs is defined in the batch control file (bcf). This script gets the formatting right. Not needed for GAMESS, etc., calculations.

Input File 3. 3_gaussian_bcf_top4lines.txt – this file could be embedded into the 2_bcf.bash file if you like. Part of the 2_bcf.bash script catenates (with cat) the contents of this file and the contents of name files in the right bcf format. This will make perfect sense after the first run.

Output File 4. 4_batchscript.bat – this file (with the numerous input files) is generated from the 1_PESscan.bash script and contains all of the input files and execution parameters for the prompt. Will be Windows- or UNIX-friendly if you did it right.

Output File 5. 5_bcf_for_gaussian.bcf – this is the batch control file for Windows-based Gaussian calculations generated from 2_bcf.bash.

Specifics of each file are provided below:

Input File 0. INPUTFILETEMPLATE

The input template file should look like the following…

%mem=500MB
%nproc=2
# scf=tight b3lyp/6-31+g(d,p) integral(grid=ultrafine)

diphenylmethanide surface scan

0 1
K             REPLACEX    REPLACEY    REPLACEZ
C             0.000000    0.000000    0.940353
C             0.000000    1.308620    0.380671
...

Note that the molecule is aligned along X=0 and that I replaced opt with scf from the molecular optimization. You don’t want to disappear for a weekend only to find that you’ve done 4 structure optimizations when you could have done 100 single-point calculations. The cation we’re sliding with is defined with its X,Y,Z coordinates as REPLACEX,REPLACEY,REPLACEZ. These variables will be replaced by values along the PES grid by running 1_PESscan.bash.

Input File 1. 1_PESscan.bash

The usage of this bash script is:

./1_PESscan.bash $1 $2 $3 $4 $5 $6

or, for instance,

./1_PESscan.bash Kdiphenylmethanide gjf g03 100 25 25

Here are what the variables are.

$1 = name of the input file template (no extension)
$2 = name of the file extension (gjf for Gaussian, inp for GAMESS, etc.)
$3 = command line executable (g03 for Gaussian, gms… for GAMESS
$4 = decimal increments for the X axis (100 = unit, no decimals)
$5 = decimal increments for the Y axis (100 = unit, no decimals)
$6 = decimal increments for the Z axis (100 = unit, no decimals)

You’re limited to nine variables in the command line, so there’s one modification you need to make to the 1_PESscan.bash file itself. In the first section, MINX through MAXZ need to be defined. These are the integer steps taken by the script to generate the surfaces. These will depend on how you oriented your molecule. The decimal increments will not (which is why they’re called in the command line).

Input File 2. 2_bcf.bash

There’s nothing to edit here. It will take all of the Gaussian input (.gjf) files in a directory and make the corresponding .bcf file. Major time-saver.

Input File 3. 3_gaussian_bcf_top4lines.txt

This file contains the following…

!
!user created batch file list
!start=1
!

Which is just the typical 4 top lines in a bcf file (start referring to which molecule in the series gets run first).
And that’s the worst of it. Definitely practice the script(s) a few times before beginning a calculation, expect some fuss (depending on how you’ve pathed your executables) initially, and start with very COARSE grid sizes before wasting a lot of time on generating and checking files (decimal increments of 100 or 50, for instance).

A brief word on the input/output files. The format for the file names generated from 1_PESscan.bash are as follows.

INPUTFILETEMPLATE_X_2.000000_Y_0.000000_Z_0.000000.gjf
INPUTFILETEMPLATE_X_2.000000_Y_0.000000_Z_0.500000.gjf
INPUTFILETEMPLATE_X_2.000000_Y_0.000000_Z_1.000000.gjf
INPUTFILETEMPLATE_X_2.000000_Y_0.000000_Z_1.500000.gjf
...

The format (with six decimal places) is used here so that a user can simply use “ls *.gjf > file.txt” to generate a text file with all of the scanned coordinates, which can then be opened in Excel or something to make the position columns. Further, of course, is that a grep for the final energies in these files will make another file with the coordinates and energies together, which is then easily tweaked and plotted.

That’s the worst of it, short of plotting a few surfaces. Any questions or better ideas, drop a line.

www.msg.ameslab.gov/GAMESS/
www.gaussian.com

I had far too much fun to not make mention of my first trip to Texas and keynote.

9/16 – Hotel. The photo above was my view of San Antonio from the 14th floor of the Crowne Plaza Hotel. Having stayed in and worked all day, it took me until the 17th to realize that San Antonio is, in fact, an actual big city. One that happens to exist to the North, East, and South of my due-West window. You can see for yourself the arrangement of the city here.

9/17 – The Alamo. My godmother’s friend’s great-grandfather, William DePriest Sutherland (web and local pdf copy), was a 17-year-old courier (perhaps performing the duties of his uncle John S. Jr.) who died during the fighting on March 6, 1836. After 170 years, it’s still a small world (if you need more proof, I link Kevin Bacon to the Alamo in 6).

9/18 – Movie. The first full day of the conference began at 5:00 am with a 14th floor fire alarm. As a chemist (well, sort of) working in a big box of laboratories full of organic vapors, my usual inclination is to run like hell when the fire alarm goes off. Much to my surprise, the directions in large hotels are to hold still until the origin of the alarm can be ascertained (you never know what… state the guests are in). The next thing I remember was waking up fully dressed in the previous day’s clothes (ready to run with nothing from the ironing board). The rest of the day was spent regretting not having taken Spanish in high school, having already regretted not taking German in high school to make my translation of German chemical journals easier. C’est dommage.

The contents of the conference are worth their own posting because, frankly, it’s too important generally to bury within a slide show. So, I skip the details…

The post-conference reception featured a 9-piece Mariachi band that were getting INTO it. Click on the image to launch a 30 second snippet (you’ll need a recent Quicktime. they’re playing my song, as it was the only Mariachi tune I knew).

9/18 – Crossroads. Carolyn Kelley is my new favorite Greek just north of the south of the border. En route to the famed Riverwalk, San Antonio’s official response to Syracuse’s Armory Square, we passed by the blurred hotel in the photo. This was the hotel, according to legend, where Robert Johnson wrote “Crossroads.” I need say no more.

9/19 – Javier. After the second day’s meeting, the assembly retired to a late lunch where I was finally able to pull my keynote translator, Javier Román, aside. It’s bad enough having to translate on the fly. It is a whole level worse when scientific lingo/jargon is being thrown around as part of the content. It is, further, a whole other matter to have to work around occasionally incoherent, rambling, unfocused presenters (like myself). On top of all that, a glitch with the translation headsets meant I had to give my presentation to him on stage in 30 second sound bites, making my 45 minute talk last about 1 hour 25 min (which, actually, was a really nice way to give a presentation, as I had plenty of time to think about what I wanted to say for the next slide AND had to make sure I curtailed my proclivity for verbosity). I don’t know what he said, but he’s AOK in my book.

9/20 – Abel and Jim. I spent several minutes trying to pack my bull horns into a suitcase already replete with my toiletries (there’s a big difference between personal grooming and personal hygiene. As a policy (and because crazy scientists are supposed to, well, LOOK the part), I focus on the latter) thanks to events at Heathrow (and note the timing of the acceptance of the PETN paper in ChemPhysChem). The rest of the morning featured a short interview for Univision and last-minute photo ops with Dr. Abel Navarro, my gracious host and conference chair, and Mr. James Dickerson, who made the presentation logistics as easy as turning my Powerbook on.

9/20 – Just of interest to note that American cities in-progress look remarkably like the Greek and Roman ones that didn’t make it over the longer haul.

www3.interscience.wiley.com/cgi-bin/jhome/72514732?CRETRY=1&SRETRY=0
www.ichotelsgroup.com/h/d/cp/1/en/hotel/satps?_requestid=631248
http://maps.google.com/maps?f=l&hl=en&q=crowne+plaza&amp…
www.tsha.utexas.edu/handbook/online/articles/SS/fsu20.html
en.wikipedia.org/wiki/Six_Degrees_of_Kevin_Bacon
en.wikipedia.org/wiki/Robert_Johnson
www.accd.edu/wfd/global/index.htm
www.thesanantonioriverwalk.com
www.somewhereville.com/?p=51
www.inspanamericano.com
www.heathrowairport.com
www.armorysquare.com
www.univision.com
www.thealamo.org
www.mariachi.org