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

Monday, September 1st, 2014

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
...
...
 ******************************************
 Gaussian 09:  EM64L-G09RevA.02 11-Jun-2009
                31-Aug-2014 
 ******************************************
...
 incident light, reduced masses (AMU), force constants (mDyne/A),
 and normal coordinates:
                     1                      2                      3
                     T                      T                      T
 Frequencies --  1356.0058              1356.0058              1356.0058
 Red. masses --     1.1789                 1.1789                 1.1789
 Frc consts  --     1.2771                 1.2771                 1.2771
 IR Inten    --    14.1123                14.1123                14.1123
  Atom  AN      X      Y      Z        X      Y      Z        X      Y      Z
     1   1    -0.03   0.42   0.43    -0.34  -0.14   0.07    -0.36  -0.23   0.23
     2   6     0.00  -0.08  -0.10     0.01   0.10  -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
...
...
 ******************************************
 Gaussian 09:  EM64L-G09RevD.01 24-Apr-2013
                31-Aug-2014 
 ******************************************
...
 incident light, reduced masses (AMU), force constants (mDyne/A),
 and normal coordinates:
                      1                      2                      3
                     ?A                     ?A                     ?A
 Frequencies --   1356.0132              1356.0132              1356.0132
 Red. masses --      1.1789                 1.1789                 1.1789
 Frc consts  --      1.2771                 1.2771                 1.2771
 IR Inten    --     14.1119                14.1119                14.1119
  Atom  AN      X      Y      Z        X      Y      Z        X      Y      Z
     1   1     0.02   0.42   0.43     0.34  -0.14   0.08    -0.36   0.23  -0.23
     2   6     0.00  -0.08  -0.09    -0.01   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
...

Two of these things are not like the other. The data’s nearly identical (and thank heavens. Unfortunately, Gaussian09 D.01 didn’t see the fully-optimized methane as belonging to the Td point group – despite all three versions being run with the same exact input file – but a rigorous re-symmetrization would have taken care of that), but there are some subtle formatting differences between all three versions (including differences between both Gaussian09 versions) that cause the venerable, all-encompassing aClimax program (developed by Timmy, the venerable, all-encompassing A. J. Ramirez-Cuesta) to throw out the following errors for all three cases when you use *.log files from a *nix (UNIX, Linux) machine.

Serious Error: A-CLIMAX has encountered an unhanded error. Please Save your data and contact support
aClimax: Quote Error Number 9
Error Loading File: Error reading data. Please check and try again.
aClimax: WARNING loaded file containing no frequencies

Problem number 1 is the existence of *nix newlines (carriage returns) in the *.log files coming off a *nix machine. Performing a conversion from *nix to DOS (for myself, using LineBreak in OSX, but tofrodos works just as well), the Gaussian03 file now opens just fine in aClimax:

File Loaded: Data Loaded Succesfully [sic].

This, unfortunately, does not improve the matter with the Gaussian09 files, which produce the following error:

Error: One of the numbers you have entered is of the wrong type.Please recheck and try again
Error Loading File: Error reading data. Please check and try again.

Given how little of the .log file aClimax actually needs to produce simulated inelastic neutron scattering (INS) spectra, I ran the methane normal mode analyses in three different Gaussian versions to determine what, in G09, was changed to make it just un-G03 enough to fail to load. With those changes figured out, I had a Perl script drafted up that would have converted everything back to the original G03 format. It was awesome. That said, after a small amount of testing to see where aClimax’s sensitivities lay, I discovered that very little of the .log file contents needed to be changed out, meaning that simple sed scripts would work just as well for those of us using our Windows boxes (or VirtualBox emulations) only for that “one stupid program” that keeps us having to log in (and, by that, I mean that we have sed already on our computers).

So, the problems between G09 and aClimax not related to carriage returns lie in two places.

1. The spacing of “Atom AN” – at the top of the eigenvector lists are the column labels, beginning with “Atom AN” – or something very close to “Atom AN” (the “|” in the boxes below mark the left edge of the output):

G03 E01 | Atom AN
G09 A02 |   Atom  AN
G09 D01 |  Atom  AN

Yes, the addition of a space or two results in a read error by aClimax. I would call this an… aggressive stringency in aClimax. That said, what did the original space in G03 versions not do that they do do in G09?

2. The spacing of “Atom N” – In the “Thermochemistry” section below the eigenvectors, atomic masses are listed as “Atom N” – or something very close to “Atom N” (again, the “|” in the boxes below mark the left edge of the output):

G03 E01 |  Atom  1
G09 A02 |    Atom     1
G09 D01 |   Atom     1

This change in spacing is also enough to cause aClimax to error out.

The Solution

A small sed script performs the necessary conversions on your *nix box (including OSX) for all .log files in a directory without issue:

#!/bin/sh

# This section converts all .log files to aClimax-friendly G03-ish format
find . -type f -name '*.log' -print | while read i
do
sed 's|  Atom  AN| Atom AN |g' $i > $i.aclimaxconversion_step1
sed 's| Atom   | Atom|g' $i.aclimaxconversion_step1 > $i.aClimaxable.log
rm $i.aclimaxconversion_step1
done

# This section converts all .out files to aClimax-friendly G03-ish format
find . -type f -name '*.out' -print | while read i
do
sed 's|  Atom  AN| Atom AN |g' $i > $i.aclimaxconversion_step1
sed 's| Atom   | Atom|g' $i.aclimaxconversion_step1 > $i.aClimaxable.out
rm $i.aclimaxconversion_step1
done

But Wait! Running G0* Jobs Under *nix? Convert To DOS Carriage Returns

The final problem halting your aClimax spectrum generation is the DOS carriage return (^M). For those running DOS-based Gaussian calculations (likely with a .out suffix), your conversion with the short script above (under *nix) likely (hopefully) worked just fine. For those running under *nix, you performed the conversion and still received the following aClimax error:

Serious Error: A-CLIMAX has encountered an unhanded error. Please Save your data and contact support
aClimax: Quote Error Number 9
Error Loading File: Error reading data. Please check and try again.
aClimax: WARNING loaded file containing no frequencies

The solution is an additional line in the sed script that will globally replace all *nix newlines with proper DOS carriage returns. The .out section remains the same.

#!/bin/sh

# This section converts all .log files to aClimax-friendly G03-ish format
find . -type f -name '*.log' -print | while read i
do
sed 's|  Atom  AN| Atom AN |g' $i > $i.aclimaxconversion_step1
sed 's| Atom   | Atom|g' $i.aclimaxconversion_step1 > $i.aclimaxconversion_step2
# This section converts your *nix newlines into DOS carriage returns
CR=`echo "\0015"`  # define the Carriage Return
sed -e "s/$/${CR}/g" $i.aclimaxconversion_step2 > $i.aClimaxable.log
done
# this cleans up your folder of temp files
rm *.aclimaxconversion_step1
rm *.aclimaxconversion_step2

# This section converts all .out files to aClimax-friendly G03-ish format
find . -type f -name '*.out' -print | while read i
do
sed 's|  Atom  AN| Atom AN |g' $i > $i.aclimaxconversion_step1
sed 's| Atom   | Atom|g' $i.aclimaxconversion_step1 > $i.aClimaxable.out
rm $i.aclimaxconversion_step1
done

Q. But what if I run the *nix-to-DOS version of the script on an already DOS-output file?

A1. The simple answer is that you’ll make your text file double-spaced (which is bad enough). aClimax will then provide the following error when you try to open it:

Error Reading File: Unexpected File End. File May be incorrect or corrupt.
Error Loading File: Error reading data. Please check and try again.

A2. I will assume that your problem is that you’re running the script in DOS to try to get your G09 to read more like G03. In this case (assuming you’re generating .out files), you’ll want to use a text editor to make the replacements described above (which is to say, that Perl script might makes it way to this page eventually. If you write a DOS .bat file or similar script for all OS’s, I’d be happy to link to it).

Commensurate Urea Inclusion Crystals With The Guest (E,E)‐1,4-Diiodo-1,3-Butadiene

Friday, December 20th, 2013

Published in Crystal Growth & Design (Cryst. Growth Des., 2013, 13 (9), pp. 3852–3855) earlier this year. The theory work is less impressive than the successful crystal growth, with initial solid-state efforts in Crystal09 only very recently now producing good results (leaving the molecular calculations to Gaussian09 in this paper). The procedure leading to the observed crystal structure of this inclusion complex is a significant step in the direction of testing the theory proposed in Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential published earlier this year in J. Mol. Struct.

2013dec20_DIBD_UIC

Caption: Two views along the ba and ca crystal axes of the (E,E)‐1,4-Diiodo-1,3-Butadiene : Urea Inclusion Complex.

Amanda F. Lashua, Tiffany M. Smith, Hegui Hu, Lihui Wei, Damian G. Allis, Michael B. Sponsler, and Bruce S. Hudson

Abstract: The urea inclusion compound (UIC) with (E,E)-1,4-diiodo-1,3-butadiene (DIBD) as a guest (DIBD:UIC) has been prepared and crystallographically characterized at 90 and 298 K as a rare example of a commensurate, fully ordered UIC. The crystal shows nearly hexagonal channels in the monoclinic space group P21/n. The DIBD guest molecules are arranged end-to-end with the nonbonding iodine atoms in the van der Waals contact. The guest structure is compared with that for DIBD at 90 K and with computations for the periodic UIC and isolated DIBD molecule.

Dipole Derivative, Polarizability Derivative, And Vibrational Polarizability Contribution Output From Gaussian09 With IOp(7/33)

Thursday, August 30th, 2012

For those itching for polarizability derivative orientation information and wondering where it is when you ask for it… what’s included below is a combination of a few points in one, specifically pointing out that the IOp options are not just “another part” of the Gaussian input file (with the IOp Overlays currently linked HERE).

The problem I realized after an email from Gaussian HQ was that, as was the case for the KMLYP density functional call discussed in previous posts about [18]-annulene, “opt” and “freq” keyword combinations are seen as two distinct runs in Gaussian that don’t pass the IOp information along (and, admittedly, I should have remembered that). Specifically, the additional print-out for the polarizability info is called by IOp(7/33=3).

What I provide below is a two-in-one input file that saves you from having to run double-duty input files in the checkpoint file. This also serves as a template for those looking for examples of combining multi-step input files that include mixed basis sets (as many of the problems I’ve been emailed stem from carriage return issues more than anything else). Note that the input file is set to run Raman intensities and produce higher-precision (hpmodes) eigenvectors (so, if you just want to test this, remove the “raman”).

%chk=C4H5Cl_B3LYP_631Gdp_LanL2DZ_IR_Raman.chk
#p scf=tight opt=tight b3lyp/GEN pseudo=read

C4H5Cl_B3LYP_631Gdp_LanL2DZ_IR_Raman Opt

0 1
 C                 -1.74671095   -0.64168298    0.00000000
 H                 -1.53944096   -1.69141587    0.00000000
 C                 -0.73010315    0.25446188    0.00000000
 H                 -0.93737314    1.30419477    0.00000000
 C                  0.73010315   -0.25446188    0.00000000
 H                  0.93737314   -1.30419477    0.00000000
 C                  1.74671095    0.64168298    0.00000000
 H                  1.53944096    1.69141587    0.00000000
 H                 -3.73526840    0.03531673    0.00000000
 Cl                 3.73526840   -0.03531673    0.00000000

C H 0
6-31G(d,p)
****
Cl
Lanl2DZ
****

Cl
Lanl2DZ

--Link1--
%chk=C4H5Cl_B3LYP_631Gdp_LanL2DZ_IR_Raman.chk
#p Geom=Check Guess=Read freq(raman,hpmodes) iop(7/33=3)
 
C4H5Cl_B3LYP_631Gdp_LanL2DZ_IR_Raman Freq
     
0 1

Note the carriage return after the second “0 1″.

For the demo molecule above, additional print-out below.

 Dipole derivatives wrt mode   1:  3.96988D-14 -1.15747D-14 -1.96904D-01
 Polarizability derivatives wrt mode          1
                 1             2             3 
      1   0.000000D+00  0.000000D+00  0.206435D+00
      2   0.000000D+00  0.000000D+00  0.143916D-01
      3   0.206435D+00  0.143916D-01  0.000000D+00
 Vibrational polarizability contributions from mode   1       0.0000000       0.0000000       0.0257731
 IFr=  0 A012= 0.23D-23 0.77D+00 0.13D+00 Act= 0.90D+00 DepolP= 0.75D+00 DepolU= 0.86D+00

Alternately, keep track of the checkpoint file.

Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential

Sunday, August 5th, 2012

In press (DOI:10.1016/j.molstruc.2012.07.051) in the Journal Of Molecular Structure. May go down in history as a hardest-fought paper acceptance. In a similar line of research as the [18]-annulene study, but exploring the infinite limit of geometry and bond length alternation energy barrier for this infinite case. If the numbers are correct, the infinite polyene chains (polyacetylene) do not exhibit bond length alternation because the Peierls’ barrier between the single-double and double-single bond alternate minima is below the vibrational zero-point level. Plenty of ramifications.

Bruce S. Hudson and Damian G. Allis

Abstract. The potential energy of the infinite periodic chain model of polyacetylene (pPA) is symmetric with two equivalent minima separated by the Peierls’ stabilization barrier. In this work it is shown how an energy scale and vibrational energy levels for this highly anharmonic Peierls’ degree of freedom can be estimated. Attention is given to the potential energy increase for large deformations. The Born-Kármán treatment of translational symmetry is applied. Two empirical methods and a direct periodic boundary condition (PBC) density functional theory (DFT) calculations are in semi-quantitative agreement, each leading to the conclusion that pPA has a zero-point level that is above the Peierls’ barrier. The argument does not depend critically on the barrier height or the other parameters of the model or the computation method. It is concluded that pPA will not exhibit bond alternation and that the zero-point average geometry does not preclude possible conductivity.

The Structure Of [18]-Annulene: Computed Raman Spectra, Zero-Point Level And Proton NMR Chemical Shifts

Saturday, August 4th, 2012

In press (DOI:10.1016/j.molstruc.2012.05.016) in the Journal Of Molecular Structure (Volume 1023, 12 September 2012, Pages 212–215) in the special issue: MOLECULAR VIBRATIONS AND STRUCTURES: THEORY AND EXPERIMENT — A collection of papers dedicated to Professor Jaan Laane on the occasion of his 70th birthday.

This paper on the “actual” geometry of [18]-annulene is part of several larger stories addressing a larger polyene (or larger-polyene) issue. First among these is the meaning of experimental results obtained by various spectroscopic methods (in this case, using previous X-ray, Raman (with the C2 (blue) and D6h (red) simulated spectra shown in the image above), IR, and NMR data that produce different results within the limitations of the methods to study the single molecule). Second is the quality of the theoretical method for reproducing certain types of spectroscopic data. In the case of the [N]-annulene series, the ever-present B3LYP density functional is found to produce the time-average geometry of [18]-annulene found in X-ray data, but another density functional (in this case, KMLYP), finds that bond-alternate minima exist. Third is the importance of the zero-point level in the treatment of systems for which bond-alternate geometries exist with transition-state barriers calculated to be below the zero-point level in the classical approximation of nuclear positions (the Born-Oppenheimer Approximation).

NOTE 1: The KMYLP density functional is called in Gaussian with the following keyword set:

BLYP iop(3/76=1000005570) iop(3/77=0000004430) iop(3/78=0448010000)

NOTE 2: Optimization and Frequency calculations must be performed as TWO SEPARATE CALCULATIONS. The iop-called density functional does not carry itself over between opt + freq (or other properties) in the same input file. If you opt + freq in the same input file, you will Opt with KMLYP but freq with BLYP. This will be obvious by the number of imaginary modes.

Bruce S. Hudson and Damian G. Allis

Abstract. [18]-annulene has been of great interest from the structural point of view of its bond alternation. High-level calculations based on structures selected for agreement with NMR spectra lead to a bond-alternate C2 form over a non-alternating planar D6h structure deduced from diffraction, infrared (IR) and electronic spectral studies. Here it is shown that computed Raman spectra for the D6h and C2 forms are expected to be very different. However, two equivalent non-D6h bond-alternate minima of D3h or C2 geometries are separated by only a small barrier along a motion that involves CC stretching and compression. It is shown here that the zero-point level is above the barrier for this species. In light of that fact, the NMR calculations are reconsidered with inclusion of zero-point level averaging.

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