609. NBO6 on a debian cluster (/w g09)

Curse blogspot and the lack of revision control and backups! I lost my post when it was almost finished.

So here's a briefer version. I have bought NBO6 and I want to integrate it with gaussian G09 rev. D (you can't use it directly with earlier binary versions)

My 'instructions' are basically copy/pasted from the NBO6 installation instructions -- this is a tl;dr version.

sudo cp nbo6.0-bin-linux-x86_64.tar.gz /opt/
cd /opt/
sudo tar xvf nbo6.0-bin-linux-x86_64.tar.gz 
sudo chown $USER:$USER nbo6 -R
vim nbo6/bin/gaunbo6

Edit:

3 set INT    = i8
  4 set BINDIR = /opt/nbo6/bin

In your queue file add

set path = ( /opt/nbo6/bin $path )

In my case, as I use ECCE I edited my apps/siteconfig/CONFIG.node files:

Gaussian-03Command{
set path = ( /opt/nbo6/bin $path )
setenv GAUSS_SCRDIR /home/me/scratch
setenv GAUSS_EXEDIR /opt/gaussian/g09d/g09/bsd:/opt/gaussian/g09d/g09/local:/opt/gaussian/g09d/g09/extras:/opt/gaussian/g09d/g09
/opt/gaussian/g09d/g09/g09< $infile > $outfile 
echo 0
}

I then tested it by running a basic gaussian calculation:

%Chk=H2O_631g.chk
#P rOPBE/6-31G 6D 10F SCRF=(PCM,Solvent=water)  Punch=(MO) pop=(nbo6)

H2O 6-31G

 0 1 ! charge and multiplicity
 O     0.00000     0.00000     0.118491
 H     0.00000     0.754898     -0.473964
 H     0.00000     -0.754898     -0.473964

and got

...
411          fchk file        "/home/me/scratch/Gau-24659.EFC"
412          mat. el file     "/home/me/scratch/Gau-24659.EUF"
413 
414  Writing Wrt12E file "/home/me/scratch/Gau-24659.EUF"
415  Gaussian matrix elements                                         Version   1 NLab= 7 Len12L=8 Len4L=8
416  Write GAUSSIAN SCALARS               from file   501 offset           0 to matrix element file.
..
429  Write ALPHA FOCK MATRIX              from file 10536 offset           0 to matrix element file.
430  No 2e integrals to process.
431  Perform NBO analysis...
432 
433  *********************************** NBO 6.0 ***********************************
434              N A T U R A L   A T O M I C   O R B I T A L   A N D
435           N A T U R A L   B O N D   O R B I T A L   A N A L Y S I S
436  ********************* Me *********************
..
447  Filename set to /home/me/scratch/Gau-24659
..
620           -------------------------------
621                  Total Lewis    9.99612  ( 99.9612%)
622            Valence non-Lewis    0.00029  (  0.0029%)
623            Rydberg non-Lewis    0.00358  (  0.0358%)
624           -------------------------------
625                Total unit  1   10.00000  (100.0000%)
626               Charge unit  1    0.00000
627 
628  $CHOOSE
629    LONE 1 2 END
630    BOND S 1 2 S 1 3 END
631  $END
632 
633  Maximum scratch memory used by NBO was 62605 words
634  Maximum scratch memory used by G09NBO was 9032 words
...

561. b3pw91 in nwchem and g09

UPDATE: there was an error in the earlier version where I gave the wrong energy for the b3pw91 functional in nwchem. In the old version the energy I provided was very close to that of acm in nwchem rather than b3pw91 in g09.

Note that for a large molecule with a medium sized basis set (101 atoms, ca 1100 functions,  ca 2200 primitives) the energy difference between b3pw91 in g09 and b3pw91 in nwchem as defined below is 0.0124 Hartree, which is pretty big (7.8 kcal/mol), although in absolute terms it's quite small (nwchem: -6187.741840960054 Hartree. g09: -6187.75427966 Hartree).

The difference is a lot smaller for the small molecule in the example below.

Original post:
According to http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id721/Are_these_definitions_correct_fo....html b3pw91 (as defined in Gaussian 09) and acm (as defined in nwchem) are identical.

Looking at the energies I've been getting, that's not true when it comes to G09 and NWCHEM.

---

That acm and b3pw91 are the same should be reasonable -- b3 indicates that it's Becke's 3-parameter hybrid exchange correlation functional model, which is also known as the Adiabatic Connection Method (ACM).

For historical reasons, g98 implemented the ACM as B3LYP, by using LYP instead of PW91, and using VWN_1_RPA and a few other tricks -- see section 2 in http://verahill.blogspot.com.au/2013/06/446-b3lyp-and-wah-confusion.html

Then it would stand to reason that B3PW91 would be the 'canonical' version of Becke's 3-parameter functional.

Looking at http://www.nwchem-sw.org/index.php/Release62:Density_Functional_Theory_for_Molecules acm is defined as

xc HFexch 0.2 slater 0.8 becke88 nonlocal 0.72 vwn_5 1 Perdew91 0.81

(there are several versions of VWN -- I know it's vwn_5 from the output)

---

Either way, using acm in a single energy calculation (no optimisation) in nwchem on a water molecule with 6-31+G* (acm/6-31+G*) gives

-76.358375905073 Hartree

G09 using B3PW91/6-31+G* (manually defined basis set so we're using the same form in both nwchem and g09) gives

 -76.3557851653 Hartree

nwchem using

xc HFexch 0.2 slater 0.8 becke88 nonlocal 0.72 vwn_5 1 Perdew91 0.81

gives

-76.358375905072 Hartree

and nwchem using

XC HFexch 0.20 slater 0.80 becke88 nonlocal 0.72 perdew91 0.81 pw91lda 1.00

obtained from http://myweb.liu.edu/~nmatsuna/gamess/refs/howto.dft.html,gives

-76.355784373093 Hartree

This last definition is thus equivalent to b3pw91 in g09.

The gaussian manual is less than helpful. In fact it is quite misleading:

"These functionals have the form devised by Becke in 1993 [Becke93a]:
A*E_X^Slater+(1-A)*E_X^HF+B*ΔE_X^Becke+E_C^VWN+C*ΔE_C^non-local
[..] B3LYP uses the non-local correlation provided by the LYP expression, and VWN functional III for local correlation (not functional V). [..]B3P86 specifies the same functional with the non-local correlation provided by Perdew 86, and B3PW91 specifies this functional with the non-local correlation provided by Perdew/Wang 91.

---

Addendum:
While I think B3PW91 should be the same as ACM in nwchem (note that nwchem does not have b3pw91 as a keyword), I decided to have a look at how different packages define b3pw91.

nwchem -- doesn't exist. Manual.

g09 (this post) -- xc HFexch 0.20 slater 0.80 becke88 nonlocal 0.72 perdew91 0.81 pw91lda 1.00

gamess US (here) -- xc HFexch 0.20 slater 0.80 becke88 nonlocal 0.72 perdew91 0.81 pw91lda 1.00

PQS (page 52, manual) Paraphrased:
"B3PW91 -- hybrid 3-parameter HF-DFT functional comprising combination of Slater local exchange, Becke nonlocal exchange, VWN 5 local correlation and PW91 nonlocal correlation together with a portion (20%) of the exact Hartree-Fock exchange (original 3-parameter hybrid recommended by Becke)". That to me sounds like ACM.

Turbomol -- not available. Manual.

Orca -- "B3PW The three-parameter hybrid version of PW91". Not informative.

molpro -- doesn't exist. manual

Dalton -- (page 285, manual).

"B3PW91 3-parameter Becke-PW91 functional, with PW91 correlation functional. Note that PW91c includes PW92c local correlation, thus only excess PW92c local correlation is required (coe cient of 0.19).
Combine HF=0.2 Slater=0.8 Becke=0.72 PW91c=0.81 PW92c=0.19"

So the local correlation is 1*PW92c= 0.81 PW91c + 0.19 PW92c. This is, I presume, is quite different from VWN.

Q-Chem -- "B3PW91 (B3 Exchange + PW91 correlation)". Not explicit enough for me.

551. Very Briefly: Getting ECCE to work with Gaussian 09 (G09) part 3: Energy gradients (EGRADVEC)

This is a really simple fix to make ECCE return the energy gradient vectors for geometry optimisation jobs in G09:

Edit apps/scripts/parsers/gaussian-03.egradvec and comment out lines 38 (if () {... ) and 70 (}):

diff --git a/ecce-v7.0/scripts/parsers/gaussian-03.egradvec b/ecce-v7.0/scripts/parsers/gaussian-03.egradvec
index a2f5633..4a4b691 100755
--- a/ecce-v7.0/scripts/parsers/gaussian-03.egradvec
+++ b/ecce-v7.0/scripts/parsers/gaussian-03.egradvec
@@ -35,7 +35,7 @@ $| = 1;
 #Don't parse gradients for runtypes with geometry optimization
 #since we can't match gradients with correct geometry.
 
-if (!($runtype =~ /Geo/i)) {
+#if (!($runtype =~ /Geo/i)) {
   $natom = 0;
   while () {
     if (/-----/) { last; }
@@ -67,4 +67,4 @@ if (!($runtype =~ /Geo/i)) {
   }
   print "units:\nHartree/Bohr\n";
   print "END\n";
-}
+#}
-- 

550. Briefly: Getting ECCE to work with Gaussian 09 (G09) part 2: Geometry trace when using NoSymm

I've made a couple of posts about how to modify ECCE to work better in general, but in particular with Gaussian 09  (G09).

See here for some of the previous posts:
Adding new basis sets, part 1: http://verahill.blogspot.com.au/2013/06/455-adding-nwchem-basis-sets-to-ecce.html
Adding new basis sets, part 2:  http://verahill.blogspot.com.au/2013/06/456-adding-nwchem-basis-sets-to-ecce.html
Adding new exchange/correlation functionals:
http://verahill.blogspot.com.au/2013/12/533-adding-new-exchangecorrelation.html
Adding new options to ECCE
http://verahill.blogspot.com.au/2013/12/534-adding-new-options-to-ecce-adding.html
Getting ECCE to read frequency calc output from G09 calcs:
http://verahill.blogspot.com.au/2013/12/536-briefly-getting-ecce-to-work-with.html


Either way, I've noticed that when I'm using the NoSymm option during optimisation ECCE fails to import the geometries from the geometry steps.

No geometry trace option

What is even worse is that if you use an optimisation job like that as the basis for another job by selecting Duplicate Setup with Last Geometry ECCE will in fact use the starting geometry -- not the optimised one.

Luckily the fix is simple -- edit apps/parsers/gaussian-03.desc and add the following lines:

[GEOMTRACE]
Script=gaussian-03.geomtrace
Begin=Z-Matrix orientation\:
Skip=5
Frequency=all
End=--------------------------------------
[END]

You can now 'Reconnect job monitoring' also to your old jobs if you still have access to the run directory. Either way, the view will now be a sweet one:

Et voila: A geometry trace

536. Briefly: Getting ECCE to work with Gaussian 09 (G09) part 1: frequency calcs

I'm slowly looking at improving the support for G09 in ECCE. One of the things that haven't worked in the past is visualising frequency calcs.

Since I'm not using G03 I've been content with editing the g03 files so that they work with G09. My changes will be submitted upstreams at a later point.

Anyway, turns out this was a very simple one.

How ECCE works:
data is extracted from the output through the use of perl parser scripts. These are located in apps/scripts/parsers, and are fairly clearly named.

The script that deals with Gaussian vibrational analyses is called gaussian-03.vib

To use it manually with a gaussian 'log' file (here called g03.output), do

./gaussian-03.vib < g03.output

So far so easy. However, if you use it on a g09 output file you'll end up with a single message: 'Zero atoms'.

Turns out that the reason is that the script looks for instances of 'Atom AN', with a single white space between m and N. In G09, however, there are two white spaces: 'Atom AN'.

The fix:
So, edit line 277:

276     while ()  {
277       if (/Atom AN/) {
278         last;

and change it to

276     while ()  {
277       if (/Atom\s*AN/) {
278         last;

Do the same thing with line 315:

314     while ()  {
315       if (/Atom\s*AN/) {
316         last;

Done!

137. Setting up Gaussian g09 on debian -- precompiled binaries

Most people would use a precompiled and pre-installed copy of gaussian on their local computational grid. If you do, however, purchase your own copy, or work at an institution with a site license, then you can install gaussian on your local beowulf cluster (or over-powered desktop).

And it's easy. I've presumed that your username is verahill, and your group is verahill.

You need csh

sudo apt-get install csh

Next set up a destination directory

mkdir /opt/gaussian
sudo chown verahill:verahill /opt/gaussian

copy the gaussian binaries to /opt/gaussian/g09 so that you have

/opt/gaussian/g09
|-- basis
|-- bsd
`-- tests
    |-- com
    |-- ia64
    `-- newz

Gaussian wants almost everything to be executable
chmod +x /opt/gaussian/g09/*
chmod +x /opt/gaussian/g09/bsd/*
cd /opt/gaussian/g09
csh bsd/install

Next, edit your ~/.bashrc and add (anywhere)

export g09root=/opt/gaussian
export GAUSS_SCRDIR=/scratch
. /opt/gaussian/g09/bsd/g09.profile
export PATH=$PATH:/opt/gaussian/g09/bsd:/opt/gaussian/g09/local

Source your bashrc to make changes take effect immediately:

source ~/.bashrc

You need to edit the bashrc of anyone wanting to use gaussian

And you're done!