Showing posts with label gaussian g09. Show all posts
Showing posts with label gaussian g09. Show all posts

04 June 2015

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
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 ...

04 March 2014

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 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

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

Looking at 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
-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,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]:
[..] 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.

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.

05 February 2014

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:
Adding new basis sets, part 2:
Adding new exchange/correlation functionals:
Adding new options to ECCE
Getting ECCE to read frequency calc output from G09 calcs:

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

17 December 2013

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;


05 May 2012

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

|-- 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!