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

549. Very briefly: Unexpected comment spam

I get about 2-3 spam comments on my blog per day. Typically they advertise money making schemes, email marketing schemes etc., and look something like this:

This site was... how do I say it? Relevant!! Finally I have found something that helped me. Kudos! Also visit my web site: minecraft 1.0

Today I got an odd one though and I'll post it here even though it kind of works in their favour:

 Anonymous has left a new comment on your post "341. Upgrading/installing BankID on 64 bit linux":

That was enjoyable to read, thanks for posting it.

My site: Bing (www.bing.com) 

I presume that spammers don't work for free, so someone must be paying them. Is Microsoft hiring less-than-reputable web marketing companies to do their bidding?