From owner-chemistry@ccl.net Fri Oct 23 02:51:01 2015
From: "Mohan maruthi sena maruthi.sena..gmail.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: ReadRadii option usage in Gaussian09
Message-Id: <-51828-151023024809-20244-iM3c1tJhmwCfSvzjHIV6lA%a%server.ccl.net>
X-Original-From: Mohan maruthi sena <maruthi.sena-.-gmail.com>
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Date: Fri, 23 Oct 2015 12:18:03 +0530
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Sent to CCL by: Mohan maruthi sena [maruthi.sena././.gmail.com]
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Dear all,
I am trying to optimize (input is shown below) a system and
I got the following error:
"Breneman (CHELPG) radii used.
GetVDW: no radius for atom 1 atomic number 33". I have seen the
earlier discussions in the forum and included the option pop=(chelpg,
ReadRadii) and mentioned the radius at the end of input file but still I
got the same error. Could someone suggest me what's wrong with the input
file. The input file is as follows:
%nprocshared=4
%mem=12GB
%chk=test.chk
# opt b3lyp/6-311+g(2df) geom=connectivity pop=(chelpg,ReadRadii)
symm=follow
optimization
-1 1
As 0.00000000 0.00000000 0.00000000
F 0.00000000 0.00000000 1.76354089
F 0.00000000 1.76354089 0.00000000
F -1.76354089 0.00000000 0.00000000
F 0.00000000 0.00000000 -1.76354089
F 0.00000000 -1.76354089 0.00000000
F 1.76354089 0.00000000 0.00000000
1 2 1.0 3 1.0 4 1.0 5 1.0 6 1.0 7 1.0
2
3
4
5
6
7
As 1.85
Thanks & Regards,
Mohan
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From owner-chemistry@ccl.net Fri Oct 23 08:56:01 2015
From: "Steven Kirk stevenrkirk-$-gmail.com" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Collection of QM method information
Message-Id: <-51829-151023012232-4827-z/qTWr2lfCmZgA0UzBXsuA.@.server.ccl.net>
X-Original-From: "Steven Kirk" <stevenrkirk{=}gmail.com>
Date: Fri, 23 Oct 2015 01:22:31 -0400
Sent to CCL by: "Steven Kirk" [stevenrkirk!=!gmail.com]
I have seen a post recently on CCL asking for clarification about the relative qualities of calculated electron densities and calculated energies produced by various electronic structure methods. There have also been posts in recent months decrying (NB. I make no judgement here on whether this is justified!) the continued use of older methods such as, e.g. B3LYP.
This prompted me to think that some sort of crowdsourced community resource with the essential features of all of the known available methods, and where they are implemented, might be generally useful. Something along the lines of the NIST Basis Set library, but for methods.
As a small naive contribution to this, I have set up the following public GitHub page:
https://github.com/srk/PsiZoo
in the document 'index.md'.
with a table to fill in details.
Of course, the table columns in the table are crude, but it's a start. If you agree on the need for such a resource, then 1) contribute with pull requests or 2) fork and do it right (or just better) elsewhere.
I'm personally hoping for option 2) to win eventually, as I'm no expert on these matters, so my qualifications (and time) to vet pull requests are very limited. I'm aware of another such attempt to rank popular DFT methods in a 'football league' metaphor - there might be some overlap there.
If this (or something even better) exists already, I'd be grateful for a contributed URL.
Thanks for your attention,
Steven Kirk
From owner-chemistry@ccl.net Fri Oct 23 11:50:01 2015
From: "Breton, Gary gbreton*berry.edu" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: Collection of QM method information
Message-Id: <-51830-151023105925-16377-Sn8pi/0nunbLS8NzEJnLuQ : server.ccl.net>
X-Original-From: "Breton, Gary" <gbreton#,#berry.edu>
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Date: Fri, 23 Oct 2015 14:59:15 +0000
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Sent to CCL by: "Breton, Gary" [gbreton*_*berry.edu]
Steven,
This is a great idea. Reading the volley (of which some were outright
spikes!) of emails that resulted recently as to which computational method
(and basis set) to employ was interesting. I can see both sides of the
argument. The theorists argue for greater accuracy in calculations and
abandonment of older, outdated methods. Everyday users (such as this
poor organic chemist), however, have to balance "extreme" accuracy with
computational facilities (i.e., a simple desktop PC) and knowledge base.
As a physical organic chemist I have to direct most of my efforts to
remain current in the physical organic world (which overlaps with the
computational chemistry world) which leaves little time to delve into the
particulars as to which method is best (or most "accurate") for a given
situation. In other words, I simply don't have the time to spend
submerged in theoretical literature when I am already submerged in
literature more specific to my field. Therefore, when presented with a
computational problem, I start with methods that have worked for others in
similar situations, run some "control" studies to check to see that it
appears to work for my new system, and go with it. The tone of some of
the theorists in the email exchange about the use of some of these methods
suggests they don't understand the time and resource constraints many of
us work under.
Hence your suggestion to set up a repository for "what works" for
different types of calculations could be a gold mine (the riches being the
joy derived from your gift to humanity and not, unfortunately, filling
your wallet).
Thanks,
Gary
On 10/23/15 1:22 AM, "owner-chemistry+gbreton==berry.edu/./ccl.net on behalf
of Steven Kirk stevenrkirk-$-gmail.com"
<owner-chemistry+gbreton==berry.edu/./ccl.net on behalf of
owner-chemistry/./ccl.net> wrote:
>
>Sent to CCL by: "Steven Kirk" [stevenrkirk!=!gmail.com]
>
>I have seen a post recently on CCL asking for clarification about the
>relative qualities of calculated electron densities and calculated
>energies produced by various electronic structure methods. There have
>also been posts in recent months decrying (NB. I make no judgement here
>on whether this is justified!) the continued use of older methods such
>as, e.g. B3LYP.
>
>This prompted me to think that some sort of crowdsourced community
>resource with the essential features of all of the known available
>methods, and where they are implemented, might be generally useful.
>Something along the lines of the NIST Basis Set library, but for methods.
>
>As a small naive contribution to this, I have set up the following public
>GitHub page:
>
>https://github.com/srk/PsiZoo
>
>in the document 'index.md'.
>
>with a table to fill in details.
>
>Of course, the table columns in the table are crude, but it's a start. If
>you agree on the need for such a resource, then 1) contribute with pull
>requests or 2) fork and do it right (or just better) elsewhere.
>
>I'm personally hoping for option 2) to win eventually, as I'm no expert
>on these matters, so my qualifications (and time) to vet pull requests
>are very limited. I'm aware of another such attempt to rank popular DFT
>methods in a 'football league' metaphor - there might be some overlap
>there.
>
>If this (or something even better) exists already, I'd be grateful for a
>contributed URL.
>
>Thanks for your attention,
>Steven Kirk>
>
From owner-chemistry@ccl.net Fri Oct 23 15:29:00 2015
From: "Margaux Toral toral|,|ccdc.cam.ac.uk" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: The CCDC Celebrates the 800,000th Entry in the Cambridge Structural Da
Message-Id: <-51831-151023131556-12450-pVTnFzbSxyCKEgdOORYJJQ,+,server.ccl.net>
X-Original-From: "Margaux Toral" <toral%x%ccdc.cam.ac.uk>
Date: Fri, 23 Oct 2015 13:15:55 -0400
Sent to CCL by: "Margaux Toral" [toral]~[ccdc.cam.ac.uk]
Hello,
The Cambridge Crystallographic Data Centre was delighted to announce this
week that there are now over 800,000 entries in the Cambridge Structural
Database. The 800,000th entry is a copper-containing metal-organic crystal
structure determined by researchers in Spain and published in Crystal
Growth & Design. You can read more about this structure and the
significance of this milestone at
http://www.ccdc.cam.ac.uk/NewsandEvents/News/Pages/NewsItem.aspx?newsid=42
and in our blog post at
http://www.ccdc.cam.ac.uk/Community/Blog/pages/BlogPost.aspx?bpid=58. We
take this opportunity to express our appreciation for the contribution made
by researchers past and present to the continuing growth and success of the
Cambridge Structural Database.
Thanks,
Margaux