From owner-chemistry@ccl.net Fri Oct 23 02:51:01 2015 From: "Mohan maruthi sena maruthi.sena..gmail.com" 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 Content-Type: multipart/alternative; boundary=001a11492bc641f6450522bffef6 Date: Fri, 23 Oct 2015 12:18:03 +0530 MIME-Version: 1.0 Sent to CCL by: Mohan maruthi sena [maruthi.sena././.gmail.com] --001a11492bc641f6450522bffef6 Content-Type: text/plain; charset=UTF-8 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 --001a11492bc641f6450522bffef6 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: base64 PGRpdiBkaXI9Imx0ciI+PGRpdj48ZGl2PjxkaXY+RGVhciBhbGwsPGJyPjwvZGl2PsKgwqDCoMKg wqDCoMKgwqDCoMKgwqDCoMKgwqAgSSBhbSB0cnlpbmcgdG8gb3B0aW1pemUgKGlucHV0IGlzIHNo b3duIGJlbG93KSBhIHN5c3RlbSBhbmQgSSBnb3QgdGhlIGZvbGxvd2luZyBlcnJvcjo8YnI+PGJy PiZxdW90O0JyZW5lbWFuIChDSEVMUEcpIHJhZGlpIHVzZWQuPGJyPsKgR2V0VkRXOsKgIG5vIHJh ZGl1cyBmb3IgYXRvbcKgwqAgMSBhdG9taWMgbnVtYmVywqAgMzMmcXVvdDsuwqAgSSBoYXZlIHNl ZW4gdGhlIGVhcmxpZXIgZGlzY3Vzc2lvbnMgaW4gdGhlIGZvcnVtIGFuZCBpbmNsdWRlZCB0aGUg b3B0aW9uIHBvcD0oY2hlbHBnLCBSZWFkUmFkaWkpIGFuZCBtZW50aW9uZWQgdGhlIHJhZGl1c8Kg IGF0IHRoZSBlbmQgb2YgaW5wdXQgZmlsZSBidXQgc3RpbGwgSSBnb3QgdGhlIHNhbWUgZXJyb3Iu IENvdWxkIHNvbWVvbmUgc3VnZ2VzdCBtZSB3aGF0JiMzOTtzIHdyb25nIHdpdGggdGhlIGlucHV0 IGZpbGUuIFRoZSBpbnB1dCBmaWxlIGlzIGFzIGZvbGxvd3M6PGJyPjxicj4lbnByb2NzaGFyZWQ9 NDxicj4lbWVtPTEyR0I8YnI+JWNoaz10ZXN0LmNoazxicj4jIG9wdCBiM2x5cC82LTMxMStnKDJk ZikgZ2VvbT1jb25uZWN0aXZpdHkgcG9wPShjaGVscGcsUmVhZFJhZGlpKTxicj5zeW1tPWZvbGxv dzxicj48YnI+b3B0aW1pemF0aW9uIDxicj48YnI+LTEgMTxicj7CoEFzwqDCoMKgwqDCoMKgwqDC oMKgwqDCoMKgwqDCoMKgwqAgMC4wMDAwMDAwMMKgwqDCoCAwLjAwMDAwMDAwwqDCoMKgIDAuMDAw MDAwMDA8YnI+wqBGwqDCoMKgwqDCoMKgwqDCoMKgwqDCoMKgwqDCoMKgwqDCoCAwLjAwMDAwMDAw wqDCoMKgIDAuMDAwMDAwMDDCoMKgwqAgMS43NjM1NDA4OTxicj7CoEbCoMKgwqDCoMKgwqDCoMKg wqDCoMKgwqDCoMKgwqDCoMKgIDAuMDAwMDAwMDDCoMKgwqAgMS43NjM1NDA4OcKgwqDCoCAwLjAw MDAwMDAwPGJyPsKgRsKgwqDCoMKgwqDCoMKgwqDCoMKgwqDCoMKgwqDCoMKgIC0xLjc2MzU0MDg5 wqDCoMKgIDAuMDAwMDAwMDDCoMKgwqAgMC4wMDAwMDAwMDxicj7CoEbCoMKgwqDCoMKgwqDCoMKg wqDCoMKgwqDCoMKgwqDCoMKgIDAuMDAwMDAwMDDCoMKgwqAgMC4wMDAwMDAwMMKgwqAgLTEuNzYz NTQwODk8YnI+wqBGwqDCoMKgwqDCoMKgwqDCoMKgwqDCoMKgwqDCoMKgwqDCoCAwLjAwMDAwMDAw wqDCoCAtMS43NjM1NDA4OcKgwqDCoCAwLjAwMDAwMDAwPGJyPsKgRsKgwqDCoMKgwqDCoMKgwqDC oMKgwqDCoMKgwqDCoMKgwqAgMS43NjM1NDA4OcKgwqDCoCAwLjAwMDAwMDAwwqDCoMKgIDAuMDAw MDAwMDA8YnI+PGJyPsKgMSAyIDEuMCAzIDEuMCA0IDEuMCA1IDEuMCA2IDEuMCA3IDEuMDxicj7C oDI8YnI+wqAzPGJyPsKgNDxicj7CoDU8YnI+wqA2PGJyPsKgNzxicj48YnI+QXMgMS44NTxicj48 YnI+PC9kaXY+VGhhbmtzICZhbXA7IFJlZ2FyZHMsPGJyPjwvZGl2Pk1vaGFuIDxicj48ZGl2Pjxk aXY+PGJyPjwvZGl2PjwvZGl2PjwvZGl2Pg0K --001a11492bc641f6450522bffef6-- From owner-chemistry@ccl.net Fri Oct 23 08:56:01 2015 From: "Steven Kirk stevenrkirk-$-gmail.com" To: CCL Subject: CCL: Collection of QM method information Message-Id: <-51829-151023012232-4827-z/qTWr2lfCmZgA0UzBXsuA.@.server.ccl.net> X-Original-From: "Steven Kirk" 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" To: CCL Subject: CCL: Collection of QM method information Message-Id: <-51830-151023105925-16377-Sn8pi/0nunbLS8NzEJnLuQ : server.ccl.net> X-Original-From: "Breton, Gary" Content-ID: <00ACBB08DFAB0747B1A9A765D53C20D8 : namprd02.prod.outlook.com> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 23 Oct 2015 14:59:15 +0000 MIME-Version: 1.0 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" 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" 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" 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