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From: Karol L. <kar...@kn...> - 2007-01-31 13:05:42
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Hi,
I'm wondering about the basis sets output by Jaguar... they have me stumped,
since the contraction coefficients for the SP gaussian primitives are totally
different than those given by GAMESS and Gaussian.
Compare the STO-3G function for carbon that I found in the cclib test
logfiles.
Gaussian:
S 3 1.00 0.000000000000
0.7161683735D+02 0.1543289673D+00
0.1304509632D+02 0.5353281423D+00
0.3530512160D+01 0.4446345422D+00
SP 3 1.00 0.000000000000
0.2941249355D+01 -0.9996722919D-01 0.1559162750D+00
0.6834830964D+00 0.3995128261D+00 0.6076837186D+00
0.2222899159D+00 0.7001154689D+00 0.3919573931D+00
Jaguar:
s j
h c i n
e o s f
l n h s
atom l t l l h z coef rcoef
-------- --- --- -- -- --- ---------- ---------- ---------
C1 1 3 0 1 0 71.6168373 0.1543290 2.7078144
C1 2 -1 0 1 0 13.0450963 0.5353281 2.6188802
C1 3 -1 0 1 0 3.5305122 0.4446345 0.8161906
C1 4 2 2 1 1 2.9412494 -0.2956454 -0.4732386
C1 5 -4 2 1 1 0.6834831 1.1815287 0.6329949
C1 6 2 -1 2 2 2.9412494 0.2213487 1.2152952
C1 7 -6 -1 2 2 0.6834831 0.8627064 0.7642102
C1 8 1 1 1 1 0.2222899 1.0000000 0.2307278
C1 9 1 -1 2 2 0.2222899 1.0000000 0.2175654
The coefficient for the S shells are the same, but the ones for SP are not.
Does anybody know how to explain this, and eventually how to interconvert? I
assume that the STO-3G functions used in both programs are identical, so it
should be possible. Or, where should I ask about this? Maybe this is the
reason why there's no gbasis attribute for the Jaguar parser yet?
Karol
--
written by Karol Langner
Wed Jan 31 14:00:32 CET 2007
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From: Noel O'B. <bao...@gm...> - 2007-01-31 14:28:58
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Yes, there are problems with gbasis for Jaguar. First I want to finish volume.py, though. I'll come back to this though and we can talk it through. If you have any ideas in the meantime I'd be happy to hear them. On 31/01/07, Karol Langner <kar...@kn...> wrote: > Hi, > > I'm wondering about the basis sets output by Jaguar... they have me stumped, > since the contraction coefficients for the SP gaussian primitives are totally > different than those given by GAMESS and Gaussian. > > Compare the STO-3G function for carbon that I found in the cclib test > logfiles. > > Gaussian: > S 3 1.00 0.000000000000 > 0.7161683735D+02 0.1543289673D+00 > 0.1304509632D+02 0.5353281423D+00 > 0.3530512160D+01 0.4446345422D+00 > SP 3 1.00 0.000000000000 > 0.2941249355D+01 -0.9996722919D-01 0.1559162750D+00 > 0.6834830964D+00 0.3995128261D+00 0.6076837186D+00 > 0.2222899159D+00 0.7001154689D+00 0.3919573931D+00 > > Jaguar: > s j > h c i n > e o s f > l n h s > atom l t l l h z coef rcoef > -------- --- --- -- -- --- ---------- ---------- --------- > C1 1 3 0 1 0 71.6168373 0.1543290 2.7078144 > C1 2 -1 0 1 0 13.0450963 0.5353281 2.6188802 > C1 3 -1 0 1 0 3.5305122 0.4446345 0.8161906 > C1 4 2 2 1 1 2.9412494 -0.2956454 -0.4732386 > C1 5 -4 2 1 1 0.6834831 1.1815287 0.6329949 > C1 6 2 -1 2 2 2.9412494 0.2213487 1.2152952 > C1 7 -6 -1 2 2 0.6834831 0.8627064 0.7642102 > C1 8 1 1 1 1 0.2222899 1.0000000 0.2307278 > C1 9 1 -1 2 2 0.2222899 1.0000000 0.2175654 > > The coefficient for the S shells are the same, but the ones for SP are not. > Does anybody know how to explain this, and eventually how to interconvert? I > assume that the STO-3G functions used in both programs are identical, so it > should be possible. Or, where should I ask about this? Maybe this is the > reason why there's no gbasis attribute for the Jaguar parser yet? > > Karol > > -- > written by Karol Langner > Wed Jan 31 14:00:32 CET 2007 > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > |
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From: Karol L. <kar...@kn...> - 2007-01-31 14:35:59
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The only thing I can imagine right now is that there is an additional contraction, or that the linear combination is summed somewhat differently than normal. I don't use the program myself, so I don't have the means to ask the Jaguar people, as I understand you must have a liscence to do so. Karol On Wednesday 31 of January 2007 15:28, you wrote: > Yes, there are problems with gbasis for Jaguar. First I want to finish > volume.py, though. I'll come back to this though and we can talk it > through. If you have any ideas in the meantime I'd be happy to hear > them. > > On 31/01/07, Karol Langner <kar...@kn...> wrote: > > Hi, > > > > I'm wondering about the basis sets output by Jaguar... they have me > > stumped, since the contraction coefficients for the SP gaussian > > primitives are totally different than those given by GAMESS and Gaussian. > > > > Compare the STO-3G function for carbon that I found in the cclib test > > logfiles. > > > > Gaussian: > > S 3 1.00 0.000000000000 > > 0.7161683735D+02 0.1543289673D+00 > > 0.1304509632D+02 0.5353281423D+00 > > 0.3530512160D+01 0.4446345422D+00 > > SP 3 1.00 0.000000000000 > > 0.2941249355D+01 -0.9996722919D-01 0.1559162750D+00 > > 0.6834830964D+00 0.3995128261D+00 0.6076837186D+00 > > 0.2222899159D+00 0.7001154689D+00 0.3919573931D+00 > > > > Jaguar: > > s j > > h c i n > > e o s f > > l n h s > > atom l t l l h z coef > > rcoef -------- --- --- -- -- --- ---------- ---------- > > --------- C1 1 3 0 1 0 71.6168373 0.1543290 > > 2.7078144 C1 2 -1 0 1 0 13.0450963 > > 0.5353281 2.6188802 C1 3 -1 0 1 0 3.5305122 > > 0.4446345 0.8161906 C1 4 2 2 1 1 > > 2.9412494 -0.2956454 -0.4732386 C1 5 -4 2 1 1 > > 0.6834831 1.1815287 0.6329949 C1 6 2 -1 2 > > 2 2.9412494 0.2213487 1.2152952 C1 7 -6 -1 > > 2 2 0.6834831 0.8627064 0.7642102 C1 8 1 > > 1 1 1 0.2222899 1.0000000 0.2307278 C1 9 > > 1 -1 2 2 0.2222899 1.0000000 0.2175654 > > > > The coefficient for the S shells are the same, but the ones for SP are > > not. Does anybody know how to explain this, and eventually how to > > interconvert? I assume that the STO-3G functions used in both programs > > are identical, so it should be possible. Or, where should I ask about > > this? Maybe this is the reason why there's no gbasis attribute for the > > Jaguar parser yet? > > > > Karol -- written by Karol Langner Wed Jan 31 15:32:18 CET 2007 |
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From: Noel O'B. <bao...@gm...> - 2007-01-31 15:24:13
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The first priority is figuring out the H coefficients...here's the
current situation for STO-3G:
PyQuante
basis_data = [
14 None,
15 [#H
16 ('S',[
17 (3.425251, 0.154329),
18 (0.623914, 0.535328),
19 (0.168855, 0.444635),
20 ]),
21 ],
The normalised coefficients for the primitives (each on their own) are:
0.2769
0.2678
0.0835
GAMESS-UK
exponents, then contraction coefficients
h
14 1s 19 3.425251 0.276934 ( 0.154329 )
14 1s 20 0.623914 0.267839 ( 0.535328 )
14 1s 21 0.168855 0.083474 ( 0.444635 )
Jag 4.2
H6 1 2 0 1 25 3.4252509 0.2405014 0.4315658
H6 2 -1 0 1 25 0.6239137 0.8342385 0.4173916
H6 3 1 0 1 25 0.1688554 1.0000000 0.1877355
Normalised coefficients
H6 1 S 26 3.425251 0.431566
H6 2 S 26 0.623914 0.417392
H6 3 S 26 0.168855 0.187735
GAMESS
H
13 S 37 3.4252509 0.154328967295
13 S 38 0.6239137 0.535328142282
13 S 39 0.1688554 0.444634542185
PC-GAMESS
THE CONTRACTED PRIMITIVE FUNCTIONS HAVE BEEN UNNORMALIZED
THE CONTRACTED BASIS FUNCTIONS ARE NOW NORMALIZED TO UNITY
H
22 S 31 3.425251 0.276934 ( 0.154329)
22 S 32 0.623914 0.267839 ( 0.535328)
22 S 33 0.168855 0.083474 ( 0.444635)
G03
Atom H7 Shell 12 S 3 bf 27 - 27
-4.468771508880 1.536663462131 0.000000000000
0.3425250914D+01 0.1543289673D+00
0.6239137298D+00 0.5353281423D+00
0.1688554040D+00 0.4446345422D+00
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From: Adam T. <a-t...@st...> - 2007-01-31 17:17:21
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Which Jaguar version are you looking at? I think my colleague just used the basis functions she normally uses for her calcs when she ran the Jaguar 6.0 calcs. Also, as I recall, the MO coeffs aren't printed for the Jaguar 4.2 files, but I may be mistaken. Adam On Jan 31, 2007, at 6:35 AM, Karol Langner wrote: > The only thing I can imagine right now is that there is an additional > contraction, or that the linear combination is summed somewhat > differently > than normal. I don't use the program myself, so I don't have the > means to ask > the Jaguar people, as I understand you must have a liscence to do so. > > Karol > > On Wednesday 31 of January 2007 15:28, you wrote: >> Yes, there are problems with gbasis for Jaguar. First I want to >> finish >> volume.py, though. I'll come back to this though and we can talk it >> through. If you have any ideas in the meantime I'd be happy to hear >> them. >> >> On 31/01/07, Karol Langner <kar...@kn...> wrote: >>> Hi, >>> >>> I'm wondering about the basis sets output by Jaguar... they have me >>> stumped, since the contraction coefficients for the SP gaussian >>> primitives are totally different than those given by GAMESS and >>> Gaussian. >>> >>> Compare the STO-3G function for carbon that I found in the cclib >>> test >>> logfiles. >>> >>> Gaussian: >>> S 3 1.00 0.000000000000 >>> 0.7161683735D+02 0.1543289673D+00 >>> 0.1304509632D+02 0.5353281423D+00 >>> 0.3530512160D+01 0.4446345422D+00 >>> SP 3 1.00 0.000000000000 >>> 0.2941249355D+01 -0.9996722919D-01 0.1559162750D+00 >>> 0.6834830964D+00 0.3995128261D+00 0.6076837186D+00 >>> 0.2222899159D+00 0.7001154689D+00 0.3919573931D+00 >>> >>> Jaguar: >>> s j >>> h c i n >>> e o s f >>> l n h s >>> atom l t l l h z coef >>> rcoef -------- --- --- -- -- --- ---------- ---------- >>> --------- C1 1 3 0 1 0 71.6168373 >>> 0.1543290 >>> 2.7078144 C1 2 -1 0 1 0 13.0450963 >>> 0.5353281 2.6188802 C1 3 -1 0 1 0 >>> 3.5305122 >>> 0.4446345 0.8161906 C1 4 2 2 1 1 >>> 2.9412494 -0.2956454 -0.4732386 C1 5 -4 2 >>> 1 1 >>> 0.6834831 1.1815287 0.6329949 C1 6 2 >>> -1 2 >>> 2 2.9412494 0.2213487 1.2152952 C1 7 >>> -6 -1 >>> 2 2 0.6834831 0.8627064 0.7642102 >>> C1 8 1 >>> 1 1 1 0.2222899 1.0000000 0.2307278 >>> C1 9 >>> 1 -1 2 2 0.2222899 1.0000000 0.2175654 >>> >>> The coefficient for the S shells are the same, but the ones for >>> SP are >>> not. Does anybody know how to explain this, and eventually how to >>> interconvert? I assume that the STO-3G functions used in both >>> programs >>> are identical, so it should be possible. Or, where should I ask >>> about >>> this? Maybe this is the reason why there's no gbasis attribute >>> for the >>> Jaguar parser yet? >>> >>> Karol > > -- > written by Karol Langner > Wed Jan 31 15:32:18 CET 2007 > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel |
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From: Noel O'B. <bao...@gm...> - 2007-02-09 08:09:32
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On 31/01/07, Karol Langner <kar...@kn...> wrote: > Hi, > > I'm wondering about the basis sets output by Jaguar... they have me stumped, > since the contraction coefficients for the SP gaussian primitives are totally > different than those given by GAMESS and Gaussian. > > Compare the STO-3G function for carbon that I found in the cclib test > logfiles. > > Gaussian: > S 3 1.00 0.000000000000 > 0.7161683735D+02 0.1543289673D+00 > 0.1304509632D+02 0.5353281423D+00 > 0.3530512160D+01 0.4446345422D+00 > SP 3 1.00 0.000000000000 > 0.2941249355D+01 -0.9996722919D-01 0.1559162750D+00 > 0.6834830964D+00 0.3995128261D+00 0.6076837186D+00 > 0.2222899159D+00 0.7001154689D+00 0.3919573931D+00 STO-3G is defined as a set of 3 GTOs (1S), 3 GTOs (2S), and 3 GTOs(2P). > Jaguar: > s j > h c i n > e o s f > l n h s > atom l t l l h z coef rcoef > -------- --- --- -- -- --- ---------- ---------- --------- > C1 1 3 0 1 0 71.6168373 0.1543290 2.7078144 > C1 2 -1 0 1 0 13.0450963 0.5353281 2.6188802 > C1 3 -1 0 1 0 3.5305122 0.4446345 0.8161906 > C1 4 2 2 1 1 2.9412494 -0.2956454 -0.4732386 > C1 5 -4 2 1 1 0.6834831 1.1815287 0.6329949 > C1 6 2 -1 2 2 2.9412494 0.2213487 1.2152952 > C1 7 -6 -1 2 2 0.6834831 0.8627064 0.7642102 > C1 8 1 1 1 1 0.2222899 1.0000000 0.2307278 > C1 9 1 -1 2 2 0.2222899 1.0000000 0.2175654 > > The coefficient for the S shells are the same, but the ones for SP are not. > Does anybody know how to explain this, and eventually how to interconvert? I > assume that the STO-3G functions used in both programs are identical, so it > should be possible. Or, where should I ask about this? Maybe this is the > reason why there's no gbasis attribute for the Jaguar parser yet? STO-3G is defined differently as a set of 3 GTOs (1S), 2 GTOs + 1 GTO (2S), 2GTOs + 1 GTO (2P). Now that we've figured this out, I will add gbasis to the Jaguar parser over the next few days. Noel |
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From: Karol L. <kar...@kn...> - 2007-02-12 18:17:50
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On Friday 09 of February 2007 09:09, Noel O'Boyle wrote: > STO-3G is defined differently as a set of 3 GTOs (1S), 2 GTOs + 1 GTO > (2S), 2GTOs + 1 GTO (2P). > > Now that we've figured this out, I will add gbasis to the Jaguar > parser over the next few days. That's a little surprising, that STO-3G is defined differently. Also, the energy zomes out exactly the same. Karol -- written by Karol Langner Mon Feb 12 19:14:36 CET 2007 |
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From: Noel O'B. <bao...@gm...> - 2007-02-13 13:29:56
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You're right - there's still something weird going on, since the total number of basis functions (which is listed in the output file) adds up to the same as in Gaussian. That is, the three GTOs are regarded as a single basis function. I've posted a question to the CCL (no response) and now I'm asking Rick Muller (of PyQuante) in case he has any ideas. I think that if this remains unresolved, we'll just have to exclude Jaguar gbasis and go with the rest. On 12/02/07, Karol Langner <kar...@kn...> wrote: > On Friday 09 of February 2007 09:09, Noel O'Boyle wrote: > > STO-3G is defined differently as a set of 3 GTOs (1S), 2 GTOs + 1 GTO > > (2S), 2GTOs + 1 GTO (2P). > > > > Now that we've figured this out, I will add gbasis to the Jaguar > > parser over the next few days. > > That's a little surprising, that STO-3G is defined differently. Also, the > energy zomes out exactly the same. > > Karol > > -- > written by Karol Langner > Mon Feb 12 19:14:36 CET 2007 > |
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From: Karol L. <kar...@kn...> - 2007-02-14 09:46:17
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I tried to look into this yesterday for a bit, but couldn't come up with anything else, again, than that there might be an adidtional sum in the contraction. I think eliminating gbasis from the Jaguar parser is the best thing to do for the moment, since there is no way be sure what exactly is going on. In the long run, it might be possible to get the infromation from the Jaguar people, but that not top-priority now, I guess. Karol On Tuesday 13 of February 2007 14:29, Noel O'Boyle wrote: > You're right - there's still something weird going on, since the total > number of basis functions (which is listed in the output file) adds up > to the same as in Gaussian. That is, the three GTOs are regarded as a > single basis function. > > I've posted a question to the CCL (no response) and now I'm asking > Rick Muller (of PyQuante) in case he has any ideas. I think that if > this remains unresolved, we'll just have to exclude Jaguar gbasis and > go with the rest. > > On 12/02/07, Karol Langner <kar...@kn...> wrote: > > On Friday 09 of February 2007 09:09, Noel O'Boyle wrote: > > > STO-3G is defined differently as a set of 3 GTOs (1S), 2 GTOs + 1 GTO > > > (2S), 2GTOs + 1 GTO (2P). > > > > > > Now that we've figured this out, I will add gbasis to the Jaguar > > > parser over the next few days. > > > > That's a little surprising, that STO-3G is defined differently. Also, the > > energy zomes out exactly the same. > > > > Karol > > > > -- > > written by Karol Langner > > Mon Feb 12 19:14:36 CET 2007 -- written by Karol Langner Wed Feb 14 10:41:13 CET 2007 |
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From: Noel O'B. <bao...@gm...> - 2007-02-14 09:57:09
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Thanks for the help. In the end ,I agree and I've just removed Jaguar gbasis. Rick Muller also checked: """ Briefly, I don't have any idea what Jaguar is doing. I just ran H2 using STO-3G with Jaguar, and the basis print out is essentially the same as that which you reference below. Which looks like it would lead to 4 bfns for H2, but in fact leads to only 2. Maybe the column labeled "jconst" isn't what they say it is in the manual. Note that the basis function index (which I believe is column 6, labeled nfsh) shows that all three primatives are in the same basis function. But maybe I'm getting "basis functions" confused with "shells". I also checked the internal Jaguar basis set data file, and it has coefficients equivalent to what you quoted from PyQuante (0.154, 0.535, 0.444...). So they just must be printing their output in a weird way. """ Interestingly, Rick points out that the data file *does* have the correct coefficients. All gbasis tests now pass. Noel On 14/02/07, Karol Langner <kar...@kn...> wrote: > I tried to look into this yesterday for a bit, but couldn't come up with > anything else, again, than that there might be an adidtional sum in the > contraction. > > I think eliminating gbasis from the Jaguar parser is the best thing to do for > the moment, since there is no way be sure what exactly is going on. In the > long run, it might be possible to get the infromation from the Jaguar people, > but that not top-priority now, I guess. > > Karol > > On Tuesday 13 of February 2007 14:29, Noel O'Boyle wrote: > > You're right - there's still something weird going on, since the total > > number of basis functions (which is listed in the output file) adds up > > to the same as in Gaussian. That is, the three GTOs are regarded as a > > single basis function. > > > > I've posted a question to the CCL (no response) and now I'm asking > > Rick Muller (of PyQuante) in case he has any ideas. I think that if > > this remains unresolved, we'll just have to exclude Jaguar gbasis and > > go with the rest. > > > > On 12/02/07, Karol Langner <kar...@kn...> wrote: > > > On Friday 09 of February 2007 09:09, Noel O'Boyle wrote: > > > > STO-3G is defined differently as a set of 3 GTOs (1S), 2 GTOs + 1 GTO > > > > (2S), 2GTOs + 1 GTO (2P). > > > > > > > > Now that we've figured this out, I will add gbasis to the Jaguar > > > > parser over the next few days. > > > > > > That's a little surprising, that STO-3G is defined differently. Also, the > > > energy zomes out exactly the same. > > > > > > Karol > > > > > > -- > > > written by Karol Langner > > > Mon Feb 12 19:14:36 CET 2007 > > -- > written by Karol Langner > Wed Feb 14 10:41:13 CET 2007 > |
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