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From: Adam T. <ate...@gm...> - 2011-03-31 18:00:01
|
Hi Xaver, Thanks for contacting us about the ORCA bug. I'm the one who started that parser (I think), and if I remember correctly, and based on the 2.6.x manual, STO-3G isn't defined; 3-21G is the next improvement. As far as the NWChem files, I would be interested in the test files. It's not a package I'm using at the moment, but I've thought about trying it out for the constrained (?) DFT methodology. I can't guarantee that there will be a rigorous parser in the near future, but I could probably hack together basic support once I can find a few hours to focus on that. Thanks again, Adam On Mar 28, 2011, at 7:46 AM, Xaver W. wrote: > Hi, > > I'm currently testing the open-source quantum chemistry application NWChem > (http://www.nwchem-sw.org). As I'm trying stuff anyway, I could prepare cclib > regression test files with it in case you want to eventually support NWChem. > Are you interested? > > Oh, and one more thing: In your wiki I read that test files should be > "b3lyp/sto-3g". It seems however that the current ORCA test files were made > with 3-21G (see e.g. > http://cclib.svn.sourceforge.net/viewvc/cclib/trunk/data/ORCA/basicORCA2.6/dvb_gopt.inp?revision=937&view=markup > ). Have I misunderstood something? > > Regards, > Xaver > > > ------------------------------------------------------------------------------ > Enable your software for Intel(R) Active Management Technology to meet the > growing manageability and security demands of your customers. Businesses > are taking advantage of Intel(R) vPro (TM) technology - will your software > be a part of the solution? Download the Intel(R) Manageability Checker > today! http://p.sf.net/sfu/intel-dev2devmar > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel |
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From: Xaver W. <xav...@we...> - 2011-03-28 14:46:21
|
Hi, I'm currently testing the open-source quantum chemistry application NWChem (http://www.nwchem-sw.org). As I'm trying stuff anyway, I could prepare cclib regression test files with it in case you want to eventually support NWChem. Are you interested? Oh, and one more thing: In your wiki I read that test files should be "b3lyp/sto-3g". It seems however that the current ORCA test files were made with 3-21G (see e.g. http://cclib.svn.sourceforge.net/viewvc/cclib/trunk/data/ORCA/basicORCA2.6/dvb_gopt.inp?revision=937&view=markup ). Have I misunderstood something? Regards, Xaver |
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From: Karol M. L. <kar...@gm...> - 2011-03-28 10:47:58
|
Dear Xaver, Looks like an easy one to fix. But could you provide us with a log file that recreates this bug, in the Public Domain? Cheers, Karol On Mon, Mar 28, 2011 at 12:38:11PM +0200, Xaver W. wrote: > Hi, > in case of dummy atoms, orcaparser can't read the atoms. Consider: > > >>> cclibdata = cfile.parse() > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "cclib/parser/logfileparser.py", line 221, in parse > self.extract(inputfile, line) > File "cclib/parser/orcaparser.py", line 196, in extract > atomnos.append(self.table.number[broken[0]]) > KeyError: '-' > > I think the lines which orcaparser is trying to read are (sth like): > > 138 --------------------------------- > 139 CARTESIAN COORDINATES (ANGSTROEM) > 140 --------------------------------- > 141 Fe 0.000000 0.000000 0.000660 > 142 O -0.592830 1.741600 -0.806850 > 143 O 0.592830 -1.741600 -0.806850 > 144 C 0.000000 2.934410 -0.176690 > 145 C 0.000000 -2.934410 -0.176690 > 146 H -0.018170 3.765540 -0.884740 > 147 H 0.018170 -3.765540 -0.884740 > 148 C 1.428890 2.563280 0.175900 > 149 C -1.428890 -2.563280 0.175900 > 150 H 2.069080 2.492180 -0.707270 > 151 H -2.069080 -2.492180 -0.707270 > 152 O 1.366300 1.233000 0.806640 > 153 O -1.366300 -1.233000 0.806640 > 154 H -0.593730 3.184280 0.706460 > 155 H 0.593730 -3.184280 0.706460 > 156 H 1.849370 3.280780 0.883620 > 157 H -1.849370 -3.280780 0.883620 > 158 H -1.264360 1.976320 -1.465620 > 159 H 1.264360 -1.976320 -1.465620 > 160 H 2.067340 1.111470 1.465270 > 161 H -2.067340 -1.111470 1.465270 > 162 - 0.408688 1.481601 0.017975 > 163 - -0.442210 -1.472899 0.045583 > > (line numbers by "vi", ignore) > > The two last lines are the coordinates of two dummy atoms. They turn up as > "DA" in the input, but apparently as " - " in the coordinate blocks of the > output. > > Drop me a line if you need more info. > > Regards, > Xaver W. > (for ccwatcher.sourceforge.net) > > ------------------------------------------------------------------------------ > Enable your software for Intel(R) Active Management Technology to meet the > growing manageability and security demands of your customers. Businesses > are taking advantage of Intel(R) vPro (TM) technology - will your software > be a part of the solution? Download the Intel(R) Manageability Checker > today! http://p.sf.net/sfu/intel-dev2devmar > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel -- written by Karol M. Langner Mon Mar 28 12:46:01 CEST 2011 |
|
From: Xaver W. <xav...@we...> - 2011-03-28 10:38:17
|
Hi,
in case of dummy atoms, orcaparser can't read the atoms. Consider:
>>> cclibdata = cfile.parse()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "cclib/parser/logfileparser.py", line 221, in parse
self.extract(inputfile, line)
File "cclib/parser/orcaparser.py", line 196, in extract
atomnos.append(self.table.number[broken[0]])
KeyError: '-'
I think the lines which orcaparser is trying to read are (sth like):
138 ---------------------------------
139 CARTESIAN COORDINATES (ANGSTROEM)
140 ---------------------------------
141 Fe 0.000000 0.000000 0.000660
142 O -0.592830 1.741600 -0.806850
143 O 0.592830 -1.741600 -0.806850
144 C 0.000000 2.934410 -0.176690
145 C 0.000000 -2.934410 -0.176690
146 H -0.018170 3.765540 -0.884740
147 H 0.018170 -3.765540 -0.884740
148 C 1.428890 2.563280 0.175900
149 C -1.428890 -2.563280 0.175900
150 H 2.069080 2.492180 -0.707270
151 H -2.069080 -2.492180 -0.707270
152 O 1.366300 1.233000 0.806640
153 O -1.366300 -1.233000 0.806640
154 H -0.593730 3.184280 0.706460
155 H 0.593730 -3.184280 0.706460
156 H 1.849370 3.280780 0.883620
157 H -1.849370 -3.280780 0.883620
158 H -1.264360 1.976320 -1.465620
159 H 1.264360 -1.976320 -1.465620
160 H 2.067340 1.111470 1.465270
161 H -2.067340 -1.111470 1.465270
162 - 0.408688 1.481601 0.017975
163 - -0.442210 -1.472899 0.045583
(line numbers by "vi", ignore)
The two last lines are the coordinates of two dummy atoms. They turn up as
"DA" in the input, but apparently as " - " in the coordinate blocks of the
output.
Drop me a line if you need more info.
Regards,
Xaver W.
(for ccwatcher.sourceforge.net)
|
|
From: Noel O'B. <bao...@gm...> - 2011-03-26 17:01:18
|
If you really want, but can you check that it installs correctly from a source distribution made after running manifest.py? - Noel On 26 March 2011 16:45, Karol M. Langner <kar...@gm...> wrote: > Noel, > > I think it would be more reasonable to NOT install them in setup.py > by default. I can take it upon myself to change this by adding an > option. Is --install-tests is OK? > > On Sat, Mar 26, 2011 at 04:01:36PM +0000, Noel O'Boyle wrote: >> There's no need for them to be packaged certainly. But I see no real >> problem with installing them (and everytime I try to change the >> installer, I break something!). >> >> - Noel >> >> On 26 March 2011 15:33, Karol M. Langner <kar...@gm...> wrote: >> > Dear cclibers, >> > >> > While working towards the cclib debian packages, a question came up >> > concerning whether the unittests should be packaged or not. Basically, >> > the user does not need them, right? If not, then I suppose we should >> > also not be installing them by default. >> > >> > What do you think? >> > >> > - Karol > > -- > written by Karol Langner > Sat Mar 26 17:43:07 CET 2011 > |
|
From: Karol M. L. <kar...@gm...> - 2011-03-26 16:45:55
|
Noel, I think it would be more reasonable to NOT install them in setup.py by default. I can take it upon myself to change this by adding an option. Is --install-tests is OK? On Sat, Mar 26, 2011 at 04:01:36PM +0000, Noel O'Boyle wrote: > There's no need for them to be packaged certainly. But I see no real > problem with installing them (and everytime I try to change the > installer, I break something!). > > - Noel > > On 26 March 2011 15:33, Karol M. Langner <kar...@gm...> wrote: > > Dear cclibers, > > > > While working towards the cclib debian packages, a question came up > > concerning whether the unittests should be packaged or not. Basically, > > the user does not need them, right? If not, then I suppose we should > > also not be installing them by default. > > > > What do you think? > > > > - Karol -- written by Karol Langner Sat Mar 26 17:43:07 CET 2011 |
|
From: Karol M. L. <kar...@gm...> - 2011-03-26 16:38:16
|
On Thu, Feb 10, 2011 at 11:02:32AM +0000, Noel O'Boyle wrote: > Unfortunately, the SF wiki > puts a huge banner at the top of the page, which is really annoying. Why? :) It really looks silly. I created a ticket for hiding it. We will see if it can be changed... -- written by Karol Langner Sat Mar 26 17:10:38 CET 2011 |
|
From: Noel O'B. <bao...@gm...> - 2011-03-26 16:01:42
|
There's no need for them to be packaged certainly. But I see no real problem with installing them (and everytime I try to change the installer, I break something!). - Noel On 26 March 2011 15:33, Karol M. Langner <kar...@gm...> wrote: > Dear cclibers, > > While working towards the cclib debian packages, a question came up > concerning whether the unittests should be packaged or not. Basically, > the user does not need them, right? If not, then I suppose we should > also not be installing them by default. > > What do you think? > > - Karol > > -- > written by Karol Langner > Sat Mar 26 16:30:18 CET 2011 > > ------------------------------------------------------------------------------ > Enable your software for Intel(R) Active Management Technology to meet the > growing manageability and security demands of your customers. Businesses > are taking advantage of Intel(R) vPro (TM) technology - will your software > be a part of the solution? Download the Intel(R) Manageability Checker > today! http://p.sf.net/sfu/intel-dev2devmar > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > |
|
From: Karol M. L. <kar...@gm...> - 2011-03-26 15:33:25
|
Dear cclibers, While working towards the cclib debian packages, a question came up concerning whether the unittests should be packaged or not. Basically, the user does not need them, right? If not, then I suppose we should also not be installing them by default. What do you think? - Karol -- written by Karol Langner Sat Mar 26 16:30:18 CET 2011 |
|
From: Karol M. L. <kar...@gm...> - 2011-03-21 09:59:55
|
On Mon, Mar 21, 2011 at 09:50:51AM +0000, Noel O'Boyle wrote: > Hi all, > > Following an email by John Simmie to CCL.net, I've added support to > extract the "X matrix of Anharmonic Constants (cm-1)" from a > FREQ=ANHARM job in Gaussian. I'm not quite sure what to call it, but > for the moment it's "vibanharms". I think there are also anharmonic > frequencies, so maybe it should instead be "vibanharmconsts". > > - Noel Hi, Isn't the frequency used in the anharmonic term the same as the harmonic? Anyway, I would propose vibaconst. - Karol -- written by Karol M. Langner Mon Mar 21 10:53:49 CET 2011 |
|
From: Noel O'B. <bao...@gm...> - 2011-03-21 09:50:58
|
Hi all, Following an email by John Simmie to CCL.net, I've added support to extract the "X matrix of Anharmonic Constants (cm-1)" from a FREQ=ANHARM job in Gaussian. I'm not quite sure what to call it, but for the moment it's "vibanharms". I think there are also anharmonic frequencies, so maybe it should instead be "vibanharmconsts". - Noel |
|
From: Karol M. L. <kar...@gm...> - 2011-03-16 14:39:21
|
On Wed, Mar 16, 2011 at 02:33:34PM +0000, Noel O'Boyle wrote: > On 16 March 2011 13:45, Karol M. Langner <kar...@gm...> wrote: > > On Wed, Mar 16, 2011 at 12:11:34PM +0000, Noel O'Boyle wrote: > >> On 16 March 2011 09:37, Noel O'Boyle <bao...@gm...> wrote: > >> > On 16 March 2011 09:36, Karol M. Langner <kar...@gm...> wrote: > >> >> On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote: > >> >>> Hi Karol, > >> >>> > >> >>> I'm just updating the changelog for cclib-1.0.1 and I see that you > >> >>> added a new attribute atommasses in r296. Can you update the wiki with > >> >>> information on this? > >> >>> > >> >>> - Noel > >> >> > >> >> Sure. I can't seem to edit pages on the wiki. Does that have something to > >> >> do with the recent software change? > >> > > >> > Probably - have you logged into SourceForge first, and then tried? > >> > >> It's looks like I needed to give you permissions - you're now an > >> editor and admin. It seems that an account is only created when you > >> visit the wiki for the first time. Then one of the wiki admins can > >> give permissions to the account. > > > > Works now. I added atommasses to both 'parsed data' pages, as I understand it made > > it into 1.0.1. The coverage is quite low among the parsers... > > That's right. 1.0.1 is basically trunk. > > A quick question: should every Gaussian calculation have atommasses set? Generally, yes, if there are atoms then I think Gaussian will always print a section with IAtWgt and AtmWgt. Althought there could be a special kind of calculation that does not have explicit atoms, it would be beyond the current scope of cclib. - Karol |
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From: Noel O'B. <bao...@gm...> - 2011-03-16 14:33:40
|
On 16 March 2011 13:45, Karol M. Langner <kar...@gm...> wrote: > On Wed, Mar 16, 2011 at 12:11:34PM +0000, Noel O'Boyle wrote: >> On 16 March 2011 09:37, Noel O'Boyle <bao...@gm...> wrote: >> > On 16 March 2011 09:36, Karol M. Langner <kar...@gm...> wrote: >> >> On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote: >> >>> Hi Karol, >> >>> >> >>> I'm just updating the changelog for cclib-1.0.1 and I see that you >> >>> added a new attribute atommasses in r296. Can you update the wiki with >> >>> information on this? >> >>> >> >>> - Noel >> >> >> >> Sure. I can't seem to edit pages on the wiki. Does that have something to >> >> do with the recent software change? >> > >> > Probably - have you logged into SourceForge first, and then tried? >> >> It's looks like I needed to give you permissions - you're now an >> editor and admin. It seems that an account is only created when you >> visit the wiki for the first time. Then one of the wiki admins can >> give permissions to the account. > > Works now. I added atommasses to both 'parsed data' pages, as I understand it made > it into 1.0.1. The coverage is quite low among the parsers... That's right. 1.0.1 is basically trunk. A quick question: should every Gaussian calculation have atommasses set? - Noel |
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From: Karol M. L. <kar...@gm...> - 2011-03-16 13:45:21
|
On Wed, Mar 16, 2011 at 12:11:34PM +0000, Noel O'Boyle wrote: > On 16 March 2011 09:37, Noel O'Boyle <bao...@gm...> wrote: > > On 16 March 2011 09:36, Karol M. Langner <kar...@gm...> wrote: > >> On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote: > >>> Hi Karol, > >>> > >>> I'm just updating the changelog for cclib-1.0.1 and I see that you > >>> added a new attribute atommasses in r296. Can you update the wiki with > >>> information on this? > >>> > >>> - Noel > >> > >> Sure. I can't seem to edit pages on the wiki. Does that have something to > >> do with the recent software change? > > > > Probably - have you logged into SourceForge first, and then tried? > > It's looks like I needed to give you permissions - you're now an > editor and admin. It seems that an account is only created when you > visit the wiki for the first time. Then one of the wiki admins can > give permissions to the account. Works now. I added atommasses to both 'parsed data' pages, as I understand it made it into 1.0.1. The coverage is quite low among the parsers... Also, I will try to make a more comprehensive update of these tables in the next few days. - Karol |
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From: Noel O'B. <bao...@gm...> - 2011-03-16 12:11:43
|
On 16 March 2011 09:37, Noel O'Boyle <bao...@gm...> wrote: > On 16 March 2011 09:36, Karol M. Langner <kar...@gm...> wrote: >> On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote: >>> Hi Karol, >>> >>> I'm just updating the changelog for cclib-1.0.1 and I see that you >>> added a new attribute atommasses in r296. Can you update the wiki with >>> information on this? >>> >>> - Noel >> >> Sure. I can't seem to edit pages on the wiki. Does that have something to >> do with the recent software change? > > Probably - have you logged into SourceForge first, and then tried? It's looks like I needed to give you permissions - you're now an editor and admin. It seems that an account is only created when you visit the wiki for the first time. Then one of the wiki admins can give permissions to the account. >> Cheers, >> Karol >> > |
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From: Noel O'B. <bao...@gm...> - 2011-03-16 09:37:40
|
On 16 March 2011 09:36, Karol M. Langner <kar...@gm...> wrote: > On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote: >> Hi Karol, >> >> I'm just updating the changelog for cclib-1.0.1 and I see that you >> added a new attribute atommasses in r296. Can you update the wiki with >> information on this? >> >> - Noel > > Sure. I can't seem to edit pages on the wiki. Does that have something to > do with the recent software change? Probably - have you logged into SourceForge first, and then tried? > Cheers, > Karol > |
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From: Karol M. L. <kar...@gm...> - 2011-03-16 09:36:39
|
On Mon, Mar 14, 2011 at 11:53:20AM +0000, Noel O'Boyle wrote: > Hi Karol, > > I'm just updating the changelog for cclib-1.0.1 and I see that you > added a new attribute atommasses in r296. Can you update the wiki with > information on this? > > - Noel Sure. I can't seem to edit pages on the wiki. Does that have something to do with the recent software change? Cheers, Karol |
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From: Noel O'B. <bao...@gm...> - 2011-03-14 14:45:54
|
Hello all, cclib 1.0.1 is now available for download from http://cclib.sf.net. This is largely a bug fix release (thanks to everyone that reported bugs or supplied patches). We've also taken the opportunity to (finally!) add instructions on the command-line application 'ccget' to our wiki, so check it out, as it's quite handy. Thanks to everyone that cited the cclib paper in the past - we really appreciate it. This paper was the 2nd most cited J Comp Chem paper in 2009. Changes since cclib-1.0: Features: * New attribute atommasses - atomic masses in Dalton * Added support for Gaussian geometry optimisations that change the number of linearly independent basis functions over the course of the calculation Bugfixes: * Handle triplet PM3 calculations in Gaussian03 (Greg Magoon) * Some Gaussian09 calculations were missing atomnos (Marius Retegan) * Handle multiple pseudopotentials in Gaussian03 (Tiago Silva) * Handle Gaussian calculations with >999 basis functions * ADF versions > 2007 no longer print overlap info by default * Handle parsing Firefly calculations that fail * Fix parsing of ORCA calculation (Marius Retegan) Regards, Noel (on behalf of the cclib dev team) |
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From: Noel O'B. <bao...@gm...> - 2011-03-14 11:53:54
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Hi Karol, I'm just updating the changelog for cclib-1.0.1 and I see that you added a new attribute atommasses in r296. Can you update the wiki with information on this? - Noel |
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From: Noel O'B. <bao...@gm...> - 2011-03-13 21:51:30
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Sounds good - when you have it, send it in. No Anaheim for me I'm afraid... - Noel On 9 March 2011 17:04, Benjamin Stein <bs...@un...> wrote: > Hi all, > > Sorry for the long silence, but I've more or less got the basis set parsing sorted out (at least in ORCA, but the foundations are there for everything). I'll try and get a cleaned up bit of code out next week (spring break, plenty of time for once...). > > Also, is anyone else planning on being at the ACS conference in Anaheim at the end of the month? > > Best, > Ben Stein > ------------------------------------------------------------------------------ > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit > for your organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ > cclib-devel mailing list > ccl...@li... > https://lists.sourceforge.net/lists/listinfo/cclib-devel > |
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From: Benjamin S. <bs...@un...> - 2011-03-09 17:04:32
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Hi all, Sorry for the long silence, but I've more or less got the basis set parsing sorted out (at least in ORCA, but the foundations are there for everything). I'll try and get a cleaned up bit of code out next week (spring break, plenty of time for once...). Also, is anyone else planning on being at the ACS conference in Anaheim at the end of the month? Best, Ben Stein |
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From: Noel O'B. <bao...@gm...> - 2011-03-06 16:33:23
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Hi all, I aim to make a new release, cclib-1.0.1 or so, in the next few days... - Noel |
