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From: <no...@so...> - 2002-11-09 12:49:18
|
Bugs item #635902, was opened at 2002-11-09 13:49 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=635902&group_id=23629 Category: User interface Group: CVS Status: Open Resolution: None Priority: 2 Submitted By: Egon Willighagen (egonw) Assigned to: Egon Willighagen (egonw) Summary: Change mode from Measure, no icon update Initial Comment: When changing the mode to MEASURE when opening the Measure dialog, or when closing it back to the original mode, the icon highlighting is not changed accordingly. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=635902&group_id=23629 |
From: Egon W. <eg...@sc...> - 2002-11-09 12:43:44
|
On Friday 08 November 2002 16:29, Fabian Dortu wrote: > Still a little bug: > > when measure is called, we are in PICK mode altough the selected icon in > the toolbar is still oldmod. Yes, indeed. I've looked at the cause, and it is not easy to solve... The problem is that the code is separated... i.e. the buttons highlighting is independant and, which is worse, in different classes... Solving this would require a redesign of the Jmol classes, which I would like to postpone to a later version... Egon |
From: mth <mt...@mt...> - 2002-11-08 21:17:25
|
I have rolled back the DisplayPanel code which uses a separate thread for recalculation. (This is the second time I have rolled something back ... I fear a dangerous pattern is developing.) Per Egon's suggestion, I put in some code which displays the rendering time in the status bar. Two numbers are shown. The first number is the number of milliseconds to calculate the most recent frame. The second number is the average of the last 50 repaints. On my machine, the threaded version was up to 25% slower on the redisplay of smaller molecules. I am still trying to find a way to isolate and/or eliminate *the bug* before I start making performance enhancements. Most of these attempts will be in the DisplayPanel code. Miguel |
From: Fabian D. <fab...@wa...> - 2002-11-08 15:29:50
|
Still a little bug: when measure is called, we are in PICK mode altough the selected icon in the toolbar is still oldmod. On Fri, 2002-11-08 at 15:48, E.L. Willighagen wrote: > On Friday 08 November 2002 15:37, E.L. Willighagen wrote: > > > By clicking on the arrow (DisplayPanel.PICK > > > mode), we should be able to pick the atoms again. Actually, I am not > > > certain of the utility of the DisplayPanel.PICK mode. Is it only to > > > highlight the atoms? Maybe we will need to add a new mode, let's say > > > DisplayPanel.PICK4MEAS (Pick for Measurement). > > > > That mode is already there, with the name MEASURE (see line 301 in > > DisplayPanel.java)... > > > > I think I've got a better idea... the PICK button is OK, but what shoul= d > > happen is this... when the PICK button is clicked, it should check weth= er > > the Measure windows is shown... if that is the case, it should enable t= he > > mode MEASURE, and PICK otherwise... >=20 > This works fine. Commiting changes now. >=20 > Egon >=20 >=20 > ------------------------------------------------------- > This sf.net email is sponsored by: See the NEW Palm=20 > Tungsten T handheld. Power & Color in a compact size! > http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0001en > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers >=20 --=20 ********** Fabian Dortu Phone : 32-475-599268 e-mail : Fab...@wa... ***********************************************=20 |
From: E.L. W. <eg...@sc...> - 2002-11-08 15:13:06
|
Forgot to mention it, but I also taged the b5 branch with "b5-merged-20021008" so that future changes to the branch can be merged with HEAD too. Egon |
From: E.L. W. <eg...@sc...> - 2002-11-08 15:07:41
|
Hi all, I've commit the changes in the branch to HEAD.. so that the HEAD now includes the recent bug fixes... Egon |
From: Dr P. Murray-R. <pm...@ca...> - 2002-11-08 14:48:47
|
On Nov 8 2002, Fabian Dortu wrote: > On Fri, 2002-11-08 at 12:38, E.L. Willighagen wrote: > > On Friday 08 November 2002 11:01, Fabian Dortu wrote: > > > so I am back from the abinit workshop where I presented Jmol. It > > > seems that Jmol is already used by few abinit users/developpers and > > > will touch more and more users if I continue to include more abinit > > > features. > > A brief reply - I am in Germany... > > > Concerning abinit: > > > > > > There is a strong motivation from the abinit leader that Jmol become > > > some kind of complete abinit output reader. To achieve this, he wants > > > to provide an abinit output in CML. I have not examine the CML DTD > > > yet, and I would like to know, Egon, if there is some specification > > > to store energy bands or phonon dispersion curves in CML. > > > > Ah, interesting... CML can hold all kinds of information for which > > there is a set of general elements, like <float>, <string> etc... If > > you could give me an example on how energy bands and phonon dispersion > > curves are stored in the current ABINIT output, I can propose a way to > > store it in CML... > I have had recent discussion with Xavier Gonze about CML and abinit. He mailed me and said he planned to include it in the next release. More generally I and Henry Rzepa are developing Computational Chemistry ML and will be issuing a spec for this fairly shortly - I have been asked to present this at a workshop in ca 2 weeks time. CCML is designed to be program-independent so that each code would create adapters for input and output. This will be a collaborative activity on our sourceforge site and we will very much welcome contributions like your message. In haste Peter > for each k-point the number of bands, the k-point coordinates and the > energies are given i.e.: > > kpt 1 : nband=4, kpt= 0.0 0.5 0.0, 0.45456 1.3455 3.5653 6.3454 > kpt 2 : nband=4, kpt= 0.1 0.5 0.0, 0.47567 1.2456 3.4365 6.1434 > ... > > *the k-point coordinates are given in reduced coordinates of the > reciprocal unit cell. > > *the energies are usually given in eV > > *the k-points are given in a specific order to constitute a line i.e.: > > kpt 1 : nband=4, kpt= 0.00 0.5 0.0, .... > kpt 2 : nband=4, kpt= 0.05 0.5 0.0, .... > kpt 3 : nband=4, kpt= 0.10 0.5 0.0, .... > .. > .. > kpt 20 : nband=4, kpt= 0.95 0.5 0.0, .... > kpt 21 : nband=4, kpt= 1.00 0.5 0.0, ... > > > for the line 0.0 0.5 0.0 --> 1.0 0.5 0.0 > I think it is important to know to which line a k point belongs because > plots are always made along lines. There is a difficulty: a given k > point can belong to several lines. This causes duplicate information > which is not good in general. > > Here is a real part of an ouput file: > > Eigenvalues ( eV ) for nkpt= 40 k points: > kpt# 1, nband= 8, wtk= 1.00000, kpt= 0.5000 0.0000 0.0000 > (reduced coord) > -3.78987 -1.16032 4.69394 4.69394 7.38388 9.23579 9.23579 > 13.45362 > kpt# 2, nband= 8, wtk= 1.00000, kpt= 0.4500 0.0000 0.0000 > (reduced coord) > -3.92925 -0.95943 4.71018 4.71018 7.40285 9.25271 9.25271 > 13.48580 > kpt# 3, nband= 8, wtk= 1.00000, kpt= 0.4000 0.0000 0.0000 > (reduced coord) > -4.25584 -0.44579 4.76451 4.76451 7.46440 9.30898 9.30898 > 13.57381 > kpt# 4, nband= 8, wtk= 1.00000, kpt= 0.3500 0.0000 0.0000 > (reduced coord) > -4.64158 0.24736 4.85456 4.85456 7.56449 9.38019 9.38019 > 13.64227 > kpt# 5, nband= 8, wtk= 1.00000, kpt= 0.3000 0.0000 0.0000 > (reduced coord) > -5.01877 1.05178 4.97950 4.97950 7.69972 9.42850 9.42850 > 13.46987 > kpt# 6, nband= 8, wtk= 1.00000, kpt= 0.2500 0.0000 0.0000 > (reduced coord) > -5.35842 1.93088 5.13615 5.13615 7.87016 9.40042 9.40042 > 12.70508 > kpt# 7, nband= 8, wtk= 1.00000, kpt= 0.2000 0.0000 0.0000 > (reduced coord) > -5.64522 2.86060 5.31982 5.31982 8.06502 9.25622 9.25622 > 11.85317 > kpt# 8, nband= 8, wtk= 1.00000, kpt= 0.1500 0.0000 0.0000 > (reduced coord) > -5.87284 3.81433 5.51838 5.51838 8.26479 9.01260 9.01260 > 10.96801 > kpt# 9, nband= 8, wtk= 1.00000, kpt= 0.1000 0.0000 0.0000 > (reduced coord) > -6.03831 4.74627 5.70919 5.70919 8.43435 8.74293 8.74293 > 10.10776 > kpt# 10, nband= 8, wtk= 1.00000, kpt= 0.0500 0.0000 0.0000 > (reduced coord) > -6.13776 5.54781 5.85776 5.85776 8.50041 8.52819 8.52819 > 9.41785 > kpt# 11, nband= 8, wtk= 1.00000, kpt= 0.0000 0.0000 0.0000 > (reduced coord) > -6.17102 5.91515 5.91515 5.91515 8.44524 8.44524 8.44524 > 9.17124 > kpt# 12, nband= 8, wtk= 1.00000, kpt= 0.0000 0.0417 0.0417 > (reduced coord) > -6.14024 5.71288 5.78441 5.78441 8.36645 8.61213 8.61213 > 9.36598 > kpt# 13, nband= 8, wtk= 1.00000, kpt= 0.0000 0.0833 0.0833 > (reduced coord) > -6.04794 5.21207 5.46952 5.46952 8.15192 9.03530 9.03530 > 9.81362 > kpt# 14, nband= 8, wtk= 1.00000, kpt= 0.0000 0.1250 0.1250 > (reduced coord) > -5.89384 4.56875 5.08418 5.08418 7.86175 9.60627 9.60627 > 10.21287 > kpt# 15, nband= 8, wtk= 1.00000, kpt= 0.0000 0.1667 0.1667 > (reduced coord) > -5.67960 3.86208 4.68977 4.68977 7.54297 10.13997 10.25582 > 10.25582 > kpt# 16, nband= 8, wtk= 1.00000, kpt= 0.0000 0.2083 0.2083 > (reduced coord) > -5.40555 3.12647 4.31688 4.31688 7.23172 9.61206 10.95216 > 10.95216 > kpt# 17, nband= 8, wtk= 1.00000, kpt= 0.0000 0.2500 0.2500 > (reduced coord) > -5.07297 2.37642 3.97975 3.97975 6.94764 8.96586 11.67483 > 11.67483 > kpt# 18, nband= 8, wtk= 1.00000, kpt= 0.0000 0.2917 0.2917 > (reduced coord) > -4.68272 1.62313 3.68845 3.68845 6.71326 8.35365 12.42265 > 12.42265 > kpt# 19, nband= 8, wtk= 1.00000, kpt= 0.0000 0.3333 0.3333 > (reduced coord) > -4.23796 0.87223 3.44463 3.44463 6.53194 7.80616 13.18559 > 13.18559 > kpt# 20, nband= 8, wtk= 1.00000, kpt= 0.0000 0.3750 0.3750 > (reduced coord) > -3.74014 0.13164 3.25437 3.25437 6.41794 7.35277 13.97613 > 13.97613 > kpt# 21, nband= 8, wtk= 1.00000, kpt= 0.0000 0.4167 0.4167 > (reduced coord) > -3.19331 -0.59332 3.11588 3.11588 6.37215 6.98112 14.75764 > 14.75764 > kpt# 22, nband= 8, wtk= 1.00000, kpt= 0.0000 0.4583 0.4583 > (reduced coord) > -2.60042 -1.29475 3.03204 3.03204 6.40106 6.70134 15.50276 > 15.50276 > kpt# 23, nband= 8, wtk= 1.00000, kpt= 0.0000 0.5000 0.5000 > (reduced coord) > -1.96598 -1.96598 3.00346 3.00346 6.50928 6.50928 15.94975 > 16.44100 > ... > ... > ... > > > > > > > > > > In my last CVS commit (sorry for the disturbance btw), I included an > > > EnergyBand object to store energy bands along (symmetry) lines. This > > > object is already used by ABINITOutputReader but there is no graphical > > > output yet. > > > > > > Concerning JAS: > > > > > > On the web site, JAS seems to be full featured and to provide > > > PostScript output. However, the interface in Jmol doesn't reflects > > > this feature. > > > > Not sure how Jmol currently makes PostScript, but the output looks > > fine. Could you elaborate on the high quality PS output, and what is > > wrong with the current output? > > > > Egon > > > > > > ------------------------------------------------------- > > This sf.net email is sponsored by: See the NEW Palm > > Tungsten T handheld. Power & Color in a compact size! > > http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0001en > > _______________________________________________ > > Jmol-developers mailing list > > Jmo...@li... > > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > |
From: E.L. W. <eg...@sc...> - 2002-11-08 14:48:31
|
On Friday 08 November 2002 15:37, E.L. Willighagen wrote: > > By clicking on the arrow (DisplayPanel.PICK > > mode), we should be able to pick the atoms again. Actually, I am not > > certain of the utility of the DisplayPanel.PICK mode. Is it only to > > highlight the atoms? Maybe we will need to add a new mode, let's say > > DisplayPanel.PICK4MEAS (Pick for Measurement). > > That mode is already there, with the name MEASURE (see line 301 in > DisplayPanel.java)... > > I think I've got a better idea... the PICK button is OK, but what should > happen is this... when the PICK button is clicked, it should check wether > the Measure windows is shown... if that is the case, it should enable the > mode MEASURE, and PICK otherwise... This works fine. Commiting changes now. Egon |
From: Fabian D. <fab...@wa...> - 2002-11-08 14:42:16
|
On Fri, 2002-11-08 at 15:37, E.L. Willighagen wrote: > On Friday 08 November 2002 15:19, Fabian Dortu wrote: > > There is some unconsistent behavior with the measure action: > > > > when the measure menu is enabled, and if you click on rotate (for > > example) there is no way to pick the atoms again. You have to close and > > reopen the measure dialog.=20 >=20 > Yes, I can confirm this strange behaviour... >=20 > > By clicking on the arrow (DisplayPanel.PICK > > mode), we should be able to pick the atoms again. Actually, I am not > > certain of the utility of the DisplayPanel.PICK mode. Is it only to > > highlight the atoms? Maybe we will need to add a new mode, let's say > > DisplayPanel.PICK4MEAS (Pick for Measurement). >=20 > That mode is already there, with the name MEASURE (see line 301 in=20 > DisplayPanel.java)... >=20 > I think I've got a better idea... the PICK button is OK, but what should=20 > happen is this... when the PICK button is clicked, it should check wether= the=20 > Measure windows is shown... if that is the case, it should enable the mod= e=20 > MEASURE, and PICK otherwise... Sounds nice >=20 > Egon >=20 >=20 > ------------------------------------------------------- > This sf.net email is sponsored by: See the NEW Palm=20 > Tungsten T handheld. Power & Color in a compact size! > http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0001en > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers >=20 --=20 ********** Fabian Dortu Phone : 32-475-599268 e-mail : Fab...@wa... ***********************************************=20 |
From: E.L. W. <eg...@sc...> - 2002-11-08 14:37:44
|
On Friday 08 November 2002 15:19, Fabian Dortu wrote: > There is some unconsistent behavior with the measure action: > > when the measure menu is enabled, and if you click on rotate (for > example) there is no way to pick the atoms again. You have to close and > reopen the measure dialog. Yes, I can confirm this strange behaviour... > By clicking on the arrow (DisplayPanel.PICK > mode), we should be able to pick the atoms again. Actually, I am not > certain of the utility of the DisplayPanel.PICK mode. Is it only to > highlight the atoms? Maybe we will need to add a new mode, let's say > DisplayPanel.PICK4MEAS (Pick for Measurement). That mode is already there, with the name MEASURE (see line 301 in DisplayPanel.java)... I think I've got a better idea... the PICK button is OK, but what should happen is this... when the PICK button is clicked, it should check wether the Measure windows is shown... if that is the case, it should enable the mode MEASURE, and PICK otherwise... Egon |
From: Fabian D. <fab...@wa...> - 2002-11-08 14:19:43
|
There is some unconsistent behavior with the measure action: when the measure menu is enabled, and if you click on rotate (for example) there is no way to pick the atoms again. You have to close and reopen the measure dialog. By clicking on the arrow (DisplayPanel.PICK mode), we should be able to pick the atoms again. Actually, I am not certain of the utility of the DisplayPanel.PICK mode. Is it only to highlight the atoms? Maybe we will need to add a new mode, let's say DisplayPanel.PICK4MEAS (Pick for Measurement). Fabian --=20 ********** Fabian Dortu Phone : 32-475-599268 e-mail : Fab...@wa... ***********************************************=20 |
From: E.L. W. <eg...@sc...> - 2002-11-08 13:09:36
|
On Wednesday 30 October 2002 18:29, Richard Muller wrote: > Thanks very much. Attached is a Jaguar optimization file for the > optimization of CH4. I also attach a Python script that I use to > convert the Jaguar output to XYZ, just so you can see what type of > patterns I search for and how I do the conversions. You can > redistribute any of this. Thanx for the example. The next Jmol release (v5) will and current b5 CVS branch supports reading of all frames in the Jaguar file. Note that it also reads the input structure, not just the output... Egon |
From: Fabian D. <fab...@wa...> - 2002-11-08 12:49:46
|
On Fri, 2002-11-08 at 12:38, E.L. Willighagen wrote: > On Friday 08 November 2002 11:01, Fabian Dortu wrote: > > so I am back from the abinit workshop where I presented Jmol. It seems > > that Jmol is already used by few abinit users/developpers and will touc= h > > more and more users if I continue to include more abinit features. >=20 > Ok. That sounds good. >=20 > > here are some of users' wishes: > > > > * direct image output as PostScript (ps/eps). > > > > * publication quality (in PostScript) graphs. >=20 > What is the difference with the File->Print menu? Right, no difference actually but the users seem a little confused about this. What do you think about adding this format into export image so=20 that File-->PrintToFile would be equivalent=20 to File->export image->eps? >=20 > > * a geometry builder. >=20 > What should it do precisely? *adding atoms by entering the coordinates. *apply an arbitrary symmetry operation (point group=20 operations and translations) to a set of atoms so that the desired structure can be build. >=20 > > * some details: > > - be able to rotate the molecule by a given angle (i.e: I want to rotat= e > > the molecule by 45=B0. around z or around any given axis). >=20 > Yes, we should implement a method to rotate around one of the axes with a= n=20 > arbitrary angle. >=20 > > - the measure->distance (or angle,...) should remain on screen after th= e > > measurement has been added to the measurement list because users > > generally want to make a lot of measurements. In other words, add a > > "dismiss" button. >=20 > Ok. >=20 > > Concerning abinit: > > > > There is a strong motivation from the abinit leader that Jmol become > > some kind of complete abinit output reader. To achieve this, he wants t= o > > provide an abinit output in CML. I have not examine the CML DTD yet, an= d > > I would like to know, Egon, if there is some specification to store > > energy bands or phonon dispersion curves in CML. >=20 > Ah, interesting... CML can hold all kinds of information for which there = is a=20 > set of general elements, like <float>, <string> etc... If you could give = me=20 > an example on how energy bands and phonon dispersion curves are stored in= the=20 > current ABINIT output, I can propose a way to store it in CML... for each k-point the number of bands, the k-point coordinates and the energies are given i.e.: kpt 1 : nband=3D4, kpt=3D 0.0 0.5 0.0, 0.45456 1.3455 3.5653 6.3454 kpt 2 : nband=3D4, kpt=3D 0.1 0.5 0.0, 0.47567 1.2456 3.4365 6.1434 ... *the k-point coordinates are given in reduced coordinates of the reciprocal unit cell. *the energies are usually given in eV *the k-points are given in a specific order to constitute a line i.e.: kpt 1 : nband=3D4, kpt=3D 0.00 0.5 0.0, .... kpt 2 : nband=3D4, kpt=3D 0.05 0.5 0.0, .... kpt 3 : nband=3D4, kpt=3D 0.10 0.5 0.0, .... .. .. kpt 20 : nband=3D4, kpt=3D 0.95 0.5 0.0, .... kpt 21 : nband=3D4, kpt=3D 1.00 0.5 0.0, ... for the line 0.0 0.5 0.0 --> 1.0 0.5 0.0 I think it is important to know to which line a k point belongs because plots are always made along lines. There is a difficulty: a given k point can belong to several lines. This causes duplicate information which is not good in general. Here is a real part of an ouput file: Eigenvalues ( eV ) for nkpt=3D 40 k points: kpt# 1, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.5000 0.0000 0.0000 (reduced coord) -3.78987 -1.16032 4.69394 4.69394 7.38388 9.23579 9.23579=20 13.45362 kpt# 2, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.4500 0.0000 0.0000 (reduced coord) -3.92925 -0.95943 4.71018 4.71018 7.40285 9.25271 9.25271=20 13.48580 kpt# 3, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.4000 0.0000 0.0000 (reduced coord) -4.25584 -0.44579 4.76451 4.76451 7.46440 9.30898 9.30898=20 13.57381 kpt# 4, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.3500 0.0000 0.0000 (reduced coord) -4.64158 0.24736 4.85456 4.85456 7.56449 9.38019 9.38019=20 13.64227 kpt# 5, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.3000 0.0000 0.0000 (reduced coord) -5.01877 1.05178 4.97950 4.97950 7.69972 9.42850 9.42850=20 13.46987 kpt# 6, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.2500 0.0000 0.0000 (reduced coord) -5.35842 1.93088 5.13615 5.13615 7.87016 9.40042 9.40042=20 12.70508 kpt# 7, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.2000 0.0000 0.0000 (reduced coord) -5.64522 2.86060 5.31982 5.31982 8.06502 9.25622 9.25622=20 11.85317 kpt# 8, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.1500 0.0000 0.0000 (reduced coord) -5.87284 3.81433 5.51838 5.51838 8.26479 9.01260 9.01260=20 10.96801 kpt# 9, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.1000 0.0000 0.0000 (reduced coord) -6.03831 4.74627 5.70919 5.70919 8.43435 8.74293 8.74293=20 10.10776 kpt# 10, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0500 0.0000 0.0000 (reduced coord) -6.13776 5.54781 5.85776 5.85776 8.50041 8.52819 8.52819 =20 9.41785 kpt# 11, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.0000 0.0000 (reduced coord) -6.17102 5.91515 5.91515 5.91515 8.44524 8.44524 8.44524 =20 9.17124 kpt# 12, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.0417 0.0417 (reduced coord) -6.14024 5.71288 5.78441 5.78441 8.36645 8.61213 8.61213 =20 9.36598 kpt# 13, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.0833 0.0833 (reduced coord) -6.04794 5.21207 5.46952 5.46952 8.15192 9.03530 9.03530 =20 9.81362 kpt# 14, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.1250 0.1250 (reduced coord) -5.89384 4.56875 5.08418 5.08418 7.86175 9.60627 9.60627=20 10.21287 kpt# 15, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.1667 0.1667 (reduced coord) -5.67960 3.86208 4.68977 4.68977 7.54297 10.13997 10.25582=20 10.25582 kpt# 16, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.2083 0.2083 (reduced coord) -5.40555 3.12647 4.31688 4.31688 7.23172 9.61206 10.95216=20 10.95216 kpt# 17, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.2500 0.2500 (reduced coord) -5.07297 2.37642 3.97975 3.97975 6.94764 8.96586 11.67483=20 11.67483 kpt# 18, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.2917 0.2917 (reduced coord) -4.68272 1.62313 3.68845 3.68845 6.71326 8.35365 12.42265=20 12.42265 kpt# 19, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.3333 0.3333 (reduced coord) -4.23796 0.87223 3.44463 3.44463 6.53194 7.80616 13.18559=20 13.18559 kpt# 20, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.3750 0.3750 (reduced coord) -3.74014 0.13164 3.25437 3.25437 6.41794 7.35277 13.97613=20 13.97613 kpt# 21, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.4167 0.4167 (reduced coord) -3.19331 -0.59332 3.11588 3.11588 6.37215 6.98112 14.75764=20 14.75764 kpt# 22, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.4583 0.4583 (reduced coord) -2.60042 -1.29475 3.03204 3.03204 6.40106 6.70134 15.50276=20 15.50276 kpt# 23, nband=3D 8, wtk=3D 1.00000, kpt=3D 0.0000 0.5000 0.5000 (reduced coord) -1.96598 -1.96598 3.00346 3.00346 6.50928 6.50928 15.94975=20 16.44100 ... ... ... >=20 > > In my last CVS commit (sorry for the disturbance btw), I included an > > EnergyBand object to store energy bands along (symmetry) lines. This > > object is already used by ABINITOutputReader but there is no graphical > > output yet. > > > > Concerning JAS: > > > > On the web site, JAS seems to be full featured and to provide PostScrip= t > > output. However, the interface in Jmol doesn't reflects this feature. >=20 > Not sure how Jmol currently makes PostScript, but the output looks fine. > Could you elaborate on the high quality PS output, and what is wrong with= the=20 > current output? >=20 > Egon >=20 >=20 > ------------------------------------------------------- > This sf.net email is sponsored by: See the NEW Palm=20 > Tungsten T handheld. Power & Color in a compact size! > http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0001en > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers >=20 --=20 ********** Fabian Dortu Phone : 32-475-599268 e-mail : Fab...@wa... ***********************************************=20 |
From: <no...@so...> - 2002-11-08 12:31:04
|
Bugs item #630456, was opened at 2002-10-29 14:29 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=630456&group_id=23629 >Category: User interface Group: v4 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Egon Willighagen (egonw) >Assigned to: Egon Willighagen (egonw) Summary: GetNearestAtom does not work properly Initial Comment: When deleting atoms, the method to determine which Atom to delete is not functioning properly. ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2002-11-08 13:31 Message: Logged In: YES user_id=25678 Bug was not in getNearestAtom() but in deleteAtom() method. It now works properly again. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=630456&group_id=23629 |
From: E.L. W. <eg...@sc...> - 2002-11-08 11:53:09
|
On Friday 08 November 2002 12:45, Fabian Dortu wrote: > about the commits to the b5 branch: do I also have to commit the changes > to the trunk or do you intend to merge the changes when release 5 is > ready? I was planning to do a merge of the changes in b5 with HEAD this afternoon... You need not apply them to HEAD manually... Egon |
From: Fabian D. <fab...@wa...> - 2002-11-08 11:45:30
|
Egon, about the commits to the b5 branch: do I also have to commit the changes to the trunk or do you intend to merge the changes when release 5 is ready? Fabian --=20 ********** Fabian Dortu Phone : 32-475-599268 e-mail : Fab...@wa... ***********************************************=20 |
From: E.L. W. <eg...@sc...> - 2002-11-08 11:38:41
|
On Friday 08 November 2002 11:01, Fabian Dortu wrote: > so I am back from the abinit workshop where I presented Jmol. It seems > that Jmol is already used by few abinit users/developpers and will touc= h > more and more users if I continue to include more abinit features. Ok. That sounds good. > here are some of users' wishes: > > * direct image output as PostScript (ps/eps). > > * publication quality (in PostScript) graphs. What is the difference with the File->Print menu? > * a geometry builder. What should it do precisely? > * some details: > - be able to rotate the molecule by a given angle (i.e: I want to rotat= e > the molecule by 45=B0. around z or around any given axis). Yes, we should implement a method to rotate around one of the axes with a= n=20 arbitrary angle. > - the measure->distance (or angle,...) should remain on screen after th= e > measurement has been added to the measurement list because users > generally want to make a lot of measurements. In other words, add a > "dismiss" button. Ok. > Concerning abinit: > > There is a strong motivation from the abinit leader that Jmol become > some kind of complete abinit output reader. To achieve this, he wants t= o > provide an abinit output in CML. I have not examine the CML DTD yet, an= d > I would like to know, Egon, if there is some specification to store > energy bands or phonon dispersion curves in CML. Ah, interesting... CML can hold all kinds of information for which there = is a=20 set of general elements, like <float>, <string> etc... If you could give = me=20 an example on how energy bands and phonon dispersion curves are stored in= the=20 current ABINIT output, I can propose a way to store it in CML... > In my last CVS commit (sorry for the disturbance btw), I included an > EnergyBand object to store energy bands along (symmetry) lines. This > object is already used by ABINITOutputReader but there is no graphical > output yet. > > Concerning JAS: > > On the web site, JAS seems to be full featured and to provide PostScrip= t > output. However, the interface in Jmol doesn't reflects this feature. Not sure how Jmol currently makes PostScript, but the output looks fine. Could you elaborate on the high quality PS output, and what is wrong with= the=20 current output? Egon |
From: <no...@so...> - 2002-11-08 11:29:58
|
Bugs item #630363, was opened at 2002-10-29 11:08 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=630363&group_id=23629 Category: None Group: CVS >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Egon Willighagen (egonw) Assigned to: Fabian Dortu (fdortu) Summary: Smoothing does not interpolate unit cell Initial Comment: Smoothing animations does not interpolate the unit cell axes. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=630363&group_id=23629 |
From: <no...@so...> - 2002-11-08 11:29:53
|
Bugs item #630359, was opened at 2002-10-29 11:02 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=630359&group_id=23629 Category: File Input/Output Group: CVS >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Egon Willighagen (egonw) Assigned to: Egon Willighagen (egonw) Summary: CML import does not set unit cell axes Initial Comment: The CML import class does not set the unit cell axes information available in estron.cml. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=630359&group_id=23629 |
From: E.L. W. <eg...@sc...> - 2002-11-08 10:57:03
|
Hi all, in my experience IRC (internet relay chat) can be a handy communication tool... especially, if you have a number short questions which do not require much thinking to answer... During the week I can reasonably often be found at the #cdk channel on irc.freenode.net. Egon |
From: Fabian D. <fab...@wa...> - 2002-11-08 10:44:07
|
On Fri, 2002-11-08 at 11:12, mth wrote: >=20 > Are the two of you seeing this on smaller molecules, or just on large > ones? I would say only on larger ones but the animation of slab_7Si_3Vac_2x_relax_2x1.out, which is only 33 atoms is jerky. Actually, I just realized that the animation speed was too high. If I reduce it, it is smooth enough. >=20 > Do you know of a technique I can use to slow down my JVM? You could try to change JVM priority with "nice" (if you are a unix user) and run some computation in the background. >=20 > > I have the same comment as Egon: > > > > *I don't see the bug anymore. > Well, the good news is that I guess it fixed the bug. > > > > but > > > > *Rotation is slower. With dna.xyz, it is *very* noticable. > My expectation is/was that on larger molecules the mouse and menus > pulldowns would be much more responsive. And that there would be a > slight delay that would fell like it was slower, but that the > refresh/repaint time would actually be almost the same. >=20 > > > > *Frame animation is also much slower. Actually, only 1 frame over 3 or > > 5 can be displayed. > I looked briefly at several of the animations, and they looked OK to me. > But I didn't look at it in detail yet. > > > > As usual, I run this on a PIII 450Mhz with the display exported to > > another machine. > I'll try running it on a remote display and see what behavior I get. >=20 >=20 > -------------------------------------------------- > Miguel Howard mi...@ho... > c/Pe=F1a Primera 11-13 esc dcha 6B > 37002 Salamanca > Espa=F1a Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US =3D > home 011 34 923 271 082 12:00 noon Eastern US =3D > cell 011 34 650 525 458 6:00 pm Spain > -------------------------------------------------- >=20 >=20 >=20 >=20 > ------------------------------------------------------- > This sf.net email is sponsored by: See the NEW Palm=20 > Tungsten T handheld. Power & Color in a compact size! > http://ads.sourceforge.net/cgi-bin/redirect.pl?palm0001en > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers >=20 --=20 ********** Fabian Dortu Phone : 32-475-599268 e-mail : Fab...@wa... ***********************************************=20 |
From: E.L. W. <eg...@sc...> - 2002-11-08 10:41:50
|
On Friday 08 November 2002 11:08, Miguel Howard wrote: > Are the two of you seeing this on smaller molecules, or just on large ones? Both seem slower. > Do you know of a technique I can use to slow down my JVM? You could turn on profiling... see java options... > > I have the same comment as Egon: > > > > *I don't see the bug anymore. > > Well, the good news is that I guess it fixed the bug. > > > but > > > > *Rotation is slower. With dna.xyz, it is *very* noticable. > > My expectation is/was that on larger molecules the mouse and menus > pulldowns would be much more responsive. And that there would be a slight > delay that would fell like it was slower, but that the refresh/repaint > time would actually be almost the same. Yes, menu's are very responsive... Egon |
From: mth <mt...@mt...> - 2002-11-08 10:12:23
|
Are the two of you seeing this on smaller molecules, or just on large ones? Do you know of a technique I can use to slow down my JVM? > I have the same comment as Egon: > > *I don't see the bug anymore. Well, the good news is that I guess it fixed the bug. > > but > > *Rotation is slower. With dna.xyz, it is *very* noticable. My expectation is/was that on larger molecules the mouse and menus pulldowns would be much more responsive. And that there would be a slight delay that would fell like it was slower, but that the refresh/repaint time would actually be almost the same. > > *Frame animation is also much slower. Actually, only 1 frame over 3 or > 5 can be displayed. I looked briefly at several of the animations, and they looked OK to me. But I didn't look at it in detail yet. > > As usual, I run this on a PIII 450Mhz with the display exported to > another machine. I'll try running it on a remote display and see what behavior I get. -------------------------------------------------- Miguel Howard mi...@ho... c/Pe=F1a Primera 11-13 esc dcha 6B 37002 Salamanca Espa=F1a Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US =3D home 011 34 923 271 082 12:00 noon Eastern US =3D cell 011 34 650 525 458 6:00 pm Spain -------------------------------------------------- |
From: Miguel H. <mi...@ho...> - 2002-11-08 10:08:25
|
Are the two of you seeing this on smaller molecules, or just on large ones? Do you know of a technique I can use to slow down my JVM? > I have the same comment as Egon: > > *I don't see the bug anymore. Well, the good news is that I guess it fixed the bug. > > but > > *Rotation is slower. With dna.xyz, it is *very* noticable. My expectation is/was that on larger molecules the mouse and menus pulldowns would be much more responsive. And that there would be a slight delay that would fell like it was slower, but that the refresh/repaint time would actually be almost the same. > > *Frame animation is also much slower. Actually, only 1 frame over 3 or 5 > can be displayed. I looked briefly at several of the animations, and they looked OK to me. But I didn't look at it in detail yet. > > As usual, I run this on a PIII 450Mhz with the display exported to > another machine. I'll try running it on a remote display and see what behavior I get. |
From: Fabian D. <fab...@wa...> - 2002-11-08 10:01:15
|
Hi all, so I am back from the abinit workshop where I presented Jmol. It seems that Jmol is already used by few abinit users/developpers and will touch more and more users if I continue to include more abinit features. here are some of users' wishes: * direct image output as PostScript (ps/eps).=20 * publication quality (in PostScript) graphs. * a geometry builder. * some details:=20 - be able to rotate the molecule by a given angle (i.e: I want to rotate the molecule by 45=B0. around z or around any given axis). - the measure->distance (or angle,...) should remain on screen after the measurement has been added to the measurement list because users generally want to make a lot of measurements. In other words, add a "dismiss" button. Concerning abinit: There is a strong motivation from the abinit leader that Jmol become some kind of complete abinit output reader. To achieve this, he wants to provide an abinit output in CML. I have not examine the CML DTD yet, and I would like to know, Egon, if there is some specification to store energy bands or phonon dispersion curves in CML. In my last CVS commit (sorry for the disturbance btw), I included an EnergyBand object to store energy bands along (symmetry) lines. This object is already used by ABINITOutputReader but there is no graphical output yet. Concerning JAS: On the web site, JAS seems to be full featured and to provide PostScript output. However, the interface in Jmol doesn't reflects this feature.=20 Fabian --=20 ********** Fabian Dortu Phone : 32-475-599268 e-mail : Fab...@wa... ***********************************************=20 |