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From: Hans H. <han...@co...> - 2014-12-07 16:19:18
|
Folks, I'm trying to load a QuantumEspresso input (see below) into the J-Ice webinterface. This what I get (copied from java console): script ERROR: unrecognized file format for file file:/D:/Aluminum/al_scf.in &control prefix='al_scf' outdir='./data' What gives? thx., H. ############################## offending input file (al_scf.in): &control prefix='al_scf' outdir='./data' pseudo_dir = '../pseudo' / &system ibrav=2, ! fcc celldm(1) =7.50, nat= 1, ntyp= 1, ecutwfc =12.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.10 / &electrons / ATOMIC_SPECIES Al 26.98 Al.pz-vbc.UPF ATOMIC_POSITIONS alat Al 0.00 0.00 0.00 K_POINTS automatic 6 6 6 1 1 1 |
|
From: cengiz s. <cen...@gm...> - 2013-03-05 07:43:06
|
Hi,
ı am a PHD student from turkey, I want use try j-ice online. I can make
crystal structure on j-ice, but I can't save or export file as VASP
(POSCAR) format. help me please !!!
1. step (continue to)
WARNING: Make sure you had selected the model you would like to export.
click ok
2. step (continue to)
Type here the job title
vasp1
click ok
3. step (continue to)
Would you like to export the structure in fractional coordinates?
If you press Cancel those will be exported as normal Cartesian. click ok
4.step (result 1)
ERROR: script ERROR: RESTORE: bonds? coords? orientation? selection? state?
structure?
----
restore >> orıentatıon << orienta
click ok
NOT SAVE !!!!
WHAT İS PROBLEM FOR THİS CASE?
|
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From: Jonas B. <jas...@ya...> - 2012-02-18 01:34:26
|
http://fallay.org/loade.html |
|
From: pieremanuele c. <pc...@ke...> - 2011-02-06 08:40:14
|
I tried to get auxiliaryInfo.models[i].name with a banal loop cycle.
I saw that it works fine for small molecule bu it doesn't work well with
most of the output you can find in the repository.
these are the function I use in cascade
function extractInfoJmol(whatToExtract){
var data = jmolGetPropertyAsArray(whatToExtract);
return data;
}
var Info = new Array();
function extractAuxiliaryJmol(){
Info = [];
Info = extractInfoJmol("auxiliaryInfo.models");
return Info;
}
function loadCryModels() {
extractAuxiliaryJmol();
for (i = 0; i < Info.length; i++) {
if (Info[i].name != null) {
var line = Info[i].name;
// alert(line)
if (line.search(/Energy/i) != -1) { // Energy
if (i > 0 && i < Info.length)
var previous = substringEnergyToFloat(Info[i - 1].name);
if (Info[i].name != null) {
addOption(getbyID("geom"), i + " " + Info[i].name, i + 1);
geomData[i] = Info[i].name;
counterFreq ++;
}
} else if (line.search(/cm/i) != -1) {
// onLoadparam();
addOption(getbyID("vib"), (i + counterFreq) + " " +
Info[i].name,
i + 1);
freqData[i + counterFreq] = Info[i].name;
}
}
}
On Sun, Feb 6, 2011 at 2:07 AM, P.Canepa <pc...@ke...> wrote:
>
> -------------------------------------------
> From: Robert Hanson[SMTP:HA...@ST...]
> Sent: Sunday, February 06, 2011 2:06:48 AM
> To: jmo...@li...
> Subject: Re: [Jmol-developers] very weird phenomenon CRYSTAL reader
> Auto forwarded by a Rule What property are you getting?
>
> On Sat, Feb 5, 2011 at 1:41 PM, pieremanuele canepa <pc...@ke...>wrote:
>
>> Dear Bob,
>>
>> I am experiencing a weird phenomenon with Jmol. When I import normal
>> CRYSTAL jobs Jmol takes relly long time to poppulate a javascript array with
>> the function jmolGetPropertyAsArray. This thing doesn't happen for other
>> reader like VASP etc... I tried with an old Jmol release and it works just
>> fine.
>> How come?
>>
>> Thanks, Bob.
>>
>>
>> --
>> *Please consider the environment before printing this e-mail.*
>> **
>> Pieremanuele Canepa
>> Room 104
>> Functional Material Group
>> School of Physical Sciences, Ingram Building,
>> University of Kent, Canterbury, Kent,
>> CT2 7NH
>> United Kingdom
>>
>> e-mail: pc...@ke...
>> mobile: +44 (0) 7772-9756456
>> -----------------------------------------------------------
>>
>>
>>
>> ------------------------------------------------------------------------------
>> The modern datacenter depends on network connectivity to access resources
>> and provide services. The best practices for maximizing a physical
>> server's
>> connectivity to a physical network are well understood - see how these
>> rules translate into the virtual world?
>> http://p.sf.net/sfu/oracle-sfdevnlfb
>> _______________________________________________
>> Jmol-developers mailing list
>> Jmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
*Please consider the environment before printing this e-mail.*
**
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@ke...
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
|
|
From: pieremanuele c. <pc...@ke...> - 2011-02-02 15:15:32
|
Yes You can definetively contribute. Download it from the download link and get a grasp as how it works. If you have question you can e-mail me. When you are happy with your release I will open a SVN account. Let me know. Piero On Wed, Feb 2, 2011 at 2:24 PM, P.Canepa <pc...@ke...> wrote: > > ------------------------------------------- > From: Jonas Baltrusaitis[SMTP:JAS...@YA...<SMTP%3AJ...@YA...>] > > Sent: Wednesday, February 02, 2011 2:24:02 PM > To: P.Canepa > Subject: Re: [J-ice-users] FW: FW: several questions on J-ICE > Auto forwarded by a Rule > I do use CRYSTAL. Band and Dos manipulation is what I need the most. I was > even looking to contribute to J-ICE on some easy things that's why I asked > > ------------------------------ > *From:* pieremanuele canepa <pc...@ke...> > *To:* j-i...@li... > *Sent:* Wed, February 2, 2011 8:11:39 AM > *Subject:* Re: [J-ice-users] FW: FW: several questions on J-ICE > > > > On Wed, Feb 2, 2011 at 2:11 PM, pieremanuele canepa < > pie...@gm...> wrote: > >> Well as I am the only the only developer I have never setup a svn! Do you >> use CRYSTAL? The code are JavaScript the rest is done on Jmol! I am Jmol >> developper >> >> >> On Wed, Feb 2, 2011 at 2:09 PM, P.Canepa <pc...@ke...> wrote: >> >>> >>> ------------------------------------------- >>> From: Jonas Baltrusaitis[SMTP:JAS...@YA...<SMTP%3AJ...@YA...>] >>> >>> Sent: Wednesday, February 02, 2011 2:09:07 PM >>> To: P.Canepa; j-i...@li... >>> Subject: Re: [J-ice-users] FW: several questions on J-ICE >>> Auto forwarded by a Rule >>> Well, you name is obvious from the sourceforge nickname. >>> >>> is there a way to download the source to look at the code, maybe I could >>> contribute somewhat. I tried, don;t know the password >>> >>> Jonas >>> >>> Jonas Baltrusaitis, PhD >>> >>> Assistant Research Scientist >>> >>> Department of Chemistry >>> >>> and >>> >>> Central Microscopy Research Facility >>> >>> EMRB 75 >>> >>> University of Iowa, Iowa City, IA 52242 >>> >>> phone: 319-335-8142 >>> >>> fax: 319-384-4469 >>> >>> >>> ------------------------------ >>> *From:* pieremanuele canepa <pc...@ke...> >>> >>> *To:* j-i...@li... >>> *Sent:* Wed, February 2, 2011 3:11:40 AM >>> *Subject:* Re: [J-ice-users] FW: several questions on J-ICE >>> >>> Jonas, >>> >>> 1st How do you know my name?:) Did I meet you before? >>> >>> I try to answer your question: >>> >>> >>> 1) J-ICE is compatible with all the operative systems, namely Windows, >>> Linux and MacOS X. >>> You can decide to run it on on the web without installing any sort of >>> thing on your machine or download it. >>> If you decide to use it on-line (best choice) goggle this address >>> http://j-ice.sourceforge.net/ondemand/index.html . >>> >>> In case you'd like to download it well you must unzip the file first and >>> secondly open with one of you browsers (Internet explorer, Firefox, Safari) >>> the file called index.html >>> >>> 2) For the time being J-ICE does not implement the BAND, DOSS >>> visualization worked out by CRYSTAL. Is something we are planing to >>> implement as those are not easy to set up in the current versions of the >>> CRYSTAL code. >>> >>> 3) The Jmol part is Java the interface is JavaScript. >>> >>> All the best, Piero >>> >>> P.S. Remember to attach a signature to your e-mails, like mine at the >>> bottom >>> >>> On Wed, Feb 2, 2011 at 2:42 AM, P.Canepa <pc...@ke...> wrote: >>> >>>> >>>> ------------------------------------------- >>>> From: Jonas Baltrusaitis[SMTP:JAS...@YA...<SMTP%3AJ...@YA...> >>>> ] >>>> Sent: Wednesday, February 02, 2011 2:42:23 AM >>>> To: j-i...@li... >>>> Subject: [J-ice-users] several questions on J-ICE >>>> Auto forwarded by a Rule >>>> >>>> Piero, >>>> >>>> is J-ICE windows compatible, e.g. how do I run it on Windows? >>>> >>>> Is BAND/DOSS visualization of CRYSTAL'09 implemented? >>>> >>>> Finally, what is the programming language used for J-ICE? >>>> >>>> Jonas >>>> >>>> >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! >>>> Finally, a world-class log management solution at an even better >>>> price-free! >>>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires >>>> February 28th, so secure your free ArcSight Logger TODAY! >>>> http://p.sf.net/sfu/arcsight-sfd2d >>>> _______________________________________________ >>>> J-ice-users mailing list >>>> J-i...@li... >>>> https://lists.sourceforge.net/lists/listinfo/j-ice-users >>>> >>> >>> >>> >>> -- >>> *Please consider the environment before printing this e-mail.* >>> ** >>> Pieremanuele Canepa >>> Room 104 >>> Functional Material Group >>> School of Physical Sciences, Ingram Building, >>> University of Kent, Canterbury, Kent, >>> CT2 7NH >>> United Kingdom >>> >>> e-mail: pc...@ke... >>> mobile: +44 (0) 7772-9756456 >>> ----------------------------------------------------------- >>> >>> >>> >> >> >> -- >> Pieremanuele Canepa >> Room 104 >> >> School of Physical Sciences, Ingram Building, >> University of Kent, Canterbury, Kent, >> CT2 7NH >> United Kingdom >> ----------------------------------------------------------- >> > > > > -- > *Please consider the environment before printing this e-mail.* > ** > Pieremanuele Canepa > Room 104 > Functional Material Group > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > e-mail: pc...@ke... > mobile: +44 (0) 7772-9756456 > ----------------------------------------------------------- > > > -- *Please consider the environment before printing this e-mail.* ** Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@ke... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- |
|
From: pieremanuele c. <pc...@ke...> - 2011-02-02 14:11:46
|
On Wed, Feb 2, 2011 at 2:11 PM, pieremanuele canepa < pie...@gm...> wrote: > Well as I am the only the only developer I have never setup a svn! Do you > use CRYSTAL? The code are JavaScript the rest is done on Jmol! I am Jmol > developper > > > On Wed, Feb 2, 2011 at 2:09 PM, P.Canepa <pc...@ke...> wrote: > >> >> ------------------------------------------- >> From: Jonas Baltrusaitis[SMTP:JAS...@YA...<SMTP%3AJ...@YA...>] >> >> Sent: Wednesday, February 02, 2011 2:09:07 PM >> To: P.Canepa; j-i...@li... >> Subject: Re: [J-ice-users] FW: several questions on J-ICE >> Auto forwarded by a Rule >> Well, you name is obvious from the sourceforge nickname. >> >> is there a way to download the source to look at the code, maybe I could >> contribute somewhat. I tried, don;t know the password >> >> Jonas >> >> Jonas Baltrusaitis, PhD >> >> Assistant Research Scientist >> >> Department of Chemistry >> >> and >> >> Central Microscopy Research Facility >> >> EMRB 75 >> >> University of Iowa, Iowa City, IA 52242 >> >> phone: 319-335-8142 >> >> fax: 319-384-4469 >> >> >> ------------------------------ >> *From:* pieremanuele canepa <pc...@ke...> >> >> *To:* j-i...@li... >> *Sent:* Wed, February 2, 2011 3:11:40 AM >> *Subject:* Re: [J-ice-users] FW: several questions on J-ICE >> >> Jonas, >> >> 1st How do you know my name?:) Did I meet you before? >> >> I try to answer your question: >> >> >> 1) J-ICE is compatible with all the operative systems, namely Windows, >> Linux and MacOS X. >> You can decide to run it on on the web without installing any sort of >> thing on your machine or download it. >> If you decide to use it on-line (best choice) goggle this address >> http://j-ice.sourceforge.net/ondemand/index.html . >> >> In case you'd like to download it well you must unzip the file first and >> secondly open with one of you browsers (Internet explorer, Firefox, Safari) >> the file called index.html >> >> 2) For the time being J-ICE does not implement the BAND, DOSS >> visualization worked out by CRYSTAL. Is something we are planing to >> implement as those are not easy to set up in the current versions of the >> CRYSTAL code. >> >> 3) The Jmol part is Java the interface is JavaScript. >> >> All the best, Piero >> >> P.S. Remember to attach a signature to your e-mails, like mine at the >> bottom >> >> On Wed, Feb 2, 2011 at 2:42 AM, P.Canepa <pc...@ke...> wrote: >> >>> >>> ------------------------------------------- >>> From: Jonas Baltrusaitis[SMTP:JAS...@YA...<SMTP%3AJ...@YA...> >>> ] >>> Sent: Wednesday, February 02, 2011 2:42:23 AM >>> To: j-i...@li... >>> Subject: [J-ice-users] several questions on J-ICE >>> Auto forwarded by a Rule >>> >>> Piero, >>> >>> is J-ICE windows compatible, e.g. how do I run it on Windows? >>> >>> Is BAND/DOSS visualization of CRYSTAL'09 implemented? >>> >>> Finally, what is the programming language used for J-ICE? >>> >>> Jonas >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! >>> Finally, a world-class log management solution at an even better >>> price-free! >>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires >>> February 28th, so secure your free ArcSight Logger TODAY! >>> http://p.sf.net/sfu/arcsight-sfd2d >>> _______________________________________________ >>> J-ice-users mailing list >>> J-i...@li... >>> https://lists.sourceforge.net/lists/listinfo/j-ice-users >>> >> >> >> >> -- >> *Please consider the environment before printing this e-mail.* >> ** >> Pieremanuele Canepa >> Room 104 >> Functional Material Group >> School of Physical Sciences, Ingram Building, >> University of Kent, Canterbury, Kent, >> CT2 7NH >> United Kingdom >> >> e-mail: pc...@ke... >> mobile: +44 (0) 7772-9756456 >> ----------------------------------------------------------- >> >> >> > > > -- > Pieremanuele Canepa > Room 104 > > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > ----------------------------------------------------------- > -- *Please consider the environment before printing this e-mail.* ** Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@ke... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- |
|
From: pieremanuele c. <pc...@ke...> - 2011-02-02 09:11:47
|
Jonas, 1st How do you know my name?:) Did I meet you before? I try to answer your question: 1) J-ICE is compatible with all the operative systems, namely Windows, Linux and MacOS X. You can decide to run it on on the web without installing any sort of thing on your machine or download it. If you decide to use it on-line (best choice) goggle this addresshttp://j-ice.sourceforge.net/ondemand/index.html. In case you'd like to download it well you must unzip the file first and secondly open with one of you browsers (Internet explorer, Firefox, Safari) the file called index.html 2) For the time being J-ICE does not implement the BAND, DOSS visualization worked out by CRYSTAL. Is something we are planing to implement as those are not easy to set up in the current versions of the CRYSTAL code. 3) The Jmol part is Java the interface is JavaScript. All the best, Piero P.S. Remember to attach a signature to your e-mails, like mine at the bottom On Wed, Feb 2, 2011 at 2:42 AM, P.Canepa <pc...@ke...> wrote: > > ------------------------------------------- > From: Jonas Baltrusaitis[SMTP:JAS...@YA...<SMTP%3AJ...@YA...> > ] > Sent: Wednesday, February 02, 2011 2:42:23 AM > To: j-i...@li... > Subject: [J-ice-users] several questions on J-ICE > Auto forwarded by a Rule > > Piero, > > is J-ICE windows compatible, e.g. how do I run it on Windows? > > Is BAND/DOSS visualization of CRYSTAL'09 implemented? > > Finally, what is the programming language used for J-ICE? > > Jonas > > > > > > > ------------------------------------------------------------------------------ > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! > Finally, a world-class log management solution at an even better > price-free! > Download using promo code Free_Logger_4_Dev2Dev. Offer expires > February 28th, so secure your free ArcSight Logger TODAY! > http://p.sf.net/sfu/arcsight-sfd2d > _______________________________________________ > J-ice-users mailing list > J-i...@li... > https://lists.sourceforge.net/lists/listinfo/j-ice-users > -- *Please consider the environment before printing this e-mail.* ** Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@ke... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- |
|
From: Jonas B. <jas...@ya...> - 2011-02-02 02:42:30
|
Piero,
is J-ICE windows compatible, e.g. how do I run it on Windows?
Is BAND/DOSS visualization of CRYSTAL'09 implemented?
Finally, what is the programming language used for J-ICE?
Jonas
|
|
From: pieremanuele c. <pie...@gm...> - 2010-09-21 09:34:13
|
prova -- Pieremanuele Canepa Room 104 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom ----------------------------------------------------------- |
|
From: Fabio C. <fab...@un...> - 2010-09-20 12:34:50
|
Email fab...@un... Message: 1. atomi evidenziati se selezionati per le distanze o angoli... 2. maggior numero di cifre significative per le distanze 3. export di vasp che si chiami solo POSCAR (senza punti e null’altro) 4. quando fai l’export delle suggestions non va a capo That's all for now!Bye bye Fabio |
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From: P.Canepa <pc...@ke...> - 2010-09-08 13:03:34
|
Hi there,
is any hidden :) Jmol command to remove blank lines once in a Jmol array?
for instance white lines appear in such cases : var script =" var array = [" + varA + ", " + varB + ", ' " varC + " ']; "
+ = 'write VAR array "?.format" '
where varA and varB are numbers whilst varC is a string.
thanks, Piero
--
Please consider the environment before printing this e-mail.
Pieremanuele Canepa
Room 104
Functional Material Group
School of Physical Sciences, Ingram Building,
University of Kent, Canterbury, Kent,
CT2 7NH
United Kingdom
e-mail: pc...@ke...
mobile: +44 (0) 7772-9756456
-----------------------------------------------------------
|
|
From: P.Canepa <pc...@ke...> - 2010-09-06 09:04:01
|
-- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc...@ke... mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- |
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