from:"Latévi Max LAWSON DAKU"

Re: [Jmol-users] Fwd: SourceForge Project of the Week March 27th, 2017

2017-03-23 Thread Latévi Max LAWSON DAKU

This is great!

Congratulations! :)

On 23. 03. 17 17:35, Jaime  Prilusky wrote:
> Congratulations!!
>
>> On 23 Mar 2017, at 16:22, Robert Hanson > > wrote:
>>
>> FYI
>>
>> -- Forwarded message --
>> Subject: SourceForge Project of the Week March 27th, 2017
>>
>> Hi,
>>
>> If you’re receiving this email it is because you are listed as an
>> admin on our next Projects of the Week Issue for March 27th, 2017 on
>> the SourceForge Blog.
>>
>> Here are the projects selected:
>>
>> *otter-browser*
>> *cyberfoxportabl*
>> *pinn*
>> *jedit*
>> *jmol*
>> *skychart*
>> *dispcalgui*
>> *emmabuntus*
>> *d3.js*
>>
>>
>> You will see them reflected live on the SourceForge homepage and blog
>> next week.
>>
>> Thanks,
>>
>> Joan Nadene
>> SourceForge Community Coordinator
>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> 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
>>
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Re: [Jmol-users] Hack-a-mol

2016-12-08 Thread Latévi Max LAWSON DAKU

Dear Bob,

This is very nice!! :)

Best,
Max



On 08. 12. 16 06:53, Robert Hanson wrote:
> This is kind of fun...
>
> https://chemapps.stolaf.edu/jmol/jsmol/hackamol.htm
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
>
>
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Re: [Jmol-users] Use of variable in a call to getProperty

2016-07-08 Thread Latévi Max LAWSON DAKU


Dear Bob,

Thanks a lot for your answer.

Your solution is also the one given by Matt and it works :)


I'm attaching a README file, which I wrote to keep track of what I did.
It's far from being perfect. But I hope it may be helpful to someone.

Thanks again, Bob, Matt and Angel!


Best,
Max




On 08. 07. 16 07:09, Robert Hanson wrote:

My message came out somewhat garbled, I think.  Trying again:

i = 7
print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')





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# 
# Animating vibrations with Jmol (600x435) & Imagemagick
# 

# Jmol
# 


# Load the results file and adjust a few settings 
# (no need here to change the orientation)
# --

load "vib_analysis.molden"

color background black;
restrict not selected;select not selected;wireframe 0.04


# Number of vibrational modes
# --

number_of_vib_modes = 177


# Index of the frame/model associated with the first normal mode 
# --

starting_frame_index = 7


# Move to the frame/model associated with the first normal mode
# and make the necessary for displaying useful information and
# animating the vibrations
# --

i_frame = @{starting_frame_index}
frame @{i_frame}
i_vib = 1
vectors on; vectors 0.04
vectors scale 3.5; color vectors yellow
vibration on; vibration scale 2

set echo bottom left; font echo 12; color echo white;
echo DOI: uu.uuu/..v

freq = getproperty('modelInfo.models['+i_frame+'].modelProperties.FreqValue')
set echo top left; font echo 16; color echo white;
echo @{format("%.1f",freq)} cm-1;

zoom 85


# Generate the JPG files for the animation of the first mode
# --

filename = "vib_" + format("%03i",i_vib) + "_"
filename += format("%04i",freq) + "_.jpg"
write vibration 4 @{filename}


# Redo, for the other vibrational modes
# --

while (i_vib < number_of_vib_modes)
{
  ++i_vib;
  ++i_frame;
  frame next;

  freq = getproperty('modelInfo.models['+i_frame+'].modelProperties.FreqValue');
  echo @{format("%.1f",freq)} cm-1;

  filename = "vib_" + format("%03i",i_vib) + "_"
  filename += format("%04i",freq) + "_.jpg"
  write vibration 4 @{filename}

  #delay 3;
}


# Imagemagick
# 

for i in $(seq 1 1 177); do x=$(printf "%03i\n" $i); PREFIX="vib_$x"; 
MP4=$(echo $(ls ${PREFIX}_*_0001.jpg) | sed -e 's/_0001.jpg/.mp4/'); echo 
${MP4}; convert ${PREFIX}_*.jpg ${MP4}; done

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Re: [Jmol-users] Use of variable in a call to getProperty

2016-07-07 Thread Latévi Max LAWSON DAKU



On 07. 07. 16 17:04, Kubasik, Matthew A. wrote:
> Max,
>

Hi Matt,

Thanks for your suggestions.

> Two suggestions.
>
> First, something like:
>
> freqvalues = getproperty('modelInfo.models.modelProperties.FreqValue')
>
> will look for frequency values of all models and put them in the array 
> "freqvalues".
>
> Unfortunately, this array will have empty entries for models lacking 
> frequency values.
>
> Second, if you know the range of models that contain freq values (say, models 
> 300 to 370), you can use something like:
>
> for (var i=300; i<370;i+=1){
> print getproperty('modelInfo.models['+i+'].modelProperties.FreqValue')
> }

I tried this latter and it works !! :D

Thanks again!

Best,
Max


>
> Perhaps more skilled coders on the list could suggest improvements to these 
> clunky lines!
>
> Matt
>
>
>
>
> 
> From: Latévi Max LAWSON DAKU [max.law...@unige.ch]
> Sent: Thursday, July 07, 2016 10:38 AM
> To: jmol-users@lists.sourceforge.net
> Subject: [Jmol-users] Use of variable in a call to getProperty
>
> Dear Jmol users/developers,
>
> I would like to be able to use a variable in a call to getProperty.
> So far, the following command works.
>
>  $ print getproperty('modelInfo.models[7].modelProperties.FreqValue')
>  129.529358
>
> But I rwould like to use a variable as follows
>
>  $ i=7
>  $ print getproperty('modelInfo.models[i].modelProperties.FreqValue')
>
> But this doesn't work. I also tried to use @{i}, with no success as
> well. I'm not comfortable with dereferencing a variable in Jmol.
>
> The reason for trying to do so us that I'ld like to iterate through the
> frames and use the variable i hold the index of the frame.
>
>
> I thank you in advance for your help.
>
> Best regards,
> Max
>
> --
> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
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Re: [Jmol-users] Use of variable in a call to getProperty

2016-07-07 Thread Latévi Max LAWSON DAKU



On 07. 07. 16 17:04, Herráez Sánchez Ángel wrote:
> Hi Max
>

Hi Herráez,

Thanks for your mail
>
> I also have trouble often using variables.
>
> @{i}  is unusual to me. The common syntax is either "i" or "@i "
>

:) I'm never sure when to use this; if using the bare name 'i' doesn't
work, i swicth to '@i'. I probably should take more time going through
the documentation :D

>
> Have you tried ...?
>
> print getproperty('modelInfo.models[@i].modelProperties.FreqValue')
>

I tried this :(

Best,
Max


> 
>
>
> --
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[Jmol-users] Use of variable in a call to getProperty

2016-07-07 Thread Latévi Max LAWSON DAKU

Dear Jmol users/developers,

I would like to be able to use a variable in a call to getProperty.
So far, the following command works.

 $ print getproperty('modelInfo.models[7].modelProperties.FreqValue')
 129.529358

But I rwould like to use a variable as follows

 $ i=7
 $ print getproperty('modelInfo.models[i].modelProperties.FreqValue')

But this doesn't work. I also tried to use @{i}, with no success as
well. I'm not comfortable with dereferencing a variable in Jmol.

The reason for trying to do so us that I'ld like to iterate through the
frames and use the variable i hold the index of the frame.


I thank you in advance for your help.

Best regards,
Max

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Re: [Jmol-users] Orbitals not being displayed (command mo)

2015-07-08 Thread Latévi Max LAWSON DAKU



On 07. 07. 15 20:59, Robert Hanson wrote:
 MO 24 in Co_ just has a very tight cutoff. So the default 0.05 is too
 large. You can see a bit of it with 0.03.
 
 I'm not seeing the problem with CuZ. Maybe the same. Also, since Jmol does
 not include G orbitals, anything that is pure G will not show up. But then
 you would see the integrated density far from 1.000. To see that issue
 
 set debug
 
 prior to the MO command, then inspect the Java console:
 
 

Hi, Bob !

Many thanks for your kind reply and your explanation. There is no bug
indeed. I was confused by the fact that no information are being
displayed. It is now clear that I should pay attention to the value of
the cutoff.

A side question: I could enable the display of the java console and
called it from a terminal with the jconsole command. Then I connected to
the jmol 'instance': various tabs are shown (Overview, Memory, Threads,
Classes, VM Summary, MBeans), but I cannot locate the place where the
jmol log goes. Could you please tell me where to look at?

Again many thanks for your help and time :)

All the best,
Max


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Re: [Jmol-users] Support for molecular orbitals in molden format

2015-04-09 Thread Latévi Max LAWSON DAKU

Dear Bob,

In order to try to understand what's going on when it
comes to render the MOs, I've called jmol with the option
-logger.info=true.

I've used three different files

- columbus.molden: s, p, d basis functions
- b1t_spdfg.molden: s, p, d, f, g basis functions
- b2q_spdfgh.molden: s, p, d, f, g, h basis functions

They are available in the viz2.tar archive at

 http://www.filedropper.com/viz2

* For the file columbus.molden, here are the relevant
information print by jmol.

The Resolver thinks Molden
[MOLDEN FORMAT]
[ATOMS] AU
[5D]
Orbital type set to [5D]
[7F]
Orbital type set to [5D][7F]
[GTO]
84 slater shells read
210 gaussian primitives read
196 MO coefficients expected for orbital type [5D][7F]
[MO]
184 molecular orbitals read in model 1
Time for openFile(columbus.molden): 115 ms
reading 10 atoms

The numbers of shells and primitives read are correct. But
the number of MO coefficients expected for orbital type
[5D][7F] is not; this should be 184. There are indeed 46 S,
26 P and 12 D shells, which corresponds for [5D][7F] orbital
type to 46*[1S]+26*[3P]+12x[5D] = 184 basis functions. The
number printed actually corresponds to [6D] orbital type.
I've rendered some random orbitals and the results were similar
to those obtained with gmolden-5.2.2.

* In b1t_spdfg.molden, there are 69 S, 50 P, 30 D, 15 F and
2 G shells. For this file, jmol reports:

[MOLDEN FORMAT]
[GTO]
166 slater shells read
1189 gaussian primitives read
579 MO coefficients expected for orbital type
[TITLE]
[ATOMS] AU
[5D7F]
Orbital type set to [5D7F]
[9G]
Unsupported orbital type ignored: [9G]
Orbital type set to [5D7F][9G]
[MO]
492 molecular orbitals read in model 1
[END OF MOLDEN OUTPUT FROM DALTON2013]
Time for openFile(b1t_spdfg.molden): 140 ms

The numbers of shells and primitives are correct, not the
number of expected MO coefficients. For [5D7F][9G] orbital
type, we should have 492 coefficients. The reported number
of MO coefficients is for [6D10F][15G] orbital type. When
plotting MOs from this file, the following message

   Unsupported basis type for atomno=1: 9G

is correctly printed out, and the calculations went fine: I
mean the plotted MOs look ok.



* In b2q_spdfgh.molden, there are 70 S, 51 P, 31 D, 16 F
and3 G and 2 H shells. I also inserted a line with [11H].
For this file, jmol reports:

[MOLDEN FORMAT]
[GTO]
173 slater shells read
1314 gaussian primitives read
656 MO coefficients expected for orbital type
[TITLE]
[ATOMS] AU
[5D7F]
Orbital type set to [5D7F]
[9G]
Unsupported orbital type ignored: [9G]
Orbital type set to [5D7F][9G]
[11H]
Unsupported orbital type ignored: [11H]
Orbital type set to [5D7F][9G][11H]
[MO]
539 molecular orbitals read in model 1
[END OF MOLDEN OUTPUT FROM DALTON2013]
Time for openFile(b2q_spdfgh.molden): 130 ms

The reported number of MO coefficients should be 539 for
[5D7F][9G][11H] orbital type. When trying to plot a MO,
there is an out-of-bound exception and the calculations
terminate.

Unsupported basis type for atomno=1: 9G
java.lang.ArrayIndexOutOfBoundsException: 10
Could not create isosurface

Please note that there is no mention of the unsupported
11H basis type, which actually are located on atomno=1.


So I guess, that the number of expected MOs coefficients
is automatically calculated for Cartesian basis functions
when reading the basis set, and that it is not updated or
printed after having determined the definitive orbital type.
It also seems that the workaround used for handling the
unsupported G basis functions is not operative for H and
possibly I basis functions. I cannot find where the
unsupported functions types are labeled as such. Could you
please point me to the corresponding portion of the code?

Thanks a lot for having gone through this lengthy mail :-)

Best,
Max


P.S. While going through the sources, I noticed that in the
method J.adapter.readers.quantum.fixOrbitalType(), nothing
is done for I basis functions. From my understanding of
J.adapter.readers-quantum.BasisFunctionReader.fixSlaterTypes(),
and of the data at the end of the file J/quantum/QS.js,
when [5D] is present, you make jmol use D, F, G and H spherical
functions; if [10F] is present, cartesian F, G and H functions
are used; and finally if [15G] is present, cartesian G and H
functions are used. Nothing seems to be done for I functions.

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Re: [Jmol-users] Support for molecular orbitals in molden format

2015-04-08 Thread Latévi Max LAWSON DAKU

Dear Bob,

I have been able to use jmol-14.3.13_2015.04.07 to view MOs in molden
format; they were obtained from different calculations using up to g
basis functions. Jmol does run nicely and fast :-)

I also give a try to MOs for which spherical h basis functions are being
used. The number of MOs is correctly detected. Unfortunately, the MOs
are not rendered in this case. I added a [11H] line to the molden file.
This line is read and the orbital types is reported as not being
supported, as expected:

Unsupported orbital type ignored: [9G]
Unsupported orbital type ignored: [11H]

539 molecular orbitals in model 1.1

But the presence of this line does not change the behavior of jmol.
I went into the sources

/jsmol/j2s/J/adapter/readers/quantumMoldenReader.js

to try to understand how this works. But, I'm really lost here.
I guess the job is done with the readMolecularOrbitals method
(line 196), but I cannot figure out how you implement skipping the
unsupported basis functions.


In case you have time for investigating this, I've made an archive
viz.tar.gz containing the molden files. It is available for download
at

http://www.filedropper.com/viztar

It contains

- viz/molden.inp_ORIG
- viz/molden.inp

which only differs by the presence of the [11H] line in the latter.


Thanks a lot for your help.

All the best,
Max


On 08. 04. 15 01:25, Latévi Max LAWSON DAKU wrote:
 Thanks a lot, Bob!  This is great! it is running nicely and fast.
 I'll also try it also on other files I don't have at hand.
 
 Thanks again.
 
 All the best,
 Max
 
 
 
 On 07. 04. 15 19:49, Robert Hanson wrote:
 see http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.04.07.zip

 On Tue, Apr 7, 2015 at 11:29 AM, Robert Hanson hans...@stolaf.edu wrote:

 OK, the new Molden format skips entries with coef 0:

 Columbus:

   43  3.393160933753838E-002
   44 -4.598253748351849E-003
   45  0.000E+000
   46  0.000E+000
   47  2.594945043892112E-002
   48 -1.534056772906609E-002


 Dalton2015:

   3290.01
   331   -0.01
   334   -0.01
   343   -0.02

 We can work around that.

 On Tue, Apr 7, 2015 at 11:25 AM, Robert Hanson hans...@stolaf.edu wrote:

  Unsupported basis type for atomno=1: 9G

 It should be able to just skip those.
 Also, there's a normalization problem

 will get back to you

 Bob


 On Tue, Apr 7, 2015 at 10:37 AM, Latévi Max LAWSON DAKU 
 max.law...@unige.ch wrote:

 Dear Bob,

 Using Jmol 13.2.0 or 14.2.13_2015.03.23, I'm not able to view molecular
 orbitals output in molden format by the program package dalton2015. I'm
 however able to see them with gmolden version 5.2.2.

 The number of available orbitals is correctly detected and printed by
 jmol. But it is not possible to view them using the mo command or the
 surfaces menu. You improved the support of the molden format for the
 13.x. release, enabling the support of g-i basis functions, which are
 actually ignored. But I haven't used jmol for visualizing MOs for long
 and I cannot tell what can go wrong.

 I used jmol 3.2.0 or 14.2.13_2015.03.23 to view the MOs in the
 columbus.molden file: this worked great! The columbus.molden file
 can be found in the archive molden_test.tar.gz which is available
 online, for 30 days, at the address

 http://dl.free.fr/f6KsenkB8

 In this archive, there is also the problematic molden file
 dalton2015.molden. The main difference I see between the formats used
 for describing the MOs in columbus.molden and in dalton2015.molden
 is that in the latter only the non-vanishing coefficients are given.


 Please do not hesitate to contact me for any further information you may
 need. I thank you in advance for your help.

 All the best,
 Max


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 it is better to take what answer we get.

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 If nature does not answer first what we want

Re: [Jmol-users] Support for molecular orbitals in molden format

2015-04-08 Thread Latévi Max LAWSON DAKU



On 08. 04. 15 19:46, Robert Hanson wrote:
 All the orbital coefficients are read, but then in creating the surfaces,
 only s-f are used.
 

Thanks a lot for the explanations, Bob.

All the best,
Max


 On Wed, Apr 8, 2015 at 11:03 AM, Latévi Max LAWSON DAKU max.law...@unige.ch
 wrote:
 
 Dear Bob,

 I have been able to use jmol-14.3.13_2015.04.07 to view MOs in molden
 format; they were obtained from different calculations using up to g
 basis functions. Jmol does run nicely and fast :-)

 I also give a try to MOs for which spherical h basis functions are being
 used. The number of MOs is correctly detected. Unfortunately, the MOs
 are not rendered in this case. I added a [11H] line to the molden file.
 This line is read and the orbital types is reported as not being
 supported, as expected:

 Unsupported orbital type ignored: [9G]
 Unsupported orbital type ignored: [11H]

 539 molecular orbitals in model 1.1

 But the presence of this line does not change the behavior of jmol.
 I went into the sources

 /jsmol/j2s/J/adapter/readers/quantumMoldenReader.js

 to try to understand how this works. But, I'm really lost here.
 I guess the job is done with the readMolecularOrbitals method
 (line 196), but I cannot figure out how you implement skipping the
 unsupported basis functions.


 In case you have time for investigating this, I've made an archive
 viz.tar.gz containing the molden files. It is available for download
 at

 http://www.filedropper.com/viztar

 It contains

 - viz/molden.inp_ORIG
 - viz/molden.inp

 which only differs by the presence of the [11H] line in the latter.


 Thanks a lot for your help.

 All the best,
 Max


 On 08. 04. 15 01:25, Latévi Max LAWSON DAKU wrote:
 Thanks a lot, Bob!  This is great! it is running nicely and fast.
 I'll also try it also on other files I don't have at hand.

 Thanks again.

 All the best,
 Max



 On 07. 04. 15 19:49, Robert Hanson wrote:
 see http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.04.07.zip

 On Tue, Apr 7, 2015 at 11:29 AM, Robert Hanson hans...@stolaf.edu
 wrote:

 OK, the new Molden format skips entries with coef 0:

 Columbus:

   43  3.393160933753838E-002
   44 -4.598253748351849E-003
   45  0.000E+000
   46  0.000E+000
   47  2.594945043892112E-002
   48 -1.534056772906609E-002


 Dalton2015:

   3290.01
   331   -0.01
   334   -0.01
   343   -0.02

 We can work around that.

 On Tue, Apr 7, 2015 at 11:25 AM, Robert Hanson hans...@stolaf.edu
 wrote:

  Unsupported basis type for atomno=1: 9G

 It should be able to just skip those.
 Also, there's a normalization problem

 will get back to you

 Bob


 On Tue, Apr 7, 2015 at 10:37 AM, Latévi Max LAWSON DAKU 
 max.law...@unige.ch wrote:

 Dear Bob,

 Using Jmol 13.2.0 or 14.2.13_2015.03.23, I'm not able to view
 molecular
 orbitals output in molden format by the program package dalton2015.
 I'm
 however able to see them with gmolden version 5.2.2.

 The number of available orbitals is correctly detected and printed by
 jmol. But it is not possible to view them using the mo command or
 the
 surfaces menu. You improved the support of the molden format for
 the
 13.x. release, enabling the support of g-i basis functions, which are
 actually ignored. But I haven't used jmol for visualizing MOs for
 long
 and I cannot tell what can go wrong.

 I used jmol 3.2.0 or 14.2.13_2015.03.23 to view the MOs in the
 columbus.molden file: this worked great! The columbus.molden file
 can be found in the archive molden_test.tar.gz which is available
 online, for 30 days, at the address

 http://dl.free.fr/f6KsenkB8

 In this archive, there is also the problematic molden file
 dalton2015.molden. The main difference I see between the formats
 used
 for describing the MOs in columbus.molden and in
 dalton2015.molden
 is that in the latter only the non-vanishing coefficients are given.


 Please do not hesitate to contact me for any further information you
 may
 need. I thank you in advance for your help.

 All the best,
 Max



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 http://www.stolaf.edu/people/hansonr


 If nature does not answer first what we

[Jmol-users] Support for molecular orbitals in molden format

2015-04-07 Thread Latévi Max LAWSON DAKU

Dear Bob,

Using Jmol 13.2.0 or 14.2.13_2015.03.23, I'm not able to view molecular
orbitals output in molden format by the program package dalton2015. I'm
however able to see them with gmolden version 5.2.2.

The number of available orbitals is correctly detected and printed by
jmol. But it is not possible to view them using the mo command or the
surfaces menu. You improved the support of the molden format for the
13.x. release, enabling the support of g-i basis functions, which are
actually ignored. But I haven't used jmol for visualizing MOs for long
and I cannot tell what can go wrong.

I used jmol 3.2.0 or 14.2.13_2015.03.23 to view the MOs in the
columbus.molden file: this worked great! The columbus.molden file
can be found in the archive molden_test.tar.gz which is available
online, for 30 days, at the address

http://dl.free.fr/f6KsenkB8

In this archive, there is also the problematic molden file
dalton2015.molden. The main difference I see between the formats used
for describing the MOs in columbus.molden and in dalton2015.molden
is that in the latter only the non-vanishing coefficients are given.


Please do not hesitate to contact me for any further information you may
need. I thank you in advance for your help.

All the best,
Max

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Re: [Jmol-users] Support for molecular orbitals in molden format

2015-04-07 Thread Latévi Max LAWSON DAKU

Thanks a lot, Bob!  This is great! it is running nicely and fast.
I'll also try it also on other files I don't have at hand.

Thanks again.

All the best,
Max



On 07. 04. 15 19:49, Robert Hanson wrote:
 see http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.13_2015.04.07.zip
 
 On Tue, Apr 7, 2015 at 11:29 AM, Robert Hanson hans...@stolaf.edu wrote:
 
 OK, the new Molden format skips entries with coef 0:

 Columbus:

   43  3.393160933753838E-002
   44 -4.598253748351849E-003
   45  0.000E+000
   46  0.000E+000
   47  2.594945043892112E-002
   48 -1.534056772906609E-002


 Dalton2015:

   3290.01
   331   -0.01
   334   -0.01
   343   -0.02

 We can work around that.

 On Tue, Apr 7, 2015 at 11:25 AM, Robert Hanson hans...@stolaf.edu wrote:

  Unsupported basis type for atomno=1: 9G

 It should be able to just skip those.
 Also, there's a normalization problem

 will get back to you

 Bob


 On Tue, Apr 7, 2015 at 10:37 AM, Latévi Max LAWSON DAKU 
 max.law...@unige.ch wrote:

 Dear Bob,

 Using Jmol 13.2.0 or 14.2.13_2015.03.23, I'm not able to view molecular
 orbitals output in molden format by the program package dalton2015. I'm
 however able to see them with gmolden version 5.2.2.

 The number of available orbitals is correctly detected and printed by
 jmol. But it is not possible to view them using the mo command or the
 surfaces menu. You improved the support of the molden format for the
 13.x. release, enabling the support of g-i basis functions, which are
 actually ignored. But I haven't used jmol for visualizing MOs for long
 and I cannot tell what can go wrong.

 I used jmol 3.2.0 or 14.2.13_2015.03.23 to view the MOs in the
 columbus.molden file: this worked great! The columbus.molden file
 can be found in the archive molden_test.tar.gz which is available
 online, for 30 days, at the address

 http://dl.free.fr/f6KsenkB8

 In this archive, there is also the problematic molden file
 dalton2015.molden. The main difference I see between the formats used
 for describing the MOs in columbus.molden and in dalton2015.molden
 is that in the latter only the non-vanishing coefficients are given.


 Please do not hesitate to contact me for any further information you may
 need. I thank you in advance for your help.

 All the best,
 Max


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 it is better to take what answer we get.

 -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900




 --
 Robert M. Hanson
 Larson-Anderson Professor of Chemistry
 Chair, Department of Chemistry
 St. Olaf College
 Northfield, MN
 http://www.stolaf.edu/people/hansonr


 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


 
 
 
 
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[Jmol-users] Problem with visualizing MOs in a molden file: h-type basis function present.

2013-08-29 Thread Latévi Max LAWSON DAKU

Dear Bob,

I'm trying to use Jmol-13 to read MOs from a molden. Something is going 
wrong when
I ask that a MO be displayed; here are the output messsages (from the 
console):

 539 molecular orbitals in model 1.1

 $ mo 4
 $ isosurface mo 4
 isosurface1 created with cutoff=NaN min=0.0 max=0.0; isosurface 
count: 0
 $ isosurface cutoff 0.01 mo 4
 isosurface1 created with cutoff=NaN min=0.0 max=0.0; isosurface 
count: 0
 $ isosurface cutoff 0.01 mo 100
 isosurface1 created with cutoff=NaN min=0.0 max=0.0; isosurface 
count: 0
 $ isosurface cutoff 0.01 mo 400
 isosurface1 created with cutoff=NaN min=0.0 max=0.0; isosurface 
count: 0
 $

I suspect this to be due to the fact that the h-type basis functions 
present in the
file are not correctly handled. As you said in a previous e-mail

 http://sourceforge.net/mailarchive/message.php?msg_id=30827892

You made the molden reader ignore the g, h and i basis functions, but, at
that time, this was not tested past the g functions.

I observed the same behavior using any of the Jmol versions 13.0.16, 
13.1.16
and 13.2.4.

With the hope that you could find time to address this issue, I've made 
the file
(fe3_nch.d2h.b1q_dk-rohf.molden.gz) available at the address below

 http://dl.free.fr/k14CG3qQn

Please, don't hesitate to contact me for any further information you may 
need.

All the best,
Max

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Universite de Genève / Quai E. Ansermet 30 / CH-1211 Genève 4


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Re: [Jmol-users] Problem with visualizing MOs in a molden file: h-type basis function present.

2013-08-29 Thread Latévi Max LAWSON DAKU


On 29. 08. 13 14:48, Susi Lehtola wrote:
 On Thu, 29 Aug 2013 14:43:01 +0200
 Latévi Max LAWSON DAKU max.law...@unige.ch wrote:
 I suspect this to be due to the fact that the h-type basis functions
 present in the
 file are not correctly handled. As you said in a previous e-mail

   http://sourceforge.net/mailarchive/message.php?msg_id=30827892

 You made the molden reader ignore the g, h and i basis functions,
 but, at that time, this was not tested past the g functions.
 I'd be surprised if anything molden handled h functions or higher.
 After all, the molden format only supports s, p, sp, d, f and g.

 http://www.cmbi.ru.nl/molden/molden_format.html
Dear Susi,

True that h and i functions are not supported by molden. Here, having Jmol
ignore them, as is already the case for the g functions, should allow 
one to
cycle through the MOs and possibly select some for CASSCF calcultions,
keeping in mind that contributions of some basis functions are ignored (and
they can anyway be read in the molden file).

Best regards,
Max


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Universite de Genève / Quai E. Ansermet 30 / CH-1211 Genève 4


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Re: [Jmol-users] visualizing molecular orbitals in molden format

2013-05-14 Thread Latévi Max LAWSON DAKU




On 13. 05. 13 20:44, Robert Hanson wrote:
OK, then that's a bug in Jmol -- it is expecting the orbitals in 
energy-order and needs to have that for displaying homo and lumo. If 
it's all right with you, I would like to add a sort to those so that 
they are in the proper energy order and not symmetry order.


This is fine with me, Bob,

Is there any real reason to keep them in symmetry order? You can 
always only load just a given symmetry if you want.




Keeping them in symmetry order may be advantageous if one wants
to identify and reorder orbitals belonging to a same or different
symmetries, for instance for defining active space in CASSCF calculations.
It this case, it indeed would suffice to load MO of a given symmetry.

Best,
Max

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Re: [Jmol-users] visualizing molecular orbitals in molden format

2013-05-14 Thread Latévi Max LAWSON DAKU




On 14. 05. 13 00:23, Robert Hanson wrote:

This version does the energy sorting so that HOMO and LUMO work properly

http://chemapps.stolaf.edu/jmol/Jmol-13.zip
To NOT sort by energy, add FILTER NOSORT to the load command.
You can also select by symmetry using FILTER SYM=AU for example.



Fantastic, Bob !!

Max :-)




Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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



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Re: [Jmol-users] visualizing molecular orbitals in molden format

2013-05-13 Thread Latévi Max LAWSON DAKU


Thanks a lot, Bob !

This is working nicely :-)

Best,
Max

On 13. 05. 13 00:13, Robert Hanson wrote:
OK, the Molden reader should  work up to orbital type i. (Untested 
past g.) Anything past f will be ignored. Assumptions here:


type spherical/cartesian: G 9/15, H 11/21, I 13/28  (all ignored)

http://chemapps.stolaf.edu/jmol/jmol-13.1.16_2013.05.12a.zip


Bob




On Sun, May 12, 2013 at 12:41 PM, Latévi Max LAWSON DAKU 
max.law...@unige.ch mailto:max.law...@unige.ch wrote:


Dear Bob,

I have been able to generate an input file, in molden format, which
can be viewed with molden/gmolden-5.0 (geometry and MOs). Trying
to open it with Jmol-13.0.14 fails with the following error message

script ERROR: Error reading file at line 442:
 g   2 1.00
8
for file /tmp/molden.inp
type Molden

 load  molden.inp 

which may correspond to the fact that g functions are not
supported.

Do you have time to look at this ? If so, the file, compressed,
(molden.inp.gz)
can be downloaded at the following address

This file (molden.inp.gz)  can be found at the a
http://dl.free.fr/muBvAUeyr

All the best,
Max




On 03. 05. 13 14:47, Robert Hanson wrote:




On Thu, May 2, 2013 at 2:40 PM, Latévi Max LAWSON DAKU
max.law...@unige.ch mailto:max.law...@unige.ch wrote:



On 02. 05. 13 19:34, Robert Hanson wrote:

Max,




Dear Bob,

I thank you a lot for your kind reply.



Well, there are a couple problems with the Malden reader --
requiring no blank line after [GTO] is an easy fix; g
orbitals not implemented (easily fixed). Maybe a bigger
issue (not solvable, probably).

Q: Are you OK with ignoring the g orbitals?



Yes. They should contribute little to the molecular orbitals,
which
I am interested in. Actually, if proceeding so, would it
possible to
ignore 'h' and 'i' functions as well ?


sure. What are the number of orbitals in h/i cartesian/spherical
sets?




There seems to be something I'm missing. There are only 492
listed MO coefficients, but there are 711 listed atomic
orbitals.

711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10)

Those numbers should match. (NEED to match.)

Q: So what is 492?



This really is the number of basis functions: the basis set
is made
of 492 contracted Gaussian functions, consisting each in a
linear
combination of some of the 711 primitive Gaussian functions.
I guess that the manner in which the MOs are listen takes the
contractions into account.


I don't see it. Please explain this particular file set in
detail. There 301 Gaussian sets listed, not 492.

301 = 166 s + 84 p + 34 d + 15 f + 2 g

For example:

 s  22 1.00
 4316265.0001.00
  646342.4000.00
  147089.7000.00
   41661.5200.00
   13590.7700.00
4905.7500.00
1912.746 tel:1912.7460.00
 792.60430000.00
 344.80650000.00
 155.89990000.00
  72.23091000.00
  32.72506000.00
  15.66762000.00
   7.50348300.00
   4.68440000.00
   3.31222300.00
   1.55847100.00
   1.22040000.00
   0.68391400.00
   0.14675700.00
   0.07058300.00
   0.03144900.00

Each set may have more than one directional component, thus we
have total number of independent coefficients:

711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10)

How do you figure that there are only 492 MO coefficients?




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Re: [Jmol-users] visualizing molecular orbitals in molden format

2013-05-13 Thread Latévi Max LAWSON DAKU




On 13. 05. 13 12:38, Robert Hanson wrote:

My pleasure. It's a fix for 13.0 and 13.1.


:-)

It so comfortable to use the MO command from the console ;-)


A couple of chemistry questions:

Q: Why in this Fe(NCH)6 complex are there only 19 occupied orbitals? 
They look great, but aren't there far more valence electrons? Many of 
them look like core orbitals. I count at least 60 valence electrons 
just in HCN. So where are they? (Only 38 electrons accounted for?)


There are 107 electrons. The MOs are in fact displayed by blocks, 
according to
their symmetry: Ag orbitals come first, then those of B3u, B2u, B1g, 
B1u, B2g,
B3g and finally Au symmetry (grep Sym molden.inp). This in ok in that 
the number

of MOs of a given symmetry can be read in the main Dalton2011 output.



Q: Why are the doubly-occupied orbitals labeled Alpha? Aren't 
alpha/beta orbitals singly occupied?


These MOs are obtained from a restricted-open-shell (actually, ROHF) 
calculation calculations,
and the spin-up and spin-down spinorbitals have the same spatial parts. 
In this case, as you
noticed, the molden driver in Dalton2011 simply outputs the MOs only 
once, with the right
occupation numbers and labeling them Alpha. The Spin= (Alpha|Beta) 
entry seems required

by molden when specifying MOs.

Please do not hesitate for any other question you may have.

Best,
Max




Bob


On Mon, May 13, 2013 at 2:59 AM, Latévi Max LAWSON DAKU 
max.law...@unige.ch mailto:max.law...@unige.ch wrote:


Thanks a lot, Bob !

This is working nicely :-)

Best,
Max

On 13. 05. 13 00:13, Robert Hanson wrote:

OK, the Molden reader should  work up to orbital type i.
(Untested past g.) Anything past f will be ignored. Assumptions here:

type spherical/cartesian: G 9/15, H 11/21, I 13/28  (all ignored)

http://chemapps.stolaf.edu/jmol/jmol-13.1.16_2013.05.12a.zip


Bob




On Sun, May 12, 2013 at 12:41 PM, Latévi Max LAWSON DAKU
max.law...@unige.ch mailto:max.law...@unige.ch wrote:

Dear Bob,

I have been able to generate an input file, in molden format,
which
can be viewed with molden/gmolden-5.0 (geometry and MOs). Trying
to open it with Jmol-13.0.14 fails with the following error
message

script ERROR: Error reading file at line 442:
 g   2 1.00
8
for file /tmp/molden.inp
type Molden

 load  molden.inp 

which may correspond to the fact that g functions are not
supported.

Do you have time to look at this ? If so, the file,
compressed, (molden.inp.gz)
can be downloaded at the following address

This file (molden.inp.gz)  can be found at the a
http://dl.free.fr/muBvAUeyr

All the best,
Max




On 03. 05. 13 14:47, Robert Hanson wrote:




On Thu, May 2, 2013 at 2:40 PM, Latévi Max LAWSON DAKU
max.law...@unige.ch mailto:max.law...@unige.ch wrote:



On 02. 05. 13 19:34, Robert Hanson wrote:

Max,




Dear Bob,

I thank you a lot for your kind reply.



Well, there are a couple problems with the Malden
reader -- requiring no blank line after [GTO] is an
easy fix; g orbitals not implemented (easily fixed).
Maybe a bigger issue (not solvable, probably).

Q: Are you OK with ignoring the g orbitals?



Yes. They should contribute little to the molecular
orbitals, which
I am interested in. Actually, if proceeding so, would it
possible to
ignore 'h' and 'i' functions as well ?


sure. What are the number of orbitals in h/i
cartesian/spherical sets?




There seems to be something I'm missing. There are only
492 listed MO coefficients, but there are 711 listed
atomic orbitals.

711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10)

Those numbers should match. (NEED to match.)

Q: So what is 492?



This really is the number of basis functions: the basis
set is made
of 492 contracted Gaussian functions, consisting each in
a linear
combination of some of the 711 primitive Gaussian
functions.
I guess that the manner in which the MOs are listen
takes the
contractions into account.


I don't see it. Please explain this particular file set in
detail. There 301 Gaussian sets listed, not 492.

301 = 166 s + 84 p + 34 d + 15 f + 2 g

For example:

 s  22 1.00
 4316265.0001.00
  646342.4000.00
  147089.7000.00
   41661.5200.00
   13590.7700.00
4905.750

Re: [Jmol-users] visualizing molecular orbitals in molden format

2013-05-03 Thread Latévi Max LAWSON DAKU




On 03. 05. 13 14:47, Robert Hanson wrote:






Dear Bob,

Thanks a lot for your reply !

[...]



Q: Are you OK with ignoring the g orbitals?



Yes. They should contribute little to the molecular orbitals, which
I am interested in. Actually, if proceeding so, would it possible to
ignore 'h' and 'i' functions as well ?



sure. What are the number of orbitals in h/i cartesian/spherical sets?


For h: we have 11 spherical and 21 cartesian functions; and for i: we
have 13 spherical and cartesian functions... if I'm not wrong.  For a
given L, there are (2L+1) spherical harmonic and (L+1)*(L+2)/2
Cartesian functions [Schlegel and Frisch, Int. J. Quantum Chem, 54,
83-87 (1995]






There seems to be something I'm missing. There are only 492
listed MO coefficients, but there are 711 listed atomic orbitals.

711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10)

Those numbers should match. (NEED to match.)

Q: So what is 492?



This really is the number of basis functions: the basis set is made
of 492 contracted Gaussian functions, consisting each in a linear
combination of some of the 711 primitive Gaussian functions.
I guess that the manner in which the MOs are listen takes the
contractions into account.


I don't see it. Please explain this particular file set in detail. 
There 301 Gaussian sets listed, not 492.


301 = 166 s + 84 p + 34 d + 15 f + 2 g

For example:

 s  22 1.00
 4316265.0001.00
  646342.4000.00
  147089.7000.00
   41661.5200.00
   13590.7700.00
4905.7500.00
1912.7460.00
 792.60430000.00
 344.80650000.00
 155.89990000.00
  72.23091000.00
  32.72506000.00
  15.66762000.00
   7.50348300.00
   4.68440000.00
   3.31222300.00
   1.55847100.00
   1.22040000.00
   0.68391400.00
   0.14675700.00
   0.07058300.00
   0.03144900.00

Each set may have more than one directional component, thus we have 
total number of independent coefficients:


711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10)

How do you figure that there are only 492 MO coefficients?





(1) My bad ! I was not clear at all. For the Fe atom, for instance, you 
only
have 9 contracted basis functions in the s shell and they are given by 
linear

combinations of the 22 primitive Gaussian listed above: this can be noted
(22s) - [9s]. In the example file, I used

for Fe, the cc-pwCVTZ-DK basis set: (22s,18p,10d,3f,2g)  - 
[9s,8p,6d,3f,2g]
for the 6 N and 6 C atoms, the cc-pVTZ-DK basis set: (10s,5p,2d,1f) 
- [4s,3p,2d,1f]

for the 6 H atoms, the cc-pVDZ-DK basis set: (4s,1p) - [2s,1p]

This is why I am expecting 492 MO coefficients

69 s + 50 p(x3) + 30 d(x5) + 15 f(x7) + 2 g(x9) = 492

(2) MY VERY BAD!!  I finally get it... I am missing that the output is 
actually
simply broken!!!  Indeed, looking again and calmly at the example file, 
I do

see that the output does not make sense! As you noticed: for each MO,
492 coefficients are given, but there is no information that may help 
connect
them with the given primitive Gaussians... Sorry! I was only staring at 
the g

functions issue ..
I will look into the sources to try to fix how the basis functions are 
written.


Thanks a lot for your valuable help and for your time.

All the best,
Max





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[Jmol-users] visualizing molecular orbitals in molden format

2013-05-02 Thread Latévi Max LAWSON DAKU

Dear Jmol users and developers,

* I am trying to visualize molecular orbitals as output by Dalton2011
in a molden format (dalton2011.molden.gz):

http://dl.free.fr/hU653l61Y

the orbitals are not detected contrarily to the molecular structure,
which is correctly displayed. This happens with the 13.0.14 and 13.1.4
releases of Jmol. Did someone already experienced this problem?

* I found that something similar happened in an earlier release
(bug #511, ticket created 2011-09-23). I have downloaded the
test file associated with this ticket (colombus.molden.gz):

http://sourceforge.net/p/jmol/bugs/_discuss/thread/3689bc64/395e/attachment/columbus.molden.gz

in this case, the orbitals are nicely displayed using both Jmol versions.

* I have therefore tried to make the structure of the Dalton2011
output file similar to the one of the colombus.molden test file.
(1) By making the [Atoms] section the first one, the orbitals are
detected but they are not displayed, using 13.0.14 or 13.1.4
(dalton2011.molden_modified.gz):

http://dl.free.fr/kILB39jxu

(2) In the test file, there is no blank line between the [GTO] header
and the 1 0 line signaling the beginning of the definition of the
first atom basis set. In the Dalton2011 out, there is one blank line.
If I remove this line, the stable or development version cannot read
the file anymore: it seems 'g' atomic orbitals cannot be processed.
Is this correct?
If so, is it possible to have 'g', and even 'h' and 'i' functions supported
in Jmol? If this not already the case.

Thanks in advance for your help :-)

All the best,
Max

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Re: [Jmol-users] visualizing molecular orbitals in molden format

2013-05-02 Thread Latévi Max LAWSON DAKU

On 02. 05. 13 10:30, Latévi Max LAWSON DAKU wrote:
Dear Jmol users and developers,

* I am trying to visualize molecular orbitals as output by Dalton2011
in a molden format (dalton2011.molden.gz):

http://dl.free.fr/hU653l61Y

Hi,

I have downloaded the sources and, from my understanding of
org.jmol.adapter.readers.quantum.BasisFunctionReader.java,
it indeed seems that 'g', 'h', and 'i' basis functions are not
supported ... may I say, yet :-)

I quickly went through org.jmol.quantum.MOCalculation.java,
and it is not obvious for me how to quickly and consistently add
the relevant support functions addData{9G,11H,13I}() and
appropriately adapt the class definition .. :-(

So, dear developpers, dear Bob, please consider my question/request
as a simple item in the users' wishlist :)

Best regards,
Max

* I found that something similar happened in an earlier release
(bug #511, ticket created 2011-09-23). I have downloaded the
test file associated with this ticket (colombus.molden.gz):

http://sourceforge.net/p/jmol/bugs/_discuss/thread/3689bc64/395e/attachment/columbus.molden.gz

in this case, the orbitals are nicely displayed using both Jmol versions.

http://dl.free.fr/kILB39jxu

Thanks in advance for your help :-)

All the best,
Max

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Re: [Jmol-users] visualizing molecular orbitals in molden format

2013-05-02 Thread Latévi Max LAWSON DAKU

On 02. 05. 13 19:34, Robert Hanson wrote:

Max,

Dear Bob,

I thank you a lot for your kind reply.

Well, there are a couple problems with the Malden reader -- requiring
no blank line after [GTO] is an easy fix; g orbitals not implemented
(easily fixed). Maybe a bigger issue (not solvable, probably).

Q: Are you OK with ignoring the g orbitals?

Yes. They should contribute little to the molecular orbitals, which
I am interested in. Actually, if proceeding so, would it possible to
ignore 'h' and 'i' functions as well ?

There seems to be something I'm missing. There are only 492 listed MO
coefficients, but there are 711 listed atomic orbitals.

711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10)

Those numbers should match. (NEED to match.)

Q: So what is 492?

This really is the number of basis functions: the basis set is made
of 492 contracted Gaussian functions, consisting each in a linear
combination of some of the 711 primitive Gaussian functions.
I guess that the manner in which the MOs are listen takes the
contractions into account.

All the best,
Max

Bob Hanson

On Thu, May 2, 2013 at 3:30 AM, Latévi Max LAWSON DAKU
max.law...@unige.ch mailto:max.law...@unige.ch wrote:

Dear Jmol users and developers,

* I am trying to visualize molecular orbitals as output by Dalton2011
in a molden format (dalton2011.molden.gz):

http://dl.free.fr/hU653l61Y

* I found that something similar happened in an earlier release
(bug #511, ticket created 2011-09-23). I have downloaded the
test file associated with this ticket (colombus.molden.gz):

http://sourceforge.net/p/jmol/bugs/_discuss/thread/3689bc64/395e/attachment/columbus.molden.gz

in this case, the orbitals are nicely displayed using both Jmol
versions.

http://dl.free.fr/kILB39jxu

Thanks in advance for your help :-)

All the best,
Max

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Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr

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it is better to take what answer we get.

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Re: [Jmol-users] how to display the original axes?

2008-11-02 Thread Latévi Max LAWSON DAKU

You can issue the command set axes molecular in the console

Regards,
Max


Egon Willighagen wrote:
 Moin!

 When I open the below XYZ file, and I display the axes, it show not
 the original reference axes, but new ones with the origin in, it
 seems, the center of mass...

 -
 9

 O 1.944591.337110.0
 C 1.523000.00.0
 C 0.00.00.0
 H 1.93156   -0.495990.90876
 H 1.93156   -0.49599   -0.90876
 H-0.351961.055880.0
 H-0.35196   -0.52794   -0.91442
 H-0.35196   -0.527940.91442
 H 1.181871.889940.0
 -

 But I need to have it show the original axes... with the second carbon
 in the origin, and the other carbon along the X-axis...

 Is this possible?

 Egon



   

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Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 

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Re: [Jmol-users] Jmol-11.5.26: two bugs

2008-04-13 Thread Latévi Max LAWSON DAKU


Many thanks, Bob ! for the fixes :-)
I will try the 11.5.27 release.

All the best,
Max

P.S. I'm sending you the missing images in a separate mail.
I first forgot to attach them. After having noticed this, I
sent an other mail with them attached. But this one got
rejected because the size of the images exceeds the list's
limit of 40kb.



Bob Hanson wrote:
Max, you have found some new and some not-so-new bugs. Thanks for 
testing this. All are fixed for 11.5.27


Bob

Latévi Max LAWSON DAKU wrote:

  

Dear Bob,
Dear Jmol developers and users,

I'm trying to use Jmol for representing in a realistic
manner the angles that describe the arrangement
of atoms around a given centre. These angles are
sketched in the attached figure model.png.

While doing this, with Jmol-11.5.26, I've found two bugs.

1) PovRay rendering of circles is buggy:  circles are
   displayed as filled cylinders.



fixed for 11.5.27

  

   - render_view.simple.jpg: this file as been obtained by
 using the save current view as a image  button - fine

   - render_view.povray.png: the PovRay rendering of the
 same view: you can notice the dark thin cylinders.



these images weren't included in the message I got.

  

  The view can be reproduced with the attached files:
  main.xyz and script_part1


2) The WIDTH and OFFSET options of the DRAW command
   show unexpected (buggy ?) behaviour.

   This can be notice with the attached file script_part2.
   It contains the commands which I'm trying to use to sketch
   the angles.

   - Drawing 'cone1_generator' with a 'WIDTH' smaller than
 0.05 gives strange results. The OFFSET option doesn't
 seem to be working.



this is also fixed for 11.5.27

  

   - The segments 'angle1_a' and 'angle1_b' are not correctly
 drawn unless a 'WIDTH' of 0.05, at least, is used to draw
 them.

Please don't hesitate to contact me for any further information.

Best regards,
Max








  


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Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 


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Re: [Jmol-users] Drawing a circle

2008-04-04 Thread Latévi Max LAWSON DAKU


Dear Bob,

Your addition is very nice: I've played with. funny.
Unfortunately, I am interested in ... 3D circle :-P

I'll try to use a(n awfull) hack to do this (with polygons)..

While playing with 11.5.25, I've noticed a bug which is probably
due to the introduction of the capability to draw circles. The bug
can be reproduced with the attached file by issuing the commands

   load test.xyz
   draw (atomno=1) (atomno=2) (atomno=3)

You will notice that an unwanted circle is drawn around the first
atom.


All the very best,
MAx


Bob Hanson wrote:

Jmol 11.5.25 draws circles.

See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm

and

http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11_5.zip

I think this is a very nice addition. Max, I hope you were thinking of 
circles the way I was -- not 3D, but 2D -- and that this will be useful 
to you. 3D would be considerably harder.


Bob


Latévi Max LAWSON DAKU wrote:

  

Many thanks, Bob, for implementing this feature.
I will download the new Jmol version and play with,
as soon as possible :-)

All the best,
Max

Bob Hanson wrote:



version=11.5.25_dev

# new feature draw circle:
#
#   A circle is a 2D object that behaves like a halo, always appearing 
circular

#
#   draw circle {molecule=1}# around specified atoms
#   draw diameter 2.0 circle {atomno=3} # 2.0 angstroms; scales
#   draw width 100 circle {_O}[1]   # 100 pixels (doesn't scale)
#   draw circle plane {*}   # a solid plane in the shape of a circle; 
can be translucent



Latévi Max LAWSON DAKU wrote:

 

  

Bob Hanson wrote:

   



Latévi Max LAWSON DAKU wrote:



 

  

Hello,

Is there a (simple) way to draw a circle using Jmol ? 
I guess there is one but cannot find it (googling or

searching the mails I received don't help).


Thanks in advance for telling me how to proceed.

All the best,
Max



  

   



no, there is not.






 

  

Many thanks, Bob, for your answer.

Could you, please, consider enabling the drawing an arc of a circle or 
a circle,

by issuing a command like

   1) circle [object_id] \
 CENTER {x y z} || (atom_expr) \
 PLANE   a_plane_id || (atom_expr) \
 RADIUS  the_radius \
 [ANGLE default=360] \
 COLOR color \
 [FILLED || NOFILLED]

or

  2) circle [object_id] \
 CENTER {x y z} || (atom_expr) \
 NORMAL   {u v w} \
 RADIUS  the_radius \
 [ANGLE default=360] \
 COLOR color \
 [FILLED || NOFILLED]

In the first case, one gives the plane in which the circle must be drawn;
in the second case, one rather gives the normal to this plane.

I don't know how demanding the implementation of this feature will
be ... but I am quite sure this may be useful for representing and/or
following in schemes structural data, such as angles or distances, as
in the case I am interested in.

Thanks in advance for considering my request.

Regards,
Max


--
***
Latevi Max LAWSON DAKU
Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 


Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
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30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 


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Re: [Jmol-users] Drawing a circle

2008-04-03 Thread Latévi Max LAWSON DAKU


Many thanks, Bob, for implementing this feature.
I will download the new Jmol version and play with,
as soon as possible :-)

All the best,
Max

Bob Hanson wrote:

version=11.5.25_dev

# new feature draw circle:
#
#   A circle is a 2D object that behaves like a halo, always appearing 
circular

#
#   draw circle {molecule=1}# around specified atoms
#   draw diameter 2.0 circle {atomno=3} # 2.0 angstroms; scales
#   draw width 100 circle {_O}[1]   # 100 pixels (doesn't scale)
#   draw circle plane {*}   # a solid plane in the shape of a circle; 
can be translucent



Latévi Max LAWSON DAKU wrote:

  

Bob Hanson wrote:



Latévi Max LAWSON DAKU wrote:

 

  

Hello,

Is there a (simple) way to draw a circle using Jmol ? 
I guess there is one but cannot find it (googling or

searching the mails I received don't help).


Thanks in advance for telling me how to proceed.

All the best,
Max



   



no, there is not.




 

  

Many thanks, Bob, for your answer.

Could you, please, consider enabling the drawing an arc of a circle or 
a circle,

by issuing a command like

1) circle [object_id] \
  CENTER {x y z} || (atom_expr) \
  PLANE   a_plane_id || (atom_expr) \
  RADIUS  the_radius \
  [ANGLE default=360] \
  COLOR color \
  [FILLED || NOFILLED]

or

   2) circle [object_id] \
  CENTER {x y z} || (atom_expr) \
  NORMAL   {u v w} \
  RADIUS  the_radius \
  [ANGLE default=360] \
  COLOR color \
  [FILLED || NOFILLED]

In the first case, one gives the plane in which the circle must be drawn;
in the second case, one rather gives the normal to this plane.

I don't know how demanding the implementation of this feature will
be ... but I am quite sure this may be useful for representing and/or
following in schemes structural data, such as angles or distances, as
in the case I am interested in.

Thanks in advance for considering my request.

Regards,
Max


--
***
Latevi Max LAWSON DAKU
Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 


Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
***
 




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Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 


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Re: [Jmol-users] Drawing a circle

2008-04-02 Thread Latévi Max LAWSON DAKU


Many thanks, Bob, for your answers.

I am especially interested in drawing a ring. But I think that,
ideally, both possibilities should be made available.
(We can readily draw the edges of polyhedra. In a equivalent
manner, this would also allow one to draw the ring that delimits
a filled-in circle).

All the best,
Max

Bob Hanson wrote:

Are we talking about a filled-in circle or a ring?

Latévi Max LAWSON DAKU wrote:

  

Bob Hanson wrote:



Latévi Max LAWSON DAKU wrote:

 

  

Hello,

Is there a (simple) way to draw a circle using Jmol ? 
I guess there is one but cannot find it (googling or

searching the mails I received don't help).


Thanks in advance for telling me how to proceed.

All the best,
Max



   



no, there is not.




 

  

Many thanks, Bob, for your answer.

Could you, please, consider enabling the drawing an arc of a circle or 
a circle,

by issuing a command like

1) circle [object_id] \
  CENTER {x y z} || (atom_expr) \
  PLANE   a_plane_id || (atom_expr) \
  RADIUS  the_radius \
  [ANGLE default=360] \
  COLOR color \
  [FILLED || NOFILLED]

or

   2) circle [object_id] \
  CENTER {x y z} || (atom_expr) \
  NORMAL   {u v w} \
  RADIUS  the_radius \
  [ANGLE default=360] \
  COLOR color \
  [FILLED || NOFILLED]

In the first case, one gives the plane in which the circle must be drawn;
in the second case, one rather gives the normal to this plane.

I don't know how demanding the implementation of this feature will
be ... but I am quite sure this may be useful for representing and/or
following in schemes structural data, such as angles or distances, as
in the case I am interested in.

Thanks in advance for considering my request.

Regards,
Max


--
***
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30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 


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CH-1211 Geneve 4 
Switzerland 


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Re: [Jmol-users] Drawing a circle

2008-04-01 Thread Latévi Max LAWSON DAKU




Bob Hanson wrote:

Latévi Max LAWSON DAKU wrote:

  

Hello,

Is there a (simple) way to draw a circle using Jmol ? 
I guess there is one but cannot find it (googling or

searching the mails I received don't help).


Thanks in advance for telling me how to proceed.

All the best,
Max

 



no, there is not.




  

Many thanks, Bob, for your answer.

Could you, please, consider enabling the drawing an arc of a circle or a 
circle,

by issuing a command like

   1) circle [object_id] \
 CENTER {x y z} || (atom_expr) \
 PLANE   a_plane_id || (atom_expr) \
 RADIUS  the_radius \
 [ANGLE default=360] \
 COLOR color \
 [FILLED || NOFILLED]

or

  2) circle [object_id] \
 CENTER {x y z} || (atom_expr) \
 NORMAL   {u v w} \
 RADIUS  the_radius \
 [ANGLE default=360] \
 COLOR color \
 [FILLED || NOFILLED]

In the first case, one gives the plane in which the circle must be drawn;
in the second case, one rather gives the normal to this plane.

I don't know how demanding the implementation of this feature will
be ... but I am quite sure this may be useful for representing and/or
following in schemes structural data, such as angles or distances, as
in the case I am interested in.

Thanks in advance for considering my request.

Regards,
Max


--
***
Latevi Max LAWSON DAKU
Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 


Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
***

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[Jmol-users] POV-Ray export of stereo rendering and referencing Jmol

2008-01-16 Thread Latévi Max LAWSON DAKU

Dear Jmol developpers and users,

The POV-Ray export feature have improved a lot
since the last time (about two months among) I tried
to use: high quality pictures and also lot of fun with !
Many thanks to Pim and Bob for the very nice job !

I am interested in exporting a stereo rendering of a
molecule to POV-Ray but only one half of the view
is exported (I would say the left one according to the
test I made by exporting the view after having issued
a stereo 90 command).
This actually also happens when the view is exported
to an image (for instance, jpeg). The Jmol versions tested
are 11.3.60,11.4.RC1 and 11.5.2.
My question is: is it possible to export a stereo rendering ?
Or is this feature missing ? If so, dear developpers, please
consider my email as a wish ?

According to the FAQ, Jmol should be referenced by its
website www.jmol.org. I would like to know if there is a
a paper or a book I could also cite. 

Best regards,
Max

-- 
***
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Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 

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Re: [Jmol-users] POV-Ray export of stereo rendering and referencing Jmol

2008-01-16 Thread Latévi Max LAWSON DAKU




Angel Herraez wrote:

According to the FAQ, Jmol should be referenced by its
website www.jmol.org. I would like to know if there is a
a paper or a book I could also cite. 



Not really. Cite the website as is described in 
http://jmol.sourceforge.net/index.en.html#How%20to%20cite%20Jmol



  

Thanks for the link!

Regards,
Max


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30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
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Re: [Jmol-users] Povray rendering of drawn objects (polyhedra, lines, ..)

2007-10-01 Thread Latévi Max LAWSON DAKU



pim schravendijk wrote:

On 9/29/07, Latévi Max LAWSON DAKU [EMAIL PROTECTED] wrote:
  

Dear all,

I cannot figure out wether it is possible to
have a povray renderering of a whole Jmol
scene that contains polyhedra and other
drawn objects. I have had no success so far.
Does support exist for doing such a thing ?

Thanks in advance for your answer,

Max



Hi!

  


Hi, Pim ! 


I thank you a lot for your email.



There was no such thing, we are working on it at the moment! Bob
Hanson has set up a general exporting method for any kind of 3D file
format, I'm now filling in the povray parts. I hope I can do a patch
for the polyhedrals by next week. If you want, you can join the
  


These are great news.


developer list and contribute.

  


Unfortunately, I don't  know the internals of the code;
furthermore I am really too busy this period, as I guess
you also are likely to be :-D

Thanks all for this nice software and your time.

Keep up the good work,
Max



Ciao, Pim

  


--
***
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Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 


Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
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[Jmol-users] Povray rendering of drawn objects (polyhedra, lines, ..)

2007-09-29 Thread Latévi Max LAWSON DAKU

Dear all,

I cannot figure out wether it is possible to
have a povray renderering of a whole Jmol
scene that contains polyhedra and other
drawn objects. I have had no success so far.
Does support exist for doing such a thing ?

Thanks in advance for your answer,

Max

-- 
***
Latevi Max LAWSON DAKU
Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 

Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
***


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Re: [Jmol-users] Axis origin

2005-08-19 Thread Latévi Max LAWSON DAKU

Dear Miguel,

Many thanks for your kind reply.


Miguel wrote:

Actually, I would like to display the
coordinate frame and have the possibility
of putting its origin at positions which allow
to easily identify  the axis with some symmetry
axis.



Not sure what you mean.

Q: Do you want the axes to be something other than the cartesian axes?

  


No, cartesian axes are fine. I just would like to
be able to put them anywhere.

If we first restrict our discussion to the cartesian axes ...

  

Ok :-)

The 'boundbox' is defined by the min  max atom center coordinate values
along the x/y/z dimensions. Try the following:

  set axes on
  set boundbox on

The origin of the axes is the center of the boundbox. The axes extend to
the center of the faces of the boundbox.

  


This works perfectly but does not suit my need.

Q: If you could position the axes at an arbitrary point, how far would the
axes extend in the +/- directions?

  


Argh... this is a good question.

Q: ... to the faces of the boundbox?

  

Not necessarily... 

In fact, the ideal solution would consist
in having the possibility to draw segments
using arbitrary styles and colors.

Best regards,
Max

Miguel


  

The coordinate frame which is shown
is the one associated with the bounding box,
and changing the rotation center does not
change this, helas...

So my question should read: is there a way to
easily draw a coordinate frame (in my case, the
one associated to the molecule will suffice).
(I could also add dummy atoms and do this
by hand. But I guess that the results would not
be satisfactory...)

I am using Jmol Version 10.00.05.

Regards,
Max

P.S. I have subscribed to the list :-))



Chris Weichenberger wrote:



I am viewing a molecule using Jmol and I am trying to put
the origin of the axis at the position of a given atom. But
I cannot figure out how to this. I did not find any tip in the
user guide.


 Your choice is the 'center' command. In order to have the origin of
the coordinate system set to the C-alpha atom of group 66, issue the
command

 center 66.CA

Rotations from now on will be centered about this atom. (If you have
opened a Jmol console window left-clicking on an atom will print its
group number and atom name and some more information.)

Hope this is what you have been looking for.

 Chris

  

--
***
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Departement de chimie physique
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet
CH-1211 Geneve 4
Switzerland

Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
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30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 

Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
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Re: [Jmol-users] Axis origin

2005-08-19 Thread Latévi Max LAWSON DAKU







Miguel wrote:

  
In fact, the "ideal" solution would consist
in having the possibility to draw segments
using arbitrary styles and colors.

  
  
Others have asked for the ability to draw arbitrary lines.

Sounds like that would meet your needs too ... the ability to draw a
line/cylinder of arbitrary radius/color between two points specified by
absolute cartesian coordinates ...

Q: Please confirm whether or not this is sufficient ...

  


Yes, this is sufficient :-)

This would be very nice if you could implement 
this feature. Whenever you need to test it before 
releasing it, please feel free to contact me.

Regards, Max


  
Miguel



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30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 

Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
***

[Jmol-users] Axis origin

2005-08-17 Thread Latévi Max LAWSON DAKU

Dear Jmol users,

I am viewing a molecule using Jmol and I am trying to put
the origin of the axis at the position of a given atom. But
I cannot figure out how to this. I did not find any tip in the
user guide.

Is there a way to do this ? I thank you in advance for your
help.

(I am not on the list; could you please Cc me the answer.)

Best regards,
LM Lawson Daku

-- 
***
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Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 

Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
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Re: [Jmol-users] Axis origin

2005-08-17 Thread Latévi Max LAWSON DAKU

Dear Chris,

Many thanks for your answer.

Unfortunately, my question was not clear
enough. Actually, I would like to display the
coordinate frame and have the possibility
of putting its origin at positions which allow
to easily identify  the axis with some symmetry
axis. The coordinate frame which is shown
is the one associated with the bounding box,
and changing the rotation center does not
change this, helas...

So my question should read: is there a way to
easily draw a coordinate frame (in my case, the
one associated to the molecule will suffice).
(I could also add dummy atoms and do this
by hand. But I guess that the results would not
be satisfactory...)

I am using Jmol Version 10.00.05.

Regards,
Max

P.S. I have subscribed to the list :-))



Chris Weichenberger wrote:


 I am viewing a molecule using Jmol and I am trying to put
 the origin of the axis at the position of a given atom. But
 I cannot figure out how to this. I did not find any tip in the
 user guide.


  Your choice is the 'center' command. In order to have the origin of
 the coordinate system set to the C-alpha atom of group 66, issue the
 command

  center 66.CA

 Rotations from now on will be centered about this atom. (If you have
 opened a Jmol console window left-clicking on an atom will print its
 group number and atom name and some more information.)

 Hope this is what you have been looking for.

  Chris


-- 
***
Latevi Max LAWSON DAKU
Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 

Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
***



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