Re: [Avogadro-Discuss] AutoOptimization

2016-10-24 Thread Marcus D. Hanwell 
It would be good to do some verification on this, because in my testing
this was consistently the location of the executable. We could add some
code to print out what it sees, or try to reproduce this locally.

There is quite a bit of work in several projects I work on where we
successfully rely upon this, and on Windows the executable needs the DLLs
in system paths or the same directory (which is why it is packaged the way
it is).

On Sun, Oct 23, 2016 at 11:55 AM, Patrick Avery <psav...@buffalo.edu> wrote:

> Indeed. I think that is BABEL_DATADIR. For Windows, I believe that is set
> here:
>
> https://github.com/cryos/avogadro/blob/2a98712f24506d023aa4b84c984136
> a913017e81/avogadro/src/main.cpp#L106
>
> Perhaps that is what we should change that setup for the next release.
>
>
> On Sunday, October 23, 2016, Marcos Verissimo Alves <
> marcos_veriss...@id.uff.br> wrote:
>
>> What if path variables with the location of the force fields are set? If
>> I'm not mistaken, Windows has those too.
>>
>> Best,
>>
>> Marcos
>>
>> Em domingo, 23 de outubro de 2016, Patrick Avery <psav...@buffalo.edu>
>> escreveu:
>>
>>> My best guess is that when you open a Gaussian file by double clicking
>>> it, it results in Avogadro's runtime location being in that directory
>>> (which means it won't find the force field files).
>>>
>>> For now, I'd always open Avogadro by using the shortcut, and then open
>>> the Gaussian file using the "Open" dialog, and it should work. I will try
>>> to figure out how to fix that sometime sooner or later...
>>>
>>> On Sunday, October 23, 2016, Željko M. Svedružić <zsved...@biol.pmf.hr>
>>> wrote:
>>>
>>>> Michael,
>>>>
>>>> most of the molecular modeling software does not tolerate "Program
>>>> Files" in the path name. The code for all those programs is written for
>>>> Linux and just adapted to windows. Linux does not recognize empty space,
>>>> i.e. "Program Files" should be "Program_Files". Thus, when I have to work
>>>> on windows I install all my modeling software in C:\\ directory, and
>>>> everything works fine. Alternatively stick with Linux.
>>>>
>>>> Hope this helps,
>>>>
>>>> Best of luck in your work, Cheers,
>>>>
>>>> www.svedruziclab.com
>>>>
>>>> On 2016-10-23 4:32, Michael Morgan wrote:
>>>>
>>>> Dear Patrick,
>>>>
>>>>
>>>>
>>>> Thank you for your kind help! The problem is solved with your help.
>>>>
>>>>
>>>>
>>>> 1)  If I run Avogadro.exe from the \bin folder, then open files, I
>>>> can use the force fields.
>>>>
>>>> 2)  If I created a shortcut link in the desktop and run it, I can
>>>> use the force fields.
>>>>
>>>> 3)  I have assigned “C:\Program Files
>>>> (x86)\Avogadro\bin\avogadro.exe” to open the Gaussian output files by
>>>> default. If I open an output
>>>> file using Avogadro by directly clicking the file, I cannot use the
>>>> force fields. Not sure what is wrong.
>>>>
>>>>
>>>>
>>>> Cheers,
>>>>
>>>> Michael
>>>>
>>>>
>>>>
>>>> *From:* Patrick Avery [mailto:psav...@buffalo.edu]
>>>> *Sent:* Saturday, October 22, 2016 9:35 AM
>>>> *To:* avogadro-discuss@lists.sourceforge.net
>>>> *Subject:* Re: [Avogadro-Discuss] AutoOptimization
>>>>
>>>>
>>>>
>>>> Hi Michael,
>>>>
>>>>
>>>>
>>>> This usually means the force field files were not found. These are the
>>>> files at this location: https://github.com/o
>>>> penbabel/openbabel/tree/master/data
>>>>
>>>>
>>>>
>>>> I can think of two likely scenarios. Either
>>>>
>>>>
>>>>
>>>> 1: you don't have the files. Check your install location (probably
>>>> C:\Program Files (x86)\Avogadro). Open the bin folder and see if the force
>>>> field files are there.
>>>>
>>>>
>>>>
>>>> 2: if you do have the files, the force field files may not be loading
>>>> if Avogadro's runtime location is not in C:\Program Files
>>>> (x86)\Avogadro\bin. You can double click the Avogadro executa

Re: [Avogadro-Discuss] AutoOptimization

2016-10-23 Thread Patrick Avery 
My best guess is that when you open a Gaussian file by double clicking it,
it results in Avogadro's runtime location being in that directory (which
means it won't find the force field files).

For now, I'd always open Avogadro by using the shortcut, and then open the
Gaussian file using the "Open" dialog, and it should work. I will try to
figure out how to fix that sometime sooner or later...

On Sunday, October 23, 2016, Željko M. Svedružić <zsved...@biol.pmf.hr>
wrote:

> Michael,
>
> most of the molecular modeling software does not tolerate "Program Files"
> in the path name. The code for all those programs is written for Linux and
> just adapted to windows. Linux does not recognize empty space, i.e.
> "Program Files" should be "Program_Files". Thus, when I have to work on
> windows I install all my modeling software in C:\\ directory, and
> everything works fine. Alternatively stick with Linux.
>
> Hope this helps,
>
> Best of luck in your work, Cheers,
>
> www.svedruziclab.com
>
> On 2016-10-23 4:32, Michael Morgan wrote:
>
> Dear Patrick,
>
>
>
> Thank you for your kind help! The problem is solved with your help.
>
>
>
> 1)  If I run Avogadro.exe from the \bin folder, then open files, I
> can use the force fields.
>
> 2)  If I created a shortcut link in the desktop and run it, I can use
> the force fields.
>
> 3)  I have assigned “C:\Program Files (x86)\Avogadro\bin\avogadro.exe”
> to open the Gaussian output files by default. If I open an output
> file using Avogadro by directly clicking the file, I cannot use the force
> fields. Not sure what is wrong.
>
>
>
> Cheers,
>
> Michael
>
>
>
> *From:* Patrick Avery [mailto:psav...@buffalo.edu
> <javascript:_e(%7B%7D,'cvml','psav...@buffalo.edu');>]
> *Sent:* Saturday, October 22, 2016 9:35 AM
> *To:* avogadro-discuss@lists.sourceforge.net
> <javascript:_e(%7B%7D,'cvml','avogadro-discuss@lists.sourceforge.net');>
> *Subject:* Re: [Avogadro-Discuss] AutoOptimization
>
>
>
> Hi Michael,
>
>
>
> This usually means the force field files were not found. These are the
> files at this location: https://github.com/openbabel/openbabel/tree/
> master/data
>
>
>
> I can think of two likely scenarios. Either
>
>
>
> 1: you don't have the files. Check your install location (probably
> C:\Program Files (x86)\Avogadro). Open the bin folder and see if the force
> field files are there.
>
>
>
> 2: if you do have the files, the force field files may not be loading if
> Avogadro's runtime location is not in C:\Program Files (x86)\Avogadro\bin.
> You can double click the Avogadro executable in C:\Program Files
> (x86)\Avogadro\bin
>
> And the force fields should work then. If you are using a shortcut, right
> click it and select "properties" and make sure it says it is starting in 
> C:\Program
> Files (x86)\Avogadro\bin and not C:\Program Files (x86)\Avogadro.
>
>
>
> I tried setting it up to make sure we wouldn't run into either of those
> problems. Perhaps I missed something, though. Did you create your own
> shortcut?
>
>
>
> Thanks,
>
> Patrick
>
>
> On Friday, October 21, 2016, Michael Morgan <michaelmorgan...@gmail.com
> <javascript:_e(%7B%7D,'cvml','michaelmorgan...@gmail.com');>> wrote:
>
> Dear All,
>
>
>
> My Avogadro’s AutoOptimization stopped working. When I clicked “Start”, it
> showed “AutoOpt: Could not setup force field…”. I have tried most simple
> molecules, as well as choosing different force field. All the same. Any
> idea what is wrong?
>
>
>
> My Avogadro version is most recent one (1.2.0). Windows 10.
>
>
>
> Thank you very much.
>
>
>
> Best
>
> Michael
>
>
>
>
>
>
>
> --
> **address file***
> Željko Svedružić ph.d.zsved...@biol.pmf.hr 
> <javascript:_e(%7B%7D,'cvml','zsved...@biol.pmf.hr');>
> web:https://profiles.google.com/106720515809875304148#106720515809875304148/about
> **
>
>
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Re: [Avogadro-Discuss] AutoOptimization

2016-10-23 Thread Željko M . Svedružić 
 

Michael, 

most of the molecular modeling software does not tolerate
"Program Files" in the path name. The code for all those programs is
written for Linux and just adapted to windows. Linux does not recognize
empty space, i.e. "Program Files" should be "Program_Files". Thus, when
I have to work on windows I install all my modeling software in C:\
directory, and everything works fine. Alternatively stick with Linux.


Hope this helps, 

Best of luck in your work, Cheers,


www.svedruziclab.com 

On 2016-10-23 4:32, Michael Morgan wrote: 

>
Dear Patrick, 
> 
> Thank you for your kind help! The problem is solved
with your help. 
> 
> 1) If I run Avogadro.exe from the bin folder, then
open files, I can use the force fields. 
> 
> 2) If I created a shortcut
link in the desktop and run it, I can use the force fields. 
> 
> 3) I
have assigned "C:Program Files (x86)Avogadrobinavogadro.exe" to open the
Gaussian output files by default. If I open an output 
> file using
Avogadro by directly clicking the file, I cannot use the force fields.
Not sure what is wrong. 
> 
> Cheers, 
> 
> Michael 
> 
> FROM: Patrick
Avery [mailto:psav...@buffalo.edu] 
> SENT: Saturday, October 22, 2016
9:35 AM
> TO: avogadro-discuss@lists.sourceforge.net
> SUBJECT: Re:
[Avogadro-Discuss] AutoOptimization 
> 
> Hi Michael, 
> 
> This usually
means the force field files were not found. These are the files at this
location: https://github.com/openbabel/openbabel/tree/master/data [1] 
>

> I can think of two likely scenarios. Either 
> 
> 1: you don't have
the files. Check your install location (probably C:Program Files
(x86)Avogadro). Open the bin folder and see if the force field files are
there. 
> 
> 2: if you do have the files, the force field files may not
be loading if Avogadro's runtime location is not in C:Program Files
(x86)Avogadrobin. You can double click the Avogadro executable in
C:Program Files (x86)Avogadrobin 
> 
> And the force fields should work
then. If you are using a shortcut, right click it and select
"properties" and make sure it says it is starting in C:Program Files
(x86)Avogadrobin and not C:Program Files (x86)Avogadro. 
> 
> I tried
setting it up to make sure we wouldn't run into either of those
problems. Perhaps I missed something, though. Did you create your own
shortcut? 
> 
> Thanks, 
> 
> Patrick 
> 
> On Friday, October 21, 2016,
Michael Morgan <michaelmorgan...@gmail.com [2]> wrote: 
> 
>> Dear All,

>> 
>> My Avogadro's AutoOptimization stopped working. When I clicked
"Start", it showed "AutoOpt: Could not setup force field…". I have tried
most simple 
>> molecules, as well as choosing different force field.
All the same. Any idea what is wrong? 
>> 
>> My Avogadro version is
most recent one (1.2.0). Windows 10. 
>> 
>> Thank you very much. 
>>

>> Best 
>> 
>> Michael

-- 
**address
file***
Željko Svedružić
Ph.D.
zsved...@biol.pmf.hr
web:
https://profiles.google.com/106720515809875304148#106720515809875304148/about
**



Links:
--
[1]
https://github.com/openbabel/openbabel/tree/master/data
[2]
mailto:michaelmorgan...@gmail.com
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Re: [Avogadro-Discuss] AutoOptimization

2016-10-23 Thread Andre Persoons 
Dear Patrick,

are these problems related to PC ?  I use MAC and have never had a problem with 
Avogadro.

Cheers,

Andre

On 22 Oct 2016, at 16:34, Patrick Avery 
> wrote:

Hi Michael,

This usually means the force field files were not found. These are the files at 
this location: https://github.com/openbabel/openbabel/tree/master/data

I can think of two likely scenarios. Either

1: you don't have the files. Check your install location (probably C:\Program 
Files (x86)\Avogadro). Open the bin folder and see if the force field files are 
there.

2: if you do have the files, the force field files may not be loading if 
Avogadro's runtime location is not in C:\Program Files (x86)\Avogadro\bin. You 
can double click the Avogadro executable in C:\Program Files (x86)\Avogadro\bin
And the force fields should work then. If you are using a shortcut, right click 
it and select "properties" and make sure it says it is starting in C:\Program 
Files (x86)\Avogadro\bin and not C:\Program Files (x86)\Avogadro.

I tried setting it up to make sure we wouldn't run into either of those 
problems. Perhaps I missed something, though. Did you create your own shortcut?

Thanks,
Patrick

On Friday, October 21, 2016, Michael Morgan 
> wrote:
Dear All,

My Avogadro’s AutoOptimization stopped working. When I clicked “Start”, it 
showed “AutoOpt: Could not setup force field…”. I have tried most simple
molecules, as well as choosing different force field. All the same. Any idea 
what is wrong?

My Avogadro version is most recent one (1.2.0). Windows 10.

Thank you very much.

Best
Michael


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Re: [Avogadro-Discuss] AutoOptimization

2016-10-22 Thread Michael Morgan 
Dear Patrick,

 

Thank you for your kind help! The problem is solved with your help.

 

1)  If I run Avogadro.exe from the \bin folder, then open files, I can use 
the force fields.

2)  If I created a shortcut link in the desktop and run it, I can use the 
force fields.

3)  I have assigned “C:\Program Files (x86)\Avogadro\bin\avogadro.exe” to 
open the Gaussian output files by default. If I open an output 
file using Avogadro by directly clicking the file, I cannot use the force 
fields. Not sure what is wrong.

 

Cheers,

Michael

 

From: Patrick Avery [mailto:psav...@buffalo.edu] 
Sent: Saturday, October 22, 2016 9:35 AM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] AutoOptimization

 

Hi Michael,

 

This usually means the force field files were not found. These are the files at 
this location: https://github.com/openbabel/openbabel/tree/master/data

 

I can think of two likely scenarios. Either

 

1: you don't have the files. Check your install location (probably C:\Program 
Files (x86)\Avogadro). Open the bin folder and see if the force field files are 
there.

 

2: if you do have the files, the force field files may not be loading if 
Avogadro's runtime location is not in C:\Program Files (x86)\Avogadro\bin. You 
can double click the Avogadro executable in C:\Program Files (x86)\Avogadro\bin 

And the force fields should work then. If you are using a shortcut, right click 
it and select "properties" and make sure it says it is starting in C:\Program 
Files (x86)\Avogadro\bin and not C:\Program Files (x86)\Avogadro.

 

I tried setting it up to make sure we wouldn't run into either of those 
problems. Perhaps I missed something, though. Did you create your own shortcut?

 

Thanks,

Patrick 


On Friday, October 21, 2016, Michael Morgan <michaelmorgan...@gmail.com> wrote:

Dear All,

 

My Avogadro’s AutoOptimization stopped working. When I clicked “Start”, it 
showed “AutoOpt: Could not setup force field…”. I have tried most simple 
molecules, as well as choosing different force field. All the same. Any idea 
what is wrong?

 

My Avogadro version is most recent one (1.2.0). Windows 10.

 

Thank you very much.

 

Best

Michael

 

 

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