From owner-chemistry@ccl.net Wed Jul 11 15:43:01 2012 From: "Gilles Frapper gilles.frapper%a%univ-poitiers.fr" To: CCL Subject: CCL: USPEX tutorial/school at CECAM (Lausanne) next october Message-Id: <-47201-120711122421-5995-zCDan1xZbpqy/AMomwo+pA],[server.ccl.net> X-Original-From: Gilles Frapper Content-Type: multipart/alternative; boundary="------------080101010807070102080305" Date: Wed, 11 Jul 2012 18:23:21 +0200 MIME-Version: 1.0 Sent to CCL by: Gilles Frapper [gilles.frapper||univ-poitiers.fr] This is a multi-part message in MIME format. --------------080101010807070102080305 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear CCL's Looking for an efficient approach to predict crystal structures, surfaces or clusters/nanoparticles? You may look at the evolutionary metadynamics code *USPEX* , a novel method developed by Artem R. Oganov (SUNY at Stony Brook) and coworkers. A tutorial/school will take place in *_october 22-26_* 2012 at CECAM - Lausanne (Switzerland). http://www.cecam.org/workshop-0-635.html Up to now, 30 participants registered from 17 different countries. There is no registration fee for the tutorial but advanced registration is required (see website ). This workshop should be extremely useful for all new users of the USPEX code and researchers looking at novel materials, surfaces and nanoparticles. We have planned an excellent scientific program - including a Quantum Espresso DFT code training -, there will be opportunities to meet the best experts on this topic and start collaborations. Best regards On behalf of the organizers: Artem Oganov and Andriy Lyakhov (SUNY Stony Brook, USA), Mario Valle (Swiss National Supercomputing Centre, Manno, Switzerland), Gilles Frapper (University of Poitiers, France) Dr Gilles Frapper ------------------------------------------------------------------- *Crystal structure prediction using the USPEX code* /October 22, 2012 to October 26, 2012 Location : CECAM-HQ-EPFL, Lausanne, Switzerland / *DETAILS* Crystal structure prediction has long remained a major unsolved problem in physical sciences [1]. A number of approaches have been formulated over years - most of these are summarized in the recent book [2]. Crystal structure prediction is a powerful tool for designing new materials "in silico", thus replacing the traditional Edisonian trial-and-error approach with design by artificial intelligence. It is also a major instrument for discovering new phenomena at extreme conditions. Crystal structure prediction should thus be an everyday tool at the hands of nearly every computational materials scientist. A major advance in this field happened with the development of the evolutionary algorithm USPEX for crystal structure prediction [3], which has led to a number of important findings [4-6]. This proved to be a very efficient and reliable method, and the USPEX code, based on it and freely distributed to academic scientists, is currently used by over 500 researchers worldwide and this number grows rapidly. We should note that in addition to the evolutionary structure prediction, USPEX code features many other techniques, such as random sampling, metadynamics, minima hopping, particle swarm optimization - all of which can be used in real applications or tested against one another. Thus, familiarity with this code will imply a solid background in other structure prediction techniques. USPEX is the widest used crystal structure prediction code and there is a need to train new users through hands-on tutorials and workshops. One such workshop was organized in Poitiers, France (June 2011) and proved to be a great success. Another workshop will take place in Xi'an, China (August 2011). Through a regular series of such pedagogical events we want to train a new generation of users and developers of crystal structure prediction techniques. Our program will consist of theory lectures, hands-on tutorial sessions, and round table discussions. Morning theory lectures will focus on the nature of the crystal structure prediction problem, various ways to address it (in particular evolutionary algorithms), theory of energy landscapes, applications of crystal structure prediction, problems related to low-dimensional systems. Afternoon tutorials will give each participant to tackle a real research project, and special attention will be paid to the tools for data analysis and visualization. References [1] Maddox J. (1988). Crystals from first principles. Nature 335, 201. [2] Oganov A.R. (Ed.) (2010). Modern methods of crystal structure prediction. Berlin: Wiley-VCH, ISBN 978-3-527-40939-6. [3] Oganov A.R., Glass C.W. (2006). Crystal structure prediction using ab initio evolutionary techniques: principles and applications. J. Chem. Phys. 124, 244704. [4] Ma Y., Eremets M.I., Oganov A.R., Xie Y., Trojan I., Medvedev S., Lyakhov A.O., Valle M., Prakapenka V. (2009). Transparent dense sodium. Nature 458, 182-185. [5] Oganov A.R., Chen J., Gatti C., Ma Y.-M., Yu T., Liu Z., Glass C.W., Ma Y.-Z., Kurakevych O.O., Solozhenko V.L. (2009). Ionic high-pressure form of elemental boron. Nature 457, 863-867. [6] Oganov A.R., Lyakhov A.O., Valle M. (2011). How evolutionary crystal structure prediction works - and why. Acc. Chem. Res. 44, 227-237. Dr Gilles Frapper Groupe Modélisation en Chimie Quantique Equipe "Catalyse, Milieux non conventionnels et Carbone Renouvelable" Institut de Chimie des Milieux et Matériaux de Poitiers IC2MP UMR 7285 CNRS - Université de Poitiers 4, rue Michel Brunet (B27) BP633 86022 Poitiers cedex tél : +33 (0)5 49 45 35 74 - fax : +33 (0) 5 49 45 34 99 http://yargla.labo.univ-poitiers.fr / gilles.frapper(!)univ-poitiers.fr --------------080101010807070102080305 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL's

Looking for an efficient approach to predict crystal structures, surfaces or clusters/nanoparticles? 

You may look at the evolutionary metadynamics code USPEX, a novel method developed by Artem R. Oganov (SUNY at Stony Brook) and coworkers.

A tutorial/school will take place in october 22-26 2012 at CECAM - Lausanne (Switzerland). http://www.cecam.org/workshop-0-635.html

Up to now, 30 participants registered from 17 different countries. There is no registration fee for the tutorial but advanced registration is required (see website).

This workshop should be extremely useful for all new users of the USPEX code and researchers looking at novel materials, surfaces and nanoparticles. We have planned an excellent scientific program - including a Quantum Espresso DFT code training -, there will be opportunities to meet the best experts on this topic and start collaborations.

Best regards

On behalf of the organizers: Artem Oganov and Andriy Lyakhov (SUNY Stony Brook, USA), Mario Valle (Swiss National Supercomputing Centre, Manno, Switzerland), Gilles Frapper (University of Poitiers, France)

Dr Gilles Frapper
 
 -------------------------------------------------------------------
Crystal structure prediction using the USPEX code
October 22, 2012 to October 26, 2012
Location : CECAM-HQ-EPFL, Lausanne, Switzerland

DETAILS

Crystal structure prediction has long remained a major unsolved problem in physical sciences [1]. A number of approaches have been formulated over years - most of these are summarized in the recent book [2]. Crystal structure prediction is a powerful tool for designing new materials "in silico", thus replacing the traditional Edisonian trial-and-error approach with design by artificial intelligence. It is also a major instrument for discovering new phenomena at extreme conditions. Crystal structure prediction should thus be an everyday tool at the hands of nearly every computational materials scientist. 
A major advance in this field happened with the development of the evolutionary algorithm USPEX for crystal structure prediction [3], which has led to a number of important findings [4-6]. This proved to be a very efficient and reliable method, and the USPEX code, based on it and freely distributed to academic scientists, is currently used by over 500 researchers worldwide and this number grows rapidly. We should note that in addition to the evolutionary structure prediction, USPEX code features many other techniques, such as random sampling, metadynamics, minima hopping, particle swarm optimization - all of which can be used in real applications or tested against one another. Thus, familiarity with this code will imply a solid background in other structure prediction techniques. USPEX is the widest used crystal structure prediction code and there is a need to train new users through hands-on tutorials and workshops. One such workshop was organized in Poitiers, France (June 2011) and proved to be a great success. Another workshop will take place in Xi'an, China (August 2011). Through a regular series of such pedagogical events we want to train a new generation of users and developers of crystal structure prediction techniques.

Our program will consist of theory lectures, hands-on tutorial sessions, and round table discussions. Morning theory lectures will focus on the nature of the crystal structure prediction problem, various ways to address it (in particular evolutionary algorithms), theory of energy landscapes, applications of crystal structure prediction, problems related to low-dimensional systems. Afternoon tutorials will give each participant to tackle a real research project, and special attention will be paid to the tools for data analysis and visualization.

References

[1] Maddox J. (1988). Crystals from first principles. Nature 335, 201.
[2] Oganov A.R. (Ed.) (2010). Modern methods of crystal structure prediction. Berlin: Wiley-VCH, ISBN 978-3-527-40939-6.
[3] Oganov A.R., Glass C.W. (2006). Crystal structure prediction using ab initio evolutionary techniques: principles and applications. J. Chem. Phys. 124, 244704.
[4] Ma Y., Eremets M.I., Oganov A.R., Xie Y., Trojan I., Medvedev S., Lyakhov A.O., Valle M., Prakapenka V. (2009). Transparent dense sodium. Nature 458, 182-185.
[5] Oganov A.R., Chen J., Gatti C., Ma Y.-M., Yu T., Liu Z., Glass C.W., Ma Y.-Z., Kurakevych O.O., Solozhenko V.L. (2009). Ionic high-pressure form of elemental boron. Nature 457, 863-867.
[6] Oganov A.R., Lyakhov A.O., Valle M. (2011). How evolutionary crystal structure prediction works - and why. Acc. Chem. Res. 44, 227-237.




 
Dr Gilles Frapper 
Groupe Modélisation en Chimie Quantique 
Equipe "Catalyse, Milieux non conventionnels et Carbone Renouvelable"   
Institut de Chimie des Milieux et Matériaux de Poitiers  
IC2MP UMR 7285 CNRS - Université de Poitiers
4, rue Michel Brunet (B27) BP633
86022 Poitiers cedex
tél : +33 (0)5 49 45 35 74 - fax : +33 (0) 5 49 45 34 99 
http://yargla.labo.univ-poitiers.fr / gilles.frapper(!)univ-poitiers.fr
--------------080101010807070102080305-- From owner-chemistry@ccl.net Wed Jul 11 16:18:00 2012 From: "Amo-Kwao Godwin amokwao::unm.edu" To: CCL Subject: CCL:G: single point mp2 electron density request in Gaussian 03 Message-Id: <-47202-120711134729-9511-PdULFzC6YswvX2dF6WYsXw+/-server.ccl.net> X-Original-From: Amo-Kwao Godwin Content-Type: multipart/alternative; boundary=90e6ba3098262e72c204c4917060 Date: Wed, 11 Jul 2012 11:46:38 -0600 MIME-Version: 1.0 Sent to CCL by: Amo-Kwao Godwin [amokwao]*[unm.edu] --90e6ba3098262e72c204c4917060 Content-Type: text/plain; charset=ISO-8859-1 Hi David, Thank you for your suggestion. The problem is I do not use GaussView at all. I run the cubgen from the command line and it works well for optimization calculations. For my research I need to generate molecular electron densities as a function of atomic separation for some fitting. To do this I need the cube file of the electron densities > from single point energy calculations. I am limited to use mp2 because I have prevoius results from mp2 and would like to maintain consistant level of theory. When I use the flag density=mp3 I get an error which I have listed below. amokwao/grid> cubegen 0 density=mp2 coinf.fchk coinf.cube -1 -2 0.0 0.0 -2 .6459 1 0.00052918 0.0 0.0 1 0.0 0.00052918 0.0 10000 0.0 0.0 0.00052918 And this is the error generated. Could not find Total MP2 Density on formatted checkpoint file. Error termination via Lnk1e at +Fri Jul 6 +10:11:29 2012. Segmentation fault Thank you Godwin On Mon, Jul 9, 2012 at 3:17 PM, Close, David M. CLOSED^_^mail.etsu.edu < owner-chemistry^ccl.net> wrote: > I had trouble with this feature last year. Part of the problem is that > Gaussian and GaussView use different keyword for this task. For the > Gaussian calculation I would use Density=MP2. I was interested in spin > densities, so in Gaussview I had to specify spin=MP2 in the cubegen file. > Regards, Dave Close. > > > From: owner-chemistry+closed==etsu.edu^^ccl.net [mailto: > owner-chemistry+closed==etsu.edu^^ccl.net] On Behalf Of Godwin Amo-Kwao > amokwao*|*gmail.com > Sent: Monday, July 09, 2012 11:55 AM > To: Close, David M. > Subject: CCL:G: single point mp2 electron density request in Gaussian 03 > > Thank you for the response to my question input on getting the mp2 > electron densities from a single point calculation. I tried the > density=current but it did not work as I wanted. > > For our research I need to generate a cube file for the electron densities > > from a calculation. This I am able to do easily for an optimization > calculation from the check point file. However there are instances where I > need to change the position of an atom in a molecule and perform a single > point mp2 calculation on the system. This is when I run into problems. > > This is the command I use to get the electron density cube file > > amokwao/grid> cubegen 0 density=mp2 coinf.fchk coinf.cube -1 > -2 0.0 0.0 -2 .6459 > 1 0.00052918 0.0 0.0 > 1 0.0 0.00052918 0.0 > 10000 0.0 0.0 0.00052918 > > And this is the error generated. > > Could not find Total MP2 Density on formatted checkpoint file. > Error termination via Lnk1e at +Fri Jul 6 +10:11:29 2012. > Segmentation fault > > > > This is my original input file > # sp mp2/6-311++G** geom=allcheck density=current pop=full IOp( +6/8=3) > > I also tried what you suggested; > %chk=coinf.chk > # geom=allcheck mp2/6-311++G** > > Any further suggestions will be appreciated. Thank you. > Godwin > > > > On Thu, Jul 5, 2012 at 3:04 PM, cina foroutan canyslopus|yahoo.co.uk< > http://yahoo.co.uk> 20ccl.net>> wrote: > Hi, > > If you want to generate electron density of post-HF methods you must > include density=current keyword too. > > Good luck, > Cina > =========================================================== > Cina Foroutan-Nejad, Ph.D. > http://independent.academia.edu/CinaForoutanNejad > > ________________________________ > > From: Godwin Amo-Kwao amokwao * unm.edu > > > To: "Foroutan-Nejad, Cina " > > Sent: Thursday, 5 July 2012, 20:04 > Subject: CCL:G: single point mp2 electron density request in Gaussian 03 > > > Sent to CCL by: "Godwin Amo-Kwao" [amokwao(!)unm.edu] > Hi, > I am trying to generate the electron density cube file from a single point > energy calculation using mp2 level of theory in Gaussian 03. > > However when I try to import the checkpoint file to generate the mp2 cube > file > it appears to re-optimize the geometry at the HF level and I get this error > "Could not find Total MP2 Density on formatted checkpoint file. > Error termination via Lnk1e at Thu Jul 5 09:52:59 2012. > Segmentation fault" > > Is there a keyword I can use in the route section to ask Gaussian to print > out > the electron density when performing a SINGLE POINT calculation. > > To clarify when I use the opt keyword I get the electron density in the > checkpoint file but I need it for a single point calculation. > > Thank you. > > > -= This is automatically added to each message by the mailing script > =-E-mail to subscribers: CHEMISTRY*ccl.net or > use:E-mail to administrators: CHEMISTRY-REQUEST*ccl.net CHEMISTRY-REQUEST*ccl.net> or usehttp:// > www.ccl.net/chemistry/sub_unsub.shtml Content-Type: text/html; charset"us-ascii" > Content-Transfer-Encoding: quoted-printable > > xmlns:o="urn:schemas-microsoft-com:office:office" > xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m=" > http://schemas.microsoft.com/office/2004/12/omml" xmlns=" > http://www.w3.org/TR/REC-html40"> > > > > > > >
>

style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I > had trouble with this feature last year.  Part of the problem is that > Gaussian and GaussView use different keyword for this task.  For the > Gaussian calculation > I would use Density=MP2.  I was interested in spin densities, so in > Gaussview I had to specify spin=MP2 in the cubegen > file.

>

style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Regards, > Dave Close.

>

style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 

>

style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From: style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> > owner-chemistry+closed==etsu.edu^^ccl.net [mailto:owner-chemistry& > #43;closed==etsu.edu^^ccl.net] > On Behalf Of Godwin Amo-Kwao amokwao*|*gmail.com
> Sent: Monday, July 09, 2012 11:55 AM
> To: Close, David M.
> Subject: CCL:G: single point mp2 electron density request in > Gaussian 03

>

 

>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222;background:white">Thank > you for the response to my question input on getting the mp2 electron > densities from a single point calculation. I tried the density=current > but it did not work as I wanted. 

>
>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"> 

>
>
>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222">For > our research I need to generate a cube file for > the electron densities from a calculation. This I am able to do > easily for an optimization > calculation from the check point file. However there are instances where > I need to change the position of an atom in > a molecule and perform a single point mp2 calculation > on the system. This is when I run into problems. style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222">

>
>
>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"> 

>
>
>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222">This > is the command I use to get the electron density cube file style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222">

>
>
>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"> 

>
>
>
>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222">amokwao/grid> > cubegen 0 density=mp2 coinf.fchk coinf.cube  class="boomerang-end-time">-1

>
>
>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222">   class="boomerang-end-time">-2         >    0.0         0.0       >    class="boomerang-end-time">-2 .6459

>
>
>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222">  >  1           0.00052918       >   0.0         0.0

>
>
>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222">  >  1            0.0       >   0.00052918        0.0

>
>
>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222">  >  10000         0.0         0.0 >         0.00052918

>
>
>
>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"> 

>
>
>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222">And > this is the error generated.

>
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>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"> 

>
>
>
>
>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#500050"> Could > not find   Total MP2 Density on formatted checkpoint > file.

>
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>
>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222"> Error > termination via Lnk1e at  style="font-size:11.5pt;font-family:"Verdana","sans-serif";color:#222222">+ class="boomerang-meeting-text"> style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:green">Fri > Jul  6 style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222">  class="b4c-add-event"> style="font-size:11.5pt;font-family:"Verdana","sans-serif";color:#222222">+ class="boomerang-meeting-text"> style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:green">10:11 style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222">:29 > 2012.

>
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>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222">Segmentation > fault

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>

style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#222222"> 

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style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"> 

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style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"> 

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>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222">This > is my original input file

>
>
>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"># > sp mp2/6-311++G** geom=allcheck density=current pop=full >  IOp( style="font-size:11.5pt;font-family:"Arial","sans-serif";color:#222222"> + class="boomerang-meeting-text"> style="font-size:10.0pt;font-family:"Arial","sans-serif";color:green">6/8 style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222">=3)

>
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style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"> 

>
>
>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222">I > also tried what you suggested; 

>
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>
>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222">%chk=coinf.chk
> # geom=allcheck mp2/6-311++G**

>
>
>
>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"> 

>
>
>

style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222">Any > further suggestions will be appreciated. Thank you.

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style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222"> 

>
>
>
>

 

>
>
>

Godwin Amo-Kwao
> Center of Advanced Research Computing
> University of New Mexico

>
>
>

 

>
>
>
>

"It is not the > critic who counts; not the man who points out how the strong man stumbles, > or where the doer of deeds could have done them better. The credit belongs > to the man who is actually in the arena, > whose face is marred by dust and sweat and blood; who strives valiantly; > who errs, who comes short again and again, because there is no effort > without error and shortcoming; but who does actually strive to do the > deeds; who knows great enthusiasms, the great > devotions; who spends himself in a worthy cause; who at the best knows in > the end the triumph of high achievement, and who at the worst, if he fails, > at least fails while daring greatly, so that his place shall never be with > those cold and timid souls who > neither know victory nor defeat." -Theodore > Roosevelt

>
>
>


>
>

>
>

On Thu, Jul 5, 2012 at 3:04 PM, cina foroutan > canyslopus|yahoo.co.uk < href="mailto:owner-chemistry%20~%20ccl.net" > target="_blank">owner-chemistry ~ ccl.net> wrote:

>
>
>
>

Hi,

>
>
>

 

>
>
>

If you want to generate electron density of > post-HF methods you must include density=current keyword > too.

>
>
>

 

>
>
>

Good luck,

>
>
>

Cina

>
>
>

===========================================================

>
>
>

Cina Foroutan-Nejad, > Ph.D.

>
> >
>

 

>
>
>
>
>
style="font-family:"Arial","sans-serif""> >
>
>

style="font-family:"Arial","sans-serif"">From: style="font-family:"Arial","sans-serif""> Godwin > Amo-Kwao amokwao * > unm.edu > <owner-chemistry*ccl.net > >
> To: "Foroutan-Nejad, Cina " <canyslopus*yahoo.co.uk> >
> Sent: Thursday, 5 July 2012, 20:04
> Subject: CCL:G: single point mp2 electron density request in > Gaussian 03

>
>
>


>
> Sent to CCL by: "Godwin  Amo-Kwao" [amokwao(!)unm.edu]
> Hi,
> I am trying to generate the electron density cube file from a single point >
> energy calculation using mp2 level of theory in Gaussian 03.
>
> However when I try to import the checkpoint file to generate the mp2 cube > file
> it appears to re-optimize the geometry at the HF level and I get this > error
> "Could not find  Total MP2 Density on formatted checkpoint > file.
> Error termination via Lnk1e at Thu Jul  5 09:52:59 2012.
> Segmentation fault"
>
> Is there a keyword I can use in the route section to ask Gaussian to print > out
> the electron density when performing a SINGLE POINT calculation.
>
> To clarify when I use the opt keyword I get the electron density in the >
> checkpoint file but I need it for a single point calculation.
>
> Thank you.
>
>
>

>
>

-= This is automatically added to each message by the > mailing script =-
>
> E-mail to subscribers: target="_blank">CHEMISTRY*ccl.net or use:
>      
>
> E-mail to administrators: target="_blank"> > CHEMISTRY-REQUEST*ccl.net or use
>      

> >
>
>
>
>
>

 

>
> > > --90e6ba3098262e72c204c4917060 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi David,
<= font face=3D"verdana,sans-serif">Thank you for your=A0suggestion. The probl= em is I do not use GaussView at all. I run the cubgen from the command line= and it works well for=A0optimization=A0calculations. For my=A0researc= h I need to generate=A0molecular=A0electron densities as a function of atom= ic separation for some fitting. To do this I need the cube file of the elec= tron densities from single point energy calculations. =A0=A0I am limited = to use mp2 because I have prevoius results from mp2 and would like to maint= ain consistant level of theory.=A0=A0When =A0I use the flag density=3Dmp3 I get an error which I have = listed below.


amokwao/grid> cubegen 0 density=3Dmp2= coinf.fchk coinf.cube=A0=A0-1
=A0= =A0=A0-2=A0=A0=A0 =A0 =A0 =A0 =A0= =A00.0 =A0 =A0 =A0 =A0 0.0 =A0 =A0 =A0 =A0=A0=A0-2=A0=A0.6459
=A0 = =A01 =A0 =A0 =A0 =A0 =A0 0.00052918 =A0 =A0 =A0 =A0 0.0 =A0 =A0 =A0 =A0 0.0=
=A0 =A01 =A0 =A0 =A0 =A0 =A0 =A00.0 =A0 =A0 =A0 =A0 0.00052918 =A0 =A0 =A0 = =A00.0
=A0 =A010000 =A0 =A0 =A0 =A0 0.0 =A0 =A0 =A0 =A0 0.0 =A0 =A0 = =A0 =A0 0.00052918

=
And this is the error generated.
=A0
<= blockquote style=3D"margin:0px 0px 0px 0.8ex;border-left-width:1px;border-l= eft-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">=A0Cou= ld not find =A0 Total MP2 Density on formatted checkpoint file.
=A0Error termination via Lnk1e at=A0+Fri Jul =A06=A0+10:11:29 2= 012.
Segme= ntation fault
Thank you
Godwin=A0


On Mon, Jul 9, 2012 at 3:17 PM, Close, D= avid M. CLOSED^_^mail.et= su.edu <owner-chemistry^ccl.net> wrote:
I had trouble with this feature last year. = =A0Part of the problem is that Gaussian and GaussView use different keyword= for this task. =A0For the Gaussian calculation I would use Density=3DMP2. = =A0I was interested in spin densities, so in Gaussview I had to specify spi= n=3DMP2 in the cubegen file.
Regards, Dave Close.

> From: owner-chemistry+closed=3D=3Detsu.edu^^ccl.= net [mailto:owner-chemistry+closed=3D=3Detsu.edu^^ccl.net] On Behalf Of Godwin Amo-Kwao amokwao*|*gmail.com
Sent: Monday, July 09, 2012 11:55 AM
To: Close, David M.
Subject: CCL:G: single point mp2 electron density request in Gaussian 03
Thank you for the response to my question input on getting the mp2 electron= densities from a single point calculation. I tried the density=3Dcurrent b= ut it did not work as I wanted.

For our research I need to generate a cube file for the electron densities = > from a calculation. This I am able to do easily for an optimization ca= lculation from the check point file. However there are instances where I ne= ed to change the position of an atom in a molecule and perform a single poi= nt mp2 calculation on the system. This is when I run into problems.

This is the command I use to get the electron density cube file

amokwao/grid> cubegen 0 density=3Dmp2 coinf.fchk coinf.cube -1
=A0 -2 =A0 =A0 =A0 =A0 =A0 =A00.0 =A0 =A0 =A0 =A0 0.0 =A0 =A0 =A0 =A0 -2 .6= 459
=A0 =A01 =A0 =A0 =A0 =A0 =A0 0.00052918 =A0 =A0 =A0 =A0 0.0 =A0 =A0 =A0 =A0= 0.0
=A0 =A01 =A0 =A0 =A0 =A0 =A0 =A00.0 =A0 =A0 =A0 =A0 0.00052918 =A0 =A0 =A0 = =A00.0
=A0 =A010000 =A0 =A0 =A0 =A0 0.0 =A0 =A0 =A0 =A0 0.0 =A0 =A0 =A0 =A0 0.0005= 2918

And this is the error generated.

=A0Could not find =A0 Total MP2 Density on formatted checkpoint file.
=A0Error termination via Lnk1e at +Fri Jul =A06 +10:11:29 2012.
Segmentation fault



This is my original input file
# sp mp2/6-311++G** geom=3Dallcheck density=3Dcurrent pop=3Dfull =A0IOp( +6= /8=3D3)

I also tried what you suggested;
%chk=3Dcoinf.chk
# geom=3Dallcheck mp2/6-311++G**

Any further suggestions will be appreciated. Thank you.
Go= dwin



On Thu, Jul 5, 2012 at 3:04 PM, cina foroutan canyslopus|yahoo.co.uk<http://yahoo.co.uk> <owner-chemistry ~ ccl.net<mailto:owner-chemistry%20~%20ccl.net>> wrote: Hi,

If you want to generate electron density of post-HF methods you must includ= e density=3Dcurrent keyword too.

Good luck,
Cina
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D
Cina Foroutan-Nejad, Ph.D.
http://independent.academia.edu/CinaForoutanNejad

________________________________
> From: Godwin Amo-Kwao amokwao * unm.edu<http://u= nm.edu> <owner-chemistry*ccl.net<http://ccl= .net>>
To: "Foroutan-Nejad, Cina " <canyslopus*yahoo.co.uk<http://yahoo.co.uk>>
Sent: Thursday, 5 July 2012, 20:04
Subject: CCL:G: single point mp2 electron density request in Gaussian 03

Sent to CCL by: "Godwin =A0Amo-Kwao" [amokwao(!)unm.edu<http://unm.edu>]
Hi,
I am trying to generate the electron density cube file from a single point<= br> energy calculation using mp2 level of theory in Gaussian 03.

However when I try to import the checkpoint file to generate the mp2 cube f= ile
it appears to re-optimize the geometry at the HF level and I get this error=
"Could not find =A0Total MP2 Density on formatted checkpoint file.
Error termination via Lnk1e at Thu Jul =A05 09:52:59 2012.
Segmentation fault"

Is there a keyword I can use in the route section to ask Gaussian to print = out
the electron density when performing a SINGLE POINT calculation.

To clarify when I use the opt keyword I get the electron density in the
checkpoint file but I need it for a single point calculation.

Thank you.


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<p class=3D"MsoNormal"><span style=3D"font-size:11.= 0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;= color:#1F497D">I had trouble with this feature last year.&nbsp;= Part of the problem is that Gaussian and GaussView use different keyword f= or this task.&nbsp; For the Gaussian calculation
=A0I would use Density=3DMP2.&nbsp; I was interested in spin densities,= so in Gaussview I had to specify spin=3DMP2 in the cubegen file.<o:p>= ;</o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.= 0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;= color:#1F497D">Regards, Dave Close.<o:p></o:p></span= ></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.= 0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;= color:#1F497D"><o:p>&nbsp;</o:p></span></p= >
<p class=3D"MsoNormal"><b><span style=3D"font= -size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&am= p;quot;">From:</span></b><span style=3D"font-si= ze:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&q= uot;"> owner-chemistry&#43;closed=3D=3Detsu.edu^^ccl.net [mailto:owner-chemistry&#43;closed=3D=3Detsu.edu^^ccl.net]
<b>On Behalf Of </b>Godwin Amo-Kwao amokwao*|*gmail.com<br>
<b>Sent:</b> Monday, July 09, 2012 11:55 AM<br>
<b>To:</b> Close, David M.<br>
<b>Subject:</b> CCL:G: single point mp2 electron density reques= t in Gaussian 03<o:p></o:p></span></p>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p><= ;/p>
<p class=3D"MsoNormal"><span style=3D"font-size:10.= 0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;= color:#222222;background:white">Thank you for the response to my qu= estion input on getting the mp2 electron densities from a single point calc= ulation. I tried the density=3Dcurrent
=A0but it did not work as I wanted.&nbsp;</span><o:p></o= :p></p>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222"><o:p>&n= bsp;</o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#222222">For our researc= h I need to generate a cube file for the&nbsp;electron&nbsp;densiti= es from a calculation. This I am able to do easily for an optimization
=A0calculation from the check point file. However there are instances where= I need to&nbsp;change&nbsp;the position of an atom in a&nbsp;m= olecule&nbsp;and perform a&nbsp;single&nbsp;point mp2 calculati= on on the system. This is when I run into problems.</span><span st= yle=3D"font-size:10.0pt;font-family:&quot;Arial&quot;,&quo= t;sans-serif&quot;;color:#222222"><o:p></o:p></s= pan></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222"><o:p>&n= bsp;</o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#222222">This is the com= mand I use to get the electron density cube file</span><span style= =3D"font-size:10.0pt;font-family:&quot;Arial&quot;,&quot;s= ans-serif&quot;;color:#222222"><o:p></o:p></span= ></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222"><o:p>&n= bsp;</o:p></span></p>
</div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#222222">amokwao/grid&am= p;gt; cubegen 0 density=3Dmp2 coinf.fchk coinf.cube&nbsp;<span class= =3D"boomerang-end-time">-1</span><o:p></o:p>= </span></p>
</blockquote>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#222222">&nbsp;&= nbsp;<span class=3D"boomerang-end-time">-2</span>&= ;nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0.0 = &nbsp; &nbsp; &nbsp; &nbsp; 0.0 &nbsp; &nbsp; &= nbsp; &nbsp;&nbsp;<span class=3D"boomerang-end-time"&g= t;-2</span>&nbsp;.6459<o:p></o:p></span></p&= gt;
</blockquote>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#222222">&nbsp; &= ;nbsp;1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0.00052918 &= amp;nbsp; &nbsp; &nbsp; &nbsp; 0.0 &nbsp; &nbsp; &n= bsp; &nbsp; 0.0<o:p></o:p></span></p>
</blockquote>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#222222">&nbsp; &= ;nbsp;1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;0.= 0 &nbsp; &nbsp; &nbsp; &nbsp; 0.00052918 &nbsp; &nb= sp; &nbsp; &nbsp;0.0<o:p></o:p></span></p><= br> </blockquote>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#222222">&nbsp; &= ;nbsp;10000 &nbsp; &nbsp; &nbsp; &nbsp; 0.0 &nbsp; &= ;nbsp; &nbsp; &nbsp; 0.0 &nbsp; &nbsp; &nbsp; &nbsp= ; 0.00052918<o:p></o:p></span></p>
</blockquote>
</blockquote>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222"><o:p>&n= bsp;</o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222">And this is the e= rror generated.<o:p></o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222">&nbsp;<o:p= ></o:p></span></p>
</div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#500050">&nbsp;Could= not find &nbsp; Total MP2 Density on formatted checkpoint file.<o:p= ></o:p></span></p>
</blockquote>
</div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#222222">&nbsp;Error= termination via Lnk1e at&nbsp;</span><span class=3D"b4c-= add-event"><span style=3D"font-size:11.5pt;font-family:&= ;quot;Verdana&quot;,&quot;sans-serif&quot;;color:#222222"&= gt;&#43;</span></span><span class=3D"boomerang-meet= ing-text"><span style=3D"font-size:10.0pt;font-family:&= quot;Verdana&quot;,&quot;sans-serif&quot;;color:green">= Fri
=A0Jul &nbsp;6</span></span><span style=3D"font-siz= e:10.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&q= uot;;color:#222222">&nbsp;</span><span class=3D"b= 4c-add-event"><span style=3D"font-size:11.5pt;font-family:&= amp;quot;Verdana&quot;,&quot;sans-serif&quot;;color:#222222&quo= t;>&#43;</span></span><span class=3D"boomerang-m= eeting-text"><span style=3D"font-size:10.0pt;font-family:&a= mp;quot;Verdana&quot;,&quot;sans-serif&quot;;color:green"&= gt;10:11</span></span><span style=3D"font-size:10.0pt;f= ont-family:&quot;Verdana&quot;,&quot;sans-serif&quot;;color= :#222222">:29
=A02012.<o:p></o:p></span></p>
</blockquote>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#222222">Segmentation fa= ult<o:p></o:p></span></p>
</blockquote>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Verdana&= quot;,&quot;sans-serif&quot;;color:#222222"><o:p>&= ;nbsp;</o:p></span></p>
</div>
</blockquote>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222"><o:p>&n= bsp;</o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222"><o:p>&n= bsp;</o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222">This is my origin= al input file<o:p></o:p></span></p>
</div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222"># sp mp2/6-311&am= p;#43;&#43;G** geom=3Dallcheck density=3Dcurrent pop=3Dfull &nbsp;I= Op(</span><span class=3D"b4c-add-event"><span styl= e=3D"font-size:11.5pt;font-family:&quot;Arial&quot;,&quot;= sans-serif&quot;;color:#222222">&nbsp;&#43;</span>= ;</span><span class=3D"boomerang-meeting-text"><sp= an style=3D"font-size:10.0pt;font-family:&quot;Arial&quot;,&am= p;quot;sans-serif&quot;;color:green">6/8</span></span&= gt;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&= quot;,&quot;sans-serif&quot;;color:#222222">=3D3)<o:p>= ;</o:p></span></p>
</blockquote>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222"><o:p>&n= bsp;</o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222">I also tried what= you suggested;&nbsp;<o:p></o:p></span></p>
</div>
<div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222">%chk=3Dcoinf.chk&= lt;br>
# geom=3Dallcheck mp2/6-311&#43;&#43;G**<o:p></o:p><= /span></p>
</blockquote>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222"><o:p>&n= bsp;</o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222">Any further sugge= stions will be appreciated. Thank you.<o:p></o:p></span>&= lt;/p>
</div>
<div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal" style=3D"background:white">= ;<span style=3D"font-size:10.0pt;font-family:&quot;Arial&qu= ot;,&quot;sans-serif&quot;;color:#222222"><o:p>&n= bsp;</o:p></span></p>
</blockquote>
</div>
<div>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p><= ;/p>
</div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal">Godwin Amo-Kwao<br>
Center of Advanced&nbsp;Research&nbsp;Computing<br>
University of New Mexico<o:p></o:p></p>
</blockquote>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal">&nbsp;<o:p></o:p><= ;/p>
</blockquote>
<div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;pa= dding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class=3D"MsoNormal"><span style=3D"font-size:7.5= pt">&quot;It is not the critic who counts; not the man who poin= ts out how the strong man stumbles, or where the doer of deeds could have d= one them better. The credit belongs to the man who is actually in the arena= ,
=A0whose face is marred by dust and sweat and blood; who strives valiantly;= who errs, who comes short again and again, because there is no effort with= out error and shortcoming; but who does actually strive to do the deeds; wh= o knows great enthusiasms, the great
=A0devotions; who spends himself in a worthy cause; who at the best knows i= n the end the triumph of high achievement, and who at the worst, if he fail= s, at least fails while daring greatly, so that his place shall never be wi= th those cold and timid souls who
=A0neither know victory nor defeat.&quot; -Theodore Roosevelt</span&= gt;<o:p></o:p></p>
</blockquote>
</div>
<p class=3D"MsoNormal" style=3D"margin-bottom:12.0pt"= ;><br>
<br>
<o:p></o:p></p>
<div>
<p class=3D"MsoNormal">On Thu, Jul 5, 2012 at 3:04 PM, cina= foroutan canyslopus|<a href=3D"http://yahoo.co.uk">yahoo.co.uk</a> &lt;<a href=3D"ma= ilto:owner-chemis= try%20~%20ccl.net&qu= ot; target=3D"_blank">owner-chemistry ~ ccl.net</a>&gt; wrote:<o:p></= o:p></p>
<div>
<div>
<div>
<p class=3D"MsoNormal"><span style=3D"font-family:&= amp;quot;Bookman Old Style&quot;,&quot;serif&quot;">Hi,= <o:p></o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal"><span style=3D"font-family:&= amp;quot;Bookman Old Style&quot;,&quot;serif&quot;"><= ;o:p>&nbsp;</o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal"><span style=3D"font-family:&= amp;quot;Bookman Old Style&quot;,&quot;serif&quot;">If = you want to generate electron density of post-HF methods you must include d= ensity=3Dcurrent keyword too.<o:p></o:p></span></p>=
</div>
<div>
<p class=3D"MsoNormal"><span style=3D"font-family:&= amp;quot;Bookman Old Style&quot;,&quot;serif&quot;"><= ;o:p>&nbsp;</o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal"><span style=3D"font-family:&= amp;quot;Bookman Old Style&quot;,&quot;serif&quot;">Goo= d luck,<o:p></o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal"><span style=3D"font-family:&= amp;quot;Bookman Old Style&quot;,&quot;serif&quot;">Cin= a<o:p></o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal"><span style=3D"font-family:&= amp;quot;Bookman Old Style&quot;,&quot;serif&quot;">=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D<o:p></o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal"><span style=3D"font-family:&= amp;quot;Bookman Old Style&quot;,&quot;serif&quot;">Cin= a Foroutan-Nejad, Ph.D.<o:p></o:p></span></p>
</div>
<div>
<p class=3D"MsoNormal"><span style=3D"font-family:&= amp;quot;Bookman Old Style&quot;,&quot;serif&quot;"><= ;a href=3D"http://independent.academia.edu/CinaForoutanNejad&= quot; target=3D"_blank">http://independent.academia.edu/C= inaForoutanNejad</a><o:p></o:p></span></p>= ;
</div>
<div>
<p class=3D"MsoNormal"><span style=3D"font-family:&= amp;quot;Bookman Old Style&quot;,&quot;serif&quot;"><= ;o:p>&nbsp;</o:p></span></p>
</div>
<div>
<div>
<div>
<div class=3D"MsoNormal" align=3D"center" style=3D&q= uot;text-align:center"><span style=3D"font-family:&quot= ;Arial&quot;,&quot;sans-serif&quot;">
<hr size=3D"1" width=3D"100%" align=3D"center&q= uot;>
</span></div>
<p class=3D"MsoNormal"><b><span style=3D"font= -family:&quot;Arial&quot;,&quot;sans-serif&quot;">F= rom:</span></b><span style=3D"font-family:&quot;Ari= al&quot;,&quot;sans-serif&quot;"> Godwin Amo-Kwao amokw= ao *
<a href=3D"http://unm.= edu" target=3D"_blank">unm.edu</a> &lt;owner-chemistry*<a href=3D&= quot;http://ccl.net" = target=3D"_blank">ccl.net</a>&gt;<br>
<b>To:</b> &quot;Foroutan-Nejad, Cina &quot; &lt;ca= nyslopus*<a href=3D"http://yahoo.co.uk" target=3D"_blank">yahoo.co.uk</a>&gt;
<br>
<b>Sent:</b> Thursday, 5 July 2012, 20:04<br>
<b>Subject:</b> CCL:G: single point mp2 electron density reques= t in Gaussian 03</span><o:p></o:p></p>
</div>
<div>
<p class=3D"MsoNormal" style=3D"margin-bottom:12.0pt"= ;><br>
<br>
Sent to CCL by: &quot;Godwin&nbsp; Amo-Kwao&quot; [amokwao(!)&l= t;a href=3D"http://unm.ed= u" target=3D"_blank">unm.edu</a>]<br>
Hi,<br>
I am trying to generate the electron density cube file from a single point = <br>
energy calculation using mp2 level of theory in Gaussian 03.<br>
<br>
However when I try to import the checkpoint file to generate the mp2 cube f= ile <br>
it appears to re-optimize the geometry at the HF level and I get this error= <br>
&quot;Could not find&nbsp; Total MP2 Density on formatted checkpoin= t file.<br>
Error termination via Lnk1e at Thu Jul&nbsp; 5 09:52:59 2012.<br>=
Segmentation fault&quot;<br>
<br>
Is there a keyword I can use in the route section to ask Gaussian to print = out <br>
the electron density when performing a SINGLE POINT calculation. <br>=
<br>
To clarify when I use the opt keyword I get the electron density in the <= ;br>
checkpoint file but I need it for a single point calculation. <br> <br>
Thank you.<br>
<br>
<br>
<o:p></o:p></p>
</div>
<p class=3D"MsoNormal">-=3D This is automatically added to = each message by the mailing script =3D-look up the X-Original-From: line in= the mail header.<br>
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http://www.ccl.net<= /a><br>
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http://www.ccl.net/chemistry/aboutccl/instructions/</a><= ;br>
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--90e6ba3098262e72c204c4917060-- From owner-chemistry@ccl.net Wed Jul 11 19:45:00 2012 From: "John Keith john.keith],[gmail.com" To: CCL Subject: CCL: Converting Molcas orbitals into Gamess orbitals Message-Id: <-47203-120711175300-19285-GVIAUuinoCohbJ/+hSItHA{=}server.ccl.net> X-Original-From: "John Keith" Date: Wed, 11 Jul 2012 17:52:56 -0400 Sent to CCL by: "John Keith" [john.keith^gmail.com] Hi All, I would like to see if someone, somewhere has a script or program that can convert ROHF orbitals from a Molcas Rasmol file into something readable with Gamess-US. I am aware this is not a trivial scripting exercise since Molcas uses pure spherical harmonics while Gamess reads and outputs orbitals in Cartesian format (even when running calculations using real spherical harmonics). Might someone know of a portable program that does the necessary transformations as Frisch and Schlegel outline? http://onlinelibrary.wiley.com/doi/10.1002/qua.560540202/abstract I checked the archive and see this issue was brought up a few years ago, but I couldn't find a solution posted. Thanks for your time, --john From owner-chemistry@ccl.net Wed Jul 11 23:33:01 2012 From: "Jun Zhang coolrainbow-x-yahoo.cn" To: CCL Subject: CCL: 'Understanding Quantum Chemistry from H2MODEL' (Manual Work) Message-Id: <-47204-120711180833-20228-qNX4UiZ3bU6KY/VwEzfYwA(_)server.ccl.net> X-Original-From: Jun Zhang Content-Type: multipart/alternative; boundary="1292221969-1170501730-1342013077=:42711" Date: Wed, 11 Jul 2012 21:24:37 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow[]yahoo.cn] --1292221969-1170501730-1342013077=:42711 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear James:=0A=0AI will be very appreciated hearing your comments and impro= ve the document!=C2=A0=0A=0ABest Regards!=0A=C2=A0=0A----------------------= ------------------------------------------=0AJun Zhang (coolrainbow(~)yahoo.c= n)=0AComputational Chemistry Group=0ANo.94, Weijinlu=0ANankai University = =0ATianjin, China=0A=0A=0A________________________________=0A =E5=8F=91=E4= =BB=B6=E4=BA=BA=EF=BC=9A "jdwhitfield(~)gmail.com" =0A= =E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A coolrainbow(~)yahoo.cn =0A=E5=8F=91=E9= =80=81=E6=97=A5=E6=9C=9F=EF=BC=9A 2012=E5=B9=B47=E6=9C=8810=E6=97=A5, =E6= =98=9F=E6=9C=9F=E4=BA=8C, =E4=B8=8A=E5=8D=88 12:17=0A=E4=B8=BB=E9=A2=98: Re= : CCL: 'Understanding Quantum Chemistry from H2MODEL' (Manual Work)=0A =0A= =0A =0AHello Jun,=0A=0AI really liked the H2MODEL document. I didn't finish= reading it but I had a few comments. Would you like feedback on the docume= nt?=0A=0ASincerely,=0AJames=0A=0AJ. D. Whitfield=0ANEC Labs America, Quantu= m Information Technology=0AColumbia University, Physics Department=0A=0Atel= : 609-903-8824=0Aweb: www.columbia.edu/~jdw2168=0A=0A=0A----- Reply message= -----=0AFrom: "Billy McCann bwm0005-#-tigermail.auburn.edu" =0ATo: "Whitfield, James Daniel " =0ASubject: CCL: 'Understanding Quantum Chemistry from H2MODEL' (Manual Wo= rk)=0ADate: Mon, Jul 9, 2012 09:00=0A=0A=0A=0A=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0 =0AVery helpful.=C2=A0 Many thanks for this contri= bution.=0A=C2=A0=0A+++++++++++++++++++++++++=0ABilly Wayne McCann=0APh.D. C= andidate=0AOrlando Acevedo Reseach=0AAuburn University, Alabama=0AOffice # = =3D 334.844.6948 =0Abwayne on irc.freenode.net=0A+++++++++++++++++++++++++= =0A=C2=A0=0AFrom:owner-chemistry+bwm0005=3D=3Dauburn.edu() ccl.net [mailto:= owner-chemistry+bwm0005=3D=3Dauburn.edu() ccl.net] On Behalf Of Jun Zhang c= oolrainbow_._yahoo.cn=0ASent: Sunday, July 08, 2012 10:16 PM=0ATo: Billy Mc= Cann=0ASubject: CCL: 'Understanding Quantum Chemistry from H2MODEL' (Manual= Work)=0A=C2=A0=0ADear CCL users:=0A=C2=A0=0ASome times ago a document name= d 'Understanding Quantum Chemistry from H2MODEL', which contains=0Adetailed= description on how ab initial computations of H2 are performed=C2=A0 was f= ound on CCL. Now the third=0Aedition of this document were released with so= me modification. =0A=C2=A0=0Adocument: http://struchem.nankai.edu.cn/softwa= re/h2model_EN.pdf=0Aprogram: http://struchem.nankai.edu.cn/software/H2MODEL= _program.rar=0A=C2=A0=0A=C2=A0=0A------------------------------------------= ----------------------=0AJun Zhang (coolrainbow*o*yahoo.cn)=0AComputational= Chemistry Group=0ANo.94, Weijinlu=0ANankai University =0ATianjin, China --1292221969-1170501730-1342013077=:42711 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Dear James= :

I will be very appreci= ated hearing your comments and improve the document! 

Best Regards!
 
----------------------------------------------------------------Jun Zhang (coolrainbow(~)yahoo.cn)
Computational Chemistry Group
No.94= , Weijinlu
Nankai University
Tianjin, China
=E5=8F=91=E4=BB=B6=E4=BA= =BA=EF=BC=9A "jdwhitfield(~)gmail.com" <jdwhitfield(~)gmail.com&g= t;
=E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A coolrainbow(~)yahoo.cn
=E5=8F= =91=E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A 2012=E5=B9=B47=E6=9C=881= 0=E6=97=A5, =E6=98=9F=E6=9C=9F=E4=BA=8C, =E4=B8=8A=E5=8D=88 12:17
=E4=B8=BB=E9=A2=98: Re: CCL: 'U= nderstanding Quantum Chemistry from H2MODEL' (Manual Work)
=0A=0A =0A =0A=0A=0A
Hello Jun,

I = really liked the H2MODEL document. I didn't finish reading it but I had a f= ew comments. Would you like feedback on the document?

Sincerely,
= James

J. D. Whitfield
NEC Labs America, Quantum Information Techn= ology
Columbia University, Physics Department

tel: 609-903-8824web: www.columbia.edu/~jdw2168

----- Reply message -----
From: "Billy McCann bwm0005-#-tige= rmail.auburn.edu" <owner-chemistry(~)ccl.net>
To: "Whitfield, James = Daniel " <jdwhitfield(~)gmail.com>
Subject: CCL: 'Understand= ing Quantum Chemistry from H2MODEL' (Manual Work)
Date: Mon, Jul 9, 2012= 09:00


=0A
=0A &= nbsp;           &nbs= p;       =0A
=0A
Very helpful.=   Many thanks for this contribution.
=0A
 
= =0A
=0A
+++++++++++++++++++++++++
=0A
Billy Wayne McCann =0A
Ph.D. Candidate
=0A
= Orlando Acevedo Reseach
=0A<= div class=3D"yiv1338834308MsoNormal">Aubu= rn University, Alabama
=0A
Office # =3D 334.844.6948=0A =0A
bwayne on irc.freenode.net
=0A
+++++++++++++++++++++++++=
=0A
=0A
 
=0A
=0A
=0A
From: owner-chemistry+bwm0005=3D=3Dauburn.ed= u() ccl.net [mailto:owner-chemistry+bwm0005=3D=3Dauburn.edu() ccl.net]=0AOn Behalf Of Jun Zhang coolrainbow_._yahoo.cn
=0ASent: Sunda= y, July 08, 2012 10:16 PM
=0ATo: Billy McCann
=0ASubject: CCL: 'Understanding Quantum Chemistry from H2MODEL' (Manual Work)=
=0A
=0A
=0A
  =0A
=0A
=0A
Dear CCL users:
= =0A
=0A
=0A
 
=0A
=0A=0A
Some times ago a document named 'Understanding Qua= ntum Chemistry from H2MODEL', which contains
=0A
=0A
= =0A
detailed description on how ab initial computations = of H2 are performed  was found on CCL. Now the third
=0A<= /div>=0A
=0A
edition of this document were released = with some modification.=0A
=0A
=0A
=0A
 
=0A
=0A=0A=
=0A
<= span style=3D"color:black;"> 
=0A
=0A
=0A
 
=0A
=0A
=0A
--= --------------------------------------------------------------
=0AJun Zh= ang (coolrainbow*o*yahoo.cn)
=0AComputational Chemistry Group
=0ANo.9= 4, Weijinlu
=0ANankai University
=0ATianjin, China
=0A<= /div>=0A
=0A
=0A
=0A=0A


<= /body> --1292221969-1170501730-1342013077=:42711--