From owner-chemistry@ccl.net Mon Jul 9 00:28:00 2012 From: "Jun Zhang coolrainbow_._yahoo.cn" To: CCL Subject: CCL: 'Understanding Quantum Chemistry from H2MODEL' (Manual Work) Message-Id: <-47181-120708231637-5220-Bl9ALGYG3m+t8Zz/bUm/ng . server.ccl.net> X-Original-From: Jun Zhang Content-Type: multipart/alternative; boundary="1770247284-282649200-1341803780=:57570" Date: Mon, 9 Jul 2012 11:16:20 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow**yahoo.cn] --1770247284-282649200-1341803780=:57570 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL users:=0A=A0=0ASome times ago a document named 'Understanding Quan= tum Chemistry from H2MODEL', which contains=0Adetailed description on how a= b initial computations of H2 are performed=A0 was found on CCL. Now the thi= rd=0Aedition of this document were released with some modification. =0A=A0= =0Adocument: http://struchem.nankai.edu.cn/software/h2model_EN.pdf=0Aprogra= m: http://struchem.nankai.edu.cn/software/H2MODEL_program.rar=0A=A0=0A=0A--= --------------------------------------------------------------=0AJun Zhang = (coolrainbow%yahoo.cn)=0AComputational Chemistry Group=0ANo.94, Weijinlu=0A= Nankai University =0ATianjin, China --1770247284-282649200-1341803780=:57570 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL u= sers:
 
Some times ago a= document named 'Understanding Quantum Chemistry from H2MODEL', which conta= ins
detailed description on how ab initial computati= ons of H2 are performed  was found on CCL. Now the third
<= div>edition of this document were released with some mod= ification.
 
document: = http://struchem.nankai.edu.cn/software/h2m= odel_EN.pdf
program: http://struchem.nankai.edu.cn/software/H2MODEL_program.r= ar
 
&nb= sp;
-------------------------------------------------------------= ---
Jun Zhang (coolrainbow%yahoo.cn)
Computational Chemistry GroupNo.94, Weijinlu
Nankai University
Tianjin, China
= --1770247284-282649200-1341803780=:57570-- From owner-chemistry@ccl.net Mon Jul 9 03:34:00 2012 From: "freitas s freitasrg!^!yahoo.com.br" To: CCL Subject: CCL: create slab with silanol groups in alpha quartz Message-Id: <-47182-120708235756-19604-cyn5crIZaOSk0BpA6k/20w : server.ccl.net> X-Original-From: "freitas s" Date: Sun, 8 Jul 2012 23:57:55 -0400 Sent to CCL by: "freitas s" [freitasrg%yahoo.com.br] hi how do I create a slab with the hydroxyl groups linked to silicon atom on the surface of alpha-quartz in the program CRYSTAL 06? From owner-chemistry@ccl.net Mon Jul 9 09:54:00 2012 From: "John McKelvey jmmckel:+:gmail.com" To: CCL Subject: CCL: Question Message-Id: <-47183-120709095158-3081-T5phcj/A6T2YPawOok8Fsw=-=server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 9 Jul 2012 09:51:52 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel{=}gmail.com] Hello... I'm trying to get 4 processes to run simultaneously on a 4 processor box and wait until they are all finished before proceeding. Don't have "fork" , "wait" or "sleep" available in free ftn compiler... I think I can do a "call system(cmd1&cmd2&cmd3&cmd4)" to get the 4 processes running at the same time, but I then need to wait till all 4 are finished before proceeding to the next step. I could do a "grep *.out > wclist" and check the value of wclist in an "infinite loop" until satisfied, i.e. wclist=4, but would this eat a lot of cycles? Would be happy to check out forums for this... Many thanks.. John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel(-)gmail.com From owner-chemistry@ccl.net Mon Jul 9 10:39:00 2012 From: "Billy McCann bwm0005-#-tigermail.auburn.edu" To: CCL Subject: CCL: 'Understanding Quantum Chemistry from H2MODEL' (Manual Work) Message-Id: <-47184-120709090116-24322-82IiQxsio9AdbHEaKJYeDQ .. server.ccl.net> X-Original-From: Billy McCann Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_9190392422E486449F1E15C0A122B1F10A0B5B7FSN2PRD0202MB119_" Date: Mon, 9 Jul 2012 13:00:58 +0000 MIME-Version: 1.0 Sent to CCL by: Billy McCann [bwm0005*|*tigermail.auburn.edu] --_000_9190392422E486449F1E15C0A122B1F10A0B5B7FSN2PRD0202MB119_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Very helpful. Many thanks for this contribution. +++++++++++++++++++++++++ Billy Wayne McCann Ph.D. Candidate Orlando Acevedo Reseach Auburn University, Alabama Office # =3D 334.844.6948 bwayne on irc.freenode.net +++++++++++++++++++++++++ > From: owner-chemistry+bwm0005=3D=3Dauburn.edu__ccl.net [mailto:owner-chemist= ry+bwm0005=3D=3Dauburn.edu__ccl.net] On Behalf Of Jun Zhang coolrainbow_._ya= hoo.cn Sent: Sunday, July 08, 2012 10:16 PM To: Billy McCann Subject: CCL: 'Understanding Quantum Chemistry from H2MODEL' (Manual Work) Dear CCL users: Some times ago a document named 'Understanding Quantum Chemistry from H2MOD= EL', which contains detailed description on how ab initial computations of H2 are performed wa= s found on CCL. Now the third edition of this document were released with some modification. document: http://struchem.nankai.edu.cn/software/h2model_EN.pdf program: http://struchem.nankai.edu.cn/software/H2MODEL_program.rar ---------------------------------------------------------------- Jun Zhang (coolrainbow*o*yahoo.cn) Computational Chemistry Group No.94, Weijinlu Nankai University Tianjin, China --_000_9190392422E486449F1E15C0A122B1F10A0B5B7FSN2PRD0202MB119_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

      &nb= sp;            =   

Very helpful.  Many thanks for thi= s contribution.

 

++++++++= ;+++++++++++++++= ;++

Billy Wayne McCann

Ph.D. Candidate

Orlando Acevedo Reseach

Auburn University, Alabama

Office # =3D 334.844.6948

bwayne on irc.freenode.net

++++++++= ;+++++++++++++++= ;++

 

From: owner-ch= emistry+bwm0005=3D=3Dauburn.edu__ccl.net [mailto:owner-chemistry+bwm= 0005=3D=3Dauburn.edu__ccl.net] On Behalf Of Jun Zhang coolrainbow_._yahoo.cn
Sent: Sunday, July 08, 2012 10:16 PM
To: Billy McCann
Subject: CCL: 'Understanding Quantum Chemistry from H2MODEL' (Manual= Work)

 

Dear CCL users:

 

Some times ago a document named 'Understanding Quantum Chemistry from H2= MODEL', which contains

detailed description on how ab initial computations of H2 are performed&= nbsp; was found on CCL. Now the third

edition of this document were released with some modification.

 

 

 

----------------------------------------------------------------
Jun Zhang (coolrainbow*o*yahoo.cn)
Computational Chemistry Group
No.94, Weijinlu
Nankai University
Tianjin, China

--_000_9190392422E486449F1E15C0A122B1F10A0B5B7FSN2PRD0202MB119_-- From owner-chemistry@ccl.net Mon Jul 9 13:09:00 2012 From: "Eric Scerri scerri(-)chem.ucla.edu" To: CCL Subject: CCL: another blog - This on the anomalous configuration in Cr Message-Id: <-47185-120709130358-1729-QtKyvBRBcANIkg63+rkrjA^server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-269-621452694 Date: Mon, 9 Jul 2012 10:03:09 -0700 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Eric Scerri [scerri~~chem.ucla.edu] --Apple-Mail-269-621452694 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii > Dear Colleagues, > Now a blog on the anomalous configuration in chromium and how to = explain it or perhaps how not to explain it. >=20 > >=20 > > http://ericscerri2.blogspot.com/ > >=20 > > comments welcome. > > either here or on the blogsite. > >=20 > > all the best > > eric scerri > >=20 >=20 ericscerri.com/ --Apple-Mail-269-621452694 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii

 

Dear Colleagues,
Now a blog on the anomalous configuration in chromium and how to explain it or perhaps how not to explain it.

>
> http://ericscerri2.blogspot.com/
>
> comments welcome.
> either here or on the blogsite.
>
> all the best
> eric scerri
>

ericscerri.com/

--Apple-Mail-269-621452694-- From owner-chemistry@ccl.net Mon Jul 9 13:43:00 2012 From: "Jaime Martell jaime_martell=-=cbu.ca" To: CCL Subject: CCL:G: New Blog on how NOT to teach Le Chatelier's Prtinciple Message-Id: <-47186-120709104543-15377-1kRxxUwPnFP7nSj2R5qDJA++server.ccl.net> X-Original-From: "Jaime Martell" Content-class: urn:content-classes:message Content-Type: multipart/related; type="multipart/alternative"; boundary="----_=_NextPart_001_01CD5DE1.7F13C0FE" Date: Mon, 9 Jul 2012 11:45:34 -0300 MIME-Version: 1.0 Sent to CCL by: "Jaime Martell" [jaime_martell{=}cbu.ca] This is a multi-part message in MIME format. ------_=_NextPart_001_01CD5DE1.7F13C0FE Content-Type: multipart/alternative; boundary="----_=_NextPart_002_01CD5DE1.7F13C0FE" ------_=_NextPart_002_01CD5DE1.7F13C0FE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable =20 Eric =20 The way I teach Le Chatelier's principle, and the way it is written in some textbooks, is to say that in each case, the equilibrium has been disturbed by placing a stress on the system. The resolution is to relieve this stress. In the case of temperature, I write the reaction including enthalpy as a reactant or product. In your example of an exothermic reaction, enthalpy is a product. Increasing the temperature increases the heat/enthalpy, so the logical way to relieve this stress is to remove some heat by driving the reaction in the endothermic reaction. =20 Explaining the principle in this manner makes it readily understandable to students, and I never have to change wording or make a 180 degree turn, as you try to claim. Thus I respectfully disagree with your rant, and I will continue with my successful manner in teaching this very important, very understandable principle. =20 Cheers Jaime =20 > From: owner-chemistry+jaime_martell=3D=3Dcbu.ca===ccl.net [mailto:owner-chemistry+jaime_martell=3D=3Dcbu.ca===ccl.net] On Behalf Of = Eric Scerri scerri:-:chem.ucla.edu Sent: July-07-12 11:30 AM To: Jaime Martell Subject: CCL:G: New Blog on how NOT to teach Le Chatelier's Prtinciple =20 =20 http://eric1scerri.blogspot.com/ =20 Comments welcome. =20 regards, eric scerri ________________________________________________________ =20 =20 ericscerri.com =20 On Twitter: =20 https://twitter.com/#!/ericscerri =20 =20 =20 =20 =20 =20 =20 =20 ------_=_NextPart_002_01CD5DE1.7F13C0FE Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

 

Eric

 

The way I teach Le Chatelier’s principle, and the way it is = written in some textbooks, is to say that in each case, the equilibrium = has been disturbed by placing a stress on the system.  The = resolution is to relieve this stress.  In the case of temperature, = I write the reaction including enthalpy as a reactant or product.  = In your example of an exothermic reaction, enthalpy is a product.  = Increasing the temperature increases the heat/enthalpy, so the logical = way to relieve this stress is to remove some heat by driving the = reaction in the endothermic reaction.

 

Explaining the principle in this manner makes it readily = understandable to students, and I never have to change wording or make a = 180 degree turn, as you try to claim.  Thus I respectfully disagree = with your rant, and I will continue with my successful manner in = teaching this very important, very understandable = principle.

 

Cheers

Jaime

 

From:= = owner-chemistry+jaime_martell=3D=3Dcbu.ca===ccl.net = [mailto:owner-chemistry+jaime_martell=3D=3Dcbu.ca===ccl.net] On Behalf = Of Eric Scerri scerri:-:chem.ucla.edu
Sent: July-07-12 = 11:30 AM
To: Jaime Martell
Subject: CCL:G: New Blog = on how NOT to teach Le Chatelier's = Prtinciple

 

 

 

Comments welcome.

 

regards,

eric scerri

________________________________________________________



       



<= div>

On Twitter:  

 

 

<= div>

 

 

 

 

 



=

 

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Content-Type: multipart/alternative; boundary=f46d043c062e322eb404c469559f Date: Mon, 9 Jul 2012 13:55:46 -0400 MIME-Version: 1.0 Sent to CCL by: Flick Coleman [wcoleman**wellesley.edu] --f46d043c062e322eb404c469559f Content-Type: text/plain; charset=ISO-8859-1 Here are two activities that I always have students do to disabuse them of the idea that there is something "special" or "anomalous" about Cr and Cu. 1. Find the ground state configurations for all elements in the first three transition series, and determine how many do not follow the Aufbau Principle or whatever "rules" you have previously learned. 2. Comment as completely as you can on the ground state configuration of Ni, Pd and Pt. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 On Mon, Jul 9, 2012 at 1:03 PM, Eric Scerri scerri(-)chem.ucla.edu < owner-chemistry_._ccl.net> wrote: > > > > Dear Colleagues, > Now a blog on the anomalous configuration in chromium and how to explain > it or perhaps how not to explain it. > > > > > http://ericscerri2.blogspot.com/ > > > > comments welcome. > > either here or on the blogsite. > > > > all the best > > eric scerri > > > > ericscerri.com/ > > --f46d043c062e322eb404c469559f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Here are two acti= vities that I always have students do to disabuse them of the idea that the= re is something "special" or "anomalous" about Cr and C= u.

1.=A0 Find the ground state configurations for all elements in the firs= t three transition series, and determine how many do not follow the Aufbau = Principle or whatever "rules" you have previously learned.=A0
2.=A0 Comment as completely as you can on the ground state configuratio= n of Ni, Pd and Pt.


Cheers,

Fl= ick

_______________
William F. Coleman
Profess= or of Chemistry
Wellesley College
Wellesl= ey MA 02481





On Mon, Jul 9, 2012 at 1:03 PM, Eric Sce= rri scerri(-)chem.ucla.edu <o= wner-chemistry_._ccl.net> wrote:
=A0

Dear Colleagues,
Now a blog on the anomalous configuration in chromium and how to explain it= or perhaps how not to explain it.

>
> http://= ericscerri2.blogspot.com/
>
> comments welcome.
> either here or on the blogsite.
>
> all the best
> eric scerri
>

ericscerri.com/

<= /blockquote>

--f46d043c062e322eb404c469559f-- From owner-chemistry@ccl.net Mon Jul 9 15:19:00 2012 From: "Godwin Amo-Kwao amokwao*|*gmail.com" To: CCL Subject: CCL:G: single point mp2 electron density request in Gaussian 03 Message-Id: <-47188-120709115544-6774-qJrEoFBxocpog82paPG/BQ:-:server.ccl.net> X-Original-From: Godwin Amo-Kwao Content-Type: multipart/alternative; boundary=f46d040838d30d956104c467a5f9 Date: Mon, 9 Jul 2012 09:54:56 -0600 MIME-Version: 1.0 Sent to CCL by: Godwin Amo-Kwao [amokwao#,#gmail.com] --f46d040838d30d956104c467a5f9 Content-Type: text/plain; charset=ISO-8859-1 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 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 < 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. > 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.**look > up the X-Original-From: line in the mail header. > > E-mail to subscribers: CHEMISTRY*ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use> > **> > > > > --f46d040838d30d956104c467a5f9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Th= ank you for the response to my question input on getting the mp2 electron d= ensities from a single point calculation. I tried the density=3Dcurrent but= it did not work as I wanted.=A0

For our= research I need to generate a cube file for the=A0electron=A0densities fro= m a calculation. This I am able to do easily for an optimization calculatio= n from the check point file. However there are instances where I need to=A0= change=A0the position of an atom in a=A0molecule=A0and perform a=A0single= =A0point mp2 calculation on the system. This is when I run into problems.

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

amokwao/grid> c= ubegen 0 density=3Dmp2 coinf.fchk coinf.cube=A0-1
=A0=A0-2=A0=A0 = =A0 =A0 =A0 =A0 =A00.0 =A0 =A0 =A0 =A0 0.0 =A0 =A0 =A0 =A0=A0-2=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 0.0005= 2918 =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
=A0Could not find =A0 Total MP2 Density on formatted checkpoint file.
=A0Error termination via Lnk1e at=A0+Fri Jul =A06=A0+1= 0:11:29 2012.
Segmentation fault



This is my original input f= ile
# sp mp2/6-311++G** geom=3Dallcheck density=3Dcurrent pop=3Dfull =A0IOp(=A0+6/8=3D3)

I also tried what you suggested;=A0
%chk=3Dcoinf.chk
# geom=3Dallcheck mp2/6-311++G**

Any further suggestions will be appreciated. Thank you.


Godwin Amo-Kwao
Center of Advanced=A0Research=A0Computing
University = of New Mexico
=A0
"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 c= omes short again and again, because there is no effort without error and sh= ortcoming; but who does actually strive to do the deeds; who knows great en= thusiasms, the great devotions; who spends himself in a worthy cause; who a= t 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 no= r defeat." -Theodore Roosevelt



On Thu, Jul 5, 2012 at 3:04 PM, cina for= outan canyslopus|yahoo.co.uk <o= wner-chemistry(_)ccl.net> wrote:
Hi,
<= br>
If you want to generate electron density of p= ost-HF methods you must include density=3Dcurrent keyword too.
=

Good luck,
Ci= na
=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 Forouta= n-Nejad, Ph.D.

From: Godwin Amo-Kwao amok= wao * unm.edu <owner-chemistry*ccl.net>
To: "Forouta= n-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=A0 Amo-Kwao" [= amokwao(!)unm.edu]
Hi,<= br>I am trying to generate the electron density cube file from a single poi= nt
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 erro= r
"Could not find=A0 Total MP2 Density on formatted checkpoint file. Error termination via Lnk1e at Thu Jul=A0 5 09:52:59 2012.
Segmentatio= n fault"

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

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

Thank you.



-=3D This is automatically added to eac= h message by the mailing script =3D-look up the X-Original-From: lin= e in the mail header.

E-mail to subscribers: CHEMISTRY*ccl.net or use:
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E= -mail to administrators: CHEMISTRY-REQUEST*ccl.net or use
=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

--f46d040838d30d956104c467a5f9-- From owner-chemistry@ccl.net Mon Jul 9 15:54:00 2012 From: "Laurence Cuffe cuffe]^[mac.com" To: CCL Subject: CCL: Question Message-Id: <-47189-120709133155-13945-0VWsJTv4lzsK8bcFsMsvJA##server.ccl.net> X-Original-From: Laurence Cuffe Content-transfer-encoding: 7BIT Content-type: text/plain; CHARSET=US-ASCII Date: Mon, 09 Jul 2012 18:31:44 +0100 MIME-version: 1.0 Sent to CCL by: Laurence Cuffe [cuffe:_:mac.com] John, can you ask each process to check on the others when it finishes? Then when the last process completes and cant see the others, it can get the whole operation going again. All the best, Laurence cuffe Sent from an iPad, On 9 Jul 2012, at 14:51, "John McKelvey jmmckel:+:gmail.com" wrote: > > Sent to CCL by: John McKelvey [jmmckel{=}gmail.com] > Hello... > > I'm trying to get 4 processes to run simultaneously on a 4 processor > box and wait until they are all finished before proceeding. Don't > have "fork" , "wait" or "sleep" available in free ftn compiler... > > I think I can do a "call system(cmd1&cmd2&cmd3&cmd4)" to get the 4 > processes running at the same time, but I then need to wait till all 4 > are finished before proceeding to the next step. I could do a "grep > *.out > wclist" and check the value of wclist in an "infinite loop" > until satisfied, i.e. wclist=4, but would this eat a lot of cycles? > > Would be happy to check out forums for this... > > > Many thanks.. > > John > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel ~ gmail.com> > From owner-chemistry@ccl.net Mon Jul 9 16:29:01 2012 From: "=?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= adrian.cereto,gmail.com" To: CCL Subject: CCL: Question Message-Id: <-47190-120709102529-3208-943p0lG8lT2Wmd2K5i+QEA-.-server.ccl.net> X-Original-From: =?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= Content-Type: multipart/alternative; boundary=20cf3036396366995304c4666212 Date: Mon, 9 Jul 2012 16:25:03 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= [adrian.cereto/a\gmail.com] --20cf3036396366995304c4666212 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello, So it seems you just need to run them in parallel and wait for them to complete, right? Then you don't need to launch the 4 of them and wait for them in fortran code, right? Your problem could be easily solved by using python's subprocess module, I think. Regards, Adri=C3=A0. 2012/7/9 John McKelvey jmmckel:+:gmail.com > > Sent to CCL by: John McKelvey [jmmckel{=3D}gmail.com] > Hello... > > I'm trying to get 4 processes to run simultaneously on a 4 processor > box and wait until they are all finished before proceeding. Don't > have "fork" , "wait" or "sleep" available in free ftn compiler... > > I think I can do a "call system(cmd1&cmd2&cmd3&cmd4)" to get the 4 > processes running at the same time, but I then need to wait till all 4 > are finished before proceeding to the next step. I could do a "grep > *.out > wclist" and check the value of wclist in an "infinite loop" > until satisfied, i.e. wclist=3D4, but would this eat a lot of cycles? > > Would be happy to check out forums for this... > > > Many thanks.. > > John > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel ~ gmail.com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --20cf3036396366995304c4666212 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello,

So it seems you just need to run them in parallel and wait fo= r them to complete, right?
Then you don't need to launch the 4 of th= em and wait for them in fortran code, right?
Your problem could be easil= y solved by using python's subprocess module, I think.

Regards,

Adri=C3=A0.

2012/7/9 = John McKelvey jmmckel:+:gmail.com <= owner-chemistry-,-ccl.net>

Sent to CCL by: John McKelvey [jmmckel{=3D}gmail.com]
Hello...

I'm trying to get 4 processes to run simultaneously on a 4 processor box and wait until they are all finished before proceeding. =C2=A0Don't=
have "fork" , "wait" or "sleep" available in = free ftn compiler...

I think I can do a "call system(cmd1&cmd2&cmd3&cmd4)"= to get the 4
processes running at the same time, but I then need to wait till all 4
are finished before proceeding to the next step. =C2=A0I could do a "g= rep
*.out > wclist" and check the value of wclist in an "infinite = loop"
until satisfied, i.e. wclist=3D4, but would this eat a lot of cycles?

Would be happy to check out forums for this...


Many thanks..

John



--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel ~ gmail.com



-=3D This is automatically added to each message by the mailing script =3D-=
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--20cf3036396366995304c4666212-- From owner-chemistry@ccl.net Mon Jul 9 17:47:00 2012 From: "Karen.Green]-[sanofi.com" To: CCL Subject: CCL:G: appropriate topic for computational chemistry list? RE: New Blog on how NOT to teach Le Chatelier's Prtinciple Message-Id: <-47191-120709150039-20808-xh3hOv/sIgYgiUQ1f7EwCQ-#-server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Type: multipart/related; type="multipart/alternative"; boundary="----_=_NextPart_001_01CD5E05.1AAB60B1" Date: Mon, 9 Jul 2012 12:00:27 -0700 MIME-Version: 1.0 Sent to CCL by: [Karen.Green]^[sanofi.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01CD5E05.1AAB60B1 Content-Type: multipart/alternative; boundary="----_=_NextPart_002_01CD5E05.1AAB60B1" ------_=_NextPart_002_01CD5E05.1AAB60B1 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Is this an appropriate topic for a computational chemistry mailing list? =20 > From: owner-chemistry+jaime_martell=3D=3Dcbu.ca:+:ccl.net [mailto:owner-chemistry+jaime_martell=3D=3Dcbu.ca:+:ccl.net] On Behalf = Of Eric Scerri scerri:-:chem.ucla.edu Sent: July-07-12 11:30 AM To: Jaime Martell Subject: CCL:G: New Blog on how NOT to teach Le Chatelier's Prtinciple =20 =20 http://eric1scerri.blogspot.com/ =20 Comments welcome. =20 regards, eric scerri ________________________________________________________ =20 =20 ericscerri.com =20 On Twitter: =20 https://twitter.com/#!/ericscerri =20 =20 =20 =20 =20 =20 =20 =20 ------_=_NextPart_002_01CD5E05.1AAB60B1 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable
Is this an appropriate topic for a = computational=20 chemistry mailing list?
 

From:=20 owner-chemistry+jaime_martell=3D=3Dcbu.ca:+:ccl.net=20 [mailto:owner-chemistry+jaime_martell=3D=3Dcbu.ca:+:ccl.net] On = Behalf Of=20 Eric Scerri scerri:-:chem.ucla.edu
Sent: July-07-12 11:30=20 AM
To: Jaime Martell
Subject: CCL:G: New Blog on how = NOT to=20 teach Le Chatelier's Prtinciple

 

 

http://eric1scerri.blogspot.com= /

 

Comments welcome.

 

regards,

eric = scerri

________________________________________________________



  =20     

ericscerri.com



On=20 Twitter:  

https://twitter.com/#!/ericsce= rri

 

 

 

 

 

 

 



=
<= /DIV>

 

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rK9ZGawVFE3frgtQwaU+FbLZ9fy4xYsbIBoXi0O2x6KRlPAo3XOMhEk8qty3ord8P0DQdN1WjaTX 9UMEviOoisLQETMjWQd25wE4+7e48Za6novw3pxqNnW2lO9xp/4q/wAYCHeoah5CX/h2eLH45qBq Ndm08kIJIO32XAxxjaDtPGbnqejfC0WyWD4immWpC5MixkEOoQC158u8/wDqDxYzTNbLp11s0Ubv qIlkZY5iNviICQGr3I5r0w0xbTHGqrdiQT3PPOYdj4Rk2n6+v+M9/rkHoOw9s8OZADyK7ZVEmwZD WR3J7k5FbO9gxocGj2wGpJ+z3fO4/wBMYgAOl3ECygs/icaidgGYtQLEA/l9cDIGUhy/lHoF7jMs SBJRP389KAXWxfk/tmMR3tZ2Hg9+/v7YbTRszEWoHpXri+kJMrKTxtPH4ZaaHsn1xXIaEbDxxrED uCgUQOcT18YDLJJtAYeXjv8A3y1IFVXFdsqJ+YiT6MQMkzpj0B0BNRU7T86GZSMCxRJJvtWLxcul /wD3k45peYSDzW4j5YBnSMSbgdhjKLx6kX9MLRB3bCK+fJwyEkgE3TGvliupdxKQGYW/POAARydr FmYgiq9OMrpAxvdsUeg98LqiRE5vnccBCA0jWAefXGQrP//Z ------_=_NextPart_001_01CD5E05.1AAB60B1-- From owner-chemistry@ccl.net Mon Jul 9 18:30:00 2012 From: "David Hall drhall[*]bu.edu" To: CCL Subject: CCL: Question Message-Id: <-47192-120709173118-10257-xbItW1+VDHdwJx0tg2R2Lg()server.ccl.net> X-Original-From: David Hall Content-Type: multipart/alternative; boundary=bcaec501c5c004a08104c46c5382 Date: Mon, 9 Jul 2012 17:29:55 -0400 MIME-Version: 1.0 Sent to CCL by: David Hall [drhall ~~ bu.edu] --bcaec501c5c004a08104c46c5382 Content-Type: text/plain; charset=ISO-8859-1 My favorite solution to this is to use gnu parallel https://savannah.gnu.org/projects/parallel/ parallel wrote: > > Sent to CCL by: John McKelvey [jmmckel{=}gmail.com] > Hello... > > I'm trying to get 4 processes to run simultaneously on a 4 processor > box and wait until they are all finished before proceeding. Don't > have "fork" , "wait" or "sleep" available in free ftn compiler... > > I think I can do a "call system(cmd1&cmd2&cmd3&cmd4)" to get the 4 > processes running at the same time, but I then need to wait till all 4 > are finished before proceeding to the next step. I could do a "grep > *.out > wclist" and check the value of wclist in an "infinite loop" > until satisfied, i.e. wclist=4, but would this eat a lot of cycles? > > Would be happy to check out forums for this... > > > Many thanks.. > > John > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel ~ gmail.com> > > --bcaec501c5c004a08104c46c5382 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable My favorite solution to this is to use gnu parallel


paralle= l <cmds.sh

will execute the commands in the file in parallel.

Assuming the commands are similar, you can see the man= page for ways to execute this without creating a file of commands

-David


On Mo= n, Jul 9, 2012 at 9:51 AM, John McKelvey jmmckel:+:gmail.com <owner-chemistry+/-ccl.net>= ; wrote:

Sent to CCL by: John McKelvey [jmmckel{=3D}gmail.com]
Hello...

I'm trying to get 4 processes to run simultaneously on a 4 processor box and wait until they are all finished before proceeding. =A0Don't have "fork" , "wait" or "sleep" available in = free ftn compiler...

I think I can do a "call system(cmd1&cmd2&cmd3&cmd4)"= to get the 4
processes running at the same time, but I then need to wait till all 4
are finished before proceeding to the next step. =A0I could do a "grep=
*.out > wclist" and check the value of wclist in an "infinite = loop"
until satisfied, i.e. wclist=3D4, but would this eat a lot of cycles?

Would be happy to check out forums for this...


Many thanks..

John



--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-4= 89-2160
jmmckel ~ gmail.com



-=3D This is automatically added to each message by the mailing script =3D-=
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--bcaec501c5c004a08104c46c5382-- From owner-chemistry@ccl.net Mon Jul 9 19:05:00 2012 From: "Close, David M. CLOSED^_^mail.etsu.edu" To: CCL Subject: CCL:G: single point mp2 electron density request in Gaussian 03 Message-Id: <-47193-120709171734-2042-V0oBIhF+iESIL7QqOQWP2g{:}server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_1F341F08F02C5D4B85F99C578AC133990A816FDFetsumd1etsuedu_" Date: Mon, 9 Jul 2012 21:17:15 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED]=[mail.etsu.edu] --_000_1F341F08F02C5D4B85F99C578AC133990A816FDFetsumd1etsuedu_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I had trouble with this feature last year. Part of the problem is that Gau= ssian and GaussView use different keyword for this task. For the Gaussian = calculation I would use Density=3DMP2. I was interested in spin densities,= so in Gaussview I had to specify spin=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 calcula= tion 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 mp= 2 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 -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=3Dallcheck density=3Dcurrent pop=3Dfull IOp( +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. 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 marre= d by dust and sweat and blood; who strives valiantly; who errs, who comes s= hort again and again, because there is no effort without error and shortcom= ing; but who does actually strive to do the deeds; who knows great enthusia= sms, 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 defe= at." -Theodore Roosevelt On Thu, Jul 5, 2012 at 3:04 PM, cina foroutan canyslopus|yahoo.co.uk > 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 > 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 f= ile 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. -=3D This is automatically added to each message by the mailing script =3D-=E-mail to subscribers: CHEMISTRY*ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml

I had trouble with this f= eature 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=3DMP2.  I was interested in spin densities, so in= Gaussview I had to specify spin=3DMP2 in the cubegen file.

Regards, Dave Close.=

 <= /p>

From: owner-ch= emistry+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 Gaussia= n 03

 

Thank yo= u for the response to my question input on getting the mp2 electron densiti= es from a single point calculation. I tried the density=3Dcurrent but it did not work as I wanted. 

=  

=

=  

=  

-1

-2   &nbs= p;        0.0         0.0   &n= bsp;     -2 .= 6459

=  

= And this is the error generated.

=  

+Fri Jul  6 +10:11= :29 2012.

=  

=  

= This is my original input file

= # sp mp2/6-311++G** geom=3Dallcheck density=3Dcurrent pop=3Dfull &n= bsp;IOp( = ;+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.

=  

 

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; w= ho errs, who comes short again and again, because there is no effort withou= t 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 canysl= opus|yahoo.co.uk <owner-chemistry ~ ccl.net> wrote:

Hi,

 

If you want to generate electron density of post-HF= methods you must include density=3Dcurrent keyword too.<= /p>

 

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.

 

From: Godwin Amo-Kwao amokwao * unm.edu <owner-chemistr= y*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 Gaussia= n 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 f= ile
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.<= br> 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.


-=3D This is automatically added to each message by = the mailing script =3D-look up the X-Original-From: line in the mail header= .

E-mail to subscribers: CHEMISTRY*ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

 

--_000_1F341F08F02C5D4B85F99C578AC133990A816FDFetsumd1etsuedu_-- From owner-chemistry@ccl.net Mon Jul 9 23:21:01 2012 From: "uekstrom-#-gmail.com uekstrom-#-gmail.com" To: CCL Subject: CCL: Question Message-Id: <-47194-120709165909-21714-R0uJMP4+b0vJ5UAmDkAhgw .. server.ccl.net> X-Original-From: "uekstrom---gmail.com" Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 9 Jul 2012 22:58:59 +0200 MIME-Version: 1.0 Sent to CCL by: "uekstrom],[gmail.com" [uekstrom],[gmail.com] > Don't > have "fork" , "wait" or "sleep" available in free ftn compiler... You can make C->Fortran wrappers easily. > I think I can do a "call system(cmd1&cmd2&cmd3&cmd4)" to get the 4 > processes running at the same time, but I then need to wait till all 4 > are finished before proceeding to the next step. Add a ;wait at the end. Ulf Ekstrom, University of Oslo