From owner-chemistry@ccl.net Fri Feb 11 08:07:01 2011 From: "Simone Marocchi simone.roz*gmail.com" To: CCL Subject: CCL: software to display all orbitals taken from an output of NWCHEM Message-Id: <-43934-110211061534-20551-in8UpaX1aKOTbTmdl7tGDw-.-server.ccl.net> X-Original-From: "Simone Marocchi" Date: Fri, 11 Feb 2011 06:15:32 -0500 Sent to CCL by: "Simone Marocchi" [simone.roz,gmail.com] Hello everyone, my name's Simone and I am a PhD student. I'm using NWCHEM, and I don't know what software (maybe molden or molekel, etc.) I can use for to visualize the electric density of the orbitals from a *.nwo file. So far the only thing I could do was to plot the electron density of a single orbital on a *.cube file (using some NWCHEM subroutine) and then view it using molekel. Sorry for this silly question But I didn't find any questions related to this in the CCL archives. Thanks in advance for your help. Best regards, Simone From owner-chemistry@ccl.net Fri Feb 11 10:54:00 2011 From: "Patrick McCarren patrick.mccarren() gmail.com" To: CCL Subject: CCL: WebMO user interface: Possible to read checkfiles? Message-Id: <-43935-110211104814-31770-caMxUKXQUELKTmESORtyLQ|-|server.ccl.net> X-Original-From: Patrick McCarren Content-Type: multipart/alternative; boundary=000e0cd34296d87730049c039f16 Date: Fri, 11 Feb 2011 10:48:07 -0500 MIME-Version: 1.0 Sent to CCL by: Patrick McCarren [patrick.mccarren,gmail.com] --000e0cd34296d87730049c039f16 Content-Type: text/plain; charset=ISO-8859-1 It reads partial files too, so you can look at the job while it is running or truncate the file. Patrick On Thu, Feb 10, 2011 at 5:02 PM, Michael Banck michael.banck],[ch.tum.de < owner-chemistry]*[ccl.net> wrote: > > Sent to CCL by: Michael Banck [michael.banck+*+ch.tum.de] > On Tue, Feb 08, 2011 at 01:33:30AM -0500, Patrick Mccarren > patrick.mccarren#%#gmail.com wrote: > > Molden is a great visualizer to keep track of a job. You get the > > energy graphs and visualization of the molecule at each step. The > > graphics aren't fancy but it is extremely fast and great for slow X11 > > connections. > > As far as I know, this visualization is after the fact though, isn't it? > I.e., you can step through a finished compute job and view each step, > but you cannot monitor a computation as it runs, right? > > > Michael> > > --000e0cd34296d87730049c039f16 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable It reads partial files too, so you can look at the job while it is running = or truncate the file.

Patrick

On = Thu, Feb 10, 2011 at 5:02 PM, Michael Banck michael.banck],[ch.tum.de <owner-chemistry]*[ccl.net> wrote:

Sent to CCL by: Michael Banck [michael.banck+*+ch.tum.de]
On Tue, Feb 08, 2011 at 01:33:30AM -0500, Patrick Mccarren patrick.mccarren= #%#gmail.com wrote:
> Molden is a great visualizer to keep track of a job. =A0You get the > energy graphs and visualization of the molecule at each step. =A0The > graphics aren't fancy but it is extremely fast and great for slow = X11
> connections.

As far as I know, this visualization is after the fact though, isn't it= ?
I.e., you can step through a finished compute job and view each step,
but you cannot monitor a computation as it runs, right?


Michael



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--000e0cd34296d87730049c039f16-- From owner-chemistry@ccl.net Fri Feb 11 12:31:00 2011 From: "Olasunkanmi Lukman Olawale walecomuk+*+yahoo.co.uk" To: CCL Subject: CCL: dissenting results Message-Id: <-43936-110211104914-32549-kpuxACbBAwFSloVFhEhSwQ ~ server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="0-1217240208-1297439325=:44250" Date: Fri, 11 Feb 2011 15:48:45 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk*o*yahoo.co.uk] --0-1217240208-1297439325=:44250 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable \a/Victor Rosas.=0AThank you for your help. Do you mean if I use a well suita= ble optimizer the =0AGradient Norm will not be as high as I have gotten usi= ng EF? Anyway I will try =0Athat and let you know what happen. I wouldn't l= ike to use "TS" because I intend =0Ato compute for the ground states. Or do= you think using "TS" would not have =0Aeffect on Ground State calculations= ?=0AThanks.=0A=0A Olasunkanmi Lukman Olawale=0A____________________________= ____=0ACurrent Address:=0ADepartment of Chemistry,=0AObafemi Awolowo Univer= sity,=0AIle-Ife, Osun State.=0ANigeria.=0A=0A+234-0-80-52401564 Or +234-0-8= 0-67161091=0A________________________________=0A =0A=0A=0A=0A=0A___________= _____________________=0AFrom: Victor Rosas Garcia rosas.victor _ gmail.com = =0ATo: "Olasunkanmi, Olawale Lukman " =0ASent: Tue, 8 February, 2011 16:53:53=0ASubject: CCL: = dissenting results=0A=0AJust do what the error message says "REDUCE GRADIEN= T USING 'TS' OR OTHER =0AGEOMETRY OPTIMIZER". You should make sure you are= using PRECISE and maybe try =0Athe different optimizers. The default is "E= F", but you can try BFGS or DFP. See =0Awhich one works best.=0A=0AI wouldn= 't worry too much about the different heats of formation because the =0Ageo= metry is essentially unconverged, so none of those numbers means much anywa= y.=0A=0AHope this helps.=0A=0AHave a nice day!=0A=0AVictor=0A=0A=0A2011/2/7= Olasunkanmi Lukman Olawale walecomuk(a)yahoo.co.uk =0A=0A=0AThank you Victor. I got your explanation but something still b= affles me.=0A>If I run the MOPAC job without the THERMO key word I will get= some parameters: =0A>e.g. final heat of formation, total energy, electroni= c energy etc. =0A>=0A>But, with THERMO key word, most often I experience th= is kind of warning/error:=0A>** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX= TO BE CALCULATED, (LIMIT=3D10) **=0A> EITHER ADD 'LET' OR REDUCE GRADIENT= =0A> USING 'TS' OR OTHER GEOMETRY OPTIMIZER=0A>=0A>It will however give a v= alue for the heat of formation again, this time around =0A>somehow differen= t from the former value. A typical case for 1,10-phenanthroline:=0A> FINAL = HEAT OF FORMATION =3D 81.10951 KCAL/MOL =3D 339.36220 KJ/MOL=0A>without u= sing the THERMO keyword.=0A>=0A>AND=0A>=0A>HEAT OF FORMATION =3D 89.3= 98345 KCALS/MOLE=0A>when the THERMO keyword was used.=0A>So what do you sug= gest I do?=0A>=0A> Olasunkanmi Lukman Olawale=0A>__________________________= ______=0A Current Address:=0A>Department of Chemistry,=0A>Obafemi Awolowo U= niversity,=0A>Ile-Ife, Osun State.=0A>Nigeria.=0A>=0A>+234-0-80-52401564 Or= +234-0-80-67161091=0A>________________________________=0A =0A>=0A>=0A>=0A>= =0A>=0A________________________________=0AFrom: Victor Rosas Garcia rosas.v= ictor*gmail.com =0A>To: "Olasunkanmi, Olawale Lu= kman " =0A>Sent: Fri, 4 February, 2011 13:53:11=0A= >Subject: CCL: dissenting results=0A>=0A>GNORM =3D 109.40376?=0A> =0A>That = is *huge*. How did you get such a specific number, by the way?=0A>=0A>Any= way, you should be careful with the use of LET. From the manual =0A>(http:= //www.openmopac.net/manual/index.html):=0A>=0A> Now LET means essentiall= y "I know what I'm doing, override safety checks".=0A> Currently, LET ha= s the following meanings:=0A> 1.In a FORCE calculation, it means that th= e supplied geometry is to be used, =0A>even if the gradients are large.So y= ou are giving MOPAC a geometry that is not =0A>converged, and telling it to= do THERMO no matter what. You could try doing the =0A>optimization using = PRECISE and then do the FORCE calc without LET and GNORM.=0A>=0A>The manual= is your friend! =0A>=0A>Hope this helps and have a nice day=0A>=0A>Victor= =0A>=0A>2011/2/3 Lukman Olawale Olasunkanmi waleolasunkanmi=3D=3D=3Dgmail.c= om =0A>=0A>=0A>Thank you.=0A>>Here are typical re= sults:=0A>>After geometry optimization without any special keyword:=0A>>FIN= AL HEAT OF FORMATION =3D 40.08240 KCAL/MOL =0A>>=0A>>With keyword "thermo"= , and LET GNORM =3D 109.40376=0A>>=0A>>HEAT OF FORMATION =3D 43.366029= KCALS/MOLE=0A>>=0A>>Sometimes the difference may be up to 10kcal/mol for s= ome calculations. =0A>>Kindly give me an advice on it.=0A>>thanks.=0A>>=0A>= >=0A>>wrote:=0A>>=0A>>=0A>>>Sent to CCL by: "Close, David M." [CLOSED!A!mai= l.etsu.edu]=0A>>>This is very interesting. But you need to tell us how muc= h the numbers differ. =0A>>> I can see how sometimes very small difference = could arise from coding errors =0A>>>arising from one subroutine using a do= uble precision variable, and another =0A>>>subroutine using the same variab= le with a different word-length. But these =0A>>>would be very small diffe= rences. Give us an example of how big the differences =0A>>>are, and what = keywords are used to control the accuracy of each SCF cycle.=0A>>> Regards,= Dave Close.=0A>>>=0A>>>-----Original Message-----=0A>>>> From: owner-chemi= stry+closed=3D=3Detsu.edu-$-ccl.net =0A>>>>[mailto:owner-chemistry+closed= =3D=3Detsu.edu-$-ccl.net] On Behalf Of Lukman Olawale =0A>>>>Olasunkanm wal= eolasunkanmi:gmail.com=0A>>>Sent: Tuesday, February 01, 2011 8:43 AM=0A>>>T= o: Close, David M.=0A>>>Subject: CCL: dissenting results=0A>>>=0A>>>=0A>>>S= ent to CCL by: "Lukman Olawale Olasunkanm" [waleolasunkanmi#,#gmail.com]=0A= >>>Hello everyone,=0A>>>I usually run my MOPAC job twice: first for ordinar= y optimization from which I =0A>>>normally get the GNORM value ( and H.O.F.= , dipole moments, HOMO-LUMO, COSMOS =0A>>>Area and volume etc.), and second= for the thermo values (with the specified =0A>>>value of the GNORM using t= he LET keyword). I discovered that the values got for =0A>>>the common para= meters like H.O.F, dipole moments etc. in both cases differ.=0A>>>What can = you advise me to do please?=0A>>>Thank =0A>>>youhttp://www.ccl.net/cgi-bin/= ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.= ccl.net/spammers.txt=0A>>>=0A>>>=0A>>>=0A>>>-=3D This is automatically adde= d to each message by the mailing script =3D- =0A>>>E-mail to subscribers: C= HEMISTRY-x-ccl.net or use:=0A>>> http://www.ccl.net/cgi-bin/ccl/send_cc= l_message=0A>>>=0A>>>E-mail to administrators: CHEMISTRY-REQUEST-x-ccl.net = or use=0A=0A>>>=0A>>= >Subscribe/Unsubscribe:=0A>>> http://www.ccl.net/chemistry/sub_unsub.sh= tml=0A>>>=0A=0A>>>= =0A>>>Job: http://www.ccl.net/jobs=0A>>>Conferences: http://server.ccl.net/= chemistry/announcements/conferences/=0A>>>=0A>>>Search Messages: http://www= .ccl.net/chemistry/searchccl/index.shtml=0A>>> http://www.ccl.net/spamm= ers.txt=0A>>>=0A>>>RTFI: http://www.ccl.net/chemistry/aboutccl/instructions= /=0A>>>=0A>>>=0A>>>=0A>>=0A>>=0A>>-- =0A>>Olasunkanmi Lukman Olawale=0A>>= =0A>>Department of Chemistry,=0A>>Obafemi Awolowo University,=0A>>Ile-Ife, = Nigeria.=0A>>+234-08052401564=0A>>=0A>>"Improving our own attitudes and our= own state of mind takes time. Haste and =0A>>impatience can only defeat ou= r purposes."=0A>>=0A>>=0A>=0A>=0A=0A=0A=0A --0-1217240208-1297439325=:44250 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
\a/Victor Rosas.
Thank you for your help. Do you mean if I us= e a well suitable optimizer the Gradient Norm will not be as high as I have= gotten using EF? Anyway I will try that and let you know what happen. I wo= uldn't like to use "TS" because I intend to compute for the ground states. = Or do you think using "TS" would not have effect on Ground State calculatio= ns?
Thanks.
 
Olasunkanmi Lukman Olawale

Current Address:
Department= of Chemistry,
Obafemi Awolowo University,

= Ile-Ife, Osun Sta= te.
Nigeria.
+234-0-80-52401564 Or +234-0-80-67161091
=


<= div style=3D"font-family: times new roman,new york,times,serif; font-size: = 12pt;">
From: Victor Rosas Garcia rosas.victor _ gmail= .com <owner-chemistry\a/ccl.net>
T= o: "Olasunkanmi, Olawale Lukman " <walecomuk\a/yahoo.co= .uk>
Sent: Tue, 8 Fe= bruary, 2011 16:53:53
Subject: CCL: dissenting results

Just do what the error message says "REDUCE = GRADIENT USING 'TS' OR OTHER GEOMETRY OPTIMIZER".  You should make sur= e you are using PRECISE and maybe try the different optimizers. The default= is "EF", but you can try BFGS or DFP. See which one works best.
=0A
= I wouldn't worry too much about the different heats of formation because th= e geometry is essentially unconverged, so none of those numbers means much = anyway.

Hope this helps.

Have a nice day!

=0AVictor
2011/2/7 Olasunkanmi Lukman Olawale walecom= uk(a)yaho= o.co.uk <owner-chemistry,+,ccl.net>
=0A
Thank you Victor. I g= ot your explanation but something still baffles me.
=0AIf I run the MOPA= C job without the THERMO key word I will get some parameters: e.g. final he= at of formation, total energy, electronic energy etc.
But, with THERMO = key word, most often I experience this kind of warning/error:
=0A** GRAD= IENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED, (LIMIT=3D10) ** EITHER ADD 'LET' OR REDUCE GRADIENT
 USING 'TS' OR OTHER GE= OMETRY OPTIMIZER

It will however give a value for the heat of format= ion again, this time around somehow different from the former value. A typi= cal case for 1,10-phenanthroline:
=0A FINAL HEAT OF FORMATION =3D&n= bsp;  81.10951 KCAL/MOL =3D 339.36220 KJ/MOL
without using the THER= MO keyword.

AND

HEAT OF FORMATION=0A =3D   &nb= sp;  89.398345 KCALS/MOLE
when the THERMO keyword was used.
So w= hat do you suggest I do?

 Olasunkanmi Lukman Olawale

=0ACurrent Ad= dress:
= Department of Chemistry,
Obafe= mi Awolowo University,
=0AIle-= Ife, Osun State.
Nigeria.
=0A
234-0-80-52401564 Or +234-0-80-67161= 091
=0A

=0A
From: Victor Rosas Gar= cia rosas.victor*gmail.com <owner-chemistry]|[ccl.net>
=0ATo: "Olasunkanmi, Olawale Lukman " <walecomuk]|= [yahoo.co= .uk>
Sent: Fri, = 4 February, 2011 13:53:11
=0ASubje= ct: CCL: dissenting results

GNORM =3D 109.40376? 
That is=0A *huge*.  How did you get such a specific number= , by the way?

Anyway, you should be careful with the use of LET.&nbs= p; From the manual (http://www.openmopac.net/manual/index.ht= ml):
=0A=0A

    Now LET means essentially = "I know what I'm doing, override safety checks".

=0A

   = ; Currently, LET has the following meanings:

=0A
 &= nbsp;  1.In a FORCE calculation, it means = that the supplied geometry is to be used, even if the gradients are large.<= /dt>=0A
So you are giving MOPAC a geometry that is not converged, and t= elling it to do THERMO no matter what.  You could try doing the optimi= zation using PRECISE and then do the FORCE calc without LET and GNORM.
= =0A
The manual is your friend!

Hope this helps and have a nice d= ay

Victor

2011/2/3 Lukman Olawale Olasunkanmi waleolasunkanmi= =3D=3D=3Dgm= ail.com <owner-chemistry**ccl.net>
=0A=0A
Thank you= .
Here are typical results:
After geometry optimization without any s= pecial keyword:
=0A=0AFINAL HEAT OF FORMATION =3D  40.08240 KCAL/MO= L

With keyword "thermo", and LET GNORM =3D 109.40376

=0AHEAT= OF FORMATION =3D      43.366029 KCALS/MOLE
Sometimes the difference may be up to 10kcal/mol for some calculations. Kindly give me an advice on it.
thanks.


wrote:
=0A=0A=0A
=0ASent to CCL by: "Close, David M." [CLOSED!A!mail.etsu.edu]=0AThis is very interesting.  But you need to tell us how much the nu= mbers differ.  I can see how sometimes very small difference could ari= se from coding errors arising from one subroutine using a double precision = variable, and another subroutine using the same variable with a different w= ord-length.  But these would be very small differences.  Give us = an example of how big the differences are, and what keywords are used to co= ntrol the accuracy of each SCF cycle.
=0A=0A=0A=0A  Regards, Dave C= lose.
=0A
=0A-----Original Message-----
=0A> From: owner-chemis= try+closed=3D=3Detsu.edu-$-ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu-$-ccl.net] On Behalf Of Lukman Olawa= le Olasunkanm waleolasunkanmi:gmail.com
=0A=0A=0A=0ASent: Tuesday, February 01,= 2011 8:43 AM
=0ATo: Close, David M.
=0ASubject: CCL: dissenting resu= lts
=0A
=0A
=0ASent to CCL by: "Lukman Olawale Olasunkanm" [waleol= asunkanmi#,#gmail.com]
=0AHello everyone,
=0AI usually run my MOPAC job twic= e: first for ordinary optimization from which I normally get the GNORM valu= e ( and H.O.F., dipole moments, HOMO-LUMO, COSMOS Area and volume etc.), an= d second for the thermo values (with the specified value of the GNORM using= the LET keyword). I discovered that the values got for the common paramete= rs like H.O.F, dipole moments etc. in both cases differ.
=0A=0A=0A=0AWha= t can you advise me to do please?
=0AThank youhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_u= nsub.shtmlhttp://www.ccl.net/spammers.txt
=0A=0A=0A=0A
=0A
=0A= -=3D This is automatically added to each message by the mailing script =3D-= =0A
=0AE-mail to subscribers: CHEM= ISTRY-x-ccl.net or use:
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=0ARTFI= : http://www.ccl.net/chemistry/aboutccl/instruction= s/
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=0A



-- =
Olasunkanmi Lukman Olawale

Department of Chemistry,
Obafemi Awolowo Uni= versity,
=0A=0A=0AIle-Ife, Nigeria.

+234-08= 052401564

"Improving our own attitudes and our own state of mind takes time. Haste= and impatience can only defeat our purposes."
=0A=0A=0A
= =0A

=0A
=0A

=0A=0A=0A=0A

=0A
=0A
=0A=0A=0A --0-1217240208-1297439325=:44250-- From owner-chemistry@ccl.net Fri Feb 11 16:56:00 2011 From: "Jose P. Ceron jpceron^um.es" To: CCL Subject: CCL:G: solvent Message-Id: <-43937-110211165311-13012-Xepe/52SZEji7/uTnHkX+A.:.server.ccl.net> X-Original-From: "Jose P. Ceron" Date: Fri, 11 Feb 2011 16:53:09 -0500 Sent to CCL by: "Jose P. Ceron" [jpceron]![um.es] Dear Mahshid, In the case of PCM you should include scrf keyword as follows: # scrf=(pcm,solvent=X) where X is the selected solvent: X=n,n-DiMethylFormamide for dmf. Please, go to www.gaussian.com/g_tech/g_ur/k_scrf.htm for further information, examples and the list of defined solvents in Gaussian. Best, Jose Sent to CCL by: "MAHSHID - SABERINASAB" [saberinasabmahshid . yahoo.com] Hi all, I've sent massages for you several times,buttill nowI didn't reseave any answetrs.in the case of opting som input files via solvent method(PCM)I facewith some problems.about that solvent such as dmf which isnot mentioned in the calculation part of gauss view,how should I run its input in a way I don't resaev any error massage?would you mind helping me in this case? in advanse thanks for your attention regards M.Saberinasab