From owner-chemistry@ccl.net Fri Dec 1 20:11:01 2017
From: "Igors Mihailovs igorsm(_)cfi.lu.lv" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian 09W program was freezing during the processing
Message-Id: <-53081-171201032753-19890-ozEdaGp5dsdpW/N1T3UIQA]~[server.ccl.net>
X-Original-From: Igors Mihailovs <igorsm]*[cfi.lu.lv>
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Dear Morad,
What exactly do You mean by freezing? Is CPU still busy (see e.g. /Task
Manager/)?
When I had problems with launching /Gaussian/ on some elderly server
station (but also with /Intel Xeon/ CPU, /64-bit Intel® Xeon® Processor
3.20 GHz, 2M Cache, 800 MHz FS//B/), I had this error message:
Error: illegal instruction, illegal opcode
This certainly means there is a problem with CPU instructions, i.e.,
/Gaussian/ is not compiled on a similar system. Do You see any error
messages if You launch /Gaussian/ from /Wind//ows Command Prompt/?
It can also be helpful if Your Route section began with #P rather than
just # – then we could have seen more specifically when the error happens.
With best intentions,
Igors Mihailovs
Research assistant
ISSP ULatvia
On 28/11/17 18:49, Morad El-Hendawy morad.elhendawy^_^yahoo.com wrote:
> Sent to CCL by: "Morad El-Hendawy" [morad.elhendawy-,-yahoo.com]
> Dear CCLers,
>
> Recently we bought a server with Intel Xeon Processor E5-2698 v4 then
> installed Windows Server 2008 (64 bit) operating system. We installed
> Gaussian 09W program properly and tested methane molecule for single
> point energy calculation but the program stopped at two electron integral
> calculations stage. Although PM6 was used for computation but the
> program was freezing. Herein, you can see the output.
>
> Gaussian 09: IA32W-G09RevA.02 11-Jun-2009
> 27-Nov-2017
> ******************************************
> -----------------------
> # pm6 geom=connectivity
> -----------------------
> 1/38=1,57=2/1;
> 2/12=2,17=6,18=5,40=1/2;
> 3/5=2,16=1,25=1,41=3900000/1,2,3;
> 4/35=1/1;
> 5/5=2,35=1,38=5/2;
> 6/7=2,8=2,9=2,10=2,28=1/1;
> 99/5=1,9=1/99;
> -------------------
> Title Card Required
> -------------------
> Symbolic Z-matrix:
> Charge = 0 Multiplicity = 1
> C 0.46908 0.2234 -0.01464
> H 0.82574 -0.78541 -0.01464
> H 0.82576 0.7278 0.85901
> H 0.82576 0.7278 -0.88829
> H -0.60092 0.22341 -0.01464
>
> Input orientation:
> ---------------------------------------------------------------------
> Center Atomic Atomic Coordinates (Angstroms)
> Number Number Type X Y Z
> ---------------------------------------------------------------------
> 1 6 0 0.469083 0.223401 -0.014643
> 2 1 0 0.825738 -0.785409 -0.014643
> 3 1 0 0.825756 0.727799 0.859009
> 4 1 0 0.825756 0.727799 -0.888294
> 5 1 0 -0.600917 0.223414 -0.014643
> ---------------------------------------------------------------------
> Distance matrix (angstroms):
> 1 2 3 4 5
> 1 C 0.000000
> 2 H 1.070000 0.000000
> 3 H 1.070000 1.747302 0.000000
> 4 H 1.070000 1.747302 1.747303 0.000000
> 5 H 1.070000 1.747303 1.747303 1.747303 0.000000
> Stoichiometry CH4
> Framework group T[O(C),4C3(H)]
> Deg. of freedom 1
> Full point group T NOp 12
> Largest Abelian subgroup D2 NOp 4
> Largest concise Abelian subgroup D2 NOp 4
> Standard orientation:
> ---------------------------------------------------------------------
> Center Atomic Atomic Coordinates (Angstroms)
> Number Number Type X Y Z
> ---------------------------------------------------------------------
> 1 6 0 0.000000 0.000000 0.000000
> 2 1 0 0.617765 0.617765 0.617765
> 3 1 0 -0.617765 -0.617765 0.617765
> 4 1 0 -0.617765 0.617765 -0.617765
> 5 1 0 0.617765 -0.617765 -0.617765
> ---------------------------------------------------------------------
> Rotational constants (GHZ): 164.2463785 164.2463785 164.2463785
> Standard basis: VSTO-6G (5D, 7F)
> There are 2 symmetry adapted basis functions of A symmetry.
> There are 2 symmetry adapted basis functions of B1 symmetry.
> There are 2 symmetry adapted basis functions of B2 symmetry.
> There are 2 symmetry adapted basis functions of B3 symmetry.
> Integral buffers will be 262144 words long.
> Regular integral format.
> Two-electron integral symmetry is turned off.
> 8 basis functions, 48 primitive gaussians, 8 cartesian basis
> functions
> 4 alpha electrons 4 beta electrons
> nuclear repulsion energy 14.5519821625 Hartrees.
> Do NDO integrals.
> One-electron integrals computed using PRISM.
> NBasis= 8 RedAO= F NBF= 2 2 2 2
> NBsUse= 8 1.00D-04 NBFU= 2 2 2 2
>
>
> The question: Is G09RevA.02 is not compiled with Windows Server 2008
> and/or server hardware?
> Any help please?
>
>
>
> Morad El-Hendawy, Ph.D.
> Assiut University, Egypt
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<font face="Liberation Sans">Dear Morad,</font><br>
<br>
<font face="Liberation Sans"> What exactly do You mean by freezing?
Is CPU still busy (see e.g. <i>Task Manager</i>)?</font><br>
<font face="Liberation Sans"> </font><br>
<font face="Liberation Sans"> When I had problems with launching <i>Gaussian</i>
on some elderly server station (but also with <i>Intel Xeon</i>
CPU, <i>64-bit Intel® Xeon® Processor 3.20 GHz, 2M Cache, 800 MHz
FS</i><i>B</i>), I had this error message:</font><br>
<font face="Liberation Sans"> </font><br>
<font face="Liberation Sans"> </font><tt>Error: illegal
instruction, illegal opcode</tt><br>
<font face="Liberation Sans"> </font><br>
<font face="Liberation Sans"> This certainly means there is a
problem with CPU instructions, i.e., <i>Gaussian</i> is not
compiled on a similar system. Do You see any error messages if You
launch <i>Gaussian</i> from <i>Wind</i><i>ows Command Prompt</i>?</font><br>
<font face="Liberation Sans"> </font><br>
<font face="Liberation Sans"> It can also be helpful if Your Route
section began with #P rather than just # – then we could have seen
more specifically when the error happens.</font><br>
<font face="Liberation Sans"> </font><br>
<font face="Liberation Sans"> With best intentions,</font><br>
<font face="Liberation Sans"> Igors Mihailovs</font><br>
<font face="Liberation Sans"> Research assistant</font><br>
<font face="Liberation Sans"> ISSP ULatvia</font><br>
<font face="Liberation Sans"> </font><br>
<div class="moz-cite-prefix">On 28/11/17 18:49, Morad El-Hendawy
morad.elhendawy^_^yahoo.com wrote:<br>
</div>
<blockquote type="cite"
cite="mid:5ce96ba3-815c-b7f2-6e09-90a2359ea6c8]=[cfi.lu.lv">
<pre wrap="">Sent to CCL by: "Morad El-Hendawy" [morad.elhendawy-,-yahoo.com]
Dear CCLers,
Recently we bought a server with Intel Xeon Processor E5-2698 v4 then
installed Windows Server 2008 (64 bit) operating system. We installed
Gaussian 09W program properly and tested methane molecule for single
point energy calculation but the program stopped at two electron integral
calculations stage. Although PM6 was used for computation but the
program was freezing. Herein, you can see the output.
Gaussian 09: IA32W-G09RevA.02 11-Jun-2009
27-Nov-2017
******************************************
-----------------------
# pm6 geom=connectivity
-----------------------
1/38=1,57=2/1;
2/12=2,17=6,18=5,40=1/2;
3/5=2,16=1,25=1,41=3900000/1,2,3;
4/35=1/1;
5/5=2,35=1,38=5/2;
6/7=2,8=2,9=2,10=2,28=1/1;
99/5=1,9=1/99;
-------------------
Title Card Required
-------------------
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
C 0.46908 0.2234 -0.01464
H 0.82574 -0.78541 -0.01464
H 0.82576 0.7278 0.85901
H 0.82576 0.7278 -0.88829
H -0.60092 0.22341 -0.01464
Input orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 6 0 0.469083 0.223401 -0.014643
2 1 0 0.825738 -0.785409 -0.014643
3 1 0 0.825756 0.727799 0.859009
4 1 0 0.825756 0.727799 -0.888294
5 1 0 -0.600917 0.223414 -0.014643
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3 4 5
1 C 0.000000
2 H 1.070000 0.000000
3 H 1.070000 1.747302 0.000000
4 H 1.070000 1.747302 1.747303 0.000000
5 H 1.070000 1.747303 1.747303 1.747303 0.000000
Stoichiometry CH4
Framework group T[O(C),4C3(H)]
Deg. of freedom 1
Full point group T NOp 12
Largest Abelian subgroup D2 NOp 4
Largest concise Abelian subgroup D2 NOp 4
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 6 0 0.000000 0.000000 0.000000
2 1 0 0.617765 0.617765 0.617765
3 1 0 -0.617765 -0.617765 0.617765
4 1 0 -0.617765 0.617765 -0.617765
5 1 0 0.617765 -0.617765 -0.617765
---------------------------------------------------------------------
Rotational constants (GHZ): 164.2463785 164.2463785 164.2463785
Standard basis: VSTO-6G (5D, 7F)
There are 2 symmetry adapted basis functions of A symmetry.
There are 2 symmetry adapted basis functions of B1 symmetry.
There are 2 symmetry adapted basis functions of B2 symmetry.
There are 2 symmetry adapted basis functions of B3 symmetry.
Integral buffers will be 262144 words long.
Regular integral format.
Two-electron integral symmetry is turned off.
8 basis functions, 48 primitive gaussians, 8 cartesian basis
functions
4 alpha electrons 4 beta electrons
nuclear repulsion energy 14.5519821625 Hartrees.
Do NDO integrals.
One-electron integrals computed using PRISM.
NBasis= 8 RedAO= F NBF= 2 2 2 2
NBsUse= 8 1.00D-04 NBFU= 2 2 2 2
The question: Is G09RevA.02 is not compiled with Windows Server 2008
and/or server hardware?
Any help please?
Morad El-Hendawy, Ph.D.
Assiut University, Egypt
</pre>
</blockquote>
</body>
</html>
--------------FB1BDE2EA7DD190BA855AC54--
From owner-chemistry@ccl.net Fri Dec 1 20:46:00 2017
From: "Jan Jensen compchemhighlights * gmail.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry Highlight: November issue
Message-Id: <-53082-171201035817-31205-anyacX30wX9BVcu1ODuwWA%%server.ccl.net>
X-Original-From: Jan Jensen <compchemhighlights-*-gmail.com>
Content-Type: multipart/alternative; boundary="001a11452ce0783b65055f439101"
Date: Fri, 1 Dec 2017 09:58:11 +0100
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Sent to CCL by: Jan Jensen [compchemhighlights===gmail.com]
--001a11452ce0783b65055f439101
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The November issue of Computational Chemistry Highlights
<http://www.compchemhighlights.org/2017_11_01_archive.html> is out.
CCH is an overlay journal <http://en.wikipedia.org/wiki/Overlay_journal> that
identifies the most important papers in computational and theoretical
chemistry published in the last 1-2 years. CCH is not affiliated with any
publisher: it is a free resource run by scientists for scientists. You can
read more about it here
<http://proteinsandwavefunctions.blogspot.com/2012/02/computational-chemistry-highlights-new.html>
.
Table of content for this issue features contributions from Steven Bachrach
and Jan Jensen:
Understanding and Breaking Scaling Relations in Single-Site Catalysis:
Methane-to-methanol Conversion by Fe(IV)=O
<http://www.compchemhighlights.org/2017/11/understanding-and-breaking-scaling.html>
Tunneling Control of Chemical Reactions: The Third Reactivity Paradigm
<http://www.compchemhighlights.org/2017/11/tunneling-control-of-chemical-reactions.html>
The Cope Rearrangement of 1,5-Dimethylsemibullvalene-2(4)-d1: Experimental
Evidence for Heavy-Atom Tunneling
<http://www.compchemhighlights.org/2017/11/the-cope-rearrangement-of-15.html>
Interested in contributing? Read more here
<http://www.compchemhighlights.org/2017/04/new-cch-contributors-wanted.html>
Interested in more? There are many ways to subscribe to CCH updates
<http://www.compchemhighlights.org/p/get-cch-updates.html>.
Also, for your daily computational chemistry fix subscribe to Computational
Chemistry Daily <https://paper.li/janhjensen/1416314690>
--001a11452ce0783b65055f439101
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<div dir=3D"ltr"><p style=3D"margin:0px;color:rgb(0,0,0);font-family:Times;=
font-size:medium;font-variant-ligatures:normal">The November issue of=C2=A0=
<a href=3D"http://www.compchemhighlights.org/2017_11_01_archive.html">Compu=
tational Chemistry Highlights</a>=C2=A0is out.</p><p style=3D"margin:0px;co=
lor:rgb(0,0,0);font-family:Times;font-size:medium;font-variant-ligatures:no=
rmal"><br></p><p style=3D"margin:0px;color:rgb(0,0,0);font-family:Times;fon=
t-size:medium;font-variant-ligatures:normal">CCH is an=C2=A0<a href=3D"http=
://en.wikipedia.org/wiki/Overlay_journal">overlay journal</a>=C2=A0that ide=
ntifies the most important papers in computational and theoretical chemistr=
y published in the last 1-2 years. CCH is not affiliated with any publisher=
: it is a free resource run by scientists for scientists.=C2=A0<a href=3D"h=
ttp://proteinsandwavefunctions.blogspot.com/2012/02/computational-chemistry=
-highlights-new.html">You can read more about it here</a>.</p><p style=3D"m=
argin:0px;color:rgb(0,0,0);font-family:Times;font-size:medium;font-variant-=
ligatures:normal"><br></p><p style=3D"margin:0px;color:rgb(0,0,0);font-fami=
ly:Times;font-size:medium;font-variant-ligatures:normal">Table of content f=
or this issue features contributions from Steven Bachrach and Jan Jensen:</=
p><p style=3D"margin:0px;color:rgb(0,0,0);font-family:Times;font-size:mediu=
m;font-variant-ligatures:normal"><br></p><p style=3D"margin:0px;color:rgb(0=
,0,0);font-family:Times;font-size:medium;font-variant-ligatures:normal"><a =
href=3D"http://www.compchemhighlights.org/2017/11/understanding-and-breakin=
g-scaling.html">Understanding and Breaking Scaling Relations in Single-Site=
Catalysis: Methane-to-methanol Conversion by Fe(IV)=3DO</a></p><p style=3D=
"margin:0px;color:rgb(0,0,0);font-family:Times;font-size:medium;font-varian=
t-ligatures:normal"><br></p><div style=3D"color:rgb(0,0,0);font-family:Time=
s;font-size:medium;font-variant-ligatures:normal"><p style=3D"margin:0px"><=
a href=3D"http://www.compchemhighlights.org/2017/11/tunneling-control-of-ch=
emical-reactions.html">Tunneling Control of Chemical Reactions: The Third R=
eactivity Paradigm</a></p></div><div style=3D"color:rgb(0,0,0);font-family:=
Times;font-size:medium;font-variant-ligatures:normal"><p style=3D"margin:0p=
x"><br></p></div><div style=3D"color:rgb(0,0,0);font-family:Times;font-size=
:medium;font-variant-ligatures:normal"><p style=3D"margin:0px"><a href=3D"h=
ttp://www.compchemhighlights.org/2017/11/the-cope-rearrangement-of-15.html"=
>The Cope Rearrangement of 1,5-Dimethylsemibullvalene-2(4)-d1: Experimental=
Evidence for Heavy-Atom Tunneling</a></p></div><div style=3D"color:rgb(0,0=
,0);font-family:Times;font-size:medium;font-variant-ligatures:normal"><p st=
yle=3D"margin:0px"><br></p><div><p style=3D"margin:0px">Interested in contr=
ibuting? =C2=A0<a href=3D"http://www.compchemhighlights.org/2017/04/new-cch=
-contributors-wanted.html">Read more here</a></p><div><p style=3D"margin:0p=
x"><br></p><p style=3D"margin:0px">Interested in more?=C2=A0<a href=3D"http=
://www.compchemhighlights.org/p/get-cch-updates.html">There are many ways t=
o subscribe to CCH updates</a>.</p><div><p style=3D"margin:0px"><br></p><p =
style=3D"margin:0px">Also, for your daily computational chemistry fix subsc=
ribe to=C2=A0<a href=3D"https://paper.li/janhjensen/1416314690">Computation=
al Chemistry Daily</a></p></div></div></div></div></div>
--001a11452ce0783b65055f439101--
From owner-chemistry@ccl.net Fri Dec 1 21:20:00 2017
From: "=?UTF-8?Q?Bj=c3=b6rn_Sommer?= bjoern*|*cellmicrocosmos.org" <owner-chemistry()server.ccl.net>
To: CCL
Subject: CCL: CfP EuroVis 2018 Workshop on Molecular Graphics and Visual Analysis of Molecular Data
Message-Id: <-53083-171201201255-20004-8q6PEwwI/YYSVc51x9NtTQ()server.ccl.net>
X-Original-From: =?UTF-8?Q?Bj=c3=b6rn_Sommer?= <bjoern%x%cellmicrocosmos.org>
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Date: Sat, 2 Dec 2017 02:12:46 +0100
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Sent to CCL by: =?UTF-8?Q?Bj=c3=b6rn_Sommer?= [bjoern~!~cellmicrocosmos.org]
"Workshop on Molecular Graphics and Visual Analysis of Molecular Data"
*
(co-located with EuroVis 2018), June 4, 2018, Brno, Czech Republic
************************************************************************************
Molecular visualization is one of the oldest branches of scientific
visualization, which has been developing for over 50 years. Due to the
continuous advances in both computational biology and computer graphics
techniques, molecular graphics and visualization are still very active
areas of research. Not only the ever-increasing dataset sizes yield a
constant challenge for visual analysis, but also new technologies like
advances in web-based graphics or augmented and virtual reality open new
possibilities. In this half-day workshop, which is held for the first
time in conjunction with EuroVis, we would like to initiate a
multidisciplinary meeting which brings visualization researchers
together working with molecular data.
Whereas molecular graphics is an established topic since many years, the
hybrid-dimensional visual analysis of molecular structures is still a
quite new research field with a lot of potential. We would like to
encourage submissions especially using new technologies, such as
immersive analytics-related approaches.
We invite short papers as well as full papers (2-4 pages for short and
up to 8 pages for full papers, both with an additional page reserved for
references). All papers will undergo a single-stage, double-blind peer
review process. Accepted papers will be published in the EG digital
library. The workshop will be held in Brno, Czech Republic, June 4th,
2018 as part of EuroVis 2018.
Suggested topics include, but are not limited to:
- Molecular Graphics
- Visual Analysis of Molecular Data (e.g., molecular structures,
biological networks and pathways, or omics data)
- Visualization of Dynamic Molecular Data
- Visualization of Large Molecular Systems
- Web-based Molecular Graphics and Visualization
- Immersive Analytics approaches using, e.g., VR/AR technologies
More info:
http://decibel.fi.muni.cz/~xbyska/molva/
Important Dates
**************************************************************************************
Paper Submission Deadline:March 5, 2018
Notification of Acceptance:April 10, 2018
Camera-ready Deadline:April 20, 2018
Workshop Date:June 4, 2018
Organizers and Contact
**************************************************************************************
- Jan Byska, University of Bergen, Norway
- Michael Krone, University of Stuttgart, Germany
- Björn Sommer, University of Konstanz
If you have any question, please contact us:
mailto: molva.eurovis*gmail.com
Submission
**************************************************************************************
Please submit your full paper via PCS (Deadline: March 5, 2018):
https://new.precisionconference.com/molva18a/
Please follow the EG guidelines for writing the paper. More info and
templates you will find here:
http://www.eurovis2018.org/public/download/EuroVis2018FullPapers_latex2e.zip
*