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Re: [Jmol-users] Natural Bond Orbital Display Issues
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From: John K. <jwk...@al...> - 2020-10-29 05:15:30
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<html 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"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} @font-face {font-family:Cambria; panose-1:2 4 5 3 5 4 6 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} pre {mso-style-priority:99; mso-style-link:"HTML Preformatted Char"; margin:0cm; margin-bottom:.0001pt; font-size:10.0pt; font-family:"Courier New";} span.HTMLPreformattedChar {mso-style-name:"HTML Preformatted Char"; mso-style-priority:99; mso-style-link:"HTML Preformatted"; font-family:"Courier New";} .MsoChpDefault {mso-style-type:export-only;} @page WordSection1 {size:612.0pt 792.0pt; margin:72.0pt 72.0pt 72.0pt 72.0pt;} div.WordSection1 {page:WordSection1;} --></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Here is what I am doing now. No need to get nbo 7.</p><p class=MsoNormal><o:p> </o:p></p><div><pre><span style='color:black'>-------------<o:p></o:p></span></pre><pre><span style='color:black'>#N B3LYP/6-31G(d,p) SP GFINPUT POP=(FULL,NBO6Read) <o:p></o:p></span></pre><pre><span style='color:black'><o:p> </o:p></span></pre><pre><span style='color:black'>C3H6O<o:p></o:p></span></pre><pre><span style='color:black'><o:p> </o:p></span></pre><pre><span style='color:black'>0 1<o:p></o:p></span></pre><pre><span style='color:black'>C 0.00000000 0.00000000 0.00000000<o:p></o:p></span></pre><pre><span style='color:black'>C 0.00000000 -1.33367900 0.77000100<o:p></o:p></span></pre><pre><span style='color:black'>C 0.00000000 -2.66735800 0.00000000<o:p></o:p></span></pre><pre><span style='color:black'>H 0.00000000 -3.49584500 0.70831500<o:p></o:p></span></pre><pre><span style='color:black'>H -0.88998100 -2.72509900 -0.62665700<o:p></o:p></span></pre><pre><span style='color:black'>H 0.88998100 -2.72509900 -0.62665700<o:p></o:p></span></pre><pre><span style='color:black'>O 0.00000000 -1.33367900 2.04500100<o:p></o:p></span></pre><pre><span style='color:black'>H 0.00000000 0.82848700 0.70831500<o:p></o:p></span></pre><pre><span style='color:black'>H 0.88998100 0.05774100 -0.62665700<o:p></o:p></span></pre><pre><span style='color:black'>H -0.88998100 0.05774100 -0.62665700<o:p></o:p></span></pre><pre><span style='color:black'><o:p> </o:p></span></pre><div style='mso-element:para-border-div;border:none;border-bottom:solid windowtext 1.0pt;padding:0cm 0cm 1.0pt 0cm'><pre style='border:none;padding:0cm'><span style='color:black'>$NBO FILE=NBODATA PLOT ARCHIVE $END<o:p></o:p></span></pre><pre style='border:none;padding:0cm'><span style='color:black'>-------------<o:p></o:p></span></pre></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>In WebMO Job Manager, Select the job, Download the Job Archive. Expand the archive on your local machine, then in Jmol:</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>$ cd <folder containing the job files></p><p class=MsoNormal>$ load nbodata.31</p><p class=MsoNormal>$ nbo type nbo</p><p class=MsoNormal>$ nbo 10</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I assume it’s possible to modify the appearance of these surfaces, and hopefully plot more than one simultaneously.</p><p class=MsoNormal>John K.</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal style='border:none;padding:0cm'><b>From: </b><a href="mailto:cbr...@ma...">Conor Broderick</a><br><b>Sent: </b>Wednesday, October 28, 2020 7:42 PM<br><b>To: </b><a href="mailto:ha...@st...">Robert Hanson</a><br><b>Cc: </b><a href="mailto:jmo...@li...">jmo...@li...</a><br><b>Subject: </b>Re: [Jmol-users] Natural Bond Orbital Display Issues</p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Amazing! Thanks for the update. Hopefully this will be the last question on my end, but do you happen to know the Gaussian command (I am using Gaussian 16) to output the .46 file? It doesn't seem to generate with "plot" and "archive," and I tried adding "label" but those runs seemed to fail immediately. I'm concerned that this may have run up against the limits of what I can do without getting NBO7.</p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>best,</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>- COnor</p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Wed, Oct 28, 2020 at 9:09 PM Robert Hanson <<a href="mailto:ha...@st...">ha...@st...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><p class=MsoNormal>(actually, it accesses those files immediately upon loading.</p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Wed, Oct 28, 2020 at 10:08 PM Robert Hanson <<a href="mailto:ha...@st..." target="_blank">ha...@st...</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Meaning, what we need are these:</p></div><p class=MsoNormal><o:p> </o:p></p><div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm'><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><b> // .31 AO basis <br> // .46 (labels)</b></p></div></div></blockquote><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>What you do is load one of these:</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal> // .32 PNAO no beta coef<br> // .33 NAO no beta coef ; adds orbital types<br> // .34 PNHO alpha+beta<br> // .35 NHO alpha+beta<br> // .36 PNBO alpha+beta<br> // .37 NBO alpha+extra+beta+extra<br> // .38 PNLMO alpha+beta<br> // .39 NLMO alpha+extra+beta+extra<br> // .40 MO alpha+beta<br> // .41 NO alpha+beta<br> // .44 PRNBO alpha+beta<br> // .45 RNBO alpha+beta</p></div></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>And it will automatically access the .31 and .46 files when you then issue the NBO command. Or you can load the .31 file and then use </p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>NBO TYPE NLMO </p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>or similar command, then </p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>NBO 10</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Bob</p></div></div></blockquote></div><p class=MsoNormal><br clear=all><br>-- </p><div><div><div><div><div><div><p class=MsoNormal>Robert M. Hanson<br>Professor of Chemistry<br>St. Olaf College<br>Northfield, MN<br><a href="http://www.stolaf.edu/people/hansonr" target="_blank">http://www.stolaf.edu/people/hansonr</a><br><br><br>If nature does not answer first what we want,<br>it is better to take what answer we get. <br><br>-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900</p></div><div><p class=MsoNormal><o:p> </o:p></p></div></div></div></div></div></div></blockquote></div><p class=MsoNormal style='margin-left:4.8pt'><i><span style='font-size:12.0pt;font-family:"Cambria",serif;color:#242121'>We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.</span></i></p><p class=MsoNormal><o:p> </o:p></p></div></body></html> |
