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From: Alexander O. <oll...@gm...> - 2006-05-26 09:23:40
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Dear XMD users! Could you prompt me reference to the detail description of algorithm, used XMD for MD integration of the equations of motion? Thanking you. Ovsjannikov Alexander. |
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From: Alexander O. <oll...@gm...> - 2006-04-11 10:27:35
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Hello! =20 I can=A1=AFt find 'xmd-2.5.34-1.rar' on 'http://xmd.sourceforge.net/download.html' :-( Only 'xmd-2.5.34-1.tar.gz=A1=AF=20 =20 =A1=B0Microsoft Visual C++=A1=B1- fine compiler and I nave no problem = with XMD compiled by it (6.0, 7.0, 7.1, 8.0 =A8C all of them). =20 Execute 'xmd.exe cavity.xm' and backup result, Execute 'xmd.exe = cavity.xm' again and compare new and old result.=20 Find difference? line 90 of cavity.xm is =A1=B0itemp 16000=A1=B1 Itemp =A8C =A1=B0Assigns random velocities=A1=AD=A1=B1 ( <http://xmd.sourceforge.net/doc/manual/xmd-8.html> http://xmd.sourceforge.net/doc/manual/xmd-8.html) And your result can=A1=AFt be the same. =20 _____ =20 From: xmd...@li... [mailto:xmd...@li...] On Behalf Of = apple__01230 Sent: Tuesday, April 11, 2006 8:21 AM To: xmd...@li... Subject: [Xmd-support] compile question =20 hello xmder: =20 I am very sorry. That enclosure is just my calculation result = last time. =20 I compile xmd with command line in Win2003.but when I circulate the = example of cavity, circulate the result have the error margin with the example = that you give as a result. The quantity class did not have problems, just the decimal point has a little the problem behind. I make the order as = 'xmd.exe ..\cavity.xm' , i don't know what is the matter. I think it may have relation with following reason fasten. =20 first:I download the 'xmd-2.5.34-1.rar' from 'http://xmd.sourceforge.net/download.html',then press with the WinRAR solution after, but the detection have no document of 'config.xmd',also = show while even circulating in the procedure'Fail to open the config.xmd'. I = want to know if the config.xmd will affect the result. =20 second:My compiler is Microsoft Visual C++. The doc don't show the particular method of using under Windows with command line .Does it must = be compiled in UNIX or Linux. =20 I really need your help ,Thanks. =20 =20 --- Weijie Liu School of Dynamics DaLian University of Technology =20 =20 =20 =D6=D0 =B9=FA =C3=BF =C4=EA =D3=C3 =B5=F4 =B6=E0 =C9=D9 =CB=AB =D2=BB = =B4=CE =D0=D4 =BF=EA =D7=D3 =A3=BF=20 450=D2=DA=CB=AB=A1=A3=D5=E2=BB=E1=BA=C4=B7=D1170=CD=F2=C1=A2=B7=BD=C3=D7=B5= =C4=C4=BE=B2=C4=A3=AC=D0=E8=D2=AA=BF=B3=B7=A5=B4=F3=D4=BC2500=CD=F2=BF=C3= =B4=F3=CA=F7=A3=A1 <http://www. 126.com/>=20 <=CD=F8=D2=D7=D3=CA=CF=E4=B9=AB=D2=E6=D0=FB=B4=AB> |
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From: apple__01230 <app...@16...> - 2006-04-11 05:21:20
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hello xmder:
I am very sorry. That enclosure is just my calculation result last time.
I compile xmd with command line in Win2003.but when I circulate the example of cavity, circulate the result have the error margin with the example that you give as a result. The quantity class did not have problems, just the decimal point has a little the problem behind. I make the order as 'xmd.exe ..\cavity.xm' , i don't know what is the matter. I think it may have relation with following reason fasten.
first:I download the 'xmd-2.5.34-1.rar' from 'http://xmd.sourceforge.net/download.html',then press with the WinRAR solution after, but the detection have no document of 'config.xmd',also show while even circulating in the procedure'Fail to open the config.xmd'. I want to know if the config.xmd will affect the result.
second:My compiler is Microsoft Visual C++. The doc don't show the particular method of using under Windows with command line .Does it must be compiled in UNIX or Linux.
I really need your help ,Thanks.
---
Weijie Liu
School of Dynamics
DaLian University of Technology
|
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From: Joel <jan...@fc...> - 2006-04-05 18:15:20
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jan...@fc... |
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From: Dr. H. Bo L. <hb...@im...> - 2005-12-14 15:31:19
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Hi colleagues, For CH4 and H2, It is better to use a Molecular Mechanics program based on FORCE FIELD. XMD does not support this type of potential. Best, Dr. Hongbo LIU Instituto Mexicano del Petroleo Tel:52-55-91756424(O); 52-55-55872927(H) Email:hb...@im...; h_...@ya... ----- Original Message ----- From: <xmd...@li...> To: <xmd...@li...> Sent: Tuesday, December 13, 2005 10:31 PM Subject: Xmd-support digest, Vol 1 #10 - 2 msgs > Send Xmd-support mailing list submissions to > xmd...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/xmd-support > or, via email, send a message with subject or body 'help' to > xmd...@li... > > You can reach the person managing the list at > xmd...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xmd-support digest..." > > > Today's Topics: > > 1. XMD for Gases (Hydrocarbons) (R. Karthik) > 2. RE: XMD for Gases (Hydrocarbons) (Alexander Ovsyannikov) > > --__--__-- > > Message: 1 > Date: Tue, 13 Dec 2005 02:31:07 -0800 (PST) > From: "R. Karthik" <kar...@ya...> > To: xmd...@li... > Subject: [Xmd-support] XMD for Gases (Hydrocarbons) > > --0-214142591-1134469867=:73834 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Hi, > > I would like to do MD on my CH4, H2 system. Can I use XMD for this, > provided I find a suitable potential? I am mainly asking this bcos in main > page its written > XMD - Molecular Dymamics for Metals and Ceramics.So I just want to know > whether it is restriced for metal/ceramics for it is generic in nature. > > thanks, > karthik > > > > > --------------------------------- > Yahoo! Shopping > Find Great Deals on Holiday Gifts at Yahoo! Shopping > --0-214142591-1134469867=:73834 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > <div id="RTEContent"> Hi,<br><br>I would like to do MD on my CH4, H2 > system. Can I use XMD for this, provided I find a suitable potential? I am > mainly asking this bcos in main page its written<br><h2 class="heading"> > XMD - Molecular Dymamics for Metals and Ceramics.</h2>So I just want to > know whether it is restriced for metal/ceramics for it is generic in > nature.<br><br>thanks,<br>karthik<br><br></div><p> > > <hr size=1>Yahoo! Shopping<br> > Find Great Deals on Holiday Gifts at <a > href="http://us.rd.yahoo.com/mail_us/footer/shopping/*http://shopping.yahoo.com/;_ylc=X3oDMTE2bzVzaHJtBF9TAzk1OTQ5NjM2BHNlYwNtYWlsdGFnBHNsawNob2xpZGF5LTA1 > ">Yahoo! Shopping</a> > --0-214142591-1134469867=:73834-- > > > --__--__-- > > Message: 2 > From: "Alexander Ovsyannikov" <ov...@im...> > To: <xmd...@li...> > Subject: RE: [Xmd-support] XMD for Gases (Hydrocarbons) > Date: Tue, 13 Dec 2005 13:43:25 +0200 > > This is a multi-part message in MIME format. > > ------=_NextPart_000_001F_01C5FFEB.3184EE80 > Content-Type: text/plain; > charset="us-ascii" > Content-Transfer-Encoding: 7bit > > Hi, R. Karthik! > > > > (http://xmd.sourceforge.net/doc/manual/xmd-2.html) > > > > "2. Introduction > > > > XMD is a program which performs Computer Molecular Dynamics (CMD) > simulations. It can use Embedded Atom Method (EAM) potentials, pair > potentials, Tersoff's silicon-carbon potential [1], or Stillinger-Weber's > Silicon potential [2]. With XMD you can generate specific lattice > structures. With these lattice structures you can perform calculations > using > both static (energies or forces) and dynamic (molecular dynamics). XMD > reads > a command file which describes a an initial atomic system, the simulation > to > be performed, and the output desired. This command file is a normal text > file (a file that can be read by a normal text editor). Normal text files > are also used for recording energies during the course of a simulation. > Special format files (files than cannot be used with text editors) are > used > for storing the particle coordinates (RCV files) and the complete CMD > state > (STA files)." > > > > EAM potential are developed for metalls; > > Tersoff's silicon-carbon potential or Stillinger-Weber's Silicon potential > - mismatch CH4 :-) > > If you can describe your system in term of pair potential, then XMD are > applicable for your task. > > > > _____ > > From: xmd...@li... > [mailto:xmd...@li...] On Behalf Of R. Karthik > Sent: Tuesday, December 13, 2005 12:31 PM > To: xmd...@li... > Subject: [Xmd-support] XMD for Gases (Hydrocarbons) > > > > Hi, > > I would like to do MD on my CH4, H2 system. Can I use XMD for this, > provided > I find a suitable potential? I am mainly asking this bcos in main page its > written > > > XMD - Molecular Dymamics for Metals and Ceramics. > > > So I just want to know whether it is restriced for metal/ceramics for it > is > generic in nature. > > thanks, > karthik > > _____ > > Yahoo! Shopping > Find Great Deals on Holiday Gifts at Yahoo! > <http://us.rd.yahoo.com/mail_us/footer/shopping/*http:/shopping.yahoo.com/;_ > ylc=X3oDMTE2bzVzaHJtBF9TAzk1OTQ5NjM2BHNlYwNtYWlsdGFnBHNsawNob2xpZGF5LTA1%20% > 0d%0a> Shopping > > > ------=_NextPart_000_001F_01C5FFEB.3184EE80 > Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > <html xmlns:v=3D"urn:schemas-microsoft-com:vml" = > xmlns:o=3D"urn:schemas-microsoft-com:office:office" = > xmlns:w=3D"urn:schemas-microsoft-com:office:word" = > xmlns=3D"http://www.w3.org/TR/REC-html40"> > > <head> > <meta http-equiv=3DContent-Type content=3D"text/html; = > charset=3Dus-ascii"> > <meta name=3DGenerator content=3D"Microsoft Word 11 (filtered medium)"> > <!--[if !mso]> > <style> > v\:* {behavior:url(#default#VML);} > o\:* {behavior:url(#default#VML);} > w\:* {behavior:url(#default#VML);} > .shape {behavior:url(#default#VML);} > </style> > <![endif]--> > <style> > <!-- > /* Font Definitions */ > @font-face > {font-family:Wingdings; > panose-1:5 0 0 0 0 0 0 0 0 0;} > @font-face > {font-family:Tahoma; > panose-1:2 11 6 4 3 5 4 4 2 4;} > /* Style Definitions */ > p.MsoNormal, li.MsoNormal, div.MsoNormal > {margin:0cm; > margin-bottom:.0001pt; > font-size:12.0pt; > font-family:"Times New Roman";} > h2 > {mso-margin-top-alt:auto; > margin-right:0cm; > mso-margin-bottom-alt:auto; > margin-left:0cm; > font-size:18.0pt; > font-family:"Times New Roman"; > font-weight:bold;} > a:link, span.MsoHyperlink > {color:blue; > text-decoration:underline;} > a:visited, span.MsoHyperlinkFollowed > {color:blue; > text-decoration:underline;} > p > {mso-margin-top-alt:auto; > margin-right:0cm; > mso-margin-bottom-alt:auto; > margin-left:0cm; > font-size:12.0pt; > font-family:"Times New Roman";} > span.EmailStyle18 > {mso-style-type:personal; > font-family:Arial; > color:navy;} > span.EmailStyle19 > {mso-style-type:personal-reply; > font-family:Arial; > color:navy;} > @page Section1 > {size:595.3pt 841.9pt; > margin:2.0cm 42.5pt 2.0cm 3.0cm;} > div.Section1 > {page:Section1;} > --> > </style> > > </head> > > <body lang=3DRU link=3Dblue vlink=3Dblue> > > <div class=3DSection1> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'>Hi, R. = > Karthik!<o:p></o:p></span></font></p> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p>= > </span></font></p> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'>(http://xmd.sourc= > eforge.net/doc/manual/xmd-2.html)<o:p></o:p></span></font></p> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p>= > </span></font></p> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'>“2. = > Introduction<o:p></o:p></span></font></p> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p>= > </span></font></p> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'>XMD is a program = > which > performs Computer Molecular Dynamics (CMD) simulations. It can use = > <b><span > style=3D'font-weight:bold'>Embedded Atom Method</span></b> (EAM) = > potentials, <b><span > style=3D'font-weight:bold'>pair</span></b> potentials, <b><span = > style=3D'font-weight: > bold'>Tersoff's silicon-carbon</span></b> potential [1], or <b><span > style=3D'font-weight:bold'>Stillinger-Weber's Silicon</span></b> = > potential [2]. > With XMD you can generate specific lattice structures. With these = > lattice > structures you can perform calculations using both static (energies or = > forces) > and dynamic (molecular dynamics). XMD reads a command file which = > describes a an > initial atomic system, the simulation to be performed, and the output = > desired. > This command file is a normal text file (a file that can be read by a = > normal > text editor). Normal text files are also used for recording energies = > during the > course of a simulation. Special format files (files than cannot be used = > with > text editors) are used for storing the particle coordinates (RCV files) = > and the > complete CMD state (STA files).”<o:p></o:p></span></font></p> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p>= > </span></font></p> > > <p class=3DMsoNormal><b><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy;font-weight:bold'>= > EAM</span></font></b><font > size=3D2 color=3Dnavy face=3DArial><span lang=3DEN-US = > style=3D'font-size:10.0pt; > font-family:Arial;color:navy'> potential are developed for metalls; = > <o:p></o:p></span></font></p> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'>Tersoff's = > <b><span > style=3D'font-weight:bold'>silicon-carbon </span></b>potential or > Stillinger-Weber's <b><span = > style=3D'font-weight:bold'>Silicon</span></b> > potential - mismatch CH4 </span></font><font size=3D2 = > color=3Dnavy > face=3DWingdings><span lang=3DEN-US = > style=3D'font-size:10.0pt;font-family:Wingdings; > color:navy'>J</span></font><font size=3D2 color=3Dnavy = > face=3DArial><span lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'><o:p></o:p></span= >></font></p> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'>If you can = > describe your > system in term of pair potential, then XMD are applicable for your = > task.<o:p></o:p></span></font></p> > > <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span = > lang=3DEN-US > style=3D'font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p>= > </span></font></p> > > <div> > > <div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><font = > size=3D3 > face=3D"Times New Roman"><span style=3D'font-size:12.0pt'> > > <hr size=3D2 width=3D"100%" align=3Dcenter tabindex=3D-1> > > </span></font></div> > > <p class=3DMsoNormal><b><font size=3D2 face=3DTahoma><span = > style=3D'font-size:10.0pt; > font-family:Tahoma;font-weight:bold'>From:</span></font></b><font = > size=3D2 > face=3DTahoma><span style=3D'font-size:10.0pt;font-family:Tahoma'> > xmd...@li... > [mailto:xmd...@li...] <b><span = > style=3D'font-weight: > bold'>On Behalf Of </span></b>R. Karthik<br> > <b><span style=3D'font-weight:bold'>Sent:</span></b> Tuesday, December = > 13, 2005 12:31 > PM<br> > <b><span style=3D'font-weight:bold'>To:</span></b> > xmd...@li...<br> > <b><span style=3D'font-weight:bold'>Subject:</span></b> [Xmd-support] = > XMD for > Gases (Hydrocarbons)</span></font><o:p></o:p></p> > > </div> > > <p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span = > style=3D'font-size: > 12.0pt'><o:p> </o:p></span></font></p> > > <div id=3DRTEContent> > > <p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span = > style=3D'font-size: > 12.0pt'> Hi,<br> > <br> > I would like to do MD on my CH4, H2 system. Can I use XMD for this, = > provided I > find a suitable potential? I am mainly asking this bcos in main page its > written<o:p></o:p></span></font></p> > > <h2><b><font size=3D5 face=3D"Times New Roman"><span = > style=3D'font-size:18.0pt'>XMD - > Molecular Dymamics for Metals and = > Ceramics.<o:p></o:p></span></font></b></h2> > > <p class=3DMsoNormal style=3D'margin-bottom:12.0pt'><font size=3D3 > face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>So I just want = > to know > whether it is restriced for metal/ceramics for it is generic in = > nature.<br> > <br> > thanks,<br> > karthik<o:p></o:p></span></font></p> > > </div> > > <div class=3DMsoNormal align=3Dcenter style=3D'text-align:center'><font = > size=3D3 > face=3D"Times New Roman"><span style=3D'font-size:12.0pt'> > > <hr size=3D1 width=3D"100%" align=3Dcenter> > > </span></font></div> > > <p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span = > style=3D'font-size: > 12.0pt'>Yahoo! Shopping<br> > Find Great Deals on Holiday Gifts at <a > href=3D"http://us.rd.yahoo.com/mail_us/footer/shopping/*http:/shopping.ya= > hoo.com/;_ylc=3DX3oDMTE2bzVzaHJtBF9TAzk1OTQ5NjM2BHNlYwNtYWlsdGFnBHNsawNob= > 2xpZGF5LTA1%20%0d%0a">Yahoo! > Shopping</a> <o:p></o:p></span></font></p> > > </div> > > </body> > > </html> > > ------=_NextPart_000_001F_01C5FFEB.3184EE80-- > > > > > --__--__-- > > _______________________________________________ > Xmd-support mailing list > Xmd...@li... > https://lists.sourceforge.net/lists/listinfo/xmd-support > > > End of Xmd-support Digest > |
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From: Alexander O. <ov...@im...> - 2005-12-13 11:46:08
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Hi, R. Karthik! (http://xmd.sourceforge.net/doc/manual/xmd-2.html) "2. Introduction XMD is a program which performs Computer Molecular Dynamics (CMD) simulations. It can use Embedded Atom Method (EAM) potentials, pair potentials, Tersoff's silicon-carbon potential [1], or Stillinger-Weber's Silicon potential [2]. With XMD you can generate specific lattice structures. With these lattice structures you can perform calculations using both static (energies or forces) and dynamic (molecular dynamics). XMD reads a command file which describes a an initial atomic system, the simulation to be performed, and the output desired. This command file is a normal text file (a file that can be read by a normal text editor). Normal text files are also used for recording energies during the course of a simulation. Special format files (files than cannot be used with text editors) are used for storing the particle coordinates (RCV files) and the complete CMD state (STA files)." EAM potential are developed for metalls; Tersoff's silicon-carbon potential or Stillinger-Weber's Silicon potential - mismatch CH4 :-) If you can describe your system in term of pair potential, then XMD are applicable for your task. _____ From: xmd...@li... [mailto:xmd...@li...] On Behalf Of R. Karthik Sent: Tuesday, December 13, 2005 12:31 PM To: xmd...@li... Subject: [Xmd-support] XMD for Gases (Hydrocarbons) Hi, I would like to do MD on my CH4, H2 system. Can I use XMD for this, provided I find a suitable potential? I am mainly asking this bcos in main page its written XMD - Molecular Dymamics for Metals and Ceramics. So I just want to know whether it is restriced for metal/ceramics for it is generic in nature. thanks, karthik _____ Yahoo! Shopping Find Great Deals on Holiday Gifts at Yahoo! <http://us.rd.yahoo.com/mail_us/footer/shopping/*http:/shopping.yahoo.com/;_ ylc=X3oDMTE2bzVzaHJtBF9TAzk1OTQ5NjM2BHNlYwNtYWlsdGFnBHNsawNob2xpZGF5LTA1%20% 0d%0a> Shopping |
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From: R. K. <kar...@ya...> - 2005-12-13 10:31:13
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Hi, I would like to do MD on my CH4, H2 system. Can I use XMD for this, provided I find a suitable potential? I am mainly asking this bcos in main page its written XMD - Molecular Dymamics for Metals and Ceramics.So I just want to know whether it is restriced for metal/ceramics for it is generic in nature. thanks, karthik --------------------------------- Yahoo! Shopping Find Great Deals on Holiday Gifts at Yahoo! Shopping |
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From: Alexander O. <ov...@im...> - 2005-12-12 14:35:29
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From: Dr. H. L. <hb...@im...> - 2005-11-21 22:53:56
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Hi AANazarov, To use the command SCALE may be an indirect method. I mean one can scale Z (or X, Y) to the original value interlacing with command CMD. About the thermonadymic average, you only can do it by output a series of xyz file or xmd input format file and make a simple program of yourself to do the average. Best, Dr. Hongbo Liu Instituto Mexicano del Petroleo Tel: 52-55-91756424(O); 52-55-55872927(H) Email: hb...@im...; h_...@ya... ----- Original Message ----- From: <xmd...@li...> To: <xmd...@li...> Sent: Saturday, November 19, 2005 10:27 PM Subject: Xmd-support digest, Vol 1 #7 - 1 msg > Send Xmd-support mailing list submissions to > xmd...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/xmd-support > or, via email, send a message with subject or body 'help' to > xmd...@li... > > You can reach the person managing the list at > xmd...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xmd-support digest..." > > > Today's Topics: > > 1. Questions (AANazarov) > > --__--__-- > > Message: 1 > Date: Sat, 19 Nov 2005 12:33:59 +0500 > From: AANazarov <AAN...@ma...> > Reply-To: AANazarov <AAN...@ma...> > Organization: UGATU > To: xmd...@li... > Subject: [Xmd-support] Questions > > *This message was transferred with a trial version of CommuniGate(tm) Pro* > Dear XMD users, > > I have a question on boundary conditions which can be applied in XMD. > I need to apply dynamic boundary conditions in two directions while > maintaining the borders in the third direction fixed. There are no > direct commands for this, since by default the borders are fixed, > while PRESSURE CLAMP makes all three borders dynamic. I wonder if an > indiract method can be used to carry out simulation in conditions I > mentioned. > > The other question concerns simulations at finite temperatures. After > equilibriating at given temperature, I would like to analyse the > structure, for which I need to output average coordinates of the atoms. > How can this be done using XMD? > > And last, is there a site where references on papers which used XMD > are put? I would like to put one later. > > Thanks. > > Airat Nazarov > > PS. This is a very nice code. On my 1.7 GHz PC I relax systems > containing 250.000 atoms in about 30 hours! > > Airat A. Nazarov > Institute of Physics of Advanced Materials > Ufa State Aviation Technical University, > 12 Karl Marx Str., > Ufa 450000 > RUSSIA > > Mail to: AAN...@ma... > > > > > > --__--__-- > > _______________________________________________ > Xmd-support mailing list > Xmd...@li... > https://lists.sourceforge.net/lists/listinfo/xmd-support > > > End of Xmd-support Digest |
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From: AANazarov <AAN...@ma...> - 2005-11-19 07:33:59
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*This message was transferred with a trial version of CommuniGate(tm) Pro* Dear XMD users, I have a question on boundary conditions which can be applied in XMD. I need to apply dynamic boundary conditions in two directions while maintaining the borders in the third direction fixed. There are no direct commands for this, since by default the borders are fixed, while PRESSURE CLAMP makes all three borders dynamic. I wonder if an indiract method can be used to carry out simulation in conditions I mentioned. The other question concerns simulations at finite temperatures. After equilibriating at given temperature, I would like to analyse the structure, for which I need to output average coordinates of the atoms. How can this be done using XMD? And last, is there a site where references on papers which used XMD are put? I would like to put one later. Thanks. Airat Nazarov PS. This is a very nice code. On my 1.7 GHz PC I relax systems containing 250.000 atoms in about 30 hours! Airat A. Nazarov Institute of Physics of Advanced Materials Ufa State Aviation Technical University, 12 Karl Marx Str., Ufa 450000 RUSSIA Mail to: AAN...@ma... |
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From: Dr. H. L. <hb...@im...> - 2005-10-31 15:31:26
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Hi everybody, Attacthed is an icosahedral structure with 309 atoms. I do not know whether it is what you required or not. Regards, Dr. Hongbo Liu Instituto Mexicano del Petroleo Tel: 52-55-91756424(O); 52-55-55872927(H) Email: hb...@im...; h_...@ya... ----- Original Message ----- From: <xmd...@li...> To: <xmd...@li...> Sent: Sunday, October 30, 2005 10:34 PM Subject: Xmd-support digest, Vol 1 #5 - 1 msg > Send Xmd-support mailing list submissions to > xmd...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/xmd-support > or, via email, send a message with subject or body 'help' to > xmd...@li... > > You can reach the person managing the list at > xmd...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xmd-support digest..." > > > Today's Topics: > > 1. XMD - icosahedron (Apu Sarkar) > > --__--__-- > > Message: 1 > Date: Mon, 31 Oct 2005 00:06:37 +0530 > From: Apu Sarkar <apu...@gm...> > To: xmd...@li... > Subject: [Xmd-support] XMD - icosahedron > > Dear XMD users, > I want to perform a simulation studies on gold nanocluster. Can anyone > tell me how to input a Mackay icosahedron structure in XMD. > > Thanking you. > > Regards, > Apu > > > > --__--__-- > > _______________________________________________ > Xmd-support mailing list > Xmd...@li... > https://lists.sourceforge.net/lists/listinfo/xmd-support > > > End of Xmd-support Digest |
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From: <ov...@im...> - 2005-10-31 13:50:55
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I have dual Xeon Nocona (with EM64T and HT) 3.2 Ghz, Xmd 2.5.34-1 compiled with gcc 4 and ( -O3 -march=Nocona; ./xmd -p4 my.xm ) 262189 atoms of Fe: --------------------------------------------------------------- DYNAMICS STATISTICS Number of MD Steps: 7950 Number of Neighbor Searchs: 617 Time spent on MD steps: 17870 (secs) Time spent on Neighbor Search: 12393 (secs) --------------------------------------------------------------- And 44447: --------------------------------------------------------------- DYNAMICS STATISTICS Number of MD Steps: 65501 Number of Neighbor Searchs: 3135 Time spent on MD steps: 14023 (secs) Time spent on Neighbor Search: 2171 (secs) --------------------------------------------------------------- You can increase you total time by increasing you "time step": Dtime 1e-15 Or even Dtime 1e-14 But this very lowering accuracy and give controversial result. " some other people can simulate millions of atoms in their laptop in a short time " - I'm think that they made "molecular STATIC simulation" and few hundreds iteration. (may be I'm not right :-) ) Sorry for broken English :-))) -----Original Message----- From: xmd...@li... [mailto:xmd...@li...] On Behalf Of Lan Li Sent: Saturday, October 29, 2005 1:53 AM To: xmd...@li... Subject: [Xmd-support] RE: Welcome to the "Xmd-support" mailing list Hi, This is Lan from the Nano-mechanical computational lab of UCLA. We are using XMD to simulate a system of 60,000 Cu atoms lattice for 250,000 steps. I am using a very fast 64bit machine but it takes 2-3 days to finish one simulation, which is very inconvenient for us. We are wondering if there are any ways that we can accelerate the simulation, maybe even with the cost of lowering some accuracy. I heard that some other people can simulate millions of atoms in their laptop in a short time. I am wondering how they can do that. Thank you for any suggestion! Sincerely yours, Lan |
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From: Apu S. <apu...@gm...> - 2005-10-30 19:35:35
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Dear XMD users, I want to perform a simulation studies on gold nanocluster. Can anyone tell me how to input a Mackay icosahedron structure in XMD. Thanking you. Regards, Apu |
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From: Lan L. <la...@uc...> - 2005-10-28 22:53:27
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Hi, This is Lan from the Nano-mechanical computational lab of UCLA. We are using XMD to simulate a system of 60,000 Cu atoms lattice for 250,000 steps. I am using a very fast 64bit machine but it takes 2-3 days to finish one simulation, which is very inconvenient for us. We are wondering if there are any ways that we can accelerate the simulation, maybe even with the cost of lowering some accuracy. I heard that some other people can simulate millions of atoms in their laptop in a short time. I am wondering how they can do that. Thank you for any suggestion! Sincerely yours, Lan -----Original Message----- From: xmd...@li... [mailto:xmd...@li...] On Behalf Of xmd...@li... Sent: Friday, October 28, 2005 3:37 PM To: la...@uc... Subject: Welcome to the "Xmd-support" mailing list Welcome to the Xmd...@li... mailing list! To post to this list, send your email to: xmd...@li... General information about the mailing list is at: https://lists.sourceforge.net/lists/listinfo/xmd-support If you ever want to unsubscribe or change your options (eg, switch to or from digest mode, change your password, etc.), visit your subscription page at: https://lists.sourceforge.net/lists/options/xmd-support/lanli%40ucla.edu You can also make such adjustments via email by sending a message to: Xmd...@li... with the word `help' in the subject or body (don't include the quotes), and you will get back a message with instructions. You must know your password to change your options (including changing the password, itself) or to unsubscribe. It is: 780702 If you forget your password, don't worry, you will receive a monthly reminder telling you what all your lists.sourceforge.net mailing list passwords are, and how to unsubscribe or change your options. There is also a button on your options page that will email your current password to you. You may also have your password mailed to you automatically off of the Web page noted above. |
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From: <ov...@im...> - 2005-08-31 10:28:42
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-----Original Message----- >... >I compile xmd under cygwin in Winxp. But I meet this error: >... For WinXP I recommend to use SFU 3.5 (http://www.microsoft.com/windowsserversystem/sfu/downloads/default.mspx), It's easy to install and gives mach more productivity. But, if it's important for you to use cigwin, I test that compiling and answer tomorrow |
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From: Hong Y. <yan...@ma...> - 2005-08-31 10:00:30
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Hi, xmder
I compile xmd under cygwin in Winxp. But I meet this error:
In file included from xmd.c:33:
strsub.h:71: error: conflicting types for 'strncasecmp'
/usr/include/string.h:68: error: previous declaration of 'strncasecmp'
was here
strsub.h:71: error: conflicting types for 'strncasecmp'
/usr/include/string.h:68: error: previous declaration of 'strncasecmp'
was here
make[2]: *** [xmd.o] Error 1
make[2]: Leaving directory `/home/md/xmd-2.5.34-1/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/md/xmd-2.5.34-1/src'
make: *** [all-recursive] Error 1
does anyone can help me? how can I solve this problem ?
best wishes.
--
Hong Yang
School of Aerospace
Tsinghua University 100084
_________________________________________
yan...@ma...
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From: <jh...@ka...> - 2005-04-22 02:19:05
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RGVhciBhbGwgWE1EIHVzZXJzLA0KDQpJIGhhdmUgYSBxdWVzdGlvbiB0byBhc2sgYWJvdXQgdGhl IHVzZSBvZiBYTUQgY29tbWFuZHMuDQoNCk15IGNhbGN1bGF0aW9uIG5lZWRzIHRvIGNvbnN0cmFp biB0aGUgb3V0ZXIgYXRvbXMgbG9jYXRlZCBvbiB0aGUgY3ViZSBzdXJmYWNlDQphdCBhIGNvbnN0 YW50IHRlbXBlcmF0dXJlLg0KSSBhbSBub3Qgc28gc3VyZSBob3cgdG8gdXNlICdDTEFNUCcgY29t bWFuZHMgZm9yIHRoZSBzZWxlY3RlZCBwYXJ0aWNsZXMuDQpJIHdpbGwgYXBwcmVjaWF0ZSBmb3Ig eW91ciBlbmxpZ2h0ZW5pbmcgbWUuDQoNCkouIEt3b24NCktvcmVhIEF0b21pYyBFbmVyZ3kgUmVz ZWFyY2ggSW5zdGl0dXRlDQpOdWNsZWFyIE1hdGVyaWFscyBUZWNobm9sb2d5IERldmVsb3BtZW50 DQpUZWwgKzgyIDQyIDg2OCA4NTg4IChPKSAvIEZheCArODIgNDIgODY4IDg1NDkgKE8pDQo= |
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From: Jon R. <jon...@uc...> - 2005-03-21 19:27:26
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This is a test of the XMD project's mailing list. |
21 messages has been excluded from this view by a project administrator.