From owner-chemistry@ccl.net Wed Dec 5 03:04:00 2007 From: "Stan van Gisbergen vangisbergen*o*scm.com" To: CCL Subject: CCL: For file conversion in ADF-reg Message-Id: <-35767-071204104536-18267-fIhzHoBEvQNEt6LVHVmyCg%%server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-262--567406997 Date: Tue, 4 Dec 2007 16:45:24 +0100 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Stan van Gisbergen [vangisbergen a scm.com] --Apple-Mail-262--567406997 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Senthilnathan, Please send future support requests for ADF to SCM directly, or use our online ADF forum. If one is using the ADF-GUI (ADF graphical user interface) there is a simple step-by-step tutorial on how to make fragments for fragment analysis: http://www.scm.com/Doc/Doc2007.01/ADFGUI/ADFGUI_tutorial/ page123.html If you're making an ADF input file yourself, several examples explain how one can do fragment analysis, e.g.: http://www.scm.com/Doc/ Doc2007.01/ADF/Examples/page88.html If you are using different .run files, use full path names to the fragment files. Typically one will rename a fragment TAPE21 to a fragment.t21, like for example, CO.t21. This one can use as fragment in a further calculation: DEFINE xyzC=2.0053211 xyzOx=3.2501913 END atoms 1. Ni 0 0 0 2. C xyzC xyzC xyzC f=CO/1 3. C -xyzC -xyzC xyzC f=CO/2 4. C xyzC -xyzC -xyzC f=CO/3 5. C -xyzC xyzC -xyzC f=CO/4 6. O xyzOx xyzOx xyzOx f=CO/1 7. O -xyzOx -xyzOx xyzOx f=CO/2 8. O xyzOx -xyzOx -xyzOx f=CO/3 9. O -xyzOx xyzOx -xyzOx f=CO/4 end fragments CO t21.CO Ni t21.Ni end Best regards, Stan van Gisbergen On Dec 4, 2007, at 2:14 PM, senthil nathan zenthil03^yahoo.co.in wrote: > > Sent to CCL by: "senthil nathan" [zenthil03[-]yahoo.co.in] > Dear CCLrs, > In connection with my privious question, I want to do > fragment analysis for particular system. My total chemical system > is neutral, but its fragment is charged species. I have done a > calculation for both the fragment files separatly and I have two > TAPE21 file for my fragments. For total fragment analysis I want to > read some basic results form TAPE21 fragment file. Now I am using > ADF trial windows version, in this version TAPE21 file will be a > binary result file. I want to do this fragment TAPE21 file as input > file for total fragment analysis. I unable to convert this binary > file as a ADF input file. Any one of you tell me a better solution > for my problem. > > thanking you inadvance > best wishes from > Senthilnathan > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen-x-scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629 --Apple-Mail-262--567406997 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Dear Senthilnathan,=A0

Please send future support = requests for ADF to SCM directly, or use our online ADF = forum.=A0

If one is using the ADF-GUI (ADF graphical user = interface) there is a simple step-by-step tutorial on=A0how to make = fragments for fragment analysis:=A0http://www.scm.com/Doc/Doc2007.01/ADFGUI/ADFGUI_tutorial/page123.html=

If you're = making an ADF input file yourself, several examples explain how one can = do=A0fragment analysis, e.g.:=A0http:/= /www.scm.com/Doc/Doc2007.01/ADF/Examples/page88.html

If you are using different .run files, use full path = names to the fragment files.=A0Typically one will rename a fragment = TAPE21 to a fragment.t21, like for example,=A0CO.t21.
This one can use as fragment in a further = calculation:

DEFINE
xyzOx=3D3.2501913
END

atoms
1. Ni =A0 0 =A0 =A0 =A0 0=A0 =A0 =A0 =A0 0=A0 2. C=A0 = =A0 xyzC=A0 =A0 xyzC =A0 =A0 xyzC =A0 =A0 f=3DCO/1
3. C =A0 -xyzC =A0 -xyzC =A0 =A0 xyzC =A0 =A0 = f=3DCO/2
4. C=A0 =A0 xyzC =A0 -xyzC=A0 =A0 = -xyzC =A0 =A0 f=3DCO/3
5. C =A0 -xyzC=A0 =A0 xyzC=A0= =A0 -xyzC =A0 =A0 f=3DCO/4
6. O=A0 =A0 = xyzOx =A0 xyzOx=A0 =A0 xyzOx =A0 =A0 f=3DCO/1
7. O =A0 -xyzOx=A0 -xyzOx=A0 =A0 xyzOx =A0 =A0 = f=3DCO/2
8. O=A0 =A0 xyzOx=A0 -xyzOx =A0 = -xyzOx =A0 =A0 f=3DCO/3
9. O =A0 = -xyzOx =A0 xyzOx =A0 -xyzOx =A0 =A0 f=3DCO/4
end

fragments
CO=A0 t21.CO
Ni=A0 = t21.Ni
end

Best = regards,
Stan van Gisbergen

On Dec 4, 2007, at = 2:14 PM, senthil nathan zenthil03^yahoo.co.in wrote:


Sent to = CCL by: "senthil=A0 nathan" = [zenthil03[-]yahoo.co.in]
Dear = CCLrs,
=A0 =A0 =A0 =A0 =A0 =A0 In = connection with my privious question, I want to do fragment analysis for = particular system. My total chemical system is neutral, but its fragment = is charged species. I have done a calculation for both the fragment = files separatly and I have two TAPE21 file for my fragments. For total = fragment analysis I want to read some basic results form TAPE21 fragment = file. Now I am using ADF trial windows version, in this version TAPE21 = file will be a binary result file. I want to do this fragment TAPE21 = file as input file for total fragment analysis. I unable to convert this = binary file as a ADF input file. Any one of you tell me a better = solution for my problem.

thanking you inadvance
best wishes from



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=
Dr. S.J.A. van Gisbergen
Scientific Computing & Modelling NV
Theoretical Chemistry, Vrije Universiteit
De Boelelaan 1083
1081 HV = Amsterdam
The Netherlands=A0=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0

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