Messages

16

General Questions and Answers / Re: Fcc NaCl including 8 atoms

« on: January 7, 2014, 07:55 »

Dear m.guo_johnson

Several atoms are occupying same coordinates.
You can check this by
Builder -> Select -> Close Neighbors
and click "Select" (see attached file).

Please check your configuration.

BR
Shinji

17

General Questions and Answers / Re: Fcc NaCl including 8 atoms

« on: January 6, 2014, 04:02 »

Dear m.guo_johnson

I suppose you construct some incorrect structure for the fcc NaCl.
For example, the lattice vectors are too short.
Could you put your input file?

BR
Shinji

18

General Questions and Answers / Re: Random Alloy

« on: December 24, 2013, 02:48 »

Dear Hesam

If you want to create a completely random structure of alloy, Packmol (http://www.ime.unicamp.br/~martinez/packmol/) will be a good tool to try.

BR
Shinji


 

19

General Questions and Answers / Re: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base

« on: December 19, 2013, 01:50 »

Dear GJK

1. I can save the mol file format only as txt after opening from the drug bank,while giving the save as option .Just help me how to save in mol format.
Right click on the mol character part in the web and save it.  

2.I lack the procedure to convert it to .xyz files using open babel.Kindly help me in sorting out this problem? so that I can start my research.
See. http://quantumwise.com/forum/index.php?topic=2543.msg11886#msg11886
and http://openbabel.org/wiki/Babel

3.Even though I tried for file conversion using open babel I could not save the output file.Kindly also specify the destination folder.
I think you can get a saved xyz file by procedure 2.

BR

20

General Questions and Answers / Re: Question about zero charge at 0 bias

« on: December 17, 2013, 14:40 »

Dear kaypu

I could get a converged result at least for the first scf step.
1.  I used a Recursion method as Anders mentioned
2.  Add extra surface layers in the central region

See input and output files I attached (compressed).

 

21

General Questions and Answers / Re: Question about zero charge at 0 bias

« on: December 17, 2013, 02:25 »

I could not get the py file you put.  The size is Zero kilobyte.

22

General Questions and Answers / Re: MOS2 bandstructure

« on: December 16, 2013, 07:59 »

I tried the calculation and could reproduce the bandstructure in the paper.
I used LDA instead of Slater-Koster.

23

General Questions and Answers / Re: outputing a file describing bond connectivity

« on: December 2, 2013, 03:08 »

if you just want to get a bond index table, you can obtain it by converting xyz file to mol file.

1. Output your structure in the XYZ format
2. Install Openbabel from http://openbabel.org/wiki/Main_Page
3. Launch your terminal or cmd.exe
4. Go to  the directory the XYZ file located
5. Command will be
> babel -ixyz C60.xyz -omol C60.mol

You will get the bond index table at the below part of the Molfile.
Like
  2  3  2  0  0  0  0
means Number 2 atom and Number 3 atom are bonding by a double bond.

As Anders mentioned these bond descriptions are not physical and just a conventional description.

24

General Questions and Answers / Re: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base

« on: November 6, 2013, 02:06 »

Dear GJK

I think you can download structures as a Mol format and
use openbabel (http://openbabel.org/wiki/Main_Page) to convert it to XYZ format.

BR
Shinji

25

General Questions and Answers / Re: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base

« on: November 1, 2013, 02:41 »

There are several drug databases.
http://www.drugbank.ca/
http://www.genome.jp/kegg/drug/

26

News and Announcements / 出展情報【2013年10月24日投稿】

« on: October 24, 2013, 06:35 »

各位

QuantumWise Japanは下記の学会に出展いたします。
皆様におかれましては、ぜひとも弊社ブースにお立ち寄りください。

ACSIN-12 & ICSPM21
期間：2013年11月5日(火) - 8日(金)
場所：Tsukuba International Congress Center, Tsukuba, Japan
　　　　大会議室101前
URL:http://dora.bk.tsukuba.ac.jp/event/acsin12/

27

General Questions and Answers / Re: broken bonds in carbon nanotube when optimization

« on: September 12, 2013, 02:44 »

If you are assuming Cu-C bonds as covalent ones the optimized bond length 2.0 Ang is reasonable.

My idea to relax the initial structure :
The Cu tube radius of your structure is too big, I mean the strain between CNT and Cu are too tight.
Making a smaller radius of Cu tube, you can construct more relaxed structure as the starting point of the optimization.

And also to enlarge the CNT radius is an alternative idea to release the strain in the system.

Hi Mr. Usui, thanks for your answer.
I am not sure about the initial distance. I did use 1.5 Angstrom as the initial one, but after relaxation, for device with less copper atoms, it always arrive at the value of around 2 Angstrom.
I am not sure if that's OK for these device results.
I mean, since it will always go through optimization, finally it would arrive at the equilibrium bond length.
Am I understanding it right?

Secondly, what do you mean by "You should make more relaxed structure as the initial configuration for the optimization"?

Please check the covalent radius of Cu and C.  
Approximate values of them are
Cu = 1.32 Ang.
C = 0.73 Ang (sp2)
by Wiki.
So the initial bond length of the Cu-C for the optimization calculation should be around 1.32 + 0.73 =~ 2.0 Ang.

Looking your initial configuration for the optimization some Cu-C length are too short ( around 1.46 Ang)
and too much forces could be applied to the system and you found the C-C bond breaking.

You should make more relaxed structure as the initial configuration for the optimization.

28

General Questions and Answers / Re: broken bonds in carbon nanotube when optimization

« on: September 11, 2013, 07:54 »

Please check the covalent radius of Cu and C.  
Approximate values of them are
Cu = 1.32 Ang.
C = 0.73 Ang (sp2)
by Wiki.
So the initial bond length of the Cu-C for the optimization calculation should be around 1.32 + 0.73 =~ 2.0 Ang.

Looking your initial configuration for the optimization some Cu-C length are too short ( around 1.46 Ang)
and too much forces could be applied to the system and you found the C-C bond breaking.

You should make more relaxed structure as the initial configuration for the optimization.

29

News and Announcements / 出展情報【2013年8月14日投稿】

« on: August 14, 2013, 09:31 »

各位

QuantumWise Japanは下記の学会に出展いたします。
皆様におかれましては、ぜひとも弊社ブースにお立ち寄りください。

第37回 日本磁気学会学術講演会
期間：2013年9月3日(火) - 6日(金)
場所：北海道大学工学部　（展示会場１Fロビーおよび１F発表会場前通路）
URL：http://www.magnetics.jp/kouenkai/2013/

5th International Conference on Recent Progress in Graphene(RPGR2013)
期間：2013年9月9日(月) - 13日(金)
場所：東京工業大学（東工大蔵前会館（目黒区大岡山））
URL：http://lt.px.tsukuba.ac.jp/RPGR2013/

30

General Questions and Answers / Re: Extra output when running parallel calculations

« on: May 23, 2013, 09:09 »

When you use the “print” command in the mpich2 parallel execution you should add “if processIsMaster():” before the print command in the input file.

print total_energy.evaluate().inUnitsOf(eV)
in the serial execution becomes
if processIsMaster(): print total_energy.evaluate().inUnitsOf(eV)
in the parallel

Your log file issue will be improved by this method.

See also
http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.processismaster.html

I could not understand the nc file issue.  But I suspect you run the calculation twice, it will generate the double data in ncfile.