[DFTB-Plus-User] DFTB-Plus-User Digest, Vol 72, Issue 5

孙萍萍 pps265616 at 126.com
Thu Jan 9 09:51:46 CET 2014 

Dear Dr. Aradi,
Is there any solution for my system? Is there any way to make the grids become the same?
Ariel
Best wishes !






At 2014-01-08 19:00:01,dftb-plus-user-request at dftb-plus.info wrote:
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>Today's Topics:
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>   1. waveplot-cubemanip error (???)
>   2. Re: waveplot-cubemanip error (B?lint Aradi)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 7 Jan 2014 20:55:18 +0800 (CST)
>From: ??? <pps265616 at 126.com>
>To: dftb-plus-user at dftb-plus.info
>Subject: [DFTB-Plus-User] waveplot-cubemanip error
>Message-ID: <78947557.d742.1436cc57c55.Coremail.pps265616 at 126.com>
>Content-Type: text/plain; charset="gbk"
>
>Dear DFTB users,
>I am wondering if any of you have used the cubemanip and got a correct result.
>In my system I have 3 parts and I would like to see the charge density difference of the three parts.
>By doing the following command operation?/cubemanip '(($1)-(($2)+($3)))' ./mha-wp-abs2.cube ./c258-wp-abs2.cube ./tio2-wp-abs2.cube >> diff.cube
>But what I got is the following presentation:
>Warning: Nr. of atoms in './mha-wp-abs2.cube' and './c258-wp-abs2.cube' differ
>Warning: Origins in './mha-wp-abs2.cube' and './c258-wp-abs2.cube' differ!
>Warning: Grid vectors in './mha-wp-abs2.cube' and './c258-wp-abs2.cube' differ!
>Warning: Grid vectors in './mha-wp-abs2.cube' and './c258-wp-abs2.cube' differ!
>Warning: Nr. of atoms in './mha-wp-abs2.cube' and './tio2-wp-abs2.cube' differ
>Warning: Origins in './mha-wp-abs2.cube' and './tio2-wp-abs2.cube' differ!
>Warning: Grid vectors in './mha-wp-abs2.cube' and './tio2-wp-abs2.cube' differ!
>Warning: Grid vectors in './mha-wp-abs2.cube' and './tio2-wp-abs2.cube' differ!
>
>When the generated diff.cube was opened by VMD, unfortunately the results was not what I expected.
>
>In my3 input files, with "PlottedRegion = OptimalCuboid{} " the same keywords, while the 3  the generated wp-abs2.cube, the look like these:
>
>mha-wp-abs2.cube' file generated by WAVEPLOT from data created by DFTB+
>Calc-Id: 2120337279, abs2
>       915 -0.3538554741E+01 -0.2998029197E+02 -0.5821002632E+01
>        50  0.1739376038E+01  0.0000000000E+00  0.0000000000E+00
>        50  0.0000000000E+00  0.1806128094E+01  0.0000000000E+00
>        50  0.0000000000E+00  0.0000000000E+00  0.1664716535E+01
>
>c258-wp-abs2.cube'  file generated by WAVEPLOT from data created by DFTB+
>Calc-Id: 1804654847, abs2
>       147  0.1169264412E+02 -0.2261664943E+02 -0.4599651333E+02
>        50  0.1074251134E+01  0.0000000000E+00  0.0000000000E+00
>        50  0.0000000000E+00  0.1440992111E+01  0.0000000000E+00
>        50  0.0000000000E+00  0.0000000000E+00  0.7818494399E+00
>
>tio2-wp-abs2.cube'  file generated by WAVEPLOT from data created by DFTB+
>Calc-Id: 1053559680, abs2
>       768 -0.5339960345E+01 -0.2996371620E+02 -0.5572606993E+01
>        50  0.1746044080E+01  0.0000000000E+00  0.0000000000E+00
>        50  0.0000000000E+00  0.1805311552E+01  0.0000000000E+00
>        50  0.0000000000E+00  0.0000000000E+00  0.4377307706E+00
>
> I hope to get your help by finding the mistake to get the correct diff.cube by using cubemanip.
>
>Best wishes.
>
>Hoping to get your good news.
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>------------------------------
>
>Message: 2
>Date: Tue, 07 Jan 2014 14:18:47 +0100
>From: B?lint Aradi <balint.aradi at bccms.uni-bremen.de>
>To: User list for DFTB+ related questions
>	<dftb-plus-user at dftb-plus.info>
>Subject: Re: [DFTB-Plus-User] waveplot-cubemanip error
>Message-ID: <52CBFEB7.7030901 at bccms.uni-bremen.de>
>Content-Type: text/plain; charset="utf-8"
>
>> By doing the following command operation?/cubemanip '(($1)-(($2)+($3)))' ./mha-wp-abs2.cube ./c258-wp-abs2.cube ./tio2-wp-abs2.cube >> diff.cube
>> But what I got is the following presentation:
>> Warning: Nr. of atoms in './mha-wp-abs2.cube' and './c258-wp-abs2.cube' differ
>> Warning: Origins in './mha-wp-abs2.cube' and './c258-wp-abs2.cube' differ!
>> Warning: Grid vectors in './mha-wp-abs2.cube' and './c258-wp-abs2.cube' differ!
>> Warning: Grid vectors in './mha-wp-abs2.cube' and './c258-wp-abs2.cube' differ!
>> Warning: Nr. of atoms in './mha-wp-abs2.cube' and './tio2-wp-abs2.cube' differ
>> Warning: Origins in './mha-wp-abs2.cube' and './tio2-wp-abs2.cube' differ!
>> Warning: Grid vectors in './mha-wp-abs2.cube' and './tio2-wp-abs2.cube' differ!
>> Warning: Grid vectors in './mha-wp-abs2.cube' and './tio2-wp-abs2.cube' differ!
>
>The cube file contains two kind of information. The geometry of your
>structure (position of your atoms) and some volumetric data (e.g. charge
>density) on a grid. The tool "cubemanip" can only handle cases
>correctly, where the grid for the volumetric data is the same, which is
>apparently not the same in your case ("Grid vectors ... differ"). You
>should only compare similar systems (similar in size and structure) with
>that tool.
>
>  Best regards,
>
>  B?lint
>
>-- 
>Dr. B?lint Aradi
>Bremen Center for Computational Materials Science, University of Bremen
>http://www.bccms.uni-bremen.de/cms/people/b_aradi/
>
>
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