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谢信锐

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Apr 13, 2020, 10:04:27 PM4/13/20
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Hi,
I encountered a problem when I use ctp as follows:
ERROR: Could not allocate MD atoms to QM atoms or weights in fragment T5H1 in segment T5H1 in molecule T5H1 due to inconsistent number of columns (MD: 93, QM: 93) Weights: 0).
NOTE: To define an MD atom without QM counterpart, insert a single ':' in the associated QM-atoms column and specify a mapping weight of 0.
an error occurred:
Inconsistency in mapping file.

I compared the sample mapping.xml, and found that the mapping.xml I prepared has not </weights> . Please see attachment!

I guess that I know how to define weights, I should define them by myself ?







Could you give me some suggestions?

system.xml

Christoph Junghans

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Apr 13, 2020, 10:10:58 PM4/13/20
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This is the votca (csg/xtp) mailing list, please ask your ctp-related
questions on votc...@googlegroups.com.

Thanks,

Christoph
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Christoph Junghans
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谢信锐

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Apr 13, 2020, 10:15:57 PM4/13/20
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OK

> -----Original Messages-----
> From: "Christoph Junghans" <jung...@votca.org>
> Sent Time: 2020-04-14 10:10:46 (Tuesday)
> To: "vo...@googlegroups.com" <vo...@googlegroups.com>
> Cc:
> Subject: Re: [votca] system

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e5SoYks5EuEQPZuex6%3DdoEj9BCadiFNAKfHnRDcCGajGA%40mail.gmail.com.

Denis Andrienko

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Apr 14, 2020, 7:29:02 AM4/14/20
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Your T5H1 seems to contain only hydrogens? How did you prepare your mapping file? Using pdb2map? Please give more details. Denis

谢信锐

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Apr 14, 2020, 9:21:39 AM4/14/20
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Yes, I use pdb2map to construct mapping file from .gro and .xyz file. I found and solved the problem. In the .xyz file,  atom label is like H12 C13 C14, there are unnecessary numbers, so I failed to prepare right mapping file.


a) There is another simple but somewhat uncertain question! If an organic molecular semiconductor contains over 100 atoms, and is also a conjugated molecule,  I don't partition it into different fragments and treat it as a whole. This opinion is right? The partitioning is optional?


b) To run the commend of kmcmultiple, it often use one thread, can we add several threads to run the task?


c) kmc calculation is time-consuming? I run an amorphous cell containing 100 molecules (100 atoms as a segment, not partitioning), and find that several hours have been spent and it still runs in one thread.


Thank you very much!


Sincerely!





-----Original Messages-----
From:"Denis Andrienko" <andr...@mpip-mainz.mpg.de>
Sent Time:2020-04-14 19:29:02 (Tuesday)
To: vo...@googlegroups.com

Cc:
Subject: Re: [votca] system

Your T5H1 seems to contain only hydrogens? How did you prepare your mapping file? Using pdb2map? Please give more details. Denis

On 14.04.2020 04:04, 谢信锐 wrote:
Hi,
I encountered a problem when I use ctp as follows:
ERROR: Could not allocate MD atoms to QM atoms or weights in fragment T5H1 in segment T5H1 in molecule T5H1 due to inconsistent number of columns (MD: 93, QM: 93) Weights: 0).
NOTE: To define an MD atom without QM counterpart, insert a single ':' in the associated QM-atoms column and specify a mapping weight of 0.
an error occurred:
Inconsistency in mapping file.

I compared the sample mapping.xml, and found that the mapping.xml I prepared has not </weights> . Please see attachment!

I guess that I know how to define weights, I should define them by myself ?



Could you give me some suggestions?
andr...@mpip-mainz.mpg.de

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谢信锐

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Apr 14, 2020, 11:03:59 PM4/14/20
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I think that I find why the kmc calculation is time-consuming. Something is wrong with the rates calculation, why the extracted rates are zero? It is very confusing!

Kind regard!


-----Original Messages-----
From:"谢信锐" <2173...@zju.edu.cn>
Sent Time:2020-04-14 21:21:30 (Tuesday)
To: vo...@googlegroups.com
Cc: andr...@mpip-mainz.mpg.de
Subject: Re: Re: [votca] system
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