Reading vector data from an external file

[Benjamin Morgan]

Is it possible to load data for showing vectors from an external file, to avoid having to add each vector by hand through the View > Vectors… dialogue?

Alternatively, is there an input file format that I could generate that would allow me to include vectors alongside the atom positions?

[Koichi Momma]

Hi,

> Is it possible to load data for showing vectors from an external file,

> to avoid having to add each vector by hand through the View > Vectors�
> dialogue?

No but I am now working on it.
I am going to fully support magnetic CIF format.
http://www.iucr.org/iucr/commissions/magnetic-structures

> Alternatively, is there an input file format that I could generate
> that would allow me to include vectors alongside the atom positions?

Currently, VESTA can only read vector information from *.vesta format.
Manually generating *.vesta files containing vector information is not a
straightforward task because you have to calculate serial number of all
the atoms in the drawing boundary using exactly the same algorithm
adopted by VESTA.

I am going to change the file format of *.vesta anyway to support
magnetic symmetry operations. So please wait a while longer.

Best regards,

Koichi

[b.lu...@gmail.com]

Hello,
I am inserting vectors with a script into the *.vesta file in the following way:

after:

DLPLY
 -1

I insert for example:

ARROW
   1 0.835 -0.631 1.174  1.000  0.500 255 0 0 1
 96 -1
 0 0 0 0 0 0 0 0 0

that should mean: on atom 96 (third line first velue) insert vector (0.835 -0.631 1.174) (second line values 2, 3 and 4) with color rgb red (255 0 0 second line values 7, 8 and 9)
and I do this for every vector by adding the same 4 lines and by changing only the number of the atom  and the coordinates of the vector.

It seams to work but I am not sure since I don't understand the meaning of the other values so I suggest this meathod but have to ask:
Is it correct?
what is the meaning of the other values?

Thank you very much,

Luigi.

[Koichi Momma]

Dear Luigi,

You are correct.
The format and meaning of each key is as follows.

ARROW
ID u v w H W R G B flag
atom_ID1 atom_ID2... -1

H is height in angstrom, and W is radius of the arrow. The actual radius is scaled by W*0.4.
Orientation of the arrow is defined by a lattice vector [u, v, w].
If flag=1, the arrow penetrates an atom sphere, and if flag=0, the arrow at the one side of an atom.

Best regards,
Koichi

b.lu...@gmail.com wrote,On (1/24/14, 3:23 AM):

> Hello,
> I am inserting vectors with a script into the *.vesta file in the following way:
>
> after:
>
> DLPLY
> -1
>
> I insert for example:
>
> ARROW
> 1 0.835 -0.631 1.174 1.000 0.500 255 0 0 1
> 96 -1
> 0 0 0 0 0 0 0 0 0
>
> that should mean: on atom 96 (third line first velue) insert vector (0.835 -0.631 1.174) (second line values 2, 3 and 4) with color rgb red (255 0 0 second line values 7, 8 and 9)
> and I do this for every vector by adding the same 4 lines and by changing only the number of the atom and the coordinates of the vector.
>
> It seams to work but I am not sure since I don't understand the meaning of the other values so I suggest this meathod but have to ask:
> Is it correct?
> what is the meaning of the other values?
>
> Thank you very much,
>
> Luigi.
>
> On Monday, November 18, 2013 1:55:30 PM UTC+1, K.M. wrote:
>
> Hi,
>
> > Is it possible to load data for showing vectors from an external file,
> > to avoid having to add each vector by hand through the View > Vectors�
> > dialogue?
>
> No but I am now working on it.
> I am going to fully support magnetic CIF format.

> http://www.iucr.org/iucr/commissions/magnetic-structures <http://www.iucr.org/iucr/commissions/magnetic-structures>

>
> > Alternatively, is there an input file format that I could generate
> > that would allow me to include vectors alongside the atom positions?
>
> Currently, VESTA can only read vector information from *.vesta format.
> Manually generating *.vesta files containing vector information is not a
> straightforward task because you have to calculate serial number of all
> the atoms in the drawing boundary using exactly the same algorithm
> adopted by VESTA.
>
> I am going to change the file format of *.vesta anyway to support
> magnetic symmetry operations. So please wait a while longer.
>
> Best regards,
>
> Koichi
>

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--
Koichi Momma
National Museum of Nature and Science
4-1-1, Amakubo, Tsukuba, Ibaraki 305-0005, Japan
TEL: +81-(0)29-853-8163
FAX: +81-(0)29-853-8998
k-m...@kahaku.go.jp
vest...@gmail.com

[Cheng Mei]

is this now can be done?

[Cheng Mei]

yes, I found it. thanks

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[S.E B.O]

Would anyone please explain how is it working now?

Best,

S.E

[Cheng Mei]

If this is that you wanted to know.

Adding arrow manually in vesta:

 

Edit>vector>new>give dimensions to the arrow.

[S.E B.O]

Thank you so much Cheng, but I'm looking for importing the vectors from file.