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How can I compute the distance formula between two specific atoms when these two atoms have different xyz coordinates each time?

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Naif Nawaf 2021-8-28

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评论： Naif Nawaf 2021-8-30

在 MATLAB Online 中打开

I have similar data table to this:

A = 10x3
 C -0.7146 0.5304 -1.1481
 C -1.1512 0.7561 0.4465
 C 0.9622 1.8652 0.1832
 C 0.2667 0.1483 -0.5122
 C -1.0791 -2.5351 -0.7354
 H -1.2107 1.7495 -1.6239
 H -0.3533 -0.4565 -1.5120
 H 1.8556 -0.3747 -0.2835
 C 0.5873 -0.5978 -1.3833
 C 0.3756 -1.4333 -1.3172
A = 10×3
 C -0.8346 0.6204 -1.0881
 C -1.7712 0.7661 0.5565
 C 0.7822 1.0052 0.6832
 C 0.2667 0.1483 -0.5122
 C -1.0791 -2.5351 -0.7354
 H -1.2111 1.7295 -1.1001
 H -0.3422 -0.4733 -1.7731
 H 1.8661 -0.3617 -0.2881
 C 0.5611 -0.5272 -1.0844
 C 0.8742 -1.9703 -1.8312

And this data is repeated 20 times with different values of xyz coordinates each time, so I want to pick up only the second row and the fourth row and calculate the distance formula for these two points of each data table. so the result has to be 20 answers of distances. How can I do that, please? I don’t know if this needs loop and how?

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DGM 2021-8-28

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编辑：DGM 2021-8-28

A is a lone 10x3 array. It's not a 10x3x20 array or something. Where did the other 19 come from? Are they coming from something overwriting A in a loop and dumping results to console? If so, they're gone. How can that be fixed? Nobody knows how to fix code that nobody can see.

What class of array is that? Is this part of some particular toolbox?

Naif Nawaf 2021-8-28

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I added part of the data table with the question to explain what I need to calculate

Walter Roberson 2021-8-28

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How does each 10 x 3 A array arrive in your workspace?

Naif Nawaf 2021-8-28

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This data is xyz coordinates of a molecule which is generated from other calculation called Siesta, so I already have the data and need to calculate the distance formula

Walter Roberson 2021-8-28

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编辑：Walter Roberson 2021-8-29

在 MATLAB Online 中打开

So could you do

N = 20;
all_A = cell(N, 1);
for K = 1 : N
   A = call_to_Siesta(parameters);
   all_A{K} = A;
end

If so then

row2s = cellfun(@(A) A(2,:), all_A, 'uniform', 0);
row4s = cellfun(@(A) A(4,:), all_A, 'uniform', 0);
dists = zeros(N,1);
for K = 1 : N
  dists(K) = norm(row2s{K} - row4s{K});
end

dists = zeros(N,1)
for K = 1 : N
  dists(K) = norm(A{K}(2,:) - A{K}(4,:));
end

which does not require the temporary variables.

Naif Nawaf 2021-8-29

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Hi,

row2s = cellfun(@(A) A(2,:), all_A, 'uniform', 0); row4s = cellfun(@(A), A(4,:), all_A, 'uniform', 0);

These have error when I run the code, I think because of @ , could you please help me to correct it

Walter Roberson 2021-8-29

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I had an extra comma in the row4s but the row2s should have been fine.

The @ is not an error in that code: the @ introduces an anonymous function that cellfun() is going to execute.

Naif Nawaf 2021-8-29

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I have sent photos for the code and the data, Are you able to see them?

Naif Nawaf 2021-8-29

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image.jpg
image.jpg

I have attached two photos of the data table and the code to be clear for you what I did, because I am still struggling with it.

Here the data is repeated 3 times for simplicity, so I put N=3;

The line A=call_to_siesta(parameters); doesn’t make sense to me!

The name of the data file is mol2.xyz

Could you help me to run the code correctly, please.

Walter Roberson 2021-8-29

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在 MATLAB Online 中打开

You need to replace

A = call_to_Siesta(parameters);

with assigning A one set of "xyz coordinates of a molecule which is generated from other calculation called Siesta". It was a placeholder line, intended to show you where you have to insert your code that makes the call to Siesta and gets back information for one molecule.

Naif Nawaf 2021-8-29

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编辑：Naif Nawaf 2021-8-29

I wrote

A=importdata(‘mol2.xyz’,’ ‘,2);
A=A.data;

and it works well.

The last question; if I want to save the results in a new file, what should I add to the code?

Walter Roberson 2021-8-29

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You can use writematrix()

Naif Nawaf 2021-8-30

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