MATLAB: How to read a txt and store specific line in matrix

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I have a long txt file and I am interested in a specific lines. The segement that I am interested in is something like:

Activities in Cartesian coordinate

          mode      1
          (       0.000000000       0.346863768       0.194956009 )
          (       0.346863768       0.000000000      -0.000000000 )
          (       0.194956009      -0.000000000       0.000000000 )
          (       0.346863768       0.000000000      -0.000000000 )
          (       0.000000000      -0.346863768       0.194956009 )
          (      -0.000000000       0.194956009      -0.000000000 )
          (       0.187247036       0.000000000       0.000000000 )
          (       0.000000000       0.187247036       0.000000000 )
          (       0.000000000       0.000000000      -0.893848809 )
           mode      2
          (       0.000000000      -0.346863768       0.194956009 )
          (      -0.346863768       0.000000000       0.000000000 )
          (       0.194956009       0.000000000       0.000000000 )
          (      -0.346863768      -0.000000000       0.000000000 )
          (      -0.000000000       0.346863768       0.194956009 )
          (       0.000000000       0.194956009      -0.000000000 )
          (       0.187247036       0.000000000       0.000000000 )
          (       0.000000000       0.187247036       0.000000000 )
          (       0.000000000       0.000000000      -0.893848809 )
           mode      3
          (      -0.000000000       0.292966545      -0.197313262 )
          (       0.292966545       0.000000000       0.000000000 )
          (      -0.197313262       0.000000000       0.000000000 )
          (       0.292966545      -0.000000000       0.000000000 )
          (      -0.000000000      -0.292966545      -0.197313262 )
          (       0.000000000      -0.197313262      -0.000000000 )
          (      -0.182193022      -0.000000000       0.000000000 )
          (      -0.000000000      -0.182193022       0.000000000 )
          (       0.000000000       0.000000000       0.894144988 )
           mode      4
          (       0.000000000      -0.292966545      -0.197313262 )
          (      -0.292966545       0.000000000      -0.000000000 )
          (      -0.197313262      -0.000000000      -0.000000000 )
          (      -0.292966545       0.000000000      -0.000000000 )
          (       0.000000000       0.292966545      -0.197313262 )
          (      -0.000000000      -0.197313262       0.000000000 )
          (      -0.182193022      -0.000000000       0.000000000 )
          (      -0.000000000      -0.182193022       0.000000000 )
          (       0.000000000       0.000000000       0.894144988 )

I want to take each mode and store the 3×3 matrices that correspond to in a variable that have a name like modeij. i is the number of the mode, and j is the index of each matrix.

I hope to hear from you.

Best Answer

fmt1='mode%n';
fmt2=['(' repmat('%f',1,3) ')'];
flds={'X','Y','Z'};
fid=fopen(fname,'r');
dat=struct([]);
i=0;
while ~feof(fid)
  i=i+1;
  dat(i).m=cell2mat(textscan(fid,fmt1,1));
  for j=1:length(flds)
    dat(i).(flds{j})=cell2mat(textscan(fid,fmt2,3,'collectoutput',1)).';
  end
end
fid=fclose(fid);

will return a stuct array dat with fields m,_X_,_Y_,_Z_

You will have to find the initial section in the file before using this code snippet (after the fopen of course) by either knowing a priori a 'headerlines' count number or using a loop and fgetl(fid) to read records until find the section wanted.

A test here returned

>> fname='ZA.dat';
>> ZA
>> whos dat
  Name      Size            Bytes  Class     Attributes
    dat       1x5              3392  struct              
>> dat(1)
ans = 
  struct with fields:
      m: 1
      X: [3×3 double]
      Y: [3×3 double]
      Z: [3×3 double]
  >> dat(1).X
  ans =
           0    0.3469    0.1950
      0.3469         0         0
      0.1950         0         0
  >> dat(2).X
  ans =
           0   -0.3469    0.1950
     -0.3469         0         0
      0.1950         0         0
  >>

Related Solutions

MATLAB: How to import .dat data

fid=fopen('yourfile.dat','r');
data=cell2mat(textscan(fid,'','CollectOutput',1,'CommentStyle','#'));
fid=fclose(fid);

looks like would do it. You'll end up w/ an array of double.

MATLAB: Find all possible combinations of 2 vectores (spin) of a system with N atoms with pondered distance

You have to bear in mind that most of us probably don't work in the same field as you do. Last time I had to worry about atom spin was some 20 years ago... So make sure to explain yourself clearly. Giving us code with syntax errors, or matrices that are not valid syntax does not help.

I want to calculate the distance between each atom,

I assume euclidean distance. That's trivially done, in just one line.

A=[ 0.000000000         0.000000000         0.000000000
    0.000000000         0.000000000         2.700000048
    0.000000000         2.700000048         0.000000000
    0.000000000         2.700000048         2.700000048
    2.700000048         0.000000000         0.000000000
    2.700000048         0.000000000         2.700000048
    2.700000048         2.700000048         0.000000000
    2.700000048         2.700000048         2.700000048
    1.350000024         1.350000024         1.350000024
    1.350000024         1.350000024         4.050000191
    1.350000024         4.050000191         1.350000024
    1.350000024         4.050000191         4.050000191
    4.050000191         1.350000024         1.350000024
    4.050000191         1.350000024         4.050000191
    4.050000191         4.050000191         1.350000024
    4.050000191         4.050000191         4.050000191];
distance = sqrt(sum((permute(A, [1 3 2]) - permute(A, [3 1 2])) .^ 2, 3))

assign the values and 1 (spin) to each atom

That;s really not clear. Going by your +- diagram, I think you want to get all possible combinations of 8 atoms out of 16 (once you've chosen 8 positive spins, the others are negative). That's trivially done again however note that for 16 atoms, there are 12870 such combinations. For more atoms, it will easily get out of hands:

ncombs = nchoosek(size(A, 1), size(A, 1)/2);   %number of combinations. If it's too large the following line will take forever and may even lock your computer
pospin = nchoosek(1:size(A, 1), size(A, 1)/2); %each row is a unique combination of 8 out 16 atoms

We can fill a matrix of -1 and +1 easily from there:

spin = -ones(size(pospin, 1), size(A, 1));  %fill with negative spin
spin(sub2ind(size(spin), repmat((1:size(spin, 1))', 1, size(pospin, 2)), pospin)) = 1; %fill selected atoms with positive spin

calculate all possible combinations of these values.

What values? Again, taking a guess based on your equation:

%using dimensional notation introduced in R2018b, here. 
%in earlier versions, you'd have to call sum twice.
result = squeeze(sum(permute(spin, [3 2 1]) .* permute(spin, [2 3 1]) .* distance, [1 2]))

Best Answer

Related Solutions

MATLAB: How to import .dat data

MATLAB: Find all possible combinations of 2 vectores (spin) of a system with N atoms with pondered distance

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