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I have following .txt file:

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
5500
ITEM: BOX BOUNDS pp pp pp
-8.3282525640612670e-02 1.2318704739253342e+01
-5.7499999999999996e-01 1.0925000000000001e+01
-5.5720358308663780e+00 5.0148322477797400e+01
ITEM: ATOMS id element xu yu zu 
1 A  1.074  0.000  4.843 
2 A  0.691  0.000  3.919 
...
ITEM: TIMESTEP
1000
ITEM: NUMBER OF ATOMS
5500
ITEM: BOX BOUNDS pp pp pp
-8.3282525640612670e-02 1.2318704739253342e+01
-5.7499999999999996e-01 1.0925000000000001e+01
-5.5720358308663780e+00 5.0148322477797400e+01
ITEM: ATOMS id element xu yu zu 
1 A  1.074  0.000  4.843 
2 A  0.691  0.000  3.919
...

What I would like to do is to, basing on the aforementioned file, create a list according to the pattern:

{{{0,1,A,1.074,0.000,4.843},{0,2,A,0.691,0.000,3.919},...},{{1000,1,A,1.074,0.000,4.843},{1000,2,A,0.691,0.000,3.919},...}

In other words, I would like to take the value which is after the line "ITEM: TIMESTEP", skip reading next lines up to line "ITEM: ATOMS id element xu yu zu", after which we take all rows till next line "ITEM: TIMESTEP". We repeat this process $n$-times, where $n$ is the number of "TIMESTEPS".

I am aware that I can do it by importing the file as a list through command IMPORT and onward use TABLE to pinpoint desired elements, but it seems to be the least efficient method.

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0
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High-performance operation on files is not my expertise, especially in Mathematica. Here is another solution that involves python along with ExternalFunction. First you need to install python from the official site:

Save this code as a python file (I will save it as "C:\file.py"):

def read_my_format(file):
    read = 0
    r1 = []
    r2 = []
    temp = []
    result = []
    with open(file,'r') as f:
        for line in f.readlines():
            if line == 'ITEM: TIMESTEP\n':
                read = 1
                continue

            elif line == 'ITEM: BOX BOUNDS pp pp pp\n' or line == 'ITEM: NUMBER OF ATOMS\n':
                read = 0
                continue

            elif line.strip() == 'ITEM: ATOMS id element xu yu zu':
                read = 2
                continue

            if read == 1:
                r1.append(int(line))
                if temp:
                    r2.append(temp)
                    temp = []
                read = 0
            
            elif read == 2:
                c = line.strip().replace('  ',' ').split(' ')
                c1 = float(c[0])
                c2 = map(float,c[2:])
                temp.append([c1,c[1],*c2])
        r2.append(temp)

    for i,vs in enumerate(r2):
        temp2 = []
        for v in vs:
            temp2.append([r1[i],*v])
        result.append(temp2)
    
    return result

Use the new function introduced in V12:

myFormat = ExternalFunction["Python", ReadString@"C:\\file.py"]

Now apply it:

myFormat["C:\\data.txt"];

Note: I test it on a 11.5 MB data file and it tooks 3.8 seconds to call python from Mathematica, read and parse the file in python and translate back the result. If you only use python and get the result in the python environment, it's around 0.6 seconds (it means Mathematica takes ~3 seconds to translate data to it's data types).

You could also register it as an import format.

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For creating a custom import format, read this article.

ImportExport`RegisterImport["MyFormat", MyFormat`MyFormatImport]
MyFormat`MyFormatImport[filename_String, options___] := 
 Module[{stream, result, lines, parser},
  
  parser1[line_String] := SemanticImportString[line, "Integer", "Rows"];
  parser2[line_String] := 
   First@SemanticImportString[
     StringReplace[line, "  " -> " "], {"Real", "String", "Real", 
      "Real", "Real"}, "Rows", Delimiters -> " "];
  
  stream = OpenRead[filename];
  lines = ReadList[stream, "String"];
  result = 
   Tuples /@ 
    Transpose@{parser1 /@ 
       Part[lines, Flatten@Position[lines, "ITEM: TIMESTEP"] + 1],
      parser2 /@
         lines[[#[[1]] + 1 ;; #[[2]] - 1]] & /@
       Flatten /@ 
        Transpose@{Position[lines, "ITEM: ATOMS id element xu yu zu "],
          Append[Position[lines, "ITEM: TIMESTEP"][[2 ;;]], {0}]}
      };
  
  Close[stream];
  Return[Map[Flatten, #, {2}] &@result]]

Import your file with the defined format:

Import["C:\\data.txt", "MyFormat"]

(*Out: {{{0, 1., "A", 1.074, 0., 4.843}, {0, 2., "A", 0.691, 0., 3.919}}, {{0, 1., "A", 1.074, 0., 4.843}, {0, 2., "A", 0.691, 0., 3.919}}} *)

Note: ITEM: BOX BOUNDS pp pp pp data should be separated by 1 or 2 spaces.

C:\\data.txt is your raw data without ....

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1
  • $\begingroup$ Very neat and stylish approach. However, when tested on file (4 MB) it takes ages for a cell to initiate, without any sign of possible successful output (after a finite time). $\endgroup$ – ATomek Mar 5 at 23:24
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Here is one way to read this. It is assumed, the data is in a file with name "name":

name = "d:/tmp/test.txt";
getDat[nam_] := Module[{fil, lin, tab}, fil = OpenRead[nam];
  tab = Reap[
     While[Find[fil, "ITEM: ATOMS"] =!= EndOfFile, 
       While[((lin = ReadLine[fil]) =!= EndOfFile) && (lin = 
            StringSplit[lin]; lin[[2]] == "A"),
         lin = MapAt[ToExpression, lin, {{1}, {3}, {4}, {5}}];
         Sow[lin];];];][[2]];
  Close[fil];
  tab]

getDat[name]

enter image description here

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  • $\begingroup$ Thanks @DanielHuber. However, your solution omits to print the first element as the timestep i.e. {Timestep, 1, A, 1.074,0,4.843} and in the case of a file that has e.g. 5500 lines between subsequent timesteps, it prints only 9 of them and not for all timesteps. $\endgroup$ – ATomek Mar 5 at 23:21
  • $\begingroup$ You are right. I did not take into account that there could be more than 9 items. I corrected this, tell me if everything is o.k. now. $\endgroup$ – Daniel Huber Mar 6 at 9:52
  • $\begingroup$ Unfortunately, still 9 items are displayed. $\endgroup$ – ATomek Mar 6 at 12:45
  • $\begingroup$ Grrrr..., I copied the old code. $\endgroup$ – Daniel Huber Mar 6 at 13:05

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