Insert data into a file at specific position

Question

I have searched all over and can't figure out how to export data into an existing preformated file (quantum espresso input file) at a specific position.

Here is what I am trying to achieve. If the preformated file has the following structure:

&control
....
/

&system
.....
/

...

ATOMIC_POSITIONS
Si    0.0    0.0    0.0
Si    0.5    0.5    0.5

K_POINTS {automatic}
5 5 5 0 0 0

Now, I have written a small program to generate the atomic positions for a series of input files I need to create to run some QE jobs. The problema is that I have to export them first into separate files in the format shown under the ATOMIC_POSITIONS section. Then I have to go copy paste them in each input file. I can post the way I am generating the positions but it is quite trivial.

My questions is: is it possible to generate the positions and then insert them under the ATOMIC_POSITIONS line directly from Mathematica?

For smaller structures with small number of atoms, I can do this from bash, although is not very nice since I have to use bc and is quite cumbersome. For larger number of atoms, becomes very laborious and I am hoping there is a Mathematica solution.

Thanks

Edit: I did some digging and I think the answer lies within string operations. However, I can't figure out how to import everything as a string and then work with lines. It would be easy if I could tell mathematica to replace all lines below the ATOMIC_POSITIONS and above K_POINTS. Within the preformatted file there is a variable that sets the number of atoms which can be used to obtain the number of lines to be replaced. I'll keep digging!

Answer 1

While it would not be difficult to do this explicitly with importing the content and some string-replacing, it seems to be a nice use case for the templating system. The following should do what I think you need:

template = FileNameJoin[{$HomeDirectory, "Desktop", "qeinput.tmp"}]
outputfile = StringReplace[template, ".tmp" -> ".inp"]
atomicpositions = {{"Si", 0.0, 0.0}, {"Si", 0.5, 0.5}};
FileTemplateApply[
  FileTemplate[template],
  <|"AtomicPositions" -> ExportString[atomicpositions, "Table"]|>,
  outputfile
]

to check the result you could do:

FilePrint[outputfile]

Some notes:

• the content of the template would contain a string `AtomicPositions` where you want those to be inserted:

  ...
  ATOMIC_POSITIONS
  `AtomicPositions`
  
  K_POINTS {automatic}
  ...
  

• if the backquotes would cause problems for your specific file format, you probably would need to resort to lower level functionality ( Import, StringReplace and Export) with which you can use markers for the template slots that are OK for your file format.

• if the program to read the file is picky about exact positions/alignments in the ATOMIC_POSITIONS section, you would need some extra effort to format the table exactly how the program expects it instead of the simple ExportString[atomicpositions,"Table"].