# Reader/writer for xyz files
import particle
import strutils
import strscans
import strformat
import linalg

proc parseXyz*(path: string): seq[Particle] =
    let f = readFile(path)
    let lines = f.split("\n")
    var i = 0
    while i <= lines.high():
        # read a single frame
        # read atom count
        let atomCount = parseInt(lines[i])
        inc i

        # the comment
        let comment = lines[i]
        inc i

        var x, y, z: float
        var name: string
        # the atoms
        if i + atomCount + 1 >= lines.high(): # tolerate empty line at end
            for j in 0..atomCount-1:
                if not lines[i + j].scanf("$s$w$s$f$s$f$s$f$s", name, x, y, z):
                    raise newException(Defect, "Invalid format on line " & $i)
                result.add(newParticle(name, vector(x, y, z), massFromName(name)))
            break
        i += atomCount

proc appendXyz*(f: File, parts: seq[Particle], t: float) =
    # f should be open in APPEND mode
    f.writeLine(parts.len()) # atom count
    f.writeLine("t = " & $t) # comment line containing the time
    for atom in parts:
        let pos = atom.pos
        f.writeLine(&"{atom.name} {pos.x} {pos.y} {pos.z}")