private void RunLammpsUsingSGE(string file, string extraArgs, string workingdir, int linknum)
{
var flagFile = Path.Combine(workingdir, "linker" + linknum + "-ave-force.d"); // says if lammps is finished
if (File.Exists(flagFile))
{
File.Delete(flagFile);
}
// Tell qsub to run with binary
const string lammpsExecutable = "/home/manion/expansion/Downloads/lammps-16Feb16/src/lmp_ubuntu";
//var lammpsExecutable = Path.Combine(Settings.OutputDirAbs, "lmp_serial");
var arguments = " -in " + file + " " + extraArgs;
var fullArguments = lammpsExecutable + arguments;
var jobname = "linker" + linknum + " -b y -wd " + workingdir + " "; //execute as binary
OBFunctions.submitlammps(fullArguments, workingdir, jobname); // lmp -v Linker "linker-" -v LinkerRoot
while (!File.Exists(flagFile))
{
}
// Console.WriteLine(flagFile);
}