Dear All,

I have written a perl script to create a new xtd file, loop over each frame, copy the contents  to a temporary document, delete the atoms that I don't want from the  temporary document and append it to the new new trajectory and repeat  for all frames, but when it debug, it has something wrong.

How to modify my script file?

Here are my script file:

#!perl

use strict;

use Getopt::Long;

use MaterialsScript qw(:all);

my \\\$xtd = "3D Atomistic";  # Name of the trajectory

my \\\$solvent = "Sketch 16"; # Set name given to the molecule

my \\\$start_frame = 1;  # Starting frame

my \\\$interval = 1;  # Extraction interval from the trajectory

#############################################################################

# Initialize

my \\\$doc = \\\$Documents{"./3D Atomistic.xtd"};

print "Document: \\\$3D Atomistic.xtdn";

my \\\$number_of_frames = \\\$doc->Trajectory->NumFrames;

print "Number of frames = \\\$number_of_frames n";

###########################################################################

# Go through frames as instructed, delete the molecule

for (my \\\$frame_counter = \\\$start_frame; \\\$frame_counter <=\\\$number_of_frames; \\\$frame_counter = \\\$frame_counter + \\\$interval) {

  print "Deleting \\\$solvent from frame \\\$frame_countern";

# copy frame to new document

  my \\\$frame = Documents->New("frame.xsd");

  \\\$doc->Trajectory->CurrentFrame = \\\$frame_counter;

  \\\$frame->CopyFrom(\\\$doc);

# delete molecules from that document

  for my \\\$molecule (@{\\\$frame->UnitCell->Molecules}) {

    if ((\\\$molecule->Name eq \\\$solvent)) { \\\$molecule->Delete;}

}

# append frame document to new trajectory

  \\\$newdoc->Trajectory->AppendFramesFrom(\\\$frame);

# delete the temporary document holding the frame.

  \\\$frame->Delete;

}

print "Deletion complete.n";

Thanks.

Best regards,

                                                                                                                                  Yours

                                                                                                                                         CHENG Xu