We wrote the perl script to calculate the center of mass. the equations are x=(m1*x1 + m2*x2...)/(m1+m2...), y=(m1*y1 + m2*y2...)/(m1+m2...) and z=(m1*z1 + m2*z2...)/(m1+m2...)

Two problems came up:

\\\$atoms -> CopyFrom(\\\$doc->DisplayRange->Sets(\\\$targetset)->Atoms); ------------------->we checked the xsd file and found it is empty.

for (my \\\$i=0; \\\$i< \\\$atoms->Atoms->Count; ++\\\$i) { ------------------------->infinite value/system. "Count" did not work. This problem might be triggered by the above one.

Please help~ here is the details of the perl script file:

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#!perl

#The system includes a water droplet on a thin film in vacuum.
#This script is to calculate the center of Mass with a specific set (water).
use strict;
use MaterialsScript qw(:all);
###########################################################################
#Begin user editable settings
#
my \\\$filename = "filename";   #Name of the trajectory
my \\\$targetset = "water";   #Name of the target set
my \\\$surfaceposition = 32.25648;  #Position of the surface
#
#End user editable settings
###########################################################################
#Defines the trajectory document
my \\\$doc = \\\$Documents{"\\\$filename.xtd"};

#create a new study table to hold the stractures and energies and set the headings
my \\\$newStudyTable = Documents->New("\\\$filename"."_CenterofMass.std");
my \\\$calcSheet = \\\$newStudyTable->Sheets->Item(0);
\\\$calcSheet->ColumnHeading(0) = "Frame Numer";
\\\$calcSheet->ColumnHeading(1) = "X";
\\\$calcSheet->ColumnHeading(2) = "Y";
\\\$calcSheet->ColumnHeading(3) = "Z";

#Get the total number of frames in the trajectory
my \\\$numFrames = \\\$doc->Trajectory->NumFrames;
print "Calculating the mass center for \\\$numFrames frames on \\\$filename trajectory\\n";

#Initialise Forcite. If you want to change the settings, you can load them or
#use a change settings command here.
my \\\$forcite = Modules->Forcite;

#Starts to loop over the frames in the trajectory
for ( my \\\$count=1; \\\$count<=\\\$numFrames; \\\$count++) {
print "Calculating the center of mass for the frame \\\$count\\n";

\\\$calcSheet->Cell(\\\$count-1, 0) = \\\$count;

#Define the frame of the trajectory
\\\$doc->Trajectorys->Item(0)->CurrentFrame = \\\$count;

#Create the target document with the target atoms

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

\\\$atoms -> CopyFrom(\\\$doc->DisplayRange->Sets(\\\$targetset)->Atoms);
 
#Calculate the center of mass in the target atoms

my \\\$xcm = 0;
my \\\$ycm = 0;
my \\\$zcm = 0;
my \\\$mcm = 0;
 
for (my \\\$i=0; \\\$i< \\\$atoms->Atoms->Count; ++\\\$i) {

  my \\\$atom = \\\$atoms->Atoms(\\\$i);
  my \\\$myx = \\\$atom-> X;
  my \\\$myy = \\\$atom-> Y;
  my \\\$myz = \\\$atom-> Z;
  my \\\$mymass = \\\$atom-> Mass; 

  if (\\\$myz >= \\\$surfaceposition) {

   my \\\$Xmass = \\\$mymass*\\\$myx;
   my \\\$Ymass = \\\$mymass*\\\$myy;
   my \\\$Zmass = \\\$mymass*\\\$myz;

   \\\$mcm = \\\$mcm + \\\$mymass;
   \\\$xcm = \\\$xcm + \\\$Xmass;
   \\\$ycm = \\\$ycm + \\\$Ymass;
   \\\$zcm = \\\$zcm + \\\$Zmass;
   \\\$Xmass->Discard;
   \\\$Ymass->Discard;
   \\\$Zmass->Discard;
  }
  else {
   \\\$mcm = \\\$mcm;
   \\\$xcm = \\\$xcm;
   \\\$ycm = \\\$ycm;
   \\\$zcm = \\\$zcm;
  }
 
  \\\$mymass->Discard;
  \\\$myx->Discard;
  \\\$myy->Discard;
  \\\$myz->Discard;
  \\\$atom->Discard;
}
my \\\$XCM = \\\$xcm/\\\$mcm;
my \\\$YCM = \\\$ycm/\\\$mcm;
my \\\$ZCM = \\\$zcm/\\\$mcm;

\\\$calcSheet->Cell(\\\$count-1, 1) = \\\$XCM;
\\\$calcSheet->Cell(\\\$count-1, 2) = \\\$YCM;
\\\$calcSheet->Cell(\\\$count-1, 3) = \\\$ZCM;

\\\$atoms->Discard;
\\\$XCM->Discard;
\\\$YCM->Discard;
\\\$ZCM->Discard;
}

print "Calculation complete.\\n";