#!perl
# Author: Stephen Todd
# This script calculates the interaction energy between two layers in a structure.# The layers have to be defined as sets called Layer 1 and Layer 2 - these are the # default names assigned by the Layer builder. 
# This also uses the default settings for Forcite - ie Universal with current charges. # You should change the settings if you want to use another forcefield or summation method.
# This script also assumes that the surface area is in the AB-plane.
# A study table is produced containing the layers, energies, interaction energy, and then# the interaction energy per angstrom^2.
# Note. The input trajectory should have a large vaccuum, greater than the# cut-off you are using in the non-bond calculation.
use strict;use MaterialsScript qw(:all);
################################################################################## Begin user editable settings#
my $filename = "Layer";    # Name of the trajectory without extensionmy $energySettings = [  CurrentForcefield => "COMPASS"]; # Change the ff if neededModules->Forcite->ChangeSettings( $energySettings );## End user editable settings#################################################################################

# Defines the trajectory document
my $doc = $Documents{"$filename.xtd"};
# Create a new study table to hold the structures and energies and set the headings
my $newStudyTable = Documents->New("$filename"."_IntEnergy.std");my $calcSheet = $newStudyTable->Sheets->Item(0);
$calcSheet->ColumnHeading(0) = "$filename Cell";$calcSheet->ColumnHeading(1) = "Energy of  $filename Cell";$calcSheet->ColumnHeading(2) = "Layer 1";$calcSheet->ColumnHeading(3) = "Energy of Layer 1";$calcSheet->ColumnHeading(4) = "Layer 2";$calcSheet->ColumnHeading(5) = "Energy of layer 2";$calcSheet->ColumnHeading(6) = "Interaction Energy";$calcSheet->ColumnHeading(7) = "Interaction Energy per angstrom^2";
# Get the total number of frames in the trajectory
my $numFrames = $doc->Trajectory->NumFrames;
print "Calculating interaction energy for $numFrames frames on $filename trajectory\n";
# Calculates the area of the surface based on the surface being in the A-B plane
my $length1 = $doc->Lattice3D->LengthA;my $length2 = $doc->Lattice3D->LengthB;my $surfaceArea = $length1 * $length2;print "The surface area is $surfaceArea angstroms^2\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 energy for frame $count\n";     # Define the frame of the trajectory     $doc->Trajectorys->Item(0)->CurrentFrame = $count;
     # Create three documents to hold the temporary layers     my $allDoc = Documents->New("all.xsd");          my $layer1Doc = Documents->New("Layer1.xsd");     my $layer2Doc = Documents->New("Layer2.xsd"); 
     # Create a copy of the structure in temporary documents and delete     # the layers that you don't need.
     $allDoc->CopyFrom($doc);
     $layer1Doc->CopyFrom($doc);     $layer1Doc->DisplayRange->Sets("Layer 2")->Atoms->Delete;   
     $layer2Doc->CopyFrom($doc);     $layer2Doc->DisplayRange->Sets("Layer 1")->Atoms->Delete;
     # Put the structures in a study table for safekeeping
     $calcSheet->Cell($count-1, 0) = $allDoc;     $calcSheet->Cell($count-1, 2) = $layer1Doc;     $calcSheet->Cell($count-1, 4) = $layer2Doc;
     #Calculate the energies for all the layers and put in the study table
     $forcite->Calculation->Run($allDoc, [Task => 'Energy']);     $calcSheet->Cell($count-1, 1) = $allDoc->PotentialEnergy;
     $forcite->Calculation->Run($layer1Doc, [Task => 'Energy']);     $calcSheet->Cell($count-1, 3) = $layer1Doc->PotentialEnergy;
     $forcite->Calculation->Run($layer2Doc, [Task => 'Energy']);     $calcSheet->Cell($count-1, 5) = $layer2Doc->PotentialEnergy;
     # Calculate the Interaction Energy from the cells in the Study Table
     my $totalEnergy = $calcSheet->Cell($count-1,1);         my $layer1Energy = $calcSheet->Cell($count-1,3);     my $layer2Energy = $calcSheet->Cell($count-1,5);    
     my $interactionEnergy = $totalEnergy - ($layer1Energy + $layer2Energy);     $calcSheet->Cell($count-1, 6) = $interactionEnergy;
     my $interactionEnergyArea = $interactionEnergy / $surfaceArea;     $calcSheet->Cell($count-1, 7) = $interactionEnergyArea;
     # Discard the temporary documents
     $allDoc->Discard;     $layer1Doc->Discard;     $layer2Doc->Discard;}print "Calculation complete.\n";