Hi everyone

I tried to the H-bond length of every H-bond between two sets of atoms, I modified Jason's hbond-life scipt to following:

#!perl

use strict;

use Getopt::Long;

use MaterialsScript qw(:all);

# Calculates hydrogen bond lifetime from a trajectory

# Considers only hydrogen bonds between two user defined sets

# User inputs

my \\\$doc = \\\$Documents{"Cs-0.5(2).xtd"};

my \\\$setA = \\\$doc->UnitCell->Sets("H");

my \\\$setB = \\\$doc->UnitCell->Sets("O");

# Relabel the atoms so names are unique (and hbond names will be unique)

my \\\$i=0;

foreach (@{\\\$doc->UnitCell->Atoms}) { \\\$i++; \\\$_->Name = \\\$_->ElementSymbol . \\\$i; }

# Label the atoms in sets A and B so they can be identified in the hbond names

foreach (@{\\\$setA->Atoms}) { \\\$_->Name .= "_HBSETA"; }

foreach (@{\\\$setB->Atoms}) { \\\$_->Name .= "_HBSETB"; }

# Calculate the initial batch of hbonds and store names

my \\\$trj = \\\$doc->Trajectory;

\\\$trj->CurrentFrame = 1;

\\\$doc->UnitCell->CalculateHBonds;

my \\\$hbonds = \\\$doc->UnitCell->HydrogenBonds;

my @hbnames;

foreach (@\\\$hbonds)

{

my \\\$a1 = \\\$_->Atom1->Name;

my \\\$a2 = \\\$_->Atom2->Name;

if (( \\\$a1 =~ /_HBSETA/ and \\\$a2 =~ /_HBSETB/) or

    ( \\\$a1 =~ /_HBSETB/ and \\\$a2 =~ /_HBSETA/))

{

push @hbnames, \\\$_->Name;

}

}

# H-bond length

my \\\$i=0;

foreach (@hbnames)

{

\\\$i++;

\\\$hbonds->Length;

printf "%4d %30s %8.2f\\n", \\\$i, \\\$_, \\\$hbonds;

}

# Discard changes so atom labels are not permanent

\\\$doc->Discard;

But I got the following error when I debug the script:

There is no function or property named "Length" on type "Collection" at -e line 53.

which is:

\\\$hbonds->Length;

I'm confused here, I checked the function list, there isn't this one, but Stephen did use this function in his hydrogen bond analysis script.

Does anyone have an idea how to get h-bond length?

Thank you.

Jingjing Bu