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MS脚本-调节分子筛硅铝比的脚本#!perl # # Purpose: Introduces substitutional disorder by replacing a percentage of atoms with another element. # If this is a zeolite, Lowenstein's rule can be used to avoid too many substitutions. # Note. When calculating the number of atoms to change, this number is rounded up. This can # be changed by modifing the line containing $numToChange. use strict; use warnings; use List::Util qw(shuffle); # Allows randomizing of the atoms in an array use POSIX; # Allows use of ceil to round-up numbers use MaterialsScript qw(:all); # Lowenstein's rule applies to substitution of Aluminium in zeolite and states that no two # Al atoms can share a common oxygen. sub CheckLowenstein { my ($atom) = @_;
#Rule states that Al-O-Al linkages are forbidden my $attached = $atom->AttachedAtoms;
foreach my $firstAtom (@$attached) { #Only care about oxygens if($firstAtom->ElementSymbol eq "O") { my $oxyAttached = $firstAtom->AttachedAtoms; foreach my $secondAtom (@$oxyAttached) { if($secondAtom->ElementSymbol eq "Al") {
return 0; #Lowenstein broken
} } } } return 1; #Lowenstein satisfied } # Main routine to substitute atoms sub SubstituteAtoms { my ($doc, $pcChange, $original, $new, $lowenstein)= @_;
# Change the symmetry to P1
$doc->MakeP1;
srand;
# Grab the collection of atoms in the unit cell
my $atoms = $doc->UnitCell->Atoms;
# Store the original atoms in an array
my @originalAtoms;
foreach my $atom (@$atoms) { if($atom->ElementSymbol eq "$original") {push(@originalAtoms, $atom);} }
# Check to see if there are any atoms to modify
if (scalar @originalAtoms == 0) {die "There are no atoms of element $original to modify\n";} # Randomize the atom positions in the array
my @shuffledOriginalAtoms = shuffle(@originalAtoms);
# calculate the number of atoms to change. The ceil commanound rounds up. If you wish to # round down, use int instead of ceil.
my $numToChange = ceil (($pcChange/100) * scalar @shuffledOriginalAtoms);
# Iterate through a counter and search for an atom to change
for(my $i=0; $i<$numToChange; ++$i) {
# Check to see if there are any atoms to modify
if (scalar @shuffledOriginalAtoms == 0) {die "Modified $i atoms. There are no atoms of element $original to modify\n";} my $attempts = 0;
# Look for an atom to modify
my $atom=undef;
while(!$atom && scalar @shuffledOriginalAtoms > 0) {
my $index = int rand( scalar @shuffledOriginalAtoms);
$atom = $shuffledOriginalAtoms[$index];
# Check we haven't already changed it and it satisfies Lowenstein rule (optionally)
if($atom->ElementSymbol eq "$new") {
splice @shuffledOriginalAtoms, $index, 1; $atom = undef;
} elsif ($lowenstein eq "Yes") {
if (!CheckLowenstein($atom)) {
splice @shuffledOriginalAtoms, $index, 1; $atom = undef; } }
++$attempts;
}
# Stop if atom is still undefined as this means Lowensteins rule has been broken
if(!$atom) { print "Unable to satisfy Lowenstein's rule\n";
# Count the number of atoms changed and report this.
my $modAtoms = 0;
foreach my $at (@{$doc->UnitCell->Atoms}) {
if ($at->ElementSymbol eq "$new") { ++$modAtoms;}
}
print "$modAtoms atoms have been modified to $new element\n";
return; } else {
#Change the element and display style $atom->ElementSymbol = "$new"; $atom->Style = "Ball and Stick";
}
} } # Specify the input document and percentage number of silicons to change my $xsd = $Documents{"TON.xsd"};# Structure name my $percentChange = 15; # Percentage of atoms of original element to change my $originalElement = "Si"; # Original element to change to new element my $newElement = "Al"; # New element my $obeyLowenstein = "Yes"; # Whether to obey Lowenstein's for zeolites SubstituteAtoms($xsd, $percentChange,$originalElement, $newElement, $obeyLowenstein); 感谢王正同学的分享 |
