请问linux下怎么使用amorphous？ - 计算化学公社

#!perl
use strict;
use Getopt::Long;
use MaterialsScript qw(:all);
my %Args;
GetOptions(\%Args, "Structure=s", "JobDir=s", "Forcefield=s", "DoRefine=s");
my $xtd = Documents->Import("$Args{JobDir}/$Args{Structure}.arc"); ##（第九行）
my $trj = $xtd->Trajectory;
my $xtdNew = Documents->New($xtd->Name . "_.xtd");
my $trjNew = $xtdNew->Trajectory;
my $currentForcefield = $Args{Forcefield};
$currentForcefield = "COMPASS" if($currentForcefield eq "compass");
Modules->Forcite->ChangeSettings([
CurrentForcefield => $currentForcefield,
"3DPeriodicvdWSummationMethod" => "Atom based",
"3DPeriodicvdWChargeGroupCubicSplineCutOff" => 8.5,
"3DPeriodicvdWChargeGroupCubicSplineWidth" => 0.0,
"3DPeriodicNonBond2BodyListBufferWidth" => 0.5,
"3DPeriodicElectrostaticSummationMethod" => "Ewald",
WriteLevel => "Silent"
]);
my $doRefine = $Args{DoRefine} =~ /[YyTt]/;
my $dynamics = Modules->Forcite->Dynamics;
my $dynamicsSettings = Settings(
NumberOfSteps => 1000,
Temperature => 298,
Ensemble3D => "NVT",
Thermostat => "Velocity Scale",
);
my $failed;
my $numFrames = $trj->NumFrames;
for(my $frame = 1; $frame <= $numFrames && !defined $failed; $frame++)
{
$trj->CurrentFrame = $frame;
my $doc = Documents->New("temp.xsd");
$doc->CopyFrom($xtd);
if ( $doRefine )
{
eval
{
print "Refining frame $frame of $numFrames...";
$dynamics->Run($doc,$dynamicsSettings)->Trajectory->Delete;
};
$failed = ($@) ? $@ : undef;
my $status = (defined $failed) ? "failed" : "OK";
print "$status\n";
}
$trjNew->AppendFramesFrom($doc);
$doc->Discard;
}
$xtdNew->Export("$Args{JobDir}/$Args{Structure}.xtd");
die $failed if defined $failed;
print "Refinement finished successfully" if $doRefine;

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