请问linux下怎么使用amorphous？

九月九

各位老师好，我想在linux下使用MS的amorphous模块，保存文件后会生成一个perl脚本以及其它输入文件，我想这个应该需要按照RunMatScript.sh来提交，于是按照说明，RunMatScript -np 4 -project test -- ../../graphene.xsd，提交之后报错Unable to import document "……graphene-box/.arc": the file does not exist (function/property "Import") at -e line 9，于是我找到.perl文件的第九行，发现好像没法修改，请问要如何处理呢？整个.perl脚本如下：

1. #!perl
   
2. 
   
3. use strict;
   
4. use Getopt::Long;
   
5. use MaterialsScript qw(:all);
   
6. 
   
7. my %Args;
   
8. GetOptions(\%Args, "Structure=s", "JobDir=s", "Forcefield=s", "DoRefine=s");
   
9. my $xtd = Documents->Import("$Args{JobDir}/$Args{Structure}.arc");       ##（第九行）
   
10. my $trj = $xtd->Trajectory;
    
11. my $xtdNew = Documents->New($xtd->Name . "_.xtd");
    
12. my $trjNew = $xtdNew->Trajectory;
    
13. 
    
14. my $currentForcefield = $Args{Forcefield};
    
15. $currentForcefield = "COMPASS" if($currentForcefield eq "compass");
    
16. 
    
17. Modules->Forcite->ChangeSettings([
    
18.    CurrentForcefield => $currentForcefield,
    
19.    "3DPeriodicvdWSummationMethod" => "Atom based",
    
20.    "3DPeriodicvdWChargeGroupCubicSplineCutOff" => 8.5,
    
21.    "3DPeriodicvdWChargeGroupCubicSplineWidth" => 0.0,
    
22.    "3DPeriodicNonBond2BodyListBufferWidth" => 0.5,
    
23.    "3DPeriodicElectrostaticSummationMethod" => "Ewald",
    
24.    WriteLevel => "Silent"
    
25. ]);
    
26. 
    
27. my $doRefine = $Args{DoRefine} =~ /[YyTt]/;
    
28. my $dynamics = Modules->Forcite->Dynamics;
    
29. my $dynamicsSettings = Settings(
    
30.    NumberOfSteps => 1000,
    
31.    Temperature => 298,
    
32.    Ensemble3D => "NVT",
    
33.    Thermostat => "Velocity Scale",
    
34. );
    
35. my $failed;
    
36. my $numFrames = $trj->NumFrames;
    
37. for(my $frame = 1; $frame <= $numFrames && !defined $failed; $frame++)
    
38. {
    
39.    $trj->CurrentFrame = $frame;
    
40.    my $doc = Documents->New("temp.xsd");
    
41.    $doc->CopyFrom($xtd);
    
42.    if ( $doRefine )
    
43.    {
    
44.        eval
    
45.        {
    
46.           print "Refining frame $frame of $numFrames...";
    
47.           $dynamics->Run($doc,$dynamicsSettings)->Trajectory->Delete;
    
48.        };
    
49.        $failed = ($@) ? $@ : undef;
    
50.        my $status = (defined $failed) ? "failed" : "OK";
    
51.        print "$status\n";
    
52.    }
    
53.    $trjNew->AppendFramesFrom($doc);
    
54.    $doc->Discard;
    
55. }
    
56. $xtdNew->Export("$Args{JobDir}/$Args{Structure}.xtd");
    
57. die $failed if defined $failed;
    
58. print "Refinement finished successfully" if $doRefine;
    

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心向暖阳

这个玩意就windows跑也很快的吧

九月九

心向暖阳 发表于 2021-7-16 11:45
这个玩意就windows跑也很快的吧

windows版MS没装好，跑不了