mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@965 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
f213705e7f
commit
9e0c6fab7a
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@ -35,17 +35,22 @@
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sub initialize
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{
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my $k = 0;
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my @options = ("-help", "-nstart", "-dn", "-cut", "-pbc",
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"-repair", "-quiet", "-focus", "-center");
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my @options = ("-help", "-nstart", "-dn", "-cut", "-repair",
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"-units", "-quiet", "-nodetect", "-data", "-pbc",
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"-focus", "-center", "-exclude");
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my @remarks = ("display this message",
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"starting frame [-1]",
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"frames to skip when creating multiple frames [0]",
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"cut bonds crossing over box edge [off]",
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"apply periodic boundary conditions [off]",
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"repair bonds [off]",
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"dump file entries have units [off]",
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"turn display information off",
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"turn auto-detection of masses off",
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"use data file other than project.data",
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"apply periodic boundary to molecules []",
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"molecules to focus on []",
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"molecules to use as center of mass []");
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"molecules to use as center of mass []",
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"exclude molecules from output []");
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my @notes = (
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"* Multiple frames are processed when dn > 0.",
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"* Only the last frame is converted when nstart < 0.",
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@ -59,14 +64,15 @@
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$program = "lammps2pdb";
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$version = "2.1";
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$year = "2005";
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$version = "2.2.5";
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$year = "2007";
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$cut = 0;
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$pbc = 0;
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$repair = 0;
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$units = 0;
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$info = 1;
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$nstart = -1;
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$dn = 0;
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$detect = 1;
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foreach (@ARGV)
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{
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@ -74,7 +80,7 @@
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{
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my $k = 0;
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my @arg = split("=");
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my $switch = ($arg[1] eq "")||($arg[1] eq "on")||($arg[1]!=0);
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my $switch = (($arg[1] eq "")||($arg[1] eq "on")||($arg[1]!=0));
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$arg[0] = lc($arg[0]);
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foreach (@options)
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{
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@ -85,11 +91,17 @@
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$nstart = $arg[1] if (!$k--);
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$dn = $arg[1] if (!$k--);
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$cut = $switch if (!$k--);
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$pbc = $switch if (!$k--);
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$repair = $switch if (!$k--);
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$info = !$switch if (!$k--);
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if (!$k--) { foreach (split(" ",$arg[1])) { $focus{uc($_)} = uc($_);}}
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if (!$k--) { foreach (split(" ",$arg[1])) { $center{uc($_)} = uc($_);}}
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$units = $switch if (!$k--);
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$info = $switch ? 0 : 1 if (!$k--);
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$detect = $switch ? 0 : 1 if (!$k--);
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$data_name = $arg[1] if (!$k--);
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if (!$k--) {
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if ($switch) { $pbc{ALL} = 1; }
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else { foreach (split(",",$arg[1])) { $pbc{uc($_)} = 1; }}}
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if (!$k--) { foreach (split(",",$arg[1])) { $focus{uc($_)} = uc($_);}}
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if (!$k--) { foreach (split(",",$arg[1])) { $center{uc($_)} = uc($_);}}
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if (!$k--) { foreach (split(",",$arg[1])) { $exclude{uc($_)}=uc($_);}}
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}
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else { $project = $_ if (!$k++); }
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}
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@ -110,14 +122,15 @@
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}
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printf("%s v%s (c)%s\n\n", $program, $version, $year) if ($info);
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$data_name = $project.".data";
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$data_name = $project.".data" if ($data_name eq "");
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$traject_name = $project.".dump";
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$pdb_name = $project."_trj.pdb";
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$psf_name = $project."_trj.psf";
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$psf_ctrl_name = $project."_ctrl.psf";
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$psf_ctrl = scalar(stat($psf_ctrl_name));
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my $flag = test($data_name)||test($traject_name);
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$traject_flag = scalar(stat($traject_name));
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my $flag = test($data_name);
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printf("Conversion aborted\n\n") if ($flag);
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exit(-1) if ($flag);
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@ -125,7 +138,7 @@
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create_atom_ids();
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create_bonds();
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open(TRAJECT, "<".$traject_name);
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open(TRAJECT, "<".$traject_name) if ($traject_flag);
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open(PSF_CTRL, "<".$psf_ctrl_name) if ($psf_ctrl);
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# open output
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@ -195,7 +208,7 @@
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{
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my $x = @_[0]/@_[1]+0.5;
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return @_[0]-@_[1]*($x<0 ? int($x)-1 : int($x));;
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return @_[0]-@_[1]*($x<0 ? int($x)-1 : int($x));
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}
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@ -483,6 +496,27 @@
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}
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# general read file operators
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sub advance_read
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{
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my $input = shift;
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my $dlines = shift;
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my $read;
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while ($dlines--) { $read = <$input>; }
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return $read;
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}
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sub rewind_read
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{
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my $input = shift;
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seek($input, 0, SEEK_SET);
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}
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# create crossreference tables
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sub create_psf_index # make an index of id
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@ -555,6 +589,13 @@
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if (join(" ",@tmp[2,3]) eq "zlo zhi");
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if (($id = $hash{$tmp[1]}) ne "") { $size{$id} = $tmp[0]; }
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}
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@l = ();
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for (my $i=0; $i<3; ++$i)
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{
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@tmp = split(" ", $L[$i]);
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$l[$i] = $tmp[0];
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$l[$i+3] = $tmp[1];
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}
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while (!eof(DATA)) # interpret data
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{
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@tmp = split(" ", <DATA>);
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@ -589,9 +630,10 @@
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my $n = goto_data(masses);
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my @mass = (1, 12, 14, 16, 32.1, 4, 20.2, 40.1, 65.4,
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55.8, 31, 35.5, 23, 24.3, 39.1, 28.1);
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my @name = (H, C, N, O, S, HE, NE, CA,
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ZN, FE, P, CL, NA, MG, K, SI);
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my @unknown = (X, Y, Z);
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my @name = ("H", "C", "N", "O", "S", "HE", "NE", "CA",
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"ZN", "FE", "P", "CL", "NA", "MG", "K", "SI");
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my @unknown = ("X", "Y", "Z");
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my @letter = ("X", "Y", "Z", "P", "Q", "R", "S", "A", "B", "C");
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my $k = 0;
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my %atom;
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@ -600,10 +642,11 @@
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for (my $i=1; $i<=$n; ++$i)
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{
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my @tmp = split(" ", <DATA>);
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my $j = $tmp[0];
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$tmp[1] = int($tmp[1]*10+0.5)/10;
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if (($names[$i] = $atom{$masses[$i] = $tmp[1]}) eq "")
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if ((($names[$j] = $atom{$masses[$j] = $tmp[1]}) eq "")||!$detect)
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{
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$names[$i] = $unknown[0].$k;
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$names[$j] = $letter[$k].$unknown[0];
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if (++$k>9) { $k = 0; shift(@unknown); }
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}
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}
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@ -613,7 +656,7 @@
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sub create_position
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{
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my @data = @_;
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my $p = $data[0]." ".$data[1];
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my $p = $data[1]." ".$data[2];
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my $k;
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for ($k=0; ($k<scalar(@data))&&(substr($data[$k],0,1) ne "#"); ++$k) { }
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@ -621,7 +664,8 @@
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foreach (@L)
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{
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my @l = split(" ");
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$p = join(" ", $p, (shift(@data)-$l[0])/$l[-1]+$data[3]);
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$p = join(" ", $p, ($data[0]-$l[0])/$l[-1]+$data[3]);
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shift(@data);
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}
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return $p;
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}
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@ -668,7 +712,6 @@
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}
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}
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$ntmp = 0;
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sub crossover
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{
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@ -688,7 +731,7 @@
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my $n = scalar(@bonds);
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my $i = 0;
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printf("Info: deleting crossovers\n") if ($info);
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printf("Info: deleting crossover bonds\n") if ($info);
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while ($i<$n) # take out crossovers
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{
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if (crossover(split(" ", $bonds[$i]))) { splice(@bonds, $i, 1); --$n; }
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@ -696,6 +739,22 @@
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}
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}
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sub delete_exclude
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{
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my $n = scalar(@bonds);
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my $i = 0;
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printf("Info: deleting excluded bonds\n") if ($info);
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while ($i<$n)
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{
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my $m = $mol[(split(" ", $bonds[$i]))[0]+1];
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if (($exclude{$m} ne "")||($exclude{$residue[$m]} ne "")
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||($exclude{$cluster[$m]} ne "")) { splice(@bonds, $i, 1); --$n; }
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else { ++$i; }
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}
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}
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sub create_bonds
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{
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@ -709,7 +768,7 @@
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}
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}
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# traject operators
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sub advance_traject
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@ -734,7 +793,7 @@
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for (my $i=0; $i<3; ++$i)
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{
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my @data = split(" ", <TRAJECT>);
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$box[$i] = 0.5*($data[0]+$data[1]); # box edge
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$box[$i] = $data[0]; # box edge
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$l[$i] = $data[1]-$data[0]; # box length
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}
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advance_traject("atoms");
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@ -828,7 +887,9 @@
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foreach (@position)
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{
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my @p = split(" ");
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$_ = join(" ", V_PBC(@p[0,1,2], @l[3,4,5]), @p[3,4]);
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my $m = $mol[$p[3]];
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$_ = join(" ", V_PBC(@p[0,1,2], @l[3,4,5]), @p[3,4])
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if ($pbc{ALL}||$pbc{$m}||$pbc{$residue[$m]}||$pbc{$cluster[$m]});
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}
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}
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@ -856,14 +917,25 @@
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my $mass;
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my @p;
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my $d;
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foreach (@traject)
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{
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my @arg = split(" ");
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my $m = $mol[$arg[0]];
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$p[0] = ($arg[2]+$arg[5]-0.5)*$l[3];
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$p[1] = ($arg[3]+$arg[6]-0.5)*$l[4];
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$p[2] = ($arg[4]+$arg[7]-0.5)*$l[5];
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next if (($exclude{$m} ne "")||($exclude{$residue[$m]} ne "")
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||($exclude{$cluster[$m]} ne ""));
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if ($units)
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{
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$p[0] = $arg[2]+$arg[5]*$l[3];
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$p[1] = $arg[3]+$arg[6]*$l[4];
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$p[2] = $arg[4]+$arg[7]*$l[5];
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}
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else
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{
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$p[0] = $l[0]+($arg[2]+$arg[5])*$l[3];
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$p[1] = $l[1]+($arg[3]+$arg[6])*$l[4];
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$p[2] = $l[2]+($arg[4]+$arg[7])*$l[5];
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}
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$position[$i++] = join(" ", @p, $arg[0], $arg[1]);
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next if (($center{$m} eq "")&&($center{$cluster[$m]} eq ""));
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$nmass += $mass = $masses[$arg[1]]; # inertia necessities:
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@ -879,7 +951,7 @@
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}
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pdb_center(M_Mult(1/$nmass, @m)) if ($nmass);
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pdb_focus(M_Mult(1/$nmass, @m)) if ($nmass && scalar(%focus));
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pdb_pbc() if ($pbc);
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pdb_pbc() if (scalar(%pbc));
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pdb_repair_bonds() if ($repair);
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}
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@ -891,12 +963,22 @@
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($psf_ctrl ? "_ctrl.psf" : ".data")." AND $project.dump\n");
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printf(PDB "REMARK CREATED BY $program v$version ON %s", `date`);
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printf(PDB "REMARK \n");
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printf(PDB "CRYST1 ");
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printf(PDB "%8.8s ", $l[3]);
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printf(PDB "%8.8s ", $l[4]);
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printf(PDB "%8.8s ", $l[5]);
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printf(PDB "%6.6s ", "90");
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printf(PDB "%6.6s ", "90");
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printf(PDB "%6.6s ", "90");
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printf(PDB "%-11.11s", "P 1");
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printf(PDB "%3.3s\n", "1");
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}
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sub pdb_atoms
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{
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my $n = 0;
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my $l = 0;
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my $last = 0;
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my @base;
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@ -907,14 +989,15 @@
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foreach (@position)
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{
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my @p = split(" ");
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my @psf = split(" ", <PSF_CTRL>) if ($psf_ctrl);
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my $nres = $mol[$p[3]];
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my @psf = split(" ", advance_read(PSF_CTRL, $p[3]-$l))
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if ($psf_ctrl);
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@base = @p[0,1,2] if ($last!=$nres);
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#@p = V_Add(V_PBC(V_Subtr(@p, @base), @l[3,4,5]), @l);
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foreach (@p) { $_ = 0 if (abs($_)<1e-4); }
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printf(PDB "ATOM "); # pdb command
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printf(PDB "%6.6s ", ++$n); # atom number
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printf(PDB "%-4.4s",
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printf(PDB "%-3.3s ",
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$psf_ctrl ? $psf[4] : $names[$p[4]]); # atom name
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printf(PDB "%-3.3s ",
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$psf_ctrl ? $psf[3] : $residue[$nres]); # residue name
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@ -927,6 +1010,7 @@
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printf(PDB "%-4.4s\n",
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$psf_ctrl ? $psf[1] : $cluster[$nres]); # cluster name
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$last = $nres;
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$l = $p[3];
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};
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printf(PDB "END\n");
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}
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@ -957,25 +1041,34 @@
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{
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my $n = goto_data(atoms);
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my $natom = 0;
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my @arg;
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my $k;
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my $l = 0;
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my $k = 0;
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my @extra;
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printf(PSF "%8.8s !NATOM\n", scalar(@position));
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for (my $i=0; $i<$n; ++$i)
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{
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@arg = split(" ", <DATA>);
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#next if (($omit{$arg[1]} ne "")||($omit{$cluster[$arg[1]]} ne ""));
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for ($k=0; ($k<scalar(@arg))&&(substr($arg[$k],0,1) ne "#"); ++$k) {}
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my @arg = split(" ", <DATA>);
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if (!$k) {
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for ($k=0; ($k<scalar(@arg))&&(substr($arg[$k],0,1) ne "#"); ++$k) {} }
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$extra[$arg[0]-1] = $arg[1]." ".$arg[2]." ".$arg[3];
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}
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printf(PSF "%8.8s !NATOM\n", scalar(@position));
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foreach (@position)
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{
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my @p = split(" ");
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my @arg = split(" ", $extra[$natom]);
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printf(PSF "%8.8s ", ++$natom); # atom number
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printf(PSF "%-4.4s ", $cluster[$arg[1]]); # cluster name
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printf(PSF "%-4.4s ", $arg[1]); # residue number
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printf(PSF "%-4.4s ", $residue[$arg[1]]); # residue name
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printf(PSF "%-4.4s ", $names[$arg[2]]); # atom name
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printf(PSF "%4.4s ", $arg[2]); # atom number
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printf(PSF "%10.10s ", $k%3 ? $arg[3] : 0); # atom charge
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printf(PSF "%-4.4s ", $cluster[$arg[0]]); # cluster name
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printf(PSF "%-4.4s ", $arg[0]); # residue number
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printf(PSF "%-4.4s ", $residue[$arg[0]]); # residue name
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printf(PSF "%-4.4s ", $names[$p[4]]); # atom name
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printf(PSF "%4.4s ", $arg[1]); # atom number
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printf(PSF "%10.10s ", $k%3 ? $arg[2] : 0); # atom charge
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printf(PSF "%4.4s ", ""); # blank entry
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printf(PSF "%8.8s ", $masses[$arg[2]]); # atom mass
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printf(PSF "%8.8s ", $masses[$arg[1]]); # atom mass
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printf(PSF "%11.11s\n", "0"); # trailing variable
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$l = $p[3];
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last if ($natom>=$n)
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}
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printf(PSF "\n");
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}
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@ -984,7 +1077,8 @@
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sub psf_bonds
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{
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my $npairs = 0;
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delete_exclude() if (scalar(%exclude)>0);
|
||||
delete_crossovers() if ($cut);
|
||||
printf(PSF "%8.8s !NBOND\n", scalar(@bonds));
|
||||
foreach (@bonds)
|
||||
|
|
@ -1005,7 +1099,7 @@
|
|||
# create .pdb file
|
||||
|
||||
$ncurrent = -1;
|
||||
while (!eof(TRAJECT))
|
||||
while ($traject_flag&&!eof(TRAJECT))
|
||||
{
|
||||
@description = read_traject();
|
||||
@l = splice(@description, -6, 6);
|
||||
|
|
@ -1026,7 +1120,7 @@
|
|||
}
|
||||
else
|
||||
{
|
||||
system("rm ".$psf_name);
|
||||
system("rm -f ".$psf_name);
|
||||
system("ln -s ".$psf_ctrl_name." ".$psf_name);
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue