properly handle -nohints flag, make -cmap flag take version as option. step version number (3b94627d) · Commits · 郑智淋 / lammps

tools/ch2lmp/charmm2lammps.pl

+14 −13

Original line number	Diff line number	Diff line
		@@ -80,12 +80,12 @@
		"rotation around x-axis",
		"rotation around y-axis",
		"rotation around z-axis",
		"generate the CMAP section"
		"generate a CMAP section in data file"
		);
		my $notes;

		$program = "charmm2lammps";
		$version = "1.8.3";
		$version = "1.9.0";
		$year = "2016";
		$add = 1;
		$water_dens = 0;
		@@ -149,8 +149,8 @@
		@R = M_Dot(M_Rotate(0, $tmp[1]), @R) if (!$k--);# -ax
		@R = M_Dot(M_Rotate(1, $tmp[1]), @R) if (!$k--);# -ay
		@R = M_Dot(M_Rotate(2, $tmp[1]), @R) if (!$k--);# -az
		$cmap = 1 if (!$k--);
		# print("Warning: ignoring unknown command line flag: $tmp[0]\n");
		$cmap = ($tmp[1] ne "" ? $tmp[1] : 22) if (!$k--); # -cmap
		print("Warning: ignoring unknown command line flag: $tmp[0]\n") unless $k;
		}
		else
		{
		@@ -161,7 +161,7 @@
		$water_dens = 1 if ($ions && !$water_dens);
		if (($k<2)\|\|$help)
		{
		printf("\n%s v%s (c)%s by Pieter J. in \'t Veld for SNL\n\n",
		printf("\n%s v%s (c)2005-%s by Pieter J. in \'t Veld and others\n\n",
		$program, $version, $year);
		printf("Usage:\n %s.pl [-option[=#] ..] forcefield project\n\n",$program);
		printf("Options:\n");
		@@ -172,7 +172,7 @@
		printf("\nNotes:\n%s\n", $notes);
		exit(-1);
		}
		else { printf("\n%s v%s (c)%s\n\n", $program, $version, $year) if ($info); }
		else { printf("\n%s v%s (c)2005-%s\n\n", $program, $version, $year) if ($info); }
		my $flag = Test($Parameters = "par_$forcefield.prm");
		$flag \|= Test($Topology = "top_$forcefield.rtf");
		$flag \|= Test($Pdb = "$project.pdb")
		@@ -1021,7 +1021,8 @@

		sub WriteLAMMPSHeader # print lammps header
		{
		printf(LAMMPS "LAMMPS data file. CGCMM style. atom_style full. Created by $program v$version on %s\n", `date`);
		printf(LAMMPS "LAMMPS data file. %sCreated by $program v$version on %s\n",
		($add ? "CGCMM Style. atom_style full. " : ""),`date`);
		printf(LAMMPS "%12d atoms\n", $natoms);
		printf(LAMMPS "%12d bonds\n", $nbonds);
		printf(LAMMPS "%12d angles\n", $nangles);
		@@ -1175,7 +1176,7 @@

		CRDGoto(atoms);
		$net_charge = 0;
		printf(LAMMPS "Atoms # full\n\n") if ($n>0);
		printf(LAMMPS "Atoms%s\n\n",($add ? " # full" : "")) if ($n>0);
		for (my $i=0; $i<$n; ++$i)
		{
		my @crd = $pdb ? NextPDB2CRD() : split(" ", <CRD>);
		@@ -1209,7 +1210,7 @@
		{
		my $mode = shift(@_)+1;
		my $header = ("Pair","Bond","Angle","Dihedral","Improper")[$mode];
		my $hint = ("lj/charmm/coul/long", "harmonic", "charmm", "charmm", "harmonic")[$mode];
		my $hint = ("# lj/charmm/coul/long", "# harmonic", "# charmm", "# charmm", "# harmonic")[$mode];
		my $n = (4, 2, 4, 4, 2)[$mode];
		my $k = 0;

		@@ -1223,7 +1224,7 @@
		@parms = Delete(1, @parms) if ($mode==3);
		}
		return 0 if (!scalar(@parms));
		printf(LAMMPS "%s Coeffs # %s\n\n", $header, $hint);
		printf(LAMMPS "%s Coeffs %s\n\n", $header, ($add ? $hint : ""));
		for (my $i=0; $i<scalar(@parms); ++$i)
		{
		if ($parms[$i] ne "")
		@@ -1446,11 +1447,11 @@
		printf(LAMMPS "improper_style harmonic\n\n") if ($nimproper_types);
		printf(LAMMPS "pair_style lj/charmm/coul/long 8 12\n");
		printf(LAMMPS "pair_modify mix arithmetic\n");
		printf(LAMMPS "kspace_style pppm 1e-4\n\n");
		printf(LAMMPS "kspace_style pppm 1e-6\n\n");

		if ($cmap) {
		printf(LAMMPS "# Modify following lines to provide directory path cmap.data and 'project'.data files\n");
		printf(LAMMPS "fix cmap all cmap /directoryPath/.../cmap36.data\n");
		printf(LAMMPS "# Modify following line to point to the desired CMAP file\n");
		printf(LAMMPS "fix cmap all cmap charmm$cmap.cmap\n");
		printf(LAMMPS "fix_modify cmap energy yes\n");
		printf(LAMMPS "read_data $project.data fix cmap crossterm CMAP\n\n");
		}else{

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