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properly handle -nohints flag, make -cmap flag take version as option. step version number

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This commit is contained in:
Axel Kohlmeyer
2016-10-03 06:52:30 -04:00
parent c2e11dffa2
commit 3b94627dfe
1 changed files with 14 additions and 13 deletions
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27
tools/ch2lmp/charmm2lammps.pl
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@ -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{