sync with GH
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15691 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -896,7 +896,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
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"lubricate/poly (o)"_pair_lubricate.html,
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"lubricateU"_pair_lubricateU.html,
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"lubricateU/poly"_pair_lubricateU.html,
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"meam (o)"_pair_meam.html,
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"meam"_pair_meam.html,
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||||
"mie/cut (o)"_pair_mie.html,
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||||
"morse (got)"_pair_morse.html,
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"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
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||||
@ -956,7 +956,7 @@ package"_Section_start.html#start_3.
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||||
"lj/sdk/coul/long (go)"_pair_sdk.html,
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"lj/sdk/coul/msm (o)"_pair_sdk.html,
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"lj/sf (o)"_pair_lj_sf.html,
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"meam/spline"_pair_meam_spline.html,
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"meam/spline (o)"_pair_meam_spline.html,
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"meam/sw/spline"_pair_meam_sw_spline.html,
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"mgpt"_pair_mgpt.html,
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"morse/smooth/linear"_pair_morse.html,
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@ -183,6 +183,16 @@ c
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real*8, external :: zbl
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real*8, external :: compute_phi
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c check for previously allocated arrays and free them
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if(allocated(phir)) deallocate(phir)
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if(allocated(phirar)) deallocate(phirar)
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if(allocated(phirar1)) deallocate(phirar1)
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if(allocated(phirar2)) deallocate(phirar2)
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if(allocated(phirar3)) deallocate(phirar3)
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if(allocated(phirar4)) deallocate(phirar4)
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if(allocated(phirar5)) deallocate(phirar5)
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if(allocated(phirar6)) deallocate(phirar6)
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c allocate memory for array that defines the potential
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allocate(phir(nr,(neltypes*(neltypes+1))/2))
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@ -460,9 +460,9 @@ void FixTMD::readfile(char *file)
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else
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n = sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg",&itag,&x,&y,&z);
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|
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if (n < 0 && me == 0) {
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error->warning(FLERR,"Ignoring empty or incorrectly formatted"
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" line in target file");
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if (n < 0) {
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if (me == 0) error->warning(FLERR,"Ignoring empty or incorrectly"
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" formatted line in target file");
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bufptr = next + 1;
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continue;
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}
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@ -41,9 +41,9 @@ should be -option=value (e.g. -border=5).
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-border add border to all sides of simulation box [default: 0 A]
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-ax rotation around x-axis
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-ay rotation around y-axis
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-az rotation around z-axis
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-az rotation around z-axis
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-cd correction for dihedral for carbohydrate systems
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-cmap add CMAP section to data file and fix cmap command lines in
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-cmap add CMAP section to data file and fix cmap command lines in
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input script" (NOTE: requires use of *.pdb file)
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In the "example" folder, you will find example files that were created
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@ -69,26 +69,26 @@ file has to the corresponding names in the charmm FF files. You'll
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need to add a "pdbalias residue x xnew" line for each change that
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needs to be made. The *.pgn should contain something like this:
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package require psfgen
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package require psfgen
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topology top_all27_na.rtf
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pdbalias residue A ADE
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pdbalias residue T THY
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pdbalias residue G GUA
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pdbalias residue C CYT
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pdbalias residue A ADE
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pdbalias residue T THY
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pdbalias residue G GUA
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pdbalias residue C CYT
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.
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.
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.
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segment A {pdb 1ac7_pared.pdb}
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coordpdb 1ac7_pared.pdb A
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guesscoord
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writepdb 1ac7.pdb
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writepsf charmm 1ac7.psf
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exit
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segment A {pdb 1ac7_pared.pdb}
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coordpdb 1ac7_pared.pdb A
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guesscoord
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||||
writepdb 1ac7.pdb
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writepsf charmm 1ac7.psf
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exit
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5) Type "vmd -e 1ac7.pgn" to build the 1ac7.psf file, and the new
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||||
1ac7.pdb file.
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||||
6) Run charmm2lammps.pl by typing:
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6) Run charmm2lammps.pl by typing:
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"perl charmm2lammps.pl all27_na 1ac7 -charmm -border=1 -pdb_ctrl -water -ions"
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7) Run lammps by typing: "lmp < 1ac7.in"
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||||
@ -105,7 +105,7 @@ molecule. The -pdb_ctrl option produces the 1ac7_ctrl.pdb file that
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||||
can be visualized in a standard visualization package such as VMD. The
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||||
-charmm option put comments into the LAMMPS data file (everything
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||||
after the # sign is a comment) for user convenience in tracking atom
|
||||
types etc. according to CHARMM nomenclature.
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||||
types etc. according to CHARMM nomenclature.
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||||
The example molecule provided above (i.e., 1ac7) is a DNA fragment.
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If instead, a peptide longer than 2 amino acid residues or a protein
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,4 +1,4 @@
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||||
# Created by charmm2lammps v1.6.2 on Fri Jun 3 14:07:02 MDT 2005
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# Created by charmm2lammps v1.9.0 on Mon Oct 3 06:55:39 EDT 2016
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||||
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units real
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||||
neigh_modify delay 2 every 1
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||||
@ -9,21 +9,23 @@ angle_style charmm
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dihedral_style charmm
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||||
improper_style harmonic
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||||
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pair_style lj/charmm/coul/long 8 10
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||||
pair_style lj/charmm/coul/long 8 12
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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kspace_style pppm 1e-6
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||||
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read_data 1ac7.data
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special_bonds charmm
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fix 1 all nve
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fix 2 all shake 1e-6 500 0 m 1.0 a 93
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||||
velocity all create 0.0 12345678 dist uniform
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||||
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||||
thermo 1
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thermo_style multi
|
||||
timestep 0.5
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||||
|
||||
minimize 0.0 0.0 1000 10000
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||||
|
||||
fix 1 all nve
|
||||
fix 2 all shake 1e-6 500 0 m 1.0 a 93
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||||
velocity all create 0.0 12345678 dist uniform
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||||
|
||||
restart 10 1ac7.restart1 1ac7.restart2
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||||
dump 1 all atom 10 1ac7.dump
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||||
dump_modify 1 image yes scale yes
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||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -8,9 +8,9 @@
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||||
# conjunction with vmd
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||||
#
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||||
# Notes: Copyright by author for Sandia National Laboratories
|
||||
# 20040903 Conception date of v1.0: rudimentary script for collagen
|
||||
# 20040903 Conception date of v1.0: rudimentary script for collagen
|
||||
# project.
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||||
# 20050423 Conception date of v2.0:
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||||
# 20050423 Conception date of v2.0:
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||||
# - changed data access through indexing data directly on disk;
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||||
# - added all command line options
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||||
# 20050425 Corrected focussing to use a target molecule's moment of
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||||
@ -22,21 +22,21 @@
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||||
# the data stream.
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||||
|
||||
# subroutines
|
||||
|
||||
|
||||
sub test
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||||
{
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||||
my $name = shift(@_);
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||||
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||||
|
||||
printf("Error: file %s not found\n", $name) if (!scalar(stat($name)));
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||||
return !scalar(stat($name));
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||||
}
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||||
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||||
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||||
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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", "-repair",
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||||
"-units", "-quiet", "-nodetect", "-data", "-pbc",
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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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||||
@ -61,7 +61,7 @@
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||||
"* Expected files in current directory: project.data, project.dump",
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||||
"* Generated output files: project_trj.psf, project_trj.pdb",
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||||
"* Uses project_ctrl.psf if available");
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||||
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||||
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||||
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||||
$program = "lammps2pdb";
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||||
$version = "2.2.5";
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@ -96,7 +96,7 @@
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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 (!$k--) {
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if (!$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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@ -120,7 +120,7 @@
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||||
printf("\n");
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exit(-1);
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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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||||
printf("%s v%s (c)%s\n\n", $program, $version, $year) if ($info);
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||||
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||||
$data_name = $project.".data" if ($data_name eq "");
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||||
$traject_name = $project.".dump";
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||||
@ -133,7 +133,7 @@
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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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||||
|
||||
|
||||
# data input
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||||
|
||||
create_atom_ids();
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||||
@ -145,9 +145,9 @@
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||||
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||||
open(PSF, ">".$psf_name) if (!$psf_ctrl);
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||||
open(PDB, ">".$pdb_name);
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||||
|
||||
|
||||
# align center with focus
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||||
|
||||
|
||||
%center = %focus if (scalar(%focus));
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||||
}
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||||
|
||||
@ -166,24 +166,24 @@
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||||
return @_;
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||||
}
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||||
|
||||
|
||||
|
||||
sub V_Add # V_Add(@a, @b) = @a + @b;
|
||||
{
|
||||
return (@_[0]+@_[3], @_[1]+@_[4], @_[2]+@_[5]);
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||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub V_Subtr # V_Subtr(@a, @b) = @a - @b;
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||||
{
|
||||
return (@_[0]-@_[3], @_[1]-@_[4], @_[2]-@_[5]);
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||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub V_Dot # V_Dot(@a, @b) = @a . @b;
|
||||
{
|
||||
return (@_[0]*@_[3]+@_[1]*@_[4]+@_[2]*@_[5]);
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||||
}
|
||||
|
||||
|
||||
|
||||
sub V_Cross # V_Cross(@a, @b) = @a x @b;
|
||||
{
|
||||
@ -191,7 +191,7 @@
|
||||
@_[0]*@_[4]-@_[1]*@_[3]);
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub V_Mult # V_Mult($f, @a) = $f * @a;
|
||||
{
|
||||
return (@_[0]*@_[1], @_[0]*@_[2], @_[0]*@_[3]);
|
||||
@ -203,11 +203,11 @@
|
||||
return V_Mult(1/sqrt(V_Dot(@_[0,1,2],@_[0,1,2])), @_[0,1,2]);
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub pbc # periodic -0.5*L <= x < 0.5*L
|
||||
{
|
||||
my $x = @_[0]/@_[1]+0.5;
|
||||
|
||||
|
||||
return @_[0]-@_[1]*($x<0 ? int($x)-1 : int($x));
|
||||
}
|
||||
|
||||
@ -216,8 +216,8 @@
|
||||
{
|
||||
return (pbc(@_[0], @_[3]), pbc(@_[1], @_[4]), pbc(@_[2], @_[5]));
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub V_Cmp # V_Cmp(abs(@a), abs(@b))
|
||||
{
|
||||
return -1 if (abs($_[0])<abs($_[3]));
|
||||
@ -228,12 +228,12 @@
|
||||
return 1 if (abs($_[2])>abs($_[5]));
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub V_Sort # sort on descending absolute
|
||||
{ # value
|
||||
my @v = @_;
|
||||
|
||||
|
||||
for (my $i=0; $i<scalar(@v)-3; $i+=3)
|
||||
{
|
||||
for (my $j=$i+3; $j<scalar(@v); $j+=3)
|
||||
@ -247,13 +247,13 @@
|
||||
return @v;
|
||||
}
|
||||
|
||||
|
||||
|
||||
# Matrix routines
|
||||
|
||||
sub M_String # M_String(@A)
|
||||
{
|
||||
my @M;
|
||||
|
||||
|
||||
for (my $i=0; $i<3; ++$i) { push(@M, V_String(splice(@_, 0, 3))); }
|
||||
return "{".join(", ", @M)."}";
|
||||
}
|
||||
@ -270,7 +270,7 @@
|
||||
return (@_[0], @_[3], @_[6], @_[1], @_[4], @_[7], @_[2], @_[5], @_[8]);
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub M_Dot # M_Dot(@A, @B) = @A . @B;
|
||||
{
|
||||
return (
|
||||
@ -288,7 +288,7 @@
|
||||
return V_Dot(@_[0,1,2], V_Cross(@_[3,4,5], @_[6,7,8]));
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub M_Mult # M_Mult($a, @A) = $a * @A
|
||||
{
|
||||
return (
|
||||
@ -296,12 +296,12 @@
|
||||
@_[0]*@_[4], @_[0]*@_[5], @_[0]*@_[6],
|
||||
@_[0]*@_[7], @_[0]*@_[8], @_[0]*@_[9]);
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub M_Unit { return (1,0,0, 0,1,0, 0,0,1); }
|
||||
|
||||
sub PI { return 4*atan2(1,1); }
|
||||
|
||||
|
||||
sub M_Rotate # M_Rotate($n, $alpha) = @R_$n;
|
||||
{ # vmd convention
|
||||
my $n = shift(@_);
|
||||
@ -316,7 +316,7 @@
|
||||
return ($cos,-$sin,0, $sin,$cos,0, 0,0,1) if ($n==2); # around z-axis
|
||||
return M_Unit();
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub M_RotateNormal # returns R.(1,0,0) = @a/|@a|;
|
||||
{
|
||||
@ -324,7 +324,7 @@
|
||||
my @n = V_Mult(1.0/sqrt(V_Dot(@_[0,1,2], @_)), @_);
|
||||
my $sina = $n[1]<0 ? -sqrt($n[1]*$n[1]+$n[2]*$n[2]) :
|
||||
sqrt($n[1]*$n[1]+$n[2]*$n[2]);
|
||||
|
||||
|
||||
if ($sina)
|
||||
{
|
||||
my $cosa = $n[0];
|
||||
@ -337,8 +337,8 @@
|
||||
}
|
||||
return @R;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub MV_Dot # MV_Dot(@A, @b) = @A . @b;
|
||||
{
|
||||
return (V_Dot(@_[0,1,2], @_[9,10,11]), V_Dot(@_[3,4,5], @_[9,10,11]),
|
||||
@ -374,14 +374,14 @@
|
||||
{
|
||||
return (@_[0]+@_[2], @_[1]+@_[3]);
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub C_Subtr # z = z1 - z2
|
||||
{
|
||||
return (@_[0]-@_[2], @_[1]-@_[3]);
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub C_Mult # z = z1 * z2
|
||||
{
|
||||
return (@_[0]*@_[2]-@_[1]*@_[3], @_[0]*@_[3]+@_[2]*@_[1]);
|
||||
@ -404,7 +404,7 @@
|
||||
return ($r*cos($a), $r*sin($a));
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub C_Correct
|
||||
{
|
||||
return (abs(@_[0])<1e-14 ? 0 : @_[0], abs(@_[1])<1e-14 ? 0 : @_[1]);
|
||||
@ -422,7 +422,7 @@
|
||||
return (@_[0], -@_[1]);
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub C_String
|
||||
{
|
||||
return @_[0]." + ".@_[1]."i";
|
||||
@ -434,12 +434,12 @@
|
||||
sub R_Sort
|
||||
{
|
||||
my $n = scalar(@_);
|
||||
|
||||
|
||||
for (my $i=0; $i<$n-2; $i+=2)
|
||||
{
|
||||
for (my $j=$i+2; $j<$n; $j+=2)
|
||||
{
|
||||
if (@_[$j]<@_[$i]) {
|
||||
if (@_[$j]<@_[$i]) {
|
||||
my @t = @_[$i,$i+1]; @_[$i,$i+1] = @_[$j,$j+1]; @_[$j,$j+1] = @t; }
|
||||
else { if ((@_[$j]==@_[$i])&&(@_[$j+1]<@_[$i+1])) {
|
||||
my @t = @_[$i,$i+1]; @_[$i,$i+1] = @_[$j,$j+1]; @_[$j,$j+1] = @t; } }
|
||||
@ -448,7 +448,7 @@
|
||||
return @_;
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub R_First
|
||||
{
|
||||
return (0, 0) if (abs(@_[1])<1e-14);
|
||||
@ -476,16 +476,16 @@
|
||||
my @B = (0, 0);
|
||||
my @z1 = (0.5, 0.5*sqrt(3));
|
||||
my @z2 = C_Conj(@z1);
|
||||
|
||||
|
||||
if (abs($f1)<1e-3) { # limit f1 -> 0
|
||||
@A = ($f2<0 ? abs(2*$f2)**(1/3) : 0, 0); }
|
||||
else {
|
||||
else {
|
||||
if (abs($f2)<1e-14) { # limit f2 -> 0
|
||||
my $f = sqrt(abs($f1))/$c3;
|
||||
@A = $f1<0 ? (-$f*$z1[1], 0.5*$f) : ($f, 0);
|
||||
@B = $f1<0 ? (-$A[0], $A[1]) : ($f, 0); }
|
||||
else {
|
||||
@B = C_Pow(C_Add(($f2, 0),
|
||||
@B = C_Pow(C_Add(($f2, 0),
|
||||
C_Pow(($f1*$f1*$f1+$f2*$f2, 0), 1/2)), 1/3);
|
||||
@A = C_Div(($f1/$c3, 0), @B);
|
||||
@B = ($B[0]/$c3, $B[1]/$c3); } }
|
||||
@ -503,21 +503,21 @@
|
||||
my $input = shift;
|
||||
my $dlines = shift;
|
||||
my $read;
|
||||
|
||||
|
||||
while ($dlines--) { $read = <$input>; }
|
||||
return $read;
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub rewind_read
|
||||
{
|
||||
my $input = shift;
|
||||
|
||||
|
||||
seek($input, 0, SEEK_SET);
|
||||
}
|
||||
|
||||
|
||||
# create crossreference tables
|
||||
# create crossreference tables
|
||||
|
||||
sub create_psf_index # make an index of id
|
||||
{ # locations
|
||||
@ -538,13 +538,13 @@
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub psf_goto # goto $ident in <PSF>
|
||||
{
|
||||
create_psf_index() if (!scalar(%PSFIndex));
|
||||
my $id = shift(@_);
|
||||
my @n = split(" ", $PSFIndex{$id});
|
||||
|
||||
|
||||
@PSFBuffer = ();
|
||||
if (!scalar(@n))
|
||||
{
|
||||
@ -571,7 +571,7 @@
|
||||
my $id;
|
||||
my %hash;
|
||||
my %size;
|
||||
|
||||
|
||||
foreach ((masses,atoms,bonds,angles,dihedrals,impropers)) { $hash{$_}=$_; }
|
||||
open(DATA, "<".$data_name);
|
||||
for (my $i=0; $i<2; ++$i) { my $tmp = <DATA>; } # skip first two lines
|
||||
@ -604,7 +604,7 @@
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub goto_data
|
||||
{
|
||||
create_data_index() if (!scalar(%DATAIndex));
|
||||
@ -623,7 +623,7 @@
|
||||
|
||||
|
||||
# create atom and residue identifiers
|
||||
|
||||
|
||||
sub create_names
|
||||
{
|
||||
return if (scalar(@names));
|
||||
@ -636,7 +636,7 @@
|
||||
my @letter = ("X", "Y", "Z", "P", "Q", "R", "S", "A", "B", "C");
|
||||
my $k = 0;
|
||||
my %atom;
|
||||
|
||||
|
||||
$names[0] = "";
|
||||
foreach (@mass) { $atom{$_} = shift(@name); }
|
||||
for (my $i=1; $i<=$n; ++$i)
|
||||
@ -658,7 +658,7 @@
|
||||
my @data = @_;
|
||||
my $p = $data[1]." ".$data[2];
|
||||
my $k;
|
||||
|
||||
|
||||
for ($k=0; ($k<scalar(@data))&&(substr($data[$k],0,1) ne "#"); ++$k) { }
|
||||
@data = splice(@data, $k-($k<8 ? 3 : 6), $k<8 ? 3 : 6);
|
||||
foreach (@L)
|
||||
@ -669,8 +669,8 @@
|
||||
}
|
||||
return $p;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub create_atom_ids
|
||||
{
|
||||
my $res = 0;
|
||||
@ -682,7 +682,7 @@
|
||||
my $id;
|
||||
my %link;
|
||||
my %special;
|
||||
|
||||
|
||||
printf("Info: creating atom ids\n") if ($info);
|
||||
create_names();
|
||||
$n = goto_data(atoms);
|
||||
@ -696,8 +696,8 @@
|
||||
{
|
||||
if ((($tmp = $link{$id = join(" ", sort(split(" ", $id)))}) eq "")&&
|
||||
(($tmp = $special{$id}) eq ""))
|
||||
{
|
||||
$link{$id} =
|
||||
{
|
||||
$link{$id} =
|
||||
$tmp = "R".($res<10 ? "0" : "").$res;
|
||||
++$res;
|
||||
}
|
||||
@ -712,12 +712,12 @@
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub crossover
|
||||
{
|
||||
my @d = V_Subtr((split(" ", $position[@_[0]]))[0,1,2],
|
||||
(split(" ", $position[@_[1]]))[0,1,2]);
|
||||
|
||||
|
||||
$d[0] /= $l[3];
|
||||
$d[1] /= $l[4];
|
||||
$d[2] /= $l[5];
|
||||
@ -744,7 +744,7 @@
|
||||
{
|
||||
my $n = scalar(@bonds);
|
||||
my $i = 0;
|
||||
|
||||
|
||||
printf("Info: deleting excluded bonds\n") if ($info);
|
||||
while ($i<$n)
|
||||
{
|
||||
@ -754,12 +754,12 @@
|
||||
else { ++$i; }
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub create_bonds
|
||||
{
|
||||
my $n = goto_data(bonds);
|
||||
|
||||
|
||||
printf("Info: creating bonds\n") if ($info);
|
||||
for (my $i=0; $i<$n; ++$i)
|
||||
{
|
||||
@ -779,20 +779,20 @@
|
||||
while (!eof(TRAJECT)&&(substr(lc(join(" ", split(" ", <TRAJECT>))),
|
||||
0,length($subject)) ne $subject)) {}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub read_traject
|
||||
{
|
||||
my @box;
|
||||
my @l;
|
||||
|
||||
|
||||
advance_traject("timestep");
|
||||
my $timestep = (split(" ", <TRAJECT>))[0];
|
||||
advance_traject("number of atoms");
|
||||
my $n = (split(" ", <TRAJECT>))[0];
|
||||
advance_traject("box bounds");
|
||||
for (my $i=0; $i<3; ++$i)
|
||||
{
|
||||
{
|
||||
my @data = split(" ", <TRAJECT>);
|
||||
$box[$i] = $data[0]; # box edge
|
||||
$l[$i] = $data[1]-$data[0]; # box length
|
||||
@ -806,9 +806,9 @@
|
||||
return ($timestep, $n, @box, @l);
|
||||
}
|
||||
|
||||
|
||||
|
||||
# pdb format
|
||||
|
||||
|
||||
sub eigen_vector # eigen_vector(@A, $l)
|
||||
{
|
||||
my @A = splice(@_,0,9);
|
||||
@ -826,8 +826,8 @@
|
||||
return (0,0,1) if ($A[8]==1);
|
||||
return (0,0,0);
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
sub pdb_inertia
|
||||
{
|
||||
my @s = (
|
||||
@ -852,13 +852,13 @@
|
||||
M_Transpose(M_RotateNormal(MV_Dot(@A,@b))));
|
||||
return M_Dot(@B, @A);
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
sub pdb_focus # using moment of inertia
|
||||
{
|
||||
my @R = pdb_inertia(@_);
|
||||
|
||||
|
||||
printf("Info: focussing\n") if ($info);
|
||||
foreach (@position)
|
||||
{
|
||||
@ -867,7 +867,7 @@
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub pdb_center
|
||||
{
|
||||
my @c = splice(@_, 0, 3);
|
||||
@ -881,7 +881,7 @@
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub pdb_pbc
|
||||
{
|
||||
printf("Info: applying periodicity\n") if ($info);
|
||||
@ -909,7 +909,7 @@
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub pdb_positions
|
||||
{
|
||||
my @m = (0,0,0,0,0,0,0,0,0);
|
||||
@ -918,7 +918,7 @@
|
||||
my $mass;
|
||||
my @p;
|
||||
my $d;
|
||||
|
||||
|
||||
foreach (@traject)
|
||||
{
|
||||
my @arg = split(" ");
|
||||
@ -974,7 +974,7 @@
|
||||
printf(PDB "%-11.11s", "P 1");
|
||||
printf(PDB "%3.3s\n", "1");
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub pdb_atoms
|
||||
{
|
||||
@ -998,15 +998,15 @@
|
||||
foreach (@p) { $_ = 0 if (abs($_)<1e-4); }
|
||||
printf(PDB "ATOM "); # pdb command
|
||||
printf(PDB "%6.6s ", ++$n); # atom number
|
||||
printf(PDB "%-3.3s ",
|
||||
printf(PDB "%-3.3s ",
|
||||
$psf_ctrl ? $psf[4] : $names[$p[4]]); # atom name
|
||||
printf(PDB "%-3.3s ",
|
||||
printf(PDB "%-3.3s ",
|
||||
$psf_ctrl ? $psf[3] : $residue[$nres]); # residue name
|
||||
printf(PDB "%5.5s ", $nres); # residue number
|
||||
printf(PDB "%3.3s ", ""); # empty placeholder
|
||||
printf(PDB "%7.7s %7.7s %7.7s ",
|
||||
$p[0], $p[1], $p[2]); # positions
|
||||
printf(PDB "%5.5s %5.5s %4.4s ",
|
||||
printf(PDB "%5.5s %5.5s %4.4s ",
|
||||
"1.00", "0.00", ""); # trailing variables
|
||||
printf(PDB "%-4.4s\n",
|
||||
$psf_ctrl ? $psf[1] : $cluster[$nres]); # cluster name
|
||||
@ -1015,7 +1015,7 @@
|
||||
};
|
||||
printf(PDB "END\n");
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub pdb_timestep
|
||||
{
|
||||
@ -1045,7 +1045,7 @@
|
||||
my $l = 0;
|
||||
my $k = 0;
|
||||
my @extra;
|
||||
|
||||
|
||||
for (my $i=0; $i<$n; ++$i)
|
||||
{
|
||||
my @arg = split(" ", <DATA>);
|
||||
@ -1073,13 +1073,13 @@
|
||||
}
|
||||
printf(PSF "\n");
|
||||
}
|
||||
|
||||
|
||||
|
||||
sub psf_bonds
|
||||
{
|
||||
my $npairs = 0;
|
||||
|
||||
delete_exclude() if (scalar(%exclude)>0);
|
||||
|
||||
delete_exclude() if (scalar(%exclude)>0);
|
||||
delete_crossovers() if ($cut);
|
||||
printf(PSF "%8.8s !NBOND\n", scalar(@bonds));
|
||||
foreach (@bonds)
|
||||
@ -1098,7 +1098,7 @@
|
||||
initialize();
|
||||
|
||||
# create .pdb file
|
||||
|
||||
|
||||
$ncurrent = -1;
|
||||
while ($traject_flag&&!eof(TRAJECT))
|
||||
{
|
||||
@ -1134,4 +1134,4 @@
|
||||
|
||||
close(TRAJECT);
|
||||
close(DATA);
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user