From 375524ed2a578a6e8d353373edbd24977c767790 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Wed, 29 Jul 2020 12:51:15 -0400
Subject: [PATCH] Tools: add PuReMD custom geometry replication to geo_tool.py.
Remove older awk scripts. Fix issue with silica 6000 atom PDB file (CRYST1
lines not 70 characters).
---
data/benchmarks/silica/silica_6000.pdb | 2 +-
tools/geo_tool.py | 61 +++++++++++++++++++++--
tools/replicate.bash | 67 --------------------------
tools/replicate_geo.awk | 60 -----------------------
4 files changed, 59 insertions(+), 131 deletions(-)
delete mode 100644 tools/replicate.bash
delete mode 100644 tools/replicate_geo.awk
diff --git a/data/benchmarks/silica/silica_6000.pdb b/data/benchmarks/silica/silica_6000.pdb
index e5c58216..ef99b2e4 100644
--- a/data/benchmarks/silica/silica_6000.pdb
+++ b/data/benchmarks/silica/silica_6000.pdb
@@ -1,4 +1,4 @@
-CRYST1 36.477 50.174 52.110 90.00 90.00 90.00 0
+CRYST1 36.477 50.174 52.110 90.00 90.00 90.00 0
ATOM 1 O REX 1 56.987 39.868 41.795 1.00 0.00 0 O
ATOM 2 O REX 1 32.795 24.104 25.968 1.00 0.00 0 O
ATOM 3 O REX 1 26.543 26.261 36.254 1.00 0.00 0 O
diff --git a/tools/geo_tool.py b/tools/geo_tool.py
index c5fc3aa7..c39cf1c1 100644
--- a/tools/geo_tool.py
+++ b/tools/geo_tool.py
@@ -130,7 +130,7 @@ def replicate(args):
with open(out_file, 'w') as outfile:
# box dimensions
- outfile.write('{:6}{:9.3f}{:9.3f}{:9.3f}{:7}{:7}{:7}{:11}{:4}'.format(
+ outfile.write('{:6}{:9.3f}{:9.3f}{:9.3f}{:7}{:7}{:7} {:11}{:4}'.format(
'CRYST1', x_dim * args.X_repl, y_dim * args.Y_repl, z_dim * args.Z_repl,
cryst_line[33:40], cryst_line[40:47], cryst_line[47:54],
cryst_line[54:65], cryst_line[65:69]) + linesep)
@@ -152,8 +152,63 @@ def replicate(args):
count = count + 1
elif args.input_format == 'PUREMD':
- #TODO
- pass
+ atom_count = 0
+ atom_lines = []
+ # simulation box info
+ x_dim = 0.0
+ y_dim = 0.0
+ z_dim = 0.0
+ x_ang = 0.0
+ y_ang = 0.0
+ z_ang = 0.0
+
+ with open(args.input_file, 'r') as infile:
+ # BOXGEO line
+ line = infile.readline()
+ line = line.split()
+ x_dim = float(line[1])
+ y_dim = float(line[2])
+ z_dim = float(line[3])
+ x_ang = float(line[4])
+ y_ang = float(line[5])
+ z_ang = float(line[6])
+
+ # atom count line
+ line = infile.readline()
+ line = line.split()
+ atom_count = int(line[0])
+
+ # atom info lines
+ for line in infile:
+ atom_lines.append(line.split())
+
+ if args.output_file:
+ out_file = args.output_file
+ else:
+ out_file = 'output.geo'
+
+ with open(out_file, 'w') as outfile:
+ # BOXGEO line
+ outfile.write('{:6} {:f} {:f} {:f} {:f} {:f} {:f}'.format(
+ 'BOXGEO', x_dim * args.X_repl, y_dim * args.Y_repl, z_dim * args.Z_repl,
+ x_ang, y_ang, z_ang) + linesep)
+
+ # atom count line
+ outfile.write('{:d}'.format(atom_count * args.X_repl * args.Y_repl * args.Z_repl) + linesep)
+
+ # atom info lines
+ count = 1
+ for x in range(args.X_repl):
+ for y in range(args.Y_repl):
+ for z in range(args.Z_repl):
+ for l in atom_lines:
+ outfile.write(' {:d} {:2} {:2} {:f} {:f} {:f}'.format(
+ count, l[1], l[2],
+ float(l[3]) + x * x_dim,
+ float(l[4]) + y * y_dim,
+ float(l[5]) + z * z_dim ) + linesep)
+
+ count = count + 1
def noise(args):
diff --git a/tools/replicate.bash b/tools/replicate.bash
deleted file mode 100644
index d5bf82f3..00000000
--- a/tools/replicate.bash
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/bin/bash
-
-function usage
-{
- echo -e "\tusage: $0 format x_dim y_dim z_dim in_file [out_file]"
- exit 1
-}
-
-
-function repl_geo
-{
- if [ -z "${5:+x}" ]; then
- FILE=$(basename "$1")
- FILE="${FILE%.*}.geo"
- else
- FILE="$5"
- fi
-
- # 1. Convert the pdb file to custom format which is an intermediate format
- "$AWK" '{if($1=="CRYST1") print "BOXGEO", $2, $3, $4, $5, $6, $7; if($1=="ATOM") print $2, $3, $12, $6, $7, $8;}' \
- "$1" >& "$FILE.cus"
-
- # 2. Convert the custom format to geo format with the following command
- # replicate_geo.awk script can also be used to replicate the box in
- # any of the x, y, z directions. They are set as 1, 1, 1 for now.
- # If you want to replicate it, just change these numbers at the beginning
- # of the replicate_geo.awk file.
- "$SED" -e "s/replicate_x = .*/replicate_x = $2;/" \
- -e "s/replicate_y = .*/replicate_y = $3;/" \
- -e "s/replicate_z = .*/replicate_z = $4;/" \
- -i "$GEO"
- "$AWK" -f "$GEO" "$FILE.cus" > "$FILE"
- rm "$FILE.cus"
-
- # 3. Open the geo file and insert a line below the BOXGEO line
- # BOXGEO is the very first line which contains the BOX geometry
- # The new line to be inserted contains the number of atoms in the
- # newly created geo file. This number should be equal to the
- # total number of lines in the geo file - (2). one is the first line
- # which is the BOXGEO line and second one is for the newly inserted line.
-
- LC=$(($(cat "$FILE" | wc -l)-1))
- "$SED" -e "s/BOXGEO.*/&\n$LC/" -i "$FILE"
-}
-
-
-function repl_pdb
-{
- #TODO
- exit
-}
-
-
-AWK="/usr/bin/awk"
-SED="/usr/bin/sed"
-
-GEO="$(dirname $0)/replicate_geo.awk"
-
-if [ "$#" -ne 5 -a "$#" -ne 6 ]; then
- usage
-fi
-
-if [ "$1" == "geo" ]; then
- repl_geo "$5" "$2" "$3" "$4" "$6"
-elif [ "$1" == "pdb" ]; then
- repl_pdb "$5" "$2" "$3" "$4" "$6"
-fi
diff --git a/tools/replicate_geo.awk b/tools/replicate_geo.awk
deleted file mode 100644
index 2231365a..00000000
--- a/tools/replicate_geo.awk
+++ /dev/null
@@ -1,60 +0,0 @@
-# replicates an orthogonal box as many times as given
-# by replicate_x, replicate_y, replicate_z parameters
-# while reading the pdb file, some problems may arise
-# if the fields are not separated as expected.
-# make sure to check for those if output is not as expected.
-
-BEGIN{
- replicate_x = 1;
- replicate_y = 1;
- replicate_z = 1;
-
- num_atoms = 0;
-}
-{
- # collect atom info
- if( $1 == "BOXGEO" ) {
- box[0] = $2;
- box[1] = $3;
- box[2] = $4;
-
- box_ang[0] = $5;
- box_ang[1] = $6;
- box_ang[2] = $7;
- }
- else if( NF == 6 ) {
- atom_id[num_atoms] = $1;
- atom_type[num_atoms] = $2;
- atom_name[num_atoms] = $3;
- atom_pos[num_atoms, 0] = $4;
- atom_pos[num_atoms, 1] = $5;
- atom_pos[num_atoms, 2] = $6;
-
- ++num_atoms;
- }
-}
-END{
- new_atoms = 0;
-
- printf( "%6s %9.3f %9.3f %9.3f %9.3f %9.3f %9.3f\n",
- "BOXGEO", box[0]*replicate_x, box[1]*replicate_y, box[2]*replicate_z,
- box_ang[0], box_ang[1], box_ang[2] );
-
- for( i = 0; i < replicate_x; ++i )
- for( j = 0; j < replicate_y; ++j )
- for( k = 0; k < replicate_z; ++k ){
- base_x = i * box[0];
- base_y = j * box[1];
- base_z = k * box[2];
-
- for( n = 0; n < num_atoms; ++n ) {
- ref = new_atoms % num_atoms;
- printf( "%d %s %s %8.3f %8.3f %8.3f\n",\
- new_atoms+1, atom_type[ref], atom_name[ref],
- base_x + atom_pos[ref,0],
- base_y + atom_pos[ref,1],
- base_z + atom_pos[ref,2] );
- ++new_atoms;
- }
- }
-}
--
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