From 028c7bc939b1f07da58ea4c9284e95f83c0a7da8 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@cse.msu.edu>
Date: Fri, 1 Jul 2016 09:44:34 -0400
Subject: [PATCH] Add more tools. Update water benchmark.
---
data/benchmarks/water/water_6540.pdb | 2 +-
tools/geo2lmp_reax.awk | 38 ++++++++++
tools/lmp2pdb.awk | 106 +++++++++++++++++++++++++++
3 files changed, 145 insertions(+), 1 deletion(-)
create mode 100644 tools/geo2lmp_reax.awk
create mode 100644 tools/lmp2pdb.awk
diff --git a/data/benchmarks/water/water_6540.pdb b/data/benchmarks/water/water_6540.pdb
index 660883aa..4c09dc51 100644
--- a/data/benchmarks/water/water_6540.pdb
+++ b/data/benchmarks/water/water_6540.pdb
@@ -1,4 +1,4 @@
-CRYST1 40.299 40.299 40.299 90.00 90.00 90.00 0
+CRYST1 40.299 40.299 40.299 90.00 90.00 90.00 0
ATOM 1 O REX 1 5.690 12.751 11.651 1.00 0.00 0 O
ATOM 2 H REX 1 4.760 12.681 11.281 1.00 0.00 0 H
ATOM 3 H REX 1 5.800 13.641 12.091 1.00 0.00 0 H
diff --git a/tools/geo2lmp_reax.awk b/tools/geo2lmp_reax.awk
new file mode 100644
index 00000000..9a5823f2
--- /dev/null
+++ b/tools/geo2lmp_reax.awk
@@ -0,0 +1,38 @@
+BEGIN{
+ comment = "water strong scaling test";
+ ntypes = 2;
+ masses[1] = 1.0080;
+ masses[2] = 15.990;
+ types["H"] = 1;
+ types["O"] = 2;
+ box[0] = box[1] = box[2] = 0;
+}
+{
+ if( $1 == "BOXGEO" ) {
+ box[0] = $2;
+ box[1] = $3;
+ box[2] = $4;
+ }
+ else if( NF == 1 ) {
+ natoms = $1;
+ # print the header
+ print "#", comment, "\n";
+
+ print natoms, "atoms";
+ print ntypes, "atom types\n";
+
+ print "0", box[0], "xlo", "xhi";
+ print "0", box[1], "ylo", "yhi";
+ print "0", box[2], "zlo", "zhi\n";
+
+ print "Masses\n";
+ for( i = 1; i <= ntypes; ++i )
+ print i, masses[i];
+
+ print "\nAtoms\n";
+ }
+ else{
+ # print the atom info
+ print $1, types[$2], "0", $4, $5, $6;
+ }
+}
\ No newline at end of file
diff --git a/tools/lmp2pdb.awk b/tools/lmp2pdb.awk
new file mode 100644
index 00000000..482bd502
--- /dev/null
+++ b/tools/lmp2pdb.awk
@@ -0,0 +1,106 @@
+BEGIN{
+ box_flag = 0;
+ natoms = -1;
+ ntypes = -1;
+ atom_style = "charge";
+}
+{
+ # num atoms
+ if( $2 == "atoms" )
+ natoms = $1;
+ # num atom types
+ else if( $2 == "atom" && $3 == "types" )
+ ntypes = $1;
+ # box geometry
+ else if( $3 == "xlo" && $4 == "xhi" ) {
+ box[0] = $2 - $1;
+ ++box_flag;
+ }
+ else if( $3 == "ylo" && $4 == "yhi" ) {
+ box[1] = $2 - $1;
+ ++box_flag;
+ }
+ else if( $3 == "zlo" && $4 == "zhi" ) {
+ box[2] = $2 - $1;
+ ++box_flag;
+ }
+ # atom masses
+ else if( $1 == "Masses" ) {
+ if( ntypes <= 0 ) {
+ printf( "number of atom types can not be %d!\n", ntypes );
+ exit;
+ }
+
+ getline; # skip the empty line
+ for( i = 0; i < ntypes; ++i ) {
+ getline;
+ if( NF != 2 ) { # expect one integer, one float
+ printf( "unexpected mass line format: %s!\n", $0 );
+ exit;
+ }
+
+ # record the atom type
+ if( $2 == 12.0000 )
+ types[$1] = "C";
+ else if( $2 == 1.0080 )
+ types[$1] = "H";
+ else if( $2 == 15.9990 )
+ types[$1] = "O";
+ else if( $2 == 14.0000 )
+ types[$1] = "N";
+ else {
+ printf( "unknown atom type!\n" );
+ exit;
+ }
+ }
+ }
+ # atom info
+ else if( $1 == "Atoms" ) {
+ if( natoms <= 0 ) {
+ printf( "number of atoms can not be %d!\n", natoms );
+ exit;
+ }
+
+ getline; # skip the empty line
+ for( i = 0; i < natoms; ++i ) {
+ getline;
+ if( NF != 6 ) { # expect 3 ints, 3 floats
+ printf( "unexpected atom line format: %s!\n", $0 );
+ exit;
+ }
+
+ atoms[i,"serial"] = $1;
+ atoms[i,"type"] = types[$2];
+ atoms[i,"q"] = $3;
+ atoms[i,"x"] = $4;
+ atoms[i,"y"] = $5;
+ atoms[i,"z"] = $6;
+ }
+ }
+ else if( $1 == "#" )
+ 1; # skip the comment
+ else if( NF == 0 )
+ 1; # skip the empty line
+ else {
+ printf( "unexpected line: %s\n", $0 );
+ exit;
+ }
+}
+END{
+ if( box_flag != 3 ) {
+ printf( "incorrect box geometry!\n" );
+ exit;
+ }
+
+ printf( "%6s%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f%11s%4d\n",
+ "CRYST1", box[0], box[1], box[2], 90, 90, 90, "P", 1 );
+
+ for( i = 0; i < natoms; ++i ) {
+ printf( "%-6s%5d%5s%c%3s %c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f "\
+ "%-4s%2s%2s\n", "ATOM", atoms[i,"serial"], atoms[i,"type"], " ",
+ "REX", " ", 1, " ", atoms[i,"x"], atoms[i,"y"], atoms[i,"z"],
+ 1.0, 0.0, "0", atoms[i,"type"], " " );
+ }
+
+ printf( "END\n" );
+}
\ No newline at end of file
--
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