[Swift-commit] r8147 - SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md
wozniak at ci.uchicago.edu
wozniak at ci.uchicago.edu
Wed Aug 13 16:19:54 CDT 2014
Author: wozniak
Date: 2014-08-13 16:19:54 -0500 (Wed, 13 Aug 2014)
New Revision: 8147
Added:
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/clean.sh
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/make-package.tcl
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.i
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.tcl
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/scan.tcl
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/test-md.tcl
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/test.sh
Modified:
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/Makefile
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/main.c
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.c
SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.h
Log:
Copy back from xsede demo
Modified: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/Makefile
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/Makefile 2014-08-13 20:17:50 UTC (rev 8146)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/Makefile 2014-08-13 21:19:54 UTC (rev 8147)
@@ -24,20 +24,30 @@
TCL_HOME = $(HOME)/sfw/tcl-8.6.0
INCLUDES += -I $(TCL_HOME)/include
+TCLSH = $(TCL_HOME)/bin/tclsh8.6
-swift-pkg: libtclmd.so
+swift-pkg: pkgIndex.tcl
-md_wrap.c: md.i
+md_wrap.c: md.i md.h
swig $(<)
+ sed -i s/Md_Init/Tclmd_Init/ $(@)
libtclmd.so: md_wrap.o $(OBJ)
gcc -shared -o $(@) $(^) -L $(TCL_HOME)/lib -l tcl8.6
-endif
+pkgIndex.tcl: libtclmd.so
+ LEAF_PKG=md LEAF_VERSION=0.0 \
+ LEAF_SO=$(<) LEAF_TCL=md.tcl \
+ $(TCLSH) ./make-package.tcl > $(@)
+clean::
+ rm -fv pkgIndex.tcl libtclmd.so md_wrap.c
+
+endif # Swift/T
+
.PHONY: clean
-clean:
- rm -f $(OBJ) $(bin)
+clean::
+ rm -fv $(OBJ) $(bin)
.PHONY: install
install:
Added: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/clean.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/clean.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/clean.sh 2014-08-13 21:19:54 UTC (rev 8147)
@@ -0,0 +1,2 @@
+#! /bin/sh
+rm -f md??.trj md.dat
Property changes on: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/clean.sh
___________________________________________________________________
Added: svn:executable
+ *
Modified: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/main.c
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/main.c 2014-08-13 20:17:50 UTC (rev 8146)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/main.c 2014-08-13 21:19:54 UTC (rev 8147)
@@ -12,7 +12,7 @@
char *outfile = "md.dat";
-char *trjfile = "md.trj.tgz";
+char *trjfile = "md.trj";
/******************************************************************************/
@@ -71,16 +71,12 @@
double ctime1;
double ctime2;
double dt = 0.0001;
- double e0;
- double *force;
int i;
int id;
- double kinetic;
double mass = 1.0 * .0001;
int nd;
int np;
- double potential;
int seed = 123456789;
int step;
int step_num;
@@ -193,8 +189,8 @@
ctime1 = cpu_time ( );
simulate (step_num, step_print_num, step_print, step_print_index,
- np, nd, mass, potential, kinetic, e0,
- dt, seed, outfile);
+ np, nd, mass,
+ dt, seed, outfile, trjfile);
ctime2 = cpu_time ( );
ctime = ctime2 - ctime1;
@@ -203,10 +199,12 @@
printf ( " Elapsed cpu time for main computation:\n" );
printf ( " %f seconds.\n", ctime );
-
+#ifdef NOTDEF
char tarcmd[2000];
sprintf(tarcmd,"tar zcf %s md??.trj",trjfile);
system(tarcmd);
+#endif
+
/*
Terminate.
*/
Added: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/make-package.tcl
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/make-package.tcl (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/make-package.tcl 2014-08-13 21:19:54 UTC (rev 8147)
@@ -0,0 +1,9 @@
+
+set name $env(LEAF_PKG)
+set version $env(LEAF_VERSION)
+set leaf_so $env(LEAF_SO)
+set leaf_tcl $env(LEAF_TCL)
+
+puts [ ::pkg::create -name $name -version $version \
+ -load $leaf_so -source $leaf_tcl ]
+
Property changes on: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/make-package.tcl
___________________________________________________________________
Added: svn:executable
+ *
Modified: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.c
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.c 2014-08-13 20:17:50 UTC (rev 8146)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.c 2014-08-13 21:19:54 UTC (rev 8147)
@@ -18,17 +18,17 @@
void snap ( int np, int nd, int t, double pos[], double vel[], double f[],
double acc[], double mass, double dt );
-static void snap_file_open(void);
-static void snap_file_close(void);
+static void trj_file_open(char *trjfile);
+static void trj_file_close(void);
void simulate (int step_num, int step_print_num,
int step_print, int step_print_index,
int np, int nd,
double mass,
- double potential, double kinetic, double e0,
double dt,
int seed,
- char* outfile)
+ char* outfile,
+ char* trjfile)
{
/*
Allocate memory.
@@ -49,7 +49,7 @@
printf ( "\n" );
printf ( " Initializing positions, velocities, and accelerations.\n" );
- snap_file_open();
+ trj_file_open(trjfile);
/*
Set initial positions, velocities, and accelerations.
@@ -61,9 +61,9 @@
printf ( "\n" );
printf ( " Computing initial forces and energies.\n" );
+ double potential, kinetic;
compute ( np, nd, pos, vel, mass, force, &potential, &kinetic );
-
- e0 = potential + kinetic;
+ double e0 = potential + kinetic;
/*
This is the main time stepping loop:
Compute forces and energies,
@@ -115,7 +115,7 @@
free ( vel );
fclose(ofile);
- snap_file_close();
+ trj_file_close();
}
/******************************************************************************/
@@ -580,20 +580,22 @@
}
static int snapid = 0;
-static FILE *snap_file = NULL;
+static FILE *trj_file = NULL;
-static void snap_file_open()
+static void trj_file_open(char *trjfile)
{
+#ifdef NOTDEF
char snapfile[100];
sprintf(snapfile, "md%02d.trj", snapid);
- snap_file = fopen(snapfile, "w");
- assert(snap_file != NULL);
+#endif
+ trj_file = fopen(trjfile, "w");
+ assert(trj_file != NULL);
}
-static void snap_file_close()
+static void trj_file_close()
{
- fclose(snap_file);
- snap_file = NULL;
+ fclose(trj_file);
+ trj_file = NULL;
}
void snap ( int np, int nd, int t, double pos[], double vel[], double f[],
@@ -603,8 +605,8 @@
for ( j = 0; j < np; j++ )
{
- fprintf(snap_file, "%i s %f %f %f %s\n",
- t, scale(pos[0+j*nd]), scale(pos[1+j*nd]), scale(pos[2+j*nd]), printinfo);
+ fprintf(trj_file, "%d s %f %f %f %s\n",
+ snapid, scale(pos[0+j*nd]), scale(pos[1+j*nd]), scale(pos[2+j*nd]), printinfo);
}
snapid++;
Modified: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.h
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.h 2014-08-13 20:17:50 UTC (rev 8146)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.h 2014-08-13 21:19:54 UTC (rev 8147)
@@ -25,9 +25,9 @@
int step_print, int step_print_index,
int np, int nd,
double mass,
- double potential, double kinetic, double e0,
double dt,
int seed,
- char* outfile);
+ char* outfile,
+ char* trjfile);
#endif
Added: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.i
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.i (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.i 2014-08-13 21:19:54 UTC (rev 8147)
@@ -0,0 +1,6 @@
+
+%module md
+%include "md.h"
+%{
+ #include "md.h"
+%}
Added: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.tcl
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.tcl (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/md.tcl 2014-08-13 21:19:54 UTC (rev 8147)
@@ -0,0 +1,4 @@
+
+namespace eval md {
+ # Nothing
+}
Added: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/scan.tcl
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/scan.tcl (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/scan.tcl 2014-08-13 21:19:54 UTC (rev 8147)
@@ -0,0 +1,21 @@
+#!/usr/bin/env tclsh8.6
+
+lappend auto_path $env(PWD)
+package require md 0.0
+
+set cmds [ info commands ]
+
+set L [list]
+
+foreach cmd $cmds {
+ puts $cmd
+ if { [ regexp .*.* $cmd ] || \
+ [ regexp .*.* $cmd ] } {
+ lappend L $cmd
+ }
+}
+
+set L [ lsort $L ]
+foreach cmd $L {
+ puts $cmd
+}
Property changes on: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/scan.tcl
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/test-md.tcl
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/test-md.tcl (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/test-md.tcl 2014-08-13 21:19:54 UTC (rev 8147)
@@ -0,0 +1,8 @@
+#!/usr/bin/env tclsh8.6
+
+lappend auto_path $env(PWD)
+package require md 0.0
+
+simulate 4 2 0 0 10 2 1 0.1 9 out.txt out.trj
+
+
Property changes on: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/test-md.tcl
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/test.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/test.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/test.sh 2014-08-13 21:19:54 UTC (rev 8147)
@@ -0,0 +1,3 @@
+#! /bin/sh
+
+./md 3 50 1000
Property changes on: SwiftTutorials/ATPESC_2014-08-14/swift-t/examples/05-md/test.sh
___________________________________________________________________
Added: svn:executable
+ *
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