[Swift-commit] r8139 - demo/xsede.2014.0425/src/md
wozniak at ci.uchicago.edu
wozniak at ci.uchicago.edu
Wed Aug 13 14:50:12 CDT 2014
Author: wozniak
Date: 2014-08-13 14:50:12 -0500 (Wed, 13 Aug 2014)
New Revision: 8139
Added:
demo/xsede.2014.0425/src/md/make-package.tcl
demo/xsede.2014.0425/src/md/md.i
demo/xsede.2014.0425/src/md/md.tcl
demo/xsede.2014.0425/src/md/test-md.tcl
Modified:
demo/xsede.2014.0425/src/md/Makefile
demo/xsede.2014.0425/src/md/main.c
demo/xsede.2014.0425/src/md/md.c
demo/xsede.2014.0425/src/md/md.h
Log:
Tcl binding and test
Modified: demo/xsede.2014.0425/src/md/Makefile
===================================================================
--- demo/xsede.2014.0425/src/md/Makefile 2014-08-13 17:47:41 UTC (rev 8138)
+++ demo/xsede.2014.0425/src/md/Makefile 2014-08-13 19:50:12 UTC (rev 8139)
@@ -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:
Modified: demo/xsede.2014.0425/src/md/main.c
===================================================================
--- demo/xsede.2014.0425/src/md/main.c 2014-08-13 17:47:41 UTC (rev 8138)
+++ demo/xsede.2014.0425/src/md/main.c 2014-08-13 19:50:12 UTC (rev 8139)
@@ -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;
@@ -193,7 +189,7 @@
ctime1 = cpu_time ( );
simulate (step_num, step_print_num, step_print, step_print_index,
- np, nd, mass, potential, kinetic, e0,
+ np, nd, mass,
dt, seed, outfile, trjfile);
ctime2 = cpu_time ( );
Added: demo/xsede.2014.0425/src/md/make-package.tcl
===================================================================
--- demo/xsede.2014.0425/src/md/make-package.tcl (rev 0)
+++ demo/xsede.2014.0425/src/md/make-package.tcl 2014-08-13 19:50:12 UTC (rev 8139)
@@ -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: demo/xsede.2014.0425/src/md/make-package.tcl
___________________________________________________________________
Added: svn:executable
+ *
Modified: demo/xsede.2014.0425/src/md/md.c
===================================================================
--- demo/xsede.2014.0425/src/md/md.c 2014-08-13 17:47:41 UTC (rev 8138)
+++ demo/xsede.2014.0425/src/md/md.c 2014-08-13 19:50:12 UTC (rev 8139)
@@ -15,7 +15,7 @@
double r8_uniform_01 ( int *seed );
void update ( int np, int nd, double pos[], double vel[], double f[],
double acc[], double mass, double dt );
-void snap ( int np, int nd, double t, double pos[], double vel[], double f[],
+void snap ( int np, int nd, int t, double pos[], double vel[], double f[],
double acc[], double mass, double dt );
static void trj_file_open(char *trjfile);
@@ -25,7 +25,6 @@
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,
@@ -62,9 +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,
@@ -104,7 +103,7 @@
( potential + kinetic - e0 ) / e0 );
step_print_index = step_print_index + 1;
step_print = ( step_print_index * step_num ) / step_print_num;
- snap (np, nd, step*dt, pos, vel, force, acc, mass, dt );
+ snap (np, nd, step, pos, vel, force, acc, mass, dt );
}
update ( np, nd, pos, vel, force, acc, mass, dt );
}
@@ -599,7 +598,7 @@
trj_file = NULL;
}
-void snap ( int np, int nd, double t, double pos[], double vel[], double f[],
+void snap ( int np, int nd, int t, double pos[], double vel[], double f[],
double acc[], double mass, double dt )
{
int j;
Modified: demo/xsede.2014.0425/src/md/md.h
===================================================================
--- demo/xsede.2014.0425/src/md/md.h 2014-08-13 17:47:41 UTC (rev 8138)
+++ demo/xsede.2014.0425/src/md/md.h 2014-08-13 19:50:12 UTC (rev 8139)
@@ -25,7 +25,6 @@
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,
Added: demo/xsede.2014.0425/src/md/md.i
===================================================================
--- demo/xsede.2014.0425/src/md/md.i (rev 0)
+++ demo/xsede.2014.0425/src/md/md.i 2014-08-13 19:50:12 UTC (rev 8139)
@@ -0,0 +1,6 @@
+
+%module md
+%include "md.h"
+%{
+ #include "md.h"
+%}
Added: demo/xsede.2014.0425/src/md/md.tcl
===================================================================
--- demo/xsede.2014.0425/src/md/md.tcl (rev 0)
+++ demo/xsede.2014.0425/src/md/md.tcl 2014-08-13 19:50:12 UTC (rev 8139)
@@ -0,0 +1,4 @@
+
+namespace eval md {
+ # Nothing
+}
Added: demo/xsede.2014.0425/src/md/test-md.tcl
===================================================================
--- demo/xsede.2014.0425/src/md/test-md.tcl (rev 0)
+++ demo/xsede.2014.0425/src/md/test-md.tcl 2014-08-13 19:50:12 UTC (rev 8139)
@@ -0,0 +1,7 @@
+#!/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
+
Property changes on: demo/xsede.2014.0425/src/md/test-md.tcl
___________________________________________________________________
Added: svn:executable
+ *
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