From 6eb09b305eb6f565d844979b68dd2542e9a0d5fa Mon Sep 17 00:00:00 2001
From: hackbard <hackbard>
Date: Mon, 20 Mar 2006 23:29:00 +0000
Subject: [PATCH] more testing

---
 clean   |  3 +++
 doit    |  9 +++++++++
 perms   |  3 +++
 posic.c | 45 +++++++++++++++++++++++++++++++++++----------
 posic.h |  2 +-
 ppm2avi |  7 +++++++
 6 files changed, 58 insertions(+), 11 deletions(-)
 create mode 100755 clean
 create mode 100755 doit
 create mode 100755 perms
 create mode 100755 ppm2avi

diff --git a/clean b/clean
new file mode 100755
index 0000000..2e1cd0e
--- /dev/null
+++ b/clean
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+rm -f saves/* video/*
diff --git a/doit b/doit
new file mode 100755
index 0000000..04ece04
--- /dev/null
+++ b/doit
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+./clean
+gcc -o posic posic.c -Wall
+./posic
+./perms
+rasmol
+./ppm2avi
+mplayer video/md.avi
diff --git a/perms b/perms
new file mode 100755
index 0000000..d1f5e41
--- /dev/null
+++ b/perms
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+chmod 640 saves/*
diff --git a/posic.c b/posic.c
index 997127e..8910ddd 100644
--- a/posic.c
+++ b/posic.c
@@ -26,7 +26,8 @@ int main(int argc,char **argv) {
 	double lj1,lj2,lj;
 
 	/* silicon */
-	amount_si=AMOUNT_SI;
+	//amount_si=AMOUNT_SI;
+	amount_si=2;
 	printf("simulating %d silicon atoms\n",amount_si);
 	si=malloc(amount_si*sizeof(t_atom));
 	if(!si) {
@@ -38,6 +39,7 @@ int main(int argc,char **argv) {
 
 	/* init */
 	printf("placing silicon atoms\n");
+	/*
 	for(i=0;i<amount_si;i++) {
 		si[i].x=RAND(LEN_X);
 		si[i].y=RAND(LEN_Y);
@@ -49,6 +51,13 @@ int main(int argc,char **argv) {
 		si[i].fy=.0;
 		si[i].fz=.0;
 	}
+	*/
+	si[0].x=-2.0;
+	si[1].x=+2.0;
+	si[0].y=0;
+	si[0].z=0;
+	si[1].y=0;
+	si[1].z=0;
 
 	/* time */
 	time=.0;
@@ -93,6 +102,10 @@ int main(int argc,char **argv) {
 		si[i].vx+=(tau*si[i].fx/m2);
 		si[i].vy+=(tau*si[i].fy/m2);
 		si[i].vz+=(tau*si[i].fz/m2);
+		/* reset of forces */
+		si[i].fx=.0;
+		si[i].fy=.0;
+		si[i].fz=.0;
 	}
 	for(i=0;i<amount_si;i++) {
 		/* calculation of forces at new positions r(t+h) */
@@ -121,21 +134,23 @@ int main(int argc,char **argv) {
 				lj1*=LJ_SIGMA_12;
 				lj2*=LJ_SIGMA_06;
 				lj=-2*lj1+lj2;
-				si[i].fx=lj*deltax;
-				si[i].fy=lj*deltay;
-				si[i].fz=lj*deltaz;
-				si[i].fx=-lj*deltax;
-				si[i].fy=-lj*deltay;
-				si[i].fz=-lj*deltaz;
+				si[i].fx-=lj*deltax;
+				si[i].fy-=lj*deltay;
+				si[i].fz-=lj*deltaz;
+				si[j].fx+=lj*deltax;
+				si[j].fy+=lj*deltay;
+				si[j].fz+=lj*deltaz;
 			}
 		}
+	}
+	for(i=0;i<amount_si;i++) {
 		/* calculation of new velocities v(t+h) */
 		si[i].vx+=(tau*si[i].fx/m2);
 		si[i].vy+=(tau*si[i].fy/m2);
 		si[i].vz+=(tau*si[i].fz/m2);
 	}
 
-	if(!(runs%10)) {
+	if(!(runs%100)) {
 
 	/* rasmol script & xyz file */
 	sprintf(xyz,"./saves/si-%.15f.xyz",time);
@@ -146,17 +161,27 @@ int main(int argc,char **argv) {
 		return -1;
 	}
 	dprintf(fd2,"load xyz %s\n",xyz);
-	dprintf(fd2,"spacefill 200\n");
+	//dprintf(fd2,"spacefill 200\n");
+	dprintf(fd2,"spacefill\n");
 	dprintf(fd2,"rotate x 11\n");
 	dprintf(fd2,"rotate y 13\n");
 	dprintf(fd2,"set ambient 20\n");
 	dprintf(fd2,"set specular on\n");
 	dprintf(fd2,"write ppm %s\n",ppm);
 	dprintf(fd2,"zap\n");
-	dprintf(fd1,"%d\nsilicon\n",amount_si);
+	dprintf(fd1,"%d\nsilicon\n",amount_si+9);
 	for(i=0;i<amount_si;i++)
 		dprintf(fd1,"Si %f %f %f %f\n",
 		        si[i].x,si[i].y,si[i].z,time);
+	dprintf(fd1,"H 0.0 0.0 0.0 %f\n",time);
+	dprintf(fd1,"He %f %f %f %f\n",LX,LY,LZ,time);
+	dprintf(fd1,"He %f %f %f %f\n",-LX,LY,LZ,time);
+	dprintf(fd1,"He %f %f %f %f\n",LX,-LY,LZ,time);
+	dprintf(fd1,"He %f %f %f %f\n",LX,LY,-LZ,time);
+	dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,LZ,time);
+	dprintf(fd1,"He %f %f %f %f\n",-LX,LY,-LZ,time);
+	dprintf(fd1,"He %f %f %f %f\n",LX,-LY,-LZ,time);
+	dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,-LZ,time);
 	close(fd1);
 
 	}
diff --git a/posic.h b/posic.h
index fa0846e..755ddc6 100644
--- a/posic.h
+++ b/posic.h
@@ -24,7 +24,7 @@
 #define LEN_Z 50
 #define LZ (1.0*LEN_Z/2)
 
-#define RUNS 1000
+#define RUNS 10000
 #define TAU 0.001
 
 #define R_CUTOFF 20
diff --git a/ppm2avi b/ppm2avi
new file mode 100755
index 0000000..febe86c
--- /dev/null
+++ b/ppm2avi
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+for i in video/*.ppm; do
+	convert $i video/$(basename $i ppm)png
+done
+
+mencoder mf://video/*.png -ovc copy -o video/md.avi
-- 
2.20.1