From: hackbard <hackbard>
Date: Wed, 5 Apr 2006 18:18:40 +0000 (+0000)
Subject: lots of mostly small changes ...
X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=commitdiff_plain;h=8358faac044f73487d64f5ba46690dd84367e532

lots of mostly small changes ...
---

diff --git a/Makefile b/Makefile
index e171354..5f25159 100644
--- a/Makefile
+++ b/Makefile
@@ -8,5 +8,6 @@ all: posic
 posic: $(OBJS) moldyn.o
 	$(CC) $(CFLAGS) -lm -o $@ $(OBJS) $(LIBS) posic.c
 
+.PHONY:clean
 clean:
 	rm -f *.o posic */*.o
diff --git a/moldyn.c b/moldyn.c
index 0fd1aca..db575e9 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -547,7 +547,7 @@ double potential_lennard_jones(t_moldyn *moldyn) {
 	params=moldyn->pot_params;
 	atom=moldyn->atom;
 	count=moldyn->count;
-	eps=params->epsilon;
+	eps=params->epsilon4;
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
@@ -559,7 +559,7 @@ double potential_lennard_jones(t_moldyn *moldyn) {
 			help=d*d; 				/* 1/r^4 */
 			help*=d; 				/* 1/r^6 */
 			d=help*help; 				/* 1/r^12 */
-			u+=eps*(sig12*d-sig6*help);
+			u+=eps*(sig6*help-sig12*d);
 		}
 	}
 	
@@ -579,7 +579,7 @@ int force_lennard_jones(t_moldyn *moldyn) {
 	atom=moldyn->atom;	
 	count=moldyn->count;
 	params=moldyn->pot_params;
-	eps=params->epsilon;
+	eps=params->epsilon4;
 	sig6=params->sigma6;
 	sig12=params->sigma12;
 
@@ -598,11 +598,13 @@ int force_lennard_jones(t_moldyn *moldyn) {
 				h1*=h2;				/* 1/r^14 */
 				h1*=sig12;
 				h2*=sig6;
-				d=12.0*h1-6.0*h2;
+				/* actually there would be a '-',	*
+				 * but f=-d/dr potential		*/
+				d=-12.0*h1+6.0*h2;
 				d*=eps;
 				v3_scale(&force,&distance,d);
-				v3_add(&(atom[j].f),&(atom[j].f),&force);
-				v3_sub(&(atom[i].f),&(atom[i].f),&force);
+				v3_add(&(atom[i].f),&(atom[i].f),&force);
+				v3_sub(&(atom[j].f),&(atom[j].f),&force);
 			}
 		}
 	}
diff --git a/moldyn.h b/moldyn.h
index 42764c5..266436b 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -22,6 +22,8 @@ typedef struct s_atom {
 	//t_list vicinity	/* verlet neighbour list */
 } t_atom;
 
+#include "visual/visual.h"
+
 typedef struct s_moldyn {
 	/* atoms, amount, dimensions */
 	int count;
@@ -68,7 +70,7 @@ typedef struct s_ho_params {
 typedef struct s_lj_params {
 	double sigma6;
 	double sigma12;
-	double epsilon;
+	double epsilon4;
 } t_lj_params;
 
 /*
diff --git a/posic.c b/posic.c
index f026abe..992f9d1 100644
--- a/posic.c
+++ b/posic.c
@@ -53,14 +53,14 @@ int main(int argc,char **argv) {
 	vis.dim.y=b*LC_SI;
 	vis.dim.z=c*LC_SI;
 
-	/* init lattice
+	/* init lattice */
 	printf("placing silicon atoms ... ");
 	count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&si);
-	printf("(%d) ok!\n",count); */
-	/* testing purpose */
+	printf("(%d) ok!\n",count);
+	/* testing purpose
 	count=2;
 	si=malloc(2*sizeof(t_atom));
-	si[0].r.x=0.35*sqrt(3.0)*LC_SI/2.0;
+	si[0].r.x=0.23*sqrt(3.0)*LC_SI/2.0;
 	si[0].r.y=0;
 	si[0].r.z=0;
 	si[0].element=SI;
@@ -70,7 +70,7 @@ int main(int argc,char **argv) {
 	si[1].r.z=0;
 	si[1].element=SI;
 	si[1].mass=M_SI;
-	/* */
+	*/
 
 	/* moldyn init (now si is a valid address) */
 	md.count=count;
@@ -90,10 +90,8 @@ int main(int argc,char **argv) {
 	md.visual=&vis;
 
 	printf("setting thermal fluctuations (T=%f K)\n",md.t);
-	//thermal_init(&md,&random,count);
-	for(a=0;a<count;a++) v3_zero(&(si[0].v));
-	//v3_zero(&(si[0].v));
-	//v3_zero(&(si[1].v));
+	thermal_init(&md,&random,count);
+	//for(a=0;a<count;a++) v3_zero(&(si[0].v));
 
 	/* check kinetic energy */
 
@@ -110,10 +108,10 @@ int main(int argc,char **argv) {
 	help=lj.sigma6*lj.sigma6;
 	lj.sigma6*=help;
 	lj.sigma12=lj.sigma6*lj.sigma6;
-	lj.epsilon=LJ_EPSILON_SI;
+	lj.epsilon4=4.0*LJ_EPSILON_SI;
 
 	ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
-	ho.spring_constant=LJ_EPSILON_SI;
+	ho.spring_constant=4.0*LJ_EPSILON_SI;
 
 	u=get_e_pot(&md);
 
diff --git a/run b/run
new file mode 100755
index 0000000..4c753fe
--- /dev/null
+++ b/run
@@ -0,0 +1,12 @@
+./clean
+./posic $@
+if [ "$?" == "0" ]; then
+	./perms
+	argv="`echo $@ | grep -- '-V'`"
+	if [ "$argv" ] ; then
+		base=`echo $argv | awk -F'-V' '{ print $2 }' | \
+			awk '{ print $2 }'`
+		rasmol -nodisplay < ${base}.scr
+		./ppm2avi
+	fi
+fi
diff --git a/visual/visual.c b/visual/visual.c
index 38ff0b0..29d9469 100644
--- a/visual/visual.c
+++ b/visual/visual.c
@@ -17,6 +17,29 @@
 #include "../moldyn.h"
 #include "../math/math.h"
 
+/* the pse, only needed here */
+static char *pse[]={
+	"*",
+	"H",
+	"He",
+	"Li",
+	"Be",
+	"B",
+	"C",
+	"N",
+	"O",
+	"F",
+	"Ne",
+	"Na",
+	"Mg",
+	"Al",
+	"Si",
+	"P",
+	"S",
+	"Cl",
+	"Ar",
+};
+
 int visual_init(t_visual *v,char *filebase) {
 
 	char file[128+8];
@@ -30,6 +53,7 @@ int visual_init(t_visual *v,char *filebase) {
 		perror("open visual fd");
 		return -1;
 	}
+	dprintf(v->fd,"set write on\n");
 
 	memset(&(v->dim),0,sizeof(t_3dvec));
 
@@ -38,7 +62,10 @@ int visual_init(t_visual *v,char *filebase) {
 
 int visual_tini(t_visual *v) {
 
-	if(v->fd) close(v->fd);
+	if(v->fd) {
+		dprintf(v->fd,"quit\n");
+		close(v->fd);
+	}
 
 	return 0;
 }
@@ -53,28 +80,6 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
 	dim.y=10e9*v->dim.y;
 	dim.z=10e9*v->dim.z;
 
-	char pse[19][4]={
-		"*",
-		"H",
-		"He",
-		"Li",
-		"Be",
-		"B",
-		"C",
-		"N",
-		"O",
-		"F",
-		"Ne",
-		"Na",
-		"Mg",
-		"Al",
-		"Si",
-		"P",
-		"S",
-		"Cl",
-		"Ar",
-	};
-
 	sprintf(file,"%s-%.15f.xyz",v->fb,time);
 	fd=open(file,O_WRONLY|O_CREAT|O_TRUNC);
 	if(fd<0) {
@@ -84,7 +89,7 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
 
 	/* script file update */
 	dprintf(v->fd,"load xyz %s\n",file);
-	dprintf(v->fd,"spacefill 300\n");
+	dprintf(v->fd,"spacefill 270\n");
 	dprintf(v->fd,"rotate x 100\n");
 	dprintf(v->fd,"rotate y 10\n");
 	dprintf(v->fd,"set ambient 20\n");
diff --git a/visual/visual.h b/visual/visual.h
index e2681d9..8726741 100644
--- a/visual/visual.h
+++ b/visual/visual.h
@@ -11,13 +11,14 @@
 #include "../moldyn.h"
 #include "../math/math.h"
 
+/* datatypes */
+
 typedef struct s_visual {
 	int fd;			/* rasmol script file descriptor */
 	char fb[128];		/* basename of the save files */
 	t_3dvec dim;		/* dimensions of the simulation cell */
 } t_visual;
 
-
 /* function prototypes */
 
 int visual_init(t_visual *v,char *filebase);
@@ -25,3 +26,5 @@ int visual_tini(t_visual *v);
 int visual_atoms(t_visual *v,double time,t_atom *atom,int n);
 
 #endif
+
+