X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=7f9745ad29ef2f8e7dd52a52301a4f0a05ad0283;hb=bdb198c5a5fe38361d10f98e7db366b0915e56fb;hp=f2ac637e64dfeb99ba82946b70a6242175ade88f;hpb=792f14f95b47989f7f12df0ea70b54619be016ee;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index f2ac637..7f9745a 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -30,9 +30,10 @@ int moldyn_usage(char **argv) {
 	printf("-M <steps> <file> (log total momentum)\n");
 	printf("-D <steps> <file> (dump total information)\n");
 	printf("-S <steps> <filebase> (single save file)\n");
+	printf("-V <steps> <filebase> (rasmol file)\n");
 	printf("--- physics options ---\n");
 	printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
-	printf("-t <timestep tau> [s] (%f)\n",MOLDYN_TAU);
+	printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
 	printf("-R <runs> (%d)\n",MOLDYN_RUNS);
 	printf("\n");
 
@@ -70,9 +71,13 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 					moldyn->swrite=atoi(argv[++i]);
 					strncpy(moldyn->sfb,argv[++i],64);
 					break;
-				case 'T':
+				case 'V':
+					moldyn->vwrite=atoi(argv[++i]);
+					strncpy(moldyn->vfb,argv[++i],64);
 					break;
+				case 'T':
 					moldyn->t=atof(argv[++i]);
+					break;
 				case 't':
 					moldyn->tau=atof(argv[++i]);
 					break;
@@ -93,9 +98,12 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
 	return 0;
 }
 
-int moldyn_log_init(t_moldyn *moldyn) {
+int moldyn_log_init(t_moldyn *moldyn,void *v) {
 
 	moldyn->lvstat=0;
+	t_visual *vis;
+
+	vis=v;
 
 	if(moldyn->ewrite) {
 		moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
@@ -130,8 +138,23 @@ int moldyn_log_init(t_moldyn *moldyn) {
 		moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
 	}
 
-	if(moldyn->dwrite)
+	if((moldyn->vwrite)&&(vis)) {
+		moldyn->visual=vis;
+		visual_init(vis,moldyn->vfb);
 		moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+	}
+
+	moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+
+	return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+	if(moldyn->efd) close(moldyn->efd);
+	if(moldyn->mfd) close(moldyn->efd);
+	if(moldyn->dfd) close(moldyn->efd);
+	if(moldyn->visual) visual_tini(moldyn->visual);
 
 	return 0;
 }
@@ -328,7 +351,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	int i;
 	unsigned int e,m,s,d,v;
-	unsigned char lvstat;
 	t_3dvec p;
 
 	int fd;
@@ -340,7 +362,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	d=moldyn->dwrite;
 	v=moldyn->vwrite;
 
-	if(!(lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
+	if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
 		printf("[moldyn] warning, lv system not initialized\n");
 		return -1;
 	}
@@ -498,7 +520,7 @@ int force_harmonic_oscillator(t_moldyn *moldyn) {
 			d=v3_norm(&distance);
 			if(d<=moldyn->cutoff) {
 				v3_scale(&force,&distance,
-				         (-sc*(1.0-(equi_dist/d))));
+				         -sc*(1.0-(equi_dist/d)));
 				v3_add(&(atom[i].f),&(atom[i].f),&force);
 				v3_sub(&(atom[j].f),&(atom[j].f),&force);
 			}
@@ -525,19 +547,19 @@ 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;
 
 	u=0.0;
 	for(i=0;i<count;i++) {
 		for(j=0;j<i;j++) {
-			v3_sub(&distance,&(atom[j].r),&(atom[i].r));
+			v3_sub(&distance,&(atom[i].r),&(atom[j].r));
 			d=1.0/v3_absolute_square(&distance); 	/* 1/r^2 */
 			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);
 		}
 	}
 	
@@ -557,15 +579,15 @@ int force_lennard_jones(t_moldyn *moldyn) {
 	atom=moldyn->atom;	
 	count=moldyn->count;
 	params=moldyn->pot_params;
-	eps=params->epsilon;
-	sig6=params->sigma6;
-	sig12=params->sigma12;
+	eps=params->epsilon4;
+	sig6=6*params->sigma6;
+	sig12=12*params->sigma12;
 
 	for(i=0;i<count;i++) v3_zero(&(atom[i].f));
 
 	for(i=0;i<count;i++) {
 		for(j=0;j<i;j++) {
-			v3_sub(&distance,&(atom[j].r),&(atom[i].r));
+			v3_sub(&distance,&(atom[i].r),&(atom[j].r));
 			v3_per_bound(&distance,&(moldyn->dim));
 			d=v3_absolute_square(&distance);
 			if(d<=moldyn->cutoff_square) {
@@ -576,11 +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=h1+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);
 			}
 		}
 	}