X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;ds=sidebyside;f=moldyn.c;h=17720675c4f5c0c76dea880ac40eb5787f772eb0;hb=877139ec35cf357c96fdb314f690fd6075554c47;hp=f2ac637e64dfeb99ba82946b70a6242175ade88f;hpb=792f14f95b47989f7f12df0ea70b54619be016ee;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index f2ac637..1772067 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -21,6 +21,7 @@
 #include "init/init.h"
 #include "random/random.h"
 #include "visual/visual.h"
+#include "list/list.h"
 
 int moldyn_usage(char **argv) {
 
@@ -30,9 +31,10 @@ 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 +72,13 @@ 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 +99,12 @@ 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 +139,23 @@ 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;
 }
@@ -315,6 +339,144 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 	return tau;	
 }
 
+/*
+ * numerical tricks
+ */
+
+/* verlet list */
+
+int verlet_list_init(t_moldyn *moldyn) {
+
+	int i,fd;
+
+	fd=open("/dev/null",O_WRONLY);
+
+	for(i=0;i<moldyn->count;i++)
+		list_init(&(moldyn->atom[i].verlet),fd);
+
+	moldyn->r_verlet=1.1*moldyn->cutoff;
+	/* +moldyn->tau*\
+		sqrt(3.0*K_BOLTZMANN*moldyn->t/moldyn->atom[0].mass); */
+
+	printf("debug: r verlet = %.15f\n",moldyn->r_verlet);
+	printf("       r cutoff = %.15f\n",moldyn->cutoff);
+	printf("       dim      = %.15f\n",moldyn->dim.x);
+
+	/* make sure to update the list in the beginning */
+	moldyn->dr_max1=moldyn->r_verlet;
+	moldyn->dr_max2=moldyn->r_verlet;
+
+	return 0;
+}
+
+int link_cell_init(t_moldyn *moldyn) {
+
+	t_linkcell *lc;
+
+	lc=&(moldyn->lc);
+
+	/* partitioning the md cell */
+	lc->nx=moldyn->dim.x/moldyn->cutoff;
+	lc->x=moldyn->dim.x/lc->nx;
+	lc->ny=moldyn->dim.y/moldyn->cutoff;
+	lc->y=moldyn->dim.y/lc->ny;
+	lc->nz=moldyn->dim.z/moldyn->cutoff;
+	lc->z=moldyn->dim.z/lc->nz;
+
+	lc->subcell=malloc(lc->nx*lc->ny*lc->nz*sizeof(t_list));
+
+ 	link_cell_update(moldyn);
+	
+	return 0;
+}
+
+int verlet_list_update(t_moldyn *moldyn) {
+
+	int i,j;
+	t_3dvec d;
+	t_atom *atom;
+
+	atom=moldyn->atom;
+
+	puts("debug: list update start");
+
+	for(i=0;i<moldyn->count;i++) {
+		list_destroy(&(atom[i].verlet));
+		for(j=0;j<moldyn->count;j++) {
+			if(i!=j) {
+				v3_sub(&d,&(atom[i].r),&(atom[j].r));
+				v3_per_bound(&d,&(moldyn->dim));
+				if(v3_norm(&d)<=moldyn->r_verlet)
+					list_add_immediate_ptr(&(atom[i].verlet),&(atom[j]));
+			}
+		}
+	}
+
+	moldyn->dr_max1=0.0;
+	moldyn->dr_max2=0.0;
+
+	puts("debug: list update end");
+
+	return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+	int count,i,j,k;
+	int nx,ny,nz;
+	t_atom *atom;
+
+	atom=moldyn->atom;
+	nx=moldyn->lc.nx; ny=moldyn->lc.ny; nz=moldyn->lc.nz;
+
+	for(i=0;i<nx*ny*nz;i++)
+		list_destroy(&(moldyn->lc.subcell[i]));
+	
+	for(count=0;count<moldyn->count;count++) {
+		for(i=0;i<nx;i++) {
+			if((atom[count].r.x>=i*moldyn->dim.x) && \
+			   (atom[count].r.x<(i+1)*moldyn->dim.x))
+				break;
+		}
+		for(j=0;j<ny;j++) {
+			if((atom[count].r.y>=j*moldyn->dim.y) && \
+			   (atom[count].r.y<(j+1)*moldyn->dim.y))
+				break;
+		}
+		for(k=0;k<nz;k++) {
+			if((atom[count].r.z>=k*moldyn->dim.z) && \
+			   (atom[count].r.z<(k+1)*moldyn->dim.z))
+				break;
+		}
+		list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+		                       &(atom[count]));
+	}
+
+	return 0;
+}
+
+int verlet_list_shutdown(t_moldyn *moldyn) {
+
+	int i;
+
+	for(i=0;i<moldyn->count;i++)
+		list_shutdown(&(moldyn->atom[i].verlet));
+
+	return 0;
+}
+
+int link_cell_shutdown(t_moldyn *moldyn) {
+
+	int i;
+	t_linkcell *lc;
+
+	lc=&(moldyn->lc);
+
+	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
+		list_shutdown(&(moldyn->lc.subcell[i]));
+
+	return 0;
+}
 
 /*
  *
@@ -328,27 +490,45 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	int i;
 	unsigned int e,m,s,d,v;
-	unsigned char lvstat;
 	t_3dvec p;
+	double rlc;
 
 	int fd;
 	char fb[128];
 
+	/* logging & visualization */
 	e=moldyn->ewrite;
 	m=moldyn->mwrite;
 	s=moldyn->swrite;
 	d=moldyn->dwrite;
 	v=moldyn->vwrite;
 
-	if(!(lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
+	/* verlet list */	
+	rlc=moldyn->r_verlet-moldyn->cutoff;
+
+	if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
 		printf("[moldyn] warning, lv system not initialized\n");
 		return -1;
 	}
 
+	/* create the neighbour list */
+	//verlet_list_update(moldyn);
+	link_cell_update(moldyn);
+
 	/* calculate initial forces */
 	moldyn->force(moldyn);
 
 	for(i=0;i<moldyn->time_steps;i++) {
+		/* show runs */
+		printf(".");
+
+		/* neighbour list update */
+		link_cell_update(moldyn);
+		//if(moldyn->dr_max1+moldyn->dr_max2>rlc) {
+		//	printf("\n");
+		//	verlet_list_update(moldyn);
+		//}
+
 		/* integration step */
 		moldyn->integrate(moldyn);
 
@@ -401,7 +581,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 int velocity_verlet(t_moldyn *moldyn) {
 
 	int i,count;
-	double tau,tau_square;
+	double tau,tau_square,dr;
 	t_3dvec delta;
 	t_atom *atom;
 
@@ -415,10 +595,20 @@ int velocity_verlet(t_moldyn *moldyn) {
 		/* new positions */
 		v3_scale(&delta,&(atom[i].v),tau);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
+		v3_add(&(atom[i].dr),&(atom[i].dr),&delta);
 		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
+		v3_add(&(atom[i].dr),&(atom[i].dr),&delta);
 		v3_per_bound(&(atom[i].r),&(moldyn->dim));
 
+		/* set maximum dr (possible list update) [obsolete] */
+		//dr=v3_norm(&(atom[i].dr));
+		//if(dr>moldyn->dr_max1) {
+		//	moldyn->dr_max2=moldyn->dr_max1;
+		//	moldyn->dr_max1=dr;
+		//}
+		//else if(dr>moldyn->dr_max2) moldyn->dr_max2=dr;
+
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
 		v3_add(&(atom[i].v),&(atom[i].v),&delta);
@@ -498,7 +688,7 @@ 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);
 			}
@@ -514,30 +704,47 @@ int force_harmonic_oscillator(t_moldyn *moldyn) {
 double potential_lennard_jones(t_moldyn *moldyn) {
 
 	t_lj_params *params;
-	t_atom *atom;
-	int i,j;
+	t_atom *atom,*btom;
+	t_linkcell *lc;
+	int i;
 	int count;
 	t_3dvec distance;
 	double d,help;
 	double u;
 	double eps,sig6,sig12;
+	int i,j,k;
+	int ni,nj,nk;
 
 	params=moldyn->pot_params;
 	atom=moldyn->atom;
+	lc=&(moldyn->lc);
 	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));
+		/* verlet list [obsolete] */
+		//list_reset(&(atom[i].verlet));
+		//if(atom[i].verlet.current==NULL) continue;
+
+		/* determine cell */
+		ni=atom[i].r.x/lc->x;
+		nj=atom[i].r.y/lc->y;
+		nk=atom[i].r.z/lc->z;
+
+		while(1) {
+			btom=atom[i].verlet.current->data;
+			v3_sub(&distance,&(atom[i].r),&(btom->r));
+			v3_per_bound(&distance,&(moldyn->dim));
 			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);
+			if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
+				break;
 		}
 	}
 	
@@ -547,8 +754,8 @@ double potential_lennard_jones(t_moldyn *moldyn) {
 int force_lennard_jones(t_moldyn *moldyn) {
 
 	t_lj_params *params;
-	int i,j,count;
-	t_atom *atom;
+	int i,count;
+	t_atom *atom,*btom;
 	t_3dvec distance;
 	t_3dvec force;
 	double d,h1,h2;
@@ -557,15 +764,18 @@ 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));
+		list_reset(&(atom[i].verlet));
+		if(atom[i].verlet.current==NULL) continue;
+		while(1) {
+			btom=atom[i].verlet.current->data;
+			v3_sub(&distance,&(atom[i].r),&(btom->r));
 			v3_per_bound(&distance,&(moldyn->dim));
 			d=v3_absolute_square(&distance);
 			if(d<=moldyn->cutoff_square) {
@@ -576,12 +786,16 @@ 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);
 			}
+			if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
+				break;
 		}
 	}