From: hackbard <hackbard>
Date: Tue, 25 Apr 2006 15:15:34 +0000 (+0000)
Subject: basic linked list / cell method support implemented
X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=881d130efd1104bd886507e3d90f262f7a82cf2d;p=physik%2Fposic.git

basic linked list / cell method support implemented
---

diff --git a/Makefile b/Makefile
index 5f25159..b696aae 100644
--- a/Makefile
+++ b/Makefile
@@ -1,10 +1,12 @@
 CC=gcc
 CFLAGS=-Wall
 
-OBJS=init/init.o visual/visual.o math/math.o random/random.o moldyn.o
+OBJS=init/init.o visual/visual.o math/math.o random/random.o list/list.o
+OBJS+=moldyn.o
 
 all: posic
 
+.PHONY:posic
 posic: $(OBJS) moldyn.o
 	$(CC) $(CFLAGS) -lm -o $@ $(OBJS) $(LIBS) posic.c
 
diff --git a/moldyn.c b/moldyn.c
index 7f9745a..dbb3e6c 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) {
 
@@ -338,6 +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;
+}
 
 /*
  *
@@ -352,25 +491,40 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	int i;
 	unsigned int e,m,s,d,v;
 	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;
 
+	/* 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 verlet list */
+	verlet_list_update(moldyn);
+
 	/* calculate initial forces */
 	moldyn->force(moldyn);
 
 	for(i=0;i<moldyn->time_steps;i++) {
+		/* check for velet list update */
+		printf(".");
+		if(moldyn->dr_max1+moldyn->dr_max2>rlc) {
+			printf("\n");
+			verlet_list_update(moldyn);
+		}
+
 		/* integration step */
 		moldyn->integrate(moldyn);
 
@@ -423,7 +577,7 @@ 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;
 
@@ -437,10 +591,20 @@ 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) */
+		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);
@@ -536,8 +700,8 @@ 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;
+	int i;
 	int count;
 	t_3dvec distance;
 	double d,help;
@@ -553,13 +717,19 @@ double potential_lennard_jones(t_moldyn *moldyn) {
 
 	u=0.0;
 	for(i=0;i<count;i++) {
-		for(j=0;j<i;j++) {
-			v3_sub(&distance,&(atom[i].r),&(atom[j].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=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*(sig6*help-sig12*d);
+			u+=eps*(sig12*d-sig6*help);
+			if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
+				break;
 		}
 	}
 	
@@ -569,8 +739,8 @@ 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;
@@ -586,8 +756,11 @@ int force_lennard_jones(t_moldyn *moldyn) {
 	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[i].r),&(atom[j].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) {
@@ -604,8 +777,10 @@ int force_lennard_jones(t_moldyn *moldyn) {
 				d*=eps;
 				v3_scale(&force,&distance,d);
 				v3_add(&(atom[i].f),&(atom[i].f),&force);
-				v3_sub(&(atom[j].f),&(atom[j].f),&force);
+				//v3_sub(&(atom[j].f),&(atom[j].f),&force);
 			}
+			if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
+				break;
 		}
 	}
 
diff --git a/moldyn.h b/moldyn.h
index 266436b..53a22fd 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -10,6 +10,7 @@
 
 #include "math/math.h"
 #include "random/random.h"
+#include "list/list.h"
 
 /* datatypes */
 
@@ -17,11 +18,18 @@ typedef struct s_atom {
 	t_3dvec r;	/* positions */
 	t_3dvec v;	/* velocities */
 	t_3dvec f;	/* forces */
+	t_3dvec dr;	/* delta r for verlet list updates */
 	int element;	/* number of element in pse */
 	double mass;	/* atom mass */
-	//t_list vicinity	/* verlet neighbour list */
+	t_list verlet;	/* verlet neighbour list */
 } t_atom;
 
+typedef struct s_linkcell {
+	int nx,ny,nz;
+	double x,y,z;
+	t_list *subcell;
+} t_linkcell;
+
 #include "visual/visual.h"
 
 typedef struct s_moldyn {
@@ -33,8 +41,14 @@ typedef struct s_moldyn {
 	double (*potential)(struct s_moldyn *moldyn);
 	int (*force)(struct s_moldyn *moldyn);
 	void *pot_params;
+	/* cut off radius, verlet list & co */
 	double cutoff;
 	double cutoff_square;
+	double r_verlet;
+	double dr_max1;
+	double dr_max2;
+	/* linked list / cell method */
+	t_linkcell lc;
 	/* temperature */
 	double t;
 	/* integration of newtons equations */
@@ -129,6 +143,13 @@ t_3dvec get_total_p(t_atom *atom,int count);
 
 double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
 
+int verlet_list_init(t_moldyn *moldyn);
+int link_cell_init(t_moldyn *moldyn);
+int verlet_list_update(t_moldyn *moldyn);
+int link_cell_update(t_moldyn *moldyn);
+int verlet_list_shutdown(t_moldyn *moldyn);
+int link_cell_shutdown(t_moldyn *moldyn);
+
 int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);
 
diff --git a/posic.c b/posic.c
index 8bbfe0e..7cde6e2 100644
--- a/posic.c
+++ b/posic.c
@@ -22,7 +22,7 @@ int main(int argc,char **argv) {
 	t_random random;
 
 	int a,b,c;
-	double e,u;
+	double e;
 	double help;
 	t_3dvec p;
 	int count;
@@ -79,8 +79,8 @@ int main(int argc,char **argv) {
 	md.force=force_lennard_jones;
 	//md.potential=potential_harmonic_oscillator;
 	//md.force=force_harmonic_oscillator;
-	md.cutoff=R_CUTOFF;
-	md.cutoff_square=(R_CUTOFF*R_CUTOFF);
+	md.cutoff=R_CUTOFF*LC_SI;
+	md.cutoff_square=md.cutoff*md.cutoff;
 	md.pot_params=&lj;
 	//md.pot_params=&ho;
 	md.integrate=velocity_verlet;
@@ -88,6 +88,14 @@ int main(int argc,char **argv) {
 	//md.tau=TAU;
 	md.status=0;
 	md.visual=&vis;
+	/* dimensions of the simulation cell */
+	md.dim.x=a*LC_SI;
+	md.dim.y=b*LC_SI;
+	md.dim.z=c*LC_SI;
+
+	/* verlet list init */
+	// later integrated in moldyn_init function!
+	verlet_list_init(&md);
 
 	printf("setting thermal fluctuations (T=%f K)\n",md.t);
 	thermal_init(&md,&random,count);
@@ -97,13 +105,14 @@ int main(int argc,char **argv) {
 
 	e=get_e_kin(si,count);
 	printf("kinetic energy: %.40f [J]\n",e);
-	printf("3/2 N k T = %.40f [J]\n",1.5*count*K_BOLTZMANN*md.t);
+	printf("3/2 N k T = %.40f [J] (T=%f [K])\n",
+	       1.5*count*K_BOLTZMANN*md.t,md.t);
 
 	/* check total momentum */
 	p=get_total_p(si,count);
 	printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
 
-	/* check potential energy */
+	/* potential paramters */
 	lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
 	help=lj.sigma6*lj.sigma6;
 	lj.sigma6*=help;
@@ -113,16 +122,6 @@ int main(int argc,char **argv) {
 	ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
 	ho.spring_constant=1.0;
 
-	u=get_e_pot(&md);
-
-	printf("potential energy: %.40f [J]\n",u);
-	printf("total energy (1): %.40f [J]\n",e+u);
-	printf("total energy (2): %.40f [J]\n",get_total_energy(&md));
-
-	md.dim.x=a*LC_SI;
-	md.dim.y=b*LC_SI;
-	md.dim.z=c*LC_SI;
-
 	printf("estimated accurate time step: %.30f [s]\n",
 	       estimate_time_step(&md,3.0,md.t));
 
@@ -140,6 +139,8 @@ int main(int argc,char **argv) {
 
 	/* close */
 
+	verlet_list_shutdown(&md);
+
 	rand_close(&random);
 
 	moldyn_shutdown(&md);
diff --git a/run b/run
index 4c753fe..584a446 100755
--- a/run
+++ b/run
@@ -1,3 +1,4 @@
+mkdir -p saves video
 ./clean
 ./posic $@
 if [ "$?" == "0" ]; then