X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=17720675c4f5c0c76dea880ac40eb5787f772eb0;hb=877139ec35cf357c96fdb314f690fd6075554c47;hp=72a672ac500591dc39694549377cae6c4157d5b3;hpb=45b27e01673a6cc5bebecb49c51d7f587917483e;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 72a672a..1772067 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -5,17 +5,160 @@
  *
  */
 
-#include "moldyn.h"
-
+#define _GNU_SOURCE
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
 #include <math.h>
 
+#include "moldyn.h"
+
 #include "math/math.h"
 #include "init/init.h"
 #include "random/random.h"
 #include "visual/visual.h"
+#include "list/list.h"
+
+int moldyn_usage(char **argv) {
+
+	printf("\n%s usage:\n\n",argv[0]);
+	printf("--- general options ---\n");
+	printf("-E <steps> <file> (log total energy)\n");
+	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] (%.15f)\n",MOLDYN_TAU);
+	printf("-R <runs> (%d)\n",MOLDYN_RUNS);
+	printf("\n");
+
+	return 0;
+}
+
+int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
+
+	int i;
+
+	memset(moldyn,0,sizeof(t_moldyn));
+
+	/* default values */
+	moldyn->t=MOLDYN_TEMP;
+	moldyn->tau=MOLDYN_TAU;
+	moldyn->time_steps=MOLDYN_RUNS;
+
+	/* parse argv */
+	for(i=1;i<argc;i++) {
+		if(argv[i][0]=='-') {
+			switch(argv[i][1]){
+				case 'E':
+					moldyn->ewrite=atoi(argv[++i]);
+					strncpy(moldyn->efb,argv[++i],64);
+					break;
+				case 'M':
+					moldyn->mwrite=atoi(argv[++i]);
+					strncpy(moldyn->mfb,argv[++i],64);
+					break;
+				case 'D':
+					moldyn->dwrite=atoi(argv[++i]);
+					strncpy(moldyn->dfb,argv[++i],64);
+					break;
+				case 'S':
+					moldyn->swrite=atoi(argv[++i]);
+					strncpy(moldyn->sfb,argv[++i],64);
+					break;
+				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;
+				case 'R':
+					moldyn->time_steps=atoi(argv[++i]);
+					break;
+				default:
+					printf("unknown option %s\n",argv[i]);
+					moldyn_usage(argv);
+					return -1;
+			}
+		} else {
+			moldyn_usage(argv);
+			return -1;
+		}
+	}
+
+	return 0;
+}
 
+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);
+		if(moldyn->efd<0) {
+			perror("[moldyn] efd open");
+			return moldyn->efd;
+		}
+		dprintf(moldyn->efd,"# moldyn total energy logfile\n");
+		moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
+	}
+
+	if(moldyn->mwrite) {
+		moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
+		if(moldyn->mfd<0) {
+			perror("[moldyn] mfd open");
+			return moldyn->mfd;
+		}
+		dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
+		moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
+	}
+
+	if(moldyn->swrite)
+		moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
+
+	if(moldyn->dwrite) {
+		moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
+                if(moldyn->dfd<0) {
+			perror("[moldyn] dfd open");
+			return moldyn->dfd;
+		}
+		write(moldyn->dfd,moldyn,sizeof(t_moldyn));
+		moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
+	}
+
+	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;
+}
 
 int create_lattice(unsigned char type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom) {
@@ -73,7 +216,7 @@ int destroy_lattice(t_atom *atom) {
 	return 0;
 }
 
-int thermal_init(t_atom *atom,t_random *random,int count,double t) {
+int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
 
 	/*
 	 * - gaussian distribution of velocities
@@ -84,11 +227,14 @@ int thermal_init(t_atom *atom,t_random *random,int count,double t) {
 	int i;
 	double v,sigma;
 	t_3dvec p_total,delta;
+	t_atom *atom;
+
+	atom=moldyn->atom;
 
 	/* gaussian distribution of velocities */
 	v3_zero(&p_total);
 	for(i=0;i<count;i++) {
-		sigma=sqrt(2.0*K_BOLTZMANN*t/atom[i].mass);
+		sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
 		/* x direction */
 		v=sigma*rand_get_gauss(random);
 		atom[i].v.x=v;
@@ -111,15 +257,18 @@ int thermal_init(t_atom *atom,t_random *random,int count,double t) {
 	}
 
 	/* velocity scaling */
-	scale_velocity(atom,count,t);
+	scale_velocity(moldyn,count);
 
 	return 0;
 }
 
-int scale_velocity(t_atom *atom,int count,double t) {
+int scale_velocity(t_moldyn *moldyn,int count) {
 
 	int i;
 	double e,c;
+	t_atom *atom;
+
+	atom=moldyn->atom;
 
 	/*
 	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
@@ -127,7 +276,7 @@ int scale_velocity(t_atom *atom,int count,double t) {
 	e=0.0;
 	for(i=0;i<count;i++)
 		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*t));
+	c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*moldyn->t));
 	for(i=0;i<count;i++)
 		v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
 
@@ -190,6 +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;
+}
 
 /*
  *
@@ -202,21 +489,87 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
 int moldyn_integrate(t_moldyn *moldyn) {
 
 	int i;
-	int write;
+	unsigned int e,m,s,d,v;
+	t_3dvec p;
+	double rlc;
+
+	int fd;
+	char fb[128];
 
-	write=moldyn->write;
+	/* 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 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);
 
-		/* check for visualiziation */
-		if(!(i%write)) {
-			visual_atoms(moldyn->visual,i*moldyn->tau,
-			             moldyn->atom,moldyn->count);
+		/* check for log & visualiziation */
+		if(e) {
+			if(!(i%e))
+				dprintf(moldyn->efd,
+				        "%.15f %.45f\n",i*moldyn->tau,
+				        get_total_energy(moldyn));
+		}
+		if(m) {
+			if(!(i%m)) {
+				p=get_total_p(moldyn->atom,moldyn->count);
+				dprintf(moldyn->mfd,
+				        "%.15f %.45f\n",i*moldyn->tau,
+				        v3_norm(&p));
+			}
+		}
+		if(s) {
+			if(!(i%s)) {
+				snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
+				         moldyn->t,i*moldyn->tau);
+				fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
+				if(fd<0) perror("[moldyn] save fd open");
+				else {
+					write(fd,moldyn,sizeof(t_moldyn));
+					write(fd,moldyn->atom,
+					      moldyn->count*sizeof(t_atom));
+				}
+			}	
+		}
+		if(d) {
+			if(!(i%d))
+				write(moldyn->dfd,moldyn->atom,
+				      moldyn->count*sizeof(t_atom));
+
+		}
+		if(v) {
+			if(!(i%v))
+				visual_atoms(moldyn->visual,i*moldyn->tau,
+				             moldyn->atom,moldyn->count);
 		}
 	}
 
@@ -228,7 +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;
 
@@ -242,10 +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);
@@ -325,7 +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);
 			}
@@ -341,30 +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;
 		}
 	}
 	
@@ -374,8 +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;
@@ -384,15 +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) {
@@ -403,12 +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;
 		}
 	}