X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=0fd1aca88d3b7243ee58cbe2d219cf0e4e2190f9;hb=512390ceb93a2dd630943165b35bba683e0ffcfc;hp=ba3c1a30c8c2bd995a2ac2264d9a79984db01015;hpb=706aed2512544b99ff34308fdb673b19ee884ce0;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index ba3c1a3..0fd1aca 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -5,14 +5,159 @@
  *
  */
 
-#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"
+
+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] (%f)\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) {
@@ -42,8 +187,8 @@ int create_lattice(unsigned char type,int element,double mass,double lc,
 			ret=diamond_init(a,b,c,lc,*atom,&origin);
 			break;
 		default:
-			ret=-1;
 			printf("unknown lattice type (%02x)\n",type);
+			return -1;
 	}
 
 	/* debug */
@@ -51,6 +196,7 @@ int create_lattice(unsigned char type,int element,double mass,double lc,
 		printf("ok, there is something wrong ...\n");
 		printf("calculated -> %d atoms\n",count);
 		printf("created -> %d atoms\n",ret);
+		return -1;
 	}
 
 	while(count) {
@@ -62,3 +208,405 @@ int create_lattice(unsigned char type,int element,double mass,double lc,
 	return ret;
 }
 
+int destroy_lattice(t_atom *atom) {
+
+	if(atom) free(atom);
+
+	return 0;
+}
+
+int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
+
+	/*
+	 * - gaussian distribution of velocities
+	 * - zero total momentum
+	 * - velocity scaling (E = 3/2 N k T), E: kinetic energy
+	 */
+
+	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*moldyn->t/atom[i].mass);
+		/* x direction */
+		v=sigma*rand_get_gauss(random);
+		atom[i].v.x=v;
+		p_total.x+=atom[i].mass*v;
+		/* y direction */
+		v=sigma*rand_get_gauss(random);
+		atom[i].v.y=v;
+		p_total.y+=atom[i].mass*v;
+		/* z direction */
+		v=sigma*rand_get_gauss(random);
+		atom[i].v.z=v;
+		p_total.z+=atom[i].mass*v;
+	}
+
+	/* zero total momentum */
+	v3_scale(&p_total,&p_total,1.0/count);
+	for(i=0;i<count;i++) {
+		v3_scale(&delta,&p_total,1.0/atom[i].mass);
+		v3_sub(&(atom[i].v),&(atom[i].v),&delta);
+	}
+
+	/* velocity scaling */
+	scale_velocity(moldyn,count);
+
+	return 0;
+}
+
+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
+	 */
+	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*moldyn->t));
+	for(i=0;i<count;i++)
+		v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+
+	return 0;
+}
+
+double get_e_kin(t_atom *atom,int count) {
+
+	int i;
+	double e;
+
+	e=0.0;
+
+	for(i=0;i<count;i++) {
+		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+	}
+
+	return e;
+}
+
+double get_e_pot(t_moldyn *moldyn) {
+
+	return(moldyn->potential(moldyn));
+}
+
+double get_total_energy(t_moldyn *moldyn) {
+
+	double e;
+
+	e=get_e_kin(moldyn->atom,moldyn->count);
+	e+=get_e_pot(moldyn);
+
+	return e;
+}
+
+t_3dvec get_total_p(t_atom *atom, int count) {
+
+	t_3dvec p,p_total;
+	int i;
+
+	v3_zero(&p_total);
+	for(i=0;i<count;i++) {
+		v3_scale(&p,&(atom[i].v),atom[i].mass);
+		v3_add(&p_total,&p_total,&p);
+	}
+
+	return p_total;
+}
+
+double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+
+	double tau;
+
+	tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
+	tau*=1.0E-9;
+	if(tau<moldyn->tau)
+		printf("[moldyn] warning: time step  (%f > %.15f)\n",
+		       moldyn->tau,tau);
+
+	return tau;	
+}
+
+
+/*
+ *
+ * 'integration of newtons equation' - algorithms
+ *
+ */
+
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+	int i;
+	unsigned int e,m,s,d,v;
+	t_3dvec p;
+
+	int fd;
+	char fb[128];
+
+	e=moldyn->ewrite;
+	m=moldyn->mwrite;
+	s=moldyn->swrite;
+	d=moldyn->dwrite;
+	v=moldyn->vwrite;
+
+	if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
+		printf("[moldyn] warning, lv system not initialized\n");
+		return -1;
+	}
+
+	/* calculate initial forces */
+	moldyn->force(moldyn);
+
+	for(i=0;i<moldyn->time_steps;i++) {
+		/* integration step */
+		moldyn->integrate(moldyn);
+
+		/* 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);
+		}
+	}
+
+	return 0;
+}
+
+/* velocity verlet */
+
+int velocity_verlet(t_moldyn *moldyn) {
+
+	int i,count;
+	double tau,tau_square;
+	t_3dvec delta;
+	t_atom *atom;
+
+	atom=moldyn->atom;
+	count=moldyn->count;
+	tau=moldyn->tau;
+
+	tau_square=tau*tau;
+
+	for(i=0;i<count;i++) {
+		/* new positions */
+		v3_scale(&delta,&(atom[i].v),tau);
+		v3_add(&(atom[i].r),&(atom[i].r),&delta);
+		v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
+		v3_add(&(atom[i].r),&(atom[i].r),&delta);
+		v3_per_bound(&(atom[i].r),&(moldyn->dim));
+
+		/* velocities */
+		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+		v3_add(&(atom[i].v),&(atom[i].v),&delta);
+	}
+
+	/* forces depending on chosen potential */
+	moldyn->force(moldyn);
+
+	for(i=0;i<count;i++) {
+		/* again velocities */
+		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+		v3_add(&(atom[i].v),&(atom[i].v),&delta);
+	}
+
+	return 0;
+}
+
+
+/*
+ *
+ * potentials & corresponding forces
+ * 
+ */
+
+/* harmonic oscillator potential and force */
+
+double potential_harmonic_oscillator(t_moldyn *moldyn) {
+
+	t_ho_params *params;
+	t_atom *atom;
+	int i,j;
+	int count;
+	t_3dvec distance;
+	double d,u;
+	double sc,equi_dist;
+
+	params=moldyn->pot_params;
+	atom=moldyn->atom;
+	sc=params->spring_constant;
+	equi_dist=params->equilibrium_distance;
+	count=moldyn->count;
+
+	u=0.0;
+	for(i=0;i<count;i++) {
+		for(j=0;j<i;j++) {
+			v3_sub(&distance,&(atom[i].r),&(atom[j].r));
+			d=v3_norm(&distance);
+			u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+		}
+	}
+
+	return u;
+}
+
+int force_harmonic_oscillator(t_moldyn *moldyn) {
+
+	t_ho_params *params;
+	int i,j,count;
+	t_atom *atom;
+	t_3dvec distance;
+	t_3dvec force;
+	double d;
+	double sc,equi_dist;
+
+	atom=moldyn->atom;	
+	count=moldyn->count;
+	params=moldyn->pot_params;
+	sc=params->spring_constant;
+	equi_dist=params->equilibrium_distance;
+
+	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));
+			v3_per_bound(&distance,&(moldyn->dim));
+			d=v3_norm(&distance);
+			if(d<=moldyn->cutoff) {
+				v3_scale(&force,&distance,
+				         (-sc*(1.0-(equi_dist/d))));
+				v3_add(&(atom[i].f),&(atom[i].f),&force);
+				v3_sub(&(atom[j].f),&(atom[j].f),&force);
+			}
+		}
+	}
+
+	return 0;
+}
+
+
+/* lennard jones potential & force for one sort of atoms */
+ 
+double potential_lennard_jones(t_moldyn *moldyn) {
+
+	t_lj_params *params;
+	t_atom *atom;
+	int i,j;
+	int count;
+	t_3dvec distance;
+	double d,help;
+	double u;
+	double eps,sig6,sig12;
+
+	params=moldyn->pot_params;
+	atom=moldyn->atom;
+	count=moldyn->count;
+	eps=params->epsilon;
+	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));
+			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);
+		}
+	}
+	
+	return u;
+}
+
+int force_lennard_jones(t_moldyn *moldyn) {
+
+	t_lj_params *params;
+	int i,j,count;
+	t_atom *atom;
+	t_3dvec distance;
+	t_3dvec force;
+	double d,h1,h2;
+	double eps,sig6,sig12;
+
+	atom=moldyn->atom;	
+	count=moldyn->count;
+	params=moldyn->pot_params;
+	eps=params->epsilon;
+	sig6=params->sigma6;
+	sig12=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_per_bound(&distance,&(moldyn->dim));
+			d=v3_absolute_square(&distance);
+			if(d<=moldyn->cutoff_square) {
+				h1=1.0/d;			/* 1/r^2 */
+				d=h1*h1;			/* 1/r^4 */
+				h2=d*d;				/* 1/r^8 */
+				h1*=d;				/* 1/r^6 */
+				h1*=h2;				/* 1/r^14 */
+				h1*=sig12;
+				h2*=sig6;
+				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);
+			}
+		}
+	}
+
+	return 0;
+}
+