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(" -- integration algo --\n");
+ printf(" -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
+ printf(" 0: velocity verlet\n");
+ printf(" -- potential --\n");
+ printf(" -P <number> <param1 param2 ...>\n");
+ printf(" 0: harmonic oscillator\n");
+ printf(" param1: spring constant\n");
+ printf(" param2: equilibrium distance\n");
+ printf(" 1: lennard jones\n");
+ printf(" param1: epsilon\n");
+ printf(" param2: sigma\n");
printf("\n");
return 0;
int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
int i;
+ t_ho_params hop;
+ t_lj_params ljp;
+ double s,e;
memset(moldyn,0,sizeof(t_moldyn));
moldyn->t=MOLDYN_TEMP;
moldyn->tau=MOLDYN_TAU;
moldyn->time_steps=MOLDYN_RUNS;
+ moldyn->integrate=velocity_verlet;
+ moldyn->potential_force_function=lennard_jones;
/* parse argv */
for(i=1;i<argc;i++) {
case 'R':
moldyn->time_steps=atoi(argv[++i]);
break;
+ case 'I':
+ /* integration algorithm */
+ switch(atoi(argv[++i])) {
+ case MOLDYN_INTEGRATE_VERLET:
+ moldyn->integrate=velocity_verlet;
+ break;
+ default:
+ printf("unknown integration algo %s\n",argv[i]);
+ moldyn_usage(argv);
+ return -1;
+ }
+
+ case 'P':
+ /* potential + params */
+ switch(atoi(argv[++i])) {
+ case MOLDYN_POTENTIAL_HO:
+ hop.spring_constant=atof(argv[++i]);
+ hop.equilibrium_distance=atof(argv[++i]);
+ moldyn->pot_params=malloc(sizeof(t_ho_params));
+ memcpy(moldyn->pot_params,&hop,sizeof(t_ho_params));
+ moldyn->potential_force_function=harmonic_oscillator;
+ break;
+ case MOLDYN_POTENTIAL_LJ:
+ e=atof(argv[++i]);
+ s=atof(argv[++i]);
+ ljp.epsilon4=4*e;
+ ljp.sigma6=s*s*s*s*s*s;
+ ljp.sigma12=ljp.sigma6*ljp.sigma6;
+ moldyn->pot_params=malloc(sizeof(t_lj_params));
+ memcpy(moldyn->pot_params,&ljp,sizeof(t_lj_params));
+ moldyn->potential_force_function=lennard_jones;
+ break;
+ default:
+ printf("unknown potential %s\n",argv[i]);
+ moldyn_usage(argv);
+ return -1;
+ }
+
default:
printf("unknown option %s\n",argv[i]);
moldyn_usage(argv);
return 0;
}
-int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
+int thermal_init(t_moldyn *moldyn,t_random *random) {
/*
* - gaussian distribution of velocities
/* gaussian distribution of velocities */
v3_zero(&p_total);
- for(i=0;i<count;i++) {
+ for(i=0;i<moldyn->count;i++) {
sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
/* x direction */
v=sigma*rand_get_gauss(random);
}
/* zero total momentum */
- v3_scale(&p_total,&p_total,1.0/count);
- for(i=0;i<count;i++) {
+ v3_scale(&p_total,&p_total,1.0/moldyn->count);
+ for(i=0;i<moldyn->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);
+ scale_velocity(moldyn);
return 0;
}
-int scale_velocity(t_moldyn *moldyn,int count) {
+int scale_velocity(t_moldyn *moldyn) {
int i;
double e,c;
* - velocity scaling (E = 3/2 N k T), E: kinetic energy
*/
e=0.0;
- for(i=0;i<count;i++)
+ for(i=0;i<moldyn->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++)
+ c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
+ for(i=0;i<moldyn->count;i++)
v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
return 0;
double get_e_pot(t_moldyn *moldyn) {
- return(moldyn->potential(moldyn));
+ return moldyn->energy;
}
double get_total_energy(t_moldyn *moldyn) {
* 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;
-}
+/* linked list / cell method */
int link_cell_init(t_moldyn *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;
+ t_linkcell *lc;
atom=moldyn->atom;
- nx=moldyn->lc.nx; ny=moldyn->lc.ny; nz=moldyn->lc.nz;
+ lc=&(moldyn->lc);
+
+ nx=lc->nx;
+ ny=lc->ny;
+ nz=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;
- }
+ i=atom[count].r.x/lc->x;
+ j=atom[count].r.y/lc->y;
+ k=atom[count].r.z/lc->z;
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 link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
- int i;
+ t_linkcell *lc;
+ int a;
+ int count1,count2;
+ int ci,cj,ck;
+ int nx,ny,nz;
+ int x,y,z;
+ unsigned char bx,by,bz;
- for(i=0;i<moldyn->count;i++)
- list_shutdown(&(moldyn->atom[i].verlet));
+ lc=&(moldyn->lc);
+ nx=lc->nx;
+ ny=lc->ny;
+ nx=lc->nz;
+ count1=1;
+ count2=27;
+ a=nx*ny;
+
+ cell[0]=lc->subcell[i+j*nx+k*a];
+ for(ci=-1;ci<=1;ci++) {
+ bx=0;
+ x=i+ci;
+ if((x<0)||(x>=nx)) {
+ x=(x+nx)%nx;
+ bx=1;
+ }
+ for(cj=-1;cj<=1;cj++) {
+ by=0;
+ y=j+cj;
+ if((y<0)||(y>=ny)) {
+ y=(y+ny)%ny;
+ by=1;
+ }
+ for(ck=-1;ck<=1;ck++) {
+ bz=0;
+ z=k+ck;
+ if((z<0)||(z>=nz)) {
+ z=(z+nz)%nz;
+ bz=1;
+ }
+ if(!(x|y|z)) continue;
+ if(bx|by|bz) {
+ cell[--count2]=lc->subcell[x+y*nx+z*a];
+ }
+ else {
+ cell[count1++]=lc->subcell[x+y*nx+z*a];
+ }
+ }
+ }
+ }
- return 0;
+ return count2;
}
int link_cell_shutdown(t_moldyn *moldyn) {
int i;
unsigned int e,m,s,d,v;
t_3dvec p;
- double rlc;
int fd;
char fb[128];
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;
}
+ /* sqaure of some variables */
+ moldyn->tau_square=moldyn->tau*moldyn->tau;
+ moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
+
/* create the neighbour list */
- //verlet_list_update(moldyn);
link_cell_update(moldyn);
/* calculate initial forces */
- moldyn->force(moldyn);
+ moldyn->potential_force_function(moldyn);
for(i=0;i<moldyn->time_steps;i++) {
/* show runs */
/* 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 log & visualiziation */
+ /* check for log & visualization */
if(e) {
if(!(i%e))
dprintf(moldyn->efd,
int velocity_verlet(t_moldyn *moldyn) {
int i,count;
- double tau,tau_square,dr;
+ double tau,tau_square;
t_3dvec delta;
t_atom *atom;
atom=moldyn->atom;
count=moldyn->count;
tau=moldyn->tau;
-
- tau_square=tau*tau;
+ tau_square=moldyn->tau_square;
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_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);
}
/* forces depending on chosen potential */
- moldyn->force(moldyn);
+ moldyn->potential_force_function(moldyn);
for(i=0;i<count;i++) {
/* again velocities */
/* harmonic oscillator potential and force */
-double potential_harmonic_oscillator(t_moldyn *moldyn) {
+int harmonic_oscillator(t_moldyn *moldyn) {
t_ho_params *params;
- t_atom *atom;
- int i,j;
+ t_atom *atom,*btom;
+ t_linkcell *lc;
+ t_list *this,neighbour[27];
+ int i,j,c;
int count;
- t_3dvec distance;
+ t_3dvec force,distance;
double d,u;
double sc,equi_dist;
+ int ni,nj,nk;
params=moldyn->pot_params;
atom=moldyn->atom;
+ lc=&(moldyn->lc);
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));
+ /* determine cell + neighbours */
+ ni=atom[i].r.x/lc->x;
+ nj=atom[i].r.y/lc->y;
+ nk=atom[i].r.z/lc->z;
+ c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
+
+ /* processing cell of atom i */
+ this=&(neighbour[0]);
+ list_reset(this); /* list has 1 element at minimum */
+ do {
+ btom=this->current->data;
+ if(btom==&(atom[i]))
+ continue;
+ v3_sub(&distance,&(atom[i].r),&(btom->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;
+ v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
+ v3_add(&(atom[i].f),&(atom[i].f),&force);
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ /* neighbours not doing boundary condition overflow */
+ for(j=1;j<c;j++) {
+ this=&(neighbour[j]);
+ list_reset(this); /* there might not be a single atom */
+ if(this->start!=NULL) {
+
+ do {
+ btom=this->current->data;
+ v3_sub(&distance,&(atom[i].r),&(btom->r));
+ d=v3_norm(&distance);
+ if(d<=moldyn->cutoff) {
+ u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+ v3_scale(&force,&distance,
+ -sc*(1.0-(equi_dist/d)));
+ v3_add(&(atom[i].f),&(atom[i].f),
+ &force);
+ }
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
- 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));
+ /* neighbours due to boundary conditions */
+ for(j=c;j<27;j++) {
+ this=&(neighbour[j]);
+ list_reset(this); /* check boundary conditions */
+ if(this->start!=NULL) {
+
+ do {
+ btom=this->current->data;
+ v3_sub(&distance,&(atom[i].r),&(btom->r));
+ v3_per_bound(&distance,&(moldyn->dim));
+ d=v3_norm(&distance);
+ if(d<=moldyn->cutoff) {
+ u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+ v3_scale(&force,&distance,
+ -sc*(1.0-(equi_dist/d)));
+ v3_add(&(atom[i].f),&(atom[i].f),
+ &force);
+ }
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
- 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);
}
}
}
+ moldyn->energy=u;
+
return 0;
}
-
/* lennard jones potential & force for one sort of atoms */
-double potential_lennard_jones(t_moldyn *moldyn) {
+int lennard_jones(t_moldyn *moldyn) {
t_lj_params *params;
t_atom *atom,*btom;
t_linkcell *lc;
- int i;
+ t_list *this,neighbour[27];
+ int i,j,c;
int count;
- t_3dvec distance;
- double d,help;
- double u;
+ t_3dvec force,distance;
+ double d,h1,h2,u;
double eps,sig6,sig12;
- int i,j,k;
int ni,nj,nk;
params=moldyn->pot_params;
u=0.0;
for(i=0;i<count;i++) {
- /* verlet list [obsolete] */
- //list_reset(&(atom[i].verlet));
- //if(atom[i].verlet.current==NULL) continue;
-
- /* determine cell */
+ /* determine cell + neighbours */
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;
+ c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
+
+ /* processing cell of atom i */
+ this=&(neighbour[0]);
+ list_reset(this); /* list has 1 element at minimum */
+ do {
+ btom=this->current->data;
+ if(btom==&(atom[i]))
+ continue;
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;
+ d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
+ h1=d*d; /* 1/r^4 */
+ h2*=d; /* 1/r^6 */
+ h1=h2*h2; /* 1/r^12 */
+ u+=eps*(sig12*h1-sig6*h2);
+ h2*=d; /* 1/r^8 */
+ h1*=d; /* 1/r^14 */
+ h2*=6*sig6;
+ h1*=12*sig12;
+ d=-h1+h2;
+ d*=eps;
+ v3_scale(&force,&distance,d);
+ v3_add(&(atom[i].f),&(atom[i].f),&force);
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ /* neighbours not doing boundary condition overflow */
+ for(j=1;j<c;j++) {
+ this=&(neighbour[j]);
+ list_reset(this); /* there might not be a single atom */
+ if(this->start!=NULL) {
+
+ do {
+ btom=this->current->data;
+ v3_sub(&distance,&(atom[i].r),&(btom->r));
+ d=v3_absolute_square(&distance); /* r^2 */
+ if(d<=moldyn->cutoff_square) {
+ d=1.0/d; /* 1/r^2 */
+ h1=d*d; /* 1/r^4 */
+ h2*=d; /* 1/r^6 */
+ h1=h2*h2; /* 1/r^12 */
+ u+=eps*(sig12*h1-sig6*h2);
+ h2*=d; /* 1/r^8 */
+ h1*=d; /* 1/r^14 */
+ h2*=6*sig6;
+ h1*=12*sig12;
+ d=-h1+h2;
+ d*=eps;
+ v3_scale(&force,&distance,d);
+ v3_add(&(atom[i].f),&(atom[i].f),
+ &force);
+ }
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
+ }
}
- }
-
- return u;
-}
-
-int force_lennard_jones(t_moldyn *moldyn) {
-
- t_lj_params *params;
- int i,count;
- t_atom *atom,*btom;
- 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->epsilon4;
- sig6=6*params->sigma6;
- sig12=12*params->sigma12;
-
- for(i=0;i<count;i++) v3_zero(&(atom[i].f));
+ /* neighbours due to boundary conditions */
+ for(j=c;j<27;j++) {
+ this=&(neighbour[j]);
+ list_reset(this); /* check boundary conditions */
+ if(this->start!=NULL) {
+
+ do {
+ btom=this->current->data;
+ v3_sub(&distance,&(atom[i].r),&(btom->r));
+ v3_per_bound(&distance,&(moldyn->dim));
+ d=v3_absolute_square(&distance); /* r^2 */
+ if(d<=moldyn->cutoff_square) {
+ d=1.0/d; /* 1/r^2 */
+ h1=d*d; /* 1/r^4 */
+ h2*=d; /* 1/r^6 */
+ h1=h2*h2; /* 1/r^12 */
+ u+=eps*(sig12*h1-sig6*h2);
+ h2*=d; /* 1/r^8 */
+ h1*=d; /* 1/r^14 */
+ h2*=6*sig6;
+ h1*=12*sig12;
+ d=-h1+h2;
+ d*=eps;
+ v3_scale(&force,&distance,d);
+ v3_add(&(atom[i].f),&(atom[i].f),
+ &force);
+ }
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
- for(i=0;i<count;i++) {
- 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) {
- 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;
- /* actually there would be a '-', *
- * but f=-d/dr potential */
- d=h1+h2;
- 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);
}
- if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
- break;
}
}
+ moldyn->energy=u;
+
return 0;
}
projects / physik / posic.git / commitdiff