#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("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
- 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");
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+ memset(moldyn,0,sizeof(t_moldyn));
+
+ rand_init(&(moldyn->random),NULL,1);
+ moldyn->random.status|=RAND_STAT_VERBOSE;
return 0;
}
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
+int moldyn_shutdown(t_moldyn *moldyn) {
- int i;
- t_ho_params hop;
- t_lj_params ljp;
- double s,e;
+ printf("[moldyn] shutdown\n");
+ moldyn_log_shutdown(moldyn);
+ link_cell_shutdown(moldyn);
+ rand_close(&(moldyn->random));
+ free(moldyn->atom);
- memset(moldyn,0,sizeof(t_moldyn));
+ return 0;
+}
- /* default values */
- 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++) {
- 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 'C':
- moldyn->cutoff=atof(argv[++i]);
- break;
- case 'R':
- moldyn->time_steps=atoi(argv[++i]);
- break;
- case 'I':
- /* integration algorithm */
- switch(atoi(argv[++i])) {
+int set_int_alg(t_moldyn *moldyn,u8 algo) {
+
+ switch(algo) {
case MOLDYN_INTEGRATE_VERLET:
moldyn->integrate=velocity_verlet;
break;
default:
- printf("unknown integration algo %s\n",argv[i]);
- moldyn_usage(argv);
+ printf("unknown integration algorithm: %02x\n",algo);
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;
- }
+ return 0;
+}
- default:
- printf("unknown option %s\n",argv[i]);
- moldyn_usage(argv);
- return -1;
- }
- } else {
- moldyn_usage(argv);
- return -1;
- }
- }
+int set_cutoff(t_moldyn *moldyn,double cutoff) {
+
+ moldyn->cutoff=cutoff;
return 0;
}
-int moldyn_log_init(t_moldyn *moldyn) {
+int set_temperature(t_moldyn *moldyn,double t_ref) {
- moldyn->lvstat=0;
- t_visual *vis;
+ moldyn->t_ref=t_ref;
- vis=&(moldyn->vis);
+ return 0;
+}
- 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;
- }
+int set_pressure(t_moldyn *moldyn,double p_ref) {
- 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;
- }
+ moldyn->p_ref=p_ref;
+
+ return 0;
+}
- if(moldyn->swrite)
- moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
- 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;
- }
+ moldyn->pt_scale=(ptype|ttype);
+ moldyn->t_tc=ttc;
+ moldyn->p_tc=ptc;
+
+ return 0;
+}
- if((moldyn->vwrite)&&(vis)) {
- moldyn->visual=vis;
- visual_init(vis,moldyn->vfb);
- moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
+
+ moldyn->dim.x=x;
+ moldyn->dim.y=y;
+ moldyn->dim.z=z;
+
+ moldyn->volume=x*y*z;
+
+ if(visualize) {
+ moldyn->vis.dim.x=x;
+ moldyn->vis.dim.y=y;
+ moldyn->vis.dim.z=z;
}
- moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+ printf("[moldyn] dimensions in A and A^3 respectively:\n");
+ printf(" x: %f\n",moldyn->dim.x);
+ printf(" y: %f\n",moldyn->dim.y);
+ printf(" z: %f\n",moldyn->dim.z);
+ printf(" volume: %f\n",moldyn->volume);
+ printf(" visualize simulation box: %s\n",visualize?"on":"off");
return 0;
}
-int moldyn_log_shutdown(t_moldyn *moldyn) {
+int set_nn_dist(t_moldyn *moldyn,double dist) {
- 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);
+ moldyn->nnd=dist;
return 0;
}
-int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
- int ret;
+ if(x)
+ moldyn->status|=MOLDYN_STAT_PBX;
- ret=moldyn_parse_argv(moldyn,argc,argv);
- if(ret<0) return ret;
+ if(y)
+ moldyn->status|=MOLDYN_STAT_PBY;
- ret=moldyn_log_init(moldyn);
- if(ret<0) return ret;
+ if(z)
+ moldyn->status|=MOLDYN_STAT_PBZ;
- rand_init(&(moldyn->random),NULL,1);
- moldyn->random.status|=RAND_STAT_VERBOSE;
+ return 0;
+}
+
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
- moldyn->status=0;
+ moldyn->func1b=func;
+ moldyn->pot1b_params=params;
return 0;
}
-int moldyn_shutdown(t_moldyn *moldyn) {
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
- moldyn_log_shutdown(moldyn);
- rand_close(&(moldyn->random));
- free(moldyn->atom);
+ moldyn->func2b=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
+
+int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+
+ moldyn->func2b_post=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
+
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+
+ moldyn->func3b=func;
+ moldyn->pot3b_params=params;
+
+ return 0;
+}
+
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
+
+ strncpy(moldyn->vlsdir,dir,127);
+
+ return 0;
+}
+
+int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
+
+ char filename[128];
+ int ret;
+
+ switch(type) {
+ case LOG_TOTAL_ENERGY:
+ moldyn->ewrite=timer;
+ snprintf(filename,127,"%s/energy",moldyn->vlsdir);
+ moldyn->efd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->efd<0) {
+ perror("[moldyn] energy log fd open");
+ return moldyn->efd;
+ }
+ dprintf(moldyn->efd,"# total energy log file\n");
+ break;
+ case LOG_TOTAL_MOMENTUM:
+ moldyn->mwrite=timer;
+ snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
+ moldyn->mfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->mfd<0) {
+ perror("[moldyn] momentum log fd open");
+ return moldyn->mfd;
+ }
+ dprintf(moldyn->efd,"# total momentum log file\n");
+ break;
+ case SAVE_STEP:
+ moldyn->swrite=timer;
+ break;
+ case VISUAL_STEP:
+ moldyn->vwrite=timer;
+ ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+ if(ret<0) {
+ printf("[moldyn] visual init failure\n");
+ return ret;
+ }
+ break;
+ default:
+ printf("[moldyn] unknown log mechanism: %02x\n",type);
+ return -1;
+ }
return 0;
}
-int create_lattice(unsigned char type,int element,double mass,double lc,
- int a,int b,int c,t_atom **atom) {
+int moldyn_log_shutdown(t_moldyn *moldyn) {
+
+ printf("[moldyn] log shutdown\n");
+ if(moldyn->efd) close(moldyn->efd);
+ if(moldyn->mfd) close(moldyn->mfd);
+ if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
+
+ return 0;
+}
+
+/*
+ * creating lattice functions
+ */
+
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
+ u8 attr,u8 bnum,int a,int b,int c) {
int count;
int ret;
count=a*b*c;
+ /* how many atoms do we expect */
if(type==FCC) count*=4;
if(type==DIAMOND) count*=8;
- *atom=malloc(count*sizeof(t_atom));
- if(*atom==NULL) {
+ /* allocate space for atoms */
+ moldyn->atom=malloc(count*sizeof(t_atom));
+ if(moldyn->atom==NULL) {
perror("malloc (atoms)");
return -1;
}
switch(type) {
case FCC:
- ret=fcc_init(a,b,c,lc,*atom,&origin);
+ ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,*atom,&origin);
+ ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
break;
default:
printf("unknown lattice type (%02x)\n",type);
/* debug */
if(ret!=count) {
- printf("ok, there is something wrong ...\n");
- printf("calculated -> %d atoms\n",count);
- printf("created -> %d atoms\n",ret);
+ printf("[moldyn] creating lattice failed\n");
+ printf(" amount of atoms\n");
+ printf(" - expected: %d\n",count);
+ printf(" - created: %d\n",ret);
return -1;
}
+ moldyn->count=count;
+ printf("[moldyn] created lattice with %d atoms\n",count);
+
while(count) {
- (*atom)[count-1].element=element;
- (*atom)[count-1].mass=mass;
count-=1;
+ moldyn->atom[count].element=element;
+ moldyn->atom[count].mass=mass;
+ moldyn->atom[count].attr=attr;
+ moldyn->atom[count].bnum=bnum;
+ check_per_bound(moldyn,&(moldyn->atom[count].r));
}
return ret;
}
-int destroy_lattice(t_atom *atom) {
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
- if(atom) free(atom);
+ int count;
+ int i,j;
+ t_3dvec o,r,n;
+ t_3dvec basis[3];
+ double help[3];
+ double x,y,z;
+
+ x=a*lc;
+ y=b*lc;
+ z=c*lc;
+
+ if(origin) v3_copy(&o,origin);
+ else v3_zero(&o);
+
+ /* construct the basis */
+ for(i=0;i<3;i++) {
+ for(j=0;j<3;j++) {
+ if(i!=j) help[j]=0.5*lc;
+ else help[j]=.0;
+ }
+ v3_set(&basis[i],help);
+ }
+
+ v3_zero(&r);
+ count=0;
+
+ /* fill up the room */
+ r.x=o.x;
+ while(r.x<x) {
+ r.y=o.y;
+ while(r.y<y) {
+ r.z=o.z;
+ while(r.z<z) {
+ v3_copy(&(atom[count].r),&r);
+ atom[count].element=1;
+ count+=1;
+ for(i=0;i<3;i++) {
+ v3_add(&n,&r,&basis[i]);
+ if((n.x<x+o.x)&&
+ (n.y<y+o.y)&&
+ (n.z<z+o.z)) {
+ v3_copy(&(atom[count].r),&n);
+ count+=1;
+ }
+ }
+ r.z+=lc;
+ }
+ r.y+=lc;
+ }
+ r.x+=lc;
+ }
+
+ /* coordinate transformation */
+ help[0]=x/2.0;
+ help[1]=y/2.0;
+ help[2]=z/2.0;
+ v3_set(&n,help);
+ for(i=0;i<count;i++)
+ v3_sub(&(atom[i].r),&(atom[i].r),&n);
+
+ return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+ int count;
+ t_3dvec o;
+
+ count=fcc_init(a,b,c,lc,atom,origin);
+
+ o.x=0.25*lc;
+ o.y=0.25*lc;
+ o.z=0.25*lc;
+
+ if(origin) v3_add(&o,&o,origin);
+
+ count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+ return count;
+}
+
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+ t_3dvec *r,t_3dvec *v) {
+
+ t_atom *atom;
+ void *ptr;
+ int count;
+
+ atom=moldyn->atom;
+ count=++(moldyn->count);
+
+ ptr=realloc(atom,count*sizeof(t_atom));
+ if(!ptr) {
+ perror("[moldyn] realloc (add atom)");
+ return -1;
+ }
+ moldyn->atom=ptr;
+
+ atom=moldyn->atom;
+ atom[count-1].r=*r;
+ atom[count-1].v=*v;
+ atom[count-1].element=element;
+ atom[count-1].mass=mass;
+ atom[count-1].bnum=bnum;
+ atom[count-1].attr=attr;
+
+ return 0;
+}
+
+int destroy_atoms(t_moldyn *moldyn) {
+
+ if(moldyn->atom) free(moldyn->atom);
return 0;
}
-int thermal_init(t_moldyn *moldyn) {
+int thermal_init(t_moldyn *moldyn,u8 equi_init) {
/*
* - gaussian distribution of velocities
/* gaussian distribution of velocities */
v3_zero(&p_total);
for(i=0;i<moldyn->count;i++) {
- sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
+ sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t_ref/atom[i].mass);
/* x direction */
v=sigma*rand_get_gauss(random);
atom[i].v.x=v;
}
/* velocity scaling */
- scale_velocity(moldyn);
+ scale_velocity(moldyn,equi_init);
return 0;
}
-int scale_velocity(t_moldyn *moldyn) {
+int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
int i;
- double e,c;
+ double e,scale;
t_atom *atom;
+ int count;
atom=moldyn->atom;
/*
* - velocity scaling (E = 3/2 N k T), E: kinetic energy
*/
+
+ /* get kinetic energy / temperature & count involved atoms */
e=0.0;
- 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*moldyn->count*K_BOLTZMANN*moldyn->t));
- for(i=0;i<moldyn->count;i++)
- v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+ count=0;
+ for(i=0;i<moldyn->count;i++) {
+ if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
+ e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ count+=1;
+ }
+ }
+ if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
+ else return 0; /* no atoms involved in scaling! */
+
+ /* (temporary) hack for e,t = 0 */
+ if(e==0.0) {
+ moldyn->t=0.0;
+ if(moldyn->t_ref!=0.0) {
+ thermal_init(moldyn,equi_init);
+ return 0;
+ }
+ else
+ return 0; /* no scaling needed */
+ }
+
+
+ /* get scaling factor */
+ scale=moldyn->t_ref/moldyn->t;
+ if(equi_init&TRUE)
+ scale*=2.0;
+ else
+ if(moldyn->pt_scale&T_SCALE_BERENDSEN)
+ scale=1.0+(scale-1.0)/moldyn->t_tc;
+ scale=sqrt(scale);
+
+ /* velocity scaling */
+ for(i=0;i<moldyn->count;i++) {
+ if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB))
+ v3_scale(&(atom[i].v),&(atom[i].v),scale);
+ }
return 0;
}
-double get_e_kin(t_atom *atom,int count) {
+int scale_volume(t_moldyn *moldyn) {
+ t_atom *atom;
+ t_3dvec *dim,*vdim;
+ double virial,scale;
+ t_linkcell *lc;
int i;
- double e;
- e=0.0;
+ atom=moldyn->atom;
+ dim=&(moldyn->dim);
+ vdim=&(moldyn->vis.dim);
+ lc=&(moldyn->lc);
- for(i=0;i<count;i++) {
- e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ for(i=0;i<moldyn->count;i++)
+ virial+=v3_norm(&(atom[i].virial));
+
+printf("%f\n",virial);
+ /* get pressure from virial */
+ moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*virial;
+ moldyn->p/=moldyn->volume;
+printf("%f\n",moldyn->p/(ATM));
+
+ /* scale factor */
+ if(moldyn->pt_scale&P_SCALE_BERENDSEN)
+ scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
+ else
+ /* should actually never be used */
+ scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
+
+printf("scale = %f\n",scale);
+ /* actual scaling */
+ dim->x*=scale;
+ dim->y*=scale;
+ dim->z*=scale;
+ if(vdim->x) vdim->x=dim->x;
+ if(vdim->y) vdim->y=dim->y;
+ if(vdim->z) vdim->z=dim->z;
+ moldyn->volume*=(scale*scale*scale);
+
+ /* check whether we need a new linkcell init */
+ if((dim->x/moldyn->cutoff!=lc->nx)||
+ (dim->y/moldyn->cutoff!=lc->ny)||
+ (dim->z/moldyn->cutoff!=lc->nx)) {
+ link_cell_shutdown(moldyn);
+ link_cell_init(moldyn);
}
- return e;
+ return 0;
+
+}
+
+double get_e_kin(t_moldyn *moldyn) {
+
+ int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+ moldyn->ekin=0.0;
+
+ for(i=0;i<moldyn->count;i++)
+ moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+
+ return moldyn->ekin;
}
double get_e_pot(t_moldyn *moldyn) {
return moldyn->energy;
}
-double get_total_energy(t_moldyn *moldyn) {
+double update_e_kin(t_moldyn *moldyn) {
- double e;
+ return(get_e_kin(moldyn));
+}
- e=get_e_kin(moldyn->atom,moldyn->count);
- e+=get_e_pot(moldyn);
+double get_total_energy(t_moldyn *moldyn) {
- return e;
+ return(moldyn->ekin+moldyn->energy);
}
-t_3dvec get_total_p(t_atom *atom, int count) {
+t_3dvec get_total_p(t_moldyn *moldyn) {
t_3dvec p,p_total;
int i;
+ t_atom *atom;
+
+ atom=moldyn->atom;
v3_zero(&p_total);
- for(i=0;i<count;i++) {
+ for(i=0;i<moldyn->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 estimate_time_step(t_moldyn *moldyn,double nn_dist) {
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);
+ /* nn_dist is the nearest neighbour distance */
+
+ tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
return tau;
}
lc=&(moldyn->lc);
- /* list log fd */
- lc->listfd=open("/dev/null",O_WRONLY);
-
/* partitioning the md cell */
lc->nx=moldyn->dim.x/moldyn->cutoff;
lc->x=moldyn->dim.x/lc->nx;
lc->cells=lc->nx*lc->ny*lc->nz;
lc->subcell=malloc(lc->cells*sizeof(t_list));
- printf("initializing linked cells (%d)\n",lc->cells);
+ printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
for(i=0;i<lc->cells;i++)
- //list_init(&(lc->subcell[i]),1);
- list_init(&(lc->subcell[i]));
+ list_init_f(&(lc->subcell[i]));
link_cell_update(moldyn);
int link_cell_update(t_moldyn *moldyn) {
int count,i,j,k;
- int nx,ny,nz;
+ int nx,ny;
t_atom *atom;
t_linkcell *lc;
+ double x,y,z;
atom=moldyn->atom;
lc=&(moldyn->lc);
nx=lc->nx;
ny=lc->ny;
- nz=lc->nz;
+
+ x=moldyn->dim.x/2;
+ y=moldyn->dim.y/2;
+ z=moldyn->dim.z/2;
for(i=0;i<lc->cells;i++)
- list_destroy(&(moldyn->lc.subcell[i]));
+ list_destroy_f(&(lc->subcell[i]));
for(count=0;count<moldyn->count;count++) {
- i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
- j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
- k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
- list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
- &(atom[count]));
+ i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
+ j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
+ k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
+ list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
}
return 0;
int ci,cj,ck;
int nx,ny,nz;
int x,y,z;
- unsigned char bx,by,bz;
+ u8 bx,by,bz;
lc=&(moldyn->lc);
nx=lc->nx;
count2=27;
a=nx*ny;
-
cell[0]=lc->subcell[i+j*nx+k*a];
for(ci=-1;ci<=1;ci++) {
bx=0;
}
}
- return count2;
+ lc->dnlc=count1;
+
+ return count1;
}
int link_cell_shutdown(t_moldyn *moldyn) {
lc=&(moldyn->lc);
for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
- list_shutdown(&(moldyn->lc.subcell[i]));
+ list_destroy_f(&(moldyn->lc.subcell[i]));
- if(lc->listfd) close(lc->listfd);
+ free(lc->subcell);
return 0;
}
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
+
+ int count;
+ void *ptr;
+ t_moldyn_schedule *schedule;
+
+ schedule=&(moldyn->schedule);
+ count=++(schedule->content_count);
+
+ ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] realloc (runs)");
+ return -1;
+ }
+ moldyn->schedule.runs=ptr;
+ moldyn->schedule.runs[count-1]=runs;
+
+ ptr=realloc(schedule->tau,count*sizeof(double));
+ if(!ptr) {
+ perror("[moldyn] realloc (tau)");
+ return -1;
+ }
+ moldyn->schedule.tau=ptr;
+ moldyn->schedule.tau[count-1]=tau;
+
+ return 0;
+}
+
+int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+
+ moldyn->schedule.hook=hook;
+ moldyn->schedule.hook_params=hook_params;
+
+ return 0;
+}
+
/*
*
* 'integration of newtons equation' - algorithms
int moldyn_integrate(t_moldyn *moldyn) {
- int i;
- unsigned int e,m,s,d,v;
+ int i,sched;
+ unsigned int e,m,s,v;
t_3dvec p;
-
+ t_moldyn_schedule *schedule;
+ t_atom *atom;
int fd;
- char fb[128];
+ char dir[128];
+ double ds;
+
+ schedule=&(moldyn->schedule);
+ atom=moldyn->atom;
/* initialize linked cell method */
link_cell_init(moldyn);
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;
- }
-
/* sqaure of some variables */
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
/* calculate initial forces */
- moldyn->potential_force_function(moldyn);
+ potential_force_calc(moldyn);
+
+ /* some stupid checks before we actually start calculating bullshit */
+ if(moldyn->cutoff>0.5*moldyn->dim.x)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.x\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.y)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.y\n");
+ if(moldyn->cutoff>0.5*moldyn->dim.z)
+ printf("[moldyn] warning: cutoff > 0.5 x dim.z\n");
+ ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+ if(ds>0.05*moldyn->nnd)
+ printf("[moldyn] warning: forces too high / tau too small!\n");
+
+ /* zero absolute time */
+ moldyn->time=0.0;
+
+ /* debugging, ignore */
+ moldyn->debug=0;
+
+ /* executing the schedule */
+ for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+
+ /* setting amount of runs and finite time step size */
+ moldyn->tau=schedule->tau[sched];
+ moldyn->tau_square=moldyn->tau*moldyn->tau;
+ moldyn->time_steps=schedule->runs[sched];
+
+ /* integration according to schedule */
for(i=0;i<moldyn->time_steps;i++) {
/* integration step */
moldyn->integrate(moldyn);
+ /* p/t scaling */
+ if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
+ scale_velocity(moldyn,FALSE);
+ if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
+ scale_volume(moldyn);
+
/* check for log & visualization */
if(e) {
if(!(i%e))
dprintf(moldyn->efd,
- "%.15f %.45f\n",i*moldyn->tau,
+ "%f %f %f %f\n",
+ moldyn->time,update_e_kin(moldyn),
+ moldyn->energy,
get_total_energy(moldyn));
}
if(m) {
if(!(i%m)) {
- p=get_total_p(moldyn->atom,moldyn->count);
+ p=get_total_p(moldyn);
dprintf(moldyn->mfd,
- "%.15f %.45f\n",i*moldyn->tau,
- v3_norm(&p));
+ "%f %f\n",moldyn->time,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);
+ snprintf(dir,128,"%s/s-%07.f.save",
+ moldyn->vlsdir,moldyn->time);
+ fd=open(dir,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));
}
+ close(fd);
}
}
- 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,
+ visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsteps: %d",i);
+ printf("\rsched: %d, steps: %d, debug: %d",
+ sched,i,moldyn->debug);
fflush(stdout);
}
}
+
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+
+ }
+
+ /* check for hooks */
+ if(schedule->hook)
+ schedule->hook(moldyn,schedule->hook_params);
+
+ /* get a new info line */
+ printf("\n");
+
}
return 0;
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));
+ check_per_bound(moldyn,&(atom[i].r));
/* velocities */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
}
/* neighbour list update */
-printf("list update ...\n");
link_cell_update(moldyn);
-printf("done\n");
/* forces depending on chosen potential */
-printf("calc potential/force ...\n");
- moldyn->potential_force_function(moldyn);
-printf("done\n");
+ potential_force_calc(moldyn);
for(i=0;i<count;i++) {
/* again velocities */
*
*/
-/* harmonic oscillator potential and force */
+/* generic potential and force calculation */
-int harmonic_oscillator(t_moldyn *moldyn) {
+int potential_force_calc(t_moldyn *moldyn) {
- t_ho_params *params;
- t_atom *atom,*btom;
+ int i,j,k,count;
+ t_atom *itom,*jtom,*ktom;
t_linkcell *lc;
- t_list *this,neighbour[27];
- int i,j,c;
- int count;
- t_3dvec force,distance;
- double d,u;
- double sc,equi_dist;
- int ni,nj,nk;
+ t_list neighbour_i[27];
+ t_list neighbour_i2[27];
+ t_list *this,*that;
+ u8 bc_ij,bc_ik;
+ int dnlc;
- params=moldyn->pot_params;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
- sc=params->spring_constant;
- equi_dist=params->equilibrium_distance;
count=moldyn->count;
+ itom=moldyn->atom;
+ lc=&(moldyn->lc);
- /* reset energy counter */
- u=0.0;
-
+ /* reset energy */
+ moldyn->energy=0.0;
+
+ /* get energy and force of every atom */
for(i=0;i<count;i++) {
+
/* reset force */
- v3_zero(&(atom[i].f));
-
- /* determine cell + neighbours */
- ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
- nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
- nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
- c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
- /*
- * processing cell of atom i
- * => no need to check for empty list (1 element at minimum)
- */
- this=&(neighbour[0]);
- list_reset(this);
- do {
- btom=this->current->data;
- if(btom==&(atom[i]))
- continue;
- 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);
+ v3_zero(&(itom[i].f));
- /*
- * direct neighbour cells
- * => no boundary condition check necessary
- */
- for(j=1;j<c;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* there might not be a single atom */
- if(this->start!=NULL) {
+ /* reset viral of atom i */
+ v3_zero(&(itom[i].virial));
- 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);
+ /* single particle potential/force */
+ if(itom[i].attr&ATOM_ATTR_1BP)
+ moldyn->func1b(moldyn,&(itom[i]));
- }
- }
+ if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
+ continue;
+
+ /* 2 body pair potential/force */
+
+ link_cell_neighbour_index(moldyn,
+ (itom[i].r.x+moldyn->dim.x/2)/lc->x,
+ (itom[i].r.y+moldyn->dim.y/2)/lc->y,
+ (itom[i].r.z+moldyn->dim.z/2)/lc->z,
+ neighbour_i);
+
+ dnlc=lc->dnlc;
- /*
- * indirect neighbour cells
- * => check boundary conditions
- */
- for(j=c;j<27;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* check boundary conditions */
- if(this->start!=NULL) {
+ for(j=0;j<27;j++) {
+
+ this=&(neighbour_i[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ bc_ij=(j<dnlc)?0:1;
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);
+ jtom=this->current->data;
+
+ if(jtom==&(itom[i]))
+ continue;
+
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP)) {
+ moldyn->func2b(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
}
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
- }
- }
- }
+ /* 3 body potential/force */
- moldyn->energy=0.5*u;
+ if(!(itom[i].attr&ATOM_ATTR_3BP)||
+ !(jtom->attr&ATOM_ATTR_3BP))
+ continue;
- return 0;
-}
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,
+ 27*sizeof(t_list));
-/* lennard jones potential & force for one sort of atoms */
-
-int lennard_jones(t_moldyn *moldyn) {
+ /* get neighbours of i */
+ for(k=0;k<27;k++) {
- t_lj_params *params;
- t_atom *atom,*btom;
- t_linkcell *lc;
- t_list *this,neighbour[27];
- int i,j,c;
- int count;
- t_3dvec force,distance;
- double d,h1,h2,u;
- double eps,sig6,sig12;
- int ni,nj,nk;
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
+
+ if(that->start==NULL)
+ continue;
- params=moldyn->pot_params;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
- count=moldyn->count;
- eps=params->epsilon4;
- sig6=params->sigma6;
- sig12=params->sigma12;
+ bc_ik=(k<dnlc)?0:1;
- /* reset energy counter */
- u=0.0;
+ do {
- for(i=0;i<count;i++) {
- /* reset force */
- v3_zero(&(atom[i].f));
-
- /* determine cell + neighbours */
- ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
- nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
- nk=(atom[i].r.z+(moldyn->dim.z/2))/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_absolute_square(&distance); /* 1/r^2 */
- if(d<=moldyn->cutoff_square) {
- d=1.0/d; /* 1/r^2 */
- h2=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);
+ ktom=that->current->data;
- /* 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) {
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
- 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 */
- h2=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);
-
- }
- }
+ if(ktom==jtom)
+ continue;
- /* neighbours due to boundary conditions */
- for(j=c;j<27;j++) {
- this=&(neighbour[j]);
- list_reset(this); /* check boundary conditions */
- if(this->start!=NULL) {
+ if(ktom==&(itom[i]))
+ continue;
+
+ moldyn->func3b(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+
+ } while(list_next_f(that)!=\
+ L_NO_NEXT_ELEMENT);
- 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 */
- h2=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);
- }
+ /* 2bp post function */
+ if(moldyn->func2b_post) {
+ moldyn->func2b_post(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
+ }
+
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+
}
+
}
- moldyn->energy=0.5*u;
-
return 0;
}
-/* tersoff potential & force for 2 sorts of atoms */
-
-int tersoff(t_moldyn *moldyn) {
-
- t_tersoff_params *params;
- t_atom *atom,*btom,*ktom;
- t_linkcell *lc;
- t_list *this,*thisk,neighbour[27],neighbourk[27];
- int i,j,k,c,ck;
- int count;
- double u;
- int ni,nj,nk;
- int ki,kj,kk;
-
+/*
+ * periodic boundayr checking
+ */
- params=moldyn->pot_params;
- atom=moldyn->atom;
- lc=&(moldyn->lc);
- count=moldyn->count;
+inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
- /* reset energy counter */
- u=0.0;
+ double x,y,z;
+ t_3dvec *dim;
- for(i=0;i<count;i++) {
- /* reset force */
- v3_zero(&(atom[i].f));
-
- /* determin cell neighbours */
- ni=(atom[i].r.x+(moldyn->dim.x/2))/lc->x;
- nj=(atom[i].r.y+(moldyn->dim.y/2))/lc->y;
- nk=(atom[i].r.z+(moldyn->dim.z/2))/lc->z;
- c=link_cell_neighbour_index(moldyn,ni,nj,nk,neighbour);
-
- /*
- * processing cell of atom i
- * => no need to check for empty list (1 element at minimum)
- */
- this=&(neighbour[0]);
- list_reset(this);
- do {
- btom=this->current->data;
- if(btom==&(atom[i]))
- continue;
+ dim=&(moldyn->dim);
- /* 2 body stuff */
+ x=dim->x/2;
+ y=dim->y/2;
+ z=dim->z/2;
- v3_sub(&dist_ij,btom,&(atom[i]));
- d_ij=v3_norm(&dist_ij);
- if(d_ij<=S) {
+ if(moldyn->status&MOLDYN_STAT_PBX) {
+ if(a->x>=x) a->x-=dim->x;
+ else if(-a->x>x) a->x+=dim->x;
+ }
+ if(moldyn->status&MOLDYN_STAT_PBY) {
+ if(a->y>=y) a->y-=dim->y;
+ else if(-a->y>y) a->y+=dim->y;
+ }
+ if(moldyn->status&MOLDYN_STAT_PBZ) {
+ if(a->z>=z) a->z-=dim->z;
+ else if(-a->z>z) a->z+=dim->z;
+ }
- S=;
- R=;
- A=;
- lambda=;
- B=;
- mu=;
+ return 0;
+}
+
- if(d_ij<=R) {
- f_c=1.0;
- df_c=0.0;
- }
- else {
- s_r=S-R;
- arg1=PI*(d_ij-R)/s_r;
- f_c=0.5+0.5*cos(arg1);
- df_c=-0.5*sin(arg1)*(PI/(s_r*d_ij));
- f_r=A*exp(-lambda*d_ij);
- f_a=-B*exp(-mu*d_ij);
- }
- }
- else
- continue;
-
-
- /* end 2 body stuff */
-
- /* determine cell neighbours of btom */
- ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
- kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
- kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
- ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
- neighbourk);
-
- /* cell of btom */
- thisk=&(neighbourk[0]);
- list_reset(thisk);
- do {
- ktom=thisk->current->data;
- if(ktom==btom)
- continue;
- if(ktom==&(atom[i]))
- continue;
-
- /* 3 body stuff (1) */
-
- theta_ijk=;
- sin_theta=;
- cos_theta=;
- hi_cos=;
- hi_cos_square=;
+/*
+ * example potentials
+ */
+/* harmonic oscillator potential and force */
- /* end 3 body stuff (1) */
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+ t_ho_params *params;
+ t_3dvec force,distance;
+ double d;
+ double sc,equi_dist;
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ params=moldyn->pot2b_params;
+ sc=params->spring_constant;
+ equi_dist=params->equilibrium_distance;
- /* direct neighbours of btom cell */
- for(k=1;k<ck;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ v3_sub(&distance,&(aj->r),&(ai->r));
+
+ if(bc) check_per_bound(moldyn,&distance);
+ d=v3_norm(&distance);
+ if(d<=moldyn->cutoff) {
+ /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
+ moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
+ /* f = -grad E; grad r_ij = -1 1/r_ij distance */
+ v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
+ v3_add(&(ai->f),&(ai->f),&force);
+ }
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+ return 0;
+}
- /* 3 body stuff (2) */
+/* lennard jones potential & force for one sort of atoms */
+
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ t_lj_params *params;
+ t_3dvec force,distance;
+ double d,h1,h2;
+ double eps,sig6,sig12;
- }
- }
+ params=moldyn->pot2b_params;
+ eps=params->epsilon4;
+ sig6=params->sigma6;
+ sig12=params->sigma12;
- /* indirect neighbours of btom cell */
- for(k=ck;k<27;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ v3_sub(&distance,&(aj->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&distance);
+ d=v3_absolute_square(&distance); /* 1/r^2 */
+ if(d<=moldyn->cutoff_square) {
+ d=1.0/d; /* 1/r^2 */
+ h2=d*d; /* 1/r^4 */
+ h2*=d; /* 1/r^6 */
+ h1=h2*h2; /* 1/r^12 */
+ /* energy is eps*..., but we will add this twice ... */
+ moldyn->energy+=0.5*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,-1.0*d); /* f = - grad E */
+ v3_add(&(ai->f),&(ai->f),&force);
+ }
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+ return 0;
+}
- /* 3 body stuff */
+/*
+ * tersoff potential & force for 2 sorts of atoms
+ */
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+/* create mixed terms from parameters and set them */
+int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
+
+ printf("[moldyn] tersoff parameter completion\n");
+ p->Smixed=sqrt(p->S[0]*p->S[1]);
+ p->Rmixed=sqrt(p->R[0]*p->R[1]);
+ p->Amixed=sqrt(p->A[0]*p->A[1]);
+ p->Bmixed=sqrt(p->B[0]*p->B[1]);
+ p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
+ p->mu_m=0.5*(p->mu[0]+p->mu[1]);
+
+ printf("[moldyn] tersoff mult parameter info:\n");
+ printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
+ printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
+ printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
+ printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
+ printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
+ p->lambda_m);
+ printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
+ printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
+ printf(" n | %f | %f\n",p->n[0],p->n[1]);
+ printf(" c | %f | %f\n",p->c[0],p->c[1]);
+ printf(" d | %f | %f\n",p->d[0],p->d[1]);
+ printf(" h | %f | %f\n",p->h[0],p->h[1]);
+ printf(" chi | %f \n",p->chi);
- }
- }
+ return 0;
+}
+/* tersoff 1 body part */
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ int num;
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ num=ai->bnum;
+ params=moldyn->pot1b_params;
+ exchange=&(params->exchange);
- /*
- * direct neighbour cells of atom i
- */
- for(j=1;j<c;j++) {
- this=&(neighbour[j]);
- list_reset(this);
- if(this->start!=NULL) {
+ /*
+ * simple: point constant parameters only depending on atom i to
+ * their right values
+ */
- do {
- btom=this->current->data;
+ exchange->beta_i=&(params->beta[num]);
+ exchange->n_i=&(params->n[num]);
+ exchange->c_i=&(params->c[num]);
+ exchange->d_i=&(params->d[num]);
+ exchange->h_i=&(params->h[num]);
- /* 2 body stuff */
+ exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
+ exchange->ci2=params->c[num]*params->c[num];
+ exchange->di2=params->d[num]*params->d[num];
+ exchange->ci2di2=exchange->ci2/exchange->di2;
+ return 0;
+}
+
+/* tersoff 2 body part */
+int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ t_3dvec dist_ij,force;
+ double d_ij;
+ double A,B,R,S,lambda,mu;
+ double f_r,df_r;
+ double f_c,df_c;
+ int num;
+ double s_r;
+ double arg;
+
+ params=moldyn->pot2b_params;
+ num=aj->bnum;
+ exchange=&(params->exchange);
+
+ /* clear 3bp and 2bp post run */
+ exchange->run3bp=0;
+ exchange->run2bp_post=0;
+
+ /* reset S > r > R mark */
+ exchange->d_ij_between_rs=0;
+
+ /*
+ * calc of 2bp contribution of V_ij and dV_ij/ji
+ *
+ * for Vij and dV_ij we need:
+ * - f_c_ij, df_c_ij
+ * - f_r_ij, df_r_ij
+ *
+ * for dV_ji we need:
+ * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
+ * - f_r_ji = f_r_ij; df_r_ji = df_r_ij
+ *
+ */
- /* determine cell neighbours of btom */
- ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
- kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
- kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
- ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
- neighbourk);
+ /* dist_ij, d_ij */
+ v3_sub(&dist_ij,&(aj->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&dist_ij);
+ d_ij=v3_norm(&dist_ij);
+
+ /* save for use in 3bp */
+ exchange->d_ij=d_ij;
+ exchange->dist_ij=dist_ij;
+
+ /* constants */
+ if(num==ai->bnum) {
+ S=params->S[num];
+ R=params->R[num];
+ A=params->A[num];
+ B=params->B[num];
+ lambda=params->lambda[num];
+ mu=params->mu[num];
+ exchange->chi=1.0;
+ }
+ else {
+ S=params->Smixed;
+ R=params->Rmixed;
+ A=params->Amixed;
+ B=params->Bmixed;
+ lambda=params->lambda_m;
+ mu=params->mu_m;
+ params->exchange.chi=params->chi;
+ }
- /* cell of btom */
- thisk=&(neighbourk[0]);
- list_reset(thisk);
- do {
- ktom=thisk->current->data;
- if(ktom==btom)
- continue;
- if(ktom==&(atom[i]))
- continue;
-
- /* 3 body stuff (1) */
+ /* if d_ij > S => no force & potential energy contribution */
+ if(d_ij>S)
+ return 0;
+
+ /* more constants */
+ exchange->beta_j=&(params->beta[num]);
+ exchange->n_j=&(params->n[num]);
+ exchange->c_j=&(params->c[num]);
+ exchange->d_j=&(params->d[num]);
+ exchange->h_j=&(params->h[num]);
+ if(num==ai->bnum) {
+ exchange->betajnj=exchange->betaini;
+ exchange->cj2=exchange->ci2;
+ exchange->dj2=exchange->di2;
+ exchange->cj2dj2=exchange->ci2di2;
+ }
+ else {
+ exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
+ exchange->cj2=params->c[num]*params->c[num];
+ exchange->dj2=params->d[num]*params->d[num];
+ exchange->cj2dj2=exchange->cj2/exchange->dj2;
+ }
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
+ f_r=A*exp(-lambda*d_ij);
+ df_r=lambda*f_r/d_ij;
+
+ /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
+ exchange->f_a=-B*exp(-mu*d_ij);
+ exchange->df_a=mu*exchange->f_a/d_ij;
+
+ /* f_c, df_c calc (again, same for ij and ji) */
+ if(d_ij<R) {
+ /* f_c = 1, df_c = 0 */
+ f_c=1.0;
+ df_c=0.0;
+ /* two body contribution (ij, ji) */
+ v3_scale(&force,&dist_ij,-df_r);
+ }
+ else {
+ s_r=S-R;
+ arg=M_PI*(d_ij-R)/s_r;
+ f_c=0.5+0.5*cos(arg);
+ //df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij)); /* MARK! */
+ df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
+ /* two body contribution (ij, ji) */
+ v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
+ /* tell 3bp that S > r > R */
+ exchange->d_ij_between_rs=1;
+ }
- /* direct neighbours of btom cell */
- for(k=1;k<ck;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ /* add forces of 2bp (ij, ji) contribution
+ * dVij = dVji and we sum up both: no 1/2) */
+ v3_add(&(ai->f),&(ai->f),&force);
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+ /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
+ moldyn->energy+=(0.5*f_r*f_c);
- /* 3 body stuff (2) */
+ /* save for use in 3bp */
+ exchange->f_c=f_c;
+ exchange->df_c=df_c;
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ /* enable the run of 3bp function and 2bp post processing */
+ exchange->run3bp=1;
+ exchange->run2bp_post=1;
- }
- }
+ /* reset 3bp sums */
+ exchange->zeta_ij=0.0;
+ exchange->zeta_ji=0.0;
+ v3_zero(&(exchange->dzeta_ij));
+ v3_zero(&(exchange->dzeta_ji));
- /* indirect neighbours of btom cell */
- for(k=ck;k<27;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ return 0;
+}
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+/* tersoff 2 body post part */
- /* 3 body stuff (3) */
+int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ /*
+ * here we have to allow for the 3bp sums
+ *
+ * that is:
+ * - zeta_ij, dzeta_ij
+ * - zeta_ji, dzeta_ji
+ *
+ * to compute the 3bp contribution to:
+ * - Vij, dVij
+ * - dVji
+ *
+ */
- }
- }
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ t_3dvec force,temp;
+ t_3dvec *dist_ij;
+ double b,db,tmp;
+ double f_c,df_c,f_a,df_a;
+ double chi,ni,betaini,nj,betajnj;
+ double zeta;
+
+ params=moldyn->pot2b_params;
+ exchange=&(params->exchange);
+
+ /* we do not run if f_c_ij was detected to be 0! */
+ if(!(exchange->run2bp_post))
+ return 0;
+
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
+ f_a=exchange->f_a;
+ df_a=exchange->df_a;
+ betaini=exchange->betaini;
+ betajnj=exchange->betajnj;
+ ni=*(exchange->n_i);
+ nj=*(exchange->n_j);
+ chi=exchange->chi;
+ dist_ij=&(exchange->dist_ij);
+
+ /* Vij and dVij */
+ zeta=exchange->zeta_ij;
+ if(zeta==0.0) {
+ moldyn->debug++; /* just for debugging ... */
+ db=0.0;
+ b=chi;
+ v3_scale(&force,dist_ij,df_a*b*f_c);
+ }
+ else {
+ tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
+ b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
+ db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
+ b=db*b; /* b_ij */
+ db*=-0.5*tmp; /* db_ij */
+ v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
+ v3_scale(&temp,dist_ij,df_a*b);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,f_c);
+ }
+ v3_scale(&temp,dist_ij,df_c*b*f_a);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-0.5);
+
+ /* add force */
+ v3_add(&(ai->f),&(ai->f),&force);
+
+ /* add energy of 3bp sum */
+ moldyn->energy+=(0.5*f_c*b*f_a);
+
+ /* dVji */
+ zeta=exchange->zeta_ji;
+ if(zeta==0.0) {
+ moldyn->debug++;
+ b=chi;
+ v3_scale(&force,dist_ij,df_a*b*f_c);
+ }
+ else {
+ tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
+ b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
+ db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
+ b=db*b; /* b_ij */
+ db*=-0.5*tmp; /* db_ij */
+ v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
+ v3_scale(&temp,dist_ij,df_a*b);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,f_c);
+ }
+ v3_scale(&temp,dist_ij,df_c*b*f_a);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-0.5);
+ /* add force */
+ v3_add(&(ai->f),&(ai->f),&force);
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ return 0;
+}
- }
- }
+/* tersoff 3 body part */
+
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ t_3dvec dist_ij,dist_ik,dist_jk;
+ t_3dvec temp1,temp2;
+ t_3dvec *dzeta;
+ double R,S,s_r;
+ double B,mu;
+ double d_ij,d_ik,d_jk;
+ double rr,dd;
+ double f_c,df_c;
+ double f_c_ik,df_c_ik,arg;
+ double f_c_jk;
+ double n,c,d,h;
+ double c2,d2,c2d2;
+ double cos_theta,d_costheta1,d_costheta2;
+ double h_cos,d2_h_cos2;
+ double frac,g,zeta,chi;
+ double tmp;
+ int num;
+
+ params=moldyn->pot3b_params;
+ exchange=&(params->exchange);
+
+ if(!(exchange->run3bp))
+ return 0;
- /*
- * indirect neighbour cells of atom i
- */
- for(j=c;j<27;j++) {
- this=&(neighbour[j]);
- list_reset(this);
- if(this->start!=NULL) {
+ /*
+ * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
+ * 2bp contribution of dV_jk
+ *
+ * for Vij and dV_ij we still need:
+ * - b_ij, db_ij (zeta_ij)
+ * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
+ *
+ * for dV_ji we still need:
+ * - b_ji, db_ji (zeta_ji)
+ * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
+ *
+ * for dV_jk we need:
+ * - f_c_jk
+ * - f_a_jk
+ * - db_jk (zeta_jk)
+ * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
+ *
+ */
- do {
- btom=this->current->data;
+ /*
+ * get exchange data
+ */
- /* 2 body stuff */
+ /* dist_ij, d_ij - this is < S_ij ! */
+ dist_ij=exchange->dist_ij;
+ d_ij=exchange->d_ij;
+ /* f_c_ij, df_c_ij (same for ji) */
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
- /* determine cell neighbours of btom */
- ki=(btom->r.x+(moldyn->dim.x/2))/lc->x;
- kj=(btom->r.y+(moldyn->dim.y/2))/lc->y;
- kk=(btom->r.z+(moldyn->dim.z/2))/lc->z;
- ck=link_cell_neighbour_index(moldyn,ki,kj,kk,
- neighbourk);
+ /*
+ * calculate unknown values now ...
+ */
- /* cell of btom */
- thisk=&(neighbourk[0]);
- list_reset(thisk);
- do {
- ktom=thisk->current->data;
- if(ktom==btom)
- continue;
- if(ktom==&(atom[i]))
- continue;
-
- /* 3 body stuff (1) */
+ /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ /* dist_ik, d_ik */
+ v3_sub(&dist_ik,&(ak->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&dist_ik);
+ d_ik=v3_norm(&dist_ik);
- /* direct neighbours of btom cell */
- for(k=1;k<ck;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ /* ik constants */
+ num=ai->bnum;
+ if(num==ak->bnum) {
+ R=params->R[num];
+ S=params->S[num];
+ }
+ else {
+ R=params->Rmixed;
+ S=params->Smixed;
+ }
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+ /* zeta_ij/dzeta_ij contribution only for d_ik < S */
+ if(d_ik<S) {
+
+ /* get constants_i from exchange data */
+ n=*(exchange->n_i);
+ c=*(exchange->c_i);
+ d=*(exchange->d_i);
+ h=*(exchange->h_i);
+ c2=exchange->ci2;
+ d2=exchange->di2;
+ c2d2=exchange->ci2di2;
+
+ /* cosine of theta_ijk by scalaproduct */
+ rr=v3_scalar_product(&dist_ij,&dist_ik);
+ dd=d_ij*d_ik;
+ cos_theta=rr/dd;
+
+ /* d_costheta */
+ tmp=1.0/dd;
+ d_costheta1=cos_theta/(d_ij*d_ij)-tmp;
+ d_costheta2=cos_theta/(d_ik*d_ik)-tmp;
+
+ /* some usefull values */
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+ frac=c2/(d2_h_cos2);
+
+ /* g(cos_theta) */
+ g=1.0+c2d2-frac;
+
+ /* d_costheta_ij and dg(cos_theta) - needed in any case! */
+ v3_scale(&temp1,&dist_ij,d_costheta1);
+ v3_scale(&temp2,&dist_ik,d_costheta2);
+ v3_add(&temp1,&temp1,&temp2);
+ v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+ /* f_c_ik & df_c_ik + {d,}zeta contribution */
+ dzeta=&(exchange->dzeta_ij);
+ if(d_ik<R) {
+ /* {d,}f_c_ik */
+ // => f_c_ik=1.0;
+ // => df_c_ik=0.0; of course we do not set this!
+
+ /* zeta_ij */
+ exchange->zeta_ij+=g;
+
+ /* dzeta_ij */
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ else {
+ /* {d,}f_c_ik */
+ s_r=S-R;
+ arg=M_PI*(d_ik-R)/s_r;
+ f_c_ik=0.5+0.5*cos(arg);
+ //df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); /* MARK */
+ df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
+
+ /* zeta_ij */
+ exchange->zeta_ij+=f_c_ik*g;
+
+ /* dzeta_ij */
+ v3_scale(&temp1,&temp1,f_c_ik);
+ v3_scale(&temp2,&dist_ik,g*df_c_ik);
+ v3_add(&temp1,&temp1,&temp2);
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ }
- /* 3 body stuff (2) */
+ /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
+
+ /* dist_jk, d_jk */
+ v3_sub(&dist_jk,&(ak->r),&(aj->r));
+ if(bc) check_per_bound(moldyn,&dist_jk);
+ d_jk=v3_norm(&dist_jk);
+
+ /* jk constants */
+ num=aj->bnum;
+ if(num==ak->bnum) {
+ R=params->R[num];
+ S=params->S[num];
+ B=params->B[num];
+ mu=params->mu[num];
+ chi=1.0;
+ }
+ else {
+ R=params->Rmixed;
+ S=params->Smixed;
+ B=params->Bmixed;
+ mu=params->mu_m;
+ chi=params->chi;
+ }
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+ /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
+ if(d_jk<S) {
+
+ /* constants_j from exchange data */
+ n=*(exchange->n_j);
+ c=*(exchange->c_j);
+ d=*(exchange->d_j);
+ h=*(exchange->h_j);
+ c2=exchange->cj2;
+ d2=exchange->dj2;
+ c2d2=exchange->cj2dj2;
+
+ /* cosine of theta_jik by scalaproduct */
+ rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
+ dd=d_ij*d_jk;
+ cos_theta=rr/dd;
+
+ /* d_costheta */
+ d_costheta1=1.0/dd;
+ d_costheta2=cos_theta/(d_ij*d_ij);
+
+ /* some usefull values */
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+ frac=c2/(d2_h_cos2);
+
+ /* g(cos_theta) */
+ g=1.0+c2d2-frac;
+
+ /* d_costheta_ij and dg(cos_theta) - needed in any case! */
+ v3_scale(&temp1,&dist_jk,d_costheta1);
+ v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
+ v3_add(&temp1,&temp1,&temp2);
+ v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+ /* store dg in temp2 and use it for dVjk later */
+ v3_copy(&temp2,&temp1);
+
+ /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
+ dzeta=&(exchange->dzeta_ji);
+ if(d_jk<R) {
+ /* f_c_jk */
+ f_c_jk=1.0;
+
+ /* zeta_ji */
+ exchange->zeta_ji+=g;
+
+ /* dzeta_ji */
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ else {
+ /* f_c_jk */
+ s_r=S-R;
+ arg=M_PI*(d_jk-R)/s_r;
+ f_c_jk=0.5+0.5*cos(arg);
+
+ /* zeta_ji */
+ exchange->zeta_ji+=f_c_jk*g;
+
+ /* dzeta_ji */
+ v3_scale(&temp1,&temp1,f_c_jk);
+ v3_add(dzeta,dzeta,&temp1);
+ }
- }
- }
+ /* dV_jk stuff | add force contribution on atom i immediately */
+ if(exchange->d_ij_between_rs) {
+ zeta=f_c*g;
+ v3_scale(&temp1,&temp2,f_c);
+ v3_scale(&temp2,&dist_ij,df_c*g);
+ v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
+ }
+ else {
+ zeta=g;
+ // dzeta_jk is simply dg, which is stored in temp2
+ }
+ /* betajnj * zeta_jk ^ nj-1 */
+ tmp=exchange->betajnj*pow(zeta,(n-1.0));
+ tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
+ v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
+ v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
+ /* scaled with 0.5 ^ */
- /* indirect neighbours of btom cell */
- for(k=ck;k<27;k++) {
- thisk=&(neighbourk[k]);
- list_reset(thisk);
- if(thisk->start!=NULL) {
+ }
- do {
- ktom=thisk->current->data;
- if(ktom==&(atom[i]))
- continue;
+ return 0;
+}
- /* 3 body stuff (3) */
- } while(list_next(thisk)!=L_NO_NEXT_ELEMENT);
+/*
+ * debugging / critical check functions
+ */
- }
- }
+int moldyn_bc_check(t_moldyn *moldyn) {
+ t_atom *atom;
+ t_3dvec *dim;
+ int i;
+double x;
+u8 byte;
+int j,k;
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ atom=moldyn->atom;
+ dim=&(moldyn->dim);
+x=dim->x/2;
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].r.x>=dim->x/2||-atom[i].r.x>dim->x/2) {
+ printf("FATAL: atom %d: x: %.20f (%.20f)\n",
+ i,atom[i].r.x,dim->x/2);
+ printf("diagnostic:\n");
+ printf("-----------\natom.r.x:\n");
+ for(j=0;j<8;j++) {
+ memcpy(&byte,(u8 *)(&(atom[i].r.x))+j,1);
+ for(k=0;k<8;k++)
+ printf("%d%c",
+ ((byte)&(1<<k))?1:0,
+ (k==7)?'\n':'|');
+ }
+ printf("---------------\nx=dim.x/2:\n");
+ for(j=0;j<8;j++) {
+ memcpy(&byte,(u8 *)(&x)+j,1);
+ for(k=0;k<8;k++)
+ printf("%d%c",
+ ((byte)&(1<<k))?1:0,
+ (k==7)?'\n':'|');
}
+ if(atom[i].r.x==x) printf("the same!\n");
+ else printf("different!\n");
}
-
+ if(atom[i].r.y>=dim->y/2||-atom[i].r.y>dim->y/2)
+ printf("FATAL: atom %d: y: %.20f (%.20f)\n",
+ i,atom[i].r.y,dim->y/2);
+ if(atom[i].r.z>=dim->z/2||-atom[i].r.z>dim->z/2)
+ printf("FATAL: atom %d: z: %.20f (%.20f)\n",
+ i,atom[i].r.z,dim->z/2);
}
- moldyn->energy=0.5*u;
-
return 0;
}
-
projects / physik / posic.git / blobdiff