moldyn->vis.dim.z=z;
}
+ printf("[moldyn] dimensions in A:\n");
+ printf(" x: %f\n",moldyn->dim.x);
+ printf(" y: %f\n",moldyn->dim.y);
+ printf(" z: %f\n",moldyn->dim.z);
+ printf(" visualize simulation box: %s\n",visualize?"on":"off");
+
return 0;
}
return 0;
}
-int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
+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;
- moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ 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] efd open");
+ 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;
- moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ 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] mfd open");
+ perror("[moldyn] momentum log fd open");
return moldyn->mfd;
}
dprintf(moldyn->efd,"# total momentum log file\n");
break;
case SAVE_STEP:
moldyn->swrite=timer;
- strncpy(moldyn->sfb,fb,63);
break;
case VISUAL_STEP:
moldyn->vwrite=timer;
- strncpy(moldyn->vfb,fb,63);
- visual_init(&(moldyn->vis),fb);
+ ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+ if(ret<0) {
+ printf("[moldyn] visual init failure\n");
+ return ret;
+ }
break;
default:
- printf("unknown log mechanism: %02x\n",type);
+ printf("[moldyn] unknown log mechanism: %02x\n",type);
return -1;
}
count=a*b*c;
+ /* how many atoms do we expect */
if(type==FCC) count*=4;
-
if(type==DIAMOND) count*=8;
+ /* allocate space for atoms */
moldyn->atom=malloc(count*sizeof(t_atom));
if(moldyn->atom==NULL) {
perror("malloc (atoms)");
/* 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;
}
check_per_bound(moldyn,&(moldyn->atom[count].r));
}
-
return ret;
}
/* (temporary) hack for e,t = 0 */
if(e==0.0) {
moldyn->t=0.0;
- if(moldyn->t_ref!=0.0)
+ if(moldyn->t_ref!=0.0) {
thermal_init(moldyn,equi_init);
+ return 0;
+ }
else
return 0; /* no scaling needed */
}
scale*=2.0;
else
if(moldyn->pt_scale&T_SCALE_BERENDSEN)
- scale=1.0+moldyn->tau*(scale-1.0)/moldyn->t_tc;
+ scale=1.0+(scale-1.0)/moldyn->t_tc;
scale=sqrt(scale);
/* velocity scaling */
- for(i=0;i<moldyn->count;i++)
+ 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;
}
/* nn_dist is the nearest neighbour distance */
- if(moldyn->t==5.0) {
- printf("[moldyn] i do not estimate timesteps below %f K!\n",
- MOLDYN_CRITICAL_EST_TEMP);
- return 23.42;
- }
-
tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
return tau;
t_moldyn_schedule *schedule;
t_atom *atom;
int fd;
- char fb[128];
+ char dir[128];
double ds;
schedule=&(moldyn->schedule);
/* zero absolute time */
moldyn->time=0.0;
- /* debugging, ignre */
+ /* debugging, ignore */
moldyn->debug=0;
/* executing the schedule */
if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
scale_velocity(moldyn,FALSE);
- /* increase absolute time */
- moldyn->time+=moldyn->tau;
-
/* check for log & visualization */
if(e) {
if(!(i%e))
dprintf(moldyn->efd,
- "%.15f %.45f %.45f %.45f\n",
+ "%f %f %f %f\n",
moldyn->time,update_e_kin(moldyn),
moldyn->energy,
get_total_energy(moldyn));
if(!(i%m)) {
p=get_total_p(moldyn);
dprintf(moldyn->mfd,
- "%.15f %.45f\n",moldyn->time,
- 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));
if(!(i%v)) {
visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsched: %d, steps: %d, theta: %d",
+ printf("\rsched: %d, steps: %d, debug: %d",
sched,i,moldyn->debug);
fflush(stdout);
}
}
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+
}
/* check for hooks */
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);
+//if(i==5) printf("v: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
check_per_bound(moldyn,&(atom[i].r));
+//if(i==5) printf("n: %f %f %f\n",atom[i].r.x,(atom[i].r.x+moldyn->dim.x/2)/moldyn->lc.x,2*atom[i].r.x/moldyn->dim.x);
/* velocities */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
+//moldyn_bc_check(moldyn);
/* neighbour list update */
link_cell_update(moldyn);
t_linkcell *lc;
t_list neighbour_i[27];
t_list neighbour_i2[27];
- //t_list neighbour_j[27];
t_list *this,*that;
u8 bc_ij,bc_ik;
int dnlc;
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 */
- if(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
- 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);
+ 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;
+ dnlc=lc->dnlc;
- for(j=0;j<27;j++) {
+ for(j=0;j<27;j++) {
- this=&(neighbour_i[j]);
- list_reset(this);
+ this=&(neighbour_i[j]);
+ list_reset(this);
- if(this->start==NULL)
- continue;
+ if(this->start==NULL)
+ continue;
- bc_ij=(j<dnlc)?0:1;
+ bc_ij=(j<dnlc)?0:1;
- do {
- jtom=this->current->data;
+ do {
+ jtom=this->current->data;
- if(jtom==&(itom[i]))
- continue;
+ 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);
+ if((jtom->attr&ATOM_ATTR_2BP)&
+ (itom[i].attr&ATOM_ATTR_2BP)) {
+ moldyn->func2b(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
- /* 3 body potential/force */
+ /* 3 body potential/force */
- if(!(itom[i].attr&ATOM_ATTR_3BP)||
- !(jtom->attr&ATOM_ATTR_3BP))
- continue;
+ if(!(itom[i].attr&ATOM_ATTR_3BP)||
+ !(jtom->attr&ATOM_ATTR_3BP))
+ continue;
- /* copy the neighbour lists */
- memcpy(neighbour_i2,neighbour_i,
- 27*sizeof(t_list));
+ /* copy the neighbour lists */
+ memcpy(neighbour_i2,neighbour_i,
+ 27*sizeof(t_list));
- /* get neighbours of i */
- for(k=0;k<27;k++) {
+ /* get neighbours of i */
+ for(k=0;k<27;k++) {
- that=&(neighbour_i2[k]);
- list_reset(that);
+ that=&(neighbour_i2[k]);
+ list_reset(that);
- if(that->start==NULL)
- continue;
+ if(that->start==NULL)
+ continue;
- bc_ik=(k<dnlc)?0:1;
+ bc_ik=(k<dnlc)?0:1;
- do {
+ do {
- ktom=that->current->data;
+ ktom=that->current->data;
- if(!(ktom->attr&ATOM_ATTR_3BP))
- continue;
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
- if(ktom==jtom)
- continue;
+ if(ktom==jtom)
+ continue;
- if(ktom==&(itom[i]))
- continue;
+ if(ktom==&(itom[i]))
+ continue;
- moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ik|bc_ij);
+ moldyn->func3b(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
- } while(list_next(that)!=\
- L_NO_NEXT_ELEMENT);
+ } while(list_next(that)!=\
+ L_NO_NEXT_ELEMENT);
+
+ }
- }
-
- } while(list_next(this)!=L_NO_NEXT_ELEMENT);
-
/* 2bp post function */
if(moldyn->func2b_post) {
-printf("DEBUG: vor 2bp post\n");
moldyn->func2b_post(moldyn,
&(itom[i]),
jtom,bc_ij);
-printf("DEBUG: nach 2bp post\n");
}
-
- }
+
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+
}
+
}
return 0;
dim=&(moldyn->dim);
- x=0.5*dim->x;
- y=0.5*dim->y;
- z=0.5*dim->z;
+ x=dim->x/2;
+ y=dim->y/2;
+ z=dim->z/2;
if(moldyn->status&MOLDYN_STAT_PBX) {
if(a->x>=x) a->x-=dim->x;
p->mu_m=0.5*(p->mu[0]+p->mu[1]);
printf("[moldyn] tersoff mult parameter info:\n");
- printf(" S (m) | %.12f | %.12f | %.12f\n",p->S[0],p->S[1],p->Smixed);
- printf(" R (m) | %.12f | %.12f | %.12f\n",p->R[0],p->R[1],p->Rmixed);
+ 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],
/* 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
/* 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;
+ 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;
+ exchange->df_a=mu*exchange->f_a/d_ij;
/* f_c, df_c calc (again, same for ij and ji) */
if(d_ij<R) {
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));
+ //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;
}
/* add forces of 2bp (ij, ji) contribution
/* Vij and dVij */
zeta=exchange->zeta_ij;
- 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); /* chi * (...)^(-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);
+ 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);
- /* add force (sub, as F = - dVij) */
- v3_sub(&(ai->f),&(ai->f),&force);
-
/* dVji */
zeta=exchange->zeta_ji;
- 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); /* chi * (...)^(-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);
+ 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 (sub, as F = - dVji) */
- v3_sub(&(ai->f),&(ai->f),&force);
+ /* add force */
+ v3_add(&(ai->f),&(ai->f),&force);
return 0;
}
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));
+ //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;
c2d2=exchange->cj2dj2;
/* cosine of theta_jik by scalaproduct */
- rr=v3_scalar_product(&dist_ij,&dist_jk); /* times -1 */
+ 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/(d_jk*d_ij);
- d_costheta2=cos_theta/(d_ij*d_ij); /* in fact -cos(), but ^ */
+ d_costheta1=1.0/dd;
+ d_costheta2=cos_theta/(d_ij*d_ij);
/* some usefull values */
h_cos=(h-cos_theta);
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) {
/* zeta_ji */
exchange->zeta_ji+=f_c_jk*g;
- /* dzeta_ij */
+ /* 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,&temp1,f_c);
- v3_scale(&temp2,&dist_ij,df_c);
- v3_add(&temp1,&temp1,&temp2);
+ 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 temp1
+ // 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(&temp1,&temp1,tmp*B*exp(-mu*d_jk)*f_c_jk);
- v3_add(&(ai->f),&(ai->f),&temp1); /* -1 skipped in f_a calc ^ */
+ 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 ^ */
+ }
+
+ return 0;
+}
+
+
+/*
+ * 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;
+
+ 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");
+ 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("---------------\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("hier gleich!\n");
+ else printf("hier NICHT gleich!\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);
}
return 0;
projects / physik / posic.git / blobdiff