]> hackdaworld.org Git - physik/posic.git/commitdiff
nearly finished tersoff 2 body part and new api
authorhackbard <hackbard>
Wed, 22 Nov 2006 15:23:42 +0000 (15:23 +0000)
committerhackbard <hackbard>
Wed, 22 Nov 2006 15:23:42 +0000 (15:23 +0000)
moldyn.c
moldyn.h

index d74b391a72362cd33d5ed6e6e698de9e2bb359de..9f8821164dd9ae3b0eb406ec21d8c3b5cbb12709 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -232,7 +232,7 @@ int moldyn_shutdown(t_moldyn *moldyn) {
        return 0;
 }
 
-int create_lattice(unsigned char type,int element,double mass,double lc,
+int create_lattice(u8 type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom) {
 
        int count;
@@ -487,7 +487,7 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
        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;
@@ -702,7 +702,7 @@ int potential_force_calc(t_moldyn *moldyn) {
        t_list neighbour[27];
        t_list *this;
        double u;
-       unsigned char bc,bc3;
+       u8 bc,bc3;
        int countn,dnlc;
 
        count=moldyn->count;
@@ -804,304 +804,174 @@ int potential_force_calc(t_moldyn *moldyn) {
        return 0;
 }
 
+/*
+ * periodic boundayr checking
+ */
+
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+       
+       double x,y,z;
+
+       x=0.5*dim->x;
+       y=0.5*dim->y;
+       z=0.5*dim->z;
+
+       if(moldyn->MOLDYN_ATTR_PBX)
+               if(a->x>=x) a->x-=dim->x;
+               else if(-a->x>x) a->x+=dim->x;
+       if(moldyn->MOLDYN_ATTR_PBY)
+               if(a->y>=y) a->y-=dim->y;
+               else if(-a->y>y) a->y+=dim->y;
+       if(moldyn->MOLDYN_ATTR_PBZ)
+               if(a->z>=z) a->z-=dim->z;
+               else if(-a->z>z) a->z+=dim->z;
+
+       return 0;
+}
+        
+
 /*
  * example potentials
  */
 
 /* harmonic oscillator potential and force */
 
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,unsigned char bc)) {
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
 
        t_ho_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,u;
+       double d;
        double sc,equi_dist;
-       int ni,nj,nk;
 
-       params=moldyn->pot_params;
-       atom=moldyn->atom;
-       lc=&(moldyn->lc);
+       params=moldyn->pot2b_params;
        sc=params->spring_constant;
        equi_dist=params->equilibrium_distance;
-       count=moldyn->count;
-
-       /* reset energy counter */
-       u=0.0;
 
-       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);
-
-               /*
-                * 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) {
-
-                       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);
-
-                       }
-               }
-
-               /*
-                * 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) {
-
-                       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);
-
-                       }
-               }
+       v3_sub(&distance,&(ai->r),&(aj->r);
+       
+       v3_per_bound(&distance,&(moldyn->dim));
+       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));
+               v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
+               v3_add(&(ai->f),&(ai->f),&force);
        }
 
-       moldyn->energy=0.5*u;
-
        return 0;
 }
 
 /* lennard jones potential & force for one sort of atoms */
  
-int lennard_jones(t_moldyn *moldyn) {
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
        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;
 
        params=moldyn->pot_params;
-       atom=moldyn->atom;
-       lc=&(moldyn->lc);
-       count=moldyn->count;
        eps=params->epsilon4;
        sig6=params->sigma6;
        sig12=params->sigma12;
 
-       /* reset energy counter */
-       u=0.0;
+       v3_sub(&distance,&(ai->r),&(aj->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,d);
+               v3_add(&(ai->f),&(aj->f),&force);
+       }
 
-       for(i=0;i<count;i++) {
-               /* reset force */
-               v3_zero(&(atom[i].f));
+       return 0;
+}
 
-               /* 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);
+/*
+ * tersoff potential & force for 2 sorts of atoms
+ */
 
-               /* 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) {
+/* tersoff 2 body part */
 
-                       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);
-                               
-                       }
-               }
+int tersoff_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
-               /* neighbours due to boundary conditions */
-               for(j=c;j<27;j++) {
-                       this=&(neighbour[j]);
-                       list_reset(this); /* check boundary conditions */
-                       if(this->start!=NULL) {
+       t_tersoff_params *params;
+       t_3dvec dist_ij;
+       double d_ij;
 
-                       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);
+       params=moldyn->pot_params;
+       
+       /*
+        * we need: f_c, df_c, f_r, df_r
+        *
+        * therefore we need: R, S
+        */
 
-                       }
+       v3_sub(&dist_ij,&(ai->r),&(aj->r));
+
+       if(bc) check_per_bound(moldyn,&dist_ij);
+
+       if(ai->bnum==aj->bnum) {
+               S=params->S[ai->bnum];
+               R=params->R[ai->bnum];
+       }
+       else {
+               S=params->Smixed;
+               R=params->Rmixed;
+       }
+
+       d_ij=v3_norm(&dist_ij);
+
+       if(d_ij<=S) {
+               f_r=A*exp(-lamda*d_ij);
+               df_r=-lambda*f_r/d_ij;
+               if(d_ij<R) {
+                       /* f_c = 1, df_c = 0 */
+                       v3_scale(&force,&dist_ij,df_r);
+               }
+               else {
+                       s_r=S-R;
+                       arg=PI*(d_ij-R)/s_r;
+                       f_c=0.5+0.5*cos(arg);
+                       df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
+                       scale=df_c*f_r+df_r*f_c;
+                       v3_scale(&force,&dist_ij,scale);
+                       v3_add(&(ai->f),&(ai->f),&force);
                }
+               moldyn->energy+=(f_r*f_c);
        }
 
-       moldyn->energy=0.5*u;
-       
        return 0;
 }
 
-/* tersoff potential & force for 2 sorts of atoms */
+/* tersoff 3 body part */
 
-int tersoff(t_moldyn *moldyn) {
+int tersoff(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc,u8 bck) {
 
        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;
-       
+       t_3dvec dist_ij;
+       double d_ij;
 
        params=moldyn->pot_params;
-       atom=moldyn->atom;
-       lc=&(moldyn->lc);
-       count=moldyn->count;
        
-       /* reset energy counter */
-       u=0.0;
-
-       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;
-
-                       /* 2 body stuff */
-
-                       /* we need: f_c, df_c, f_r, df_r */
+       /* 2 body part of the tersoff potential */
 
-                       v3_sub(&dist_ij,btom,&(atom[i]));
-                       d_ij=v3_norm(&dist_ij);
-                       if(d_ij<=S) {
+       v3_sub(&dist_ij,&(ai->r),&(aj->r));
+       if(bc) check_per_bound(moldyn,&dist_ij);
+       d_ij=v3_norm(&dist_ij);
+               if(d_ij<=S) {
 
                                /* determine the tersoff parameters */
                                if(atom[i].element!=btom->element) {
index 66f774eb068cd1b296d7f7277682a74b3bf461ba..d98b4286268ce6dfaebace9bb1fb9d234d43630f 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -25,7 +25,8 @@ typedef struct s_atom {
        t_3dvec f;              /* force */
        int element;            /* number of element in pse */
        double mass;            /* atom mass */
-       unsigned char attr;     /* attributes */
+       u8 bnum;                /* brand number */
+       u8 attr;                /* attributes */
 } t_atom;
 
 #define ATOM_ATTR_FP   0x01    /* fixed position (bulk material) */
@@ -58,12 +59,14 @@ typedef struct s_moldyn {
 
        t_3dvec dim;            /* dimensions of the simulation volume */
 
-       /* potential force function pointer and parameters */
+       /* potential force function and parameter pointers */
        int (*pf_func1b)(struct s_moldyn *,t_atom *);
+       void *pot1b_params;
        int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+       void *pot2b_params;
        int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+       void *pot3b_params;
        //int (*potential_force_function)(struct s_moldyn *moldyn);
-       void *pot_params;       /* parameters describing the potential */ 
 
        double cutoff;          /* cutoff radius */
        double cutoff_square;   /* square of the cutoff radius */
@@ -81,7 +84,7 @@ typedef struct s_moldyn {
        double energy;          /* energy */
 
        t_visual vis;           /* visualization/log/save interface structure */
-       unsigned char lvstat;   /* log & vis properties */
+       u8 lvstat;      /* log & vis properties */
        unsigned int ewrite;    /* how often to log energy */
        char efb[64];           /* energy log filename */
        int efd;                /* fd for energy log */
@@ -93,7 +96,7 @@ typedef struct s_moldyn {
        void *visual;           /* pointer (hack!) */
        unsigned int swrite;    /* how often to create a save file */
 
-       unsigned char status;   /* general moldyn properties */
+       u8 status;      /* general moldyn properties */
 
        t_random random;        /* random interface */
 } t_moldyn;
@@ -120,6 +123,11 @@ typedef struct s_lj_params {
 } t_lj_params;
 
 typedef struct s_tersoff_params {
+       double S[2];            /* tersoff cutoff radii */
+       double R[2];            /* tersoff cutoff radii */
+       double Smixed           /* mixed S radius */
+       double Rmixed           /* mixed R radius */
+
        double l_1,l_2;
        double m_1,m_2;
        double a_1,a_2;
@@ -171,7 +179,7 @@ int moldyn_log_init(t_moldyn *moldyn);
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
 int moldyn_shutdown(t_moldyn *moldyn);
 
-int create_lattice(unsigned char type,int element,double mass,double lc,
+int create_lattice(u8 type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom);
 int destroy_lattice(t_atom *atom);
 int thermal_init(t_moldyn *moldyn);