completed crt implementation

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 12cb49b..a6f5c45 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -55,6 +55,11 @@ pthread_mutex_t *amutex;
 pthread_mutex_t emutex;
 #endif
 
+/* fully constrained relaxation technique - global pointers */
+u8 crtt;
+u8 *constraints;
+double *trafo_angle;
+
 /*
  * the moldyn functions
  */
@@ -78,6 +83,9 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
        pthread_mutex_init(&emutex,NULL);
 #endif
 
+       if(crtt)
+               printf("USING CRT\n");
+
        return 0;
 }
 
@@ -516,7 +524,8 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 
 int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
                    u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin,
-                   t_part_params *p_params,t_defect_params *d_params) {
+                   t_part_params *p_params,t_defect_params *d_params,
+                   t_offset_params *o_params) {
 
        int new,count;
        int ret;
@@ -588,6 +597,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
 
        switch(type) {
                case CUBIC:
+                       if(o_params->use)
+                               v3_add(&orig,&orig,&(o_params->o));
                        set_nn_dist(moldyn,lc);
                        ret=cubic_init(a,b,c,lc,atom,&orig,p_params,d_params);
                        strcpy(name,"cubic");
@@ -595,6 +606,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
                case FCC:
                        if(!origin)
                                v3_scale(&orig,&orig,0.5);
+                       if(o_params->use)
+                               v3_add(&orig,&orig,&(o_params->o));
                        set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
                        ret=fcc_init(a,b,c,lc,atom,&orig,p_params,d_params);
                        strcpy(name,"fcc");
@@ -602,6 +615,8 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,
                case DIAMOND:
                        if(!origin)
                                v3_scale(&orig,&orig,0.25);
+                       if(o_params->use)
+                               v3_add(&orig,&orig,&(o_params->o));
                        set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
                        ret=diamond_init(a,b,c,lc,atom,&orig,p_params,d_params);
                        strcpy(name,"diamond");
@@ -802,8 +817,6 @@ int del_atom(t_moldyn *moldyn,int tag) {
                        case DEFECT_STYPE_DB_Z:\
                                d_o.z=d_params->od;\
                                d_d.z=d_params->dd;\
-d_d.x=0.9;\
-d_d.y=0.9;\
                                break;\
                        case DEFECT_STYPE_DB_R:\
                                break;\
@@ -2228,6 +2241,59 @@ printf("sched:%d, steps:%d/%d, T:%4.1f/%4.1f P:%4.1f/%4.1f V:%6.1f (%d)\n",
 
        }
 
+       /* writing a final save file! */
+       if(s) {
+               snprintf(dir,128,"%s/s-final.save",moldyn->vlsdir);
+               fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
+               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);
+       }
+       /* writing a final visual file! */
+       if(a)
+               visual_atoms(moldyn);
+
+       return 0;
+}
+
+/* basis trafo */
+
+#define FORWARD                0
+#define BACKWARD       1
+
+int basis_trafo(t_3dvec *r,u8 dir,double z,double x) {
+
+       t_3dvec tmp;
+
+       if(dir==FORWARD) {
+               if(z!=0.0) {
+                       v3_copy(&tmp,r);
+                       r->x=cos(z)*tmp.x-sin(z)*tmp.y;
+                       r->y=sin(z)*tmp.x+cos(z)*tmp.y;
+               }
+               if(x!=0.0) {
+                       v3_copy(&tmp,r);
+                       r->y=cos(x)*tmp.y-sin(x)*tmp.z;
+                       r->z=sin(x)*tmp.y+cos(x)*tmp.z;
+               }
+       }
+       else {
+               if(x!=0.0) {
+                       v3_copy(&tmp,r);
+                       r->y=cos(-x)*tmp.y-sin(-x)*tmp.z;
+                       r->z=sin(-x)*tmp.y+cos(-x)*tmp.z;
+               }
+               if(z!=0.0) {
+                       v3_copy(&tmp,r);
+                       r->x=cos(-z)*tmp.x-sin(-z)*tmp.y;
+                       r->y=sin(-z)*tmp.x+cos(-z)*tmp.y;
+               }
+       }
+
        return 0;
 }
 
@@ -2246,13 +2312,32 @@ int velocity_verlet(t_moldyn *moldyn) {
        tau_square=moldyn->tau_square;
 
        for(i=0;i<count;i++) {
+
                /* check whether fixed atom */
                if(atom[i].attr&ATOM_ATTR_FP)
                        continue;
+
                /* new positions */
                h=0.5/atom[i].mass;
+
+               /* constraint relaxation */
+               if(crtt) {
+                       basis_trafo(&(atom[i].f),FORWARD,
+                                   trafo_angle[2*i],trafo_angle[2*i+1]);
+                       if(constraints[3*i])
+                               atom[i].f.x=0;
+                       if(constraints[3*i+1])
+                               atom[i].f.y=0;
+                       if(constraints[3*i+2])
+                               atom[i].f.z=0;
+                       basis_trafo(&(atom[i].f),BACKWARD,
+                                   trafo_angle[2*i],trafo_angle[2*i+1]);
+               }
+
+#ifndef QUENCH
                v3_scale(&delta,&(atom[i].v),tau);
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
+#endif
                v3_scale(&delta,&(atom[i].f),h*tau_square);
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
                //check_per_bound_and_care_for_pbc(moldyn,&(atom[i]));
@@ -2284,6 +2369,21 @@ int velocity_verlet(t_moldyn *moldyn) {
                /* check whether fixed atom */
                if(atom[i].attr&ATOM_ATTR_FP)
                        continue;
+
+               /* constraint relaxation */
+               if(crtt) {
+                       basis_trafo(&(atom[i].f),FORWARD,
+                                   trafo_angle[2*i],trafo_angle[2*i+1]);
+                       if(constraints[3*i])
+                               atom[i].f.x=0;
+                       if(constraints[3*i+1])
+                               atom[i].f.y=0;
+                       if(constraints[3*i+2])
+                               atom[i].f.z=0;
+                       basis_trafo(&(atom[i].f),BACKWARD,
+                                   trafo_angle[2*i],trafo_angle[2*i+1]);
+               }
+
                /* again velocities [actually v(t+tau)] */
                v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
                v3_add(&(atom[i].v),&(atom[i].v),&delta);
@@ -2862,7 +2962,7 @@ int moldyn_read_save_file(t_moldyn *moldyn,char *file) {
        if(fsize!=sizeof(t_moldyn)+size) {
                corr=fsize-sizeof(t_moldyn)-size;
                printf("[moldyn] WARNING: lsf (illegal file size)\n");
-               printf("  moifying offset:\n");
+               printf("  modifying offset:\n");
                printf("  - current pos: %d\n",sizeof(t_moldyn));
                printf("  - atom size: %d\n",size);
                printf("  - file size: %d\n",fsize);
@@ -3148,6 +3248,57 @@ int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
        return 0;
 }
 
+int calculate_msd(t_moldyn *moldyn,double *msd) {
+
+       int i;
+       t_atom *atom;
+       t_3dvec dist;
+       t_3dvec final_r;
+       double d2;
+       int a_cnt;
+       int b_cnt;
+
+       atom=moldyn->atom;
+       msd[0]=0;
+       msd[1]=0;
+       msd[2]=0;
+       a_cnt=0;
+       b_cnt=0;
+
+       for(i=0;i<moldyn->count;i++) {
+
+               /* care for pb crossing */
+               if(atom[i].pbc[0]|atom[i].pbc[1]|atom[i].pbc[2]) {
+                       printf("[moldyn] msd pb crossings for atom %d\n",i);
+                       printf("  x: %d y: %d z: %d\n",
+                              atom[i].pbc[0],atom[i].pbc[1],atom[i].pbc[2]);
+               }
+               final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
+               final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
+               final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
+               /* calculate distance */
+               v3_sub(&dist,&final_r,&(atom[i].r_0));
+               d2=v3_absolute_square(&dist);
+
+               if(atom[i].brand) {
+                       b_cnt+=1;
+                       msd[1]+=d2;
+               }
+               else {
+                       a_cnt+=1;
+                       msd[0]+=d2;
+               }
+
+               msd[2]+=d2;
+       }
+
+       msd[0]/=a_cnt;
+       msd[1]/=b_cnt;
+       msd[2]/=moldyn->count;
+               
+       return 0;
+}
+
 int bonding_analyze(t_moldyn *moldyn,double *cnt) {
 
        return 0;