visual atoms using moldyn func now, updated TODO, atom_match build by

Makefile

diff --git a/Makefile b/Makefile
index 4de3dcc..462a9b7 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -33,7 +33,7 @@ SRC += potentials/tersoff.c potentials/albe.c
 SRC += potentials/albe_fast.c
 
 ALL = mdrun sic fluctuation_calc postproc pair_correlation_calc diffusion_calc
-ALL += bond_analyze search_bonds visual_atoms display_atom_data
+ALL += bond_analyze search_bonds visual_atoms display_atom_data atom_match
 
 all: $(ALL)
 
@@ -57,6 +57,8 @@ visual_atoms: $(DEPS)
 
 display_atom_data: $(DEPS)
 
+atom_match: $(DEPS)
+
 .PHONY:clean
 clean:
        rm -vf $(ALL) *.o */*.o

diff --git a/TODO.txt b/TODO.txt
index bf6f4ad..570ee54 100644 (file)
--- a/TODO.txt
+++ b/TODO.txt
@@ -11,17 +11,20 @@ implement
 
  - improve ins_m_atoms (merge to general ins_atoms function maybe)
  - clean up mdrun
+ - config sanity checks
  - introduce/improve fill command (multiple fills)
 
  - check virial calc, where does the - come from?
 
  - angular distribution
- - structfactoranalyze (see nordlund paper)
+ - structurfactoranalyze (see nordlund paper)
 
  - filled atoms need atom attrib?!?!? or aattr pre prerun
 
  - bond_analyze to dump xyz file of atoms
 
+ - improve diff calc
+
  - make it parallel! (mpi/openmp) <- email to ralfu (asap)
    * openmp: doch auf verlet listen (pointer problem!)
 
@@ -56,13 +59,13 @@ simulation runs
 - cryst simulations: reasonable pctrl?
 - even higher temperatures
 - tctrl only in outer regions
-- cryst of molten area with cryst area next to it
 - only 1 atom per timestep
 - EXTENDED C-C cutoff
 - different sized SiC prec in Si (4:5! diff temperatures)
-- more interstitial combinations
 - melting exps (both, anneal + interface method)
-- characterize interstitials by PCF, then inc temperature
+- interstitials:
+  - more interstitial combinations
+  - characterize interstitials by PCF, then inc temperature
 
 learn
 *****

diff --git a/visual_atoms.c b/visual_atoms.c
index a98ecd6..68901ec 100644 (file)
--- a/visual_atoms.c
+++ b/visual_atoms.c
@@ -23,6 +23,14 @@
 #undef PSE_NAME
 #undef PSE_COL
 
+typedef struct s_data {
+       int ca;
+       double radius;
+       double lc;
+       int ma;
+       double ox,oy,oz;
+} t_data;
+
 int usage(char *prog) {
 
        printf("\nusage:\n");
@@ -32,33 +40,47 @@ int usage(char *prog) {
        return -1;
 }
 
+int process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,void *ptr,u8 bc) {
+
+       t_3dvec dist;
+       double d;
+       t_data *data;
+
+       data=ptr;
+
+       v3_sub(&dist,&(itom->r),&(jtom->r));
+       if(bc) check_per_bound(moldyn,&dist);
+       d=v3_norm(&dist);
+
+       if(d<=data->radius) {
+               printf("%s %f %f %f %s %f\n",
+                      pse_name[jtom->element],
+                      jtom->r.x+data->ox,jtom->r.y+data->oy,jtom->r.z+data->oz,
+                      (jtom->tag==data->ma)?"Red":pse_col[jtom->element],
+                      jtom->ekin);
+       }
+
+       return 0;
+}
+
 int main(int argc,char **argv) {
 
        t_moldyn moldyn;
-       t_atom *itom,*jtom;
-       int j;
+       t_data data;
        int ret;
-       t_list n[27];
-       t_list *this;
-       t_linkcell *lc;
-       t_3dvec dist;
-       double d,radius;
-       double ox,oy,oz;
-       int ma,ca;
-       double lac;
+       t_atom *atom;
 
        if(argc<4) {
                usage(argv[0]);
                return -1;
        }
-
-       ca=atoi(argv[2]);
-       radius=atof(argv[3]);
-       lac=atof(argv[4]);
-
-       ma=-1;
+       
+       data.ca=atoi(argv[2]);
+       data.radius=atof(argv[3]);
+       data.lc=atof(argv[4]);
+       data.ma=-1;
        if(argc==6)
-               ma=atoi(argv[5]);
+               data.ma=atoi(argv[5]);
 
        memset(&moldyn,0,sizeof(t_moldyn));
 
@@ -70,87 +92,52 @@ int main(int argc,char **argv) {
        }
 
        /* link cell init */
-       moldyn.cutoff=radius;
+       moldyn.cutoff=data.radius;
        link_cell_init(&moldyn,VERBOSE);
-       lc=&(moldyn.lc);
-
-       /* serach atoms */
-       itom=&(moldyn.atom[ca]);
-       link_cell_neighbour_index(&moldyn,
-                                 (itom->r.x+moldyn.dim.x/2)/lc->x,
-                                 (itom->r.y+moldyn.dim.y/2)/lc->y,
-                                 (itom->r.z+moldyn.dim.z/2)/lc->z,
-                                 n);
 
+       atom=&(moldyn.atom[data.ca]);
 
        /* prepare offset */
-       ox=0.0;
-       if(itom->r.x<0) {
-               while((itom->r.x+ox)<(-lac/2.0))
-                       ox+=lac;
+       data.ox=0.0;
+       if(atom->r.x<0) {
+               while((atom->r.x+data.ox)<(-data.lc/2.0))
+                       data.ox+=data.lc;
        }
        else {
-               while((itom->r.x+ox)>(lac/2.0))
-                       ox-=lac;
+               while((atom->r.x+data.ox)>(data.lc/2.0))
+                       data.ox-=data.lc;
        }
 
-       oy=0.0;
-       if(itom->r.y<0) {
-               while((itom->r.y+oy)<(-lac/2.0))
-                       oy+=lac;
+       data.oy=0.0;
+       if(atom->r.y<0) {
+               while((atom->r.y+data.oy)<(-data.lc/2.0))
+                       data.oy+=data.lc;
        }
        else {
-               while((itom->r.y+oy)>(lac/2.0))
-                       oy-=lac;
+               while((atom->r.y+data.oy)>(data.lc/2.0))
+                       data.oy-=data.lc;
        }
 
-       oz=0.0;
-       if(itom->r.z<0) {
-               while((itom->r.z+oz)<(-lac/2.0))
-                       oz+=lac;
+       data.oz=0.0;
+       if(atom->r.z<0) {
+               while((atom->r.z+data.oz)<(-data.lc/2.0))
+                       data.oz+=data.lc;
        }
        else {
-               while((itom->r.z+oz)>(lac/2.0))
-                       oz-=lac;
+               while((atom->r.z+data.oz)>(data.lc/2.0))
+                       data.oz-=data.lc;
        }
 
-
+       /* print the centered atom */
        printf("%s %f %f %f %s %f\n",
-              pse_name[itom->element],itom->r.x+ox,itom->r.y+oy,itom->r.z+oz,
-              "Green",itom->ekin);
-
-       for(j=0;j<27;j++) {
-               this=&(n[j]);
-               list_reset_f(this);
-
-               if(this->start==NULL)
-                       continue;
-
-               do {
-
-                       jtom=this->current->data;
-
-                       if(jtom==itom)
-                               continue;
-
-                       v3_sub(&dist,&(itom->r),&(jtom->r));
-                       check_per_bound(&moldyn,&dist);
-                       d=v3_norm(&dist);
-
-                       if(d<=radius) {
-                               printf("%s %f %f %f %s %f\n",
-                                      pse_name[jtom->element],
-                                      jtom->r.x+ox,jtom->r.y+oy,jtom->r.z+oz,
-                                      (jtom->tag==ma)?"Red":pse_col[jtom->element],
-                                      jtom->ekin);
-                       }
-
-               } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
-       }
+              pse_name[atom->element],atom->r.x+data.ox,atom->r.y+data.oy,
+               atom->r.z+data.oz,"Green",atom->ekin);
 
+       process_neighbours(&moldyn,&data,atom,process);
+       
        link_cell_shutdown(&moldyn);
-
        moldyn_free_save_file(&moldyn);
 
        return 0;
 }
+