implemented continue featue + skipped d calc in bond_analyze function

[physik/posic.git] / moldyn.c

diff --git a/moldyn.c b/moldyn.c
index 832d171..a4fef49 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -30,101 +30,6 @@
 #include "potentials/tersoff.h"
 #endif
 
-
-/*
- * global variables, pse and atom colors (only needed here)
- */ 
-
-static char *pse_name[]={
-       "*",
-       "H",
-       "He",
-       "Li",
-       "Be",
-       "B",
-       "C",
-       "N",
-       "O",
-       "F",
-       "Ne",
-       "Na",
-       "Mg",
-       "Al",
-       "Si",
-       "P",
-       "S",
-       "Cl",
-       "Ar",
-};
-
-static char *pse_col[]={
-       "*",
-       "White",
-       "He",
-       "Li",
-       "Be",
-       "B",
-       "Gray",
-       "N",
-       "Blue",
-       "F",
-       "Ne",
-       "Na",
-       "Mg",
-       "Al",
-       "Yellow",
-       "P",
-       "S",
-       "Cl",
-       "Ar",
-};
-
-/*
-static double pse_mass[]={
-       0,
-       0,
-       0,
-       0,
-       0,
-       0,
-       M_C,
-       0,
-       0,
-       0,
-       0,
-       0,
-       0,
-       0,
-       M_SI,
-       0,
-       0,
-       0,
-       0,
-};
-
-static double pse_lc[]={
-       0,
-       0,
-       0,
-       0,
-       0,
-       0,
-       LC_C,
-       0,
-       0,
-       0,
-       0,
-       0,
-       0,
-       0,
-       LC_SI,
-       0,
-       0,
-       0,
-       0,
-};
-*/
-
 /*
  * the moldyn functions
  */
@@ -208,7 +113,7 @@ int set_p_scale(t_moldyn *moldyn,u8 ptype,double ptc) {
        moldyn->pt_scale|=ptype;
        moldyn->p_tc=ptc;
 
-       printf("[moldyn] p/t scaling:\n");
+       printf("[moldyn] p scaling:\n");
 
        printf("  p: %s",ptype?"yes":"no ");
        if(ptype)
@@ -224,7 +129,7 @@ int set_t_scale(t_moldyn *moldyn,u8 ttype,double ttc) {
        moldyn->pt_scale|=ttype;
        moldyn->t_tc=ttc;
 
-       printf("[moldyn] p/t scaling:\n");
+       printf("[moldyn] t scaling:\n");
 
        printf("  t: %s",ttype?"yes":"no ");
        if(ttype)
@@ -574,6 +479,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
        t_3dvec orig;
        void *ptr;
        t_atom *atom;
+       char name[16];
 
        new=a*b*c;
        count=moldyn->count;
@@ -608,18 +514,21 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
                case CUBIC:
                        set_nn_dist(moldyn,lc);
                        ret=cubic_init(a,b,c,lc,atom,&orig);
+                       strcpy(name,"cubic");
                        break;
                case FCC:
                        if(!origin)
                                v3_scale(&orig,&orig,0.5);
                        set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
                        ret=fcc_init(a,b,c,lc,atom,&orig);
+                       strcpy(name,"fcc");
                        break;
                case DIAMOND:
                        if(!origin)
                                v3_scale(&orig,&orig,0.25);
                        set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
                        ret=diamond_init(a,b,c,lc,atom,&orig);
+                       strcpy(name,"diamond");
                        break;
                default:
                        printf("unknown lattice type (%02x)\n",type);
@@ -636,7 +545,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
        }
 
        moldyn->count+=new;
-       printf("[moldyn] created lattice with %d atoms\n",new);
+       printf("[moldyn] created %s lattice with %d atoms\n",name,new);
 
        for(ret=0;ret<new;ret++) {
                atom[ret].element=element;
@@ -1670,8 +1579,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
                printf("[moldyn] WARNING: forces too high / tau too small!\n");
 
        /* zero absolute time */
-       moldyn->time=0.0;
-       moldyn->total_steps=0;
+       // should have right values!
+       //moldyn->time=0.0;
+       //moldyn->total_steps=0;
 
        /* debugging, ignore */
        moldyn->debug=0;
@@ -1703,7 +1613,11 @@ int moldyn_integrate(t_moldyn *moldyn) {
                temperature_calc(moldyn);
                virial_sum(moldyn);
                pressure_calc(moldyn);
-               //thermodynamic_pressure_calc(moldyn);
+               /*
+               thermodynamic_pressure_calc(moldyn);
+               printf("\n\nDEBUG: numeric pressure calc: %f\n\n",
+                      moldyn->tp/BAR);
+               */
 
                /* calculate fluctuations + averages */
                average_and_fluctuation_calc(moldyn);
@@ -2414,9 +2328,6 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
        t_list *this;
 
        lc=&(moldyn->lc);
-
-       link_cell_init(moldyn,VERBOSE);
-
        itom=moldyn->atom;
        
        for(i=0;i<moldyn->count;i++) {
@@ -2676,8 +2587,6 @@ int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
        if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
                return 0;
 
-       d=sqrt(d);
-
        /* now count this bonding ... */
        ba=data;