X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.c;h=a4fef49f1f6f7d1a431e584d56a8d7c3c815038d;hb=98f5c05d17d1077aaca379e755bf36f5d8f61776;hp=832d171be44b345c61a6f05306bfe1b12e9c8c3d;hpb=3592f3b0cf641729566674a7cdfd8eff3f61f59a;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 832d171..a4fef49 100644
--- 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;