X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=mdrun.c;h=26fbc871708c262a19eead0b398d8773a2941902;hp=bb1cd21377ee706a31ecc489d19ac58fdf5d5450;hb=HEAD;hpb=fe84cdc3fc897581636aff89b6f4fd12db1d2718

diff --git a/mdrun.c b/mdrun.c
index bb1cd21..26fbc87 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -11,6 +11,7 @@
 #include "potentials/harmonic_oscillator.h"
 #include "potentials/lennard_jones.h"
 #include "potentials/albe.h"
+#include "potentials/albe_orig.h"
 #ifdef TERSOFF_ORIG
 #include "potentials/tersoff_orig.h"
 #else
@@ -234,6 +235,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		if(!strncmp(word[0],"potential",9)) {
 			if(!strncmp(word[1],"albe",4))
 				mdrun->potential=MOLDYN_POTENTIAL_AM;
+			if(!strncmp(word[1],"albe_o",6))
+				mdrun->potential=MOLDYN_POTENTIAL_AO;
 			if(!strncmp(word[1],"tersoff",7))
 				mdrun->potential=MOLDYN_POTENTIAL_TM;
 			if(!strncmp(word[1],"ho",2))
@@ -803,18 +806,35 @@ int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	t_del_atoms_params *delp;
 	int i;
 	t_3dvec dist;
-	
+	u8 outer;
+
+	outer=0;	
 	stage=mdrun->stage.current->data;
 	delp=stage->params;
 
+	if(delp->r<0)
+		outer=1;
+
 	for(i=0;i<moldyn->count;i++) {
 		v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
 //printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
 		if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
-			del_atom(moldyn,moldyn->atom[i].tag);
-			printf("%s atom deleted: %d %d %d\n",ME,
-                               moldyn->atom[i].tag,moldyn->atom[i].element,
-			       moldyn->atom[i].brand);
+			if(!outer) {
+				del_atom(moldyn,moldyn->atom[i].tag);
+				printf("%s atom deleted: %d %d %d\n",ME,
+		                       moldyn->atom[i].tag,
+				       moldyn->atom[i].element,
+			 	       moldyn->atom[i].brand);
+			}
+		}
+		else {
+			if(outer) {
+				del_atom(moldyn,moldyn->atom[i].tag);
+				printf("%s atom deleted: %d %d %d\n",ME,
+             	  	               moldyn->atom[i].tag,
+				       moldyn->atom[i].element,
+				       moldyn->atom[i].brand);
+			}
 		}
 	}
 
@@ -1308,6 +1328,8 @@ int crt(t_moldyn *moldyn,t_mdrun *mdrun) {
 		      moldyn->count*sizeof(t_atom));
 	}
 	close(fd);
+	/* visualize atoms */
+	visual_atoms(moldyn);
 
 	/* output energy */
 	printf("  crt energy: %d - %f\n\n",
@@ -1634,6 +1656,11 @@ int main(int argc,char **argv) {
 			                     mdrun.element1,
 			                     mdrun.element2);
 			break;
+		case MOLDYN_POTENTIAL_AO:
+			albe_orig_mult_set_params(&moldyn,
+			                          mdrun.element1,
+			                          mdrun.element2);
+			break;
 		case MOLDYN_POTENTIAL_TM:
 			tersoff_mult_set_params(&moldyn,
 			                        mdrun.element1,