X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=mdrun.c;h=26fbc871708c262a19eead0b398d8773a2941902;hp=3266dd3804a0ac0668049988c30ecfac554a8fca;hb=HEAD;hpb=ff44bcba9df0d021568abcb553d1d490c442f696

diff --git a/mdrun.c b/mdrun.c
index 3266dd3..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);
+			}
 		}
 	}
 
@@ -1286,6 +1306,7 @@ int crt(t_moldyn *moldyn,t_mdrun *mdrun) {
 			// done reading
 			acount+=1;
 		}
+		close(fd);
 		// allocate trafo angles
 		trafo_angle=malloc(acount*2*sizeof(double));
 		if(trafo_angle==NULL) {
@@ -1296,18 +1317,41 @@ int crt(t_moldyn *moldyn,t_mdrun *mdrun) {
 		crtt=crtp->type;
 	}
 
+	/* write a save file s-crt_xofy.save */
+	snprintf(line,128,"%s/s-crt_%03dof%03d.save",
+	         moldyn->vlsdir,crtp->count,crtp->steps);
+	fd=open(line,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
+	if(fd<0) perror("[mdrun] crt save fd open");
+	else {
+		write(fd,moldyn,sizeof(t_moldyn));
+		write(fd,moldyn->atom,
+		      moldyn->count*sizeof(t_atom));
+	}
+	close(fd);
+	/* visualize atoms */
+	visual_atoms(moldyn);
+
+	/* output energy */
+	printf("  crt energy: %d - %f\n\n",
+	       crtp->count,(moldyn->ekin+moldyn->energy)/EV);
+
 	/* crt routines: calculate displacement + set individual constraints */
 
 	printf("  crt step %d of %d in total\n\n",crtp->count+1,crtp->steps);
 
+	if((crtp->type==1)|(crtp->count==0))
+		printf("  crt angle update\n\n");
+		
 	for(i=0;i<moldyn->count;i++) {
 		// calc displacements
 		atom=moldyn->atom;
 		v3_sub(&disp,&(crtp->r_fin[i]),&(atom[i].r));
 		// angles
-		trafo_angle[2*i]=atan2(disp.x,disp.y);
-		trafo_angle[2*i+1]=-atan2(disp.z,
-		                          sqrt(disp.x*disp.x+disp.y*disp.y));
+		if((crtp->type==1)|(crtp->count==0)) {
+			trafo_angle[2*i]=atan2(disp.x,disp.y);
+			trafo_angle[2*i+1]=-atan2(disp.z,
+			                   sqrt(disp.x*disp.x+disp.y*disp.y));
+		}
 		// move atoms
 		frac=1.0/(crtp->steps-crtp->count);
 		v3_scale(&disp,&disp,frac);
@@ -1612,6 +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,