X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=83f501ce2074cb568b7637bc0f8f2c4d2a00146e;hb=787848dc9bf3daa2ccb76296de904688cc504a45;hp=b5abe87ed61b6a8a8e782e07f565e1c20e735a05;hpb=55cd4d049604f2cf1d0fff095e6bcd13ec25780f;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index b5abe87..83f501c 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -17,6 +17,11 @@
 #include "potentials/tersoff.h"
 #endif
 
+/* pse */
+#define PSE_MASS
+#include "pse.h"
+#undef PSE_MASS
+
 #define ME	"[mdrun]"
 
 /*
@@ -279,6 +284,14 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			mdrun->ly=atoi(word[3]);
 			mdrun->lz=atoi(word[4]);
 			mdrun->lc=atof(word[5]);
+			if(wcnt==8) {
+				mdrun->fill_element=atoi(word[6]);
+				mdrun->fill_brand=atoi(word[7]);
+			}
+			else {
+				mdrun->fill_element=mdrun->element1;
+				mdrun->fill_brand=0;
+			}
 		}
 		else if(!strncmp(word[0],"aattr",5)) {
 			// for aatrib line we need a special stage
@@ -517,6 +530,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				ap.count=0;
 				ap.runs=atoi(word[2]);
 				ap.dt=atof(word[3]);
+				ap.interval=atoi(word[4]);
 				add_stage(mdrun,STAGE_ANNEAL,&ap);
 			}
 			else if(!strncmp(word[1],"set_temp",8)) {
@@ -1006,6 +1020,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 					set_temperature(moldyn,
 					                moldyn->t_ref+ap->dt);
 				ap->count+=1;
+				steps=ap->interval;
 				break;
 			case STAGE_CHAATTR:
 				stage_print("  -> change atom attributes\n\n");
@@ -1148,24 +1163,27 @@ int main(int argc,char **argv) {
 	set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
 	switch(mdrun.lattice) {
 		case FCC:
-			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
-			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
-			               mdrun.ly,mdrun.lz,NULL);
+			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,
+                                       mdrun.fill_brand,mdrun.lx,
+			               mdrun.ly,mdrun.lz,NULL,0,NULL);
 			break;
 		case DIAMOND:
-			create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
-			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
-			               mdrun.ly,mdrun.lz,NULL);
+			create_lattice(&moldyn,DIAMOND,mdrun.lc,
+                                       mdrun.fill_element,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,
+                                       mdrun.fill_brand,mdrun.lx,
+			               mdrun.ly,mdrun.lz,NULL,0,NULL);
 			break;
 		case ZINCBLENDE:
 			o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
 			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
-			               mdrun.ly,mdrun.lz,&o);
+			               mdrun.ly,mdrun.lz,&o,0,NULL);
 			o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
 			               mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
-			               mdrun.ly,mdrun.lz,&o);
+			               mdrun.ly,mdrun.lz,&o,0,NULL);
 			break;
 		case NONE:
 			set_nn_dist(&moldyn,mdrun.nnd);