X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=mdrun.c;h=6effe1aff6c56f33b635da11e332e27a4252b65e;hb=d843bfcc38ac4ad1ceffbb82a1aba8096f791b41;hp=b5abe87ed61b6a8a8e782e07f565e1c20e735a05;hpb=55cd4d049604f2cf1d0fff095e6bcd13ec25780f;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index b5abe87..6effe1a 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]"
 
 /*
@@ -117,6 +122,12 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_SET_TIMESTEP:
 			psize=sizeof(t_set_timestep_params);
 			break;
+		case STAGE_FILL:
+			psize=sizeof(t_fill_params);
+			break;
+		case STAGE_THERMAL_INIT:
+			psize=0;
+			break;
 		default:
 			printf("%s unknown stage type: %02x\n",ME,type);
 			return -1;
@@ -163,6 +174,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	t_chsattr_params csp;
 	t_set_temp_params stp;
 	t_set_timestep_params stsp;
+	t_fill_params fp;
 
 	/* open config file */
 	fd=open(mdrun->cfile,O_RDONLY);
@@ -194,6 +206,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		memset(&csp,0,sizeof(t_chsattr_params));
 		memset(&stp,0,sizeof(t_set_temp_params));
 		memset(&stsp,0,sizeof(t_set_timestep_params));
+		memset(&fp,0,sizeof(t_fill_params));
 
 		// get command + args
 		wcnt=0;
@@ -274,11 +287,60 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			mdrun->m2=pse_mass[mdrun->element2];
 		}
 		else if(!strncmp(word[0],"fill",6)) {
-			// only lc mode by now
-			mdrun->lx=atoi(word[2]);
-			mdrun->ly=atoi(word[3]);
-			mdrun->lz=atoi(word[4]);
-			mdrun->lc=atof(word[5]);
+			fp.lx=atoi(word[2]);
+			fp.ly=atoi(word[3]);
+			fp.lz=atoi(word[4]);
+			fp.lc=atof(word[5]);
+			mdrun->lc=fp.lc;
+			if(!strncmp(word[1],"lc",2)) {
+				if(wcnt==8) {
+					fp.fill_element=atoi(word[6]);
+					fp.fill_brand=atoi(word[7]);
+				}
+				else {
+					fp.fill_element=mdrun->element1;
+					fp.fill_brand=0;
+				}
+			}
+			else {
+				switch(word[6][0]) {
+					case 'i':
+						if(word[6][1]=='r')
+							fp.p_type=PART_INSIDE_R;
+						else
+							fp.p_type=PART_INSIDE_D;
+						break;
+					case 'o':
+						if(word[6][1]=='r')
+						fp.p_type=PART_OUTSIDE_R;
+						else
+						fp.p_type=PART_OUTSIDE_D;
+						break;
+					default:
+						break;
+				}
+			}
+			if((fp.p_type==PART_INSIDE_R)||
+                           (fp.p_type==PART_OUTSIDE_R)) {
+				fp.p_vals.r=atof(word[7]);	
+				fp.p_vals.p.x=atof(word[8]);	
+				fp.p_vals.p.y=atof(word[9]);	
+				fp.p_vals.p.z=atof(word[10]);
+			}
+			if((fp.p_type==PART_INSIDE_D)||
+                           (fp.p_type==PART_OUTSIDE_D)) {
+				fp.p_vals.p.x=atof(word[7]);	
+				fp.p_vals.p.y=atof(word[8]);	
+				fp.p_vals.p.z=atof(word[9]);
+				fp.p_vals.d.x=atof(word[10]);	
+				fp.p_vals.d.y=atof(word[11]);	
+				fp.p_vals.d.z=atof(word[12]);
+			}
+			fp.lattice=mdrun->lattice;
+			add_stage(mdrun,STAGE_FILL,&fp);
+		}
+		else if(!strncmp(word[0],"thermal_init",12)) {
+			add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
 		}
 		else if(!strncmp(word[0],"aattr",5)) {
 			// for aatrib line we need a special stage
@@ -517,6 +579,7 @@ 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)) {
@@ -923,6 +986,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	t_list *sl;
 	int steps;
 	u8 change_stage;
+	t_3dvec o;
 
 	t_insert_atoms_params *iap;
 	t_insert_mixed_atoms_params *imp;
@@ -930,6 +994,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	t_anneal_params *ap;
 	t_set_temp_params *stp;
 	t_set_timestep_params *stsp;
+	t_fill_params *fp;
 
 	moldyn=ptr1;
 	mdrun=ptr2;
@@ -1006,6 +1071,7 @@ 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");
@@ -1034,6 +1100,51 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				mdrun->timestep=stsp->tau;
 				change_stage=TRUE;
 				break;
+			case STAGE_FILL:
+				stage_print("  -> fill lattice\n\n");
+				fp=stage->params;
+				if(fp->lattice!=ZINCBLENDE) {
+					create_lattice(moldyn,
+					               fp->lattice,fp->lc,
+					               mdrun->element1,
+					               mdrun->m1,
+					               DEFAULT_ATOM_ATTR,0,
+					               fp->lx,fp->ly,fp->lz,
+					               NULL,fp->p_type,
+					               &(fp->p_vals));
+				}
+				else {
+					o.x=0.5*0.25*fp->lc;
+					o.y=o.x;
+					o.z=o.x;
+					create_lattice(moldyn,
+					               FCC,fp->lc,
+					               mdrun->element1,
+					               mdrun->m1,
+					               DEFAULT_ATOM_ATTR,0,
+					               fp->lx,fp->ly,fp->lz,
+					               &o,fp->p_type,
+					               &(fp->p_vals));
+					o.x+=0.25*fp->lc;
+					o.y=o.x;
+					o.z=o.x;
+					create_lattice(moldyn,
+					               FCC,fp->lc,
+					               mdrun->element2,
+					               mdrun->m2,
+					               DEFAULT_ATOM_ATTR,1,
+					               fp->lx,fp->ly,fp->lz,
+					               &o,fp->p_type,
+					               &(fp->p_vals));
+				}
+				moldyn_bc_check(moldyn);
+				change_stage=TRUE;
+				break;
+			case STAGE_THERMAL_INIT:
+				stage_print("  -> thermal init\n\n");
+				thermal_init(moldyn,TRUE);
+				change_stage=TRUE;
+				break;
 			default:
 				printf("%s unknwon stage type\n",ME);
 				break;
@@ -1071,7 +1182,7 @@ int main(int argc,char **argv) {
 
 	t_mdrun mdrun;
 	t_moldyn moldyn;
-	t_3dvec o;
+	//t_3dvec o;
 
 	/* clear structs */
 	memset(&mdrun,0,sizeof(t_mdrun));
@@ -1146,26 +1257,30 @@ int main(int argc,char **argv) {
 	/* initial lattice and dimensions */
 	set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
 	set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
+	/* replaced by fill stage !! 
 	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);
@@ -1176,11 +1291,14 @@ int main(int argc,char **argv) {
 			return -1;
 	}
 	moldyn_bc_check(&moldyn);
+	replaced by fill stage !! */
 
 	/* temperature and pressure */
 	set_temperature(&moldyn,mdrun.temperature);
 	set_pressure(&moldyn,mdrun.pressure);
+	/* replaced thermal_init stage
 	thermal_init(&moldyn,TRUE);
+	*/
 
 addsched:
 	/* first schedule */