X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=29d3160acdc9375864ff56788a293704e8c3ccee;hb=959801961cfdd51e080e6500f51647b3397d336c;hp=b2e67f371810946b5c4b67b82e6a03caab311dfe;hpb=d1ceb8d3fc8e7a2e067f7576b3e787928d556277;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index b2e67f3..29d3160 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -90,6 +90,9 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 	t_stage *stage;
 
 	switch(type) {
+		case STAGE_DISPLACE_ATOM:
+			psize=sizeof(t_displace_atom_params);
+			break;
 		case STAGE_INSERT_ATOMS:
 			psize=sizeof(t_insert_atoms_params);
 			break;
@@ -138,10 +141,11 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	char error[128];
 	char line[128];
 	char *wptr;
-	char word[16][32];
+	char word[16][64];
 	int wcnt;
 	int i,o;
 
+	t_displace_atom_params dap;
 	t_insert_atoms_params iap;
 	t_continue_params cp;
 	t_anneal_params ap;
@@ -185,7 +189,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				wptr=strtok(line," \t");
 			if(wptr==NULL)
 				break;
-			strncpy(word[wcnt],wptr,32);
+			strncpy(word[wcnt],wptr,64);
 			wcnt+=1;
 		}
 
@@ -199,6 +203,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			if(!strncmp(word[1],"lj",2))
 				mdrun->potential=MOLDYN_POTENTIAL_LJ;
 		}
+		else if(!strncmp(word[0],"continue",8))
+			strncpy(mdrun->continue_file,word[1],128);
 		else if(!strncmp(word[0],"cutoff",6))
 			mdrun->cutoff=atof(word[1]);
 		else if(!strncmp(word[0],"nnd",3))
@@ -368,7 +374,14 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			mdrun->visualize=atoi(word[1]);
 		else if(!strncmp(word[0],"stage",5)) {
 			// for every stage line, add a stage
-			if(!strncmp(word[1],"ins_atoms",9)) {
+			if(!strncmp(word[1],"displace",8)) {
+				dap.nr=atoi(word[2]);	
+				dap.dx=atof(word[3]);
+				dap.dy=atof(word[4]);
+				dap.dz=atof(word[5]);
+				add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
+			}
+			else if(!strncmp(word[1],"ins_atoms",9)) {
 				iap.ins_steps=atoi(word[2]);
 				iap.ins_atoms=atoi(word[3]);
 				iap.element=atoi(word[4]);
@@ -494,6 +507,23 @@ int check_temperature(t_moldyn *moldyn,t_mdrun *mdrun) {
 	return TRUE;
 }
 
+int displace_atom(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+	t_displace_atom_params *dap;
+	t_stage *stage;
+	t_atom *atom;
+
+	stage=mdrun->stage.current->data;
+	dap=stage->params;
+
+	atom=&(moldyn->atom[dap->nr]);
+	atom->r.x+=dap->dx;
+	atom->r.y+=dap->dy;
+	atom->r.z+=dap->dz;
+
+	return 0;
+}
+
 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 
 	t_insert_atoms_params *iap;
@@ -742,6 +772,11 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 		
 		/* stage specific stuff */
 		switch(stage->type) {
+			case STAGE_DISPLACE_ATOM:
+				stage_print("  -> displace atom\n\n");
+				displace_atom(moldyn,mdrun);
+				change_stage=TRUE;
+				break;
 			case STAGE_INSERT_ATOMS:
 				stage_print("  -> insert atoms\n\n");
 				iap=stage->params;
@@ -751,7 +786,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				}
 				insert_atoms(moldyn,mdrun);
 				iap->cnt_steps+=1;
-					break;
+				break;
 			case STAGE_CONTINUE:
 				stage_print("  -> continue\n\n");
 				if(stage->executed==TRUE) {
@@ -760,7 +795,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				}
 				cp=stage->params;
 				steps=cp->runs;
-					break;
+				break;
 			case STAGE_ANNEAL:
 				stage_print("  -> anneal\n\n");
 				ap=stage->params;
@@ -843,9 +878,24 @@ int main(int argc,char **argv) {
 	/* sanity check! */
 
 	/* prepare simulation */
-	moldyn_init(&moldyn,argc,argv);
+
+	if(mdrun.continue_file[0]) {
+		// read the save file
+		moldyn_read_save_file(&moldyn,mdrun.continue_file);
+		// manualaadjusting some stuff
+		moldyn.argc=argc;
+		moldyn.args=argv;
+		rand_init(&(moldyn.random),NULL,1);
+		moldyn.random.status|=RAND_STAT_VERBOSE;
+	}
+	else {
+		moldyn_init(&moldyn,argc,argv);
+	}
+	
 	if(set_int_alg(&moldyn,mdrun.intalgo)<0)
 		return -1;
+
+	/* potential */
 	set_cutoff(&moldyn,mdrun.cutoff);
 	if(set_potential(&moldyn,mdrun.potential)<0)
 		return -1;
@@ -871,6 +921,14 @@ int main(int argc,char **argv) {
 			       ME,mdrun.potential);
 			return -1;
 	}
+
+	/* if it is a continue run, reset schedule and skip lattice init */
+	if(mdrun.continue_file[0]) {
+		memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
+		goto addsched;
+	}
+
+	/* 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);
 	switch(mdrun.lattice) {
@@ -900,10 +958,17 @@ int main(int argc,char **argv) {
 			return -1;
 	}
 	moldyn_bc_check(&moldyn);
+
+	/* temperature and pressure */
 	set_temperature(&moldyn,mdrun.temperature);
 	set_pressure(&moldyn,mdrun.pressure);
 	thermal_init(&moldyn,TRUE);
+
+addsched:
+	/* first schedule */
 	moldyn_add_schedule(&moldyn,mdrun.prerun,mdrun.timestep);
+
+	/* log */
 	moldyn_set_log_dir(&moldyn,mdrun.sdir);
 	moldyn_set_report(&moldyn,"CHANGE ME","CHANGE ME TOO");
 	if(mdrun.elog)