From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Tue, 13 May 2008 09:54:41 +0000 (+0200)
Subject: implemented continue featue + skipped d calc in bond_analyze function
X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=commitdiff_plain;h=d1c8623aedde670da01eb2e85cf36d0b2a7c340f

implemented continue featue + skipped d calc in bond_analyze function
---

diff --git a/mdrun.c b/mdrun.c
index bd045fe..d99bd7a 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -141,7 +141,7 @@ 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;
 
@@ -189,7 +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;
 		}
 
@@ -203,6 +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))
@@ -876,9 +878,16 @@ int main(int argc,char **argv) {
 	/* sanity check! */
 
 	/* prepare simulation */
+
 	moldyn_init(&moldyn,argc,argv);
+
+	if(mdrun.continue_file)
+		moldyn_read_save_file(&moldyn,mdrun.continue_file);
+	
 	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;
@@ -904,6 +913,14 @@ 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) {
+		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) {
@@ -933,10 +950,17 @@ 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)
diff --git a/mdrun.h b/mdrun.h
index 3b24946..d065d57 100644
--- a/mdrun.h
+++ b/mdrun.h
@@ -51,6 +51,8 @@ typedef struct s_stage {
 typedef struct s_mdrun {
 	char cfile[128];			// config file
 
+	char continue_file[128];		// moldyn save file to continue
+
 	u8 intalgo;				// integration algorithm
 	double timestep;			// timestep
 
diff --git a/moldyn.c b/moldyn.c
index caafc4c..a4fef49 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -1579,8 +1579,9 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		printf("[moldyn] WARNING: forces too high / tau too small!\n");
 
 	/* zero absolute time */
-	moldyn->time=0.0;
-	moldyn->total_steps=0;
+	// should have right values!
+	//moldyn->time=0.0;
+	//moldyn->total_steps=0;
 
 	/* debugging, ignore */
 	moldyn->debug=0;
@@ -2586,8 +2587,6 @@ int bond_analyze_process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,
 	if(moldyn->check_2b_bond(moldyn,itom,jtom,bc)==FALSE)
 		return 0;
 
-	d=sqrt(d);
-
 	/* now count this bonding ... */
 	ba=data;