From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Tue, 29 Apr 2008 11:44:49 +0000 (+0200)
Subject: safety checkin before mensa
X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=2dddad627c54f294c4c5b5d736178c3ef3288159;p=physik%2Fposic.git

safety checkin before mensa
---

diff --git a/config.default b/config.default
index e9181be..d63e401 100644
--- a/config.default
+++ b/config.default
@@ -4,8 +4,9 @@
 
 ## potential ##
 
-potential albe
+potential albe 14 6
 cutoff 2.96
+nnd 2.351
 
 ## integration algorithm ##
 
@@ -14,20 +15,20 @@ timestep 1.0
 
 ## simulation volume ##
 
-volume 
+volume 48.861 48.861 48.861
 pbc 1 1 1
 
 ## temperature / pressure ##
 
-temperature 450.0
+temperature -273.0
 pressure 0.0
 
 ## initial lattice ##
 
 lattice diamond
 #lattice zincblende
-element1 silicon
-#element2 carbon
+element1 14
+element2 6
 fill lc 9 9 9
 
 ## atom attributes ##
diff --git a/mdrun.c b/mdrun.c
index c4b6df2..63899a6 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -201,6 +201,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		}
 		else if(!strncmp(word[0],"cutoff",6))
 			mdrun->cutoff=atof(word[1]);
+		else if(!strncmp(word[0],"nnd",3))
+			mdrun->nnd=atof(word[1]);
 		else if(!strncmp(word[0],"intalgo",7)) {
 			if(!strncmp(word[1],"verlet",5))
 				mdrun->intalgo=MOLDYN_INTEGRATE_VERLET;
@@ -242,33 +244,11 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		}
 		else if(!strncmp(word[0],"element1",8)) {
 			mdrun->element1=atoi(word[1]);
-			switch(mdrun->element1) {
-				case SI:
-					mdrun->m1=M_SI;
-					break;
-				case C:
-					mdrun->m1=M_C;
-					break;
-				default:
-					printf("%s unknown element1: %s|%d\n",
-					       ME,word[1],mdrun->element1);
-					return -1;
-			}
+			mdrun->m1=pse_mass[mdrun->element1];
 		}
 		else if(!strncmp(word[0],"element2",8)) {
 			mdrun->element2=atoi(word[1]);
-			switch(mdrun->element2) {
-				case SI:
-					mdrun->m2=M_SI;
-					break;
-				case C:
-					mdrun->m2=M_C;
-					break;
-				default:
-					printf("%s unknown element2: %s|%d\n",
-					       ME,word[1],mdrun->element2);
-					return -1;
-			}
+			mdrun->m2=pse_mass[mdrun->element2];
 		}
 		else if(!strncmp(word[0],"fill",6)) {
 			// only lc mode by now
@@ -341,24 +321,31 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		else if(!strncmp(word[0],"sattr",5)) {
 			// for satrib line we need a special stage
 			// containing one schedule of 0 loops ...
+			csp.type=0;
 			for(i=1;i<wcnt;i++) {
 				if(!strncmp(word[i],"pctrl",5)) {
-					csp.ptau=atof(word[++i]);
+					csp.ptau=0.01/(atof(word[++i])*GPA);
+					csp.type|=CHSATTR_PCTRL;
 				}
 				if(!strncmp(word[i],"tctrl",5)) {
 					csp.ttau=atof(word[++i]);
+					csp.type|=CHSATTR_TCTRL;
 				}
 				if(!strncmp(word[i],"prelax",6)) {
 					csp.dp=atof(word[++i]);
+					csp.type|=CHSATTR_PRELAX;
 				}
 				if(!strncmp(word[i],"trelax",6)) {
 					csp.dt=atof(word[++i]);
+					csp.type|=CHSATTR_TRELAX;
 				}
 				if(!strncmp(word[i],"rsteps",6)) {
 					csp.rsteps=atoi(word[++i]);
+					csp.type|=CHSATTR_RSTEPS;
 				}
 				if(!strncmp(word[i],"avgrst",6)) {
 					csp.avgrst=atoi(word[++i]);
+					csp.type|=CHSATTR_AVGRST;
 				}
 			}
 			add_stage(mdrun,STAGE_CHSATTR,&csp);
@@ -654,6 +641,9 @@ int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 	return 0;
 }
 
+#define stage_print(m)	if(!(stage->executed)) \
+				printf("%s",m)
+
 int mdrun_hook(void *ptr1,void *ptr2) {
 
 	t_moldyn *moldyn;
@@ -684,15 +674,22 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 
 	/* default steps and tau values */
 	steps=mdrun->relax_steps;
+printf("-------> %d\n",mdrun->relax_steps);
 	tau=mdrun->timestep;
 
 	/* check whether relaxation steps are necessary */
 	if(!((check_pressure(moldyn,mdrun)==FALSE)|\
 	     (check_temperature(moldyn,mdrun)==FALSE))) {
+	
+		/* be verbose */
+		stage_print("\n###########################\n");
+		stage_print("# [mdrun] executing stage #\n");
+		stage_print("###########################\n\n");
 		
 		/* stage specific stuff */
 		switch(stage->type) {
 			case STAGE_INSERT_ATOMS:
+				stage_print("  -> insert atoms\n\n");
 				iap=stage->params;
 				if(iap->cnt_steps==iap->ins_steps) {
 					change_stage=TRUE;
@@ -702,6 +699,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				iap->cnt_steps+=1;
 					break;
 			case STAGE_CONTINUE:
+				stage_print("  -> continue\n\n");
 				if(stage->executed==TRUE) {
 					change_stage=TRUE;
 					break;
@@ -710,6 +708,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				steps=cp->runs;
 					break;
 			case STAGE_ANNEAL:
+				stage_print("  -> anneal\n\n");
 				ap=stage->params;
 				if(ap->count==ap->runs) {
 					change_stage=TRUE;
@@ -719,10 +718,12 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				ap->count+=1;
 				break;
 			case STAGE_CHAATTR:
+				stage_print("  -> chaattr\n\n");
 				chaatr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
 			case STAGE_CHSATTR:
+				stage_print("  -> chsattr\n\n");
 				chsattr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
@@ -789,6 +790,7 @@ int main(int argc,char **argv) {
 	if(set_int_alg(&moldyn,mdrun.intalgo)<0)
 		return -1;
 	set_cutoff(&moldyn,mdrun.cutoff);
+	set_nn_dist(&moldyn,mdrun.nnd);
 	if(set_potential(&moldyn,mdrun.potential)<0)
 		return -1;
 	switch(mdrun.potential) {
diff --git a/mdrun.h b/mdrun.h
index 20d68d7..83a8196 100644
--- a/mdrun.h
+++ b/mdrun.h
@@ -57,8 +57,9 @@ typedef struct s_mdrun {
 	double timestep;			// timestep
 
 	u8 potential;				// potential
-
 	double cutoff;				// cutoff radius
+	double nnd;				// next neighbour distance
+
 	t_3dvec dim;				// simulation volume
 	u8 pbcx;				// periodic boundary conditions
 	u8 pbcy;
diff --git a/moldyn.c b/moldyn.c
index 832d171..6fa9df2 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -1635,6 +1635,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	atom=moldyn->atom;
 
 	/* initialize linked cell method */
+printf(" hier soll es sein\n");
 	link_cell_init(moldyn,VERBOSE);
 
 	/* logging & visualization */
@@ -2415,6 +2416,8 @@ int process_2b_bonds(t_moldyn *moldyn,void *data,
 
 	lc=&(moldyn->lc);
 
+	/* only init link cell if it doesn't exist! */
+	HIER WEITER
 	link_cell_init(moldyn,VERBOSE);
 
 	itom=moldyn->atom;