X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=mdrun.c;h=8c5cf71c974f8816c58ee97805a9189d69ea7daa;hb=0d1dfb1e5027d215fced8ca306dd658f692a2a44;hp=c4b6df2a09badbeb2107df086f930ad444bde24c;hpb=3592f3b0cf641729566674a7cdfd8eff3f61f59a;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index c4b6df2..8c5cf71 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -140,7 +140,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	char *wptr;
 	char word[16][32];
 	int wcnt;
-	int i;
+	int i,o;
 
 	t_insert_atoms_params iap;
 	t_continue_params cp;
@@ -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;
@@ -242,39 +244,18 @@ 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
 			mdrun->lx=atoi(word[2]);
 			mdrun->ly=atoi(word[3]);
 			mdrun->lz=atoi(word[4]);
+			mdrun->lc=atof(word[5]);
 		}
 		else if(!strncmp(word[0],"aattr",5)) {
 			// for aatrib line we need a special stage
@@ -294,7 +275,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 						break;
 				}
 			}
-			i=1;
+			i=2;
 			if(cap.type&CHAATTR_REGION) {
 				cap.x0=atof(word[1]);	
 				cap.y0=atof(word[2]);	
@@ -308,9 +289,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				cap.element=atoi(word[i]);
 				i+=1;
 			}
-			wptr=word[i];
-			for(i=0;i<strlen(wptr);i++) {
-				switch(word[2][i]) {
+			for(o=0;o<strlen(word[i]);o++) {
+				switch(word[i][o]) {
 					case 'b':
 						cap.attr|=ATOM_ATTR_VB;
 						break;
@@ -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;
@@ -689,10 +679,16 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	/* 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 +698,7 @@ 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 +707,7 @@ 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 +717,12 @@ 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;
@@ -766,8 +766,9 @@ int main(int argc,char **argv) {
 	t_moldyn moldyn;
 	t_3dvec o;
 
-	/* clear mdrun struct */
+	/* clear structs */
 	memset(&mdrun,0,sizeof(t_mdrun));
+	memset(&moldyn,0,sizeof(t_moldyn));
 
 	/* parse arguments */
 	if(mdrun_parse_argv(&mdrun,argc,argv)<0)
@@ -818,22 +819,22 @@ int main(int argc,char **argv) {
 	switch(mdrun.lattice) {
 		case FCC:
 			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
-			               mdrun.m1,0,0,mdrun.lx,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 			               mdrun.ly,mdrun.lz,NULL);
 			break;
 		case DIAMOND:
 			create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
-			               mdrun.m1,0,0,mdrun.lx,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 			               mdrun.ly,mdrun.lz,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.m1,0,0,mdrun.lx,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
 			               mdrun.ly,mdrun.lz,&o);
 			o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
 			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
-			               mdrun.m2,0,1,mdrun.lx,
+			               mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
 			               mdrun.ly,mdrun.lz,&o);
 			break;
 		default: