X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=mdrun.c;h=b5abe87ed61b6a8a8e782e07f565e1c20e735a05;hb=55cd4d049604f2cf1d0fff095e6bcd13ec25780f;hp=31943efc65bd39680dc8dec02fec465ce39c7e90;hpb=67df6b3a722a44e36fd56f3f040c3c9726b3fc3f;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index 31943ef..b5abe87 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -111,6 +111,12 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_CHSATTR:
 			psize=sizeof(t_chsattr_params);
 			break;
+		case STAGE_SET_TEMP:
+			psize=sizeof(t_set_temp_params);
+			break;
+		case STAGE_SET_TIMESTEP:
+			psize=sizeof(t_set_timestep_params);
+			break;
 		default:
 			printf("%s unknown stage type: %02x\n",ME,type);
 			return -1;
@@ -155,6 +161,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	t_anneal_params ap;
 	t_chaattr_params cap;
 	t_chsattr_params csp;
+	t_set_temp_params stp;
+	t_set_timestep_params stsp;
 
 	/* open config file */
 	fd=open(mdrun->cfile,O_RDONLY);
@@ -184,6 +192,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		memset(&ap,0,sizeof(t_anneal_params));
 		memset(&cap,0,sizeof(t_chaattr_params));
 		memset(&csp,0,sizeof(t_chsattr_params));
+		memset(&stp,0,sizeof(t_set_temp_params));
+		memset(&stsp,0,sizeof(t_set_timestep_params));
 
 		// get command + args
 		wcnt=0;
@@ -459,7 +469,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				imp.amount2=atoi(word[5]);
 				imp.brand1=atoi(word[6]);
 				imp.brand2=atoi(word[7]);
-				imp.cr=atof(word[8]);
+				imp.crmin=atof(word[8]);
+				imp.crmax=atof(word[9]);
 				/* do this later ...
 				for(i=0;i<strlen(word[8]);i++) {
 					switch(word[8][i]) {
@@ -489,8 +500,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 					}
 				}
 				*/
-				imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
-				imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
+				imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
+				imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
 				add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
 			}
 
@@ -508,6 +519,21 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				ap.dt=atof(word[3]);
 				add_stage(mdrun,STAGE_ANNEAL,&ap);
 			}
+			else if(!strncmp(word[1],"set_temp",8)) {
+				if(word[2][0]=='c') {
+					stp.type=SET_TEMP_CURRENT;
+					stp.val=0.0;
+				}
+				else {
+					stp.type=SET_TEMP_VALUE;
+					stp.val=atof(word[2]);
+				}
+				add_stage(mdrun,STAGE_SET_TEMP,&stp);
+			}
+			else if(!strncmp(word[1],"set_timestep",12)) {
+				stsp.tau=atof(word[2]);
+				add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
+			}
 			else {
 				printf("%s unknown stage type: %s\n",
 				       ME,word[1]);
@@ -706,7 +732,7 @@ int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	t_insert_mixed_atoms_params *imp;
 	t_atom *atom;
 	double x,x0,y,y0,z,z0;
-	double dmin,d,c;
+	double dmin,d,cmin,cmax;
 	u8 retry;
 	t_3dvec r,v,dist;
 	int i;
@@ -726,7 +752,8 @@ int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	v.y=0.0;
 	v.z=0.0;
 
-	c=imp->cr*imp->cr;
+	cmin=imp->crmin*imp->crmin;
+	cmax=imp->crmax*imp->crmax;
 
 	while(imp->amount1|imp->amount2) {
 		if(imp->amount1) {
@@ -745,20 +772,22 @@ int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 					v3_sub(&dist,&(atom->r),&r);
 					check_per_bound(moldyn,&dist);
 					d=v3_absolute_square(&dist);
-					if(d<c) {
+					if(d<cmin) {
 						retry=1;
 						break;
 					}
 					if(d<dmin)
 						dmin=d;
-					
 				}
+				if(dmin!=1000.0)
+					if(dmin>cmax)
+						retry=1;
 			}
 			add_atom(moldyn,imp->element1,pse_mass[imp->element1],
                                  imp->brand1,imp->attr1,&r,&v);
 			printf("%s (mixed) atom inserted (%d): %f %f %f\n",
                                ME,imp->amount1,r.x,r.y,r.z);
-			printf("  -> d2 = %f/%f\n",dmin,c);
+			printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 			imp->amount1-=1;
 		}
 		if(imp->amount2) {
@@ -777,20 +806,22 @@ int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 					v3_sub(&dist,&(atom->r),&r);
 					check_per_bound(moldyn,&dist);
 					d=v3_absolute_square(&dist);
-					if(d<c) {
+					if(d<cmin) {
 						retry=1;
 						break;
 					}
 					if(d<dmin)
 						dmin=d;
-					
 				}
+				if(dmin!=1000.0)
+					if(dmin>cmax)
+						retry=1;
 			}
 			add_atom(moldyn,imp->element2,pse_mass[imp->element2],
                                  imp->brand2,imp->attr2,&r,&v);
 			printf("%s (mixed) atom inserted (%d): %f %f %f\n",
                                ME,imp->amount2,r.x,r.y,r.z);
-			printf("  -> d2 = %f/%f\n",dmin,c);
+			printf("  -> d2 = %f/%f/%f\n",dmin,cmin,cmax);
 			imp->amount2-=1;
 		}
 	}
@@ -891,13 +922,14 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	t_stage *stage;
 	t_list *sl;
 	int steps;
-	double tau;
 	u8 change_stage;
 
 	t_insert_atoms_params *iap;
 	t_insert_mixed_atoms_params *imp;
 	t_continue_params *cp;
 	t_anneal_params *ap;
+	t_set_temp_params *stp;
+	t_set_timestep_params *stsp;
 
 	moldyn=ptr1;
 	mdrun=ptr2;
@@ -913,9 +945,8 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	/* get stage description */
 	stage=sl->current->data;
 
-	/* default steps and tau values */
+	/* steps in next schedule */
 	steps=mdrun->relax_steps;
-	tau=mdrun->timestep;
 
 	/* check whether relaxation steps are necessary */
 	if((check_pressure(moldyn,mdrun)==TRUE)&\
@@ -950,6 +981,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				stage_print("  -> insert mixed atoms\n\n");
 				imp=stage->params;
 				insert_mixed_atoms(moldyn,mdrun);
+				change_stage=TRUE;
 				break;
 
 
@@ -976,15 +1008,32 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				ap->count+=1;
 				break;
 			case STAGE_CHAATTR:
-				stage_print("  -> chaattr\n\n");
+				stage_print("  -> change atom attributes\n\n");
 				chaatr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
 			case STAGE_CHSATTR:
-				stage_print("  -> chsattr\n\n");
+				stage_print("  -> change sys attributes\n\n");
 				chsattr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
+			case STAGE_SET_TEMP:
+				stage_print("  -> set temperature\n\n");
+				stp=stage->params;
+				if(stp->type&SET_TEMP_CURRENT) {
+					set_temperature(moldyn,moldyn->t_avg);
+				}
+				else {
+					set_temperature(moldyn,stp->val);
+				}
+				change_stage=TRUE;
+				break;
+			case STAGE_SET_TIMESTEP:
+				stage_print("  -> set timestep\n\n");
+				stsp=stage->params;
+				mdrun->timestep=stsp->tau;
+				change_stage=TRUE;
+				break;
 			default:
 				printf("%s unknwon stage type\n",ME);
 				break;
@@ -1001,7 +1050,6 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				return 0;
 			}
 			steps=0;
-			tau=mdrun->timestep;
 		}
 
 	}
@@ -1014,7 +1062,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	}
 
 	/* continue simulation */
-	moldyn_add_schedule(moldyn,steps,tau);
+	moldyn_add_schedule(moldyn,steps,mdrun->timestep);
 
 	return 0;
 }
@@ -1120,6 +1168,7 @@ int main(int argc,char **argv) {
 			               mdrun.ly,mdrun.lz,&o);
 			break;
 		case NONE:
+			set_nn_dist(&moldyn,mdrun.nnd);
 			break;
 		default:
 			printf("%s unknown lattice type: %02x\n",