X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=130725d48fc70c74fcaf47146e963ff578928b15;hb=98c1ca4feaacee4f319a6c288aa2b0cef65033e4;hp=31e5f0a162a9d0d296e4959037bc6a92b3545b52;hpb=beac6be36b6859ff09d1d5c426b762a9fb34c03d;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index 31e5f0a..130725d 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -129,6 +129,9 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_THERMAL_INIT:
 			psize=0;
 			break;
+		case STAGE_CONSTRAINT_RELAXATION_TECHNIQUE:
+			psize=sizeof(t_constraint_relaxation_technique);
+			break;
 		default:
 			printf("%s unknown stage type: %02x\n",ME,type);
 			return -1;
@@ -178,6 +181,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	t_set_timestep_params stsp;
 	t_fill_params fp;
 	t_del_atoms_params delp;
+	t_crt_params crtp;
 
 	/* open config file */
 	fd=open(mdrun->cfile,O_RDONLY);
@@ -212,6 +216,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		memset(&stsp,0,sizeof(t_set_timestep_params));
 		memset(&fp,0,sizeof(t_fill_params));
 		memset(&delp,0,sizeof(t_del_atoms_params));
+		memset(&crtp,0,sizeof(t_crt_params));
 
 		// get command + args
 		wcnt=0;
@@ -393,6 +398,14 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 					continue;
 
 				}
+				// offset
+				if(word[i][0]=='o') {
+					fp.o_params.o.x=atof(word[++i])*fp.lc;
+					fp.o_params.o.y=atof(word[++i])*fp.lc;
+					fp.o_params.o.z=atof(word[++i])*fp.lc;
+					fp.o_params.use=1;
+					continue;
+				}
 				i+=1;
 			}
 			add_stage(mdrun,STAGE_FILL,&fp);
@@ -414,6 +427,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 					case 'e':
 						cap.type|=CHAATTR_ELEMENT;
 						break;
+					case 'n':
+						cap.type|=CHAATTR_NUMBER;
 					default:
 						break;
 				}
@@ -432,6 +447,10 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				cap.element=atoi(word[i]);
 				i+=1;
 			}
+			if(cap.type&CHAATTR_NUMBER) {
+				cap.element=atoi(word[i]);
+				i+=1;
+			}
 			for(o=0;o<strlen(word[i]);o++) {
 				switch(word[i][o]) {
 					case 'b':
@@ -583,6 +602,12 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 						iap.y0=atof(word[9]);
 						iap.z0=atof(word[10]);
 						break;
+					case 'P':
+						iap.type=INS_RELPOS;
+						iap.x0=atof(word[8]);
+						iap.y0=atof(word[9]);
+						iap.z0=atof(word[10]);
+						break;
 					case 'r':
 						switch(word[8][0]) {
 
@@ -693,6 +718,12 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				stsp.tau=atof(word[2]);
 				add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
 			}
+			else if(!strncmp(word[1],"crt",3)) {
+				crtp.type=atoi(word[2]);
+				crtp.steps=atoi(word[3]);
+				strncpy(crtp.file,word[4],127);
+				add_stage(mdrun,STAGE_CRT,&crtp);
+			}
 			else {
 				printf("%s unknown stage type: %s\n",
 				       ME,word[1]);
@@ -888,6 +919,7 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 			cr_check=TRUE;
 			break;
 		case INS_POS:
+		case INS_RELPOS:
 			x0=iap->x0;
 			y0=iap->y0;
 			z0=iap->z0;
@@ -903,7 +935,7 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	while(cnt<iap->ins_atoms) {
 		run=1;
 		while(run) {
-			if(iap->type!=INS_POS) {
+			if((iap->type!=INS_POS)&&(iap->type!=INS_RELPOS)) {
 				r.x=rand_get_double(&(moldyn->random))*x;
 				r.y=rand_get_double(&(moldyn->random))*y;
 				r.z=rand_get_double(&(moldyn->random))*z;
@@ -913,9 +945,16 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 				r.y=0.0;
 				r.z=0.0;
 			}
-			r.x+=x0;
-			r.y+=y0;
-			r.z+=z0;
+			if(iap->type==INS_RELPOS) {
+				r.x+=x0*mdrun->lc;
+				r.y+=y0*mdrun->lc;
+				r.z+=z0*mdrun->lc;
+			}
+			else {
+				r.x+=x0;
+				r.y+=y0;
+				r.z+=z0;
+			}
 			// offset
 			if(iap->type!=INS_TOTAL) {
 				r.x+=o;
@@ -1094,6 +1133,10 @@ int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 			if(cap->element!=atom->element)
 				continue;
 		}
+		if(cap->type&CHAATTR_NUMBER) {
+			if(cap->element!=atom->tag)
+				continue;
+		}
 		if(cap->type&CHAATTR_REGION) {
 			if(cap->x0>atom->r.x)
 				continue;
@@ -1108,7 +1151,9 @@ int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 			if(cap->z1<atom->r.z)
 				continue;
 		}
-		printf("  changing attributes of atom %d (0x%x)\n",i,cap->attr);
+		if(!(cap->type&CHAATTR_TOTALV))
+			printf("  changing attributes of atom %d (0x%x)\n",
+			       i,cap->attr);
 		atom->attr=cap->attr;
 	}
 
@@ -1164,6 +1209,106 @@ int chsattr(t_moldyn *moldyn,t_mdrun *mdrun) {
 	return 0;
 }
 
+int crt(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+	t_stage *stage;
+	t_crt_params *crtp;
+
+	int fd;
+	char line[128];
+	char *wptr;
+	int acount;
+	int ret;
+	void *ptr;
+
+	extern u8 crt;
+	extern u8 *constraints;
+	extern double *trafo_angles;
+
+	t_atom *atom;
+	double dx,dy,dz;
+	
+	stage=mdrun->stage.current->data;
+	crtp=stage->params;
+
+	acount=0;
+
+	/* initial stuff */
+
+	if(crtp->count==0) {
+		printf("  crt init\n",acount);
+		// read final positions, constraints and do the alloc
+		fd=open(crtp->file,O_RDONLY);
+		if(fd<0) {
+			perror("[mdrun] FATAL reading constraints file");
+			return fd;
+		}
+		while(1) {
+			ret=get_line(fd,line,128);
+			// check for end of file
+			if(ret<=0) {
+				printf("  -> read %d atom positions\n",acount);
+				crtp->acnt=acount;
+				break;
+			}
+			// ignore # lines and \n
+			if((line[0]=='#')|(ret==1))
+				continue;
+			// allocate new memory
+			ptr=realloc(crtp->r_fin,(acount+1)*sizeof(t_3dvec));
+			if(ptr==NULL) {
+				perror("[mdrun] FATAL realloc crt positions");
+				return -1;
+			}
+			crtp->r_fin=ptr;
+			ptr=realloc(constraints,(acount+1)*3*sizeof(u8));
+			if(ptr==NULL) {
+				perror("[mdrun] FATAL realloc crt constraints");
+				return -1;
+			}
+			constraints=ptr;
+			// ignore type
+			wptr=strtok(line," \t");
+			// read x y z
+			wptr=strtok(NULL," \t");
+			crtp->r_fin.x=atof(wptr);
+			wptr=strtok(NULL," \t");
+			crtp->r_fin.y=atof(wptr);
+			wptr=strtok(NULL," \t");
+			crtp->r_fin.z=atof(wptr);
+			// read constraints
+			wptr=strtok(NULL," \t");
+			constraints[acount]=atoi(wptr);
+			wptr=strtok(NULL," \t");
+			constraints[acount+1]=atoi(wptr);
+			wptr=strtok(NULL," \t");
+			constraints[acount+2]=atoi(wptr);
+			// done reading
+			acount+=1;
+		}
+		// allocate trafo angles
+		trafo_angle=malloc(acount*2*sizeof(double));
+		if(trafo_angle==NULL) {
+			perror("[mdrun] FATAL alloc trafo angles");
+			return -1;
+		}
+		// set crt mode
+		crt=crtp->type;
+	}
+
+	/* crt routines: calculate displacement + set individual constraints */
+
+	for(i=0;i<moldyn->count;i++) {
+		atom=moldyn->atom;
+		dx=atom[i].r.x-crtp->r_fin[i].x;
+		dy=atom[i].r.y-crtp->r_fin[i].y;
+		dz=atom[i].r.z-crtp->r_fin[i].z;
+		// HIER WEITER
+	}
+
+	return 0;
+}
+
 #define stage_print(m)	if(!(stage->executed)) \
 				printf("%s",m)
 
@@ -1315,7 +1460,8 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 					               fp->lx,fp->ly,fp->lz,
 					               &o,
 					               &(fp->p_params),
-					               &(fp->d_params));
+					               &(fp->d_params),
+					               &(fp->o_params));
 					o.x+=0.25*fp->lc;
 					o.y=o.x;
 					o.z=o.x;
@@ -1326,7 +1472,8 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 					               fp->lx,fp->ly,fp->lz,
 					               &o,
 					               &(fp->p_params),
-					               &(fp->d_params));
+					               &(fp->d_params),
+					               &(fp->o_params));
 					break;
 
 					default:
@@ -1339,7 +1486,8 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 					               fp->lx,fp->ly,fp->lz,
 					               NULL,
 					               &(fp->p_params),
-					               &(fp->d_params));
+					               &(fp->d_params),
+					               &(fp->o_params));
 					break;
 				}
 				moldyn_bc_check(moldyn);
@@ -1350,6 +1498,17 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				thermal_init(moldyn,TRUE);
 				change_stage=TRUE;
 				break;
+			case STAGE_CRT:
+				stage_print("  -> constraint relaxation")
+				stage_print(" technique\n\n");
+				crtp=stage->params;
+				if(crtp->count==crtp->steps) {
+					change_stage=TRUE;
+					break;
+				}
+				crt(moldyn,mdrun);
+				crtp->count+=1;
+				break;
 			default:
 				printf("%s unknwon stage type\n",ME);
 				break;