X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=3266dd3804a0ac0668049988c30ecfac554a8fca;hb=ff44bcba9df0d021568abcb553d1d490c442f696;hp=29e5e487fcf9058048e30e522a5159ce1a20a993;hpb=e6ca71aa985ab3c6885784e0cd1b8141672902fb;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index 29e5e48..3266dd3 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_CRT:
+			psize=sizeof(t_crt_params);
+			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;
@@ -713,6 +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]);
@@ -1198,6 +1209,114 @@ 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;
+
+	t_atom *atom;
+	t_3dvec disp;
+	double frac;
+	int i;
+	
+	stage=mdrun->stage.current->data;
+	crtp=stage->params;
+
+	acount=0;
+
+	/* initial stuff */
+
+	if(crtp->count==0) {
+		printf("  crt init\n");
+		// 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);
+				if(acount!=moldyn->count)
+					printf("  atom count mismatch!!!\n");
+				printf("\n");
+				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[acount].x=atof(wptr);
+			wptr=strtok(NULL," \t");
+			crtp->r_fin[acount].y=atof(wptr);
+			wptr=strtok(NULL," \t");
+			crtp->r_fin[acount].z=atof(wptr);
+			// read constraints
+			wptr=strtok(NULL," \t");
+			constraints[3*acount]=atoi(wptr);
+			wptr=strtok(NULL," \t");
+			constraints[3*acount+1]=atoi(wptr);
+			wptr=strtok(NULL," \t");
+			constraints[3*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
+		crtt=crtp->type;
+	}
+
+	/* crt routines: calculate displacement + set individual constraints */
+
+	printf("  crt step %d of %d in total\n\n",crtp->count+1,crtp->steps);
+
+	for(i=0;i<moldyn->count;i++) {
+		// calc displacements
+		atom=moldyn->atom;
+		v3_sub(&disp,&(crtp->r_fin[i]),&(atom[i].r));
+		// angles
+		trafo_angle[2*i]=atan2(disp.x,disp.y);
+		trafo_angle[2*i+1]=-atan2(disp.z,
+		                          sqrt(disp.x*disp.x+disp.y*disp.y));
+		// move atoms
+		frac=1.0/(crtp->steps-crtp->count);
+		v3_scale(&disp,&disp,frac);
+		v3_add(&(atom[i].r),&(atom[i].r),&disp);
+	}
+
+	return 0;
+}
+
 #define stage_print(m)	if(!(stage->executed)) \
 				printf("%s",m)
 
@@ -1218,6 +1337,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	t_set_temp_params *stp;
 	t_set_timestep_params *stsp;
 	t_fill_params *fp;
+	t_crt_params *crtp;
 
 	moldyn=ptr1;
 	mdrun=ptr2;
@@ -1387,6 +1507,20 @@ 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) {
+					free(constraints);
+					free(trafo_angle);
+					free(crtp->r_fin);
+					change_stage=TRUE;
+					break;
+				}
+				crt(moldyn,mdrun);
+				crtp->count+=1;
+				break;
 			default:
 				printf("%s unknwon stage type\n",ME);
 				break;
@@ -1430,6 +1564,11 @@ int main(int argc,char **argv) {
 	memset(&mdrun,0,sizeof(t_mdrun));
 	memset(&moldyn,0,sizeof(t_moldyn));
 
+	/* init crt variables */
+	crtt=0;
+	constraints=NULL;
+	trafo_angle=NULL;
+
 	/* parse arguments */
 	if(mdrun_parse_argv(&mdrun,argc,argv)<0)
 		return -1;