From bc17c58e6e7c5adde9e7cf89efd6dfe37147446d Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Tue, 18 May 2010 17:46:18 +0200
Subject: [PATCH] started with crt ...

---
 mdrun.c  | 122 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 mdrun.h  |  10 +++++
 moldyn.c |   7 ++++
 3 files changed, 139 insertions(+)

diff --git a/mdrun.c b/mdrun.c
index 29e5e48..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;
@@ -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 +1209,106 @@ 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)
 
@@ -1387,6 +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;
diff --git a/mdrun.h b/mdrun.h
index 0a5ceab..102c3d2 100644
--- a/mdrun.h
+++ b/mdrun.h
@@ -54,6 +54,7 @@ typedef struct s_stage {
 #define STAGE_THERMAL_INIT			0x10
 #define STAGE_DEL_ATOMS				0x11
 #define STAGE_MODIFY_ATOMS			0x12
+#define STAGE_CRT				0x13
 
 typedef struct s_mdrun {
 	char cfile[128];			// config file
@@ -218,6 +219,15 @@ typedef struct s_fill_params {
 	t_offset_params o_params;
 } t_fill_params;
 
+typedef struct s_crt_params {
+	u8 type;
+	char file[128];
+	t_3dvec *r_fin;
+	u8 *constraints;
+	int steps;
+	int count;
+} t_crt_params;
+
 /*
  * function prototypes
  */
diff --git a/moldyn.c b/moldyn.c
index bd29afc..ccc0b56 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -55,6 +55,13 @@ pthread_mutex_t *amutex;
 pthread_mutex_t emutex;
 #endif
 
+#ifdef CRT
+/* fully constrained relaxation technique - global pointers */
+u8 crt;
+u8 *constraints;
+double *trafo_angle;
+#endif
+
 /*
  * the moldyn functions
  */
-- 
2.20.1