From fe84cdc3fc897581636aff89b6f4fd12db1d2718 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Thu, 20 May 2010 16:54:35 +0200
Subject: [PATCH] introduced crt type 2 (initial diplacement vector for
 constraints) + write out crt save files

---
 mdrun.c  | 28 +++++++++++++++++++++++++---
 moldyn.c |  3 ---
 2 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/mdrun.c b/mdrun.c
index 3266dd3..bb1cd21 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -1286,6 +1286,7 @@ int crt(t_moldyn *moldyn,t_mdrun *mdrun) {
 			// done reading
 			acount+=1;
 		}
+		close(fd);
 		// allocate trafo angles
 		trafo_angle=malloc(acount*2*sizeof(double));
 		if(trafo_angle==NULL) {
@@ -1296,18 +1297,39 @@ int crt(t_moldyn *moldyn,t_mdrun *mdrun) {
 		crtt=crtp->type;
 	}
 
+	/* write a save file s-crt_xofy.save */
+	snprintf(line,128,"%s/s-crt_%03dof%03d.save",
+	         moldyn->vlsdir,crtp->count,crtp->steps);
+	fd=open(line,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
+	if(fd<0) perror("[mdrun] crt save fd open");
+	else {
+		write(fd,moldyn,sizeof(t_moldyn));
+		write(fd,moldyn->atom,
+		      moldyn->count*sizeof(t_atom));
+	}
+	close(fd);
+
+	/* output energy */
+	printf("  crt energy: %d - %f\n\n",
+	       crtp->count,(moldyn->ekin+moldyn->energy)/EV);
+
 	/* crt routines: calculate displacement + set individual constraints */
 
 	printf("  crt step %d of %d in total\n\n",crtp->count+1,crtp->steps);
 
+	if((crtp->type==1)|(crtp->count==0))
+		printf("  crt angle update\n\n");
+		
 	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));
+		if((crtp->type==1)|(crtp->count==0)) {
+			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);
diff --git a/moldyn.c b/moldyn.c
index a6f5c45..d715c52 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -83,9 +83,6 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 	pthread_mutex_init(&emutex,NULL);
 #endif
 
-	if(crtt)
-		printf("USING CRT\n");
-
 	return 0;
 }
 
-- 
2.39.2