From 03dbca0a50d2f2e929c1feac3b145abf5575490b Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Thu, 28 May 2009 21:11:10 +0200
Subject: [PATCH] added modify atom function (velocity only by now!)

---
 mdrun.c | 76 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
 mdrun.h |  8 ++++++
 2 files changed, 83 insertions(+), 1 deletion(-)

diff --git a/mdrun.c b/mdrun.c
index f402e40..f0edd0b 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -96,6 +96,9 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_DEL_ATOMS:
 			psize=sizeof(t_del_atoms_params);
 			break;
+		case STAGE_MODIFY_ATOMS:
+			psize=sizeof(t_modify_atoms_params);
+			break;
 		case STAGE_INSERT_ATOMS:
 			psize=sizeof(t_insert_atoms_params);
 			break;
@@ -164,6 +167,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 	int i,o;
 
 	t_displace_atom_params dap;
+	t_modify_atoms_params map;
 	t_insert_atoms_params iap;
 	t_insert_mixed_atoms_params imp;
 	t_continue_params cp;
@@ -198,6 +202,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 
 		// reset
 		memset(&iap,0,sizeof(t_insert_atoms_params));
+		memset(&map,0,sizeof(t_modify_atoms_params));
 		memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
 		memset(&cp,0,sizeof(t_continue_params));
 		memset(&ap,0,sizeof(t_anneal_params));
@@ -522,6 +527,22 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				delp.r=atof(word[5]);
 				add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
 			}
+			else if(!strncmp(word[1],"mod_atoms",8)) {
+				i=2;
+				while(i<wcnt) {
+					if(!strncmp(word[i],"t",1)) {
+						map.tag=atoi(word[++i]);
+						i+=1;
+					}
+					if(!strncmp(word[i],"ekin",5)) {
+						map.ekin.x=atof(word[++i])*EV;
+						map.ekin.y=atof(word[++i])*EV;
+						map.ekin.z=atof(word[++i])*EV;
+						i+=1;
+					}
+				}
+				add_stage(mdrun,STAGE_MODIFY_ATOMS,&map);
+			}
 			else if(!strncmp(word[1],"ins_atoms",9)) {
 				iap.ins_steps=atoi(word[2]);
 				iap.ins_atoms=atoi(word[3]);
@@ -767,7 +788,39 @@ int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	}
 
 	return 0;
+}
+
+int modify_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+	t_modify_atoms_params *map;
+	t_stage *stage;
+	t_atom *atom;
+	t_3dvec v;
+	int i;
+
+	atom=moldyn->atom;
+	stage=mdrun->stage.current->data;
+	map=stage->params;
+	v.x=0.0; v.y=0.0; v.z=0.0;
+
+	for(i=0;i<moldyn->count;i++) {
+		if(atom[i].tag==map->tag) {
+			v.x=sqrt(2.0*fabs(map->ekin.x)/atom[i].mass);
+			if(map->ekin.x<0.0)
+				v.x=-v.x;
+			v.y=sqrt(2.0*fabs(map->ekin.y)/atom[i].mass);
+			if(map->ekin.y<0.0)
+				v.y=-v.y;
+			v.z=sqrt(2.0*fabs(map->ekin.z)/atom[i].mass);
+			if(map->ekin.z<0.0)
+				v.z=-v.z;
+			v3_copy(&(atom[i].v),&v);
+			printf("%s atom modified: v = (%f %f %f)\n",
+                               ME,v.x,v.y,v.z);
+		}
+	}	
 
+	return 0;
 }
 
 int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
@@ -899,7 +952,23 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 		printf("%s atom inserted (%d/%d): %f %f %f\n",
 		       ME,(iap->cnt_steps+1)*iap->ins_atoms,
 		       iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
-		printf("  -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
+		printf("  attributes: ");
+		if(iap->attr&ATOM_ATTR_VB)
+			printf("b ");
+		if(iap->attr&ATOM_ATTR_HB)
+			printf("h ");
+		if(iap->attr&ATOM_ATTR_VA)
+			printf("v ");
+		if(iap->attr&ATOM_ATTR_FP)
+			printf("f ");
+		if(iap->attr&ATOM_ATTR_1BP)
+			printf("1 ");
+		if(iap->attr&ATOM_ATTR_2BP)
+			printf("2 ");
+		if(iap->attr&ATOM_ATTR_3BP)
+			printf("3 ");
+		printf("\n");
+		printf("  d2 = %f/%f\n",dmin,iap->cr*iap->cr);
 		cnt+=1;
 	}
 
@@ -1151,6 +1220,11 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				del_atoms(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
+			case STAGE_MODIFY_ATOMS:
+				stage_print(" -> modify atoms\n\n");
+				modify_atoms(moldyn,mdrun);
+				change_stage=TRUE;
+				break;
 			case STAGE_INSERT_ATOMS:
 				stage_print("  -> insert atoms\n\n");
 				iap=stage->params;
diff --git a/mdrun.h b/mdrun.h
index be09d5a..102d00e 100644
--- a/mdrun.h
+++ b/mdrun.h
@@ -53,6 +53,7 @@ typedef struct s_stage {
 #define STAGE_FILL				0x09
 #define STAGE_THERMAL_INIT			0x10
 #define STAGE_DEL_ATOMS				0x11
+#define STAGE_MODIFY_ATOMS			0x12
 
 typedef struct s_mdrun {
 	char cfile[128];			// config file
@@ -114,6 +115,12 @@ typedef struct s_del_atoms_params {
 	t_3dvec o;
 } t_del_atoms_params;
 
+typedef struct s_modify_aoms_params {
+	u8 type;
+	int tag;
+	t_3dvec ekin;
+} t_modify_atoms_params;
+
 typedef struct s_insert_atoms_params {
 	u8 type;
 	double x0,y0,z0,x1,y1,z1;
@@ -206,6 +213,7 @@ typedef struct s_fill_params {
 	u8 fill_brand;
 	t_part_params p_params;
 	t_defect_params d_params;
+	t_offset_params o_params;
 } t_fill_params;
 
 /*
-- 
2.20.1