From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Mon, 18 Aug 2008 15:02:44 +0000 (+0200)
Subject: insert mixed atoms feature added (will be renamed an cleand up later)
X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=67df6b3a722a44e36fd56f3f040c3c9726b3fc3f;p=physik%2Fposic.git

insert mixed atoms feature added (will be renamed an cleand up later)
still problematic!
---

diff --git a/mdrun.c b/mdrun.c
index 29d3160..31943ef 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -96,6 +96,9 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_INSERT_ATOMS:
 			psize=sizeof(t_insert_atoms_params);
 			break;
+		case STAGE_INSERT_MIXED_ATOMS:
+			psize=sizeof(t_insert_mixed_atoms_params);
+			break;
 		case STAGE_CONTINUE:
 			psize=sizeof(t_continue_params);
 			break;
@@ -147,6 +150,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 
 	t_displace_atom_params dap;
 	t_insert_atoms_params iap;
+	t_insert_mixed_atoms_params imp;
 	t_continue_params cp;
 	t_anneal_params ap;
 	t_chaattr_params cap;
@@ -175,6 +179,7 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 
 		// reset
 		memset(&iap,0,sizeof(t_insert_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));
 		memset(&cap,0,sizeof(t_chaattr_params));
@@ -247,6 +252,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				mdrun->lattice=FCC;
 			if(!strncmp(word[1],"diamond",7))
 				mdrun->lattice=DIAMOND;
+			if(!strncmp(word[1],"none",4))
+				mdrun->lattice=NONE;
 		}
 		else if(!strncmp(word[0],"element1",8)) {
 			mdrun->element1=atoi(word[1]);
@@ -441,6 +448,56 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				}
 				add_stage(mdrun,STAGE_INSERT_ATOMS,&iap);
 			}
+
+
+			// HERE WE GO ...
+
+			else if(!strncmp(word[1],"ins_m_atoms",11)) {
+				imp.element1=atoi(word[2]);
+				imp.element2=atoi(word[3]);
+				imp.amount1=atoi(word[4]);
+				imp.amount2=atoi(word[5]);
+				imp.brand1=atoi(word[6]);
+				imp.brand2=atoi(word[7]);
+				imp.cr=atof(word[8]);
+				/* do this later ...
+				for(i=0;i<strlen(word[8]);i++) {
+					switch(word[8][i]) {
+						case 'b':
+							imp.attr|=ATOM_ATTR_VB;
+							break;
+						case 'h':
+							imp.attr|=ATOM_ATTR_HB;
+							break;
+						case 'v':
+							imp.attr|=ATOM_ATTR_VA;
+							break;
+						case 'f':
+							imp.attr|=ATOM_ATTR_FP;
+							break;
+						case '1':
+							imp.attr|=ATOM_ATTR_1BP;
+							break;
+						case '2':
+							imp.attr|=ATOM_ATTR_2BP;
+							break;
+						case '3':
+							imp.attr|=ATOM_ATTR_3BP;
+							break;
+						default:
+							break;
+					}
+				}
+				*/
+				imp.attr1=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
+				imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
+				add_stage(mdrun,STAGE_INSERT_MIXED_ATOMS,&imp);
+			}
+
+
+
+
+
 			else if(!strncmp(word[1],"continue",8)) {
 				cp.runs=atoi(word[2]);
 				add_stage(mdrun,STAGE_CONTINUE,&cp);
@@ -643,6 +700,104 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	return 0;
 }
 
+int insert_mixed_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+	t_stage *stage;
+	t_insert_mixed_atoms_params *imp;
+	t_atom *atom;
+	double x,x0,y,y0,z,z0;
+	double dmin,d,c;
+	u8 retry;
+	t_3dvec r,v,dist;
+	int i;
+	
+
+	stage=mdrun->stage.current->data;
+	imp=stage->params;
+
+	x=moldyn->dim.x;
+	x0=-x/2.0;
+	y=moldyn->dim.y;
+	y0=-y/2.0;
+	z=moldyn->dim.z;
+	z0=-z/2.0;
+
+	v.x=0.0;
+	v.y=0.0;
+	v.z=0.0;
+
+	c=imp->cr*imp->cr;
+
+	while(imp->amount1|imp->amount2) {
+		if(imp->amount1) {
+			retry=1;
+			while(retry) {
+				retry=0;
+				r.x=rand_get_double(&(moldyn->random))*x;
+				r.y=rand_get_double(&(moldyn->random))*y;
+				r.z=rand_get_double(&(moldyn->random))*z;
+				r.x+=x0;
+				r.y+=y0;
+				r.z+=z0;
+				dmin=1000.0;	// for sure too high!
+				for(i=0;i<moldyn->count;i++) {
+					atom=&(moldyn->atom[i]);
+					v3_sub(&dist,&(atom->r),&r);
+					check_per_bound(moldyn,&dist);
+					d=v3_absolute_square(&dist);
+					if(d<c) {
+						retry=1;
+						break;
+					}
+					if(d<dmin)
+						dmin=d;
+					
+				}
+			}
+			add_atom(moldyn,imp->element1,pse_mass[imp->element1],
+                                 imp->brand1,imp->attr1,&r,&v);
+			printf("%s (mixed) atom inserted (%d): %f %f %f\n",
+                               ME,imp->amount1,r.x,r.y,r.z);
+			printf("  -> d2 = %f/%f\n",dmin,c);
+			imp->amount1-=1;
+		}
+		if(imp->amount2) {
+			retry=1;
+			while(retry) {
+				retry=0;
+				r.x=rand_get_double(&(moldyn->random))*x;
+				r.y=rand_get_double(&(moldyn->random))*y;
+				r.z=rand_get_double(&(moldyn->random))*z;
+				r.x+=x0;
+				r.y+=y0;
+				r.z+=z0;
+				dmin=1000.0;	// for sure too high!
+				for(i=0;i<moldyn->count;i++) {
+					atom=&(moldyn->atom[i]);
+					v3_sub(&dist,&(atom->r),&r);
+					check_per_bound(moldyn,&dist);
+					d=v3_absolute_square(&dist);
+					if(d<c) {
+						retry=1;
+						break;
+					}
+					if(d<dmin)
+						dmin=d;
+					
+				}
+			}
+			add_atom(moldyn,imp->element2,pse_mass[imp->element2],
+                                 imp->brand2,imp->attr2,&r,&v);
+			printf("%s (mixed) atom inserted (%d): %f %f %f\n",
+                               ME,imp->amount2,r.x,r.y,r.z);
+			printf("  -> d2 = %f/%f\n",dmin,c);
+			imp->amount2-=1;
+		}
+	}
+
+	return 0;
+}
+
 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 
 	t_stage *stage;
@@ -740,6 +895,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	u8 change_stage;
 
 	t_insert_atoms_params *iap;
+	t_insert_mixed_atoms_params *imp;
 	t_continue_params *cp;
 	t_anneal_params *ap;
 
@@ -787,6 +943,17 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				insert_atoms(moldyn,mdrun);
 				iap->cnt_steps+=1;
 				break;
+
+
+
+			case STAGE_INSERT_MIXED_ATOMS:
+				stage_print("  -> insert mixed atoms\n\n");
+				imp=stage->params;
+				insert_mixed_atoms(moldyn,mdrun);
+				break;
+
+
+
 			case STAGE_CONTINUE:
 				stage_print("  -> continue\n\n");
 				if(stage->executed==TRUE) {
@@ -952,6 +1119,8 @@ int main(int argc,char **argv) {
 			               mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
 			               mdrun.ly,mdrun.lz,&o);
 			break;
+		case NONE:
+			break;
 		default:
 			printf("%s unknown lattice type: %02x\n",
 			       ME,mdrun.lattice);
diff --git a/mdrun.h b/mdrun.h
index d065d57..b1c2e06 100644
--- a/mdrun.h
+++ b/mdrun.h
@@ -43,10 +43,11 @@ typedef struct s_stage {
 
 #define STAGE_DISPLACE_ATOM			0x00
 #define STAGE_INSERT_ATOMS			0x01
-#define STAGE_CONTINUE				0x02
-#define STAGE_ANNEAL				0x03
-#define STAGE_CHAATTR				0x04
-#define STAGE_CHSATTR				0x05
+#define STAGE_INSERT_MIXED_ATOMS		0x02
+#define STAGE_CONTINUE				0x03
+#define STAGE_ANNEAL				0x04
+#define STAGE_CHAATTR				0x05
+#define STAGE_CHSATTR				0x06
 
 typedef struct s_mdrun {
 	char cfile[128];			// config file
@@ -119,6 +120,18 @@ typedef struct s_insert_atoms_params {
 	u8 attr;
 } t_insert_atoms_params;
 
+typedef struct s_insert_mixed_atoms_params {
+	int element1;
+	int element2;
+	int amount1;
+	int amount2;
+	u8 brand1;
+	u8 brand2;
+	u8 attr1;
+	u8 attr2;
+	double cr;
+} t_insert_mixed_atoms_params;
+
 #define INS_TOTAL				0x01
 #define INS_REGION				0x02
 #define INS_POS					0x03
diff --git a/moldyn.c b/moldyn.c
index b79dea6..eb3c4b0 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -485,6 +485,10 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	count=moldyn->count;
 
 	/* how many atoms do we expect */
+	if(type==NONE) {
+		new*=1;
+		printf("[moldyn] WARNING: create 'none' lattice called");
+	}
 	if(type==CUBIC) new*=1;
 	if(type==FCC) new*=4;
 	if(type==DIAMOND) new*=8;
@@ -1574,9 +1578,11 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		printf("[moldyn] WARNING: cutoff > 0.5 x dim.y\n");
 	if(moldyn->cutoff>0.5*moldyn->dim.z)
 		printf("[moldyn] WARNING: cutoff > 0.5 x dim.z\n");
-	ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
-	if(ds>0.05*moldyn->nnd)
+	if(moldyn->count) {
+		ds=0.5*atom[0].f.x*moldyn->tau_square/atom[0].mass;
+		if(ds>0.05*moldyn->nnd)
 		printf("[moldyn] WARNING: forces too high / tau too small!\n");
+	}
 
 	/* zero absolute time */
 	// should have right values!
diff --git a/moldyn.h b/moldyn.h
index ca40103..11fdf6b 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -352,6 +352,7 @@ typedef struct s_vb {
 #define FCC			0x02
 #define DIAMOND			0x04
 #define ZINCBLENDE		0x08
+#define NONE			0x80
 
 /*
  * more includes