X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=mdrun.c;h=17ce2776544d765276f48a68eae4ffc11328f2f9;hb=302ab3d5071520fcfd17be54c13dc44bb1f39ab7;hp=d99bd7a169f4637afd0266dfbba3f2fc36a3f3c7;hpb=d1c8623aedde670da01eb2e85cf36d0b2a7c340f;p=physik%2Fposic.git

diff --git a/mdrun.c b/mdrun.c
index d99bd7a..17ce277 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -17,6 +17,11 @@
 #include "potentials/tersoff.h"
 #endif
 
+/* pse */
+#define PSE_MASS
+#include "pse.h"
+#undef PSE_MASS
+
 #define ME	"[mdrun]"
 
 /*
@@ -96,6 +101,9 @@ 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;
@@ -108,6 +116,12 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_CHSATTR:
 			psize=sizeof(t_chsattr_params);
 			break;
+		case STAGE_SET_TEMP:
+			psize=sizeof(t_set_temp_params);
+			break;
+		case STAGE_SET_TIMESTEP:
+			psize=sizeof(t_set_timestep_params);
+			break;
 		default:
 			printf("%s unknown stage type: %02x\n",ME,type);
 			return -1;
@@ -147,10 +161,13 @@ 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;
 	t_chsattr_params csp;
+	t_set_temp_params stp;
+	t_set_timestep_params stsp;
 
 	/* open config file */
 	fd=open(mdrun->cfile,O_RDONLY);
@@ -175,10 +192,13 @@ 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));
 		memset(&csp,0,sizeof(t_chsattr_params));
+		memset(&stp,0,sizeof(t_set_temp_params));
+		memset(&stsp,0,sizeof(t_set_timestep_params));
 
 		// get command + args
 		wcnt=0;
@@ -247,6 +267,8 @@ 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]);
@@ -262,6 +284,14 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 			mdrun->ly=atoi(word[3]);
 			mdrun->lz=atoi(word[4]);
 			mdrun->lc=atof(word[5]);
+			if(wcnt==8) {
+				mdrun->fill_element=atoi(word[6]);
+				mdrun->fill_brand=atoi(word[7]);
+			}
+			else {
+				mdrun->fill_element=mdrun->element1;
+				mdrun->fill_brand=0;
+			}
 		}
 		else if(!strncmp(word[0],"aattr",5)) {
 			// for aatrib line we need a special stage
@@ -441,6 +471,57 @@ 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.crmin=atof(word[8]);
+				imp.crmax=atof(word[9]);
+				/* 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|ATOM_ATTR_FP;
+				imp.attr2=ATOM_ATTR_HB|ATOM_ATTR_VA|ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_FP;
+				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);
@@ -449,8 +530,24 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				ap.count=0;
 				ap.runs=atoi(word[2]);
 				ap.dt=atof(word[3]);
+				ap.interval=atoi(word[4]);
 				add_stage(mdrun,STAGE_ANNEAL,&ap);
 			}
+			else if(!strncmp(word[1],"set_temp",8)) {
+				if(word[2][0]=='c') {
+					stp.type=SET_TEMP_CURRENT;
+					stp.val=0.0;
+				}
+				else {
+					stp.type=SET_TEMP_VALUE;
+					stp.val=atof(word[2]);
+				}
+				add_stage(mdrun,STAGE_SET_TEMP,&stp);
+			}
+			else if(!strncmp(word[1],"set_timestep",12)) {
+				stsp.tau=atof(word[2]);
+				add_stage(mdrun,STAGE_SET_TIMESTEP,&stsp);
+			}
 			else {
 				printf("%s unknown stage type: %s\n",
 				       ME,word[1]);
@@ -643,6 +740,109 @@ 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,cmin,cmax;
+	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;
+
+	cmin=imp->crmin*imp->crmin;
+	cmax=imp->crmax*imp->crmax;
+
+	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<cmin) {
+						retry=1;
+						break;
+					}
+					if(d<dmin)
+						dmin=d;
+				}
+				if(dmin!=1000.0)
+					if(dmin>cmax)
+						retry=1;
+			}
+			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/%f\n",dmin,cmin,cmax);
+			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<cmin) {
+						retry=1;
+						break;
+					}
+					if(d<dmin)
+						dmin=d;
+				}
+				if(dmin!=1000.0)
+					if(dmin>cmax)
+						retry=1;
+			}
+			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/%f\n",dmin,cmin,cmax);
+			imp->amount2-=1;
+		}
+	}
+
+	return 0;
+}
+
 int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 
 	t_stage *stage;
@@ -736,12 +936,14 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	t_stage *stage;
 	t_list *sl;
 	int steps;
-	double tau;
 	u8 change_stage;
 
 	t_insert_atoms_params *iap;
+	t_insert_mixed_atoms_params *imp;
 	t_continue_params *cp;
 	t_anneal_params *ap;
+	t_set_temp_params *stp;
+	t_set_timestep_params *stsp;
 
 	moldyn=ptr1;
 	mdrun=ptr2;
@@ -757,9 +959,8 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	/* get stage description */
 	stage=sl->current->data;
 
-	/* default steps and tau values */
+	/* steps in next schedule */
 	steps=mdrun->relax_steps;
-	tau=mdrun->timestep;
 
 	/* check whether relaxation steps are necessary */
 	if((check_pressure(moldyn,mdrun)==TRUE)&\
@@ -787,6 +988,18 @@ 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);
+				change_stage=TRUE;
+				break;
+
+
+
 			case STAGE_CONTINUE:
 				stage_print("  -> continue\n\n");
 				if(stage->executed==TRUE) {
@@ -807,17 +1020,35 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 					set_temperature(moldyn,
 					                moldyn->t_ref+ap->dt);
 				ap->count+=1;
+				steps=ap->interval;
 				break;
 			case STAGE_CHAATTR:
-				stage_print("  -> chaattr\n\n");
+				stage_print("  -> change atom attributes\n\n");
 				chaatr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
 			case STAGE_CHSATTR:
-				stage_print("  -> chsattr\n\n");
+				stage_print("  -> change sys attributes\n\n");
 				chsattr(moldyn,mdrun);
 				change_stage=TRUE;
 				break;
+			case STAGE_SET_TEMP:
+				stage_print("  -> set temperature\n\n");
+				stp=stage->params;
+				if(stp->type&SET_TEMP_CURRENT) {
+					set_temperature(moldyn,moldyn->t_avg);
+				}
+				else {
+					set_temperature(moldyn,stp->val);
+				}
+				change_stage=TRUE;
+				break;
+			case STAGE_SET_TIMESTEP:
+				stage_print("  -> set timestep\n\n");
+				stsp=stage->params;
+				mdrun->timestep=stsp->tau;
+				change_stage=TRUE;
+				break;
 			default:
 				printf("%s unknwon stage type\n",ME);
 				break;
@@ -834,7 +1065,6 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 				return 0;
 			}
 			steps=0;
-			tau=mdrun->timestep;
 		}
 
 	}
@@ -847,7 +1077,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	}
 
 	/* continue simulation */
-	moldyn_add_schedule(moldyn,steps,tau);
+	moldyn_add_schedule(moldyn,steps,mdrun->timestep);
 
 	return 0;
 }
@@ -879,10 +1109,18 @@ int main(int argc,char **argv) {
 
 	/* prepare simulation */
 
-	moldyn_init(&moldyn,argc,argv);
-
-	if(mdrun.continue_file)
+	if(mdrun.continue_file[0]) {
+		// read the save file
 		moldyn_read_save_file(&moldyn,mdrun.continue_file);
+		// manualaadjusting some stuff
+		moldyn.argc=argc;
+		moldyn.args=argv;
+		rand_init(&(moldyn.random),NULL,1);
+		moldyn.random.status|=RAND_STAT_VERBOSE;
+	}
+	else {
+		moldyn_init(&moldyn,argc,argv);
+	}
 	
 	if(set_int_alg(&moldyn,mdrun.intalgo)<0)
 		return -1;
@@ -915,7 +1153,7 @@ int main(int argc,char **argv) {
 	}
 
 	/* if it is a continue run, reset schedule and skip lattice init */
-	if(mdrun.continue_file) {
+	if(mdrun.continue_file[0]) {
 		memset(&(moldyn.schedule),0,sizeof(t_moldyn_schedule));
 		goto addsched;
 	}
@@ -925,13 +1163,16 @@ int main(int argc,char **argv) {
 	set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
 	switch(mdrun.lattice) {
 		case FCC:
-			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
-			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
+			create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,
+                                       mdrun.fill_brand,mdrun.lx,
 			               mdrun.ly,mdrun.lz,NULL);
 			break;
 		case DIAMOND:
-			create_lattice(&moldyn,DIAMOND,mdrun.lc,mdrun.element1,
-			               mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
+			create_lattice(&moldyn,DIAMOND,mdrun.lc,
+                                       mdrun.fill_element,
+			               mdrun.m1,DEFAULT_ATOM_ATTR,
+                                       mdrun.fill_brand,mdrun.lx,
 			               mdrun.ly,mdrun.lz,NULL);
 			break;
 		case ZINCBLENDE:
@@ -944,6 +1185,9 @@ int main(int argc,char **argv) {
 			               mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
 			               mdrun.ly,mdrun.lz,&o);
 			break;
+		case NONE:
+			set_nn_dist(&moldyn,mdrun.nnd);
+			break;
 		default:
 			printf("%s unknown lattice type: %02x\n",
 			       ME,mdrun.lattice);