X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=mdrun.c;h=26fbc871708c262a19eead0b398d8773a2941902;hp=062224b99f65ff80a9b5f97c338ed184e9524538;hb=HEAD;hpb=f0e4c6422ec1aff0cf86597fef919335bba75c1b

diff --git a/mdrun.c b/mdrun.c
index 062224b..26fbc87 100644
--- a/mdrun.c
+++ b/mdrun.c
@@ -11,6 +11,7 @@
 #include "potentials/harmonic_oscillator.h"
 #include "potentials/lennard_jones.h"
 #include "potentials/albe.h"
+#include "potentials/albe_orig.h"
 #ifdef TERSOFF_ORIG
 #include "potentials/tersoff_orig.h"
 #else
@@ -129,6 +130,9 @@ int add_stage(t_mdrun *mdrun,u8 type,void *params) {
 		case STAGE_THERMAL_INIT:
 			psize=0;
 			break;
+		case STAGE_CRT:
+			psize=sizeof(t_crt_params);
+			break;
 		default:
 			printf("%s unknown stage type: %02x\n",ME,type);
 			return -1;
@@ -178,6 +182,7 @@ 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 +217,7 @@ 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;
@@ -229,6 +235,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 		if(!strncmp(word[0],"potential",9)) {
 			if(!strncmp(word[1],"albe",4))
 				mdrun->potential=MOLDYN_POTENTIAL_AM;
+			if(!strncmp(word[1],"albe_o",6))
+				mdrun->potential=MOLDYN_POTENTIAL_AO;
 			if(!strncmp(word[1],"tersoff",7))
 				mdrun->potential=MOLDYN_POTENTIAL_TM;
 			if(!strncmp(word[1],"ho",2))
@@ -422,6 +430,8 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 					case 'e':
 						cap.type|=CHAATTR_ELEMENT;
 						break;
+					case 'n':
+						cap.type|=CHAATTR_NUMBER;
 					default:
 						break;
 				}
@@ -440,6 +450,10 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 				cap.element=atoi(word[i]);
 				i+=1;
 			}
+			if(cap.type&CHAATTR_NUMBER) {
+				cap.element=atoi(word[i]);
+				i+=1;
+			}
 			for(o=0;o<strlen(word[i]);o++) {
 				switch(word[i][o]) {
 					case 'b':
@@ -591,6 +605,12 @@ int mdrun_parse_config(t_mdrun *mdrun) {
 						iap.y0=atof(word[9]);
 						iap.z0=atof(word[10]);
 						break;
+					case 'P':
+						iap.type=INS_RELPOS;
+						iap.x0=atof(word[8]);
+						iap.y0=atof(word[9]);
+						iap.z0=atof(word[10]);
+						break;
 					case 'r':
 						switch(word[8][0]) {
 
@@ -701,6 +721,12 @@ 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]);
@@ -780,18 +806,35 @@ int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	t_del_atoms_params *delp;
 	int i;
 	t_3dvec dist;
-	
+	u8 outer;
+
+	outer=0;	
 	stage=mdrun->stage.current->data;
 	delp=stage->params;
 
+	if(delp->r<0)
+		outer=1;
+
 	for(i=0;i<moldyn->count;i++) {
 		v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
 //printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
 		if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
-			del_atom(moldyn,moldyn->atom[i].tag);
-			printf("%s atom deleted: %d %d %d\n",ME,
-                               moldyn->atom[i].tag,moldyn->atom[i].element,
-			       moldyn->atom[i].brand);
+			if(!outer) {
+				del_atom(moldyn,moldyn->atom[i].tag);
+				printf("%s atom deleted: %d %d %d\n",ME,
+		                       moldyn->atom[i].tag,
+				       moldyn->atom[i].element,
+			 	       moldyn->atom[i].brand);
+			}
+		}
+		else {
+			if(outer) {
+				del_atom(moldyn,moldyn->atom[i].tag);
+				printf("%s atom deleted: %d %d %d\n",ME,
+             	  	               moldyn->atom[i].tag,
+				       moldyn->atom[i].element,
+				       moldyn->atom[i].brand);
+			}
 		}
 	}
 
@@ -896,6 +939,7 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 			cr_check=TRUE;
 			break;
 		case INS_POS:
+		case INS_RELPOS:
 			x0=iap->x0;
 			y0=iap->y0;
 			z0=iap->z0;
@@ -911,7 +955,7 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 	while(cnt<iap->ins_atoms) {
 		run=1;
 		while(run) {
-			if(iap->type!=INS_POS) {
+			if((iap->type!=INS_POS)&&(iap->type!=INS_RELPOS)) {
 				r.x=rand_get_double(&(moldyn->random))*x;
 				r.y=rand_get_double(&(moldyn->random))*y;
 				r.z=rand_get_double(&(moldyn->random))*z;
@@ -921,9 +965,16 @@ int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
 				r.y=0.0;
 				r.z=0.0;
 			}
-			r.x+=x0;
-			r.y+=y0;
-			r.z+=z0;
+			if(iap->type==INS_RELPOS) {
+				r.x+=x0*mdrun->lc;
+				r.y+=y0*mdrun->lc;
+				r.z+=z0*mdrun->lc;
+			}
+			else {
+				r.x+=x0;
+				r.y+=y0;
+				r.z+=z0;
+			}
 			// offset
 			if(iap->type!=INS_TOTAL) {
 				r.x+=o;
@@ -1102,6 +1153,10 @@ int chaatr(t_moldyn *moldyn,t_mdrun *mdrun) {
 			if(cap->element!=atom->element)
 				continue;
 		}
+		if(cap->type&CHAATTR_NUMBER) {
+			if(cap->element!=atom->tag)
+				continue;
+		}
 		if(cap->type&CHAATTR_REGION) {
 			if(cap->x0>atom->r.x)
 				continue;
@@ -1174,6 +1229,138 @@ 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;
+
+	t_atom *atom;
+	t_3dvec disp;
+	double frac;
+	int i;
+	
+	stage=mdrun->stage.current->data;
+	crtp=stage->params;
+
+	acount=0;
+
+	/* initial stuff */
+
+	if(crtp->count==0) {
+		printf("  crt init\n");
+		// 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);
+				if(acount!=moldyn->count)
+					printf("  atom count mismatch!!!\n");
+				printf("\n");
+				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[acount].x=atof(wptr);
+			wptr=strtok(NULL," \t");
+			crtp->r_fin[acount].y=atof(wptr);
+			wptr=strtok(NULL," \t");
+			crtp->r_fin[acount].z=atof(wptr);
+			// read constraints
+			wptr=strtok(NULL," \t");
+			constraints[3*acount]=atoi(wptr);
+			wptr=strtok(NULL," \t");
+			constraints[3*acount+1]=atoi(wptr);
+			wptr=strtok(NULL," \t");
+			constraints[3*acount+2]=atoi(wptr);
+			// done reading
+			acount+=1;
+		}
+		close(fd);
+		// 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
+		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);
+	/* visualize atoms */
+	visual_atoms(moldyn);
+
+	/* 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
+		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);
+		v3_add(&(atom[i].r),&(atom[i].r),&disp);
+	}
+
+	return 0;
+}
+
 #define stage_print(m)	if(!(stage->executed)) \
 				printf("%s",m)
 
@@ -1194,6 +1381,7 @@ int mdrun_hook(void *ptr1,void *ptr2) {
 	t_set_temp_params *stp;
 	t_set_timestep_params *stsp;
 	t_fill_params *fp;
+	t_crt_params *crtp;
 
 	moldyn=ptr1;
 	mdrun=ptr2;
@@ -1363,6 +1551,20 @@ 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) {
+					free(constraints);
+					free(trafo_angle);
+					free(crtp->r_fin);
+					change_stage=TRUE;
+					break;
+				}
+				crt(moldyn,mdrun);
+				crtp->count+=1;
+				break;
 			default:
 				printf("%s unknwon stage type\n",ME);
 				break;
@@ -1406,6 +1608,11 @@ int main(int argc,char **argv) {
 	memset(&mdrun,0,sizeof(t_mdrun));
 	memset(&moldyn,0,sizeof(t_moldyn));
 
+	/* init crt variables */
+	crtt=0;
+	constraints=NULL;
+	trafo_angle=NULL;
+
 	/* parse arguments */
 	if(mdrun_parse_argv(&mdrun,argc,argv)<0)
 		return -1;
@@ -1449,6 +1656,11 @@ int main(int argc,char **argv) {
 			                     mdrun.element1,
 			                     mdrun.element2);
 			break;
+		case MOLDYN_POTENTIAL_AO:
+			albe_orig_mult_set_params(&moldyn,
+			                          mdrun.element1,
+			                          mdrun.element2);
+			break;
 		case MOLDYN_POTENTIAL_TM:
 			tersoff_mult_set_params(&moldyn,
 			                        mdrun.element1,