X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=4d736179550d68c7402e89b4412dec3dfc9d40bb;hb=0b96eb313c9bfec6272b1f8de0d99c4ce26d1686;hp=9a62b9f7c93d5142f5b15d57d099f4ba160604ce;hpb=ea612b88a0588b8f46fafaebf3b37fb46c83c0cf;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 9a62b9f..4d73617 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -82,7 +82,7 @@ int set_pressure(t_moldyn *moldyn,double p_ref) {
 
 	moldyn->p_ref=p_ref;
 
-	printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
+	printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
 
 	return 0;
 }
@@ -176,16 +176,37 @@ int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
 	return 0;
 }
 
-int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func) {
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
 
-	moldyn->func2b_post=func;
+	moldyn->func3b_j1=func;
 
 	return 0;
 }
 
-int set_potential3b(t_moldyn *moldyn,pf_func3b func) {
+int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
 
-	moldyn->func3b=func;
+	moldyn->func3b_j2=func;
+
+	return 0;
+}
+
+int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
+
+	moldyn->func3b_j3=func;
+
+	return 0;
+}
+
+int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
+
+	moldyn->func3b_k1=func;
+
+	return 0;
+}
+
+int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
+
+	moldyn->func3b_k2=func;
 
 	return 0;
 }
@@ -294,6 +315,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				perror("[moldyn] report fd open");	
 				return moldyn->rfd;
 			}
+			printf("report -> ");
 			if(moldyn->efd) {
 				snprintf(filename,127,"%s/e_plot.scr",
 				         moldyn->vlsdir);
@@ -306,6 +328,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				}
 				dprintf(moldyn->epfd,e_plot_script);
 				close(moldyn->epfd);
+				printf("energy ");
 			}
 			if(moldyn->pfd) {
 				snprintf(filename,127,"%s/pressure_plot.scr",
@@ -319,6 +342,7 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				}
 				dprintf(moldyn->ppfd,pressure_plot_script);
 				close(moldyn->ppfd);
+				printf("pressure ");
 			}
 			if(moldyn->tfd) {
 				snprintf(filename,127,"%s/temperature_plot.scr",
@@ -332,9 +356,11 @@ int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
 				}
 				dprintf(moldyn->tpfd,temperature_plot_script);
 				close(moldyn->tpfd);
+				printf("temperature ");
 			}
 			dprintf(moldyn->rfd,report_start,
 			        moldyn->rauthor,moldyn->rtitle);
+			printf("\n");
 			break;
 		default:
 			printf("unknown log type: %02x\n",type);
@@ -672,6 +698,8 @@ double temperature_calc(t_moldyn *moldyn) {
 	/* assume up to date kinetic energy, which is 3/2 N k_B T */
 
 	moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
+	moldyn->t_sum+=moldyn->t;
+	moldyn->mean_t=moldyn->t_sum/moldyn->total_steps;
 
 	return moldyn->t;
 }
@@ -769,6 +797,16 @@ double pressure_calc(t_moldyn *moldyn) {
 	/* assume up to date kinetic energy */
 	moldyn->p=2.0*moldyn->ekin+v;
 	moldyn->p/=(3.0*moldyn->volume);
+	moldyn->p_sum+=moldyn->p;
+	moldyn->mean_p=moldyn->p_sum/moldyn->total_steps;
+
+	/* pressure from 'absolute coordinates' virial */
+	virial=&(moldyn->virial);
+	v=virial->xx+virial->yy+virial->zz;
+	moldyn->gp=2.0*moldyn->ekin+v;
+	moldyn->gp/=(3.0*moldyn->volume);
+	moldyn->gp_sum+=moldyn->gp;
+	moldyn->mean_gp=moldyn->gp_sum/moldyn->total_steps;
 
 	return moldyn->p;
 }	
@@ -788,7 +826,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
 	 * dV: dx,y,z = 0.001 x,y,z
 	 */
 
-	scale=1.00001;
+	scale=1.00000000000001;
 printf("\n\nP-DEBUG:\n");
 
 	tp=&(moldyn->tp);
@@ -806,13 +844,12 @@ printf("\n\nP-DEBUG:\n");
 	/* derivative with respect to x direction */
 	scale_dim(moldyn,scale,TRUE,0,0);
 	scale_atoms(moldyn,scale,TRUE,0,0);
-	dv=0.00001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
+	dv=0.00000000000001*moldyn->dim.x*moldyn->dim.y*moldyn->dim.z;
 	link_cell_shutdown(moldyn);
 	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
 	tp->x=(moldyn->energy-u)/dv;
 	p=tp->x*tp->x;
-printf("e: %f eV de: %f eV dV: %f A^3\n",moldyn->energy/moldyn->count/EV,(moldyn->energy-u)/moldyn->count/EV,dv);
 
 	/* restore atomic configuration + dim */
 	memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
@@ -821,7 +858,7 @@ printf("e: %f eV de: %f eV dV: %f A^3\n",moldyn->energy/moldyn->count/EV,(moldyn
 	/* derivative with respect to y direction */
 	scale_dim(moldyn,scale,0,TRUE,0);
 	scale_atoms(moldyn,scale,0,TRUE,0);
-	dv=0.00001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
+	dv=0.00000000000001*moldyn->dim.y*moldyn->dim.x*moldyn->dim.z;
 	link_cell_shutdown(moldyn);
 	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
@@ -835,7 +872,7 @@ printf("e: %f eV de: %f eV dV: %f A^3\n",moldyn->energy/moldyn->count/EV,(moldyn
 	/* derivative with respect to z direction */
 	scale_dim(moldyn,scale,0,0,TRUE);
 	scale_atoms(moldyn,scale,0,0,TRUE);
-	dv=0.00001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
+	dv=0.00000000000001*moldyn->dim.z*moldyn->dim.x*moldyn->dim.y;
 	link_cell_shutdown(moldyn);
 	link_cell_init(moldyn,QUIET);
 	potential_force_calc(moldyn);
@@ -939,7 +976,7 @@ moldyn->debug=scale;
 
 }
 
-double get_e_kin(t_moldyn *moldyn) {
+double e_kin_calc(t_moldyn *moldyn) {
 
 	int i;
 	t_atom *atom;
@@ -953,11 +990,6 @@ double get_e_kin(t_moldyn *moldyn) {
 	return moldyn->ekin;
 }
 
-double update_e_kin(t_moldyn *moldyn) {
-
-	return(get_e_kin(moldyn));
-}
-
 double get_total_energy(t_moldyn *moldyn) {
 
 	return(moldyn->ekin+moldyn->energy);
@@ -1018,7 +1050,12 @@ int link_cell_init(t_moldyn *moldyn,u8 vol) {
 	if(lc->cells<27)
 		printf("[moldyn] FATAL: less then 27 subcells!\n");
 
-	if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+	if(vol) {
+		printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+		printf("  x: %d x %f A\n",lc->nx,lc->x);
+		printf("  y: %d x %f A\n",lc->ny,lc->y);
+		printf("  z: %d x %f A\n",lc->nz,lc->z);
+	}
 
 	for(i=0;i<lc->cells;i++)
 		list_init_f(&(lc->subcell[i]));
@@ -1053,7 +1090,7 @@ int link_cell_update(t_moldyn *moldyn) {
 		i=((atom[count].r.x+(moldyn->dim.x/2))/lc->x);
 		j=((atom[count].r.y+(moldyn->dim.y/2))/lc->y);
 		k=((atom[count].r.z+(moldyn->dim.z/2))/lc->z);
-		list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+		list_add_immediate_f(&(lc->subcell[i+j*nx+k*nx*ny]),
 		                     &(atom[count]));
 	}
 
@@ -1229,6 +1266,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 	/* zero absolute time */
 	moldyn->time=0.0;
+	moldyn->total_steps=0;
 
 	/* debugging, ignore */
 	moldyn->debug=0;
@@ -1252,10 +1290,11 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		moldyn->integrate(moldyn);
 
 		/* calculate kinetic energy, temperature and pressure */
-		update_e_kin(moldyn);
+		e_kin_calc(moldyn);
 		temperature_calc(moldyn);
 		pressure_calc(moldyn);
 		//tp=thermodynamic_pressure_calc(moldyn);
+//printf("thermodynamic p: %f %f %f - %f\n",moldyn->tp.x/BAR,moldyn->tp.y/BAR,moldyn->tp.z/BAR,tp/BAR);
 
 		/* p/t scaling */
 		if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
@@ -1284,13 +1323,16 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		if(p) {
 			if(!(i%p)) {
 				dprintf(moldyn->pfd,
-				        "%f %f\n",moldyn->time,moldyn->p/ATM);
+				        "%f %f %f %f %f\n",moldyn->time,
+				         moldyn->p/BAR,moldyn->mean_p/BAR,
+				         moldyn->gp/BAR,moldyn->mean_gp/BAR);
 			}
 		}
 		if(t) {
 			if(!(i%t)) {
 				dprintf(moldyn->tfd,
-				        "%f %f\n",moldyn->time,moldyn->t);
+				        "%f %f %f\n",
+				        moldyn->time,moldyn->t,moldyn->mean_t);
 			}
 		}
 		if(s) {
@@ -1316,14 +1358,18 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
 		/* display progress */
 		if(!(i%10)) {
-			printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
+			printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
 			       sched->count,i,
-			       moldyn->t,moldyn->p/ATM,moldyn->volume);
+			       moldyn->mean_t,
+			       moldyn->mean_p/BAR,
+			       moldyn->mean_gp/BAR,
+			       moldyn->volume);
 			fflush(stdout);
 		}
 
 		/* increase absolute time */
 		moldyn->time+=moldyn->tau;
+		moldyn->total_steps+=1;
 
 	}
 
@@ -1410,6 +1456,9 @@ int potential_force_calc(t_moldyn *moldyn) {
 	/* reset energy */
 	moldyn->energy=0.0;
 
+	/* reset global virial */
+	memset(&(moldyn->virial),0,sizeof(t_virial));
+
 	/* reset force, site energy and virial of every atom */
 	for(i=0;i<count;i++) {
 
@@ -1430,7 +1479,9 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	}
 
-	/* get energy,force and virial of every atom */
+	/* get energy, force and virial of every atom */
+
+	/* first (and only) loop over atoms i */
 	for(i=0;i<count;i++) {
 
 		/* single particle potential/force */
@@ -1450,6 +1501,45 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 		dnlc=lc->dnlc;
 
+		/* first loop over atoms j */
+		if(moldyn->func2b) {
+			for(j=0;j<27;j++) {
+
+				this=&(neighbour_i[j]);
+				list_reset_f(this);
+
+				if(this->start==NULL)
+					continue;
+
+				bc_ij=(j<dnlc)?0:1;
+
+				do {
+					jtom=this->current->data;
+
+					if(jtom==&(itom[i]))
+						continue;
+
+					if((jtom->attr&ATOM_ATTR_2BP)&
+					   (itom[i].attr&ATOM_ATTR_2BP)) {
+						moldyn->func2b(moldyn,
+						               &(itom[i]),
+						               jtom,
+					        	       bc_ij);
+					}
+				} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+
+			}
+		}
+
+		/* 3 body potential/force */
+
+		if(!(itom[i].attr&ATOM_ATTR_3BP))
+			continue;
+
+		/* copy the neighbour lists */
+		memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+
+		/* second loop over atoms j */
 		for(j=0;j<27;j++) {
 
 			this=&(neighbour_i[j]);
@@ -1466,25 +1556,70 @@ int potential_force_calc(t_moldyn *moldyn) {
 				if(jtom==&(itom[i]))
 					continue;
 
-				if((jtom->attr&ATOM_ATTR_2BP)&
-				   (itom[i].attr&ATOM_ATTR_2BP)) {
-					moldyn->func2b(moldyn,
-					               &(itom[i]),
-					               jtom,
-					               bc_ij);
-				}
+				if(!(jtom->attr&ATOM_ATTR_3BP))
+					continue;
 
-				/* 3 body potential/force */
+				/* reset 3bp run */
+				moldyn->run3bp=1;
 
-				if(!(itom[i].attr&ATOM_ATTR_3BP)||
-				   !(jtom->attr&ATOM_ATTR_3BP))
+				if(moldyn->func3b_j1)
+					moldyn->func3b_j1(moldyn,
+					                  &(itom[i]),
+					                  jtom,
+					                  bc_ij);
+
+				/* in first j loop, 3bp run can be skipped */
+				if(!(moldyn->run3bp))
 					continue;
+			
+				/* first loop over atoms k */
+				if(moldyn->func3b_k1) {
+
+				for(k=0;k<27;k++) {
+
+					that=&(neighbour_i2[k]);
+					list_reset_f(that);
+					
+					if(that->start==NULL)
+						continue;
+
+					bc_ik=(k<dnlc)?0:1;
 
-				/* copy the neighbour lists */
-				memcpy(neighbour_i2,neighbour_i,
-				       27*sizeof(t_list));
+					do {
+
+						ktom=that->current->data;
+
+						if(!(ktom->attr&ATOM_ATTR_3BP))
+							continue;
+
+						if(ktom==jtom)
+							continue;
+
+						if(ktom==&(itom[i]))
+							continue;
+
+						moldyn->func3b_k1(moldyn,
+						                  &(itom[i]),
+						                  jtom,
+						                  ktom,
+						                  bc_ik|bc_ij);
+
+					} while(list_next_f(that)!=\
+					        L_NO_NEXT_ELEMENT);
+
+				}
+
+				}
+
+				if(moldyn->func3b_j2)
+					moldyn->func3b_j2(moldyn,
+					                  &(itom[i]),
+					                  jtom,
+					                  bc_ij);
+
+				/* second loop over atoms k */
+				if(moldyn->func3b_k2) {
 
-				/* get neighbours of i */
 				for(k=0;k<27;k++) {
 
 					that=&(neighbour_i2[k]);
@@ -1508,37 +1643,53 @@ int potential_force_calc(t_moldyn *moldyn) {
 						if(ktom==&(itom[i]))
 							continue;
 
-						moldyn->func3b(moldyn,
-						               &(itom[i]),
-						               jtom,
-						               ktom,
-						               bc_ik|bc_ij);
+						moldyn->func3b_k2(moldyn,
+						                  &(itom[i]),
+						                  jtom,
+						                  ktom,
+						                  bc_ik|bc_ij);
 
 					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
 
 				}
+				
+				}
 
 				/* 2bp post function */
-				if(moldyn->func2b_post) {
-					moldyn->func2b_post(moldyn,
-					                    &(itom[i]),
-					                    jtom,bc_ij);
+				if(moldyn->func3b_j3) {
+					moldyn->func3b_j3(moldyn,
+					                  &(itom[i]),
+					                  jtom,bc_ij);
 				}
 					
 			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 		
 		}
+		
+#ifdef DEBUG
+	//printf("\n\n");
+#endif
+#ifdef VDEBUG
+	printf("\n\n");
+#endif
 
 	}
 
 #ifdef DEBUG
-printf("\n\n");
-#endif
-#ifdef VDEBUG
-printf("\n\n");
+	printf("\nATOM 0: %f %f %f\n\n",itom->f.x,itom->f.y,itom->f.z);
 #endif
 
+	/* calculate global virial */
+	for(i=0;i<count;i++) {
+		moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
+		moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
+		moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
+		moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
+		moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
+		moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+	}
+
 	return 0;
 }