X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=a310e912a0567941248bcabeb690c5643bfd4081;hb=e1348f10aff2c0bb1040108181d13fcb48db5af2;hp=e0881de5db49b1669c5a0b02641e66760dc957a0;hpb=e2c5d8b0eb4ce6faeb48830634eef522dbdb52b0;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index e0881de..a310e91 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -24,6 +24,9 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 	memset(moldyn,0,sizeof(t_moldyn));
 
+	moldyn->argc=argc;
+	moldyn->args=argv;
+
 	rand_init(&(moldyn->random),NULL,1);
 	moldyn->random.status|=RAND_STAT_VERBOSE;
 
@@ -510,6 +513,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 		atom[ret].brand=brand;
 		atom[ret].tag=count+ret;
 		check_per_bound(moldyn,&(atom[ret].r));
+		atom[ret].r_0=atom[ret].r;
 	}
 
 	/* update total system mass */
@@ -518,6 +522,40 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	return ret;
 }
 
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+             t_3dvec *r,t_3dvec *v) {
+
+	t_atom *atom;
+	void *ptr;
+	int count;
+	
+	atom=moldyn->atom;
+	count=(moldyn->count)++;
+
+	ptr=realloc(atom,(count+1)*sizeof(t_atom));
+	if(!ptr) {
+		perror("[moldyn] realloc (add atom)");
+		return -1;
+	}
+	moldyn->atom=ptr;
+
+	atom=moldyn->atom;
+	atom[count].r=*r;
+	atom[count].v=*v;
+	atom[count].element=element;
+	atom[count].mass=mass;
+	atom[count].brand=brand;
+	atom[count].tag=count;
+	atom[count].attr=attr;
+	check_per_bound(moldyn,&(atom[count].r));
+	atom[count].r_0=atom[count].r;
+
+	/* update total system mass */
+	total_mass_calc(moldyn);
+
+	return 0;
+}
+
 /* cubic init */
 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 
@@ -630,38 +668,6 @@ int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 	return count;
 }
 
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
-             t_3dvec *r,t_3dvec *v) {
-
-	t_atom *atom;
-	void *ptr;
-	int count;
-	
-	atom=moldyn->atom;
-	count=(moldyn->count)++;
-
-	ptr=realloc(atom,(count+1)*sizeof(t_atom));
-	if(!ptr) {
-		perror("[moldyn] realloc (add atom)");
-		return -1;
-	}
-	moldyn->atom=ptr;
-
-	atom=moldyn->atom;
-	atom[count].r=*r;
-	atom[count].v=*v;
-	atom[count].element=element;
-	atom[count].mass=mass;
-	atom[count].brand=brand;
-	atom[count].tag=count;
-	atom[count].attr=attr;
-
-	/* update total system mass */
-	total_mass_calc(moldyn);
-
-	return 0;
-}
-
 int destroy_atoms(t_moldyn *moldyn) {
 
 	if(moldyn->atom) free(moldyn->atom);
@@ -810,12 +816,29 @@ double ideal_gas_law_pressure(t_moldyn *moldyn) {
 	return p;
 }
 
-double pressure_calc(t_moldyn *moldyn) {
+double virial_sum(t_moldyn *moldyn) {
 
 	int i;
 	double v;
 	t_virial *virial;
 
+	/* virial (sum over atom virials) */
+	v=0.0;
+	for(i=0;i<moldyn->count;i++) {
+		virial=&(moldyn->atom[i].virial);
+		v+=(virial->xx+virial->yy+virial->zz);
+	}
+	moldyn->virial=v;
+
+	/* global virial (absolute coordinates) */
+	virial=&(moldyn->gvir);
+	moldyn->gv=virial->xx+virial->yy+virial->zz;
+
+	return moldyn->virial;
+}
+
+double pressure_calc(t_moldyn *moldyn) {
+
 	/*
 	 * PV = NkT + <W>
 	 * with W = 1/3 sum_i f_i r_i (- skipped!)
@@ -824,34 +847,15 @@ double pressure_calc(t_moldyn *moldyn) {
 	 * => P = (2 Ekin + virial) / (3V)
 	 */
 
-	v=0.0;
-	for(i=0;i<moldyn->count;i++) {
-		virial=&(moldyn->atom[i].virial);
-		v+=(virial->xx+virial->yy+virial->zz);
-	}
+	/* assume up to date virial & up to date kinetic energy */
 
-	/* virial sum and average virial */
-	if(moldyn->total_steps>=moldyn->avg_skip) {
-		moldyn->virial_sum+=v;
-		moldyn->virial_avg=moldyn->virial_sum/
-		                   (moldyn->total_steps+1-moldyn->avg_skip);
-		moldyn->p=2.0*moldyn->k_avg+moldyn->virial_avg;
-		moldyn->p/=(3.0*moldyn->volume);
-		moldyn->p_sum+=moldyn->p;
-		moldyn->p_avg=moldyn->p_sum/
-		              (moldyn->total_steps+1-moldyn->avg_skip);
-	}
+	/* pressure (atom virials) */
+	moldyn->p=2.0*moldyn->ekin+moldyn->virial;
+	moldyn->p/=(3.0*moldyn->volume);
 
-	/* pressure from 'absolute coordinates' virial */
-	virial=&(moldyn->virial);
-	v=virial->xx+virial->yy+virial->zz;
-	moldyn->gp=2.0*moldyn->ekin+v;
+	/* pressure (absolute coordinates) */
+	moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
 	moldyn->gp/=(3.0*moldyn->volume);
-	if(moldyn->total_steps>=moldyn->avg_skip) {
-		moldyn->gp_sum+=moldyn->gp;
-		moldyn->gp_avg=moldyn->gp_sum/
-		               (moldyn->total_steps+1-moldyn->avg_skip);
-	}
 
 	return moldyn->p;
 }
@@ -861,31 +865,39 @@ int average_and_fluctuation_calc(t_moldyn *moldyn) {
 	if(moldyn->total_steps<moldyn->avg_skip)
 		return 0;
 
+	int denom=moldyn->total_steps+1-moldyn->avg_skip;
+
 	/* assume up to date energies, temperature, pressure etc */
 
 	/* kinetic energy */
 	moldyn->k_sum+=moldyn->ekin;
 	moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
-	moldyn->k_avg=moldyn->k_sum/(moldyn->total_steps+1-moldyn->avg_skip);
-	moldyn->k2_avg=moldyn->k2_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+	moldyn->k_avg=moldyn->k_sum/denom;
+	moldyn->k2_avg=moldyn->k2_sum/denom;
 	moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
 
 	/* potential energy */
 	moldyn->v_sum+=moldyn->energy;
 	moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
-	moldyn->v_avg=moldyn->v_sum/(moldyn->total_steps+1-moldyn->avg_skip);
-	moldyn->v2_avg=moldyn->v2_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+	moldyn->v_avg=moldyn->v_sum/denom;
+	moldyn->v2_avg=moldyn->v2_sum/denom;
 	moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
 
 	/* temperature */
 	moldyn->t_sum+=moldyn->t;
-	moldyn->t_avg=moldyn->t_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+	moldyn->t_avg=moldyn->t_sum/denom;
 
 	/* virial */
-	
+	moldyn->virial_sum+=moldyn->virial;
+	moldyn->virial_avg=moldyn->virial_sum/denom;
+	moldyn->gv_sum+=moldyn->gv;
+	moldyn->gv_avg=moldyn->gv_sum/denom;
 
 	/* pressure */
-
+	moldyn->p_sum+=moldyn->p;
+	moldyn->p_avg=moldyn->p_sum/denom;
+	moldyn->gp_sum+=moldyn->gp;
+	moldyn->gp_avg=moldyn->gp_sum/denom;
 
 	return 0;
 }
@@ -1091,8 +1103,10 @@ double e_kin_calc(t_moldyn *moldyn) {
 	atom=moldyn->atom;
 	moldyn->ekin=0.0;
 
-	for(i=0;i<moldyn->count;i++)
-		moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+	for(i=0;i<moldyn->count;i++) {
+		atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+		moldyn->ekin+=atom[i].ekin;
+	}
 
 	return moldyn->ekin;
 }
@@ -1385,7 +1399,8 @@ return 0;
 	printf("[moldyn] integration start, go get a coffee ...\n");
 
 	/* executing the schedule */
-	for(sched->count=0;sched->count<sched->total_sched;sched->count++) {
+	sched->count=0;
+	while(sched->count<sched->total_sched) {
 
 		/* setting amount of runs and finite time step size */
 		moldyn->tau=sched->tau[sched->count];
@@ -1402,6 +1417,7 @@ return 0;
 		/* calculate kinetic energy, temperature and pressure */
 		e_kin_calc(moldyn);
 		temperature_calc(moldyn);
+		virial_sum(moldyn);
 		pressure_calc(moldyn);
 		average_and_fluctuation_calc(moldyn);
 
@@ -1467,14 +1483,12 @@ return 0;
 
 		/* display progress */
 		if(!(i%10)) {
-			printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
-			       sched->count,i,
-			       moldyn->t_avg,
-			       //moldyn->p_avg/BAR,
-			       moldyn->p/BAR,
-			       moldyn->gp_avg/BAR,
-			       moldyn->volume);
-			fflush(stdout);
+	printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
+	       sched->count,i,
+	       moldyn->t,moldyn->t_avg,
+	       moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
+	       moldyn->volume);
+	fflush(stdout);
 		}
 
 		/* increase absolute time */
@@ -1484,13 +1498,15 @@ return 0;
 	}
 
 		/* check for hooks */
-		if(sched->count+1<sched->total_sched)
-			if(sched->hook) {
-				printf("\n ## schedule hook %d/%d start ##\n",
-				       sched->count+1,sched->total_sched);
-				sched->hook(moldyn,sched->hook_params);
-				printf(" ## schedule hook end ##\n");
-			}
+		if(sched->hook) {
+			printf("\n ## schedule hook %d/%d start ##\n",
+			       sched->count+1,sched->total_sched-1);
+			sched->hook(moldyn,sched->hook_params);
+			printf(" ## schedule hook end ##\n");
+		}
+
+		/* increase the schedule counter */
+		sched->count+=1;
 
 	}
 
@@ -1569,7 +1585,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 	moldyn->energy=0.0;
 
 	/* reset global virial */
-	memset(&(moldyn->virial),0,sizeof(t_virial));
+	memset(&(moldyn->gvir),0,sizeof(t_virial));
 
 	/* reset force, site energy and virial of every atom */
 	for(i=0;i<count;i++) {
@@ -1795,12 +1811,12 @@ int potential_force_calc(t_moldyn *moldyn) {
 
 	/* 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;
+		moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
+		moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
+		moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
+		moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
+		moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
+		moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
 	}
 
 	return 0;