X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=415581c475fef1e8bb85b4fb8a1595135de3a88f;hb=684bf7c398cdfa98549b0c7a1fa37e6dc5b35bea;hp=e0881de5db49b1669c5a0b02641e66760dc957a0;hpb=e2c5d8b0eb4ce6faeb48830634eef522dbdb52b0;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index e0881de..415581c 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -13,6 +13,8 @@
 #include <sys/stat.h>
 #include <fcntl.h>
 #include <unistd.h>
+#include <sys/time.h>
+#include <time.h>
 #include <math.h>
 
 #include "moldyn.h"
@@ -24,6 +26,9 @@ 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 +515,7 @@ 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 +524,40 @@ 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 +670,6 @@ 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 +818,29 @@ 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 +849,15 @@ 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 +867,39 @@ 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 +1105,10 @@ 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;
 }
@@ -1334,6 +1350,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	char dir[128];
 	double ds;
 	double energy_scale;
+	struct timeval t1,t2;
 	//double tp;
 
 	sched=&(moldyn->schedule);
@@ -1354,8 +1371,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	moldyn->tau_square=moldyn->tau*moldyn->tau;
 	moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
 
-	/* energy scaling factor */
-	energy_scale=moldyn->count*EV;
+	/* get current time */
+	gettimeofday(&t1,NULL);
 
 	/* calculate initial forces */
 	potential_force_calc(moldyn);
@@ -1385,13 +1402,17 @@ 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];
 		moldyn->tau_square=moldyn->tau*moldyn->tau;
 		moldyn->time_steps=sched->runs[sched->count];
 
+		/* energy scaling factor (might change!) */
+		energy_scale=moldyn->count*EV;
+
 	/* integration according to schedule */
 
 	for(i=0;i<moldyn->time_steps;i++) {
@@ -1402,6 +1423,7 @@ 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);
 
@@ -1413,7 +1435,7 @@ return 0;
 
 		/* check for log & visualization */
 		if(e) {
-			if(!(i%e))
+			if(!(moldyn->total_steps%e))
 				dprintf(moldyn->efd,
 				        "%f %f %f %f\n",
 				        moldyn->time,moldyn->ekin/energy_scale,
@@ -1421,7 +1443,7 @@ return 0;
 				        get_total_energy(moldyn)/energy_scale);
 		}
 		if(m) {
-			if(!(i%m)) {
+			if(!(moldyn->total_steps%m)) {
 				momentum=get_total_p(moldyn);
 				dprintf(moldyn->mfd,
 				        "%f %f %f %f %f\n",moldyn->time,
@@ -1430,7 +1452,7 @@ return 0;
 			}
 		}
 		if(p) {
-			if(!(i%p)) {
+			if(!(moldyn->total_steps%p)) {
 				dprintf(moldyn->pfd,
 				        "%f %f %f %f %f\n",moldyn->time,
 				         moldyn->p/BAR,moldyn->p_avg/BAR,
@@ -1438,17 +1460,18 @@ return 0;
 			}
 		}
 		if(t) {
-			if(!(i%t)) {
+			if(!(moldyn->total_steps%t)) {
 				dprintf(moldyn->tfd,
 				        "%f %f %f\n",
 				        moldyn->time,moldyn->t,moldyn->t_avg);
 			}
 		}
 		if(s) {
-			if(!(i%s)) {
+			if(!(moldyn->total_steps%s)) {
 				snprintf(dir,128,"%s/s-%07.f.save",
 				         moldyn->vlsdir,moldyn->time);
-				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
+				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
+				        S_IRUSR|S_IWUSR);
 				if(fd<0) perror("[moldyn] save fd open");
 				else {
 					write(fd,moldyn,sizeof(t_moldyn));
@@ -1459,22 +1482,27 @@ return 0;
 			}	
 		}
 		if(v) {
-			if(!(i%v)) {
+			if(!(moldyn->total_steps%v)) {
 				visual_atoms(&(moldyn->vis),moldyn->time,
 				             moldyn->atom,moldyn->count);
 			}
 		}
 
 		/* 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);
+		if(!(moldyn->total_steps%10)) {
+			/* get current time */
+			gettimeofday(&t2,NULL);
+
+	printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f (%d)",
+	       sched->count,i,
+	       moldyn->t,moldyn->t_avg,
+	       moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
+	       moldyn->volume,
+	       (int)(t2.tv_sec-t1.tv_sec));
+	fflush(stdout);
+
+			/* copy over time */
+			t1=t2;
 		}
 
 		/* increase absolute time */
@@ -1484,13 +1512,15 @@ 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 +1599,7 @@ 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 +1825,12 @@ 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;
@@ -1907,6 +1937,17 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 	return 0;
 }
 
+/*
+ * restore function
+ */
+
+int moldyn_load(t_moldyn *moldyn) {
+
+	// later ...
+
+	return 0;
+}
+
 /*
  * post processing functions
  */
@@ -1929,3 +1970,11 @@ int get_line(int fd,char *line,int max) {
 	}
 }
 
+int analyze_bonds(t_moldyn *moldyn) {
+
+	
+	
+
+	return 0;
+}
+