X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=moldyn.c;h=3c4d87399dcaceffb42f6d91ffe97a58bd8e841f;hb=c40d54eb3e319b17b2f6174c4eddcfd6ee3a407b;hp=a310e912a0567941248bcabeb690c5643bfd4081;hpb=e1348f10aff2c0bb1040108181d13fcb48db5af2;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index a310e91..3c4d873 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -13,11 +13,65 @@
 #include <sys/stat.h>
 #include <fcntl.h>
 #include <unistd.h>
+#include <sys/time.h>
+#include <time.h>
 #include <math.h>
 
 #include "moldyn.h"
 #include "report/report.h"
 
+/*
+ * global variables, pse and atom colors (only needed here)
+ */ 
+
+static char *pse_name[]={
+	"*",
+	"H",
+	"He",
+	"Li",
+	"Be",
+	"B",
+	"C",
+	"N",
+	"O",
+	"F",
+	"Ne",
+	"Na",
+	"Mg",
+	"Al",
+	"Si",
+	"P",
+	"S",
+	"Cl",
+	"Ar",
+};
+
+static char *pse_col[]={
+	"*",
+	"White",
+	"He",
+	"Li",
+	"Be",
+	"B",
+	"Gray",
+	"N",
+	"Blue",
+	"F",
+	"Ne",
+	"Na",
+	"Mg",
+	"Al",
+	"Yellow",
+	"P",
+	"S",
+	"Cl",
+	"Ar",
+};
+
+/*
+ * the moldyn functions
+ */
+
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 	printf("[moldyn] init\n");
@@ -425,7 +479,6 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
 		         moldyn->vlsdir);
 		system(sc);
 	}
-	if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
 
 	return 0;
 }
@@ -556,6 +609,35 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 	return 0;
 }
 
+int del_atom(t_moldyn *moldyn,int tag) {
+
+	t_atom *new,*old;
+	int cnt;
+
+	old=moldyn->atom;
+
+	new=(t_atom *)malloc((moldyn->count-1)*sizeof(t_atom));
+	if(!new) {
+		perror("[moldyn]malloc (del atom)");
+		return -1;
+	}
+
+	for(cnt=0;cnt<tag;cnt++)
+		new[cnt]=old[cnt];
+	
+	for(cnt=tag+1;cnt<moldyn->count;cnt++) {
+		new[cnt-1]=old[cnt];
+		new[cnt-1].tag=cnt-1;
+	}
+
+	moldyn->count-=1;
+	moldyn->atom=new;
+
+	free(old);
+
+	return 0;
+}
+
 /* cubic init */
 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 
@@ -1348,6 +1430,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	char dir[128];
 	double ds;
 	double energy_scale;
+	struct timeval t1,t2;
 	//double tp;
 
 	sched=&(moldyn->schedule);
@@ -1368,8 +1451,8 @@ 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);
@@ -1407,6 +1490,9 @@ return 0;
 		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++) {
@@ -1429,7 +1515,7 @@ 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,
@@ -1437,7 +1523,7 @@ 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,
@@ -1446,7 +1532,7 @@ 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,
@@ -1454,17 +1540,18 @@ 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));
@@ -1475,20 +1562,27 @@ 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:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
+		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);
+	       moldyn->volume,
+	       (int)(t2.tv_sec-t1.tv_sec));
 	fflush(stdout);
+
+			/* copy over time */
+			t1=t2;
 		}
 
 		/* increase absolute time */
@@ -1923,6 +2017,17 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 	return 0;
 }
 
+/*
+ * restore function
+ */
+
+int moldyn_load(t_moldyn *moldyn) {
+
+	// later ...
+
+	return 0;
+}
+
 /*
  * post processing functions
  */
@@ -1945,3 +2050,101 @@ int get_line(int fd,char *line,int max) {
 	}
 }
 
+int analyze_bonds(t_moldyn *moldyn) {
+
+	
+	
+
+	return 0;
+}
+
+/*
+ * visualization code
+ */
+
+int visual_init(t_visual *v,char *filebase) {
+
+	char file[128+8];
+
+	strncpy(v->fb,filebase,128);
+	memset(file,0,128+8);
+
+	return 0;
+}
+
+int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
+
+	int i,fd;
+ 	char file[128+64];
+	t_3dvec dim;
+	double help;
+
+	dim.x=v->dim.x;
+	dim.y=v->dim.y;
+	dim.z=v->dim.z;
+
+	help=(dim.x+dim.y);
+
+	sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,time);
+	fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
+	if(fd<0) {
+		perror("open visual save file fd");
+		return -1;
+	}
+
+	/* write the actual data file */
+	dprintf(fd,"# [P] %d %07.f <%f,%f,%f>\n",
+	        n,time,help/40.0,help/40.0,-0.8*help);
+	for(i=0;i<n;i++)
+		dprintf(fd,"%s %f %f %f %s %f\n",pse_name[atom[i].element],
+		                                 atom[i].r.x,
+		                                 atom[i].r.y,
+		                                 atom[i].r.z,
+		                                 pse_col[atom[i].element],
+		                                 atom[i].ekin);
+	if(dim.x) {
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        -dim.x/2,-dim.y/2,-dim.z/2,
+		        dim.x/2,-dim.y/2,-dim.z/2);
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        -dim.x/2,-dim.y/2,-dim.z/2,
+		        -dim.x/2,dim.y/2,-dim.z/2);
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        dim.x/2,dim.y/2,-dim.z/2,
+		        dim.x/2,-dim.y/2,-dim.z/2);
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        -dim.x/2,dim.y/2,-dim.z/2,
+		        dim.x/2,dim.y/2,-dim.z/2);
+
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        -dim.x/2,-dim.y/2,dim.z/2,
+		        dim.x/2,-dim.y/2,dim.z/2);
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        -dim.x/2,-dim.y/2,dim.z/2,
+		        -dim.x/2,dim.y/2,dim.z/2);
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        dim.x/2,dim.y/2,dim.z/2,
+		        dim.x/2,-dim.y/2,dim.z/2);
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        -dim.x/2,dim.y/2,dim.z/2,
+		        dim.x/2,dim.y/2,dim.z/2);
+
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        -dim.x/2,-dim.y/2,dim.z/2,
+		        -dim.x/2,-dim.y/2,-dim.z/2);
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        -dim.x/2,dim.y/2,dim.z/2,
+		        -dim.x/2,dim.y/2,-dim.z/2);
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        dim.x/2,-dim.y/2,dim.z/2,
+		        dim.x/2,-dim.y/2,-dim.z/2);
+		dprintf(fd,"# [D] %f %f %f %f %f %f\n",
+		        dim.x/2,dim.y/2,dim.z/2,
+		        dim.x/2,dim.y/2,-dim.z/2);
+	}
+
+	close(fd);
+
+	return 0;
+}
+