added another diff calc code

diff --git a/diffusion_calc_ver2.c b/diffusion_calc_ver2.c
new file mode 100644 (file)
index 0000000..ef071a0
--- /dev/null
+++ b/diffusion_calc_ver2.c
@@ -0,0 +1,113 @@
+/*
+ * calculation of diffusion coefficient (version 2)
+ *
+ * author: frank.zirkelbach@physik.uni-augsburg.de
+ *
+ */
+
+#define _GNU_SOURCE
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+
+#include "moldyn.h"
+
+#define CM     1.0e8
+
+int usage(char *prog) {
+
+       printf("\nusage:\n");
+       printf("  %s <save file 1> <save file 2>\n\n",prog);
+
+       return -1;
+}
+
+int main(int argc,char **argv) {
+
+       t_moldyn moldyn_0,moldyn_1;
+       int ret,i,a_cnt,b_cnt;
+       double dx,dy,dz,dc[3];
+
+       if(argc!=3) {
+               usage(argv[0]);
+               return -1;
+       }
+
+       memset(&moldyn_0,0,sizeof(t_moldyn));
+       memset(&moldyn_1,0,sizeof(t_moldyn));
+
+       a_cnt=0;
+       b_cnt=0;
+
+       dc[0]=0.0;
+       dc[1]=0.0;
+       dc[2]=0.0;
+
+       printf("[diffusion calc] reading save files ...\n");
+       ret=moldyn_read_save_file(&moldyn_0,argv[1]);
+       if(ret) {
+               printf("[diffusion calc] exit!\n");
+               return ret;
+       }
+       ret=moldyn_read_save_file(&moldyn_1,argv[2]);
+       if(ret) {
+               printf("[diffusion calc] exit!\n");
+               return ret;
+       }
+
+       if(moldyn_0.count!=moldyn_1.count) {
+               printf("[diffusion calc] atom count mismatch\n");
+               return -1;
+       }
+
+       for(i=0;i<moldyn_0.count;i++) {
+               dx=moldyn_0.atom[i].r.x/moldyn_0.dim.x;
+               dy=moldyn_0.atom[i].r.y/moldyn_0.dim.y;
+               dz=moldyn_0.atom[i].r.z/moldyn_0.dim.z;
+               dx-=(moldyn_1.atom[i].r.x/moldyn_1.dim.x);
+               dy-=(moldyn_1.atom[i].r.y/moldyn_1.dim.y);
+               dz-=(moldyn_1.atom[i].r.z/moldyn_1.dim.z);
+               if(dx>0.5)
+                       dx-=0.5;
+               if(dx<-0.5)
+                       dx+=0.5;
+               if(dy>0.5)
+                       dy-=0.5;
+               if(dy<-0.5)
+                       dy+=0.5;
+               if(dz>0.5)
+                       dz-=0.5;
+               if(dz<-0.5)
+                       dz+=0.5;
+               dx*=moldyn_1.dim.x;
+               dy*=moldyn_1.dim.y;
+               dz*=moldyn_1.dim.z;
+               if(moldyn_0.atom[i].brand) {
+                       b_cnt+=1;
+                       dc[1]+=dx*dx+dy*dy+dz*dz;
+               }
+               else {
+                       a_cnt+=1;
+                       dc[0]+=dx*dx+dy*dy+dz*dz;
+               }
+               dc[2]+=dx*dx+dy*dy+dz*dz;
+       }
+
+       dc[0]*=(1.0/(6.0*(moldyn_1.time-moldyn_0.time)*a_cnt));
+       dc[1]*=(1.0/(6.0*(moldyn_1.time-moldyn_0.time)*b_cnt));
+       dc[2]*=(1.0/(6.0*(moldyn_1.time-moldyn_0.time)*moldyn_0.count));
+
+       dc[0]*=(SECOND/(CM*CM));
+       dc[1]*=(SECOND/(CM*CM));
+       dc[2]*=(SECOND/(CM*CM));
+
+       printf("diffusion coefficients: %.10f %.10f %.10f [cm^2/s]\n",
+              dc[0],dc[1],dc[2]);
+
+       return 0;
+}
+