Merge branch 'leadoff'

[physik/posic.git] / potentials / lennard_jones.c

diff --git a/potentials/lennard_jones.c b/potentials/lennard_jones.c
index 7d45a17..2424b98 100644 (file)
--- a/potentials/lennard_jones.c
+++ b/potentials/lennard_jones.c
@@ -16,8 +16,64 @@
 #include <math.h>
 
 #include "../moldyn.h"
-#inlcude "../math/math.h"
-//#include "lennard_jones.h"
+#include "../math/math.h"
+#include "lennard_jones.h"
+
+int lennard_jones_set_params(t_moldyn *moldyn,int element) {
+
+       t_lj_params *p;
+       t_atom a,b;
+
+       // set cutoff before parameters (actually only necessary for some pots)
+       if(moldyn->cutoff==0.0) {
+               printf("[lennard jones] WARNING: no cutoff!\n");
+               return -1;
+       }
+
+       /* atoms for correction term */
+       a.r.x=0.0; a.r.y=0.0; a.r.z=0.0;
+       b.r.x=0.0; b.r.y=0.0; b.r.z=moldyn->cutoff;
+
+       /* alloc mem for potential parameters */
+       moldyn->pot_params=malloc(sizeof(t_lj_params));
+       if(moldyn->pot_params==NULL) {
+               perror("[lennard jones] pot params alloc");
+               return -1;
+       }
+
+       /* these are now lennard jones parameters */
+       p=moldyn->pot_params;
+
+       switch(element) {
+               case SI:
+                       /* type: silicon */
+                       p->sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI*LJ_SIGMA_SI;
+                       p->sigma6+=p->sigma6;
+                       p->sigma12=p->sigma6*p->sigma6;
+                       p->epsilon4=4.0*LJ_EPSILON_SI;
+                       p->uc=0.0; // calc it now!
+                       lennard_jones(moldyn,&a,&b,0);
+                       p->uc=moldyn->energy;
+                       moldyn->energy=0.0;
+                       break;
+               case C:
+                       /* type: carbon */
+                       p->sigma6=LJ_SIGMA_C*LJ_SIGMA_C*LJ_SIGMA_C;
+                       p->sigma6+=p->sigma6;
+                       p->sigma12=p->sigma6*p->sigma6;
+                       p->epsilon4=4.0*LJ_EPSILON_C;
+                       p->uc=0.0; // calc it now!
+                       lennard_jones(moldyn,&a,&b,0);
+                       p->uc=moldyn->energy;
+                       moldyn->energy=0.0;
+                       break;
+               default:
+                       printf("[lennard jones] WARNING: element\n");
+                       return -1;
+       }
+
+       return 0;
+}
 
 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
@@ -25,8 +81,9 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
        t_3dvec force,distance;
        double d,h1,h2;
        double eps,sig6,sig12;
+       double energy;
 
-       params=moldyn->pot2b_params;
+       params=moldyn->pot_params;
        eps=params->epsilon4;
        sig6=params->sigma6;
        sig12=params->sigma12;
@@ -35,12 +92,16 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
        v3_sub(&distance,&(aj->r),&(ai->r));
        if(bc) check_per_bound(moldyn,&distance);
-       d=v3_absolute_square(&distance);        /* 1/r^2 */
+       d=v3_absolute_square(&distance);        /* r^2 */
        if(d<=moldyn->cutoff_square) {
                d=1.0/d;                        /* 1/r^2 */
                h2=d*d;                         /* 1/r^4 */
+               h2*=d;                          /* 1/r^6 */
                h1=h2*h2;                       /* 1/r^12 */
-               moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
+               energy=(eps*(sig12*h1-sig6*h2)-params->uc);
+               moldyn->energy+=energy;         /* total energy */
+               ai->e+=0.5*energy;              /* site energy */
+               aj->e+=0.5*energy;
                h2*=d;                          /* 1/r^8 */
                h1*=d;                          /* 1/r^14 */
                h2*=6*sig6;
@@ -58,3 +119,17 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
        return 0;
 }
 
+int lennard_jones_check_2b_bond(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+        t_3dvec dist;
+        double d;
+
+       v3_sub(&dist,&(aj->r),&(ai->r));
+       if(bc) check_per_bound(moldyn,&dist);
+       d=v3_absolute_square(&dist);
+
+       if(d>moldyn->cutoff_square)
+               return FALSE;
+
+       return TRUE;
+}