testing foo

diff --git a/moldyn.c b/moldyn.c
index 5aa6d87..db91859 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -519,7 +519,8 @@ int scale_volume(t_moldyn *moldyn) {
 
        t_atom *atom;
        t_3dvec *dim,*vdim;
-       double virial,scale;
+       double scale,v;
+       t_virial virial;
        t_linkcell *lc;
        int i;
 
@@ -528,12 +529,23 @@ int scale_volume(t_moldyn *moldyn) {
        vdim=&(moldyn->vis.dim);
        lc=&(moldyn->lc);
 
-       for(i=0;i<moldyn->count;i++)
-               virial+=v3_norm(&(atom[i].virial));
+       memset(&virial,0,sizeof(t_virial));
+
+       for(i=0;i<moldyn->count;i++) {
+               virial.xx+=atom[i].virial.xx;
+               virial.yy+=atom[i].virial.yy;
+               virial.zz+=atom[i].virial.zz;
+               virial.xy+=atom[i].virial.xy;
+               virial.xz+=atom[i].virial.xz;
+               virial.yz+=atom[i].virial.yz;
+       }
+
+       /* just a guess so far ... */
+       v=sqrt(virial.xx*virial.xx+virial.yy*virial.yy+virial.zz+virial.zz);
 
-printf("%f\n",virial);
+printf("%f\n",v);
        /* get pressure from virial */
-       moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*virial;
+       moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*v;
        moldyn->p/=moldyn->volume;
 printf("%f\n",moldyn->p/(ATM));
 
@@ -984,6 +996,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 
        int i,j,k,count;
        t_atom *itom,*jtom,*ktom;
+       t_virial *virial;
        t_linkcell *lc;
        t_list neighbour_i[27];
        t_list neighbour_i2[27];
@@ -1005,7 +1018,13 @@ int potential_force_calc(t_moldyn *moldyn) {
                v3_zero(&(itom[i].f));
 
                /* reset viral of atom i */
-               v3_zero(&(itom[i].virial));
+               virial=&(itom[i].virial);
+               virial->xx=0.0;
+               virial->yy=0.0;
+               virial->zz=0.0;
+               virial->xy=0.0;
+               virial->xz=0.0;
+               virial->yz=0.0;
 
                /* reset site energy */
                itom[i].e=0.0;
@@ -1224,7 +1243,10 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 int tersoff_mult_complete_params(t_tersoff_mult_params *p) {
 
        printf("[moldyn] tersoff parameter completion\n");
+       p->S2[0]=p->S[0]*p->S[0];
+       p->S2[1]=p->S[1]*p->S[1];
        p->Smixed=sqrt(p->S[0]*p->S[1]);
+       p->S2mixed=p->Smixed*p->Smixed;
        p->Rmixed=sqrt(p->R[0]*p->R[1]);
        p->Amixed=sqrt(p->A[0]*p->A[1]);
        p->Bmixed=sqrt(p->B[0]*p->B[1]);
@@ -1285,8 +1307,8 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
        t_tersoff_mult_params *params;
        t_tersoff_exchange *exchange;
        t_3dvec dist_ij,force;
-       double d_ij;
-       double A,B,R,S,lambda,mu;
+       double d_ij,d_ij2;
+       double A,B,R,S,S2,lambda,mu;
        double f_r,df_r;
        double f_c,df_c;
        int brand;
@@ -1317,18 +1339,10 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
         *
         */
 
-       /* dist_ij, d_ij */
-       v3_sub(&dist_ij,&(aj->r),&(ai->r));
-       if(bc) check_per_bound(moldyn,&dist_ij);
-       d_ij=v3_norm(&dist_ij);
-
-       /* save for use in 3bp */
-       exchange->d_ij=d_ij;
-       exchange->dist_ij=dist_ij;
-
        /* constants */
        if(brand==ai->brand) {
                S=params->S[brand];
+               S2=params->S2[brand];
                R=params->R[brand];
                A=params->A[brand];
                B=params->B[brand];
@@ -1338,6 +1352,7 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
        }
        else {
                S=params->Smixed;
+               S2=params->S2mixed;
                R=params->Rmixed;
                A=params->Amixed;
                B=params->Bmixed;
@@ -1346,10 +1361,23 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
                params->exchange.chi=params->chi;
        }
 
-       /* if d_ij > S => no force & potential energy contribution */
-       if(d_ij>S)
+       /* dist_ij, d_ij */
+       v3_sub(&dist_ij,&(aj->r),&(ai->r));
+       if(bc) check_per_bound(moldyn,&dist_ij);
+       d_ij2=v3_absolute_square(&dist_ij);
+
+       /* if d_ij2 > S2 => no force & potential energy contribution */
+       if(d_ij2>S2)
                return 0;
 
+       /* now we will need the distance */
+       //d_ij=v3_norm(&dist_ij);
+       d_ij=sqrt(d_ij2);
+
+       /* save for use in 3bp */
+       exchange->d_ij=d_ij;
+       exchange->dist_ij=dist_ij;
+
        /* more constants */
        exchange->beta_j=&(params->beta[brand]);
        exchange->n_j=&(params->n[brand]);
@@ -1389,7 +1417,6 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
                s_r=S-R;
                arg=M_PI*(d_ij-R)/s_r;
                f_c=0.5+0.5*cos(arg);
-               //df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij)); /* MARK! */
                df_c=0.5*sin(arg)*(M_PI/(s_r*d_ij));
                /* two body contribution (ij, ji) */
                v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
@@ -1685,7 +1712,6 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
                        s_r=S-R;
                        arg=M_PI*(d_ik-R)/s_r;
                        f_c_ik=0.5+0.5*cos(arg);
-                       //df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik)); /* MARK */
                        df_c_ik=0.5*sin(arg)*(M_PI/(s_r*d_ik));
 
                        /* zeta_ij */

diff --git a/moldyn.h b/moldyn.h
index 38e4999..dd94b0e 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -22,12 +22,22 @@
 /* general */
 typedef unsigned char u8;
 
+/* virial */
+typedef struct s_virial {
+       double xx;      /*                      | xx     xy     xz |    */
+       double yy;      /*      V       =       | yx     yy     yz |    */
+       double zz;      /*                      | zx     zy     zz |    */
+       double xy;      /*                                              */
+       double xz;      /*      with:   xy=yx, xz=zx, yz=zy             */
+       double yz;      /*                                              */
+} t_virial;
+
 /* the atom of the md simulation */
 typedef struct s_atom {
        t_3dvec r;              /* position */
        t_3dvec v;              /* velocity */
        t_3dvec f;              /* force */
-       t_3dvec virial;         /* virial (v_xx, v_yy, v_zz) */
+       t_virial virial;        /* virial */
        double e;               /* site energy */
        int element;            /* number of element in pse */
        double mass;            /* atom mass */
@@ -222,8 +232,10 @@ typedef struct s_tersoff_exchange {
 /* tersoff multi (2!) potential parameters */
 typedef struct s_tersoff_mult_params {
        double S[2];            /* tersoff cutoff radii */
+       double S2[2];           /* tersoff cutoff radii squared */
        double R[2];            /* tersoff cutoff radii */
        double Smixed;          /* mixed S radius */
+       double S2mixed;         /* mixed S radius squared */
        double Rmixed;          /* mixed R radius */
        double A[2];            /* factor of tersoff attractive part */
        double B[2];            /* factor of tersoff repulsive part */
@@ -310,6 +322,7 @@ typedef struct s_tersoff_mult_params {
 #define SI                     0x0e
 #define LC_SI                  (0.543105e-9*METER)             /* A */
 #define M_SI                   28.08553                        /* amu */
+
 #define LJ_SIGMA_SI            ((0.25*sqrt(3.0)*LC_SI)/1.122462)       /* A */
 #define LJ_EPSILON_SI          (2.1678*EV)                             /* NA */
 

diff --git a/sic.c b/sic.c
index 35931e0..c4355b3 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -112,24 +112,26 @@ int main(int argc,char **argv) {
 
        /* create the lattice / place atoms */
        printf("[sic] creating atoms\n");
-       create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
-                      ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
-                      0,5,5,5);
-       moldyn_bc_check(&md);
+       //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
+       //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+       //               0,5,5,5);
+       //moldyn_bc_check(&md);
 
        /* testing configuration */
-       //r.x=2.95/2;   v.x=0;
-       //r.y=0;                v.y=0;
-       //r.z=0;                v.z=0;
-       //add_atom(&md,SI,M_SI,0,
-       //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,//|ATOM_ATTR_HB,
-       //           &r,&v);
-       //r.x=-2.95/2;  v.x=0;
-       //r.y=0;                v.y=0;
-       //r.z=0;                v.z=0;
-       //add_atom(&md,SI,M_SI,0,
-       //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,//|ATOM_ATTR_HB,
-       //           &r,&v);
+       r.x=2.8/2;      v.x=0;
+       r.y=0;          v.y=0;
+       r.z=0;          v.z=0;
+       add_atom(&md,SI,M_SI,0,
+                  ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,//|ATOM_ATTR_HB,
+       //           ATOM_ATTR_2BP,
+                  &r,&v);
+       r.x=-2.8/2;     v.x=0;
+       r.y=0;          v.y=0;
+       r.z=0;          v.z=0;
+       add_atom(&md,SI,M_SI,0,
+                  ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,//|ATOM_ATTR_HB,
+       //           ATOM_ATTR_2BP,
+                  &r,&v);
 
        /* setting a nearest neighbour distance for the moldyn checks */
        set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */
@@ -151,25 +153,21 @@ int main(int argc,char **argv) {
        printf("[sic] set p/t scaling\n");
        //set_pt_scale(&md,P_SCALE_BERENDSEN,100.0,
        //                 T_SCALE_BERENDSEN,100.0);
-       set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
+       //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
        
        /* initial thermal fluctuations of particles (in equilibrium) */
        printf("[sic] thermal init\n");
-       thermal_init(&md,TRUE);
+       //thermal_init(&md,TRUE);
 
        /* create the simulation schedule */
        printf("[sic] adding schedule\n");
-       moldyn_add_schedule(&md,20000,.1);
-       moldyn_add_schedule(&md,10000,.2);
-       moldyn_add_schedule(&md,6667,.3);
-       moldyn_add_schedule(&md,5000,.4);
-       moldyn_add_schedule(&md,4001,.5);
+       moldyn_add_schedule(&md,10000,.1);
 
        /* activate logging */
        printf("[sic] activate logging\n");
        moldyn_set_log_dir(&md,argv[1]);
-       moldyn_set_log(&md,LOG_TOTAL_ENERGY,100);
-       moldyn_set_log(&md,VISUAL_STEP,100);
+       moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
+       moldyn_set_log(&md,VISUAL_STEP,20);
 
        /*
         * let's do the actual md algorithm now