still full of bugs ...

diff --git a/Makefile b/Makefile
index 39457f7..c51f8bd 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -4,7 +4,8 @@ CFLAGS=-Wall
 CFLAGS+=-O3
 CFLAGS+=-ffloat-store
 CFLAGS+=-g
-CFLAGS+=-DDEBUG
+#CFLAGS+=-DDEBUG
+#CFLAGS+=-DVDEBUG
 LDFLAGS=-lm
 
 OBJS=visual/visual.o random/random.o

diff --git a/moldyn.c b/moldyn.c
index c21f59f..d33de02 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -460,6 +460,28 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
        return 0;
 }
 
+double temperature_calc(t_moldyn *moldyn) {
+
+       double double_ekin;
+       int i;
+       t_atom *atom;
+
+       atom=moldyn->atom;
+
+       for(i=0;i<moldyn->count;i++)
+               double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
+
+       /* kinetic energy = 3/2 N k_B T */
+       moldyn->t=double_ekin/(3.0*K_BOLTZMANN*moldyn->count);
+
+       return moldyn->t;
+}
+
+double get_temperature(t_moldyn *moldyn) {
+
+       return moldyn->t;
+}
+
 int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
 
        int i;
@@ -478,10 +500,11 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
        count=0;
        for(i=0;i<moldyn->count;i++) {
                if((equi_init&TRUE)||(atom[i].attr&ATOM_ATTR_HB)) {
-                       e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+                       e+=atom[i].mass*v3_absolute_square(&(atom[i].v));
                        count+=1;
                }
        }
+       e*=0.5;
        if(count!=0) moldyn->t=e/(1.5*count*K_BOLTZMANN);
        else return 0;  /* no atoms involved in scaling! */
        
@@ -515,6 +538,34 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
        return 0;
 }
 
+double pressure_calc(t_moldyn *moldyn) {
+
+       int i;
+       t_atom *atom;
+       double p1,p2,p=0;
+       
+       for(i=0;i<moldyn->count;i++) {
+               
+
+       }
+
+       p1=(moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*moldyn->vt1);
+       p1/=moldyn->volume;
+
+       p2=(moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*moldyn->vt2);
+       p2/=moldyn->volume;
+
+       printf("compare pressures: %f %f\n",p1/ATM,p2/ATM);
+
+       return moldyn->p;
+}      
+
+double get_pressure(t_moldyn *moldyn) {
+
+       return moldyn->p;
+
+}
+
 int scale_volume(t_moldyn *moldyn) {
 
        t_atom *atom;
@@ -592,11 +643,6 @@ double get_e_kin(t_moldyn *moldyn) {
        return moldyn->ekin;
 }
 
-double get_e_pot(t_moldyn *moldyn) {
-
-       return moldyn->energy;
-}
-
 double update_e_kin(t_moldyn *moldyn) {
 
        return(get_e_kin(moldyn));
@@ -659,6 +705,9 @@ int link_cell_init(t_moldyn *moldyn) {
        lc->cells=lc->nx*lc->ny*lc->nz;
        lc->subcell=malloc(lc->cells*sizeof(t_list));
 
+       if(lc->cells<27)
+               printf("[moldyn] FATAL: less then 27 subcells!\n");
+
        printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
        for(i=0;i<lc->cells;i++)
@@ -885,13 +934,21 @@ int moldyn_integrate(t_moldyn *moldyn) {
                        scale_volume(moldyn);
 
                /* check for log & visualization */
+//double ax;
+//double ao;
+//double av;
                if(e) {
                        if(!(i%e))
+//ao=sqrt(0.1/M_SI);
+//ax=((0.28-0.25)*sqrt(3)*LC_SI/2)*cos(ao*i);
+//av=ao*(0.28-0.25)*sqrt(3)*LC_SI/2*sin(ao*i);
+                               update_e_kin(moldyn);
                                dprintf(moldyn->efd,
                                        "%f %f %f %f\n",
-                                       moldyn->time,update_e_kin(moldyn),
+                                       moldyn->time,moldyn->ekin,
                                        moldyn->energy,
                                        get_total_energy(moldyn));
+//moldyn->atom[0].r.x,ax,av*av*M_SI,0.1*ax*ax,av*av*M_SI+0.1*ax*ax);
                }
                if(m) {
                        if(!(i%m)) {
@@ -946,7 +1003,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 int velocity_verlet(t_moldyn *moldyn) {
 
        int i,count;
-       double tau,tau_square;
+       double tau,tau_square,h;
        t_3dvec delta;
        t_atom *atom;
 
@@ -957,14 +1014,15 @@ int velocity_verlet(t_moldyn *moldyn) {
 
        for(i=0;i<count;i++) {
                /* new positions */
+               h=0.5/atom[i].mass;
                v3_scale(&delta,&(atom[i].v),tau);
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
-               v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
+               v3_scale(&delta,&(atom[i].f),h*tau_square);
                v3_add(&(atom[i].r),&(atom[i].r),&delta);
                check_per_bound(moldyn,&(atom[i].r));
 
-               /* velocities */
-               v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+               /* velocities [actually v(t+tau/2)] */
+               v3_scale(&delta,&(atom[i].f),h*tau);
                v3_add(&(atom[i].v),&(atom[i].v),&delta);
        }
 
@@ -975,7 +1033,7 @@ int velocity_verlet(t_moldyn *moldyn) {
        potential_force_calc(moldyn);
 
        for(i=0;i<count;i++) {
-               /* again velocities */
+               /* again velocities [actually v(t+tau)] */
                v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
                v3_add(&(atom[i].v),&(atom[i].v),&delta);
        }
@@ -986,7 +1044,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 /*
  *
- * potentials & corresponding forces
+ * potentials & corresponding forces & virial routine
  * 
  */
 
@@ -1010,6 +1068,8 @@ int potential_force_calc(t_moldyn *moldyn) {
 
        /* reset energy */
        moldyn->energy=0.0;
+
+       moldyn->vt2=0.0;
        
        /* get energy and force of every atom */
        for(i=0;i<count;i++) {
@@ -1025,6 +1085,7 @@ int potential_force_calc(t_moldyn *moldyn) {
                virial->xy=0.0;
                virial->xz=0.0;
                virial->yz=0.0;
+               moldyn->vt1=0.0;
 
                /* reset site energy */
                itom[i].e=0.0;
@@ -1134,6 +1195,30 @@ printf("\n\n");
 printf("\n\n");
 #endif
 
+       moldyn->vt2=0.0;
+       for(i=0;i<count;i++)
+               moldyn->vt2-=v3_scalar_product(&(itom[i].r),&(itom[i].f));
+
+printf("compare: vt1: %f vt2: %f\n",moldyn->vt1,moldyn->vt2);
+
+pressure_calc(moldyn);
+
+       return 0;
+}
+
+/*
+ * virial calculation
+ */
+
+inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d) {
+
+       a->virial.xx-=f->x*d->x;
+       a->virial.yy-=f->y*d->y;
+       a->virial.zz-=f->z*d->z;
+       a->virial.xy-=f->x*d->y;
+       a->virial.xz-=f->x*d->z;
+       a->virial.yz-=f->y*d->z;
+
        return 0;
 }
 
@@ -1179,23 +1264,29 @@ int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
        t_ho_params *params;
        t_3dvec force,distance;
-       double d;
+       double d,f;
        double sc,equi_dist;
 
        params=moldyn->pot2b_params;
        sc=params->spring_constant;
        equi_dist=params->equilibrium_distance;
 
+       if(ai<aj) return 0;
+
        v3_sub(&distance,&(aj->r),&(ai->r));
        
        if(bc) check_per_bound(moldyn,&distance);
        d=v3_norm(&distance);
        if(d<=moldyn->cutoff) {
-               /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
-               moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
+               moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
                /* f = -grad E; grad r_ij = -1 1/r_ij distance */
-               v3_scale(&force,&distance,sc*(1.0-(equi_dist/d)));
+               f=sc*(1.0-equi_dist/d);
+               v3_scale(&force,&distance,f);
                v3_add(&(ai->f),&(ai->f),&force);
+               virial_calc(ai,&force,&distance);
+               virial_calc(aj,&force,&distance); /* f and d signe switched */
+               v3_scale(&force,&distance,-f);
+               v3_add(&(aj->f),&(aj->f),&force);
        }
 
        return 0;
@@ -1215,6 +1306,8 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
        sig6=params->sigma6;
        sig12=params->sigma12;
 
+       if(ai<aj) return 0;
+
        v3_sub(&distance,&(aj->r),&(ai->r));
        if(bc) check_per_bound(moldyn,&distance);
        d=v3_absolute_square(&distance);        /* 1/r^2 */
@@ -1223,16 +1316,20 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
                h2=d*d;                         /* 1/r^4 */
                h2*=d;                          /* 1/r^6 */
                h1=h2*h2;                       /* 1/r^12 */
-               /* energy is eps*..., but we will add this twice ... */
-               moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+               moldyn->energy+=(eps*(sig12*h1-sig6*h2)-params->uc);
                h2*=d;                          /* 1/r^8 */
                h1*=d;                          /* 1/r^14 */
                h2*=6*sig6;
                h1*=12*sig12;
                d=+h1-h2;
                d*=eps;
+               v3_scale(&force,&distance,d);
+               v3_add(&(aj->f),&(aj->f),&force);
                v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
                v3_add(&(ai->f),&(ai->f),&force);
+               virial_calc(ai,&force,&distance);
+               virial_calc(aj,&force,&distance); /* f and d signe switched */
+               moldyn->vt1-=v3_scalar_product(&force,&distance);
        }
 
        return 0;
@@ -1526,7 +1623,6 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
        zeta=exchange->zeta_ij;
        if(zeta==0.0) {
                moldyn->debug++;                /* just for debugging ... */
-               db=0.0;
                b=chi;
                v3_scale(&force,dist_ij,df_a*b*f_c);
        }
@@ -1602,12 +1698,13 @@ if(ai==&(moldyn->atom[0])) {
        v3_add(&(ai->f),&(ai->f),&force);
 
        /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
-       ai->virial.xx+=force.x*dist_ij->x;
-       ai->virial.yy+=force.y*dist_ij->y;
-       ai->virial.zz+=force.z*dist_ij->z;
-       ai->virial.xy+=force.x*dist_ij->y;
-       ai->virial.xz+=force.x*dist_ij->z;
-       ai->virial.yz+=force.y*dist_ij->z;
+// TEST ... with a minus instead
+       ai->virial.xx-=force.x*dist_ij->x;
+       ai->virial.yy-=force.y*dist_ij->y;
+       ai->virial.zz-=force.z*dist_ij->z;
+       ai->virial.xy-=force.x*dist_ij->y;
+       ai->virial.xz-=force.x*dist_ij->z;
+       ai->virial.yz-=force.y*dist_ij->z;
 
 #ifdef DEBUG
 if(ai==&(moldyn->atom[0])) {

diff --git a/moldyn.h b/moldyn.h
index 23b5100..c5cc064 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -82,6 +82,7 @@ typedef struct s_moldyn {
 
        t_3dvec dim;            /* dimensions of the simulation volume */
        double volume;          /* volume of sim cell (dim.x*dim.y*dim.z) */
+       double vt1,vt2;
 
        /* potential force function and parameter pointers */
        int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
@@ -183,6 +184,7 @@ typedef struct s_lj_params {
        double sigma6;
        double sigma12;
        double epsilon4;
+       double uc;
 } t_lj_params;
 
 /*
@@ -401,11 +403,15 @@ int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
 int destroy_atoms(t_moldyn *moldyn);
 
 int thermal_init(t_moldyn *moldyn,u8 equi_init);
+double temperature_calc(t_moldyn *moldyn);
+double get_temperature(t_moldyn *moldyn);
 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
+double pressure_calc(t_moldyn *moldyn);
+double get_pressure(t_moldyn *moldyn);
 int scale_volume(t_moldyn *moldyn);
 
 double get_e_kin(t_moldyn *moldyn);
-double get_e_pot(t_moldyn *moldyn);
+double update_e_kin(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
 t_3dvec get_total_p(t_moldyn *moldyn);
 
@@ -423,9 +429,10 @@ int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);
 
 int potential_force_calc(t_moldyn *moldyn);
+inline int virial_calc(t_atom *a,t_3dvec *f,t_3dvec *d)
+       __attribute__((always_inline));
 inline int check_per_bound(t_moldyn *moldyn,t_3dvec *a)
        __attribute__((always_inline));
-int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
 int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
 int tersoff_mult_complete_params(t_tersoff_mult_params *p);

diff --git a/sic.c b/sic.c
index aabb79c..e2e8626 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -46,11 +46,17 @@ int main(int argc,char **argv) {
 
        /* choose potential */
        printf("[sic] selecting potential\n");
-       set_potential1b(&md,tersoff_mult_1bp,&tp);
-       set_potential2b(&md,tersoff_mult_2bp,&tp);
-       set_potential2b_post(&md,tersoff_mult_post_2bp,&tp);
-       set_potential3b(&md,tersoff_mult_3bp,&tp);
-       //set_potential2b(&md,lennard_jones,&lj);
+       //set_potential1b(&md,tersoff_mult_1bp,&tp);
+       //set_potential2b(&md,tersoff_mult_2bp,&tp);
+       //set_potential2b_post(&md,tersoff_mult_post_2bp,&tp);
+       //set_potential3b(&md,tersoff_mult_3bp,&tp);
+       set_potential2b(&md,lennard_jones,&lj);
+       //set_potential2b(&md,harmonic_oscillator,&ho);
+
+       /* cutoff radius */
+       printf("[sic] setting cutoff radius\n");
+       //set_cutoff(&md,TM_S_SI);
+       set_cutoff(&md,3*LC_SI);
 
        /*
         * potential parameters
@@ -61,10 +67,11 @@ int main(int argc,char **argv) {
        lj.sigma6*=lj.sigma6;
        lj.sigma12=lj.sigma6*lj.sigma6;
        lj.epsilon4=4.0*LJ_EPSILON_SI;
+       lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
 
        /* harmonic oscillator */
        ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
-       ho.spring_constant=1;
+       ho.spring_constant=.1;
 
        /*
          * tersoff mult potential parameters for SiC
@@ -97,14 +104,9 @@ int main(int argc,char **argv) {
 
        tersoff_mult_complete_params(&tp);
 
-       /* cutoff radius */
-       printf("[sic] setting cutoff radius\n");
-       set_cutoff(&md,TM_S_SI);
-       //set_cutoff(&md,2*LC_SI);
-
        /* set (initial) dimensions of simulation volume */
        printf("[sic] setting dimensions\n");
-       set_dim(&md,5*LC_SI,5*LC_SI,5*LC_SI,TRUE);
+       set_dim(&md,10*LC_SI,10*LC_SI,10*LC_SI,TRUE);
 
        /* set periodic boundary conditions in all directions */
        printf("[sic] setting periodic boundary conditions\n");
@@ -113,24 +115,26 @@ 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);
+       //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+                      ATOM_ATTR_2BP|ATOM_ATTR_HB,
+                      0,10,10,10);
        moldyn_bc_check(&md);
 
        /* testing configuration */
-       //r.x=2.8/2;    v.x=0;
+       //r.x=0.28*sqrt(3)*LC_SI/2;     v.x=0;
+       //r.x=1.75*LC_SI;       v.x=-0.01;
        //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,
+       //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
        //           &r,&v);
-       //r.x=-2.8/2;   v.x=0;
+       //r.x=-r.x;     v.x=-v.x;
        //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,
+       //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
        //           &r,&v);
 
        /* setting a nearest neighbour distance for the moldyn checks */
@@ -153,21 +157,22 @@ 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);
+       //set_pt_scale(&md,P_SCALE_BERENDSEN,100.0,0,0);
        
        /* 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,100,1.0);
+       moldyn_add_schedule(&md,10001,1.0);
 
        /* activate logging */
        printf("[sic] activate logging\n");
        moldyn_set_log_dir(&md,argv[1]);
-       moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
-       moldyn_set_log(&md,VISUAL_STEP,1);
+       moldyn_set_log(&md,LOG_TOTAL_ENERGY,10);
+       moldyn_set_log(&md,VISUAL_STEP,100);
 
        /*
         * let's do the actual md algorithm now