...

diff --git a/clean b/clean
index ca57788..1f359db 100755 (executable)
--- a/clean
+++ b/clean
@@ -1 +1,2 @@
-rm -f $1/* > /dev/null 2>&1
+rm -rf $1
+mkdir -p $1

diff --git a/moldyn.c b/moldyn.c
index 9db5cd9..94d596e 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -121,12 +121,15 @@ int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
                moldyn->vis.dim.z=z;
        }
 
+       moldyn->dv=0.0001*moldyn->volume;
+
        printf("[moldyn] dimensions in A and A^3 respectively:\n");
        printf("  x: %f\n",moldyn->dim.x);
        printf("  y: %f\n",moldyn->dim.y);
        printf("  z: %f\n",moldyn->dim.z);
        printf("  volume: %f\n",moldyn->volume);
        printf("  visualize simulation box: %s\n",visualize?"yes":"no");
+       printf("  delta volume (pressure calc): %f\n",moldyn->dv);
 
        return 0;
 }
@@ -279,6 +282,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
        count=moldyn->count;
 
        /* how many atoms do we expect */
+       if(type==CUBIC) new*=1;
        if(type==FCC) new*=4;
        if(type==DIAMOND) new*=8;
 
@@ -294,6 +298,9 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
        v3_zero(&origin);
 
        switch(type) {
+               case CUBIC:
+                       ret=cubic_init(a,b,c,atom,&origin);
+                       break;
                case FCC:
                        ret=fcc_init(a,b,c,lc,atom,&origin);
                        break;
@@ -329,6 +336,15 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
        return ret;
 }
 
+/* cubic init */
+int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+       int count;
+       t_3dvec r
+
+HIER WEITER !
+}
+
 /* fcc lattice init */
 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 
@@ -507,6 +523,7 @@ double temperature_calc(t_moldyn *moldyn) {
 
        atom=moldyn->atom;
 
+       double_ekin=0;
        for(i=0;i<moldyn->count;i++)
                double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
 
@@ -577,34 +594,153 @@ int scale_velocity(t_moldyn *moldyn,u8 equi_init) {
        return 0;
 }
 
+double ideal_gas_law_pressure(t_moldyn *moldyn) {
+
+       double p;
+
+       p=moldyn->count*moldyn->t*K_BOLTZMANN/moldyn->volume;
+printf("temp = %f => ideal gas law pressure: %f\n",moldyn->t,p/ATM);
+
+       return p;
+}
+
 double pressure_calc(t_moldyn *moldyn) {
 
        int i;
-       t_atom *atom;
-       double p1,p2,p=0;
-       
-       for(i=0;i<moldyn->count;i++) {
-               
+       double p1,p;
+       double v,h;
+       t_virial *virial;
 
+       v=0.0;
+       for(i=0;i<moldyn->count;i++) {
+               virial=&(moldyn->atom[i].virial);
+               v+=(virial->xx+virial->yy+virial->zz);
        }
 
+       h=moldyn->count*K_BOLTZMANN*moldyn->t;
+
+       p=(h-ONE_THIRD*v);
+       p/=moldyn->volume;
+
        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("debug: vt1=%f v=%f nkt=%f\n",moldyn->vt1,v,h);
 
-       printf("compare pressures: %f %f\n",p1/ATM,p2/ATM);
+       printf("compare pressures: %f %f %f\n",p1/ATM,p/ATM,h/moldyn->volume/ATM);
 
        return moldyn->p;
 }      
 
+double thermodynamic_pressure_calc(t_moldyn *moldyn) {
+
+       t_3dvec dim,*tp;
+       double u,p;
+       double scale;
+       t_atom *store;
+
+       tp=&(moldyn->tp);
+       store=malloc(moldyn->count*sizeof(t_atom));
+       if(store==NULL) {
+               printf("[moldyn] allocating store mem failed\n");
+               return -1;
+       }
+
+       /* save unscaled potential energy + atom/dim configuration */
+       u=moldyn->energy;
+       memcpy(store,moldyn->atom,moldyn->count*sizeof(t_atom));
+       dim=moldyn->dim;
+
+       /* derivative with respect to x direction */
+       scale=1.0+moldyn->dv/(moldyn->dim.y*moldyn->dim.z);
+       scale_dim(moldyn,scale,TRUE,0,0);
+       scale_atoms(moldyn,scale,TRUE,0,0);
+       potential_force_calc(moldyn);
+       tp->x=(moldyn->energy-u)/moldyn->dv;
+       p=tp->x*tp->x;
+
+       /* restore atomic configuration + dim */
+       memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+       moldyn->dim=dim;
+
+       /* derivative with respect to y direction */
+       scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.z);
+       scale_dim(moldyn,scale,0,TRUE,0);
+       scale_atoms(moldyn,scale,0,TRUE,0);
+       potential_force_calc(moldyn);
+       tp->y=(moldyn->energy-u)/moldyn->dv;
+       p+=tp->y*tp->y;
+
+       /* restore atomic configuration + dim */
+       memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+       moldyn->dim=dim;
+
+       /* derivative with respect to z direction */
+       scale=1.0+moldyn->dv/(moldyn->dim.x*moldyn->dim.y);
+       scale_dim(moldyn,scale,0,0,TRUE);
+       scale_atoms(moldyn,scale,0,0,TRUE);
+       potential_force_calc(moldyn);
+       tp->z=(moldyn->energy-u)/moldyn->dv;
+       p+=tp->z*tp->z;
+
+       /* restore atomic configuration + dim */
+       memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+       moldyn->dim=dim;
+
+       printf("dU/dV komp addiert = %f\n",(tp->x+tp->y+tp->z)/ATM);
+
+       scale=1.0+pow(moldyn->dv/moldyn->volume,ONE_THIRD);
+
+       scale_dim(moldyn,scale,1,1,1);
+       scale_dim(moldyn,scale,1,1,1);
+       potential_force_calc(moldyn);
+
+       printf("dU/dV einfach = %f\n",(moldyn->energy-u)/moldyn->dv/ATM);
+
+       /* restore atomic configuration + dim */
+       memcpy(moldyn->atom,store,moldyn->count*sizeof(t_atom));
+       moldyn->dim=dim;
+
+       /* restore energy */
+       moldyn->energy=u;
+
+       return sqrt(p);
+}
+
 double get_pressure(t_moldyn *moldyn) {
 
        return moldyn->p;
 
 }
 
+int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+       t_3dvec *dim;
+
+       dim=&(moldyn->dim);
+
+       if(x) dim->x*=scale;
+       if(y) dim->y*=scale;
+       if(z) dim->z*=scale;
+
+       return 0;
+}
+
+int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
+
+       int i;
+       t_3dvec *r;
+
+       for(i=0;i<moldyn->count;i++) {
+               r=&(moldyn->atom[i].r);
+               if(x) r->x*=scale;
+               if(y) r->y*=scale;
+               if(z) r->z*=scale;
+       }
+
+       return 0;
+}
+
 int scale_volume(t_moldyn *moldyn) {
 
        t_atom *atom;
@@ -979,22 +1115,17 @@ int moldyn_integrate(t_moldyn *moldyn) {
                if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
                        scale_volume(moldyn);
 
+printf("-> %f\n",thermodynamic_pressure_calc(moldyn)/ATM);
+
                /* 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,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)) {
@@ -1115,27 +1246,32 @@ int potential_force_calc(t_moldyn *moldyn) {
        /* reset energy */
        moldyn->energy=0.0;
 
-       moldyn->vt2=0.0;
-       
-       /* get energy and force of every atom */
+       /* reset virial */
+       moldyn->vt1=0.0;
+
+       /* reset force, site energy and virial of every atom */
        for(i=0;i<count;i++) {
 
                /* reset force */
                v3_zero(&(itom[i].f));
 
-               /* reset viral of atom i */
-               virial=&(itom[i].virial);
+               /* reset 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;
-               moldyn->vt1=0.0;
-
+       
                /* reset site energy */
                itom[i].e=0.0;
 
+       }
+
+       /* get energy,force and virial of every atom */
+       for(i=0;i<count;i++) {
+
                /* single particle potential/force */
                if(itom[i].attr&ATOM_ATTR_1BP)
                        moldyn->func1b(moldyn,&(itom[i]));
@@ -1241,13 +1377,9 @@ 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);
+temperature_calc(moldyn);
+pressure_calc(moldyn);
+ideal_gas_law_pressure(moldyn);
 
        return 0;
 }

diff --git a/moldyn.h b/moldyn.h
index 8254568..c910d7f 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -105,7 +105,9 @@ typedef struct s_moldyn {
        double t;               /* actual temperature */
 
        double p_ref;           /* reference pressure */
-       double p;               /* actual pressure */
+       double p;               /* actual pressure (computed by virial) */
+       t_3dvec tp;             /* thermodynamic pressure dU/dV */
+       double dv;              /* dV for thermodynamic pressure calc */
 
        /* pressure and temperature control (velocity/volume scaling) */
        /* (t_tc in units of tau, p_tc in units of tau * isoth. compressib.) */
@@ -407,8 +409,11 @@ 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 thermodynamic_pressure_calc(t_moldyn *moldyn);
 double get_pressure(t_moldyn *moldyn);
 int scale_volume(t_moldyn *moldyn);
+int scale_dim(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
+int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z);
 
 double get_e_kin(t_moldyn *moldyn);
 double update_e_kin(t_moldyn *moldyn);

diff --git a/sic.c b/sic.c
index a890270..5cfbb03 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -17,8 +17,16 @@ int hook(void *moldyn,void *hook_params) {
 
        md=moldyn;
 
-       /* decrease temperature in every hook */
-       set_temperature(md,md->t_ref-100.0);
+       /* switch to direct scaling in first hook */    
+       if(md->schedule.count==0)
+               set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+       /* switch off temp scaling in second hook */
+       if(md->schedule.count==1)
+               set_pt_scale(md,0,0,0,0);
+               
+       
+       //set_temperature(md,md->t_ref-100.0);
+
 
        return 0;
 }
@@ -153,29 +161,24 @@ int main(int argc,char **argv) {
        /* set p/t scaling */
        //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_DIRECT,1.0);
        //set_pt_scale(&md,P_SCALE_BERENDSEN,100.0,0,0);
        
        /* initial thermal fluctuations of particles (in equilibrium) */
        thermal_init(&md,TRUE);
 
        /* create the simulation schedule */
-       moldyn_add_schedule(&md,100,1.0);
-       moldyn_add_schedule(&md,100,1.0);
-       moldyn_add_schedule(&md,100,1.0);
-       moldyn_add_schedule(&md,100,1.0);
-       moldyn_add_schedule(&md,100,1.0);
-       moldyn_add_schedule(&md,100,1.0);
-       moldyn_add_schedule(&md,100,1.0);
-       moldyn_add_schedule(&md,100,1.0);
+       moldyn_add_schedule(&md,1001,3.0);
+       moldyn_add_schedule(&md,501,1.0);
+       moldyn_add_schedule(&md,501,1.0);
 
        /* schedule hook function */
        moldyn_set_schedule_hook(&md,&hook,NULL);
 
        /* activate logging */
        moldyn_set_log_dir(&md,argv[1]);
-       moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
-       moldyn_set_log(&md,VISUAL_STEP,10);
+       moldyn_set_log(&md,LOG_TOTAL_ENERGY,5);
+       moldyn_set_log(&md,VISUAL_STEP,50);
 
        /*
         * let's do the actual md algorithm now