#CFLAGS+=-DVDEBUG
LDFLAGS=-lm
-OBJS=visual/visual.o random/random.o
-OBJS+=moldyn.o
+SOURCE=moldyn.c visual/visual.c random/random.c
-all: clean sic
+POT_SRC=potentials/tersoff.c potentials/lennard_jones.c
+POT_SRC+= potentials/harmonic_oscillator.c
-sic: $(OBJS)
+all: sic
+
+sic:
+ $(CC) $(CFLAGS) $(LDFLAGS) $(SOURCE) $(POT_SRC) sic.c -o sic
.PHONY:clean
clean:
- rm -f *.o sic */*.o
+ rm -f sic
return 0;
}
-/* lennard jones potential & force for one sort of atoms */
-
-int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
- t_lj_params *params;
- t_3dvec force,distance;
- double d,h1,h2;
- double eps,sig6,sig12;
-
- params=moldyn->pot2b_params;
- eps=params->epsilon4;
- 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 */
- 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);
- 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,&force,-1.0); /* f = - grad E */
- v3_add(&(ai->f),&(ai->f),&force);
- virial_calc(ai,&force,&distance);
-if(force.x*distance.x<=0) printf("virial xx: %.15f -> %f %f %f\n",force.x*distance.x,distance.x,distance.y,distance.z);
- virial_calc(aj,&force,&distance); /* f and d signe switched */
- }
-
- return 0;
-}
-
-/*
- * tersoff potential & force for 2 sorts of atoms
- */
-
-/* create mixed terms from parameters and set them */
-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]);
- p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
- p->mu_m=0.5*(p->mu[0]+p->mu[1]);
-
- printf("[moldyn] tersoff mult parameter info:\n");
- printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
- printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
- printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
- printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
- printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
- p->lambda_m);
- printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
- printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
- printf(" n | %f | %f\n",p->n[0],p->n[1]);
- printf(" c | %f | %f\n",p->c[0],p->c[1]);
- printf(" d | %f | %f\n",p->d[0],p->d[1]);
- printf(" h | %f | %f\n",p->h[0],p->h[1]);
- printf(" chi | %f \n",p->chi);
-
- return 0;
-}
-
-/* tersoff 1 body part */
-int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
-
- int brand;
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
-
- brand=ai->brand;
- params=moldyn->pot1b_params;
- exchange=&(params->exchange);
-
- /*
- * simple: point constant parameters only depending on atom i to
- * their right values
- */
-
- exchange->beta_i=&(params->beta[brand]);
- exchange->n_i=&(params->n[brand]);
- exchange->c_i=&(params->c[brand]);
- exchange->d_i=&(params->d[brand]);
- exchange->h_i=&(params->h[brand]);
-
- exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
- exchange->ci2=params->c[brand]*params->c[brand];
- exchange->di2=params->d[brand]*params->d[brand];
- exchange->ci2di2=exchange->ci2/exchange->di2;
-
- return 0;
-}
-
-/* tersoff 2 body part */
-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,d_ij2;
- double A,B,R,S,S2,lambda,mu;
- double f_r,df_r;
- double f_c,df_c;
- int brand;
- double s_r;
- double arg;
-
- params=moldyn->pot2b_params;
- brand=aj->brand;
- exchange=&(params->exchange);
-
- /* clear 3bp and 2bp post run */
- exchange->run3bp=0;
- exchange->run2bp_post=0;
-
- /* reset S > r > R mark */
- exchange->d_ij_between_rs=0;
-
- /*
- * calc of 2bp contribution of V_ij and dV_ij/ji
- *
- * for Vij and dV_ij we need:
- * - f_c_ij, df_c_ij
- * - f_r_ij, df_r_ij
- *
- * for dV_ji we need:
- * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
- * - f_r_ji = f_r_ij; df_r_ji = df_r_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];
- lambda=params->lambda[brand];
- mu=params->mu[brand];
- exchange->chi=1.0;
- }
- else {
- S=params->Smixed;
- S2=params->S2mixed;
- R=params->Rmixed;
- A=params->Amixed;
- B=params->Bmixed;
- lambda=params->lambda_m;
- mu=params->mu_m;
- params->exchange.chi=params->chi;
- }
-
- /* 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->d_ij2=d_ij2;
- exchange->dist_ij=dist_ij;
-
- /* more constants */
- exchange->beta_j=&(params->beta[brand]);
- exchange->n_j=&(params->n[brand]);
- exchange->c_j=&(params->c[brand]);
- exchange->d_j=&(params->d[brand]);
- exchange->h_j=&(params->h[brand]);
- if(brand==ai->brand) {
- exchange->betajnj=exchange->betaini;
- exchange->cj2=exchange->ci2;
- exchange->dj2=exchange->di2;
- exchange->cj2dj2=exchange->ci2di2;
- }
- else {
- exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
- exchange->cj2=params->c[brand]*params->c[brand];
- exchange->dj2=params->d[brand]*params->d[brand];
- exchange->cj2dj2=exchange->cj2/exchange->dj2;
- }
-
- /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
- f_r=A*exp(-lambda*d_ij);
- df_r=lambda*f_r/d_ij;
-
- /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
- exchange->f_a=-B*exp(-mu*d_ij);
- exchange->df_a=mu*exchange->f_a/d_ij;
-
- /* f_c, df_c calc (again, same for ij and ji) */
- if(d_ij<R) {
- /* f_c = 1, df_c = 0 */
- f_c=1.0;
- df_c=0.0;
- /* two body contribution (ij, ji) */
- v3_scale(&force,&dist_ij,-df_r);
- }
- else {
- 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));
- /* two body contribution (ij, ji) */
- v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
- /* tell 3bp that S > r > R */
- exchange->d_ij_between_rs=1;
- }
-
- /* add forces of 2bp (ij, ji) contribution
- * dVij = dVji and we sum up both: no 1/2) */
- v3_add(&(ai->f),&(ai->f),&force);
-
- /* virial */
- 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])) {
- printf("dVij, dVji (2bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij, dVji (2bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
-}
-#endif
-
- /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
- moldyn->energy+=(0.5*f_r*f_c);
-
- /* save for use in 3bp */
- exchange->f_c=f_c;
- exchange->df_c=df_c;
-
- /* enable the run of 3bp function and 2bp post processing */
- exchange->run3bp=1;
- exchange->run2bp_post=1;
-
- /* reset 3bp sums */
- exchange->zeta_ij=0.0;
- exchange->zeta_ji=0.0;
- v3_zero(&(exchange->dzeta_ij));
- v3_zero(&(exchange->dzeta_ji));
-
- return 0;
-}
-
-/* tersoff 2 body post part */
-
-int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-
- /*
- * here we have to allow for the 3bp sums
- *
- * that is:
- * - zeta_ij, dzeta_ij
- * - zeta_ji, dzeta_ji
- *
- * to compute the 3bp contribution to:
- * - Vij, dVij
- * - dVji
- *
- */
-
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
-
- t_3dvec force,temp;
- t_3dvec *dist_ij;
- double b,db,tmp;
- double f_c,df_c,f_a,df_a;
- double chi,ni,betaini,nj,betajnj;
- double zeta;
-
- params=moldyn->pot2b_params;
- exchange=&(params->exchange);
-
- /* we do not run if f_c_ij was detected to be 0! */
- if(!(exchange->run2bp_post))
- return 0;
-
- f_c=exchange->f_c;
- df_c=exchange->df_c;
- f_a=exchange->f_a;
- df_a=exchange->df_a;
- betaini=exchange->betaini;
- betajnj=exchange->betajnj;
- ni=*(exchange->n_i);
- nj=*(exchange->n_j);
- chi=exchange->chi;
- dist_ij=&(exchange->dist_ij);
-
- /* Vij and dVij */
- zeta=exchange->zeta_ij;
- if(zeta==0.0) {
- moldyn->debug++; /* just for debugging ... */
- b=chi;
- v3_scale(&force,dist_ij,df_a*b*f_c);
- }
- else {
- tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
- b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
- db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
- b=db*b; /* b_ij */
- db*=-0.5*tmp; /* db_ij */
- v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
- v3_scale(&temp,dist_ij,df_a*b);
- v3_add(&force,&force,&temp);
- v3_scale(&force,&force,f_c);
- }
- v3_scale(&temp,dist_ij,df_c*b*f_a);
- v3_add(&force,&force,&temp);
- v3_scale(&force,&force,-0.5);
-
- /* add force */
- v3_add(&(ai->f),&(ai->f),&force);
-
- /* virial */
- 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])) {
- printf("dVij (3bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVij (3bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
-}
-#endif
-
- /* add energy of 3bp sum */
- moldyn->energy+=(0.5*f_c*b*f_a);
-
- /* dVji */
- zeta=exchange->zeta_ji;
- if(zeta==0.0) {
- moldyn->debug++;
- b=chi;
- v3_scale(&force,dist_ij,df_a*b*f_c);
- }
- else {
- tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
- b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
- db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
- b=db*b; /* b_ij */
- db*=-0.5*tmp; /* db_ij */
- v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
- v3_scale(&temp,dist_ij,df_a*b);
- v3_add(&force,&force,&temp);
- v3_scale(&force,&force,f_c);
- }
- v3_scale(&temp,dist_ij,df_c*b*f_a);
- v3_add(&force,&force,&temp);
- v3_scale(&force,&force,-0.5);
-
- /* add force */
- v3_add(&(ai->f),&(ai->f),&force);
-
- /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
-// 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])) {
- printf("dVji (3bp) contrib:\n");
- printf("%f | %f\n",force.x,ai->f.x);
- printf("%f | %f\n",force.y,ai->f.y);
- printf("%f | %f\n",force.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVji (3bp) contrib:\n");
- printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
- printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
- printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
-}
-#endif
-
- return 0;
-}
-
-/* tersoff 3 body part */
-
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
-
- t_tersoff_mult_params *params;
- t_tersoff_exchange *exchange;
- t_3dvec dist_ij,dist_ik,dist_jk;
- t_3dvec temp1,temp2;
- t_3dvec *dzeta;
- double R,S,S2,s_r;
- double B,mu;
- double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
- double rr,dd;
- double f_c,df_c;
- double f_c_ik,df_c_ik,arg;
- double f_c_jk;
- double n,c,d,h;
- double c2,d2,c2d2;
- double cos_theta,d_costheta1,d_costheta2;
- double h_cos,d2_h_cos2;
- double frac,g,zeta,chi;
- double tmp;
- int brand;
-
- params=moldyn->pot3b_params;
- exchange=&(params->exchange);
-
- if(!(exchange->run3bp))
- return 0;
-
- /*
- * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
- * 2bp contribution of dV_jk
- *
- * for Vij and dV_ij we still need:
- * - b_ij, db_ij (zeta_ij)
- * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
- *
- * for dV_ji we still need:
- * - b_ji, db_ji (zeta_ji)
- * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
- *
- * for dV_jk we need:
- * - f_c_jk
- * - f_a_jk
- * - db_jk (zeta_jk)
- * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
- *
- */
-
- /*
- * get exchange data
- */
-
- /* dist_ij, d_ij - this is < S_ij ! */
- dist_ij=exchange->dist_ij;
- d_ij=exchange->d_ij;
- d_ij2=exchange->d_ij2;
-
- /* f_c_ij, df_c_ij (same for ji) */
- f_c=exchange->f_c;
- df_c=exchange->df_c;
-
- /*
- * calculate unknown values now ...
- */
-
- /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
-
- /* dist_ik, d_ik */
- v3_sub(&dist_ik,&(ak->r),&(ai->r));
- if(bc) check_per_bound(moldyn,&dist_ik);
- d_ik2=v3_absolute_square(&dist_ik);
-
- /* ik constants */
- brand=ai->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
- S=params->S[brand];
- S2=params->S2[brand];
- }
- else {
- R=params->Rmixed;
- S=params->Smixed;
- S2=params->S2mixed;
- }
-
- /* zeta_ij/dzeta_ij contribution only for d_ik < S */
- if(d_ik2<S2) {
-
- /* now we need d_ik */
- d_ik=sqrt(d_ik2);
-
- /* get constants_i from exchange data */
- n=*(exchange->n_i);
- c=*(exchange->c_i);
- d=*(exchange->d_i);
- h=*(exchange->h_i);
- c2=exchange->ci2;
- d2=exchange->di2;
- c2d2=exchange->ci2di2;
-
- /* cosine of theta_ijk by scalaproduct */
- rr=v3_scalar_product(&dist_ij,&dist_ik);
- dd=d_ij*d_ik;
- cos_theta=rr/dd;
-
- /* d_costheta */
- tmp=1.0/dd;
- d_costheta1=cos_theta/d_ij2-tmp;
- d_costheta2=cos_theta/d_ik2-tmp;
-
- /* some usefull values */
- h_cos=(h-cos_theta);
- d2_h_cos2=d2+(h_cos*h_cos);
- frac=c2/(d2_h_cos2);
-
- /* g(cos_theta) */
- g=1.0+c2d2-frac;
-
- /* d_costheta_ij and dg(cos_theta) - needed in any case! */
- v3_scale(&temp1,&dist_ij,d_costheta1);
- v3_scale(&temp2,&dist_ik,d_costheta2);
- v3_add(&temp1,&temp1,&temp2);
- v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
-
- /* f_c_ik & df_c_ik + {d,}zeta contribution */
- dzeta=&(exchange->dzeta_ij);
- if(d_ik<R) {
- /* {d,}f_c_ik */
- // => f_c_ik=1.0;
- // => df_c_ik=0.0; of course we do not set this!
-
- /* zeta_ij */
- exchange->zeta_ij+=g;
-
- /* dzeta_ij */
- v3_add(dzeta,dzeta,&temp1);
- }
- else {
- /* {d,}f_c_ik */
- 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));
-
- /* zeta_ij */
- exchange->zeta_ij+=f_c_ik*g;
-
- /* dzeta_ij */
- v3_scale(&temp1,&temp1,f_c_ik);
- v3_scale(&temp2,&dist_ik,g*df_c_ik);
- v3_add(&temp1,&temp1,&temp2);
- v3_add(dzeta,dzeta,&temp1);
- }
- }
-
- /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
-
- /* dist_jk, d_jk */
- v3_sub(&dist_jk,&(ak->r),&(aj->r));
- if(bc) check_per_bound(moldyn,&dist_jk);
- d_jk2=v3_absolute_square(&dist_jk);
-
- /* jk constants */
- brand=aj->brand;
- if(brand==ak->brand) {
- R=params->R[brand];
- S=params->S[brand];
- S2=params->S2[brand];
- B=params->B[brand];
- mu=params->mu[brand];
- chi=1.0;
- }
- else {
- R=params->Rmixed;
- S=params->Smixed;
- S2=params->S2mixed;
- B=params->Bmixed;
- mu=params->mu_m;
- chi=params->chi;
- }
-
- /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
- if(d_jk2<S2) {
-
- /* now we need d_ik */
- d_jk=sqrt(d_jk2);
-
- /* constants_j from exchange data */
- n=*(exchange->n_j);
- c=*(exchange->c_j);
- d=*(exchange->d_j);
- h=*(exchange->h_j);
- c2=exchange->cj2;
- d2=exchange->dj2;
- c2d2=exchange->cj2dj2;
-
- /* cosine of theta_jik by scalaproduct */
- rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
- dd=d_ij*d_jk;
- cos_theta=rr/dd;
-
- /* d_costheta */
- d_costheta1=1.0/dd;
- d_costheta2=cos_theta/d_ij2;
-
- /* some usefull values */
- h_cos=(h-cos_theta);
- d2_h_cos2=d2+(h_cos*h_cos);
- frac=c2/(d2_h_cos2);
-
- /* g(cos_theta) */
- g=1.0+c2d2-frac;
-
- /* d_costheta_jik and dg(cos_theta) - needed in any case! */
- v3_scale(&temp1,&dist_jk,d_costheta1);
- v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
- //v3_add(&temp1,&temp1,&temp2);
- v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
- v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
-
- /* store dg in temp2 and use it for dVjk later */
- v3_copy(&temp2,&temp1);
-
- /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
- dzeta=&(exchange->dzeta_ji);
- if(d_jk<R) {
- /* f_c_jk */
- f_c_jk=1.0;
-
- /* zeta_ji */
- exchange->zeta_ji+=g;
-
- /* dzeta_ji */
- v3_add(dzeta,dzeta,&temp1);
- }
- else {
- /* f_c_jk */
- s_r=S-R;
- arg=M_PI*(d_jk-R)/s_r;
- f_c_jk=0.5+0.5*cos(arg);
-
- /* zeta_ji */
- exchange->zeta_ji+=f_c_jk*g;
-
- /* dzeta_ji */
- v3_scale(&temp1,&temp1,f_c_jk);
- v3_add(dzeta,dzeta,&temp1);
- }
-
- /* dV_jk stuff | add force contribution on atom i immediately */
- if(exchange->d_ij_between_rs) {
- zeta=f_c*g;
- v3_scale(&temp1,&temp2,f_c);
- v3_scale(&temp2,&dist_ij,df_c*g);
- v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
- }
- else {
- zeta=g;
- // dzeta_jk is simply dg, which is stored in temp2
- }
- /* betajnj * zeta_jk ^ nj-1 */
- tmp=exchange->betajnj*pow(zeta,(n-1.0));
- tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
- v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
- v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
- /* scaled with 0.5 ^ */
-
- /* virial */
- ai->virial.xx-=temp2.x*dist_jk.x;
- ai->virial.yy-=temp2.y*dist_jk.y;
- ai->virial.zz-=temp2.z*dist_jk.z;
- ai->virial.xy-=temp2.x*dist_jk.y;
- ai->virial.xz-=temp2.x*dist_jk.z;
- ai->virial.yz-=temp2.y*dist_jk.z;
-
-#ifdef DEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVjk (3bp) contrib:\n");
- printf("%f | %f\n",temp2.x,ai->f.x);
- printf("%f | %f\n",temp2.y,ai->f.y);
- printf("%f | %f\n",temp2.z,ai->f.z);
-}
-#endif
-#ifdef VDEBUG
-if(ai==&(moldyn->atom[0])) {
- printf("dVjk (3bp) contrib:\n");
- printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
- printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
- printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
-}
-#endif
-
- }
-
- return 0;
-}
-
-
/*
* debugging / critical check functions
*/
--- /dev/null
+/*
+ * harmonic_oscillator.c - harmonic oscillator potential
+ *
+ * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
+ *
+ */
+
+#define _GNU_SOURCE
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <math.h>
+
+#include "../moldyn.h"
+#include "../math/math.h"
+//#include "harmonic_oscillator.h"
+
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_ho_params *params;
+ t_3dvec force,distance;
+ 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) {
+ moldyn->energy+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+ /* f = -grad E; grad r_ij = -1 1/r_ij distance */
+ 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;
+}
+
--- /dev/null
+/*
+ * lennard_jones.c - lennard jones potential
+ *
+ * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
+ *
+ */
+
+#define _GNU_SOURCE
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <math.h>
+
+#include "../moldyn.h"
+#inlcude "../math/math.h"
+//#include "lennard_jones.h"
+
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ t_lj_params *params;
+ t_3dvec force,distance;
+ double d,h1,h2;
+ double eps,sig6,sig12;
+
+ params=moldyn->pot2b_params;
+ eps=params->epsilon4;
+ 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 */
+ if(d<=moldyn->cutoff_square) {
+ d=1.0/d; /* 1/r^2 */
+ h2=d*d; /* 1/r^4 */
+ h1=h2*h2; /* 1/r^12 */
+ 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,&force,-1.0); /* 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 */
+ }
+
+ return 0;
+}
+
--- /dev/null
+/*
+ * tersoff.c - tersoff potential
+ *
+ * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
+ *
+ */
+
+#define _GNU_SOURCE
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <math.h>
+
+#include "../moldyn.h"
+#include "../math/math.h"
+//#include "tersoff.h"
+
+/* create mixed terms from parameters and set them */
+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]);
+ p->lambda_m=0.5*(p->lambda[0]+p->lambda[1]);
+ p->mu_m=0.5*(p->mu[0]+p->mu[1]);
+
+ printf("[moldyn] tersoff mult parameter info:\n");
+ printf(" S (A) | %f | %f | %f\n",p->S[0],p->S[1],p->Smixed);
+ printf(" R (A) | %f | %f | %f\n",p->R[0],p->R[1],p->Rmixed);
+ printf(" A (eV) | %f | %f | %f\n",p->A[0]/EV,p->A[1]/EV,p->Amixed/EV);
+ printf(" B (eV) | %f | %f | %f\n",p->B[0]/EV,p->B[1]/EV,p->Bmixed/EV);
+ printf(" lambda | %f | %f | %f\n",p->lambda[0],p->lambda[1],
+ p->lambda_m);
+ printf(" mu | %f | %f | %f\n",p->mu[0],p->mu[1],p->mu_m);
+ printf(" beta | %.10f | %.10f\n",p->beta[0],p->beta[1]);
+ printf(" n | %f | %f\n",p->n[0],p->n[1]);
+ printf(" c | %f | %f\n",p->c[0],p->c[1]);
+ printf(" d | %f | %f\n",p->d[0],p->d[1]);
+ printf(" h | %f | %f\n",p->h[0],p->h[1]);
+ printf(" chi | %f \n",p->chi);
+
+ return 0;
+}
+
+/* tersoff 1 body part */
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
+
+ int brand;
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ brand=ai->brand;
+ params=moldyn->pot1b_params;
+ exchange=&(params->exchange);
+
+ /*
+ * simple: point constant parameters only depending on atom i to
+ * their right values
+ */
+
+ exchange->beta_i=&(params->beta[brand]);
+ exchange->n_i=&(params->n[brand]);
+ exchange->c_i=&(params->c[brand]);
+ exchange->d_i=&(params->d[brand]);
+ exchange->h_i=&(params->h[brand]);
+
+ exchange->betaini=pow(*(exchange->beta_i),*(exchange->n_i));
+ exchange->ci2=params->c[brand]*params->c[brand];
+ exchange->di2=params->d[brand]*params->d[brand];
+ exchange->ci2di2=exchange->ci2/exchange->di2;
+
+ return 0;
+}
+
+/* tersoff 2 body part */
+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,d_ij2;
+ double A,B,R,S,S2,lambda,mu;
+ double f_r,df_r;
+ double f_c,df_c;
+ int brand;
+ double s_r;
+ double arg;
+
+ params=moldyn->pot2b_params;
+ brand=aj->brand;
+ exchange=&(params->exchange);
+
+ /* clear 3bp and 2bp post run */
+ exchange->run3bp=0;
+ exchange->run2bp_post=0;
+
+ /* reset S > r > R mark */
+ exchange->d_ij_between_rs=0;
+
+ /*
+ * calc of 2bp contribution of V_ij and dV_ij/ji
+ *
+ * for Vij and dV_ij we need:
+ * - f_c_ij, df_c_ij
+ * - f_r_ij, df_r_ij
+ *
+ * for dV_ji we need:
+ * - f_c_ji = f_c_ij, df_c_ji = df_c_ij
+ * - f_r_ji = f_r_ij; df_r_ji = df_r_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];
+ lambda=params->lambda[brand];
+ mu=params->mu[brand];
+ exchange->chi=1.0;
+ }
+ else {
+ S=params->Smixed;
+ S2=params->S2mixed;
+ R=params->Rmixed;
+ A=params->Amixed;
+ B=params->Bmixed;
+ lambda=params->lambda_m;
+ mu=params->mu_m;
+ params->exchange.chi=params->chi;
+ }
+
+ /* 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->d_ij2=d_ij2;
+ exchange->dist_ij=dist_ij;
+
+ /* more constants */
+ exchange->beta_j=&(params->beta[brand]);
+ exchange->n_j=&(params->n[brand]);
+ exchange->c_j=&(params->c[brand]);
+ exchange->d_j=&(params->d[brand]);
+ exchange->h_j=&(params->h[brand]);
+ if(brand==ai->brand) {
+ exchange->betajnj=exchange->betaini;
+ exchange->cj2=exchange->ci2;
+ exchange->dj2=exchange->di2;
+ exchange->cj2dj2=exchange->ci2di2;
+ }
+ else {
+ exchange->betajnj=pow(*(exchange->beta_j),*(exchange->n_j));
+ exchange->cj2=params->c[brand]*params->c[brand];
+ exchange->dj2=params->d[brand]*params->d[brand];
+ exchange->cj2dj2=exchange->cj2/exchange->dj2;
+ }
+
+ /* f_r_ij = f_r_ji, df_r_ij = df_r_ji */
+ f_r=A*exp(-lambda*d_ij);
+ df_r=lambda*f_r/d_ij;
+
+ /* f_a, df_a calc (again, same for ij and ji) | save for later use! */
+ exchange->f_a=-B*exp(-mu*d_ij);
+ exchange->df_a=mu*exchange->f_a/d_ij;
+
+ /* f_c, df_c calc (again, same for ij and ji) */
+ if(d_ij<R) {
+ /* f_c = 1, df_c = 0 */
+ f_c=1.0;
+ df_c=0.0;
+ /* two body contribution (ij, ji) */
+ v3_scale(&force,&dist_ij,-df_r);
+ }
+ else {
+ 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));
+ /* two body contribution (ij, ji) */
+ v3_scale(&force,&dist_ij,-df_c*f_r-df_r*f_c);
+ /* tell 3bp that S > r > R */
+ exchange->d_ij_between_rs=1;
+ }
+
+ /* add forces of 2bp (ij, ji) contribution
+ * dVij = dVji and we sum up both: no 1/2) */
+ v3_add(&(ai->f),&(ai->f),&force);
+
+ /* virial */
+ 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])) {
+ printf("dVij, dVji (2bp) contrib:\n");
+ printf("%f | %f\n",force.x,ai->f.x);
+ printf("%f | %f\n",force.y,ai->f.y);
+ printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVij, dVji (2bp) contrib:\n");
+ printf("%f | %f\n",force.x*dist_ij.x,ai->virial.xx);
+ printf("%f | %f\n",force.y*dist_ij.y,ai->virial.yy);
+ printf("%f | %f\n",force.z*dist_ij.z,ai->virial.zz);
+}
+#endif
+
+ /* energy 2bp contribution (ij, ji) is 0.5 f_r f_c ... */
+ moldyn->energy+=(0.5*f_r*f_c);
+
+ /* save for use in 3bp */
+ exchange->f_c=f_c;
+ exchange->df_c=df_c;
+
+ /* enable the run of 3bp function and 2bp post processing */
+ exchange->run3bp=1;
+ exchange->run2bp_post=1;
+
+ /* reset 3bp sums */
+ exchange->zeta_ij=0.0;
+ exchange->zeta_ji=0.0;
+ v3_zero(&(exchange->dzeta_ij));
+ v3_zero(&(exchange->dzeta_ji));
+
+ return 0;
+}
+
+/* tersoff 2 body post part */
+
+int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
+
+ /*
+ * here we have to allow for the 3bp sums
+ *
+ * that is:
+ * - zeta_ij, dzeta_ij
+ * - zeta_ji, dzeta_ji
+ *
+ * to compute the 3bp contribution to:
+ * - Vij, dVij
+ * - dVji
+ *
+ */
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+
+ t_3dvec force,temp;
+ t_3dvec *dist_ij;
+ double b,db,tmp;
+ double f_c,df_c,f_a,df_a;
+ double chi,ni,betaini,nj,betajnj;
+ double zeta;
+
+ params=moldyn->pot2b_params;
+ exchange=&(params->exchange);
+
+ /* we do not run if f_c_ij was detected to be 0! */
+ if(!(exchange->run2bp_post))
+ return 0;
+
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
+ f_a=exchange->f_a;
+ df_a=exchange->df_a;
+ betaini=exchange->betaini;
+ betajnj=exchange->betajnj;
+ ni=*(exchange->n_i);
+ nj=*(exchange->n_j);
+ chi=exchange->chi;
+ dist_ij=&(exchange->dist_ij);
+
+ /* Vij and dVij */
+ zeta=exchange->zeta_ij;
+ if(zeta==0.0) {
+ moldyn->debug++; /* just for debugging ... */
+ b=chi;
+ v3_scale(&force,dist_ij,df_a*b*f_c);
+ }
+ else {
+ tmp=betaini*pow(zeta,ni-1.0); /* beta^n * zeta^n-1 */
+ b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
+ db=chi*pow(b,-1.0/(2*ni)-1); /* x(...)^(-1/2n - 1) */
+ b=db*b; /* b_ij */
+ db*=-0.5*tmp; /* db_ij */
+ v3_scale(&force,&(exchange->dzeta_ij),f_a*db);
+ v3_scale(&temp,dist_ij,df_a*b);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,f_c);
+ }
+ v3_scale(&temp,dist_ij,df_c*b*f_a);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-0.5);
+
+ /* add force */
+ v3_add(&(ai->f),&(ai->f),&force);
+
+ /* virial */
+ 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])) {
+ printf("dVij (3bp) contrib:\n");
+ printf("%f | %f\n",force.x,ai->f.x);
+ printf("%f | %f\n",force.y,ai->f.y);
+ printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVij (3bp) contrib:\n");
+ printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
+ printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
+ printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+}
+#endif
+
+ /* add energy of 3bp sum */
+ moldyn->energy+=(0.5*f_c*b*f_a);
+
+ /* dVji */
+ zeta=exchange->zeta_ji;
+ if(zeta==0.0) {
+ moldyn->debug++;
+ b=chi;
+ v3_scale(&force,dist_ij,df_a*b*f_c);
+ }
+ else {
+ tmp=betajnj*pow(zeta,nj-1.0); /* beta^n * zeta^n-1 */
+ b=(1+zeta*tmp); /* 1 + beta^n zeta^n */
+ db=chi*pow(b,-1.0/(2*nj)-1); /* x(...)^(-1/2n - 1) */
+ b=db*b; /* b_ij */
+ db*=-0.5*tmp; /* db_ij */
+ v3_scale(&force,&(exchange->dzeta_ji),f_a*db);
+ v3_scale(&temp,dist_ij,df_a*b);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,f_c);
+ }
+ v3_scale(&temp,dist_ij,df_c*b*f_a);
+ v3_add(&force,&force,&temp);
+ v3_scale(&force,&force,-0.5);
+
+ /* add force */
+ v3_add(&(ai->f),&(ai->f),&force);
+
+ /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
+// 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])) {
+ printf("dVji (3bp) contrib:\n");
+ printf("%f | %f\n",force.x,ai->f.x);
+ printf("%f | %f\n",force.y,ai->f.y);
+ printf("%f | %f\n",force.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVji (3bp) contrib:\n");
+ printf("%f | %f\n",force.x*dist_ij->x,ai->virial.xx);
+ printf("%f | %f\n",force.y*dist_ij->y,ai->virial.yy);
+ printf("%f | %f\n",force.z*dist_ij->z,ai->virial.zz);
+}
+#endif
+
+ return 0;
+}
+
+/* tersoff 3 body part */
+
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ t_3dvec dist_ij,dist_ik,dist_jk;
+ t_3dvec temp1,temp2;
+ t_3dvec *dzeta;
+ double R,S,S2,s_r;
+ double B,mu;
+ double d_ij,d_ik,d_jk,d_ij2,d_ik2,d_jk2;
+ double rr,dd;
+ double f_c,df_c;
+ double f_c_ik,df_c_ik,arg;
+ double f_c_jk;
+ double n,c,d,h;
+ double c2,d2,c2d2;
+ double cos_theta,d_costheta1,d_costheta2;
+ double h_cos,d2_h_cos2;
+ double frac,g,zeta,chi;
+ double tmp;
+ int brand;
+
+ params=moldyn->pot3b_params;
+ exchange=&(params->exchange);
+
+ if(!(exchange->run3bp))
+ return 0;
+
+ /*
+ * calc of 3bp contribution of V_ij and dV_ij/ji/jk &
+ * 2bp contribution of dV_jk
+ *
+ * for Vij and dV_ij we still need:
+ * - b_ij, db_ij (zeta_ij)
+ * - f_c_ik, df_c_ik, constants_i, cos_theta_ijk, d_costheta_ijk
+ *
+ * for dV_ji we still need:
+ * - b_ji, db_ji (zeta_ji)
+ * - f_c_jk, d_c_jk, constants_j, cos_theta_jik, d_costheta_jik
+ *
+ * for dV_jk we need:
+ * - f_c_jk
+ * - f_a_jk
+ * - db_jk (zeta_jk)
+ * - f_c_ji, df_c_ji, constants_j, cos_theta_jki, d_costheta_jki
+ *
+ */
+
+ /*
+ * get exchange data
+ */
+
+ /* dist_ij, d_ij - this is < S_ij ! */
+ dist_ij=exchange->dist_ij;
+ d_ij=exchange->d_ij;
+ d_ij2=exchange->d_ij2;
+
+ /* f_c_ij, df_c_ij (same for ji) */
+ f_c=exchange->f_c;
+ df_c=exchange->df_c;
+
+ /*
+ * calculate unknown values now ...
+ */
+
+ /* V_ij and dV_ij stuff (in b_ij there is f_c_ik) */
+
+ /* dist_ik, d_ik */
+ v3_sub(&dist_ik,&(ak->r),&(ai->r));
+ if(bc) check_per_bound(moldyn,&dist_ik);
+ d_ik2=v3_absolute_square(&dist_ik);
+
+ /* ik constants */
+ brand=ai->brand;
+ if(brand==ak->brand) {
+ R=params->R[brand];
+ S=params->S[brand];
+ S2=params->S2[brand];
+ }
+ else {
+ R=params->Rmixed;
+ S=params->Smixed;
+ S2=params->S2mixed;
+ }
+
+ /* zeta_ij/dzeta_ij contribution only for d_ik < S */
+ if(d_ik2<S2) {
+
+ /* now we need d_ik */
+ d_ik=sqrt(d_ik2);
+
+ /* get constants_i from exchange data */
+ n=*(exchange->n_i);
+ c=*(exchange->c_i);
+ d=*(exchange->d_i);
+ h=*(exchange->h_i);
+ c2=exchange->ci2;
+ d2=exchange->di2;
+ c2d2=exchange->ci2di2;
+
+ /* cosine of theta_ijk by scalaproduct */
+ rr=v3_scalar_product(&dist_ij,&dist_ik);
+ dd=d_ij*d_ik;
+ cos_theta=rr/dd;
+
+ /* d_costheta */
+ tmp=1.0/dd;
+ d_costheta1=cos_theta/d_ij2-tmp;
+ d_costheta2=cos_theta/d_ik2-tmp;
+
+ /* some usefull values */
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+ frac=c2/(d2_h_cos2);
+
+ /* g(cos_theta) */
+ g=1.0+c2d2-frac;
+
+ /* d_costheta_ij and dg(cos_theta) - needed in any case! */
+ v3_scale(&temp1,&dist_ij,d_costheta1);
+ v3_scale(&temp2,&dist_ik,d_costheta2);
+ v3_add(&temp1,&temp1,&temp2);
+ v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+ /* f_c_ik & df_c_ik + {d,}zeta contribution */
+ dzeta=&(exchange->dzeta_ij);
+ if(d_ik<R) {
+ /* {d,}f_c_ik */
+ // => f_c_ik=1.0;
+ // => df_c_ik=0.0; of course we do not set this!
+
+ /* zeta_ij */
+ exchange->zeta_ij+=g;
+
+ /* dzeta_ij */
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ else {
+ /* {d,}f_c_ik */
+ 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));
+
+ /* zeta_ij */
+ exchange->zeta_ij+=f_c_ik*g;
+
+ /* dzeta_ij */
+ v3_scale(&temp1,&temp1,f_c_ik);
+ v3_scale(&temp2,&dist_ik,g*df_c_ik);
+ v3_add(&temp1,&temp1,&temp2);
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ }
+
+ /* dV_ji stuff (in b_ji there is f_c_jk) + dV_jk stuff! */
+
+ /* dist_jk, d_jk */
+ v3_sub(&dist_jk,&(ak->r),&(aj->r));
+ if(bc) check_per_bound(moldyn,&dist_jk);
+ d_jk2=v3_absolute_square(&dist_jk);
+
+ /* jk constants */
+ brand=aj->brand;
+ if(brand==ak->brand) {
+ R=params->R[brand];
+ S=params->S[brand];
+ S2=params->S2[brand];
+ B=params->B[brand];
+ mu=params->mu[brand];
+ chi=1.0;
+ }
+ else {
+ R=params->Rmixed;
+ S=params->Smixed;
+ S2=params->S2mixed;
+ B=params->Bmixed;
+ mu=params->mu_m;
+ chi=params->chi;
+ }
+
+ /* zeta_ji/dzeta_ji contribution only for d_jk < S_jk */
+ if(d_jk2<S2) {
+
+ /* now we need d_ik */
+ d_jk=sqrt(d_jk2);
+
+ /* constants_j from exchange data */
+ n=*(exchange->n_j);
+ c=*(exchange->c_j);
+ d=*(exchange->d_j);
+ h=*(exchange->h_j);
+ c2=exchange->cj2;
+ d2=exchange->dj2;
+ c2d2=exchange->cj2dj2;
+
+ /* cosine of theta_jik by scalaproduct */
+ rr=-v3_scalar_product(&dist_ij,&dist_jk); /* -1, as ij -> ji */
+ dd=d_ij*d_jk;
+ cos_theta=rr/dd;
+
+ /* d_costheta */
+ d_costheta1=1.0/dd;
+ d_costheta2=cos_theta/d_ij2;
+
+ /* some usefull values */
+ h_cos=(h-cos_theta);
+ d2_h_cos2=d2+(h_cos*h_cos);
+ frac=c2/(d2_h_cos2);
+
+ /* g(cos_theta) */
+ g=1.0+c2d2-frac;
+
+ /* d_costheta_jik and dg(cos_theta) - needed in any case! */
+ v3_scale(&temp1,&dist_jk,d_costheta1);
+ v3_scale(&temp2,&dist_ij,-d_costheta2); /* ji -> ij => -1 */
+ //v3_add(&temp1,&temp1,&temp2);
+ v3_sub(&temp1,&temp1,&temp2); /* there is a minus! */
+ v3_scale(&temp1,&temp1,-2.0*frac*h_cos/d2_h_cos2); /* dg */
+
+ /* store dg in temp2 and use it for dVjk later */
+ v3_copy(&temp2,&temp1);
+
+ /* f_c_jk + {d,}zeta contribution (df_c_jk = 0) */
+ dzeta=&(exchange->dzeta_ji);
+ if(d_jk<R) {
+ /* f_c_jk */
+ f_c_jk=1.0;
+
+ /* zeta_ji */
+ exchange->zeta_ji+=g;
+
+ /* dzeta_ji */
+ v3_add(dzeta,dzeta,&temp1);
+ }
+ else {
+ /* f_c_jk */
+ s_r=S-R;
+ arg=M_PI*(d_jk-R)/s_r;
+ f_c_jk=0.5+0.5*cos(arg);
+
+ /* zeta_ji */
+ exchange->zeta_ji+=f_c_jk*g;
+
+ /* dzeta_ji */
+ v3_scale(&temp1,&temp1,f_c_jk);
+ v3_add(dzeta,dzeta,&temp1);
+ }
+
+ /* dV_jk stuff | add force contribution on atom i immediately */
+ if(exchange->d_ij_between_rs) {
+ zeta=f_c*g;
+ v3_scale(&temp1,&temp2,f_c);
+ v3_scale(&temp2,&dist_ij,df_c*g);
+ v3_add(&temp2,&temp2,&temp1); /* -> dzeta_jk in temp2 */
+ }
+ else {
+ zeta=g;
+ // dzeta_jk is simply dg, which is stored in temp2
+ }
+ /* betajnj * zeta_jk ^ nj-1 */
+ tmp=exchange->betajnj*pow(zeta,(n-1.0));
+ tmp=-chi/2.0*pow((1+tmp*zeta),(-1.0/(2.0*n)-1))*tmp;
+ v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
+ v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
+ /* scaled with 0.5 ^ */
+
+ /* virial */
+ ai->virial.xx-=temp2.x*dist_jk.x;
+ ai->virial.yy-=temp2.y*dist_jk.y;
+ ai->virial.zz-=temp2.z*dist_jk.z;
+ ai->virial.xy-=temp2.x*dist_jk.y;
+ ai->virial.xz-=temp2.x*dist_jk.z;
+ ai->virial.yz-=temp2.y*dist_jk.z;
+
+#ifdef DEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVjk (3bp) contrib:\n");
+ printf("%f | %f\n",temp2.x,ai->f.x);
+ printf("%f | %f\n",temp2.y,ai->f.y);
+ printf("%f | %f\n",temp2.z,ai->f.z);
+}
+#endif
+#ifdef VDEBUG
+if(ai==&(moldyn->atom[0])) {
+ printf("dVjk (3bp) contrib:\n");
+ printf("%f | %f\n",temp2.x*dist_jk.x,ai->virial.xx);
+ printf("%f | %f\n",temp2.y*dist_jk.y,ai->virial.yy);
+ printf("%f | %f\n",temp2.z*dist_jk.z,ai->virial.zz);
+}
+#endif
+
+ }
+
+ return 0;
+}
+
projects / physik / posic.git / commitdiff