#include "potentials/harmonic_oscillator.h"
#include "potentials/lennard_jones.h"
#include "potentials/albe.h"
+#include "potentials/albe_orig.h"
#ifdef TERSOFF_ORIG
#include "potentials/tersoff_orig.h"
#else
pthread_mutex_t emutex;
#endif
+/* fully constrained relaxation technique - global pointers */
+u8 crtt;
+u8 *constraints;
+double *trafo_angle;
+
/*
* the moldyn functions
*/
pthread_mutex_init(&emutex,NULL);
#endif
-#ifdef CONSTRAINT_110_5832
- printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n");
- printf("\n\n\n!! -- constraints enabled -- !!\n\n\n");
-#endif
return 0;
}
moldyn->func3b_k2=tersoff_mult_3bp_k2;
moldyn->check_2b_bond=tersoff_mult_check_2b_bond;
break;
+ case MOLDYN_POTENTIAL_AO:
+ moldyn->func_j1=albe_orig_mult_3bp_j1;
+ moldyn->func_j1_k0=albe_orig_mult_3bp_k1;
+ moldyn->func_j1c=albe_orig_mult_3bp_j2;
+ moldyn->func_j1_k1=albe_orig_mult_3bp_k2;
+ moldyn->check_2b_bond=albe_orig_mult_check_2b_bond;
+ break;
case MOLDYN_POTENTIAL_AM:
- moldyn->func3b_j1=albe_mult_3bp_j1;
- moldyn->func3b_k1=albe_mult_3bp_k1;
- moldyn->func3b_j2=albe_mult_3bp_j2;
- moldyn->func3b_k2=albe_mult_3bp_k2;
+ moldyn->func_i0=albe_mult_i0;
+ moldyn->func_j0=albe_mult_i0_j0;
+ moldyn->func_j0_k0=albe_mult_i0_j0_k0;
+ moldyn->func_j0e=albe_mult_i0_j1;
+ moldyn->func_j1=albe_mult_i0_j2;
+ moldyn->func_j1_k0=albe_mult_i0_j2_k0;
+ moldyn->func_j1c=albe_mult_i0_j3;
moldyn->check_2b_bond=albe_mult_check_2b_bond;
break;
case MOLDYN_POTENTIAL_HO:
- moldyn->func2b=harmonic_oscillator;
+ moldyn->func_j0=harmonic_oscillator;
moldyn->check_2b_bond=harmonic_oscillator_check_2b_bond;
break;
case MOLDYN_POTENTIAL_LJ:
- moldyn->func2b=lennard_jones;
+ moldyn->func_j0=lennard_jones;
moldyn->check_2b_bond=lennard_jones_check_2b_bond;
break;
default:
return 0;
}
+/* basis trafo */
+
+#define FORWARD 0
+#define BACKWARD 1
+
+int basis_trafo(t_3dvec *r,u8 dir,double z,double x) {
+
+ t_3dvec tmp;
+
+ if(dir==FORWARD) {
+ if(z!=0.0) {
+ v3_copy(&tmp,r);
+ r->x=cos(z)*tmp.x-sin(z)*tmp.y;
+ r->y=sin(z)*tmp.x+cos(z)*tmp.y;
+ }
+ if(x!=0.0) {
+ v3_copy(&tmp,r);
+ r->y=cos(x)*tmp.y-sin(x)*tmp.z;
+ r->z=sin(x)*tmp.y+cos(x)*tmp.z;
+ }
+ }
+ else {
+ if(x!=0.0) {
+ v3_copy(&tmp,r);
+ r->y=cos(-x)*tmp.y-sin(-x)*tmp.z;
+ r->z=sin(-x)*tmp.y+cos(-x)*tmp.z;
+ }
+ if(z!=0.0) {
+ v3_copy(&tmp,r);
+ r->x=cos(-z)*tmp.x-sin(-z)*tmp.y;
+ r->y=sin(-z)*tmp.x+cos(-z)*tmp.y;
+ }
+ }
+
+ return 0;
+}
+
/* velocity verlet */
int velocity_verlet(t_moldyn *moldyn) {
tau=moldyn->tau;
tau_square=moldyn->tau_square;
-#ifdef CONSTRAINT_110_5832
- if(count==5833) {
- atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
- atom[5832].f.y=-atom[5832].f.x;
- }
-#endif
for(i=0;i<count;i++) {
+
/* check whether fixed atom */
if(atom[i].attr&ATOM_ATTR_FP)
continue;
+
/* new positions */
h=0.5/atom[i].mass;
- v3_scale(&delta,&(atom[i].v),tau);
-#ifdef CONSTRAINT_110_5832
- if(i==5832) {
- delta.y=-delta.x;
+
+ /* constraint relaxation */
+ if(crtt) {
+ // forces
+ basis_trafo(&(atom[i].f),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].f.x=0;
+ if(constraints[3*i+1])
+ atom[i].f.y=0;
+ if(constraints[3*i+2])
+ atom[i].f.z=0;
+ basis_trafo(&(atom[i].f),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ // velocities
+ basis_trafo(&(atom[i].v),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].v.x=0;
+ if(constraints[3*i+1])
+ atom[i].v.y=0;
+ if(constraints[3*i+2])
+ atom[i].v.z=0;
+ basis_trafo(&(atom[i].v),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
}
-#endif
+
#ifndef QUENCH
+ v3_scale(&delta,&(atom[i].v),tau);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
#endif
v3_scale(&delta,&(atom[i].f),h*tau_square);
-#ifdef CONSTRAINT_110_5832
- if(i==5832) {
- delta.y=-delta.x;
- }
-#endif
v3_add(&(atom[i].r),&(atom[i].r),&delta);
//check_per_bound_and_care_for_pbc(moldyn,&(atom[i]));
check_per_bound(moldyn,&(atom[i].r));
albe_potential_force_calc(moldyn);
#endif
-#ifdef CONSTRAINT_110_5832
- if(count==5833) {
- atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
- atom[5832].f.y=-atom[5832].f.x;
- }
-#endif
for(i=0;i<count;i++) {
/* check whether fixed atom */
if(atom[i].attr&ATOM_ATTR_FP)
continue;
+
+ /* constraint relaxation */
+ if(crtt) {
+ // forces
+ basis_trafo(&(atom[i].f),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].f.x=0;
+ if(constraints[3*i+1])
+ atom[i].f.y=0;
+ if(constraints[3*i+2])
+ atom[i].f.z=0;
+ basis_trafo(&(atom[i].f),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ // velocities
+ basis_trafo(&(atom[i].v),FORWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ if(constraints[3*i])
+ atom[i].v.x=0;
+ if(constraints[3*i+1])
+ atom[i].v.y=0;
+ if(constraints[3*i+2])
+ atom[i].v.z=0;
+ basis_trafo(&(atom[i].v),BACKWARD,
+ trafo_angle[2*i],trafo_angle[2*i+1]);
+ }
+
/* 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);
/* single particle potential/force */
if(itom[i].attr&ATOM_ATTR_1BP)
- if(moldyn->func1b)
- moldyn->func1b(moldyn,&(itom[i]));
+ if(moldyn->func_i0)
+ moldyn->func_i0(moldyn,&(itom[i]));
if(!(itom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)))
continue;
dnlc=lc->dnlc;
+#ifndef STATIC_LISTS
+ /* check for later 3 body interaction */
+ if(itom[i].attr&ATOM_ATTR_3BP)
+ memcpy(neighbour_i2,neighbour_i,27*sizeof(t_list));
+#endif
+
/* first loop over atoms j */
- if(moldyn->func2b) {
+ if(moldyn->func_j0) {
for(j=0;j<27;j++) {
bc_ij=(j<dnlc)?0:1;
if(jtom==&(itom[i]))
continue;
+ /* reset 3bp run */
+ moldyn->run3bp=1;
+
if((jtom->attr&ATOM_ATTR_2BP)&
(itom[i].attr&ATOM_ATTR_2BP)) {
- moldyn->func2b(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
+ moldyn->func_j0(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
+ }
+
+ /* 3 body potential/force */
+
+ /* in j loop, 3bp run can be skipped */
+ if(!(moldyn->run3bp))
+ continue;
+
+ if(!(itom[i].attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(!(jtom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(moldyn->func_j0_k0==NULL)
+ continue;
+
+ /* first loop over atoms k in first j loop */
+ for(k=0;k<27;k++) {
+
+ bc_ik=(k<dnlc)?0:1;
+#ifdef STATIC_LISTS
+ q=0;
+
+ while(neighbour_i[j][q]!=0) {
+
+ ktom=&(atom[neighbour_i[k][q]]);
+ q++;
+#else
+ that=&(neighbour_i2[k]);
+ list_reset_f(that);
+
+ if(that->start==NULL)
+ continue;
+
+ do {
+ ktom=that->current->data;
+#endif
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ //if(ktom==jtom)
+ // continue;
+
+ if(ktom==&(itom[i]))
+ continue;
+
+ moldyn->func_j0_k0(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
+#ifdef STATIC_LISTS
}
#ifdef STATIC_LISTS
}
}
}
- /* 3 body potential/force */
+ /* continued 3 body potential/force */
if(!(itom[i].attr&ATOM_ATTR_3BP))
continue;
/* reset 3bp run */
moldyn->run3bp=1;
- if(moldyn->func3b_j1)
- moldyn->func3b_j1(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
+ if(moldyn->func_j1)
+ moldyn->func_j1(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
- /* in first j loop, 3bp run can be skipped */
+ /* in j loop, 3bp run can be skipped */
if(!(moldyn->run3bp))
continue;
- /* first loop over atoms k */
- if(moldyn->func3b_k1) {
+ /* first loop over atoms k in second j loop */
+ if(moldyn->func_j1_k0) {
for(k=0;k<27;k++) {
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
- if(ktom==jtom)
- continue;
+ //if(ktom==jtom)
+ // continue;
if(ktom==&(itom[i]))
continue;
}
- if(moldyn->func3b_j2)
- moldyn->func3b_j2(moldyn,
- &(itom[i]),
- jtom,
- bc_ij);
+ /* continued j loop after first k loop */
+ if(moldyn->func_j1c)
+ moldyn->func_j1c(moldyn,
+ &(itom[i]),
+ jtom,
+ bc_ij);
/* second loop over atoms k */
- if(moldyn->func3b_k2) {
+ if(moldyn->func_j1_k1) {
for(k=0;k<27;k++) {
if(!(ktom->attr&ATOM_ATTR_3BP))
continue;
- if(ktom==jtom)
- continue;
+ //if(ktom==jtom)
+ // continue;
if(ktom==&(itom[i]))
continue;
- moldyn->func3b_k2(moldyn,
- &(itom[i]),
- jtom,
- ktom,
- bc_ik|bc_ij);
+ moldyn->func_j1_k1(moldyn,
+ &(itom[i]),
+ jtom,
+ ktom,
+ bc_ik|bc_ij);
#ifdef STATIC_LISTS
}
}
- /* 2bp post function */
- if(moldyn->func3b_j3) {
- moldyn->func3b_j3(moldyn,
- &(itom[i]),
- jtom,bc_ij);
+ /* finish of j loop after second k loop */
+ if(moldyn->func_j1e) {
+ moldyn->func_j1e(moldyn,
+ &(itom[i]),
+ jtom,bc_ij);
}
#ifdef STATIC_LISTS
}
#endif
}
-
+
#ifdef DEBUG
//printf("\n\n");
#endif
return 0;
}
+int calculate_msd(t_moldyn *moldyn,double *msd) {
+
+ int i;
+ t_atom *atom;
+ t_3dvec dist;
+ t_3dvec final_r;
+ double d2;
+ int a_cnt;
+ int b_cnt;
+
+ atom=moldyn->atom;
+ msd[0]=0;
+ msd[1]=0;
+ msd[2]=0;
+ a_cnt=0;
+ b_cnt=0;
+
+ for(i=0;i<moldyn->count;i++) {
+
+ /* care for pb crossing */
+ if(atom[i].pbc[0]|atom[i].pbc[1]|atom[i].pbc[2]) {
+ printf("[moldyn] msd pb crossings for atom %d\n",i);
+ printf(" x: %d y: %d z: %d\n",
+ atom[i].pbc[0],atom[i].pbc[1],atom[i].pbc[2]);
+ }
+ final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
+ final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
+ final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
+ /* calculate distance */
+ v3_sub(&dist,&final_r,&(atom[i].r_0));
+ d2=v3_absolute_square(&dist);
+
+ if(atom[i].brand) {
+ b_cnt+=1;
+ msd[1]+=d2;
+ }
+ else {
+ a_cnt+=1;
+ msd[0]+=d2;
+ }
+
+ msd[2]+=d2;
+ }
+
+ msd[0]/=a_cnt;
+ msd[1]/=b_cnt;
+ msd[2]/=moldyn->count;
+
+ return 0;
+}
+
int bonding_analyze(t_moldyn *moldyn,double *cnt) {
return 0;
projects / physik / posic.git / blobdiff