mirror of https://github.com/lammps/lammps.git
Refactored pair body rounded/polyhedron so that kernel_force() can be derived for other styles
This commit is contained in:
Trung Nguyen
parent
7aab932731
commit
d4cca615fb
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@ -1,9 +1,9 @@
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# 2d rounded polygon bodies
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variable r index 3
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variable r index 4
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variable steps index 100000
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variable T index 0.5
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variable P index 0.2
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variable P index 0.1
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variable seed index 980411
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units lj
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@ -48,9 +48,7 @@ dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
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thermo_style custom step ke pe etotal press
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thermo 1000
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restart 100000 restart1.bin restart2.bin
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#dump 2 all image 10000 image.*.jpg type type zoom 2.0 adiam 1.5 body yes 0 0
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#dump_modify 2 pad 6
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run ${steps}
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run ${steps}
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@ -123,7 +123,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
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int i,j,ii,jj,inum,jnum,itype,jtype;
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int ni,nj,npi,npj,ifirst,jfirst,nei,nej,iefirst,jefirst;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,facc[3];
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double rsq,eradi,eradj,k_nij,k_naij;
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double rsq,eradi,eradj;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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@ -215,9 +215,6 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
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nej = ednum[j];
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jefirst = edfirst[j];
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eradj = enclosing_radius[j];
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k_nij = k_n[itype][jtype];
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k_naij = k_na[itype][jtype];
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// no interaction
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@ -227,8 +224,8 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
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// sphere-sphere interaction
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if (npi == 1 && npj == 1) {
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sphere_against_sphere(i, j, delx, dely, delz, rsq,
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k_nij, k_naij, v, f, evflag);
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sphere_against_sphere(i, j, itype, jtype, delx, dely, delz,
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rsq, v, f, evflag);
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continue;
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}
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@ -265,15 +262,15 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
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// one of the two bodies is a sphere
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if (npj == 1) {
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sphere_against_face(i, j, k_nij, k_naij, x, v, f, torque,
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sphere_against_face(i, j, itype, jtype, x, v, f, torque,
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angmom, evflag);
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sphere_against_edge(i, j, k_nij, k_naij, x, v, f, torque,
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sphere_against_edge(i, j, itype, jtype, x, v, f, torque,
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angmom, evflag);
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continue;
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} else if (npi == 1) {
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sphere_against_face(j, i, k_nij, k_naij, x, v, f, torque,
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sphere_against_face(j, i, jtype, itype, x, v, f, torque,
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angmom, evflag);
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sphere_against_edge(j, i, k_nij, k_naij, x, v, f, torque,
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sphere_against_edge(j, i, jtype, itype, x, v, f, torque,
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angmom, evflag);
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continue;
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}
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@ -287,21 +284,21 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
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#ifdef _POLYHEDRON_DEBUG
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printf("INTERACTION between edges of %d vs. faces of %d:\n", i, j);
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#endif
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interact = edge_against_face(i, j, k_nij, k_naij, x, contact_list,
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interact = edge_against_face(i, j, itype, jtype, x, contact_list,
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num_contacts, evdwl, facc);
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// check interaction between j's edges and i' faces
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#ifdef _POLYHEDRON_DEBUG
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printf("\nINTERACTION between edges of %d vs. faces of %d:\n", j, i);
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#endif
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interact = edge_against_face(j, i, k_nij, k_naij, x, contact_list,
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interact = edge_against_face(j, i, jtype, itype, x, contact_list,
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num_contacts, evdwl, facc);
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// check interaction between i's edges and j' edges
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#ifdef _POLYHEDRON_DEBUG
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printf("INTERACTION between edges of %d vs. edges of %d:\n", i, j);
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#endif
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interact = edge_against_edge(i, j, k_nij, k_naij, x, contact_list,
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interact = edge_against_edge(i, j, itype, jtype, x, contact_list,
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num_contacts, evdwl, facc);
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// estimate the contact area
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@ -309,7 +306,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
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if (num_contacts > 0) {
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rescale_cohesive_forces(x, f, torque, contact_list, num_contacts,
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k_nij, k_naij, facc);
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itype, jtype, facc);
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}
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if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,
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@ -594,9 +591,8 @@ void PairBodyRoundedPolyhedron::body2space(int i)
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---------------------------------------------------------------------- */
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void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody,
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double delx, double dely, double delz, double rsq,
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double k_n, double k_na, double** v, double** f,
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int evflag)
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int itype, int jtype, double delx, double dely, double delz, double rsq,
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double** v, double** f, int evflag)
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{
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double rradi,rradj,contact_dist;
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double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
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@ -612,7 +608,7 @@ void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody,
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R = rij - contact_dist;
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energy = 0;
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kernel_force(R, k_n, k_na, energy, fpair);
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kernel_force(R, itype, jtype, energy, fpair);
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/*
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if (R <= 0) { // deformation occurs
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fpair = -k_n * R - shift;
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@ -686,9 +682,8 @@ void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody,
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---------------------------------------------------------------------- */
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void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
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double k_n, double k_na, double** x, double** v,
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double** f, double** torque, double** angmom,
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int evflag)
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int itype, int jtype, double** x, double** v, double** f, double** torque,
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double** angmom, int evflag)
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{
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int ni,nei,ifirst,iefirst,npi1,npi2,ibonus;
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double xi1[3],xi2[3],vti[3],h[3],fn[3],ft[3],d,t;
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@ -760,7 +755,7 @@ void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
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R = rij - contact_dist;
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energy = 0;
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kernel_force(R, k_n, k_na, energy, fpair);
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kernel_force(R, itype, jtype, energy, fpair);
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/*
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if (R <= 0) { // deformation occurs
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fpair = -k_n * R - shift;
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@ -844,9 +839,8 @@ void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
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---------------------------------------------------------------------- */
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void PairBodyRoundedPolyhedron::sphere_against_face(int ibody, int jbody,
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double k_n, double k_na, double** x, double** v,
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double** f, double** torque, double** angmom,
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int evflag)
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int itype, int jtype, double** x, double** v, double** f, double** torque,
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double** angmom, int evflag)
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{
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int ni,nfi,inside,ifirst,iffirst,npi1,npi2,npi3,ibonus,tmp;
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double xi1[3],xi2[3],xi3[3],ui[3],vi[3],vti[3],n[3],h[3],fn[3],ft[3],d;
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@ -913,7 +907,7 @@ void PairBodyRoundedPolyhedron::sphere_against_face(int ibody, int jbody,
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R = rij - contact_dist;
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energy = 0;
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kernel_force(R, k_n, k_na, energy, fpair);
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kernel_force(R, itype, jtype, energy, fpair);
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/*
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if (R <= 0) { // deformation occurs
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fpair = -k_n * R - shift;
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@ -1009,8 +1003,8 @@ void PairBodyRoundedPolyhedron::sphere_against_face(int ibody, int jbody,
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---------------------------------------------------------------------- */
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int PairBodyRoundedPolyhedron::edge_against_edge(int ibody, int jbody,
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double k_n, double k_na, double** x, Contact* contact_list,
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int &num_contacts, double &evdwl, double* facc)
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int itype, int jtype, double** x, Contact* contact_list, int &num_contacts,
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double &evdwl, double* facc)
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{
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int ni,nei,nj,nej,contact,interact;
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double rradi,rradj,energy;
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@ -1037,7 +1031,7 @@ int PairBodyRoundedPolyhedron::edge_against_edge(int ibody, int jbody,
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interact = interaction_edge_to_edge(ibody, ni, x[ibody], rradi,
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jbody, nj, x[jbody], rradj,
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k_n, k_na, cut_inner,
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itype, jtype, cut_inner,
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contact_list, num_contacts,
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energy, facc);
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}
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@ -1065,8 +1059,8 @@ int PairBodyRoundedPolyhedron::edge_against_edge(int ibody, int jbody,
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---------------------------------------------------------------------- */
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int PairBodyRoundedPolyhedron::edge_against_face(int ibody, int jbody,
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double k_n, double k_na, double** x, Contact* contact_list,
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int &num_contacts, double &evdwl, double* facc)
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int itype, int jtype, double** x, Contact* contact_list, int &num_contacts,
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double &evdwl, double* facc)
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{
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int ni,nei,nj,nfj,contact,interact;
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double rradi,rradj,energy;
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@ -1095,7 +1089,7 @@ int PairBodyRoundedPolyhedron::edge_against_face(int ibody, int jbody,
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interact = interaction_face_to_edge(jbody, nj, x[jbody], rradj,
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ibody, ni, x[ibody], rradi,
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k_n, k_na, cut_inner,
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itype, jtype, cut_inner,
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contact_list, num_contacts,
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energy, facc);
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}
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@ -1132,20 +1126,10 @@ int PairBodyRoundedPolyhedron::edge_against_face(int ibody, int jbody,
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------------------------------------------------------------------------- */
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int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody,
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int edge_index_i,
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double *xmi,
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double rounded_radius_i,
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int jbody,
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int edge_index_j,
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double *xmj,
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double rounded_radius_j,
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double k_n,
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double k_na,
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double cut_inner,
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Contact* contact_list,
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int &num_contacts,
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double &energy,
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double* facc)
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int edge_index_i, double *xmi, double rounded_radius_i,
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int jbody, int edge_index_j, double *xmj, double rounded_radius_j,
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int itype, int jtype, double cut_inner,
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Contact* contact_list, int &num_contacts, double &energy, double* facc)
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{
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int ifirst,iefirst,jfirst,jefirst,npi1,npi2,npj1,npj2,interact;
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double xi1[3],xi2[3],xpj1[3],xpj2[3];
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@ -1219,7 +1203,7 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody,
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if (t1 >= 0 && t1 <= 1 && t2 >= 0 && t2 <= 1 &&
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r < contact_dist + cut_inner) {
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pair_force_and_torque(jbody, ibody, h1, h2, r, contact_dist,
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k_n, k_na, x, v, f, torque, angmom,
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jtype, itype, x, v, f, torque, angmom,
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jflag, energy, facc);
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interact = EE_INTERACT;
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@ -1270,20 +1254,10 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody,
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------------------------------------------------------------------------- */
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int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
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int face_index,
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double *xmi,
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double rounded_radius_i,
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int jbody,
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int edge_index,
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double *xmj,
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double rounded_radius_j,
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double k_n,
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double k_na,
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double cut_inner,
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Contact* contact_list,
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int &num_contacts,
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double &energy,
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double* facc)
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int face_index, double *xmi, double rounded_radius_i,
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int jbody, int edge_index, double *xmj, double rounded_radius_j,
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int itype, int jtype, double cut_inner,
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Contact* contact_list, int &num_contacts, double &energy, double* facc)
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{
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if (face_index >= facnum[ibody]) return EF_INVALID;
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@ -1397,7 +1371,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
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if (inside1) {
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if (static_cast<int>(discrete[jfirst+npj1][6]) == 0) {
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pair_force_and_torque(jbody, ibody, xpj1, hi1, d1, contact_dist,
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k_n, k_na, x, v, f, torque, angmom,
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jtype, itype, x, v, f, torque, angmom,
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jflag, energy, facc);
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#ifdef _POLYHEDRON_DEBUG
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printf(" - compute pair force between vertex %d from edge %d of body %d "
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@ -1436,7 +1410,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
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if (inside2) {
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if (static_cast<int>(discrete[jfirst+npj2][6]) == 0) {
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pair_force_and_torque(jbody, ibody, xpj2, hi2, d2, contact_dist,
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k_n, k_na, x, v, f, torque, angmom,
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jtype, itype, x, v, f, torque, angmom,
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jflag, energy, facc);
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#ifdef _POLYHEDRON_DEBUG
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printf(" - compute pair force between vertex %d from edge %d of body %d "
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@ -1502,11 +1476,11 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
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int jflag = 1;
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if (d1 < d2)
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pair_force_and_torque(jbody, ibody, xpj1, hi1, d1, contact_dist,
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k_n, k_na, x, v, f, torque, angmom,
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jtype, itype, x, v, f, torque, angmom,
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jflag, energy, facc);
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else
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pair_force_and_torque(jbody, ibody, xpj2, hi2, d2, contact_dist,
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k_n, k_na, x, v, f, torque, angmom,
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jtype, itype, x, v, f, torque, angmom,
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jflag, energy, facc);
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}
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@ -1520,7 +1494,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
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void PairBodyRoundedPolyhedron::pair_force_and_torque(int ibody, int jbody,
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double* pi, double* pj, double r, double contact_dist,
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double k_n, double k_na, double** x,
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int itype, int jtype, double** x,
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double** v, double** f, double** torque, double** angmom,
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int jflag, double& energy, double* facc)
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{
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@ -1531,7 +1505,7 @@ void PairBodyRoundedPolyhedron::pair_force_and_torque(int ibody, int jbody,
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delz = pi[2] - pj[2];
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R = r - contact_dist;
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kernel_force(R, k_n, k_na, energy, fpair);
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kernel_force(R, itype, jtype, energy, fpair);
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/*
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if (R <= 0) { // deformation occurs
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fpair = -k_n * R - shift;
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@ -1583,17 +1557,19 @@ void PairBodyRoundedPolyhedron::pair_force_and_torque(int ibody, int jbody,
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here is the harmonic potential (linear piece-wise forces) in Wang et al.
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------------------------------------------------------------------------- */
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void PairBodyRoundedPolyhedron::kernel_force(double R, double k_n, double k_na,
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void PairBodyRoundedPolyhedron::kernel_force(double R, int itype, int jtype,
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double& energy, double& fpair)
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{
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double shift = k_na * cut_inner;
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double kn = k_n[itype][jtype];
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double kna = k_na[itype][jtype];
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double shift = kna * cut_inner;
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double e = 0;
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if (R <= 0) { // deformation occurs
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fpair = -k_n * R - shift;
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e = (0.5 * k_n * R + shift) * R;
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fpair = -kn * R - shift;
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e = (0.5 * kn * R + shift) * R;
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} else if (R <= cut_inner) { // not deforming but cohesive ranges overlap
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fpair = k_na * R - shift;
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e = (-0.5 * k_na * R + shift) * R;
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fpair = kna * R - shift;
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e = (-0.5 * kna * R + shift) * R;
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} else fpair = 0.0;
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energy += e;
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}
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@ -1710,7 +1686,7 @@ void PairBodyRoundedPolyhedron::contact_forces(int ibody, int jbody,
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void PairBodyRoundedPolyhedron::rescale_cohesive_forces(double** x,
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double** f, double** torque, Contact* contact_list, int &num_contacts,
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double k_n, double k_na, double* facc)
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int itype, int jtype, double* facc)
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{
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int m,ibody,jbody;
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double delx,dely,delz,fx,fy,fz,R,fpair,r,contact_area;
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@ -1766,7 +1742,7 @@ void PairBodyRoundedPolyhedron::rescale_cohesive_forces(double** x,
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R = contact_list[m].separation;
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double energy = 0;
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kernel_force(R, k_n, k_na, energy, fpair);
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kernel_force(R, itype, jtype, energy, fpair);
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/*
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if (R <= 0) { // deformation occurs
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fpair = -k_n * R - shift;
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@ -34,7 +34,7 @@ class PairBodyRoundedPolyhedron : public Pair {
|
|||
void init_style();
|
||||
double init_one(int, int);
|
||||
|
||||
virtual void kernel_force(double R, double k_n, double k_na,
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||||
virtual void kernel_force(double R, int itype, int jtype,
|
||||
double& energy, double& fpair);
|
||||
|
||||
struct Contact {
|
||||
|
|
@ -88,23 +88,23 @@ class PairBodyRoundedPolyhedron : public Pair {
|
|||
void body2space(int);
|
||||
|
||||
// sphere-sphere interaction
|
||||
void sphere_against_sphere(int ibody, int jbody, double delx, double dely, double delz,
|
||||
double rsq, double k_n, double k_na,
|
||||
void sphere_against_sphere(int ibody, int jbody, int itype, int jtype,
|
||||
double delx, double dely, double delz, double rsq,
|
||||
double** v, double** f, int evflag);
|
||||
// sphere-edge interaction
|
||||
void sphere_against_edge(int ibody, int jbody,
|
||||
double k_n, double k_na, double** x, double** v,
|
||||
double** f, double** torque, double** angmom, int evflag);
|
||||
void sphere_against_edge(int ibody, int jbody, int itype, int jtype,
|
||||
double** x, double** v, double** f, double** torque,
|
||||
double** angmom, int evflag);
|
||||
// sphere-face interaction
|
||||
void sphere_against_face(int ibody, int jbody,
|
||||
double k_n, double k_na, double** x, double** v,
|
||||
double** f, double** torque, double** angmom, int evflag);
|
||||
void sphere_against_face(int ibody, int jbody, int itype, int jtype,
|
||||
double** x, double** v, double** f, double** torque,
|
||||
double** angmom, int evflag);
|
||||
// edge-edge interactions
|
||||
int edge_against_edge(int ibody, int jbody, double k_n, double k_na,
|
||||
int edge_against_edge(int ibody, int jbody, int itype, int jtype,
|
||||
double** x,Contact* contact_list, int &num_contacts,
|
||||
double &evdwl, double* facc);
|
||||
// edge-face interactions
|
||||
int edge_against_face(int ibody, int jbody, double k_n, double k_na,
|
||||
int edge_against_face(int ibody, int jbody, int itype, int jtype,
|
||||
double** x, Contact* contact_list, int &num_contacts,
|
||||
double &evdwl, double* facc);
|
||||
|
||||
|
|
@ -112,14 +112,14 @@ class PairBodyRoundedPolyhedron : public Pair {
|
|||
int interaction_face_to_edge(int ibody, int face_index, double* xmi,
|
||||
double rounded_radius_i, int jbody, int edge_index,
|
||||
double* xmj, double rounded_radius_j,
|
||||
double k_n, double k_na, double cut_inner,
|
||||
int itype, int jtype, double cut_inner,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
double& energy, double* facc);
|
||||
// an edge vs. an edge from another body
|
||||
int interaction_edge_to_edge(int ibody, int edge_index_i, double* xmi,
|
||||
double rounded_radius_i, int jbody, int edge_index_j,
|
||||
double* xmj, double rounded_radius_j,
|
||||
double k_n, double k_na, double cut_inner,
|
||||
int itype, int jtype, double cut_inner,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
double& energy, double* facc);
|
||||
|
||||
|
|
@ -131,14 +131,14 @@ class PairBodyRoundedPolyhedron : public Pair {
|
|||
|
||||
// compute force and torque between two bodies given a pair of interacting points
|
||||
void pair_force_and_torque(int ibody, int jbody, double* pi, double* pj,
|
||||
double r, double contact_dist, double k_n,
|
||||
double k_na, double** x, double** v,
|
||||
double** f, double** torque, double** angmom,
|
||||
int jflag, double& energy, double* facc);
|
||||
double r, double contact_dist, int itype, int jtype,
|
||||
double** x, double** v, double** f, double** torque,
|
||||
double** angmom, int jflag, double& energy, double* facc);
|
||||
|
||||
// rescale the cohesive forces if a contact area is detected
|
||||
void rescale_cohesive_forces(double** x, double** f, double** torque,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
double k_n, double k_na, double* facc);
|
||||
int itype, int jtype, double* facc);
|
||||
|
||||
// compute the separation between two contacts
|
||||
double contact_separation(const Contact& c1, const Contact& c2);
|
||||
|
|
|
|||
Loading…
Reference in New Issue