Commit dadd1c8b authored by Sebastian Hütter's avatar Sebastian Hütter
Browse files

Remove neigh_f2c/c2f, related cleanup 

- neighbour lists now use C indexing
- removed many arr*v() macros
- removed some unneccessary pointers
- minor reformatting
parent f092da80

src/USER-MEAMC/meam.h

+16 −12
Original line number Diff line number Diff line
@@ -141,20 +141,24 @@ public: 
  void interpolate_meam(int);

  double compute_phi(double, int, int);

 public:

  void meam_setup_global(int, lattice_t*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*);

  void meam_setup_param(int, double, int, int*, int*);

  void meam_setup_done(double*);

  void meam_dens_setup(int, int, int);

  void meam_dens_init(int* i, int* ntype, int* type, int* fmap, double** x,

                int* numneigh, int* firstneigh, int* numneigh_full,

  void meam_setup_global(int nelt, lattice_t* lat, double* z, int* ielement, double* atwt,

                   double* alpha, double* b0, double* b1, double* b2,

                   double* b3, double* alat, double* esub, double* asub,

                   double* t0, double* t1, double* t2, double* t3,

                   double* rozero, int* ibar);

  void meam_setup_param(int which, double value, int nindex, int* index /*index(3)*/, int* errorflag);

  void meam_setup_done(double* cutmax);

  void meam_dens_setup(int atom_nmax, int nall, int n_neigh);

  void meam_dens_init(int i, int ntype, int* type, int* fmap, double** x,

                int numneigh, int* firstneigh, int numneigh_full,

                int* firstneigh_full, int fnoffset, int* errorflag);

  void meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global,

                 int* eflag_atom, double* eng_vdwl, double* eatom, int* ntype,

  void meam_dens_final(int nlocal, int eflag_either, int eflag_global,

                 int eflag_atom, double* eng_vdwl, double* eatom, int ntype,

                 int* type, int* fmap, int* errorflag);

  void meam_force(int* iptr, int* eflag_either, int* eflag_global,

            int* eflag_atom, int* vflag_atom, double* eng_vdwl, double* eatom,

            int* ntype, int* type, int* fmap, double** x, int* numneigh,

            int* firstneigh, int* numneigh_full, int* firstneigh_full,

  void meam_force(int i, int eflag_either, int eflag_global,

            int eflag_atom, int vflag_atom, double* eng_vdwl, double* eatom,

            int ntype, int* type, int* fmap, double** x, int numneigh,

            int* firstneigh, int numneigh_full, int* firstneigh_full,

            int fnoffset, double** f, double** vatom,

            int* errorflag);

};

src/USER-MEAMC/meam_dens_final.cpp

+53 −55
Original line number Diff line number Diff line
@@ -21,8 +21,8 @@ using namespace LAMMPS_NS; 
//



void

MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global,

                 int* eflag_atom, double* eng_vdwl, double* eatom, int* ntype,

MEAM::meam_dens_final(int nlocal, int eflag_either, int eflag_global,

                 int eflag_atom, double* eng_vdwl, double* eatom, int ntype,

                 int* type, int* fmap, int* errorflag)

{

  int i, elti;
@@ -32,56 +32,54 @@ MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global, 


  //     Complete the calculation of density



  for (i = 1; i <= *nlocal; i++) {

    elti = fmap[arr1v(type, i)];

  for (i = 0; i < nlocal; i++) {

    elti = fmap[type[i]];

    if (elti >= 0) {

      arr1v(rho1, i) = 0.0;

      arr1v(rho2, i) = -1.0 / 3.0 * arr1v(arho2b, i) * arr1v(arho2b, i);

      arr1v(rho3, i) = 0.0;

      rho1[i] = 0.0;

      rho2[i] = -1.0 / 3.0 * arho2b[i] * arho2b[i];

      rho3[i] = 0.0;

      for (m = 1; m <= 3; m++) {

        arr1v(rho1, i) =

          arr1v(rho1, i) + arr2v(arho1, m, i) * arr2v(arho1, m, i);

        arr1v(rho3, i) = arr1v(rho3, i) -

                         3.0 / 5.0 * arr2v(arho3b, m, i) * arr2v(arho3b, m, i);

        rho1[i] = rho1[i] + arr2v(arho1, m, i+1) * arr2v(arho1, m, i+1);

        rho3[i] = rho3[i] - 3.0 / 5.0 * arr2v(arho3b, m, i+1) * arr2v(arho3b, m, i+1);

      }

      for (m = 1; m <= 6; m++) {

        arr1v(rho2, i) =

          arr1v(rho2, i) +

          this->v2D[m] * arr2v(arho2, m, i) * arr2v(arho2, m, i);

        rho2[i] =

          rho2[i] +

          this->v2D[m] * arr2v(arho2, m, i+1) * arr2v(arho2, m, i+1);

      }

      for (m = 1; m <= 10; m++) {

        arr1v(rho3, i) =

          arr1v(rho3, i) +

          this->v3D[m] * arr2v(arho3, m, i) * arr2v(arho3, m, i);

        rho3[i] =

          rho3[i] +

          this->v3D[m] * arr2v(arho3, m, i+1) * arr2v(arho3, m, i+1);

      }



      if (arr1v(rho0, i) > 0.0) {

      if (rho0[i] > 0.0) {

        if (this->ialloy == 1) {

          arr2v(t_ave, 1, i) = arr2v(t_ave, 1, i) / arr2v(tsq_ave, 1, i);

          arr2v(t_ave, 2, i) = arr2v(t_ave, 2, i) / arr2v(tsq_ave, 2, i);

          arr2v(t_ave, 3, i) = arr2v(t_ave, 3, i) / arr2v(tsq_ave, 3, i);

          t_ave[i][0] = t_ave[i][0] / tsq_ave[i][0];

          t_ave[i][1] = t_ave[i][1] / tsq_ave[i][1];

          t_ave[i][2] = t_ave[i][2] / tsq_ave[i][2];

        } else if (this->ialloy == 2) {

          arr2v(t_ave, 1, i) = this->t1_meam[elti];

          arr2v(t_ave, 2, i) = this->t2_meam[elti];

          arr2v(t_ave, 3, i) = this->t3_meam[elti];

          t_ave[i][0] = this->t1_meam[elti];

          t_ave[i][1] = this->t2_meam[elti];

          t_ave[i][2] = this->t3_meam[elti];

        } else {

          arr2v(t_ave, 1, i) = arr2v(t_ave, 1, i) / arr1v(rho0, i);

          arr2v(t_ave, 2, i) = arr2v(t_ave, 2, i) / arr1v(rho0, i);

          arr2v(t_ave, 3, i) = arr2v(t_ave, 3, i) / arr1v(rho0, i);

          t_ave[i][0] = t_ave[i][0] / rho0[i];

          t_ave[i][1] = t_ave[i][1] / rho0[i];

          t_ave[i][2] = t_ave[i][2] / rho0[i];

        }

      }



      arr1v(gamma, i) = arr2v(t_ave, 1, i) * arr1v(rho1, i) +

                        arr2v(t_ave, 2, i) * arr1v(rho2, i) +

                        arr2v(t_ave, 3, i) * arr1v(rho3, i);

      gamma[i] = t_ave[i][0] * rho1[i] +

                 t_ave[i][1] * rho2[i] +

                 t_ave[i][2] * rho3[i];



      if (arr1v(rho0, i) > 0.0) {

        arr1v(gamma, i) = arr1v(gamma, i) / (arr1v(rho0, i) * arr1v(rho0, i));

      if (rho0[i] > 0.0) {

        gamma[i] = gamma[i] / (rho0[i] * rho0[i]);

      }



      Z = this->Z_meam[elti];



      G_gam(arr1v(gamma, i), this->ibar_meam[elti], &G, errorflag);

      G_gam(gamma[i], this->ibar_meam[elti], &G, errorflag);

      if (*errorflag != 0)

        return;

      get_shpfcn(shp, this->lattce_meam[elti][elti]);
@@ -90,8 +88,8 @@ MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global, 
        dGbar = 0.0;

      } else {

        if (this->mix_ref_t == 1) {

          gam = (arr2v(t_ave, 1, i) * shp[1] + arr2v(t_ave, 2, i) * shp[2] +

                 arr2v(t_ave, 3, i) * shp[3]) /

          gam = (t_ave[i][0] * shp[1] + t_ave[i][1] * shp[2] +

                 t_ave[i][2] * shp[3]) /

                (Z * Z);

        } else {

          gam = (this->t1_meam[elti] * shp[1] +
@@ -101,15 +99,15 @@ MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global, 
        }

        G_gam(gam, this->ibar_meam[elti], &Gbar, errorflag);

      }

      arr1v(rho, i) = arr1v(rho0, i) * G;

      rho[i] = rho0[i] * G;



      if (this->mix_ref_t == 1) {

        if (this->ibar_meam[elti] <= 0) {

          Gbar = 1.0;

          dGbar = 0.0;

        } else {

          gam = (arr2v(t_ave, 1, i) * shp[1] + arr2v(t_ave, 2, i) * shp[2] +

                 arr2v(t_ave, 3, i) * shp[3]) /

          gam = (t_ave[i][0] * shp[1] + t_ave[i][1] * shp[2] +

                 t_ave[i][2] * shp[3]) /

                (Z * Z);

          dG_gam(gam, this->ibar_meam[elti], &Gbar, &dGbar);

        }
@@ -121,57 +119,57 @@ MEAM::meam_dens_final(int* nlocal, int* eflag_either, int* eflag_global, 
          rho_bkgd = this->rho_ref_meam[elti];

        }

      }

      rhob = arr1v(rho, i) / rho_bkgd;

      rhob = rho[i] / rho_bkgd;

      denom = 1.0 / rho_bkgd;



      dG_gam(arr1v(gamma, i), this->ibar_meam[elti], &G, &dG);

      dG_gam(gamma[i], this->ibar_meam[elti], &G, &dG);



      arr1v(dgamma1, i) = (G - 2 * dG * arr1v(gamma, i)) * denom;

      dgamma1[i] = (G - 2 * dG * gamma[i]) * denom;



      if (!iszero(arr1v(rho0, i))) {

        arr1v(dgamma2, i) = (dG / arr1v(rho0, i)) * denom;

      if (!iszero(rho0[i])) {

        dgamma2[i] = (dG / rho0[i]) * denom;

      } else {

        arr1v(dgamma2, i) = 0.0;

        dgamma2[i] = 0.0;

      }



      //     dgamma3 is nonzero only if we are using the "mixed" rule for

      //     computing t in the reference system (which is not correct, but

      //     included for backward compatibility

      if (this->mix_ref_t == 1) {

        arr1v(dgamma3, i) = arr1v(rho0, i) * G * dGbar / (Gbar * Z * Z) * denom;

        dgamma3[i] = rho0[i] * G * dGbar / (Gbar * Z * Z) * denom;

      } else {

        arr1v(dgamma3, i) = 0.0;

        dgamma3[i] = 0.0;

      }



      B = this->A_meam[elti] * this->Ec_meam[elti][elti];



      if (!iszero(rhob)) {

        if (this->emb_lin_neg == 1 && rhob <= 0) {

          arr1v(frhop, i) = -B;

          frhop[i] = -B;

        } else {

          arr1v(frhop, i) = B * (log(rhob) + 1.0);

          frhop[i] = B * (log(rhob) + 1.0);

        }

        if (*eflag_either != 0) {

          if (*eflag_global != 0) {

        if (eflag_either != 0) {

          if (eflag_global != 0) {

            if (this->emb_lin_neg == 1 && rhob <= 0) {

              *eng_vdwl = *eng_vdwl - B * rhob;

            } else {

              *eng_vdwl = *eng_vdwl + B * rhob * log(rhob);

            }

          }

          if (*eflag_atom != 0) {

          if (eflag_atom != 0) {

            if (this->emb_lin_neg == 1 && rhob <= 0) {

              arr1v(eatom, i) = arr1v(eatom, i) - B * rhob;

              eatom[i] = eatom[i] - B * rhob;

            } else {

              arr1v(eatom, i) = arr1v(eatom, i) + B * rhob * log(rhob);

              eatom[i] = eatom[i] + B * rhob * log(rhob);

            }

          }

        }

      } else {

        if (this->emb_lin_neg == 1) {

          arr1v(frhop, i) = -B;

          frhop[i] = -B;

        } else {

          arr1v(frhop, i) = B;

          frhop[i] = B;

        }

      }

    }

src/USER-MEAMC/meam_dens_init.cpp

+87 −105
Original line number Diff line number Diff line
@@ -101,18 +101,18 @@ MEAM::meam_dens_setup(int atom_nmax, int nall, int n_neigh) 
//



void

MEAM::meam_dens_init(int* i, int* ntype, int* type, int* fmap, double** x,

                int* numneigh, int* firstneigh, int* numneigh_full,

MEAM::meam_dens_init(int i, int ntype, int* type, int* fmap, double** x,

                int numneigh, int* firstneigh, int numneigh_full,

                int* firstneigh_full, int fnoffset, int* errorflag)

{

  *errorflag = 0;



  //     Compute screening function and derivatives

  getscreen(*i, &scrfcn[fnoffset], &dscrfcn[fnoffset], &fcpair[fnoffset], x, *numneigh, firstneigh,

            *numneigh_full, firstneigh_full, *ntype, type, fmap);

  getscreen(i, &scrfcn[fnoffset], &dscrfcn[fnoffset], &fcpair[fnoffset], x, numneigh, firstneigh,

            numneigh_full, firstneigh_full, ntype, type, fmap);



  //     Calculate intermediate density terms to be communicated

  calc_rho1(*i, *ntype, type, fmap, x, *numneigh, firstneigh, &scrfcn[fnoffset], &fcpair[fnoffset]);

  calc_rho1(i, ntype, type, fmap, x, numneigh, firstneigh, &scrfcn[fnoffset], &fcpair[fnoffset]);

}



// ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
@@ -135,24 +135,24 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, 
  double rnorm, fc, dfc, drinv;



  drinv = 1.0 / this->delr_meam;

  elti = fmap[arr1v(type, i)];

  elti = fmap[type[i]];



  if (elti >= 0) {



    xitmp = arr2v(x, 1, i);

    yitmp = arr2v(x, 2, i);

    zitmp = arr2v(x, 3, i);

    xitmp = x[i][0];

    yitmp = x[i][1];

    zitmp = x[i][2];



    for (jn = 1; jn <= numneigh; jn++) {

      j = arr1v(firstneigh, jn);

    for (jn = 0; jn < numneigh; jn++) {

      j = firstneigh[jn];



      eltj = fmap[arr1v(type, j)];

      eltj = fmap[type[j]];

      if (eltj >= 0) {



        //     First compute screening function itself, sij

        xjtmp = arr2v(x, 1, j);

        yjtmp = arr2v(x, 2, j);

        zjtmp = arr2v(x, 3, j);

        xjtmp = x[j][0];

        yjtmp = x[j][1];

        zjtmp = x[j][2];

        delxij = xjtmp - xitmp;

        delyij = yjtmp - yitmp;

        delzij = zjtmp - zitmp;
@@ -171,21 +171,21 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, 
        }



        //     Now compute derivatives

        arr1v(dscrfcn, jn) = 0.0;

        dscrfcn[jn] = 0.0;

        sfcij = sij * fcij;

        if (iszero(sfcij) || iszero(sfcij - 1.0))

          goto LABEL_100;

        rbound = this->ebound_meam[elti][eltj] * rij2;

        for (kn = 1; kn <= numneigh_full; kn++) {

          k = arr1v(firstneigh_full, kn);

        for (kn = 0; kn < numneigh_full; kn++) {

          k = firstneigh_full[kn];

          if (k == j)

            continue;

          eltk = fmap[arr1v(type, k)];

          eltk = fmap[type[k]];

          if (eltk < 0)

            continue;

          xktmp = arr2v(x, 1, k);

          yktmp = arr2v(x, 2, k);

          zktmp = arr2v(x, 3, k);

          xktmp = x[k][0];

          yktmp = x[k][1];

          zktmp = x[k][2];

          delxjk = xktmp - xjtmp;

          delyjk = yktmp - yjtmp;

          delzjk = zktmp - zjtmp;
@@ -223,16 +223,16 @@ MEAM::getscreen(int i, double* scrfcn, double* dscrfcn, double* fcpair, 
            dfcut(cikj, &sikj, &dfikj);

            coef1 = dfikj / (delc * sikj);

            dCfunc(rij2, rik2, rjk2, &dCikj);

            arr1v(dscrfcn, jn) = arr1v(dscrfcn, jn) + coef1 * dCikj;

            dscrfcn[jn] = dscrfcn[jn] + coef1 * dCikj;

          }

        }

        coef1 = sfcij;

        coef2 = sij * dfcij / rij;

        arr1v(dscrfcn, jn) = arr1v(dscrfcn, jn) * coef1 - coef2;

        dscrfcn[jn] = dscrfcn[jn] * coef1 - coef2;



      LABEL_100:

        arr1v(scrfcn, jn) = sij;

        arr1v(fcpair, jn) = fcij;

        scrfcn[jn] = sij;

        fcpair[jn] = fcij;

      }

    }

  }
@@ -252,20 +252,20 @@ MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x, 
  double ro0i, ro0j;

  double rhoa0i, rhoa1i, rhoa2i, rhoa3i, A1i, A2i, A3i;



  elti = fmap[arr1v(type, i)];

  xtmp = arr2v(x, 1, i);

  ytmp = arr2v(x, 2, i);

  ztmp = arr2v(x, 3, i);

  for (jn = 1; jn <= numneigh; jn++) {

    if (!iszero(arr1v(scrfcn, jn))) {

      j = arr1v(firstneigh, jn);

      sij = arr1v(scrfcn, jn) * arr1v(fcpair, jn);

      delij[1] = arr2v(x, 1, j) - xtmp;

      delij[2] = arr2v(x, 2, j) - ytmp;

      delij[3] = arr2v(x, 3, j) - ztmp;

  elti = fmap[type[i]];

  xtmp = x[i][0];

  ytmp = x[i][1];

  ztmp = x[i][2];

  for (jn = 0; jn < numneigh; jn++) {

    if (!iszero(scrfcn[jn])) {

      j = firstneigh[jn];

      sij = scrfcn[jn] * fcpair[jn];

      delij[1] = x[j][0] - xtmp;

      delij[2] = x[j][1] - ytmp;

      delij[3] = x[j][2] - ztmp;

      rij2 = delij[1] * delij[1] + delij[2] * delij[2] + delij[3] * delij[3];

      if (rij2 < this->cutforcesq) {

        eltj = fmap[arr1v(type, j)];

        eltj = fmap[type[j]];

        rij = sqrt(rij2);

        ai = rij / this->re_meam[elti][elti] - 1.0;

        aj = rij / this->re_meam[eltj][eltj] - 1.0;
@@ -287,45 +287,27 @@ MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x, 
          rhoa2i = rhoa2i * this->t2_meam[elti];

          rhoa3i = rhoa3i * this->t3_meam[elti];

        }

        arr1v(rho0, i) = arr1v(rho0, i) + rhoa0j;

        arr1v(rho0, j) = arr1v(rho0, j) + rhoa0i;

        rho0[i] = rho0[i] + rhoa0j;

        rho0[j] = rho0[j] + rhoa0i;

        // For ialloy = 2, use single-element value (not average)

        if (this->ialloy != 2) {

          arr2v(t_ave, 1, i) =

            arr2v(t_ave, 1, i) + this->t1_meam[eltj] * rhoa0j;

          arr2v(t_ave, 2, i) =

            arr2v(t_ave, 2, i) + this->t2_meam[eltj] * rhoa0j;

          arr2v(t_ave, 3, i) =

            arr2v(t_ave, 3, i) + this->t3_meam[eltj] * rhoa0j;

          arr2v(t_ave, 1, j) =

            arr2v(t_ave, 1, j) + this->t1_meam[elti] * rhoa0i;

          arr2v(t_ave, 2, j) =

            arr2v(t_ave, 2, j) + this->t2_meam[elti] * rhoa0i;

          arr2v(t_ave, 3, j) =

            arr2v(t_ave, 3, j) + this->t3_meam[elti] * rhoa0i;

          t_ave[i][0] = t_ave[i][0] + this->t1_meam[eltj] * rhoa0j;

          t_ave[i][1] = t_ave[i][1] + this->t2_meam[eltj] * rhoa0j;

          t_ave[i][2] = t_ave[i][2] + this->t3_meam[eltj] * rhoa0j;

          t_ave[j][0] = t_ave[j][0] + this->t1_meam[elti] * rhoa0i;

          t_ave[j][1] = t_ave[j][1] + this->t2_meam[elti] * rhoa0i;

          t_ave[j][2] = t_ave[j][2] + this->t3_meam[elti] * rhoa0i;

        }

        if (this->ialloy == 1) {

          arr2v(tsq_ave, 1, i) =

            arr2v(tsq_ave, 1, i) +

            this->t1_meam[eltj] * this->t1_meam[eltj] * rhoa0j;

          arr2v(tsq_ave, 2, i) =

            arr2v(tsq_ave, 2, i) +

            this->t2_meam[eltj] * this->t2_meam[eltj] * rhoa0j;

          arr2v(tsq_ave, 3, i) =

            arr2v(tsq_ave, 3, i) +

            this->t3_meam[eltj] * this->t3_meam[eltj] * rhoa0j;

          arr2v(tsq_ave, 1, j) =

            arr2v(tsq_ave, 1, j) +

            this->t1_meam[elti] * this->t1_meam[elti] * rhoa0i;

          arr2v(tsq_ave, 2, j) =

            arr2v(tsq_ave, 2, j) +

            this->t2_meam[elti] * this->t2_meam[elti] * rhoa0i;

          arr2v(tsq_ave, 3, j) =

            arr2v(tsq_ave, 3, j) +

            this->t3_meam[elti] * this->t3_meam[elti] * rhoa0i;

        }

        arr1v(arho2b, i) = arr1v(arho2b, i) + rhoa2j;

        arr1v(arho2b, j) = arr1v(arho2b, j) + rhoa2i;

          tsq_ave[i][0] = tsq_ave[i][0] + this->t1_meam[eltj] * this->t1_meam[eltj] * rhoa0j;

          tsq_ave[i][1] = tsq_ave[i][1] + this->t2_meam[eltj] * this->t2_meam[eltj] * rhoa0j;

          tsq_ave[i][2] = tsq_ave[i][2] + this->t3_meam[eltj] * this->t3_meam[eltj] * rhoa0j;

          tsq_ave[j][0] = tsq_ave[j][0] + this->t1_meam[elti] * this->t1_meam[elti] * rhoa0i;

          tsq_ave[j][1] = tsq_ave[j][1] + this->t2_meam[elti] * this->t2_meam[elti] * rhoa0i;

          tsq_ave[j][2] = tsq_ave[j][2] + this->t3_meam[elti] * this->t3_meam[elti] * rhoa0i;

        }

        arho2b[i] = arho2b[i] + rhoa2j;

        arho2b[j] = arho2b[j] + rhoa2i;



        A1j = rhoa1j / rij;

        A2j = rhoa2j / rij2;
@@ -336,21 +318,21 @@ MEAM::calc_rho1(int i, int ntype, int* type, int* fmap, double** x, 
        nv2 = 1;

        nv3 = 1;

        for (m = 1; m <= 3; m++) {

          arr2v(arho1, m, i) = arr2v(arho1, m, i) + A1j * delij[m];

          arr2v(arho1, m, j) = arr2v(arho1, m, j) - A1i * delij[m];

          arr2v(arho3b, m, i) = arr2v(arho3b, m, i) + rhoa3j * delij[m] / rij;

          arr2v(arho3b, m, j) = arr2v(arho3b, m, j) - rhoa3i * delij[m] / rij;

          arr2v(arho1, m, i+1) = arr2v(arho1, m, i+1) + A1j * delij[m];

          arr2v(arho1, m, j+1) = arr2v(arho1, m, j+1) - A1i * delij[m];

          arr2v(arho3b, m, i+1) = arr2v(arho3b, m, i+1) + rhoa3j * delij[m] / rij;

          arr2v(arho3b, m, j+1) = arr2v(arho3b, m, j+1) - rhoa3i * delij[m] / rij;

          for (n = m; n <= 3; n++) {

            arr2v(arho2, nv2, i) =

              arr2v(arho2, nv2, i) + A2j * delij[m] * delij[n];

            arr2v(arho2, nv2, j) =

              arr2v(arho2, nv2, j) + A2i * delij[m] * delij[n];

            arr2v(arho2, nv2, i+1) =

              arr2v(arho2, nv2, i+1) + A2j * delij[m] * delij[n];

            arr2v(arho2, nv2, j+1) =

              arr2v(arho2, nv2, j+1) + A2i * delij[m] * delij[n];

            nv2 = nv2 + 1;

            for (p = n; p <= 3; p++) {

              arr2v(arho3, nv3, i) =

                arr2v(arho3, nv3, i) + A3j * delij[m] * delij[n] * delij[p];

              arr2v(arho3, nv3, j) =

                arr2v(arho3, nv3, j) - A3i * delij[m] * delij[n] * delij[p];

              arr2v(arho3, nv3, i+1) =

                arr2v(arho3, nv3, i+1) + A3j * delij[m] * delij[n] * delij[p];

              arr2v(arho3, nv3, j+1) =

                arr2v(arho3, nv3, j+1) - A3i * delij[m] * delij[n] * delij[p];

              nv3 = nv3 + 1;

            }

          }
@@ -379,26 +361,26 @@ MEAM::screen(int i, int j, double** x, double rijsq, double* sij, 
  double Cmax, Cmin, rbound;



  *sij = 1.0;

  elti = fmap[arr1v(type, i)];

  eltj = fmap[arr1v(type, j)];

  elti = fmap[type[i]];

  eltj = fmap[type[j]];



  //     if rjksq > ebound*rijsq, atom k is definitely outside the ellipse

  rbound = this->ebound_meam[elti][eltj] * rijsq;



  for (nk = 1; nk <= numneigh_full; nk++) {

    k = arr1v(firstneigh_full, nk);

    eltk = fmap[arr1v(type, k)];

  for (nk = 0; nk < numneigh_full; nk++) {

    k = firstneigh_full[nk];

    eltk = fmap[type[k]];

    if (k == j)

      continue;

    delxjk = arr2v(x, 1, k) - arr2v(x, 1, j);

    delyjk = arr2v(x, 2, k) - arr2v(x, 2, j);

    delzjk = arr2v(x, 3, k) - arr2v(x, 3, j);

    delxjk = x[k][0] - x[j][0];

    delyjk = x[k][1] - x[j][1];

    delzjk = x[k][2] - x[j][2];

    rjksq = delxjk * delxjk + delyjk * delyjk + delzjk * delzjk;

    if (rjksq > rbound)

      continue;

    delxik = arr2v(x, 1, k) - arr2v(x, 1, i);

    delyik = arr2v(x, 2, k) - arr2v(x, 2, i);

    delzik = arr2v(x, 3, k) - arr2v(x, 3, i);

    delxik = x[k][0] - x[i][0];

    delyik = x[k][1] - x[i][1];

    delzik = x[k][2] - x[i][2];

    riksq = delxik * delxik + delyik * delyik + delzik * delzik;

    if (riksq > rbound)

      continue;
@@ -450,10 +432,10 @@ MEAM::dsij(int i, int j, int k, int jn, int numneigh, double rij2, 
  double rbound, delc, sij, xik, xjk, cikj, sikj, dfc, a;

  double Cmax, Cmin, dCikj1, dCikj2;



  sij = arr1v(scrfcn, jn) * arr1v(fcpair, jn);

  elti = fmap[arr1v(type, i)];

  eltj = fmap[arr1v(type, j)];

  eltk = fmap[arr1v(type, k)];

  sij = scrfcn[jn] * fcpair[jn];

  elti = fmap[type[i]];

  eltj = fmap[type[j]];

  eltk = fmap[type[k]];

  Cmax = this->Cmax_meam[elti][eltj][eltk];

  Cmin = this->Cmin_meam[elti][eltj][eltk];
@@ -462,14 +444,14 @@ MEAM::dsij(int i, int j, int k, int jn, int numneigh, double rij2, 
  if (!iszero(sij) && !iszero(sij - 1.0)) {

    rbound = rij2 * this->ebound_meam[elti][eltj];

    delc = Cmax - Cmin;

    dxjk = arr2v(x, 1, k) - arr2v(x, 1, j);

    dyjk = arr2v(x, 2, k) - arr2v(x, 2, j);

    dzjk = arr2v(x, 3, k) - arr2v(x, 3, j);

    dxjk = x[k][0] - x[j][0];

    dyjk = x[k][1] - x[j][1];

    dzjk = x[k][2] - x[j][2];

    rjk2 = dxjk * dxjk + dyjk * dyjk + dzjk * dzjk;

    if (rjk2 <= rbound) {

      dxik = arr2v(x, 1, k) - arr2v(x, 1, i);

      dyik = arr2v(x, 2, k) - arr2v(x, 2, i);

      dzik = arr2v(x, 3, k) - arr2v(x, 3, i);

      dxik = x[k][0] - x[i][0];

      dyik = x[k][1] - x[i][1];

      dzik = x[k][2] - x[i][2];

      rik2 = dxik * dxik + dyik * dyik + dzik * dzik;

      if (rik2 <= rbound) {

        xik = rik2 / rij2;

src/USER-MEAMC/meam_force.cpp

+145 −155

File changed.

Preview size limit exceeded, changes collapsed.

src/USER-MEAMC/pair_meamc.cpp

+9 −53
Original line number Diff line number Diff line
@@ -129,24 +129,17 @@ void PairMEAMC::compute(int eflag, int vflag) 
  int *type = atom->type;

  int ntype = atom->ntypes;



  // change neighbor list indices to Fortran indexing



  neigh_c2f(inum_half,ilist_half,numneigh_half,firstneigh_half);

  neigh_c2f(inum_half,ilist_half,numneigh_full,firstneigh_full);



  // 3 stages of MEAM calculation

  // loop over my atoms followed by communication



  int ifort;

  int offset = 0;

  errorflag = 0;



  for (ii = 0; ii < inum_half; ii++) {

    i = ilist_half[ii];

    ifort = i+1;

    meam_inst->meam_dens_init(&ifort,&ntype,type,map,x,

                    &numneigh_half[i],firstneigh_half[i],

                    &numneigh_full[i],firstneigh_full[i],

    meam_inst->meam_dens_init(i,ntype,type,map,x,

                    numneigh_half[i],firstneigh_half[i],

                    numneigh_full[i],firstneigh_full[i],

                    offset,

                    &errorflag);

    if (errorflag) {
@@ -159,8 +152,8 @@ void PairMEAMC::compute(int eflag, int vflag) 


  comm->reverse_comm_pair(this);



  meam_inst->meam_dens_final(&nlocal,&eflag_either,&eflag_global,&eflag_atom,

                   &eng_vdwl,eatom,&ntype,type,map,

  meam_inst->meam_dens_final(nlocal,eflag_either,eflag_global,eflag_atom,

                   &eng_vdwl,eatom,ntype,type,map,

                   &errorflag);

  if (errorflag) {

    char str[128];
@@ -181,11 +174,10 @@ void PairMEAMC::compute(int eflag, int vflag) 


  for (ii = 0; ii < inum_half; ii++) {

    i = ilist_half[ii];

    ifort = i+1;

    meam_inst->meam_force(&ifort,&eflag_either,&eflag_global,&eflag_atom,

                &vflag_atom,&eng_vdwl,eatom,&ntype,type,map,x,

                &numneigh_half[i],firstneigh_half[i],

                &numneigh_full[i],firstneigh_full[i],

    meam_inst->meam_force(i,eflag_either,eflag_global,eflag_atom,

                vflag_atom,&eng_vdwl,eatom,ntype,type,map,x,

                numneigh_half[i],firstneigh_half[i],

                numneigh_full[i],firstneigh_full[i],

                offset,

                f,vptr,&errorflag);

    if (errorflag) {
@@ -196,11 +188,6 @@ void PairMEAMC::compute(int eflag, int vflag) 
    offset += numneigh_half[i];

  }



  // change neighbor list indices back to C indexing



  neigh_f2c(inum_half,ilist_half,numneigh_half,firstneigh_half);

  neigh_f2c(inum_half,ilist_half,numneigh_full,firstneigh_full);



  if (vflag_fdotr) virial_fdotr_compute();

}
@@ -806,34 +793,3 @@ void PairMEAMC::neigh_strip(int inum, int *ilist, 
    for (j = 0; j < jnum; j++) jlist[j] &= NEIGHMASK;

  }

}
 


/* ----------------------------------------------------------------------

   toggle neighbor list indices between zero- and one-based values

   needed for access by MEAM Fortran library

------------------------------------------------------------------------- */



void PairMEAMC::neigh_f2c(int inum, int *ilist, int *numneigh, int **firstneigh)

{

  int i,j,ii,jnum;

  int *jlist;



  for (ii = 0; ii < inum; ii++) {

    i = ilist[ii];

    jlist = firstneigh[i];

    jnum = numneigh[i];

    for (j = 0; j < jnum; j++) jlist[j]--;

  }

}



void PairMEAMC::neigh_c2f(int inum, int *ilist, int *numneigh, int **firstneigh)

{

  int i,j,ii,jnum;

  int *jlist;



  for (ii = 0; ii < inum; ii++) {

    i = ilist[ii];

    jlist = firstneigh[i];

    jnum = numneigh[i];

    for (j = 0; j < jnum; j++) jlist[j]++;

  }

}

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