forked from lijiext/lammps
whitespace cleanup
This commit is contained in:
Axel Kohlmeyer
parent
6c5edf6c70
commit
390ceb1475
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@ -102,7 +102,7 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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const double* const * const x = atom->x;
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double* const * const forces = atom->f;
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const int ntypes = atom->ntypes;
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if (eflag || vflag) {
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ev_setup(eflag, vflag);
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} else {
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@ -123,7 +123,7 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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int newMaxNeighbors = 0;
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for(int ii = 0; ii < listfull->inum; ii++) {
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int jnum = listfull->numneigh[listfull->ilist[ii]];
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if(jnum > newMaxNeighbors)
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if(jnum > newMaxNeighbors)
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newMaxNeighbors = jnum;
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}
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@ -151,24 +151,24 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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for(int jj = 0; jj < listfull->numneigh[i]; jj++) {
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int j = listfull->firstneigh[i][jj];
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j &= NEIGHMASK;
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double jdelx = x[j][0] - x[i][0];
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double jdely = x[j][1] - x[i][1];
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double jdelz = x[j][2] - x[i][2];
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double rij_sq = jdelx*jdelx + jdely*jdely + jdelz*jdelz;
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if(rij_sq < cutoff*cutoff) {
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double rij = sqrt(rij_sq);
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double partial_sum = 0;
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const int jtype = atom->type[j];
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nextTwoBodyInfo->tag = j;
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nextTwoBodyInfo->r = rij;
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nextTwoBodyInfo->f = fs[i_to_potl(jtype)].eval(rij, nextTwoBodyInfo->fprime);
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nextTwoBodyInfo->del[0] = jdelx / rij;
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nextTwoBodyInfo->del[1] = jdely / rij;
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nextTwoBodyInfo->del[2] = jdelz / rij;
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for(int kk = 0; kk < numBonds; kk++) {
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const MEAM2Body& bondk = twoBodyInfo[kk];
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double cos_theta = (nextTwoBodyInfo->del[0]*bondk.del[0] +
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@ -176,10 +176,10 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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nextTwoBodyInfo->del[2]*bondk.del[2]);
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partial_sum += bondk.f * gs[ij_to_potl(jtype,atom->type[bondk.tag],ntypes)].eval(cos_theta);
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}
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rho_value += nextTwoBodyInfo->f * partial_sum;
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rho_value += rhos[i_to_potl(jtype)].eval(rij);
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numBonds++;
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nextTwoBodyInfo++;
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}
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@ -189,7 +189,7 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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double Uprime_i;
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double embeddingEnergy = Us[i_to_potl(itype)].eval(rho_value, Uprime_i)
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- zero_atom_energies[i_to_potl(itype)];
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Uprime_values[i] = Uprime_i;
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if(eflag) {
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if(eflag_global)
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@ -204,17 +204,17 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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const MEAM2Body bondj = twoBodyInfo[jj];
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double rij = bondj.r;
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int j = bondj.tag;
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double f_rij_prime = bondj.fprime;
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double f_rij = bondj.f;
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double forces_j[3] = {0, 0, 0};
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const int jtype = atom->type[j];
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MEAM2Body const* bondk = twoBodyInfo;
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for(int kk = 0; kk < jj; kk++, ++bondk) {
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double rik = bondk->r;
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double cos_theta = (bondj.del[0]*bondk->del[0] +
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bondj.del[1]*bondk->del[1] +
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bondj.del[2]*bondk->del[2]);
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@ -222,37 +222,37 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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double g_value = gs[ij_to_potl(jtype,atom->type[bondk->tag],ntypes)].eval(cos_theta, g_prime);
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double f_rik_prime = bondk->fprime;
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double f_rik = bondk->f;
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double fij = -Uprime_i * g_value * f_rik * f_rij_prime;
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double fik = -Uprime_i * g_value * f_rij * f_rik_prime;
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double prefactor = Uprime_i * f_rij * f_rik * g_prime;
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double prefactor_ij = prefactor / rij;
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double prefactor_ik = prefactor / rik;
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fij += prefactor_ij * cos_theta;
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fik += prefactor_ik * cos_theta;
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double fj[3], fk[3];
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fj[0] = bondj.del[0] * fij - bondk->del[0] * prefactor_ij;
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fj[1] = bondj.del[1] * fij - bondk->del[1] * prefactor_ij;
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fj[2] = bondj.del[2] * fij - bondk->del[2] * prefactor_ij;
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forces_j[0] += fj[0];
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forces_j[1] += fj[1];
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forces_j[2] += fj[2];
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fk[0] = bondk->del[0] * fik - bondj.del[0] * prefactor_ik;
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fk[1] = bondk->del[1] * fik - bondj.del[1] * prefactor_ik;
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fk[2] = bondk->del[2] * fik - bondj.del[2] * prefactor_ik;
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forces_i[0] -= fk[0];
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forces_i[1] -= fk[1];
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forces_i[2] -= fk[2];
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int k = bondk->tag;
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forces[k][0] += fk[0];
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forces[k][1] += fk[1];
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forces[k][2] += fk[2];
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if(evflag) {
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double delta_ij[3];
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double delta_ik[3];
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@ -265,7 +265,7 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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ev_tally3(i, j, k, 0.0, 0.0, fj, fk, delta_ij, delta_ik);
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}
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}
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forces[i][0] -= forces_j[0];
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forces[i][1] -= forces_j[1];
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forces[i][2] -= forces_j[2];
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@ -273,7 +273,7 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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forces[j][1] += forces_j[1];
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forces[j][2] += forces_j[2];
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}
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forces[i][0] += forces_i[0];
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forces[i][1] += forces_i[1];
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forces[i][2] += forces_i[2];
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@ -287,17 +287,17 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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for(int ii = 0; ii < listhalf->inum; ii++) {
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int i = listhalf->ilist[ii];
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const int itype = atom->type[i];
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for(int jj = 0; jj < listhalf->numneigh[i]; jj++) {
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int j = listhalf->firstneigh[i][jj];
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j &= NEIGHMASK;
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double jdel[3];
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jdel[0] = x[j][0] - x[i][0];
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jdel[1] = x[j][1] - x[i][1];
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jdel[2] = x[j][2] - x[i][2];
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double rij_sq = jdel[0]*jdel[0] + jdel[1]*jdel[1] + jdel[2]*jdel[2];
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if(rij_sq < cutoff*cutoff) {
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double rij = sqrt(rij_sq);
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const int jtype = atom->type[j];
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@ -327,7 +327,7 @@ void PairMEAMSpline::compute(int eflag, int vflag)
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}
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}
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if(vflag_fdotr)
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if(vflag_fdotr)
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virial_fdotr_compute();
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}
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@ -410,12 +410,12 @@ void PairMEAMSpline::coeff(int narg, char **arg)
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}
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}
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// clear setflag since coeff() called once with I,J = * *
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n = atom->ntypes;
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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// set setflag i,j for type pairs where both are mapped to elements
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int count = 0;
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@ -442,19 +442,19 @@ void PairMEAMSpline::read_file(const char* filename)
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sprintf(str,"Cannot open spline MEAM potential file %s", filename);
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error->one(FLERR,str);
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}
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// Skip first line of file. It's a comment.
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char line[MAXLINE];
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char *ptr;
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fgets(line, MAXLINE, fp);
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// Second line holds potential type ("meam/spline")
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// in new potential format.
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bool isNewFormat = false;
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fgets(line, MAXLINE, fp);
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ptr = strtok(line, " \t\n\r\f");
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if (strcmp(ptr, "meam/spline") == 0) {
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isNewFormat = true;
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// parse the rest of the line!
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@ -484,13 +484,13 @@ void PairMEAMSpline::read_file(const char* filename)
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rewind(fp);
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fgets(line, MAXLINE, fp);
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}
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nmultichoose2 = ((nelements+1)*nelements)/2;
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// allocate!!
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allocate();
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// Parse spline functions.
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for (int i = 0; i < nmultichoose2; i++)
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phis[i].parse(fp, error, isNewFormat);
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for (int i = 0; i < nelements; i++)
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@ -501,7 +501,7 @@ void PairMEAMSpline::read_file(const char* filename)
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fs[i].parse(fp, error, isNewFormat);
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for (int i = 0; i < nmultichoose2; i++)
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gs[i].parse(fp, error, isNewFormat);
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fclose(fp);
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}
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@ -532,11 +532,11 @@ void PairMEAMSpline::read_file(const char* filename)
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Us[i].communicate(world, comm->me);
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for (int i = 0; i < nmultichoose2; i++)
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gs[i].communicate(world, comm->me);
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// Calculate 'zero-point energy' of single atom in vacuum.
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for (int i = 0; i < nelements; i++)
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zero_atom_energies[i] = Us[i].eval(0.0);
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// Determine maximum cutoff radius of all relevant spline functions.
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cutoff = 0.0;
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for (int i = 0; i < nmultichoose2; i++)
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@ -548,7 +548,7 @@ void PairMEAMSpline::read_file(const char* filename)
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for (int i = 0; i < nelements; i++)
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if(fs[i].cutoff() > cutoff)
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cutoff = fs[i].cutoff();
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// Set LAMMPS pair interaction flags.
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for(int i = 1; i <= atom->ntypes; i++) {
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for(int j = 1; j <= atom->ntypes; j++) {
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@ -556,7 +556,7 @@ void PairMEAMSpline::read_file(const char* filename)
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cutsq[i][j] = cutoff;
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}
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}
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}
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/* ----------------------------------------------------------------------
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@ -643,27 +643,27 @@ void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error,
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bool isNewFormat)
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{
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char line[MAXLINE];
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// If new format, read the spline format. Should always be "spline3eq" for now.
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if (isNewFormat)
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fgets(line, MAXLINE, fp);
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// Parse number of spline knots.
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fgets(line, MAXLINE, fp);
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int n = atoi(line);
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if(n < 2)
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error->one(FLERR,"Invalid number of spline knots in MEAM potential file");
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// Parse first derivatives at beginning and end of spline.
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fgets(line, MAXLINE, fp);
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double d0 = atof(strtok(line, " \t\n\r\f"));
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double dN = atof(strtok(NULL, " \t\n\r\f"));
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init(n, d0, dN);
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// Skip line in old format
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if (!isNewFormat)
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fgets(line, MAXLINE, fp);
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// Parse knot coordinates.
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for(int i=0; i<n; i++) {
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fgets(line, MAXLINE, fp);
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@ -673,7 +673,7 @@ void PairMEAMSpline::SplineFunction::parse(FILE* fp, Error* error,
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}
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setKnot(i, x, y);
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}
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prepareSpline(error);
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}
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@ -682,11 +682,11 @@ void PairMEAMSpline::SplineFunction::prepareSpline(Error* error)
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{
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xmin = X[0];
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xmax = X[N-1];
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isGridSpline = true;
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h = (xmax-xmin)/(N-1);
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hsq = h*h;
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double* u = new double[N];
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Y2[0] = -0.5;
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u[0] = (3.0/(X[1]-X[0])) * ((Y[1]-Y[0])/(X[1]-X[0]) - deriv0);
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@ -696,20 +696,20 @@ void PairMEAMSpline::SplineFunction::prepareSpline(Error* error)
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Y2[i] = (sig - 1.0) / p;
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u[i] = (Y[i+1]-Y[i]) / (X[i+1]-X[i]) - (Y[i]-Y[i-1])/(X[i]-X[i-1]);
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u[i] = (6.0 * u[i]/(X[i+1]-X[i-1]) - sig*u[i-1])/p;
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if(fabs(h*i+xmin - X[i]) > 1e-8)
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isGridSpline = false;
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}
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double qn = 0.5;
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double un = (3.0/(X[N-1]-X[N-2])) * (derivN - (Y[N-1]-Y[N-2])/(X[N-1]-X[N-2]));
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Y2[N-1] = (un - qn*u[N-2]) / (qn * Y2[N-2] + 1.0);
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for(int k = N-2; k >= 0; k--) {
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Y2[k] = Y2[k] * Y2[k+1] + u[k];
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}
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delete[] u;
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#if !SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES
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if(!isGridSpline)
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error->one(FLERR,"Support for MEAM potentials with non-uniform cubic splines has not been enabled in the MEAM potential code. Set SPLINE_MEAM_SUPPORT_NON_GRID_SPLINES in pair_spline_meam.h to 1 to enable it");
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@ -51,21 +51,21 @@ public:
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void init_style();
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void init_list(int, class NeighList *);
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double init_one(int, int);
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// helper functions for compute()
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int ij_to_potl(const int itype, const int jtype, const int ntypes) const {
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return jtype - 1 + (itype-1)*ntypes - (itype-1)*itype/2;
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}
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int i_to_potl(const int itype) const { return itype-1; }
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int pack_forward_comm(int, int *, double *, int, int *);
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void unpack_forward_comm(int, int, double *);
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int pack_reverse_comm(int, int, double *);
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void unpack_reverse_comm(int, int *, double *);
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double memory_usage();
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protected:
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char **elements; // names of unique elements
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int *map; // mapping from atom types to elements
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@ -75,7 +75,7 @@ protected:
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public:
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/// Default constructor.
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SplineFunction() : X(NULL), Xs(NULL), Y(NULL), Y2(NULL), Ydelta(NULL), N(0) {}
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/// Destructor.
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~SplineFunction() {
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delete[] X;
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@ -84,7 +84,7 @@ protected:
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delete[] Y2;
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delete[] Ydelta;
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}
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/// Initialization of spline function.
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void init(int _N, double _deriv0, double _derivN) {
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N = _N;
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@ -101,19 +101,19 @@ protected:
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Y2 = new double[N];
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Ydelta = new double[N];
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}
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/// Adds a knot to the spline.
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void setKnot(int n, double x, double y) { X[n] = x; Y[n] = y; }
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/// Returns the number of knots.
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int numKnots() const { return N; }
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/// Parses the spline knots from a text file.
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void parse(FILE* fp, Error* error, bool isNewFormat);
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/// Calculates the second derivatives of the cubic spline.
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void prepareSpline(Error* error);
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/// Evaluates the spline function at position x.
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inline double eval(double x) const
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{
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@ -151,7 +151,7 @@ protected:
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#endif
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}
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}
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/// Evaluates the spline function and its first derivative at position x.
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inline double eval(double x, double& deriv) const
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{
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@ -197,16 +197,16 @@ protected:
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#endif
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}
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}
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/// Returns the number of bytes used by this function object.
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double memory_usage() const { return sizeof(*this) + sizeof(X[0]) * N * 3; }
|
||||
|
||||
/// Returns the cutoff radius of this function.
|
||||
double cutoff() const { return X[N-1]; }
|
||||
|
||||
|
||||
/// Writes a Gnuplot script that plots the spline function.
|
||||
void writeGnuplot(const char* filename, const char* title = NULL) const;
|
||||
|
||||
|
||||
/// Broadcasts the spline function parameters to all processors.
|
||||
void communicate(MPI_Comm& world, int me);
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||||
|
||||
|
|
@ -226,7 +226,7 @@ protected:
|
|||
double hsq; // The squared distance between knots if this is a grid spline with equidistant knots.
|
||||
double xmax_shifted; // The end of the spline interval after it has been shifted to begin at X=0.
|
||||
};
|
||||
|
||||
|
||||
/// Helper data structure for potential routine.
|
||||
struct MEAM2Body {
|
||||
int tag; // holds the index of the second atom (j)
|
||||
|
|
@ -234,26 +234,26 @@ protected:
|
|||
double f, fprime;
|
||||
double del[3];
|
||||
};
|
||||
|
||||
|
||||
SplineFunction* phis; // Phi_i(r_ij)
|
||||
SplineFunction* rhos; // Rho_ij(r_ij)
|
||||
SplineFunction* fs; // f_i(r_ij)
|
||||
SplineFunction* Us; // U_i(rho)
|
||||
SplineFunction* gs; // g_ij(cos_theta)
|
||||
double* zero_atom_energies; // Shift embedding energy by this value to make it zero for a single atom in vacuum.
|
||||
|
||||
|
||||
double cutoff; // The cutoff radius
|
||||
|
||||
|
||||
double* Uprime_values; // Used for temporary storage of U'(rho) values
|
||||
int nmax; // Size of temporary array.
|
||||
int maxNeighbors; // The last maximum number of neighbors a single atoms has.
|
||||
MEAM2Body* twoBodyInfo; // Temporary array.
|
||||
|
||||
|
||||
void read_file(const char* filename);
|
||||
void allocate();
|
||||
|
||||
|
||||
};
|
||||
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -305,7 +305,7 @@ void PairMEAMSplineOMP::eval(int iifrom, int iito, ThrData * const thr)
|
|||
rhos[i_to_potl(itype)].eval(rij,rho_prime_i);
|
||||
rhos[i_to_potl(jtype)].eval(rij,rho_prime_j);
|
||||
double fpair = rho_prime_j * Uprime_values[i] + rho_prime_i*Uprime_values[j];
|
||||
|
||||
|
||||
double pair_pot_deriv;
|
||||
double pair_pot = phis[ij_to_potl(itype,jtype,ntypes)].eval(rij, pair_pot_deriv);
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue