void *lammps_extract_compute(void *ptr, char *id, int style, int type) { LAMMPS *lmp = (LAMMPS *) ptr; int icompute = lmp->modify->find_compute(id); if (icompute < 0) return NULL; Compute *compute = lmp->modify->compute[icompute]; if (style == 0) { if (type == 0) { if (!compute->scalar_flag) return NULL; if (compute->invoked_scalar != lmp->update->ntimestep) compute->compute_scalar(); return (void *) &compute->scalar; } if (type == 1) { if (!compute->vector_flag) return NULL; if (compute->invoked_vector != lmp->update->ntimestep) compute->compute_vector(); return (void *) compute->vector; } if (type == 2) { if (!compute->array_flag) return NULL; if (compute->invoked_array != lmp->update->ntimestep) compute->compute_array(); return (void *) compute->array; } } if (style == 1) { if (!compute->peratom_flag) return NULL; if (type == 1) { if (compute->invoked_peratom != lmp->update->ntimestep) compute->compute_peratom(); return (void *) compute->vector_atom; } if (type == 2) { if (compute->invoked_peratom != lmp->update->ntimestep) compute->compute_peratom(); return (void *) compute->array_atom; } } if (style == 2) { if (!compute->local_flag) return NULL; if (type == 1) { if (compute->invoked_local != lmp->update->ntimestep) compute->compute_local(); return (void *) compute->vector_local; } if (type == 2) { if (compute->invoked_local != lmp->update->ntimestep) compute->compute_local(); return (void *) compute->array_local; } } return NULL; }
double ComputeReduceRegion::compute_one(int m, int flag) { int i; Region *region = domain->regions[iregion]; region->prematch(); // invoke the appropriate attribute,compute,fix,variable // compute scalar quantity by summing over atom scalars // only include atoms in group index = -1; double **x = atom->x; int *mask = atom->mask; int nlocal = atom->nlocal; int n = value2index[m]; int j = argindex[m]; double one; if (mode == SUM) one = 0.0; else if (mode == MINN) one = BIG; else if (mode == MAXX) one = -BIG; else if (mode == AVE) one = 0.0; if (which[m] == X) { if (flag < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,x[i][j],i); } else one = x[flag][j]; } else if (which[m] == V) { double **v = atom->v; if (flag < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,v[i][j],i); } else one = v[flag][j]; } else if (which[m] == F) { double **f = atom->f; if (flag < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,f[i][j],i); } else one = f[flag][j]; // invoke compute if not previously invoked } else if (which[m] == COMPUTE) { Compute *compute = modify->compute[n]; if (flavor[m] == PERATOM) { if (!(compute->invoked_flag & INVOKED_PERATOM)) { compute->compute_peratom(); compute->invoked_flag |= INVOKED_PERATOM; } if (j == 0) { double *compute_vector = compute->vector_atom; int n = nlocal; if (flag < 0) { for (i = 0; i < n; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,compute_vector[i],i); } else one = compute_vector[flag]; } else { double **compute_array = compute->array_atom; int n = nlocal; int jm1 = j - 1; if (flag < 0) { for (i = 0; i < n; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,compute_array[i][jm1],i); } else one = compute_array[flag][jm1]; } } else if (flavor[m] == LOCAL) { if (!(compute->invoked_flag & INVOKED_LOCAL)) { compute->compute_local(); compute->invoked_flag |= INVOKED_LOCAL; } if (j == 0) { double *compute_vector = compute->vector_local; int n = compute->size_local_rows; if (flag < 0) for (i = 0; i < n; i++) combine(one,compute_vector[i],i); else one = compute_vector[flag]; } else { double **compute_array = compute->array_local; int n = compute->size_local_rows; int jm1 = j - 1; if (flag < 0) for (i = 0; i < n; i++) combine(one,compute_array[i][jm1],i); else one = compute_array[flag][jm1]; } } // check if fix frequency is a match } else if (which[m] == FIX) { if (update->ntimestep % modify->fix[n]->peratom_freq) error->all(FLERR,"Fix used in compute reduce not computed at " "compatible time"); Fix *fix = modify->fix[n]; if (flavor[m] == PERATOM) { if (j == 0) { double *fix_vector = fix->vector_atom; int n = nlocal; if (flag < 0) { for (i = 0; i < n; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,fix_vector[i],i); } else one = fix_vector[flag]; } else { double **fix_array = fix->array_atom; int jm1 = j - 1; if (flag < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,fix_array[i][jm1],i); } else one = fix_array[flag][jm1]; } } else if (flavor[m] == LOCAL) { if (j == 0) { double *fix_vector = fix->vector_local; int n = fix->size_local_rows; if (flag < 0) for (i = 0; i < n; i++) combine(one,fix_vector[i],i); else one = fix_vector[flag]; } else { double **fix_array = fix->array_local; int n = fix->size_local_rows; int jm1 = j - 1; if (flag < 0) for (i = 0; i < n; i++) combine(one,fix_array[i][jm1],i); else one = fix_array[flag][jm1]; } } // evaluate atom-style variable } else if (which[m] == VARIABLE) { if (nlocal > maxatom) { maxatom = atom->nmax; memory->destroy(varatom); memory->create(varatom,maxatom,"reduce/region:varatom"); } input->variable->compute_atom(n,igroup,varatom,1,0); if (flag < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) combine(one,varatom[i],i); } else one = varatom[flag]; } return one; }
double ComputeReduce::compute_one(int m, int flag) { int i; // invoke the appropriate attribute,compute,fix,variable // for flag = -1, compute scalar quantity by scanning over atom properties // only include atoms in group for atom properties and per-atom quantities index = -1; int vidx = value2index[m]; int aidx = argindex[m]; int *mask = atom->mask; int nlocal = atom->nlocal; double one; if (mode == SUM) one = 0.0; else if (mode == MINN) one = BIG; else if (mode == MAXX) one = -BIG; else if (mode == AVE) one = 0.0; if (which[m] == X) { double **x = atom->x; if (flag < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one,x[i][aidx],i); } else one = x[flag][aidx]; } else if (which[m] == V) { double **v = atom->v; if (flag < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one,v[i][aidx],i); } else one = v[flag][aidx]; } else if (which[m] == F) { double **f = atom->f; if (flag < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one,f[i][aidx],i); } else one = f[flag][aidx]; // invoke compute if not previously invoked } else if (which[m] == COMPUTE) { Compute *compute = modify->compute[vidx]; if (flavor[m] == PERATOM) { if (!(compute->invoked_flag & INVOKED_PERATOM)) { compute->compute_peratom(); compute->invoked_flag |= INVOKED_PERATOM; } if (aidx == 0) { double *comp_vec = compute->vector_atom; int n = nlocal; if (flag < 0) { for (i = 0; i < n; i++) if (mask[i] & groupbit) combine(one,comp_vec[i],i); } else one = comp_vec[flag]; } else { double **carray_atom = compute->array_atom; int n = nlocal; int aidxm1 = aidx - 1; if (flag < 0) { for (i = 0; i < n; i++) if (mask[i] & groupbit) combine(one,carray_atom[i][aidxm1],i); } else one = carray_atom[flag][aidxm1]; } } else if (flavor[m] == LOCAL) { if (!(compute->invoked_flag & INVOKED_LOCAL)) { compute->compute_local(); compute->invoked_flag |= INVOKED_LOCAL; } if (aidx == 0) { double *comp_vec = compute->vector_local; int n = compute->size_local_rows; if (flag < 0) for (i = 0; i < n; i++) combine(one,comp_vec[i],i); else one = comp_vec[flag]; } else { double **carray_local = compute->array_local; int n = compute->size_local_rows; int aidxm1 = aidx - 1; if (flag < 0) for (i = 0; i < n; i++) combine(one,carray_local[i][aidxm1],i); else one = carray_local[flag][aidxm1]; } } // access fix fields, check if fix frequency is a match } else if (which[m] == FIX) { if (update->ntimestep % modify->fix[vidx]->peratom_freq) error->all("Fix used in compute reduce not computed at compatible time"); Fix *fix = modify->fix[vidx]; if (flavor[m] == PERATOM) { if (aidx == 0) { double *fix_vector = fix->vector_atom; int n = nlocal; if (flag < 0) { for (i = 0; i < n; i++) if (mask[i] & groupbit) combine(one,fix_vector[i],i); } else one = fix_vector[flag]; } else { double **fix_array = fix->array_atom; int aidxm1 = aidx - 1; if (flag < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one,fix_array[i][aidxm1],i); } else one = fix_array[flag][aidxm1]; } } else if (flavor[m] == LOCAL) { if (aidx == 0) { double *fix_vector = fix->vector_local; int n = fix->size_local_rows; if (flag < 0) for (i = 0; i < n; i++) combine(one,fix_vector[i],i); else one = fix_vector[flag]; } else { double **fix_array = fix->array_local; int n = fix->size_local_rows; int aidxm1 = aidx - 1; if (flag < 0) for (i = 0; i < n; i++) combine(one,fix_array[i][aidxm1],i); else one = fix_array[flag][aidxm1]; } } // evaluate atom-style variable } else if (which[m] == VARIABLE) { if (nlocal > maxatom) { maxatom = atom->nmax; memory->destroy(varatom); memory->create(varatom,maxatom,"reduce:varatom"); } input->variable->compute_atom(vidx,igroup,varatom,1,0); if (flag < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) combine(one,varatom[i],i); } else one = varatom[flag]; } return one; }
void FixAveHisto::end_of_step() { int i,j,m; // skip if not step which requires doing something // error check if timestep was reset in an invalid manner bigint ntimestep = update->ntimestep; if (ntimestep < nvalid_last || ntimestep > nvalid) error->all(FLERR,"Invalid timestep reset for fix ave/histo"); if (ntimestep != nvalid) return; nvalid_last = nvalid; // zero if first step if (irepeat == 0) { stats[0] = stats[1] = 0.0; stats[2] = BIG; stats[3] = -BIG; for (i = 0; i < nbins; i++) bin[i] = 0.0; } // accumulate results of computes,fixes,variables to local copy // compute/fix/variable may invoke computes so wrap with clear/add modify->clearstep_compute(); for (i = 0; i < nvalues; i++) { m = value2index[i]; j = argindex[i]; // atom attributes if (which[i] == X) bin_atoms(&atom->x[0][j],3); else if (which[i] == V) bin_atoms(&atom->v[0][j],3); else if (which[i] == F) bin_atoms(&atom->f[0][j],3); // invoke compute if not previously invoked if (which[i] == COMPUTE) { Compute *compute = modify->compute[m]; if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { if (!(compute->invoked_flag & INVOKED_SCALAR)) { compute->compute_scalar(); compute->invoked_flag |= INVOKED_SCALAR; } bin_one(compute->scalar); } else { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } bin_one(compute->vector[j-1]); } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } bin_vector(compute->size_vector,compute->vector,1); } else { if (!(compute->invoked_flag & INVOKED_ARRAY)) { compute->compute_array(); compute->invoked_flag |= INVOKED_ARRAY; } if (compute->array) bin_vector(compute->size_array_rows,&compute->array[0][j-1], compute->size_array_cols); } } else if (kind == PERATOM) { if (!(compute->invoked_flag & INVOKED_PERATOM)) { compute->compute_peratom(); compute->invoked_flag |= INVOKED_PERATOM; } if (j == 0) bin_atoms(compute->vector_atom,1); else if (compute->array_atom) bin_atoms(&compute->array_atom[0][j-1],compute->size_peratom_cols); } else if (kind == LOCAL) { if (!(compute->invoked_flag & INVOKED_LOCAL)) { compute->compute_local(); compute->invoked_flag |= INVOKED_LOCAL; } if (j == 0) bin_vector(compute->size_local_rows,compute->vector_local,1); else if (compute->array_local) bin_vector(compute->size_local_rows,&compute->array_local[0][j-1], compute->size_local_cols); } // access fix fields, guaranteed to be ready } else if (which[i] == FIX) { Fix *fix = modify->fix[m]; if (kind == GLOBAL && mode == SCALAR) { if (j == 0) bin_one(fix->compute_scalar()); else bin_one(fix->compute_vector(j-1)); } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { int n = fix->size_vector; for (i = 0; i < n; i++) bin_one(fix->compute_vector(i)); } else { int n = fix->size_vector; for (i = 0; i < n; i++) bin_one(fix->compute_array(i,j-1)); } } else if (kind == PERATOM) { if (j == 0) bin_atoms(fix->vector_atom,1); else if (fix->array_atom) bin_atoms(fix->array_atom[j-1],fix->size_peratom_cols); } else if (kind == LOCAL) { if (j == 0) bin_vector(fix->size_local_rows,fix->vector_local,1); else if (fix->array_local) bin_vector(fix->size_local_rows,&fix->array_local[0][j-1], fix->size_local_cols); } // evaluate equal-style variable } else if (which[i] == VARIABLE && kind == GLOBAL) { bin_one(input->variable->compute_equal(m)); } else if (which[i] == VARIABLE && kind == PERATOM) { if (atom->nlocal > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo:vector"); } input->variable->compute_atom(m,igroup,vector,1,0); bin_atoms(vector,1); } } // done if irepeat < nrepeat // else reset irepeat and nvalid irepeat++; if (irepeat < nrepeat) { nvalid += nevery; modify->addstep_compute(nvalid); return; } irepeat = 0; nvalid = ntimestep + nfreq - (nrepeat-1)*nevery; modify->addstep_compute(nvalid); // merge histogram stats across procs if necessary if (kind == PERATOM || kind == LOCAL) { MPI_Allreduce(stats,stats_all,2,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&stats[2],&stats_all[2],1,MPI_DOUBLE,MPI_MIN,world); MPI_Allreduce(&stats[3],&stats_all[3],1,MPI_DOUBLE,MPI_MAX,world); MPI_Allreduce(bin,bin_all,nbins,MPI_DOUBLE,MPI_SUM,world); stats[0] = stats_all[0]; stats[1] = stats_all[1]; stats[2] = stats_all[2]; stats[3] = stats_all[3]; for (i = 0; i < nbins; i++) bin[i] = bin_all[i]; } // if ave = ONE, only single Nfreq timestep value is needed // if ave = RUNNING, combine with all previous Nfreq timestep values // if ave = WINDOW, combine with nwindow most recent Nfreq timestep values if (ave == ONE) { stats_total[0] = stats[0]; stats_total[1] = stats[1]; stats_total[2] = stats[2]; stats_total[3] = stats[3]; for (i = 0; i < nbins; i++) bin_total[i] = bin[i]; } else if (ave == RUNNING) { stats_total[0] += stats[0]; stats_total[1] += stats[1]; stats_total[2] = MIN(stats_total[2],stats[2]); stats_total[3] = MAX(stats_total[3],stats[3]); for (i = 0; i < nbins; i++) bin_total[i] += bin[i]; } else if (ave == WINDOW) { stats_total[0] += stats[0]; if (window_limit) stats_total[0] -= stats_list[iwindow][0]; stats_list[iwindow][0] = stats[0]; stats_total[1] += stats[1]; if (window_limit) stats_total[1] -= stats_list[iwindow][1]; stats_list[iwindow][1] = stats[1]; if (window_limit) m = nwindow; else m = iwindow+1; stats_list[iwindow][2] = stats[2]; stats_total[2] = stats_list[0][2]; for (i = 1; i < m; i++) stats_total[2] = MIN(stats_total[2],stats_list[i][2]); stats_list[iwindow][3] = stats[3]; stats_total[3] = stats_list[0][3]; for (i = 1; i < m; i++) stats_total[3] = MAX(stats_total[3],stats_list[i][3]); for (i = 0; i < nbins; i++) { bin_total[i] += bin[i]; if (window_limit) bin_total[i] -= bin_list[iwindow][i]; bin_list[iwindow][i] = bin[i]; } iwindow++; if (iwindow == nwindow) { iwindow = 0; window_limit = 1; } } // output result to file if (fp && me == 0) { if (overwrite) fseek(fp,filepos,SEEK_SET); fprintf(fp,BIGINT_FORMAT " %d %g %g %g %g\n",ntimestep,nbins, stats_total[0],stats_total[1],stats_total[2],stats_total[3]); if (stats_total[0] != 0.0) for (i = 0; i < nbins; i++) fprintf(fp,"%d %g %g %g\n", i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]); else for (i = 0; i < nbins; i++) fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0); fflush(fp); if (overwrite) { long fileend = ftell(fp); ftruncate(fileno(fp),fileend); } } }