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; }
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); } } }
void FixAveTime::invoke_scalar(bigint ntimestep) { int i,m; double scalar; // zero if first step if (irepeat == 0) for (i = 0; i < nvalues; i++) vector[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]; // invoke compute if not previously invoked if (which[i] == COMPUTE) { Compute *compute = modify->compute[m]; if (argindex[i] == 0) { if (!(compute->invoked_flag & INVOKED_SCALAR)) { compute->compute_scalar(); compute->invoked_flag |= INVOKED_SCALAR; } scalar = compute->scalar; } else { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } scalar = compute->vector[argindex[i]-1]; } // access fix fields, guaranteed to be ready } else if (which[i] == FIX) { if (argindex[i] == 0) scalar = modify->fix[m]->compute_scalar(); else scalar = modify->fix[m]->compute_vector(argindex[i]-1); // evaluate equal-style variable } else if (which[i] == VARIABLE) scalar = input->variable->compute_equal(m); // add value to vector or just set directly if offcol is set if (offcol[i]) vector[i] = scalar; else vector[i] += scalar; } // 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); // average the final result for the Nfreq timestep double repeat = nrepeat; for (i = 0; i < nvalues; i++) if (offcol[i] == 0) vector[i] /= repeat; // 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 (ntimestep >= startstep) { if (ave == ONE) { for (i = 0; i < nvalues; i++) vector_total[i] = vector[i]; norm = 1; } else if (ave == RUNNING) { for (i = 0; i < nvalues; i++) vector_total[i] += vector[i]; norm++; } else if (ave == WINDOW) { for (i = 0; i < nvalues; i++) { vector_total[i] += vector[i]; if (window_limit) vector_total[i] -= vector_list[iwindow][i]; vector_list[iwindow][i] = vector[i]; } iwindow++; if (iwindow == nwindow) { iwindow = 0; window_limit = 1; } if (window_limit) norm = nwindow; else norm = iwindow; } } // insure any columns with offcol set are effectively set to last value for (i = 0; i < nvalues; i++) if (offcol[i]) vector_total[i] = norm*vector[i]; // output result to file if (fp && me == 0) { fprintf(fp,BIGINT_FORMAT,ntimestep); for (i = 0; i < nvalues; i++) fprintf(fp," %g",vector_total[i]/norm); fprintf(fp,"\n"); fflush(fp); } }
void FixAveTime::invoke_scalar(bigint ntimestep) { int i,m; double scalar; // zero if first sample within single Nfreq epoch // NOTE: doc this // are not checking for returned length, just initialize it // check for exceeding length is done below if (irepeat == 0) { if (any_variable_length) { modify->clearstep_compute(); column_length(1); modify->addstep_compute(ntimestep+nevery); modify->addstep_compute(ntimestep+nfreq); } for (i = 0; i < nvalues; i++) vector[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]; // invoke compute if not previously invoked if (which[i] == COMPUTE) { Compute *compute = modify->compute[m]; if (argindex[i] == 0) { if (!(compute->invoked_flag & INVOKED_SCALAR)) { compute->compute_scalar(); compute->invoked_flag |= INVOKED_SCALAR; } scalar = compute->scalar; } else { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } // insure no out-of-range access to variable-length compute vector if (varlen[i] && compute->size_vector < argindex[i]) scalar = 0.0; else scalar = compute->vector[argindex[i]-1]; } // access fix fields, guaranteed to be ready } else if (which[i] == FIX) { if (argindex[i] == 0) scalar = modify->fix[m]->compute_scalar(); else scalar = modify->fix[m]->compute_vector(argindex[i]-1); // evaluate equal-style variable } else if (which[i] == VARIABLE) scalar = input->variable->compute_equal(m); // add value to vector or just set directly if offcol is set if (offcol[i]) vector[i] = scalar; else vector[i] += scalar; } // 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); // average the final result for the Nfreq timestep double repeat = nrepeat; for (i = 0; i < nvalues; i++) if (offcol[i] == 0) vector[i] /= repeat; // 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) { for (i = 0; i < nvalues; i++) vector_total[i] = vector[i]; norm = 1; } else if (ave == RUNNING) { for (i = 0; i < nvalues; i++) vector_total[i] += vector[i]; norm++; } else if (ave == WINDOW) { for (i = 0; i < nvalues; i++) { vector_total[i] += vector[i]; if (window_limit) vector_total[i] -= vector_list[iwindow][i]; vector_list[iwindow][i] = vector[i]; } iwindow++; if (iwindow == nwindow) { iwindow = 0; window_limit = 1; } if (window_limit) norm = nwindow; else norm = iwindow; } // insure any columns with offcol set are effectively set to last value for (i = 0; i < nvalues; i++) if (offcol[i]) vector_total[i] = norm*vector[i]; // output result to file if (fp && me == 0) { clearerr(fp); if (overwrite) fseek(fp,filepos,SEEK_SET); fprintf(fp,BIGINT_FORMAT,ntimestep); for (i = 0; i < nvalues; i++) fprintf(fp,format,vector_total[i]/norm); fprintf(fp,"\n"); if (ferror(fp)) error->one(FLERR,"Error writing out time averaged data"); fflush(fp); if (overwrite) { long fileend = ftell(fp); if (fileend > 0) ftruncate(fileno(fp),fileend); } } }
void FixAveCorrelate::end_of_step() { int i,j,m; double scalar; // 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/correlate"); if (ntimestep != nvalid) return; nvalid_last = nvalid; // accumulate results of computes,fixes,variables to origin // compute/fix/variable may invoke computes so wrap with clear/add modify->clearstep_compute(); // lastindex = index in values ring of latest time sample lastindex++; if (lastindex == nrepeat) lastindex = 0; for (i = 0; i < nvalues; i++) { m = value2index[i]; // invoke compute if not previously invoked if (which[i] == COMPUTE) { Compute *compute = modify->compute[m]; if (argindex[i] == 0) { if (!(compute->invoked_flag & INVOKED_SCALAR)) { compute->compute_scalar(); compute->invoked_flag |= INVOKED_SCALAR; } scalar = compute->scalar; } else { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } scalar = compute->vector[argindex[i]-1]; } // access fix fields, guaranteed to be ready } else if (which[i] == FIX) { if (argindex[i] == 0) scalar = modify->fix[m]->compute_scalar(); else scalar = modify->fix[m]->compute_vector(argindex[i]-1); // evaluate equal-style variable } else if (which[i] == VARIABLE) scalar = input->variable->compute_equal(m); values[lastindex][i] = scalar; } // fistindex = index in values ring of earliest time sample // nsample = number of time samples in values ring if (nsample < nrepeat) nsample++; else { firstindex++; if (firstindex == nrepeat) firstindex = 0; } nvalid += nevery; modify->addstep_compute(nvalid); // calculate all Cij() enabled by latest values accumulate(); if (ntimestep % nfreq) return; // save results in save_count and save_corr for (i = 0; i < nrepeat; i++) { save_count[i] = count[i]; if (count[i]) for (j = 0; j < npair; j++) save_corr[i][j] = prefactor*corr[i][j]/count[i]; else for (j = 0; j < npair; j++) save_corr[i][j] = 0.0; } // output result to file if (fp && me == 0) { if (overwrite) fseek(fp,filepos,SEEK_SET); fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrepeat); for (i = 0; i < nrepeat; i++) { fprintf(fp,"%d %d %d",i+1,i*nevery,count[i]); if (count[i]) for (j = 0; j < npair; j++) fprintf(fp," %g",prefactor*corr[i][j]/count[i]); else for (j = 0; j < npair; j++) fprintf(fp," 0.0"); fprintf(fp,"\n"); } fflush(fp); if (overwrite) { long fileend = ftell(fp); ftruncate(fileno(fp),fileend); } } // zero accumulation if requested // recalculate Cij(0) if (ave == ONE) { for (i = 0; i < nrepeat; i++) { count[i] = 0; for (j = 0; j < npair; j++) corr[i][j] = 0.0; } nsample = 1; accumulate(); } }