convert compute slice
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,3 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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@ -27,96 +26,84 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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nvalues(0), which(nullptr), argindex(nullptr), value2index(nullptr), ids(nullptr)
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ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
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{
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if (narg < 7) error->all(FLERR,"Illegal compute slice command");
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if (narg < 7) utils::missing_cmd_args(FLERR, "compute slice", error);
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MPI_Comm_rank(world,&me);
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nstart = utils::inumeric(FLERR, arg[3], false, lmp);
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nstop = utils::inumeric(FLERR, arg[4], false, lmp);
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nskip = utils::inumeric(FLERR, arg[5], false, lmp);
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nstart = utils::inumeric(FLERR,arg[3],false,lmp);
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nstop = utils::inumeric(FLERR,arg[4],false,lmp);
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nskip = utils::inumeric(FLERR,arg[5],false,lmp);
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if (nstart < 1) error->all(FLERR, "Invalid compute slice nstart value {} < 1", nstart);
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if (nstop < nstart) error->all(FLERR, "Invalid compute slice nstop value {} < {}", nstop, nstart);
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if (nskip < 1) error->all(FLERR, "Invalid compute slice nskip value < 1: {}", nskip);
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if (nstart < 1 || nstop < nstart || nskip < 1)
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error->all(FLERR,"Illegal compute slice command");
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// parse remaining values until one isn't recognized
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which = new int[narg-6];
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argindex = new int[narg-6];
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ids = new char*[narg-6];
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value2index = new int[narg-6];
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nvalues = 0;
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// parse values
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values.clear();
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for (int iarg = 6; iarg < narg; iarg++) {
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ArgInfo argi(arg[iarg]);
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which[nvalues] = argi.get_type();
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argindex[nvalues] = argi.get_index1();
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ids[nvalues] = argi.copy_name();
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value_t val;
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val.which = argi.get_type();
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val.argindex = argi.get_index1();
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val.id = argi.get_name();
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val.val.c = nullptr;
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if ((which[nvalues] == ArgInfo::UNKNOWN) || (which[nvalues] == ArgInfo::NONE)
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|| (argi.get_dim() > 1))
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error->all(FLERR,"Illegal compute slice command");
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if ((val.which == ArgInfo::UNKNOWN) || (val.which == ArgInfo::NONE) || (argi.get_dim() > 1))
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error->all(FLERR, "Illegal compute slice argument: {}", arg[iarg]);
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nvalues++;
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values.push_back(val);
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}
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// setup and error check
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == ArgInfo::COMPUTE) {
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int icompute = modify->find_compute(ids[i]);
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if (icompute < 0)
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error->all(FLERR,"Compute ID for compute slice does not exist");
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if (modify->compute[icompute]->vector_flag) {
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if (argindex[i])
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error->all(FLERR,"Compute slice compute does not "
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"calculate a global array");
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if (nstop > modify->compute[icompute]->size_vector)
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error->all(FLERR,"Compute slice compute vector is "
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"accessed out-of-range");
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} else if (modify->compute[icompute]->array_flag) {
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if (argindex[i] == 0)
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error->all(FLERR,"Compute slice compute does not "
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"calculate a global vector");
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if (argindex[i] > modify->compute[icompute]->size_array_cols)
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error->all(FLERR,"Compute slice compute array is "
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"accessed out-of-range");
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if (nstop > modify->compute[icompute]->size_array_rows)
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error->all(FLERR,"Compute slice compute array is "
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"accessed out-of-range");
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} else error->all(FLERR,"Compute slice compute does not calculate "
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"global vector or array");
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} else if (which[i] == ArgInfo::FIX) {
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auto ifix = modify->get_fix_by_id(ids[i]);
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if (!ifix)
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error->all(FLERR,"Fix ID {} for compute slice does not exist", ids[i]);
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if (ifix->vector_flag) {
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if (argindex[i])
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error->all(FLERR,"Compute slice fix {} does not calculate a global array", ids[i]);
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if (nstop > ifix->size_vector)
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error->all(FLERR,"Compute slice fix {} vector is accessed out-of-range", ids[i]);
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} else if (ifix->array_flag) {
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if (argindex[i] == 0)
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error->all(FLERR,"Compute slice fix {} does not calculate a global vector", ids[i]);
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if (argindex[i] > ifix->size_array_cols)
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error->all(FLERR,"Compute slice fix {} array is accessed out-of-range", ids[i]);
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if (nstop > ifix->size_array_rows)
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error->all(FLERR,"Compute slice fix {} array is accessed out-of-range", ids[i]);
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} else error->all(FLERR,"Compute slice fix {} does not calculate global vector or array", ids[i]);
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} else if (which[i] == ArgInfo::VARIABLE) {
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int ivariable = input->variable->find(ids[i]);
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if (ivariable < 0)
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error->all(FLERR,"Variable name for compute slice does not exist");
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if (argindex[i] == 0 && input->variable->vectorstyle(ivariable) == 0)
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error->all(FLERR,"Compute slice variable is not vector-style variable");
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if (argindex[i])
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error->all(FLERR,"Compute slice vector variable cannot be indexed");
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for (auto &val : values) {
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if (val.which == ArgInfo::COMPUTE) {
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val.val.c = modify->get_compute_by_id(val.id);
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if (!val.val.c) error->all(FLERR, "Compute ID {} for compute slice does not exist", val.id);
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if (val.val.c->vector_flag) {
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if (val.argindex)
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error->all(FLERR, "Compute slice compute {} does not calculate a global array", val.id);
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if (nstop > val.val.c->size_vector)
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error->all(FLERR, "Compute slice compute {} vector is accessed out-of-range", val.id);
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} else if (val.val.c->array_flag) {
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if (val.argindex == 0)
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error->all(FLERR, "Compute slice compute {} does not calculate a global vector", val.id);
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if (val.argindex > val.val.c->size_array_cols)
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error->all(FLERR, "Compute slice compute {} array is accessed out-of-range", val.id);
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if (nstop > val.val.c->size_array_rows)
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error->all(FLERR, "Compute slice compute {} array is accessed out-of-range", val.id);
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} else {
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error->all(FLERR, "Compute slice compute {} does not calculate global vector or array",
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val.id);
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}
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} else if (val.which == ArgInfo::FIX) {
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val.val.f = modify->get_fix_by_id(val.id);
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if (!val.val.f) error->all(FLERR, "Fix ID {} for compute slice does not exist", val.id);
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if (val.val.f->vector_flag) {
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if (val.argindex)
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error->all(FLERR, "Compute slice fix {} does not calculate a global array", val.id);
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if (nstop > val.val.f->size_vector)
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error->all(FLERR, "Compute slice fix {} vector is accessed out-of-range", val.id);
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} else if (val.val.f->array_flag) {
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if (val.argindex == 0)
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error->all(FLERR, "Compute slice fix {} does not calculate a global vector", val.id);
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if (val.argindex > val.val.f->size_array_cols)
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error->all(FLERR, "Compute slice fix {} array is accessed out-of-range", val.id);
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if (nstop > val.val.f->size_array_rows)
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error->all(FLERR, "Compute slice fix {} array is accessed out-of-range", val.id);
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} else {
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error->all(FLERR, "Compute slice fix {} does not calculate global vector or array", val.id);
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}
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} else if (val.which == ArgInfo::VARIABLE) {
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val.val.v = input->variable->find(val.id.c_str());
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if (val.val.v < 0)
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error->all(FLERR, "Variable name {} for compute slice does not exist", val.id);
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if (val.argindex == 0 && input->variable->vectorstyle(val.val.v) == 0)
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error->all(FLERR, "Compute slice variable {} is not vector-style variable", val.id);
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if (val.argindex)
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error->all(FLERR, "Compute slice vector variable {} cannot be indexed", val.id);
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}
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}
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@ -124,68 +111,65 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
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// for vector, set intensive/extensive to mirror input values
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// for array, set intensive if all input values are intensive, else extensive
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if (nvalues == 1) {
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if (values.size() == 1) {
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auto &val = values[0];
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vector_flag = 1;
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size_vector = (nstop-nstart) / nskip;
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memory->create(vector,size_vector,"slice:vector");
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size_vector = (nstop - nstart) / nskip;
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memory->create(vector, size_vector, "slice:vector");
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if (which[0] == ArgInfo::COMPUTE) {
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int icompute = modify->find_compute(ids[0]);
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if (argindex[0] == 0) {
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extvector = modify->compute[icompute]->extvector;
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if (modify->compute[icompute]->extvector == -1) {
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if (val.which == ArgInfo::COMPUTE) {
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if (val.argindex == 0) {
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extvector = val.val.c->extvector;
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if (val.val.c->extvector == -1) {
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extlist = new int[size_vector];
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int j = 0;
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for (int i = nstart; i < nstop; i += nskip)
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extlist[j++] = modify->compute[icompute]->extlist[i-1];
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for (int i = nstart; i < nstop; i += nskip) extlist[j++] = val.val.c->extlist[i - 1];
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}
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} else extvector = modify->compute[icompute]->extarray;
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} else if (which[0] == ArgInfo::FIX) {
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auto ifix = modify->get_fix_by_id(ids[0]);
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if (argindex[0] == 0) {
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extvector = ifix->extvector;
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if (ifix->extvector == -1) {
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} else
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extvector = val.val.c->extarray;
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} else if (val.which == ArgInfo::FIX) {
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if (val.argindex == 0) {
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extvector = val.val.f->extvector;
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if (val.val.f->extvector == -1) {
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extlist = new int[size_vector];
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int j = 0;
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for (int i = nstart; i < nstop; i += nskip)
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extlist[j++] = ifix->extlist[i-1];
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for (int i = nstart; i < nstop; i += nskip) extlist[j++] = val.val.f->extlist[i - 1];
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}
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} else extvector = ifix->extarray;
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} else if (which[0] == ArgInfo::VARIABLE) {
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} else
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extvector = val.val.f->extarray;
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} else if (val.which == ArgInfo::VARIABLE) {
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extvector = 0;
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}
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} else {
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array_flag = 1;
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size_array_rows = (nstop-nstart) / nskip;
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size_array_cols = nvalues;
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memory->create(array,size_array_rows,size_array_cols,"slice:array");
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size_array_rows = (nstop - nstart) / nskip;
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size_array_cols = values.size();
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memory->create(array, size_array_rows, size_array_cols, "slice:array");
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extarray = 0;
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == ArgInfo::COMPUTE) {
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int icompute = modify->find_compute(ids[i]);
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if (argindex[i] == 0) {
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if (modify->compute[icompute]->extvector == 1) extarray = 1;
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if (modify->compute[icompute]->extvector == -1) {
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for (int j = 0; j < modify->compute[icompute]->size_vector; j++)
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if (modify->compute[icompute]->extlist[j]) extarray = 1;
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for (auto &val : values) {
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if (val.which == ArgInfo::COMPUTE) {
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if (val.argindex == 0) {
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if (val.val.c->extvector == 1) extarray = 1;
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if (val.val.c->extvector == -1) {
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for (int j = 0; j < val.val.c->size_vector; j++)
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if (val.val.c->extlist[j]) extarray = 1;
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}
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} else {
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if (modify->compute[icompute]->extarray) extarray = 1;
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if (val.val.c->extarray) extarray = 1;
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}
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} else if (which[i] == ArgInfo::FIX) {
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auto ifix = modify->get_fix_by_id(ids[i]);
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if (argindex[i] == 0) {
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if (ifix->extvector == 1) extarray = 1;
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if (ifix->extvector == -1) {
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for (int j = 0; j < ifix->size_vector; j++)
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if (ifix->extlist[j]) extarray = 1;
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} else if (val.which == ArgInfo::FIX) {
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if (val.argindex == 0) {
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if (val.val.f->extvector == 1) extarray = 1;
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if (val.val.f->extvector == -1) {
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for (int j = 0; j < val.val.f->size_vector; j++)
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if (val.val.f->extlist[j]) extarray = 1;
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}
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} else {
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if (ifix->extarray) extarray = 1;
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if (val.val.f->extarray) extarray = 1;
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}
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} else if (which[i] == ArgInfo::VARIABLE) {
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} else if (val.which == ArgInfo::VARIABLE) {
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// variable is always intensive, does not change extarray
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}
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}
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@ -196,12 +180,7 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
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ComputeSlice::~ComputeSlice()
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{
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delete [] which;
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delete [] argindex;
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for (int m = 0; m < nvalues; m++) delete [] ids[m];
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delete [] ids;
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delete [] value2index;
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delete [] extlist;
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delete[] extlist;
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memory->destroy(vector);
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memory->destroy(array);
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@ -213,22 +192,17 @@ void ComputeSlice::init()
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{
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// set indices and check validity of all computes,fixes
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for (int m = 0; m < nvalues; m++) {
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if (which[m] == ArgInfo::COMPUTE) {
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int icompute = modify->find_compute(ids[m]);
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if (icompute < 0)
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error->all(FLERR,"Compute ID for compute slice does not exist");
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value2index[m] = icompute;
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} else if (which[m] == ArgInfo::FIX) {
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int ifix = modify->find_fix(ids[m]);
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if (ifix < 0)
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error->all(FLERR,"Fix ID for compute slice does not exist");
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value2index[m] = ifix;
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} else if (which[m] == ArgInfo::VARIABLE) {
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int ivariable = input->variable->find(ids[m]);
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if (ivariable < 0)
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error->all(FLERR,"Variable name for compute slice does not exist");
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value2index[m] = ivariable;
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for (auto &val : values) {
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if (val.which == ArgInfo::COMPUTE) {
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val.val.c = modify->get_compute_by_id(val.id);
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if (!val.val.c) error->all(FLERR, "Compute ID {} for compute slice does not exist", val.id);
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} else if (val.which == ArgInfo::FIX) {
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val.val.f = modify->get_fix_by_id(val.id);
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if (!val.val.f) error->all(FLERR, "Fix ID {} for compute slice does not exist", val.id);
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} else if (val.which == ArgInfo::VARIABLE) {
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val.val.v = input->variable->find(val.id.c_str());
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if (val.val.v < 0)
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error->all(FLERR, "Variable name {} for compute slice does not exist", val.id);
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}
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}
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}
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@ -239,7 +213,7 @@ void ComputeSlice::compute_vector()
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{
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invoked_vector = update->ntimestep;
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extract_one(0,vector,1);
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extract_one(0, vector, 1);
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}
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/* ---------------------------------------------------------------------- */
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@ -248,8 +222,7 @@ void ComputeSlice::compute_array()
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{
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invoked_array = update->ntimestep;
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for (int m = 0; m < nvalues; m++)
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extract_one(0,&array[m][0],nvalues);
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for (int m = 0; m < values.size(); m++) extract_one(0, &array[m][0], values.size());
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}
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/* ----------------------------------------------------------------------
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@ -259,72 +232,67 @@ void ComputeSlice::compute_array()
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void ComputeSlice::extract_one(int m, double *vec, int stride)
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{
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int i,j;
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auto &val = values[m];
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// invoke the appropriate compute if needed
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if (which[m] == ArgInfo::COMPUTE) {
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Compute *compute = modify->compute[value2index[m]];
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if (argindex[m] == 0) {
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if (!(compute->invoked_flag & Compute::INVOKED_VECTOR)) {
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compute->compute_vector();
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compute->invoked_flag |= Compute::INVOKED_VECTOR;
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if (val.which == ArgInfo::COMPUTE) {
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if (val.argindex == 0) {
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if (!(val.val.c->invoked_flag & Compute::INVOKED_VECTOR)) {
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val.val.c->compute_vector();
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val.val.c->invoked_flag |= Compute::INVOKED_VECTOR;
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}
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double *cvector = compute->vector;
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j = 0;
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for (i = nstart; i < nstop; i += nskip) {
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vec[j] = cvector[i-1];
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double *cvector = val.val.c->vector;
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int j = 0;
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for (int i = nstart; i < nstop; i += nskip) {
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vec[j] = cvector[i - 1];
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j += stride;
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}
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} else {
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if (!(compute->invoked_flag & Compute::INVOKED_ARRAY)) {
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compute->compute_array();
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compute->invoked_flag |= Compute::INVOKED_ARRAY;
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if (!(val.val.c->invoked_flag & Compute::INVOKED_ARRAY)) {
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val.val.c->compute_array();
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val.val.c->invoked_flag |= Compute::INVOKED_ARRAY;
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}
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double **carray = compute->array;
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int icol = argindex[m]-1;
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j = 0;
|
||||
for (i = nstart; i < nstop; i += nskip) {
|
||||
vec[j] = carray[i-1][icol];
|
||||
double **carray = val.val.c->array;
|
||||
int icol = val.argindex - 1;
|
||||
int j = 0;
|
||||
for (int i = nstart; i < nstop; i += nskip) {
|
||||
vec[j] = carray[i - 1][icol];
|
||||
j += stride;
|
||||
}
|
||||
}
|
||||
|
||||
// access fix fields, check if fix frequency is a match
|
||||
// access fix fields, check if fix frequency is a match
|
||||
|
||||
} else if (which[m] == ArgInfo::FIX) {
|
||||
if (update->ntimestep % modify->fix[value2index[m]]->global_freq)
|
||||
error->all(FLERR,"Fix used in compute slice not "
|
||||
"computed at compatible time");
|
||||
Fix *fix = modify->fix[value2index[m]];
|
||||
} else if (val.which == ArgInfo::FIX) {
|
||||
if (update->ntimestep % val.val.f->global_freq)
|
||||
error->all(FLERR, "Fix {} used in compute slice not computed at compatible time", val.id);
|
||||
|
||||
if (argindex[m] == 0) {
|
||||
j = 0;
|
||||
for (i = nstart; i < nstop; i += nskip) {
|
||||
vec[j] = fix->compute_vector(i-1);
|
||||
if (val.argindex == 0) {
|
||||
int j = 0;
|
||||
for (int i = nstart; i < nstop; i += nskip) {
|
||||
vec[j] = val.val.f->compute_vector(i - 1);
|
||||
j += stride;
|
||||
}
|
||||
} else {
|
||||
int icol = argindex[m]-1;
|
||||
j = 0;
|
||||
for (i = nstart; i < nstop; i += nskip) {
|
||||
vec[j] = fix->compute_array(i-1,icol);
|
||||
int icol = val.argindex - 1;
|
||||
int j = 0;
|
||||
for (int i = nstart; i < nstop; i += nskip) {
|
||||
vec[j] = val.val.f->compute_array(i - 1, icol);
|
||||
j += stride;
|
||||
}
|
||||
}
|
||||
|
||||
// invoke vector-style variable
|
||||
|
||||
} else if (which[m] == ArgInfo::VARIABLE) {
|
||||
} else if (val.which == ArgInfo::VARIABLE) {
|
||||
double *varvec;
|
||||
int nvec = input->variable->compute_vector(value2index[m],&varvec);
|
||||
if (nvec < nstop)
|
||||
error->all(FLERR,"Compute slice variable is not long enough");
|
||||
j = 0;
|
||||
for (i = nstart; i < nstop; i += nskip) {
|
||||
vec[j] = varvec[i-1];
|
||||
int nvec = input->variable->compute_vector(val.val.v, &varvec);
|
||||
if (nvec < nstop) error->all(FLERR, "Compute slice variable {} is not long enough", val.id);
|
||||
int j = 0;
|
||||
for (int i = nstart; i < nstop; i += nskip) {
|
||||
vec[j] = varvec[i - 1];
|
||||
j += stride;
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user