enable and apply clang-format
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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@ -33,8 +32,7 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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MLIAPModelNN::MLIAPModelNN(LAMMPS* _lmp, char* coefffilename) :
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MLIAPModel(_lmp, coefffilename)
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MLIAPModelNN::MLIAPModelNN(LAMMPS *_lmp, char *coefffilename) : MLIAPModel(_lmp, coefffilename)
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{
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nnodes = nullptr;
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activation = nullptr;
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@ -47,9 +45,9 @@ MLIAPModelNN::MLIAPModelNN(LAMMPS* _lmp, char* coefffilename) :
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MLIAPModelNN::~MLIAPModelNN()
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{
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memory->destroy(nnodes);
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memory->destroy(activation);
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memory->destroy(scale);
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memory->destroy(nnodes);
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memory->destroy(activation);
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memory->destroy(scale);
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}
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/* ----------------------------------------------------------------------
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@ -59,7 +57,7 @@ MLIAPModelNN::~MLIAPModelNN()
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int MLIAPModelNN::get_nparams()
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{
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if (nparams == 0)
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if (ndescriptors == 0) error->all(FLERR,"ndescriptors not defined");
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if (ndescriptors == 0) error->all(FLERR, "ndescriptors not defined");
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return nparams;
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}
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@ -71,9 +69,9 @@ void MLIAPModelNN::read_coeffs(char *coefffilename)
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FILE *fpcoeff;
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if (comm->me == 0) {
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fpcoeff = utils::open_potential(coefffilename,lmp,nullptr);
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fpcoeff = utils::open_potential(coefffilename, lmp, nullptr);
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if (fpcoeff == nullptr)
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error->one(FLERR,"Cannot open MLIAPModel coeff file {}: {}", coefffilename,
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error->one(FLERR, "Cannot open MLIAPModel coeff file {}: {}", coefffilename,
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utils::getsyserror());
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}
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@ -84,24 +82,24 @@ void MLIAPModelNN::read_coeffs(char *coefffilename)
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int nwords = 0;
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while (nwords == 0) {
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if (comm->me == 0) {
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ptr = fgets(line,MAXLINE,fpcoeff);
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ptr = fgets(line, MAXLINE, fpcoeff);
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if (ptr == nullptr) {
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eof = 1;
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fclose(fpcoeff);
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} else n = strlen(line) + 1;
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} else
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n = strlen(line) + 1;
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}
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MPI_Bcast(&eof,1,MPI_INT,0,world);
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MPI_Bcast(&eof, 1, MPI_INT, 0, world);
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if (eof) break;
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MPI_Bcast(&n,1,MPI_INT,0,world);
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MPI_Bcast(line,n,MPI_CHAR,0,world);
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MPI_Bcast(&n, 1, MPI_INT, 0, world);
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MPI_Bcast(line, n, MPI_CHAR, 0, world);
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// strip comment, skip line if blank
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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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if ((ptr = strchr(line, '#'))) *ptr = '\0';
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nwords = utils::count_words(line);
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}
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if (nwords != 2)
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error->all(FLERR,"Incorrect format in MLIAPModel coefficient file");
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if (nwords != 2) error->all(FLERR, "Incorrect format in MLIAPModel coefficient file");
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// words = ptrs to all words in line
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// strip single and double quotes from words
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@ -111,13 +109,13 @@ void MLIAPModelNN::read_coeffs(char *coefffilename)
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nelements = coeffs.next_int();
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nparams = coeffs.next_int();
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} catch (TokenizerException &e) {
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error->all(FLERR,"Incorrect format in MLIAPModel coefficient file: {}",e.what());
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error->all(FLERR, "Incorrect format in MLIAPModel coefficient file: {}", e.what());
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}
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// set up coeff lists
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memory->destroy(coeffelem);
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memory->create(coeffelem,nelements,nparams,"mliap_snap_model:coeffelem");
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memory->create(coeffelem, nelements, nparams, "mliap_snap_model:coeffelem");
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int stats = 0;
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int ielem = 0;
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@ -125,47 +123,53 @@ void MLIAPModelNN::read_coeffs(char *coefffilename)
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while (true) {
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if (comm->me == 0) {
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ptr = fgets(line,MAXLINE,fpcoeff);
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ptr = fgets(line, MAXLINE, fpcoeff);
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if (ptr == nullptr) {
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eof = 1;
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fclose(fpcoeff);
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} else n = strlen(line) + 1;
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} else
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n = strlen(line) + 1;
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}
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MPI_Bcast(&eof,1,MPI_INT,0,world);
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MPI_Bcast(&eof, 1, MPI_INT, 0, world);
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if (eof) break;
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MPI_Bcast(&n,1,MPI_INT,0,world);
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MPI_Bcast(line,n,MPI_CHAR,0,world);
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MPI_Bcast(&n, 1, MPI_INT, 0, world);
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MPI_Bcast(line, n, MPI_CHAR, 0, world);
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// strip comment, skip line if blank
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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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if ((ptr = strchr(line, '#'))) *ptr = '\0';
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nwords = utils::trim_and_count_words(line);
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if (nwords == 0) continue;
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ValueTokenizer values(line, "\"' \t\n\t\f");
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if (stats == 0) { // Header NET
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if (stats == 0) { // Header NET
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auto tstr = values.next_string();
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if (tstr.substr(0,3) != "NET")
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error->all(FLERR,"Incorrect format in MLIAPModel coefficient file");
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if (tstr.substr(0, 3) != "NET")
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error->all(FLERR, "Incorrect format in MLIAPModel coefficient file");
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ndescriptors = values.next_int();
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nlayers = values.next_int();
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memory->create(activation,nlayers,"mliap_model:activation");
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memory->create(nnodes,nlayers,"mliap_model:nnodes");
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memory->create(scale,nelements,2,ndescriptors,"mliap_model:scale");
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memory->create(activation, nlayers, "mliap_model:activation");
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memory->create(nnodes, nlayers, "mliap_model:nnodes");
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memory->create(scale, nelements, 2, ndescriptors, "mliap_model:scale");
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for (int ilayer = 0; ilayer < nlayers; ilayer++) {
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tstr = values.next_string();
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nnodes[ilayer] = values.next_int();
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if (tstr == "linear") activation[ilayer] = 0;
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else if (tstr == "sigmoid") activation[ilayer] = 1;
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else if (tstr == "tanh") activation[ilayer] = 2;
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else if (tstr == "relu") activation[ilayer] = 3;
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else activation[ilayer] = 4;
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if (tstr == "linear")
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activation[ilayer] = 0;
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else if (tstr == "sigmoid")
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activation[ilayer] = 1;
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else if (tstr == "tanh")
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activation[ilayer] = 2;
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else if (tstr == "relu")
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activation[ilayer] = 3;
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else
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activation[ilayer] = 4;
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}
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stats = 1;
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@ -173,7 +177,7 @@ void MLIAPModelNN::read_coeffs(char *coefffilename)
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} else if (stats == 1) {
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scale[ielem][0][l] = values.next_double();
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for (int icoeff = 1; icoeff < nwords; icoeff++) {
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scale[ielem][0][l+icoeff] = values.next_double();
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scale[ielem][0][l + icoeff] = values.next_double();
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}
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l += nwords;
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if (l == ndescriptors) {
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@ -184,7 +188,7 @@ void MLIAPModelNN::read_coeffs(char *coefffilename)
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} else if (stats == 2) {
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scale[ielem][1][l] = values.next_double();
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for (int icoeff = 1; icoeff < nwords; icoeff++) {
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scale[ielem][1][l+icoeff] = values.next_double();
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scale[ielem][1][l + icoeff] = values.next_double();
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}
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l += nwords;
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if (l == ndescriptors) {
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@ -195,11 +199,11 @@ void MLIAPModelNN::read_coeffs(char *coefffilename)
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// set up coeff lists
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} else if (stats == 3) {
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if (nwords > 30) error->all(FLERR,"Incorrect format in MLIAPModel coefficient file");
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if (nwords > 30) error->all(FLERR, "Incorrect format in MLIAPModel coefficient file");
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coeffelem[ielem][l] = values.next_double();
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for (int icoeff = 1; icoeff < nwords; icoeff++) {
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coeffelem[ielem][l+icoeff] = values.next_double();
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coeffelem[ielem][l + icoeff] = values.next_double();
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}
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l += nwords;
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if (l == nparams) {
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@ -216,153 +220,127 @@ void MLIAPModelNN::read_coeffs(char *coefffilename)
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for each atom beta_i = dE(B_i)/dB_i
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---------------------------------------------------------------------- */
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void MLIAPModelNN::compute_gradients(MLIAPData* data)
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void MLIAPModelNN::compute_gradients(MLIAPData *data)
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{
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data->energy = 0.0;
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for (int ii = 0; ii < data->nlistatoms; ii++) {
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const int ielem = data->ielems[ii];
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const int nl = nlayers;
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const int ielem = data->ielems[ii];
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const int nl = nlayers;
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double* coeffi = coeffelem[ielem];
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double** scalei = scale[ielem];
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double **nodes, **dnodes, **bnodes;
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double *coeffi = coeffelem[ielem];
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double **scalei = scale[ielem];
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double **nodes, **dnodes, **bnodes;
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nodes = new double*[nl];
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dnodes = new double*[nl];
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bnodes = new double*[nl];
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for (int l=0; l<nl; ++l) {
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nodes[l] = new double[nnodes[l]];
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dnodes[l] = new double[nnodes[l]];
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bnodes[l] = new double[nnodes[l]];
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}
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nodes = new double *[nl];
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dnodes = new double *[nl];
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bnodes = new double *[nl];
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for (int l = 0; l < nl; ++l) {
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nodes[l] = new double[nnodes[l]];
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dnodes[l] = new double[nnodes[l]];
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bnodes[l] = new double[nnodes[l]];
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}
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// forwardprop
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// input - hidden1
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for (int n=0; n < nnodes[0]; n++) {
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nodes[0][n] = 0;
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for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++) {
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nodes[0][n] += coeffi[n*((data->ndescriptors)+1)+icoeff+1] *
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(data->descriptors[ii][icoeff] - scalei[0][icoeff]) /
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scalei[1][icoeff];
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}
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if (activation[0] == 1) {
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nodes[0][n] = sigm(nodes[0][n] +
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coeffi[n*((data->ndescriptors)+1)],
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dnodes[0][n]);
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}
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else if (activation[0] == 2) {
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nodes[0][n] = tanh(nodes[0][n] +
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coeffi[n*((data->ndescriptors)+1)],
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dnodes[0][n]);
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}
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else if (activation[0] == 3) {
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nodes[0][n] = relu(nodes[0][n] +
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coeffi[n*((data->ndescriptors)+1)],
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dnodes[0][n]);
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}
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else {
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nodes[0][n] += coeffi[n*((data->ndescriptors)+1)];
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dnodes[0][n] = 1;
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}
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}
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// hidden~output
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int k = 0;
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if (nl > 1) {
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k += ((data->ndescriptors)+1)*nnodes[0];
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for (int l=1; l < nl; l++) {
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for (int n=0; n < nnodes[l]; n++) {
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nodes[l][n] = 0;
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for (int j=0; j < nnodes[l-1]; j++) {
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nodes[l][n] += coeffi[k+n*(nnodes[l-1]+1)+j+1] *
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nodes[l-1][j];
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}
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if (activation[l] == 1) {
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nodes[l][n] = sigm(nodes[l][n] +
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coeffi[k+n*(nnodes[l-1]+1)],
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dnodes[l][n]);
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}
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else if (activation[l] == 2) {
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nodes[l][n] = tanh(nodes[l][n] +
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coeffi[k+n*(nnodes[l-1]+1)],
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dnodes[l][n]);
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}
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else if (activation[l] == 3) {
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nodes[l][n] = relu(nodes[l][n] +
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coeffi[k+n*(nnodes[l-1]+1)],
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dnodes[l][n]);
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}
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else {
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nodes[l][n] += coeffi[k+n*(nnodes[l-1]+1)];
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dnodes[l][n] = 1;
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}
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}
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k += (nnodes[l-1]+1)*nnodes[l];
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}
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}
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// backwardprop
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// output layer dnode initialized to 1.
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for (int n=0; n<nnodes[nl-1]; n++) {
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if (activation[nl-1] == 0) {
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bnodes[nl-1][n] = 1;
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}
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else {
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bnodes[nl-1][n] = dnodes[nl-1][n];
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}
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}
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if (nl > 1) {
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for (int l=nl-1; l>0; l--) {
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k -= (nnodes[l-1]+1)*nnodes[l];
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for (int n=0; n<nnodes[l-1]; n++) {
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bnodes[l-1][n] = 0;
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for (int j=0; j<nnodes[l]; j++) {
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bnodes[l-1][n] += coeffi[k+j*(nnodes[l-1]+1)+n+1] *
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bnodes[l][j];
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}
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if (activation[l-1] >= 1) {
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bnodes[l-1][n] *= dnodes[l-1][n];
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}
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}
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}
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}
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// forwardprop
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// input - hidden1
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for (int n = 0; n < nnodes[0]; n++) {
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nodes[0][n] = 0;
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for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++) {
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data->betas[ii][icoeff] = 0;
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for (int j=0; j<nnodes[0]; j++) {
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data->betas[ii][icoeff] +=
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coeffi[j*((data->ndescriptors)+1)+icoeff+1] *
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bnodes[0][j];
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}
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data->betas[ii][icoeff] = data->betas[ii][icoeff]/scalei[1][icoeff];
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nodes[0][n] += coeffi[n * ((data->ndescriptors) + 1) + icoeff + 1] *
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(data->descriptors[ii][icoeff] - scalei[0][icoeff]) / scalei[1][icoeff];
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}
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if (activation[0] == 1) {
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nodes[0][n] = sigm(nodes[0][n] + coeffi[n * ((data->ndescriptors) + 1)], dnodes[0][n]);
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} else if (activation[0] == 2) {
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nodes[0][n] = tanh(nodes[0][n] + coeffi[n * ((data->ndescriptors) + 1)], dnodes[0][n]);
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} else if (activation[0] == 3) {
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nodes[0][n] = relu(nodes[0][n] + coeffi[n * ((data->ndescriptors) + 1)], dnodes[0][n]);
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} else {
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nodes[0][n] += coeffi[n * ((data->ndescriptors) + 1)];
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dnodes[0][n] = 1;
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}
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}
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if (data->eflag) {
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// hidden~output
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int k = 0;
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if (nl > 1) {
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k += ((data->ndescriptors) + 1) * nnodes[0];
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for (int l = 1; l < nl; l++) {
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for (int n = 0; n < nnodes[l]; n++) {
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nodes[l][n] = 0;
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for (int j = 0; j < nnodes[l - 1]; j++) {
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nodes[l][n] += coeffi[k + n * (nnodes[l - 1] + 1) + j + 1] * nodes[l - 1][j];
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}
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if (activation[l] == 1) {
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nodes[l][n] = sigm(nodes[l][n] + coeffi[k + n * (nnodes[l - 1] + 1)], dnodes[l][n]);
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} else if (activation[l] == 2) {
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nodes[l][n] = tanh(nodes[l][n] + coeffi[k + n * (nnodes[l - 1] + 1)], dnodes[l][n]);
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} else if (activation[l] == 3) {
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nodes[l][n] = relu(nodes[l][n] + coeffi[k + n * (nnodes[l - 1] + 1)], dnodes[l][n]);
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} else {
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nodes[l][n] += coeffi[k + n * (nnodes[l - 1] + 1)];
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dnodes[l][n] = 1;
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}
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}
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k += (nnodes[l - 1] + 1) * nnodes[l];
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}
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}
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// backwardprop
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// output layer dnode initialized to 1.
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for (int n = 0; n < nnodes[nl - 1]; n++) {
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if (activation[nl - 1] == 0) {
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bnodes[nl - 1][n] = 1;
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} else {
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bnodes[nl - 1][n] = dnodes[nl - 1][n];
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}
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}
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if (nl > 1) {
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for (int l = nl - 1; l > 0; l--) {
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k -= (nnodes[l - 1] + 1) * nnodes[l];
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for (int n = 0; n < nnodes[l - 1]; n++) {
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bnodes[l - 1][n] = 0;
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for (int j = 0; j < nnodes[l]; j++) {
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bnodes[l - 1][n] += coeffi[k + j * (nnodes[l - 1] + 1) + n + 1] * bnodes[l][j];
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}
|
||||
if (activation[l - 1] >= 1) { bnodes[l - 1][n] *= dnodes[l - 1][n]; }
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++) {
|
||||
data->betas[ii][icoeff] = 0;
|
||||
for (int j = 0; j < nnodes[0]; j++) {
|
||||
data->betas[ii][icoeff] +=
|
||||
coeffi[j * ((data->ndescriptors) + 1) + icoeff + 1] * bnodes[0][j];
|
||||
}
|
||||
data->betas[ii][icoeff] = data->betas[ii][icoeff] / scalei[1][icoeff];
|
||||
}
|
||||
|
||||
if (data->eflag) {
|
||||
|
||||
// energy of atom I (E_i)
|
||||
|
||||
double etmp = nodes[nl-1][0];
|
||||
double etmp = nodes[nl - 1][0];
|
||||
|
||||
data->energy += etmp;
|
||||
data->eatoms[ii] = etmp;
|
||||
}
|
||||
// Deleting the variables
|
||||
data->energy += etmp;
|
||||
data->eatoms[ii] = etmp;
|
||||
}
|
||||
// Deleting the variables
|
||||
|
||||
for (int n=0; n<nl; n++) {
|
||||
delete[] nodes[n];
|
||||
delete[] dnodes[n];
|
||||
delete[] bnodes[n];
|
||||
}
|
||||
|
||||
delete[] nodes;
|
||||
delete[] dnodes;
|
||||
delete[] bnodes;
|
||||
for (int n = 0; n < nl; n++) {
|
||||
delete[] nodes[n];
|
||||
delete[] dnodes[n];
|
||||
delete[] bnodes[n];
|
||||
}
|
||||
|
||||
delete[] nodes;
|
||||
delete[] dnodes;
|
||||
delete[] bnodes;
|
||||
}
|
||||
}
|
||||
|
||||
@ -383,7 +361,7 @@ void MLIAPModelNN::compute_gradients(MLIAPData* data)
|
||||
|
||||
void MLIAPModelNN::compute_gradgrads(class MLIAPData * /*data*/)
|
||||
{
|
||||
error->all(FLERR,"compute_gradgrads not implemented");
|
||||
error->all(FLERR, "compute_gradgrads not implemented");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -393,7 +371,7 @@ void MLIAPModelNN::compute_gradgrads(class MLIAPData * /*data*/)
|
||||
|
||||
void MLIAPModelNN::compute_force_gradients(class MLIAPData * /*data*/)
|
||||
{
|
||||
error->all(FLERR,"compute_force_gradients not implemented");
|
||||
error->all(FLERR, "compute_force_gradients not implemented");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -410,9 +388,9 @@ double MLIAPModelNN::memory_usage()
|
||||
{
|
||||
double bytes = 0;
|
||||
|
||||
bytes += (double)nelements*nparams*sizeof(double); // coeffelem
|
||||
bytes += (double)nelements*2*ndescriptors*sizeof(double); // scale
|
||||
bytes += (int)nlayers*sizeof(int); // nnodes
|
||||
bytes += (int)nlayers*sizeof(int); // activation
|
||||
bytes += (double) nelements * nparams * sizeof(double); // coeffelem
|
||||
bytes += (double) nelements * 2 * ndescriptors * sizeof(double); // scale
|
||||
bytes += (int) nlayers * sizeof(int); // nnodes
|
||||
bytes += (int) nlayers * sizeof(int); // activation
|
||||
return bytes;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user