Commit 59768dbf authored by Gerhard Bräunlich's avatar Gerhard Bräunlich
Browse files

main: Avoid using namespace ...

parent f59e63f0

.clang-tidy

+1 −1
Original line number Diff line number Diff line
@@ -14,7 +14,7 @@ 
# You should have received a copy of the GNU General Public License along with

# aqcnes. If not, see <https://www.gnu.org/licenses/>.

---

Checks: '*,-abseil-*,-altera-*,-android-*,-darwin-*,-fuchsia-*,-llvmlibc-*,linuxkernel-*,-zirkon-*,-objc-*,-google-objc-*,-google-readability-*,-llvm-include-order,-llvm-prefer-register-over-unsigned,-llvm-twine-local,-llvm-header-guard,-cppcoreguidelines-pro-bounds-constant-array-index,-cppcoreguidelines-avoid-magic-numbers,-cppcoreguidelines-non-private-member-variables-in-classes,-readability-magic-numbers,-readability-identifier-length,-readability-braces-around-statements,-readability-use-anyofallof,-readability-named-parameter,-readability-avoid-const-params-in-decls,-hicpp-named-parameter,-hicpp-braces-around-statements,-modernize-use-trailing-return-type,-misc-non-private-member-variables-in-classes,-misc-no-recursion,-bugprone-easily-swappable-parameters,-cert-msc32-c,-cert-msc51-cpp,-clang-analyzer-optin.mpi.MPI-Checker,-todo,-readability-function-cognitive-complexity,-cert-err34-c,-cert-msc30-c,-cert-msc50-cpp,-bugprone-exception-escape,-concurrency-mt-unsafe,-google-build-using-namespace,-google-runtime-int'

Checks: '*,-abseil-*,-altera-*,-android-*,-darwin-*,-fuchsia-*,-llvmlibc-*,linuxkernel-*,-zirkon-*,-objc-*,-google-objc-*,-google-readability-*,-llvm-include-order,-llvm-prefer-register-over-unsigned,-llvm-twine-local,-llvm-header-guard,-cppcoreguidelines-pro-bounds-constant-array-index,-cppcoreguidelines-avoid-magic-numbers,-cppcoreguidelines-non-private-member-variables-in-classes,-readability-magic-numbers,-readability-identifier-length,-readability-braces-around-statements,-readability-use-anyofallof,-readability-named-parameter,-readability-avoid-const-params-in-decls,-hicpp-named-parameter,-hicpp-braces-around-statements,-modernize-use-trailing-return-type,-misc-non-private-member-variables-in-classes,-misc-no-recursion,-bugprone-easily-swappable-parameters,-cert-msc32-c,-cert-msc51-cpp,-clang-analyzer-optin.mpi.MPI-Checker,-todo,-readability-function-cognitive-complexity,-cert-err34-c,-cert-msc30-c,-cert-msc50-cpp,-bugprone-exception-escape,-concurrency-mt-unsafe,-google-runtime-int'

WarningsAsErrors: '*'

HeaderFilterRegex: 'src/.*\.(h|ipp)'

AnalyzeTemporaryDtors: false

src/main/elastic_constants.cpp

+35 −29
Original line number Diff line number Diff line
@@ -40,7 +40,6 @@ 
#include <boost/mpi.hpp>

#include <string_view>



using namespace std;

namespace array_ops = qcmesh::array_ops;



constexpr static std::string_view HELP = "using petsc.\n\n";
@@ -84,12 +83,14 @@ int main(int argc, char *argv[]) { 
      lattice::load_lattice_cache<DIM>(solver_variables.input.lattice_file)));



  if (mpi_rank == 0) {

    cout << "--------------------------------------------------------" << endl;

    cout << " WARNING! Please double-check the crystal lattice structure."

         << endl;

    cout << "	running :- "

         << "FCC" << endl;

    cout << "--------------------------------------------------------" << endl;

    std::cout << "--------------------------------------------------------"

              << std::endl;

    std::cout << " WARNING! Please double-check the crystal lattice structure."

              << std::endl;

    std::cout << "	running :- "

              << "FCC" << std::endl;

    std::cout << "--------------------------------------------------------"

              << std::endl;

  }



  const auto &restart_file_name = solver_variables.input.restart_file_name;
@@ -122,7 +123,7 @@ int main(int argc, char *argv[]) { 
                     solver_variables.local_mesh.periodic_lengths)

              << std::endl;



    cout << " periodic offsets : " << std::endl;

    std::cout << " periodic offsets : " << std::endl;

    for (const auto &offset : solver_variables.local_mesh.periodic_offsets)

      std::cout << array_ops::as_streamable(offset) << std::endl;

  }
@@ -133,20 +134,20 @@ int main(int argc, char *argv[]) { 


  if (!restart_file_name.has_value()) {

    if (mpi_rank == 0) {

      cout << "--------------------------------------------" << endl;

      cout << "domain is bound within " << endl;

      cout << "lower : "

      std::cout << "--------------------------------------------" << std::endl;

      std::cout << "domain is bound within " << std::endl;

      std::cout << "lower : "

                << array_ops::as_streamable(

                       solver_variables.local_mesh.domain_bound.lower)

           << endl;

      cout << "upper : "

                << std::endl;

      std::cout << "upper : "

                << array_ops::as_streamable(

                       solver_variables.local_mesh.domain_bound.upper)

           << endl;

      cout << "Verlet list buffer "

                << std::endl;

      std::cout << "Verlet list buffer "

                << solver_variables.input.verlet_buffer_factor *

                       solver_variables.input.neighbour_update_displacement

           << endl;

                << std::endl;

    }

  }
@@ -167,9 +168,12 @@ int main(int argc, char *argv[]) { 


  if (!restart_file_name.has_value()) {

    if (mpi_rank == 0) {

      cout << "-------------------------------------------------" << endl;

      cout << "--------------- Attempting initial repair--------" << endl;

      cout << "-------------------------------------------------" << endl;

      std::cout << "-------------------------------------------------"

                << std::endl;

      std::cout << "--------------- Attempting initial repair--------"

                << std::endl;

      std::cout << "-------------------------------------------------"

                << std::endl;

    }

    // initial repair after triangulation

    meshing::repair_mesh(solver_variables.local_mesh);
@@ -221,17 +225,18 @@ int main(int argc, char *argv[]) { 
    }



    if (min_distance < 1.0) {

      cout << mpi_rank << " , " << id << " , "

      std::cout << mpi_rank << " , " << id << " , "

                << array_ops::as_streamable(

                       solver_variables.local_mesh.nodes

                      .at(solver_variables.local_mesh.node_index_to_key.at(id))

                           .at(solver_variables.local_mesh.node_index_to_key.at(

                               id))

                           .position)

           << endl;

                << std::endl;

    }

  }



  if (mpi_rank == 0) {

    cout << "Neighbourhood udpdate styles, "

    std::cout << "Neighbourhood udpdate styles, "

              << "Verlet : "

              << (solver_variables.input.neighbour_update_style ==

                  input::NeighbourUpdateStyle::VERLET)
@@ -241,7 +246,7 @@ int main(int argc, char *argv[]) { 
              << " :: "

              << static_cast<std::size_t>(

                     solver_variables.input.neighbour_update_style)

         << endl;

              << std::endl;

  }



  solver_variables.relaxation_fire_parameters.time_step =
@@ -339,10 +344,10 @@ int main(int argc, char *argv[]) { 


  mesh_volume = solver_variables.local_mesh.volume();



  string filename =

  std::string filename =

      "energy_volume_" + solver_variables.materials[0].material_name;



  ofstream f_external;

  std::ofstream f_external;



#ifdef FINITE_TEMPERATURE

  const auto output_t = std::to_string(solver_variables.input.T_ref);
@@ -364,7 +369,7 @@ int main(int argc, char *argv[]) { 
    f_external.close();

  }



  vector<geometry::Point<DIM>> initial_locations;

  std::vector<geometry::Point<DIM>> initial_locations;

  initial_locations = solver_variables.local_mesh.repatoms.locations;



  for (auto &val : solver_variables.input.periodicity)
@@ -450,13 +455,14 @@ int main(int argc, char *argv[]) { 


  const auto elapsed_time = clock.toc();



  cout << "rank " << mpi_rank << " took " << elapsed_time << " with "

  std::cout

      << "rank " << mpi_rank << " took " << elapsed_time << " with "

      << solver_variables.local_mesh.sampling_atoms.nodal_locations.size()

      << " nodal sampling atoms "

      << solver_variables.local_mesh.sampling_atoms.central_locations.size()

      << " central sampling atoms " << solver_variables.local_mesh.nodes.size()

      << " nodes and " << solver_variables.local_mesh.cells.size()

       << " elements" << endl;

      << " elements" << std::endl;



  PetscFinalize();

  // MPI_Finalize();

src/main/energy_minima.cpp

+18 −24
Original line number Diff line number Diff line
@@ -30,8 +30,6 @@ 
#include <chrono>

#include <string_view>



using namespace std;

using namespace geometry;

namespace array_ops = qcmesh::array_ops;



constexpr static std::string_view HELP = "using petsc.\n\n";
@@ -47,8 +45,7 @@ using Matrix = Eigen::Matrix<double, DIM, DIM>; 
using SolverKernel = solver::Solver;



int main(int argc, char *argv[]) {

  using namespace std::chrono;

  high_resolution_clock::time_point t1 = high_resolution_clock::now();

  const auto t1 = std::chrono::high_resolution_clock::now();



  solver::SolverVariables<DIM> solver_variables;
@@ -70,28 +67,28 @@ int main(int argc, char *argv[]) { 


  geometry::Point<DIM> center = {{0.0, 0.0, 0.0}};



  array<array<double, DIM>, DIM> basis =

  std::array<std::array<double, DIM>, DIM> basis =

      solver_variables.materials[0].basis_vectors;



  geometry::Point<DIM> px = {{basis[0][0], basis[1][0], basis[2][0]}};

  geometry::Point<DIM> py = {{basis[0][1], basis[1][1], basis[2][1]}};

  geometry::Point<DIM> pz = {{basis[0][2], basis[1][2], basis[2][2]}};



  vector<geometry::Point<DIM>> lattice;

  std::vector<geometry::Point<DIM>> lattice;

  geometry::Point<DIM> lattice_point;

  vector<geometry::Point<DIM>> neighbours;

  std::vector<geometry::Point<DIM>> neighbours;



  const auto args = utils::DynamicSpan(argv, argc);



  const auto r_r0 = stod(args[1]);

  const auto dr = stod(args[2]);

  const std::size_t nr = static_cast<std::size_t>(stoi(args[3]));

  const auto r_r0 = std::stod(args[1]);

  const auto dr = std::stod(args[2]);

  const std::size_t nr = static_cast<std::size_t>(std::stoi(args[3]));

  double min_energy = 0.0;

  double r_min{};



  string file_name;

  string thermal_expansion_file_name;

  string force_file_name;

  std::string file_name;

  std::string thermal_expansion_file_name;

  std::string force_file_name;

  std::ofstream f_energies;

  std::ofstream f_forces;

  std::ofstream f_thermal_expansion;
@@ -105,12 +102,12 @@ int main(int argc, char *argv[]) { 
  std::vector<double> thermal_forces_atom;

  std::vector<double> thermal_forces_neigh;

  ThermalPoint atom_thermal_coordinates;

  vector<ThermalPoint> neighbours_thermal_coordinates;

  std::vector<ThermalPoint> neighbours_thermal_coordinates;

  double temp = solver_variables.input.T_ref;



  const auto sigma_start = stod(args[4]);

  const auto dsigma = stod(args[5]);

  const std::size_t nsigma = static_cast<std::size_t>(stoi(args[6]));

  const auto sigma_start = std::stod(args[4]);

  const auto dsigma = std::stod(args[5]);

  const std::size_t nsigma = static_cast<std::size_t>(std::stoi(args[6]));

  double sigma_min{};

  double entropy = 0.0;
@@ -175,8 +172,6 @@ int main(int argc, char *argv[]) { 
        // Compute forces and energy

        double energy{};

        double kenergy{};

        // std::vector<point<DIM>> forces;

        // std::vector<double> thermal_forces_atom, thermal_forces_neigh;



        kenergy = 3.0 * exp(-atom_thermal_coordinates[0]) / 2;

        energy = 0.0;
@@ -210,12 +205,10 @@ int main(int argc, char *argv[]) { 
    std::cout << " Minimising parameters: Spacing coefficient " << r_min

              << " and Sigma " << sigma_min << std::endl;



    // f_energies.close();

    f_thermal_expansion << temp << " " << r_min << " " << sigma_min << " "

                        << min_energy << '\n';

  }

  f_thermal_expansion.close();

  // f_forces.close();



#else
@@ -293,9 +286,10 @@ int main(int argc, char *argv[]) { 


  PetscFinalize();



  high_resolution_clock::time_point t2 = high_resolution_clock::now();

  duration<double> time_span = duration_cast<duration<double>>(t2 - t1);

  std::cout << "duration: " << time_span.count() << endl;

  const auto t2 = std::chrono::high_resolution_clock::now();

  const auto time_span =

      std::chrono::duration_cast<std::chrono::duration<double>>(t2 - t1);

  std::cout << "duration: " << time_span.count() << std::endl;



  return 0;

}

src/main/external_shear.cpp

+37 −31
Original line number Diff line number Diff line
@@ -13,6 +13,7 @@ 
//

// You should have received a copy of the GNU General Public License along with

// aqcnes. If not, see <https://www.gnu.org/licenses/>.



/** @file

 * @brief Example to perform a quasistatic displacement driven shear of a mesh with staggered relaxation steps

 * @author P. Gupta
@@ -39,7 +40,6 @@ 
#include <boost/mpi.hpp>

#include <string_view>



using namespace std;

namespace array_ops = qcmesh::array_ops;



constexpr static std::string_view HELP = "using petsc.\n\n";
@@ -88,12 +88,14 @@ int main(int argc, char *argv[]) { 
      lattice::load_lattice_cache<DIM>(solver_variables.input.lattice_file)));



  if (mpi_rank == 0) {

    cout << "--------------------------------------------------------" << endl;

    cout << " WARNING! Please double-check the crystal lattice structure."

         << endl;

    cout << "	running :- "

         << "FCC" << endl;

    cout << "--------------------------------------------------------" << endl;

    std::cout << "--------------------------------------------------------"

              << std::endl;

    std::cout << " WARNING! Please double-check the crystal lattice structure."

              << std::endl;

    std::cout << "	running :- "

              << "FCC" << std::endl;

    std::cout << "--------------------------------------------------------"

              << std::endl;

  }



  const auto &restart_file_name = solver_variables.input.restart_file_name;
@@ -114,13 +116,13 @@ int main(int argc, char *argv[]) { 
  //=-=-=-=-=-=-=-=-=<Initialize periodic lengths and flags>-=-=-=-=-=-//



  if (mpi_rank == 0) {

    cout << "periodic lengths : "

    std::cout << "periodic lengths : "

              << array_ops::as_streamable(

                     solver_variables.local_mesh.domain_bound.lower)

              << " , "

              << array_ops::as_streamable(

                     solver_variables.local_mesh.domain_bound.upper)

         << endl;

              << std::endl;

  }



  // redistribute the mesh again after this so periodic connectivities are
@@ -131,20 +133,20 @@ int main(int argc, char *argv[]) { 


  if (!restart_file_name.has_value()) {

    if (mpi_rank == 0) {

      cout << "--------------------------------------------" << endl;

      cout << "domain is bound within " << endl;

      cout << "lower : "

      std::cout << "--------------------------------------------" << std::endl;

      std::cout << "domain is bound within " << std::endl;

      std::cout << "lower : "

                << array_ops::as_streamable(

                       solver_variables.local_mesh.domain_bound.lower)

           << endl;

      cout << "upper : "

                << std::endl;

      std::cout << "upper : "

                << array_ops::as_streamable(

                       solver_variables.local_mesh.domain_bound.upper)

           << endl;

      cout << "Verlet list buffer "

                << std::endl;

      std::cout << "Verlet list buffer "

                << solver_variables.input.verlet_buffer_factor *

                       solver_variables.input.neighbour_update_displacement

           << endl;

                << std::endl;

    }

  }
@@ -165,9 +167,12 @@ int main(int argc, char *argv[]) { 


  if (!restart_file_name.has_value()) {

    if (mpi_rank == 0) {

      cout << "-------------------------------------------------" << endl;

      cout << "--------------- Attempting initial repair--------" << endl;

      cout << "-------------------------------------------------" << endl;

      std::cout << "-------------------------------------------------"

                << std::endl;

      std::cout << "--------------- Attempting initial repair--------"

                << std::endl;

      std::cout << "-------------------------------------------------"

                << std::endl;

    }

    // initial repair after triangulation

    meshing::repair_mesh(solver_variables.local_mesh);
@@ -235,7 +240,7 @@ int main(int argc, char *argv[]) { 
  }



  if (mpi_rank == 0) {

    cout << "Neighbourhood udpdate styles, "

    std::cout << "Neighbourhood udpdate styles, "

              << "Verlet : "

              << (solver_variables.input.neighbour_update_style ==

                  input::NeighbourUpdateStyle::VERLET)
@@ -245,7 +250,7 @@ int main(int argc, char *argv[]) { 
              << " :: "

              << static_cast<std::size_t>(

                     solver_variables.input.neighbour_update_style)

         << endl;

              << std::endl;

  }



  solver_variables.relaxation_fire_parameters.time_step =
@@ -291,7 +296,7 @@ int main(int argc, char *argv[]) { 
  SolverKernel::allocate_initial_neighbourhoods<

      meshing::NodalDataMultispecies<NOI>, DIM, NIDOF>(solver_variables);



  ofstream f_external;

  std::ofstream f_external;



  solver_variables.local_mesh.compute_nodal_centro_symmetry();
@@ -398,9 +403,9 @@ int main(int argc, char *argv[]) { 
  w_all_global = qcmesh::mpi::all_reduce_sum(w_all_local);



  if (mpi_rank == 0) {

    cout << "beginning with external shear " << restart_data.external_strain

         << " and shear increment " << restart_data.external_strain_increment

         << endl;

    std::cout << "beginning with external shear "

              << restart_data.external_strain << " and shear increment "

              << restart_data.external_strain_increment << std::endl;

  }



  // get the left and right dislocations
@@ -467,7 +472,7 @@ int main(int argc, char *argv[]) { 
  array_ops::as_eigen(dislocation_r) /= mass_r;



  solver_variables.local_mesh.repatoms.get_fixed_region_force(external_force);

  string filename = "ExternalStrainForce";

  std::string filename = "ExternalStrainForce";



#ifdef FINITE_TEMPERATURE

  filename += "_" +
@@ -484,7 +489,7 @@ int main(int argc, char *argv[]) { 
               << array_ops::as_streamable(external_force) << " "

               << array_ops::distance(dislocation_l, dislocation_r) << " "

               << v_all_global << " " << k_all_global << " " << w_all_global

               << endl;

               << std::endl;

    f_external.close();

  }
@@ -646,7 +651,7 @@ int main(int argc, char *argv[]) { 
                 << array_ops::as_streamable(external_force) << " "

                 << array_ops::distance(dislocation_l, dislocation_r) << " "

                 << v_all_global << " " << k_all_global << " " << w_all_global

                 << endl;

                 << std::endl;

      f_external.close();

    }
@@ -659,13 +664,14 @@ int main(int argc, char *argv[]) { 


  const auto elapsed_time = clock.toc();



  cout << "rank " << mpi_rank << " took " << elapsed_time << " with "

  std::cout

      << "rank " << mpi_rank << " took " << elapsed_time << " with "

      << solver_variables.local_mesh.sampling_atoms.nodal_locations.size()

      << " nodal sampling atoms "

      << solver_variables.local_mesh.sampling_atoms.central_locations.size()

      << " central sampling atoms " << solver_variables.local_mesh.nodes.size()

      << " nodes and " << solver_variables.local_mesh.cells.size()

       << " elements" << endl;

      << " elements" << std::endl;



  PetscFinalize();

  // MPI_Finalize();

src/main/infinite_model_deformation.cpp

+4 −6
Original line number Diff line number Diff line
@@ -23,16 +23,13 @@ 
#include "solver/infinite_model_relaxation.hpp"

#include <string_view>



using namespace geometry;



static constexpr std::size_t DIM = 3;

static constexpr std::size_t NIDOF = 2;

static constexpr std::size_t NOI = 1;

constexpr static std::string_view HELP = "using petsc.\n\n";



int main(int argc, char *argv[]) {

  using namespace std::chrono;

  high_resolution_clock::time_point t1 = high_resolution_clock::now();

  const auto t1 = std::chrono::high_resolution_clock::now();



  solver::SolverVariables<DIM> solver_variables;
@@ -92,8 +89,9 @@ int main(int argc, char *argv[]) { 


  PetscFinalize();



  high_resolution_clock::time_point t2 = high_resolution_clock::now();

  duration<double> time_span = duration_cast<duration<double>>(t2 - t1);

  const auto t2 = std::chrono::high_resolution_clock::now();

  const auto time_span =

      std::chrono::duration_cast<std::chrono::duration<double>>(t2 - t1);

  std::cout << "duration: " << time_span.count() << std::endl;



  return 0;