From 970aa6ea9a63d264596463645c17566cc5d26047 Mon Sep 17 00:00:00 2001
From: jingang <liangjg2008@gmail.com>
Date: Wed, 5 Jun 2019 11:26:39 -0400
Subject: [PATCH 01/10] fixed compiling errors with visual studio, mostly VLAs

---
 include/openmc/error.h               |  2 +-
 include/openmc/hdf5_interface.h      | 23 ++++++++++++---
 src/cell.cpp                         |  2 +-
 src/finalize.cpp                     |  4 +--
 src/hdf5_interface.cpp               |  9 ++++--
 src/initialize.cpp                   |  2 +-
 src/lattice.cpp                      | 12 ++++----
 src/math_functions.cpp               | 13 +++++----
 src/mesh.cpp                         | 43 ++++++++++++++--------------
 src/mgxs.cpp                         |  3 +-
 src/surface.cpp                      |  1 +
 src/tallies/filter_legendre.cpp      |  4 +--
 src/tallies/filter_mesh.cpp          |  4 +--
 src/tallies/filter_sph_harm.cpp      |  8 +++---
 src/tallies/filter_sptl_legendre.cpp |  4 +--
 src/tallies/filter_zernike.cpp       |  8 +++---
 16 files changed, 81 insertions(+), 61 deletions(-)

diff --git a/include/openmc/error.h b/include/openmc/error.h
index 5f30f0252d..32ed36c8b8 100644
--- a/include/openmc/error.h
+++ b/include/openmc/error.h
@@ -44,7 +44,7 @@ void fatal_error(const std::stringstream& message)
 [[noreturn]] inline
 void fatal_error(const char* message)
 {
-  fatal_error({message, std::strlen(message)});
+  fatal_error(std::string{message, std::strlen(message)});
 }
 
 void warning(const std::string& message);
diff --git a/include/openmc/hdf5_interface.h b/include/openmc/hdf5_interface.h
index 0be98718ce..e52d6c8054 100644
--- a/include/openmc/hdf5_interface.h
+++ b/include/openmc/hdf5_interface.h
@@ -187,11 +187,12 @@ read_attribute(hid_t obj_id, const char* name, std::string& str)
 {
   // Create buffer to read data into
   auto n = attribute_typesize(obj_id, name);
-  char buffer[n];
+  char* buffer = new char[n];
 
   // Read attribute and set string
   read_attr_string(obj_id, name, n, buffer);
   str = std::string{buffer, n};
+  delete[] buffer;
 }
 
 // overload for std::vector<std::string>
@@ -203,7 +204,10 @@ read_attribute(hid_t obj_id, const char* name, std::vector<std::string>& vec)
 
   // Allocate a C char array to get strings
   auto n = attribute_typesize(obj_id, name);
-  char buffer[m][n];
+  char** buffer = new char*[m];
+  for (int i = 0; i < m; i++) {
+    buffer[i] = new char[n];
+  }
 
   // Read char data in attribute
   read_attr_string(obj_id, name, n, buffer[0]);
@@ -216,7 +220,9 @@ read_attribute(hid_t obj_id, const char* name, std::vector<std::string>& vec)
 
     // Create string based on (char*, size_t) constructor
     vec.emplace_back(&buffer[i][0], k);
+    delete[] buffer[i];
   }
+  delete[] buffer;
 }
 
 //==============================================================================
@@ -240,7 +246,7 @@ read_dataset(hid_t obj_id, const char* name, std::string& str, bool indep=false)
 {
   // Create buffer to read data into
   auto n = dataset_typesize(obj_id, name);
-  char buffer[n];
+  char* buffer = new char[n];
 
   // Read attribute and set string
   read_string(obj_id, name, n, buffer, indep);
@@ -458,7 +464,10 @@ write_dataset(hid_t obj_id, const char* name, const std::vector<std::string>& bu
   }
 
   // Copy data into contiguous buffer
-  char temp[n][m];
+  char** temp = new char*[n];
+  for (int i = 0; i < n; i++) {
+    temp[i] = new char[m];
+  }
   std::fill(temp[0], temp[0] + n*m, '\0');
   for (int i = 0; i < n; ++i) {
     std::copy(buffer[i].begin(), buffer[i].end(), temp[i]);
@@ -466,6 +475,12 @@ write_dataset(hid_t obj_id, const char* name, const std::vector<std::string>& bu
 
   // Write 2D data
   write_string(obj_id, 1, dims, m, name, temp[0], false);
+
+  // Free temp array
+  for (int i = 0; i < n; i++) {
+    delete[] temp[i];
+  }
+  delete[] temp;
 }
 
 template<typename T> inline void
diff --git a/src/cell.cpp b/src/cell.cpp
index 650a18a8a0..157d0d1a2c 100644
--- a/src/cell.cpp
+++ b/src/cell.cpp
@@ -560,7 +560,7 @@ CSGCell::contains_complex(Position r, Direction u, int32_t on_surface) const
 {
   // Make a stack of booleans.  We don't know how big it needs to be, but we do
   // know that rpn.size() is an upper-bound.
-  bool stack[rpn_.size()];
+  std::vector<bool> stack(rpn_.size());
   int i_stack = -1;
 
   for (int32_t token : rpn_) {
diff --git a/src/finalize.cpp b/src/finalize.cpp
index 34c4b9781b..81d7559b8e 100644
--- a/src/finalize.cpp
+++ b/src/finalize.cpp
@@ -117,7 +117,7 @@ int openmc_finalize()
   data::energy_max = {INFTY, INFTY};
   data::energy_min = {0.0, 0.0};
   model::root_universe = -1;
-  openmc_set_seed(DEFAULT_SEED);
+  openmc::openmc_set_seed(DEFAULT_SEED);
 
   // Deallocate arrays
   free_memory();
@@ -159,6 +159,6 @@ int openmc_hard_reset()
   simulation::total_gen = 0;
 
   // Reset the random number generator state
-  openmc_set_seed(DEFAULT_SEED);
+  openmc::openmc_set_seed(DEFAULT_SEED);
   return 0;
 }
diff --git a/src/hdf5_interface.cpp b/src/hdf5_interface.cpp
index 1fb10b7066..729f008914 100644
--- a/src/hdf5_interface.cpp
+++ b/src/hdf5_interface.cpp
@@ -366,10 +366,11 @@ member_names(hid_t group_id, H5O_type_t type)
                                   i, nullptr, 0, H5P_DEFAULT);
 
     // Read name
-    char buffer[size];
+    char* buffer = new char[size];
     H5Lget_name_by_idx(group_id, ".", H5_INDEX_NAME, H5_ITER_INC, i,
                        buffer, size, H5P_DEFAULT);
     names.emplace_back(&buffer[0]);
+    delete[] buffer;
   }
   return names;
 }
@@ -404,11 +405,13 @@ object_name(hid_t obj_id)
 {
   // Determine size and create buffer
   size_t size = 1 + H5Iget_name(obj_id, nullptr, 0);
-  char buffer[size];
+  char* buffer = new char[size];
 
   // Read and return name
   H5Iget_name(obj_id, buffer, size);
-  return buffer;
+  std::string str = buffer;
+  delete[] buffer;
+  return str;
 }
 
 
diff --git a/src/initialize.cpp b/src/initialize.cpp
index f8a4f4a39a..fd524a2de9 100644
--- a/src/initialize.cpp
+++ b/src/initialize.cpp
@@ -68,7 +68,7 @@ int openmc_init(int argc, char* argv[], const void* intracomm)
 
   // Initialize random number generator -- if the user specifies a seed, it
   // will be re-initialized later
-  openmc_set_seed(DEFAULT_SEED);
+  openmc::openmc_set_seed(DEFAULT_SEED);
 
   // Read XML input files
   read_input_xml();
diff --git a/src/lattice.cpp b/src/lattice.cpp
index b16fecc6e3..5e679042ad 100644
--- a/src/lattice.cpp
+++ b/src/lattice.cpp
@@ -388,7 +388,7 @@ RectLattice::to_hdf5_inner(hid_t lat_group) const
     hsize_t nx {static_cast<hsize_t>(n_cells_[0])};
     hsize_t ny {static_cast<hsize_t>(n_cells_[1])};
     hsize_t nz {static_cast<hsize_t>(n_cells_[2])};
-    int out[nx*ny*nz];
+    std::vector<int> out(nx*ny*nz);
 
     for (int m = 0; m < nz; m++) {
       for (int k = 0; k < ny; k++) {
@@ -401,12 +401,12 @@ RectLattice::to_hdf5_inner(hid_t lat_group) const
     }
 
     hsize_t dims[3] {nz, ny, nx};
-    write_int(lat_group, 3, dims, "universes", out, false);
+    write_int(lat_group, 3, dims, "universes", &out[0], false);
 
   } else {
     hsize_t nx {static_cast<hsize_t>(n_cells_[0])};
     hsize_t ny {static_cast<hsize_t>(n_cells_[1])};
-    int out[nx*ny];
+    std::vector<int> out(nx*ny);
 
     for (int k = 0; k < ny; k++) {
       for (int j = 0; j < nx; j++) {
@@ -417,7 +417,7 @@ RectLattice::to_hdf5_inner(hid_t lat_group) const
     }
 
     hsize_t dims[3] {1, ny, nx};
-    write_int(lat_group, 3, dims, "universes", out, false);
+    write_int(lat_group, 3, dims, "universes", &out[0], false);
   }
 }
 
@@ -877,7 +877,7 @@ HexLattice::to_hdf5_inner(hid_t lat_group) const
   hsize_t nx {static_cast<hsize_t>(2*n_rings_ - 1)};
   hsize_t ny {static_cast<hsize_t>(2*n_rings_ - 1)};
   hsize_t nz {static_cast<hsize_t>(n_axial_)};
-  int out[nx*ny*nz];
+  std::vector<int> out(nx*ny*nz);
 
   for (int m = 0; m < nz; m++) {
     for (int k = 0; k < ny; k++) {
@@ -897,7 +897,7 @@ HexLattice::to_hdf5_inner(hid_t lat_group) const
   }
 
   hsize_t dims[3] {nz, ny, nx};
-  write_int(lat_group, 3, dims, "universes", out, false);
+  write_int(lat_group, 3, dims, "universes", &out[0], false);
 }
 
 //==============================================================================
diff --git a/src/math_functions.cpp b/src/math_functions.cpp
index 54d0e93441..ec5d64eac7 100644
--- a/src/math_functions.cpp
+++ b/src/math_functions.cpp
@@ -110,12 +110,13 @@ void calc_pn_c(int n, double x, double pnx[])
 
 double evaluate_legendre(int n, const double data[], double x)
 {
-  double pnx[n + 1];
+  double* pnx = new double[n + 1];
   double val = 0.0;
   calc_pn_c(n, x, pnx);
   for (int l = 0; l <= n; l++) {
     val += (l + 0.5) * data[l] * pnx[l];
   }
+  delete[] pnx;
   return val;
 }
 
@@ -536,8 +537,8 @@ void calc_zn(int n, double rho, double phi, double zn[]) {
   double sin_phi = std::sin(phi);
   double cos_phi = std::cos(phi);
 
-  double sin_phi_vec[n + 1]; // Sin[n * phi]
-  double cos_phi_vec[n + 1]; // Cos[n * phi]
+  std::vector<double> sin_phi_vec(n + 1); // Sin[n * phi]
+  std::vector<double> cos_phi_vec(n + 1); // Cos[n * phi]
   sin_phi_vec[0] = 1.0;
   cos_phi_vec[0] = 1.0;
   sin_phi_vec[1] = 2.0 * cos_phi;
@@ -554,8 +555,8 @@ void calc_zn(int n, double rho, double phi, double zn[]) {
 
   // ===========================================================================
   // Calculate R_pq(rho)
-  double zn_mat[n + 1][n + 1]; // Matrix forms of the coefficients which are
-                               // easier to work with
+  // Matrix forms of the coefficients which are easier to work with
+  std::vector<std::vector<double>> zn_mat(n + 1, std::vector<double>(n + 1));
 
   // Fill the main diagonal first (Eq 3.9 in Chong)
   for (int p = 0; p <= n; p++) {
@@ -763,7 +764,7 @@ void broaden_wmp_polynomials(double E, double dopp, int n, double factors[])
 
 void spline(int n, const double x[], const double y[], double z[])
 {
-  double c_new[n-1];
+  std::vector<double> c_new(n-1);
 
   // Set natural boundary conditions
   c_new[0] = 0.0;
diff --git a/src/mesh.cpp b/src/mesh.cpp
index ddfa272a6d..075e58de24 100644
--- a/src/mesh.cpp
+++ b/src/mesh.cpp
@@ -181,13 +181,13 @@ int RegularMesh::get_bin(Position r) const
   }
 
   // Determine indices
-  int ijk[n_dimension_];
+  std::vector<int> ijk(n_dimension_);
   bool in_mesh;
-  get_indices(r, ijk, &in_mesh);
+  get_indices(r, &ijk[0], &in_mesh);
   if (!in_mesh) return -1;
 
   // Convert indices to bin
-  return get_bin_from_indices(ijk);
+  return get_bin_from_indices(&ijk[0]);
 }
 
 int RegularMesh::get_bin_from_indices(const int* ijk) const
@@ -495,11 +495,11 @@ void RegularMesh::bins_crossed(const Particle* p, std::vector<int>& bins,
 
   // Determine the mesh indices for the starting and ending coords.
   int n = n_dimension_;
-  int ijk0[n], ijk1[n];
+  std::vector<int> ijk0(n), ijk1(n);
   bool start_in_mesh;
-  get_indices(r0, ijk0, &start_in_mesh);
+  get_indices(r0, &ijk0[0], &start_in_mesh);
   bool end_in_mesh;
-  get_indices(r1, ijk1, &end_in_mesh);
+  get_indices(r1, &ijk1[0], &end_in_mesh);
 
   // Reset coordinates and check for a mesh intersection if necessary.
   if (start_in_mesh) {
@@ -509,7 +509,7 @@ void RegularMesh::bins_crossed(const Particle* p, std::vector<int>& bins,
     // The initial coords do not lie in the mesh.  Check to see if the particle
     // eventually intersects the mesh and compute the relevant coords and
     // indices.
-    if (!intersects(r0, r1, ijk0)) return;
+    if (!intersects(r0, r1, &ijk0[0])) return;
   }
   r1 = r;
 
@@ -517,17 +517,17 @@ void RegularMesh::bins_crossed(const Particle* p, std::vector<int>& bins,
   // Find which mesh cells are traversed and the length of each traversal.
 
   while (true) {
-    if (std::equal(ijk0, ijk0+n, ijk1)) {
+    if (ijk0 == ijk1) {
       // The track ends in this cell.  Use the particle end location rather
       // than the mesh surface and stop iterating.
       double distance = (r1 - r0).norm();
-      bins.push_back(get_bin_from_indices(ijk0));
+      bins.push_back(get_bin_from_indices(&ijk0[0]));
       lengths.push_back(distance / total_distance);
       break;
     }
 
     // The track exits this cell.  Determine the distance to each mesh surface.
-    double d[n];
+    std::vector<double> d(n);
     for (int k = 0; k < n; ++k) {
       if (std::fabs(u[k]) < FP_PRECISION) {
         d[k] = INFTY;
@@ -541,9 +541,9 @@ void RegularMesh::bins_crossed(const Particle* p, std::vector<int>& bins,
     }
 
     // Pick the closest mesh surface and append this traversal to the output.
-    auto j = std::min_element(d, d+n) - d;
+    auto j = std::min_element(d.begin(), d.end()) - d.begin();
     double distance = d[j];
-    bins.push_back(get_bin_from_indices(ijk0));
+    bins.push_back(get_bin_from_indices(&ijk0[0]));
     lengths.push_back(distance / total_distance);
 
     // Translate to the oncoming mesh surface.
@@ -582,18 +582,17 @@ void RegularMesh::surface_bins_crossed(const Particle* p,
 
   // Determine indices for starting and ending location.
   int n = n_dimension_;
-  int ijk0[n], ijk1[n];
+  std::vector<int> ijk0(n), ijk1(n);
   bool start_in_mesh;
-  get_indices(r0, ijk0, &start_in_mesh);
+  get_indices(r0, &ijk0[0], &start_in_mesh);
   bool end_in_mesh;
-  get_indices(r1, ijk1, &end_in_mesh);
+  get_indices(r1, &ijk1[0], &end_in_mesh);
 
   // Check if the track intersects any part of the mesh.
   if (!start_in_mesh) {
     Position r0_copy = r0;
-    int ijk0_copy[n];
-    for (int i = 0; i < n; ++i) ijk0_copy[i] = ijk0[i];
-    if (!intersects(r0_copy, r1, ijk0_copy)) return;
+    std::vector<int> ijk0_copy(ijk0);
+    if (!intersects(r0_copy, r1, &ijk0_copy[0])) return;
   }
 
   // ========================================================================
@@ -651,7 +650,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p,
           // Outward current on i max surface
           if (in_mesh) {
             int i_surf = 4*i + 3;
-            int i_mesh = get_bin_from_indices(ijk0);
+            int i_mesh = get_bin_from_indices(&ijk0[0]);
             int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
@@ -672,7 +671,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p,
           // i min surface
           if (in_mesh) {
             int i_surf = 4*i + 2;
-            int i_mesh = get_bin_from_indices(ijk0);
+            int i_mesh = get_bin_from_indices(&ijk0[0]);
             int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
@@ -684,7 +683,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p,
           // Outward current on i min surface
           if (in_mesh) {
             int i_surf = 4*i + 1;
-            int i_mesh = get_bin_from_indices(ijk0);
+            int i_mesh = get_bin_from_indices(&ijk0[0]);
             int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
@@ -705,7 +704,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p,
           // i max surface
           if (in_mesh) {
             int i_surf = 4*i + 4;
-            int i_mesh = get_bin_from_indices(ijk0);
+            int i_mesh = get_bin_from_indices(&ijk0[0]);
             int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
diff --git a/src/mgxs.cpp b/src/mgxs.cpp
index efe562fa28..3aac41f35b 100644
--- a/src/mgxs.cpp
+++ b/src/mgxs.cpp
@@ -96,7 +96,7 @@ Mgxs::metadata_from_hdf5(hid_t xs_id, const std::vector<double>& temperature,
   // Determine the available temperatures
   hid_t kT_group = open_group(xs_id, "kTs");
   int num_temps = get_num_datasets(kT_group);
-  char* dset_names[num_temps];
+  char** dset_names = new char*[num_temps];
   for (int i = 0; i < num_temps; i++) {
     dset_names[i] = new char[151];
   }
@@ -111,6 +111,7 @@ Mgxs::metadata_from_hdf5(hid_t xs_id, const std::vector<double>& temperature,
     // Done with dset_names, so delete it
     delete[] dset_names[i];
   }
+  delete[] dset_names;
   std::sort(available_temps.begin(), available_temps.end());
 
   // If only one temperature is available, lets just use nearest temperature
diff --git a/src/surface.cpp b/src/surface.cpp
index f30b444310..9361fa4241 100644
--- a/src/surface.cpp
+++ b/src/surface.cpp
@@ -4,6 +4,7 @@
 #include <cmath>
 #include <sstream>
 #include <utility>
+#include <ciso646>
 
 #include "openmc/error.h"
 #include "openmc/hdf5_interface.h"
diff --git a/src/tallies/filter_legendre.cpp b/src/tallies/filter_legendre.cpp
index 1d1d440b28..0446cb2955 100644
--- a/src/tallies/filter_legendre.cpp
+++ b/src/tallies/filter_legendre.cpp
@@ -18,8 +18,8 @@ void
 LegendreFilter::get_all_bins(const Particle* p, int estimator,
                              FilterMatch& match) const
 {
-  double wgt[n_bins_];
-  calc_pn_c(order_, p->mu_, wgt);
+  std::vector<double> wgt(n_bins_);
+  calc_pn_c(order_, p->mu_, &wgt[0]);
   for (int i = 0; i < n_bins_; i++) {
     match.bins_.push_back(i);
     match.weights_.push_back(wgt[i]);
diff --git a/src/tallies/filter_mesh.cpp b/src/tallies/filter_mesh.cpp
index f69a966523..c62578b47e 100644
--- a/src/tallies/filter_mesh.cpp
+++ b/src/tallies/filter_mesh.cpp
@@ -58,8 +58,8 @@ MeshFilter::text_label(int bin) const
   auto& mesh = *model::meshes[mesh_];
   int n_dim = mesh.n_dimension_;
 
-  int ijk[n_dim];
-  mesh.get_indices_from_bin(bin, ijk);
+  std::vector<int> ijk(n_dim);
+  mesh.get_indices_from_bin(bin, &ijk[0]);
 
   std::stringstream out;
   out << "Mesh Index (" << ijk[0];
diff --git a/src/tallies/filter_sph_harm.cpp b/src/tallies/filter_sph_harm.cpp
index 1e97e64c1b..bbb34b16cc 100644
--- a/src/tallies/filter_sph_harm.cpp
+++ b/src/tallies/filter_sph_harm.cpp
@@ -35,16 +35,16 @@ SphericalHarmonicsFilter::get_all_bins(const Particle* p, int estimator,
                                        FilterMatch& match) const
 {
   // Determine cosine term for scatter expansion if necessary
-  double wgt[order_ + 1];
+  std::vector<double> wgt(order_ + 1);
   if (cosine_ == SphericalHarmonicsCosine::scatter) {
-    calc_pn_c(order_, p->mu_, wgt);
+    calc_pn_c(order_, p->mu_, &wgt[0]);
   } else {
     for (int i = 0; i < order_ + 1; i++) wgt[i] = 1;
   }
 
   // Find the Rn,m values
-  double rn[n_bins_];
-  calc_rn(order_, p->u_last_, rn);
+  std::vector<double> rn(n_bins_);
+  calc_rn(order_, p->u_last_, &rn[0]);
 
   int j = 0;
   for (int n = 0; n < order_ + 1; n++) {
diff --git a/src/tallies/filter_sptl_legendre.cpp b/src/tallies/filter_sptl_legendre.cpp
index 616dbbbd4d..6727bfed10 100644
--- a/src/tallies/filter_sptl_legendre.cpp
+++ b/src/tallies/filter_sptl_legendre.cpp
@@ -50,8 +50,8 @@ SpatialLegendreFilter::get_all_bins(const Particle* p, int estimator,
     double x_norm = 2.0*(x - min_) / (max_ - min_) - 1.0;
 
     // Compute and return the Legendre weights.
-    double wgt[order_ + 1];
-    calc_pn_c(order_, x_norm, wgt);
+    std::vector<double> wgt(order_ + 1);
+    calc_pn_c(order_, x_norm, &wgt[0]);
     for (int i = 0; i < order_ + 1; i++) {
       match.bins_.push_back(i);
       match.weights_.push_back(wgt[i]);
diff --git a/src/tallies/filter_zernike.cpp b/src/tallies/filter_zernike.cpp
index 9f66a68f98..9ab7b4bcda 100644
--- a/src/tallies/filter_zernike.cpp
+++ b/src/tallies/filter_zernike.cpp
@@ -36,8 +36,8 @@ ZernikeFilter::get_all_bins(const Particle* p, int estimator,
 
   if (r <= 1.0) {
     // Compute and return the Zernike weights.
-    double zn[n_bins_];
-    calc_zn(order_, r, theta, zn);
+    std::vector<double> zn(n_bins_);
+    calc_zn(order_, r, theta, &zn[0]);
     for (int i = 0; i < n_bins_; i++) {
       match.bins_.push_back(i);
       match.weights_.push_back(zn[i]);
@@ -93,8 +93,8 @@ ZernikeRadialFilter::get_all_bins(const Particle* p, int estimator,
 
   if (r <= 1.0) {
     // Compute and return the Zernike weights.
-    double zn[n_bins_];
-    calc_zn_rad(order_, r, zn);
+    std::vector<double> zn(n_bins_);
+    calc_zn_rad(order_, r, &zn[0]);
     for (int i = 0; i < n_bins_; i++) {
       match.bins_.push_back(i);
       match.weights_.push_back(zn[i]);

From 12b5f337d45e533c9eb6a0e6cfeab01d0a529508 Mon Sep 17 00:00:00 2001
From: jingang <liangjg2008@gmail.com>
Date: Wed, 5 Jun 2019 15:19:24 -0400
Subject: [PATCH 02/10] HDF5 linking errors

---
 CMakeLists.txt         | 6 ++++++
 src/hdf5_interface.cpp | 2 ++
 2 files changed, 8 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index fea014f12d..7448713663 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -272,6 +272,12 @@ if(GIT_SHA1_SUCCESS EQUAL 0)
   target_compile_definitions(libopenmc PRIVATE -DGIT_SHA1="${GIT_SHA1}")
 endif()
 
+# To use the shared HDF5 libraries on Windows with Visual Studio,
+# the H5_BUILT_AS_DYNAMIC_LIB compile definition must be specified.
+if(MSVC)
+  target_compile_definitions(libopenmc PRIVATE -DH5_BUILT_AS_DYNAMIC_LIB)
+endif()
+
 # target_link_libraries treats any arguments starting with - but not -l as
 # linker flags. Thus, we can pass both linker flags and libraries together.
 target_link_libraries(libopenmc ${ldflags} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES}
diff --git a/src/hdf5_interface.cpp b/src/hdf5_interface.cpp
index 729f008914..b1a90cb8f7 100644
--- a/src/hdf5_interface.cpp
+++ b/src/hdf5_interface.cpp
@@ -792,6 +792,8 @@ const hid_t H5TypeMap<int>::type_id = H5T_NATIVE_INT;
 template<>
 const hid_t H5TypeMap<unsigned long>::type_id = H5T_NATIVE_ULONG;
 template<>
+const hid_t H5TypeMap<unsigned long long>::type_id = H5T_NATIVE_ULLONG;
+template<>
 const hid_t H5TypeMap<unsigned int>::type_id = H5T_NATIVE_UINT;
 template<>
 const hid_t H5TypeMap<int64_t>::type_id = H5T_NATIVE_INT64;

From 97b8b6bef71b812c7e0376ef91a776ca10d09b96 Mon Sep 17 00:00:00 2001
From: jingang <liangjg2008@gmail.com>
Date: Wed, 5 Jun 2019 16:22:23 -0400
Subject: [PATCH 03/10] read windows cross section libaries

---
 src/cross_sections.cpp | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/cross_sections.cpp b/src/cross_sections.cpp
index 5d8d18c219..8ea59c1f08 100644
--- a/src/cross_sections.cpp
+++ b/src/cross_sections.cpp
@@ -402,6 +402,10 @@ void read_ce_cross_sections_xml()
     // If no directory is listed in cross_sections.xml, by default select the
     // directory in which the cross_sections.xml file resides
     auto pos = filename.rfind("/");
+    if (pos == std::string::npos) {
+      // no '/' found, probably a Windows directory
+      pos = filename.rfind("\\");
+    }
     directory = filename.substr(0, pos);
   }
 

From e5b108be7a14a1bc6a42034dc5e0bd801a4219fe Mon Sep 17 00:00:00 2001
From: jingang <liangjg2008@gmail.com>
Date: Thu, 6 Jun 2019 10:36:15 -0400
Subject: [PATCH 04/10] fix write 2D char arrays in HDF5

---
 include/openmc/hdf5_interface.h | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/include/openmc/hdf5_interface.h b/include/openmc/hdf5_interface.h
index e52d6c8054..c87abd84a1 100644
--- a/include/openmc/hdf5_interface.h
+++ b/include/openmc/hdf5_interface.h
@@ -464,22 +464,16 @@ write_dataset(hid_t obj_id, const char* name, const std::vector<std::string>& bu
   }
 
   // Copy data into contiguous buffer
-  char** temp = new char*[n];
-  for (int i = 0; i < n; i++) {
-    temp[i] = new char[m];
-  }
-  std::fill(temp[0], temp[0] + n*m, '\0');
+  char* temp = new char[n*m];
+  std::fill(temp, temp + n*m, '\0');
   for (int i = 0; i < n; ++i) {
-    std::copy(buffer[i].begin(), buffer[i].end(), temp[i]);
+    std::copy(buffer[i].begin(), buffer[i].end(), temp + i*m);
   }
 
   // Write 2D data
-  write_string(obj_id, 1, dims, m, name, temp[0], false);
+  write_string(obj_id, 1, dims, m, name, temp, false);
 
   // Free temp array
-  for (int i = 0; i < n; i++) {
-    delete[] temp[i];
-  }
   delete[] temp;
 }
 

From 950c684e6ce92b9c7b39cf0bdab548813ba21b4e Mon Sep 17 00:00:00 2001
From: jingang <liangjg2008@gmail.com>
Date: Thu, 6 Jun 2019 10:46:01 -0400
Subject: [PATCH 05/10] Set libopenmc as static library in CMake for MSVC:
 Built openmc.exe successfully with visual studio

---
 CMakeLists.txt | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7448713663..70ff63e978 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -159,7 +159,7 @@ target_compile_options(faddeeva PRIVATE ${cxxflags})
 # libopenmc
 #===============================================================================
 
-add_library(libopenmc SHARED
+list(APPEND libopenmc_SOURCES
   src/bank.cpp
   src/bremsstrahlung.cpp
   src/dagmc.cpp
@@ -246,6 +246,18 @@ add_library(libopenmc SHARED
   src/xml_interface.cpp
   src/xsdata.cpp)
 
+# For Visual Studio compilers
+if(MSVC)
+  # Use static library (otherwise explicit symbol portings are needed)
+  add_library(libopenmc STATIC ${libopenmc_SOURCES})
+
+  # To use the shared HDF5 libraries on Windows, the H5_BUILT_AS_DYNAMIC_LIB
+  # compile definition must be specified.
+  target_compile_definitions(libopenmc PRIVATE -DH5_BUILT_AS_DYNAMIC_LIB)
+else()
+  add_library(libopenmc SHARED ${libopenmc_SOURCES})
+endif()
+
 set_target_properties(libopenmc PROPERTIES
   OUTPUT_NAME openmc)
 
@@ -272,12 +284,6 @@ if(GIT_SHA1_SUCCESS EQUAL 0)
   target_compile_definitions(libopenmc PRIVATE -DGIT_SHA1="${GIT_SHA1}")
 endif()
 
-# To use the shared HDF5 libraries on Windows with Visual Studio,
-# the H5_BUILT_AS_DYNAMIC_LIB compile definition must be specified.
-if(MSVC)
-  target_compile_definitions(libopenmc PRIVATE -DH5_BUILT_AS_DYNAMIC_LIB)
-endif()
-
 # target_link_libraries treats any arguments starting with - but not -l as
 # linker flags. Thus, we can pass both linker flags and libraries together.
 target_link_libraries(libopenmc ${ldflags} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES}

From 59046be677cd4526bb568330e385da07d718b485 Mon Sep 17 00:00:00 2001
From: Jingang Liang <liangjg2008@gmail.com>
Date: Thu, 6 Jun 2019 17:20:14 +0000
Subject: [PATCH 06/10] fix reading 2D string vector from attribute in hdf5

---
 include/openmc/hdf5_interface.h | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/include/openmc/hdf5_interface.h b/include/openmc/hdf5_interface.h
index c87abd84a1..d0474c8344 100644
--- a/include/openmc/hdf5_interface.h
+++ b/include/openmc/hdf5_interface.h
@@ -204,23 +204,19 @@ read_attribute(hid_t obj_id, const char* name, std::vector<std::string>& vec)
 
   // Allocate a C char array to get strings
   auto n = attribute_typesize(obj_id, name);
-  char** buffer = new char*[m];
-  for (int i = 0; i < m; i++) {
-    buffer[i] = new char[n];
-  }
+  char* buffer = new char[m*n];
 
   // Read char data in attribute
-  read_attr_string(obj_id, name, n, buffer[0]);
+  read_attr_string(obj_id, name, n, buffer);
 
   for (int i = 0; i < m; ++i) {
     // Determine proper length of string -- strlen doesn't work because
     // buffer[i] might not have any null characters
     std::size_t k = 0;
-    for (; k < n; ++k) if (buffer[i][k] == '\0') break;
+    for (; k < n; ++k) if (buffer[i*n + k] == '\0') break;
 
     // Create string based on (char*, size_t) constructor
-    vec.emplace_back(&buffer[i][0], k);
-    delete[] buffer[i];
+    vec.emplace_back(&buffer[i*n], k);
   }
   delete[] buffer;
 }

From f57c4b919c6f067668eb1691942089fcb24488bc Mon Sep 17 00:00:00 2001
From: jingang <liangjg2008@gmail.com>
Date: Thu, 6 Jun 2019 11:36:39 -0400
Subject: [PATCH 07/10] do not set compile/link flags for visual studio
 generator

---
 CMakeLists.txt | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 70ff63e978..5c0734d23f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -72,6 +72,9 @@ endif()
 # Set compile/link flags based on which compiler is being used
 #===============================================================================
 
+# Skip for Visual Stduio which has its own configurations through GUI
+if(NOT MSVC)
+
 if(openmp)
   # Requires CMake 3.1+
   find_package(OpenMP)
@@ -104,6 +107,8 @@ endif()
 message(STATUS "OpenMC C++ flags: ${cxxflags}")
 message(STATUS "OpenMC Linker flags: ${ldflags}")
 
+endif()
+
 #===============================================================================
 # pugixml library
 #===============================================================================

From e5b2c6b477ae517419c6f7be813a43c095838ee5 Mon Sep 17 00:00:00 2001
From: jingang <liangjg2008@gmail.com>
Date: Fri, 14 Jun 2019 19:59:27 -0400
Subject: [PATCH 08/10] &name[0] -> name.data()

---
 src/initialize.cpp                   |  2 +-
 src/lattice.cpp                      |  6 +++---
 src/mesh.cpp                         | 28 ++++++++++++++--------------
 src/tallies/filter_legendre.cpp      |  2 +-
 src/tallies/filter_mesh.cpp          |  2 +-
 src/tallies/filter_sph_harm.cpp      |  4 ++--
 src/tallies/filter_sptl_legendre.cpp |  2 +-
 src/tallies/filter_zernike.cpp       |  4 ++--
 8 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/src/initialize.cpp b/src/initialize.cpp
index fd524a2de9..8331c30b5d 100644
--- a/src/initialize.cpp
+++ b/src/initialize.cpp
@@ -102,7 +102,7 @@ void initialize_mpi(MPI_Comm intracomm)
   // Create bank datatype
   Particle::Bank b;
   MPI_Aint disp[6];
-  MPI_Get_address(&b.r, &disp[0]);
+  MPI_Get_address(c&b.r, &disp[0]);
   MPI_Get_address(&b.u, &disp[1]);
   MPI_Get_address(&b.E, &disp[2]);
   MPI_Get_address(&b.wgt, &disp[3]);
diff --git a/src/lattice.cpp b/src/lattice.cpp
index 5e679042ad..42e15013d4 100644
--- a/src/lattice.cpp
+++ b/src/lattice.cpp
@@ -401,7 +401,7 @@ RectLattice::to_hdf5_inner(hid_t lat_group) const
     }
 
     hsize_t dims[3] {nz, ny, nx};
-    write_int(lat_group, 3, dims, "universes", &out[0], false);
+    write_int(lat_group, 3, dims, "universes", out.data(), false);
 
   } else {
     hsize_t nx {static_cast<hsize_t>(n_cells_[0])};
@@ -417,7 +417,7 @@ RectLattice::to_hdf5_inner(hid_t lat_group) const
     }
 
     hsize_t dims[3] {1, ny, nx};
-    write_int(lat_group, 3, dims, "universes", &out[0], false);
+    write_int(lat_group, 3, dims, "universes", out.data(), false);
   }
 }
 
@@ -897,7 +897,7 @@ HexLattice::to_hdf5_inner(hid_t lat_group) const
   }
 
   hsize_t dims[3] {nz, ny, nx};
-  write_int(lat_group, 3, dims, "universes", &out[0], false);
+  write_int(lat_group, 3, dims, "universes", out.data(), false);
 }
 
 //==============================================================================
diff --git a/src/mesh.cpp b/src/mesh.cpp
index 075e58de24..01ad329b7a 100644
--- a/src/mesh.cpp
+++ b/src/mesh.cpp
@@ -183,11 +183,11 @@ int RegularMesh::get_bin(Position r) const
   // Determine indices
   std::vector<int> ijk(n_dimension_);
   bool in_mesh;
-  get_indices(r, &ijk[0], &in_mesh);
+  get_indices(r, ijk.data(), &in_mesh);
   if (!in_mesh) return -1;
 
   // Convert indices to bin
-  return get_bin_from_indices(&ijk[0]);
+  return get_bin_from_indices(ijk.data());
 }
 
 int RegularMesh::get_bin_from_indices(const int* ijk) const
@@ -497,9 +497,9 @@ void RegularMesh::bins_crossed(const Particle* p, std::vector<int>& bins,
   int n = n_dimension_;
   std::vector<int> ijk0(n), ijk1(n);
   bool start_in_mesh;
-  get_indices(r0, &ijk0[0], &start_in_mesh);
+  get_indices(r0, ijk0.data(), &start_in_mesh);
   bool end_in_mesh;
-  get_indices(r1, &ijk1[0], &end_in_mesh);
+  get_indices(r1, ijk1.data(), &end_in_mesh);
 
   // Reset coordinates and check for a mesh intersection if necessary.
   if (start_in_mesh) {
@@ -509,7 +509,7 @@ void RegularMesh::bins_crossed(const Particle* p, std::vector<int>& bins,
     // The initial coords do not lie in the mesh.  Check to see if the particle
     // eventually intersects the mesh and compute the relevant coords and
     // indices.
-    if (!intersects(r0, r1, &ijk0[0])) return;
+    if (!intersects(r0, r1, ijk0.data())) return;
   }
   r1 = r;
 
@@ -521,7 +521,7 @@ void RegularMesh::bins_crossed(const Particle* p, std::vector<int>& bins,
       // The track ends in this cell.  Use the particle end location rather
       // than the mesh surface and stop iterating.
       double distance = (r1 - r0).norm();
-      bins.push_back(get_bin_from_indices(&ijk0[0]));
+      bins.push_back(get_bin_from_indices(ijk0.data()));
       lengths.push_back(distance / total_distance);
       break;
     }
@@ -543,7 +543,7 @@ void RegularMesh::bins_crossed(const Particle* p, std::vector<int>& bins,
     // Pick the closest mesh surface and append this traversal to the output.
     auto j = std::min_element(d.begin(), d.end()) - d.begin();
     double distance = d[j];
-    bins.push_back(get_bin_from_indices(&ijk0[0]));
+    bins.push_back(get_bin_from_indices(ijk0.data()));
     lengths.push_back(distance / total_distance);
 
     // Translate to the oncoming mesh surface.
@@ -584,15 +584,15 @@ void RegularMesh::surface_bins_crossed(const Particle* p,
   int n = n_dimension_;
   std::vector<int> ijk0(n), ijk1(n);
   bool start_in_mesh;
-  get_indices(r0, &ijk0[0], &start_in_mesh);
+  get_indices(r0, ijk0.data(), &start_in_mesh);
   bool end_in_mesh;
-  get_indices(r1, &ijk1[0], &end_in_mesh);
+  get_indices(r1, ijk1.data(), &end_in_mesh);
 
   // Check if the track intersects any part of the mesh.
   if (!start_in_mesh) {
     Position r0_copy = r0;
     std::vector<int> ijk0_copy(ijk0);
-    if (!intersects(r0_copy, r1, &ijk0_copy[0])) return;
+    if (!intersects(r0_copy, r1, ijk0_copy.data())) return;
   }
 
   // ========================================================================
@@ -650,7 +650,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p,
           // Outward current on i max surface
           if (in_mesh) {
             int i_surf = 4*i + 3;
-            int i_mesh = get_bin_from_indices(&ijk0[0]);
+            int i_mesh = get_bin_from_indices(ijk0.data());
             int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
@@ -671,7 +671,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p,
           // i min surface
           if (in_mesh) {
             int i_surf = 4*i + 2;
-            int i_mesh = get_bin_from_indices(&ijk0[0]);
+            int i_mesh = get_bin_from_indices(ijk0.data());
             int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
@@ -683,7 +683,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p,
           // Outward current on i min surface
           if (in_mesh) {
             int i_surf = 4*i + 1;
-            int i_mesh = get_bin_from_indices(&ijk0[0]);
+            int i_mesh = get_bin_from_indices(ijk0.data());
             int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
@@ -704,7 +704,7 @@ void RegularMesh::surface_bins_crossed(const Particle* p,
           // i max surface
           if (in_mesh) {
             int i_surf = 4*i + 4;
-            int i_mesh = get_bin_from_indices(&ijk0[0]);
+            int i_mesh = get_bin_from_indices(ijk0.data());
             int i_bin = 4*n*i_mesh + i_surf - 1;
 
             bins.push_back(i_bin);
diff --git a/src/tallies/filter_legendre.cpp b/src/tallies/filter_legendre.cpp
index 0446cb2955..6fa041c76b 100644
--- a/src/tallies/filter_legendre.cpp
+++ b/src/tallies/filter_legendre.cpp
@@ -19,7 +19,7 @@ LegendreFilter::get_all_bins(const Particle* p, int estimator,
                              FilterMatch& match) const
 {
   std::vector<double> wgt(n_bins_);
-  calc_pn_c(order_, p->mu_, &wgt[0]);
+  calc_pn_c(order_, p->mu_, wgt.data());
   for (int i = 0; i < n_bins_; i++) {
     match.bins_.push_back(i);
     match.weights_.push_back(wgt[i]);
diff --git a/src/tallies/filter_mesh.cpp b/src/tallies/filter_mesh.cpp
index c62578b47e..babc4b6e61 100644
--- a/src/tallies/filter_mesh.cpp
+++ b/src/tallies/filter_mesh.cpp
@@ -59,7 +59,7 @@ MeshFilter::text_label(int bin) const
   int n_dim = mesh.n_dimension_;
 
   std::vector<int> ijk(n_dim);
-  mesh.get_indices_from_bin(bin, &ijk[0]);
+  mesh.get_indices_from_bin(bin, ijk.data());
 
   std::stringstream out;
   out << "Mesh Index (" << ijk[0];
diff --git a/src/tallies/filter_sph_harm.cpp b/src/tallies/filter_sph_harm.cpp
index bbb34b16cc..0b3a371187 100644
--- a/src/tallies/filter_sph_harm.cpp
+++ b/src/tallies/filter_sph_harm.cpp
@@ -37,14 +37,14 @@ SphericalHarmonicsFilter::get_all_bins(const Particle* p, int estimator,
   // Determine cosine term for scatter expansion if necessary
   std::vector<double> wgt(order_ + 1);
   if (cosine_ == SphericalHarmonicsCosine::scatter) {
-    calc_pn_c(order_, p->mu_, &wgt[0]);
+    calc_pn_c(order_, p->mu_, wgt.data());
   } else {
     for (int i = 0; i < order_ + 1; i++) wgt[i] = 1;
   }
 
   // Find the Rn,m values
   std::vector<double> rn(n_bins_);
-  calc_rn(order_, p->u_last_, &rn[0]);
+  calc_rn(order_, p->u_last_, rn.data());
 
   int j = 0;
   for (int n = 0; n < order_ + 1; n++) {
diff --git a/src/tallies/filter_sptl_legendre.cpp b/src/tallies/filter_sptl_legendre.cpp
index 6727bfed10..6562ff01c7 100644
--- a/src/tallies/filter_sptl_legendre.cpp
+++ b/src/tallies/filter_sptl_legendre.cpp
@@ -51,7 +51,7 @@ SpatialLegendreFilter::get_all_bins(const Particle* p, int estimator,
 
     // Compute and return the Legendre weights.
     std::vector<double> wgt(order_ + 1);
-    calc_pn_c(order_, x_norm, &wgt[0]);
+    calc_pn_c(order_, x_norm, wgt.data());
     for (int i = 0; i < order_ + 1; i++) {
       match.bins_.push_back(i);
       match.weights_.push_back(wgt[i]);
diff --git a/src/tallies/filter_zernike.cpp b/src/tallies/filter_zernike.cpp
index 9ab7b4bcda..125bfada89 100644
--- a/src/tallies/filter_zernike.cpp
+++ b/src/tallies/filter_zernike.cpp
@@ -37,7 +37,7 @@ ZernikeFilter::get_all_bins(const Particle* p, int estimator,
   if (r <= 1.0) {
     // Compute and return the Zernike weights.
     std::vector<double> zn(n_bins_);
-    calc_zn(order_, r, theta, &zn[0]);
+    calc_zn(order_, r, theta, zn.data());
     for (int i = 0; i < n_bins_; i++) {
       match.bins_.push_back(i);
       match.weights_.push_back(zn[i]);
@@ -94,7 +94,7 @@ ZernikeRadialFilter::get_all_bins(const Particle* p, int estimator,
   if (r <= 1.0) {
     // Compute and return the Zernike weights.
     std::vector<double> zn(n_bins_);
-    calc_zn_rad(order_, r, &zn[0]);
+    calc_zn_rad(order_, r, zn.data());
     for (int i = 0; i < n_bins_; i++) {
       match.bins_.push_back(i);
       match.weights_.push_back(zn[i]);

From 23d7e41592609c6d782d044ea436ff17e4d26bd6 Mon Sep 17 00:00:00 2001
From: jingang <liangjg2008@gmail.com>
Date: Fri, 14 Jun 2019 20:07:42 -0400
Subject: [PATCH 09/10] and -> &&, or -> ||

---
 src/surface.cpp | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/surface.cpp b/src/surface.cpp
index 9361fa4241..f329fda6d2 100644
--- a/src/surface.cpp
+++ b/src/surface.cpp
@@ -4,7 +4,6 @@
 #include <cmath>
 #include <sstream>
 #include <utility>
-#include <ciso646>
 
 #include "openmc/error.h"
 #include "openmc/hdf5_interface.h"
@@ -298,7 +297,7 @@ template<int i> double
 axis_aligned_plane_distance(Position r, Direction u, bool coincident, double offset)
 {
   const double f = offset - r[i];
-  if (coincident or std::abs(f) < FP_COINCIDENT or u[i] == 0.0) return INFTY;
+  if (coincident || std::abs(f) < FP_COINCIDENT || u[i] == 0.0) return INFTY;
   const double d = f / u[i];
   if (d < 0.0) return INFTY;
   return d;
@@ -494,7 +493,7 @@ SurfacePlane::distance(Position r, Direction u, bool coincident) const
 {
   const double f = A_*r.x + B_*r.y + C_*r.z - D_;
   const double projection = A_*u.x + B_*u.y + C_*u.z;
-  if (coincident or std::abs(f) < FP_COINCIDENT or projection == 0.0) {
+  if (coincident || std::abs(f) < FP_COINCIDENT || projection == 0.0) {
     return INFTY;
   } else {
     const double d = -f / projection;
@@ -574,7 +573,7 @@ axis_aligned_cylinder_distance(Position r, Direction u,
     // No intersection with cylinder.
     return INFTY;
 
-  } else if (coincident or std::abs(c) < FP_COINCIDENT) {
+  } else if (coincident || std::abs(c) < FP_COINCIDENT) {
     // Particle is on the cylinder, thus one distance is positive/negative
     // and the other is zero. The sign of k determines if we are facing in or
     // out.
@@ -744,7 +743,7 @@ double SurfaceSphere::distance(Position r, Direction u, bool coincident) const
     // No intersection with sphere.
     return INFTY;
 
-  } else if (coincident or std::abs(c) < FP_COINCIDENT) {
+  } else if (coincident || std::abs(c) < FP_COINCIDENT) {
     // Particle is on the sphere, thus one distance is positive/negative and
     // the other is zero. The sign of k determines if we are facing in or out.
     if (k >= 0.0) {
@@ -821,7 +820,7 @@ axis_aligned_cone_distance(Position r, Direction u,
     // No intersection with cone.
     return INFTY;
 
-  } else if (coincident or std::abs(c) < FP_COINCIDENT) {
+  } else if (coincident || std::abs(c) < FP_COINCIDENT) {
     // Particle is on the cone, thus one distance is positive/negative
     // and the other is zero. The sign of k determines if we are facing in or
     // out.
@@ -1009,7 +1008,7 @@ SurfaceQuadric::distance(Position r, Direction ang, bool coincident) const
     // No intersection with surface.
     return INFTY;
 
-  } else if (coincident or std::abs(c) < FP_COINCIDENT) {
+  } else if (coincident || std::abs(c) < FP_COINCIDENT) {
     // Particle is on the surface, thus one distance is positive/negative and
     // the other is zero. The sign of k determines which distance is zero and
     // which is not.
@@ -1156,27 +1155,27 @@ void read_surfaces(pugi::xml_node node)
 
       // See if this surface makes part of the global bounding box.
       BoundingBox bb = surf->bounding_box();
-      if (bb.xmin > -INFTY and bb.xmin < xmin) {
+      if (bb.xmin > -INFTY && bb.xmin < xmin) {
         xmin = bb.xmin;
         i_xmin = i_surf;
       }
-      if (bb.xmax < INFTY and bb.xmax > xmax) {
+      if (bb.xmax < INFTY && bb.xmax > xmax) {
         xmax = bb.xmax;
         i_xmax = i_surf;
       }
-      if (bb.ymin > -INFTY and bb.ymin < ymin) {
+      if (bb.ymin > -INFTY && bb.ymin < ymin) {
         ymin = bb.ymin;
         i_ymin = i_surf;
       }
-      if (bb.ymax < INFTY and bb.ymax > ymax) {
+      if (bb.ymax < INFTY && bb.ymax > ymax) {
         ymax = bb.ymax;
         i_ymax = i_surf;
       }
-      if (bb.zmin > -INFTY and bb.zmin < zmin) {
+      if (bb.zmin > -INFTY && bb.zmin < zmin) {
         zmin = bb.zmin;
         i_zmin = i_surf;
       }
-      if (bb.zmax < INFTY and bb.zmax > zmax) {
+      if (bb.zmax < INFTY && bb.zmax > zmax) {
         zmax = bb.zmax;
         i_zmax = i_surf;
       }

From 7cf9bca90845ca8f94108553fca79915f5175b72 Mon Sep 17 00:00:00 2001
From: jingang <liangjg2008@gmail.com>
Date: Fri, 14 Jun 2019 20:39:49 -0400
Subject: [PATCH 10/10] added include <cctype> in cell.cpp

---
 src/cell.cpp       | 1 +
 src/initialize.cpp | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/cell.cpp b/src/cell.cpp
index 157d0d1a2c..a60f20fbea 100644
--- a/src/cell.cpp
+++ b/src/cell.cpp
@@ -4,6 +4,7 @@
 #include <sstream>
 #include <set>
 #include <string>
+#include <cctype>
 
 #include "openmc/capi.h"
 #include "openmc/constants.h"
diff --git a/src/initialize.cpp b/src/initialize.cpp
index 8331c30b5d..fd524a2de9 100644
--- a/src/initialize.cpp
+++ b/src/initialize.cpp
@@ -102,7 +102,7 @@ void initialize_mpi(MPI_Comm intracomm)
   // Create bank datatype
   Particle::Bank b;
   MPI_Aint disp[6];
-  MPI_Get_address(c&b.r, &disp[0]);
+  MPI_Get_address(&b.r, &disp[0]);
   MPI_Get_address(&b.u, &disp[1]);
   MPI_Get_address(&b.E, &disp[2]);
   MPI_Get_address(&b.wgt, &disp[3]);