Re-applied code formatting on C++ code with clang-format --style=llvm.

include/SM_Helpers.hpp

@@ -128,7 +128,7 @@ template <typename T> bool is_identity(T *A, unsigned int M, double tolerance) {
   return true;
 }
 
-template <typename T> T norm_max(T * A, unsigned int Dim) {
+template <typename T> T norm_max(T *A, unsigned int Dim) {
   T res = 0;
   for (unsigned int i = 0; i < Dim; i++) {
     for (unsigned int j = 0; j < Dim; j++) {
@@ -142,37 +142,37 @@ template <typename T> T norm_max(T * A, unsigned int Dim) {
   return res;
 }
 
-template  <typename T> T norm_frobenius2(T * A, unsigned int Dim) {
+template <typename T> T norm_frobenius2(T *A, unsigned int Dim) {
   T res = 0;
   for (unsigned int i = 0; i < Dim; i++) {
     for (unsigned int j = 0; j < Dim; j++) {
       T delta = A[i * Dim + j];
-      res += delta*delta;
+      res += delta * delta;
     }
   }
   return res;
 }
 
-template <typename T> T residual_max(T * A, unsigned int Dim) {
+template <typename T> T residual_max(T *A, unsigned int Dim) {
-  T res = 0;
-  for (unsigned int i = 0; i < Dim; i++) {
-    for (unsigned int j = 0; j < Dim; j++) {
-      T  delta = A[i * Dim + j] - (i == j);
-      delta = fabs(delta);
-      if (delta > res) {
-        res = delta;
-      }
-    }
-  }
-  return res;
-}
-
-template <typename T> T residual_frobenius2(T * A, unsigned int Dim) {
   T res = 0;
   for (unsigned int i = 0; i < Dim; i++) {
     for (unsigned int j = 0; j < Dim; j++) {
       T delta = A[i * Dim + j] - (i == j);
-      res += delta*delta;
+      delta = fabs(delta);
+      if (delta > res) {
+        res = delta;
+      }
+    }
+  }
+  return res;
+}
+
+template <typename T> T residual_frobenius2(T *A, unsigned int Dim) {
+  T res = 0;
+  for (unsigned int i = 0; i < Dim; i++) {
+    for (unsigned int j = 0; j < Dim; j++) {
+      T delta = A[i * Dim + j] - (i == j);
+      res += delta * delta;
     }
   }
   return res;

src/SM_Maponi.cpp

@@ -184,7 +184,7 @@ void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
       }
     }
 #ifdef DEBUG
-    showVector(ylk[0][k], Dim+1, "");
+    showVector(ylk[0][k], Dim + 1, "");
 #endif
   }
 
@@ -237,7 +237,10 @@ void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
             (i == j) - (j == component - 1) * ylk[l][p[l + 1]][i + 1] * ibeta;
       }
     }
-    matMul(Al, last, next, Dim); tmp = next; next = last; last = tmp;
+    matMul(Al, last, next, Dim);
+    tmp = next;
+    next = last;
+    last = tmp;
 #ifdef DEBUG
     showMatrix(last, Dim, "last");
 #endif
@@ -275,17 +278,17 @@ void MaponiA3S(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
 }
 
 extern "C" {
-  void MaponiA3_f(double **linSlater_inv, unsigned int *Dim,
+void MaponiA3_f(double **linSlater_inv, unsigned int *Dim,
-                  unsigned int *N_updates, double **linUpdates,
+                unsigned int *N_updates, double **linUpdates,
-                  unsigned int **Updates_index) {
+                unsigned int **Updates_index) {
-    MaponiA3(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
+  MaponiA3(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
-  }
+}
 }
 
 extern "C" {
-  void MaponiA3S_f(double **linSlater_inv, unsigned int *Dim,
+void MaponiA3S_f(double **linSlater_inv, unsigned int *Dim,
-                  unsigned int *N_updates, double **linUpdates,
+                 unsigned int *N_updates, double **linUpdates,
-                  unsigned int **Updates_index) {
+                 unsigned int **Updates_index) {
-    MaponiA3S(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
+  MaponiA3S(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
-  }
+}
 }

src/SM_Standard.cpp

@@ -173,7 +173,8 @@ void SM3(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
 }
 
 // Sherman Morrison, mix between SM3 + SM2
-// Leave zero denominators for later (SM3), and when none are left then split (SM2)
+// Leave zero denominators for later (SM3), and when none are left then split
+// (SM2)
 void SM4(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
          double *Updates, unsigned int *Updates_index) {
   std::cerr << "Called SM4 with " << N_updates << " updates" << std::endl;
@@ -237,27 +238,23 @@ void SM4(double *Slater_inv, unsigned int Dim, unsigned int N_updates,
 }
 
 extern "C" {
-  void SM1_f(double **linSlater_inv, unsigned int *Dim,
+void SM1_f(double **linSlater_inv, unsigned int *Dim, unsigned int *N_updates,
-                  unsigned int *N_updates, double **linUpdates,
+           double **linUpdates, unsigned int **Updates_index) {
-                  unsigned int **Updates_index) {
+  SM1(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
-    SM1(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
+}
-  }
+
-
+void SM2_f(double **linSlater_inv, unsigned int *Dim, unsigned int *N_updates,
-  void SM2_f(double **linSlater_inv, unsigned int *Dim,
+           double **linUpdates, unsigned int **Updates_index) {
-                  unsigned int *N_updates, double **linUpdates,
+  SM2(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
-                  unsigned int **Updates_index) {
+}
-    SM2(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
+
-  }
+void SM3_f(double **linSlater_inv, unsigned int *Dim, unsigned int *N_updates,
-
+           double **linUpdates, unsigned int **Updates_index) {
-  void SM3_f(double **linSlater_inv, unsigned int *Dim,
+  SM3(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
-                  unsigned int *N_updates, double **linUpdates,
+}
-                  unsigned int **Updates_index) {
+
-    SM3(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
+void SM4_f(double **linSlater_inv, unsigned int *Dim, unsigned int *N_updates,
-  }
+           double **linUpdates, unsigned int **Updates_index) {
-
+  SM4(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
-  void SM4_f(double **linSlater_inv, unsigned int *Dim,
+}
-                  unsigned int *N_updates, double **linUpdates,
-                  unsigned int **Updates_index) {
-    SM4(*linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index);
-  }
 }

tests/cMaponiA3_test_3x3_3.cpp

@@ -1,53 +1,61 @@
 // main.cpp
-#include "SM_Maponi.hpp"
 #include "SM_Helpers.hpp"
+#include "SM_Maponi.hpp"
 
 int main() {
 
-    unsigned int M = 3; // Dimension of the Slater-matrix
+  unsigned int M = 3; // Dimension of the Slater-matrix
-    unsigned int i, j; // Indices for iterators
+  unsigned int i, j;  // Indices for iterators
 
-    // Declare, allocate all vectors and matrices and fill them with zeros
+  // Declare, allocate all vectors and matrices and fill them with zeros
-    unsigned int *Ar_index = new unsigned int[M];
+  unsigned int *Ar_index = new unsigned int[M];
-    double *A = new double[M*M]; // The matrix to be inverted
+  double *A = new double[M * M]; // The matrix to be inverted
-    double *A0 = new double[M*M]; // A diagonal matrix with the digonal elements of A
+  double *A0 =
-    double *Ar = new double[M*M]; // The update matrix
+      new double[M * M]; // A diagonal matrix with the digonal elements of A
-    double *A0_inv = new double[M*M]; // The inverse
+  double *Ar = new double[M * M];     // The update matrix
+  double *A0_inv = new double[M * M]; // The inverse
 
-    // Fill with zeros
+  // Fill with zeros
-    for (i = 0; i < M; i++) {
+  for (i = 0; i < M; i++) {
-        for (j = 0; j < M; j++) {
+    for (j = 0; j < M; j++) {
-            A0[i*M+j] = 0;
+      A0[i * M + j] = 0;
-            Ar[i*M+j] = 0;
+      Ar[i * M + j] = 0;
-            A0_inv[i*M+j] = 0;
+      A0_inv[i * M + j] = 0;
-        }
     }
+  }
 
-    // Initialize A with M=3 and fill acc. to Eq. (17) from paper
+  // Initialize A with M=3 and fill acc. to Eq. (17) from paper
-    A[0] = 1;    A[3] = 1;    A[6] = -1;
+  A[0] = 1;
-    A[1] = 1;    A[4] = 1;    A[7] = 0;
+  A[3] = 1;
-    A[2] = -1;   A[5] = 0;    A[8] = -1;
+  A[6] = -1;
+  A[1] = 1;
+  A[4] = 1;
+  A[7] = 0;
+  A[2] = -1;
+  A[5] = 0;
+  A[8] = -1;
 
-    showMatrix(A, M, "A");
+  showMatrix(A, M, "A");
 
-    // Initialize the diagonal matrix A0,
+  // Initialize the diagonal matrix A0,
-    // the inverse of A0_inv of diagonal matrix A0_inv
+  // the inverse of A0_inv of diagonal matrix A0_inv
-    // and the update matrix Ar
+  // and the update matrix Ar
-    for (i = 0; i < M; i++) {
+  for (i = 0; i < M; i++) {
-        A0[i*M + i] = A[i*M + i];
+    A0[i * M + i] = A[i * M + i];
-        A0_inv[i*M + i] = 1.0/A[i*M + i];
+    A0_inv[i * M + i] = 1.0 / A[i * M + i];
-        Ar_index[i] = i+1; // ! First column needs to start with 1 !
+    Ar_index[i] = i + 1; // ! First column needs to start with 1 !
-        for (j = 0; j < M; j++) {
+    for (j = 0; j < M; j++) {
-            Ar[i*M + j] = A[i*M + j] - A0[i*M + j];
+      Ar[i * M + j] = A[i * M + j] - A0[i * M + j];
-        }
     }
+  }
 
-    // Define pointers dim and n_updates to use in Sherman-Morrison(...) function call
+  // Define pointers dim and n_updates to use in Sherman-Morrison(...) function
-    MaponiA3(A0_inv, M, M, Ar, Ar_index);
+  // call
-    showMatrix(A0_inv, M, "A0_inv");
+  MaponiA3(A0_inv, M, M, Ar, Ar_index);
+  showMatrix(A0_inv, M, "A0_inv");
 
-    // Deallocate all vectors and matrices
+  // Deallocate all vectors and matrices
-    delete [] A, A0, A0_inv, Ar, Ar_index;
+  delete[] A, A0, A0_inv, Ar, Ar_index;
 
-    return 0;
+  return 0;
 }

tests/test_h5.cpp

@@ -1,22 +1,22 @@
-#include "hdf5/serial/hdf5.h"
 #include "hdf5/serial/H5Cpp.h"
+#include "hdf5/serial/hdf5.h"
 
+#include "SM_Helpers.hpp"
 #include "SM_Maponi.hpp"
 #include "SM_Standard.hpp"
-#include "SM_Helpers.hpp"
 
 using namespace H5;
 // #define DEBUG
 
-const H5std_string FILE_NAME( "dataset.hdf5" );
+const H5std_string FILE_NAME("dataset.hdf5");
 
-void read_int(H5File file, std::string key, unsigned int * data) {
+void read_int(H5File file, std::string key, unsigned int *data) {
   DataSet ds = file.openDataSet(key);
   ds.read(data, PredType::STD_U32LE);
   ds.close();
 }
 
-void read_double(H5File file, std::string key, double * data) {
+void read_double(H5File file, std::string key, double *data) {
   DataSet ds = file.openDataSet(key);
   ds.read(data, PredType::IEEE_F64LE);
   ds.close();
@@ -32,19 +32,19 @@ int test_cycle(H5File file, int cycle, std::string version, double tolerance) {
   read_int(file, group + "/slater_matrix_dim", &dim);
   read_int(file, group + "/nupdates", &nupdates);
 
-  double * slater_matrix = new double[dim*dim];
+  double *slater_matrix = new double[dim * dim];
   read_double(file, group + "/slater_matrix", slater_matrix);
 
-  double * slater_inverse = new double[dim*dim];
+  double *slater_inverse = new double[dim * dim];
   read_double(file, group + "/slater_inverse", slater_inverse);
 
-  unsigned int * col_update_index = new unsigned int[nupdates];
+  unsigned int *col_update_index = new unsigned int[nupdates];
   read_int(file, group + "/col_update_index", col_update_index);
 
-  double * updates = new double[nupdates*dim];
+  double *updates = new double[nupdates * dim];
   read_double(file, group + "/updates", updates);
 
-  double * u = new double[nupdates*dim];
+  double *u = new double[nupdates * dim];
 
   /* Test */
 #ifdef DEBUG
@@ -55,8 +55,9 @@ int test_cycle(H5File file, int cycle, std::string version, double tolerance) {
   for (j = 0; j < nupdates; j++) {
     for (i = 0; i < dim; i++) {
       col = col_update_index[j];
-      u[i + j*dim] = updates[i + j*dim] - slater_matrix[i*dim + (col - 1)];
+      u[i + j * dim] =
-      slater_matrix[i*dim + (col - 1)] = updates[i + j*dim];
+          updates[i + j * dim] - slater_matrix[i * dim + (col - 1)];
+      slater_matrix[i * dim + (col - 1)] = updates[i + j * dim];
     }
   }
 
@@ -93,20 +94,20 @@ int test_cycle(H5File file, int cycle, std::string version, double tolerance) {
   showMatrix(slater_inverse, dim, "NEW Inverse");
 #endif
 
-  double * res = new double[dim*dim] {0};
+  double *res = new double[dim * dim]{0};
   matMul(slater_matrix, slater_inverse, res, dim);
   bool ok = is_identity(res, dim, tolerance);
 
   double res_max = residual_max(res, dim);
   double res2 = residual_frobenius2(res, dim);
-  std::cout << "Residual = " << version << " " << cycle << " " << res_max << " " << res2 << std::endl;
+  std::cout << "Residual = " << version << " " << cycle << " " << res_max << " "
+            << res2 << std::endl;
 
 #ifdef DEBUG
   showMatrix(res, dim, "Result");
 #endif
 
-  delete [] res, updates, u, col_update_index,
+  delete[] res, updates, u, col_update_index, slater_matrix, slater_inverse;
-            slater_matrix, slater_inverse;
 
   return ok;
 }
@@ -114,7 +115,9 @@ int test_cycle(H5File file, int cycle, std::string version, double tolerance) {
 int main(int argc, char **argv) {
   if (argc != 5) {
     std::cerr << "Execute from within 'datasets/'" << std::endl;
-    std::cerr << "usage: test_h5 <version> <start cycle> <stop cycle> <tolerance>" << std::endl;
+    std::cerr
+        << "usage: test_h5 <version> <start cycle> <stop cycle> <tolerance>"
+        << std::endl;
     return 1;
   }
   std::string version(argv[1]);
@@ -124,15 +127,12 @@ int main(int argc, char **argv) {
   H5File file(FILE_NAME, H5F_ACC_RDONLY);
 
   bool ok;
-  for (int cycle = start_cycle; cycle < stop_cycle+1; cycle++) {
+  for (int cycle = start_cycle; cycle < stop_cycle + 1; cycle++) {
     ok = test_cycle(file, cycle, version, tolerance);
     if (ok) {
-      std::cerr << "ok -- cycle " << std::to_string(cycle)
+      std::cerr << "ok -- cycle " << std::to_string(cycle) << std::endl;
-      << std::endl;
+    } else {
-    }
+      std::cerr << "failed -- cycle " << std::to_string(cycle) << std::endl;
-    else {
-      std::cerr << "failed -- cycle " << std::to_string(cycle)
-      << std::endl;
     }
   }
 

tests/vfc_test_h5.cpp

@@ -3,31 +3,30 @@
 // cycles in a CSV file, instead of accepting a start and an end cycle (which
 // makes it easier to select the exact cycles we are interested in with vfc_ci).
 
-#include <hdf5/serial/hdf5.h>
 #include <hdf5/serial/H5Cpp.h>
+#include <hdf5/serial/hdf5.h>
 
-#include <vector>
 #include <fstream>
 #include <sstream>
+#include <vector>
 
-
+#include "SM_Helpers.hpp"
 #include "SM_Maponi.hpp"
 #include "SM_Standard.hpp"
-#include "SM_Helpers.hpp"
 #include "vfc_probe.h"
 
 using namespace H5;
 // #define DEBUG
 
-const H5std_string FILE_NAME( "datasets/ci_dataset.hdf5" );
+const H5std_string FILE_NAME("datasets/ci_dataset.hdf5");
 
-void read_int(H5File file, std::string key, unsigned int * data) {
+void read_int(H5File file, std::string key, unsigned int *data) {
   DataSet ds = file.openDataSet(key);
   ds.read(data, PredType::STD_U32LE);
   ds.close();
 }
 
-void read_double(H5File file, std::string key, double * data) {
+void read_double(H5File file, std::string key, double *data) {
   DataSet ds = file.openDataSet(key);
   ds.read(data, PredType::IEEE_F64LE);
   ds.close();
@@ -42,14 +41,15 @@ std::vector<int> get_cycles_list(std::string path) {
   std::string cycle_str;
   std::vector<int> cycles_list = {};
 
-  while(string_stream >> cycle_str) {
+  while (string_stream >> cycle_str) {
     cycles_list.push_back(std::stoi(cycle_str));
   }
 
   return cycles_list;
 }
 
-int test_cycle(H5File file, int cycle, std::string version, vfc_probes * probes) {
+int test_cycle(H5File file, int cycle, std::string version,
+               vfc_probes *probes) {
 
   /* Read the data */
 
@@ -59,11 +59,12 @@ int test_cycle(H5File file, int cycle, std::string version, vfc_probes * probes)
   // being zero-padded. This is used when calling vfc_put_probe later on.
   std::string zero_padded_group = std::to_string(cycle);
   zero_padded_group = "cycle_" +
-  std::string(5 - zero_padded_group.length(), '0') + zero_padded_group;
+                      std::string(5 - zero_padded_group.length(), '0') +
+                      zero_padded_group;
 
-  try{
+  try {
     file.openGroup(group);
-  } catch(H5::Exception& e){
+  } catch (H5::Exception &e) {
     std::cerr << "group " << group << "not found" << std::endl;
     return 0;
   }
@@ -72,21 +73,20 @@ int test_cycle(H5File file, int cycle, std::string version, vfc_probes * probes)
   read_int(file, group + "/slater_matrix_dim", &dim);
   read_int(file, group + "/nupdates", &nupdates);
 
-
+  double *slater_matrix = new double[dim * dim];
-  double * slater_matrix = new double[dim*dim];
   read_double(file, group + "/slater_matrix", slater_matrix);
 
-  double * slater_inverse = new double[dim*dim];
+  double *slater_inverse = new double[dim * dim];
   read_double(file, group + "/slater_inverse", slater_inverse);
-  //slater_inverse = transpose(slater_inverse, dim);
+  // slater_inverse = transpose(slater_inverse, dim);
 
-  unsigned int * col_update_index = new unsigned int[nupdates];
+  unsigned int *col_update_index = new unsigned int[nupdates];
   read_int(file, group + "/col_update_index", col_update_index);
 
-  double * updates = new double[nupdates*dim];
+  double *updates = new double[nupdates * dim];
   read_double(file, group + "/updates", updates);
 
-  double * u = new double[nupdates*dim];
+  double *u = new double[nupdates * dim];
 
   /* Test */
 #ifdef DEBUG
@@ -100,8 +100,9 @@ int test_cycle(H5File file, int cycle, std::string version, vfc_probes * probes)
   for (j = 0; j < nupdates; j++) {
     for (i = 0; i < dim; i++) {
       col = col_update_index[j];
-      u[i + j*dim] = updates[i + j*dim] - slater_matrix[i*dim + (col - 1)];
+      u[i + j * dim] =
-      slater_matrix[i*dim + (col - 1)] = updates[i + j*dim];
+          updates[i + j * dim] - slater_matrix[i * dim + (col - 1)];
+      slater_matrix[i * dim + (col - 1)] = updates[i + j * dim];
     }
   }
 
@@ -128,7 +129,7 @@ int test_cycle(H5File file, int cycle, std::string version, vfc_probes * probes)
   showMatrix(slater_inverse, dim, "NEW Inverse");
 #endif
 
-  double * res = new double[dim*dim] {0};
+  double *res = new double[dim * dim]{0};
   matMul(slater_matrix, slater_inverse, res, dim);
   bool ok = is_identity(res, dim, 1e-3);
 
@@ -139,11 +140,11 @@ int test_cycle(H5File file, int cycle, std::string version, vfc_probes * probes)
   showMatrix(res, dim, "Result");
 #endif
 
-  vfc_put_probe(probes, &(zero_padded_group)[0], &("res_max_" + version)[0], res_max);
+  vfc_put_probe(probes, &(zero_padded_group)[0], &("res_max_" + version)[0],
+                res_max);
   vfc_put_probe(probes, &(zero_padded_group)[0], &("res2_" + version)[0], res2);
 
-  delete [] res, updates, u, col_update_index,
+  delete[] res, updates, u, col_update_index, slater_matrix, slater_inverse;
-            slater_matrix, slater_inverse;
 
   return ok;
 }
@@ -165,12 +166,9 @@ int main(int argc, char **argv) {
   for (int i = 0; i < cycles_list.size(); i++) {
     ok = test_cycle(file, cycles_list[i], version, &probes);
     if (ok) {
-      std::cout << "ok -- cycle " << std::to_string(i)
+      std::cout << "ok -- cycle " << std::to_string(i) << std::endl;
-      << std::endl;
+    } else {
-    }
+      std::cerr << "failed -- cycle " << std::to_string(i) << std::endl;
-    else {
-      std::cerr << "failed -- cycle " << std::to_string(i)
-      << std::endl;
     }
   }