Cleanup the codes

alm/alamode.h

@@ -40,4 +40,3 @@ namespace ALM_NS
         std::string mode;
     };
 }
-

alm/combination.h

@@ -25,7 +25,9 @@ namespace ALM_NS
 
 
     public:
-        CombinationWithRepetition() {};
+        CombinationWithRepetition()
+        {
+        };
 
         template <class InputIter>
         CombinationWithRepetition(InputIter begin,
@@ -75,4 +77,3 @@ namespace ALM_NS
         }
     };
 }
-

alm/constraint.h

@@ -164,7 +164,6 @@ namespace ALM_NS
         void rref(std::vector<std::vector<double>> &, const double tolerance = eps12);
 
         void generate_symmetry_constraint_in_cartesian(std::vector<ConstraintClass> *);
-
     };
 
     extern "C"

alm/error.h

@@ -27,4 +27,3 @@ namespace ALM_NS
         void exit(const char *, const char *, const char *);
     };
 }
-

alm/interaction.h

@@ -177,13 +177,13 @@ namespace ALM_NS
     {
     public:
         std::vector<int> atom;
-        std::vector<std::vector<int> > cell;
+        std::vector<std::vector<int>> cell;
         double distmax;
 
         MinimumDistanceCluster();
 
         MinimumDistanceCluster(const std::vector<int> atom_in,
-                               const std::vector<std::vector<int> > cell_in,
+                               const std::vector<std::vector<int>> cell_in,
                                const double dist_in)
         {
             for (int i = 0; i < atom_in.size(); ++i) {
@@ -196,7 +196,7 @@ namespace ALM_NS
         }
 
         MinimumDistanceCluster(const std::vector<int> atom_in,
-                               const std::vector<std::vector<int> > cell_in)
+                               const std::vector<std::vector<int>> cell_in)
         {
             for (int i = 0; i < atom_in.size(); ++i) {
                 atom.push_back(atom_in[i]);
@@ -279,11 +279,10 @@ namespace ALM_NS
                                     std::vector<DistInfo> **,
                                     int *, std::set<MinimumDistanceCluster> **);
 
-        void cell_combination(std::vector<std::vector<int> >,
+        void cell_combination(std::vector<std::vector<int>>,
                               int, std::vector<int>,
-                              std::vector<std::vector<int> > &);
+                              std::vector<std::vector<int>> &);
 
         void generate_pairs(std::set<IntList> *, std::set<MinimumDistanceCluster> **);
     };
 }
-

alm/memory.h

@@ -169,4 +169,3 @@ namespace ALM_NS
         }
     };
 }
-

alm/pointers.h

@@ -31,9 +31,13 @@ namespace ALM_NS
             displace(ptr->displace),
             writes(ptr->writes),
             error(ptr->error),
-            timer(ptr->timer) {}
+            timer(ptr->timer)
+        {
+        }
 
-        virtual ~Pointers() {}
+        virtual ~Pointers()
+        {
+        }
 
     protected:
         ALM *alm;
@@ -52,4 +56,3 @@ namespace ALM_NS
         Timer *&timer;
     };
 }
-

alm/system.h

@@ -68,4 +68,3 @@ namespace ALM_NS
         void setup_atomic_class(int *);
     };
 }
-

alm/timer.h

@@ -42,4 +42,3 @@ namespace ALM_NS
 #endif
     };
 }
-

alm/writes.cpp

@@ -495,7 +495,7 @@ void Writes::write_misc_xml()
     std::sort(fcs->fc_table[0].begin(), fcs->fc_table[0].end());
 
     for (std::vector<FcProperty>::iterator it = fcs->fc_table[0].begin();
-        it != fcs->fc_table[0].end(); ++it) {
+         it != fcs->fc_table[0].end(); ++it) {
         FcProperty fctmp = *it;
         ip = fctmp.mother;
 
@@ -530,7 +530,7 @@ void Writes::write_misc_xml()
         std::sort(fcs->fc_table[order].begin(), fcs->fc_table[order].end());
 
         for (std::vector<FcProperty>::iterator it = fcs->fc_table[order].begin();
-            it != fcs->fc_table[order].end(); ++it) {
+             it != fcs->fc_table[order].end(); ++it) {
             FcProperty fctmp = *it;
             ip = fctmp.mother + ishift;
 
@@ -652,45 +652,45 @@ void Writes::write_hessian()
 
     std::cout << " Complete Hessian matrix                    : " << files->file_hes << std::endl;
 
-  /*
-    std::string file_fc2 = files->job_title + ".fc2";
-    std::ofstream ofs_fc2;
-    ofs_fc2.open(file_fc2.c_str(), std::ios::out);
-    ofs_fc2 << " # iat, icrd, jat, icrd, icell, relvec, fc2" << std::endl;
-    double vec[3];
-    for (std::vector<FcProperty>::iterator it = fcs->fc_table[0].begin();
-         it != fcs->fc_table[0].end(); ++it) {
-        FcProperty fctmp = *it;
-        ip = fctmp.mother;
-
-        for (i = 0; i < 2; ++i) pair_tmp[i] = fctmp.elems[i] / 3;
-        for (itran = 0; itran < symmetry->ntran; ++itran) {
-            for (i = 0; i < 2; ++i) {
-                pair_tran[i] = symmetry->map_sym[pair_tmp[i]][symmetry->symnum_tran[itran]];
-            }
-            for (std::vector<DistInfo>::iterator
-                 it2  = interaction->mindist_pairs[pair_tran[0]][pair_tran[1]].begin();
-                 it2 != interaction->mindist_pairs[pair_tran[0]][pair_tran[1]].end(); ++it2) {
-                  int multiplicity = interaction->mindist_pairs[pair_tran[0]][pair_tran[1]].size();
-                  for (i = 0; i < 3; ++i) {
-                    vec[i] = interaction->x_image[(*it2).cell][pair_tran[1]][i]
-                           - interaction->x_image[0][pair_tran[0]][i];
-                  }
-                  ofs_fc2 << std::setw(5) << pair_tran[0] + 1 << std::setw(5) << fctmp.elems[0] % 3 + 1;
-                  ofs_fc2 << std::setw(5) << pair_tran[1] + 1 << std::setw(5) << fctmp.elems[1] % 3 + 1;
-                  ofs_fc2 << std::setw(5) << (*it2).cell + 1;
-                  ofs_fc2 << std::setw(15) << vec[0];
-                  ofs_fc2 << std::setw(15) << vec[1];
-                  ofs_fc2 << std::setw(15) << vec[2];
-
-                  ofs_fc2 << std::setw(15)
-                  << fitting->params[ip] * fctmp.sign / static_cast<double>(multiplicity);
-                  ofs_fc2 << std::endl;
-            }
-        }
-    }
-    ofs_fc2.close();
-   */
+    /*
+      std::string file_fc2 = files->job_title + ".fc2";
+      std::ofstream ofs_fc2;
+      ofs_fc2.open(file_fc2.c_str(), std::ios::out);
+      ofs_fc2 << " # iat, icrd, jat, icrd, icell, relvec, fc2" << std::endl;
+      double vec[3];
+      for (std::vector<FcProperty>::iterator it = fcs->fc_table[0].begin();
+           it != fcs->fc_table[0].end(); ++it) {
+          FcProperty fctmp = *it;
+          ip = fctmp.mother;
+  
+          for (i = 0; i < 2; ++i) pair_tmp[i] = fctmp.elems[i] / 3;
+          for (itran = 0; itran < symmetry->ntran; ++itran) {
+              for (i = 0; i < 2; ++i) {
+                  pair_tran[i] = symmetry->map_sym[pair_tmp[i]][symmetry->symnum_tran[itran]];
+              }
+              for (std::vector<DistInfo>::iterator
+                   it2  = interaction->mindist_pairs[pair_tran[0]][pair_tran[1]].begin();
+                   it2 != interaction->mindist_pairs[pair_tran[0]][pair_tran[1]].end(); ++it2) {
+                    int multiplicity = interaction->mindist_pairs[pair_tran[0]][pair_tran[1]].size();
+                    for (i = 0; i < 3; ++i) {
+                      vec[i] = interaction->x_image[(*it2).cell][pair_tran[1]][i]
+                             - interaction->x_image[0][pair_tran[0]][i];
+                    }
+                    ofs_fc2 << std::setw(5) << pair_tran[0] + 1 << std::setw(5) << fctmp.elems[0] % 3 + 1;
+                    ofs_fc2 << std::setw(5) << pair_tran[1] + 1 << std::setw(5) << fctmp.elems[1] % 3 + 1;
+                    ofs_fc2 << std::setw(5) << (*it2).cell + 1;
+                    ofs_fc2 << std::setw(15) << vec[0];
+                    ofs_fc2 << std::setw(15) << vec[1];
+                    ofs_fc2 << std::setw(15) << vec[2];
+  
+                    ofs_fc2 << std::setw(15)
+                    << fitting->params[ip] * fctmp.sign / static_cast<double>(multiplicity);
+                    ofs_fc2 << std::endl;
+              }
+          }
+      }
+      ofs_fc2.close();
+     */
 }
 
 std::string Writes::double2string(const double d, const int nprec)

alm/writes.h

@@ -24,11 +24,15 @@ namespace ALM_NS
         int kind;
         int atom, tran;
 
-        AtomProperty() {};
+        AtomProperty()
+        {
+        };
 
         AtomProperty(const AtomProperty &other)
             : x(other.x), y(other.y), z(other.z),
-              kind(other.kind), atom(other.atom), tran(other.tran) {};
+              kind(other.kind), atom(other.atom), tran(other.tran)
+        {
+        };
 
         AtomProperty(const double *pos,
                      const int kind_in,
@@ -52,7 +56,9 @@ namespace ALM_NS
         int nat, natmin, ntran;
         int nspecies;
 
-        SystemInfo() {};
+        SystemInfo()
+        {
+        };
     };
 
     class Writes: protected Pointers

anphon/pointers.h

@@ -40,9 +40,13 @@ namespace PHON_NS
             isotope(ptr->isotope),
             scph(ptr->scph),
             ewald(ptr->ewald),
-            timer(ptr->timer) {}
+            timer(ptr->timer)
+        {
+        }
 
-        virtual ~Pointers() {}
+        virtual ~Pointers()
+        {
+        }
 
     protected:
         PHON *phon;
@@ -70,4 +74,3 @@ namespace PHON_NS
         Timer *&timer;
     };
 }
-

anphon/relaxation.cpp

@@ -1208,7 +1208,7 @@ void Relaxation::calc_frequency_resolved_final_state(const unsigned int N,
                         n1 = f1 + f2 + 1.0;
                         n2 = f1 - f2;
                     }
-   
+
                     if (integration->ismear == 0) {
                         prod_tmp[0] = n1
                             * (delta_lorentz(omega0 - omega_inner[0] - omega_inner[1], epsilon)
@@ -2542,7 +2542,7 @@ void Relaxation::print_momentum_resolved_final_state(const unsigned int NT,
                                 n1 = f1 + f2 + 1.0;
                                 n2 = f1 - f2;
                             }
- 
+
 
                             if (selection_type == 0) {
                                 gamma_k[k][iT] += V3norm * n1;
@@ -3120,7 +3120,7 @@ void Relaxation::calc_self3omega_tetrahedron(const double Temp,
                             n1 = f1 + f2 + 1.0;
                             n2 = f1 - f2;
                         }
-  
+
                         //#pragma omp critical
                         ret_private[nomega * ithread + iomega]
                             += v3_arr[ik][ib] * (n1 * weight_tetra[0][ik] - 2.0 * n2 * weight_tetra[1][ik]);

anphon/scph.cpp

@@ -115,7 +115,7 @@ void Scph::exec_scph()
             write_scph_bands(eval_anharm);
         } else if (kpoint->kpoint_mode == 2) {
             write_scph_dos(eval_anharm);
- //           write_scph_thermodynamics(eval_anharm);
+            //           write_scph_thermodynamics(eval_anharm);
             if (writes->print_msd) {
                 write_scph_msd(eval_anharm, evec_anharm);
             }

anphon/selfenergy.cpp

@@ -127,7 +127,7 @@ void Selfenergy::selfenergy_tadpole(const unsigned int N,
                     } else {
                         n2 = thermodynamics->fB(omega2, T_tmp);
                         ret_mpi[i] += v3_tmp2 * (2.0 * n2 + 1.0);
-                    } 
+                    }
                 }
             }
         }

anphon/thermodynamics.cpp

@@ -273,7 +273,7 @@ double Thermodynamics::free_energy(const double T)
             x = omega / (T * T_to_Ryd);
             ret += std::log(x);
         }
-        
+
         return T * T_to_Ryd * ret / static_cast<double>(nk);
 
     } else {
@@ -297,7 +297,6 @@ double Thermodynamics::free_energy(const double T)
 
         return T * T_to_Ryd * ret / static_cast<double>(nk);
     }
-
 }
 
 double Thermodynamics::disp2_avg(const double T,
@@ -325,7 +324,7 @@ double Thermodynamics::disp2_avg(const double T,
             if (omega < eps8) continue;
 
             ret += real(dynamical->evec_phonon[ik][is][ns1]
-                * std::conj(dynamical->evec_phonon[ik][is][ns2]))
+                    * std::conj(dynamical->evec_phonon[ik][is][ns2]))
                 * T * T_to_Ryd / (omega * omega);
         }
     } else {
@@ -340,7 +339,7 @@ double Thermodynamics::disp2_avg(const double T,
             if (omega < eps8) continue;
 
             ret += real(dynamical->evec_phonon[ik][is][ns1]
-                * std::conj(dynamical->evec_phonon[ik][is][ns2]))
+                    * std::conj(dynamical->evec_phonon[ik][is][ns2]))
                 * (fB(omega, T) + 0.5) / omega;
         }
     }

anphon/write_phonons.cpp

@@ -282,7 +282,7 @@ void Writes::setup_result_io()
             }
             if (static_cast<bool>(is_classical) != thermodynamics->classical) {
                 error->warn("setup_result_io",
-                    "CLASSICAL val is not consistent");
+                            "CLASSICAL val is not consistent");
             }
 
             found_tag = false;
@@ -610,8 +610,8 @@ void Writes::write_phonon_bands()
         for (i = 0; i < nk; ++i) {
             ofs_bands << std::setw(8) << std::fixed << kaxis[i];
             for (j = 0; j < nbands; ++j) {
-                ofs_bands << std::setw(15) << std::scientific 
-                << in_kayser(eval[i][dynamical->index_bconnect[i][j]]);
+                ofs_bands << std::setw(15) << std::scientific
+                    << in_kayser(eval[i][dynamical->index_bconnect[i][j]]);
             }
             ofs_bands << std::endl;
         }
@@ -629,7 +629,7 @@ void Writes::write_phonon_bands()
         ofs_connect.open(file_connect.c_str(), std::ios::out);
         if (!ofs_connect)
             error->exit("write_phonon_bands",
-                "cannot open file_connect");
+                        "cannot open file_connect");
 
         ofs_connect << "# " << str_kpath << std::endl;
         ofs_connect << "#" << str_kval << std::endl;

tools/analyze_phonons.cpp

@@ -563,7 +563,7 @@ void calc_kappa_cumulative(double max_length, double delta_length, int itemp)
                 } else {
                     c_tmp = Cv(omega[ik][is], temp[itemp]);
                 }
-                
+
                 vel_tmp = pow(vel[ik][is][0][0], 2)
                     + pow(vel[ik][is][0][1], 2)
                     + pow(vel[ik][is][0][2], 2);
@@ -782,7 +782,7 @@ void calc_kappa_boundary2(double max_length, double delta_length, int itemp, int
                     c_tmp = k_Boltzmann;
                 } else {
                     c_tmp = Cv(omega[ik][is], temp[itemp]);
-                }          
+                }
 
                 for (i = 0; i < nsame; ++i) {