Clearn up codes. (Need more refactoring)

anphon/conductivity.cpp

@@ -9,42 +9,74 @@
 */
 
 #include "mpi_common.h"
-#include <iostream>
-#include <fstream>
-#include <iomanip>
 #include "conductivity.h"
+#include "constants.h"
 #include "dynamical.h"
 #include "error.h"
 #include "integration.h"
+#include "isotope.h"
 #include "kpoint.h"
+#include "mathfunctions.h"
 #include "memory.h"
 #include "parsephon.h"
+#include "phonon_dos.h"
 #include "thermodynamics.h"
 #include "phonon_velocity.h"
 #include "relaxation.h"
 #include "system.h"
 #include "write_phonons.h"
-#include "constants.h"
+#include <iostream>
+#include <fstream>
+#include <iomanip>
 #include <set>
 #include <vector>
-#include "mathfunctions.h"
-#include "isotope.h"
-#include "phonon_dos.h"
 
 using namespace PHON_NS;
 
 Conductivity::Conductivity(PHON *phon): Pointers(phon)
 {
+    set_default_variables();
 }
 
 Conductivity::~Conductivity()
 {
+    deallocate_variables();
 };
 
+void Conductivity::set_default_variables()
+{
+    calc_kappa_spec = 0;
+    ntemp = 0;
+    damping3 = nullptr;
+    kappa = nullptr;
+    kappa_spec = nullptr;
+    Temperature = nullptr;
+    vel = nullptr;
+}
+
+void Conductivity::deallocate_variables()
+{
+    if (damping3) {
+        memory->deallocate(damping3);
+    }
+    if (kappa) {
+        memory->deallocate(kappa);
+    }
+    if (kappa_spec) {
+        memory->deallocate(kappa_spec);
+    }
+    if (Temperature) {
+        memory->deallocate(Temperature);
+    }
+    if (vel) {
+        memory->deallocate(vel);
+    }
+}
+
+
 void Conductivity::setup_kappa()
 {
     unsigned int i, j, k;
-    unsigned int nks_total, nks_each_thread, nrem;
 
     nk = kpoint->nk;
     ns = dynamical->neval;
@@ -56,9 +88,9 @@ void Conductivity::setup_kappa()
         Temperature[i] = system->Tmin + static_cast<double>(i) * system->dT;
     }
 
-    nks_total = kpoint->nk_irred * ns;
-    nks_each_thread = nks_total / mympi->nprocs;
-    nrem = nks_total - nks_each_thread * mympi->nprocs;
+    unsigned int nks_total = kpoint->nk_irred * ns;
+    unsigned int nks_each_thread = nks_total / mympi->nprocs;
+    unsigned int nrem = nks_total - nks_each_thread * mympi->nprocs;
 
     if (nrem > 0) {
         memory->allocate(damping3, (nks_each_thread + 1) * mympi->nprocs, ntemp);
@@ -190,22 +222,9 @@ void Conductivity::prepare_restart()
     vks_done.clear();
 }
 
-void Conductivity::finish_kappa()
-{
-    if (mympi->my_rank == 0) {
-        memory->deallocate(vel);
-        memory->deallocate(kappa);
-        if (calc_kappa_spec) {
-            memory->deallocate(kappa_spec);
-        }
-    }
-    memory->deallocate(damping3);
-    memory->deallocate(Temperature);
-}
 
 void Conductivity::calc_anharmonic_imagself()
 {
-    unsigned int nks_g;
     unsigned int i, j;
     unsigned int knum, snum;
     unsigned int *nks_thread;
@@ -216,7 +235,7 @@ void Conductivity::calc_anharmonic_imagself()
 
     // Distribute (k,s) to individual MPI threads
 
-    nks_g = vks_job.size();
+    unsigned int nks_g = vks_job.size();
     vks_l.clear();
 
     unsigned int icount = 0;
@@ -304,11 +323,11 @@ void Conductivity::write_result_gamma(const unsigned int ik, const unsigned int
                                       double ***vel_in, double **damp_in)
 {
     unsigned int np = mympi->nprocs;
-    unsigned int j, k, iks_g;
+    unsigned int k, iks_g;
     unsigned int nk_equiv;
     unsigned int ktmp;
 
-    for (j = 0; j < np; ++j) {
+    for (unsigned int j = 0; j < np; ++j) {
 
         iks_g = ik * np + j + nshift;
 
@@ -368,7 +387,7 @@ void Conductivity::compute_kappa()
                 snum = iks % ns;
                 if (relaxation->is_imaginary[iks / ns][snum]) {
                     for (i = 0; i < ntemp; ++i) {
-                        lifetime[iks][i] = 0.0;;
+                        lifetime[iks][i] = 0.0;
                     }
                 } else {
                     for (i = 0; i < ntemp; ++i) {

anphon/conductivity.h

@@ -25,7 +25,6 @@ namespace PHON_NS
         void prepare_restart();
         void calc_anharmonic_imagself();
         void compute_kappa();
-        void finish_kappa();
 
         int calc_kappa_spec;
         unsigned int ntemp;
@@ -35,21 +34,24 @@ namespace PHON_NS
         double *Temperature;
 
     private:
+        void set_default_variables();
+        void deallocate_variables();
+
         double ***vel;
         unsigned int nk, ns;
         int nshift_restart;
         std::vector<int> vks, vks_l, vks_done;
         std::set<int> vks_job;
 
-        void write_result_gamma(const unsigned int,
-                                const unsigned int,
+        void write_result_gamma(unsigned int,
+                                unsigned int,
                                 double ***,
                                 double **);
-        void average_self_energy_at_degenerate_point(const int,
-                                                     const int,
+        void average_self_energy_at_degenerate_point(int,
+                                                     int,
                                                      double **);
-        void compute_frequency_resolved_kappa(const int,
+        void compute_frequency_resolved_kappa(int,
                                               double ****,
-                                              const int);
+                                              int);
     };
 }

anphon/error.h

@@ -10,7 +10,6 @@
 
 #pragma once
 
-#include <string>
 #include "pointers.h"
 
 namespace PHON_NS

anphon/isotope.cpp

@@ -62,7 +62,9 @@ void Isotope::setup_isotope_scattering()
         if (mympi->my_rank == 0) {
             if (!isotope_factor) {
                 memory->allocate(isotope_factor, nkd);
-                set_isotope_factor_from_database(nkd, system->symbol_kd, isotope_factor);
+                set_isotope_factor_from_database(nkd,
+                                                 system->symbol_kd,
+                                                 isotope_factor);
             }
         }
 

anphon/mpi_common.cpp

@@ -9,7 +9,6 @@
 */
 
 #include "mpi_common.h"
-#include <iostream>
 #include <string>
 #include <cstring>
 
@@ -21,9 +20,7 @@ MyMPI::MyMPI(PHON *phon, MPI_Comm comm): Pointers(phon)
     MPI_Comm_size(comm, &nprocs);
 }
 
-MyMPI::~MyMPI()
-{
-}
+MyMPI::~MyMPI() {}
 
 void MyMPI::MPI_Bcast_string(std::string &str, int root, MPI_Comm comm)
 {

anphon/phonons.cpp

@@ -258,12 +258,6 @@ void PHON::execute_RTA()
         writes->write_kappa();
         writes->write_selfenergy_isotope();
     }
-
-    relaxation->finish_relaxation();
-
-    if (!relaxation->ks_analyze_mode) {
-        conductivity->finish_kappa();
-    }
 }
 
 void PHON::execute_self_consistent_phonon()