Merge branch 'develop' of github.com:ttadano/alamode into develop

alm/alamode.cpp

@@ -33,12 +33,12 @@ using namespace ALM_NS;
 
 ALM::ALM(int narg, char **arg)
 {
-    std::cout << " +------------------------------------------------------------+" << std::endl;
-    std::cout << " +                      Program ALM                           +" << std::endl;
-    std::cout << " +                           Ver.";
+    std::cout << " +-----------------------------------------------------------------+" << std::endl;
+    std::cout << " +                         Program ALM                             +" << std::endl;
+    std::cout << " +                             Ver.";
     std::cout << std::setw(7) << ALAMODE_VERSION;
-    std::cout << "                      +" << std::endl;
-    std::cout << " +------------------------------------------------------------+" << std::endl;
+    std::cout << "                         +" << std::endl;
+    std::cout << " +-----------------------------------------------------------------+" << std::endl;
     std::cout << std::endl;
 
     timer = new Timer(this);

alm/constraint.cpp

@@ -65,22 +65,23 @@ void Constraint::setup()
     case 1:
         impose_inv_T = true;
         impose_inv_R = false;
-        std::cout << "  ICONST = 1: Constraints for translational invariance will be considered." << std::endl;
+        std::cout << "  ICONST = 1: Constraints for translational invariance" << std::endl;
+        std::cout << "              will be considered." << std::endl;
         break;
     case 2:
         impose_inv_T = true;
         impose_inv_R = true;
         exclude_last_R = true;
-        std::cout << "  ICONST = 2: Constraints for translational and rotational invariance will be considered." << std::endl;
-        std::cout << "              Axis of rotation is " << rotation_axis << std::endl;
+        std::cout << "  ICONST = 2: Constraints for translational and rotational invariance" << std::endl;
+        std::cout << "              will be considered. Axis of rotation is " << rotation_axis << std::endl;
         std::cout << "              Rotational invariance of the maximum order will be neglected" << std::endl;
         break;
     case 3:
         impose_inv_T = true;
         impose_inv_R = true;
         exclude_last_R = false;
-        std::cout << "  ICONST = 3: Constraints for translational and rotational invariance will be considered." << std::endl;
-        std::cout << "              Axis of rotation is " << rotation_axis << std::endl;
+        std::cout << "  ICONST = 3: Constraints for translational and rotational invariance" << std::endl;
+        std::cout << "              will be considered. Axis of rotation is " << rotation_axis << std::endl;
         break;
     default:
         error->exit("Constraint::setup", "invalid constraint_mode", constraint_mode);
@@ -277,7 +278,7 @@ void Constraint::setup()
         memory->deallocate(const_self);
 
         timer->print_elapsed();
-        std::cout << " --------------------------------------------------------------" << std::endl;
+        std::cout << " -------------------------------------------------------------------" << std::endl;
         std::cout << std::endl;
     }
 }

alm/fcs.cpp

@@ -75,7 +75,7 @@ void Fcs::init()
     memory->deallocate(nints);
     memory->deallocate(nzero);
     timer->print_elapsed();
-    std::cout << " --------------------------------------------------------------" << std::endl;
+    std::cout << " -------------------------------------------------------------------" << std::endl;
     std::cout << std::endl;
 }
 

alm/fitting.cpp

@@ -217,7 +217,7 @@ void Fitting::fitmain()
 
     std::cout << std::endl;
     timer->print_elapsed();
-    std::cout << " --------------------------------------------------------------" << std::endl;
+    std::cout << " -------------------------------------------------------------------" << std::endl;
     std::cout << std::endl;
 }
 
@@ -307,8 +307,8 @@ void Fitting::data_multiplier(const int nat,
 
     } else if (multiply_data == 1) {
 
-        std::cout << "  MULTDAT = 1: Generate symmetrically equivalent displacement-force data sets " << std::endl;
-        std::cout << "               by using pure translational operations only." << std::endl << std::endl;
+        std::cout << "  MULTDAT = 1: Generate symmetrically equivalent displacement-force " << std::endl;
+        std::cout << "               data sets by using pure translational operations only." << std::endl << std::endl;
 
         nmulti = symmetry->ntran;
 
@@ -338,8 +338,8 @@ void Fitting::data_multiplier(const int nat,
 
         double u_rot[3], f_rot[3];
 
-        std::cout << "  MULTDAT = 2: Generate symmetrically equivalent displacement-force data sets." << std::endl;
-        std::cout << "               (including rotational part) " << std::endl << std::endl;
+        std::cout << "  MULTDAT = 2: Generate symmetrically equivalent displacement-force" << std::endl;
+        std::cout << "                data sets. (including rotational part) " << std::endl << std::endl;
 
         nmulti = symmetry->nsym;
 

alm/interaction.cpp

@@ -93,7 +93,7 @@ void Interaction::init()
     generate_pairs(pairs, mindist_cluster);
 
     timer->print_elapsed();
-    std::cout << " --------------------------------------------------------------" << std::endl;
+    std::cout << " -------------------------------------------------------------------" << std::endl;
     std::cout << std::endl;
 }
 

alm/symmetry.cpp

@@ -83,7 +83,8 @@ void Symmetry::init()
     symop_availability_check(symrel, sym_available, nsym, nsym_fc);
 
     if (nsym_fc == nsym) {
-        std::cout << "  All symmetry operations will be used to reduce the number of force constants." << std::endl;
+        std::cout << "  All symmetry operations will be used to" << std::endl;
+        std::cout << "  reduce the number of force constants." << std::endl;
     } else {
         std::cout << "  " << nsym_fc << " symmetry operations out of "
             << nsym << " will be used to reduce the number of parameters." << std::endl;
@@ -117,7 +118,7 @@ void Symmetry::init()
     std::cout << std::endl;
 
     timer->print_elapsed();
-    std::cout << " --------------------------------------------------------------" << std::endl;
+    std::cout << " -------------------------------------------------------------------" << std::endl;
     std::cout << std::endl;
 }
 

alm/system.cpp

@@ -150,7 +150,7 @@ void System::init()
     }
 
     timer->print_elapsed();
-    cout << " --------------------------------------------------------------" << endl;
+    cout << " -------------------------------------------------------------------" << endl;
     cout << endl;
 }
 

alm/writes.cpp

@@ -39,8 +39,8 @@ void Writes::write_input_vars()
     unsigned int i;
 
     std::cout << std::endl;
-    std::cout << " Input variables below:" << std::endl;
-    std::cout << " --------------------------------------------------------------" << std::endl;
+    std::cout << " Input variables:" << std::endl;
+    std::cout << " -------------------------------------------------------------------" << std::endl;
     std::cout << " General:" << std::endl;
     std::cout << "  PREFIX = " << files->job_title << std::endl;
     std::cout << "  MODE = " << alm->mode << std::endl;
@@ -85,15 +85,17 @@ void Writes::write_input_vars()
         std::cout << "  FC3XML = " << constraint->fc3_file << std::endl;
         std::cout << std::endl;
     }
-    std::cout << " --------------------------------------------------------------" << std::endl;
+    std::cout << " -------------------------------------------------------------------" << std::endl;
     std::cout << std::endl;
 }
 
 void Writes::writeall()
 {
+    std::cout << " The following files are created:" << std::endl << std::endl;
     write_force_constants();
     write_misc_xml();
     if (print_hessian) write_hessian();
+    std::cout << std::endl;
 }
 
 void Writes::write_force_constants()
@@ -262,7 +264,7 @@ void Writes::write_force_constants()
     memory->deallocate(str_fcs);
     ofs_fcs.close();
 
-    std::cout << std::endl << " Force constants are written to file: "
+    std::cout << " Force constants in a human-readable format : "
         << files->file_fcs << std::endl;
 }
 
@@ -591,7 +593,7 @@ void Writes::write_misc_xml()
 
     memory->deallocate(pair_tmp);
 
-    std::cout << " Information for post-process is stored to file: " << file_xml << std::endl;
+    std::cout << " Input data for the phonon code ANPHON      : " << file_xml << std::endl;
 }
 
 void Writes::write_hessian()
@@ -629,7 +631,7 @@ void Writes::write_hessian()
     ofs_hes.open(files->file_hes.c_str(), std::ios::out);
     if (!ofs_hes) error->exit("write_hessian", "cannot create hessian file");
 
-    ofs_hes << "# iat, icrd, jat, jcrd, FC2 (Ryd/Bohr^2)" << std::endl;
+    ofs_hes << "# atom1, xyz1, atom2, xyz2, FC2 (Ryd/Bohr^2)" << std::endl;
     for (i = 0; i < nat3; ++i) {
         for (j = 0; j < nat3; ++j) {
             ofs_hes << std::setw(5) << i / 3 + 1;
@@ -644,7 +646,7 @@ void Writes::write_hessian()
     ofs_hes.close();
     memory->deallocate(hessian);
 
-    std::cout << " Hessian is written to file: " << files->file_hes << std::endl;
+    std::cout << " Complete Hessian matrix                    : " << files->file_hes << std::endl;
 }
 
 std::string Writes::double2string(const double d, const int nprec)

anphon/conductivity.cpp

@@ -522,6 +522,7 @@ void Conductivity::compute_frequency_resolved_kappa(const int ntemp,
     int *kmap_identity;
     double **eval;
 
+    std::cout << std::endl;
     std::cout << " KAPPA_SPEC = 1 : Calculating thermal conductivity spectra ... ";
 
     memory->allocate(kappa_spec, dos->n_energy, ntemp, 3);

anphon/dynamical.cpp

@@ -115,7 +115,8 @@ void Dynamical::setup_dynamical(std::string mode)
 
     if (mympi->my_rank == 0) {
         std::cout << std::endl;
-        std::cout << " ------------------------------------------------------------" << std::endl << std::endl;
+        std::cout << " -----------------------------------------------------------------" 
+            << std::endl << std::endl;
     }
 }
 
@@ -788,16 +789,12 @@ double Dynamical::fold(double x)
 
 double Dynamical::freq(const double x)
 {
-    if (std::abs(x) < eps) {
-        // Special treatment to avoid the divergence of computation.
-        return eps15;
-    } else {
-        if (x > 0.0) {
-            return std::sqrt(x);
-        } else {
-            return -std::sqrt(-x);
-        }
-    }
+    // Special treatment to avoid the divergence of computation.
+    if (std::abs(x) < eps)  return eps15;
+
+    if (x > 0.0) return std::sqrt(x);
+
+    return -std::sqrt(-x);
 }
 
 

anphon/phonons.cpp

@@ -47,12 +47,12 @@ PHON::PHON(int narg, char **arg, MPI_Comm comm)
     create_pointers();
 
     if (mympi->my_rank == 0) {
-        std::cout << " +------------------------------------------------------------+" << std::endl;
-        std::cout << " +                      Program ANPHON                        +" << std::endl;
-        std::cout << " +                           Ver.";
+        std::cout << " +-----------------------------------------------------------------+" << std::endl;
+        std::cout << " +                         Program ANPHON                          +" << std::endl;
+        std::cout << " +                             Ver.";
         std::cout << std::setw(7) << ALAMODE_VERSION;
-        std::cout << "                      +" << std::endl;
-        std::cout << " +------------------------------------------------------------+" << std::endl;
+        std::cout << "                         +" << std::endl;
+        std::cout << " +-----------------------------------------------------------------+" << std::endl;
 
         std::cout << std::endl;
         std::cout << " Job started at " << timer->DateAndTime() << std::endl;

anphon/relaxation.cpp

@@ -56,7 +56,7 @@ void Relaxation::setup_relaxation()
 
     if (mympi->my_rank == 0) {
         std::cout << std::endl;
-        std::cout << " ------------------------------------------------------------" << std::endl << std::endl;
+        std::cout << " -----------------------------------------------------------------" << std::endl << std::endl;
         std::cout << " Now, move on to phonon lifetime calculations." << std::endl;
     }
 

anphon/system.cpp

@@ -78,7 +78,7 @@ void System::setup()
     }
 
     if (mympi->my_rank == 0) {
-        cout << " ------------------------------------------------------------" << endl;
+        cout << " -----------------------------------------------------------------" << endl;
         cout << endl;
         cout << " Crystal structure" << endl;
         cout << " =================" << endl << endl;

anphon/write_phonons.cpp

@@ -49,8 +49,8 @@ void Writes::write_input_vars()
     unsigned int i;
 
     std::cout << std::endl;
-    std::cout << " Input variables :" << std::endl;
-    std::cout << " ------------------------------------------------------------" << std::endl;
+    std::cout << " Input variables:" << std::endl;
+    std::cout << " -----------------------------------------------------------------" << std::endl;
     std::cout << " General:" << std::endl;
     std::cout << "  PREFIX = " << input->job_title << std::endl;
     std::cout << "  MODE = " << phon->mode << std::endl;
@@ -150,7 +150,7 @@ void Writes::write_input_vars()
             std::cout << "  ISOFACT = ";
             for (i = 0; i < system->nkd; ++i) {
                 std::cout << std::scientific
-                    << std::setw(12) << isotope->isotope_factor[i];
+                    << std::setw(13) << isotope->isotope_factor[i];
             }
             std::cout << std::endl;
         }
@@ -169,7 +169,7 @@ void Writes::write_input_vars()
     }
 
     std::cout << std::endl << std::endl;
-    std::cout << " ------------------------------------------------------------" << std::endl;
+    std::cout << " -----------------------------------------------------------------" << std::endl;
     std::cout << std::endl;
 }
 
@@ -365,7 +365,7 @@ void Writes::print_phonon_energy()
     double kayser_to_THz = 0.0299792458;
 
     std::cout << std::endl;
-    std::cout << " ------------------------------------------------------------" << std::endl << std::endl;
+    std::cout << " -----------------------------------------------------------------" << std::endl << std::endl;
     std::cout << " Phonon frequencies below:" << std::endl << std::endl;
 
     if (kpoint->kpoint_mode == 0 || kpoint->kpoint_mode == 1) {
@@ -440,7 +440,7 @@ void Writes::write_phonon_info()
     }
 
     std::cout << std::endl;
-    std::cout << " ------------------------------------------------------------" << std::endl << std::endl;
+    std::cout << " -----------------------------------------------------------------" << std::endl << std::endl;
     std::cout << " The following files are created: " << std::endl;
 
 
@@ -1226,7 +1226,7 @@ void Writes::write_kappa()
         }
 
         std::cout << std::endl;
-        std::cout << " ------------------------------------------------------------" << std::endl << std::endl;
+        std::cout << " -----------------------------------------------------------------" << std::endl << std::endl;
         std::cout << " Lattice thermal conductivity is stored in the file " << file_kappa << std::endl;
         if (conductivity->calc_kappa_spec) {
             std::cout << " Thermal conductivity spectra is stored in the file " << file_kappa2 << std::endl;
@@ -1320,7 +1320,7 @@ void Writes::write_normal_mode_animation(const double xk_in[3],
     for (i = 0; i < 3; ++i) {
         xk[i] = xk_in[i];
     }
-    std::cout << " ------------------------------------------------------------" << std::endl << std::endl;
+    std::cout << " -----------------------------------------------------------------" << std::endl << std::endl;
     std::cout << " ANIME-tag is given: Making animation files for the given" << std::endl;
     std::cout << "                     k point ( ";
     std::cout << std::setw(5) << xk[0] << ", "