Updating k-point output and atomic coordinates

I added a line to give the number of k-points even at
Iprint 0, and added a flag IO.AtomCoordsXYZ to allow output
at the start in XYZ format.  I copied periodic_table_module.f90
from the BasisGeneration utility to write out element symbols

src/initial_read_module.f90

@@ -858,7 +858,7 @@ contains
          pdb_output, banner, get_file_name, time_max, &
          flag_MatrixFile_RankFromZero, flag_MatrixFile_BinaryFormat, &
          flag_MatrixFile_BinaryFormat_Grab, flag_MatrixFile_BinaryFormat_Dump, &
-         flag_MatrixFile_BinaryFormat_Dump_END, atom_output_threshold
+         flag_MatrixFile_BinaryFormat_Dump_END, atom_output_threshold, flag_coords_xyz
 
     use group_module,     only: part_method, HILBERT, PYTHON
     use H_matrix_module,  only: locps_output, locps_choice
@@ -1086,6 +1086,7 @@ contains
        InitAtomicDistance_min = fdf_double('IO.InitAtomicDistance_min',  0.5_double)
     end if
     atom_output_threshold = fdf_integer('IO.AtomOutputThreshold',200)
+    flag_coords_xyz = fdf_boolean('IO.AtomCoordsXYZ',.false.)
     call my_barrier()
     !
     !
@@ -2789,6 +2790,7 @@ contains
     real(double), allocatable, dimension(:)   :: wtk_tmp
     integer :: nkp_tmp
     integer :: counter
+    character(len=2) :: suffix
 
     !****lat<$    
     call start_backtrace(t=backtrace_timer,who='readDiagInfo',where=1,level=2)
@@ -2907,7 +2909,11 @@ contains
        flag_lines_kpoints = fdf_boolean('Diag.KspaceLines',.false.)
        if(flag_lines_kpoints) then
           nkp_lines = fdf_integer('Diag.NumKptLines',1)
-          if(iprint_init>1.AND.inode==ionode) write(io_lun,fmt='(8x,"Number of Kpoint lines: ",i4)') nkp_lines
+          if(iprint_init>1.AND.inode==ionode) then
+             write(io_lun,fmt='(8x,"Number of Kpoint lines: ",i4)') nkp_lines
+          else
+             write(io_lun,fmt='(4x,"Using ",i3," lines of k-points specified by user")')
+          end if
           if(nkp_lines<1) call cq_abort("Need to specify how many kpoint lines !",nkp_lines)
           nkp = fdf_integer('Diag.NumKpts',2)
           if(iprint_init>1.AND.inode==ionode) write(io_lun,fmt='(8x,"Number of Kpoints in a line: ",i4)') nkp
@@ -2959,7 +2965,9 @@ contains
        else
           ! Read k-point number and allocate
           nkp = fdf_integer('Diag.NumKpts',1)
-          if(iprint_init>1.AND.inode==ionode) write(io_lun,fmt='(8x,"Number of Kpoints: ",i4)') nkp
+          if(iprint_init>1.AND.inode==ionode) then
+             write(io_lun,fmt='(8x,"Number of Kpoints: ",i4)') nkp
+          end if
           if(nkp<1) call cq_abort("Need to specify how many kpoints !",nkp)
           allocate(kk(3,nkp),wtk(nkp),STAT=stat)
           if(stat/=0) call cq_abort('FindEvals: couldnt allocate kpoints',nkp)
@@ -2967,6 +2975,13 @@ contains
           sum = zero
           ! Read k-points
           if(fdf_block('Diag.Kpoints'))then
+             if(iprint_init==0) then
+                if(nkp==1) then
+                   write(io_lun,fmt='(4x,"Using ",i1," k-point specified by user")') nkp
+                else
+                   write(io_lun,fmt='(4x,"Using ",i3," k-points specified by user")') nkp
+                endif
+             end if
              if(1+block_end-block_start<nkp) &
                   call cq_abort("Kpoint error: ",1+block_end-block_start,nkp)
              do i=1,nkp
@@ -2981,7 +2996,7 @@ contains
              call fdf_endblock
              wtk = wtk/sum
           else ! Force gamma point dependence
-             if(inode==ionode) write(io_lun,4)
+             if(inode==ionode) write(io_lun,fmt='(4x,"Default k-point sampling of Gamma point only")')
              nkp = 1
              kk(1,1) = zero
              kk(2,1) = zero
@@ -3014,6 +3029,14 @@ contains
              write (io_lun,fmt='(/8x,a, i3," x ",i3," x ",i3)') &
                   ' Monkhorst-Pack mesh: ', (mp(i), i=1,3)
           end if
+       else if(inode==ionode) then
+          if(flag_gamma) then
+             suffix = " G"
+          else
+             suffix = "  "
+          end if
+          write (io_lun,fmt='(4x,"Using a MP mesh for k-points: ", i3," x ",i3," x ",i3,a2)') &
+               (mp(i), i=1,3), suffix
        end if
        if (mp(1) <= 0 .OR. mp(2) <= 0 .OR. mp(3) <= 0) &
             call cq_abort('K-points: number of k-points must be > 0!')

src/io_module.f90

@@ -114,6 +114,7 @@ module io_module
   ! Moved here from read_and_write so that it can be used for extended XYZ output
   ! Moved here from initial_read_module to slove the dependence problem
   character(len=80), save :: titles
+  logical          :: flag_coords_xyz
 
 !!***
 
@@ -3098,7 +3099,9 @@ second:   do
     use global_module, only: atom_coord, iprint_MD, ni_in_cell, species_glob
     use dimens,         only: r_super_x, r_super_y, r_super_z
     use GenComms, only: inode, ionode
-    use units, only: dist_conv, d_units, dist_units
+    use units, only: dist_conv, d_units, dist_units, BohrToAng, bohr
+    use periodic_table, only: pte
+    use pseudo_tm_info, only: pseudo
 
     implicit none
 
@@ -3108,11 +3111,27 @@ second:   do
        write(io_lun,fmt='(/4x,"Simulation cell dimensions: ",f10.4,a3," x ",f10.4,a3," x ",f10.4,a3)') &
             r_super_x*dist_conv, d_units(dist_units), r_super_y*dist_conv, d_units(dist_units), &
             r_super_z*dist_conv, d_units(dist_units)
-       write(io_lun,fmt='(/4x,"Atomic coordinates (",a2,")")') d_units(dist_units)
-       write(io_lun,fmt='(4x,"   Atom         X         Y         Z  Species")')
-       do i = 1, ni_in_cell
-          write (io_lun,fmt='(4x, i7, 3f10.4, 6x, i3)') i,atom_coord(1:3,i), species_glob(i)
-       end do
+       if(flag_coords_xyz) then
+          write(io_lun,fmt='(4x,"           X         Y         Z")')
+          if(dist_units==bohr) then
+             write(io_lun,fmt='(/4x,"Atomic coordinates (",a2,")")') "A "
+             do i = 1, ni_in_cell
+                write (io_lun,fmt='(4x, a2, 3f10.4)') pte(pseudo(species_glob(i))%z), atom_coord(1:3,i)*BohrToAng
+             end do
+             write(io_lun,fmt='(6x,"N.B. units above converted to Angstroms for xyz output")')
+          else
+             write(io_lun,fmt='(/4x,"Atomic coordinates (",a2,")")') d_units(dist_units)
+             do i = 1, ni_in_cell
+                write (io_lun,fmt='(4x, a2, 3f10.4)') pte(pseudo(species_glob(i))%z), atom_coord(1:3,i)
+             end do
+          end if
+       else
+          write(io_lun,fmt='(/4x,"Atomic coordinates (",a2,")")') d_units(dist_units)
+          write(io_lun,fmt='(4x,"   Atom         X         Y         Z  Species")')
+          do i = 1, ni_in_cell
+             write (io_lun,fmt='(4x, i7, 3f10.4, 6x, i3)') i,atom_coord(1:3,i), species_glob(i)
+          end do
+       end if
     end if
     return
     

src/odd.obj

@@ -15,4 +15,5 @@ ODD_OBJS = global_module.o \
            rng_module.o \
            biblio_module.o \
            references.o \
+           periodic_table_module.o \
            fft_module.o $(FFT_OBJ)

src/periodic_table_module.f90

@@ -0,0 +1,40 @@
+module periodic_table
+
+  use datatypes
+
+  implicit none
+  
+  integer, parameter  :: n_species=94
+
+  real(double), parameter ::  atomic_mass(n_species) = (/ &
+       1.01_double,    4.00_double,  6.94_double,  9.01_double, 10.81_double, 12.01_double, &
+       14.01_double,  16.00_double, 19.00_double, 20.18_double, 22.99_double, 24.31_double, &
+       26.98_double,  28.09_double, 30.97_double, 32.07_double, 35.45_double, 39.95_double, &
+       39.10_double,  40.08_double, 44.96_double, 47.88_double, 50.94_double, 52.00_double, &
+       54.94_double,  55.85_double, 58.93_double, 58.69_double, 63.55_double, 65.39_double, &
+       69.72_double,  72.61_double, 74.92_double, 78.96_double, 79.90_double, 83.80_double, & 
+       85.47_double,  87.62_double, 88.91_double, 91.22_double, 92.91_double, 95.94_double, & 
+       98.91_double, 101.07_double,102.91_double,106.42_double,107.87_double,112.41_double, &
+       114.82_double,118.71_double,121.75_double,127.60_double,126.90_double,131.29_double, &
+       132.91_double,137.33_double,138.91_double,140.12_double,140.91_double,144.24_double, &
+       146.92_double,150.36_double,151.97_double,157.25_double,158.93_double,162.50_double, &
+       164.93_double,167.26_double,168.93_double,173.04_double,174.97_double,178.49_double, &
+       180.95_double,183.85_double,186.21_double,190.20_double,192.22_double,195.08_double, &
+       196.97_double,200.59_double,204.38_double,207.20_double,208.98_double,208.98_double, &
+       209.99_double,222.02_double,223.02_double,226.03_double,227.03_double,232.04_double, &
+       231.04_double,238.03_double,237.05_double,244.06_double/)
+  
+  character(len=2), dimension(103) :: pte = &
+       (/  "H ", "He", "Li", "Be", "B ", "C ", "N ", "O ", "F ", "Ne", &
+         "Na", "Mg", "Al", "Si", "P ", "S ", "Cl", "Ar", "K ", "Ca", &
+         "Sc", "Ti", "V ", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", &
+         "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y ", "Zr", &
+         "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", &
+         "Sb", "Te", "I ", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", &
+         "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", &
+         "Lu", "Hf", "Ta", "W ", "Re", "Os", "Ir", "Pt", "Au", "Hg", &
+         "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", &
+         "Pa", "U ", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", &
+         "Md", "No", "Lr"/)
+
+end module periodic_table