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Merged
AugustinLu merged 3 commits into from
Aug 17, 2026
Merged

Fix issue 465 #469

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6874edb
Modified cell volume print format.
AugustinLu Aug 7, 2026
77c4148
Fix atomic coordinate unit conversion in output.
AugustinLu Aug 13, 2026
0f06fa5
Removed flag_coords_xyz and related keyword IO.AtomCoordsXYZ.
AugustinLu Aug 13, 2026
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10 changes: 8 additions & 2 deletions src/control.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -2243,6 +2243,8 @@ end subroutine sqnm
!! MODIFICATION HISTORY
!! 2022/08/17 15:18 dave
!! Introduced scaling to improve conditioning in arxiv/2206.07339
!! 2026/08/13 Augustin Lu
!! Set a wider format and user-selected units for simulation cell volume output.
!! SOURCE
!!
subroutine cell_sqnm(fixed_potential, vary_mu, total_energy)
Expand Down Expand Up @@ -2582,7 +2584,8 @@ subroutine cell_sqnm(fixed_potential, vary_mu, total_energy)
iter, max_stress*volume, enthalpy1, en_conv*dH
if (iprint_MD > 1) then
write(io_lun,'(4x,"Maximum stress ",e14.6," Ha/Bohr**3")') max_stress
write(io_lun,'(4x,"Simulation cell volume ",e14.6," Bohr**3")') volume
write(io_lun,'(4x,"Simulation cell volume ",f18.6,1x,a2,a3)') &
volume * dist_conv**3, d_units(dist_units), '**3'
write(io_lun,'(4x,"Maximum stress ",f14.6," GPa")') &
max_stress*HaBohr3ToGPa
write(io_lun,'(4x,"Stress tolerance: ",f14.6," GPa")') &
Expand Down Expand Up @@ -3764,6 +3767,8 @@ end subroutine full_double_loop
! alternating full ionic and full cell optimisation (full_cg_run_double_loop)
! and full ionic with single line minimisation cell optimisation (this routine)
! Use cell optimisation method 4 for this
! 2026/08/13 Augustin Lu
! Set a wider format and user-selected units for simulation cell volume output.
subroutine full_cg_run_double_loop_alt(fixed_potential, vary_mu, total_energy)

! Module usage
Expand Down Expand Up @@ -4059,7 +4064,8 @@ subroutine full_cg_run_double_loop_alt(fixed_potential, vary_mu, total_energy)
write(io_lun,'(4x,"Force tolerance: ",f19.8)') MDcgtol
write(io_lun,'(4x,"Maximum stress ",e14.6," Ha/Bohr**3")') &
max_stress
write(io_lun,'(4x,"Simulation cell volume ",e14.6," Bohr**3")') volume
write(io_lun,'(4x,"Simulation cell volume ",f18.6,1x,a2,a3)') &
volume * dist_conv**3, d_units(dist_units), '**3'
write(io_lun,'(4x,"Maximum stress ",f14.6," GPa")') &
max_stress*HaBohr3ToGPa
write(io_lun,'(4x,"Stress tolerance: ",f14.6," GPa")') &
Expand Down
5 changes: 3 additions & 2 deletions src/initial_read_module.f90
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Expand Up @@ -874,6 +874,8 @@ end subroutine read_and_write
!! Set flag_out_wf = .true. expricitly when flag_write_projected_DOS is .true.
!! 2026/07/03 09:47 dave
!! Turn off WF and/or pDOS output except for static, diagonalisation runs
!! 2026/08/13 Augustin Lu
!! Remove the obsolete IO.AtomCoordsXYZ input option.
!! TODO
!! SOURCE
!!
Expand Down Expand Up @@ -995,7 +997,7 @@ subroutine read_input(start, start_L, titles, vary_mu,&
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_coords_xyz
flag_MatrixFile_BinaryFormat_Dump_END, atom_output_threshold

use group_module, only: part_method, HILBERT, PYTHON
use H_matrix_module, only: flag_write_locps, flag_dump_locps, &
Expand Down Expand Up @@ -1253,7 +1255,6 @@ subroutine read_input(start, start_L, titles, vary_mu,&
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()
!
!
Expand Down
55 changes: 22 additions & 33 deletions src/io_module.f90
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Expand Up @@ -78,6 +78,8 @@
!! they don't exist
!! 2019/11/04 11:36 dave
!! Removed redundant code (old SFC routines)
!! 2026/08/13 Augstin Lu
!! Removed unused flag_coords_xyz
module io_module

use datatypes, only: double
Expand Down Expand Up @@ -114,7 +116,6 @@ 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

!!***

Expand Down Expand Up @@ -3271,50 +3272,38 @@ end subroutine print_process_info
!! CREATION DATE
!! 2020/03/11
!! MODIFICATION HISTORY
!! 2026/08/13 Augustin Lu
!! Set a wider format and user-selected units for cell output
!! Convert printed atomic coordinates to the selected distance units
!! Remove the obsolete IO.AtomCoordsXYZ output mode.
!!
!! SOURCE
!!
subroutine print_atomic_positions

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, atomicnum, volume
use global_module, only: atom_coord, ni_in_cell, species_glob
use dimens, only: r_super_x, r_super_y, r_super_z, volume
use GenComms, only: inode, ionode
use units, only: dist_conv, d_units, dist_units, BohrToAng, bohr
use periodic_table, only: pte
use pseudo_tm_info, only: pseudo
use units, only: dist_conv, d_units, dist_units

implicit none

integer :: i

if(inode==ionode) then
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,"Simulation cell volume: ",f10.4,a3,a3)') &
volume*dist_conv*dist_conv*dist_conv, d_units(dist_units),'**3'
if(flag_coords_xyz) then
write(io_lun,fmt='(6x," X Y Z")')
if(dist_units==bohr) then
write(io_lun,fmt='(/6x,"Atomic coordinates in XYZ format (",a2,")")') "A "
do i = 1, ni_in_cell
write (io_lun,fmt='(4x, a2, 3f10.4)') pte(atomicnum(species_glob(i))), atom_coord(1:3,i)*BohrToAng
end do
write(io_lun,fmt='(8x,"N.B. units above converted to Angstroms for xyz output")')
else
write(io_lun,fmt='(/6x,"Atomic coordinates (",a2,")")') d_units(dist_units)
do i = 1, ni_in_cell
write (io_lun,fmt='(4x, a2, 3f10.4)') pte(atomicnum(species_glob(i))), atom_coord(1:3,i)
end do
end if
else
write(io_lun,fmt='(/6x,"Atomic coordinates (",a2,")")') d_units(dist_units)
write(io_lun,fmt='(6x," Atom X Y Z Species")')
do i = 1, ni_in_cell
write (io_lun,fmt='(6x, i7, 3f10.4, 6x, i3)') i,atom_coord(1:3,i), species_glob(i)
end do
end if
if(inode==ionode) then
write(io_lun,fmt='(/4x,"Simulation cell dimensions: ",f18.4,1x,a2," x ",f18.4,1x,a2," x ",f18.4,1x,a2)') &
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,"Simulation cell volume: ",f18.6,1x,a2,a3)') &
volume * dist_conv * dist_conv * dist_conv, d_units(dist_units),'**3'
write(io_lun,fmt='(/6x,"Atomic coordinates (",a2,")")') d_units(dist_units)
write(io_lun,fmt='(6x," Atom X Y Z Species")')
do i = 1, ni_in_cell
write (io_lun,fmt='(6x, i7, 3f10.4, 6x, i3)') i, atom_coord(1:3,i) * dist_conv, &
species_glob(i)
end do
end if

return

end subroutine print_atomic_positions
Expand Down
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