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1220 lines
46 KiB
1220 lines
46 KiB
module io
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use elements
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use parameters
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use atoms
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use box
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use str
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implicit none
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integer :: outfilenum = 0, infilenum = 0
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character(len=100) :: outfiles(100), infiles(100), in_lattice_type=''
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logical :: force_overwrite
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real(kind=dp) :: in_lapa=0.0
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public
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contains
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Subroutines for writing out data files !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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subroutine get_out_file(filename)
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implicit none
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character(len=100), intent(in) :: filename
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character(len=100) :: temp_outfile
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character(len=1) :: overwrite
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logical :: file_exists
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!If no filename is provided then this function is called with none and prompts user input
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if (filename=='none') then
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print *, "Please specify a filename or extension to output to:"
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read(*,*) temp_outfile
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else
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temp_outfile = filename
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end if
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!Infinite loop which only exists if user provides valid filetype
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overwrite = 'r'
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do while(.true.)
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!Check to see if file exists, if it does then ask user if they would like to overwrite the file
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inquire(file=trim(temp_outfile), exist=file_exists)
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if (file_exists.and.(.not.(force_overwrite))) then
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if (overwrite == 'r') print *, "File ", trim(temp_outfile), " already exists. Would you like to overwrite? (Y/N)"
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read(*,*) overwrite
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if((scan(overwrite, "n") > 0).or.(scan(overwrite, "N") > 0)) then
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print *, "Please specify a new filename with extension:"
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read(*,*) temp_outfile
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else if((scan(overwrite, "y") > 0).or.(scan(overwrite, "Y") > 0)) then
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continue
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else
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print *, "Please pick either y or n"
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read(*,*) overwrite
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end if
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end if
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if (scan(temp_outfile,'.',.true.) == 0) then
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print *, "No extension included on filename, please type a full filename that includes an extension."
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read(*,*) temp_outfile
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cycle
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end if
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select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
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case('xyz', 'lmp', 'vtk', 'mb', 'restart', 'dump')
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outfilenum=outfilenum+1
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outfiles(outfilenum) = temp_outfile
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exit
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case('cac')
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lmpcac = .true.
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outfilenum=outfilenum+1
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outfiles(outfilenum) = temp_outfile
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exit
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case default
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print *, "File type: ", trim(temp_outfile(scan(temp_outfile,'.',.true.):)), " not currently accepted. ", &
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"please input a filename with extension from following list: xyz, lmp, vtk, cac."
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read(*,*) temp_outfile
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end select
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end do
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end subroutine get_out_file
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subroutine write_out
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!This subroutine loops over alll of the outfile types defined and calls the correct writing subroutine
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integer :: i
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!Find max esize which will be needed later
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call set_max_esize
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do i = 1, outfilenum
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print *, "Writing data out to ", trim(adjustl(outfiles(i)))
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!Pull out the extension of the file and call the correct write subroutine
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select case(trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))))
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case('xyz')
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call write_xyz(outfiles(i))
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case('lmp')
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call write_lmp(outfiles(i))
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case('vtk')
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call write_vtk(outfiles(i))
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case('mb')
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call write_mb(outfiles(i))
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case('restart')
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call write_pycac(outfiles(i))
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case('cac')
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call write_lmpcac(outfiles(i))
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case('dump')
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call write_ldump(outfiles(i))
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case default
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print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
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" is not accepted for writing. Please select from: xyz, lmp, vtk, mb, restart, cac and try again"
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stop
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end select
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end do
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end subroutine write_out
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subroutine write_xyz(file)
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!This is the simplest visualization subroutine, it writes out all nodal positions and atom positions to an xyz file
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character(len=100), intent(in) :: file
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integer :: i, inod, ibasis, outn
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open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
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!Write total number of atoms + elements
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write(11, '(i16)') node_atoms+atom_num
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!Write comment line
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write(11, '(a)') "#Node + atom file created using cacmb"
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outn=0
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!Write nodal positions
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do i = 1, ele_num
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do inod = 1, ng_node(lat_ele(i))
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do ibasis = 1, basisnum(lat_ele(i))
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write(11, '(2i16, 3f23.15)') basis_type(ibasis,lat_ele(i)), 1, r_node(:,ibasis,inod,i)
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outn = outn + 1
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end do
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end do
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end do
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if(outn /= node_atoms) then
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print *, "outn", outn, " doesn't equal node_atoms ", node_atoms
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end if
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!Write atom positions
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do i = 1, atom_num
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write(11, '(2i16, 3f23.15)') type_atom(i), 0, r_atom(:,i)
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outn = outn + 1
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end do
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if((outn-node_atoms) /= atom_num) then
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print *, "outn", (outn-node_atoms), " doesn't equal atom_num ", atom_num
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end if
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!Finish writing
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close(11)
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end subroutine write_xyz
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subroutine write_lmp(file)
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!This subroutine writes out a .lmp style dump file
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character(len=100), intent(in) :: file
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integer :: write_num, i, iatom, type_interp(max_basisnum*max_esize**3), interp_num
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real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), mass
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open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
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!Comment line
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write(11, '(a)') '# lmp file made with cacmb'
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write(11, '(a)')
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!Calculate total atom number
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write_num = atom_num
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do i = 1,ele_num
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if(type_ele(i) == 'fcc') write_num = write_num + size_ele(i)**3
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if(type_ele(i) == 'bcc') write_num = write_num + size_ele(i)**3
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end do
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!Write total number of atoms + elements
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write(11, '(i16, a)') write_num, ' atoms'
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!Write number of atom types
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write(11, '(i16, a)') atom_types, ' atom types'
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write(11,'(a)') ' '
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!Write box bd
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write(11, '(2f23.15, a)') box_bd(1:2), ' xlo xhi'
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write(11, '(2f23.15, a)') box_bd(3:4), ' ylo yhi'
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write(11, '(2f23.15, a)') box_bd(5:6), ' zlo zhi'
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!Masses
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write(11, '(a)') 'Masses'
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write(11, '(a)') ' '
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do i =1, atom_types
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call atommass(type_to_name(i),mass)
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write(11, '(i16, f23.15)') i, mass
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end do
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write(11, '(a)') ' '
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!Write atom positions
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write(11, '(a)') 'Atoms'
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write(11, '(a)') ' '
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do i = 1, atom_num
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write(11, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i)
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end do
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!Write refined element atomic positions
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interp_num = 0
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do i = 1, ele_num
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call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
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select case(trim(adjustl(type_ele(i))))
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case('fcc','bcc')
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do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
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interp_num = interp_num+1
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call apply_periodic(r_interp(:,iatom))
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write(11, '(2i16, 3f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom)
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end do
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end select
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end do
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end subroutine write_lmp
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subroutine write_ldump(file)
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!This subroutine will only work if element data is defined
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character(len = *), intent(in) :: file
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integer :: write_num, i, iatom
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logical :: write_dat
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integer :: type_interp(max_basisnum*max_esize**3), interp_num
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real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), data_interp(10, max_basisnum*max_esize**3)
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1 format('ITEM: TIMESTEP'/i16)
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2 format('ITEM: NUMBER OF ATOMS' /i16)
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3 format('ITEM: BOX BOUNDS ', 2a1, ' ', 2a1, ' ', 2a1 / &
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2f23.15 / 2f23.15 / 2f23.15)
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4 format('ITEM: ATOMS id type x y z energy fx fy fz s11 s22 s33 s23 s13 s12')
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5 format('ITEM: ATOMS id type x y z')
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open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
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!Write header information
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write(11,1) timestep
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!Calculate total atom number
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write_num = atom_num
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do i = 1,ele_num
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if(type_ele(i) == 'fcc') write_num = write_num + size_ele(i)**3
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if(type_ele(i) == 'bcc') write_num = write_num + size_ele(i)**3
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end do
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!Write total number of atoms
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write(11,2) write_num
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!Write box information
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write(11,3) box_bc(1:1), box_bc(1:1), box_bc(2:2), box_bc(2:2), box_bc(3:3), box_bc(3:3), box_bd(:)
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!Now pick if we are interpolating data or not
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if(allocated(force_node).or.allocated(force_atom)) then
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write(11, 4)
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write_dat = .true.
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else
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write(11, 5)
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write_dat = .false.
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end if
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if (write_dat) then
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do i = 1, atom_num
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write(11, '(2i16, 13f23.15)') i, type_atom(i), r_atom(:,i), energy_atom(i), force_atom(:,i), virial_atom(:,i)
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end do
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else
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do i = 1, atom_num
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write(11, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i)
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end do
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end if
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!Write refined element atomic positions
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interp_num = 0
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do i = 1, ele_num
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if(write_dat) then
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call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp, &
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energy_node(:,:,i), force_node(:,:,:,i), virial_node(:,:,:,i), data_interp)
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else
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call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
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end if
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select case(trim(adjustl(type_ele(i))))
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case('fcc','bcc')
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if(write_dat) then
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do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
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interp_num = interp_num+1
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call apply_periodic(r_interp(:,iatom))
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write(11, '(2i16, 13f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom), &
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data_interp(:,iatom)
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end do
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else
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do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
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interp_num = interp_num+1
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call apply_periodic(r_interp(:,iatom))
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write(11, '(2i16, 3f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom)
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end do
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end if
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end select
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end do
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end subroutine write_ldump
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subroutine write_lmpcac(file)
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!This subroutine writes out a .lmp style dump file
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character(len=100), intent(in) :: file
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integer :: write_num, i, inod, ibasis
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real(kind=dp) :: mass, fcc_adjust(3,8), local_adjust(3,8), rout(3)
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1 format(i16, ' Eight_Node', 4i16)
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2 format(i16, ' Atom', 4i16)
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3 format(3i16,3f23.15)
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open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
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!Comment line
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write(11, '(a)') '# CAC input file made with cacmb'
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write(11, '(a)')
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!Calculate total atom number
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write_num = atom_num + ele_num
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!Write total number of atoms + elements
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write(11, '(i16, a)') write_num, ' cac elements'
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!Write number of atom types
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write(11, '(i16, a)') atom_types, ' atom types'
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write(11,'(a)') ' '
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!Write box bd
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write(11, '(2f23.15, a)') box_bd(1:2), ' xlo xhi'
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write(11, '(2f23.15, a)') box_bd(3:4), ' ylo yhi'
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write(11, '(2f23.15, a)') box_bd(5:6), ' zlo zhi'
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!Masses
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write(11, '(a)') 'Masses'
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write(11, '(a)') ' '
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do i =1, atom_types
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call atommass(type_to_name(i),mass)
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write(11, '(i16, f23.15, 2a)') i, mass, ' # ', type_to_name(i)
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end do
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write(11, '(a)') ' '
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write(11, '(a)') 'CAC Elements'
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write(11, '(a)') ' '
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!Set up the nodal adjustment variables for all the different element types. This adjusts the node centers
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!from the center of the unit cell (as formulated in this code) to the corners of the unit cells
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do inod = 1, 8
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do i = 1,3
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if(is_equal(cubic_cell(i, inod),0.0_dp)) then
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fcc_adjust(i,inod) = -0.5_dp
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else
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fcc_adjust(i, inod) = 0.5_dp
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end if
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end do
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end do
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fcc_adjust = matmul(fcc_mat, fcc_adjust)
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!Write element nodal positions
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do i = 1, ele_num
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select case(trim(adjustl(type_ele(i))))
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case('fcc')
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!Now orient the current adjustment vector to the correct orientation
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local_adjust = matmul(sub_box_ori(:,:,sbox_ele(i)), fcc_adjust) * lapa(lat_ele(i))
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!The first entry is the element specifier
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write(11,1) i, basisnum(lat_ele(i)), size_ele(i), size_ele(i), size_ele(i)
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do ibasis = 1, basisnum(lat_ele(i))
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do inod = 1, 8
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!Nodal information for every node
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rout = r_node(:,ibasis,inod,i) + local_adjust(:,inod)
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write(11,3) inod, ibasis, basis_type(ibasis,lat_ele(i)), rout
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end do
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end do
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end select
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end do
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do i = 1, atom_num
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!Element specifier dictating that it is an atom
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write(11,2) ele_num+i, 1, 1, 1, 1
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!Write the atomic information
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write(11,3) 1, 1, type_atom(i), r_atom(:,i)
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end do
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end subroutine write_lmpcac
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subroutine write_vtk(file)
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!This subroutine writes out a vtk style dump file
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integer :: i, j, inod, ibasis
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character(len=100), intent(in) :: file
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1 format('# vtk DataFile Version 4.0.1', / &
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'CAC output -- cg', / &
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'ASCII')
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11 format('# vtk DataFile Version 4.0.1', / &
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'CACmb output -- atoms', / &
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'ASCII')
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2 format('DATASET UNSTRUCTURED_GRID')
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3 format('POINTS', i16, ' float')
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4 format(/'CELLS', 2i16)
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5 format(/'CELL_TYPES', i16)
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12 format(/'CELL_DATA', i16)
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16 format(/'POINT_DATA', i16)
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17 format('SCALARS weight float', / &
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'LOOKUP_TABLE default')
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18 format('SCALARS atom_type float', / &
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'LOOKUP_TABLE default')
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20 format('SCALARS lattice_type float', /&
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'LOOKUP_TABLE default')
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21 format('SCALARS esize float', /&
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'LOOKUP_TABLE default')
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!First we write the vtk file containing the atoms
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open(unit=11, file='atoms_'//trim(adjustl(file)), action='write', status='replace',position='rewind')
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write(11, 11)
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write(11, 2)
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write(11, 3) atom_num
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do i = 1, atom_num
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write(11, '(3f23.15)') r_atom(:,i)
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end do
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write(11,4) atom_num, atom_num*2
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do i = 1, atom_num
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write(11, '(2i16)') 1, i-1
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end do
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write(11, 5) atom_num
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do i = 1, atom_num
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write(11, '(i16)') 1
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end do
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write(11, 16) atom_num
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write(11, 18)
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do i = 1, atom_num
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write(11, '(i16)') type_atom(i)
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end do
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close(11)
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!Now we write the vtk file for the elements
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open(unit=11, file='cg_'//trim(adjustl(file)), action='write', status='replace',position='rewind')
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write(11,1)
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write(11,2)
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write(11,3) node_num
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do i = 1, ele_num
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do inod=1, ng_node(lat_ele(i))
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do ibasis = 1, basisnum(lat_ele(i))
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write(11, '(3f23.15)') sum(r_node(:,:,inod,i),2)/basisnum(lat_ele(i))
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end do
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end do
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end do
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write(11, 4) ele_num, ele_num + node_num
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do i =1, ele_num
|
|
write(11, '(9i16)') ng_node(lat_ele(i)), (j, j = (i-1)*ng_node(lat_ele(i)), i*ng_node(lat_ele(i))-1)
|
|
end do
|
|
write(11,5) ele_num
|
|
do i = 1, ele_num
|
|
if(trim(adjustl(type_ele(i))) == 'fcc') write(11, '(i16)') 12
|
|
if(trim(adjustl(type_ele(i))) == 'bcc') write(11, '(i16)') 12
|
|
end do
|
|
write(11,12) ele_num
|
|
write(11,20)
|
|
do i = 1, ele_num
|
|
write(11, '(i16)') lat_ele(i)
|
|
end do
|
|
write(11,21)
|
|
do i = 1, ele_num
|
|
write(11, '(i16)') size_ele(i)
|
|
end do
|
|
close(11)
|
|
end subroutine
|
|
|
|
subroutine write_pycac(file)
|
|
!This subroutine writes restart files meant to be used with the McDowell Group CAC code.
|
|
!NOTE: This code doesn't work for arbitrary number of basis atoms per node. It assumes that the
|
|
!each element has only 1 atom type at the node.
|
|
character(len=100), intent(in) :: file
|
|
integer :: interp_max, i, j, inod, ibasis, ip, unique_index(50), unique_size(50), unique_type(50), unique_num, &
|
|
etype
|
|
real(kind=dp) :: box_vec(3), masses(10)
|
|
|
|
1 format('time' / i16, f23.15)
|
|
2 format('number of elements' / i16)
|
|
3 format('number of nodes' / i16)
|
|
5 format('number of atoms' / i16)
|
|
7 format('boundary ' / 3a1)
|
|
8 format('box bound' / 6f23.15)
|
|
9 format('box length' / 3f23.15)
|
|
10 format('box matrix')
|
|
11 format(3f23.15)
|
|
12 format('coarse-grained domain')
|
|
13 format('ie basis_num ng_node esize'/ 'ip ibasis type x y z')
|
|
14 format('atomistic domain' / 'ia type_atom x y z')
|
|
19 format('max nodes per element and basis per nodes' / 2i16)
|
|
20 format('max interpo per element' / i16)
|
|
21 format('atom types to elements')
|
|
|
|
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
|
|
|
|
!Below writes the header information for the restart file
|
|
write(11,1) timestep, total_time
|
|
write(11,2) ele_num
|
|
|
|
!Calculate the max number of atoms per element
|
|
select case(max_ng_node)
|
|
case(8)
|
|
interp_max = (max_esize)**3
|
|
case default
|
|
interp_max = 0
|
|
end select
|
|
|
|
write(11,20) interp_max
|
|
!Write
|
|
write(11,3) node_num
|
|
write(11,19) max_ng_node, max_basisnum
|
|
write(11,5) atom_num
|
|
do i = 1, atom_types
|
|
call atommass(type_to_name(i),masses(i))
|
|
end do
|
|
write(11,*) "masses: "
|
|
write(11, *) (masses(i), i = 1, atom_types)
|
|
write(11,7) box_bc(1:1), box_bc(2:2), box_bc(3:3)
|
|
write(11,8) box_bd
|
|
write(11,10)
|
|
!Current boxes are limited to being rectangular
|
|
do i = 1,3
|
|
box_vec(:) = 0.0_dp
|
|
box_vec(i) = box_bd(2*i) - box_bd(2*i-1)
|
|
write(11,11) box_vec
|
|
end do
|
|
|
|
!write the element information
|
|
if(ele_num > 0) then
|
|
write(11,12)
|
|
ip = 0
|
|
write(11,13)
|
|
do i = 1, ele_num
|
|
write(11, '(4i16)') i, basisnum(lat_ele(i)), 2, (size_ele(i)-1)
|
|
do inod = 1, ng_node(lat_ele(i))
|
|
do ibasis = 1, basisnum(lat_ele(i))
|
|
ip = ip + 1
|
|
write(11, '(3i16, 3f23.15)') ip, ibasis, basis_type(ibasis, lat_ele(i)), r_node(:, ibasis, inod, i)
|
|
end do
|
|
end do
|
|
end do
|
|
end if
|
|
|
|
!Now write the atomic information
|
|
if(atom_num /= 0) then
|
|
write(11,14)
|
|
do i = 1, atom_num
|
|
write(11, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i)
|
|
end do
|
|
end if
|
|
|
|
close(11)
|
|
end subroutine write_pycac
|
|
|
|
subroutine write_mb(file)
|
|
|
|
!This subroutine writes the cacmb formatted file which provides necessary information for building models
|
|
character(len=100), intent(in) :: file
|
|
|
|
integer :: i, j, k, inod, ibasis
|
|
|
|
!Open the .mb file for writing
|
|
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
|
|
|
|
!First write the box boundary information
|
|
!Write the global box boundaries
|
|
write(11,*) box_bd(:)
|
|
!Write the number of sub_boxes in the system
|
|
write(11,*) sub_box_num
|
|
!For every subbox write the orientation, sub box boundar
|
|
do i = 1, sub_box_num
|
|
write(11,*) sub_box_ori(:,:,i)
|
|
write(11,*) sub_box_bd(:,i)
|
|
end do
|
|
|
|
!Write the number of atom types in the current model and all of their names
|
|
write(11,*) atom_types, (type_to_name(i)//' ', i=1, atom_types)
|
|
!Write the number of lattice_types, basisnum and number of nodes for each lattice type
|
|
write(11,*) lattice_types, (basisnum(i), i = 1, lattice_types), (ng_node(i), i = 1, lattice_types)
|
|
!Now for every lattice type write the basis atom types
|
|
write(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_types)
|
|
!Now for every lattice type write the lattice parameters
|
|
write(11,*) (lapa(i), i = 1, lattice_types)
|
|
|
|
!Now write the numbers of elements and atoms
|
|
write(11,*) atom_num, ele_num
|
|
|
|
!Write out atoms first
|
|
do i = 1, atom_num
|
|
write(11,*) tag_atom(i), type_atom(i), sbox_atom(i), r_atom(:,i)
|
|
end do
|
|
|
|
!Write out the elements, this is written in two stages, one line for the element and then 1 line for
|
|
!every basis at every node
|
|
do i = 1, ele_num
|
|
write(11, *) tag_ele(i), lat_ele(i), size_ele(i), sbox_ele(i), type_ele(i)
|
|
do inod = 1, ng_node(lat_ele(i))
|
|
do ibasis =1, basisnum(lat_ele(i))
|
|
write(11,*) inod, ibasis, r_node(:, ibasis, inod, i)
|
|
end do
|
|
end do
|
|
end do
|
|
|
|
close(11)
|
|
end subroutine write_mb
|
|
|
|
|
|
!!!!!!!!!!!!! Below are subroutines for reading files !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
|
|
subroutine get_in_file(filename)
|
|
|
|
implicit none
|
|
|
|
character(len=100), intent(in) :: filename
|
|
character(len=100) :: temp_infile
|
|
logical :: file_exists
|
|
|
|
!If no filename is provided then this function is called with none and prompts user input
|
|
if (filename=='none') then
|
|
print *, "Please specify a filename or extension to output to:"
|
|
read(*,*) temp_infile
|
|
else
|
|
temp_infile = filename
|
|
end if
|
|
|
|
!Check to see if file exists, if it does then ask user if they would like to overwrite the file
|
|
inquire(file=trim(temp_infile), exist=file_exists)
|
|
if (.not.file_exists) then
|
|
print *, "The file ", trim(adjustl(filename)), " does not exist. Please input an existing file to read."
|
|
stop 3
|
|
end if
|
|
|
|
select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
|
|
case('restart', 'mb', 'cac')
|
|
infilenum=infilenum+1
|
|
infiles(infilenum) = temp_infile
|
|
case('out')
|
|
if(atom_types == 0) then
|
|
print *, "Please run -set_types command prior to running code requiring reading in pycac_*.out files"
|
|
stop 3
|
|
end if
|
|
select case(trim(adjustl(mode)))
|
|
case('--calc', '--convert','--metric')
|
|
infilenum = infilenum+1
|
|
infiles(infilenum) = temp_infile
|
|
case default
|
|
print *, "Files of type .out cannot be used with mode ", trim(adjustl(mode))
|
|
stop 3
|
|
end select
|
|
|
|
case default
|
|
print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
|
|
"please input a filename with extension from following list: mb, restart, cac, or out."
|
|
stop 3
|
|
end select
|
|
|
|
end subroutine get_in_file
|
|
|
|
subroutine read_in(i, displace, temp_box_bd)
|
|
!This subroutine reads in file i
|
|
|
|
integer, intent(in) :: i
|
|
real(kind=dp), dimension(3), intent(in) :: displace
|
|
real(kind=dp), dimension(6), intent(out) :: temp_box_bd
|
|
|
|
!Pull out the extension of the file and call the correct write subroutine
|
|
select case(trim(adjustl(infiles(i)(scan(infiles(i),'.',.true.)+1:))))
|
|
case('mb')
|
|
call read_mb(infiles(i), displace, temp_box_bd)
|
|
case('restart')
|
|
call read_pycac(infiles(i), displace, temp_box_bd)
|
|
case('cac')
|
|
call read_lmpcac(infiles(i), displace, temp_box_bd)
|
|
case('out')
|
|
call read_pycac_out(infiles(i), displace, temp_box_bd)
|
|
case default
|
|
print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
|
|
" is not accepted for reading. Please select from: mb,restart,cac,out and try again"
|
|
stop
|
|
|
|
end select
|
|
|
|
end subroutine read_in
|
|
|
|
subroutine read_mb(file, displace, temp_box_bd)
|
|
!This subroutine reads in an mb file for operation
|
|
|
|
character(len=100), intent(in) :: file
|
|
real(kind=dp), dimension(3), intent(in) :: displace
|
|
real(kind = dp), dimension(6), intent(out) :: temp_box_bd
|
|
|
|
integer :: i, j, k, l, n, inod, ibasis, type, size, in_atoms, in_eles, new_atom_types, &
|
|
new_type_to_type(10), new_lattice_types, sbox, new_lattice_map(10)
|
|
character(len=100) :: etype
|
|
real(kind=dp) :: r(3), newdisplace(3)
|
|
real(kind=dp), allocatable :: r_innode(:,:,:)
|
|
character(len = 2) :: new_type_to_name(10)
|
|
!First open the file
|
|
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
|
|
|
|
!Read in the box boundary and grow the current active box bd
|
|
read(11, *) temp_box_bd(:)
|
|
|
|
do i = 1, 3
|
|
if (abs(displace(i)) > lim_zero) then
|
|
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
|
|
else
|
|
newdisplace(i)=displace(i)
|
|
end if
|
|
temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
|
|
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
|
|
end do
|
|
|
|
call grow_box(temp_box_bd)
|
|
!Read in the number of sub_boxes and allocate the variables
|
|
read(11, *) n
|
|
|
|
if (sub_box_num == 0) then
|
|
call alloc_sub_box(n)
|
|
else
|
|
call grow_sub_box(n)
|
|
end if
|
|
|
|
!Read in subbox orientations and boundaries
|
|
do i = 1, n
|
|
!Read in orientation with column major ordering
|
|
read(11,*) ((sub_box_ori(j, k, sub_box_num+i), j = 1, 3), k = 1, 3)
|
|
!Read in subbox boundaries
|
|
read(11,*) sub_box_bd(:,sub_box_num+i)
|
|
|
|
do j = 1, 3
|
|
sub_box_bd(2*j-1,sub_box_num+i) = sub_box_bd(2*j-1, sub_box_num+i) + displace(j)
|
|
sub_box_bd(2*j,sub_box_num+i) = sub_box_bd(2*j, sub_box_num+i) + displace(j)
|
|
end do
|
|
end do
|
|
|
|
!Read in the number of atom types and all their names
|
|
read(11, *) new_atom_types, (new_type_to_name(i), i = 1, new_atom_types)
|
|
!Now fit these into the global list of atom types, after this new_type_to_type is the actual global
|
|
!type of the atoms within this file
|
|
do i = 1, new_atom_types
|
|
call add_atom_type(new_type_to_name(i), new_type_to_type(i))
|
|
end do
|
|
!Read the number of lattice types, basisnum, and number of nodes for each lattice type
|
|
read(11,*) new_lattice_types, (basisnum(i), i = lattice_types+1, lattice_types+new_lattice_types), &
|
|
(ng_node(i), i = lattice_types+1, lattice_types+new_lattice_types)
|
|
!Define max_ng_node and max_basis_num
|
|
max_basisnum = maxval(basisnum)
|
|
max_ng_node = maxval(ng_node)
|
|
!Read the basis atom types for every lattice
|
|
read(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = lattice_types+1, lattice_types+new_lattice_types)
|
|
!Convert the basis_atom types
|
|
do j = lattice_types+1, lattice_types+new_lattice_types
|
|
do i = 1, basisnum(j)
|
|
basis_type(i,j) = new_type_to_type(basis_type(i,j))
|
|
end do
|
|
end do
|
|
!Read the lattice parameters for every lattice type
|
|
read(11,*) (lapa(i), i = lattice_types+1, lattice_types+new_lattice_types)
|
|
|
|
!Now we loop over all new lattice types and check to see if they are exactly the same as any old lattice types
|
|
!If they are then we map the new type to the old type.
|
|
k = lattice_types + 1
|
|
new_lattice_map(:) = 0
|
|
new_loop:do i = 1, new_lattice_types
|
|
old_loop:do j = 1, lattice_types
|
|
!First check all the lattice level variables
|
|
if ((basisnum(lattice_types + i) == basisnum(j)).and. &
|
|
(ng_node(lattice_types + i) == ng_node(j))) then
|
|
!Now check the basis level variables
|
|
do ibasis =1, basisnum(i)
|
|
if(basis_type(ibasis,lattice_types+i) /= basis_type(ibasis,j)) then
|
|
cycle old_loop
|
|
end if
|
|
end do
|
|
new_lattice_map(i) = j
|
|
cycle new_loop
|
|
end if
|
|
end do old_loop
|
|
new_lattice_map(i) = k
|
|
k = k+1
|
|
end do new_loop
|
|
|
|
!Read number of elements and atoms and allocate arrays
|
|
read(11, *) in_atoms, in_eles
|
|
call grow_ele_arrays(in_eles, in_atoms)
|
|
allocate(r_innode(3,max_basisnum, max_ng_node))
|
|
|
|
print *, "Read in ", in_eles, " elements and ", in_atoms, " atoms from ", trim(adjustl(file))
|
|
print *, "New box dimensions are: ", box_bd
|
|
|
|
!Read the atoms
|
|
do i = 1, in_atoms
|
|
read(11,*) j, type, sbox, r(:)
|
|
r = r+newdisplace
|
|
call add_atom(j, new_type_to_type(type), sbox+sub_box_num, r)
|
|
end do
|
|
|
|
!Read the elements
|
|
do i = 1, in_eles
|
|
read(11, *) j, type, size, sbox, etype
|
|
do inod = 1, ng_node(type)
|
|
do ibasis =1, basisnum(type)
|
|
read(11,*) k, l, r_innode(:, ibasis, inod)
|
|
r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace
|
|
end do
|
|
end do
|
|
call add_element(j, etype, size, new_lattice_map(type), sbox+sub_box_num, r_innode)
|
|
end do
|
|
|
|
!Close the file being read
|
|
close(11)
|
|
|
|
!Only increment the lattice types if there are elements, if there are no elements then we
|
|
!just overwrite the arrays
|
|
lattice_types = maxval(new_lattice_map)
|
|
|
|
|
|
sub_box_num = sub_box_num + n
|
|
|
|
call set_max_esize
|
|
end subroutine read_mb
|
|
|
|
subroutine read_pycac(file, displace, temp_box_bd)
|
|
!Add subroutine for reading in restart files from PyCAC. This code currently only
|
|
!works for 8 node elements.
|
|
character(len=100), intent(in) :: file
|
|
real(kind=dp), dimension(3), intent(in) :: displace
|
|
real(kind = dp), dimension(6), intent(out) :: temp_box_bd
|
|
|
|
integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
|
|
atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), &
|
|
atom_type, stat
|
|
real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), atomic_masses(10)
|
|
character(len=100) :: textholder, in_lattype_map(10)
|
|
character(len=2) :: atomic_element
|
|
!First open the file
|
|
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
|
|
|
|
!Read the timestep information
|
|
read(11,*) textholder
|
|
read(11,*) timestep, total_time
|
|
|
|
!Read element number
|
|
read(11,*) textholder
|
|
read(11,*) in_eles
|
|
|
|
!Discard info and read ng_max_node and max_basisnum
|
|
do i = 1, 5
|
|
read(11,*) textholder
|
|
end do
|
|
read(11,*) max_ng_node, max_basisnum
|
|
|
|
!Read in atom num
|
|
read(11,*) textholder
|
|
read(11,*) in_atoms
|
|
|
|
!read in atom masses
|
|
read(11, *) textholder
|
|
read(11, '(a)') textholder
|
|
j = tok_count(textholder)
|
|
read(textholder, *) (atomic_masses(i), i=1, j)
|
|
|
|
!Read define atom_types by mass
|
|
do i = 1, in_atom_types
|
|
call atommassspecies(atomic_masses(i), atomic_element)
|
|
call add_atom_type(atomic_element, atom_type_map(i))
|
|
end do
|
|
|
|
!Read in the boundary
|
|
read(11,*) textholder
|
|
read(11,*) box_bc
|
|
|
|
!Read box boundaries and displace them if necessary
|
|
read(11,*) temp_box_bd(:)
|
|
do i = 1, 3
|
|
if (abs(displace(i)) > lim_zero) then
|
|
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
|
|
else
|
|
newdisplace(i)=displace(i)
|
|
end if
|
|
temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
|
|
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
|
|
end do
|
|
|
|
call grow_box(temp_box_bd)
|
|
|
|
!Allocate sub_box
|
|
if (sub_box_num == 0) then
|
|
call alloc_sub_box(1)
|
|
else
|
|
call grow_sub_box(1)
|
|
end if
|
|
|
|
!Because orientations and other needed sub_box information isn't really
|
|
!present within the restart file we just default a lot of it.
|
|
sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
|
|
sub_box_bd(:, sub_box_num+1) = temp_box_bd
|
|
|
|
!Read in more useless info
|
|
do i = 1, 9
|
|
read(11,*) textholder
|
|
end do
|
|
|
|
!Now start reading the elements
|
|
if(in_eles > 0) then
|
|
read(11,*) textholder
|
|
read(11,*) textholder
|
|
do i = 1, in_eles
|
|
read(11,*) j, etype, k, lat_type
|
|
do inod = 1, 8
|
|
read(11, *) k, l, r_in(:,1,inod)
|
|
r_in(:,1,inod) = r_in(:,1,inod) + newdisplace
|
|
end do
|
|
call add_element(j, in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in)
|
|
end do
|
|
end if
|
|
|
|
if(in_atoms > 0) then
|
|
|
|
if (in_eles > 0) then
|
|
!Read useless data
|
|
read(11,*) textholder
|
|
read(11,*) textholder
|
|
end if
|
|
|
|
do i = 1, in_atoms
|
|
read(11,*, iostat=stat) j, k, atom_type, r_in_atom(:)
|
|
if(stat > 0) then
|
|
print *, j
|
|
stop
|
|
end if
|
|
r_in_atom = r_in_atom + newdisplace
|
|
call add_atom(j,atom_type_map(atom_type), sub_box_num + 1, r_in_atom)
|
|
end do
|
|
!Close file
|
|
close(11)
|
|
|
|
lattice_types = maxval(new_lattice_map)
|
|
|
|
sub_box_num = sub_box_num + 1
|
|
|
|
call set_max_esize
|
|
end if
|
|
end subroutine read_pycac
|
|
|
|
subroutine read_pycac_out(file, displace, temp_box_bd)
|
|
!This subroutine reads in the pyCAC dump file
|
|
|
|
|
|
!Arguments
|
|
character(len=100), intent(in) :: file
|
|
real(kind=dp), dimension(3), intent(in) :: displace
|
|
real(kind=dp), dimension(6), intent(out) :: temp_box_bd
|
|
|
|
!Internal Variables
|
|
integer :: i, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
|
|
id, type_node, ilat, esize, tag, type, bnum, n, ibasis, ip
|
|
real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), &
|
|
ee(10,8), fe(3,10,8), ve(6,10,8), re(3,10,8)
|
|
character(len=100) :: textholder, fcc
|
|
character(len=1000) :: line
|
|
|
|
|
|
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
|
|
|
|
!Now initialize some important variables if they aren't defined
|
|
if (max_basisnum==0) max_basisnum = 10
|
|
if (max_ng_node==0) max_ng_node=8
|
|
fcc="fcc"
|
|
|
|
!Skip header comment lines
|
|
read(11, *) textholder
|
|
read(11, *) textholder
|
|
|
|
!Read the timestep
|
|
read(11, *) textholder, timestep
|
|
|
|
!Read atom number and element number and grow element arrays by needed amount
|
|
read(11,*) textholder, in_atoms, textholder, in_eles
|
|
call grow_ele_arrays(in_eles, in_atoms)
|
|
call alloc_dat_arrays(in_eles, in_atoms)
|
|
|
|
!Read boundary information
|
|
read(11,*) textholder, box_bc(1:1), box_bc(2:2), box_bc(3:3), temp_box_bd(:)
|
|
do i = 1, 3
|
|
if (abs(displace(i)) > lim_zero) then
|
|
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
|
|
else
|
|
newdisplace(i)=displace(i)
|
|
end if
|
|
temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
|
|
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
|
|
end do
|
|
|
|
call grow_box(temp_box_bd)
|
|
|
|
!Allocate sub_box boundaries
|
|
if (sub_box_num == 0) then
|
|
call alloc_sub_box(1)
|
|
else
|
|
call grow_sub_box(1)
|
|
end if
|
|
|
|
!Because orientations and other needed sub_box information isn't really
|
|
!present within the .cac file we just default a lot of it.
|
|
sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
|
|
sub_box_bd(:, sub_box_num+1) = temp_box_bd
|
|
sub_box_num = sub_box_num + 1
|
|
|
|
if(in_atoms > 0 ) then
|
|
!Read atom header
|
|
read(11,*) textholder
|
|
do ia = 1, in_atoms
|
|
read(11,'(a)') line(:)
|
|
read(line,*) tag, type, ra(:), ea, fa(:), va(:)
|
|
call add_atom(tag, type, sub_box_num, ra)
|
|
call add_atom_data(atom_num, ea, fa, va)
|
|
end do
|
|
|
|
end if
|
|
|
|
if(in_eles > 0) then
|
|
!Read element and node headers
|
|
read(11,*) textholder
|
|
read(11,*) textholder
|
|
|
|
!read element information, currently only 8 node elements with 1 basis
|
|
do ie =1, in_eles
|
|
read(11,*) tag, n, bnum, esize
|
|
inbtypes(:) = 0
|
|
do inod =1, n*bnum
|
|
read(11,*) ip, ibasis, inbtypes(ibasis), re(:,ibasis,ip), ee(ibasis,ip), fe(:,ibasis,ip), ve(:,ibasis,ip)
|
|
end do
|
|
call lattice_map(bnum, inbtypes, n, 1.0_dp, lat_type)
|
|
call add_element(tag, fcc, esize+1, lat_type, sub_box_num, re)
|
|
call add_element_data(ele_num, ee, fe, ve)
|
|
end do
|
|
end if
|
|
call set_max_esize
|
|
return
|
|
end subroutine
|
|
|
|
|
|
|
|
subroutine read_lmpcac(file, displace, temp_box_bd)
|
|
!This subroutine is used to read .cac files which are used with the lammpsCAC format
|
|
character(len=100), intent(in) :: file
|
|
real(kind=dp), dimension(3), intent(in) :: displace
|
|
real(kind = dp), dimension(6), intent(out) :: temp_box_bd
|
|
|
|
character(len=100) :: textholder, element_type
|
|
character(len=2) :: atom_species
|
|
integer :: i, j, k, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10), esize, &
|
|
lat_type
|
|
real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3,3), in_ori(3,3), newdisplace(3)
|
|
|
|
!First check to make sure that we have set the needed variables
|
|
if(is_equal(in_lapa,0.0_dp).or.(in_lattice_type=='')) then
|
|
print *, "Please use set_cac to set needed parameters to read in .cac file"
|
|
stop 3
|
|
end if
|
|
!Open the file
|
|
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
|
|
|
|
!Now initialize some important variables if they aren't defined
|
|
if (max_basisnum==0) max_basisnum = 10
|
|
if (max_ng_node==0) max_ng_node=8
|
|
|
|
!Read header information
|
|
read(11, *) textholder
|
|
|
|
!Read number of elements
|
|
read(11, *) ele_in, textholder
|
|
read(11, *) type_in, textholder
|
|
|
|
!Read box_boundaries
|
|
read(11,*) temp_box_bd(1:2), textholder
|
|
read(11,*) temp_box_bd(3:4), textholder
|
|
read(11,*) temp_box_bd(5:6), textholder
|
|
|
|
!Shift the box boundaries if needed
|
|
do i = 1, 3
|
|
if (abs(displace(i)) > lim_zero) then
|
|
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
|
|
else
|
|
newdisplace(i)=displace(i)
|
|
end if
|
|
temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
|
|
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
|
|
end do
|
|
|
|
!Grow box boundaries
|
|
call grow_box(temp_box_bd)
|
|
|
|
!Allocate sub_box
|
|
if (sub_box_num == 0) then
|
|
call alloc_sub_box(1)
|
|
else
|
|
call grow_sub_box(1)
|
|
end if
|
|
|
|
!Because orientations and other needed sub_box information isn't really
|
|
!present within the .cac file we just default a lot of it.
|
|
sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
|
|
sub_box_bd(:, sub_box_num+1) = temp_box_bd
|
|
sub_box_num = sub_box_num + 1
|
|
|
|
|
|
!Read useless information
|
|
read(11,*) textholder
|
|
|
|
!Read atomic masses
|
|
do i = 1, type_in
|
|
read(11,*) j, mass, textholder
|
|
call ATOMMASSSPECIES(mass, atom_species)
|
|
call add_atom_type(atom_species, type_map(i))
|
|
end do
|
|
|
|
!Read useless info
|
|
read(11,*) textholder
|
|
|
|
!Start the reading loop
|
|
do i = 1, ele_in
|
|
read(11,*) j, element_type, in_basis, esize
|
|
!Check to see if we need to grow the max_basis_num
|
|
select case(trim(adjustl(element_type)))
|
|
case('Eight_Node')
|
|
!Read in all the data
|
|
do j = 1, 8*in_basis
|
|
read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,ibasis,inod)
|
|
end do
|
|
|
|
!Now calculate the lattice vectors and shift the nodal points from the corners to the center of the unit cell
|
|
!Please check the nodal numbering figure in the readme in order to understand which nodes are used for the
|
|
!calculation
|
|
lat_vec(:,1) = (r_in(:,1,2) - r_in(:,1,1))/(2*esize)
|
|
lat_vec(:,2) = (r_in(:,1,4) - r_in(:,1,1))/(2*esize)
|
|
lat_vec(:,3) = (r_in(:,1,5) - r_in(:,1,1))/(2*esize)
|
|
|
|
!Now shift all the nodal positions
|
|
select case(trim(adjustl(in_lattice_type)))
|
|
case('fcc','FCC')
|
|
do ibasis = 1, in_basis
|
|
r_in(:,ibasis,1) = r_in(:,ibasis,1) + lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
|
|
r_in(:,ibasis,2) = r_in(:,ibasis,2) - lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
|
|
r_in(:,ibasis,3) = r_in(:,ibasis,3) - lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
|
|
r_in(:,ibasis,4) = r_in(:,ibasis,4) + lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
|
|
r_in(:,ibasis,5) = r_in(:,ibasis,5) + lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
|
|
r_in(:,ibasis,6) = r_in(:,ibasis,6) - lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
|
|
r_in(:,ibasis,7) = r_in(:,ibasis,7) - lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
|
|
r_in(:,ibasis,8) = r_in(:,ibasis,8) + lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
|
|
end do
|
|
case default
|
|
print *, in_lattice_type, " is not an accepted lattice type. Please select from: fcc"
|
|
end select
|
|
!Now map it to either an existing or new lattice type
|
|
call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
|
|
|
|
!Now add the element
|
|
call add_element(0,in_lattice_type, esize, lat_type, sub_box_num, r_in(:,1:max_basisnum,1:max_ng_node))
|
|
|
|
case('Atom')
|
|
read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,1,1)
|
|
call add_atom(0,in_basis_types(ibasis), sub_box_num, r_in(:,1,1))
|
|
end select
|
|
end do
|
|
|
|
end subroutine read_lmpcac
|
|
|
|
subroutine set_cac(apos)
|
|
!This code parses input values
|
|
integer, intent(in) :: apos
|
|
integer :: arglen, arg_pos
|
|
|
|
character(len=100) :: textholder
|
|
|
|
arg_pos = apos + 1
|
|
call get_command_argument(arg_pos, textholder, arglen)
|
|
if (arglen==0) then
|
|
print *, "Missing lattice parameter for set_input_lat"
|
|
end if
|
|
read(textholder,*) in_lapa
|
|
print *, in_lapa
|
|
|
|
arg_pos = arg_pos + 1
|
|
call get_command_argument(arg_pos, textholder, arglen)
|
|
if (arglen==0) then
|
|
print *, "Missing lattice type for set_input_lat"
|
|
end if
|
|
read(textholder,*) in_lattice_type
|
|
print *, in_lattice_type
|
|
|
|
end subroutine set_cac
|
|
|
|
subroutine set_types(apos)
|
|
!This code
|
|
integer, intent(in) :: apos
|
|
integer :: i, j,arglen, arg_pos, ntypes
|
|
|
|
character(len=100) :: textholder
|
|
|
|
arg_pos = apos + 1
|
|
call get_command_argument(arg_pos, textholder, arglen)
|
|
if (arglen==0) stop "Missing numtypes in io"
|
|
read(textholder,*) ntypes
|
|
|
|
do i=1,ntypes
|
|
arg_pos = arg_pos + 1
|
|
call get_command_argument(arg_pos, textholder, arglen)
|
|
call add_atom_type(textholder, j)
|
|
end do
|
|
|
|
return
|
|
end subroutine set_types
|
|
end module io
|