Working read from pycac.out file format
This commit is contained in:
Alex Selimov
parent
dadc1f7a4a
commit
5949f04103
7 changed files with 213 additions and 16 deletions
144
src/io.f90
144
src/io.f90
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@ -106,7 +106,7 @@ module io
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call write_lmpcac(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 and try again"
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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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@ -599,9 +599,24 @@ module io
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infilenum=infilenum+1
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infiles(infilenum) = temp_infile
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exit
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case('out')
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if(atom_types == 0) then
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print *, "Please run -set_types command prior to running code requiring reading in pycac_*.out files"
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stop 3
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end if
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select case(trim(adjustl(mode)))
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case('--convert','--metric')
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infilenum = infilenum+1
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infiles(infilenum) = temp_infile
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exit
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case default
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print *, "Files of type .out cannot be used with mode ", trim(adjustl(mode))
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stop 3
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end select
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case default
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print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
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"please input a filename with extension from following list: mb, restart."
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"please input a filename with extension from following list: mb, restart, cac, or out."
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read(*,*) temp_infile
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end select
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@ -624,9 +639,11 @@ module io
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call read_pycac(infiles(i), displace, temp_box_bd)
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case('cac')
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call read_lmpcac(infiles(i), displace, temp_box_bd)
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case('out')
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call read_pycac_out(infiles(i), displace, temp_box_bd)
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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: mb and try again"
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" is not accepted for reading. Please select from: mb,restart,cac,out and try again"
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stop
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end select
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@ -781,7 +798,7 @@ module io
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integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
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atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), &
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atom_type, stat
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atom_type, stat
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real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3)
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character(len=100) :: textholder, in_lattype_map(10)
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character(len=2) :: atomic_element
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@ -960,6 +977,102 @@ module io
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end if
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end subroutine read_pycac
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subroutine read_pycac_out(file, displace, temp_box_bd)
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!This subroutine reads in the pyCAC dump file
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!Arguments
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character(len=100), intent(in) :: file
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real(kind=dp), dimension(3), intent(in) :: displace
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real(kind=dp), dimension(6), intent(out) :: temp_box_bd
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!Internal Variables
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integer :: i, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
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id, type_node, ilat, esize, tag, type
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real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), &
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ee(1,8), fe(3,1,8), ve(3,1,8), re(3,1,8)
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character(len=100) :: textholder, fcc
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open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
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!Now initialize some important variables if they aren't defined
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if (max_basisnum==0) max_basisnum = 1
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if (max_ng_node==0) max_ng_node=8
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fcc="fcc"
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!Skip header comment lines
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read(11, *) textholder
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read(11, *) textholder
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!Read atom number and element number and grow element arrays by needed amount
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read(11,*) textholder, in_atoms, textholder, in_eles
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call grow_ele_arrays(in_eles, in_atoms)
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call alloc_dat_arrays(in_eles, in_atoms)
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!Read boundary information
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read(11,*) textholder, box_bc(1:1), box_bc(2:2), box_bc(3:3), temp_box_bd(:)
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do i = 1, 3
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if (abs(displace(i)) > lim_zero) then
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newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
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else
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newdisplace(i)=displace(i)
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end if
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temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
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temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
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end do
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call grow_box(temp_box_bd)
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!Allocate sub_box boundaries
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if (sub_box_num == 0) then
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call alloc_sub_box(1)
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else
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call grow_sub_box(1)
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end if
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!Because orientations and other needed sub_box information isn't really
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!present within the .cac file we just default a lot of it.
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sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
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sub_box_bd(:, sub_box_num+1) = temp_box_bd
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sub_box_num = sub_box_num + 1
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if(in_atoms > 0 ) then
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!Read atom header
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read(11,*) textholder
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do ia = 1, in_atoms
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read(11,*) tag, type, ra(:), ea, fa(:), va(:)
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call add_atom(tag, type, sub_box_num, ra)
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call add_atom_data(atom_num, ea, fa, va)
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end do
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end if
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if(in_eles > 0) then
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!Add the lattice_types based on the atom types
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inbtypes=0
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do i = 1, maxval(type_atom)
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inbtypes(1) = i
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call lattice_map(1, inbtypes, 8 , 1.0_dp, ilat) !Please check documentation on pycac.out formats
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end do
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!Read element and node headers
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read(11,*) textholder
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read(11,*) textholder
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!read element information, currently only 8 node elements with 1 basis
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do ie =1, in_eles
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read(11,*) tag, lat_type, textholder, textholder, esize
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do inod =1, 8
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read(11,*) textholder, textholder, textholder, re(:,1,inod), ee(1,inod), fe(:,1,inod), ve(:,1,inod)
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end do
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call add_element(tag, fcc, esize+1, lat_type, sub_box_num, re)
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call add_element_data(ele_num, ee, fe, ve)
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end do
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end if
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call set_max_esize
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return
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end subroutine
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subroutine read_lmpcac(file, displace, temp_box_bd)
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!This subroutine is used to read .cac files which are used with the lammpsCAC format
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character(len=100), intent(in) :: file
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@ -980,7 +1093,7 @@ module io
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!Open the file
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open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
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!Now initialiaze some important variables if they aren't defined
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!Now initialize some important variables if they aren't defined
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if (max_basisnum==0) max_basisnum = 10
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if (max_ng_node==0) max_ng_node=8
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@ -1109,4 +1222,25 @@ module io
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print *, in_lattice_type
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end subroutine set_cac
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subroutine set_types(apos)
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!This code
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integer, intent(in) :: apos
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integer :: i, j,arglen, arg_pos, ntypes
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character(len=100) :: textholder
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arg_pos = apos + 1
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call get_command_argument(arg_pos, textholder, arglen)
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if (arglen==0) stop "Missing numtypes in io"
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read(textholder,*) ntypes
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do i=1,ntypes
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, textholder, arglen)
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call add_atom_type(textholder, j)
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end do
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return
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end subroutine set_types
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end module io
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