diff --git a/README.md b/README.md index 6068e39..8dd0971 100644 --- a/README.md +++ b/README.md @@ -329,7 +329,6 @@ This command will delete all overlapping atoms within a specific cutoff radius ` This option is primarily used when reading data from non .mb formats. This code simply sets the orientation variable for the specified sub box `sbox`. **** - ## Position Specification Specifying positions in cacmb can be done through a variety of ways. Examples of each format is shown below. diff --git a/src/call_option.f90 b/src/call_option.f90 index ead7af0..368e542 100644 --- a/src/call_option.f90 +++ b/src/call_option.f90 @@ -33,8 +33,10 @@ subroutine call_option(option, arg_pos) call sbox_ori(arg_pos) case('-delete') call run_delete(arg_pos) + case('-set_cac') + arg_pos=arg_pos +3 case default print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.' stop 3 end select -end subroutine call_option \ No newline at end of file +end subroutine call_option diff --git a/src/elements.f90 b/src/elements.f90 index 954719f..010b476 100644 --- a/src/elements.f90 +++ b/src/elements.f90 @@ -36,13 +36,13 @@ module elements integer :: lattice_types = 0 integer :: max_ng_node, ng_node(10) !Max number of nodes per element and number of nodes per element for each lattice type integer :: max_esize=0 !Maximum number of atoms per side of element + real(kind=dp) :: lapa(10) !These variables contain information on the basis, for simplicities sake we limit !the user to the definition of 10 lattice types with 10 basis atoms at each lattice point. !This can be easily increased with no change to efficiency integer :: max_basisnum, basisnum(10) !Max basis atom number, number of basis atoms in each lattice type integer :: basis_type(10,10) - real(kind=dp) :: lapa(10) !Additional module level variables we need logical :: wrap_flag @@ -323,8 +323,6 @@ module elements integer :: i - max_ng_node = 0 - do i=1, n select case(trim(adjustl(element_types(i)))) case('fcc') @@ -676,4 +674,39 @@ module elements end select end subroutine + subroutine lattice_map(in_bnum, in_btypes, in_ngnodes, in_lapa, lat_type) + !This subroutine maps an input lattice type to either a new lattice type or an existing one depending on basis_type and + !number of nodes at the atoms + + integer, intent(in) :: in_ngnodes, in_bnum, in_btypes(10) !Input variables + real(kind=dp), intent(in) :: in_lapa + integer, intent(out) :: lat_type + + integer j, ibasis + + lat_type = 0 + lat_loop:do j = 1, lattice_types + !Check all the lattice level variables + if ((basisnum(j) == in_bnum).and.(ng_node(j) == in_ngnodes).and.(is_equal(lapa(j),in_lapa))) then + !Now check lattice level variables + do ibasis = 1, basisnum(j) + if(basis_type(ibasis,j) /= in_btypes(ibasis)) cycle lat_loop + end do + lat_type = j + exit lat_loop + end if + end do lat_loop + + !If it doesn't match an existing lattice type we add it + if( lat_type == 0) then + lattice_types = lattice_types + 1 + basisnum(lattice_types) = in_bnum + basis_type(:,lattice_types) = in_btypes + ng_node(lattice_types) = in_ngnodes + lapa(lattice_types) = in_lapa + lat_type = lattice_types + end if + + end subroutine lattice_map + end module elements diff --git a/src/io.f90 b/src/io.f90 index 6aafafc..79e63d4 100644 --- a/src/io.f90 +++ b/src/io.f90 @@ -8,9 +8,9 @@ module io implicit none integer :: outfilenum = 0, infilenum = 0 - character(len=100) :: outfiles(100), infiles(100) + character(len=100) :: outfiles(100), infiles(100), in_lattice_type='' logical :: force_overwrite - + real(kind=dp) :: in_lapa=0.0 public contains @@ -196,7 +196,7 @@ module io do i = 1, ele_num call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp) select case(trim(adjustl(type_ele(i)))) - case('fcc') + case('fcc','bcc') do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3 interp_num = interp_num+1 call apply_periodic(r_interp(:,iatom)) @@ -591,7 +591,7 @@ module io end if select case(temp_infile(scan(temp_infile,'.',.true.)+1:)) - case('restart', 'mb') + case('restart', 'mb', 'cac') infilenum=infilenum+1 infiles(infilenum) = temp_infile exit @@ -618,6 +618,8 @@ module io 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 default print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), & " is not accepted for writing. Please select from: mb and try again" @@ -776,7 +778,7 @@ module io 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 - real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), new_displace(3) + real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3) character(len=100) :: textholder, in_lattype_map(10) character(len=2) :: atomic_element !First open the file @@ -949,4 +951,154 @@ module io call set_max_esize end if end subroutine read_pycac + + 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 initialiaze 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(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(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 end module io diff --git a/src/main.f90 b/src/main.f90 index 958a3c0..53fa4fa 100644 --- a/src/main.f90 +++ b/src/main.f90 @@ -60,6 +60,9 @@ program main !This lets us know if we need to wrap atomic positions back into the cell case('-wrap') wrap_flag=.true. + + case('-set_cac') + call set_cac(i) end select end do !Determine if a mode is being used and what it is. The first argument has to be the mode