Merge pull request #4 from aselimov/bg--fixes-to-mode-merge-reading
Fixes to file reading to ensure that mode_merge works correctly
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aselimov
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ce2e3d17f4
@ -1,6 +1,6 @@
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FC=ifort
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FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
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#FFLAGS=-c -mcmodel=large -Ofast
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#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
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FFLAGS=-mcmodel=large -Ofast
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MODES=mode_create.o mode_merge.o mode_convert.o
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OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES)
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28
src/io.f90
28
src/io.f90
@ -394,10 +394,12 @@ module io
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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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integer :: i, j, k, n, inod, ibasis, type, size, in_atoms, in_eles
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integer :: i, j, k, n, inod, ibasis, type, size, in_atoms, in_eles, new_atom_types, &
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new_type_to_type(10), new_lattice_types
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character(len=100) :: etype
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real(kind=dp) :: r(3), newdisplace(3)
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real(kind=dp), allocatable :: r_innode(:,:,:)
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character(len = 2) :: new_type_to_name(10)
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!First open the file
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open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
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@ -433,15 +435,26 @@ module io
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sub_box_num = sub_box_num + n
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!Read in the number of atom types and all their names
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read(11, *) atom_types, (type_to_name(i), i = 1, atom_types)
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read(11, *) new_atom_types, (new_type_to_name(i), i = 1, new_atom_types)
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!Now fit these into the global list of atom types, after this new_type_to_type is the actual global
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!type of the atoms within this file
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do i = 1, new_atom_types
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call add_atom_type(new_type_to_name(i), new_type_to_type(i))
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end do
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!Read the number of lattice types, basisnum, and number of nodes for each lattice type
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read(11,*) lattice_types, (basisnum(i), i = 1, lattice_types), (ng_node(i), i = 1, lattice_types)
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read(11,*) new_lattice_types, (basisnum(i), i = lattice_types+1, lattice_types+new_lattice_types), &
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(ng_node(i), i = lattice_types+1, lattice_types+new_lattice_types)
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!Define max_ng_node and max_basis_num
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max_basisnum = maxval(basisnum)
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max_ng_node = maxval(ng_node)
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!Read the basis atom types for every lattice
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read(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_types)
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read(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = lattice_types+1, lattice_types+new_lattice_types)
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!Convert the basis_atom types
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do j = lattice_types+1, lattice_types+new_lattice_types
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do i = 1, basisnum(j)
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basis_type(i,j) = new_type_to_type(basis_type(i,j))
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end do
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end do
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!Read number of elements and atoms and allocate arrays
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read(11, *) in_atoms, in_eles
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call grow_ele_arrays(in_eles, in_atoms)
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@ -450,7 +463,7 @@ module io
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!Read the atoms
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do i = 1, in_atoms
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read(11,*) j, type, r(:)
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call add_atom(type, r+newdisplace)
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call add_atom(new_type_to_type(type), r+newdisplace)
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end do
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!Read the elements
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@ -462,11 +475,12 @@ module io
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r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace
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end do
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end do
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type = type + lattice_types
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call add_element(etype, size, type, r_innode)
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end do
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!Close the file being read
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close(11)
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lattice_types = lattice_types + new_lattice_types
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end subroutine read_mb
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end module io
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@ -12,8 +12,8 @@ module mode_create
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character(len=100) :: name, element_type
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real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), &
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orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3)
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integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
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orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3)
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integer :: esize, ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
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basis_pos(3,10)
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logical :: dup_flag, dim_flag
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@ -58,16 +58,15 @@ module mode_create
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allocate(r_node_temp(3,max_basisnum,max_ng_node))
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!Get the inverse orientation matrix we will need later
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call matrix_inverse(orient,3,orient_inv)
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if(dup_flag) then
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!We initialize the cell with a lattice_parameter of 1 because we will add the lattice parameter later
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call cell_init(1.0_dp, esize, element_type, orient, cell_mat)
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!Define box vertices
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do i = 1, 8
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box_vert(:,i) = duplicate(:)*esize*lattice_space(:)*cubic_cell(:,i) + origin(:)
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box_vert(:,i) = duplicate(:)*esize*lattice_space(:)*cubic_cell(:,i) + (origin(:)/lattice_parameter)
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end do
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call matrix_inverse(orient,3,orient_inv)
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!Now get the rotated box vertex positions in lattice space. Should be integer units
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box_lat_vert = int(matmul(fcc_inv, matmul(orient_inv, box_vert)))+1
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!Find the new maxlen
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@ -76,21 +75,25 @@ module mode_create
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box_bd(2*i) = maxval(box_vert(i,:)) - 0.25_dp*lattice_space(i)
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box_bd(2*i-1) = origin(i)-0.25_dp*lattice_space(i)
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end do
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!and then call the build function with the correct transformation matrix
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select case(trim(adjustl(element_type)))
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case('fcc')
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call build_with_rhomb(box_lat_vert, fcc_mat)
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case default
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print *, "Element type ", trim(adjustl(element_type)), " not accepted in mode create, please specify a supported ", &
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"element type"
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stop 3
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end select
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!Now that it is multiply by the lattice parameter
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box_bd = box_bd*lattice_parameter
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else if(dim_flag) then
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continue
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!As a note everything is defined so that the lattice parameter is multiplied in at the end
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!so we have to divide all the real Angstroms units by the lattice parameter
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!Define box_vertices
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do i = 1, 8
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box_vert(:,i) = (cubic_cell(:,i)*box_len(:) + origin(:))/lattice_parameter
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end do
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!Now get the rotated box vertex positions in lattice space. Should be integer units
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box_lat_vert = int(matmul(fcc_inv, matmul(orient_inv, box_vert)))+1
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!Now get the box_bd in lattice units
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do i = 1, 3
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box_bd(2*i) = (box_len(i)+origin(i))/lattice_parameter
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box_bd(2*i-1) = origin(i)/lattice_parameter
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end do
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else
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call cell_init(lattice_parameter, esize, element_type, orient, cell_mat)
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@ -112,6 +115,19 @@ module mode_create
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!If we passed the dup_flag or dim_flag then we have to convert the lattice points and add them to the atom/element arrays
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if(dup_flag.or.dim_flag) then
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!Call the build function with the correct transformation matrix
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select case(trim(adjustl(element_type)))
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case('fcc')
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call build_with_rhomb(box_lat_vert, fcc_mat)
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case default
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print *, "Element type ", trim(adjustl(element_type)), " not accepted in mode create, please specify a supported ", &
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"element type"
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stop 3
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end select
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!Now that it is built multiply by the lattice parameter
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box_bd = box_bd*lattice_parameter
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!Allocate variables
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call alloc_ele_arrays(lat_ele_num, lat_atom_num*basisnum(1))
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if(lat_atom_num > 0) then
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@ -208,13 +224,21 @@ module mode_create
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!If the duplicate command is passed then we extract the information on the new bounds.
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case('duplicate')
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if(dim_flag) STOP "Both duplicate and dim options cannot be used in mode_create"
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dup_flag = .true.
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do i = 1, 3
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call get_command_argument(arg_pos, textholder)
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read(textholder, *) duplicate(i)
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arg_pos = arg_pos + 1
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end do
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case('dim')
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if(dup_flag) STOP "Both duplicate and dim options cannot be used in mode_create"
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dim_flag = .true.
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do i = 1, 3
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call get_command_argument(arg_pos, textholder)
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read(textholder, *) box_len(i)
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arg_pos = arg_pos + 1
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end do
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case('origin')
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do i = 1, 3
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call get_command_argument(arg_pos, textholder)
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