Merge pull request #4 from aselimov/bg--fixes-to-mode-merge-reading

Fixes to file reading to ensure that mode_merge works correctly
master
aselimov 5 years ago committed by GitHub
commit ce2e3d17f4
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@ -1,6 +1,6 @@
FC=ifort FC=ifort
FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin #FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
#FFLAGS=-c -mcmodel=large -Ofast FFLAGS=-mcmodel=large -Ofast
MODES=mode_create.o mode_merge.o mode_convert.o MODES=mode_create.o mode_merge.o mode_convert.o
OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES) OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES)

@ -394,10 +394,12 @@ module io
real(kind=dp), dimension(3), intent(in) :: displace real(kind=dp), dimension(3), intent(in) :: displace
real(kind = dp), dimension(6), intent(out) :: temp_box_bd real(kind = dp), dimension(6), intent(out) :: temp_box_bd
integer :: i, j, k, n, inod, ibasis, type, size, in_atoms, in_eles integer :: i, j, k, n, inod, ibasis, type, size, in_atoms, in_eles, new_atom_types, &
new_type_to_type(10), new_lattice_types
character(len=100) :: etype character(len=100) :: etype
real(kind=dp) :: r(3), newdisplace(3) real(kind=dp) :: r(3), newdisplace(3)
real(kind=dp), allocatable :: r_innode(:,:,:) real(kind=dp), allocatable :: r_innode(:,:,:)
character(len = 2) :: new_type_to_name(10)
!First open the file !First open the file
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind') open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
@ -433,15 +435,26 @@ module io
sub_box_num = sub_box_num + n sub_box_num = sub_box_num + n
!Read in the number of atom types and all their names !Read in the number of atom types and all their names
read(11, *) atom_types, (type_to_name(i), i = 1, atom_types) 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 the number of lattice types, basisnum, and number of nodes for each lattice type
read(11,*) lattice_types, (basisnum(i), i = 1, lattice_types), (ng_node(i), i = 1, lattice_types) 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 !Define max_ng_node and max_basis_num
max_basisnum = maxval(basisnum) max_basisnum = maxval(basisnum)
max_ng_node = maxval(ng_node) max_ng_node = maxval(ng_node)
!Read the basis atom types for every lattice !Read the basis atom types for every lattice
read(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_types) 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 number of elements and atoms and allocate arrays !Read number of elements and atoms and allocate arrays
read(11, *) in_atoms, in_eles read(11, *) in_atoms, in_eles
call grow_ele_arrays(in_eles, in_atoms) call grow_ele_arrays(in_eles, in_atoms)
@ -450,7 +463,7 @@ module io
!Read the atoms !Read the atoms
do i = 1, in_atoms do i = 1, in_atoms
read(11,*) j, type, r(:) read(11,*) j, type, r(:)
call add_atom(type, r+newdisplace) call add_atom(new_type_to_type(type), r+newdisplace)
end do end do
!Read the elements !Read the elements
@ -462,11 +475,12 @@ module io
r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace
end do end do
end do end do
type = type + lattice_types
call add_element(etype, size, type, r_innode) call add_element(etype, size, type, r_innode)
end do end do
!Close the file being read !Close the file being read
close(11) close(11)
lattice_types = lattice_types + new_lattice_types
end subroutine read_mb end subroutine read_mb
end module io end module io

@ -12,8 +12,8 @@ module mode_create
character(len=100) :: name, element_type character(len=100) :: name, element_type
real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), & real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), &
orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3) orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3)
integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), & integer :: esize, ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
basis_pos(3,10) basis_pos(3,10)
logical :: dup_flag, dim_flag logical :: dup_flag, dim_flag
@ -58,16 +58,15 @@ module mode_create
allocate(r_node_temp(3,max_basisnum,max_ng_node)) allocate(r_node_temp(3,max_basisnum,max_ng_node))
if(dup_flag) then !Get the inverse orientation matrix we will need later
call matrix_inverse(orient,3,orient_inv)
!We initialize the cell with a lattice_parameter of 1 because we will add the lattice parameter later if(dup_flag) then
call cell_init(1.0_dp, esize, element_type, orient, cell_mat)
!Define box vertices
do i = 1, 8 do i = 1, 8
box_vert(:,i) = duplicate(:)*esize*lattice_space(:)*cubic_cell(:,i) + origin(:) box_vert(:,i) = duplicate(:)*esize*lattice_space(:)*cubic_cell(:,i) + (origin(:)/lattice_parameter)
end do end do
call matrix_inverse(orient,3,orient_inv)
!Now get the rotated box vertex positions in lattice space. Should be integer units !Now get the rotated box vertex positions in lattice space. Should be integer units
box_lat_vert = int(matmul(fcc_inv, matmul(orient_inv, box_vert)))+1 box_lat_vert = int(matmul(fcc_inv, matmul(orient_inv, box_vert)))+1
!Find the new maxlen !Find the new maxlen
@ -76,21 +75,25 @@ module mode_create
box_bd(2*i) = maxval(box_vert(i,:)) - 0.25_dp*lattice_space(i) box_bd(2*i) = maxval(box_vert(i,:)) - 0.25_dp*lattice_space(i)
box_bd(2*i-1) = origin(i)-0.25_dp*lattice_space(i) box_bd(2*i-1) = origin(i)-0.25_dp*lattice_space(i)
end do end do
!and then call the build function with the correct transformation matrix
select case(trim(adjustl(element_type)))
case('fcc')
call build_with_rhomb(box_lat_vert, fcc_mat)
case default
print *, "Element type ", trim(adjustl(element_type)), " not accepted in mode create, please specify a supported ", &
"element type"
stop 3
end select
!Now that it is multiply by the lattice parameter
box_bd = box_bd*lattice_parameter
else if(dim_flag) then else if(dim_flag) then
continue !As a note everything is defined so that the lattice parameter is multiplied in at the end
!so we have to divide all the real Angstroms units by the lattice parameter
!Define box_vertices
do i = 1, 8
box_vert(:,i) = (cubic_cell(:,i)*box_len(:) + origin(:))/lattice_parameter
end do
!Now get the rotated box vertex positions in lattice space. Should be integer units
box_lat_vert = int(matmul(fcc_inv, matmul(orient_inv, box_vert)))+1
!Now get the box_bd in lattice units
do i = 1, 3
box_bd(2*i) = (box_len(i)+origin(i))/lattice_parameter
box_bd(2*i-1) = origin(i)/lattice_parameter
end do
else else
call cell_init(lattice_parameter, esize, element_type, orient, cell_mat) call cell_init(lattice_parameter, esize, element_type, orient, cell_mat)
@ -112,6 +115,19 @@ module mode_create
!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 !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
if(dup_flag.or.dim_flag) then if(dup_flag.or.dim_flag) then
!Call the build function with the correct transformation matrix
select case(trim(adjustl(element_type)))
case('fcc')
call build_with_rhomb(box_lat_vert, fcc_mat)
case default
print *, "Element type ", trim(adjustl(element_type)), " not accepted in mode create, please specify a supported ", &
"element type"
stop 3
end select
!Now that it is built multiply by the lattice parameter
box_bd = box_bd*lattice_parameter
!Allocate variables !Allocate variables
call alloc_ele_arrays(lat_ele_num, lat_atom_num*basisnum(1)) call alloc_ele_arrays(lat_ele_num, lat_atom_num*basisnum(1))
if(lat_atom_num > 0) then if(lat_atom_num > 0) then
@ -208,13 +224,21 @@ module mode_create
!If the duplicate command is passed then we extract the information on the new bounds. !If the duplicate command is passed then we extract the information on the new bounds.
case('duplicate') case('duplicate')
if(dim_flag) STOP "Both duplicate and dim options cannot be used in mode_create"
dup_flag = .true. dup_flag = .true.
do i = 1, 3 do i = 1, 3
call get_command_argument(arg_pos, textholder) call get_command_argument(arg_pos, textholder)
read(textholder, *) duplicate(i) read(textholder, *) duplicate(i)
arg_pos = arg_pos + 1 arg_pos = arg_pos + 1
end do end do
case('dim')
if(dup_flag) STOP "Both duplicate and dim options cannot be used in mode_create"
dim_flag = .true.
do i = 1, 3
call get_command_argument(arg_pos, textholder)
read(textholder, *) box_len(i)
arg_pos = arg_pos + 1
end do
case('origin') case('origin')
do i = 1, 3 do i = 1, 3
call get_command_argument(arg_pos, textholder) call get_command_argument(arg_pos, textholder)

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