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@ -520,6 +520,8 @@ module io
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12 format('coarse-grained domain')
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12 format('coarse-grained domain')
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13 format('ie basis_num ng_node esize'/ 'ip ibasis type x y z')
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13 format('ie basis_num ng_node esize'/ 'ip ibasis type x y z')
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14 format('atomistic domain' / 'ia type_atom x y z')
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14 format('atomistic domain' / 'ia type_atom x y z')
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15 format('ie basis_num ng_node esize'/ 'ip ibasis type x y z velx vely velz')
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16 format('atomistic domain' / 'ia type_atom x y z velx vely velz')
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19 format('max nodes per element and basis per nodes' / 2i16)
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19 format('max nodes per element and basis per nodes' / 2i16)
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20 format('max interpo per element' / i16)
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20 format('max interpo per element' / i16)
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21 format('atom types to elements')
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21 format('atom types to elements')
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@ -562,7 +564,11 @@ module io
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if(ele_num > 0) then
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if(ele_num > 0) then
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write(11,12)
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write(11,12)
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ip = 0
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ip = 0
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if(allocated(vel_node)) then
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write(11,15)
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else
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write(11,13)
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write(11,13)
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end if
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do i = 1, ele_num
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do i = 1, ele_num
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select case(type_ele(i))
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select case(type_ele(i))
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case('fcc','bcc')
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case('fcc','bcc')
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@ -570,22 +576,39 @@ module io
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case('20fcc')
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case('20fcc')
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write(11, '(4i16)') i, basisnum(lat_ele(i)), 3, (size_ele(i)-1)
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write(11, '(4i16)') i, basisnum(lat_ele(i)), 3, (size_ele(i)-1)
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end select
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end select
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if(allocated(vel_node)) then
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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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ip = ip + 1
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write(11, '(3i16, 6f23.15)') ip, ibasis, basis_type(ibasis, lat_ele(i)), r_node(:, ibasis, inod, i), &
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vel_node(:,ibasis,inod,i)
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end do
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end do
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else
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do inod = 1, ng_node(lat_ele(i))
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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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do ibasis = 1, basisnum(lat_ele(i))
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ip = ip + 1
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ip = ip + 1
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write(11, '(3i16, 3f23.15)') ip, ibasis, basis_type(ibasis, lat_ele(i)), r_node(:, ibasis, inod, i)
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write(11, '(3i16, 3f23.15)') ip, ibasis, basis_type(ibasis, lat_ele(i)), r_node(:, ibasis, inod, i)
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end do
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end do
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end do
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end do
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end if
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end do
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end do
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end if
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end if
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!Now write the atomic information
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!Now write the atomic information
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if(atom_num /= 0) then
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if(atom_num /= 0) then
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if(allocated(vel_atom)) then
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write(11, 16)
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do i = 1, atom_num
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write(11, '(2i16, 6f23.15)') i, type_atom(i), r_atom(:,i), vel_atom(:, i)
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end do
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else
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write(11,14)
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write(11,14)
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do i = 1, atom_num
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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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write(11, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i)
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end do
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end do
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end if
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end if
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end if
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close(11)
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close(11)
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end subroutine write_pycac
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end subroutine write_pycac
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@ -730,9 +753,10 @@ module io
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real(kind = dp), dimension(6), intent(out) :: temp_box_bd
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real(kind = dp), dimension(6), intent(out) :: temp_box_bd
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integer :: i, j, k, l, n, inod, ibasis, type, size, in_atoms, in_eles, new_atom_types, &
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integer :: i, j, k, l, n, inod, ibasis, type, size, in_atoms, in_eles, new_atom_types, &
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new_type_to_type(10), new_lattice_types, sbox, new_lattice_map(10)
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new_type_to_type(10), new_lattice_types, sbox, new_lattice_map(10), btype_map(10,10), bnum_map(10), &
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node_map(10)
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character(len=100) :: etype
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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) :: r(3), newdisplace(3), lapa_map(10)
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real(kind=dp), allocatable :: r_innode(:,:,:)
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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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character(len = 2) :: new_type_to_name(10)
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!First open the file
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!First open the file
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@ -782,45 +806,29 @@ module io
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call add_atom_type(new_type_to_name(i), new_type_to_type(i), all_new)
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call add_atom_type(new_type_to_name(i), new_type_to_type(i), all_new)
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end do
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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 the number of lattice types, basisnum, and number of nodes for each lattice type
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read(11,*) new_lattice_types, (basisnum(i), i = lattice_types+1, lattice_types+new_lattice_types), &
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read(11,*) new_lattice_types, (bnum_map(i), i = 1, new_lattice_types),(node_map(i), i =1, 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 the basis atom types for every lattice
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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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read(11,*) ((btype_map(i,j), i = 1, bnum_map(j)), j = 1, new_lattice_types)
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!Convert the basis_atom 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 j =1, new_lattice_types
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do i = 1, basisnum(j)
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do i = 1, bnum_map(j)
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basis_type(i,j) = new_type_to_type(basis_type(i,j))
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btype_map(i,j) = new_type_to_type(btype_map(i,j))
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end do
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end do
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end do
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end do
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!Read the lattice parameters for every lattice type
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!Read the lattice parameters for every lattice type
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read(11,*) (lapa(i), i = lattice_types+1, lattice_types+new_lattice_types)
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read(11,*) (lapa_map(i), i = 1, new_lattice_types)
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!Now we loop over all new lattice types and check to see if they are exactly the same as any old lattice types
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!Now we loop over all new lattice types and check to see if they are exactly the same as any old lattice types
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!If they are then we map the new type to the old type.
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!If they are then we map the new type to the old type.
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k = lattice_types + 1
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new_lattice_map(:) = 0
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new_lattice_map(:) = 0
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new_loop:do i = 1, new_lattice_types
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new_loop:do i = 1, new_lattice_types
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old_loop:do j = 1, lattice_types
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call lattice_map(bnum_map(i), btype_map(:,i), node_map(i), lapa_map(i), new_lattice_map(i))
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!First check all the lattice level variables
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if ((basisnum(lattice_types + i) == basisnum(j)).and. &
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(ng_node(lattice_types + i) == ng_node(j))) then
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!Now check the basis level variables
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do ibasis =1, basisnum(i)
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if(basis_type(ibasis,lattice_types+i) /= basis_type(ibasis,j)) then
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cycle old_loop
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end if
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end do
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new_lattice_map(i) = j
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cycle new_loop
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end if
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end do old_loop
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new_lattice_map(i) = k
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k = k+1
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end do new_loop
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end do new_loop
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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 number of elements and atoms and allocate arrays
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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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read(11, *) in_atoms, in_eles
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call grow_ele_arrays(in_eles, in_atoms)
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call grow_ele_arrays(in_eles, in_atoms)
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@ -909,7 +917,7 @@ module io
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!Read define atom_types by mass
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!Read define atom_types by mass
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print *, j
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print *, j
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do i = 1, j
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do i = 1, j
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call atommassspecies(atomic_masses(i), atomic_element)
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call realatomspecies(atomic_masses(i), atomic_element)
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call add_atom_type(atomic_element, atom_type_map(i), all_new)
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call add_atom_type(atomic_element, atom_type_map(i), all_new)
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print *, i, atom_type_map(i)
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print *, i, atom_type_map(i)
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end do
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end do
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@ -1009,13 +1017,15 @@ module io
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!Internal Variables
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!Internal Variables
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integer :: i, j, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
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integer :: i, j, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
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id, type_node, ilat, esize, tag, type, bnum, n, ibasis, ip, atom_type_map(100)
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id, type_node, ilat, esize, tag, type, bnum, n, ibasis, ip, atom_type_map(100)
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real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), &
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real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), vela(3),&
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ee(10,20), fe(3,10,20), ve(6,10,20), re(3,10,20), atomic_masses(10)
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ee(10,20), fe(3,10,20), ve(6,10,20), re(3,10,20), vele(3,10,20), atomic_masses(10)
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character(len=100) :: textholder, fcc
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character(len=100) :: textholder, fcc
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character(len=1000) :: line
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character(len=1000) :: line
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character(len=2) :: atomic_element
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character(len=2) :: atomic_element
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logical :: read_vel
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read_vel =.false.
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open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
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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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!Now initialize some important variables if they aren't defined
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@ -1063,7 +1073,7 @@ module io
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!Read define atom_types by mass
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!Read define atom_types by mass
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do i = 1, j
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do i = 1, j
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call atommassspecies(atomic_masses(i), atomic_element)
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call realatomspecies(atomic_masses(i), atomic_element)
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call add_atom_type(atomic_element, atom_type_map(i), all_new)
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call add_atom_type(atomic_element, atom_type_map(i), all_new)
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end do
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end do
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@ -1077,12 +1087,22 @@ module io
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if(in_atoms > 0 ) then
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if(in_atoms > 0 ) then
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!Read atom header
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!Read atom header
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read(11,*) textholder
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read(11,'(a)') line
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read(line, *) (textholder, i=1, 18)
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if(textholder=="velx") then
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call alloc_vel_arrays(in_eles, in_atoms)
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read_vel = .true.
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end if
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do ia = 1, in_atoms
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do ia = 1, in_atoms
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read(11,'(a)') line(:)
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read(11,'(a)') line(:)
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if(read_vel) then
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read(line,*) tag, type, ra(:), ea, fa(:), va(:), vela(:)
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else
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read(line,*) tag, type, ra(:), ea, fa(:), va(:)
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read(line,*) tag, type, ra(:), ea, fa(:), va(:)
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end if
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call add_atom(tag, atom_type_map(type), sub_box_num, ra)
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call add_atom(tag, atom_type_map(type), sub_box_num, ra)
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call add_atom_data(atom_num, ea, fa, va)
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call add_atom_data(atom_num, ea, fa, va)
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if(read_vel) vel_atom(:,atom_num) = vela
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end do
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end do
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end if
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end if
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@ -1096,9 +1116,16 @@ module io
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do ie =1, in_eles
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do ie =1, in_eles
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read(11,*) tag, n, bnum, esize
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read(11,*) tag, n, bnum, esize
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inbtypes(:) = 0
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inbtypes(:) = 0
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if(read_vel) then
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do inod =1, n*bnum
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read(11,*) ip, ibasis, inbtypes(ibasis), re(:,ibasis,ip), ee(ibasis,ip), fe(:,ibasis,ip), &
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ve(:,ibasis,ip), vele(:,ibasis,ip)
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end do
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else
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do inod =1, n*bnum
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do inod =1, n*bnum
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read(11,*) ip, ibasis, inbtypes(ibasis), re(:,ibasis,ip), ee(ibasis,ip), fe(:,ibasis,ip), ve(:,ibasis,ip)
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read(11,*) ip, ibasis, inbtypes(ibasis), re(:,ibasis,ip), ee(ibasis,ip), fe(:,ibasis,ip), ve(:,ibasis,ip)
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end do
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end do
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end if
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do i = 1, bnum
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do i = 1, bnum
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inbtypes(ibasis) = atom_type_map(inbtypes(ibasis))
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inbtypes(ibasis) = atom_type_map(inbtypes(ibasis))
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end do
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end do
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@ -1110,11 +1137,12 @@ module io
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end if
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end if
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call add_element(tag, fcc, esize+1, lat_type, sub_box_num, re)
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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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call add_element_data(ele_num, ee, fe, ve)
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if(read_vel) vel_node(:, :, :, ele_num) = vele(:,1:max_basisnum, 1:max_ng_node)
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end do
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end do
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end if
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end if
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call set_max_esize
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call set_max_esize
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return
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return
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end subroutine
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end subroutine read_pycac_out
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subroutine read_lmp(file, displace, temp_box_bd)
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subroutine read_lmp(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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!This subroutine is used to read .cac files which are used with the lammpsCAC format
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@ -1184,7 +1212,7 @@ module io
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!Read atomic masses
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!Read atomic masses
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do i = 1, type_in
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do i = 1, type_in
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read(11,*) j, mass
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read(11,*) j, mass
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call ATOMMASSSPECIES(mass, atom_species)
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call realatomspecies(mass, atom_species)
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call add_atom_type(atom_species, type_map(i), all_new)
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call add_atom_type(atom_species, type_map(i), all_new)
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end do
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end do
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@ -1272,7 +1300,7 @@ module io
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!Read atomic masses
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!Read atomic masses
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do i = 1, type_in
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do i = 1, type_in
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read(11,*) j, mass, textholder
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read(11,*) j, mass, textholder
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call ATOMMASSSPECIES(mass, atom_species)
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call realatomspecies(mass, atom_species)
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call add_atom_type(atom_species, type_map(i), all_new)
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call add_atom_type(atom_species, type_map(i), all_new)
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end do
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end do
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Alex Selimov
3 years ago