Changes to how the adjustment to nodal positions is performed for lammpscac output
This commit is contained in:
Alex Selimov
parent
55fbe679e5
commit
849da1d24a
4 changed files with 69 additions and 54 deletions
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@ -12,7 +12,7 @@ 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), duplicate(3), adjustVar(3,8)
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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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@ -105,7 +105,7 @@ module mode_create
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box_bd(2*i) = maxval(r_node_temp(i,:,:))
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box_bd(2*i-1) = origin(i)
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end do
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call add_element(element_type, esize, 1, r_node_temp)
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call add_element(element_type, esize, 1, 1, r_node_temp)
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end if
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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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@ -141,7 +141,7 @@ module mode_create
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r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis)
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end do
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end do
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call add_element(element_type, esize, 1, r_node_temp)
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call add_element(element_type, esize, 1, 1, r_node_temp)
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end do
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end if
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end if
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@ -199,7 +199,20 @@ module mode_create
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call get_command_argument(arg_pos, orient_string, arglen)
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if (arglen==0) STOP "Missing orientation in orient command of mode create"
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arg_pos = arg_pos+1
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call parse_ori_vec(orient_string, orient(i,:))
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ori_pos=2
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do j = 1,3
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if (orient_string(ori_pos:ori_pos) == '-') then
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ori_pos = ori_pos + 1
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read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
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if (stat>0) STOP "Error reading orient value"
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orient(i,j) = -orient(i,j)
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ori_pos = ori_pos + 1
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else
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read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
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if(stat>0) STOP "Error reading orient value"
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ori_pos=ori_pos + 1
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end if
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end do
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end do
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@ -234,6 +247,7 @@ module mode_create
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exit
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end select
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end do
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!Calculate the lattice periodicity length in lattice units
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do i = 1, 3
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lattice_space(i) = norm2(orient(i,:))
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@ -264,8 +278,9 @@ module mode_create
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!Now normalize the orientation matrix
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orient = matrix_normal(orient,3)
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!Set lattice_num to 1
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!Set lattice_num to 1 and add the lattice_parameter to the elements module lattice paramter variable
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lattice_types = 1
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lapa(1) = lattice_parameter
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!If we haven't defined a basis then define the basis and add the default basis atom type and position
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if (basisnum(1) == 0) then
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@ -286,7 +301,7 @@ module mode_create
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!Internal variables
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integer :: i, inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz, numlatpoints, ele(3,8), rzero(3), &
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vlat(3), temp_lat(3,8), m, n, o
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real(kind=dp) :: v(3), temp_nodes(3,1,8), adjustVar(3,8)
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real(kind=dp) :: v(3), temp_nodes(3,1,8)
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real(kind=dp), allocatable :: resize_lat_array(:,:)
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logical, allocatable :: lat_points(:,:,:)
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logical :: node_in_bd(8)
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@ -294,23 +309,6 @@ module mode_create
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!Do some value initialization
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max_esize = esize
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!If we are writing out to lammpscac format then we have to adjust the nodal positions
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if(lmpcac) then
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do inod = 1, 8
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do i = 1,3
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if(is_equal(cubic_cell(i, inod),0.0_dp)) then
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adjustVar(i,inod) = -0.5_dp
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else
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adjustVar(i, inod) = 0.5_dp
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end if
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end do
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end do
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adjustVar(:,1:8) = matmul(orient,matmul(fcc_mat,adjustVar(:,1:8)))
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else
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adjustVar(:,:)=0.0_dp
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end if
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!First find the bounding lattice points (min and max points for the box in each dimension)
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numlatpoints = 1
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do i = 1, 3
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@ -328,6 +326,7 @@ module mode_create
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continue
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end select
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!Loop over all of lattice points within the boundary, we choose between two loops. One for the atomistic case
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!and one for the regular case
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if (esize==2) then
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@ -440,11 +439,9 @@ module mode_create
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end do
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if(all(node_in_bd)) then
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lat_ele_num = lat_ele_num+1
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do inod = 1, 8
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r_lat(:,inod,lat_ele_num) = temp_nodes(:,1,inod) + adjustVar(:,inod)
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end do
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lat_ele_num = lat_ele_num+1
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r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
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!Now set all the lattice points contained within an element to false
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do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:))
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do n = minval(temp_lat(2,:)), maxval(temp_lat(2,:))
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@ -510,4 +507,4 @@ module mode_create
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end subroutine error_message
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end module mode_create
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end module mode_create
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