Added deform box option and allowed for reading time information from restart files
This commit is contained in:
Alex Selimov
parent
8d939ed942
commit
724e573287
@ -2,7 +2,7 @@ FC=ifort
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FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
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#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays
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MODES=mode_create.o mode_merge.o mode_convert.o
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OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o
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OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o opt_deform.o
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OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES) $(OPTIONS) call_option.o sorts.o
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.SUFFIXES:
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@ -14,7 +14,6 @@ module box
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real(kind=dp), allocatable :: sub_box_ori(:,:,:)!Orientations for each of the subboxes
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real(kind=dp), allocatable :: sub_box_bd(:,:)!Boundaries for each of the sub_boxes
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!Below are some simulation parameters which may be adjusted if reading in restart files
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integer :: timestep=0
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real(kind=dp) :: total_time=0.0_dp
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@ -98,4 +97,4 @@ module box
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end do
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return
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end subroutine in_sub_box
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end module box
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end module box
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@ -3,6 +3,7 @@ subroutine call_option(option, arg_pos)
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use opt_disl
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use opt_group
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use opt_orient
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use opt_deform
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use opt_delete
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use box
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implicit none
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@ -31,6 +32,8 @@ subroutine call_option(option, arg_pos)
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bound_called = .true.
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case('-sbox_ori')
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call sbox_ori(arg_pos)
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case('-deform')
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call deform(arg_pos)
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case('-delete')
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call run_delete(arg_pos)
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case('-set_cac')
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@ -503,6 +503,7 @@ module elements
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size_ele(sorted_index(i)) = 0
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lat_ele(sorted_index(i)) = 0
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sbox_ele(sorted_index(i)) = 0
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tag_ele(sorted_index(i)) = 0
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else
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node_num = node_num - ng_node(lat_ele(sorted_index(i)))
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r_node(:,:,:,sorted_index(i)) = r_node(:,:,:,ele_num)
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@ -510,6 +511,7 @@ module elements
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size_ele(sorted_index(i)) = size_ele(ele_num)
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lat_ele(sorted_index(i)) = lat_ele(ele_num)
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sbox_ele(sorted_index(i)) = sbox_ele(ele_num)
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tag_ele(sorted_index(i)) = tag_ele(ele_num)
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end if
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ele_num = ele_num - 1
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end do
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20
src/io.f90
20
src/io.f90
@ -491,7 +491,7 @@ module io
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exit
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endif
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end do
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write(11, '(4i16)') i, etype, 1, basis_type(1,lat_ele(i))
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write(11, '(4i16)') tag_ele(i), etype, 1, basis_type(1,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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ip = ip + 1
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@ -505,7 +505,7 @@ module io
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if(atom_num /= 0) then
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write(11,14)
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do i = 1, atom_num
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write(11, '(3i16, 3f23.15)') i, 1, type_atom(i), r_atom(:,i)
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write(11, '(3i16, 3f23.15)') tag_atom(i), 1, type_atom(i), r_atom(:,i)
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end do
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end if
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@ -781,19 +781,19 @@ module io
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integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
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atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), &
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atom_type
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atom_type, stat
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real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3)
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character(len=100) :: textholder, in_lattype_map(10)
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character(len=2) :: atomic_element
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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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!Disregard unneeded information
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do i = 1, 3
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read(11,*) textholder
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end do
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!Read the timestep information
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read(11,*) textholder
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read(11,*) timestep, total_time
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!Read element number
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read(11,*) textholder
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read(11,*) in_eles
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!Discard info and read ng_max_node
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@ -941,7 +941,11 @@ module io
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end if
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do i = 1, in_atoms
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read(11,*) j, k, atom_type, r_in_atom(:)
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read(11,*, iostat=stat) j, k, atom_type, r_in_atom(:)
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if(stat > 0) then
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print *, j
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stop
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end if
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r_in_atom = r_in_atom + newdisplace
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call add_atom(j,atom_type_map(atom_type), sub_box_num + 1, r_in_atom)
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end do
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98
src/opt_deform.f90
Normal file
98
src/opt_deform.f90
Normal file
@ -0,0 +1,98 @@
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module opt_deform
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!This module constains the deform option which applies a uniaxial strain to the system
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use parameters
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use subroutines
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use elements
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use box
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implicit none
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real(kind=dp), save :: applied_strain
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integer, save :: sdim
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public
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contains
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subroutine deform(arg_pos)
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!This subroutine applies the simulation box deformation to the system
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integer, intent(inout) :: arg_pos
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character(len=1) :: dims(3)
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integer :: i, j, k
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real(kind=dp) :: frac_atom(atom_num), frac_node(max_basisnum, max_ng_node, ele_num)
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!initialize some variables
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dims(1) = 'x'
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dims(2) = 'y'
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dims(3) = 'z'
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!First parse the input command
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call parse_deform(arg_pos)
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print *, '-----------------------Option Deform------------------------'
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!Now convert all positions in the specified dimension to fractional coordinates
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do i = 1, atom_num
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frac_atom(i) = (r_atom(sdim, i) - box_bd(2*sdim-1))/(box_bd(2*sdim)-box_bd(2*sdim-1))
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end do
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do i = 1, ele_num
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do j = 1, ng_node(lat_ele(i))
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do k = 1, basisnum(lat_ele(i))
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frac_node(k,j,i) = (r_node(sdim,k,j,i) - box_bd(2*sdim-1))/(box_bd(2*sdim)-box_bd(2*sdim-1))
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end do
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end do
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end do
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print *, "Original box bounds in ", dims(sdim), " are ", box_bd(2*sdim-1:2*sdim)
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box_bd(2*sdim) = box_bd(2*sdim) + applied_strain
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print *, "New box bounds are ", box_bd(2*sdim-1:2*sdim)
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!Now reassign the positions
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do i = 1, atom_num
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r_atom(sdim,i) = frac_atom(i)*(box_bd(2*sdim)-box_bd(2*sdim-1)) + box_bd(2*sdim-1)
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end do
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do i = 1, ele_num
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do j = 1, ng_node(lat_ele(i))
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do k = 1, basisnum(lat_ele(i))
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r_node(sdim,k,j,i) = frac_node(k,j,i)*(box_bd(2*sdim)-box_bd(2*sdim-1)) + box_bd(2*sdim-1)
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end do
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end do
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end do
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end subroutine deform
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subroutine parse_deform(arg_pos)
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integer, intent(inout) :: arg_pos
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integer :: arg_len
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character(len=100) :: textholder
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!Pull out the dimension to be strained
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arg_pos=arg_pos+1
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call get_command_argument(arg_pos, textholder, arg_len)
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if (arg_len == 0) stop "Missing dim in deform command"
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select case(trim(adjustl(textholder)))
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case('x','X')
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sdim = 1
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case('y','Y')
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sdim = 2
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case('z','Z')
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sdim = 3
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case default
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print *, "Dimension ", trim(adjustl(textholder)), " is not accepted. Please select either x, y, or z"
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end select
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!Now pull out the strain vector, currently only accepts a real number by which to reduce the simulation cell size by in
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!that dimension
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, textholder, arg_len)
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if (arg_len == 0) stop "Missing strain in deform command"
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read(textholder, *) applied_strain
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arg_pos = arg_pos + 1
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end subroutine parse_deform
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end module opt_deform
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