Alex Selimov
5 years ago
commit
d09ebfa7e0
@ -0,0 +1,82 @@
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module box
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!This module contains information on the properties of the current box.
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use parameters
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implicit none
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real(kind=dp) :: box_bd(6) !Global box boundaries
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character(len=3) :: box_bc !Box boundary conditions (periodic or shrinkwrapped)
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!The subbox variables contain values for each subbox, being the boxes read in through some
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!command. Currently only mode_merge will require sub_boxes, for mode_create it will always
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!allocate to only 1 sub_box
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integer :: sub_box_num = 0
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integer, allocatable :: sub_box_array_bd(:,:,:)!Boundaries in the atom and element arrays for each sub_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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public
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contains
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subroutine box_init
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!Initialize some box functions
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box_bd(:) = 0.0_dp
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box_bc = 'ppp'
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end subroutine box_init
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subroutine alloc_sub_box(n)
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!Allocate the sub_box variables
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integer, intent(in) :: n
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allocate(sub_box_ori(3,3,n), sub_box_bd(6,n), sub_box_array_bd(2,2,n))
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end subroutine alloc_sub_box
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subroutine grow_sub_box(n)
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!Grows sub box arrays, this is only called when a new file is read in
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integer, intent(in) :: n
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integer, allocatable :: temp_array_bd(:,:,:), temp_file(:)
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real(kind=dp), allocatable :: temp_ori(:,:,:), temp_bd(:,:)
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!Allocate temporary arrays
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allocate(temp_ori(3,3,sub_box_num+n),temp_bd(6,sub_box_num+n), &
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temp_array_bd(2,2,sub_box_num+n), temp_file(sub_box_num+n))
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!Move allocation for all sub_box_arrays
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temp_ori(:,:,1:sub_box_num) = sub_box_ori
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temp_ori(:,:,sub_box_num+1:) = 0.0_dp
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call move_alloc(temp_ori, sub_box_ori)
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temp_bd(:, 1:sub_box_num) = sub_box_bd
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temp_bd(:, sub_box_num+1:) = 0.0_dp
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call move_alloc(temp_bd, sub_box_bd)
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temp_array_bd(:,:,1:sub_box_num) = sub_box_array_bd
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temp_array_bd(:,:,sub_box_num+1:) = 0.0_dp
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call move_alloc(temp_array_bd, sub_box_array_bd)
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return
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end subroutine grow_sub_box
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subroutine grow_box(temp_box_bd)
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!This function takes in a temporary box boundary and adjusts the overall box boundaries
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!to include it
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real(kind=dp), dimension(6), intent(in) :: temp_box_bd
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integer :: i
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do i = 1, 3
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if(temp_box_bd(2*i-1) < box_bd(2*i-1)) box_bd(2*i-1) = temp_box_bd(2*i-1)
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if(temp_box_bd(2*i) > box_bd(2*i)) box_bd(2*i) = temp_box_bd(2*i)
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end do
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return
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end subroutine grow_box
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end module box
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@ -0,0 +1,26 @@
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module mode_convert
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use parameters
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use box
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use elements
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use io
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public
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contains
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subroutine convert(arg_pos)
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!This subroutine converts a single input file from one format to another
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integer, intent(out) :: arg_pos
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character(len=100) :: infile, outfile
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real(kind = dp) :: temp_box_bd(6)
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!We have to allocate the element and atom arrays with a size of 1 for the read in code to work
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call alloc_ele_arrays(1,1)
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!First read in the file
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call get_command_argument(2, infile)
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call get_in_file(infile)
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call read_in(1, (/0.0_dp,0.0_dp,0.0_dp/), temp_box_bd)
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call grow_box(temp_box_bd)
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arg_pos = 3
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end subroutine convert
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end module mode_convert
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@ -0,0 +1,100 @@
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module mode_merge
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!This module contains the code needed for merging several .mb files together
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use parameters
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use atoms
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use io
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use subroutines
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use elements
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character(len=4) :: dim
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integer :: in_num
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public
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contains
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subroutine merge(arg_pos)
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integer, intent(out) :: arg_pos
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integer :: i
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real(kind=dp) :: displace(3), temp_box_bd(6)
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!First we parse the merge command
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call parse_command(arg_pos)
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!Now loop over all files and stack them
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do i = 1, in_num
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displace(:) = 0.0_dp
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if ((i==1).or.(trim(adjustl(dim)) == 'none')) then
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call read_in(i, displace, temp_box_bd)
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call grow_box(temp_box_bd)
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else
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select case(trim(adjustl(dim)))
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case('x')
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displace(1) = box_bd(2)
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case('y')
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displace(2) = box_bd(4)
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case('z')
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displace(3) = box_bd(6)
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end select
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call read_in(i, displace, temp_box_bd)
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call grow_box(temp_box_bd)
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end if
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end do
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return
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end subroutine merge
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subroutine parse_command(arg_pos)
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integer, intent(out) :: arg_pos
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character(len=100) :: textholder
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integer :: i, stat, arglen
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!Get dimension to concatenate along
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call get_command_argument(2, dim, arglen)
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if (arglen == 0) STOP "Missing dim in mode_merge command"
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select case(trim(adjustl(dim)))
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case('x','y','z','none')
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continue
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case default
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print *, dim, " not accepted as a dimension in mode_merge"
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stop 3
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end select
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!Get number of files to read in
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call get_command_argument(3, textholder, arglen)
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if (arglen == 0) STOP "Number of files to read missing in mode_merge command"
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read(textholder, *, iostat = stat) in_num
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if (stat > 0) STOP "Error reading number of files in, must be integer"
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!Now loop and pull out all files
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do i = 1, in_num
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call get_command_argument(3+i, textholder, arglen)
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if (arglen == 0) STOP "Fewer files to read in then specified"
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!Make sure this file is readable
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call get_in_file(textholder)
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end do
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!Set argpos accordingly
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arg_pos = 3+in_num+1
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!Now options loop
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!Check for optional keywords
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do while(.true.)
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if(arg_pos > command_argument_count()) exit
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!Pull out the next argument which should either be a keyword or an option
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call get_command_argument(arg_pos, textholder)
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textholder=adjustl(textholder)
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arg_pos=arg_pos+1
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!Choose what to based on what the option string is
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select case(trim(textholder))
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case default
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!If it isn't an available option to mode merge then we just exit
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exit
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end select
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end do
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end subroutine parse_command
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end module mode_merge
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