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Current working changes to control-box code

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development
Alex Selimov 4 years ago
parent 5949f04103
commit 95e2ad0b4d
6 changed files with 50 additions and 97 deletions
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7
README.md
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@ -58,7 +58,7 @@ Default duplicate is `1 1 1`. This is used to replicate the element along each d
**Dimensions**
```
dimensions dimx dimy dimz
dim dimx dimy dimz
```
There is no default dimensions as duplicate is the default option. This command assigns a box with user-assigned dimensions and fills it with the desired element. By default atoms fill in the jagged edges at the boundaries if the dimensions command is included.
@ -129,6 +129,11 @@ wrap
This will wrap atomic positions back inside the box. Effectively as if periodic boundary conditions are applied so that atoms which exit from one side of the simulation cell enter back in through the other.
###Mode Metric
```
--metric cmetric nfiles {filepaths}
```
## Options
Options are additional portions of code which have additional functionality. Options are performed in the order that they appear in the argument list and can be added to any mode. If wanting to use strictly options use `--convert` to specify input and output files.

6
src/box.f90
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@ -97,4 +97,10 @@ module box
end do
return
end subroutine in_sub_box
subroutine reset_box
!This subroutine just resets the box boundary and position
box_bc = "ppp"
box_bd(:) = 0
end subroutine reset_box
end module box

7
src/elements.f90
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@ -793,4 +793,11 @@ module elements
virial_node(:,:,:,ie) = virial
return
end subroutine add_element_data
subroutine reset_data
!This function resets all of the data arrays for the elements and atoms
atom_num = 0
ele_num = 0
node_num = 0
end subroutine reset_data
end module elements

63
src/io.f90
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@ -583,49 +583,41 @@ module io
temp_infile = filename
end if
!Infinite loop which only exists if user provides valid filetype
do while(.true.)
!Check to see if file exists, if it does then ask user if they would like to overwrite the file
inquire(file=trim(temp_infile), exist=file_exists)
if (.not.file_exists) then
print *, "The file ", trim(adjustl(filename)), " does not exist. Please input an existing file to read."
stop 3
end if
!Check to see if file exists, if it does then ask user if they would like to overwrite the file
inquire(file=trim(temp_infile), exist=file_exists)
if (.not.file_exists) then
print *, "The file ", trim(adjustl(filename)), " does not exist. Please input a filename that exists"
read(*,*) temp_infile
cycle
select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
case('restart', 'mb', 'cac')
infilenum=infilenum+1
infiles(infilenum) = temp_infile
case('out')
if(atom_types == 0) then
print *, "Please run -set_types command prior to running code requiring reading in pycac_*.out files"
stop 3
end if
select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
case('restart', 'mb', 'cac')
infilenum=infilenum+1
infiles(infilenum) = temp_infile
exit
case('out')
if(atom_types == 0) then
print *, "Please run -set_types command prior to running code requiring reading in pycac_*.out files"
stop 3
end if
select case(trim(adjustl(mode)))
case('--convert','--metric')
infilenum = infilenum+1
infiles(infilenum) = temp_infile
exit
case default
print *, "Files of type .out cannot be used with mode ", trim(adjustl(mode))
stop 3
end select
select case(trim(adjustl(mode)))
case('--convert','--metric')
infilenum = infilenum+1
infiles(infilenum) = temp_infile
case default
print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
"please input a filename with extension from following list: mb, restart, cac, or out."
read(*,*) temp_infile
print *, "Files of type .out cannot be used with mode ", trim(adjustl(mode))
stop 3
end select
end do
case default
print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
"please input a filename with extension from following list: mb, restart, cac, or out."
stop 3
end select
end subroutine get_in_file
subroutine read_in(i, displace, temp_box_bd)
!This subroutine loops over alll of the outfile types defined and calls the correct writing subroutine
!This subroutine reads in file i
integer, intent(in) :: i
real(kind=dp), dimension(3), intent(in) :: displace
@ -1067,6 +1059,7 @@ module io
end do
call add_element(tag, fcc, esize+1, lat_type, sub_box_num, re)
call add_element_data(ele_num, ee, fe, ve)
node_num = node_num + 8
end do
end if
call set_max_esize

1
src/opt_delete.f90
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@ -3,6 +3,7 @@ module opt_delete
use parameters
use subroutines
use elements
use neighbors
implicit none

61
src/subroutines.f90
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@ -198,66 +198,6 @@ module subroutines
end do
end subroutine
subroutine build_cell_list(numinlist, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
!This subroutine builds a cell list based on rc_off
!----------------------------------------Input/output variables-------------------------------------------
integer, intent(in) :: numinlist !The number of points within r_list
real(kind=dp), dimension(3,numinlist), intent(in) :: r_list !List of points to be used for the construction of
!the cell list.
real(kind=dp), intent(in) :: rc_off ! Cutoff radius which dictates the size of the cells
integer, dimension(3), intent(inout) :: cell_num !Number of cells in each dimension.
integer, allocatable, intent(inout) :: num_in_cell(:,:,:) !Number of points within each cell
integer, allocatable, intent(inout) :: cell_list(:,:,:,:) !Index of points from r_list within each cell.
integer, dimension(3,numinlist), intent(out) :: which_cell !The cell index for each point in r_list
!----------------------------------------Begin Subroutine -------------------------------------------
integer :: i, j, cell_lim, c(3)
real(kind=dp) :: box_len(3)
integer, allocatable :: resize_cell_list(:,:,:,:)
!First calculate the number of cells that we need in each dimension
do i = 1,3
box_len(i) = box_bd(2*i) - box_bd(2*i-1)
cell_num(i) = int(box_len(i)/(rc_off/2))+1
end do
!Initialize/allocate variables
cell_lim = 10
allocate(num_in_cell(cell_num(1),cell_num(2),cell_num(3)), cell_list(cell_lim, cell_num(1), cell_num(2), cell_num(3)))
!Now place points within cell
do i = 1, numinlist
!c is the position of the cell that the point belongs to
do j = 1, 3
c(j) = int((r_list(j,i)-box_bd(2*j-1))/(rc_off/2)) + 1
end do
!Place the index in the correct position, growing if necessary
num_in_cell(c(1),c(2),c(3)) = num_in_cell(c(1),c(2),c(3)) + 1
if (num_in_cell(c(1),c(2),c(3)) > cell_lim) then
allocate(resize_cell_list(cell_lim+10,cell_num(1),cell_num(2),cell_num(3)))
resize_cell_list(1:cell_lim, :, :, :) = cell_list
resize_cell_list(cell_lim+1:, :, :, :) = 0
call move_alloc(resize_cell_list, cell_list)
end if
cell_list(num_in_cell(c(1),c(2),c(3)),c(1),c(2),c(3)) = i
which_cell(:,i) = c
end do
return
end subroutine build_cell_list
subroutine check_right_ortho(ori, isortho, isrighthanded)
!This subroutine checks whether provided orientations in the form:
! | x1 x2 x3 |
@ -301,4 +241,5 @@ module subroutines
return
end subroutine check_right_ortho
end module subroutines

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