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First working version of reading in .cac format. Works for two separate orientations

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This commit is contained in:
Alex Selimov 2020-06-02 16:42:12 -04:00
parent 4038cab76f
commit b52d7761e0
4 changed files with 34 additions and 29 deletions
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2
src/call_option.f90
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@ -34,7 +34,7 @@ subroutine call_option(option, arg_pos)
case('-delete')
call run_delete(arg_pos)
case('-set_cac')
arg_pos = arg_pos+3
arg_pos=arg_pos +3
case default
print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
stop 3

5
src/elements.f90
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@ -646,7 +646,7 @@ module elements
if ((basisnum(j) == in_bnum).and.(ng_node(j) == in_ngnodes).and.(is_equal(lapa(j),in_lapa))) then
!Now check lattice level variables
do ibasis = 1, basisnum(j)
if(basis_type(ibasis,j) /= in_btypes(ibasis)) cycle old_loop
if(basis_type(ibasis,j) /= in_btypes(ibasis)) cycle lat_loop
end do
lat_type = j
exit lat_loop
@ -657,9 +657,10 @@ module elements
if( lat_type == 0) then
lattice_types = lattice_types + 1
basisnum(lattice_types) = in_bnum
basis_types(:,lattice_types) = in_btypes
basis_type(:,lattice_types) = in_btypes
ng_node(lattice_types) = in_ngnodes
lapa(lattice_types) = in_lapa
lat_type = lattice_types
end if
end subroutine lattice_map

54
src/io.f90
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@ -591,7 +591,7 @@ module io
end if
select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
case('restart', 'mb')
case('restart', 'mb', 'cac')
infilenum=infilenum+1
infiles(infilenum) = temp_infile
exit
@ -618,6 +618,8 @@ module io
call read_mb(infiles(i), displace, temp_box_bd)
case('restart')
call read_pycac(infiles(i), displace, temp_box_bd)
case('cac')
call read_lmpcac(infiles(i), displace, temp_box_bd)
case default
print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
" is not accepted for writing. Please select from: mb and try again"
@ -956,10 +958,11 @@ module io
real(kind=dp), dimension(3), intent(in) :: displace
real(kind = dp), dimension(6), intent(out) :: temp_box_bd
character(len=100) :: textholder, element_type, esize
character(len=100) :: textholder, element_type
character(len=2) :: atom_species
integer :: i, j, k, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3,3), in_ori(3,3), temp_box_bd(6), newdisplace(3)
integer :: i, j, k, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10), esize, &
lat_type
real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3,3), in_ori(3,3), newdisplace(3)
!First check to make sure that we have set the needed variables
if(is_equal(in_lapa,0.0_dp).or.(in_lattice_type=='')) then
@ -969,22 +972,21 @@ module io
!Open the file
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
!Now initialiaze some important variables
max_basis_num = 10
!Now initialiaze some important variables if they aren't defined
if (max_basisnum==0) max_basisnum = 10
if (max_ng_node==0) max_ng_node=8
!Read header information
read(11, *) textholder
read(11, *) textholder
!Read number of elements
read(11, *) ele_in, textholder
read(11, *) type_in, textholder
!Read box_boundaries
read(11,*) textholder
read(11,*) temp_box_bd(1:2), texholder
read(11,*) temp_box_bd(3:4), texholder
read(11,*) temp_box_bd(5:6), texholder
read(11,*) temp_box_bd(1:2), textholder
read(11,*) temp_box_bd(3:4), textholder
read(11,*) temp_box_bd(5:6), textholder
!Shift the box boundaries if needed
do i = 1, 3
@ -1016,7 +1018,6 @@ module io
!Read useless information
read(11,*) textholder
read(11,*) textholder
!Read atomic masses
do i = 1, type_in
@ -1026,13 +1027,11 @@ module io
end do
!Read useless info
do i = 1, 3
read(11,*) textholder
end do
read(11,*) textholder
!Start the reading loop
do i = 1, ele_in
read(11,*) j, ele, element_type, in_basis, esize
read(11,*) j, element_type, in_basis, esize
!Check to see if we need to grow the max_basis_num
select case(trim(adjustl(element_type)))
case('Eight_Node')
@ -1044,10 +1043,10 @@ module io
!Now calculate the lattice vectors and shift the nodal points from the corners to the center of the unit cell
!Please check the nodal numbering figure in the readme in order to understand which nodes are used for the
!calculation
lat_vec(:,1) = (r_node(:,1,2) - r_node(:,1,1))/esize
lat_vec(:,2) = (r_node(:,1,4) - r_node(:,1,1))/esize
lat_vec(:,3) = (r_node(:,1,5) - r_node(:,1,1))/esize
lat_vec(:,1) = (r_in(:,1,2) - r_in(:,1,1))/(2*esize)
lat_vec(:,2) = (r_in(:,1,4) - r_in(:,1,1))/(2*esize)
lat_vec(:,3) = (r_in(:,1,5) - r_in(:,1,1))/(2*esize)
!Now shift all the nodal positions
select case(trim(adjustl(in_lattice_type)))
case('fcc','FCC')
@ -1068,7 +1067,7 @@ module io
call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
!Now add the element
call add_element(in_lattice_type, esize, lat_type, sub_box_num, r_in)
call add_element(in_lattice_type, esize, lat_type, sub_box_num, r_in(:,1:max_basisnum,1:max_ng_node))
case('Atom')
read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,1,1)
@ -1082,17 +1081,24 @@ module io
!This code parses input values
integer, intent(in) :: apos
integer :: arglen, arg_pos
character(len=100) :: textholder
arg_pos = apos + 1
call get_command_argument(arg_pos, in_lapa, arglen)
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) then
print *, "Missing lattice parameter for set_input_lat"
end if
read(textholder,*) in_lapa
print *, in_lapa
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, in_lattice_type, arglen)
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) then
print *, "Missing lattice type for set_input_lat"
end if
end subroutine set_input_lat(arg_pos)
read(textholder,*) in_lattice_type
print *, in_lattice_type
end subroutine set_cac
end module io

2
src/main.f90
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@ -61,10 +61,8 @@ program main
case('-wrap')
wrap_flag=.true.
!This gives necessary information in order to correctly read .cac files
case('-set_cac')
call set_cac(i)
end select
end do
!Determine if a mode is being used and what it is. The first argument has to be the mode