Added group option and shift command
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Alex
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README.md
21
README.md
@ -153,4 +153,23 @@ This option deletes vacancies on a plane which when minimized should result in a
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`bx by bz` - The burgers vector for the dislocation
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`poisson` - Poisson ratio for continuum solution
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`poisson` - Poisson ratio for continuum solution
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### Option Group
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`-group select_type group_shape shape_arguments additional keywords`
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This option selects a group of either elements, nodes, atoms and applies some transformation to them.
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`select_type` - Either `nodes`, `atoms`, `elements`, `nodes/atoms`, `all`. When using the option `nodes` only nodes which are within the group are selected, `elements` selects elements based on whether the element center is within the group, `nodes/atoms` selects both nodes and atoms for the group. `all` selects elements based on the element center and atoms based on their position.
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`group_shape` - Specifies what shape the group takes and dictates which options must be passed. Each shape requires different arguments and these arguments are represented by the placeholder `shape_arguments`. The accepted group shapes and arguments are below:
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*Block:*
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`-group nodes block xlo xhi ylo yhi zlo zhi`
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This selects a group residing in a block with edges perpendicular to the simulation cell. The block boundaries are given by `xlo xhi ylo yhi zlo zhi`.
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`additional keywords`- Represents the various transformations which can be performed on a group. These additional keywords are given below.
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@ -2,8 +2,8 @@ FC=ifort
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FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
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#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin
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MODES=mode_create.o mode_merge.o mode_convert.o
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OPTIONS=opt_disl.o
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OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o call_option.o $(MODES) $(OPTIONS)
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OPTIONS=opt_disl.o opt_group.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
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.SUFFIXES:
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.SUFFIXES: .c .f .f90 .F90 .o
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@ -38,6 +38,6 @@ atoms.o subroutines.o testfuncs.o box.o : functions.o
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main.o io.o $(MODES) $(OPTIONS) : elements.o
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call_mode.o : $(MODES)
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call_option.o : $(OPTIONS)
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$(MODES) io.o: atoms.o box.o
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$(MODES) $(OPTIONS) io.o : atoms.o box.o
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$(MODES) main.o : io.o
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testfuncs.o elements.o mode_create.o opt_disl.o: subroutines.o
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testfuncs.o elements.o mode_create.o $(OPTIONS): subroutines.o
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@ -399,6 +399,8 @@ module io
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select case(max_ng_node)
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case(8)
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interp_max = (max_esize)**3
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case default
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interp_max = 0
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end select
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write(11,20) interp_max
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write(11,3) node_num
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200
src/opt_group.f90
Normal file
200
src/opt_group.f90
Normal file
@ -0,0 +1,200 @@
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module opt_group
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!This module contains all code associated with dislocations
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use parameters
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use elements
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use subroutines
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use box
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implicit none
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integer :: group_ele_num, group_atom_num
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character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
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real(kind=dp) :: block_bd(6), disp_vec(3)
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logical :: displace, wrap
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integer, allocatable :: element_index(:), atom_index(:)
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public
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contains
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subroutine group(arg_pos)
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!Main calling function for the group option
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integer, intent(inout) :: arg_pos
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group_ele_num = 0
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group_atom_num = 0
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if(allocated(element_index)) deallocate(element_index)
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if(allocated(atom_index)) deallocate(atom_index)
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call parse_group(arg_pos)
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call get_group
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!Now call the transformation functions for the group
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if(displace) call displace_group
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end subroutine group
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subroutine parse_group(arg_pos)
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!Parse the group command
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integer, intent(inout) :: arg_pos
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integer :: i,arglen
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character(len=100) :: textholder
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!Parse type and shape command
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, type, arglen)
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if (arglen==0) STOP "Missing select_type in group command"
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select case(trim(adjustl(type)))
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case('atoms', 'elements', 'both')
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continue
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case default
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print *, "Select_type ", trim(adjustl(type)), " is not an accept group selection criteria. ", &
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"Please select from atoms, nodes, or both."
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end select
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, shape, arglen)
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if (arglen==0) STOP "Missing group_shape in group command"
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!Now parse the arguments required by the user selected shape
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select case(trim(adjustl(shape)))
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case('block')
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do i= 1, 6
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, textholder, arglen)
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if (arglen==0) STOP "Missing block boundary in dislgen command"
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call parse_pos(int((i+1)/2), textholder, block_bd(i))
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end do
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case default
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print *, "Group shape ", trim(adjustl(shape)), " is not currently accepted. Please check documentation ", &
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"for accepted group shapes."
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end select
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!Now parse the additional options which may be present
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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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arg_pos=arg_pos+1
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call get_command_argument(arg_pos, textholder)
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textholder=adjustl(textholder)
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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('displace')
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displace = .true.
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do i = 1,3
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, textholder, arglen)
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if (arglen==0) stop "Missing vector component for shift command"
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read(textholder, *) disp_vec(i)
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end do
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case('wrap')
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wrap = .true.
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case default
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!If it isn't an available option to opt_disl 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_group
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subroutine get_group
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!This subroutine finds all elements and/or atoms within the group boundaries
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!specified by the user.
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integer :: i, inod, ibasis
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integer, allocatable :: resize_array(:)
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real(kind=dp) :: r_center(3)
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select case(trim(adjustl(shape)))
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case('block')
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!Allocate variables to arbitrary size
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allocate(element_index(1024), atom_index(1024))
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!Check the type to see whether we need to find the elements within the group
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select case(trim(adjustl(type)))
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case('elements', 'both')
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do i = 1, ele_num
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r_center(:) = 0.0_dp
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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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r_center = r_center + r_node(:,ibasis,inod,i)/(basisnum(lat_ele(i))*ng_node(lat_ele(i)))
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end do
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end do
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if (in_block_bd(r_center, block_bd)) then
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group_ele_num = group_ele_num + 1
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if(group_ele_num > size(element_index)) then
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allocate(resize_array(size(element_index) + 1024))
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resize_array(1:group_ele_num-1) = element_index
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resize_array(group_ele_num:) = 0
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call move_alloc(resize_array, element_index)
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end if
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element_index(group_ele_num) = i
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end if
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end do
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end select
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!Check the type to see if we need to find the atoms within the group
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select case(trim(adjustl(type)))
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case('atoms','both')
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do i = 1, atom_num
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if(in_block_bd(r_atom(:,i),block_bd)) then
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group_atom_num = group_atom_num + 1
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if (group_atom_num > size(atom_index)) then
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allocate(resize_array(size(atom_index) + 1024))
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resize_array(1:group_atom_num -1) = atom_index
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resize_array(group_atom_num:) = 0
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call move_alloc(resize_array, atom_index)
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end if
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atom_index(group_atom_num) = i
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end if
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end do
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end select
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end select
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end subroutine get_group
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subroutine displace_group
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!This subroutine applies a displacement to elements/atoms in the groups
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integer :: i, inod, ibasis
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!Displace atoms
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do i = 1, group_atom_num
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r_atom(:,atom_index(i)) = r_atom(:,atom_index(i)) + disp_vec
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end do
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!Displace elements
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do i = 1, group_ele_num
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do inod = 1, ng_node(lat_ele(element_index(i)))
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do ibasis = 1, basisnum(lat_ele(element_index(i)))
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r_node(:,ibasis,inod,element_index(i)) = r_node(:,ibasis,inod,element_index(i)) + disp_vec
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end do
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end do
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end do
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!Now either apply periodic boundaries if wrap command was passed or adjust box dimensions
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!Now we check if we have to wrap the atoms, nodes are not wrapped. For elements the periodic
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!boundary conditions are applied in the actual CAC codes
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if(wrap) then
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do i = 1, atom_num
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call apply_periodic(r_atom(:,i))
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end do
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!If we don't include the wrap command then we have to increase the size of the box
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else
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do i = 1,3
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if (disp_vec(i) < -lim_zero) then
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box_bd(2*i-1) = box_bd(2*i-1) - disp_vec(i)
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else if (disp_vec(i) > lim_zero) then
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box_bd(2*i) = box_bd(2*i) + disp_vec(i)
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end if
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end do
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end if
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end subroutine displace_group
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end module opt_group
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@ -178,6 +178,8 @@ module subroutines
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real(kind=dp), intent(out) :: pos !The output parsed position value
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integer :: iospara
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iospara = 0
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if(trim(adjustl(pos_string)) == 'inf') then
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pos=box_bd(2*i)
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else if(trim(adjustl(pos_string)) == '-inf') then
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@ -258,12 +260,13 @@ module subroutines
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real(kind=dp), dimension(3), intent(inout) :: r
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integer :: j
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real(kind=dp) ::box_len
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do j = 1, 3
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box_len = box_bd(2*j) - box_bd(2*j-1)
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if (r(j) > box_bd(2*j)) then
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r(j) = r(j) - box_bd(2*j)
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r(j) = r(j) - box_len
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else if (r(j) < box_bd(2*j-1)) then
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r(j) = r(j) + box_bd(2*j-1)
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r(j) = r(j) + box_len
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end if
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end do
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end subroutine
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