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Added orient and unorient options

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master
Alex Selimov 5 years ago
parent 58ad74ca9a
commit 44efb4be4a
6 changed files with 77 additions and 30 deletions
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4
src/Makefile
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@ -2,7 +2,7 @@ FC=ifort
FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin #FFLAGS=-mcmodel=large -Ofast -no-wrap-margin
MODES=mode_create.o mode_merge.o mode_convert.o MODES=mode_create.o mode_merge.o mode_convert.o
OPTIONS=opt_disl.o opt_group.o OPTIONS=opt_disl.o opt_group.o opt_orient.o
OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES) $(OPTIONS) call_option.o OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES) $(OPTIONS) call_option.o
.SUFFIXES: .SUFFIXES:
@ -40,4 +40,4 @@ call_mode.o : $(MODES)
call_option.o : $(OPTIONS) call_option.o : $(OPTIONS)
$(MODES) $(OPTIONS) subroutines.o io.o : atoms.o box.o $(MODES) $(OPTIONS) subroutines.o io.o : atoms.o box.o
$(MODES) main.o : io.o $(MODES) main.o : io.o
testfuncs.o elements.o mode_create.o $(OPTIONS): subroutines.o testfuncs.o elements.o mode_create.o $(OPTIONS) $(MODES): subroutines.o

9
src/call_option.f90
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@ -2,6 +2,7 @@ subroutine call_option(option, arg_pos)
use parameters use parameters
use opt_disl use opt_disl
use opt_group use opt_group
use opt_orient
use box use box
implicit none implicit none
@ -15,14 +16,16 @@ subroutine call_option(option, arg_pos)
call group(arg_pos) call group(arg_pos)
case('-ow') case('-ow')
arg_pos = arg_pos + 1 arg_pos = arg_pos + 1
continue
case('-wrap') case('-wrap')
arg_pos = arg_pos + 1 arg_pos = arg_pos + 1
continue case('-orient')
call orient(arg_pos)
case('-unorient')
call unorient
arg_pos = arg_pos + 1
case('-boundary') case('-boundary')
arg_pos=arg_pos+1 arg_pos=arg_pos+1
call get_command_argument(arg_pos, box_bc) call get_command_argument(arg_pos, box_bc)
print *, box_bc
arg_pos=arg_pos+1 arg_pos=arg_pos+1
case default case default
print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.' print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'

48
src/elements.f90
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@ -5,6 +5,7 @@ module elements
use parameters use parameters
use functions use functions
use subroutines use subroutines
use box
implicit none implicit none
!Data structures used to represent the CAC elements. Each index represents an element !Data structures used to represent the CAC elements. Each index represents an element
@ -17,6 +18,7 @@ module elements
!Data structure used to represent atoms !Data structure used to represent atoms
integer, allocatable :: type_atom(:)!atom type integer, allocatable :: type_atom(:)!atom type
integer, allocatable :: sbox_atom(:)
real(kind =dp),allocatable :: r_atom(:,:) !atom position real(kind =dp),allocatable :: r_atom(:,:) !atom position
integer :: atom_num=0 !Number of atoms integer :: atom_num=0 !Number of atoms
@ -153,7 +155,7 @@ module elements
if(m > 0) then if(m > 0) then
!Allocate atom arrays !Allocate atom arrays
allocate(type_atom(m), r_atom(3,m), stat=allostat) allocate(type_atom(m), sbox_atom(m), r_atom(3,m), stat=allostat)
if(allostat > 0) then if(allostat > 0) then
print *, "Error allocating atom arrays in elements.f90 because of: ", allostat print *, "Error allocating atom arrays in elements.f90 because of: ", allostat
stop stop
@ -211,6 +213,11 @@ module elements
temp_int(atom_size+1:) = 0 temp_int(atom_size+1:) = 0
call move_alloc(temp_int, type_atom) call move_alloc(temp_int, type_atom)
allocate(temp_int(m+atom_num+buffer_size))
temp_int(1:atom_size) = sbox_atom
temp_int(atom_size+1:) = 0
call move_alloc(temp_int, sbox_atom)
allocate(temp_real(3,m+atom_num+buffer_size)) allocate(temp_real(3,m+atom_num+buffer_size))
temp_real(:,1:atom_size) = r_atom temp_real(:,1:atom_size) = r_atom
temp_real(:, atom_size+1:) = 0.0_dp temp_real(:, atom_size+1:) = 0.0_dp
@ -237,9 +244,9 @@ module elements
end subroutine add_element end subroutine add_element
subroutine add_atom(type, r) subroutine add_atom(type, sbox, r)
!Subroutine which adds an atom to the atom arrays !Subroutine which adds an atom to the atom arrays
integer, intent(in) :: type integer, intent(in) :: type, sbox
real(kind=dp), intent(in), dimension(3) :: r real(kind=dp), intent(in), dimension(3) :: r
atom_num = atom_num+1 atom_num = atom_num+1
@ -247,6 +254,7 @@ module elements
call grow_ele_arrays(0,1) call grow_ele_arrays(0,1)
type_atom(atom_num) = type type_atom(atom_num) = type
r_atom(:,atom_num) = r(:) r_atom(:,atom_num) = r(:)
sbox_atom(atom_num) = sbox
end subroutine add_atom end subroutine add_atom
@ -449,4 +457,38 @@ module elements
end do end do
end subroutine wrap_atoms end subroutine wrap_atoms
subroutine def_new_box
!This subroutine calculates new box boundaries based on minimum and maximum nodal/atomic positions
integer :: i, j, inod, ibasis
real(kind=dp) :: max_bd(3), min_bd(3)
max_bd(:) = -huge(1.0_dp)
min_bd(:) = huge(1.0_dp)
do i = 1, atom_num
do j = 1, 3
if (r_atom(j,i) > max_bd(j)) max_bd(j) = r_atom(j,i) + lim_zero
if (r_atom(j,i) < min_bd(j)) min_bd(j) = r_atom(j,i) - lim_zero
end do
end do
do i = 1, ele_num
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
do j = 1, 3
if (r_node(j,ibasis,inod,i) > max_bd(j)) max_bd(j) = r_node(j,ibasis,inod,i) + lim_zero
if (r_node(j,ibasis,inod,i) < min_bd(j)) min_bd(j) = r_node(j,ibasis,inod,i) -lim_zero
end do
end do
end do
end do
do j = 1, 3
box_bd(2*j) = max_bd(j)
box_bd(2*j-1) = min_bd(j)
end do
end subroutine
end module elements end module elements

12
src/io.f90
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@ -8,7 +8,7 @@ module io
implicit none implicit none
integer :: outfilenum = 0, infilenum = 0 integer :: outfilenum = 0, infilenum = 0
character(len=100) :: outfiles(10), infiles(10) character(len=100) :: outfiles(100), infiles(100)
logical :: force_overwrite logical :: force_overwrite
public public
@ -130,14 +130,14 @@ module io
do i = 1, ele_num do i = 1, ele_num
do inod = 1, ng_node(lat_ele(i)) do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i)) do ibasis = 1, basisnum(lat_ele(i))
write(11, '(a, 3f23.15)') basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i) write(11, '(i16, 3f23.15)') basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i)
end do end do
end do end do
end do end do
!Write atom positions !Write atom positions
do i = 1, atom_num do i = 1, atom_num
write(11, '(a, 3f23.15)') type_atom(i), r_atom(:,i) write(11, '(i16, 3f23.15)') type_atom(i), r_atom(:,i)
end do end do
!Finish writing !Finish writing
@ -520,7 +520,7 @@ module io
!Write out atoms first !Write out atoms first
do i = 1, atom_num do i = 1, atom_num
write(11,*) i, type_atom(i), r_atom(:,i) write(11,*) i, type_atom(i), sbox_atom(i), r_atom(:,i)
end do end do
!Write out the elements, this is written in two stages, one line for the element and then 1 line for !Write out the elements, this is written in two stages, one line for the element and then 1 line for
@ -713,8 +713,8 @@ module io
!Read the atoms !Read the atoms
do i = 1, in_atoms do i = 1, in_atoms
read(11,*) j, type, r(:) read(11,*) j, type, sbox, r(:)
call add_atom(new_type_to_type(type), r+newdisplace) call add_atom(new_type_to_type(type), sbox, r+newdisplace )
end do end do
!Read the elements !Read the elements

32
src/mode_create.f90
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@ -135,7 +135,7 @@ module mode_create
if(lat_atom_num > 0) then if(lat_atom_num > 0) then
do i = 1, lat_atom_num do i = 1, lat_atom_num
do ibasis = 1, basisnum(1) do ibasis = 1, basisnum(1)
call add_atom(basis_type(ibasis, 1), (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis)) call add_atom(basis_type(ibasis, 1), 1, (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis))
end do end do
end do end do
deallocate(r_atom_lat) deallocate(r_atom_lat)
@ -205,21 +205,23 @@ module mode_create
do i = 1, 3 do i = 1, 3
call get_command_argument(arg_pos, orient_string, arglen) call get_command_argument(arg_pos, orient_string, arglen)
if (arglen==0) STOP "Missing orientation in orient command of mode create" if (arglen==0) STOP "Missing orientation in orient command of mode create"
call parse_ori_vec(orient_string, orient(i,:))
arg_pos = arg_pos+1 arg_pos = arg_pos+1
ori_pos=2
do j = 1,3 ! ori_pos=2
if (orient_string(ori_pos:ori_pos) == '-') then ! do j = 1,3
ori_pos = ori_pos + 1 ! if (orient_string(ori_pos:ori_pos) == '-') then
read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j) ! ori_pos = ori_pos + 1
if (stat>0) STOP "Error reading orient value" ! read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
orient(i,j) = -orient(i,j) ! if (stat>0) STOP "Error reading orient value"
ori_pos = ori_pos + 1 ! orient(i,j) = -orient(i,j)
else ! ori_pos = ori_pos + 1
read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j) ! else
if(stat>0) STOP "Error reading orient value" ! read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
ori_pos=ori_pos + 1 ! if(stat>0) STOP "Error reading orient value"
end if ! ori_pos=ori_pos + 1
end do ! end if
! end do
end do end do

2
src/opt_group.f90
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@ -229,7 +229,7 @@ module opt_group
!here as well to make sure they are in the box !here as well to make sure they are in the box
do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3 do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3
call apply_periodic(r_interp(:,j)) call apply_periodic(r_interp(:,j))
call add_atom(type_interp(j), r_interp(:,j)) call add_atom(type_interp(j), sbox_ele(ie), r_interp(:,j))
end do end do
end do end do

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