Added deform box option and allowed for reading time information from restart files

development
Alex Selimov 4 years ago
parent 8d939ed942
commit 724e573287

@ -2,7 +2,7 @@ FC=ifort
FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays
MODES=mode_create.o mode_merge.o mode_convert.o
OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o
OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o opt_deform.o
OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES) $(OPTIONS) call_option.o sorts.o
.SUFFIXES:

@ -14,7 +14,6 @@ module box
real(kind=dp), allocatable :: sub_box_ori(:,:,:)!Orientations for each of the subboxes
real(kind=dp), allocatable :: sub_box_bd(:,:)!Boundaries for each of the sub_boxes
!Below are some simulation parameters which may be adjusted if reading in restart files
integer :: timestep=0
real(kind=dp) :: total_time=0.0_dp

@ -3,6 +3,7 @@ subroutine call_option(option, arg_pos)
use opt_disl
use opt_group
use opt_orient
use opt_deform
use opt_delete
use box
implicit none
@ -31,6 +32,8 @@ subroutine call_option(option, arg_pos)
bound_called = .true.
case('-sbox_ori')
call sbox_ori(arg_pos)
case('-deform')
call deform(arg_pos)
case('-delete')
call run_delete(arg_pos)
case('-set_cac')

@ -503,6 +503,7 @@ module elements
size_ele(sorted_index(i)) = 0
lat_ele(sorted_index(i)) = 0
sbox_ele(sorted_index(i)) = 0
tag_ele(sorted_index(i)) = 0
else
node_num = node_num - ng_node(lat_ele(sorted_index(i)))
r_node(:,:,:,sorted_index(i)) = r_node(:,:,:,ele_num)
@ -510,6 +511,7 @@ module elements
size_ele(sorted_index(i)) = size_ele(ele_num)
lat_ele(sorted_index(i)) = lat_ele(ele_num)
sbox_ele(sorted_index(i)) = sbox_ele(ele_num)
tag_ele(sorted_index(i)) = tag_ele(ele_num)
end if
ele_num = ele_num - 1
end do

@ -491,7 +491,7 @@ module io
exit
endif
end do
write(11, '(4i16)') i, etype, 1, basis_type(1,lat_ele(i))
write(11, '(4i16)') tag_ele(i), etype, 1, basis_type(1,lat_ele(i))
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
ip = ip + 1
@ -505,7 +505,7 @@ module io
if(atom_num /= 0) then
write(11,14)
do i = 1, atom_num
write(11, '(3i16, 3f23.15)') i, 1, type_atom(i), r_atom(:,i)
write(11, '(3i16, 3f23.15)') tag_atom(i), 1, type_atom(i), r_atom(:,i)
end do
end if
@ -781,19 +781,19 @@ module io
integer :: i, inod, ibasis, j, k, l, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
atom_type_map(100), etype_map(100), etype, lat_type, new_lattice_map(100), &
atom_type
atom_type, stat
real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3)
character(len=100) :: textholder, in_lattype_map(10)
character(len=2) :: atomic_element
!First open the file
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
!Disregard unneeded information
do i = 1, 3
read(11,*) textholder
end do
!Read the timestep information
read(11,*) textholder
read(11,*) timestep, total_time
!Read element number
read(11,*) textholder
read(11,*) in_eles
!Discard info and read ng_max_node
@ -941,7 +941,11 @@ module io
end if
do i = 1, in_atoms
read(11,*) j, k, atom_type, r_in_atom(:)
read(11,*, iostat=stat) j, k, atom_type, r_in_atom(:)
if(stat > 0) then
print *, j
stop
end if
r_in_atom = r_in_atom + newdisplace
call add_atom(j,atom_type_map(atom_type), sub_box_num + 1, r_in_atom)
end do

@ -0,0 +1,98 @@
module opt_deform
!This module constains the deform option which applies a uniaxial strain to the system
use parameters
use subroutines
use elements
use box
implicit none
real(kind=dp), save :: applied_strain
integer, save :: sdim
public
contains
subroutine deform(arg_pos)
!This subroutine applies the simulation box deformation to the system
integer, intent(inout) :: arg_pos
character(len=1) :: dims(3)
integer :: i, j, k
real(kind=dp) :: frac_atom(atom_num), frac_node(max_basisnum, max_ng_node, ele_num)
!initialize some variables
dims(1) = 'x'
dims(2) = 'y'
dims(3) = 'z'
!First parse the input command
call parse_deform(arg_pos)
print *, '-----------------------Option Deform------------------------'
!Now convert all positions in the specified dimension to fractional coordinates
do i = 1, atom_num
frac_atom(i) = (r_atom(sdim, i) - box_bd(2*sdim-1))/(box_bd(2*sdim)-box_bd(2*sdim-1))
end do
do i = 1, ele_num
do j = 1, ng_node(lat_ele(i))
do k = 1, basisnum(lat_ele(i))
frac_node(k,j,i) = (r_node(sdim,k,j,i) - box_bd(2*sdim-1))/(box_bd(2*sdim)-box_bd(2*sdim-1))
end do
end do
end do
print *, "Original box bounds in ", dims(sdim), " are ", box_bd(2*sdim-1:2*sdim)
box_bd(2*sdim) = box_bd(2*sdim) + applied_strain
print *, "New box bounds are ", box_bd(2*sdim-1:2*sdim)
!Now reassign the positions
do i = 1, atom_num
r_atom(sdim,i) = frac_atom(i)*(box_bd(2*sdim)-box_bd(2*sdim-1)) + box_bd(2*sdim-1)
end do
do i = 1, ele_num
do j = 1, ng_node(lat_ele(i))
do k = 1, basisnum(lat_ele(i))
r_node(sdim,k,j,i) = frac_node(k,j,i)*(box_bd(2*sdim)-box_bd(2*sdim-1)) + box_bd(2*sdim-1)
end do
end do
end do
end subroutine deform
subroutine parse_deform(arg_pos)
integer, intent(inout) :: arg_pos
integer :: arg_len
character(len=100) :: textholder
!Pull out the dimension to be strained
arg_pos=arg_pos+1
call get_command_argument(arg_pos, textholder, arg_len)
if (arg_len == 0) stop "Missing dim in deform command"
select case(trim(adjustl(textholder)))
case('x','X')
sdim = 1
case('y','Y')
sdim = 2
case('z','Z')
sdim = 3
case default
print *, "Dimension ", trim(adjustl(textholder)), " is not accepted. Please select either x, y, or z"
end select
!Now pull out the strain vector, currently only accepts a real number by which to reduce the simulation cell size by in
!that dimension
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arg_len)
if (arg_len == 0) stop "Missing strain in deform command"
read(textholder, *) applied_strain
arg_pos = arg_pos + 1
end subroutine parse_deform
end module opt_deform
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