Added writing to pycac restart file format

master
Alex Selimov 5 years ago
parent c291ec65b4
commit b3a9577cc2

@ -5,7 +5,7 @@ module box
implicit none implicit none
real(kind=dp) :: box_bd(6) !Global box boundaries real(kind=dp) :: box_bd(6) !Global box boundaries
character(len=3) :: box_bc !Box boundary conditions (periodic or shrinkwrapped)
!The subbox variables contain values for each subbox, being the boxes read in through some !The subbox variables contain values for each subbox, being the boxes read in through some
!command. Currently only mode_merge will require sub_boxes, for mode_create it will always !command. Currently only mode_merge will require sub_boxes, for mode_create it will always
!allocate to only 1 sub_box !allocate to only 1 sub_box
@ -14,12 +14,19 @@ module box
real(kind=dp), allocatable :: sub_box_ori(:,:,:)!Orientations for each of the subboxes 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 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
public public
contains contains
subroutine box_init subroutine box_init
!Initialize some box functions !Initialize some box functions
box_bd(:) = 0.0_dp box_bd(:) = 0.0_dp
box_bc = 'ppp'
end subroutine box_init end subroutine box_init
subroutine alloc_sub_box(n) subroutine alloc_sub_box(n)

@ -11,8 +11,8 @@ module elements
integer, allocatable :: size_ele(:), lat_ele(:) !Element siz integer, allocatable :: size_ele(:), lat_ele(:) !Element siz
real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array
integer :: ele_num=0 !Number of elements integer, save :: ele_num !Number of elements
integer :: node_num=0 !Total number of nodes integer, save :: node_num !Total number of nodes
!Data structure used to represent atoms !Data structure used to represent atoms
integer, allocatable :: type_atom(:)!atom type integer, allocatable :: type_atom(:)!atom type
@ -85,6 +85,9 @@ module elements
max_basisnum = 0 max_basisnum = 0
basisnum(:) = 0 basisnum(:) = 0
ng_node(:) = 0 ng_node(:) = 0
node_num = 0
ele_num = 0
atom_num = 0
end subroutine lattice_init end subroutine lattice_init
subroutine cell_init(lapa,esize,ele_type, orient_mat, cell_mat) subroutine cell_init(lapa,esize,ele_type, orient_mat, cell_mat)

@ -58,7 +58,7 @@ module io
cycle cycle
end if end if
select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:)) select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
case('xyz', 'lmp', 'vtk', 'mb') case('xyz', 'lmp', 'vtk', 'mb', 'restart')
outfilenum=outfilenum+1 outfilenum=outfilenum+1
outfiles(outfilenum) = temp_outfile outfiles(outfilenum) = temp_outfile
exit exit
@ -92,6 +92,8 @@ module io
call write_vtk(outfiles(i)) call write_vtk(outfiles(i))
case('mb') case('mb')
call write_mb(outfiles(i)) call write_mb(outfiles(i))
case('restart')
call write_pycac(outfiles(i))
case default case default
print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), & print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
" is not accepted for writing. Please select from: xyz and try again" " is not accepted for writing. Please select from: xyz and try again"
@ -107,16 +109,10 @@ module io
!This is the simplest visualization subroutine, it writes out all nodal positions and atom positions to an xyz file !This is the simplest visualization subroutine, it writes out all nodal positions and atom positions to an xyz file
character(len=100), intent(in) :: file character(len=100), intent(in) :: file
integer :: node_num, i, inod, ibasis integer :: i, inod, ibasis
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind') open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
!Calculate total node number
node_num=0
do i = 1, ele_num
node_num = node_num + basisnum(lat_ele(i))*ng_node(lat_ele(i))
end do
!Write total number of atoms + elements !Write total number of atoms + elements
write(11, '(i16)') node_num+atom_num write(11, '(i16)') node_num+atom_num
@ -273,6 +269,123 @@ module io
close(11) close(11)
end subroutine end subroutine
subroutine write_pycac(file)
!This subroutine writes restart files meant to be used with the McDowell Group CAC code.
!NOTE: This code doesn't work for arbitrary number of basis atoms per node. It assumes that the
!each element has only 1 atom type at the node.
character(len=100), intent(in) :: file
integer :: interp_max, i, j, lat_size, inod, ibasis, ip
real(kind=dp) :: box_vec(3)
1 format('time' / i16, f23.15)
2 format('number of elements' / i16)
3 format('number of nodes' / i16)
4 format('element types' / i16)
5 format('number of atoms' / i16)
6 format('number of grains' / i16)
7 format('boundary ' / 3a1)
8 format('box bound' / 6f23.15)
9 format('box length' / 3f23.15)
10 format('box matrix')
11 format(3f23.15)
12 format('coarse-grained domain')
13 format('ie ele_type grain_ele lat_type_ele'/ 'ip ibasis type x y z')
14 format('atomistic domain' / 'ia grain_atom type_atom x y z')
15 format('maximum lattice periodicity length' / 3f23.15)
16 format('Number of lattice types and atom types '/ 2i16)
17 format('lattice type IDs')
18 format('lattice types for grains')
19 format('max nodes per element' / i16)
20 format('max interpo per element' / i16)
21 format('atom types to elements')
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
write(11,1) timestep, total_time
write(11,2) ele_num
!Below writes the header information for the restart file
!Calculate the max number of atoms per element
select case(max_ng_node)
case(8)
interp_max = (max_esize)**3
end select
write(11,20) interp_max
write(11,3) node_num
write(11,19) max_ng_node
write(11,4) lattice_types
write(11,2) atom_num
write(11,6) 1 !Grain_num is ignored
write(11,16) lattice_types, atom_types
write(11,21)
do i = 1, atom_types
write(11,*) i, type_to_name(i)
end do
write(11,7) box_bc(1:1), box_bc(2:2), box_bc(3:3)
write(11,18)
write(11,'(2i16)') 1,1 !This is another throwaway line that is meaningless
write(11,17)
!This may have to be updated in the future but currently the only 8 node element is fcc
do i = 1, lattice_types
select case(ng_node(i))
case(8)
write(11, *) i, 'fcc'
end select
end do
write(11,15) 1.0_dp, 1.0_dp, 1.0_dp !Another throwaway line that isn't needed
write(11,8) box_bd
write(11,9) box_bd(2)-box_bd(1), box_bd(4) - box_bd(3), box_bd(6)-box_bd(5)
write(11,10)
!Current boxes are limited to being rectangular
do i = 1,3
box_vec(:) = 0.0_dp
box_vec(i) = box_bd(2*i) - box_bd(2*i-1)
write(11,11) box_vec
end do
!We write this as box_mat ori and box_mat current
do i = 1,3
box_vec(:) = 0.0_dp
box_vec(i) = box_bd(2*i) - box_bd(2*i-1)
write(11,11) box_vec
end do
!write the element information
if(ele_num > 0) then
write(11,12)
do i = 1, lattice_types
do j = 1, ele_num
if (lat_ele(j) == i) then
lat_size = size_ele(j)-1
exit
end if
end do
write(11,'(3i16)') i, lat_size, basis_type(1,i)
end do
ip = 0
write(11,13)
do i = 1, ele_num
write(11, '(4i16)') i, lat_ele(i), 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
write(11, '(2i16, 3f23.15)') ip, ibasis, r_node(:, ibasis, inod, i)
end do
end do
end do
end if
!Now write the atomic information
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)
end do
end if
close(11)
end subroutine write_pycac
subroutine write_mb(file) subroutine write_mb(file)
!This subroutine writes the cacmb formatted file which provides necessary information for building models !This subroutine writes the cacmb formatted file which provides necessary information for building models
@ -321,8 +434,10 @@ module io
end do end do
end do end do
close(11)
end subroutine write_mb end subroutine write_mb
!!!!!!!!!!!!! Below are subroutines for reading files !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!! Below are subroutines for reading files !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine get_in_file(filename) subroutine get_in_file(filename)
@ -481,6 +596,9 @@ module io
!Close the file being read !Close the file being read
close(11) close(11)
lattice_types = lattice_types + new_lattice_types
!Only increment the lattice types if there are elements, if there are no elements then we
!just overwrite the arrays
if(in_eles > 0) lattice_types = lattice_types + new_lattice_types
end subroutine read_mb end subroutine read_mb
end module io end module io
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