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Update to match new cac inputs/output formats

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development
Alex Selimov 4 years ago
parent 90bdc160cb
commit fc8186f3a1
4 changed files with 184 additions and 179 deletions
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18
src/Makefile.dep
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@ -9,7 +9,6 @@ obj/main : \
obj/io.o \
obj/main.o \
obj/mode_calc.o \
obj/mode_check.o \
obj/mode_convert.o \
obj/mode_create.o \
obj/mode_merge.o \
@ -24,6 +23,7 @@ obj/main : \
obj/opt_slip_plane.o \
obj/parameters.o \
obj/sorts.o \
obj/str.o \
obj/subroutines.o
obj/atoms.o : \
@ -37,7 +37,6 @@ obj/box.o : \
obj/caller.o : \
obj/box.o \
obj/mode_calc.o \
obj/mode_check.o \
obj/mode_convert.o \
obj/mode_create.o \
obj/mode_merge.o \
@ -65,7 +64,8 @@ obj/io.o : \
obj/atoms.o \
obj/box.o \
obj/elements.o \
obj/parameters.o
obj/parameters.o \
obj/str.o
obj/main.o : \
obj/caller.o \
@ -80,16 +80,6 @@ obj/mode_calc.o : \
obj/parameters.o \
obj/subroutines.o
obj/mode_check.o : \
obj/atoms.o \
obj/box.o \
obj/elements.o \
obj/functions.o \
obj/io.o \
obj/neighbors.o \
obj/parameters.o \
obj/subroutines.o
obj/mode_convert.o : \
obj/box.o \
obj/elements.o \
@ -169,6 +159,8 @@ obj/parameters.o :
obj/sorts.o : \
obj/parameters.o
obj/str.o :
obj/subroutines.o : \
obj/box.o \
obj/functions.o \

17
src/elements.f90
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@ -14,10 +14,11 @@ module elements
integer, allocatable :: size_ele(:), lat_ele(:), sbox_ele(:), tag_ele(:) !Element size
real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array
!Element result data structures
real(kind=8), allocatable :: force_node(:,:,:,:), virial_node(:,:,:,:), energy_node(:,:,:)
real(kind=dp), allocatable :: force_node(:,:,:,:), virial_node(:,:,:,:), energy_node(:,:,:)
integer, save :: ele_num !Number of elements
integer, save :: node_num !Total number of nodes
integer, save :: node_atoms !Count of all basis atoms at nodes summed over all nodes
!Data structure used to represent atoms
integer, allocatable :: type_atom(:)!atom type
@ -120,6 +121,7 @@ module elements
basisnum(:) = 0
ng_node(:) = 0
node_num = 0
node_atoms = 0
ele_num = 0
atom_num = 0
end subroutine lattice_init
@ -288,6 +290,7 @@ module elements
ele_num = ele_num + 1
node_num = node_num + ng_node(lat)
node_atoms = node_atoms + ng_node(lat)*basisnum(lat)
if (tag==0) then
newtag = ele_num !If we don't assign a tag then pass the tag as the ele_num
@ -386,7 +389,7 @@ module elements
end if
end subroutine
subroutine interpolate_atoms(type, esize, lat_type, r_in, type_interp, r_interp)
subroutine interpolate_atoms(type, esize, lat_type, r_in, type_interp, r_interp, eng, f, v, data_interp)
!This subroutine returns the interpolated atoms from the elements.
!Arguments
@ -396,6 +399,9 @@ module elements
real(kind=dp), dimension(3,max_basisnum, max_ng_node), intent(in) :: r_in !Nodal positions
integer, dimension(max_basisnum*max_esize**3), intent(out) :: type_interp !Interpolated atomic positions
real(kind=dp), dimension(3, max_basisnum*max_esize**3), intent(out) :: r_interp !Interpolated atomic positions
real(kind = dp), optional, intent(in) :: eng(max_basisnum, max_ng_node), f(3, max_basisnum, max_ng_node), &
v(6, max_basisnum, max_ng_node)
real(kind=dp), dimension(10, max_basisnum*max_esize**3), optional,intent(out) :: data_interp !Interpolated atomic positions
!Internal variables
integer :: it, is, ir, ibasis, inod, ia, bnum, lat_type_temp
@ -405,6 +411,7 @@ module elements
!Initialize some variables
r_interp(:,:) = 0.0_dp
type_interp(:) = 0
if(present(data_interp)) data_interp = 0.0_dp
ia = 0
!Define bnum based on the input lattice type. If lat_type=0 then we are interpolating lattice points which means
@ -437,6 +444,12 @@ module elements
type_interp(ia) = basis_type(ibasis,lat_type_temp)
r_interp(:,ia) = r_interp(:,ia) + a_shape(inod) * r_in(:,ibasis,inod)
if(present(data_interp)) then
!If data is present then interpolate data arrays as well
data_interp(1,ia) = data_interp(1,ia) + eng(ibasis, inod)*a_shape(inod)
data_interp(2:4,ia) = data_interp(2:4,ia) + f(:, ibasis, inod)*a_shape(inod)
data_interp(5:10,ia) = data_interp(5:10,ia) + v(:, ibasis, inod)*a_shape(inod)
end if
end do
end do

291
src/io.f90
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@ -4,6 +4,7 @@ module io
use parameters
use atoms
use box
use str
implicit none
@ -59,7 +60,7 @@ module io
cycle
end if
select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
case('xyz', 'lmp', 'vtk', 'mb', 'restart')
case('xyz', 'lmp', 'vtk', 'mb', 'restart', 'dump')
outfilenum=outfilenum+1
outfiles(outfilenum) = temp_outfile
exit
@ -104,6 +105,8 @@ module io
call write_pycac(outfiles(i))
case('cac')
call write_lmpcac(outfiles(i))
case('dump')
call write_ldump(outfiles(i))
case default
print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
" is not accepted for writing. Please select from: xyz, lmp, vtk, mb, restart, cac and try again"
@ -124,7 +127,7 @@ module io
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
!Write total number of atoms + elements
write(11, '(i16)') node_num+atom_num
write(11, '(i16)') node_atoms+atom_num
!Write comment line
write(11, '(a)') "#Node + atom file created using cacmb"
@ -140,8 +143,8 @@ module io
end do
end do
if(outn /= node_num) then
print *, "outn", outn, " doesn't equal node_num ", node_num
if(outn /= node_atoms) then
print *, "outn", outn, " doesn't equal node_atoms ", node_atoms
end if
!Write atom positions
@ -150,8 +153,8 @@ module io
outn = outn + 1
end do
if((outn-node_num) /= atom_num) then
print *, "outn", (outn-node_num), " doesn't equal atom_num ", atom_num
if((outn-node_atoms) /= atom_num) then
print *, "outn", (outn-node_atoms), " doesn't equal atom_num ", atom_num
end if
!Finish writing
@ -219,6 +222,87 @@ module io
end do
end subroutine write_lmp
subroutine write_ldump(file)
!This subroutine will only work if element data is defined
character(len = *), intent(in) :: file
integer :: write_num, i, iatom
logical :: write_dat
integer :: type_interp(max_basisnum*max_esize**3), interp_num
real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), data_interp(10, max_basisnum*max_esize**3)
1 format('ITEM: TIMESTEP'/i16)
2 format('ITEM: NUMBER OF ATOMS' /i16)
3 format('ITEM: BOX BOUNDS ', 2a1, ' ', 2a1, ' ', 2a1 / &
2f23.15 / 2f23.15 / 2f23.15)
4 format('ITEM: ATOMS id type x y z energy fx fy fz s11 s22 s33 s23 s13 s12')
5 format('ITEM: ATOMS id type x y z')
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
!Write header information
write(11,1) timestep
!Calculate total atom number
write_num = atom_num
do i = 1,ele_num
if(type_ele(i) == 'fcc') write_num = write_num + size_ele(i)**3
if(type_ele(i) == 'bcc') write_num = write_num + size_ele(i)**3
end do
!Write total number of atoms
write(11,2) write_num
!Write box information
write(11,3) box_bc(1:1), box_bc(1:1), box_bc(2:2), box_bc(2:2), box_bc(3:3), box_bc(3:3), box_bd(:)
!Now pick if we are interpolating data or not
if(allocated(force_node).or.allocated(force_atom)) then
write(11, 4)
write_dat = .true.
else
write(11, 5)
write_dat = .false.
end if
if (write_dat) then
do i = 1, atom_num
write(11, '(2i16, 13f23.15)') i, type_atom(i), r_atom(:,i), energy_atom(i), force_atom(:,i), virial_atom(:,i)
end do
else
do i = 1, atom_num
write(11, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i)
end do
end if
!Write refined element atomic positions
interp_num = 0
do i = 1, ele_num
if(write_dat) then
call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp, &
energy_node(:,:,i), force_node(:,:,:,i), virial_node(:,:,:,i), data_interp)
else
call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
end if
select case(trim(adjustl(type_ele(i))))
case('fcc','bcc')
if(write_dat) then
do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
interp_num = interp_num+1
call apply_periodic(r_interp(:,iatom))
write(11, '(2i16, 13f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom), &
data_interp(:,iatom)
end do
else
do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
interp_num = interp_num+1
call apply_periodic(r_interp(:,iatom))
write(11, '(2i16, 3f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom)
end do
end if
end select
end do
end subroutine write_ldump
subroutine write_lmpcac(file)
!This subroutine writes out a .lmp style dump file
character(len=100), intent(in) :: file
@ -392,54 +476,30 @@ module io
character(len=100), intent(in) :: file
integer :: interp_max, i, j, inod, ibasis, ip, unique_index(50), unique_size(50), unique_type(50), unique_num, &
etype
real(kind=dp) :: box_vec(3)
real(kind=dp) :: box_vec(3), masses(10)
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 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)
13 format('ie basis_num ng_node esize'/ 'ip ibasis type x y z')
14 format('atomistic domain' / 'ia type_atom x y z')
19 format('max nodes per element and basis per nodes' / 2i16)
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')
!Below writes the header information for the restart file
write(11,1) timestep, total_time
write(11,2) ele_num
!Below writes the header information for the restart file
!First figure out all of the unique element types
unique_num = 0
unique_index(:) = 0
eleloop:do i = 1, ele_num
do j =1 , unique_num
if ( ( size_ele(i) == size_ele( unique_index(j) ) ).and. &
( lat_ele(i) == lat_ele(unique_index(j)) ) ) then
cycle eleloop
end if
end do
unique_num = unique_num + 1
unique_index(unique_num) = i
unique_size(unique_num) = size_ele(i)
unique_type(unique_num) = lat_ele(i)
end do eleloop
!Calculate the max number of atoms per element
select case(max_ng_node)
case(8)
@ -447,31 +507,19 @@ module io
case default
interp_max = 0
end select
write(11,20) interp_max
!Write
write(11,3) node_num
write(11,19) max_ng_node
write(11,4) unique_num
write(11,19) max_ng_node, max_basisnum
write(11,5) 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)
call atommass(type_to_name(i),masses(i))
end do
write(11,*) "masses: "
write(11, *) (masses(i), i = 1, atom_types)
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
@ -479,35 +527,18 @@ module io
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, unique_num
write(11,'(3i16)') i, size_ele(unique_index(i))-1, basis_type(1,lat_ele(unique_index(i)))
end do
ip = 0
write(11,13)
do i = 1, ele_num
!Figure out the ele type
do j = 1, unique_num
if ( (unique_size(j) == size_ele(i)).and.(unique_type(j) == lat_ele(i))) then
etype = j
exit
endif
end do
write(11, '(4i16)') i, etype, 1, basis_type(1,lat_ele(i))
write(11, '(4i16)') i, basisnum(lat_ele(i)), 2, (size_ele(i)-1)
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)
write(11, '(3i16, 3f23.15)') ip, ibasis, basis_type(ibasis, lat_ele(i)), r_node(:, ibasis, inod, i)
end do
end do
end do
@ -517,7 +548,7 @@ 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, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i)
end do
end if
@ -803,7 +834,7 @@ 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, stat
real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3)
real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), atomic_masses(10)
character(len=100) :: textholder, in_lattype_map(10)
character(len=2) :: atomic_element
!First open the file
@ -817,31 +848,25 @@ module io
read(11,*) textholder
read(11,*) in_eles
!Discard info and read ng_max_node
!Discard info and read ng_max_node and max_basisnum
do i = 1, 5
read(11,*) textholder
end do
read(11,*) max_ng_node
!Read element types (only needed inside this subroutine)
read(11,*) textholder
read(11,*) ele_types
read(11,*) max_ng_node, max_basisnum
!Read in atom num
read(11,*) textholder
read(11,*) in_atoms
!read in lattice_types and atom types
do i = 1,3
read(11,*) textholder
end do
read(11,*) in_lat_num, in_atom_types
!read in atom masses
read(11, *) textholder
read(11, '(a)') textholder
j = tok_count(textholder)
read(textholder, *) (atomic_masses(i), i=1, j)
!Read define atom_types by name
read(11,*) textholder
!Read define atom_types by mass
do i = 1, in_atom_types
read(11,*) j, atomic_element
call atommassspecies(atomic_masses(i), atomic_element)
call add_atom_type(atomic_element, atom_type_map(i))
end do
@ -849,22 +874,6 @@ module io
read(11,*) textholder
read(11,*) box_bc
!Disregard useless info
do i = 1, 3
read(11,*) textholder
end do
!Read in lat_type map
do i = 1, in_lat_num
read(11,*) j, in_lattype_map(i)
ng_node(lattice_types+i) = 8 !Only cubic elements are currently supported in pyCAC
end do
!Disregard useless info
do i =1 , 3
read(11,*) textholder
end do
!Read box boundaries and displace them if necessary
read(11,*) temp_box_bd(:)
do i = 1, 3
@ -892,56 +901,13 @@ module io
sub_box_bd(:, sub_box_num+1) = temp_box_bd
!Read in more useless info
do i = 1, 10
do i = 1, 9
read(11,*) textholder
end do
!Now read the ele_type to size and lat map
do i = 1, ele_types
read(11,*) j, etype_map(i)
etype_map(i) = etype_map(i) + 1
end do
!Now set up the lattice types. In this code it assumes that lattice_type 1 maps to
!atom type 1 because it only allows 1 atom per basis in pyCAC at the moment.
do i = 1, in_lat_num
basisnum(lattice_types+i) = 1
basis_type(1,lattice_types+i) = atom_type_map(i)
end do
!Figure out the lattice type maps in case we have repeated lattice_types
k = lattice_types + 1
new_lattice_map(:) = 0
new_loop:do i = 1, in_lat_num
old_loop:do j = 1, lattice_types
!First check all the lattice level variables
if ((basisnum(lattice_types+i) == basisnum(j)).and. &
(ng_node(lattice_types+i) == ng_node(j))) then
!Now check the basis level variables
do ibasis =1, basisnum(i)
if(basis_type(ibasis,lattice_types+i) /= basis_type(ibasis,j)) then
cycle old_loop
end if
end do
new_lattice_map(i) = j
cycle new_loop
end if
end do old_loop
new_lattice_map(i) = k
k = k+1
end do new_loop
!Read more useless data
read(11,*) textholder
!set max values and allocate variables
max_basisnum = maxval(basisnum)
max_ng_node = maxval(ng_node)
call grow_ele_arrays(in_eles, in_atoms)
!Now start reading the elements
if(in_eles > 0) then
read(11,*) textholder
read(11,*) textholder
do i = 1, in_eles
read(11,*) j, etype, k, lat_type
@ -992,9 +958,9 @@ module io
!Internal Variables
integer :: i, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
id, type_node, ilat, esize, tag, type
id, type_node, ilat, esize, tag, type, bnum, n, ibasis, ip
real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), &
ee(1,8), fe(3,1,8), ve(3,1,8), re(3,1,8)
ee(10,8), fe(3,10,8), ve(6,10,8), re(3,10,8)
character(len=100) :: textholder, fcc
character(len=1000) :: line
@ -1002,7 +968,7 @@ module io
open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
!Now initialize some important variables if they aren't defined
if (max_basisnum==0) max_basisnum = 1
if (max_basisnum==0) max_basisnum = 10
if (max_ng_node==0) max_ng_node=8
fcc="fcc"
@ -1010,6 +976,9 @@ module io
read(11, *) textholder
read(11, *) textholder
!Read the timestep
read(11, *) textholder, timestep
!Read atom number and element number and grow element arrays by needed amount
read(11,*) textholder, in_atoms, textholder, in_eles
call grow_ele_arrays(in_eles, in_atoms)
@ -1055,22 +1024,18 @@ module io
end if
if(in_eles > 0) then
!Add the lattice_types based on the atom types
inbtypes=0
do i = 1, maxval(type_atom)
inbtypes(1) = i
call lattice_map(1, inbtypes, 8 , 1.0_dp, ilat) !Please check documentation on pycac.out formats
end do
!Read element and node headers
read(11,*) textholder
read(11,*) textholder
!read element information, currently only 8 node elements with 1 basis
do ie =1, in_eles
read(11,*) tag, lat_type, textholder, textholder, esize
do inod =1, 8
read(11,*) textholder, textholder, textholder, re(:,1,inod), ee(1,inod), fe(:,1,inod), ve(:,1,inod)
read(11,*) tag, n, bnum, esize
inbtypes(:) = 0
do inod =1, n*bnum
read(11,*) ip, ibasis, inbtypes(ibasis), re(:,ibasis,ip), ee(ibasis,ip), fe(:,ibasis,ip), ve(:,ibasis,ip)
end do
call lattice_map(bnum, inbtypes, n, 1.0_dp, lat_type)
call add_element(tag, fcc, esize+1, lat_type, sub_box_num, re)
call add_element_data(ele_num, ee, fe, ve)
end do
@ -1079,6 +1044,8 @@ module io
return
end subroutine
subroutine read_lmpcac(file, displace, temp_box_bd)
!This subroutine is used to read .cac files which are used with the lammpsCAC format
character(len=100), intent(in) :: file

33
src/str.f90
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@ -0,0 +1,33 @@
module str
!this module has some string manipulation commands
public
contains
pure function tok_count(text)
!counts number of tokens in a string
character(len = *), intent(in) :: text
integer :: tok_count
integer :: i, j
logical :: in_tok
j = len(trim(adjustl(text)))
in_tok = .false.
tok_count = 0
do i = 1, j
!This checks if it is a white space character which is the delimiter
if(trim(adjustl(text(i:i))) == ' ') then
!If previously we were in token and the current character is the delimiter
!Then we are no longer in the token
if(in_tok) in_tok = .false.
!If the character isn't a white space character and we previously weren't in the token then set in_tok
!to true and increment token count
else if(.not.in_tok) then
in_tok = .true.
tok_count = tok_count + 1
end if
end do
return
end function tok_count
end module str
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