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Initial commit with file writing and create mode working for atoms

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Alex 2019-11-25 18:19:25 -05:00
parent 624886bbe9
commit 8217e8b51c
15 changed files with 2465 additions and 271 deletions
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32
src/Makefile
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CC=ifort
FC=ifort
FFLAGS=-c -mcmodel=large -debug -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone
OBJECTS= main.o elements.o lattice.o subroutines.o precision_comm_module.o
#FFLAGS=-c -mcmodel=large -debug -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone
FFLAGS=-c -mcmodel=large -Ofast
MODES=mode_create.o
OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o build_subroutines.o $(MODES)
.SUFFIXES:
.SUFFIXES: .c .f .f90 .F90 .o
builder: $(OBJECTS)
cacmb: $(OBJECTS)
$(FC) $(OBJECTS) -o $@
.f90.o:
$(FC) $(FFLAGS) $<
main.o lattice.o elements.o region.o subroutines.o : precision_comm_module.o
lattice.o : subroutines.o
main.o : elements.o lattice.o region.o
.PHONY: clean
clean:
$(RM) cacmb *.o
testfuncs: testfuncs.o functions.o subroutines.o
$(FC) testfuncs.o functions.o build_subroutines.o subroutines.o elements.o -o $@
.PHONY: cleantest
cleantest:
$(RM) testfuncs testfuncs.o
$(OBJECTS) : parameters.o
atoms.o subroutines.o testfuncs.o : functions.o
main.o io.o build_subroutines.o: elements.o
call_mode.o : $(MODES)
$(MODES) io.o: atoms.o
$(MODES) main.o : io.o
testfuncs.o elements.o mode_create.o: subroutines.o
testfuncs.o : build_subroutines.o

1167
src/atoms.f90 Normal file
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24
src/call_mode.f90 Normal file
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subroutine call_mode(arg_num,mode)
!This code is used to parse the command line argument for the mode information and calls the required
!mode module.
use mode_create
use parameters
implicit none
integer, intent(in) :: arg_num
character(len=100), intent(in) :: mode
select case(mode)
case('--create')
call create(arg_num)
case default
print *, "Mode ", mode, " currently not accepted. Please check documentation for ", &
"accepted modes and rerun."
stop 3
end select
end subroutine call_mode

199
src/elements.f90
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module elements
use precision_comm_module
!This module contains the elements data structures, structures needed for building regions
!and operations that are done on elements
use parameters
use subroutines
implicit none
!This is the data structure which is used to represent the CAC elements
type element
integer :: tag = 0 !Element tag (used to keep track of id's
integer :: type = 0 !Lattice type of the element
integer :: size = 0 !Element size
!Nodal position array below only works for wedge or fcc elements
real(kind=wp) :: r_node(3,8)
end type
!Data structures used to represent the CAC elements. Each index represents an element
integer,allocatable :: tag_ele(:) !Element tag (used to keep track of id's
character(len=100), allocatable :: type_ele(:) !Element type
integer, allocatable :: size_ele(:), lat_ele(:) !Element siz
real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array
!Finite element array
type(element), allocatable :: element_array(:)
integer :: ele_num=0 !Number of elements
integer :: ele_num
!Data structure used to represent atoms
integer, allocatable :: tag_atom(:) !atom id
character(len=100), allocatable:: type_atom(:) !atom type
real(kind =dp),allocatable :: r_atom(:,:) !atom position
integer :: atom_num=0 !Number of atoms
!Data structure used to represent atoms
type atom
integer :: tag = 0
integer :: type = 0
real(kind =wp) :: r
end type
!Variables for creating elements based on primitive cells
real(kind=dp) :: cubic_cell(3,8), fcc_cell(3,8), fcc_mat(3,3), fcc_inv(3,3)
integer :: cubic_faces(4,6)
type(atom), allocatable :: atoms(:)
!Below are lattice type arrays which provide information on the general form of the elements.
!We currently have a limit of 10 lattice types for simplicities sake but this can be easily increased.
integer :: max_ng_node, ng_node(10) !Max number of nodes per element and number of nodes per element for each lattice type
integer :: atom_num
!These variables contain information on the basis, for simplicities sake we limit
!the user to the definition of 10 lattice types with 10 basis atoms at each lattice point.
!This can be easily increased with no change to efficiency
integer :: max_basisnum, basisnum(10)!Max basis atom number, number of basis atoms in each lattice type
character(len=2) :: basis_type(10,10) !Atom type of each basis
real(kind=dp) :: basis_pos(3,10,10) !Basis atom positions
!Simulation cell parameters
real(kind=dp) :: box_bd(6)
public
contains
subroutine lattice_init
!This subroutine just intializes variables needed for building the different finite
!element types
!First initialize the cubic cell
cubic_cell = reshape((/ 0.0_dp, 0.0_dp, 0.0_dp, &
1.0_dp, 0.0_dp, 0.0_dp, &
1.0_dp, 1.0_dp, 0.0_dp, &
0.0_dp, 1.0_dp, 0.0_dp, &
0.0_dp, 0.0_dp, 1.0_dp, &
1.0_dp, 0.0_dp, 1.0_dp, &
1.0_dp, 1.0_dp, 1.0_dp, &
0.0_dp, 1.0_dp, 1.0_dp /), &
shape(fcc_cell))
!Now we create a list containing the list of vertices needed to describe the 6 cube faces
cubic_faces(:,1) = (/ 1, 4, 8, 5 /)
cubic_faces(:,2) = (/ 2, 3, 7, 6 /)
cubic_faces(:,3) = (/ 1, 2, 6, 5 /)
cubic_faces(:,4) = (/ 3, 4, 8, 7 /)
cubic_faces(:,5) = (/ 1, 2, 3, 4 /)
cubic_faces(:,6) = (/ 5, 6, 7, 8 /)
!!Now initialize the fcc primitive cell
fcc_cell = reshape((/ 0.0_dp, 0.0_dp, 0.0_dp, &
0.5_dp, 0.5_dp, 0.0_dp, &
0.5_dp, 1.0_dp, 0.5_dp, &
0.0_dp, 0.5_dp, 0.5_dp, &
0.5_dp, 0.0_dp, 0.5_dp, &
1.0_dp, 0.5_dp, 0.5_dp, &
1.0_dp, 1.0_dp, 1.0_dp, &
0.5_dp, 0.5_dp, 1.0_dp /), &
shape(fcc_cell))
fcc_mat = reshape((/ 0.5_dp, 0.5_dp, 0.0_dp, &
0.0_dp, 0.5_dp, 0.5_dp, &
0.5_dp, 0.0_dp, 0.5_dp /), &
shape(fcc_mat))
call matrix_inverse(fcc_mat,3,fcc_inv)
max_basisnum = 0
basisnum(:) = 0
basis_pos(:,:,:) = 0.0_dp
ng_node(:) = 0
end subroutine lattice_init
subroutine cell_init(lapa,esize,ele_type, orient_mat, cell_mat)
!This subroutine uses the user provided information to transform the finite element cell to the correct
!size, orientation, and dimensions using the esize, lattice parameter, element_type, and orientation provided
!by the user
integer, intent(in) :: esize
real(kind=dp), intent(in) :: lapa, orient_mat(3,3)
character(len=100), intent(in) :: ele_type
real(kind=dp), dimension(3,max_ng_node), intent(out) :: cell_mat
select case(trim(ele_type))
case('fcc')
cell_mat(:,1:8) = lapa * ((esize-1)*matmul(orient_mat, fcc_cell))
case default
print *, "Element type ", trim(ele_type), " currently not accepted"
stop
end select
end subroutine cell_init
subroutine alloc_ele_arrays(n,m)
!This subroutine used to provide initial allocation for the atom and element arrays
integer, intent(in) :: n, m !n-size of element arrays, m-size of atom arrays
integer :: allostat
!Allocate element arrays
if(n > 0) then
allocate(tag_ele(n), type_ele(n), size_ele(n), lat_ele(n), r_node(3,max_basisnum, max_ng_node,n), &
stat=allostat)
if(allostat > 0) then
print *, "Error allocating element arrays in elements.f90 because of: ", allostat
stop
end if
end if
if(m > 0) then
!Allocate atom arrays
allocate(tag_atom(m), type_atom(m), r_atom(3,m), stat=allostat)
if(allostat > 0) then
print *, "Error allocating atom arrays in elements.f90 because of: ", allostat
stop
end if
end if
end subroutine
subroutine add_element(type, size, lat, r)
!Subroutine which adds an element to the element arrays
integer, intent(in) :: size, lat
character(len=100), intent(in) :: type
real(kind=dp), intent(in) :: r(3, max_basisnum, max_ng_node)
ele_num = ele_num + 1
tag_ele(ele_num) = ele_num
type_ele(ele_num) = type
size_ele(ele_num) = size
lat_ele(ele_num) = lat
r_node(:,:,:,ele_num) = r(:,:,:)
end subroutine add_element
subroutine add_atom(type, r)
!Subroutine which adds an atom to the atom arrays
character(len=2), intent(in) :: type
real(kind=dp), intent(in), dimension(3) :: r
atom_num = atom_num+1
tag_atom(atom_num) = atom_num
type_atom(atom_num) = type
r_atom(:,atom_num) = r(:)
end subroutine add_atom
subroutine def_ng_node(n, element_types)
!This subroutine defines the maximum node number among n element types
integer, intent(in) :: n !Number of element types
character(len=100), dimension(n) :: element_types !Array of element type strings
integer :: i
max_ng_node = 0
do i=1, n
select case(trim(adjustl(element_types(i))))
case('fcc')
ng_node(i) = 8
end select
if(ng_node(i) > max_ng_node) max_ng_node = ng_node(i)
end do
end subroutine def_ng_node
end module elements

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module functions
use parameters
implicit none
public
contains
! Functions below this comment are taken from the functions module of atomsk
!********************************************************
! STRUPCASE
! This function reads a string of any length
! and capitalizes all letters.
!********************************************************
FUNCTION StrUpCase (input_string) RESULT (UC_string)
!
IMPLICIT NONE
CHARACTER(*),PARAMETER:: lower_case = 'abcdefghijklmnopqrstuvwxyz'
CHARACTER(*),PARAMETER:: upper_case = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
CHARACTER(*),INTENT(IN):: input_string
CHARACTER(LEN(Input_String)):: UC_string !Upper-Case string that is produced
INTEGER:: i, n
!
IF(LEN(input_string)==0) RETURN
UC_string = input_string
! Loop over string elements
DO i=1,LEN(UC_string)
!Find location of letter in lower case constant string
n = INDEX( lower_case, UC_string(i:i) )
!If current substring is a lower case letter, make it upper case
IF(n>0) THEN
UC_string(i:i) = upper_case(n:n)
ENDIF
END DO
!
END FUNCTION StrUpCase
!********************************************************
! STRDNCASE
! This function reads a string of any length
! and transforms all letters to lower case.
!********************************************************
FUNCTION StrDnCase (input_string) RESULT (lc_string)
!
IMPLICIT NONE
CHARACTER(*),PARAMETER:: lower_case = 'abcdefghijklmnopqrstuvwxyz'
CHARACTER(*),PARAMETER:: upper_case = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
CHARACTER(*),INTENT(IN):: input_string
CHARACTER(LEN(Input_String)):: lc_string !Lower-Case string that is produced
INTEGER:: i, n
!
IF(LEN(input_string)==0) RETURN
lc_string = input_string
! Loop over string elements
DO i=1,LEN(lc_string)
!Find location of letter in upper case constant string
n = INDEX( upper_case, lc_string(i:i) )
!If current substring is an upper case letter, make it lower case
IF(n>0) THEN
lc_string(i:i) = lower_case(n:n)
ENDIF
END DO
!
END FUNCTION StrDnCase
pure function matrix_normal(a, n)
integer :: i
integer, intent(in) :: n
real(kind = dp), dimension(n) :: v
real(kind = dp), dimension(n, n),intent(in) :: a
real(kind = dp), dimension(n,n) :: matrix_normal
matrix_normal(:, :) = a(:, :)
do i = 1, n
v(:) = a(i,:)
matrix_normal(i, :) = v(:) / norm2(v)
end do
return
end function matrix_normal
pure function cross_product(a, b)
!Function which finds the cross product of two vectors
real(kind = dp), dimension(3), intent(in) :: a, b
real(kind = dp), dimension(3) :: cross_product
cross_product(1) = a(2) * b(3) - a(3) * b(2)
cross_product(2) = a(3) * b(1) - a(1) * b(3)
cross_product(3) = a(1) * b(2) - a(2) * b(1)
return
end function cross_product
pure function identity_mat(n)
!Returns the nxn identity matrix
integer :: i
integer, intent(in) :: n
real(kind = dp), dimension(n, n) :: identity_mat
identity_mat(:, :) = 0.0_dp
do i = 1, n
identity_mat(i, i) = 1.0_dp
end do
return
end function identity_mat
pure function triple_product(a, b, c)
!triple product between three 3*1 vectors
real(kind = dp) :: triple_product
real(kind = dp), dimension(3), intent(in) :: a, b, c
triple_product = dot_product(a, cross_product(b, c))
return
end function triple_product
function in_bd_lat(v, box_faces, box_norms)
!This function returns whether the point is within the transformed box boundaries. The transformed
!box being the transformed simulation cell in the lattice basis
!Input/output variables
real(kind=dp), dimension(3), intent(in) :: v !integer lattice position
real(kind=dp), dimension(3,6), intent(in) :: box_faces !Centroid of all the box faces
real(kind=dp), dimension(3,6), intent(in) :: box_norms !Box face normals
logical :: in_bd_lat
!Other variables
integer :: i
real(kind=dp) :: pt_to_face(3)
in_bd_lat = .true.
!Check if point is in box bounds, this works by comparing the dot product of the face normal and the
!vector from the point to the face. If the dot product is greater than 0 then the point is behind the face
!if it is equal to zero then the point is on the face, if is less than 0 the the point is in front of the face.
do i = 1, 6
pt_to_face(:) = box_faces(:, i) - v
if(dot_product(pt_to_face, box_norms(:,i)) <= 0) then
in_bd_lat = .false.
exit
end if
end do
return
end function in_bd_lat
function in_block_bd(v, box_bd)
!This function returns whether a point is within a block in 3d
!Input/output
real(kind=dp), dimension(3), intent(in) :: v
real(kind=dp), dimension(6), intent(in) :: box_bd
logical :: in_block_bd
!Other variables
integer :: i
in_block_bd = .true.
do i =1 ,3
!Check upper bound
if(v(i) > (box_bd(2*i)+10.0_dp**(-10)) ) then
in_block_bd =.false.
exit
!Check lower bound
else if (v(i) < (box_bd(2*i-1)-10.0_dp**(-10))) then
in_block_bd = .false.
exit
end if
end do
end function in_block_bd
function lcm(a,b)
!This function returns the smallest least common multiple of two numbers
real(kind=dp), intent(in) :: a, b
real(kind=dp) :: lcm
integer :: aint, bint, gcd, remainder, placeholder
!Cast the vector positions to ints. There will be some error associated with this calculation
aint = a*10**2
bint = b*10**2
!Calculate greated common divisor
gcd = aint
placeholder = bint
do while(placeholder /= 0)
remainder = modulo(gcd, placeholder)
gcd = placeholder
placeholder=remainder
end do
lcm = real((aint*bint),dp)/(real(gcd,dp))* 10.0_dp**(-2.0_dp)
end function lcm
function is_neighbor(rl, rk, r_in, r_out)
!This function checks to see if two atoms are within a shell with an inner radius r_in and outer radius
!r_out
real(kind=dp), intent(in) :: r_in, r_out
real(kind=dp), dimension(3), intent(in) :: rl, rk
logical :: is_neighbor
!Internal variable
real(kind=dp) :: rlk
rlk = norm2(rk - rl)
is_neighbor=.true.
if((rlk>r_out).or.(rlk < r_in)) is_neighbor = .false.
return
end function is_neighbor
function is_equal(A, B)
!This function checks if too numbers are equal within a tolerance
real(kind=dp), intent(in) :: A, B
logical :: is_equal
if((A>(B - 10.0_dp**-10)).and.(A < (B+10.0_dp**-10))) then
is_equal = .true.
else
is_equal = .false.
end if
return
end function is_equal
end module functions

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module io
use elements
use parameters
use atoms
implicit none
integer :: outfilenum = 0
character(len=100) :: outfiles(10)
public
contains
subroutine get_out_file(filename)
implicit none
character(len=100), intent(in) :: filename
character(len=100) :: temp_outfile
character(len=1) :: overwrite
logical :: file_exists
!If no filename is provided then this function is called with none and prompts user input
if (filename=='none') then
print *, "Please specify a filename or extension to output to:"
read(*,*) temp_outfile
else
temp_outfile = filename
end if
!Infinite loop which only exists if user provides valid filetype
overwrite = 'r'
do while(.true.)
!Check to see if file exists, if it does then ask user if they would like to overwrite the file
inquire(file=trim(temp_outfile), exist=file_exists)
if (file_exists) then
if (overwrite == 'r') print *, "File ", trim(temp_outfile), " already exists. Would you like to overwrite? (Y/N)"
read(*,*) overwrite
if((scan(overwrite, "n") > 0).or.(scan(overwrite, "N") > 0)) then
print *, "Please specify a new filename with extension:"
read(*,*) temp_outfile
else if((scan(overwrite, "y") > 0).or.(scan(overwrite, "Y") > 0)) then
continue
else
print *, "Please pick either y or n"
read(*,*) overwrite
end if
end if
if (scan(temp_outfile,'.',.true.) == 0) then
print *, "No extension included on filename, please type a full filename that includes an extension."
read(*,*) temp_outfile
cycle
end if
select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
case('xyz')
outfilenum=outfilenum+1
outfiles(outfilenum) = temp_outfile
exit
case('lmp')
outfilenum=outfilenum+1
outfiles(outfilenum) = temp_outfile
exit
case default
print *, "File type: ", trim(temp_outfile(scan(temp_outfile,'.',.true.):)), "not currently accepted. ", &
"please input a filename with extension from following list: xyz."
read(*,*) temp_outfile
end select
end do
end subroutine get_out_file
subroutine write_out
!This subroutine loops over alll of the outfile types defined and calls the correct writing subroutine
integer :: i
do i = 1, outfilenum
!Pull out the extension of the file and call the correct write subroutine
select case(trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))))
case('xyz')
call write_xyz(outfiles(i))
case('lmp')
call write_lmp(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 and try again"
stop
end select
end do
end subroutine write_out
subroutine write_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
integer :: node_num, i, inod, ibasis
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(11, '(i16)') node_num+atom_num
!Write comment line
write(11, '(a)') "#Node + atom file created using cacmb"
!Write nodal positions
do i = 1, ele_num
do inod = 1, ng_node(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)
end do
end do
end do
!Write atom positions
do i = 1, atom_num
write(11, '(a, 3f23.15)') type_atom(i), r_atom(:,i)
end do
!Finish writing
close(11)
end subroutine write_xyz
subroutine write_lmp(file)
integer :: write_num, i
character(len=100), intent(in) :: file
!This subroutine writes out a .lmp style dump file
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
!Comment line
write(11, '(a)') '# lmp file made with cacmb'
write(11, '(a)')
!Calculate total atom number
write_num = atom_num
!Write total number of atoms + elements
write(11, '(i16, a)') write_num, ' atoms'
!Write number of atom types
write(11, '(i16, a)') 1, ' atom types'
write(11,'(a)') ' '
!Write box bd
write(11, '(2f23.15, a)') box_bd(1:2), ' xlo xhi'
write(11, '(2f23.15, a)') box_bd(3:4), ' ylo yhi'
write(11, '(2f23.15, a)') box_bd(5:6), ' zlo zhi'
!Masses
write(11, '(a)') 'Masses'
write(11, '(a)') ' '
write(11, '(i16, f23.15)') 1, 63.546
write(11, '(a)') ' '
!Write atom positions
write(11, '(a)') 'Atoms'
write(11, '(a)') ' '
do i = 1, atom_num
write(11, '(2i16, 3f23.15)') i, 1, r_atom(:,i)
end do
end subroutine write_lmp
end module io

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module lattice
use precision_comm_module
use subroutines
implicit none
integer :: atom_types
!Atom type variables
character(len=2), dimension(10) :: atom_names
real(kind=wp), dimension(10) :: atom_masses
!Lattice_type variables
integer :: lat_num
character(len=10), dimension(10) :: lattice_id, lattice_type
real(kind=wp), dimension(10) :: lapa
integer(kind=wp), dimension(10) :: basis_atom_num
integer(kind=wp), dimension(10,10) :: basis_type
real(kind=wp), dimension(3,10,10) ::basis_pos
!Unit Cell variables
real(kind = wp) :: fcc_cell(3,8), fcc_mat(3,3)
public
contains
subroutine lattice_init
!Initialize needed variables
lat_num=0
basis_atom_num(:) = 0
!Initialize finite element cells to be used
!First initialize the primitive fcc cell
fcc_cell = reshape((/ 0.0_wp, 0.0_wp, 0.0_wp, &
0.5_wp, 0.5_wp, 0.0_wp, &
0.5_wp, 1.0_wp, 0.5_wp, &
0.0_wp, 0.5_wp, 0.5_wp, &
0.5_wp, 0.0_wp, 0.5_wp, &
1.0_wp, 0.5_wp, 0.5_wp, &
1.0_wp, 1.0_wp, 1.0_wp, &
0.5_wp, 0.5_wp, 1.0_wp /), &
shape(fcc_cell))
fcc_mat = reshape((/ 0.5_wp, 0.5_wp, 0.0_wp, &
0.5_wp, 0.5_wp, 0.5_wp, &
0.5_wp, 0.0_wp, 0.5_wp /), &
shape(fcc_mat))
end subroutine lattice_init
!This subroutine defines the atom type arrays
subroutine atom_type_parse(line)
character(len=100), intent(in) :: line
character(len=100) :: errorloc
integer :: ia, error
character(len=20) :: label
read(line, *, iostat=error) label, atom_types, (atom_names(ia), atom_masses(ia), ia=1, atom_types)
errorloc="lattice:22"
call read_error_check(error,errorloc)
end subroutine atom_type_parse
!This subroutine defines the lattice types and the unit cells for the lattice types
subroutine lattice_parse(line)
character(len=100), intent(in) :: line
integer :: ia, error
character(len=20) :: label, kw
character(len=100) :: errorloc
lat_num = lat_num + 1
read(line, *, iostat=error) label, lattice_id(lat_num), lattice_type(lat_num), lapa(lat_num), kw
errorloc="lattice:77"
call read_error_check(error, errorloc)
select case(kw)
case("type")
read(line(scan(line, "type"):), *, iostat=error) label, basis_type(1,1)
errorloc="lattice:56"
call read_error_check(error,errorloc)
case("basis")
read(line(scan(line, "basis"):), *, iostat=error) label, basis_atom_num(lat_num), (basis_type(ia, lat_num) ,&
basis_pos(1:3,ia,lat_num), ia = 1, basis_atom_num(lat_num))
errorloc="lattice:59"
call read_error_check(error,errorloc)
case default
print *, "Keyword ", kw, " is not accepted in the lattice command"
stop "Exit with error"
end select
end subroutine lattice_parse
end module lattice

71
src/main.f90
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@ -1,52 +1,39 @@
program main
use precision_comm_module
!**************************** CACmb *******************************
!* CAC model building toolkit *
! ____________ *
! / / *
! / / *
! /___________/ *
! _|_ _|_ _|____________ *
! / / *
! / / *
! /___________/ *
! *
!*******************************************************************
use parameters
use elements
use lattice
use region
use io
integer :: iosline, iospara
logical :: flags(4)
character(len=100) :: line, command, errorloc
iosline = 0
iospara = 0
flags(:) = .false.
integer :: arg_num
character(len=100) :: mode
call lattice_init
!Main command loop
do while (iosline == 0)
! Command line parsing
arg_num = command_argument_count()
read(*, '(a)', iostat=iosline) line
errorloc="read_input:line"
call read_error_check(iosline, errorloc)
!Determine if a mode is being used and what it is. The first argument has to be the mode
!if a mode is being used
call get_command_argument(1, mode)
!Check for comment character (#)
if ((scan(line, '#')/= 1).and.(line/='')) then
read(line, *, iostat = iospara) command
errorloc="read_input:command"
call read_error_check(iosline, errorloc)
mode = trim(adjustl(mode))
if (mode(1:2) == '--') then
call call_mode(arg_num, mode)
end if
select case(command)
case('atom_types')
call atom_type_parse(line)
flags(1) = .true.
case('lattice')
if(flags(1).eqv..false.) then
print *, "Please define atom types before defining lattice types"
stop 3
end if
call lattice_parse(line)
flags(2) =.true.
! case('region')
! call build_region(line)
! case('write')
! call write_parse(line)
case default
print *, "The command ", trim(command), " is not currently accepted",&
" please check input script and try again."
end select
end if
end do
!Finish by writing the files
call write_out
end program main

432
src/mode_create.f90 Normal file
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@ -0,0 +1,432 @@
module mode_create
!This mode is intended for creating element/atom regions and writing them to specific files.
use parameters
use atoms
use io
use subroutines
implicit none
character(len=100) :: name, element_type
real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), &
orient_inv(3,3), box_vert(3,8), ox_bd(6), maxbd(3), lattice_space(3)
integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_num, lat_atom_num, bd_in_lat(6)
logical :: dup_flag, dim_flag
real(kind=dp), allocatable :: r_lat(:,:,:), r_atom_lat(:,:)
public
contains
subroutine create(arg_num)
! Main subroutine which controls execution
integer, intent(in) :: arg_num
character(len=100) :: textholder
integer :: i, ibasis, inod
real(kind=dp) :: r(3), periodvone(3), periodvtwo(3)
real(kind=dp), allocatable :: r_node(:,:,:)
!Initialize default parameters
orient = reshape((/ 1.0_dp, 0.0_dp, 0.0_dp, 0.0_dp, 1.0_dp, 0.0_dp, 0.0_dp, 0.0_dp, 1.0_dp /), shape(orient))
cell_mat(:,:)=0.0_dp
name =''
element_type = ''
esize=0
lattice_parameter=0.0_dp
duplicate(:) = 0
box_len(:) = 0.0_dp
dup_flag = .false.
dim_flag = .false.
basisnum = 0
lat_num = 0
lat_atom_num = 0
!First we parse the command
call parse_command(arg_num)
! Before building do a check on the file
if (outfilenum == 0) then
textholder = 'none'
call get_out_file(textholder)
end if
!Now we setup the unit element and call other init subroutines
call def_ng_node(1, element_type)
allocate(r_node(3,max_basisnum,max_ng_node))
if(dup_flag) then
!We initialize the cell with a lattice_parameter of 1 because we will add the lattice parameter later
call cell_init(1.0_dp, esize, element_type, orient, cell_mat)
do i = 1, 8
box_vert(:,i) = duplicate(:)*lattice_space(:)*cubic_cell(:,i) + origin(:)
end do
call matrix_inverse(orient,3,orient_inv)
!Now get the rotated box vertex positions in lattice space. Should be integer units
box_lat_vert = int(matmul(fcc_inv, matmul(orient_inv, box_vert)))+1
!Find the new maxlen
maxbd = maxval(matmul(orient,matmul(fcc_mat,box_lat_vert)),2)
do i = 1, 3
box_bd(2*i) = maxval(box_vert(i,:)) - 0.1_dp*lattice_space(i)
box_bd(2*i-1) = origin(i)
end do
!and then call the build function with the correct transformation matrix
select case(trim(adjustl(element_type)))
case('fcc')
! periodvone(:) = matmul(orient, reshape((/ 1, 1, 0 /),(/ 3 /)))
! periodvtwo(:) = matmul(orient, reshape((/ 1, 1, 2 /),(/ 3 /)))
! do i = 1, 3
! if (periodvone(i) < lim_zero) then
! ! box_bd(2*i) =floor(box_bd(2*i)/periodvtwo(i))*periodvtwo(i)
! box_bd(2*i) = box_bd(2*i) - 0.5*periodvtwo(i)
! else if(periodvtwo(i) < lim_zero) then
! ! box_bd(2*i) =floor(box_bd(2*i)/periodvone(i))*periodvone(i)
! box_bd(2*i) = box_bd(2*i) - 0.5*periodvone(i)
! else
! ! box_bd(2*i) = floor(box_bd(2*i)/lcm(periodvone(i),periodvtwo(i)))*lcm(periodvone(i),periodvtwo(i))
! box_bd(2*i) = box_bd(2*i) - 0.5*lcm(periodvone(i),periodvtwo(i))
! end if
! end do
call lattice_in_box(box_lat_vert, fcc_mat)
case default
print *, "Element type ", trim(adjustl(element_type)), " not accepted in mode create, please specify a supported ", &
"element type"
stop 3
end select
!Now that it is multiply by the lattice parameter
box_bd = box_bd*lattice_parameter
else if(dim_flag) then
continue
else
call cell_init(lattice_parameter, esize, element_type, orient, cell_mat)
!If the user doesn't pass any build instructions than we just put the cell mat into the element_array
call alloc_ele_arrays(1,0)
!Add the basis atoms to the unit cell
do inod = 1, max_ng_node
do ibasis = 1, basisnum(1)
r_node(:,ibasis,inod) = cell_mat(:,inod) + basis_pos(:,ibasis,1) + origin(:)
end do
end do
call add_element(element_type, esize, 1, r_node)
end if
!If we passed the dup_flag or dim_flag then we have to convert the lattice points and add them to the atom/element arrays
if(dup_flag.or.dim_flag) then
!Allocate variables
call alloc_ele_arrays(lat_num, lat_atom_num*basisnum(1))
if(lat_atom_num > 0) then
!Check for periodicity
do i = 1, lat_atom_num
do ibasis = 1, basisnum(1)
call add_atom(basis_type(ibasis,1), (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis,1))
end do
end do
deallocate(r_atom_lat)
end if
end if
end subroutine create
!This subroutine parses the command and pulls out information needed for mode_create
subroutine parse_command(arg_num)
integer, intent(in) :: arg_num
integer :: arg_pos, ori_pos, i, j, arglen, stat
character(len=100) :: textholder
character(len=8) :: orient_string
!Pull out all required positional arguments
call get_command_argument(2, name, arglen)
if(arglen==0) STOP "Name is missing in mode create"
call get_command_argument(3,element_type, arglen)
if(arglen==0) STOP "Element_type is missing in mode create"
call get_command_argument(4,textholder, arglen)
if(arglen==0) STOP "Lattice Parameter is missing in mode create"
read(textholder, *, iostat=stat) lattice_parameter
if(stat > 0) STOP "Error reading lattice parameter"
call get_command_argument(5, textholder, arglen)
if(arglen==0) STOP "Esize missing in mode create"
read(textholder, *, iostat=stat) esize
if(stat > 0) STOP "Error reading esize"
arg_pos = 6
!Check for optional keywords
do while(.true.)
if(arg_pos > command_argument_count()) exit
!Pull out the next argument which should either be a keyword or an option
call get_command_argument(arg_pos, textholder)
textholder=adjustl(textholder)
arg_pos=arg_pos+1
!Choose what to based on what the option string is
select case(trim(textholder))
!If orient command is passed extract the orientation to numeric array format
case('orient')
do i = 1, 3
call get_command_argument(arg_pos, orient_string, arglen)
if (arglen==0) STOP "Missing orientation in orient command of mode create"
arg_pos = arg_pos+1
ori_pos=2
do j = 1,3
if (orient_string(ori_pos:ori_pos) == '-') then
ori_pos = ori_pos + 1
read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
if (stat>0) STOP "Error reading orient value"
orient(i,j) = -orient(i,j)
ori_pos = ori_pos + 1
else
read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
if(stat>0) STOP "Error reading orient value"
ori_pos=ori_pos + 1
end if
end do
end do
!If the duplicate command is passed then we extract the information on the new bounds.
case('duplicate')
dup_flag = .true.
do i = 1, 3
call get_command_argument(arg_pos, textholder)
read(textholder, *) duplicate(i)
arg_pos = arg_pos + 1
end do
case('origin')
do i = 1, 3
call get_command_argument(arg_pos, textholder)
read(textholder, *) origin(i)
arg_pos = arg_pos + 1
end do
print *, origin
!If a filetype is passed then we add name.ext to the outfiles list
case('xyz')
textholder = trim(adjustl(name)) //'.xyz'
call get_out_file(textholder)
case default
!Check to see if it is an option command, if so then mode_create must be finished
if(textholder(1:1) == '-') then
exit
!Check to see if a filename was passed
elseif(scan(textholder,'.',.true.) > 0) then
call get_out_file(textholder)
end if
end select
end do
!Calculate the lattice periodicity length in lattice units
do i = 1, 3
lattice_space(i) = norm2(orient(i,:))
end do
!Check special periodicity relations
select case(trim(adjustl(element_type)))
case('fcc')
do i = 1,3
print *, orient(i,:)
!Check if one of the directions is 110
if ((is_equal(abs(orient(i,1)), abs(orient(i,2))).and.(is_equal(orient(i,3),0.0_dp))).or.&
(is_equal(abs(orient(i,2)), abs(orient(i,3))).and.(is_equal(orient(i,1),0.0_dp))).or.&
(is_equal(abs(orient(i,3)), abs(orient(i,1))).and.(is_equal(orient(i,2),0.0_dp)))) then
print *, '110', i
lattice_space(i) = 0.5_dp * lattice_space(i)
!Check if one direction is 112
else if ((is_equal(abs(orient(i,1)), abs(orient(i,2))).and.(is_equal(abs(orient(i,3)),2.0_dp*abs(orient(i,1))))).or.&
(is_equal(abs(orient(i,2)), abs(orient(i,3))).and.(is_equal(abs(orient(i,1)),2.0_dp*abs(orient(i,2))))).or.&
(is_equal(abs(orient(i,3)), abs(orient(i,1))).and.(is_equal(abs(orient(i,2)),2.0_dp*abs(orient(i,3))))))&
then
print *, '112 ', i
lattice_space(i) = 0.5_dp * lattice_space(i)
end if
end do
end select
!Now normalize the orientation matrix
orient = matrix_normal(orient,3)
!If we haven't defined a basis then define the basis and add the default basis atom type and position
if (basisnum(1) == 0) then
max_basisnum = 1
basisnum(1) = 1
basis_type(1,1) = name !If basis command not defined then we use name as the atom_name
basis_pos(:,1,1) = 0.0_dp
end if
end subroutine
subroutine lattice_in_box(box_in_lat, transform_matrix)
!This subroutine returns all the lattice points in the box in r_lat
!Inputs
integer, dimension(3,8), intent(in) :: box_in_lat !The box vertices transformed to lattice space
real(kind=dp), dimension(3,3), intent(in) :: transform_matrix !The transformation matrix from lattice_space to real space
!Internal variables
integer :: i, j, bd_in_lat(6), ix, iy, iz, numlatpoints
real(kind=dp) :: box_face_center(3,6), face_normals(3,6), Cx(2), Cy, Cz, A(2), v(3)
real(kind=dp), allocatable :: resize_lat_array(:,:)
!First find the bounding lattice points (min and max points for the box in each dimension)
numlatpoints = 1
do i = 1, 3
bd_in_lat(2*i-1) = minval(box_in_lat(i,:))
bd_in_lat(2*i) = maxval(box_in_lat(i,:))
numlatpoints = numlatpoints*(bd_in_lat(2*i)-bd_in_lat(2*i-1))
end do
!Allocate the correct lat variable
select case(esize)
!Atomistics
case(2)
allocate(r_atom_lat(3,numlatpoints))
case default
continue
end select
!Calculate the box_face centroids and box face normals. This is used in the centroid code.
box_face_center(:,:) = 0.0_dp
face_normals = reshape((/ -1.0_dp, 0.0_dp, 0.0_dp, &
1.0_dp, 0.0_dp, 0.0_dp, &
0.0_dp, -1.0_dp, 0.0_dp, &
0.0_dp, 1.0_dp, 0.0_dp, &
0.0_dp, 0.0_dp, -1.0_dp, &
0.0_dp, 0.0_dp, 1.0_dp /),&
shape(face_normals))
!Face normals
select case(trim(adjustl(element_type)))
case('fcc')
do i = 1, 6
!Box face normal
face_normals(:,i) = matmul(fcc_inv, matmul(orient_inv, face_normals(:,i)))
end do
end select
!Face centroids
do i =1, 6
!Initialize variables
A(:) = 0.0_dp
Cx(:) = 0.0_dp
Cy = 0.0_dp
Cz = 0.0_dp
!Calculate all terms using a projection onto the xy and xz planes and then using the 2d equation
!for centroid of a plane. This is why we calculate the x centroid twice.
do j = 1, 4
! A(1) = A(1) + 0.5*(box_in_lat(1,cubic_faces(j,i))*box_in_lat(2,cubic_faces(j+1,i)) &
! - box_in_lat(1,cubic_faces(j+1,i))*box_in_lat(2,cubic_faces(j,i)))
! !Centroid in x from xy plane
! Cx(1) = Cx(1) + (box_in_lat(1,cubic_faces(j,i))+box_in_lat(1,cubic_faces(j+1,i)))* &
! (box_in_lat(1,cubic_faces(j,i))*box_in_lat(2,cubic_faces(j+1,i)) &
! - box_in_lat(1,cubic_faces(j+1,i))*box_in_lat(2,cubic_faces(j,i)))
! !Centroid in y from xy plane
! Cy = Cy + (box_in_lat(2,cubic_faces(j,i))+box_in_lat(2,cubic_faces(j+1,i)))* &
! (box_in_lat(1,cubic_faces(j,i))*box_in_lat(2,cubic_faces(j+1,i)) &
! - box_in_lat(1,cubic_faces(j+1,i))*box_in_lat(2,cubic_faces(j,i)))
! A(2) = A(2) + 0.5*(box_in_lat(1,cubic_faces(j,i))*box_in_lat(3,cubic_faces(j+1,i)) &
! - box_in_lat(1,cubic_faces(j+1,i))*box_in_lat(3,cubic_faces(j,i)))
! !Centroid in x from xz plane
! Cx(2) = Cx(2) + (box_in_lat(1,cubic_faces(j,i))+box_in_lat(1,cubic_faces(j+1,i)))* &
! (box_in_lat(1,cubic_faces(j,i))*box_in_lat(3,cubic_faces(j+1,i)) &
! - box_in_lat(1,cubic_faces(j+1,i))*box_in_lat(3,cubic_faces(j,i)))
! !Centroid in z from xz plane
! Cz = Cz + (box_in_lat(3,cubic_faces(j,i))+box_in_lat(3,cubic_faces(j+1,i)))* &
! (box_in_lat(1,cubic_faces(j,i))*box_in_lat(3,cubic_faces(j+1,i)) &
! - box_in_lat(1,cubic_faces(j+1,i))*box_in_lat(3,cubic_faces(j,i)))
! print *, j, i, Cx, Cy, Cz, A
Cx(1) = Cx(1) + box_in_lat(1,cubic_faces(j,i))*0.25
Cy = Cy + box_in_lat(2,cubic_faces(j,i))*0.25
Cz = Cz + box_in_lat(3,cubic_faces(j,i))*0.25
end do
! Cx = Cx * 1/(6*A)
! if(Cx(1) /= Cx(2)) then
! call error_message(7)
! end if
! Cy = Cy* 1/(6*A(1))
! Cz = Cz*1/(6*A(2))
box_face_center(:,i) = (/ Cx(1), Cy, Cz /)
end do
!Loop over all of lattice points within the boundary, we choose between two loops. One for the atomistic case
!and one for the regular case
print *, box_bd
if (esize==2) then
!atomistics
do iz = bd_in_lat(5)-5, bd_in_lat(6)+5
do iy = bd_in_lat(3)-5, bd_in_lat(4)+5
do ix = bd_in_lat(1)-5, bd_in_lat(2)+5
v= (/ real(ix,dp), real(iy, dp), real(iz,dp) /)
!Transform point back to real space for easier checking
v = matmul(orient, matmul(transform_matrix,v))
!If within the boundaries
if(in_block_bd(v, box_bd)) then
lat_atom_num = lat_atom_num + 1
r_atom_lat(:,lat_atom_num) = v
end if
end do
end do
end do
else
continue
end if
end subroutine lattice_in_box
subroutine error_message(errorid)
integer, intent(in) :: errorid
select case(errorid)
case(1)
STOP "Name is missing."
case(2)
print *, "Element_type is missing"
case(3)
print *, "Lattice_parameter is missing"
case(4)
print *, "Lattice parameter is not in float form"
case(5)
print *, "Esize is missing"
case(6)
print *, "Esize is not in integer form"
case(7)
print *, "Cx(1) should equal Cx(2) in plane centroid finding algorithm. Please double check implementation"
end select
STOP 3
end subroutine error_message
end module mode_create

8
src/parameters.f90 Normal file
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@ -0,0 +1,8 @@
module parameters
implicit none
integer, parameter :: dp= selected_real_kind(15,307)
real(kind=dp), parameter :: lim_zero = epsilon(1.0_dp), &
lim_large = huge(1.0_dp)
end module parameters

13
src/precision_comm_module.f90
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@ -1,13 +0,0 @@
module precision_comm_module
implicit none
integer, parameter :: &
dp = selected_real_kind(15, 307), & ! double real
qp = selected_real_kind(33, 4931), & ! quadrupole real
wp = dp
integer, save :: &
mpi_wp
end module precision_comm_module

14
src/region.f90
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@ -1,14 +0,0 @@
module region
use precision_comm_module
implicit none
public
contains
subroutine build_region(line)
character(len=100), intent(in) :: line
end subroutine build_region
end module region

132
src/subroutines.f90
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@ -1,13 +1,12 @@
module subroutines
use precision_comm_module
use parameters
use functions
implicit none
integer :: allostat, deallostat
public
contains
!This subroutine is just used to break the code and exit on an error
subroutine read_error_check(para, loc)
@ -18,7 +17,132 @@ module subroutines
print *, "Read error in ", trim(loc), " because of ", para
stop "Exit with error"
end if
end subroutine
subroutine matrix_inverse(a, n, a_inv)
integer :: i, j, k, piv_loc
integer, intent(in) :: n
real(kind = dp) :: coeff, sum_l, sum_u
real(kind = dp), dimension(n) :: b, x, y, b_piv
real(kind = dp), dimension(n, n) :: l, u, p
real(kind = dp), dimension(n, n), intent(in) :: a
real(kind = dp), dimension(n, n), intent(out) :: a_inv
real(kind = dp), allocatable :: v(:), u_temp(:), l_temp(:), p_temp(:)
l(:, :) = identity_mat(n)
u(:, :) = a(:, :)
p(:, :) = identity_mat(n)
!LU decomposition with partial pivoting
do j = 1, n-1
allocate(v(n-j+1), stat = allostat)
if(allostat /=0 ) then
print *, 'Fail to allocate v in matrix_inverse'
stop
end if
v(:) = u(j:n, j)
if(maxval(abs(v)) < lim_zero) then
print *, 'Fail to inverse matrix', a
stop
end if
piv_loc = maxloc(abs(v), 1)
deallocate(v, stat = deallostat)
if(deallostat /=0 ) then
print *, 'Fail to deallocate v in matrix_inverse'
stop
end if
!partial pivoting
if(piv_loc /= 1) then
allocate( u_temp(n-j+1), p_temp(n), stat = allostat)
if(allostat /=0 ) then
print *, 'Fail to allocate p_temp and/or u_temp in matrix_inverse'
stop
end if
u_temp(:) = u(j, j:n)
u(j, j:n) = u(piv_loc+j-1, j:n)
u(piv_loc+j-1, j:n) = u_temp(:)
p_temp(:) = p(j, :)
p(j, :) = p(piv_loc+j-1, :)
p(piv_loc+j-1, :) = p_temp(:)
deallocate( u_temp, p_temp, stat = deallostat)
if(deallostat /=0 ) then
print *, 'Fail to deallocate p_temp and/or u_temp in matrix_inverse'
stop
end if
if(j > 1) then
allocate( l_temp(j-1), stat = allostat)
if(allostat /= 0) then
print *, 'Fail to allocate l_temp in matrix_inverse'
stop
end if
l_temp(:) = l(j, 1:j-1)
l(j, 1:j-1) = l(piv_loc+j-1, 1:j-1)
l(piv_loc+j-1, 1:j-1) = l_temp(:)
deallocate( l_temp, stat = deallostat)
if(deallostat /=0 ) then
print *, 'Fail to deallocate l_temp in matrix_inverse'
stop
end if
end if
end if
!LU decomposition
do i = j+1, n
coeff = u(i, j)/u(j, j)
l(i, j) = coeff
u(i, j:n) = u(i, j:n)-coeff*u(j, j:n)
end do
end do
a_inv(:, :) = 0.0_dp
do j = 1, n
b(:) = 0.0_dp
b(j) = 1.0_dp
b_piv(:) = matmul(p, b)
!Now we have LUx = b_piv
!the first step is to solve y from Ly = b_piv
!forward substitution
do i = 1, n
if(i == 1) then
y(i) = b_piv(i)/l(i, i)
else
sum_l = 0
do k = 1, i-1
sum_l = sum_l+l(i, k)*y(k)
end do
y(i) = (b_piv(i)-sum_l)/l(i, i)
end if
end do
!then we solve x from ux = y
!backward subsitution
do i = n, 1, -1
if(i == n) then
x(i) = y(i)/u(i, i)
else
sum_u = 0
do k = i+1, n
sum_u = sum_u+u(i, k)*x(k)
end do
x(i) = (y(i)-sum_u)/u(i, i)
end if
end do
!put x into j column of a_inv
a_inv(:, j) = x(:)
end do
return
end subroutine matrix_inverse
end module subroutines