Program allo
Implicit none
integer :: A,ok,i,B,k
Real, Dimension (:,:), Allocatable :: note
Print*, "enter line A"
Read*, A
Print*, "enter range B"
Read* ,B
Allocate (note(A,B), STAT=ok)
If (ok/=0) then
print*, "failed"
STOP
end if
Do i=1,A
Do k=1,B
Read*, note(i,k)
End do
End do
print*,shape(note, /A,B/)
Deallocate (note)
End Program allo
When I compile it normally without the "shape" option, it gives me an array on 1 line, I want to have the (A,B) array. I tried to shape it to have my perfect table but it gives me error.
The shape intrinsic returns the shape of your array, here the result will be an array [ A, B ].
What you are trying to do is reshaping the array, for which you need to use the reshape intrinsic.
However, the array is already in the desired shape. It is just not printed that way.
I would propose a loop to print the array:
do i=1,A
print *, note(i,:)
enddo !i
Related
I am trying to read a text file using a Fortran code. I have a file with 1999 rows and the number of columns vary with each row. Can someone please tell me how one can code such a problem. This is my code for reading a 4*2 text file but I am using do loops which I can't use in my current case.
PROGRAM myread2
IMPLICIT NONE
INTEGER, DIMENSION(100) :: a, b
INTEGER :: row,col,max_rows,max_cols
OPEN(UNIT=11, file='text.txt')
DO row = 1,4
READ(11,*) a(row), b(row)
END DO
PRINT *, a(1)
PRINT *, a(4)
PRINT*, b(4)
END PROGRAM myread2
The best way of reading a file like this depends on how you want to store the data. I'm going to use a ragged array as it's probably simplest, although other container types may be better suited depending on your requirements.
Fortran doesn't have ragged arrays natively, so first you need to define a type to hold each row. This can be done as
type :: RowData
integer, allocatable :: cols(:)
end type
type(RowData), allocatable :: rows(:)
When this container is filled out, the value in the i'th column of the j'th row will be accessed as
value = rows(j)%cols(i)
We can then write a program to read the file, e.g.
type :: RowData
integer, allocatable :: cols(:)
end type
type(RowData), allocatable :: rows(:)
integer :: no_rows
integer :: i
open(unit=11, file='text.txt')
no_rows = count_lines(11)
allocate(rows(no_rows))
do i=1,no_rows
rows(i)%cols = read_row(11)
enddo
Now we just need to write the functions count_lines, which counts the number of lines in the file, and read_row, which reads a line from the file and returns the contents of that line as an array of integers.
Following this question, count_lines can be written as
! Takes a file unit, and returns the number of lines in the file.
! N.B. the file must be at the start of the file.
function count_lines(file_unit) result(output)
integer, intent(in) :: file_unit
integer :: output
integer :: iostat
output = 0
iostat = 0
do while (iostat==0)
read(file_unit, *, iostat=iostat)
if (iostat==0) then
output = output+1
endif
enddo
rewind(file_unit)
end function
Writing read_row, to parse a line of unknown length from a file, can be done by following this question.
I need to call some fortran code that dynamically allocates arrays similar to this basic example. (unlike this example in the code I'm working with the size of the array is not known at the beginning of the function)
subroutine getIdentity(n,I)
integer, intent(in) :: n
integer, allocatable,dimension(:,:), intent(out) :: I
integer :: j,k
write(*,*) "creating " ,n, "x", n, "identity matrix"
allocate(I(n,n))
do j=1,n
do k=1,n
if(k==j) then
I(j,k) = 1
else
I(j,k) = 0
end if
end do
end do
end subroutine getIdentity
When I call this with this julia code:
I = zeros(Int32,1,1)
n = Ref{Int32}(3)
ccall((:__myModule_MOD_getidentity,"./test.so"), Cvoid ,
(Ref{Int32},Ref{Int32}), n,I)
println(I)
When I look at I in julia it is just garbage, not the Identity matrix I would expect. What would be the correct way to do this?
I'm writing a subroutine that transform a regular vector into the one with only non-zero elements. Say, vector a=(0,0,1,2,3)' (n by 1). Then the non-zero vector is c=(1,2,3), and the row index is recorded as ic=(0,0,0,1,2,3) where ic(1)=0, ic(i+1)-ic(i) is the number of non-zero elements in i-th row. The vector index jc=(1,1,1) with size 3 as there are 3 non-zero entries. See the sparse matrix wiki for FYI: https://en.wikipedia.org/wiki/Sparse_matrix.
Despite its simplicity, I'm having troubles in running the following code named sparsem.f90
!This subroutine coverts a regular sparse matrix a into a CSR form
MODULE SPARSEM
CONTAINS
SUBROUTINE vsparse(a,c,jc,ic,counta,ierr,myid)
IMPLICIT NONE
REAL(8), INTENT(IN):: a(:)
INTEGER, INTENT(IN):: counta,myid
REAL(8), INTENT(OUT):: c(counta)
INTEGER, INTENT(OUT):: jc(counta),ic(size(a)+1)
INTEGER:: ierr,countaa,i
character(len=90):: filename
ierr=0
jc=0
c=0.0d0
ic=0
PRINT *, 'SIZE OF A IN VSPARSE', size(a),count(a>0.0d0),counta
IF (COUNT(a>0.0d0) /= counta) THEN
ierr=1
PRINT *, 'ERROR: number count of non-zero a(i,j) is not', counta
ELSE
countaa=0
ic(1)=0
DO i=1,size(a)
IF (a(i) > 0.0d0 ) THEN
countaa=countaa+1
c(countaa)=a(i)
ic(i+1)=ic(i)+1
jc(countaa)=1
IF (countaa<100) PRINT *,'checkcheckcheck', a(i), &
countaa,jc(countaa),c(countaa)，jc(1:5)
ELSE
ic(i+1)=ic(i)
END IF
END DO
PRINT *, 'JCJCJCJC',jc(1:5)
END IF
IF (myid==7) THEN
WRITE(filename,'("sparsedens_dcheck",I1,".txt")') myid+1
OPEN(UNIT=212101, FILE="/home/wenya/Workspace/Model4/valuef/"//filename,ACTION='write',status='replace')
DO i=1,counta+1
IF (i<=counta) THEN
WRITE(212101,*) c(i),jc(i)
ELSE
WRITE(212101,*) 0.0D0,0
END IF
END DO
CLOSE(212101)
END IF
return
END SUBROUTINE vsparse
END MODULE SPARSEM
So the three print jc codes shall give 1 1 1 1 1.... Yet starting from the second print jc code, the result is 6750960 6750691 6750692 .... The array of jc has size 9,000,000. And I know the first 2250000 element is 0.
To replicate this problem, here is the main program
PROGRAM MAIN
USE SPARSEM
IMPICIT NONE
REAL(8):: dens_last(9000000)
REAL(8), ALLOCATABLE :: dens(:)
INTEGER, ALLOCATABLE :: ic(:),jc(:)
INTEGER:: i
dens_last(1:2250000)=0.0d0
dens_last(2250001:9000000)=1.0d0/6750000.0d0
ncount=count(dens_last>0.0d0)
ALLOCATE(dens(ncount), ic(9000000+1), jc(ncount)_
CALL VSPASEM(dens_last, dens, jc, ic, ncount,ierr)
DEALLOCATE(dens,ic,jc)
END PROGRAM MAIN
I am using gfortran 6.3.0 and openmpi latest version on a UBUNTU 17.04 computer. Although openmpi is not used in this example, it's used in the rest of the program. Any thoughts? Thanks!
There are several threads with similar titles of mine, but I do not believe they are the same. One was very similar fortran pass allocated array to main procedure, but the answer required Fortran 2008. I am after a Fortran 90/95 solution.
Another very good, and quite similar thread is Dynamic array allocation in fortran90. However in this method while they allocate in the subroutine, they don't ever appear to deallocate, which seems odd. My method looks on the surface at least to be the same, yet when I print the array in the main program, only blank spaces are printed. When I print in the subroutine itself, the array prints to screen the correct values, and the correct number of values.
In the following a MAIN program calls a subroutine. This subroutine reads data into an allocatable array, and passes the array back to the main program. I do this by using small subroutines each designed to look for specific terms in the input file. All of these subroutines are in one module file. So there are three files: Main.f90, input_read.f90 and filename.inp.
It seems then that I do not know how to pass an array that is allocatable in program Main.f90 as well as in the called subroutine where it is actually allocated, sized, and then deallocated before being passed to program Main. This perhaps sounds confusing, so here is the code for all three programs. I apologize for the poor formatting when I pasted it. I tried to separate all the rows.
main.f90:
Program main
use input_read ! the module with the subroutines used for reading filename.inp
implicit none
REAL, Allocatable :: epsilstar(:)
INTEGER :: natoms
call Obtain_LJ_Epsilon(epsilstar, natoms)
print*, 'LJ Epsilon : ', epsilstar
END Program main
Next is the module with a subroutine (I removed all but the necessary one for space), input_read.f90:
module input_read
contains
!===============================================================
!===============================================================
Subroutine Obtain_LJ_Epsilon(epsilstar,natoms)
! Reads epsilon and sigma parameters for Lennard-Jones Force-Field and also
! counts the number of types of atoms in the system
!===============================================================
!===============================================================
INTEGER :: error,line_number,natoms_eps,i
CHARACTER(120) :: string, next_line, next_next_line,dummy_char
CHARACTER(8) :: dummy_na,dummy_eps
INTEGER,intent(out) :: natoms
LOGICAL :: Proceed
real, intent(out), allocatable :: epsilstar(:)
error = 0
line_number = 0
Proceed = .true.
open(10,file='filename.inp',status='old')
!=============================================
! Find key word LJ_Epsilon
!=============================================
DO
line_number = line_number + 1
Read(10,'(A120)',iostat=error) string
IF (error .NE. 0) THEN
print*, "Error, stopping read input due to an error reading line"
exit
END IF
IF (string(1:12) == '$ LJ_epsilon') THEN
line_number = line_number + 1
exit
ELSE IF (string(1:3) == 'END' .or. line_number > 2000) THEN
print*, "Hit end of file before reading '$ LJ_epsilon' "
Proceed = .false.
exit
ENDIF
ENDDO
!========================================================
! Key word found, now determine number of parameters
! needing to be read
!========================================================
natoms_eps = -1
dummy_eps = 'iii'
do while ((dummy_eps(1:1) .ne. '$') .and. (dummy_eps(1:1) .ne. ' '))
natoms_eps = natoms_eps + 1
read(10,*) dummy_eps
enddo !we now know the number of atoms in the system (# of parameters)
close(10)
Allocate(epsilstar(natoms_eps))
epsilstar = 0.0
!============================================================
! Number of parameters found, now read their values
!============================================================
if(Proceed) then
open(11,file='filename.inp',status='old')
do i = 1,line_number-1
read(11,*) ! note it is not recording anything for this do loop
enddo
do i = 1,natoms_eps
read(11,*) dummy_char
read(dummy_char,*) epsilstar(i) ! convert string read in to real, and store in epsilstar
enddo
close(11)
PRINT*, 'LJ_epsilon: ', epsilstar ! printing to make sure it worked
endif
deallocate(epsilstar)
END Subroutine Obtain_LJ_Epsilon
end module input_read
And finally the input file: filename.inp
# Run_Type
NVT
# Run_Name
Test_Name
# Pressure
1.0
# Temperature
298.15
# Number_Species
# LJ_epsilon
117.1
117.1
117.1
# LJ_sigma
3.251
3.251
3.251
END
And again, I can't figure out how to pass the allocated epsilstar array to the main program. I have tried passing an unallocated array to the subroutine from the main.f90, allocating it inside, passing it back, and deallocating it in the main.f90, but that did not work. I have tried it as the code currently is... the code works (i.e. is bug free) but it does not pass epsilstar from the subroutine where it correctly finds it and creates an array.
It turns out that the mistake I made was in deallocating the array in the subroutine before passing it to the main program. By NOT deallocating, the array was sent back fine. Also, I do not deallocate in the main program either.
I am trying to write a wrapper for 'allocate' function, i.e. function which receives an array and dimensions, allocates memory and returns allocated array. The most important thing is that the function must work with arrays of different rank. But I have to explicitly state rank of array in function interface, and in this case code only compiles if I pass arrays of certain rank as a parameter. For example, this code does not compile:
module memory_allocator
contains
subroutine memory(array, length)
implicit none
real(8), allocatable, intent(out), dimension(:) :: array
integer, intent(in) :: length
integer :: ierr
print *, "memory: before: ", allocated(array)
allocate(array(length), stat=ierr)
if (ierr /= 0) then
print *, "error allocating memory: ierr=", ierr
end if
print *, "memory: after: ", allocated(array)
end subroutine memory
subroutine freem(array)
implicit none
real(8), allocatable, dimension(:) :: array
print *, "freem: before: ", allocated(array)
deallocate(array)
print *, "freem: after: ", allocated(array)
end subroutine freem
end module memory_allocator
program alloc
use memory_allocator
implicit none
integer, parameter :: n = 3
real(8), allocatable, dimension(:,:,:) :: foo
integer :: i, j, k
print *, "main: before memory: ", allocated(foo)
call memory(foo, n*n*n)
print *, "main: after memory: ", allocated(foo)
do i = 1,n
do j = 1,n
do k = 1, n
foo(i, j, k) = real(i*j*k)
end do
end do
end do
print *, foo
print *, "main: before freem: ", allocated(foo)
call freem(foo)
print *, "main: after freem: ", allocated(foo)
end program alloc
Compilation error:
gfortran -o alloc alloc.f90 -std=f2003
alloc.f90:46.14:
call memory(foo, n*n*n)
1
Error: Rank mismatch in argument 'array' at (1) (1 and 3)
alloc.f90:60.13:
call freem(foo)
1
Error: Rank mismatch in argument 'array' at (1) (1 and 3)
Is there any way of implementing such wrapper?..
Thanks!
This can be done via a generic interface block. You have to create procedures for each rank that you want to handle, e.g., memory_1d, memory_2d, ... memory_4d. (Obviously a lot of cut & pasting.) Then you write a generic interface block that gives all of these procedures the alternative name memory as a generic procedure name. When you call memory, the compiler distinguishes which memory_Xd should be called based on the rank of the argument. The same for your freem functions.
This is how intrinsic functions such as sin have long worked -- you can call sin with a real arguments of various previsions, or with a complex argument, and the compiler figures out with actual sin function to call. In really old FORTRAN you had to use different names for the different sin functions. Now modern Fortran you can setup the same thing with your own routines.
Edit: adding a code example demonstrating the method & syntax:
module double_array_mod
implicit none
interface double_array
module procedure double_vector
module procedure double_array_2D
end interface double_array
private ! hides items not listed on public statement
public :: double_array
contains
subroutine double_vector (vector)
integer, dimension (:), intent (inout) :: vector
vector = 2 * vector
end subroutine double_vector
subroutine double_array_2D (array)
integer, dimension (:,:), intent (inout) :: array
array = 2 * array
end subroutine double_array_2D
end module double_array_mod
program demo_user_generic
use double_array_mod
implicit none
integer, dimension (2) :: A = [1, 2]
integer, dimension (2,2) :: B = reshape ( [11, 12, 13, 14], [2,2] )
integer :: i
write (*, '( / "vector before:", / 2(2X, I3) )' ) A
call double_array (A)
write (*, '( / "vector after:", / 2(2X, I3) )' ) A
write (*, '( / "2D array before:" )' )
do i=1, 2
write (*, '( 2(2X, I3) )' ) B (i, :)
end do
call double_array (B)
write (*, '( / "2D array after:" )' )
do i=1, 2
write (*, '( 2(2X, I3) )' ) B (i, :)
end do
stop
end program demo_user_generic
subroutine memory(array, length) has as it first dummy parameter 1-dimensional array (real(8), allocatable, intent(out), dimension(:) :: array).
Calling this subroutine from your main program with 3-dimensional array foo (real(8), allocatable, dimension(:,:,:) :: foo) is error obviously. And this is what compiler actually said.
If you really need such subroutines write one pair memory/freem subroutines for each array of different dimension - one subroutines pair for 1-dimensional array, another for 2-dimensional array, etc.
By the way, memory subroutines will be different in general because in order to allocate n-dimensional array you need to pass n extents to above-mentioned subroutine.