Assignment of 2D array

  • Fortran
  • Thread starter davidfur
  • Start date
  • #1
18
2
Hi guys,
On with my Fortran adventures...I'm trying to accomplish a simple task: assign a 2D array with some reals. Here's an excerpt from the code:

Fortran:
subroutine get_energy_and_grad(natoms_,coords,ereal,gradmat)

    include 'cbka.blk'
    include 'opt.blk'
    integer, intent(in)    :: natoms_
    double precision, intent(in)    :: coords(3*natoms_)
    real*8, intent(out)    :: ereal    ! total energy
    real*8, dimension(3,3), intent(out)    :: gradmat

    call vlist
    call srtbon1
    call encalc
     
    ereal = estrc ! total energy

!    write (*,*) 'natoms_ is: ', natoms_

    write (*,*) 'size of gradmat is:', size(gradmat)
    write (*,*) 'size of d is:', size(d)
    write (*,*) 'shape of gradmat is:', shape(gradmat)
    write (*,*) 'shape of d is:', shape(d)

    gradmat = reshape((/ 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0 /),(/3, 3/))

    write(*,*) 'gradmat is: ', gradmat(2,3)

end subroutine get_energy_and_grad
This just won't assign the 1.0-9.0 reals into gradmat and throws out the following:

Code:
 size of gradmat is:           9
 size of d is:        7500
 shape of gradmat is:           3           3
 shape of d is:           3        2500

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7F3B8F78EE08
#1  0x7F3B8F78DF90
#2  0x7F3B8F0D54AF
#3  0x40151C in __reaxff_interface_MOD_get_energy_and_grad
#4  0x402C5E in MAIN__ at main.f90:?
Segmentation fault (core dumped)
I'm obviously doing something really stupid, but I just can't figure out what's wrong... need help!

Dave
 
Last edited:

Answers and Replies

  • #2
12,477
6,262
Here's a tutorial on the reshape function:

https://www.tutorialspoint.com/fortran/reshape.htm

I don't see what wrong but a memory error often indicates referencing an element outside the array bounds.

Perhaps, you could try being more explicit and breaking the statement up a bit:

Fortran:
 real*8, dimension (1:9) :: b = (/ 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0 /)

 gradmat = reshape( b , (/3, 3/) )
 
  • #3
18
2
Thanks jedishrfu, but it doesn't work either. I suspect there's something wrong with my declarations....
I post here the full code if this helps

Main program

Fortran:
program main

use reaxff_interface
implicit none

integer natoms_
real*8 ereal
real*8, allocatable :: coords(:,:)
real*8, allocatable :: gradvec(:,:)

call get_energy_and_grad(gradvec)

write (*,*) "This is main. grad(3,3) is : ", gradvec(3,3)

end program main
Module

Fortran:
    module reaxff_interface
    implicit none

subroutine get_energy_and_grad(grad)
    include 'cbka.blk'
    include 'opt.blk'
    real*8, dimension(3,3), intent(out)     :: grad
    real*8, dimension (1:9) :: b

    b = (/ 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0 /)
    grad = reshape( b , (/3, 3/) ) 
end subroutine get_energy_and_grad

end module reaxff_interface
output:
Code:
Program received signal SIGBUS: Access to an undefined portion of a memory object.

Backtrace for this error:
#0  0x7F4FB566DE08
#1  0x7F4FB566CF90
#2  0x7F4FB4FB44AF
#3  0x7F4FB574563F
#4  0x7F4FB5748154
#5  0x7F4FB5748D3E
#6  0x402DBF in MAIN__ at main.f90:?
Bus error (core dumped)
 
  • #4
34,667
6,379
Here's an excerpt from the code:
Fortran:
subroutine get_energy_and_grad(natoms_,coords,ereal,gradmat)

    include 'cbka.blk'
    include 'opt.blk'
    integer, intent(in)    :: natoms_
    double precision, intent(in)    :: coords(3*natoms_)
    real*8, intent(out)    :: ereal    ! total energy
    real*8, dimension(3,3), intent(out)    :: gradmat

    call vlist
    call srtbon1
    call encalc
    
    ereal = estrc ! total energy

!    write (*,*) 'natoms_ is: ', natoms_

    write (*,*) 'size of gradmat is:', size(gradmat)
    write (*,*) 'size of d is:', size(d)
    write (*,*) 'shape of gradmat is:', shape(gradmat)
    write (*,*) 'shape of d is:', shape(d)

    gradmat = reshape((/ 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0 /),(/3, 3/))

    write(*,*) 'gradmat is: ', gradmat(2,3)

end subroutine get_energy_and_grad
I see two or maybe three problems:
1. In your three call statements, none of the subroutine calls is written correctly. The syntax for a call statement is
call SubName(argument1, argument2, ...). If a subroutine has no parameters, the parentheses still must be used. See http://pages.mtu.edu/~shene/COURSES/cs201/NOTES/F90-Subprograms.pdf, on page titled "Subroutines: 2/2".
You don't show the definitions for the three subroutines, so I can't tell if any of them takes any arguments.

2. What is d? There is no declaration for d in either the parameter list or in the declarations for local variables, so d apparently is a global variable. It's very bad practice for a function of subroutine to access global variables. At the very least, doing this makes debugging much more difficult.

3. I'm not sure that reshape will take a list of constants as its first argument. Per the GNU Fortran Compiler man page for reshape (https://gcc.gnu.org/onlinedocs/gfortran/RESHAPE.html), it appears to me that the first argument has to be a variable, but I'm not certain of this.
 
  • Like
Likes jim mcnamara
  • #5
18
2
Thanks Mark44 for your help!
I managed to solve the problem by properly declaring and allocating coords and gradvec variables outside the get_energy_and_grad subroutine.

Cheers!
 

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