simplified pfio.c

fort_io/README.md

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+# PF_FORT_IO
+
+Python wrapped Fortran PF IO codes
+
+## Prerequisites
+
+* Fortran compiler
+* Numpy
+
+## Install
+
+Recommend that this tool is installed in it's own virtual environment, like a conda environment, rather than at the system level.
+
+```
+git clone https://github.com/arezaii/pf_tools.git
+cd pf_tools/fort_io
+pip install .
+```
+
+## Usage
+
+Brief overview of the pf_read usage
+
+```
+>>>import pf_pytools.pf_fort_io as pf_fort_io
+>>>import numpy as np
+>>>pfb_data = np.asfortranarray(np.zeros((3342,1888,17)))
+>>>pf_fort_io.pfb_read(pfb_data,'filename')
+```
+

fort_io/pf_fort_io.f90

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+ subroutine pfb_read(value,fname,nx,ny,nz) 
+  implicit none
+  real*8 value(nx,ny,nz)
+  real*8 dx, dy, dz, x1, y1, z1								
+  integer*4 i,j,k, nni, nnj, nnk, ix, iy, iz,			&
+            ns,  rx, ry, rz,nx,ny,nz, nnx, nny, nnz,is
+  character*100 fname
+
+  open(100,file=trim(adjustl(fname)),form='unformatted',   &
+                 access='stream',convert='BIG_ENDIAN')         !binary outputfile of Parflow
+  ! Read in header info
+
+! Start: reading of domain spatial information
+  read(100) x1 !X
+  read(100) y1 !Y 
+  read(100) z1 !Z
+
+  read(100) nx !NX
+  read(100) ny !NY
+  read(100) nz !NZ
+
+  read(100) dx !DX
+  read(100) dy !DY
+  read(100) dz !DZ
+
+  read(100) ns !num_subgrids
+! End: reading of domain spatial information
+
+! Start: loop over number of sub grids
+  do is = 0, (ns-1)
+
+! Start: reading of sub-grid spatial information
+   read(100) ix
+   read(100) iy
+   read(100) iz
+
+   read(100) nnx
+   read(100) nny
+   read(100) nnz
+   read(100) rx
+   read(100) ry
+   read(100) rz
+
+! End: reading of sub-grid spatial information
+
+! Start: read in saturation data from each individual subgrid
+!  do  k=iz +1 , iz + nnz
+!   do  j=iy +1 , iy + nny
+!    do  i=ix +1 , ix + nnx
+read(100) value((ix+1):(ix+nnx),(iy+1):(iy+nny),(iz+1):(iz+nnz))
+!     read(100) value(i,j,k)
+!    end do
+!   end do
+!  end do
+! End: read in saturation data from each individual subgrid
+
+! End: read in saturation data from each individual subgrid
+
+  end do
+! End: loop over number of sub grids
+
+
+
+  close(100)
+  end subroutine
+
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+! Subroutine to write output as PFB
+subroutine pfb_write(value,fname,nx,ny,nz,x1,y1,z1,dx,dy,dz)
+  implicit none
+  real*8        value(nx,ny,nz)
+  real*8        dx,dy,dz,x1,y1,z1
+  integer*4     i,j,k,nni,nnj,nnk,ix,iy,iz,                   &
+                ns,rx,ry,rz,nx,ny,nz,nnx,nny,nnz,is
+  character*200 fname
+
+  ! ifort
+  ! open(100,file=trim(fname),form='unformatted',accconvert='BIG_ENDIAN',status='unknown')
+
+  ! gfortran
+  open(100,file=trim(fname),form='unformatted',access='stream',convert='BIG_ENDIAN',status='unknown')
+
+  nnx=nx; nny=ny; nnz=nz
+  ns=1
+  ix=0;iy=0;iz=0
+  rx=0;ry=0;rz=0
+
+  ! Start: writing of domain spatial information
+  write(100) x1 !X
+  write(100) y1 !Y 
+  write(100) z1 !Z
+
+  write(100) nx !NX
+  write(100) ny !NY
+  write(100) nz !NZ
+
+  write(100) dx !DX
+  write(100) dy !DY
+  write(100) dz !DZ
+
+  write(100) ns !num_subgrids
+  ! End: writing of domain spatial information
+
+  ! Start: loop over number of sub grids
+  do is = 0, (ns-1)
+
+   ! Start: writing of sub-grid spatial information
+   write(100) ix
+   write(100) iy
+   write(100) iz
+   write(100) nnx
+   write(100) nny
+   write(100) nnz
+   write(100) rx
+   write(100) ry
+   write(100) rz
+   ! End: writing of sub-grid spatial information
+
+   ! Start: write in data from each individual subgrid
+    !write(100) value((ix+1):(ix+nnx),(iy+1):(iy+nny),(iz+1):(iz+nnz))
+    write(100) value
+ ! do  k=iz +1 , iz + nnz
+  !  do  j=iy +1 , iy + nny
+  !   do  i=ix +1 , ix + nnx
+  !    write(100) value(i,j,k)
+  !   end do
+  !  end do
+  ! end do
+
+   ! End: write data from each individual subgrid
+
+  end do
+  ! End: loop over number of sub grids
+
+  close(100)
+end subroutine
+

fort_io/pf_fort_io.pyf

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+!    -*- f90 -*-
+! Note: the context of this file is case sensitive.
+
+python module pf_fort_io ! in 
+    interface  ! in :pf_fort_io
+        subroutine pfb_read(value,fname,nx,ny,nz) ! in :pf_fort_io:pf_fort_io.f90
+            real*8 intent(inout),dimension(nx,ny,nz) :: value
+            character*100 intent(in) :: fname
+            integer*4 intent(in),optional,check(shape(value,0)==nx),depend(value) :: nx=shape(value,0)
+            integer*4 intent(in),optional,check(shape(value,1)==ny),depend(value) :: ny=shape(value,1)
+            integer*4 intent(in),optional,check(shape(value,2)==nz),depend(value) :: nz=shape(value,2)
+        end subroutine pfb_read
+        subroutine pfb_write(value,fname,nx,ny,nz,x1,y1,z1,dx,dy,dz) ! in :pf_fort_io:pf_fort_io.f90
+            real*8 dimension(nx,ny,nz) :: value
+            character*200 :: fname
+            integer*4, optional,check(shape(value,0)==nx),depend(value) :: nx=shape(value,0)
+            integer*4, optional,check(shape(value,1)==ny),depend(value) :: ny=shape(value,1)
+            integer*4, optional,check(shape(value,2)==nz),depend(value) :: nz=shape(value,2)
+            real*8 :: x1
+            real*8 :: y1
+            real*8 :: z1
+            real*8 :: dx
+            real*8 :: dy
+            real*8 :: dz
+        end subroutine pfb_write
+    end interface 
+end python module pf_fort_io
+
+! This file was auto-generated with f2py (version:2).
+! See http://cens.ioc.ee/projects/f2py2e/

fort_io/setup.py

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+
+def configuration(parent_package='', top_path=None):
+    from numpy.distutils.misc_util import Configuration
+    config = Configuration('pf_pytools',parent_package, top_path)
+    config.add_extension('pf_fort_io', sources=['pf_fort_io.pyf','pf_fort_io.f90'])
+    return config
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(**configuration(top_path='').todict())