I try to read a file as such (the numbers here are equal just to have an idea of the format of the file):
0.7498000E-01 0.1046400E+00 0.4006199E-01 0.1978479E+01
0.7498000E-01 0.1046400E+00 0.4006199E-01 0.1978479E+01
0.7498000E-01 0.1046400E+00 0.4006199E-01 0.1978479E+01
0.7498000E-01 0.1046400E+00 0.4006199E-01 0.1978479E+01
0.7498000E-01 0.1046400E+00 0.4006199E-01 0.1978479E+01
0.7498000E-01 0.1046400E+00 0.4006199E-01 0.1978479E+01
0.7498000E-01 0.1046400E+00 0.4006199E-01 0.1978479E+01
0.7498000E-01 0.1046400E+00 0.4006199E-01 0.1978479E+01
0.7498000E-01 0.1046400E+00 0.4006199E-01 0.1978479E+01
My code is the follow one:
CASE 1
program selection
implicit none
integer :: i,n,s,j
REAL*8,allocatable:: dum1(:),dum2(:),dum3(:),dum4(:)
open(10,file='file.txt')
n=0
DO
READ(10,*,END=100)
n=n+1
END DO
100 continue
rewind(10)
allocate(dum1(n),dum2(n),dum3(n)dum4(n))
s=0
do s=1, n
read(10,*) dum1(s),dum2(s),dum3(s),dum4(s)
end do
end program selection
The problem are the spaces between two different set of data that give to me forrtl: severe (24): end-of-file during read during the reading.
So I solve this problem just saying to the code how many lines the file has, and I modify the code as such:
CASE 2
program selection
implicit none
integer :: i,n,s,j
REAL*8,allocatable:: dum1(:),dum2(:),dum3(:),dum4(:)
open(10,file='file.txt')
n = 9 ! number of rows in the particular file in this example
allocate(dum1(n),dum2(n),dum3(n)dum4(n))
s=0
do s=1, n
read(10,*) dum1(s),dum2(s),dum3(s),dum4(s)
end do
end program selection
My question is: is there some way to modify the iterative process in CASE 1 such as I can automatically read empty lines, too?
A minimal change to count non-empty lines. More checking can be added if desirable or necessary.
character(max_line_length) :: line
open(10,file='file.txt')
n=0
DO
read(10,'(a)',end=100) line
if (len_trim(line)>0) n = n + 1
END DO
100 continue
Normally, I prefer to stop counting on any end-of-file condition or error-condition using iostat=)
character(max_line_length) :: line
integer :: ie
open(10,file='file.txt')
n=0
DO
read(10,'(a)',iostat=ie) line
if (ie/=0) exit
if (len_trim(line)>0) n = n + 1
END DO
Related
I have only limited experience with FORTRAN and I need to parse files with a structure similar to this:
H s 13.010000 0.019685
1.962000 0.137977
0.444600 0.478148
s 0.122000 1.000000
p 0.727000 1.000000
***
He s 38.360000 0.023809
5.770000 0.154891
1.240000 0.469987
s 0.297600 1.000000
p 1.275000 1.000000
***
I need to search for the label (e.g. He) and then read the corresponding blocks into an array.
I know I can parse file by specifying the format each line is supposed to have, but here there are different formats possible.
In Python I would just split each line by the white spaces and deal with it depending on the number of columns. But how to approach this in FORTRAN?
You can read each line as a character string and then process it. If, as it seems, the format is fixed (element symbol in first two characters, orbital letter in sixth character, etc.), the following program could serve you as inspiration:
program elms
implicit none
integer, parameter :: MAX_LEN = 40
character(len=MAX_LEN) :: line_el, line
integer :: u
integer :: is
integer :: nlin
character(len=2) :: element = 'He'
integer, parameter :: MAX_LINES = 20
real, dimension(MAX_LINES) :: e, f
open(newunit=u, file='elms.dat', status='old', action='read')
main_loop: do
! Read line
read(u, '(a)', iostat=is) line_el
if (eof_iostat(is)) exit main_loop
! Check first two characters of the line vs. chemical element.
if (line_el(1:2) .eq. element) then
! This is the beginning of an element block
nlin = 0
line = line_el
do
if (line .ne. '') then
! Line is not empty or only spaces.
nlin = nlin + 1
if (line(6:6) .ne. ' ') then
! Line contains an orbital letter - process it.
end if
! Read the real values in the rest of the line
read(line(7:),*) e(nlin), f(nlin)
end if
! Read next line
read(u, '(a)', iostat=is) line
if (eof_iostat(is)) exit main_loop
if (line(1:2) .ne. ' ') then
! Finished processing element block.
exit main_loop
end if
end do
end if
end do main_loop
! Close file
close(u)
contains
logical function eof_iostat(istat)
! Returns true if the end of file has been reached
use, intrinsic :: iso_fortran_env, only: IOSTAT_END
implicit none
integer, intent(in) :: istat
select case (istat)
case (0) ! No error
eof_iostat = .false.
case (IOSTAT_END) ! End of file reached
eof_iostat = .true.
case default ! Error
STOP
end select
end function eof_iostat
end program
You will probably need to make the program a subroutine, make element an intent(in) dummy argument, process the orbital symbols, etc.
Note that, if possible, it would be easier to just read all the data from the file in one go, and then search for the relevant data in the memory (e.g., having an array with the chemical symbols).
I'm trying to open 6 different files (at least) and then read the number of lines in each file, which should be about 20,000 lines each. I've read some posts on this forum about how to do that as I'm a newbie, and I've tried to implement it for my purposes.
I can do this individually without any problem, but when I try to read in all the files, I get an error message. I get either the "Killed: 9" error message or a malloc error:
malloc: *** mach_vm_map(size=63032829050880) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
What does this error mean regarding memory allocation? What am I doing wrong? How do I go about correcting this?
PROGRAM X
IMPLICIT NONE
INTEGER :: J,IO,NFILES,NLINES
CHARACTER (LEN=128) :: FILENAME
NFILES = 6
NLINES = 0
DO J = 0,NFILES-1
WRITE(FILENAME,'(A,I7.7,A)') 'data_',J*200,'.txt'
OPEN(1,FILE='FILENAME',FORM='FORMATTED')
DO
READ(1,*,IOSTAT=IO)
IF (IO/=0) EXIT
NLINES = NLINES + 1
END DO
WRITE(*,*) NLINES
CLOSE(1)
END DO
END PROGRAM X
I am using gfortran to compile.
UPDATE
I created 6 test files, data_0000000.txt, data_0000200.txt, ..., data_0001000.txt, each with less than 10 lines where there are less than 100 characters in each line. Unfortunately, I get the same error.
Obligatory disclaimer: If you just want to know the number of lines in a file, use wc -l <filename>. Don't reinvent the wheel if you don't have to.
I write this not necessarily because I think you didn't know that, but because someone else might come along, and think they need to write their own program to get the number of lines of files.
As for your question: I don't know why you get a malloc error. Maybe tell us which compiler and system you're using (including versions)? That said, there are three things that I noticed when reading your code:
You create a variable FILENAME, but then you don't use it. You're quoting it: FILE='FILENAME' which means that the open command looks for a file literally called FILENAME, not for a file with the name stored in the variable FILENAME. Remove the quotes:
OPEN(1, FILENAME=FILENAME, FORM='FORMATTED')
You use the unit number 1 -- that is dangerous. Different version of Fortran use specific unit numbers for specific uses. Use a handle far larger (at least 10, or more), or, even better, use the newunit descriptor in the open statement:
INTEGER :: u
OPEN(NEWUNIT=u, FILE=FILENAME, ACTION='READ', FORM='FORMATTED')
READ(u, *, IOSTAT=IO)
CLOSE(u)
You're not resetting the NLINES variable to 0 between files. The program will print a cumulative sum, not the number of lines for each file directly.
Adding to #chw21's response, if your sole purpose is to count the number of records (lines) in a file, here is a modular solution and a test program along with it (the counting is done inside subroutine getNumRecordInFile()):
module NumRecord_mod
implicit none
type :: Err_type
logical :: occurred = .false.
integer :: stat = -huge(0)
character(:), allocatable :: msg
end type Err_type
contains
! returns the number of lines in a file.
subroutine getNumRecordInFile(filePath,numRecord,Err)
implicit none
character(len=*), intent(in) :: filePath
integer, intent(out) :: numRecord
type(Err_type), intent(out) :: Err
character(len=8) :: record
integer :: fileUnit
logical :: fileExists, isOpen
integer :: iostat
character(*), parameter :: PROCEDURE_NAME = "#getNumRecordInFile()"
Err%occurred = .false.
Err%msg = ""
! Check if file exists
inquire( file=filePath, exist=fileExists, opened=isOpen, number=fileUnit, iostat=Err%stat )
if (Err%stat/=0) then
Err%occurred = .true.
Err%msg = PROCEDURE_NAME // ": Error occurred while inquiring the status of file='" // filePath // "'."
return
end if
if (.not.fileExists) then
Err%occurred = .true.
Err%msg = PROCEDURE_NAME // ": The input file='" // filePath // "' does not exist."
return
end if
if (isOpen) close(unit=fileUnit,iostat=Err%stat)
if (Err%stat>0) then
Err%occurred = .true.
Err%msg = PROCEDURE_NAME // ": Error occurred while attempting to close the open input file='" // filePath // "'."
return
end if
open(newunit=fileUnit,file=filePath,status="old",iostat=Err%stat)
if (Err%stat>0) then
Err%occurred = .true.
Err%msg = PROCEDURE_NAME // ": Error occurred while opening input file='" // filePath // "'."
return
end if
numRecord = 0
do
read(fileUnit,'(A)',iostat=iostat) record
if(iostat==0) then
numRecord = numRecord + 1
cycle
elseif(is_iostat_end(iostat)) then
exit
else
Err%occurred = .true.
Err%stat = iostat
Err%msg = PROCEDURE_NAME // ": Error occurred while reading input file='" // filePath // "'."
return
end if
end do
close(fileUnit,iostat=Err%stat)
if (Err%stat>0) then
Err%occurred = .true.
Err%msg = PROCEDURE_NAME // ": Error occurred while attempting to close the open input file='" // &
filePath // "' after counting the number of records in file."
return
end if
end subroutine getNumRecordInFile
end module NumRecord_mod
program test_numRecord
use NumRecord_mod
implicit none
type(Err_type) :: Err
integer :: numRecord
character(:), allocatable :: filePath
filePath = "main.f95"
call getNumRecordInFile(filePath=filePath,numRecord=numRecord,Err=Err)
if (Err%occurred) then
write(*,*) Err%msg
write(*,*) Err%stat
error stop
else
write(*,*) "Total number of records in file='" // filePath // "': ", numRecord
end if
end program test_numRecord
Now if you put this code in a file named "main.f95" and compile it under Fortran 2008 standard, then it should output the number of lines in your "main.f95" file, which should be something like the following:
$gfortran -std=f2008 *.f95 -o main
$main
Total number of records in file='main.f95': 98
For testing, you can simply copy paste the entire code in the online Fortran compiler here: https://www.tutorialspoint.com/compile_fortran_online.php
But keep in mind to change the compile option -std=f95 to -std=f2008 by going to Project -> Compile Options before executing the code.
Try this change (declaration and read line), there was no variable specified where the line contents shall go, here insert now dummy...
character(len=1000) :: dummy
...
READ(u, '(a)' , IOSTAT=IO) dummy
....
This is a small portion of the data I am trying to read:
01/06/2009,Tom Sanders,,264,220,73,260
01/08/2009,Adam Apple,158,,260,,208
01/13/2009,Lori Freeman,230,288,218,282,234
01/15/2009,Diane Greenberg,170,,250,321,197
01/20/2009,Adam Apple,257,,263,256,190
01/21/2009,Diane Greenberg,201,,160,195,142
01/27/2009,Tom Sanders,267,,143,140,206
01/29/2009,Tina Workman,153,,124,155,140
02/03/2009,Tina Workman,233,,115,,163
02/03/2009,Adam Apple,266,130,310,,310
the numbers between each comma are from a different location
Where two commas would represent missing data and a trailing comma would mean the fifth data point is missing
My goal is to organize the data into a table after calculating the average of each site and person, hence my two dim arrays
I want my output to look something like the following:
(obviously neater formatting but a table nonetheless)
Average Observed TDS (mg/l)
Name Site 1 Site 2 Site 3 Site 4 Site 5
------------------------------------------------------
Tom Sanders 251.0 172.5 251.7 160.0 229.0
Adam Apple 227.0 130.0 277.7 256.0 236.0
Lori Freeman 194.0 288.0 216.7 279.0 202.7
Diane Greenberg 185.5 190.0 205.0 258.0 169.5
Tina Workman 193.0 140.0 119.5 155.0 163.0
This is my program so far:
program name_finder
implicit none
integer, parameter :: wp = selected_real_kind(15)
real(wp) :: m, tds
real(wp), dimension(20,5) :: avg_site, site_sum
integer, dimension(20) :: nobs
integer, dimension(5) :: x
integer :: ierror, i, nemp, cp, non, ni, n
character(len=40), dimension(20) :: names
character(len=200) :: line, aname
character(len=20) :: output, filename
character(len=3), parameter :: a = "(A)"
do
write(*,*) "Enter file to open."
read(*,*) filename
open(unit=10,file = filename, status = "old", iostat = ierror)
if (ierror==0) exit
end do
write(*,*) "File, ",trim(filename)," has been opened."
non = 0
outer: do
read(10,a, iostat = ierror) line
if (ierror/=0) exit
cp = index(line(12:),",") + 11
aname = line(12:cp-1)
n=0
middle: do
read(line,'(Tcp,f4.2)') tds
write(*,*) "tds=", tds
n=n+1
if (n>10) exit
i = 1
inner: do
if (i > non) then
non = non +1
names(non) = trim(aname)
!ni = non
exit
end if
if (aname == names(i)) then
!ni = i
!cycle outer
exit inner
end if
i = i + 1
end do inner
end do middle
end do outer
write(*,*)
write(*,*) "Names:"
do i = 1,non
write(*,*) i, names(i)
end do
close(10)
close(20)
STOP
end program name_finder
TLDR; I am having trouble reading the data from the file shown at the top of each site after the names.
Suggestions? Thanks!
I hope the following is helpful. I have omitted any easily assumed declarations or any further data manipulation or writing to another file. The code is used just to read the data line by line.
character(150) :: word
read(fileunit, '(A)') word ! read the entire line
comma_ind = index(word,',') ! find the position of first comma
! Find the position of next comma
data_begin = index(word(comma_ind+1:),',')
! Save the name
thename = word(comma_ind+1:comma_ind+data_begin-1)
! Define next starting point
data_begin = comma_ind+data_begin
! Read the rest of the data
outer: do
if (word(data_begin+1:data_begin+1) == ',') then
! decide what to do when missing an entry
data_begin = data_begin + 1
cycle outer
else if (word(data_begin+1:data_begin+1) == ' ') then
! Missing last entry
exit outer
else
! Use it to find the length of current entry
st_ind = index(word(data_begin+1:),',')
if (st_ind == 0) then
! You reached the last entry, read it and exit
read(word(data_begin+1:), *) realData
exit outer
else
! Read current entry
read(word(data_begin+1: data_begin+st_ind-1),*) realData
end if
! Update starting point
data_begin = data_begin + st_ind
end if
end do outer
There could be a more elegant way to do it but I cannot think of any at the moment.
I have a certain piece of code in fortran. The code takes 'pq' as an input from the user and is a single point. Instead of doing this I want to read a set of points 'pq' from a file points.txt and run it for those number of points instead of just one single user input. Is it possible? The code is as follows:
program prop
use module
implicit none
character(len=80) :: ErrorMsg
character(2) :: xy
real(8) :: Conc(20) = 0.d0
character(len=20) :: fn, fl
real(8) :: Mmolar, Tcritical, Pcritical, Tmininimum, Tmaximum, x, y
call Init_module()
write(*,*) 'Insert the gas name:'
read(*,*) fn
write(*,*) 'Insert the gas library:'
read(*,*) fl
write(*,*) 'Insert the copule pq:'
read(*,*) pq
write(*,*) 'Insert the value of ', pq(1:1)
read(*,*) x
write(*,*) 'Insert the value of ', pq(2:2)
read(*,*) y
write(*,*) 'Pres = ', Pres( pq, x, y, ErrorMsg)
write(*,*) 'Temp = ', Temperature( pq, x, y, ErrorMsg)
call ReleaseObjects()
end program prop
Instead of reading pq as a single point x,y from the user in the above code, I want to read a set of points from file.txt, for example 50 points and then run subroutines Pres and Temperature.
Each line of the file contains one point x,y and x and y in each line are separated by a few space characters.
The first few lines of file.txt are:
Ts
500
0.04781564 159.81587875
0.20396084 165.46398084
0.08159885 166.81382894
0.03879184 164.17497877
0.12585959 165.37000305
0.09895530 165.95997769
0.10389518 170.74235496
It must be noted that the length and the sign of the floating numbers can vary. The file.txt is originally written through python with the formatting for x, y being '%-12.8f %-12.8f\n'%. I have the following code to try and read the file but am not able to read from the 3rd line onwards:
real, allocatable :: x(:),y(:)
integer :: np
open(12,file=trim('file.txt'),status='old', &
access='sequential', form='formatted', action='read' )
read(12,*)pq
write(*,*)'pq:', pq
read(12,*)np
write(*,*)'number of points:',np
allocate (x(np))
allocate (y(np))
do i=1,np
read(12,*)x(i),y(i)
write(*,*)x(i),y(i)
enddo
Instead of using the READ statement with the asterisk (*) as the first argument asking for an user input, use a file identifier. You need to OPEN your file containing the set of points, assuming it is ASCII :
OPEN(UNIT=10,FILE=file.txt,ACTION='read',STATUS='old')
I think the arguments of this command are quite explanatory.
Then assuming your file contains multiple lines with x and y values, you can read each line of your file by doing :
READ(10,*) x,y
If you have multiple points to read, just use a DO if you know the number of points to read, a DO WHILE otherwise. To take your example with 50 points, something like this should work :
OPEN(UNIT=10,FILE=file.txt,ACTION='read',STATUS='old') ! Open file
DO i=1,50
READ(10,*) x,y
write(*,*) 'Pres = ', Pres( pq, x, y, ErrorMsg)
write(*,*) 'Temp = ', Temperature( pq, x, y, ErrorMsg)
END DO
CLOSE(10) ! Close file
EDIT
Your suggestion is almost correct. You forgot to declare pq as a character(len=2). You should not have been able to pass line 1 because of that.
As I said, there is a space separator that is naturally treated by a asterisk as a format. Anyway, if you want to exactly match the format, use the same with which you wrote your data. Reading your format Python, I assume you wrote two floats with a space separator, and indeed if you count the number of character of your digits :
0.04781564 159.81587875
^^^^^^^^^^^^|^^^^^^^^^^^^
1 12|1 12
|
space
which gives the following format in Fortran :
read(12,'(f12.8,1X,f12.8)') x(i),y(i)
X means a space separator in Fortran formats.
Then you can write you data onscreen with the same format to check :
write(*,'(f12.8,1X,f12.8)') x(i),y(i)
It gives :
pq:Ts
number of points: 500
0.04781564 159.81587219
0.20396084 165.46397400
0.08159885 166.81382751
0.03879184 164.17497253
0.12585959 165.37001038
0.09895530 165.95997620
0.10389518 170.74235535
You may have noticed that you lost precision on the last digits. It is because you have declared a simple real (4 bytes). Switch your real to 8 bytes with real(kind=8) or real*8 according to your compiler (be aware, not the right way to do it, not portable but sufficient in your case)
Do not forget to close your file when you are done dealing with it :
close(12)
I am new to Fortran but I am trying to adapt a Fortran code and I am having trouble doing something which I think is probably quite simple.
I want to adapt a Fortran file called original.f so that it makes an input file called input.inp and populates it with 4 integers calculated earlier in original.f so that input.inp looks like, for example:
&input
A = 1
B = 2
C = 3
D = 4
&end
I know how to write this format:
OPEN(UNIT=10,FILE='input.inp')
WRITE (10,00001) 1,2,3,4
...
...
...
00001 Format (/2x,'&input',
& /2x,'A = ',i4,
& /2x,'B = ',i4,
& /2x,'C = ',i4,
& /2x,'D = ',i4,
& /2x,'&end')
(or something like this that I can fiddle with when I get it working) but I am not sure how to create the input.inp file write this into it and then use this input file.
The input file needs to be used to run an executable called "exec". I would run this in bash as:
./exec < input.inp > output.out
Where output.out contains two arrays called eg(11) and ai(11,6,2) (with dimensions given) like:
eg(1)= 1
eg(2)= 2
...
...
...
eg(11)= 11
ai(1,1,1)= 111
ai(1,2,1)= 121
...
...
...
ai(11,6,2)=1162
Finally I need to read these inputs back into original.f so that they can be used further down in file. I have defined these arrays at the beginning of original.f as:
COMMON /DATA / eg(11),ai(11,6,2)
But I am not sure of the Fortran to read data line by linw from output.out to populate these arrays.
Any help for any of the stages in this process would be hugely appreciated.
Thank you very much
James
Since you have shown how you create the input file, I assume the question is how to read it. The code shows how "a" and "b" can be read from successive lines after skipping the first line. On Windows, if the resulting executable is a.exe, the commands a.exe < data.txt or type data.txt | a.exe will read from data.txt.
program xread
implicit none
character (len=10) :: words(3)
integer, parameter :: iu = 5 ! assuming unit 5 is standard input
integer :: a,b
read (iu,*) ! skip line with &input
read (iu,*) words ! read "a", "=", and "1" into 3 strings
read (words(3),*) a ! read integer from 3rd string
read (iu,*) words ! read "b", "=", and "1" into 3 strings
read (words(3),*) b ! read integer from 3rd string
print*,"a =",a," b =",b
end program xread
If I understand the expanded question correctly, you have to work with an output file, produced by some other code you did not write, with lines like eg(1) = ....
For the simplest case where you know the number of elements and their ordering beforehand, you can simply search each line for the equals sign from behind:
program readme
implicit none
character(100) :: buffer
integer :: i, j, k, pos, eg(11), ai(11,6,2)
do i = 1,11
read*, buffer
pos = index(buffer, '=', back = .true.)
read(buffer(pos+1:), *) eg(i)
enddo
! I have assumed an arbitrary ordering here
do k = 1,2
do i = 1,11
do j = 1,6
read*, buffer
pos = index(buffer, '=', back = .true.)
read(buffer(pos+1:), *) ai(i,j,k)
enddo
enddo
enddo
end program
Assuming here for simplicity that the data are provided to standard input.