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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).
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'm learning how to programming with fortran90 and i need receive data from a txt file by the command prompt (something like that:
program.exe"<"data.txt).
at the Input txt file I'll always have a single line with at least 6 numbers till infinity.
if the data was wrote line by line it runs fine but as single line I'm receiving the error: "traceback:not available,compile with - ftrace=frame or - ftrace=full fortran runtime error:end file"
*note: i'm using Force fortran 2.0
here is example of data:
0 1 0.001 5 3 1 0 -9 3
edit: just clarifying: the code is working fine itself except for the read statement, which is a simple "read*,". I want know how To read a entire line from a txt once the entrance will be made by the promt command with stream direction.
( you can see more about that here: https://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/redirection.mspx?mfr=true).
there is no need to read the code, i've posted it just for knowledge.
I'm sorry about the whole inconvenience.
here is the code so far:
program bissecao
implicit none
integer::cont,int,e,k,intc,t1,t2,t3
doubleprecision::ii,is,pre,prec,erro,somaa,somab,xn
doubleprecision,dimension(:),allocatable::co
t1=0
t2=0
t3=0
! print*,"insira um limite inf da funcao"
read*,ii
!print*,"insira o limite superior da func"
read*,is
! print*,"insira a precisÆo admissivel"
read*,pre
if (erro<=0) then !elimina criterio de parada negativo ou zero
Print*,"erro"
go to 100
end if
!print*,"insira a qtd iteracoes admissiveis"
read*,int
!print*,"insira o grau da f(x)"
read*,e
if (e<=0) then ! elimina expoente negativo
e=(e**2)**(0.5)
end if
allocate(co(e+1))
!print*, "insira os coeficientes na ordem:&
! &c1x^n+...+(cn-1)x^1+cnx^0"
read(*,*)(co(k),k=e+1,1,-1)
somab=2*pre
intc=0
do while (intc<int.and.(somab**2)**0.5>pre.and.((is-ii)**2)**0.5>pre)
somab=0
somaa=0
xn =(ii+is)/2
do k=1,e+1,1
if (ii /=0) then
somaa=ii**(k-1)*co(k)+somaa
else
somaa=co(1)
end if
! print*,"somaa",k,"=",somaa
end do
do k=1,(e+1),1
if (xn/=0) then
somab=xn**(k-1)*co(k)+somab
else
somab=co(1)
end if
!print*,"somab",k,"=",somab
end do
if ((somaa*somab)<0) then
is=xn
else if((somaa*somab)>0)then
ii=xn
else if ((somaa*somab)==0) then
xn=(ii+is)/2
go to 100
end if
intc =intc+1
prec=is-ii
if ((((is-ii)**2)**.5)< pre) then
t3=1
end if
if (((somab**2)**.5)< pre) then
t2=1.
end if
if (intc>=int) then
t1=1
end if
end do
somab=0
xn=(ii+is)/2
do k=1,(e+1),1
if (xn/=0) then
somab=xn**(k-1)*co(k)+somab
else
somab=co(1)
end if
end do
100 write(*,'(A,F20.15,A,F20.15,A,A,F20.15,A,F20.15,A,I2)'),"I:[",ii,",",is,"]","raiz:",xn,"Fraiz:",somab,"Iteracoes:",intc
end program !----------------------------------------------------------------------------
In your program, you are using the "list-directed input" (i.e., read *, or read(*,*))
read *, ii
read *, is
read *, pre
read *, int
read *, e
read *, ( co( k ), k = e+1, 1, -1 )
which means that the program goes to the next line of the data file after each read statement (by neglecting any remaining data in the same line). So, the program works if the data file (say "multi.dat") consists of separate lines (as suggested by OP):
0
1
0.001
5
3
1 0 -9 3
But now you are trying to read an input file containing only a single line (say "single.dat")
0 1 0.001 5 3 1 0 -9 3
In this case, we need to read all the values with a single read statement (if list-directed input is to be used).
A subtle point here is that the range of array co depends on e, which also needs to be read by the same read statement. A workaround might be to just pre-allocate co with a sufficiently large number of elements (say 100) and read the data in a single line, e.g.,
integer :: k
allocate( co( 100 ) )
read *, ii, is, pre, int, e, ( co( k ), k = e+1, 1, -1 )
For completeness, here is a test program where you can choose method = 1 or 2 to read "multi.dat" or "single.dat".
program main
implicit none
integer :: int, e, k, method
double precision :: ii, is, pre
double precision, allocatable :: co(:)
allocate( co( 1000 ) )
method = 1 !! 1:multi-line-data, 2:single-line-data
if ( method == 1 ) then
call system( "cat multi.dat" )
read*, ii
read*, is
read*, pre
read*, int
read*, e
read*, ( co( k ), k = e+1, 1, -1 )
else
call system( "cat single.dat" )
read*, ii, is, pre, int, e, ( co( k ), k = e+1, 1, -1 )
endif
print *, "Input data obtained:"
print *, "ii = ", ii
print *, "is = ", is
print *, "pre = ", pre
print *, "int = ", int
print *, "e = ", e
do k = 1, e+1
print *, "co(", k, ") = ", co( k )
enddo
end program
You can pass the input file from standard input as
./a.out < multi.dat (for method=1)
./a.out < single.dat (for method=2)
Please note that "multi.dat" can also be read directly by using "<".
I want to read data from some files in Fortran, I can do that when the file names have a regular order. but now it's not regular, although all have same prefix for example : Fix001, Fix002, Fix023, Fix432, ...
I want the program get the prefix from the user and open all the files in a loop, read the data and write them in a single file.
any idea ?
Thanks.
PROGRAM Output
Implicit none
Integer ::n=5 !number of files
Integer ::nn=50 !number of rows in each file
Integer ::i,j
Real,Dimension(:),Allocatable::t,x,y,z
Character(len=12)::TD
Open(11,file='outputX.txt')
Allocate (t(1000),x(1000),y(1000),z(1000))
j=0
Do i=1,n
Write(TD,10)i
Write(*,*)TD
Open(1,file=TD)
Read(1,*)(t(j),x(j),j=1,nn)
Write(11,20)(x(j),j=1,nn)
j=j+1
Enddo
10 Format('100',i3.3,'')
20 Format(<nn>E25.8E3)
Deallocate(x,y,z,t)
END PROGRAM Output
If you do have an upper limit, you can try to open the file and test with the iostat parameter whether that was successful. If it wasn't, you skip the file.
This is an example that reads only the first integer variable from a file and appends it to the output file:
program read_files
implicit none
integer :: i, d
integer :: ioerr
character(len=len("FixXXX.txt")) :: fname
open(unit=30, file="Output.txt", action="write", iostat=ioerr)
if (ioerr /= 0) stop 1
do i = 0, 999
write(fname, '(A, I3.3, A)') "Fix", i, ".txt"
open(unit = 40, file=fname, status="old", action="read", iostat=ioerr)
if (ioerr /= 0) cycle
read(40, *) d
write(30, *) d
close(40)
end do
end program read_files
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)