I'm trying to write a rudimentary bit of code to print a 50*50 array called 'arr'. Unfortunately it so far only prints the first row of the array, although the formatting for that row is correct. I've attached the code below and was wondering if anyone could point out where I was going wrong? Thank you!
program testing
implicit none
integer :: i, j
integer, dimension (1:50, 1:50) :: arr
arr = 1
do i=1,50
open(unit=6, file= "array.txt", action="write")
write(6, '(2500I3)') (arr(i,j), j=1,50)
close(6)
end do
end program testing
Your open statement is inside loop (along with a matching close statement). That means for every row of the array, you open the file. That's probably not what you meant to do.
The default position specifier for an OPEN statement if there is no POSITION specifier is 'ASIS'. For a file that already exists (your case after the first iteration, and perhaps even for the first iteration) that means that the position is unspecified. Your processor probably takes that to be the start of the file. That means that each iteration of the loop you simply overwrite the first record, over and over again.
If you must open the file each iteration, then use the POSITION='APPEND' specifier to position the file at the end when the open statement is executed. Otherwise, move the open and close statements out of the loop.
(The way that the default of 'ASIS' behaves means that you should always specify the initial position of a file via a POSITION specifier when executing an OPEN statement for an existing "on disk" file.)
IanH's answer is correct. Your program can be fixed as follows. Note that output units should be parameterized and not set to 6 and that arrays and array sections can be written as shown.
program testing
implicit none
integer :: i
integer, dimension (1:50, 1:50) :: arr
integer, parameter :: outu = 20 ! better to parameterize unit and
! not to use the number 6, which most compilers
! use for standard output
arr = 1
open(unit=outu, file= "array.txt", action="write")
do i=1,50
write(outu, '(2500I3)') arr(i,:) ! can write array section without implied do loop
end do
close(outu)
end program testing
Related
How do I fix the Fortran runtime error: Bad integer for item 0 in list input?
Below is the Fortran program which generates a runtime error.
CHARACTER CNFILE*(*)
REAL BOX
INTEGER CNUNIT
PARAMETER ( CNUNIT = 10 )
INTEGER NN
OPEN ( UNIT = CNUNIT, FILE = CNFILE, STATUS = 'OLD' )
READ ( CNUNIT,* ) NN, BOX
The error message received from gdb is :
At line 688 of file MCNPT.f (unit = 10, file = 'LATTICE-256.txt')
Fortran runtime error: Bad integer for item 0 in list input
[Inferior 1 (process 3052) exited with code 02]
(gdb)
I am not sure what options must be specified for READ() to read to numbers from the text file. Does it matter if the two numbers on the same line are specified as either an integer or a real in the text file?
Below is the gdb execution of the program using a break point at the open call
Breakpoint 1, readcn (
cnfile=<error reading variable: Cannot access memory at address 0x7fffffffdff0>,
box=-3.37898272e+33, _cnfile=30) at MCNPT.f:686
Since you did not specify form="unformatted" on the open statement, the unit / file is opened for formatted IO. This is appropriate for a human-readable text file. ("unformatted" would be used for a non-human readable file in computer-native format, sometimes called "binary".) Therefore you should provide a format on the read, or use list-directed read, i.e., read(unit, *). To advise on a particular format we would have to know the layout of the numbers in the file. A possible read with format is: read (CNUINT, '(I4, 2X, F6.2)' ) NN, BOX
P.S. I'm answering the question in your question and not the title, which seems unrelated.
EDIT: now that you are show the text data file, a list-directed read looks easier. That is because the data doesn't line up in columns. It seems that the file has two integers on the first line, then three real numbers on each of the following lines. Most likely you need a different read for the first line. Is the code sample that you are showing us trying to read the first line, or one of the later lines? If the first line, it would seem plausible to read into two integer variables. If a later line, into two or three real variables. Two if you wish to skip the third data item on the line.
EDIT 2: the question has been substantially altered several times, which is very confusing. The first line of the text file that was shown in one version of the question contained integers, with later lines having reals. Since the listed-directed read is reading into an integer and a floating variable, it will have problems if you attempt to use it on the later lines that have two real values.
How do we read a specific file line by line while skipping some columns in it?
For example, I have a text file which has data, sorted out in 5 columns, but I need to read only two columns out of it, they can be first two or any other random combination (I mean, need a solution which would work with any combination of columns like first and third only).
Code something like this
open(1, file=data_file)
read (1,*) ! to skip first line, with metadata
lmax = 0
do while (.true.)
! read column 1 and 3 here, either write
! that to an array or just loop through each row
end do
99 continue
close (1)
Any explanation or example would help a lot.
High Performance Mark's answer gives the essentials of simple selective column reading: one still reads the column but transfers it to a then-ignored variable.
To extend that answer, then, consider that we want to read the second and fourth columns of a five-column line:
read(*,*) junk, x, junk, y
The first value is transferred into junk, then the second into x, then the third (replacing the one just acquired a moment ago) into junk and finally the fourth into y. The fifth is ignored because we've run out of input items and the transfer statement terminates (and the next read in a loop will go to the next record).
Of course, this is fine when we know it's those columns we want. Let's generalize to when we don't know in advance:
integer col1, col2 ! The columns we require, defined somehow (assume col1<col2)
<type>, dimension(nrows) :: x, y, junk(3) ! For the number of rows
integer i
do i=1,nrows
read(*,*) junk(:col1-1), x(i), junk(:col2-col1-1), y(i)
end do
Here, we transfer a number of values (which may be zero) up to just before the first column of interest, then the value of interest. After that, more to-be-ignored values (possibly zero), then the final value of interest. The rest of the row is skipped.
This is still very basic and avoids many potential complications in requirements. To some extent, it's such a basic approach one may as well just consider:
do i=1,nrows
read(*,*) allofthem(:5)
x(i) = allofthem(col1)
y(i) = allofthem(col2)
end do
(where that variable is a row-by-row temporary) but variety and options are good.
This is very easy. You simply read 5 variables from each line and ignore the ones you have no further use for. Something like
do i = 1, 100
read(*,*) a(i), b, c(i), d, e
end do
This will overwrite the values in b, d, and e at every iteration.
Incidentally, your line
99 continue
is redundant; it's not used as the closing line for the do loop and you're not branching to it from anywhere else. If you are branching to it from unseen code you could just attach the label 99 to the next line and delete the continue statement. Generally, continue is redundant in modern Fortran; specifically it seems redundant in your code.
This should be an easy one.. I can't figure out why my read statement has a syntax error. I have a file 7477 lines long and I want each of those variables to correspond in each line like my format specifies. Any help here would be great. Thanks!
implicit none
integer :: spe, flen = 7477, i
real, dimension (7477):: wnum,s,A,abh
character :: other
integer :: lun = 11
write(*,*) 'Opening File!'
open(lun,file ='h2o_allbands',status = 'old',action ='read')
write(*,*) 'Success!'
17 format (1x,i2,3x,F9.6,1x,E9.3,1x,E9.3,F5.5,A120)
do i = 1, 7477
read(lun,17) spe(i),wnum(i),s(i),A(i),abh(i),other
write(*,*) wnum(i)
end do
The read has spe(i) as an input list item. spe is not declared as an array, so the compiler probably thinks spe(i) is a reference to an integer function. You cannot read "into" the result of a plain integer function.
Perhaps spe should be declared as an array?
Without seeing a line from your input file, it is difficult to say what the exact problem is: However:
First of all, you should not use a format statement when reading entities (unless in special cases), as this can lead to all sort of different errors, if your line is not well formatted for whatever reasons. So just replace the read line with:
read(lun,*) spe(i), wnum(i), s(i), A(i), abh(i), other
If all the lines are read in well apart the last one, then make sure, that you have a newline at the end of the last line.
I have been tasked with writing a Fortran 95 program that will read character input from a file, and then (to start with) simply spit it back out again.
The tricky part is that these lines of input are of varying length (no maximum length given) and there can be any number of lines within the file.
I've used
do
read( 1, *, iostat = IO ) DNA ! reads to EOF -- GOOD!!
if ( IO < 0 ) exit ! if EOF is reached, exit do
I = I + 1
NumRec = I ! used later for total no. of records
allocate( Seq(I) )
Seq(I) = DNA
print*, I, Seq(I)
X = Len_Trim( Seq(I) ) ! length of individual sequence
print*, 'Sequence size: ', X
print*
end do
However, my initial statements list
character(100), dimension(:), allocatable :: Seq
character(100) DNA
and the appropriate integers etc.
I guess what I'm asking is if there is any way to NOT list the size of the character strings in the first instance. Say I've got a string of DNA that is 200+ characters, and then another that is only 25, is there a way that the program can just read what there is and not need to include all the additional blanks? Can this be done without needing to use len_trim, since it can't be referenced in the declaration statements?
To progressively read a record in Fortran 95, use non-advancing input. For example:
CHARACTER(10) :: buffer
INTEGER :: size
READ (unit, "(A)", ADVANCE='NO', SIZE=size, EOR=10, END=20) buffer
will read up to 10 characters worth (the length of buffer) each time it is called. The file position will only advance to the next record (the next line) once the entire record has been read by a series of one or more non-advancing reads.
Barring an end of file condition, the size variable will be defined with the actual number of characters read into buffer each time the read statement is executed.
The EOR and END and specifiers are used to control execution flow (execution will jump to the appropriately labelled statement) when end of record or end of file conditions occur respectively. You can also use an IOSTAT specifier to detect these conditions, but the particular negative values to use for the two conditions are processor dependent.
You can sum size within a particular record to work out the length of that particular record.
Wrap such a non-advancing read in a loop that appropriately detects for end of file and end of record and you have the incremental reading part.
In Fortran 95, the length specification for a local character variable must be a specification expression - essentially an expression that can be safely evaluated prior to the first executable statement of the scope that contains the variable's declaration. Constants represent the simplest case, but a specification expression in a procedure can involve dummy arguments of that procedure, amongst other things.
Reading the entire record of arbitrary length in is then a multi stage process:
Determine the length of the current record by using a series of incremental reads. These incremental reads for a particular record finish when the end of record condition occurs, at which time the file position will have moved to the next record.
Backspace the file back to the record of interest.
Call a procedure, passing the length of the current record as a dummy argument. Inside that procedure have an character variable whose length is given by the dummy argument.
Inside that called procedure, read the current record into that character variable using normal advancing input.
Carry out further processing on that character variable!
Note that each record ends up being read twice - once to determine its length, the second to actually read the data into the correctly "lengthed" character variable.
Alternative approaches exist that use allocatable (or automatic) character arrays of length one. The overall strategy is the same. Look at the code of the Get procedures in the common ISO_VARYING_STRING implementation for an example.
Fortran 2003 introduces deferred length character variables, which can have their length specified by an arbitrary expression in an allocate statement or, for allocatable variables, by the length of the right hand side in an assignment statement. This (in conjunction with other "allocatable" enhancements) allows the progressive read that determines the record length to also build the character variable that holds the contents of the record. Your supervisor needs to bring his Fortran environment up to date.
Here's a function for Fortran 2003, which sets an allocatable string (InLine) of exactly the length of the input string (optionally trimmed), or returns .false. if end of file
function ReadLine(aunit, InLine, trimmed) result(OK)
integer, intent(IN) :: aunit
character(LEN=:), allocatable, optional :: InLine
logical, intent(in), optional :: trimmed
integer, parameter :: line_buf_len= 1024*4
character(LEN=line_buf_len) :: InS
logical :: OK, set
integer status, size
OK = .false.
set = .true.
do
read (aunit,'(a)',advance='NO',iostat=status, size=size) InS
OK = .not. IS_IOSTAT_END(status)
if (.not. OK) return
if (present(InLine)) then
if (set) then
InLine = InS(1:size)
set=.false.
else
InLine = InLine // InS(1:size)
end if
end if
if (IS_IOSTAT_EOR(status)) exit
end do
if (present(trimmed) .and. present(InLine)) then
if (trimmed) InLine = trim(adjustl(InLine))
end if
end function ReadLine
For example to do something with all lines in a file with unit "aunit" do
character(LEN=:), allocatable :: InLine
do while (ReadLine(aunit, InLine))
[.. something with InLine]
end do
I have used the following. Let me know if it is better or worse than yours.
!::::::::::::::::::::: SUBROUTINE OR FUNCTION :::::::::::::::::::::::::::::::::::::::
!__________________ SUBROUTINE lineread(filno,cargout,ios) __________________________
subroutine lineread(filno,cargout,ios)
Use reallocate,ErrorMsg,SumStr1,ChCount
! this subroutine reads
! 1. following row in a file except a blank line or the line begins with a !#*
! 2. the part of the string until first !#*-sign is found or to end of string
!
! input Arguments:
! filno (integer) input file number
!
! output Arguments:
! cargout (character) output chArActer string, converted so that all unecessay spaces/tabs/control characters removed.
implicit none
integer,intent(in)::filno
character*(*),intent(out)::cargout
integer,intent(out)::ios
integer::nlen=0,i,ip,ich,isp,nsp,size
character*11,parameter::sep='=,;()[]{}*~'
character::ch,temp*100
character,pointer::crad(:)
nullify(crad)
cargout=''; nlen=0; isp=0; nsp=0; ich=-1; ios=0
Do While(ios/=-1) !The eof() isn't standard Fortran.
READ(filno,"(A)",ADVANCE='NO',SIZE=size,iostat=ios,ERR=9,END=9)ch ! start reading file
! read(filno,*,iostat=ios,err=9)ch;
if(size>0.and.ios>=0)then
ich=iachar(ch)
else
READ(filno,"(A)",ADVANCE='no',SIZE=size,iostat=ios,EOR=9); if(nlen>0)exit
end if
if(ich<=32)then ! tab(9) or space(32) character
if(nlen>0)then
if(isp==2)then
isp=0;
else
isp=1;
end if
eend if; cycle;
elseif(ich==33.or.ich==35.or.ich==38)then !if char is comment !# or continue sign &
READ(filno,"(A)",ADVANCE='yes',SIZE=size,iostat=ios,EOR=9)ch; if(nlen>0.and.ich/=38)exit;
else
ip=scan(ch,sep);
if(isp==1.and.ip==0)then; nlen=nlen+1; crad=>reallocate(crad,nlen); nsp=nsp+1; endif
nlen=nlen+1; crad=>reallocate(crad,nlen); crad(nlen)=ch;
isp=0; if(ip==1)isp=2;
end if
end do
9 if(size*ios>0)call ErrorMsg('Met error in reading file in [lineread]',-1)
! ios<0: Indicating an end-of-file or end-of-record condition occurred.
if(nlen==0)return
!write(6,'(a,l)')SumStr1(crad),eof(filno)
!do i=1,nlen-1; write(6,'(a,$)')crad(i:i); end do; if(nlen>0)write(6,'(a)')crad(i:i)
cargout=SumStr1(crad)
nsp=nsp+1; i=ChCount(SumStr1(crad),' ',',')+1;
if(len(cargout)<nlen)then
call ErrorMsg(SumStr1(crad)// " is too long!",-1)
!elseif(i/=nsp.and.nlen>=0)then
! call ErrorMsg(SumStr1(crad)// " has unrecognizable data number!",-1)
end if
end subroutine lineread
I'm using Fortran 90 to do this:
X = Len_Trim( Seq(I) ) ! length of individual sequence
write(*,'(a<X>)') Seq(I)(1:X)
You can simply declare Seq to be a large character string and then trim it as your write it out. I don't know how kosher this solution is but it certainly works for my purpose. I know that some compilers do not support "variable format expressions", but there are various workarounds to do the same thing almost as simply.
GNU Fortran variable expression workaround.
I am writing a FORTRAN code that uses data in a file made by a MD program. the data is a list of values but has breaks in the data for list updates in the form (# Neighbor list update .. 6527 indexes in list), These breaks are at random intervals so I can't just skip every x
I when I do my code it doesn't ignore these lines and randomly adds the value from the previous step.
1, 0.98510699999999995, 0.98510699999999995
2, 1.9654170000000000, 0.98031000000000001
3, 2.9427820000000002, 0.97736500000000004
4, 3.9186540000000001, 0.97587199999999996
4, 4.8945259999999999, 0.97587199999999996
5, 5.8697910000000002, 0.97526500000000005
note the double step 4 with an identical value from the true step 4
How would I go about skipping this line. Please find the sample code below
Open(Unit=10,File='prod._100.tup')
do i=1,50
Read(10,*,IOSTAT=ios)step,temp,kinetic,potential,total,pressure
If(IS_IOSTAT_END(ios)) Exit
test=test+temp
print*, step, test, temp
End Do
It is not clear to me what the "breaks" in the file are. Are they blank lines? If so, the following code should work:
use, intrinsic :: iso_fortran_env
character (len=200) :: line
Open(Unit=10,File='prod._100.tup')
read_loop: do
Read (10,'(A)',IOSTAT=ios) line
If(ios == iostat_end) exit read_loop
if (len_trim (line) == 0) then
write (*, *) "blank line"
cycle read_loop
end if
read (line, *) step,temp,kinetic,potential,total,pressure
test=test+temp
print*, step, test, temp
end do: read_loop
write (*, *) "total is", test
The above is not tested. The "len_trim" test is based on bad records being blank lines. If breaks are otherwise defined you will have to create a different test.
Try:
i=1
do while (i<=50)
Read(10,*,IOSTAT=ios)step,temp,kinetic,potential,total,pressure
If(IS_IOSTAT_END(ios)) Exit
IF(ios.ne.0) cycle
test=test+temp
i=i+1
enddo
When a bad record is read, ios is assigned a system dependent non-zero number (it is zero on success). Apparently you've written a function (IS_IOSTAT_END) to tell if you've reached the end of the file, but other error conditions can exist (for example, the read statement doesn't match the data). That will return a different non-zero ios than an end-file record, so you should just restart the loop at that point (e.g. cycle)
I assume you want to read exactly 50 lines from the file, so I changed your do loop to a do while, but if the number of records you read doesn't actually matter, then feel free to change it back.