I am faced with this problem that I couldn't figure out yet, if you can point me to some direction that'll be of great help. So here's what I want to do.
I have let's say 10000 files which contains same number of Z coordinates in each file. I have to find the distance of those coordinates from a metal atom whose coordinate is constant, create an interval array (like 0.1,0.2...) then check how many atoms lie between 0.1 & 0.2, 0.2 & 0.3...Then I have to find the probability, just dividing by number of total atoms for each interval. At last I have to add those probabilities of each interval from all 10000 files and average those. I will try to make my self easier with example.
So what I did was a loop over files that will read coordinates, calculate distances. But how do I count or get probabilities for the intervals? I tried creating mask and using a loop for counting before file loop starts but honestly I have no clue how should I progress. Cause has to go through all the distances to check how many atoms lie in that interval. I thought of giving this post last night but I slept over it but still have nothing. I also tried creating a mask but I'm pretty sure I'm doing it wrong.
I'm showing the audacity to post my terrible code here, if you have sometime to look over it.
Code:
program zdistribution
implicit none
!Initializing inpputs
integer, parameter:: dp = selected_real_kind(15, 307)
real,parameter::waterlength=10.0
real(dp)::boxs,topl
integer::waterno
integer::ierror,stat_err
real(dp),allocatable::coord(:)
character(len=20)::filename
!Initializing outputs
integer::i,j
integer::int_size=waterlength/0.1
integer::array_int
integer::nlines
real(dp),allocatable::distance(:)
real(dp),allocatable::interval(:)
real(dp),allocatable::countw(:)
logical,allocatable::mask(:)
real(dp),allocatable::probability(:)
!prompt for boxsize, top layer metal and water layer length
write(*,*)"Enter the box size with at least one decimal place:"
read(*,*) boxs
write(*,*)"Enter the top layer metal surface coordinate with at least one decimal place:"
read(*,*) topl
write(*,*)"Enter the Total number of water in the box :"
read(*,*) waterno
!Counting lines in a file to allocate arrays
nlines=0
OPEN(unit=10,file='OwZ-1.xyz',status='old',action='read',&
iostat=ierror)
do ! count loop
read(10,*,iostat=ierror)
if (ierror /= 0) exit
nlines=nlines+1
end do !end count loop
CLOSE(unit=10)
!allocating input arrays
allocate (coord(nlines))
allocate (distance(nlines))
!allocating output arrays
allocate (interval(int_size))
allocate (countw(int_size))
allocate (mask(int_size))
allocate (probability(int_size))
do j=1,int_size
do i=1,2 ! file loop
write(filename,100)i
100 format('OwZ-',I1,'.xyz')
write(*,*)"This is for OwZ-",i,".xyz"
OPEN(unit=10,file=filename,status='old',action='read',&
iostat=ierror)
do
if (ierror /= 0) exit
read(10,*,iostat=ierror) coord(nlines)
write(*,*) "This is the coord: ",coord(nlines)
if (coord(nlines) < topl) then
distance(nlines)=coord(nlines)+(boxs-topl)
else
distance(nlines)=coord(nlines)-topl
end if
write(*,*)"This is the distance from top layer metal",&
": ",distance(nlines)
mask=((distance(nlines))>(interval(j)) .and. (distance(nlines))<(interval(j+1)))
countw(j)=count(mask)
probability(j)=countw(j)/waterno
end do
end do !file loop
CLOSE(10)
end do ! j loop
end program zdistribution
This code shows run time error after showing distance for the 1st coord of the 1st file. Obviously cause I have no idea what I'm doing. Also I've 10000's of files to read. So if in the loop over files I put I4 instead of I1 it can't read files which are numbered as 1,2 or 10,100,1000. It can only read 10000. And if I put I1, it can only read up to 9. Also I don't know how to average those probabilities at the end. In essence I'm in a big mess. If you guys could just point me to a direction, that will be of great help.
What be the verbatim msg of your run time error? I don't know what happens if you open a unit twice without closing it, but this is what you do in the file loop.
Thanks RudiC. But It seems like the concatenation operator only works for character strings, doesn't work with character and integer. I tried this way too.
Code:
do i=1,9 ! file loop
write(filename,*)'OwZ-',i,'.xyz'
Shows run time error!Seems like this damn thing vowed not to work.
Thanks a lot man!
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Hi.
Using the short code:
Code:
program one
character(len=20)::filename
integer i
do i=1,10000 ! file loop
! write(*,*)'OwZ-',i,'.xyz'
write(*,9) i
end do
9 format('OwZ-',I0,'.xyz')
end
compiling with gfortran one.f90 and running ./a.out | specimen 5:5:5
produces:
Thanks a lot drl! I actually had no time at that moment so I just converted all the files to 5 digits, like 1 to 10001 and 10000 to 20000. Your solution is the one I was looking for. I'll try it sometime.
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04-29-2015
