program indexes_
use iso_fortran_env, only: real64, int64
use chemfiles
implicit none
! Chemfiles types declaration uses the "chfl_" prefix
type(chfl_trajectory) :: trajectory
type(chfl_frame) :: frame
real(real64), dimension(:, :), pointer :: positions
integer(int64), dimension(:), allocatable :: indexes
integer(int64) :: natoms, i, j
integer :: status
call frame%init()
call trajectory%open("filename.xyz", "r")
call trajectory%read(frame, status=status)
if (status /= 0) then
stop "Error"
end if
call frame%positions(positions, natoms)
allocate(indexes(natoms))
indexes = -1
j = 1
do i=1,natoms
if (positions(1, i) < 5) then
indexes(j) = i
j = j + 1
end if
end do
write(*,*) "Atoms with x < 5: "
do i=1,natoms
if (indexes(i) == -1) then
exit
end if
write(*,*) " - ", indexes(i)
end do
! Cleanup the allocated memory
deallocate(indexes, positions)
call trajectory%close()
call frame%free()
end program
program rmsd_
use iso_fortran_env, only: real64, int64
use chemfiles
implicit none
type(chfl_trajectory) :: trajectory
type(chfl_frame) :: frame
real(real64), dimension(:, :), pointer :: positions
real(real64), dimension(:), allocatable :: distances
integer(int64) :: nsteps = 0, natoms=0, i
real(real64) :: distance = 0, mean = 0, rmsd = 0
integer :: status
call trajectory%open("filename.nc", "r", status=status)
if (status /= 0) stop "Error while opening input file"
call frame%init()
call trajectory%nsteps(nsteps)
allocate(distances(nsteps))
! Accumulate the distances to the origin of the 10th atom throughtout the
! trajectory
do i=1,nsteps
call trajectory%read(frame, status)
if (status /= 0) stop "Error while reading the frame"
! Only allocate on the first iteration. This assume a constant number
! of particles
if (i == 0) then
call frame%atoms_count(natoms)
allocate(positions(3, natoms))
end if
! Position of the 10th atom
call frame%positions(positions, natoms, status)
if (status /= 0) stop "Error while getting the positions"
distance = sqrt(positions(1, 10)*positions(1, 10) + &
positions(2, 10)*positions(2, 10) + &
positions(3, 10)*positions(3, 10))
distances(i) = distance
end do
do i=1,nsteps
mean = mean + distances(i)
end do
mean = mean / nsteps
do i=1,nsteps
rmsd = rmsd + (mean - distances(i))*(mean - distances(i));
end do
rmsd = rmsd / nsteps;
rmsd = sqrt(rmsd);
write(*, *) "Root-mean square displacement is: ", rmsd
! Cleanup the allocated memory
call trajectory%close()
call frame%free()
deallocate(distances, positions)
end program
program convert
use iso_fortran_env, only: int64
use chemfiles
implicit none
type(chfl_trajectory) :: input, ouput_file
type(chfl_frame) :: frame
type(chfl_cell) :: cell
type(chfl_topology) :: water_topology
type(chfl_atom) :: O, H
integer(int64) :: nsteps, i
integer :: status
call input%open("water.xyz", "r", status=status)
if (status /= 0) stop "Error while opening input file"
call ouput_file%open("water.pdb", "w")
call frame%init()
call water_topology%init()
! Orthorombic UnitCell with lengths of 20, 15 and 35 A
call cell%init([20d0, 15d0, 35d0])
! Create Atoms
call O%init("O")
call H%init("H")
! Fill the topology with one water molecule
call water_topology%add_atom(O)
call water_topology%add_atom(H)
call water_topology%add_atom(H)
call water_topology%add_bond(0_int64, 1_int64)
call water_topology%add_bond(0_int64, 2_int64)
call input%nsteps(nsteps)
do i=1,nsteps
call input%read(frame, status)
if (status /= 0) stop "Error while reading input file"
! Set the frame cell and topology
call frame%set_cell(cell)
call frame%set_topology(water_topology)
! Write the frame to the output file, using PDB format
call ouput_file%write(frame, status)
if (status /= 0) stop "Error while writing ouput file"
end do
! Cleanup the allocated memory
call input%close()
call ouput_file%close()
call frame%free()
call cell%free()
call water_topology%free()
call O%free()
call H%free()
end program