xtcio

The xtc format is a portable format for trajectories. It uses the xdr routines for writing and reading data which was created for the Unix NFS system. The trajectories are written using a reduced precision algorithm which works in the following way: the coordinates (in nm) are multiplied by a scale factor, typically 1000, so that you have coordinates in pm. These are rounded to integer values. Then several other tricks are performed, for instance making use of the fact that atoms close in sequence are usually close in space too (e.g. a water molecule). To this end, the xdr library is extended with a special routine to write 3-D float coordinates.

NOTE: xrdfile read is same as write. He he he.

---

xtc_open

Open file for reading and check for errors. Frame offset table is constructed (byte position where frame starts). Move to selected frame with xdr_seek. If the function fails stat is a positive number, otherwise it is set to zero. If stat is not present end error occurs error stop is raised.

call xtc_open (file, xd, nframes, offset, stat, errmsg)

Parameters

character(*), intent(IN) :: file

Input file name.

type(XDRFILE), pointer, intent(INOUT) :: xd

XDR file pointer.

integer, intent(OUT) :: nframes

Number of frames in file.

integer(INT64), allocatable, dimension(:), intent(INOUT) :: offset

Frame offset table. Array size same as nframes.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

---

xtc_close

Close opened file.

call xtc_close (xd, stat, errmsg)

Parameters

type(XDRFILE), pointer, intent(INOUT) :: xd

XDR file pointer.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

---

xtc_do_header

Read/write file header information in XTC format.

call xtc_do_header (xd, natoms, step, time, stat, errmsg)

type(XDRFILE), pointer, intent(IN) :: xd

XDR file pointer.

integer, intent(INOUT) :: natoms

Number of atoms in current frame.

integer, intent(INOUT) :: step

Current simulation step number.

integer, intent(INOUT) :: time

Time of current frame in ps.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

---

xtc_do_data

Read/write data in XTC format.

call xtc_do_data (xd, bRead, natoms, prec, coor, box, stat, errmsg)

Parameters

type(XDRFILE), pointer, intent(IN) :: xd

XDR file pointer.

logical, intent(IN) :: bRead

Read data? Else write it.

integer, intent(INOUT) :: natoms

Number of atoms in current frame.

real, intent(INOUT) :: prec

Coordinate precission.

real, dimension(DIM,natoms), intent(INOUT) :: coor

Atom cartesian coordinates in nm.

real, dimension(DIM,DIM), intent(INOUT) :: box

Simulation box dimensions in nm.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

---

xtc_do_skip

Read through file (skip) in XTC format but do not store any data.

call xtc_do_skip (xd, natoms, stat, errmsg)

Parameters

type(XDRFILE), pointer, intent(IN) :: xd

XDR file pointer.

integer, intent(IN) :: natoms

number of atoms in current frame.

integer, intent(OUT), optional :: stat

Error status code. Returns zero if no error.

character(*), intent(OUT), optional :: errmsg

Error status message. Empty if no error.

---

Example

program main
  use xdrfor
  use atomlib_xtcio
  use iso_fortran_env, only: INT64
  implicit none
  integer, paramete
  type(xdrfile), pointer :: xd => null()
  integer(INT64), allocatable :: offset(:)
  real, allocatable :: coor(:,:)
  real :: box(DIM,DIM)
  real :: time, precision
  integer :: natoms, nframes, step, status

  ! Read
  call xtc_open ("traj.xtc", xd, nframes, offset, STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  call xtc_do_header (xd, natoms, step, time, STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  allocate (coor(DIM,natoms), STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  call xtc_do_data (xd, .True., natoms, prec, coor, box, STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  call xtc_close (unit, STAT=status, ERRMSG=message)
  if (status /= 0) error stop message  

  ! Write
  call xdr_open (xd, "out.xtc", .False., STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  call xtc_do_header (xd, natoms, step, time, STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  call xtc_do_data (xd, .False., natoms, prec, coor, box, STAT=status, ERRMSG=message)
  if (status /= 0) error stop message

  call xdr_close (xd, STAT=status, ERRMSG=message)
  if (status /= 0) error stop messa

end program main