dcdfort_trajectory Module Reference

Module that contains Trajectory type. More...

Data Types
type	trajectory
	Trajectory class. More...

Functions/Subroutines
subroutine	trajectory_open (this, filename_in, ndxfile)
	Trajectory class method which opens DCD file and optionally index file. More...
integer function	trajectory_get_natoms (this, group)
	Trajectory class method which gets the number of atoms in the system or an index group. More...
integer function	trajectory_skip_next (this, F)
	Trajectory class method which skips a specified number of frames. More...
integer function	trajectory_read_next (this, F, ndxgrp)
	Trajectory class method which reads a specified number of frames into memory after using the open() method. More...
real function, dimension(3)	trajectory_get_xyz (this, frame, atom, group)
	Trajectory class method which returns the coordinates of a particle. More...
subroutine	trajectory_read (this, dcdfile, ndxfile, ndxgrp)
	Trajectory class method which opens, reads, and closes a trajectory file. More...
real(8) function, dimension(6)	trajectory_get_box (this, frame)
	Trajectory class method which returns the box from a simulation frame. More...
subroutine	trajectory_close (this)
	Trajectory class method which closes a DCD file which was opened with open() More...

Detailed Description

Module that contains Trajectory type.

Function/Subroutine Documentation

trajectory_close()

subroutine dcdfort_trajectory::trajectory_close ( class(trajectory), intent(inout)  this )

private

Trajectory class method which closes a DCD file which was opened with open()

Parameters

[in,out]

this

Trajectory class

        implicit none
        class(trajectory), intent(inout) :: this

        call this%dcd%close()

trajectory_get_box()

real(8) function, dimension(6) dcdfort_trajectory::trajectory_get_box ( class(trajectory), intent(in)  this, integer, intent(in)  frame  )

private

Trajectory class method which returns the box from a simulation frame.

Parameters

[in,out]	this	Trajectory class
[in]	frame	Which frame to return the box dimensions

Returns

A real(8) array with 6 elements containing the x, y, and z dimensions of the box as well as the alpha, beta, and gamma angles

        implicit none
        real(8) :: trajectory_get_box(6)
        class(trajectory), intent(in) :: this
        integer, intent(in) :: frame

        call trajectory_check_frame(this, frame)
        trajectory_get_box = this%frameArray(frame)%box

trajectory_get_natoms()

integer function dcdfort_trajectory::trajectory_get_natoms ( class(trajectory), intent(inout)  this, character (len=*), intent(in), optional  group  )

private

Trajectory class method which gets the number of atoms in the system or an index group.

Parameters

[in,out]	this	the Trajectory object
[in]	group	name of index group

Returns

number of atoms in index group (if specified) or in system

        implicit none
        integer :: trajectory_get_natoms
        class(trajectory), intent(inout) :: this
        character (len=*), intent(in), optional :: group

        if (this%read_only_index_group .and. present(group)) then
            call error_stop_program("Do not specify an index group in natoms() when already specifying an & 
                &index group with read() or read_next().")
        end if

        trajectory_get_natoms = merge(this%ndx%get_natoms(group), this%NUMATOMS, present(group))

trajectory_get_xyz()

real function, dimension(3) dcdfort_trajectory::trajectory_get_xyz ( class(trajectory), intent(inout)  this, integer, intent(in)  frame, integer, intent(in)  atom, character (len=*), intent(in), optional  group  )

private

Trajectory class method which returns the coordinates of a particle.

Gets the coordinates of a particle from the read in trajectory. Returns a real array with 3 elements (x, y, and z). An optional index group can be specified; if so, the atomid is in relationship to the group.

Parameters

[in,out]	this	Trajectory class
[in]	frame
[in]	atom	atomid of particle to get
[in]	group	optional index group

Returns

coordinate of the particle

        implicit none
        real :: trajectory_get_xyz(3)
        integer, intent(in) :: frame, atom
        integer :: atom_tmp, natoms
        class(trajectory), intent(inout) :: this
        character (len=1024) :: message
        character (len=*), intent(in), optional :: group

        call trajectory_check_frame(this, frame)

        if (this%read_only_index_group .and. present(group)) then
            call error_stop_program("Do not specify an index group in x() when already specifying an & 
                &index group with read() or read_next().")
        end if

        atom_tmp = merge(this%ndx%get(group, atom), atom, present(group))
        natoms = merge(this%natoms(group), this%natoms(), present(group))

        if (atom > natoms .or. atom < 1) then
            write(message, "(a,i0,a,i0,a)") "Tried to access atom number ", atom_tmp, " when there are ", &
                natoms, ". Note that Fortran uses one-based indexing."
            call error_stop_program(trim(message))
        end if

        trajectory_get_xyz = this%frameArray(frame)%xyz(:,atom_tmp)

trajectory_open()

subroutine dcdfort_trajectory::trajectory_open	(	class(trajectory), intent(inout)	this,
		character (len=*), intent(in)	filename_in,
		character (len=*), intent(in), optional	ndxfile
	)

Trajectory class method which opens DCD file and optionally index file.

Parameters

[in,out]	this	the Trajectory object
[in]	filename_in	name of DCD file
[in]	ndxfile	name of GROMACS style index file

        implicit none
        class(trajectory), intent(inout) :: this
        character (len=*), intent(in) :: filename_in
        character (len=*), intent(in), optional :: ndxfile
        character (len=206) :: filetype
        logical :: ex
        integer :: i, j

        call this%dcd%open(trim(filename_in))

        write(error_unit,'(a)') "Opened "//trim(filename_in)//" for reading."
        call this%dcd%read_header(this%nframes, this%istart, this%nevery, this%iend, this%timestep, this%NUMATOMS)

        write(error_unit,'(i0,a)') this%NUMATOMS, " atoms present in system."
        write(error_unit,'(i0,a)') this%NFRAMES, " frames present in trajectory file."
        write(error_unit,'(a,i0)') "First timestep saved: ", this%ISTART
        write(error_unit,'(a,i0)') "Last timestep saved: ", this%IEND
        write(error_unit,'(a,f12.6)') "Simulation timestep: ", this%timestep
        write(error_unit,'(a,i0,a)') "Trajectory written every ", this%nevery, " timesteps."

        this%FRAMES_REMAINING = this%NFRAMES

        this%N = this%NUMATOMS ! Save for use when user selects just one group
        if (present(ndxfile)) call this%ndx%read(ndxfile, this%NUMATOMS)

trajectory_read()

subroutine dcdfort_trajectory::trajectory_read ( class(trajectory), intent(inout)  this, character (len=*)  dcdfile, character (len=*), optional  ndxfile, character (len=*), optional  ndxgrp  )

private

Trajectory class method which opens, reads, and closes a trajectory file.

Parameters

[in,out]	this	Trajectory class
[in]	dcdfile	Name of DCD trajectory file
[in]	ndxfile	Name of optional index file
[in]	ndxgrp	Name of optional group. If specified, only that group will be read into memory.

        implicit none
        class(trajectory), intent(inout) :: this
        character (len=*), optional :: ndxfile, ndxgrp
        character (len=*) :: dcdfile
        integer :: n

        call this%open(dcdfile, ndxfile)

        n = this%read_next(this%NFRAMES, ndxgrp)

        call this%close()

trajectory_read_next()

integer function dcdfort_trajectory::trajectory_read_next ( class(trajectory), intent(inout)  this, integer, intent(in), optional  F, character (len=*), optional  ndxgrp  )

private

Trajectory class method which reads a specified number of frames into memory after using the open() method.

Parameters

[in,out]	this	Trajectory class
[in]	F	number of frames to read in; if not specified, 1 frame is read
[in]	ndxgrp	read only this index group into memory

Returns

number of frames read in

        implicit none
        integer :: trajectory_read_next
        class(trajectory), intent(inout) :: this
        integer, intent(in), optional :: f
        character (len=*), optional :: ndxgrp
        integer :: i, j, n, stat
        real, allocatable :: xyz(:,:)

        ! If the user specified how many frames to read and it is greater than one, use it
        n = merge(f, 1, present(f))

        ! Are we near the end of the file?
        n = min(this%FRAMES_REMAINING, n)
        this%FRAMES_REMAINING = this%FRAMES_REMAINING - n

        if (allocated(this%frameArray)) deallocate(this%frameArray)
        allocate(this%frameArray(n))

        write(error_unit,*)

        this%read_only_index_group = .false.

        if (present(ndxgrp)) then

            allocate(xyz(3,this%N))
            this%NUMATOMS = this%natoms(trim(ndxgrp))
            do i = 1, n

                if (modulo(i, 1000) .eq. 0) call print_frames_saved(i)

                allocate(this%frameArray(i)%xyz(3,this%NUMATOMS))
                call this%dcd%read_next(xyz, this%frameArray(i)%box)

                do j = 1, size(this%ndx%group)
                    if (trim(this%ndx%group(j)%title) .eq. trim(ndxgrp)) then
                        this%frameArray(i)%xyz = xyz(:,this%ndx%group(j)%LOC)
                        exit
                    end if
                end do

            end do
            deallocate(xyz)

            this%read_only_index_group = .true.

        else

            do i = 1, n

                if (modulo(i, 1000) .eq. 0) call print_frames_saved(i)

                allocate(this%frameArray(i)%xyz(3,this%NUMATOMS))
                call this%dcd%read_next(this%frameArray(i)%xyz, this%frameArray(i)%box)

            end do

        end if

        this%frames_read = n
        trajectory_read_next = n
        call print_frames_saved(n)

trajectory_skip_next()

integer function dcdfort_trajectory::trajectory_skip_next ( class(trajectory), intent(inout)  this, integer, intent(in), optional  F  )

private

Trajectory class method which skips a specified number of frames.

Parameters

[in,out]	this	Trajectory class
[in]	F	number of frames to skip; if not specified, 1 frame is skipped

Returns

number of frames skipped

        class(trajectory), intent(inout) :: this
        integer, intent(in), optional :: f
        integer :: trajectory_skip_next, i, stat, n

        ! If the user specified how many frames to read and it is greater than one, use it
        n = merge(f, 1, present(f))

        ! Are we near the end of the file?
        n = min(this%FRAMES_REMAINING, n)
        this%FRAMES_REMAINING = this%FRAMES_REMAINING - n

        do i = 1, n
            call this%dcd%skip_next()
            if (stat .ne. 0) then
                write(error_unit,'(a,i0,a)') "Skipped ", i-1, " frames."
                trajectory_skip_next = i-1
                exit
            end if
        end do
        write(error_unit,'(a,i0,a)') "Skipped ", n, " frames."
        trajectory_skip_next = n