dcdfort_writer Module Reference

Module that contains dcdwriter class. More...

Data Types
type	dcdwriter
	dcdwriter class More...

Functions/Subroutines
subroutine	dcdwriter_open (this, filename)
	Opens new file to write to. More...
subroutine	dcdwriter_write_header (this, istart, nevery, timestep, natoms)
	Writes header to new DCD file. More...
subroutine	dcdwriter_close (this)
	Closes DCD file. More...
subroutine	dcdwriter_write_next (this, xyz, box_in)
	Writes snapshot to an open DCD file. More...

Detailed Description

Module that contains dcdwriter class.

Function/Subroutine Documentation

dcdwriter_close()

subroutine dcdfort_writer::dcdwriter_close ( class(dcdwriter), intent(inout)  this )

private

Closes DCD file.

Parameters

[in,out]

this

dcdwriter object

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

        close(this%u)

dcdwriter_open()

subroutine dcdfort_writer::dcdwriter_open	(	class(dcdwriter), intent(inout)	this,
		character (len=*), intent(in)	filename
	)

Opens new file to write to.

Parameters

[in,out]	this	dcdwriter object
[in]	filename	name of new DCD file to write to

        implicit none
        character (len=*), intent(in) :: filename
        class(dcdwriter), intent(inout) :: this

        open(newunit=this%u, file=trim(filename), form="unformatted", access="stream", status="replace")

dcdwriter_write_header()

subroutine dcdfort_writer::dcdwriter_write_header ( class(dcdwriter), intent(inout)  this, integer(kind=int32), intent(in)  istart, integer(kind=int32), intent(in)  nevery, real(kind=real32), intent(in)  timestep, integer(kind=int32), intent(in)  natoms  )

private

Writes header to new DCD file.

Parameters

[in,out]	this	dcdwriter object
[in]	istart	first timestep in file
[in]	nevery	how often snapshots written (in timesteps)
[in]	timestep	simulation timestep
[in]	natoms	number of atoms in each snapshot

        implicit none

        integer(kind=int32) :: i
        integer(kind=int32), intent(in) :: istart, nevery, natoms
        real(kind=real32), intent(in) :: timestep
        class(dcdwriter), intent(inout) :: this
        character (len=79) :: remarks1, remarks2
        character (len=8) :: date
        character (len=10) :: time

        do i = 1, 79
            remarks1(i:i) = ' '
            remarks2(i:i) = ' '
        end do
        call date_and_time(date=date,time=time)
        remarks1 = "Created by libdcdfort"
        remarks2 = "REMARK Created on "//date//" "//time

        this%nframes = 0
        this%iend = istart
        this%nevery = nevery

        write(this%u) 84
        write(this%u) "CORD"

        inquire(unit=this%u, pos=this%nframes_pos)
        ! Number of snapshots in file
        write(this%u) this%nframes

        ! Timestep of first snapshot
        write(this%u) istart

        ! Save snapshots every this many steps
        write(this%u) nevery

        inquire(unit=this%u, pos=this%iend_pos)
        ! Timestep of last snapshot
        write(this%u) this%iend

        do i = 1, 5
            write(this%u) 0
        end do

        ! Simulation timestep
        write(this%u) timestep

        ! Has unit cell
        write(this%u) 1

        do i = 1, 8
            write(this%u) 0
        end do

        ! Pretend to be CHARMM version 24
        write(this%u) 24
        write(this%u) 84
        write(this%u) 164

        write(this%u) 2
        write(this%u) remarks1//c_null_char
        write(this%u) remarks2//c_null_char

        write(this%u) 164
        write(this%u) 4

        ! Number of atoms in each snapshot
        write(this%u) natoms

        write(this%u) 4

        flush(this%u)

dcdwriter_write_next()

subroutine dcdfort_writer::dcdwriter_write_next ( class(dcdwriter), intent(inout)  this, real(kind=real32), dimension(:,:), intent(in)  xyz, real(kind=real64), dimension(6), intent(in)  box_in  )

private

Writes snapshot to an open DCD file.

Writes a new snapshot to a DCD file. Header should have already been written.

Parameters

[in,out]	this	dcdwriter object
[in]	xyz	coordinates of all atoms in this snapshot
[in]	box_in	box dimensions for this snapshot

        implicit none
        real(kind=real32), intent(in) :: xyz(:,:)
        real(kind=real64), intent(in) :: box_in(6)
        real(kind=real64) :: box(6)
        class(dcdwriter), intent(inout) :: this
        integer(kind=int32) :: coord_size

        coord_size = size(xyz,1)*4
        box = box_in
    
        ! Should be 48 (6 double precision floats)
        write(this%u) 48

        write(this%u) box(1) ! A
        write(this%u) box(6) ! gamma
        write(this%u) box(2) ! B
        write(this%u) box(5) ! beta
        write(this%u) box(4) ! alpha
        write(this%u) box(3) ! C

        write(this%u) 48
        write(this%u) coord_size

        write(this%u) xyz(:,1)

        write(this%u) coord_size
        write(this%u) coord_size

        write(this%u) xyz(:,2)

        write(this%u) coord_size
        write(this%u) coord_size

        write(this%u) xyz(:,3)

        write(this%u) coord_size

        inquire(unit=this%u, pos=this%curr_pos)

        this%nframes = this%nframes+1
        this%iend = this%iend + this%nevery

        ! Go back and update header
        write(this%u, pos=this%nframes_pos) this%nframes
        write(this%u, pos=this%iend_pos) this%iend
        write(this%u, pos=this%curr_pos)

        flush(this%u)