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config_io_module.f90
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config_io_module.f90
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! config_io_module.f90
! Routines for atomic/molecular configuration I/O
MODULE config_io_module
!------------------------------------------------------------------------------------------------!
! This software was written in 2016/17 !
! by Michael P. Allen <m.p.allen@warwick.ac.uk>/<m.p.allen@bristol.ac.uk> !
! and Dominic J. Tildesley <d.tildesley7@gmail.com> ("the authors"), !
! to accompany the book "Computer Simulation of Liquids", second edition, 2017 ("the text"), !
! published by Oxford University Press ("the publishers"). !
! !
! LICENCE !
! Creative Commons CC0 Public Domain Dedication. !
! To the extent possible under law, the authors have dedicated all copyright and related !
! and neighboring rights to this software to the PUBLIC domain worldwide. !
! This software is distributed without any warranty. !
! You should have received a copy of the CC0 Public Domain Dedication along with this software. !
! If not, see <http://creativecommons.org/publicdomain/zero/1.0/>. !
! !
! DISCLAIMER !
! The authors and publishers make no warranties about the software, and disclaim liability !
! for all uses of the software, to the fullest extent permitted by applicable law. !
! The authors and publishers do not recommend use of this software for any purpose. !
! It is made freely available, solely to clarify points made in the text. When using or citing !
! the software, you should not imply endorsement by the authors or publishers. !
!------------------------------------------------------------------------------------------------!
USE, INTRINSIC :: iso_fortran_env, ONLY : error_unit, iostat_end, iostat_eor
IMPLICIT NONE
PRIVATE
! Public routines
PUBLIC :: read_cnf_atoms, write_cnf_atoms, read_cnf_mols, write_cnf_mols
CONTAINS
SUBROUTINE read_cnf_atoms ( filename, n, box, r, v ) ! Read in atomic configuration
IMPLICIT NONE
CHARACTER(len=*), INTENT(in) :: filename ! Supplied filename
INTEGER, INTENT(inout) :: n ! Number of atoms
REAL, INTENT(out) :: box ! Simulation box length (assumed cubic)
REAL, DIMENSION(:,:), OPTIONAL, INTENT(out) :: r ! Atomic positions (3,n)
REAL, DIMENSION(:,:), OPTIONAL, INTENT(out) :: v ! Atomic velocities (3,n)
! The first call of this routine is just to get n and box, used to allocate arrays
! The second call attempts to read in the atomic positions and optionally velocities
INTEGER :: cnf_unit, ioerr, i
! Open given filename, will terminate on any errors
OPEN ( newunit=cnf_unit, file=filename, status='old', action='read', iostat=ioerr )
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error opening ', filename, ioerr
STOP 'Error in read_cnf_atoms'
END IF
! Read number of atoms from first record
READ ( unit=cnf_unit, fmt=*, iostat=ioerr ) n
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error reading n from ', filename, ioerr
IF ( ioerr == iostat_eor ) WRITE ( unit=error_unit, fmt='(a)') 'End of record'
IF ( ioerr == iostat_end ) WRITE ( unit=error_unit, fmt='(a)') 'End of file'
STOP 'Error in read_cnf_atoms'
END IF
! Read box length from second record
READ ( unit=cnf_unit, fmt=*, iostat=ioerr ) box
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error reading box from ', filename, ioerr
IF ( ioerr == iostat_eor ) WRITE ( unit=error_unit, fmt='(a)') 'End of record'
IF ( ioerr == iostat_end ) WRITE ( unit=error_unit, fmt='(a)') 'End of file'
STOP 'Error in read_cnf_atoms'
END IF
! Expected format is one record per atom containing either r(:,i), v(:,i) or just r(:,i)
IF ( PRESENT ( r ) ) THEN
IF ( n > SIZE ( r, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of r ', n, SIZE ( r, dim=2 )
STOP 'Error in read_cnf_atoms'
END IF
IF ( PRESENT ( v ) ) THEN
IF ( n > SIZE ( v, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of v ', n, SIZE ( v, dim=2 )
STOP 'Error in read_cnf_atoms'
END IF
! Read positions, velocities
DO i = 1, n
READ ( unit=cnf_unit, fmt=*, iostat=ioerr ) r(:,i), v(:,i)
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error reading r, v from ', filename, ioerr
IF ( ioerr == iostat_eor ) WRITE ( unit=error_unit, fmt='(a)') 'End of record'
IF ( ioerr == iostat_end ) WRITE ( unit=error_unit, fmt='(a)') 'End of file'
STOP 'Error in read_cnf_atoms'
END IF
END DO
ELSE
! Read positions
DO i = 1, n
READ ( unit=cnf_unit, fmt=*, iostat=ioerr ) r(:,i)
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error reading r from ', filename, ioerr
IF ( ioerr == iostat_eor ) WRITE ( unit=error_unit, fmt='(a)') 'End of record'
IF ( ioerr == iostat_end ) WRITE ( unit=error_unit, fmt='(a)') 'End of file'
STOP 'Error in read_cnf_atoms'
END IF
END DO
END IF
END IF
CLOSE ( unit=cnf_unit )
END SUBROUTINE read_cnf_atoms
SUBROUTINE write_cnf_atoms ( filename, n, box, r, v ) ! Write out atomic configuration
IMPLICIT NONE
CHARACTER(len=*), INTENT(in) :: filename ! Supplied filename
INTEGER, INTENT(in) :: n ! Number of atoms
REAL, INTENT(in) :: box ! Simulation box length (assumed cubic)
REAL, DIMENSION(:,:), INTENT(in) :: r ! Atomic positions (3,n)
REAL, DIMENSION(:,:), OPTIONAL, INTENT(in) :: v ! Atomic velocities
INTEGER :: cnf_unit, ioerr, i
! Open given filename, replacing it if it already exists, will terminate on any errors
OPEN ( newunit=cnf_unit, file=filename, status='replace', iostat=ioerr )
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error opening ', filename, ioerr
STOP 'Error in write_cnf_atoms'
END IF
! Write number of atoms to first record, box length to second record
WRITE ( unit=cnf_unit, fmt='(i15)' ) n
WRITE ( unit=cnf_unit, fmt='(f15.8)') box
IF ( n > SIZE ( r, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of r ', n, SIZE ( r, dim=2 )
STOP 'Error in write_cnf_atoms'
END IF
IF ( PRESENT ( v ) ) THEN
IF ( n > SIZE ( v, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of v ', n, SIZE ( v, dim=2 )
STOP 'Error in write_cnf_atoms'
END IF
! Write positions, velocities
DO i = 1, n
WRITE ( unit=cnf_unit, fmt='(*(f15.10))' ) r(:,i), v(:,i)
END DO
ELSE
! Write positions
DO i = 1, n
WRITE ( unit=cnf_unit, fmt='(*(f15.10))' ) r(:,i)
END DO
END IF
CLOSE ( unit=cnf_unit )
END SUBROUTINE write_cnf_atoms
SUBROUTINE read_cnf_mols ( filename, n, box, r, e, v, w ) ! Read in molecular configuration
IMPLICIT NONE
CHARACTER(len=*), INTENT(in) :: filename ! Supplied filename
INTEGER, INTENT(inout) :: n ! Number of molecules
REAL, INTENT(out) :: box ! Simulation box length (assumed cubic)
REAL, DIMENSION(:,:), OPTIONAL, INTENT(out) :: r ! Molecular positions (3,n)
REAL, DIMENSION(:,:), OPTIONAL, INTENT(out) :: e ! Orientation vectors (3,n) or quaternions (4,n)
REAL, DIMENSION(:,:), OPTIONAL, INTENT(out) :: v ! Molecular velocities (3,n)
REAL, DIMENSION(:,:), OPTIONAL, INTENT(out) :: w ! Angular velocities/momenta (3,n)
! The first call of this routine is just to get n and box, used to allocate arrays
! The second call attempts to read in the molecular positions, orientations
! and optionally velocities, angular velocities/momenta
INTEGER :: cnf_unit, ioerr, i
! Open given filename, will terminate on any errors
OPEN ( newunit=cnf_unit, file=filename, status='old', action='read', iostat=ioerr )
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error opening ', filename, ioerr
STOP 'Error opening file in read_cnf_mols'
END IF
! Read number of molecules from first record
READ ( unit=cnf_unit, fmt=*, iostat=ioerr ) n
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error reading n from ', filename, ioerr
IF ( ioerr == iostat_eor ) WRITE ( unit=error_unit, fmt='(a)') 'End of record'
IF ( ioerr == iostat_end ) WRITE ( unit=error_unit, fmt='(a)') 'End of file'
STOP 'Error in read_cnf_mols'
END IF
! Read box length from second record
READ ( unit=cnf_unit, fmt=*, iostat=ioerr ) box
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error reading box from ', filename, ioerr
IF ( ioerr == iostat_eor ) WRITE ( unit=error_unit, fmt='(a)') 'End of record'
IF ( ioerr == iostat_end ) WRITE ( unit=error_unit, fmt='(a)') 'End of file'
STOP 'Error in read_cnf_mols'
END IF
! Expected format is one line per atom containing either r(:,i), e(:,i), v(:,i), w(:,i) or just r(:,i), e(:,i)
! The first dimension of the e array can be 3 elements (vector) or 4 elements (quaternion)
IF ( PRESENT ( r ) ) THEN
IF ( .NOT. PRESENT ( e ) ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'r and e arguments must be present together'
STOP 'Error in read_cnf_mols'
END IF
IF ( n > SIZE ( r, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of r ', n, SIZE ( r, dim=2 )
STOP 'Error in read_cnf_mols'
END IF
IF ( n > SIZE ( e, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of e ', n, SIZE ( e, dim=2 )
STOP 'Error in read_cnf_mols'
END IF
IF ( PRESENT ( v ) ) THEN
IF ( .NOT. PRESENT ( w ) ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'v and w arguments must be present together'
STOP 'Error in read_cnf_mols'
END IF
IF ( n > SIZE ( v, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of v ', n, SIZE ( v, dim=2 )
STOP 'Error in read_cnf_mols'
END IF
IF ( n > SIZE ( w, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of w ', n, SIZE ( w, dim=2 )
STOP 'Error in read_cnf_mols'
END IF
! Read positions, orientation vectors or quaternions, velocities, angular velocities/momenta
DO i = 1, n
READ ( unit=cnf_unit, fmt=*, iostat=ioerr ) r(:,i), e(:,i), v(:,i), w(:,i)
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error reading r, e, v, w from ', filename, ioerr
IF ( ioerr == iostat_eor ) WRITE ( unit=error_unit, fmt='(a)') 'End of record'
IF ( ioerr == iostat_end ) WRITE ( unit=error_unit, fmt='(a)') 'End of file'
STOP 'Error in read_cnf_mols'
END IF
END DO
ELSE
! Read positions, orientation vectors or quaternions
DO i = 1, n
READ ( unit=cnf_unit, fmt=*, iostat=ioerr ) r(:,i), e(:,i)
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error reading r, e from ', filename, ioerr
IF ( ioerr == iostat_eor ) WRITE ( unit=error_unit, fmt='(a)') 'End of record'
IF ( ioerr == iostat_end ) WRITE ( unit=error_unit, fmt='(a)') 'End of file'
STOP 'Error in read_cnf_mols'
END IF
END DO
END IF
END IF
CLOSE ( unit=cnf_unit )
END SUBROUTINE read_cnf_mols
SUBROUTINE write_cnf_mols ( filename, n, box, r, e, v, w ) ! Write out molecular configuration
IMPLICIT NONE
CHARACTER(len=*), INTENT(in) :: filename ! Supplied filename
INTEGER, INTENT(in) :: n ! Number of molecules
REAL, INTENT(in) :: box ! Simulation box length (assumed cubic)
REAL, DIMENSION(:,:), INTENT(in) :: r ! Molecular positions (3,n)
REAL, DIMENSION(:,:), INTENT(in) :: e ! Orientation vectors (3,n) or quaternions (0:3,n)
REAL, DIMENSION(:,:), OPTIONAL, INTENT(in) :: v ! Molecular velocities (3,n)
REAL, DIMENSION(:,:), OPTIONAL, INTENT(in) :: w ! Angular velocities/momenta (3,n)
INTEGER :: cnf_unit, ioerr, i
! Open given filename, replacing it if it already exists, will terminate on any errors
OPEN ( newunit=cnf_unit, file=filename, status='replace', iostat=ioerr )
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'Error opening ', filename, ioerr
STOP 'Error in write_cnf_mols'
END IF
! Write number of molecules to first record, box length to second record
WRITE(cnf_unit,'(i15)' ) n
WRITE(cnf_unit,'(f15.8)') box
IF ( n > SIZE ( r, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of r ', n, SIZE ( r, dim=2 )
STOP 'Error in write_cnf_mols'
END IF
IF ( n > SIZE ( e, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of e ', n, SIZE ( e, dim=2 )
STOP 'Error in write_cnf_mols'
END IF
IF ( PRESENT ( v ) ) THEN
IF ( .NOT. PRESENT ( w ) ) THEN
WRITE ( unit=error_unit, fmt='(a,a,i15)') 'v and w arguments must be present together'
STOP 'Error in write_cnf_mols'
END IF
IF ( n > SIZE ( v, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of v ', n, SIZE ( v, dim=2 )
STOP 'Error in write_cnf_mols'
END IF
IF ( n > SIZE ( w, dim=2 ) ) THEN
WRITE ( unit=error_unit, fmt='(a,2i15)') 'Error in size of w ', n, SIZE ( w, dim=2 )
STOP 'Error in write_cnf_mols'
END IF
! Write positions, orientation vectors or quaternions, velocities, angular velocities/momenta
DO i = 1, n
WRITE ( unit=cnf_unit, fmt='(*(f15.10))') r(:,i), e(:,i), v(:,i), w(:,i)
END DO
ELSE
! Write positions, orientation vectors or quaternions
DO i = 1, n
WRITE ( unit=cnf_unit, fmt='(*(f15.10))') r(:,i), e(:,i)
END DO
END IF
CLOSE ( unit=cnf_unit )
END SUBROUTINE write_cnf_mols
END MODULE config_io_module