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grint.f90
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grint.f90
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! grint.f90
! g(z,c,r) in a planar interface
PROGRAM grint
!------------------------------------------------------------------------------------------------!
! This software was written in 2016/17 !
! by Michael P. Allen <[email protected]>/<[email protected]> !
! and Dominic J. Tildesley <[email protected]> ("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. !
!------------------------------------------------------------------------------------------------!
! Reads a trajectory from a sequence of configuration files
! Calculates pair distribution function for a planar interface in the xy plane,
! including dependence on z and symmetry breaking with respect to z direction
! Single-particle density profile in box coordinates is written to a file 'den.out'
! The combined profile for both interfaces, relative to interface position, is written to rho.out
! Slices through the pair distribution function g2(z,c,r) where z=z1 is the z-coordinate of atom 1
! and c=cos(theta) is the angle of the r12 vector, are written out to files as a function of r.
! Assuming that the liquid phase is more-or-less central in the box, the interfaces are combined
! in the analysis and oriented so that z<0 is towards the gas and z>0 is towards the liquid.
! The cosine is defined so that c<0 corresponds to z1<z2 and c>0 to z1>z2.
! For illustration and simplicity, we adopt a scheme of formatted files of the same kind
! as those that are saved at the end of each block of our MD simulation examples
! We assume that the initial configuration of a run has been copied to cnf.000
! and subsequent configurations are called cnf.001 cnf.002 etc., up to (at most) cnf.999
! Obviously, in a practical application, a binary trajectory file would fulfil this role.
! Cubic periodic boundary conditions are assumed
! r and box are assumed to be in the same units (e.g. LJ sigma)
! box is assumed to be unchanged throughout
! Values of basic parameters are read from standard input using a namelist nml
USE, INTRINSIC :: iso_fortran_env, ONLY : input_unit, output_unit, error_unit, iostat_end, iostat_eor
USE config_io_module, ONLY : read_cnf_atoms
USE grint_module, ONLY : fit
IMPLICIT NONE
! Most important variables
INTEGER :: n ! Number of atoms
INTEGER :: t ! Time (in blocks, equivalent to number of file)
REAL :: box ! Box length
REAL :: dz ! Spacing in z-direction
REAL :: dz_box ! Spacing in z-direction adjusted to fit box
REAL :: dr ! Spacing in r_ij
REAL :: dc ! Spacing in cos(theta_ij)
REAL :: z_mid ! Rough estimate of mid-point of liquid slab
INTEGER :: nz ! Number of z points relative to interface location
INTEGER :: nr ! Number of r points in pair density
INTEGER :: nc ! Number of cos(theta) points in pair density
INTEGER :: nk ! Number of z points in simulation box
REAL, DIMENSION(:,:), ALLOCATABLE :: r ! Positions (3,n)
REAL, DIMENSION(:), ALLOCATABLE :: rz ! Saved z-coordinates (n)
REAL, DIMENSION(:), ALLOCATABLE :: d ! Single-particle density profile snapshot (nk)
REAL, DIMENSION(:), ALLOCATABLE :: dens ! Single-particle density profile average (nk)
REAL, DIMENSION(:), ALLOCATABLE :: z_box ! Positions for density profile (nk)
REAL, DIMENSION(:), ALLOCATABLE :: rho1 ! One-particle density relative to interface location (-nz:nz)
REAL, DIMENSION(:,:,:), ALLOCATABLE :: rho2 ! Two-particle density relative to interface location (-nz:nz,-nc:nc,nr)
REAL, DIMENSION(:,:,:), ALLOCATABLE :: g2 ! Pair distribution relative to interface location (-nz:nz,-nc:nc,nr)
REAL, DIMENSION(:), ALLOCATABLE :: z ! Positions for rho1, rho2, g2 (-nz:nz)
REAL, DIMENSION(4) :: c1tanh ! Coefficients for 1-tanh fit
REAL, DIMENSION(5) :: c2tanh ! Coefficients for 2-tanh fit
CHARACTER(len=4), PARAMETER :: cnf_prefix = 'cnf.'
CHARACTER(len=3), PARAMETER :: den_prefix = 'den'
CHARACTER(len=3), PARAMETER :: rho_prefix = 'rho'
CHARACTER(len=3), PARAMETER :: g2_prefix = 'g2_'
CHARACTER(len=4), PARAMETER :: out_tag = '.out' ! NB with dot
CHARACTER(len=3) :: sav_tag, z_tag, c_tag
INTEGER :: i, k, unit, ioerr, zskip, cskip, iz, ir, ic, ic_max, iz_max
LOGICAL :: exists, fail
REAL :: norm, area, rij_mag, c, z1, z2, rho1_z1, rho1_z2
REAL, PARAMETER :: pi = 4.0*ATAN(1.0), twopi = 2.0*pi
NAMELIST /nml/ dz, dr, z_mid, nz, nc, nr, zskip, cskip, iz_max
! Example default values
dz = 0.2 ! Spacing in z-direction
nz = 15 ! Number of z-points relative to interface location (-nz:+nz)
nc = 6 ! Number of cos(theta) points covering range (-1,1) (-nc:+nc)
dr = 0.02 ! r-spacing
z_mid = 0.0 ! First estimate of location of liquid slab midpoint
iz_max = 10 ! Limit on z values for g2 output
zskip = 5 ! With iz_max=10 will give output files at iz = -10, -5, 0, +5, +10
cskip = 3 ! With nc=6 will give output files at ic = -6, -3, 0, +3, +6
nr = 200 ! Number of r-points
! Namelist from standard input
READ ( unit=input_unit, nml=nml, iostat=ioerr )
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,i15)') 'Error reading namelist nml from standard input', 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 grint'
END IF
dc = 2.0 / REAL(2*nc+1) ! Cosine spacing to cover the range (-1,1)
WRITE ( unit=output_unit, fmt='(a,t40,f15.6)' ) 'Spacing in z-direction', dz
WRITE ( unit=output_unit, fmt='(a,t40,i15)' ) 'Number of z points', nz
WRITE ( unit=output_unit, fmt='(a,t40,f15.6)' ) '+/- zmax', nz*dz
WRITE ( unit=output_unit, fmt='(a,t40,f15.6)' ) 'Spacing in cos(theta)', dc
WRITE ( unit=output_unit, fmt='(a,t40,i15)' ) 'Number of cos(theta) points', nc
WRITE ( unit=output_unit, fmt='(a,t40,f15.6)' ) 'Spacing in r', dr
WRITE ( unit=output_unit, fmt='(a,t40,i15)' ) 'Number of r points', nr
WRITE ( unit=output_unit, fmt='(a,t40,f15.6)' ) 'rmax', nr*dr
WRITE ( unit=output_unit, fmt='(a,t40,i15)' ) 'Output z skip', zskip
WRITE ( unit=output_unit, fmt='(a,t40,i15)' ) 'Output z max', iz_max
WRITE ( unit=output_unit, fmt='(a,t40,i15)' ) 'Output c skip', cskip
WRITE ( unit=output_unit, fmt='(a,t40,f15.6)' ) 'Liquid slab midpoint (guess)', z_mid
sav_tag = '000' ! Use initial configuration to get N
INQUIRE ( file = cnf_prefix//sav_tag, exist = exists ) ! Check the file exists
IF ( .NOT. exists ) THEN
WRITE ( unit=error_unit, fmt='(a,a)') 'File does not exist: ', cnf_prefix//sav_tag
STOP 'Error in grint'
END IF
CALL read_cnf_atoms ( cnf_prefix//sav_tag, n, box ) ! Read n and box
! We must remember that artefacts are expected whenever z approaches the "other" interface
! This depends on widths of the two phases, on nz*dz, and on nr*dr
! It's up to you if you ignore this warning
IF ( ( nz*dz + nr*dr ) > 0.25*box ) THEN
WRITE ( unit=output_unit, fmt='(a,t40,2f15.6)' ) 'Warning: max z > box/4 = ', (nz*dz+nr*dr), 0.25*box
END IF
! We define dz_box to fit the box exactly
nk = NINT(box/dz)
dz_box = box / REAL(nk)
area = box**2
ALLOCATE ( r(3,n), rz(n), d(nk), dens(nk), z_box(nk) )
ALLOCATE ( rho1(-nz:nz), rho2(-nz:nz,-nc:nc,nr), g2(-nz:nz,-nc:nc,nr), z(-nz:nz) )
z_box(:) = [ ( -0.5*box + (REAL(k)-0.5)*dz_box, k = 1, nk ) ] ! Coordinates in simulation box
z(:) = [ ( REAL(k)*dz, k = -nz, nz ) ] ! Coordinates around interface
dens = 0.0
rho1 = 0.0
rho2 = 0.0
norm = 0.0
t = 0
! Initial guesses at slab fit parameters
! These will be passed on at each step, assuming that changes are small
c2tanh(1) = -0.25*box ! Gas-liquid interface position
c2tanh(2) = 0.25*box ! Liquid-gas interface position
c2tanh(3) = 1.0 ! Width of interface
c2tanh(4) = 0.0 ! Gas density
c2tanh(5) = 0.8 ! Liquid density
DO ! Loop through configuration files
IF ( t > 999 ) EXIT ! Our naming scheme only goes up to cnf.999
WRITE ( sav_tag, fmt='(i3.3)' ) t ! Number of this configuration
INQUIRE ( file = cnf_prefix//sav_tag, exist = exists ) ! Check the file exists
IF ( .NOT. exists ) EXIT ! We have come to the end of the data
IF ( MOD(t,10)==0 ) WRITE ( unit=output_unit, fmt='(a)' ) 'Processing file '//cnf_prefix//sav_tag
CALL read_cnf_atoms ( cnf_prefix//sav_tag, n, box, r ) ! Read configuration
r(3,:) = r(3,:) - z_mid ! Place liquid slab approximately in centre of box
r = r - ANINT ( r / box ) * box ! Apply periodic boundary conditions
d(:) = 0.0
DO i = 1, n
k = 1 + FLOOR ( ( r(3,i) + box/2.0 ) / dz_box )
k = MAX ( 1, k ) ! Guard against roundoff
k = MIN ( nk, k ) ! Guard against roundoff
d(k) = d(k) + 1.0
dens(k) = dens(k) + 1.0
END DO
d(:) = d(:) / ( area * dz_box )
! Fit profile in order to obtain interface positions in c2tanh(1) and c2tanh(2)
CALL fit ( z_box, d, c2tanh, f2tanh, d2tanh, fail )
IF ( fail ) THEN
WRITE ( unit=error_unit, fmt='(a)') 'Failed in fit routine'
STOP 'Error in grint'
END IF
rz(:) = r(3,:) ! Save z-coordinates of all atoms
! Process gas-liquid interface
r(3,:) = rz(:) - c2tanh(1) ! Shift gas-liquid interface to origin
r(3,:) = r(3,:) - ANINT ( r(3,:) / box ) * box ! Apply PBC
CALL calculate
! Process liquid-gas interface
r(3,:) = c2tanh(2) - rz(:) ! Shift liquid-gas interface to origin and reflect
r(3,:) = r(3,:) - ANINT ( r(3,:) / box ) * box ! Apply PBC
CALL calculate
norm = norm + 1.0
t = t + 1 ! Ready for next file
z_mid = z_mid + 0.5*(c2tanh(1)+c2tanh(2)) ! Refine estimate of slab midpoint for next time
END DO ! End loop through configuration files
! Normalize (including factor for 2 interfaces)
dens = dens / ( norm * area * dz_box )
rho1 = rho1 / ( 2.0 * norm * area * dz )
rho2 = rho2 / ( 2.0 * twopi * norm * area * dr * dc * dz )
! Fit the averaged density profile
CALL fit ( z_box, dens, c2tanh, f2tanh, d2tanh, fail )
! Fit the single particle density
c1tanh(1) = 0.0 ! Position of interface
c1tanh(2) = c2tanh(3) ! Width of interface
c1tanh(3) = c2tanh(4) ! Gas density
c1tanh(4) = c2tanh(5) ! Liquid density
CALL fit ( z, rho1, c1tanh, f1tanh, d1tanh, fail )
! Convert rho2 to g2, normalizing by fitted single-particle densities at z1 and z2
DO iz = -nz, nz ! Loop over z coordinate
z1 = z(iz)
rho1_z1 = f1tanh ( z1, c1tanh ) ! Use fitted single-particle density (an approximation)
DO ic = -nc, nc ! Loop over cos(theta)
c = REAL(ic) * dc
DO ir = 1, nr ! Loop over radial distance
rij_mag = ( REAL( ir ) - 0.5 ) * dr
z2 = z1 - c * rij_mag
rho1_z2 = f1tanh ( z2, c1tanh ) ! Use fitted single-particle density (an approximation)
g2(iz,ic,ir) = rho2(iz,ic,ir) / ( rho1_z1 * rho1_z2 )
END DO ! End loop over radial distance
END DO ! End loop over cos(theta)
END DO ! End loop over z coordinate
! Output results
WRITE ( unit=output_unit, fmt='(a)' ) 'Box average density profile output to ' // den_prefix//out_tag
OPEN ( newunit=unit, file=den_prefix//out_tag, status='replace', iostat=ioerr )
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,i15)') 'Error opening dens file', ioerr
STOP 'Error in grint'
END IF
DO k = 1, nk
WRITE ( unit=unit, fmt='(3f15.6)' ) z_box(k), dens(k), f2tanh(z_box(k),c2tanh)
END DO
CLOSE(unit=unit)
WRITE ( unit=output_unit, fmt='(a)' ) 'Single-particle density profile rho1 output to ' // rho_prefix//out_tag
OPEN ( newunit=unit, file=rho_prefix//out_tag, status='replace', iostat=ioerr )
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,i15)') 'Error opening rho file', ioerr
STOP 'Error in grint'
END IF
DO k = -nz, nz
WRITE ( unit=unit, fmt='(3f15.6)' ) z(k), rho1(k), f1tanh(z(k),c1tanh)
END DO
CLOSE(unit=unit)
WRITE ( unit=output_unit, fmt='(a)' ) 'Pair distribution function g2 output in selected slices'
WRITE ( unit=output_unit, fmt='(a)' ) 'Each slice has fixed z=z1 and c=cos(theta)'
WRITE ( unit=output_unit, fmt='(a)' ) 'Filenames have the form g2_ZZZ_CCC'//out_tag
! Slices for selected values of iz, ic
iz_max = MIN ( iz_max, nz )
iz_max = iz_max / zskip
iz_max = iz_max * zskip
IF ( iz_max>99 ) STOP 'The output filename format will only cope with iz_max<100'
WRITE ( unit=output_unit, fmt='(a)' ) 'ZZZ z1'
DO iz = -iz_max, iz_max, zskip
WRITE ( unit=output_unit, fmt='(sp,i3.2,f15.5)' ) iz, z(iz)
END DO
WRITE ( unit=output_unit, fmt='(a)' ) '-ve sign means z1 on gas side, +ve sign means z1 on liquid side'
ic_max = nc / cskip
ic_max = ic_max * cskip
IF ( ic_max>99 ) STOP 'The output filename format will only cope with ic_max<100'
WRITE ( unit=output_unit, fmt='(a)' ) 'CCC cos(theta)'
DO ic = -ic_max, ic_max, cskip
WRITE ( unit=output_unit, fmt='(sp,i3.2,f15.5)' ) ic, REAL(ic) * dc
END DO
WRITE ( unit=output_unit, fmt='(a)' ) '-ve sign means z1<z2, +ve sign means z1>z2'
DO iz = -iz_max, iz_max, zskip
WRITE ( z_tag, fmt='(sp,i3.2)' ) iz ! encoded with +/- sign
DO ic = -ic_max, ic_max, cskip
WRITE ( c_tag, fmt='(sp,i3.2)' ) ic ! encode with +/- sign
OPEN ( newunit=unit, file=g2_prefix//z_tag//'_'//c_tag//out_tag, status='replace', iostat=ioerr )
IF ( ioerr /= 0 ) THEN
WRITE ( unit=error_unit, fmt='(a,i15)') 'Error opening g2 file', ioerr
STOP 'Error in grint'
END IF
DO ir = 1, nr ! Loop over radial distance
rij_mag = ( REAL( ir ) - 0.5 ) * dr
WRITE ( unit=unit, fmt='(2f15.6)' ) rij_mag, g2(iz,ic,ir)
END DO
CLOSE(unit=unit)
END DO
END DO
DEALLOCATE ( r, rz, d, dens, rho1, rho2, g2, z_box, z )
CONTAINS
SUBROUTINE calculate
! This routine carries out the histogramming for rho1 and rho2
IMPLICIT NONE
INTEGER :: i, j, ic, ir, iz
REAL :: rij_sq, rij_mag, c, r_cut, r_cut_sq
REAL, DIMENSION(3) :: rij
r_cut = REAL(nr)*dr
r_cut_sq = r_cut ** 2
DO i = 1, n ! Loop over atoms
iz = NINT ( r(3,i) / dz )
IF ( ABS(iz) > nz ) CYCLE ! No need to consider i-atoms outside range
rho1(iz) = rho1(iz) + 1.0
DO j = 1, n ! Loop over all other atoms
IF ( i==j ) CYCLE ! Skip self
rij = r(:,i) - r(:,j)
rij = rij - ANINT ( rij / box ) * box ! Apply PBC
rij_sq = SUM(rij**2) ! Squared magnitude of separation
IF ( rij_sq > r_cut_sq ) CYCLE ! No need to consider separations out of range
rij_mag = SQRT ( rij_sq ) ! Magnitude of separation
ir = 1 + FLOOR ( rij_mag/dr )
ir = MAX ( 1, ir ) ! Guard against roundoff
ir = MIN ( nr, ir ) ! Guard against roundoff
c = rij(3) / rij_mag ! Cosine of angle
ic = NINT ( c / dc )
ic = MAX ( -nc, ic ) ! Guard against roundoff
ic = MIN ( nc, ic ) ! Guard against roundoff
rho2(iz,ic,ir) = rho2(iz,ic,ir) + 1.0 / rij_sq ! Incorporating r**2 factor here
END DO ! End loop over all other atoms
END DO ! End loop over atoms
END SUBROUTINE calculate
FUNCTION f1tanh ( x, c ) RESULT ( f )
IMPLICIT NONE
REAL :: f ! Returns fitting function
REAL, INTENT(in) :: x ! Abscissa
REAL, DIMENSION(:), INTENT(in) :: c ! Coefficients
REAL :: t
! 1-tanh fit function (function value)
IF ( SIZE(c) /= 4 ) STOP 'Error in function f1tanh'
t = TANH ( ( x - c(1) ) / c(2) )
f = 0.5 * ( c(4) + c(3) ) + 0.5 * ( c(4) - c(3) ) * t
END FUNCTION f1tanh
FUNCTION d1tanh ( x, c ) RESULT ( d )
IMPLICIT NONE
REAL, INTENT(in) :: x ! Abscissa
REAL, DIMENSION(:), INTENT(in) :: c ! Coefficients
REAL, DIMENSION(SIZE(c)) :: d ! Returns fitting function derivatives
REAL :: t
! 1-tanh fit function (derivatives)
IF ( SIZE(c) /= 4 ) STOP 'Error in function d1tanh'
t = TANH ( ( x - c(1) ) / c(2) )
d(1) = 0.5 * ( c(4) - c(3) ) * ( t**2 - 1.0 ) / c(2)
d(2) = 0.5 * ( c(4) - c(3) ) * ( x - c(1) ) * ( t**2 - 1.0 ) / c(2)**2
d(3) = 0.5 - 0.5 * t
d(4) = 0.5 + 0.5 * t
END FUNCTION d1tanh
FUNCTION f2tanh ( x, c ) RESULT ( f )
IMPLICIT NONE
REAL :: f ! Returns fitting function
REAL, INTENT(in) :: x ! Abscissa
REAL, DIMENSION(:), INTENT(in) :: c ! Coefficients
REAL :: t1, t2
! 2-tanh fit function (function value)
IF ( SIZE(c) /= 5 ) STOP 'Error in function f2tanh'
t1 = TANH ( ( x - c(1) ) / c(3) )
t2 = TANH ( ( x - c(2) ) / c(3) )
f = c(4) + 0.5 * ( c(5) - c(4) ) * ( t1 - t2 )
END FUNCTION f2tanh
FUNCTION d2tanh ( x, c ) RESULT ( d )
IMPLICIT NONE
REAL, INTENT(in) :: x ! Abscissa
REAL, DIMENSION(:), INTENT(in) :: c ! Coefficients
REAL, DIMENSION(SIZE(c)) :: d ! Returns fitting function derivatives
REAL :: t1, t2
! 2-tanh fit function (derivatives)
IF ( SIZE(c) /= 5 ) STOP 'Error in function d2tanh'
t1 = TANH ( ( x - c(1) ) / c(3) )
t2 = TANH ( ( x - c(2) ) / c(3) )
d(1) = 0.5 * ( c(5) - c(4) ) * ( t1**2 - 1.0 ) / c(3)
d(2) = 0.5 * ( c(5) - c(4) ) * ( 1.0 - t2**2 ) / c(3)
d(3) = 0.5 * ( c(5) - c(4) ) * ( ( x - c(1) ) * ( t1**2 - 1.0 ) + ( x - c(2) ) * ( 1.0 - t2**2 ) ) / c(3)**2
d(4) = 1.0 - 0.5 * ( t1 - t2 )
d(5) = 0.5 * ( t1 - t2 )
END FUNCTION d2tanh
END PROGRAM grint