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| Program nonorthoSA
!
! This program calculates the accessible surface area by using a simple Monte
! Carlo integration for both orthorhombic and non-orthorhombic unit cells.
! To run the program the following files are needed:
! 1) an input file containing the name of the file containing the diameters of
! the atoms, the name of the file containing the coordinates of the
! framework atoms, the diameter of the probe, the number of random trials
! around each framework atom, the lenghts of the unit cells (a, b, c), the
! cell angles (alpha, beta and gamma) and the crystal density.
! 2) A file containing the diameters of the framework atoms. The program is
! written to read in an xyz file. Please note that the coordinates of all
! framework atoms need to be specified (P1) as the program does not handle
! symmetry operations.
!
! Things that you might have to change:
! - The maximum number of framework atoms 5000 at the moment. Change the value
! of max_no if your unit cells contains more atoms.
!
! Changes to the code
!
! 9/3/2009 Tina Duren
! fixed a bug that wrote the error message to a file rather than
! the screen if an atom type was not specified in the diameter list
! Thanks to Kenji Sumida from the University of Berkeley for
! pointing this out.
!
Use matrix
Use defaults
Implicit None
!
! Maximum number of atoms in your unit cell. Increase if your unit cell
! contains more atoms.
!
Integer, Parameter :: max_no = 5000
Character(len = 3) :: atom
Character(len = 2) :: symbol
Character(len = 10) :: atomname(1:max_no), atomtype(1:100)
Character(len = 100) :: atom_file, coord_file, output_file
Type(MatrixType) :: lij, lijinv
Real(kind=RDbl) :: sigmatype(1:100), atomsigma(1:4000)
Real(kind=RDbl) :: x(1:max_no), y(1:max_no), z(1:max_no)
Real(kind=RDbl) :: xnew(1:max_no), ynew(1:max_no), znew(1:max_no)
Real(kind=RDbl) :: alpha, beta, gamma, alpha_r, beta_r, gamma_r
Real(kind=RDbl) :: a, b, c, ai, bi, ci, aj, bj, cj, ak, bk, ck
Real(kind=RDbl) :: xpoint, ypoint, zpoint, xpointnew, ypointnew, zpointnew
Real(kind=RDbl) :: phi, costheta, theta
Real(kind=RDbl) :: rho_crys, dprobe, Nsample
Real(kind=RDbl) :: dx, dy, dz, dx_trans, dy_trans, dz_trans, dist2
Real(kind=RDbl) :: sjreal, stotal, sfrac, uc_volume, stotalreduced
Real(kind=RDbl) :: ran_num1, ran_num2, trash
Real(kind=RDBL) :: ran0
Integer :: seed, N, ntypes, i, j, k, ncount
Integer :: ierror
Logical :: match, deny
!
! Seed for the random number generator, change if you want to start from a
! different random number
!
seed = -52907
!
! to properly initialise the random number generator, a negative seed is
! needed
!
If (seed> 0) seed = -1 * seed
!
! Read the data from the input file
!
Read(*,('(A)')) atom_file ! file containing the diameters of atoms
Read(*,('(A)')) coord_file ! file containing the cartesian coordinates
Read(*,*) dprobe ! diameter of probe in A
Read(*,*) Nsample ! Number of trials per framework atom
Read(*,*) a, b, c ! Cell parameters in A
Read(*,*) alpha, beta, gamma ! cell angles
Read(*,*) rho_crys ! density of crystal in g / cm3
alpha_r = alpha*degtorad
beta_r = beta*degtorad
gamma_r = gamma*degtorad
ai = a
aj = 0
ak = 0
bi = b*cos(gamma_r)
bj = b*sin(gamma_r)
bk = 0
ci = c*cos(beta_r)
cj = (b*c*cos(alpha_r)-bi*ci)/bj
ck = sqrt(c**2-ci**2-cj**2)
lij%comp = 0
lij%comp(1,1) = ai
lij%comp(1,2) = bi
lij%comp(1,3) = ci
lij%comp(2,1) = aj
lij%comp(2,2) = bj
lij%comp(2,3) = cj
lij%comp(3,1) = ak
lij%comp(3,2) = bk
lij%comp(3,3) = ck
lijinv=matrix_inverse(lij)
!
! Open the files and read the data
!
Open(10, file=atom_file, status='old', IOSTAT = ierror)
If (ierror /= 0) Then
Write(*,*) 'Error opening file: ',atom_file
Write(*,*) 'Make sure it exists or check the spelling of the filename'
END IF
ntypes = 0
Do
Read(10,*) atom
IF(Trim(atom) == 'EOF') EXIT
ntypes = ntypes + 1
END DO
Rewind(10)
Do i = 1, ntypes
Read(10,*) atomtype(i), sigmatype(i)
End do
!
! Openeing and reading the coord file
!
Open(20, file=coord_file, status='old', IOSTAT = ierror)
If (ierror /= 0) Then
Write(*,*) 'Error opening file: ',coord_file
Write(*,*) 'Make sure it exists or check the spelling of the filename'
END IF
!
! The first line contains the number of framework atoms
!
Read(20,*) N
!
! Skip the blank line of the xyz file
!
Read(20,*)
Do i=1, N
!
! The format of the coordinate file corresponds to an xyz file as exported
! from Diamond.
! x(i), y(i), z(i): x,y,z coordinates in Angstrom
! symbol: chemical symbol of framework atom.
!
! Change the following read statement if you want to use a different
! file format. But ensure that you end up with the coordinates in A and
! the name of the framework atoms!
Read(20,*) symbol, x(i), y(i), z(i)
!
! The diameters of the framework atoms are stored together with the atom
! name. So assign atom name according to chemical symbol.
!
symbol = Trim(symbol)
SELECT CASE(symbol)
CASE('H')
atomname(i) = 'Hydrogen'
CASE('C')
atomname(i) = 'Carbon'
CASE('O')
atomname(i) = 'Oxygen'
CASE('Zn')
atomname(i) = 'Zinc'
CASE('Cr')
atomname(i) = 'Chromium'
CASE('Cd')
atomname(i) = 'Cadmium'
CASE default
Write(*,*) symbol ,' not in list'
Write(*,*) 'List can be found in nonorthoSA.F90'
END SELECT
! Transform molecules coordinates
xnew(i) = x(i)*lijinv%comp(1,1) + y(i)*lijinv%comp(1,2) + &
z(i)*lijinv%comp(1,3)
ynew(i) = x(i)*lijinv%comp(2,1) + y(i)*lijinv%comp(2,2) + &
z(i)*lijinv%comp(2,3)
znew(i) = x(i)*lijinv%comp(3,1) + y(i)*lijinv%comp(3,2) + &
z(i)*lijinv%comp(3,3)
xnew(i) = a*xnew(i)
ynew(i) = b*ynew(i)
znew(i) = c*znew(i)
! Translate the transformed coordinates so they lie in the box a,b,c
If(xnew(i)<0.0) xnew(i) = xnew(i) + a
If(xnew(i)>=a) xnew(i) = xnew(i) - a
If(ynew(i)<0.0) ynew(i) = ynew(i) + b
If(ynew(i)>=b) ynew(i) = ynew(i) - b
If(znew(i)<0.0) znew(i) = znew(i) + c
If(znew(i)>=c) znew(i) = znew(i) - c
! Match sigmas with coordinates
atomname(i)=Trim(atomname(i))
match=.False.
Do j=1, ntypes
If(atomname(i)==atomtype(j)) Then
atomsigma(i)=sigmatype(j)+dprobe
match=.True.
Exit
End If
End Do
If(.Not.match) Then
Write(*,*) 'Could not find match for atom: ', i, ' ', atomname(i)
Write(*,*) 'The name is either read in incorrectly or does not exist'
Write(*,*) 'in the list of available atoms in ',atom_file
Stop
End If
End Do
Write(*,*)
Write(*,*) 'Calculating the accessible surface area for the following input parameters'
Write(*,*) '-------------------------------------------------------------------------'
Write(*,*) 'File with framework coordinates: ',TRIM(coord_file)
Write(*,*) 'File with atom diameters: ', TRIM(atom_file)
Write(*,'(A,F12.3)') ' Probe diameter in A: ',dprobe
! Main sampling cycle
stotal=0.0
Do i=1, N ! Loop over all framework atoms
ncount=0
Do j=1, Nsample ! Number of trial positions around each framework atom
!
! Generate random vector of length 1
! First generate phi 0:+2pi
!
phi = ran0(seed)*twopi
!
!
! Generate cosTheta -1:1 to allow for even distribution of random vectors
! on the unit sphere.See <a href="http://mathworld.wolfram.com/SpherePointPicking.html" target="_blank">http://mathworld.wolfram.com/SpherePointPicking.html</a>
! for further explanations
!
costheta = 1 - ran0(seed) * 2.0
theta = Acos(costheta)
xpoint = sin(theta)*cos(phi)
ypoint = sin(theta)*sin(phi)
zpoint = costheta
! Make this vector of (sigma+probe_diameter)/2.0 length
xpoint=xpoint*atomsigma(i)/2.0
ypoint=ypoint*atomsigma(i)/2.0
zpoint=zpoint*atomsigma(i)/2.0
! Transform random vector
xpointnew = xpoint*lijinv%comp(1,1) + ypoint*lijinv%comp(1,2) &
+ zpoint*lijinv%comp(1,3)
ypointnew = xpoint*lijinv%comp(2,1) + ypoint*lijinv%comp(2,2) &
+ zpoint*lijinv%comp(2,3)
zpointnew = xpoint*lijinv%comp(3,1) + ypoint*lijinv%comp(3,2) &
+ zpoint*lijinv%comp(3,3)
xpointnew = a*xpointnew
ypointnew = b*ypointnew
zpointnew = c*zpointnew
! Translate the center of coordinate to the particle i center and apply PBC
xpointnew = xpointnew + xnew(i)
ypointnew = ypointnew + ynew(i)
zpointnew = zpointnew + znew(i)
If(xpointnew < 0.0) xpointnew = xpointnew + a
If(xpointnew >= a) xpointnew = xpointnew - a
If(ypointnew < 0.0) ypointnew = ypointnew + b
If(ypointnew >= b) ypointnew = ypointnew - b
If(zpointnew < 0.0) zpointnew = zpointnew + c
If(zpointnew >= c) zpointnew = zpointnew - c
! Now we check for overlap
deny=.False.
Do k=1,N
if(k==i) cycle
dx = xpointnew - xnew(k)
dx = dx - a*int(2.0*dx/a)
dy = ypointnew - ynew(k)
dy = dy - b*int(2.0*dy/b)
dz = zpointnew-znew(k)
dz = dz-c*int(2.0*dz/c)
dx = dx / a
dy = dy / b
dz = dz / c
dx_trans = dx*lij%comp(1,1) + dy*lij%comp(1,2) + dz*lij%comp(1,3)
dy_trans = dx*lij%comp(2,1) + dy*lij%comp(2,2) + dz*lij%comp(2,3)
dz_trans = dx*lij%comp(3,1) + dy*lij%comp(3,2) + dz*lij%comp(3,3)
dist2=dx_trans*dx_trans+dy_trans*dy_trans+dz_trans*dz_trans
If(sqrt(dist2)<0.999*atomsigma(k)/2.0) then
deny=.True.
Exit
End If
End Do
If(deny) Cycle
ncount=ncount+1
End Do
! Fraction of the accessible surface area for sphere i
sfrac=Real(ncount)/Real(Nsample)
! Surface area for sphere i in real units (A^2)
sjreal=pi*atomsigma(i)*atomsigma(i)*sfrac
stotal=stotal+sjreal
End Do
! Converting stotal on Surface per Volume
! Unit volume calculated from the absolute value of the determinate of the 3x3
! matrix containing the vectors defining the unit cell.
! See e.g. Marsden, et al. "Basic Multivariable Calculus" 1993 pg. 53
uc_volume=abs(ai*(bj*ck-bk*cj)-aj*(bi*ck-bk*ci)+ak*(bi*cj-bj*ci))
stotalreduced=stotal/uc_volume*1.E4
! Report results
Write(*,'(A,F12.2)') ' Total surface area in Angstroms^2: ', stotal
Write(*,'(A,F12.2)') ' Total surface area per volume in m^2/cm^3: ', &
stotalreduced
Write(*,'(A,F12.2)') ' Total surface area per volume in m^2/g: ', &
stotalreduced / rho_crys
End Program NonorthoSA
!----------------FUNCTIONS-------------------------------------
FUNCTION ran0(idum)
!
! Random number generator from W.H. Press et al, Numerical Recipes in
! FORTRAN, Cambridge University Press, 1992
!
INTEGER idum,IA,IM,IQ,IR,NTAB,NDIV
REAL(kind = 8) ran0,AM,EPS,RNMX
PARAMETER (IA=16807,IM=2147483647,AM=1./IM,IQ=127773,IR=2836, &
NTAB=32,NDIV=1+(IM-1)/NTAB,EPS=1.2e-7,RNMX=1.-EPS)
INTEGER j,k,iv(NTAB),iy
SAVE iv,iy
DATA iv /NTAB*0/, iy /0/
if (idum.le.0.or.iy.eq.0) then
idum=max(-idum,1)
do 11 j=NTAB+8,1,-1
k=idum/IQ
idum=IA*(idum-k*IQ)-IR*k
if (idum.lt.0) idum=idum+IM
if (j.le.NTAB) iv(j)=idum
11 continue
iy=iv(1)
endif
k=idum/IQ
idum=IA*(idum-k*IQ)-IR*k
if (idum.lt.0) idum=idum+IM
j=1+iy/NDIV
iy=iv(j)
iv(j)=idum
ran0=min(AM*iy,RNMX)
return
END FUNCTION ran0 |
