Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/tools/micelle2d.f
e9c79e2ccc41lammm-master-deprecated

Last Change
Raw File

micelle2d.f
View Options

c Create LAMMPS 2003 input file for 2d LJ simulation of micelles
c
c Syntax: micelle2d < def.micelle2d > data.file
c
c def file contains size of system and number to turn into surfactants
c attaches a random surfactant tail(s) to random head
c if nonflag is set, will attach 2nd-neighbor bonds in surfactant
c solvent atoms = type 1
c micelle heads = type 2
c micelle tails = type 3,4,5,etc.
program micelle2d
parameter (maxatom=100000,maxbond=10000)
real*4 x(2,maxatom)
integer type(maxatom),molecule(maxatom)
integer bondatom(2,maxbond),bondtype(maxbond)
common xprd,yprd,zprd,xboundlo,xboundhi,yboundlo,yboundhi,
$ zboundlo,zboundhi
999 format (3i7,3f8.3)
998 format (4i7)
read (5,*)
read (5,*)
read (5,*) rhostar
read (5,*) iseed
read (5,*) nx,ny
read (5,*) nsurf
read (5,*) r0
read (5,*) ntails
read (5,*) nonflag
natoms = nx*ny
if (natoms+nsurf*ntails.gt.maxatom) then
write (6,*) 'Too many atoms - boost maxatom'
call exit(0)
endif
nbonds = nsurf*ntails
if (nonflag.eq.1) nbonds = nbonds + nsurf*(ntails-1)
if (nbonds.gt.maxbond) then
write (6,*) 'Too many surfactants - boost maxbond'
call exit(0)
endif
c box size
rlattice = (1.0/rhostar) ** 0.5
xboundlo = 0.0
xboundhi = nx*rlattice
yboundlo = 0.0
yboundhi = ny*rlattice
zboundlo = -0.1
zboundhi = 0.1
sigma = 1.0
xprd = xboundhi - xboundlo
yprd = yboundhi - yboundlo
zprd = zboundhi - zboundlo
c initial square lattice of solvents
m = 0
do j = 1,ny
do i = 1,nx
m = m + 1
x(1,m) = xboundlo + (i-1)*rlattice
x(2,m) = yboundlo + (j-1)*rlattice
molecule(m) = 0
type(m) = 1
enddo
enddo
c turn some into surfactants with molecule ID
c head changes to type 2
c create ntails for each head of types 3,4,...
c each tail is at distance r0 away in straight line with random orientation
do i = 1,nsurf
10 m = random(iseed)*natoms + 1
if (m.gt.natoms) m = natoms
if (molecule(m) .ne. 0) goto 10
molecule(m) = i
type(m) = 2
angle = random(iseed)*2.0*3.1415926
do j = 1,ntails
k = (i-1)*ntails + j
x(1,natoms+k) = x(1,m) + cos(angle)*j*r0*sigma
x(2,natoms+k) = x(2,m) + sin(angle)*j*r0*sigma
molecule(natoms+k) = i
type(natoms+k) = 2+j
call pbc(x(1,natoms+k),x(2,natoms+k))
if (j.eq.1) bondatom(1,k) = m
if (j.ne.1) bondatom(1,k) = natoms+k-1
bondatom(2,k) = natoms+k
bondtype(k) = 1
enddo
enddo
c if nonflag is set, add (ntails-1) 2nd nearest neighbor bonds to end
c of bond list
c k = location in bondatom list where nearest neighbor bonds for
c this surfactant are stored
if (nonflag.eq.1) then
nbonds = nsurf*ntails
do i = 1,nsurf
do j = 1,ntails-1
k = (i-1)*ntails + j
nbonds = nbonds + 1
bondatom(1,nbonds) = bondatom(1,k)
bondatom(2,nbonds) = bondatom(2,k+1)
bondtype(nbonds) = 2
enddo
enddo
endif
c write LAMMPS data file
natoms = natoms + nsurf*ntails
nbonds = nsurf*ntails
if (nonflag.eq.1) nbonds = nbonds + nsurf*(ntails-1)
ntypes = 2 + ntails
nbondtypes = 1
if (nonflag.eq.1) nbondtypes = 2
if (nsurf.eq.0) then
ntypes = 1
nbondtypes = 0
endif
write (6,*) 'LAMMPS 2d micelle data file'
write (6,*)
write (6,*) natoms,' atoms'
write (6,*) nbonds,' bonds'
write (6,*) 0,' angles'
write (6,*) 0,' dihedrals'
write (6,*) 0,' impropers'
write (6,*)
write (6,*) ntypes,' atom types'
write (6,*) nbondtypes,' bond types'
write (6,*) 0,' angle types'
write (6,*) 0,' dihedral types'
write (6,*) 0,' improper types'
write (6,*)
write (6,*) xboundlo,xboundhi,' xlo xhi'
write (6,*) yboundlo,yboundhi,' ylo yhi'
write (6,*) zboundlo,zboundhi,' zlo zhi'
write (6,*)
write (6,*) 'Masses'
write (6,*)
do i = 1,ntypes
write (6,*) i,1.0
enddo
write (6,*)
write (6,*) 'Atoms'
write (6,*)
do i = 1,natoms
write (6,999) i,molecule(i),type(i),x(1,i),x(2,i),0.0
enddo
if (nsurf.gt.0) then
write (6,*)
write (6,*) 'Bonds'
write (6,*)
do i = 1,nbonds
write (6,998) i,bondtype(i),bondatom(1,i),bondatom(2,i)
enddo
endif
c write Xmovie bond geometry file
open(1,file='bond.micelle')
write (1,*) 'ITEM: BONDS'
do i = 1,nbonds
write (1,*) bondtype(i),bondatom(1,i),bondatom(2,i)
enddo
close(1)
end
c ************
c Subroutines
c ************
c periodic boundary conditions - map atom back into periodic box
subroutine pbc(x,y)
common xprd,yprd,zprd,xboundlo,xboundhi,yboundlo,yboundhi,
$ zboundlo,zboundhi
if (x.lt.xboundlo) x = x + xprd
if (x.ge.xboundhi) x = x - xprd
if (y.lt.yboundlo) y = y + yprd
if (y.ge.yboundhi) y = y - yprd
return
end
c RNG - compute in double precision, return single
real*4 function random(iseed)
real*8 aa,mm,sseed
parameter (aa=16807.0D0,mm=2147483647.0D0)
sseed = iseed
sseed = mod(aa*sseed,mm)
random = sseed/mm
iseed = sseed
return
end
c4science · Help