2006-09-28 03:51:49 +08:00
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c Create LAMMPS data file for collection of
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c polymer bead-spring chains of various lengths and bead sizes
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c Syntax: chain < def.chain > data.file
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c def.chain is input file that specifies the chains
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c data.file is output file that will be input for LAMMPS
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c includes image flags in data file so chains can be unraveled later
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program chain
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integer swaptype
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integer, allocatable :: nchain(:),nmonomer(:)
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integer, allocatable :: ntype(:),nbondtype(:)
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integer, allocatable :: type(:),molecule(:)
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integer, allocatable :: imagex(:),imagey(:),imagez(:)
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real*8, allocatable :: x(:),y(:),z(:)
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real*8, allocatable :: bondlength(:),restrict(:)
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common xprd,yprd,zprd,xboundlo,xboundhi,
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$ yboundlo,yboundhi,zboundlo,zboundhi
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real*8 random
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900 format(a)
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2015-04-14 22:18:40 +08:00
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901 format(2f15.6,a)
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2006-09-28 03:51:49 +08:00
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902 format(i3,f5.1)
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2006-12-07 08:43:04 +08:00
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903 format(i10,i8,i8,3f10.4,3i4)
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2015-04-14 22:18:40 +08:00
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904 format(i9,i3,2i9)
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2006-09-28 03:51:49 +08:00
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c read chain definitions
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read (5,*)
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read (5,*)
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read (5,*) rhostar
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read (5,*) iseed
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read (5,*) nsets
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read (5,*) swaptype
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allocate(nchain(nsets))
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allocate(nmonomer(nsets))
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allocate(ntype(nsets))
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allocate(nbondtype(nsets))
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allocate(bondlength(nsets))
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allocate(restrict(nsets))
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do iset = 1,nsets
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read (5,*)
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read (5,*) nchain(iset)
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read (5,*) nmonomer(iset)
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read (5,*) ntype(iset)
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read (5,*) nbondtype(iset)
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read (5,*) bondlength(iset)
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read (5,*) restrict(iset)
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enddo
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c natoms = total # of monomers
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natoms = 0
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do iset = 1,nsets
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natoms = natoms + nchain(iset)*nmonomer(iset)
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enddo
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allocate(x(natoms))
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allocate(y(natoms))
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allocate(z(natoms))
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allocate(type(natoms))
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allocate(molecule(natoms))
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allocate(imagex(natoms))
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allocate(imagey(natoms))
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allocate(imagez(natoms))
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c setup box size (sigma = 1.0)
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volume = natoms/rhostar
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xprd = volume**(1.0/3.0)
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yprd = xprd
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zprd = xprd
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xboundlo = -xprd/2.0
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xboundhi = -xboundlo
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yboundlo = xboundlo
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yboundhi = xboundhi
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zboundlo = xboundlo
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zboundhi = xboundhi
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c generate random chains
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c loop over sets and chains in each set
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n = 0
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nmolecule = 0
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do iset = 1,nsets
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do ichain = 1,nchain(iset)
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nmolecule = nmolecule + 1
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c random starting point for the chain in the box
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x1 = 0.0
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y1 = 0.0
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z1 = 0.0
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x2 = xboundlo + random(iseed)*xprd
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y2 = yboundlo + random(iseed)*yprd
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z2 = zboundlo + random(iseed)*zprd
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c store 1st monomer of chain
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c 1st monomer is always in original box (image = 0)
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call pbc(x2,y2,z2)
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n = n + 1
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x(n) = x2
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y(n) = y2
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z(n) = z2
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type(n) = ntype(iset)
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imagex(n) = 0
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imagey(n) = 0
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imagez(n) = 0
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if (swaptype == 0) then
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molecule(n) = nmolecule
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else
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molecule(n) = 1
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endif
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c generate rest of monomers in this chain
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do imonomer = 2,nmonomer(iset)
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x0 = x1
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y0 = y1
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z0 = z1
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x1 = x2
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y1 = y2
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z1 = z2
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c random point inside sphere of unit radius
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10 xinner = 2.0*random(iseed) - 1.0
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yinner = 2.0*random(iseed) - 1.0
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zinner = 2.0*random(iseed) - 1.0
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rsq = xinner*xinner + yinner*yinner + zinner*zinner
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if (rsq > 1.0) goto 10
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c project point to surface of sphere of unit radius
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r = sqrt(rsq)
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xsurf = xinner/r
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ysurf = yinner/r
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zsurf = zinner/r
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c create new point by scaling unit offsets by bondlength (sigma = 1.0)
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x2 = x1 + xsurf*bondlength(iset)
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y2 = y1 + ysurf*bondlength(iset)
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z2 = z1 + zsurf*bondlength(iset)
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c check that new point meets restriction requirement
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c only for 3rd monomer and beyond
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dx = x2 - x0
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dy = y2 - y0
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dz = z2 - z0
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r = sqrt(dx*dx + dy*dy + dz*dz)
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if (imonomer > 2 .and. r <= restrict(iset)) goto 10
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c store new point
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c if delta to previous bead is large, then increment/decrement image flag
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call pbc(x2,y2,z2)
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n = n + 1
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x(n) = x2
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y(n) = y2
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z(n) = z2
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type(n) = ntype(iset)
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if (abs(x(n)-x(n-1)) < 2.0*bondlength(iset)) then
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imagex(n) = imagex(n-1)
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else if (x(n) - x(n-1) < 0.0) then
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imagex(n) = imagex(n-1) + 1
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else if (x(n) - x(n-1) > 0.0) then
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imagex(n) = imagex(n-1) - 1
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endif
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if (abs(y(n)-y(n-1)) < 2.0*bondlength(iset)) then
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imagey(n) = imagey(n-1)
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else if (y(n) - y(n-1) < 0.0) then
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imagey(n) = imagey(n-1) + 1
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else if (y(n) - y(n-1) > 0.0) then
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imagey(n) = imagey(n-1) - 1
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endif
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if (abs(z(n)-z(n-1)) < 2.0*bondlength(iset)) then
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imagez(n) = imagez(n-1)
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else if (z(n) - z(n-1) < 0.0) then
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imagez(n) = imagez(n-1) + 1
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else if (z(n) - z(n-1) > 0.0) then
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imagez(n) = imagez(n-1) - 1
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endif
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if (swaptype == 0) then
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molecule(n) = nmolecule
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else if (swaptype == 1) then
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molecule(n) = imonomer
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else if (swaptype == 2) then
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if (imonomer <= nmonomer(iset)/2) then
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molecule(n) = imonomer
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else
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molecule(n) = nmonomer(iset)+1-imonomer
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endif
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endif
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enddo
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enddo
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enddo
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c compute quantities needed for LAMMPS file
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nbonds = 0
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ntypes = 0
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nbondtypes = 0
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do iset = 1,nsets
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nbonds = nbonds + nchain(iset)*(nmonomer(iset)-1)
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if (ntype(iset) > ntypes) ntypes = ntype(iset)
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if (nbondtype(iset) > nbondtypes)
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$ nbondtypes = nbondtype(iset)
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enddo
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c write out LAMMPS file
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write (6,900) 'LAMMPS FENE chain data file'
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write (6,*)
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write (6,*) natoms,' atoms'
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write (6,*) nbonds,' bonds'
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write (6,*) 0,' angles'
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write (6,*) 0,' dihedrals'
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write (6,*) 0,' impropers'
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write (6,*)
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write (6,*) ntypes,' atom types'
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write (6,*) nbondtypes,' bond types'
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write (6,*) 0,' angle types'
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write (6,*) 0,' dihedral types'
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write (6,*) 0,' improper types'
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write (6,*)
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write (6,901) xboundlo,xboundhi,' xlo xhi'
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write (6,901) yboundlo,yboundhi,' ylo yhi'
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write (6,901) zboundlo,zboundhi,' zlo zhi'
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write (6,*)
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write (6,900) 'Masses'
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write (6,*)
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do i = 1,ntypes
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write (6,902) i,1.0
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enddo
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write (6,*)
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write (6,900) 'Atoms'
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write (6,*)
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do i = 1,natoms
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write (6,903) i,molecule(i),type(i),x(i),y(i),z(i),
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$ imagex(i),imagey(i),imagez(i)
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enddo
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if (nbonds > 0) then
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write (6,*)
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write (6,900) 'Bonds'
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write (6,*)
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n = 0
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m = 0
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do iset = 1,nsets
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do ichain = 1,nchain(iset)
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do imonomer = 1,nmonomer(iset)
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n = n + 1
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if (imonomer /= nmonomer(iset)) then
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m = m + 1
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write (6,904) m,nbondtype(iset),n,n+1
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endif
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enddo
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enddo
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enddo
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endif
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end
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c ************
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c Subroutines
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c ************
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c periodic boundary conditions - map atom back into periodic box
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subroutine pbc(x,y,z)
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common xprd,yprd,zprd,xboundlo,xboundhi,
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$ yboundlo,yboundhi,zboundlo,zboundhi
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if (x < xboundlo) x = x + xprd
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if (x >= xboundhi) x = x - xprd
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if (y < yboundlo) y = y + yprd
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if (y >= yboundhi) y = y - yprd
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if (z < zboundlo) z = z + zprd
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if (z >= zboundhi) z = z - zprd
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return
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end
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c RNG from Numerical Recipes
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real*8 function random(iseed)
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real*8 aa,mm,sseed
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parameter (aa=16807.0D0,mm=2147483647.0D0)
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sseed = iseed
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sseed = mod(aa*sseed,mm)
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random = sseed/mm
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iseed = sseed
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return
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end
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