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EcoSLIM.f90
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EcoSLIM.f90
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!--------------------------------------------------------------------
! **EcoSLIM** is a Lagrangian, particle-tracking that simulates advective
! and diffusive movement of water parcels. This code can be used to
! simulate age, diagnosing travel times, source water composition and
! flowpaths. It integrates seamlessly with **ParFlow-CLM**.
!
! Developed by: Reed Maxwell-August 2016 (rmaxwell@mines.edu)
!
! Contributors: Laura Condon (lecondon@email.arizona.edu)
! Mohammad Danesh-Yazdi (danesh@sharif.edu)
! Lindsay Bearup (lbearup@usbr.gov)
! Zach Perzan (zperzan@stanford.edu)
!
! released under GNU LPGL, see LICENSE file for details
!
!--------------------------------------------------------------------
! MAIN FORTRAN CODE
!--------------------------------------------------------------------
! EcoSLIM_main.f90: The main fortran code performing particle tracking
! Use Makefile provided to build.
!
!
!
!--------------------------------------------------------------------
! INPUTS
!--------------------------------------------------------------------
! slimin.txt: Includes the domain's geometric information,
! ParFlow timesteps and their total number, and particles
! initial locations.
!
!--------------------------------------------------------------------
! SUBROUTINES
!--------------------------------------------------------------------
! pfb_read(arg1,...,arg5).f90: Reads a ParFlow .pfb output file and
! stores it in a matrix. Arguments
! in order are:
!
! - arg1: Name of the matrix in which
! ParFlow .pfb is stored
! - arg2: Corresponding .pfb file name,
! e.g., test.out.press.00100.pfb
! - arg3: Number of cells in x-direction
! - arg4: Number of cells in y-direction
! - arg5: Number of cells in z-direction
!
!--------------------------------------------------------------------
! OUTPUTS
!--------------------------------------------------------------------
! XXXX_log.txt: Reports the domain's geometric information,
! ParFlow's timesteps and their total number,
! and particles initial condition. XXXX is the name of
! the SLIM2 run already set in slimin.txt
!
! XXXX_particle.3D: Contains particles' trajectory information in
! space (i.e., X, Y, Z) and time (i.e., residence
! time). XXXX is the name of the SLIM2 run
! already set in slimin.txt
!
! XXXX_endparticle.txt: Contains the final X, Y, Z location of all
! particles as well as their travel time.
! XXXX is the name of the SLIM2 run already set
! in slimin.txt
!
!--------------------------------------------------------------------
! CODE STRUCTURE
!--------------------------------------------------------------------
! (1) Define variables
!
! (2) Read inputs, set up domain, write the log file, and
! initialize particles,
!
! (3) For each timestep, loop over all particles to find and
! update their new locations
!--------------------------------------------------------------------
program EcoSLIM
use ran_mod
implicit none
!--------------------------------------------------------------------
! (1) Define variables
!--------------------------------------------------------------------
real*8,allocatable::P(:,:)
! P = Particle array [np,attributes]
! np = Number of particles
! P(np,1) = X coordinate [L]
! P(np,2) = Y coordinate [L]
! P(np,3) = Z coordinate [L]
! P(np,4) = Particle residence time [T]
! P(np,5) = Saturated particle residence time [T]
! P(np,6) = Particle mass; assigned via preciptiation or snowmelt rate (Evap_Trans*density*volume*dT)
! P(np,7) = Particle source (1=IC, 2=rain, 3=snowmelt...)
! P(np,8) = Particle Status (1=active, 0=inactive)
! P(np,9) = concentration
! P(np,10) = Exit status (1=surface outflow, 2=ET, 3=subsurface outflow, 4=well outflow)
! P(np,11) = Particle Number (This is a unique integer identifier for the particle)
! P(np,12) = Partical Initial X coordinate [L]
! P(np,13) = Partical Initial Y coordinate [L]
! P(np,14) = Partical Initial Z coordinate [L]
! P(np,15) = Time that particle was added [T]
! P(np,16) = Length of flow path [L]
! P(np,17) = Length of saturated flow path [L]
! P(np,18:(17+nind)) = Length of flow path in indicator i [L]
! P(np,(18+nind):(17+nind*2)) = particle age in indicator i [T]
!@ RMM, why is this needed?
real*8,allocatable::PInLoc(:,:)
! PInLoc(np,1) = Particle initial X location
! PInLoc(np,2) = Particle initial Y location
! PInLoc(np,3) = Particle initial Z location
real*8,allocatable::Vx(:,:,:)
real*8,allocatable::Vy(:,:,:)
real*8,allocatable::Vz(:,:,:)
! Vx = Velocity x-direction [nx+1,ny,nz] -- ParFlow output
! Vy = Velocity y-direction [nx,ny+1,nz] -- ParFlow output
! Vz = Velocity z-direction [nx,ny,nz+1] -- ParFlow output
real*8,allocatable::C(:,:,:,:)
! Concentration array, in i,j,k with l (first index) as consituent or
! property. These are set by user at runtime using input
!real*8,allocatable::ET_grid(:,:,:,:)
! ET array, in i,j,k with l (first index) as consituent or property
CHARACTER*20,allocatable:: conc_header(:)
! name for variables written in the C array above. Dimensioned as l above.
real*8,allocatable::Time_Next(:)
! Vector of real times at which ParFlow dumps outputs
real*8,allocatable::dz(:), Zt(:)
! Delta Z values in the vertical direction
! Elevations in z-direction in local coordinates
real*8,allocatable::Sx(:,:) ! Sx: Slopes in x-direction (not used)
real*8,allocatable::Sy(:,:) ! Sy: Slopes in y-direction (not used)
real*8,allocatable::Saturation(:,:,:) ! Saturation (read from ParFlow)
real*8,allocatable::Porosity(:,:,:) ! Porosity (read from ParFlow)
real*8,allocatable::EvapTrans(:,:,:) ! CLM EvapTrans (read from ParFlow, [1/T] units)
real*8,allocatable::CLMvars(:,:,:) ! CLM Output (read from ParFlow, following single file
! CLM output as specified in the manual)
real*8,allocatable::Pnts(:,:), DEM(:,:) ! DEM and grid points for concentration output
real*8,allocatable::Ind(:,:,:) ! Flowpath indicator file
real*8,allocatable::BoundFlux(:,:,:) ! An array of flux across each domain boundary
real*8,allocatable::PSourceBool(:,:,:) ! Boolean particle source file
integer Ploc(3)
! Particle's location whithin a cell
integer nind, itemp
! Number of units in the indicator file, temporary integer to store current indicator
integer nx, nnx, ny, nny, nz, nnz, nztemp
! number of cells in the domain and cells+1 in x, y, and z directions
integer np_ic, np, np_active, np_active2, icwrite, jj, npnts, ncell, npout
! number of particles for intial pulse IC, total, and running active
integer nt, n_constituents
! number of timesteps ParFlow; numer of C vectors written for VTK output
integer pid
! Counter for particle ID number
real*8 pfdt, advdt(3), Ltemp
! ParFlow timestep value, advection timestep for each direction
! for each individual particle step; used to chose optimal particle timestep
! Temporary storage for step length calculations
integer pft1, pft2, tout1, pfnt, n_cycle
! parflow start and stop file numbers number of ParFlow timesteps
! flag specifying the number for the first output write (0= start with pft1)
! number of timestep cycles
real*8 Time_first, part_tstart
! initial timestep for Parflow ((pft1-1)*pfdt)
! initial time for particles (used for recording the particle insert time)
integer kk, ktemp
! Loop counter for the time steps (pfnt)
! temporary loop counter
integer pfkk, outkk
! Counter for the file numbers starts at pft1
! Counter for the output writing
integer ii
! Loop counter for the number of particles (np)
integer iflux_p_res, i_added_particles
! Number of particles per cell for flux input and
! number of particle added total for precip input per
! timestep
integer i, j, k, l, ik, ji, m, ij, nzclm, nCLMsoil
integer itime_loc
! Local indices / counters
integer*4 ir
character*200 runname, filenum, filenumout, pname, fname, vtk_file, DEMname, Indname, Boolname
! runname = SLIM runname
! filenum = ParFlow file number
! filenumout = File number for Ecoslim writing
! pname = ParFlow output runname
! fname = Full name of a ParFlow's output
! vtk_file = concentration file
! DEMname = DEM file name
! Indname = Indicator File name
! Boolname = Boolean particle source file name
integer nlines
! number of lines in slimin.txt
real*8 Clocx, Clocy, Clocz, Z, maxz
! The fractional location of each particle within it's grid cell
! Particle Z location
real*8 V_mult
! Multiplier for forward/backward particle tracking
! If V_mult = 1, forward tracking
! If V_mult = -1, backward tracking
logical clmtrans, clmfile, velfile, boolfile
! logical for mode of operation with CLM, will add particles with P-ET > 0
! will remove particles if ET > 0
! clmfile governs reading of the full CLM output, not just evaptrans
! velfile governs addition of particles to the domain via velocity pfb output
! boolfile governs reading of a PSourceBool file, which spatially limits particle addition
real*8 dtfrac
! fraction of dx/Vx (as well as dy/Vy and dz/Vz) assuring
! numerical stability while advecting a particle to a new
! location.
real*8 Xmin, Xmax, Ymin, Ymax, Zmin, Zmax
! Domain boundaries in local / grid coordinates. min values set to zero,
! DEM is read in later to output to Terrain Following Grid used by ParFlow.
real*8 dx, dy
! Domain's number of cells in x and y directions
real*8 Vpx, Vpy, Vpz
! Particle velocity in x, y, and z directions
real*8 particledt, delta_time
! The time it takes for a particle to displace from
! one location to another and the local particle from-to time
! for each PF timestep
real*8 mean_age, mean_comp, mean_mass, total_mass
! mean age and composition and mass of all particles in domain
real*8 local_flux, et_flux, water_vol, Zr, z1, z2, z3
! The local cell flux convergence
! The volumetric ET flux
! The availble water volume in a cell
! random variable
real*8 Xlow, Xhi, Ylow, Yhi, Zlow, Zhi
! Particles initial locations i.e., where they are injected
! into the domain.
integer, dimension(2):: xbd, ybd, zbd, vxbd, vybd, vzbd
! used to calculate flux at corners of domain
! xbd = (/ 1, nx /)
! vxbd = (/ 1, nx+1 /)
real*8, dimension(2):: fluxsign
! sign (+/-) of velocity at the each end of the domain that
! corresponds to flux into the domain
! fluxsign = (/ 1, -1 \)
real*8 velx, vely, velz
! float of an individual value of Vx, Vy, Vz
integer xi, yi, zi
! counters within xbd, etc and xfluxsign, etc
! density of water (M/L3), molecular diffusion (L2/T), fractionation
real*8 denh2o, moldiff, Efract !, ran1
! time history of ET, time (1,:) and mass for rain (2,:), snow (3,:),
! PET balance is water balance flux from PF accumulated over the domain at each
! timestep
real*8, allocatable::ET_age(:,:), ET_comp(:,:), water_balance(:,:), ET_mass(:)
real*8, allocatable::Surf_age(:,:), Surf_mass(:,:), Surf_comp(:,:)
real*8, allocatable::Subsurf_age(:,:), Subsurf_mass(:,:), Subsurf_comp(:,:)
real*8, allocatable::Well_age(:,:), Well_mass(:), Well_comp(:,:)
integer, allocatable:: ET_np(:), Surf_np(:), Subsurf_np(:), Well_np(:)
real*8 ET_dt, DR_Temp
! time interval for ET
! integer counters and operators.
! the first set are used for total run timing the latter for component timing
integer Total_time1, Total_time2, t1, t2, IO_time_read, IO_time_write, parallel_time
integer sort_time
!! integers for writing C or point based output
integer ipwrite, ibinpntswrite
! integers for writing gridded ET outputs
integer etwrite
!! IO control
!! ipwrite controls an ASCII, .3D particle file not recommended due to poor performance
!! this is left as a compiler option, currently disabled
!!!!!!!
!! icwrite controls VTK, binary grid based output where particle masses, concentrations,
!! ages are mapped to a grid and written every N timesteps. This is the most effiecient output
!! but loses some accuracy or flexbility becuase individual particle locations are aggregated
!! to the grid
!!!!!!!!
!! ibinpntswrite controls VTK, binary output of particle locations and attributes. This is much faster
!! than the .3D ASCII output but is still much slower than grid based output. It provides the most
!! information as particle locations are preserved
interface
SUBROUTINE vtk_write(time,x,conc_header,ixlim,iylim,izlim,icycle,n_constituents,Pnts,vtk_file)
real*8 :: time
REAL*8 :: x(:,:,:,:)
CHARACTER (LEN=20) :: conc_header(:)
INTEGER*4 :: ixlim
INTEGER*4 :: iylim
INTEGER*4 :: izlim
REAL*8 :: dx
REAL*8 :: dy
REAL*8 :: dz(izlim)
REAL*8 :: Pnts(:,:)
INTEGER :: icycle
INTEGER :: n_constituents
CHARACTER (LEN=200) :: vtk_file
end subroutine vtk_write
SUBROUTINE vtk_write_points(P,np_active, np,icycle,vtk_file,dx,dy,nx,ny,maxZ,DEM)
REAL*8 :: P(:,:)
INTEGER :: icycle
INTEGER*4 :: np_active
INTEGER*4 :: np
INTEGER :: n_constituents
REAL*8 :: dx
REAL*8 :: dy
INTEGER*4 :: nx
INTEGER*4 :: ny
REAL*8 :: maxZ
REAL*8 :: DEM(:,:)
CHARACTER (LEN=200) :: vtk_file
end subroutine vtk_write_points
end interface
!Set up timing
Total_time1 = 0
Total_time2 = 0
t1 = 0
t2 = 0
IO_time_read = 0
IO_time_write = 0
parallel_time = 0
sort_time = 0
call system_clock(Total_time1)
!--------------------------------------------------------------------
! (2) Read inputs, set up domain, write the log file, and
! initialize particles
!--------------------------------------------------------------------
! Note: The following file numbers refer to
!
! - #10: slimin.txt
! - #11: runname_log.txt
! - #12: runname_particle.3D (visualizes particles in VisIT)
! - #13: runname_endparticle.txt
call system_clock(T1)
! Count number of lines in slimin.txt to determine file version
! if nlines >= 31, then velfile option has been provided (even if false) and
! if nlines >= 32, then boolfile name has been provided (even if '')
nlines = 0
open (10,file='slimin.txt')
do
read (10,*,end=1010)
nlines = nlines + 1
end do
1010 close(10)
! open SLIM input .txt file
open (10,file='slimin.txt')
! read SLIM run name
read(10,*) runname
! read ParFlow run name
read(10,*) pname
! read DEM file name
read(10,*) DEMname
! open/create/write the output log.txt file. If doesn't exist, it's created.
open(11,file=trim(runname)//'_log.txt')
write(11,*) '### EcoSLIM Log File'
write(11,*)
write(11,*) 'run name:',trim(runname)
write(11,*)
write(11,*) 'ParFlow run name:',trim(pname)
write(11,*)
if (DEMname /= '') then
write(11,*) 'ParFlow DEM name:',trim(DEMname)
else
write(11,*) 'Not reading ParFlow DEM'
end if
write(11,*)
! read domain number of cells and number of particles to be injected
read(10,*) nx
read(10,*) ny
read(10,*) nz
! read in number of particles for IC (if np_ic = -1 then restart from a file)
read(10,*) np_ic
! read in the number of particles total
read(10,*) np
! check to make sure we don't assign more particles for IC than we have allocated
! in total
if (np_ic > np) then
write(11,*) ' warning NP_IC greater than NP total'
np = np_ic
end if
! write nx, ny, nz, and np in the log file
write(11,*) ' Grid information'
write(11,*) 'nx:',nx
write(11,*) 'ny:',ny
write(11,*) 'nz:',nz
write(11,*)
write(11,*) ' Particle IC Information'
write(11,*) 'np IC:',np_ic
if (np_ic == -1) &
write(11,*) 'Reading particle restart file:',trim(runname)//'_particle_restart.bin'
write(11,*) 'np:',np
! grid +1 variables
nnx=nx+1
nny=ny+1
nnz=nz+1
itemp=0
nCLMsoil = 10 ! number of CLM soil layers over the root zone
nzclm = 13+nCLMsoil ! CLM output is 13+nCLMsoil layers for different variables not domain NZ,
! e.g. 23 for 10 soil layers (default) and 17 for 4 soil layers (Noah soil
! layer setup)
! number of things written to C array, hard wired at 2 now for Testing
!n_constituents = 5
!n_constituents = 9
n_constituents = 13 ! additional 4 for Well
!allocate arrays
allocate(PInLoc(np,3))
allocate(Sx(nx,ny),Sy(nx,ny), DEM(nx,ny))
allocate(dz(nz), Zt(0:nz))
allocate(Vx(nnx,ny,nz), Vy(nx,nny,nz), Vz(nx,ny,nnz))
allocate(Saturation(nx,ny,nz), Porosity(nx,ny,nz),EvapTrans(nx,ny,nz), Ind(nx,ny,nz), BoundFlux(nx,ny,nz))
allocate(PSourceBool(nx,ny,nz))
allocate(CLMvars(nx,ny,nzclm))
allocate(C(n_constituents,nx,ny,nz))
!allocate(ET_grid(1,nx,ny,nz))
allocate(conc_header(n_constituents))
!Intialize everything to Zero
Vx = 0.0d0
Vy = 0.0d0
Vz = 0.0d0
Saturation = 0.0D0
Porosity = 0.0D0
EvapTrans = 0.0d0
BoundFlux = 0.0d0
C = 0.0d0
!ET_grid=0.0d0
! read dx, dy as scalars
read(10,*) dx
read(10,*) dy
! read dz as an array
read(10,*) dz(1:nz)
! read in (constant for now) ParFlow dt
read(10,*) pfdt
! read in parflow start and stop times
read(10,*) pft1
read(10,*) pft2
read(10,*) tout1
read(10,*) part_tstart
read(10,*) n_cycle
pfnt=n_cycle*(pft2-pft1+1)
if (tout1 == 0) then
outkk = pft1
tout1 = pft1
else
outkk = tout1
end if
! set ET DT to ParFlow one and allocate ET arrays accordingly
ET_dt = pfdt
allocate(ET_age(pfnt,5), ET_comp(pfnt,3), ET_mass(pfnt), ET_np(pfnt))
allocate(water_balance(pfnt,2))
ET_age = 0.0d0
ET_mass = 0.0d0
ET_comp = 0.0d0
ET_np = 0
water_balance = 0.0D0
allocate(Surf_age(pfnt,5), Surf_comp(pfnt,3), Surf_mass(pfnt,5), Surf_np(pfnt))
Surf_age = 0.0d0
Surf_mass = 0.0d0
Surf_comp = 0.0d0
Surf_np = 0
allocate(Subsurf_age(pfnt,5), Subsurf_comp(pfnt,3), Subsurf_mass(pfnt,5), Subsurf_np(pfnt))
Subsurf_age = 0.0d0
Subsurf_mass = 0.0d0
Subsurf_comp = 0.0d0
Subsurf_np = 0
allocate(Well_age(pfnt,5), Well_comp(pfnt,3), Well_mass(pfnt), Well_np(pfnt))
Well_age = 0.0d0
Well_mass = 0.0d0
Well_comp = 0.0d0
Well_np = 0
! clear out output particles
npout = 0
!! IO control, each value is a timestep interval, e.g. 1= every timestep, 2=every other, 0 = no writing
read(10,*) ipwrite ! controls an ASCII, .3D particle file not recommended due to poor performance
read(10,*) ibinpntswrite ! controls VTK, binary output of particle locations and attributes
read(10,*) etwrite ! controls ASCII ET output
read(10,*) icwrite ! controls VTK, binary grid based output where particle masses, concentrations,
! ages are mapped to a grid and written every N timesteps
! allocate and assign timesteps
allocate(Time_Next(pfnt))
do kk = 1, pfnt
Time_Next(kk) = float(kk+outkk-1)*pfdt
end do
Time_first = float(outkk-1)*pfdt
! read in velocity multiplier
read(10,*) V_mult
! do we read in clm evap trans?
read(10,*) clmtrans
! do we read in clm output file?
read(10,*) clmfile
! read in IC number of particles for flux
read(10,*) iflux_p_res
! read in density h2o
read(10,*) denh2o
! read in diffusivity
!moldiff = (1.15e-9)*3600.d0
read(10,*) moldiff
!saving Efract for a later time
!read(10,*) Efract
! fraction of dx/Vx
read(10,*) dtfrac
!wite out log file
write(11,*)
write(11,*) ' Grid Dimensions'
write(11,'("dx:",e12.5)') dx
write(11,'("dy:",e12.5)') dy
write(11,'("dz:",*(e12.5,", "))') dz(1:nz)
write(11,*)
write(11,*) 'Timestepping Information'
write(11,'("ParFlow delta-T, pfdt:",e12.5)') pfdt
write(11,'("ParFlow timesteps, pfnt:",i12)') pfnt
write(11,'("ParFlow start step, pft1:",i12)') pft1
write(11,'("ParFlow end step, pft2:",i12)') pft2
write(11,'("Output step start:",i12)') outkk
write(11,'("Time loops, cycles, n_cycle:",i12)') n_cycle
write(11,'("Total time steps:",i12)') pfnt
write(11,*)
write(11,*) 'V mult: ',V_mult,' for forward/backward particle tracking'
write(11,*) 'CLM Trans: ',clmtrans,' adds / removes particles based on LSM fluxes'
write(11,*)
write(11,*) 'Physical Constants'
write(11,*) 'denh2o: ',denh2o,' M/L^3'
write(11,*) 'Molecular Diffusivity: ',moldiff,' '
!write(11,*) 'Fractionation: ',Efract,' '
write(11,*)
write(11,*) 'Numerical Stability Information'
write(11,'("dtfrac: ",e12.5," fraction of dx/Vx")') dtfrac
read(10,*) nind !read in the number of indicators
read(10,*) Indname
write(11,*)
write(11,*) 'Indicator File'
write(11,*) nind, 'Indicators'
! allocate P, Sx, dz, Vx, Vy, Vz, Saturation, and Porosity arrays
if (nind<=0) then
allocate(P(np,17))
P(1:np,1:6) = 0.0 ! clear out all particle attributes
P(1:np,7:9) = 1.0 ! make all particles active to start with and original from 1 = GW/IC
P(1:np,10) = 0.0 ! no exit
P(1:np,11:14) = 0.0 ! Clear initial ID and location
P(1:np,15) = 0.0 ! Set initial start time to zero
P(1:np,16:17) = 0.0 ! Set initial lengths to zero
write(11,*) 'Zero indicators setting up regular P array'
else
allocate(P(np,(17+nind*2)))
P(1:np,1:6) = 0.0 ! clear out all particle attributes
P(1:np,7:9) = 1.0 ! make all particles active to start with and original from 1 = GW/IC
P(1:np,10) = 0.0 ! no exit
P(1:np,11:14) = 0.0 ! Clear initial ID and location
P(1:np,15) = 0.0 ! Set initial start time to zero
P(1:np,16:17) = 0.0 ! Set initial lengths to zero
P(1:np, 18:(17+nind*2))=0.0 !initizling indicator file times and lengths to zero
write(11,*) 'Adding columns for',nind, 'indicators'
!Read in the indictor file
end if
! Read in velfile and boolfile, if that line has been provided
if (nlines >= 31) then
read(10,*) velfile !bool of whether or not to add particles using velocity fluxes
write(11,*)
write(11,*) 'velfile: ',velfile,' whether or not to add particles from velocity fluxes'
if (nlines >= 32) then
read(10,*) Boolname
write(11,*)
if (Boolname /= '') then
boolfile = .TRUE.
write(11,*) 'Using boolean source files: ', Boolname
else
boolfile = .FALSE.
write(11,*) 'Not using boolean source file'
end if
end if
! If neither of these lines are provided, turn velfile and boolfile off
else
velfile = .FALSE.
boolfile = .FALSE.
write(11,*)
write(11,*) 'Did not find velfile line in slimin.txt. Setting velfile = False'
write(11,*)
write(11,*) 'Did not find PSourceBool line in slimin.txt. Setting boolfile = False'
end if
! end of SLIM input
close(10)
call system_clock(T2)
IO_time_read = IO_time_read + (T2-T1)
!! set up domain boundaries
Xmin = 0.0d0
Ymin = 0.0d0
Zmin = 0.0d0
Xmax = float(nx)*dx
Ymax = float(ny)*dy
Zmax = 0.0d0
do k = 1, nz
Zmax = Zmax + dz(k)
end do
DEM = 0.0d0
! read in DEM
if (DEMname /= '') then
fname = trim(adjustl(DEMname))
call pfb_read(DEM,fname,nx,ny,nztemp)
end if ! DEM
Ind = 1.0d0
! read in Indicator file
if (nind>0) then
if (Indname /= '') then
fname = trim(adjustl(Indname))
call pfb_read(Ind,fname,nx,ny,nz)
write(11,*) 'Read Indicator File:', fname
!write(11,*) 'IndREAD:', nx, ny, nztemp
else
write(11,*) 'WARNING: indicator flag >0 but no indicator file provided'
end if ! Ind
end if
!! hard wire DEM @RMM, to do, need to make this input
!do i = 1, nx
! do j = 1, ny
!DEM(i,j) = 0.0D0 + float(i)*dx*0.05
!end do
!end do
write(11,*)
write(11,*) '## Domain Info'
write(11,'("Xmin:",e12.5," Xmax:",e12.5)') Xmin, Xmax
write(11,'("Ymin:",e12.5," Ymax:",e12.5)') Ymin, Ymax
write(11,'("Zmin:",e12.5," Zmax:",e12.5)') Zmin, Zmax
!! DEM set to zero but will be read in as input
!! Set up grid locations for file output
npnts=nnx*nny*nnz
ncell=nx*ny*nz
allocate(Pnts(npnts,3))
Pnts=0
m=1
! Need the maximum height of the model and elevation locations
Z = 0.0d0
Zt(0) = 0.0D0
do ik = 1, nz
Z = Z + dz(ik)
Zt(ik) = Z
!print*, Z, dz(ik), Zt(ik), ik
end do
maxZ=Z
!! candidate loops for OpenMP
do k=1,nnz
do j=1,nny
do i=1,nnx
Pnts(m,1)=DBLE(i-1)*dx
Pnts(m,2)=DBLE(j-1)*dy
! This is a simple way of handling the maximum edges
if (i <= nx) then
ii=i
else
ii=nx
endif
if (j <= ny) then
jj=j
else
jj=ny
endif
! This step translates the DEM
! The specified initial heights in the pfb (z1) are ignored and the
! offset is computed based on the model thickness
Pnts(m,3)=(DEM(ii,jj)-maxZ)+Zt(k-1)
m=m+1
end do
end do
end do
! Read porosity values from ParFlow .pfb file
fname=trim(adjustl(pname))//'.out.porosity.pfb'
call pfb_read(Porosity,fname,nx,ny,nz)
! Read the in initial Saturation from ParFlow
kk = 0
pfkk=pft1-1
!print*, pfkk
write(filenum,'(i5.5)') pfkk
fname=trim(adjustl(pname))//'.out.satur.'//trim(adjustl(filenum))//'.pfb'
call pfb_read(Saturation,fname,nx,ny,nz)
! By default, add particles everywhere
PSourceBool = 1.0d0
! If we are limiting particles according to boolfile, read in Boolname to PSourceBool
if (boolfile) then
fname=trim(adjustl(Boolname))//'.'//trim(adjustl(filenum))//'.pfb'
call pfb_read(PSourceBool,fname,nx,ny,nz)
end if
! Intialize random seed
ir = -3333
!Initialize np_active2
np_active = 0
!Initialize Ltemp
Ltemp = 0.0
!! Define initial particles' locations and mass
!!
if (np_ic == 0) then
np_active = 0
pid = np_active
end if
if (np_ic > 0) then
np_active = 0
pid = 0
PInLoc=0.0d0
!call srand(333)
do i = 1, nx
do j = 1, ny
do k = 1, nz
if (np_active < np) then ! check if we have particles left
if (Saturation(i,j,k) > 0.0) then ! check if we are in the active domain
if (PSourceBool(i,j,k) == 1.0d0) then ! check if we should add particles here
do ij = 1, np_ic
np_active = np_active + 1
pid=pid + 1
ii = np_active
P(ii,11)=float(pid) !Saving a particle ID number
! assign X, Y, Z locations randomly to each cell
! assign X, Y, Z locations randomly to each cell
P(ii,1) = float(i-1)*dx +ran1(ir)*dx
PInLoc(ii,1) = P(ii,1)
P(ii,12)=P(ii,1) ! Saving the initial location
P(ii,2) = float(j-1)*dy +ran1(ir)*dy
PInLoc(ii,2) = P(ii,2)
P(ii,13)=P(ii,2)
P(ii,15) = part_tstart + 0.0 !setting insert time to the start time
Z = 0.0d0
do ik = 1, k
Z = Z + dz(ik)
end do
P(ii,3) = Z -dz(k)*ran1(ir)
PInLoc(ii,3) = P(ii,3)
P(ii,14)=P(ii,3) ! Saving the initial location
! assign mass of particle by the volume of the cells
! and the water contained in that cell
P(ii,6) = dx*dy*dz(k)*(Porosity(i,j,k) &
*Saturation(i,j,k))*denh2o*(1.0d0/float(np_ic))
P(ii,7) = 1.0d0
P(ii,8) = 1.0d0
! set up intial concentrations
C(1,i,j,k) = C(1,i,j,k) + P(ii,8)*P(ii,6) / &
(dx*dy*dz(k)*(Porosity(i,j,k) &
*Saturation(i,j,k)))
C(2,i,j,k) = C(2,i,j,k) + P(ii,8)*P(ii,4)*P(ii,6)
C(4,i,j,k) = C(4,i,j,k) + P(ii,8)*P(ii,7)*P(ii,6)
C(3,i,j,k) = C(3,i,j,k) + P(ii,8)*P(ii,6)
end do ! particles per cell
end if ! end-if for PSourceBool
end if ! active domain
else
write(11,*) ' **Warning IC input but no paricles left'
write(11,*) ' **Exiting code gracefully writing restart '
goto 9090
end if
end do ! i
end do ! j
end do ! k
!! if np_ic = -1 then we read a restart file
else if (np_ic == -1) then
write(11,*) 'Reading particle restart File:',trim(runname)//'_particle_restart.bin'
! read in full particle array as binary restart file, should name change?,
! potential overwrite confusion
open(116,file=trim(runname)//'_particle_restart.bin', FORM='unformatted', &
access='stream')
read(116) np_active
read(116) pid
if (np_active < np) then ! check if we have particles left
!do ii = 1, np_active
if (nind > 0) then
read(116) P(1:np_active,1:(nind*2+17))
else
read(116) P(1:np_active,1:17)
endif
!end do !11
close(116)
!pid = np_active
write(11,*) 'RESTART np_active :',np_active
write(11,*) 'RESTART pid:',pid
else
write(11,*) ' **Warning restart IC input but no paricles left'
write(11,*) ' **Exiting code *not* (over)writing restart '
close(116)
stop
end if
end if
!! Define initial particles' locations by surface water
!!
if (np_ic < -1) then
write(11,*) 'River IC activated'
np_active = 0
pid = np_active
PInLoc=0.0d0
!call srand(333)
ir = -3333
do i = 1, nx
do j = 1, ny
k = nz
if (np_active < np) then ! check if we have particles left
!if (saturation(i,j,k) >= 0.95d0) then
do ij = 1, abs(np_ic)
np_active = np_active + 1
pid = pid +1
ii = np_active
P(ii,11) = float(pid)
! assign X, Y, Z locations randomly to each cell
! assign X, Y, Z locations randomly to each cell
P(ii,1) = float(i-1)*dx +ran1(ir)*dx
PInLoc(ii,1) = P(ii,1)
P(ii,12)=P(ii,1) ! Saving the initial location
P(ii,2) = float(j-1)*dy +ran1(ir)*dy
PInLoc(ii,2) = P(ii,2)
P(ii,13)=P(ii,2) ! Saving the initial location
P(ii,15) = part_tstart + 0.0 !setting insert time to the start time
Z = 0.0d0
do ik = 1, k
Z = Z + dz(ik)
end do
P(ii,3) = Z !-dz(k)*ran1(ir)
PInLoc(ii,3) = P(ii,3)
P(ii,14)=P(ii,3) ! Saving the initial location
! assign mass of particle by the volume of the cells
! and the water contained in that cell
P(ii,6) = dx*dy*dz(k)*(Porosity(i,j,k) &
*Saturation(i,j,k))*denh2o*(1.0d0/float(np_ic))
P(ii,7) = 1.0d0
P(ii,8) = 1.0d0
! set up intial concentrations
C(1,i,j,k) = C(1,i,j,k) + P(ii,8)*P(ii,6) / &
(dx*dy*dz(k)*(Porosity(i,j,k) &
*Saturation(i,j,k)))
C(2,i,j,k) = C(2,i,j,k) + P(ii,8)*P(ii,4)*P(ii,6)
C(4,i,j,k) = C(4,i,j,k) + P(ii,8)*P(ii,7)*P(ii,6)
C(3,i,j,k) = C(3,i,j,k) + P(ii,8)*P(ii,6)
end do ! particles per cell
!end if !! saturated at top
else
write(11,*) ' **Warning IC input but no paricles left'
write(11,*) ' **Exiting code gracefully writing restart '
goto 9090
end if
end do ! i
end do ! j
end if !! river IC
! Write out intial concentrations
! normalize ages by mass
where (C(3,:,:,:)>0.0) C(2,:,:,:) = C(2,:,:,:) / C(3,:,:,:)
where (C(3,:,:,:)>0.0) C(4,:,:,:) = C(4,:,:,:) / C(3,:,:,:)
!! Set up output options for VTK grid output
!icwrite = 1
vtk_file=trim(runname)//'_cgrid'
conc_header(1) = 'Concentration'
conc_header(2) = 'Age'
conc_header(3) = 'Mass'
conc_header(4) = 'Comp'
conc_header(5) = 'Delta'
conc_header(6) = 'ET_Npart'
conc_header(7) = 'ET_Mass'
conc_header(8) = 'ET_Age'
conc_header(9) = 'ET_Comp'
if(icwrite > 0) &
call vtk_write(Time_first,C,conc_header,nx,ny,nz,0,n_constituents,Pnts,vtk_file)
!! clear out C arrays
C = 0.0D0
!! write timestep header
write(11,*)
write(11,*)
write(11,*) ' **** Transient Simulation Particle Accounting ****'
write(11,*) ' Timestep PFTimestep OutStep Time Mean_Age Mean_Comp Mean_Mass Total_Mass PrecipIn ETOut &
NP_PrecipIn NP_ETOut &
NP_WellOut NP_QOut NP_active_old NP_filtered'
flush(11)
!! open exited particle file and write header
!open(114,file=trim(runname)//'_exited_particles.txt')
open(114,file=trim(runname)//'_exited_particles.bin', FORM='unformatted', &
access='stream')
!write(114,*) 'Time X Y Z PTime Mass Comp ExitStatus'