Commits

Glenn Hammond  committed 68b9958 Merge

merge

  • Participants
  • Parent commits e3201bf, 2961f9e

Comments (0)

Files changed (268)

File docs/readiness/pflotran_1.in

 \begin{verbatim}
-:Description: 3D infiltration problem
+#Description: 3D infiltration problem
  
-: == debugging ================================================================
+# == debugging ================================================================
 DEBUG
-:MATVIEW_JACOBIAN
-:VECVIEW_RESIDUAL
-:VECVIEW_SOLUTION
+#MATVIEW_JACOBIAN
+#VECVIEW_RESIDUAL
+#VECVIEW_SOLUTION
 /
 
-: == mode =====================================================================
+# == mode =====================================================================
 MODE RICHARDS
 
-: == reference variables ======================================================
+# == reference variables ======================================================
 REFERENCE_POROSITY 0.25d0
 
-: == time stepping ============================================================
+# == time stepping ============================================================
 TIMESTEPPER
 TS_ACCELERATION 8
 /
 
-: == discretization ===========================================================
+# == discretization ===========================================================
 GRID
 TYPE structured
 NXYZ 20 20 80
 /
 /
 
-: == flow solvers =============================================================
+# == flow solvers =============================================================
 NEWTON_SOLVER FLOW
 PRECONDITIONER_MATRIX_TYPE AIJ
 RTOL 1.d-8
 ATOL 1.d-8
 STOL 1.d-30
 ITOL_UPDATE 1.d0
-:NO_INFINITY_NORM
-:NO_PRINT_CONVERGENCE
-:PRINT_DETAILED_CONVERGENCE
+#NO_INFINITY_NORM
+#NO_PRINT_CONVERGENCE
+#PRINT_DETAILED_CONVERGENCE
 /
 
 LINEAR_SOLVER FLOW
-:KSP_TYPE FGMRES
-:KSP_TYPE PREONLY
-:PC_TYPE LU
+#KSP_TYPE FGMRES
+#KSP_TYPE PREONLY
+#PC_TYPE LU
 /
 
-: == transport solvers ========================================================
+# == transport solvers ========================================================
 NEWTON_SOLVER TRANSPORT
 PRECONDITIONER_MATRIX_TYPE AIJ
 RTOL 1.d-12
 ATOL 1.d-12
 STOL 1.d-30
-:NO_INFINITY_NORM
-:NO_PRINT_CONVERGENCE
-:PRINT_DETAILED_CONVERGENCE
+#NO_INFINITY_NORM
+#NO_PRINT_CONVERGENCE
+#PRINT_DETAILED_CONVERGENCE
 /
 
 LINEAR_SOLVER TRANSPORT
-:KSP_TYPE PREONLY
-:PC_TYPE LU
+#KSP_TYPE PREONLY
+#PC_TYPE LU
 /
 
-: == fluid properties =========================================================
+# == fluid properties =========================================================
 FLUID_PROPERTY
 DIFFUSION_COEFFICIENT 1.d-9
 /
 
-: == material properties ======================================================
+# == material properties ======================================================
 MATERIAL_PROPERTY HD
 ID 1
 SATURATION_FUNCTION HD
 /
 /
 
-: == saturation / permeability functions ======================================
+# == saturation / permeability functions ======================================
 SATURATION_FUNCTION HD
 SATURATION_FUNCTION_TYPE VAN_GENUCHTEN
 RESIDUAL_SATURATION 0.115
 ALPHA 1.4295d-4
 /
 
-: == output ===================================================================
+# == output ===================================================================
 OUTPUT
-:PERIODIC TIMESTEP 1
+#PERIODIC TIMESTEP 1
 PERIODIC TIME .1 y
 FORMAT TECPLOT BLOCK
 /
 
-: == times ====================================================================
+# == times ====================================================================
 TIME
 FINAL_TIME 1. y
 INITIAL_TIMESTEP_SIZE 1. d
 MAXIMUM_TIMESTEP_SIZE 1. d
 /
 
-: == regions ==================================================================
+# == regions ==================================================================
 REGION all
 COORDINATES
 -1.d20 -1.d20 0.d0
 /
 /
 
-: == flow conditions ==============================
+# == flow conditions ==============================
 FLOW_CONDITION Inlet
 TYPE
 FLUX neumann
 /
-:FLUX 0.317098d-7 ! 1 m/y
+#FLUX 0.317098d-7 ! 1 m/y
 FLUX 1.5855d-9 ! 5 cm/y
-:FLUX file 200w_recharge_1951-2000_daily.dat
+#FLUX file 200w_recharge_1951-2000_daily.dat
 /
 
 FLOW_CONDITION Initial
 PRESSURE 101325.d0
 /
 
-: == couplers ====================================
+# == couplers ====================================
 BOUNDARY_CONDITION Inlet
 FLOW_CONDITION Inlet
 REGION Top
 REGION all
 /
 
-: == stratigraphy ================================
+# == stratigraphy ================================
 STRATA
 MATERIAL HD
 REGION HD

File docs/readiness/pflotran_2.in

-:Description: 3D infiltration problem
+#Description: 3D infiltration problem
  
-: == debugging ================================================================
+# == debugging ================================================================
 DEBUG
-:MATVIEW_JACOBIAN
-:VECVIEW_RESIDUAL
-:VECVIEW_SOLUTION
+#MATVIEW_JACOBIAN
+#VECVIEW_RESIDUAL
+#VECVIEW_SOLUTION
 /
 
-: == mode =====================================================================
+# == mode =====================================================================
 MODE RICHARDS
 
-: == chemistry ================================================================
+# == chemistry ================================================================
 CHEMISTRY
 PRIMARY_SPECIES
 Tracer
 /
 /
 
-: == reference variables ======================================================
+# == reference variables ======================================================
 REFERENCE_POROSITY 0.25d0
 
-: == time stepping ============================================================
+# == time stepping ============================================================
 TIMESTEPPER
 TS_ACCELERATION 8
 /
 
-: == discretization ===========================================================
+# == discretization ===========================================================
 GRID
 TYPE structured
 NXYZ 20 20 80
 /
 /
 
-: == flow solvers =============================================================
+# == flow solvers =============================================================
 NEWTON_SOLVER FLOW
 PRECONDITIONER_MATRIX_TYPE AIJ
 RTOL 1.d-8
 ATOL 1.d-8
 STOL 1.d-30
 ITOL_UPDATE 1.d0
-:NO_INFINITY_NORM
-:NO_PRINT_CONVERGENCE
-:PRINT_DETAILED_CONVERGENCE
+#NO_INFINITY_NORM
+#NO_PRINT_CONVERGENCE
+#PRINT_DETAILED_CONVERGENCE
 /
 
 LINEAR_SOLVER FLOW
-:KSP_TYPE FGMRES
-:KSP_TYPE PREONLY
-:PC_TYPE LU
+#KSP_TYPE FGMRES
+#KSP_TYPE PREONLY
+#PC_TYPE LU
 /
 
-: == transport solvers ========================================================
+# == transport solvers ========================================================
 NEWTON_SOLVER TRANSPORT
 PRECONDITIONER_MATRIX_TYPE AIJ
 RTOL 1.d-12
 ATOL 1.d-12
 STOL 1.d-30
-:NO_INFINITY_NORM
-:NO_PRINT_CONVERGENCE
-:PRINT_DETAILED_CONVERGENCE
+#NO_INFINITY_NORM
+#NO_PRINT_CONVERGENCE
+#PRINT_DETAILED_CONVERGENCE
 /
 
 LINEAR_SOLVER TRANSPORT
-:KSP_TYPE PREONLY
-:PC_TYPE LU
+#KSP_TYPE PREONLY
+#PC_TYPE LU
 /
 
-: == fluid properties =========================================================
+# == fluid properties =========================================================
 FLUID_PROPERTY
 DIFFUSION_COEFFICIENT 1.d-9
 /
 
-: == material properties ======================================================
+# == material properties ======================================================
 MATERIAL_PROPERTY HD
 ID 1
 SATURATION_FUNCTION HD
 /
 /
 
-: == saturation / permeability functions ======================================
+# == saturation / permeability functions ======================================
 SATURATION_FUNCTION HD
 SATURATION_FUNCTION_TYPE VAN_GENUCHTEN
 RESIDUAL_SATURATION 0.115
 ALPHA 1.4295d-4
 /
 
-: == output ===================================================================
+# == output ===================================================================
 OUTPUT
-:PERIODIC TIMESTEP 1
+#PERIODIC TIMESTEP 1
 PERIODIC TIME .1 y
 FORMAT TECPLOT BLOCK
 /
 
-: == times ====================================================================
+# == times ====================================================================
 TIME
 FINAL_TIME 1. y
 INITIAL_TIMESTEP_SIZE 1. d
 MAXIMUM_TIMESTEP_SIZE 1. d
 /
 
-: == regions ==================================================================
+# == regions ==================================================================
 REGION all
 COORDINATES
 -1.d20 -1.d20 0.d0
 /
 /
 
-: == flow conditions ==========================================================
+# == flow conditions ==========================================================
 FLOW_CONDITION Inlet
 TYPE
 FLUX neumann
 /
-:FLUX 0.317098d-7 ! 1 m/y
+#FLUX 0.317098d-7 ! 1 m/y
 FLUX 1.5855d-9 ! 5 cm/y
-:FLUX file 200w_recharge_1951-2000_daily.dat
+#FLUX file 200w_recharge_1951-2000_daily.dat
 /
 
 FLOW_CONDITION Initial
 RATE file src.dat ! 0.187 kg/s for 2 weeks (60,000 gallons)
 /
 
-: == transport conditions =====================================================
+# == transport conditions =====================================================
 TRANSPORT_CONDITION Inlet
 TYPE dirichlet
 CONSTRAINT_LIST
 /
 /
 
-: == transport constraints ====================================================
+# == transport constraints ====================================================
 CONSTRAINT Initial
 CONCENTRATIONS
 Tracer   1.e-10            F
 /
 /
 
-: == couplers =================================================================
+# == couplers =================================================================
 BOUNDARY_CONDITION Inlet
 FLOW_CONDITION Inlet
 TRANSPORT_CONDITION Inlet
 REGION all
 /
 
-: == stratigraphy =============================================================
+# == stratigraphy =============================================================
 STRATA
 MATERIAL HD
 REGION HD

File docs/readiness/pflotran_amr_1.in

 }
 
 TimerManager{
-   timer_list = "xfer::*::*", "FAC::*::*", "AMRUtilities::*::*", "apps::main::main", "RD2T::*::*", "LevelSolver::*::*"
+   timer_list = "xfer#:*::*", "FAC::*::*", "AMRUtilities::*::*", "apps::main::main", "RD2T::*::*", "LevelSolver::*::*"
 }

File docs/user_manual/inputfiles/ionex.in

-:Description: 3D 5-spot copper leaching problem
+#Description: 3D 5-spot copper leaching problem
  
-: == debugging ================================================================
-:DEBUG
-:MATVIEW_JACOBIAN
-:VECVIEW_RESIDUAL
-:VECVIEW_SOLUTION
-:/
+# == debugging ================================================================
+#DEBUG
+#MATVIEW_JACOBIAN
+#VECVIEW_RESIDUAL
+#VECVIEW_SOLUTION
+#/
 
-: == mode =====================================================================
-:MODE RICHARDS
+# == mode =====================================================================
+#MODE RICHARDS
 
-:UNIFORM_VELOCITY 0.317098d-7 0.d0 0.d0
+#UNIFORM_VELOCITY 0.317098d-7 0.d0 0.d0
 UNIFORM_VELOCITY 5.69333e-4 0.d0 0.d0
 
-:=========================== runtime ==========================================
-:CHECKPOINT 100
-:WALLCLOCK_STOP 11.75
+#=========================== runtime ==========================================
+#CHECKPOINT 100
+#WALLCLOCK_STOP 11.75
 
-: == chemistry ================================================================
+# == chemistry ================================================================
 CHEMISTRY
-:OPERATOR_SPLIT
+#OPERATOR_SPLIT
 PRIMARY_SPECIES
 Na+
-:K+
+#K+
 Ca++
 Mg++
 H+
 MgHCO3+
 MgCl+
 HCl(aq)
-:KCl(aq)
+#KCl(aq)
 NaCl(aq)
 NaOH(aq)
 /
 MINERALS
 Halite
 /
-:
+#
 MINERAL_KINETICS
 Halite
 RATE_CONSTANT 1.e-30
 SORPTION
 ION_EXCHANGE_RXN
 MINERAL Halite
-:CEC 68.676  ! mol/m^3
+#CEC 68.676  ! mol/m^3
 CEC 71.004
 CATIONS
 Na+   7.94328
 /
 /
 
-: == reference variables ======================================================
+# == reference variables ======================================================
 REFERENCE_POROSITY 0.61d0
 
-: == time stepping ============================================================
+# == time stepping ============================================================
 TIMESTEPPER
 TS_ACCELERATION 8
 MAX_STEPS 100000
-:MAX_STEPS 1
+#MAX_STEPS 1
 /
 
-: == discretization ===========================================================
+# == discretization ===========================================================
 GRID
 TYPE structured 
 NXYZ 250 1 1
 /
 /
 
-: == flow solvers =============================================================
+# == flow solvers =============================================================
 NEWTON_SOLVER FLOW
 PRECONDITIONER_MATRIX_TYPE AIJ
 RTOL 1.d-8
 ATOL 1.d-8
 STOL 1.d-30
 ITOL_UPDATE 1.d0
-:NO_INFINITY_NORM
-:NO_PRINT_CONVERGENCE
-:PRINT_DETAILED_CONVERGENCE
+#NO_INFINITY_NORM
+#NO_PRINT_CONVERGENCE
+#PRINT_DETAILED_CONVERGENCE
 /
 
 LINEAR_SOLVER FLOW
-:KSP_TYPE PREONLY
-:PC_TYPE LU
-:KSP_TYPE FGMRES !samrai
-:PC_TYPE SHELL !samrai
+#KSP_TYPE PREONLY
+#PC_TYPE LU
+#KSP_TYPE FGMRES !samrai
+#PC_TYPE SHELL !samrai
 /
 
-: == transport solvers ========================================================
+# == transport solvers ========================================================
 NEWTON_SOLVER TRANSPORT
 PRECONDITIONER_MATRIX_TYPE AIJ
 RTOL 1.d-8
 ATOL 1.d-8
 STOL 1.d-30
-:NO_INFINITY_NORM
-:NO_PRINT_CONVERGENCE
-:PRINT_DETAILED_CONVERGENCE
+#NO_INFINITY_NORM
+#NO_PRINT_CONVERGENCE
+#PRINT_DETAILED_CONVERGENCE
 /
 
 LINEAR_SOLVER TRANSPORT
-:PC_TYPE LU
-:KSP_TYPE PREONLY
-:KSP_TYPE FGMRES ! samrai
-:PC_TYPE SHELL !samrai
+#PC_TYPE LU
+#KSP_TYPE PREONLY
+#KSP_TYPE FGMRES ! samrai
+#PC_TYPE SHELL !samrai
 /
 
-: == fluid properties =========================================================
+# == fluid properties =========================================================
 FLUID_PROPERTY
 DIFFUSION_COEFFICIENT 1.d-9
-:DIFFUSION_COEFFICIENT 9.33333e-7
+#DIFFUSION_COEFFICIENT 9.33333e-7
 /
 
-: == material properties ======================================================
+# == material properties ======================================================
 MATERIAL_PROPERTY HD
 ID 1
 SATURATION_FUNCTION default
 POROSITY 0.61
 TORTUOSITY 1.0
-:LONGITUDINAL_DISPERSIVITY 0.001
+#LONGITUDINAL_DISPERSIVITY 0.001
 PERMEABILITY
 PERM_ISO 5.43d-13
 /
 /
 
-: == saturation / permeability functions ======================================
+# == saturation / permeability functions ======================================
 SATURATION_FUNCTION HD
 SATURATION_FUNCTION_TYPE VAN_GENUCHTEN
 RESIDUAL_SATURATION 0.115
 ALPHA 1.9401d-4
 /
 
-:=========================== saturation functions =============================
+#=========================== saturation functions =============================
 SATURATION_FUNCTION default
 /
 
-: == output ===================================================================
+# == output ===================================================================
 OUTPUT
 TIMES s 10307.1 33498.2 41228.6
 PERIODIC_OBSERVATION TIMESTEP 1
-:PERIODIC TIMESTEP 1
-:PERIODIC TIME 0.04 y
+#PERIODIC TIMESTEP 1
+#PERIODIC TIME 0.04 y
 SCREEN PERIODIC 10
-:FORMAT HDF5
+#FORMAT HDF5
 FORMAT TECPLOT POINT
 VELOCITIES
 /
 
-: == times ====================================================================
+# == times ====================================================================
 TIME
 FINAL_TIME 41228.6 s
 INITIAL_TIMESTEP_SIZE 1. s
 MAXIMUM_TIMESTEP_SIZE 20. s at 33600 s
 /
 
-: == regions ==================================================================
+# == regions ==================================================================
 REGION all
 COORDINATES
 0.d0 0.d0 0.d0
 REGION east
 /
 
-: == flow conditions ==========================================================
+# == flow conditions ==========================================================
 skip
 FLOW_CONDITION west
 TYPE
 FLUX neumann
 /
 FLUX 0.317098d-7 ! 1 m/y
-:FLUX 1.5855d-9 ! 5 cm/y
-:FLUX file 200w_recharge_1951-2000_daily.dat
+#FLUX 1.5855d-9 ! 5 cm/y
+#FLUX file 200w_recharge_1951-2000_daily.dat
 /
 noskip
 
 PRESSURE 101325.d0
 END
 
-: == transport conditions =====================================================
+# == transport conditions =====================================================
 TRANSPORT_CONDITION Initial
 TYPE dirichlet
 CONSTRAINT_LIST
 /
 /
 
-: == couplers =================================================================
+# == couplers =================================================================
 
 INITIAL_CONDITION Initial
-:FLOW_CONDITION Initial
+#FLOW_CONDITION Initial
 TRANSPORT_CONDITION Initial
 REGION all
 /
 
 BOUNDARY_CONDITION
-:FLOW_CONDITION west
+#FLOW_CONDITION west
 TRANSPORT_CONDITION west
 REGION west
 END
 
 BOUNDARY_CONDITION
-:FLOW_CONDITION east
+#FLOW_CONDITION east
 TRANSPORT_CONDITION east
 REGION east
 END
 
-: == stratigraphy =============================================================
+# == stratigraphy =============================================================
 STRATA
 MATERIAL HD
 REGION all
 /
 
-: == transport constraints ====================================================
+# == transport constraints ====================================================
 CONSTRAINT Initial
 CONCENTRATIONS
 Na+           4.65d-3  T
-:K+            2.d-4    T
+#K+            2.d-4    T
 Ca++          5.2d-3   T
 Mg++          4.55e-3  T
 H+            4.6     pH
 CONSTRAINT Inlet1
 CONCENTRATIONS
 Na+           1.d-16  T
-:K+            1.d-10  T
+#K+            1.d-10  T
 Ca++          5.3d-3  T
 Mg++          1.e-16  T
 H+            4.6    pH
 CONSTRAINT Inlet2
 CONCENTRATIONS
 Na+           4.6d-3  T
-:K+            1.d-10  T
+#K+            1.d-10  T
 Ca++          1.d-16  T
 Mg++          2.4e-3  T
 H+            4.6    pH
 CONSTRAINT Inlet3
 CONCENTRATIONS
 Na+           4.65d-3 T
-:K+            1.d-10  T
+#K+            1.d-10  T
 Ca++          5.2d-3  T
 Mg++          4.55e-3 T
 H+            4.6    pH

File docs/user_manual/inputfiles/sx115/sx115.in

-:Description: 1D test problem for tracer transport
+#Description: 1D test problem for tracer transport
 
-:=========================== flow mode ========================================
+#=========================== flow mode ========================================
 MODE RICHARDS
 
-:=========================== chemistry ========================================
+#=========================== chemistry ========================================
 CHEMISTRY
   PRIMARY_SPECIES
     Tracer
   /
 END
 
-:=========================== runtime ==========================================
+#=========================== runtime ==========================================
 CHECKPOINT 100000
-:RESTART restart.chk 0.d0
-:OVERWRITE_RESTART_TRANSPORT
-:WALLCLOCK_STOP 11.75
+#RESTART restart.chk 0.d0
+#OVERWRITE_RESTART_TRANSPORT
+#WALLCLOCK_STOP 11.75
 
-:=========================== solver options ===================================
+#=========================== solver options ===================================
 TIMESTEPPER
-  :MAX_STEPS -1
+  #MAX_STEPS -1
   TS_ACCELERATION 8
   INITIALIZE_TO_STEADY_STATE 1.d0
 END
 
 NEWTON_SOLVER FLOW
-  :RTOL 1.d-12
+  #RTOL 1.d-12
   RTOL 1.d-20
-  :ATOL 1.d-12
-  :STOL 1.e-60
-  :DTOL 1.e4
+  #ATOL 1.d-12
+  #STOL 1.e-60
+  #DTOL 1.e4
   ITOL_UPDATE 1.d0
-  :NO_INFINITY_NORM
-  ::NO_PRINT_CONVERGENCE
-  :PRINT_DETAILED_CONVERGENCE
+  #NO_INFINITY_NORM
+  #:NO_PRINT_CONVERGENCE
+  #PRINT_DETAILED_CONVERGENCE
 END
 
 LINEAR_SOLVER FLOW
-  :KSP_TYPE GMRES
-  :PC_TYPE NONE
-  :KSP_TYPE PREONLY
-  :PC_TYPE LU
-  :SOLVER GMRES
+  #KSP_TYPE GMRES
+  #PC_TYPE NONE
+  #KSP_TYPE PREONLY
+  #PC_TYPE LU
+  #SOLVER GMRES
 END
 
 NEWTON_SOLVER TRANSPORT
   ATOL 1.d-12
   STOL 1.e-60
   DTOL 1.e4
-  :ITOL_UPDATE 1.d-4
-  :NO_INFINITY_NORM
-  :NO_PRINT_CONVERGENCE
-  :PRINT_DETAILED_CONVERGENCE
+  #ITOL_UPDATE 1.d-4
+  #NO_INFINITY_NORM
+  #NO_PRINT_CONVERGENCE
+  #PRINT_DETAILED_CONVERGENCE
 END
 
 LINEAR_SOLVER TRANSPORT
-  :KSP_TYPE GMRES
-  :PC_TYPE NONE
-  :KSP_TYPE PREONLY
-  :PC_TYPE LU
-  :SOLVER GMRES
+  #KSP_TYPE GMRES
+  #PC_TYPE NONE
+  #KSP_TYPE PREONLY
+  #PC_TYPE LU
+  #SOLVER GMRES
 END
 
-:=========================== discretization ===================================
+#=========================== discretization ===================================
 GRID
   TYPE structured
   ORIGIN 0.d0 0.d0 0.d0
   /
 END
 
-:=========================== fluid properties =================================
+#=========================== fluid properties =================================
 FLUID_PROPERTY 
   DIFFUSION_COEFFICIENT 1.d-9
 END
 
-:=========================== material properties ==============================
+#=========================== material properties ==============================
 MATERIAL_PROPERTY Backfill
   ID 1
   POROSITY 0.2585d0
   /
 END
 
-:=========================== saturation functions =============================
+#=========================== saturation functions =============================
 SATURATION_FUNCTION BF
   SATURATION_FUNCTION_TYPE VAN_GENUCHTEN
   PERMEABILITY_FUNCTION_TYPE MUALEM
   POWER 1.d0
 END
 
-:=========================== output options ===================================
+#=========================== output options ===================================
 OUTPUT
-  :SCREEN PERIODIC 10
-  :MASS_BALANCE
-  :TIMES y 0.5 1.0 2.0 5.0 10.0
+  #SCREEN PERIODIC 10
+  #MASS_BALANCE
+  #TIMES y 0.5 1.0 2.0 5.0 10.0
   TIMES y  100. 250. 500. 750. 1000.
   FORMAT TECPLOT POINT
   VELOCITIES
 END
 
-:=========================== times ============================================
+#=========================== times ============================================
 TIME
   FINAL_TIME 1000.d0 y
   INITIAL_TIMESTEP_SIZE 1.d-6 y
   MAXIMUM_TIMESTEP_SIZE 1.d-0 y
 END
 
-:=========================== regions ==========================================
+#=========================== regions ==========================================
 REGION all
   COORDINATES
     0.d0 0.d0 0.d0
   /
 END
 
-:=============boundaries=================
+#=============boundaries=================
 
 REGION west
   FACE WEST
   /
 END
 
-:=========================== flow conditions ==================================
+#=========================== flow conditions ==================================
 FLOW_CONDITION initial
   TYPE
     PRESSURE hydrostatic
   TYPE
     FLUX neumann
   /
-  :FLUX 2.53678e-9 ! 0.08 m/yr
-  :FLUX 2.53678e-10 ! 8 mm/yr
+  #FLUX 2.53678e-9 ! 0.08 m/yr
+  #FLUX 2.53678e-10 ! 8 mm/yr
   FLUX 0.d0
 END
 
   /
   DATUM 0.d0 0.d0 6.d0
   PRESSURE 101325.d0 
-  :PRESSURE 1.4e5 ! 200 meter piezometric head (200*997.32*9.81)
+  #PRESSURE 1.4e5 ! 200 meter piezometric head (200*997.32*9.81)
 END
 
 FLOW_CONDITION source
   TYPE
     RATE mass_rate
   /
-  :RATE 8.5d-4 ! kg/s
+  #RATE 8.5d-4 ! kg/s
   RATE file src.dat ! 8.4e-4 kg/s for 2 weeks (60,000 gallons)
 END
 
-:=========================== transport conditions =============================
+#=========================== transport conditions =============================
 TRANSPORT_CONDITION initial
   TYPE zero_gradient
   CONSTRAINT_LIST
   /
 /
 
-:=========================== condition couplers ===============================
-: initial condition
+#=========================== condition couplers ===============================
+# initial condition
 INITIAL_CONDITION
   FLOW_CONDITION initial
   TRANSPORT_CONDITION initial
   REGION all
 END
 
-: top boundary condition
+# top boundary condition
 BOUNDARY_CONDITION top
-  :FLOW_CONDITION initial
+  #FLOW_CONDITION initial
   FLOW_CONDITION infiltration
   TRANSPORT_CONDITION initial
   REGION top
 END
 
-: bottom boundary condition
+# bottom boundary condition
 BOUNDARY_CONDITION bottom
   FLOW_CONDITION water_table
   TRANSPORT_CONDITION initial
   REGION bottom
 END
 
-: well source/sink
+# well source/sink
 skip
 SOURCE_SINK well
   FLOW_CONDITION source
 END
 noskip
 
-: infiltration source/sink
+# infiltration source/sink
 skip
 SOURCE_SINK infil
   FLOW_CONDITION infiltration
 END
 noskip
 
-:=========================== stratigraphy couplers ============================
+#=========================== stratigraphy couplers ============================
 STRATA
   REGION MRG
   MATERIAL Middle-Ringold-Gravel
 END
 noskip
 
-:=========================== constraints ======================================
+#=========================== constraints ======================================
 
 CONSTRAINT well
   CONCENTRATIONS

File example_problems/100_100_100/calcite/pflotran.in

-:Description: 3D test problem for diffusion of tracer and reaction of calcite in a cubic domain
+#Description: 3D test problem for diffusion of tracer and reaction of calcite in a cubic domain
 
-:=========================== chemistry ========================================
+#=========================== chemistry ========================================
 CHEMISTRY
 PRIMARY_SPECIES
 Ca++
 RATE_CONSTANT 1.e-8 
 /
 /
-:DATABASE /Users/lichtner/projects/parallel/repository/pflotran/database/hanford.dat
-:DATABASE /Users/lichtner/flotran/database/hanford.dat
+#DATABASE /Users/lichtner/projects/parallel/repository/pflotran/database/hanford.dat
+#DATABASE /Users/lichtner/flotran/database/hanford.dat
 DATABASE ../../../database/hanford.dat
 LOG_FORMULATION
 ACTIVITY_COEFFICIENTS
 MOLAL
 /
-:=========================== solver options ===================================
+#=========================== solver options ===================================
 TIMESTEPPER
 TS_ACCELERATION 8
 /
 
 NEWTON_SOLVER TRANSPORT
-:RTOL 1.d-4
-:ATOL 1.d-4
-:STOL 1.e-60
-:DTOL 1.e4
-:ITOL_UPDATE 1.d-4
+#RTOL 1.d-4
+#ATOL 1.d-4
+#STOL 1.e-60
+#DTOL 1.e4
+#ITOL_UPDATE 1.d-4
 NO_INFINITY_NORM
-:NO_PRINT_CONVERGENCE
-:PRINT_DETAILED_CONVERGENCE
+#NO_PRINT_CONVERGENCE
+#PRINT_DETAILED_CONVERGENCE
 /
 
 LINEAR_SOLVER TRANSPORT
 KSP_TYPE GMRES
-:PC_TYPE NONE
-:KSP_TYPE PREONLY
-:PC_TYPE LU
-:SOLVER GMRES
+#PC_TYPE NONE
+#KSP_TYPE PREONLY
+#PC_TYPE LU
+#SOLVER GMRES
 /
 
-:=========================== discretization ===================================
+#=========================== discretization ===================================
 GRID
 TYPE structured
 ORIGIN 0.d0 0.d0 0.d0
 /
 END
 
-:=========================== fluid properties =================================
+#=========================== fluid properties =================================
 FLUID_PROPERTY 
 DIFFUSION_COEFFICIENT 1.d-9
 /
 
-:=========================== material properties ==============================
+#=========================== material properties ==============================
 MATERIAL_PROPERTY soil1
 ID 1
 POROSITY 0.25d0
 /
 /
 
-:=========================== saturation functions =============================
+#=========================== saturation functions =============================
 SATURATION_FUNCTION default
 /
 
-:=========================== output options ===================================
+#=========================== output options ===================================
 OUTPUT
 PERIODIC TIME 1.d0 y
 FORMAT TECPLOT BLOCK
 /
 
-:=========================== times ============================================
+#=========================== times ============================================
 TIME
 FINAL_TIME 10.d0 y
 INITIAL_TIMESTEP_SIZE 1.d-6 y
 MAXIMUM_TIMESTEP_SIZE 1.d0 y
 /
 
-:=========================== regions ==========================================
+#=========================== regions ==========================================
 REGION all
 COORDINATES
 0.d0 0.d0 0.d0
 /
 END
 
-:=========================== transport conditions =============================
+#=========================== transport conditions =============================
 TRANSPORT_CONDITION initial
 TYPE zero_gradient
 CONSTRAINT_LIST
 /
 /
 
-:=========================== constraints ======================================
+#=========================== constraints ======================================
 CONSTRAINT pulse
 CONCENTRATIONS
 Ca++   1.e-8 T
 /
 /
 
-:=========================== condition couplers ===============================
-: initial condition
+#=========================== condition couplers ===============================
+# initial condition
 INITIAL_CONDITION
 TRANSPORT_CONDITION initial
 REGION all
 END
 
-: initial pulse condition
+# initial pulse condition
 INITIAL_CONDITION
 TRANSPORT_CONDITION initial_pulse
 REGION center
 END
 
-: west boundary condition
+# west boundary condition
 BOUNDARY_CONDITION west
 TRANSPORT_CONDITION initial
 REGION west
 END
 
-: east boundary condition
+# east boundary condition
 BOUNDARY_CONDITION east
 TRANSPORT_CONDITION initial
 REGION east
 END
 
-: north boundary condition
+# north boundary condition
 BOUNDARY_CONDITION north
 TRANSPORT_CONDITION initial
 REGION north
 END
 
-: south boundary condition
+# south boundary condition
 BOUNDARY_CONDITION south
 TRANSPORT_CONDITION initial
 REGION south
 END
 
-: top boundary condition
+# top boundary condition
 BOUNDARY_CONDITION top
 TRANSPORT_CONDITION initial
 REGION top
 END
 
-: bottom boundary condition
+# bottom boundary condition
 BOUNDARY_CONDITION bottom
 TRANSPORT_CONDITION initial
 REGION bottom
 END
 
-:=========================== stratigraphy couplers ============================
+#=========================== stratigraphy couplers ============================
 STRATA
 REGION top_layer
 MATERIAL soil1

File example_problems/100_100_100/checker/pflotran.in

-:Description: 1D test problem for tracer transport
+#Description: 1D test problem for tracer transport
 
-:=========================== flow mode ========================================
+#=========================== flow mode ========================================
 MODE RICHARDS
 
-:=========================== chemistry ========================================
+#=========================== chemistry ========================================
 skip
 CHEMISTRY
 PRIMARY_SPECIES
 /
 noskip
 
-:=========================== solver options ===================================
+#=========================== solver options ===================================
 TIMESTEPPER
 TS_ACCELERATION 8
 /
 
 NEWTON_SOLVER FLOW
-:RTOL 1.d-4
-:ATOL 1.d-4
-:STOL 1.e-60
-:DTOL 1.e4
+#RTOL 1.d-4
+#ATOL 1.d-4
+#STOL 1.e-60
+#DTOL 1.e4
 ITOL_UPDATE 1.d0
-:NO_INFINITY_NORM
-::NO_PRINT_CONVERGENCE
-:PRINT_DETAILED_CONVERGENCE
+#NO_INFINITY_NORM
+#:NO_PRINT_CONVERGENCE
+#PRINT_DETAILED_CONVERGENCE
 /
 
 LINEAR_SOLVER FLOW
 KSP_TYPE GMRES
 PC_TYPE NONE
-:KSP_TYPE PREONLY
-:PC_TYPE LU
-:SOLVER GMRES
+#KSP_TYPE PREONLY
+#PC_TYPE LU
+#SOLVER GMRES
 /
 
 NEWTON_SOLVER TRANSPORT
-:RTOL 1.d-4
-:ATOL 1.d-4
-:STOL 1.e-60
-:DTOL 1.e4
-:ITOL_UPDATE 1.d-4
+#RTOL 1.d-4
+#ATOL 1.d-4
+#STOL 1.e-60
+#DTOL 1.e4
+#ITOL_UPDATE 1.d-4
 NO_INFINITY_NORM
-:NO_PRINT_CONVERGENCE
-:PRINT_DETAILED_CONVERGENCE
+#NO_PRINT_CONVERGENCE
+#PRINT_DETAILED_CONVERGENCE
 /
 
 LINEAR_SOLVER TRANSPORT
 KSP_TYPE GMRES
 PC_TYPE NONE
-:KSP_TYPE PREONLY
-:PC_TYPE LU
-:SOLVER GMRES
+#KSP_TYPE PREONLY
+#PC_TYPE LU
+#SOLVER GMRES
 /
 
-:=========================== discretization ===================================
+#=========================== discretization ===================================
 GRID
 TYPE structured
 ORIGIN 0.d0 0.d0 0.d0
-:NXYZ 8 8 8
+#NXYZ 8 8 8
 NXYZ 32 32 32
 BOUNDS
 0.d0 100.d0
 /
 END
 
-:=========================== fluid properties =================================
+#=========================== fluid properties =================================
 FLUID_PROPERTY 
 DIFFUSION_COEFFICIENT 1.d-9
 /
 
-:=========================== material properties ==============================
+#=========================== material properties ==============================
 MATERIAL_PROPERTY soil1
 ID 1
 POROSITY 0.25d0
 ID 2
 POROSITY 0.25d0
 TORTUOSITY 1.d0
-:SATURATION_FUNCTION sf2
+#SATURATION_FUNCTION sf2
 SATURATION_FUNCTION sf1
 PERMEABILITY
 PERM_X 1.d-13
 /
 /
 
-:=========================== saturation functions =============================
+#=========================== saturation functions =============================
 SATURATION_FUNCTION sf1
 SATURATION_FUNCTION_TYPE VAN_GENUCHTEN
 RESIDUAL_SATURATION 0.2d0
-:LAMBDA 0.25d0
+#LAMBDA 0.25d0
 LAMBDA 0.75d0
 ALPHA 1.d-4
 MAX_CAPILLARY_PRESSURE 1.d8
 POWER 1.d0
 /
 
-:=========================== output options ===================================
+#=========================== output options ===================================
 OUTPUT
-:MASS_BALANCE
-:TIMES y 0.25d0 0.5d0 0.75d0
+#MASS_BALANCE
+#TIMES y 0.25d0 0.5d0 0.75d0
 PERIODIC TIME 0.5 y
 FORMAT TECPLOT BLOCK
 VELOCITIES
 /
 
-:=========================== times ============================================
+#=========================== times ============================================
 TIME
 FINAL_TIME 10.d0 y
 INITIAL_TIMESTEP_SIZE 1.d-6 y
 MAXIMUM_TIMESTEP_SIZE 1.d-1 y
 /
 
-:=========================== regions ==========================================
+#=========================== regions ==========================================
 REGION all
 COORDINATES
 0.d0 0.d0 0.d0
 /
 END
 
-: Layer 1
+# Layer 1
 REGION region_1_1_1
 COORDINATES
 0.d0 0.d0 0.d0
 /
 END
 
-: Layer 2
+# Layer 2
 REGION region_1_1_2
 COORDINATES
 0.d0 0.d0 25.d0
 /
 END
 
-: Layer 3
+# Layer 3
 REGION region_1_1_3
 COORDINATES
 0.d0 0.d0 50.d0
 /
 END
 
-: Layer 4
+# Layer 4
 REGION region_1_1_4
 COORDINATES
 0.d0 0.d0 75.d0
 /
 END
 
-:=========================== flow conditions ==================================
+#=========================== flow conditions ==================================
 FLOW_CONDITION initial
 TYPE
 PRESSURE hydrostatic
 /
 noskip
 
-:=========================== transport conditions =============================
+#=========================== transport conditions =============================
 skip
 TRANSPORT_CONDITION initial
 TYPE zero_gradient
 /
 /
 
-:=========================== constraints ======================================
+#=========================== constraints ======================================
 CONSTRAINT well
 CONCENTRATIONS
 Tracer 1.d0 T
 END
 noskip
 
-:=========================== condition couplers ===============================
-: initial condition
+#=========================== condition couplers ===============================
+# initial condition
 INITIAL_CONDITION
 FLOW_CONDITION initial
-:TRANSPORT_CONDITION initial
+#TRANSPORT_CONDITION initial
 REGION all
 END
 
 skip
-: west boundary condition
+# west boundary condition
 BOUNDARY_CONDITION west
 FLOW_CONDITION initial
 TRANSPORT_CONDITION initial
 REGION west
 END
 
-: east boundary condition
+# east boundary condition
 BOUNDARY_CONDITION east
 FLOW_CONDITION initial
 TRANSPORT_CONDITION initial
 REGION east
 END
 
-: north boundary condition
+# north boundary condition
 BOUNDARY_CONDITION north
 FLOW_CONDITION initial
 TRANSPORT_CONDITION initial
 REGION north
 END
 
-: south boundary condition
+# south boundary condition
 BOUNDARY_CONDITION south
 FLOW_CONDITION initial
 TRANSPORT_CONDITION initial
 END
 noskip
 
-: top boundary condition
+# top boundary condition
 BOUNDARY_CONDITION top
 FLOW_CONDITION recharge
-:TRANSPORT_CONDITION initial
+#TRANSPORT_CONDITION initial
 REGION top
 END
 
-: bottom boundary condition
+# bottom boundary condition
 BOUNDARY_CONDITION bottom
-:FLOW_CONDITION initial
+#FLOW_CONDITION initial
 FLOW_CONDITION variable
-:FLOW_CONDITION atmospheric
-:TRANSPORT_CONDITION initial
+#FLOW_CONDITION atmospheric
+#TRANSPORT_CONDITION initial
 REGION bottom
 END
 
 skip
-: well source/sink
+# well source/sink
 SOURCE_SINK well
 FLOW_CONDITION source
 TRANSPORT_CONDITION source
 END
 noskip
 
-:=========================== stratigraphy couplers ============================
-: Layer 1
+#=========================== stratigraphy couplers ============================
+# Layer 1
 STRATA
 REGION region_1_1_1
 MATERIAL soil1
 MATERIAL soil1
 END
 
-: Layer 2
+# Layer 2
 STRATA
 REGION region_1_1_2
 MATERIAL soil2
 MATERIAL soil2
 END
 
-: Layer 3
+# Layer 3
 STRATA
 REGION region_1_1_3
 MATERIAL soil1
 MATERIAL soil1
 END
 
-: Layer 4
+# Layer 4
 STRATA
 REGION region_1_1_4
 MATERIAL soil2

File example_problems/100_100_100/diffusion/pflotran.in

-:Description: 1D test problem for diffusion of tracer in a cubic domain
+#Description: 1D test problem for diffusion of tracer in a cubic domain
 
-:=========================== chemistry ========================================
+#=========================== chemistry ========================================
 CHEMISTRY
 PRIMARY_SPECIES
 Tracer
 /
 /
 
-:=========================== solver options ===================================
+#=========================== solver options ===================================
 TIMESTEPPER
 TS_ACCELERATION 8
 /
 
 NEWTON_SOLVER TRANSPORT
-:RTOL 1.d-4
-:ATOL 1.d-4
-:STOL 1.e-60
-:DTOL 1.e4
-:ITOL_UPDATE 1.d-4
+#RTOL 1.d-4
+#ATOL 1.d-4
+#STOL 1.e-60
+#DTOL 1.e4
+#ITOL_UPDATE 1.d-4
 NO_INFINITY_NORM
-:NO_PRINT_CONVERGENCE
-:PRINT_DETAILED_CONVERGENCE
+#NO_PRINT_CONVERGENCE
+#PRINT_DETAILED_CONVERGENCE
 /
 
 LINEAR_SOLVER TRANSPORT
 KSP_TYPE GMRES
 PC_TYPE NONE
-:KSP_TYPE PREONLY
-:PC_TYPE LU
-:SOLVER GMRES
+#KSP_TYPE PREONLY
+#PC_TYPE LU
+#SOLVER GMRES
 /
 
-:=========================== discretization ===================================
+#=========================== discretization ===================================
 GRID
 TYPE structured
 ORIGIN 0.d0 0.d0 0.d0
 /
 END
 
-:=========================== fluid properties =================================
+#=========================== fluid properties =================================
 FLUID_PROPERTY 
 DIFFUSION_COEFFICIENT 1.d-9
 /
 
-:=========================== material properties ==============================
+#=========================== material properties ==============================
 MATERIAL_PROPERTY soil1
 ID 1
 POROSITY 0.25d0
 /
 /
 
-:=========================== saturation functions =============================
+#=========================== saturation functions =============================
 SATURATION_FUNCTION default
 /
 
-:=========================== output options ===================================
+#=========================== output options ===================================
 OUTPUT
 PERIODIC TIME 1.d0 y
 FORMAT TECPLOT BLOCK
 /
 
-:=========================== times ============================================
+#=========================== times ============================================
 TIME
 FINAL_TIME 10.d0 y
 INITIAL_TIMESTEP_SIZE 1.d-3 y
 MAXIMUM_TIMESTEP_SIZE 1.d0 y
 /
 
-:=========================== regions ==========================================
+#=========================== regions ==========================================
 REGION all
 COORDINATES
 0.d0 0.d0 0.d0
 /
 END
 
-:=========================== transport conditions =============================
+#=========================== transport conditions =============================
 TRANSPORT_CONDITION initial
 TYPE zero_gradient
 CONSTRAINT_LIST
 /
 /
 
-:=========================== constraints ======================================
+#=========================== constraints ======================================
 CONSTRAINT pulse
 CONCENTRATIONS
 Tracer 1.d0 T
 /
 END
 
-:=========================== condition couplers ===============================
-: initial condition
+#=========================== condition couplers ===============================
+# initial condition
 INITIAL_CONDITION
 TRANSPORT_CONDITION initial
 REGION all
 END
 
-: initial pulse condition
+# initial pulse condition
 INITIAL_CONDITION
 TRANSPORT_CONDITION initial_pulse
 REGION center
 END
 
-: west boundary condition
+# west boundary condition
 BOUNDARY_CONDITION west
 TRANSPORT_CONDITION initial
 REGION west
 END