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committed f19ff59

Added residual and jacobian for Richards eqn.

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# File docs/user_manual/developer_guide.tex


 \subsection{Finite Volume Discretization}

+The number of degrees of freedom is equal to the number of control volumes $N$ with one degree of freedom, fluid pressure $P$, per control volume. The following applies to both structured and unstructured grids assuming a two-point flux approximation. For accuracy this requires in the case of an unstructured grid that the line connecting neighboring control volumes be perpendicular to their common interface.
+
+\subsubsection{Residual Function}
+
+The residual function for the Richards equation at the $k+1$st time level is given by
+\EQ
+R_n \eq \varphi\Big((s\rho)_n^{k+1} - (s\rho)_n^k\Big)\frac{V_n}{\Delta t} + \sum_{n' \ne n} F_{nn'}^{k+1} A_{nn'}^{} - Q_{wn}^{} V_n^{},
+\EN
+for the $n$th control volume with volume $V_n$ and interfacial area $A_{nn'}$, where the sum over $n'$ is over all control volumes connecting with the $n$th control volume. The finite volume form of the flux $F_{nn'}$ is given by
+\EQ
+F_{nn'}^{k+1} \eq \big(\rho_{nn'}\big)_{nn'}^{k+1} \, \big(q\big)_{nn'}^{k+1}.
+\EN
+The Darcy velocity $q_{nn'}$ is evaluated as (the superscript $k+1$ is omitted in the following)
+\EQ
+q_{nn'}\eq -\Big(\frac{kk_r}{\mu}\Big)_{nn'} \left[\frac{P_{n'} - P_n}{d_{n'}+d_n}-W_w \rho_{nn'} g z_{nn'}\right],
+\EN
+where the subscript $nn'$ implies the quantity is evaluated at the interface between $n$ and $n'$. The density $\rho_{nn'}$ is set equal to the {\color{red} arithmetic mean---check code}
+\EQ
+\rho_{nn'} \eq \omega_n \rho_n + (1-\omega_n) \rho_{n'},
+\EN
+where
+\EQ
+\omega_n \eq \frac{d_n}{d_{n'}+d_n} \eq 1-\omega_{n'}.
+\EN
+The quantity in brackets is evaluated using the harmonic mean for permeability and unwinding for mobility $\lambda = k_r/\mu$
+\EQ
+\Big(\frac{kk_r}{\mu}\Big)_{nn'} \eq \frac{k_n k_{n'} (d_{n'}+d_n)}{d_n k_{n'}+d_{n'}k_n} \lambda_{nn'},
+\EN
+where
+\EQ
+\lambda_{nn'} \eq \left\{
+\begin{array}{ll}
+\lambda_n, & q_{nn'} > 0,\\
+\lambda_{n'}, & q_{nn'} < 0,
+\end{array} \right.
+\EN
+where $q_{nn'} > 0$ for flow from $n$ to $n'$, and $q_{nn'} < 0$ for flow from $n'$ to $n$. Combining these relations it follows that
+\EQ
+q_{nn'}\eq -\frac{k_n k_{n'}}{d_n k_{n'}+d_{n'}k_n} \lambda_{nn'} \Big[P_{n'} - P_n -W_w \rho_{nn'} g z_{nn'} (d_{n'}+d_n)\Big].
+\EN
+
+\subsubsection{Jacobian}
+
+The Jacobian $J_{nn'}$ is given by the derivatives of the residual function with respect to pressure as
+\BA
+J_{nn'} &\eq \frac{\p R_n}{\p P_{n'}}.
+\EA
+From the expression for the residual function it follows that
+\EQ
+\frac{\p R_n}{\p P_n} \eq \frac{V_n \varphi}{\Delta t} \frac{\p}{\p P_n} \big(s_n\rho_n\big) + \sum_{n' \ne n} \frac{\p F_{nn'}}{\p P_n} A_{nn'}^{} - \frac{\p Q_{wn}^{}}{\p P_n} V_n^{},
+\EN
+and for $n' \ne n$
+\EQ
+\frac{\p R_n}{\p P_{n'}} \eq \sum_{n' \ne n} \frac{\p F_{nn'}}{\p P_{n'}} A_{nn'}^{} - \frac{\p Q_{wn}^{}}{\p P_{n'}} V_n^{}.
+\EN
+For the accumulation term one has
+\EQ
+\frac{\p}{\p P_n} \big(s_n\rho_n\big) \eq \rho_n \frac{\p s_n}{\p P_n} + s_n \frac{\p\rho_n}{\p P_n}.
+\EN
+The derivative of the flux terms is found to be
+\EQ
+\frac{\p F_{nn'}}{\p P_n} \eq \omega_n \frac{\p\rho_n}{\p P_n} q_{nn'} + \rho_{nn'} \frac{\p q_{nn'}}{\p P_n},
+\EN
+and
+\EQ
+\frac{\p F_{nn'}}{\p P_{n'}} \eq \omega_{n'} \frac{\p\rho_n}{\p P_{n'}} q_{nn'} + \rho_{nn'} \frac{\p q_{nn'}}{\p P_{n'}},
+\EN
+with
+\EQ
+\frac{\p q_{nn'}}{\p P_n} \eq \frac{k_n k_{n'}}{d_n k_{n'}+d_{n'}k_n} \left\{
+\lambda_{nn'} - \frac{\p \ln\lambda_{nn'}}{\p P_{n}} q_{nn'}
+\right\},
+\EN
+and
+\EQ
+\frac{\p q_{nn'}}{\p P_{n'}} \eq -\frac{k_n k_{n'}}{d_n k_{n'}+d_{n'}k_n} \left\{
+\lambda_{nn'} + \frac{\p \ln\lambda_{nn'}}{\p P_{n'}} q_{nn'}
+\right\}.
+\EN
+
+\begin{comment}
+For a 1D system the Jacobian reduces to
+\EQ
+J_{nn'} \eq \delta_{n-1,n'} \frac{\p R_n}{\p P_{n-1}}
++ \delta_{nn'} \frac{\p R_n}{\p P_{n}}
++ \delta_{n+1,n'} \frac{\p R_n}{\p P_{n+1}}.
+\EN
+It follows that
+\EQ
+J_{n,n-1} \eq -\frac{k_n k_{n'}}{d_n k_{n'}+d_{n'}k_n} \lambda_{nn'},
+\EN
+\EQ
+J_{n,n} \eq \frac{k_n k_{n'}}{d_n k_{n'}+d_{n'}k_n} \lambda_{nn'} \Big(1+d_n\frac{\p\rho_n}{\p P_n}W_w g z_{nn'}\Big),
+\EN
+and
+\EQ
+J_{n,n+1} \eq -\frac{k_n k_{n'}}{d_n k_{n'}+d_{n'}k_n} \lambda_{nn'}.
+\EN
+\end{comment}
+
 %+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

 \section{Supercritical CO$_2$}

# File docs/user_manual/quick_guide.tex

 \EQ
 \frac{\p}{\p t}\left(\varphi s\rho\right) + \bnabla\cdot\left(\rho\bq\right) = Q_w,
 \EN
-and
+with Darcy flux $\bq$ defined as
 \EQ
 \bq = -\frac{kk_r(s)}{\mu}\bnabla\left(P-W_w\rho g z\right).
 \EN
 \item Andreas Voegelin, Vijay M. Vulava, Florian Kuhnen, Ruben Kretzschmar (2000) Multicomponent transport of major cations predicted from binary adsorption experiments, Journal of Contaminant Hydrology, 46, 319--338.
 \end{description}

-\begin{comment}
-\newpage
-
-\section{Appendix: List of Subroutines in PFLOTRAN}
-
-\footnotesize
-\begin{verbatim}
-grep '^subroutine' *.F90
-amrgrid.F90:subroutine samr_physical_dimensions(p_hierarchy, nx, ny, nz)
-amrgrid.F90:subroutine AMRGridComputeLocalBounds(amrgrid)
-amrgrid.F90:subroutine AMRGridComputeGridSpacing(amrgrid)
-amrgrid.F90:subroutine AMRGridInitialize(amrgrid)
-amrgrid.F90:subroutine samr_physical_dimensions(p_hierarchy, nx, ny, nz)
-amrgrid.F90:subroutine samr_get_origin(p_hierarchy, x0, y0, z0)
-amrgrid.F90:subroutine samr_get_upper_corner(p_hierarchy, x1, y1, z1)
-amrgrid.F90:subroutine AMRGridCreateVector(amrgrid, dof, vector,vector_type, &
-amrgrid.F90:subroutine create_samrai_vec(p_application, dof, centering, use_ghost, use_components, vec)
-amrgrid.F90:subroutine AMRGridCreateJacobian(dm_ptr,Jacobian,option)
-amrgrid.F90:subroutine AMRGridComputeGeometryInformation(amrgrid, origin_global, field, &
-amrgrid.F90:subroutine AMRGridReadDXYZ(amrgrid, input, option)
-amrgrid.F90:subroutine AMRGridReadDXDYDZ(array,ndim,input,option)
-amrgrid.F90:subroutine AMRGridGlobalToLocal(dm_ptr,global_vec,local_vec)
-amrgrid.F90:subroutine AMRGridLocalToGlobal(dm_ptr,local_vec,global_vec)
-amrgrid.F90:subroutine AMRGridLocalToLocal(dm_ptr,local_vec1,local_vec2)
-amrgrid.F90:subroutine AMRGridDestroy(amrgrid)
-amrstubs.F90:subroutine create_samrai_vec(p_application, dof, centering, use_ghost, use_components, vec)
-amrstubs.F90:subroutine samr_patch_get_corners(p_patch, nxs, nys, nzs, nlx, nly, nlz)
-amrstubs.F90:subroutine samr_patch_get_origin(p_patch, xs, ys, zs)
-amrstubs.F90:subroutine samr_patch_get_ghostcorners(p_patch, nxs, nys, nzs, nlx, nly, nlz)
-amrstubs.F90:subroutine samr_physical_dimensions(p_application, nx, ny, nz)
-amrstubs.F90:subroutine samr_get_origin(p_application, x0, y0, z0)
-amrstubs.F90:subroutine samr_get_upper_corner(p_application, x0, y0, z0)
-amrstubs.F90:subroutine assign_c_array_ptr(return_arg, pointer_arg)
-amrstubs.F90:subroutine samr_vecgetarraycellf90(patch, petscvec, f90wrap)
-amrstubs.F90:subroutine samr_vecgetarraysidef90(patch, axis, petscvec, f90wrap)
-amrstubs.F90:subroutine samrvecgetmaskarraycellf90(patch, petscvec, f90wrap)
-amrstubs.F90:subroutine samr_patch_get_spacing(p_samr_patch, dx, dy, dz)
-amrstubs.F90:subroutine SAMRCreateMatrix(p_application, ndof, stencilsize, flowortransport, p_matrix)
-amrstubs.F90:subroutine SAMRGlobalToLocal(p_application, gvec, lvec, ierr)
-amrstubs.F90:subroutine SAMRLocalToLocal(p_application, gvec, lvec, ierr)
-amrstubs.F90:subroutine SAMRCoarsenVector(p_application, vec)
-amrstubs.F90:subroutine SAMRCoarsenFaceFluxes(p_application, vec, ierr)
-amrstubs.F90:subroutine SAMRSetCurrentJacobianPatch(mat,patch)
-amrstubs.F90:subroutine SAMRSetJacobianSourceOnPatch(which_pc, index, val, application, patch)
-amrstubs.F90:subroutine SAMRSetJacobianSrcCoeffsOnPatch(which_pc, p_application, p_patch)
-amrstubs.F90:subroutine samrpetscobjectstateincrease(vec)
-amrstubs.F90:subroutine samr_mpi_min(x,y,z)
-amrstubs.F90:subroutine samr_mpi_max(x,y,z)
-amrstubs.F90:subroutine SAMRBarrier()
-amrstubs.F90:subroutine SAMRCopyVecToVecComponent(vec,svec, component)
-amrstubs.F90:subroutine SAMRRegisterForViz(ptr,vec,component,dname,dnamec, string)
-amrstubs.F90:subroutine SAMRRegisterForViz(ptr,vec,component,dname,dnamec)
-amrstubs.F90:subroutine SAMRWritePlotData(ptr, time)
-amrstubs.F90:subroutine SAMRInitializePreconditioner(p_application, which_pc, pc)
-amrstubs.F90:subroutine SAMRGetRealization(p_application, realization)
-amrstubs.F90:subroutine SAMRSetPetscTransportMatrix(p_application, transportMat)
-auxilliary.F90:subroutine AuxInit(aux)
-auxilliary.F90:subroutine AuxDestroy(aux)
-checkpoint.F90:subroutine Checkpoint(realization, &
-checkpoint.F90:subroutine Restart(realization, &
-co2_span_wagner.F90:subroutine initialize_span_wagner(itable,myrank)
-co2_span_wagner.F90:subroutine co2_span_wagner(pl,tl,rho,dddt,dddp,fg,dfgdp,dfgdt, &
-co2_span_wagner.F90:subroutine guess(lguess,uguess)
-co2_span_wagner.F90:subroutine co2den(den,f,df)
-co2_span_wagner.F90:subroutine dphiodtau(dr,del2,tau2)
-co2_span_wagner.F90:subroutine dphiodtautau(dr,del2,tau2)
-co2_span_wagner.F90:subroutine phir(r_helm,del2,tau2)
-co2_span_wagner.F90:subroutine dphirddel(dr,del2,tau2)
-co2_span_wagner.F90:subroutine dphirdddel(dpdd,del2,tau2)
-co2_span_wagner.F90:subroutine dphirdtau(dpdtau,del2,tau2)
-co2_span_wagner.F90:subroutine dphirdtautau(dpdtt,del2,tau2)
-co2_span_wagner.F90:subroutine dphirddeldtau(dpddt,del2,tau2)
-co2_span_wagner.F90:subroutine vappr(tm,ps,dertp,derpt,ifl1)
-co2_span_wagner.F90:subroutine viscosity(p,t,rho,drhodp,drhodt,mu,dmudt,dmudp)
-co2_span_wagner.F90:subroutine dissco2(p,t,mco2,fg,mol)
-co2_span_wagner_orig.F90:subroutine initialize_span_wagner(itable,myrank)
-co2_span_wagner_orig.F90:subroutine co2_span_wagner(pl,tl,rho,dddt,dddp,fg,dfgdp,dfgdt, &
-co2_span_wagner_orig.F90:subroutine guess(lguess,uguess)
-co2_span_wagner_orig.F90:subroutine co2den(den,f,df)
-co2_span_wagner_orig.F90:subroutine dphiodtautau(dr,del2,tau2)
-co2_span_wagner_orig.F90:subroutine phir(r_helm,del2,tau2)
-co2_span_wagner_orig.F90:subroutine dphirddel(dr,del2,tau2)
-co2_span_wagner_orig.F90:subroutine dphirdddel(dpdd,del2,tau2)
-co2_span_wagner_orig.F90:subroutine dphirdtau(dpdtau,del2,tau2)
-co2_span_wagner_orig.F90:subroutine dphirdtautau(dpdtt,del2,tau2)
-co2_span_wagner_orig.F90:subroutine dphirddeldtau(dpddt,del2,tau2)
-co2_span_wagner_orig.F90:subroutine vappr(tm,ps,dertp,derpt,ifl1)
-co2_span_wagner_orig.F90:subroutine viscosity(p,t,rho,drhodp,drhodt,mu,dmudt,dmudp)
-co2_span_wagner_orig.F90:subroutine dissco2(p,t,mco2,fg,mol)
-co2_span_wagner_spline.F90:subroutine sw_spline_read
-co2_span_wagner_spline.F90:subroutine sw_prop(tx,px,rho,h,u,fg)
-co2_sw.F90:subroutine initialize_sw_interp(itable,myrank)
-co2_sw.F90:subroutine interp(x1,x2,y)
-co2_sw.F90:subroutine co2_sw_interp(p,tc,rho,dddt,dddp,fg,dfgdp,dfgdt, &
-co2_sw_rtsafe.F90:subroutine bracket(func,x1,x2)
-co2eos.F90:subroutine CO2(TX,PCX,DC,FC,PHI,HC)
-co2eos.F90:subroutine MRK(Y,T,PCX,V,DV,AT)
-co2eos.F90:subroutine FUGACITY(Y,T,V,Z,PHI)
-co2eos.F90:subroutine ENTHALPY(T,V,Z,H)
-co2eos.F90:subroutine duanco2 (tt,p,dc,fc,phi)
-co2eos.F90:subroutine Henry_duan_sun_0NaCl (p,tc,henry)
-co2eos.F90:subroutine Henry_duan_sun(tc,p,mco2,phico2,lngamco2,mc,ma,psat,co2_aq_actcoef)
-co2eos.F90:subroutine duan_sun_param(t,p,c,par)
-co2eos.F90:subroutine HENRY_co2_noderiv(xmole,x1m,tx,pcx,xphi,rkh,poyn)
-co2eos.F90:subroutine HENRY_sullivan (TX,PCX,PS,FC,X1M,XCO2,HP)
-co2eos.F90:subroutine SOLUT(PCX,TX,HSOL)
-co2eos.F90:subroutine DENMIX(TX,DW,X1M,D1M)
-co2eos.F90:subroutine VISCO2(TX,DC,VC)
-co2eos.F90:subroutine SAT(T,P)
-co2eos.F90:subroutine COWAT0(TF,PP,D,U)
-co2eos.F90:subroutine SUPST(T,P,D,U)
-co2eos.F90:subroutine TSAT(PX,TX00,TS)
-co2eos.F90:subroutine SIGMA(T,ST)
-co2eos.F90:subroutine VIS(T,P,D,VW,VS,PS)
-co2eos.F90:subroutine VISW0(T,P,PS,VW)
-co2eos.F90:subroutine VISS(T,P,D,VS)
-co2eos.F90:subroutine THERC(T,P,D,CONW,CONS,PS)
-condition.F90:subroutine FlowConditionDatasetInit(dataset)
-condition.F90:subroutine FlowSubConditionVerify(option, condition, sub_condition_name, &
-condition.F90:subroutine FlowConditionDatasetVerify(option, condition_name, sub_condition_name, &
-condition.F90:subroutine FlowConditionDatasetGetTimes(option, sub_condition, &
-condition.F90:subroutine FlowConditionRead(condition,input,option)
-condition.F90:subroutine FlowConditionGeneralRead(condition,input,option)
-condition.F90:subroutine TranConditionRead(condition,constraint_list,reaction,input,option)
-condition.F90:subroutine TranConstraintRead(constraint,reaction,input,option)
-condition.F90:subroutine FlowConditionReadValues(input,option,keyword,string,dataset,units)
-condition.F90:subroutine FlowConditionReadValuesFromFile(input,dataset,option)
-condition.F90:subroutine FlowConditionReadValuesFromFile2(input,dataset,option)
-condition.F90:subroutine FlowConditionPrint(condition,option)
-condition.F90:subroutine FlowConditionPrintSubCondition(subcondition,option)
-condition.F90:subroutine FlowConditionPrintDataset(dataset,option)
-condition.F90:subroutine FlowConditionUpdate(condition_list,option,time)
-condition.F90:subroutine FlowSubConditionUpdateDataset(option,time,dataset)
-condition.F90:subroutine TranConditionUpdate(condition_list,option,time)
-condition.F90:subroutine FlowConditionInitList(list)
-condition.F90:subroutine FlowConditionAddToList(new_condition,list)
-condition.F90:subroutine TranConditionInitList(list)
-condition.F90:subroutine TranConstraintInitList(list)
-condition.F90:subroutine TranConditionAddToList(new_condition,list)
-condition.F90:subroutine TranConstraintAddToList(new_constraint,list)
-condition.F90:subroutine FlowConditionDestroyList(condition_list)
-condition.F90:subroutine FlowConditionDestroy(condition)
-condition.F90:subroutine FlowGeneralConditionDestroy(general_condition)
-condition.F90:subroutine FlowSubConditionDestroy(sub_condition)
-condition.F90:subroutine FlowConditionDatasetDestroy(dataset)
-condition.F90:subroutine TranConditionDestroyList(condition_list)
-condition.F90:subroutine TranConstraintDestroy(constraint)
-condition.F90:subroutine TranConstraintDestroyList(constraint_list)
-condition.F90:subroutine TranConditionDestroy(condition)
-condition.F90:subroutine TranConstraintCouplerDestroy(coupler_list)
-connection.F90:subroutine ConnectionInitList(list)
-connection.F90:subroutine ConnectionAddToList(new_connection_set,list)
-connection.F90:subroutine ConnectionConvertListToArray(list)
-connection.F90:subroutine ConnectionDestroy(connection)
-connection.F90:subroutine ConnectionDestroyList(list)
-convergence.F90:subroutine ConvergenceTest(snes_,it,xnorm,pnorm,fnorm,reason,context,ierr)
-convergence.F90:subroutine ConvergenceContextDestroy(context)
-coupler.F90:subroutine CouplerInitList(list)
-coupler.F90:subroutine CouplerRead(coupler,input,option)
-coupler.F90:subroutine CouplerAddToList(new_coupler,list)
-coupler.F90:subroutine CouplerListComputeConnections(grid,option,coupler_list)
-coupler.F90:subroutine CouplerComputeConnections(grid,option,coupler)
-coupler.F90:subroutine CouplerComputeConnectionsFaces(grid,option,coupler)
-coupler.F90:subroutine CouplerAssignBCtoCells(grid,option,coupler)
-coupler.F90:subroutine CouplerDestroyList(coupler_list)
-coupler.F90:subroutine CouplerDestroy(coupler)
-database.F90:subroutine DatabaseRead(reaction,option)
-database.F90:subroutine BasisInit(reaction,option)
-database.F90:subroutine BasisAlignSpeciesInRxn(num_basis_species,basis_names, &
-database.F90:subroutine BasisSubSpeciesInGasOrSecRxn(name1,dbaserxn1,dbaserxn2)
-database.F90:subroutine BasisSubSpeciesInMineralRxn(name,sec_dbaserxn,mnrl_dbaserxn)
-database.F90:subroutine BasisPrint(reaction,title,option)
-dataset.F90:subroutine DatasetRead(dataset,input,option)
-dataset.F90:subroutine DatasetAddToList(dataset,list)
-debug.F90:subroutine DebugReadFlow(debug,input,option)
-discretization.F90:subroutine DiscretizationRead(discretization,input,first_time,option)
-discretization.F90:subroutine DiscretizationCreateDMs(discretization,option)
-discretization.F90:subroutine DiscretizationCreateDM(discretization,dm_ptr,ndof,stencil_width, &
-discretization.F90:subroutine DiscretizationCreateVector(discretization,dm_index,vector, &
-discretization.F90:subroutine DiscretizationDuplicateVector(discretization,vector1,vector2)
-discretization.F90:subroutine DiscretizationCreateJacobian(discretization,dm_index,mat_type,Jacobian,option)
-discretization.F90:subroutine SAMRCreateMatrix(p_application, ndof, stencilsize, flowortransport, p_matrix)
-discretization.F90:subroutine DiscretizationCreateInterpolation(discretization,dm_index, &
-discretization.F90:subroutine DiscretizationCreateColoring(discretization,dm_index,option,coloring)
-discretization.F90:subroutine DiscretizationGlobalToLocal(discretization,global_vec,local_vec,dm_index)
-discretization.F90:subroutine SAMRGlobalToLocal(p_application, gvec, lvec, ierr)
-discretization.F90:subroutine DiscretizationGlobalToLocalFaces(discretization,global_vec,local_vec,dm_index)
-discretization.F90:subroutine DiscretizationLocalToGlobal(discretization,local_vec,global_vec,dm_index)
-discretization.F90:subroutine DiscretizationLocalToLocal(discretization,local_vec1,local_vec2,dm_index)
-discretization.F90:subroutine SAMRLocalToLocal(p_application, gvec, lvec, ierr)
-discretization.F90:subroutine DiscretizationLocalToLocalFaces(discretization,local_vec1,local_vec2,dm_index)
-discretization.F90:subroutine DiscretizationGlobalToNatural(discretization,global_vec,natural_vec,dm_index)
-discretization.F90:subroutine DiscretizationNaturalToGlobal(discretization,natural_vec,global_vec,dm_index)
-discretization.F90:subroutine DiscretizationGlobalToLocalBegin(discretization,global_vec,local_vec,dm_index)
-discretization.F90:subroutine DiscretizationGlobalToLocalEnd(discretization,global_vec,local_vec,dm_index)
-discretization.F90:subroutine DiscretizLocalToLocalFacesBegin(discretization,local_vec1,local_vec2,dm_index)
-discretization.F90:subroutine DiscretizLocalToLocalFacesEnd(discretization,local_vec1,local_vec2,dm_index)
-discretization.F90:subroutine DiscretizGlobalToLocalFacesBegin(discretization,global_vec,local_vec,dm_index)
-discretization.F90:subroutine DiscretizGlobalToLocalFacesEnd(discretization,global_vec,local_vec,dm_index)
-discretization.F90:subroutine DiscretizationLocalToLocalBegin(discretization,local_vec1,local_vec2,dm_index)
-discretization.F90:subroutine DiscretizationLocalToLocalEnd(discretization,local_vec1,local_vec2,dm_index)
-discretization.F90:subroutine DiscretizGlobalToNaturalBegin(discretization,global_vec,natural_vec,dm_index)
-discretization.F90:subroutine DiscretizGlobalToNaturalEnd(discretization,global_vec,natural_vec,dm_index)
-discretization.F90:subroutine DiscretizNaturalToGlobalBegin(discretization,natural_vec,global_vec,dm_index)
-discretization.F90:subroutine DiscretizNaturalToGlobalEnd(discretization,natural_vec,global_vec,dm_index)
-discretization.F90:subroutine DiscretizationDestroy(discretization)
-field.F90:subroutine FieldDestroy(field)
-flash2.F90:subroutine Flash2TimeCut(realization)
-flash2.F90:subroutine Flash2Setup(realization)
-flash2.F90:subroutine Flash2SetupPatch(realization)
-flash2.F90:subroutine Flash2UpdateReasonPatch(reason,realization)
-flash2.F90:subroutine Flash2UpdateReason(reason, realization)
-flash2.F90:subroutine Flash2UpdateAuxVars(realization)
-flash2.F90:subroutine Flash2UpdateAuxVarsPatch(realization)
-flash2.F90:subroutine Flash2InitializeTimestep(realization)
-flash2.F90:subroutine Flash2UpdateSolution(realization)
-flash2.F90:subroutine Flash2UpdateFixedAccumulation(realization)
-flash2.F90:subroutine Flash2UpdateFixedAccumPatch(realization)
-flash2.F90:subroutine Flash2Accumulation(aux_var,global_aux_var,por,vol,rock_dencpr,option,iireac,Res)
-flash2.F90:subroutine Flash2SourceSink(mmsrc,psrc,tsrc,hsrc,aux_var,isrctype,Res, energy_flag, option)
-flash2.F90:subroutine Flash2Flux(aux_var_up,por_up,tor_up,sir_up,dd_up,perm_up,Dk_up, &
-flash2.F90:subroutine Flash2FluxAdv(aux_var_up,por_up,tor_up,sir_up,dd_up,perm_up,Dk_up, &
-flash2.F90:subroutine Flash2FluxDiffusion(aux_var_up,por_up,tor_up,sir_up,dd_up,perm_up,Dk_up, &
-flash2.F90:subroutine Flash2BCFlux(ibndtype,aux_vars,aux_var_up,aux_var_dn, &
-flash2.F90:subroutine Flash2BCFluxAdv(ibndtype,aux_vars,aux_var_up,aux_var_dn, &
-flash2.F90:subroutine Flash2BCFluxDiffusion(ibndtype,aux_vars,aux_var_up,aux_var_dn, &
-flash2.F90:subroutine Flash2Residual(snes,xx,r,realization,ierr)
-flash2.F90:subroutine samrpetscobjectstateincrease(vec)
-flash2.F90:subroutine SAMRCoarsenFaceFluxes(p_application, vec, ierr)
-flash2.F90:subroutine Flash2ResidualPatch(snes,xx,r,realization,ierr)
-flash2.F90:subroutine Flash2ResidualFluxContribPatch(r,realization,ierr)
-flash2.F90:subroutine Flash2ResidualPatch1(snes,xx,r,realization,ierr)
-flash2.F90:subroutine Flash2ResidualPatch0(snes,xx,r,realization,ierr)
-flash2.F90:subroutine Flash2ResidualPatch2(snes,xx,r,realization,ierr)
-flash2.F90:subroutine Flash2Jacobian(snes,xx,A,B,flag,realization,ierr)
-flash2.F90:subroutine SAMRSetCurrentJacobianPatch(mat,patch)
-flash2.F90:subroutine Flash2JacobianPatch(snes,xx,A,B,flag,realization,ierr)
-flash2.F90:subroutine Flash2JacobianPatch1(snes,xx,A,B,flag,realization,ierr)
-flash2.F90:subroutine Flash2JacobianPatch2(snes,xx,A,B,flag,realization,ierr)
-flash2.F90:subroutine SAMRSetJacobianSourceOnPatch(which_pc, index, val, p_application, p_patch)
-flash2.F90:subroutine SAMRSetJacobianSrcCoeffsOnPatch(which_pc, p_application, p_patch)
-flash2.F90:subroutine Flash2CreateZeroArray(patch,option)
-flash2.F90:subroutine Flash2MaxChange(realization)
-flash2.F90:subroutine Flash2Destroy(patch)
-flash2.F90:subroutine Flash2CheckpointWrite(discretization, viewer)
-flash2.F90:subroutine Flash2CheckpointRead(discretization,viewer)
-flash2_aux.F90:subroutine Flash2AuxVarInit(aux_var,option)
-flash2_aux.F90:subroutine Flash2AuxVarCopy(aux_var,aux_var2,option)
-flash2_aux.F90:subroutine Flash2AuxVarCompute_NINC(x,aux_var,global_aux_var, &
-flash2_aux.F90:subroutine Flash2AuxVarCompute_WINC(x, delx, aux_var,global_auxvar,saturation_function, &
-flash2_aux.F90:subroutine Flash2AuxVarDestroy(aux_var)
-flash2_aux.F90:subroutine Flash2AuxDestroy(aux, option)
-fluid.F90:subroutine FluidPropertyRead(fluid_property,input,option)
-fluid.F90:subroutine FluidPropertyAddToList(fluid_property,list)
-gaseos_mod.F90:subroutine ideal_gaseos_noderiv(p,tc,energyscale,d,h,u)
-gaseos_mod.F90:subroutine ideal_gaseos(p,tc,energyscale,d,d_p,d_t,h,h_p,h_t,u,u_p,u_t)
-gaseos_mod.F90:subroutine visgas_noderiv(t,pa,p,ds,visg)
-gaseos_mod.F90:subroutine Henry_air_noderiv(p,tc,ps,Henry)
-gaseos_mod.F90:subroutine Henry_air(p,tc,ps,ps_p,ps_t,Henry,Henry_p,Henry_t)
-general.F90:subroutine GeneralTimeCut(realization)
-general.F90:subroutine GeneralTimeCutPatch(realization)
-general.F90:subroutine GeneralSetup(realization)
-general.F90:subroutine GeneralSetupPatch(realization)
-general.F90:subroutine GeneralComputeMassBalance(realization,mass_balance)
-general.F90:subroutine GeneralComputeMassBalancePatch(realization,mass_balance)
-general.F90:subroutine GeneralZeroMassBalDeltaPatch(realization)
-general.F90:subroutine GeneralUpdateMassBalancePatch(realization)
-general.F90:subroutine GeneralUpdateAuxVars(realization)
-general.F90:subroutine GeneralUpdateAuxVarsPatch(realization,update_state)
-general.F90:subroutine GeneralInitializeTimestep(realization)
-general.F90:subroutine GeneralUpdateSolution(realization)
-general.F90:subroutine GeneralUpdateSolutionPatch(realization)
-general.F90:subroutine GeneralUpdateFixedAccum(realization)
-general.F90:subroutine GeneralUpdateFixedAccumPatch(realization)
-general.F90:subroutine GeneralNumericalJacTest(xx,realization)
-general.F90:subroutine GeneralAuxVarPerturb(gen_aux_var,global_aux_var, &
-general.F90:subroutine GeneralAccumulation(gen_aux_var,global_aux_var,dencpr,por,vol, &
-general.F90:subroutine GeneralAccumDerivative(gen_aux_var,global_aux_var,dencpr,por,vol, &
-general.F90:subroutine GeneralFlux(gen_aux_var_up,global_aux_var_up, &
-general.F90:subroutine GeneralFluxDerivative(gen_aux_var_up,global_aux_var_up,por_up, &
-general.F90:subroutine GeneralBCFlux(ibndtype,aux_vars, &
-general.F90:subroutine GeneralBCFluxDerivative(ibndtype,aux_vars, &
-general.F90:subroutine GeneralSrcSink(option,qsrc,flow_src_sink_type, &
-general.F90:subroutine GeneralResidual(snes,xx,r,realization,ierr)
-general.F90:subroutine GeneralResidualPatch1(snes,xx,r,realization,ierr)
-general.F90:subroutine GeneralResidualPatch2(snes,xx,r,realization,ierr)
-general.F90:subroutine GeneralJacobian(snes,xx,A,B,flag,realization,ierr)
-general.F90:subroutine GeneralJacobianPatch1(snes,xx,A,B,flag,realization,ierr)
-general.F90:subroutine GeneralJacobianPatch2(snes,xx,A,B,flag,realization,ierr)
-general.F90:subroutine GeneralCreateZeroArray(patch,option)
-general.F90:subroutine GeneralMaxChange(realization)
-general.F90:subroutine GeneralUpdateState(x,gen_aux_var,global_aux_var, &
-general.F90:subroutine GeneralDestroy(realization)
-general.F90:subroutine GeneralDestroyPatch(realization)
-general_aux.F90:subroutine GeneralAuxVarInit(aux_var,option)
-general_aux.F90:subroutine GeneralAuxVarCopy(aux_var,aux_var2,option)
-general_aux.F90:subroutine GeneralAuxVarCompute(x,gen_aux_var, global_aux_var,&
-general_aux.F90:subroutine GeneralAuxVarDestroy(aux_var)
-general_aux.F90:subroutine GeneralAuxDestroy(aux)
-general_grid.F90:subroutine ReadStructuredGridHDF5(realization)
-general_grid.F90:subroutine ReadStructuredGridHDF5(realization)
-general_grid.F90:subroutine SetupConnectionIndices(grid,option,file_id,indices)
-general_grid.F90:subroutine UpdateGlobalToLocal(discretization,field)
-general_phase.F90:subroutine GeneralPhaseTimeCut(realization)
-general_phase.F90:subroutine GeneralPhaseSetup(realization)
-general_phase.F90:subroutine GeneralPhaseSetupPatch(realization)
-general_phase.F90:subroutine GeneralPhaseComputeMassBalance(realization,mass_balance)
-general_phase.F90:subroutine GeneralPhaseComputeMassBalancePatch(realization,mass_balance)
-general_phase.F90:subroutine GeneralPhaseZeroMassBalDeltaPatch(realization)
-general_phase.F90:subroutine GeneralPhaseUpdateMassBalancePatch(realization)
-general_phase.F90:subroutine GeneralPhaseUpdateAuxVars(realization)
-general_phase.F90:subroutine GeneralPhaseUpdateAuxVarsPatch(realization)
-general_phase.F90:subroutine GeneralPhaseInitializeTimestep(realization)
-general_phase.F90:subroutine GeneralPhaseUpdateSolution(realization)
-general_phase.F90:subroutine GeneralPhaseUpdateSolutionPatch(realization)
-general_phase.F90:subroutine GeneralPhaseUpdateFixedAccum(realization)
-general_phase.F90:subroutine GeneralPhaseLiUpdateFixedAccumPatch(realization)
-general_phase.F90:subroutine GeneralPhaseNumericalJacTest(xx,realization)
-general_phase.F90:subroutine GeneralPhaseAccumDerivative(rich_aux_var,global_aux_var,por,vol, &
-general_phase.F90:subroutine GeneralPhaseAccumulation(rich_aux_var,global_aux_var,por,vol,rock_dencpr, &
-general_phase.F90:subroutine GeneralPhaseFluxDerivative(rich_aux_var_up,global_aux_var_up,por_up, &
-general_phase.F90:subroutine GeneralPhaseFlux(rich_aux_var_up,global_aux_var_up, &
-general_phase.F90:subroutine GeneralPhaseBCFluxDerivative(ibndtype,aux_vars, &
-general_phase.F90:subroutine GeneralPhaseBCFlux(ibndtype,aux_vars, &
-general_phase.F90:subroutine GeneralPhaseResidual(snes,xx,r,realization,ierr)
-general_phase.F90:subroutine samrpetscobjectstateincrease(vec)
-general_phase.F90:subroutine GeneralPhaseResidualPatch(snes,xx,r,realization,ierr)
-general_phase.F90:subroutine GeneralPhaseJacobian(snes,xx,A,B,flag,realization,ierr)
-general_phase.F90:subroutine SAMRSetCurrentJacobianPatch(mat,patch)
-general_phase.F90:subroutine GeneralPhaseJacobianPatch(snes,xx,A,B,flag,realization,ierr)
-general_phase.F90:subroutine GeneralPhaseCreateZeroArray(patch,option)
-general_phase.F90:subroutine GeneralPhaseMaxChange(realization)
-general_phase.F90:subroutine GeneralPhaseDestroy(patch)
-general_phase_aux.F90:subroutine GeneralPhaseAuxVarInit(aux_var,option)
-general_phase_aux.F90:subroutine GeneralPhaseAuxVarCopy(aux_var,aux_var2,option)
-general_phase_aux.F90:subroutine GeneralPhaseAuxVarCompute(x,aux_var,global_aux_var,iphase,&
-general_phase_aux.F90:subroutine AuxVarDestroy(aux_var)
-general_phase_aux.F90:subroutine GeneralPhaseAuxDestroy(aux)
-global.F90:subroutine GlobalSetup(realization)
-global.F90:subroutine GlobalSetupPatch(realization)
-global.F90:subroutine GlobalSetAuxVarScalar(realization,value,ivar)
-global.F90:subroutine GlobalSetAuxVarScalarPatch(realization,value,ivar)
-global.F90:subroutine GlobalSetAuxVarVecLoc(realization,vec_loc,ivar,isubvar)
-global.F90:subroutine GlobalSetAuxVarVecLocPatch(realization,vec_loc,ivar,isubvar)
-global.F90:subroutine GlobalUpdateDenAndSat(realization,weight)
-global.F90:subroutine GlobalUpdateDenAndSatPatch(realization,weight)
-global.F90:subroutine GlobalUpdateAuxVars(realization,time_level)
-global_aux.F90:subroutine GlobalAuxVarInit(aux_var,option)
-global_aux.F90:subroutine GlobalAuxVarCopy(aux_var,aux_var2,option)
-global_aux.F90:subroutine GlobalAuxVarDestroy(aux_var)
-global_aux.F90:subroutine GlobalAuxDestroy(aux)
-grid.F90:subroutine GridComputeInternalConnect(grid,option,ugdm)
-grid.F90:subroutine GridPopulateConnection(grid,connection,iface,iconn,cell_id_local)
-grid.F90:subroutine GridPopulateFaces(grid, option)
-grid.F90:subroutine GridComputeCell2FaceConnectivity(grid, MFD_aux, option)
-grid.F90:subroutine GridComputeGlobalCell2FaceConnectivity( grid, MFD_aux, DOF, option)
-grid.F90:subroutine GridMapIndices(grid, sgdm)
-grid.F90:subroutine GridComputeSpacing(grid,option)
-grid.F90:subroutine GridComputeCoordinates(grid,origin_global,option,ugdm)
-grid.F90:subroutine GridComputeVolumes(grid,volume,option)
-grid.F90:subroutine GridLocalizeRegions(grid,region_list,option)
-grid.F90:subroutine GridLocalizeRegionsForUGrid(grid, region_list, option)
-grid.F90:subroutine GridCopyIntegerArrayToVec(grid, array,vector,num_values)
-grid.F90:subroutine GridCopyRealArrayToVec(grid,array,vector,num_values)
-grid.F90:subroutine GridCopyVecToIntegerArray(grid,array,vector,num_values)
-grid.F90:subroutine GridCopyVecToRealArray(grid,array,vector,num_values)
-grid.F90:subroutine GridCreateNaturalToGhostedHash(grid,option)
-grid.F90:subroutine GridDestroyHashTable(grid)
-grid.F90:subroutine GridPrintHashTable(grid)
-grid.F90:subroutine GridGetGhostedNeighbors(grid,ghosted_id,stencil_type, &
-grid.F90:subroutine GridDestroy(grid)
-grid.F90:subroutine GridVecGetMaskArrayCellF90(grid, vec, f90ptr, ierr)
-grid.F90:subroutine GridVecGetArrayCellF90(grid, vec, f90ptr, ierr)
-grid.F90:subroutine GridVecGetArraySideF90(grid, axis, vec, f90ptr, ierr)
-grid.F90:subroutine GridVecRestoreArrayF90(grid, vec, f90ptr, ierr)
-hdf5.F90:subroutine HDF5MapLocalToNaturalIndices(grid,option,file_id, &
-hdf5.F90:subroutine HDF5MapLocalToNaturalIndices(grid,option,file_id, &
-hdf5.F90:subroutine HDF5ReadRealArray(option,file_id,dataset_name,dataset_size, &
-hdf5.F90:subroutine HDF5ReadRealArray(option,file_id,dataset_name,dataset_size, &
-hdf5.F90:subroutine HDF5ReadIntegerArray(option,file_id,dataset_name,dataset_size, &
-hdf5.F90:subroutine HDF5ReadIntegerArray(option,file_id,dataset_name,dataset_size, &
-hdf5.F90:subroutine HDF5WriteIntegerArray(option,dataset_name,dataset_size,file_id, &
-hdf5.F90:subroutine HDF5WriteStructuredDataSet(name,array,file_id,data_type,option, &
-hdf5.F90:subroutine HDF5WriteStructuredDataSet(name,array,file_id,data_type,option, &
-hdf5.F90:subroutine HDF5ReadIndices(grid,option,file_id,dataset_name,dataset_size, &
-hdf5.F90:subroutine HDF5ReadArray(discretization,grid,option,file_id,dataset_name, &
-hdf5.F90:subroutine HDF5ReadRegionFromFile(realization,region,filename)
-hdf5.F90:subroutine HDF5ReadUnstructuredGridRegionFromFile(realization,region,filename)
-hdf5.F90:subroutine HDF5ReadRegionFromFile(realization,region,filename)
-hdf5.F90:subroutine HDF5ReadCellIndexedIntegerArray(realization,global_vec,filename, &
-hdf5.F90:subroutine HDF5ReadCellIndexedIntegerArray(realization,global_vec,filename, &
-hdf5.F90:subroutine HDF5ReadCellIndexedRealArray(realization,global_vec,filename, &
-hdf5.F90:subroutine HDF5ReadCellIndexedRealArray(realization,global_vec,filename, &
-hdf5.F90:subroutine HDF5WriteStructDataSetFromVec(name,realization,vec,file_id,data_type)
-hdf5.F90:subroutine HDF5WriteStructDataSetFromVec(name,realization,vec,file_id,data_type)
-hdf5.F90:subroutine HDF5ReadUnstructuredGridRegionFromFile(realization,region,filename)
-hdf5_aux.F90:subroutine HDF5ReadNDimRealArray(option,file_id,dataset_name,ndims,dims, &
-hdf5_aux.F90:subroutine HDF5ReadDatasetInteger2D(filename,dataset_name,read_option,option, &
-hdf5_aux.F90:subroutine HDF5ReadDatasetReal2D(filename,dataset_name,read_option,option, &
-hdf5_dataset.F90:subroutine WriteHDF5DataSet(string,int_array,real_array,length,file_id, &
-hydrostatic.F90:subroutine HydrostaticUpdateCoupler(coupler,option,grid)
-hydrostatic.F90:subroutine HydrostaticTest()
-immis.F90:subroutine ImmisTimeCut(realization)
-immis.F90:subroutine ImmisSetup(realization)
-immis.F90:subroutine ImmisSetupPatch(realization)
-immis.F90:subroutine ImmisUpdateReasonPatch(reason,realization)
-immis.F90:subroutine ImmisUpdateReason(reason, realization)
-immis.F90:subroutine ImmisUpdateAuxVars(realization)
-immis.F90:subroutine ImmisUpdateAuxVarsPatch(realization)
-immis.F90:subroutine ImmisInitializeTimestep(realization)
-immis.F90:subroutine ImmisUpdateSolution(realization)
-immis.F90:subroutine ImmisUpdateFixedAccumulation(realization)
-immis.F90:subroutine ImmisUpdateFixedAccumPatch(realization)
-immis.F90:subroutine ImmisAccumulation(aux_var,por,vol,rock_dencpr,option,iireac,Res)
-immis.F90:subroutine ImmisSourceSink(mmsrc,psrc,tsrc,hsrc,aux_var,isrctype,Res, energy_flag, option)
-immis.F90:subroutine ImmisFlux(aux_var_up,por_up,tor_up,sir_up,dd_up,perm_up,Dk_up, &
-immis.F90:subroutine ImmisBCFlux(ibndtype,aux_vars,aux_var_up,aux_var_dn, &
-immis.F90:subroutine ImmisResidual(snes,xx,r,realization,ierr)
-immis.F90:subroutine samrpetscobjectstateincrease(vec)
-immis.F90:subroutine ImmisResidualPatch(snes,xx,r,realization,ierr)
-immis.F90:subroutine ImmisJacobian(snes,xx,A,B,flag,realization,ierr)
-immis.F90:subroutine SAMRSetCurrentJacobianPatch(mat,patch)
-immis.F90:subroutine ImmisJacobianPatch(snes,xx,A,B,flag,realization,ierr)
-immis.F90:subroutine ImmisCreateZeroArray(patch,option)
-immis.F90:subroutine ImmisMaxChange(realization)
-immis.F90:subroutine ImmisDestroy(patch)
-immis.F90:subroutine ImmisCheckpointWrite(discretization, viewer)
-immis.F90:subroutine ImmisCheckpointRead(discretization,viewer)
-immis_aux.F90:subroutine ImmisAuxVarInit(aux_var,option)
-immis_aux.F90:subroutine ImmisAuxVarCopy(aux_var,aux_var2,option)
-immis_aux.F90:subroutine ImmisAuxVarCompute_NINC(x,aux_var,saturation_function, &
-immis_aux.F90:subroutine ImmisAuxVarCompute_WINC(x, delx, aux_var,saturation_function, &
-immis_aux.F90:subroutine ImmisAuxVarDestroy(aux_var)
-immis_aux.F90:subroutine ImmisAuxDestroy(aux, option)
-init.F90:subroutine Init(simulation)
-init.F90:subroutine SAMRInitializePreconditioner(p_application, which_pc, pc)
-init.F90:subroutine InitReadStochasticCardFromInput(stochastic,option)
-init.F90:subroutine InitReadInputFilenames(option,filenames)
-init.F90:subroutine InitReadRequiredCardsFromInput(realization)
-init.F90:subroutine InitReadInput(simulation)
-init.F90:subroutine setFlowMode(option)
-init.F90:subroutine assignMaterialPropToRegions(realization)
-init.F90:subroutine assignSubcontinuumPropToRegions(realization)
-init.F90:subroutine verifyAllCouplers(realization)
-init.F90:subroutine verifyCoupler(realization,patch,coupler_list)
-init.F90:subroutine readRegionFiles(realization)
-init.F90:subroutine readMaterialsFromFile(realization,filename)
-init.F90:subroutine readPermeabilitiesFromFile(realization,material_property)
-init.F90:subroutine readVectorFromFile(realization,vector,filename,vector_type)
-init.F90:subroutine readFlowInitialCondition(realization,filename)
-init.F90:subroutine readTransportInitialCondition(realization,filename)
-init.F90:subroutine Create_IOGroups(option)
-init.F90:subroutine InitReadHDF5CardsFromInput(realization)
-input.F90:subroutine InputDefaultMsg1(input,option,buffer)
-input.F90:subroutine InputDefaultMsg2(input,option)
-input.F90:subroutine InputErrorMsg1(input,option,buffer1,buffer2)
-input.F90:subroutine InputErrorMsg2(input,option)
-input.F90:subroutine InputReadStringErrorMsg1(input, option, buffer)
-input.F90:subroutine InputReadStringErrorMsg2(input, option)
-input.F90:subroutine InputFindStringErrorMsg(input, option, string)
-input.F90:subroutine InputReadInt1(input, option, int)
-input.F90:subroutine InputReadInt2(string, option, int, ierr)
-input.F90:subroutine InputReadDouble1(input, option, double)
-input.F90:subroutine InputReadDouble2(string, option, double, ierr)
-input.F90:subroutine InputReadNDoubles1(input, option, double, n)
-input.F90:subroutine InputReadNDoubles2(string, option, double, n, ierr)
-input.F90:subroutine InputReadFlotranString1(option, fid, string, ierr)
-input.F90:subroutine InputReadFlotranString2(input, option)
-input.F90:subroutine InputReadFlotranStringSlave(input, option)
-input.F90:subroutine InputReadWord1(input, option, word, return_blank_error)
-input.F90:subroutine InputReadWord2(string, word, return_blank_error, ierr)
-input.F90:subroutine InputReadNChars1(input, option, chars, n, return_blank_error)
-input.F90:subroutine InputReadNChars2(string, chars, n, return_blank_error, ierr)
-input.F90:subroutine InputReadQuotedWord(input, option, word, return_blank_error)
-input.F90:subroutine InputReadPath(string, word, return_blank_error, ierr)
-input.F90:subroutine InputFindStringInFile1(input, option, string)
-input.F90:subroutine InputFindStringInFile2(input, option, string, print_warning)
-input.F90:subroutine InputSkipToEND(input,option,string)
-input.F90:subroutine InputGetCommandLineInt(string,int_value,found,option)
-input.F90:subroutine InputGetCommandLineReal(string,double_value,found,option)
-input.F90:subroutine InputGetCommandLineString(string,string_value,found,option)
-input.F90:subroutine InputGetCommandLineTruth(string,truth_value,found,option)
-input.F90:subroutine getCommandLineArgument(i,arg)
-input.F90:subroutine InputDestroy(input)
-level.F90:subroutine LevelAddPatch(new_patch,level)
-level.F90:subroutine LevelAddToList(new_level,level_list)
-level.F90:subroutine LevelConvertListToArray(level_list)
-level.F90:subroutine LevelProcessCouplers(level,flow_conditions,transport_conditions, &
-level.F90:subroutine LevelInitAllCouplerAuxVars(level,option)
-level.F90:subroutine LevelInitCouplerAuxVars(level,option)
-level.F90:subroutine LevelUpdateAllCouplerAuxVars(level,force_update_flag,option)
-level.F90:subroutine LevelUpdateCouplerAuxVars(level,force_update_flag,field,option)
-level.F90:subroutine LevelDestroyList(level_list)
-level.F90:subroutine LevelDestroy(level)
-logging.F90:subroutine LoggingCreate()
-logging.F90:subroutine LoggingDestroy()
-mass_balance.F90:subroutine MassBalanceCreate(realization)
-mass_balance.F90:subroutine MassBalanceUpdate(realization,flow_solver,tran_solver)
-material.F90:subroutine MaterialPropertyRead(material_property,input,option)
-material.F90:subroutine MaterialPropertyAddToList(material_property,list)
-material.F90:subroutine MaterialPropConvertListToArray(list,array,option)
-material_aux.F90:subroutine MaterialAuxVarInit(aux_var,option)
-material_aux.F90:subroutine MaterialAuxVarCopy(aux_var,aux_var2,option)
-material_aux.F90:subroutine AuxVarDestroy(aux_var)
-material_aux.F90:subroutine MaterialAuxDestroy(aux)
-matrix_block_aux.F90:subroutine MatrixBlockAuxVarInit1(aux_var,dim1,dim2,dim3,option)
-matrix_block_aux.F90:subroutine MatrixBlockAuxVarInit2(aux_var,matrix_info,option)
-matrix_block_aux.F90:subroutine MatrixBlockAuxVarCopy(aux_var,aux_var2,option)
-matrix_block_aux.F90:subroutine MatrixBlockAuxVarDestroy(aux_var)
-matrix_block_aux.F90:subroutine MatrixBlockInfoDestroy(matrix_info)
-matrix_buffer.F90:subroutine MatrixBufferInit(A,matrix_buffer,grid)
-matrix_buffer.F90:subroutine MatrixBufferZero(matrix_buffer)
-matrix_buffer.F90:subroutine MatrixBufferAdd(matrix_buffer,irow,icol,value)
-matrix_buffer.F90:subroutine MatrixBufferZeroRows(matrix_buffer,nrows,rows)
-matrix_buffer.F90:subroutine MatrixBufferSetValues(A,matrix_buffer)
-matrix_buffer.F90:subroutine MatrixBufferSetValuesHypre(A,matrix_buffer)
-matrix_buffer.F90:subroutine MatrixBufferSetValuesAij(A,matrix_buffer)
-matrix_buffer.F90:subroutine MatrixBufferDestroy(matrix_buffer)
-mfd.F90:subroutine MFDCreateJacobian(grid, mfd_aux, mat_type, J, option)
-mfd.F90:subroutine MFDInitializeMassMatrices(grid, field, &
-mfd.F90:subroutine MFDAuxGenerateStiffMatrix(aux_var, rich_aux_var, global_aux_var,  &
-mfd.F90:subroutine MFDAuxGenerateRhs(patch, grid, ghosted_cell_id, PermTensor, bc_g, source_f,  bc_h, aux_var, &
-mfd.F90:subroutine MFDAuxJacobianLocal( grid, aux_var, &
-mfd.F90:subroutine MFDAuxReconstruct(face_pr, source_f, aux_var, rich_aux_var, global_aux_var, Accum, &
-mfd.F90:subroutine  MFDAuxUpdateCellPressure(face_pres, face_DELTA_pres, mfd_aux_var,&
-mfd.F90:subroutine MFDAuxFluxes(patch, grid, ghosted_cell_id, xx, face_pr, aux_var, PermTensor, rich_aux_var, global_aux_var, &
-mfd.F90:subroutine MFDComputeDensity(global_aux_var, pres, den, dden_dp, option)
-mfd.F90:subroutine MFDAuxComputeGeometricValues (grid, ghosted_cell_id, aux_var, PermTensor, option)
-mfd.F90:subroutine MFDAuxGenerateMassMatrixInv(grid, ghosted_cell_id,  aux_var, volume, PermTensor, option)
-mfd_aux.F90:subroutine MFDAuxInit(aux, num_aux, option)
-mfd_aux.F90:subroutine MFDAuxVarInit(aux_var, numfaces, option)
-mfd_aux.F90:subroutine MFDAuxAddFace(aux_var, option, face_id)
-mfd_aux.F90:subroutine MFDAuxVarDestroy(aux_var)
-mfd_aux.F90:subroutine MFDAuxDestroy(aux)
-mfd_aux.F90:subroutine MFDAuxInitResidDerivArrays(aux_var, option)
-mfd_aux.F90:subroutine MFDAuxInitStiffMatrix(aux_var, option)
-mixed_fluid_eos.F90:subroutine mixture_eos_noderiv (p,t,xga,sg,energyscale,num_phase,num_spec,&
-mixed_fluid_eos.F90:subroutine mixture_eos(p,t,xga,sg,energyscale,num_phase,num_spec, &
-mphase.F90:subroutine MphaseTimeCut(realization)
-mphase.F90:subroutine init_span_wanger(realization)
-mphase.F90:subroutine MphaseSetup(realization)
-mphase.F90:subroutine MphaseSetupPatch(realization)
-mphase.F90:subroutine MphaseComputeMassBalance(realization,mass_balance)
-mphase.F90:subroutine MphaseComputeMassBalancePatch(realization,mass_balance)
-mphase.F90:subroutine MphaseZeroMassBalDeltaPatch(realization)
-mphase.F90:subroutine MphaseUpdateMassBalancePatch(realization)
-mphase.F90:subroutine MPhaseUpdateReason(reason, realization)
-mphase.F90:subroutine MphaseUpdateAuxVars(realization)
-mphase.F90:subroutine MphaseUpdateAuxVarsPatch(realization)
-mphase.F90:subroutine MphaseInitializeTimestep(realization)
-mphase.F90:subroutine MphaseUpdateSolution(realization)
-mphase.F90:subroutine MphaseUpdateSolutionPatch(realization)
-mphase.F90:subroutine MphaseUpdateFixedAccumulation(realization)
-mphase.F90:subroutine MphaseUpdateFixedAccumPatch(realization)
-mphase.F90:subroutine MphaseAccumulation(aux_var,global_aux_var,por,vol,rock_dencpr, &
-mphase.F90:subroutine MphaseSourceSink(mmsrc,nsrcpara,psrc,tsrc,hsrc,csrc,aux_var,isrctype,Res, &
-mphase.F90:subroutine MphaseFlux(aux_var_up,por_up,tor_up,sir_up,dd_up,perm_up,Dk_up, &
-mphase.F90:subroutine MphaseFlux(aux_var_up,por_up,tor_up,sir_up,dd_up,perm_up,Dk_up, &
-mphase.F90:subroutine MphaseBCFlux(ibndtype,aux_vars,aux_var_up,aux_var_dn, &
-mphase.F90:subroutine MphaseResidual(snes,xx,r,realization,ierr)
-mphase.F90:subroutine samrpetscobjectstateincrease(vec)
-mphase.F90:subroutine MphaseVarSwitchPatch(xx, realization, icri, ichange)
-mphase.F90:subroutine MphaseResidualPatch(snes,xx,r,realization,ierr)
-mphase.F90:subroutine MphaseJacobian(snes,xx,A,B,flag,realization,ierr)
-mphase.F90:subroutine SAMRSetCurrentJacobianPatch(mat,patch)
-mphase.F90:subroutine MphaseJacobianPatch(snes,xx,A,B,flag,realization,ierr)
-mphase.F90:subroutine MphaseCreateZeroArray(patch,option)
-mphase.F90:subroutine MphaseMaxChange(realization)
-mphase.F90:subroutine MphaseMaxChangePatch(realization,  max_c, max_s)
-mphase.F90:subroutine MphaseDestroy(patch)
-mphase.F90:subroutine MphaseCheckpointWrite(discretization, viewer)
-mphase.F90:subroutine MphaseCheckpointRead(discretization,viewer)
-mphase_aux.F90:subroutine MphaseAuxVarInit(aux_var,option)
-mphase_aux.F90:subroutine MphaseAuxVarCopy(aux_var,aux_var2,option)
-mphase_aux.F90:subroutine MphaseAuxVarCompute_NINC(x,aux_var,global_aux_var,iphase,saturation_function, &
-mphase_aux.F90:subroutine MphaseAuxVarCompute_WINC(x, delx, aux_var, global_auxvar,iphase,saturation_function, &
-mphase_aux.F90:subroutine MphaseAuxVarDestroy(aux_var)
-mphase_aux.F90:subroutine MphaseAuxDestroy(aux, option)
-observation.F90:subroutine ObservationRead(observation,input,option)
-observation.F90:subroutine ObservationInitList(list)
-observation.F90:subroutine ObservationAddToList(new_observation,list)
-observation.F90:subroutine ObservationRemoveFromList(observation,list)
-observation.F90:subroutine ObservationDestroyList(observation_list)
-observation.F90:subroutine ObservationDestroy(observation)
-oil_eos.F90:subroutine Vis_oil(p,t,viso, ierr)
-oil_eos.F90:subroutine PSAT_oil(t,psat,ierr)
-oil_eos.F90:subroutine oil_eos(t,p, x_mid, x_heavy, denoil, h, scale, ierr)
-oil_eos.F90:subroutine Meth_Eos
-option.F90:subroutine OptionInitAll(option)
-option.F90:subroutine OptionInitRealization(option)
-option.F90:subroutine OptionCheckCommandLine(option)
-option.F90:subroutine printErrMsg1(option)
-option.F90:subroutine printErrMsg2(option,string)
-option.F90:subroutine printWrnMsg1(option)
-option.F90:subroutine printWrnMsg2(option,string)
-option.F90:subroutine printMsg1(option)
-option.F90:subroutine printMsg2(option,string)
-option.F90:subroutine OptionMaxMinMeanVariance(value,max,min,mean,variance, &
-option.F90:subroutine OptionMeanVariance(value,mean,variance,calculate_variance,option)
-option.F90:subroutine OutputOptionDestroy(output_option)
-option.F90:subroutine OptionDestroy(option)
-output.F90:subroutine OutputInit(realization,num_steps)
-output.F90:subroutine Output(realization,plot_flag,transient_plot_flag)
-output.F90:subroutine OutputObservation(realization)
-output.F90:subroutine OutputTecplotBlock(realization)
-output.F90:subroutine OutputVelocitiesTecplotBlock(realization)
-output.F90:subroutine OutputFluxVelocitiesTecplotBlk(realization,iphase, &
-output.F90:subroutine OutputTecplotPoint(realization)
-output.F90:subroutine OutputVelocitiesTecplotPoint(realization)
-output.F90:subroutine OutputVectorTecplot(filename,dataset_name,realization,vector)
-output.F90:subroutine WriteTecplotDataSetFromVec(fid,realization,vec,datatype)
-output.F90:subroutine WriteTecplotStructuredGrid(fid,realization)
-output.F90:subroutine WriteTecplotDataSet(fid,realization,array,datatype,size_flag)
-output.F90:subroutine OutputObservationTecplot(realization)
-output.F90:subroutine WriteObservationHeaderForCell(fid,realization,region,icell, &
-output.F90:subroutine WriteObservationHeaderForCoord(fid,realization,region, &
-output.F90:subroutine WriteObservationHeaderForBC(fid,realization,coupler_name)
-output.F90:subroutine WriteObservationDataForCell(fid,realization,local_id)
-output.F90:subroutine WriteObservationDataForCoord(fid,realization,region)
-output.F90:subroutine WriteObservationDataForBC(fid,realization,patch,connection_set)
-output.F90:subroutine WriteVelocityAtCell(fid,realization,local_id)
-output.F90:subroutine WriteVelocityAtCoord(fid,realization,region)
-output.F90:subroutine OutputVTK(realization)
-output.F90:subroutine OutputVelocitiesVTK(realization)
-output.F90:subroutine WriteVTKGrid(fid,realization)
-output.F90:subroutine WriteVTKDataSetFromVec(fid,realization,dataset_name,vec,datatype)
-output.F90:subroutine WriteVTKDataSet(fid,realization,dataset_name,array,datatype, &
-output.F90:subroutine OutputHDF5(realization)
-output.F90:subroutine SAMRCopyVecToVecComponent(vec,svec, component)
-output.F90:subroutine SAMRRegisterForViz(ptr,vec,component, namestr)
-output.F90:subroutine SAMRWritePlotData(ptr, time)
-output.F90:subroutine OutputMAD(realization)
-output.F90:subroutine WriteHDF5FluxVelocities(name,realization,iphase,direction,file_id)
-output.F90:subroutine WriteHDF5Coordinates(name,option,length,array,file_id)
-output.F90:subroutine GetCoordinates(grid,vec,direction)
-output.F90:subroutine ConvertArrayToNatural(indices,array,local_size,global_size,option)
-output.F90:subroutine OutputGetVarFromArray(realization,vec,ivar,isubvar,isubvar1)
-output.F90:subroutine GetCellCenteredVelocities(realization,vec,iphase,direction)
-output.F90:subroutine ComputeFlowMassBalance(realization)
-output.F90:subroutine OutputMassBalanceNew(realization)
-output.F90:subroutine ComputeFlowCellVelocityStats(realization)
-output.F90:subroutine ComputeFlowFluxVelocityStats(realization)
-output.F90:subroutine OutputPermeability(realization)
-patch.F90:subroutine PatchAddToList(new_patch,patch_list)
-patch.F90:subroutine PatchConvertListToArray(patch_list)
-patch.F90:subroutine PatchLocalizeRegions(patch,regions,option)
-patch.F90:subroutine PatchProcessCouplers(patch,flow_conditions,transport_conditions, &
-patch.F90:subroutine PatchInitAllCouplerAuxVars(patch,reaction,option)
-patch.F90:subroutine PatchInitCouplerAuxVars(coupler_list,reaction,option)
-patch.F90:subroutine PatchUpdateAllCouplerAuxVars(patch,force_update_flag,option)
-patch.F90:subroutine PatchUpdateCouplerAuxVars(patch,coupler_list,force_update_flag, &
-patch.F90:subroutine PatchScaleSourceSink(patch,option)
-patch.F90:subroutine PatchInitConstraints(patch,reaction,option)
-patch.F90:subroutine PatchInitCouplerConstraints(coupler_list,reaction,option)
-patch.F90:subroutine PatchUpdateUniformVelocity(patch,velocity,option)
-patch.F90:subroutine PatchGetDataset(patch,field,reaction,option,output_option,vec,ivar, &
-patch.F90:subroutine PatchSetDataset(patch,field,option,vec,vec_format,ivar,isubvar)
-patch.F90:subroutine PatchCountCells(patch,total_count,active_count)
-patch.F90:subroutine PatchCalculateCFL1Timestep(patch,option,max_dt_cfl_1)
-patch.F90:subroutine PatchGetIvarsFromKeyword(keyword,ivar,isubvar,var_type,option)
-patch.F90:subroutine PatchDestroyList(patch_list)
-patch.F90:subroutine PatchDestroy(patch)
-pckr_mod.F90:subroutine pflow_pckr(ipckrtype,pckr_swir,pckr_lambda,pckr_alpha,&
-pckr_mod.F90:subroutine pflow_pckr_noderiv_exec(ipckrtype,pckr_sir,pckr_lambda, &
-pckr_mod.F90:subroutine pckrNH_noderiv( sat, pc, kr, saturation_function, option)
-pckr_mod.F90:subroutine pckrHY_noderiv(sat, hysdat, pc, kr, saturation_function, option)
-reaction.F90:subroutine ReactionRead(reaction,input,option)
-reaction.F90:subroutine ReactionReadMineralKinetics(reaction,input,option)
-reaction.F90:subroutine ReactionReadRedoxSpecies(reaction,input,option)
-reaction.F90:subroutine ReactionProcessConstraint(reaction,constraint_name, &
-reaction.F90:subroutine ReactionEquilibrateConstraint(rt_auxvar,global_auxvar, &
-reaction.F90:subroutine ReactionPrintConstraint(constraint_coupler,reaction,option)
-reaction.F90:subroutine DoubleLayer(constraint_coupler,reaction,option)
-reaction.F90:subroutine srfcmplx(irxn,icplx,lnQK,logK,Z,potential,tempk, &
-reaction.F90:subroutine ReactionReadOutput(reaction,input,option)
-reaction.F90:subroutine RJumpStartKineticSorption(rt_auxvar,global_auxvar, &
-reaction.F90:subroutine RReact(rt_auxvar,global_auxvar,total,volume,porosity, &
-reaction.F90:subroutine RReaction(Res,Jac,derivative,rt_auxvar,global_auxvar,porosity, &
-reaction.F90:subroutine RReactionDerivative(Res,Jac,rt_auxvar,global_auxvar,porosity, &
-reaction.F90:subroutine CO2AqActCoeff(rt_auxvar,global_auxvar,reaction,option)
-reaction.F90:subroutine RActivityCoefficients(rt_auxvar,global_auxvar,reaction,option)
-reaction.F90:subroutine RTotal(rt_auxvar,global_auxvar,reaction,option)
-reaction.F90:subroutine RTotalSorb(rt_auxvar,global_auxvar,reaction,option)
-reaction.F90:subroutine RTotalSorbKD(rt_auxvar,global_auxvar,reaction,option)
-reaction.F90:subroutine RTotalSorbEqSurfCplx(rt_auxvar,global_auxvar,reaction,option)
-reaction.F90:subroutine RTotalSorbEqIonx(rt_auxvar,global_auxvar,reaction,option)
-reaction.F90:subroutine RMultiRateSorption(Res,Jac,compute_derivative,rt_auxvar, &
-reaction.F90:subroutine RKineticSurfCplx(Res,Jac,compute_derivative,rt_auxvar, &
-reaction.F90:subroutine RKineticMineral(Res,Jac,compute_derivative,rt_auxvar, &
-reaction.F90:subroutine RAccumulationSorb(rt_aux_var,global_aux_var,vol,reaction, &
-reaction.F90:subroutine RAccumulationSorbDerivative(rt_aux_var,global_aux_var, &
-reaction.F90:subroutine RGeneral(Res,Jac,compute_derivative,rt_auxvar,global_auxvar, &
-reaction.F90:subroutine RSolve(Res,Jac,conc,update,ncomp,use_log_formulation)
-reaction.F90:subroutine ReactionFitLogKCoef(coefs,logK,name,option,reaction)
-reaction.F90:subroutine ReactionInitializeLogK(logKcoef,logKs,logK,option,reaction)
-reaction.F90:subroutine ReactionInterpolateLogK(coefs,logKs,temp,n)
-reaction.F90:subroutine ReactionComputeKd(icomp,retardation,rt_auxvar,global_auxvar, &
-reaction.F90:subroutine RAge(rt_aux_var,global_aux_var,por,vol,option,reaction,Res)
-reaction.F90:subroutine RTAuxVarCompute(rt_aux_var,global_aux_var,reaction,option)
-reaction.F90:subroutine RTAccumulation(rt_aux_var,global_aux_var,por,vol,reaction,option,Res)
-reaction.F90:subroutine RTAccumulationDerivative(rt_aux_var,global_aux_var, &
-reaction.F90:subroutine RCalculateCompression(global_auxvar,rt_auxvar,reaction,option)
-reaction.F90:subroutine RTPrintAuxVar(rt_auxvar,reaction,option)
-reaction_aux.F90:subroutine SpeciesIndexDestroy(species_idx)
-reaction_aux.F90:subroutine AqueousSpeciesDestroy(species)
-reaction_aux.F90:subroutine AqueousSpeciesListDestroy(aq_species_list)
-reaction_aux.F90:subroutine GasSpeciesDestroy(species)
-reaction_aux.F90:subroutine MineralDestroy(mineral)
-reaction_aux.F90:subroutine ColloidDestroy(colloid)
-reaction_aux.F90:subroutine DatabaseRxnDestroy(dbaserxn)
-reaction_aux.F90:subroutine SurfaceComplexationRxnDestroy(srfcplxrxn)
-reaction_aux.F90:subroutine SurfaceComplexDestroy(srfcplx)
-reaction_aux.F90:subroutine IonExchangeRxnDestroy(ionxrxn)
-reaction_aux.F90:subroutine GeneralRxnDestroy(rxn)
-reaction_aux.F90:subroutine KDRxnDestroy(rxn)
-reaction_aux.F90:subroutine AqueousSpeciesConstraintDestroy(constraint)
-reaction_aux.F90:subroutine MineralConstraintDestroy(constraint)
-reaction_aux.F90:subroutine SurfaceComplexConstraintDestroy(constraint)
-reaction_aux.F90:subroutine ColloidConstraintDestroy(constraint)
-reaction_aux.F90:subroutine ReactionDestroy(reaction)
-reaction_chunk.F90:subroutine RPack(rt_auxvar,global_auxvar,total,rt_auxvar_chunk,volume, &
-reaction_chunk.F90:subroutine RUnpack(rt_auxvar,free_ion,rt_auxvar_chunk,ichunk,ithread,reaction)
-reaction_chunk.F90:subroutine RReactChunk(auxvar,num_iterations_,reaction,vector_length, &
-reaction_chunk.F90:subroutine RReactionChunk(Res,Jac,derivative,auxvar,vector_length,ithread,reaction,option)
-reaction_chunk.F90:subroutine RActivityCoefficientsChunk(auxvar,vector_length,ithread,reaction,option)
-reaction_chunk.F90:subroutine RTotalChunk(auxvar,vector_length,ithread,reaction,option)
-reaction_chunk.F90:subroutine RTotalSorbChunk(auxvar,vector_length,ithread,reaction,option)
-reaction_chunk.F90:subroutine RTotalSorbEqSurfCplxChunk(auxvar,vector_length,ithread,reaction,option)
-reaction_chunk.F90:subroutine RKineticMineralChunk(Res,Jac,compute_derivative,auxvar,vector_length,ithread,reaction, &
-reaction_chunk.F90:subroutine RAccumulationSorbChunk(auxvar,vector_length,ithread,reaction,option,Res)
-reaction_chunk.F90:subroutine RAccumulationSorbDerivChunk(auxvar,vector_length,ithread,reaction,option,J)
-reaction_chunk.F90:subroutine RTAuxVarComputeChunk(auxvar,vector_length,ithread,reaction,option)
-reaction_chunk.F90:subroutine RTAccumulationChunk(auxvar,vector_length,ithread,reaction,option,Res)
-reaction_chunk.F90:subroutine RTAccumulationDerivativeChunk(auxvar,vector_length,ithread,reaction,option,J)
-reactive_transport.F90:subroutine RTTimeCut(realization)
-reactive_transport.F90:subroutine RTSetup(realization)
-reactive_transport.F90:subroutine RTSetupPatch(realization)
-reactive_transport.F90:subroutine RTCheckUpdate(snes_,C,dC,realization,changed,ierr)
-reactive_transport.F90:subroutine RTCheckUpdatePatch(snes_,C,dC,realization,changed,ierr)
-reactive_transport.F90:subroutine RTComputeMassBalance(realization,mass_balance)
-reactive_transport.F90:subroutine RTComputeMassBalancePatch(realization,mass_balance)
-reactive_transport.F90:subroutine RTZeroMassBalanceDeltaPatch(realization)
-reactive_transport.F90:subroutine RTUpdateMassBalancePatch(realization)
-reactive_transport.F90:subroutine RTInitializeTimestep(realization)
-reactive_transport.F90:subroutine RTInitializeTimestepPatch(realization)
-reactive_transport.F90:subroutine RTUpdateSolution(realization)
-reactive_transport.F90:subroutine RTUpdateSolutionPatch(realization)
-reactive_transport.F90:subroutine RTUpdateFixedAccumulationPatch(realization)
-reactive_transport.F90:subroutine RTUpdateTransportCoefs(realization)
-reactive_transport.F90:subroutine RTUpdateTransportCoefsPatch(realization)
-reactive_transport.F90:subroutine RTUpdateRHSCoefs(realization)
-reactive_transport.F90:subroutine RTUpdateRHSCoefsPatch(realization)
-reactive_transport.F90:subroutine RTCalculateRHS_t0(realization)
-reactive_transport.F90:subroutine RTCalculateRHS_t0Patch(realization)
-reactive_transport.F90:subroutine RTCalculateRHS_t1(realization)
-reactive_transport.F90:subroutine RTCalculateRHS_t1Patch(realization)
-reactive_transport.F90:subroutine RTCalculateTransportMatrix(realization,T)
-reactive_transport.F90:subroutine SAMRSetCurrentJacobianPatch(mat,patch)
-reactive_transport.F90:subroutine RTCalculateTranMatrixPatch1(realization,T)
-reactive_transport.F90:subroutine RTCalculateTranMatrixPatch2(realization,T)
-reactive_transport.F90:subroutine SAMRSetJacobianSrcCoeffsOnPatch(which_pc, p_application, p_patch)
-reactive_transport.F90:subroutine RTReact(realization)
-reactive_transport.F90:subroutine SAMRCoarsenVector(p_application, vec)
-reactive_transport.F90:subroutine RTReactPatch(realization)
-reactive_transport.F90:subroutine RTComputeBCMassBalanceOSPatch(realization)
-reactive_transport.F90:subroutine RTTransportResidual(realization,solution_loc,residual,idof)
-reactive_transport.F90:subroutine samrpetscobjectstateincrease(vec)
-reactive_transport.F90:subroutine RTTransportResidualPatch1(realization,solution_loc,residual,idof)
-reactive_transport.F90:subroutine RTTransportResidualPatch2(realization,solution_loc,residual,idof)
-reactive_transport.F90:subroutine RTTransportMatVecPatch2(realization,solution_loc,residual,idof)
-reactive_transport.F90:subroutine RTTransportMatVec(mat, x, y)
-reactive_transport.F90:subroutine SAMRGetRealization(p_application, realization)
-reactive_transport.F90:subroutine SAMRGetPetscTransportMatrix(p_application, transportMat)
-reactive_transport.F90:subroutine RTTransportResidualFluxContribPatch(r,realization,ierr)
-reactive_transport.F90:subroutine RTNumericalJacobianTest(realization)
-reactive_transport.F90:subroutine RTResidual(snes,xx,r,realization,ierr)
-reactive_transport.F90:subroutine samrpetscobjectstateincrease(vec)
-reactive_transport.F90:subroutine RTResidualFluxContribPatch(r,realization,ierr)
-reactive_transport.F90:subroutine RTResidualPatch1(snes,xx,r,realization,ierr)
-reactive_transport.F90:subroutine RTResidualPatch2(snes,xx,r,realization,ierr)
-reactive_transport.F90:subroutine RTJacobian(snes,xx,A,B,flag,realization,ierr)
-reactive_transport.F90:subroutine RTJacobianPatch1(snes,xx,A,B,flag,realization,ierr)
-reactive_transport.F90:subroutine RTJacobianPatch2(snes,xx,A,B,flag,realization,ierr)
-reactive_transport.F90:subroutine SAMRSetJacobianSrcCoeffsOnPatch(which_pc, p_application, p_patch)
-reactive_transport.F90:subroutine RTUpdateAuxVars(realization,update_cells,update_bcs, &
-reactive_transport.F90:subroutine RTUpdateAuxVarsPatch(realization,update_cells,update_bcs, &
-reactive_transport.F90:subroutine RTCreateZeroArray(patch,reaction,option)
-reactive_transport.F90:subroutine RTMaxChange(realization)
-reactive_transport.F90:subroutine RTJumpStartKineticSorption(realization)
-reactive_transport.F90:subroutine RTJumpStartKineticSorptionPatch(realization)
-reactive_transport.F90:subroutine RTCheckpointKineticSorption(realization,viewer,checkpoint)
-reactive_transport.F90:subroutine RTDestroy(realization)
-reactive_transport.F90:subroutine RTDestroyPatch(realization)
-reactive_transport_aux.F90:subroutine RTAuxVarInit(aux_var,reaction,option)
-reactive_transport_aux.F90:subroutine RTAuxVarCopy(aux_var,aux_var2,option)
-reactive_transport_aux.F90:subroutine RTAuxVarChunkDestroy(auxvar)
-reactive_transport_aux.F90:subroutine RTAuxVarDestroy(aux_var)
-reactive_transport_aux.F90:subroutine RTAuxDestroy(aux)
-realization.F90:subroutine RealizationCreateDiscretization(realization)
-realization.F90:subroutine RealizationLocalizeRegions(realization)
-realization.F90:subroutine RealizatonPassFieldPtrToPatches(realization)
-realization.F90:subroutine RealizationAddCoupler(realization,coupler)
-realization.F90:subroutine RealizationAddStrata(realization,strata)
-realization.F90:subroutine RealizationAddObservation(realization,observation)
-realization.F90:subroutine RealizationProcessCouplers(realization)
-realization.F90:subroutine RealizationProcessConditions(realization)
-realization.F90:subroutine RealProcessMatPropAndSatFunc(realization)
-realization.F90:subroutine RealProcessSubcontinuumProp(realization)
-realization.F90:subroutine RealProcessFluidProperties(realization)
-realization.F90:subroutine RealProcessTranConditions(realization)
-realization.F90:subroutine RealizationInitConstraints(realization)
-realization.F90:subroutine RealizationPrintCouplers(realization)
-realization.F90:subroutine RealizationPrintCoupler(coupler,reaction,option)
-realization.F90:subroutine RealizationInitAllCouplerAuxVars(realization)
-realization.F90:subroutine RealizUpdateAllCouplerAuxVars(realization,force_update_flag)
-realization.F90:subroutine RealizationUpdate(realization)
-realization.F90:subroutine RealizAssignInitialConditions(realization)
-realization.F90:subroutine RealizAssignFlowInitCond(realization)
-realization.F90:subroutine RealizAssignTransportInitCond(realization)
-realization.F90:subroutine RealizationScaleSourceSink(realization)
-realization.F90:subroutine RealizationRevertFlowParameters(realization)
-realization.F90:subroutine RealizUpdateUniformVelocity(realization)
-realization.F90:subroutine RealizationAddWaypointsToList(realization)
-realization.F90:subroutine RealizationGetDataset(realization,vec,ivar,isubvar,isubvar1)
-realization.F90:subroutine RealizationSetDataset(realization,vec,vec_format,ivar,isubvar)
-realization.F90:subroutine RealizationUpdateProperties(realization)
-realization.F90:subroutine RealizationUpdatePropertiesPatch(realization)
-realization.F90:subroutine RealLocalToLocalWithArray(realization,array_id)
-realization.F90:subroutine RealizationCountCells(realization,global_total_count, &
-realization.F90:subroutine RealizationSetUpBC4Faces(realization)
-realization.F90:subroutine RealizationPrintGridStatistics(realization)
-realization.F90:subroutine RealizationCalculateCFL1Timestep(realization,max_dt_cfl_1)
-realization.F90:subroutine RealizationDestroy(realization)
-region.F90:subroutine RegionInitList(list)
-region.F90:subroutine RegionAddToList(new_region,list)
-region.F90:subroutine RegionRead(region,input,option)
-region.F90:subroutine RegionReadFromFilename(region,option,filename)
-region.F90:subroutine RegionReadFromFileId(region,input,option)
-region.F90:subroutine RegionDestroyList(region_list)
-region.F90:subroutine RegionDestroy(region)
-richards.F90:subroutine RichardsTimeCut(realization)
-richards.F90:subroutine RichardsSetup(realization)
-richards.F90:subroutine RichardsSetupPatch(realization)
-richards.F90:subroutine RichardsComputeMassBalance(realization,mass_balance)
-richards.F90:subroutine RichardsComputeMassBalancePatch(realization,mass_balance)
-richards.F90:subroutine RichardsCheckMassBalancePatch(realization)
-richards.F90:subroutine RichardsZeroMassBalDeltaPatch(realization)
-richards.F90:subroutine RichardsUpdateMassBalancePatch(realization)
-richards.F90:subroutine RichardsUpdateAuxVars(realization)
-richards.F90:subroutine RichardsInitialPressureReconstruction(realization)
-richards.F90:subroutine RichardsUpdateCellPressure(realization)
-richards.F90:subroutine RichardsUpdateAuxVarsPatch(realization)
-richards.F90:subroutine RichardsInitialPressureReconstructionPatch(realization)
-richards.F90:subroutine RichardsUpdateCellPressurePatch(realization)
-richards.F90:subroutine RichardsUpdateAuxVarsPatchMFD(realization)
-richards.F90:subroutine RichardsInitializeTimestep(realization)
-richards.F90:subroutine RichardsUpdateSolution(realization)
-richards.F90:subroutine RichardsUpdateSolutionPatch(realization)
-richards.F90:subroutine RichardsUpdateFixedAccum(realization)
-richards.F90:subroutine RichardsUpdateFixedAccumPatch(realization)
-richards.F90:subroutine RichardsNumericalJacTest(xx,realization)
-richards.F90:subroutine RichardsAccumDerivative(rich_aux_var,global_aux_var,por,vol, &
-richards.F90:subroutine RichardsAccumulation(rich_aux_var,global_aux_var,por,vol, &
-richards.F90:subroutine RichardsFluxDerivative(rich_aux_var_up,global_aux_var_up,por_up, &
-richards.F90:subroutine RichardsFlux(rich_aux_var_up,global_aux_var_up, &
-richards.F90:subroutine RichardsBCFluxDerivative(ibndtype,aux_vars, &
-richards.F90:subroutine RichardsBCFlux(ibndtype,aux_vars, &
-richards.F90:subroutine RichardsResidual(snes,xx,r,realization,ierr)
-richards.F90:subroutine samrpetscobjectstateincrease(vec)
-richards.F90:subroutine SAMRCoarsenFaceFluxes(p_application, vec, ierr)
-richards.F90:subroutine RichardsResidualMFD(snes,xx,r,realization,ierr)
-richards.F90:subroutine RichardsResidualFluxContribPatch(r,realization,ierr)
-richards.F90:subroutine RichardsResidualPatch1(snes,xx,r,realization,ierr)
-richards.F90:subroutine RichardsResidualPatch2(snes,xx,r,realization,ierr)
-richards.F90:subroutine RichardsResidualPatchMFD1(snes,xx,r,realization,ierr)
-richards.F90:subroutine RichardsResidualPatchMFD2(snes,xx,r,realization,ierr)
-richards.F90:subroutine RichardsJacobian(snes,xx,A,B,flag,realization,ierr)
-richards.F90:subroutine SAMRSetCurrentJacobianPatch(mat,patch)
-richards.F90:subroutine RichardsJacobianMFD(snes,xx,A,B,flag,realization,ierr)
-richards.F90:subroutine SAMRSetCurrentJacobianPatch(mat,patch)
-richards.F90:subroutine RichardsJacobianPatch1(snes,xx,A,B,flag,realization,ierr)
-richards.F90:subroutine RichardsJacobianPatch2(snes,xx,A,B,flag,realization,ierr)
-richards.F90:subroutine SAMRSetJacobianSourceOnPatch(which_pc, index, val, p_application, p_patch)
-richards.F90:subroutine SAMRSetJacobianSrcCoeffsOnPatch(which_pc, p_application, p_patch)
-richards.F90:subroutine RichardsJacobianPatchMFD (snes,xx,A,B,flag,realization,ierr)
-richards.F90:subroutine RichardsCreateZeroArray(patch,option)
-richards.F90:subroutine RichardsMaxChange(realization)
-richards.F90:subroutine RichardsDestroy(realization)
-richards.F90:subroutine RichardsDestroyPatch(realization)
-richards_aux.F90:subroutine RichardsAuxVarInit(aux_var,option)
-richards_aux.F90:subroutine RichardsAuxVarCopy(aux_var,aux_var2,option)
-richards_aux.F90:subroutine RichardsAuxVarCompute(x,aux_var,global_aux_var,&
-richards_aux.F90:subroutine AuxVarDestroy(aux_var)
-richards_aux.F90:subroutine RichardsAuxDestroy(aux)
-saturation.F90:subroutine SaturationUpdateCoupler(coupler,option,grid,saturation_functions, &
-saturation_function.F90:subroutine SaturationFunctionRead(saturation_function,input,option)
-saturation_function.F90:subroutine SaturationFunctionComputeSpline(option,saturation_function)
-saturation_function.F90:subroutine SaturationFunctionAddToList(saturation_function,list)
-saturation_function.F90:subroutine SaturatFuncConvertListToArray(list,array,option)
-saturation_function.F90:subroutine SaturationFunctionCompute(pressure,saturation,relative_perm, &
-saturation_function.F90:subroutine SatFuncGetRelPermFromSat(saturation,relative_perm,dkr_Se, &
-saturation_function.F90:subroutine SatFuncGetCapillaryPressure(capillary_pressure,saturation, &
-simulation.F90:subroutine SimulationCreateProcessorGroups(option,num_groups)
-simulation.F90:subroutine SimulationResetTimeSteppers(simulation)
-simulation.F90:subroutine SimulationDestroy(simulation)
-solver.F90:subroutine SolverCreateSNES(solver,comm)
-solver.F90:subroutine SolverSetSNESOptions(solver)
-solver.F90:subroutine SolverReadLinear(solver,input,option)
-solver.F90:subroutine SolverReadNewton(solver,input,option)
-solver.F90:subroutine SolverPrintLinearInfo(solver,print_to_screen,print_to_file,fid, &
-solver.F90:subroutine SolverPrintNewtonInfo(solver,print_to_screen,print_to_file,fid, &
-solver.F90:subroutine SolverCheckCommandLine(solver)
-solver.F90:subroutine SolverDestroy(solver)
-spline.F90:subroutine spline(x,y,n,y2)
-spline.F90:subroutine splint(xa,ya,y2a,n,x,y)
-spline.F90:subroutine locate(xx,n,x,j)
-stochastic.F90:subroutine StochasticInit(stochastic,option)
-stochastic.F90:subroutine StochasticRun(stochastic,option)
-stochastic_aux.F90:subroutine StochasticRead(stochastic,input,option)
-stochastic_aux.F90:subroutine StochasticDestroy(stochastic)
-strata.F90:subroutine StrataInitList(list)
-strata.F90:subroutine StrataRead(strata,input,option)
-strata.F90:subroutine StrataAddToList(new_strata,list)
-strata.F90:subroutine StrataDestroyList(strata_list)
-strata.F90:subroutine StrataDestroy(strata)
-string.F90:subroutine StringToUpper(string)
-string.F90:subroutine StringToLower(string)
-string.F90:subroutine StringReadQuotedWord(string, name, return_blank_error, ierr)
-string.F90:subroutine StringAdjustl(string)
-structured_grid.F90:subroutine StructuredGridCreateDM(structured_grid,da,ndof,stencil_width, &
-structured_grid.F90:subroutine StructGridComputeLocalBounds(structured_grid,da)
-structured_grid.F90:subroutine samr_patch_get_corners(p_patch, nxs, nys, nzs, nlx, nly, nlz)
-structured_grid.F90:subroutine samr_patch_get_ghostcorners(p_patch, nxs, nys, nzs, nlx, nly, nlz)
-structured_grid.F90:subroutine StructuredGridCreateVecFromDM(da,vector,vector_type)
-structured_grid.F90:subroutine StructuredGridReadDXYZ(structured_grid,input,option)
-structured_grid.F90:subroutine StructuredGridReadArray(a,n,input,option)
-structured_grid.F90:subroutine StructuredGridReadArrayNew(array,array_size,axis,input,option)
-structured_grid.F90:subroutine StructuredGridComputeSpacing(structured_grid,nG2A,nG2L,option)
-structured_grid.F90:subroutine StructuredGridComputeCoord(structured_grid,option,origin_global, &
-structured_grid.F90:subroutine samr_patch_get_origin(p_patch, xs, ys, zs)
-structured_grid.F90:subroutine StructGridGetIJKFromCoordinate(structured_grid,x,y,z,i,j,k)
-structured_grid.F90:subroutine StructGridGetIJKFromLocalID(structured_grid,local_id,i,j,k)
-structured_grid.F90:subroutine StructGridGetIJKFromGhostedID(structured_grid,ghosted_id,i,j,k)
-structured_grid.F90:subroutine StructGridPopulateConnection(radius,structured_grid,connection,iface, &
-structured_grid.F90:subroutine StructuredGridComputeVolumes(radius,structured_grid,option,nL2G,volume)
-structured_grid.F90:subroutine StructuredGridMapIndices(structured_grid,nG2L,nL2G,nL2A,nG2A)
-structured_grid.F90:subroutine StructGridGetGhostedNeighbors(structured_grid,ghosted_id, &
-structured_grid.F90:subroutine StructuredGridDestroy(structured_grid)
-structured_grid.F90:subroutine StructuredGridVecGetMaskArrayCellF90(structured_grid, vec, f90ptr, ierr)
-structured_grid.F90:subroutine samrvecgetmaskarraycellf90(patch, petscvec, f90wrap)
-structured_grid.F90:subroutine StructuredGridVecGetArrayCellF90(structured_grid, vec, f90ptr, ierr)
-structured_grid.F90:subroutine samr_vecgetarraycellf90(patch, petscvec, f90wrap)
-structured_grid.F90:subroutine StructuredGridVecGetArraySideF90(structured_grid, axis, vec, f90ptr, ierr)
-structured_grid.F90:subroutine samr_vecgetarraysidef90(patch, axis, petscvec, f90wrap)
-structured_grid.F90:subroutine StructGridVecRestoreArrayF90(structured_grid, vec, f90ptr, ierr)
-sub_grid.F90:subroutine SubGridRead(sub_grid,fid,myrank)
-sub_grid.F90:subroutine SubGridAllocateLists(list)
-sub_grid.F90:subroutine SubGridInitList(list)
-sub_grid.F90:subroutine SubGridAddToList(new_sub_grid,list)
-sub_grid.F90:subroutine SubGridConvertListToArray(list)
-sub_grid.F90:subroutine SubGridDestroy(sub_grid)
-sub_grid.F90:subroutine SubGridDestroyList(list)
-subcontinuum.F90:subroutine SubcontinuumPropertyRead(subcontinuum_property,input,option)
-subcontinuum.F90:subroutine SubcontinuumPropertyAddToList(subcontinuum_property,list)
-subcontinuum.F90:subroutine SubcontinuumPropConvertListToArray(list,array)
-subcontinuum.F90:subroutine SubcontinuumFieldCreatePatch(patch)
-subcontinuum.F90:subroutine SubcontinuumFieldCreateRealization(realization)
-subcontinuum.F90:subroutine GridPopulateSubcontinuum(realization)
-subcontinuum_transport.F90:subroutine RTSetup(realization)
-subcontinuum_transport.F90:subroutine STSetupPatch(realization)
-subcontinuum_transport_aux.F90:subroutine STAuxVarInit(aux_var,reaction,option)
-subcontinuum_transport_aux.F90:subroutine STAuxVarCopy(aux_var,aux_var2,option)
-subcontinuum_transport_aux.F90:subroutine STAuxVarDestroy(aux_var)
-subcontinuum_transport_aux.F90:subroutine STAuxDestroy(aux)
-thc.F90:subroutine THCTimeCut(realization)
-thc.F90:subroutine THCSetup(realization)
-thc.F90:subroutine THCSetupPatch(realization)
-thc.F90:subroutine THCComputeMassBalance(realization, mass_balance)
-thc.F90:subroutine THCComputeMassBalancePatch(realization,mass_balance)
-thc.F90:subroutine THCUpdateAuxVars(realization)
-thc.F90:subroutine THCUpdateAuxVarsPatch(realization)
-thc.F90:subroutine THCInitializeTimestep(realization)
-thc.F90:subroutine THCUpdateSolution(realization)
-thc.F90:subroutine THCUpdateFixedAccumulation(realization)
-thc.F90:subroutine THCUpdateFixedAccumPatch(realization)
-thc.F90:subroutine THCNumericalJacobianTest(xx,realization)
-thc.F90:subroutine THCAccumDerivative(thc_aux_var,global_aux_var,por,vol, &
-thc.F90:subroutine THCAccumulation(aux_var,global_aux_var,por,vol,rock_dencpr,option,Res)
-thc.F90:subroutine THCFluxDerivative(aux_var_up,global_aux_var_up,por_up,tor_up, &
-thc.F90:subroutine THCFlux(aux_var_up,global_aux_var_up, &
-thc.F90:subroutine THCBCFluxDerivative(ibndtype,aux_vars, &
-thc.F90:subroutine THCBCFlux(ibndtype,aux_vars,aux_var_up,global_aux_var_up, &
-thc.F90:subroutine THCResidual(snes,xx,r,realization,ierr)
-thc.F90:subroutine samrpetscobjectstateincrease(vec)
-thc.F90:subroutine SAMRCoarsenFaceFluxes(p_application, vec, ierr)
-thc.F90:subroutine THCResidualFluxContribPatch(r,realization,ierr)
-thc.F90:subroutine THCResidualPatch(snes,xx,r,realization,ierr)
-thc.F90:subroutine THCJacobian(snes,xx,A,B,flag,realization,ierr)
-thc.F90:subroutine SAMRSetCurrentJacobianPatch(mat,patch)
-thc.F90:subroutine THCJacobianPatch(snes,xx,A,B,flag,realization,ierr)
-thc.F90:subroutine THCCreateZeroArray(patch,option)
-thc.F90:subroutine THCMaxChange(realization)
-thc.F90:subroutine THCResidualToMass(realization)
-thc.F90:subroutine THCDestroy(patch)
-thc_aux.F90:subroutine THCAuxVarInit(aux_var,option)
-thc_aux.F90:subroutine THCAuxVarCopy(aux_var,aux_var2,option)
-thc_aux.F90:subroutine THCAuxVarCompute(x,aux_var,global_aux_var, &
-thc_aux.F90:subroutine AuxVarDestroy(aux_var)
-thc_aux.F90:subroutine THCAuxDestroy(aux)
-timestepper.F90:subroutine TimestepperReset(stepper,dt_min)
-timestepper.F90:subroutine TimestepperRead(stepper,input,option)
-timestepper.F90:subroutine StepperRun(realization,flow_stepper,tran_stepper)
-timestepper.F90:subroutine StepperUpdateDT(flow_stepper,tran_stepper,option)
-timestepper.F90:subroutine StepperSetTargetTimes(flow_stepper,tran_stepper,option,plot_flag, &
-timestepper.F90:subroutine StepperStepFlowDT(realization,stepper,step_to_steady_state,failure)
-timestepper.F90:subroutine StepperStepTransportDT_GI(realization,stepper,flow_t0,flow_t1, &
-timestepper.F90:subroutine StepperStepTransportDT_OS(realization,stepper,flow_t0,flow_t1, &
-timestepper.F90:subroutine StepperRunSteadyState(realization,flow_stepper,tran_stepper)
-timestepper.F90:subroutine StepperSolveFlowSteadyState(realization,stepper,failure)
-timestepper.F90:subroutine StepperSolveTranSteadyState(realization,stepper,failure)
-timestepper.F90:subroutine StepperUpdateSolution(realization)
-timestepper.F90:subroutine StepperUpdateFlowSolution(realization)
-timestepper.F90:subroutine StepperUpdateTransportSolution(realization)
-timestepper.F90:subroutine StepperJumpStart(realization)
-timestepper.F90:subroutine StepperUpdateFlowAuxVars(realization)
-timestepper.F90:subroutine StepperUpdateTranAuxVars(realization)
-timestepper.F90:subroutine StepperSandbox(realization)
-timestepper.F90:subroutine StepperCheckpoint(realization,flow_stepper,tran_stepper,id)
-timestepper.F90:subroutine StepperRestart(realization,flow_stepper,tran_stepper, &
-timestepper.F90:subroutine TimestepperSetTranWeights(option,flow_t0, flow_t1)
-timestepper.F90:subroutine TimestepperCheckCFLLimit(stepper,realization)
-timestepper.F90:subroutine TimestepperEnforceCFLLimit(stepper,option,output_option)
-timestepper.F90:subroutine TimestepperPrintInfo(stepper,fid,header,option)
-timestepper.F90:subroutine TimestepperDestroy(stepper)
-transport.F90:subroutine TDiffusion(global_aux_var_up,por_up,tor_up,dist_up, &
-transport.F90:subroutine TDiffusionBC(ibndtype,global_aux_var_up,global_aux_var_dn, &
-transport.F90:subroutine TFlux(rt_parameter, &
-transport.F90:subroutine TFlux_CD(rt_parameter, &
-transport.F90:subroutine TFluxDerivative(rt_parameter, &
-transport.F90:subroutine TFluxDerivative_CD(rt_parameter, &
-transport.F90:subroutine TFluxCoef(option,area,velocity,diffusion,fraction_upwind,T_up,T_dn)
-transport.F90:subroutine TFluxCoef_CD(option,area,velocity,diffusion,fraction_upwind, &
-transport.F90:subroutine TSrcSinkCoef(option,qsrc,flow_src_sink_type,tran_src_sink_type, &
-transport.F90:subroutine TSrcSinkCoefNew(option,qsrc,tran_src_sink_type,T_in,T_out)
-unstructured_grid.F90:subroutine UnstGridCreateNatToGhostedHash(unstructured_grid,nG2A)
-unstructured_grid.F90:subroutine UnstructGridPrintHashTable(unstructured_grid)
-unstructured_grid.F90:subroutine UGridRead(unstructured_grid,filename,option)
-unstructured_grid.F90:subroutine UGridReadHDF5(unstructured_grid,filename,option)
-unstructured_grid.F90:subroutine UGridReadHDF5PIOLib(unstructured_grid, filename, &
-unstructured_grid.F90:subroutine UGridDecompose(unstructured_grid,option)
-unstructured_grid.F90:subroutine UGridCreateUGDM(unstructured_grid,ugdm,ndof,option)
-unstructured_grid.F90:subroutine UGridPopulateConnection(unstructured_grid, connection, iface, &
-unstructured_grid.F90:subroutine UGridGetCellFaceVertices(option,cell_type,iface,vertex_ids)
-unstructured_grid.F90:subroutine UGridComputeCoord(unstructured_grid,option, &
-unstructured_grid.F90:subroutine UGridComputeVolumes(unstructured_grid,option,nL2G,volume)
-unstructured_grid.F90:subroutine ComputePlane(plane,point1,point2,point3)
-unstructured_grid.F90:subroutine GetPlaneIntercept(plane,point1,point2,intercept)
-unstructured_grid.F90:subroutine UGridDMCreateJacobian(unstructured_grid,ugdm,mat_type,J,option)
-unstructured_grid.F90:subroutine UGridDMCreateVector(unstructured_grid,ugdm,vec,vec_type,option)
-unstructured_grid.F90:subroutine UGridMapIndices(unstructured_grid,ugdm,nG2L,nL2G,nL2A,nG2A)
-unstructured_grid.F90:subroutine UGridDestroy(unstructured_grid)
-unstructured_grid.F90:subroutine UGridDMDestroy(ugdm)
-utility.F90:subroutine Natural2LocalIndex(ir, nl, llist, llength)
-utility.F90:subroutine reallocateIntArray(array,size)
-utility.F90:subroutine reallocateRealArray(array,size)
-utility.F90:subroutine ludcmp(A,N,INDX,D)
-utility.F90:subroutine lubksb(A,N,INDX,B)
-utility.F90:subroutine ludcmp_chunk(A,N,INDX,D,chunk_size,ithread,num_threads)
-utility.F90:subroutine lubksb_chunk(A,N,INDX,B,chunk_size,ithread,num_threads)
-utility.F90:subroutine Interpolate(x_high,x_low,x,y_high,y_low,y)
-utility.F90:subroutine UtilityReadArray(array,array_size,comment,input,option)
-velocity.F90:subroutine VelocityDatasetRead(dataset,input,option)
-velocity.F90:subroutine VelocityDatasetReadValues(input,option,keyword,string,dataset,units)
-velocity.F90:subroutine VelocityDatasetReadFromFile(input,dataset,option)
-velocity.F90:subroutine VelocityDatasetVerify(option, dataset)
-velocity.F90:subroutine VelocityDatasetUpdate(option,time,dataset)
-velocity.F90:subroutine VelocityDatasetDestroy(dataset)
-water_eos.F90:subroutine VISW_FLO (t,dw,vw)
-water_eos.F90:subroutine PSAT_orig (T, P, ierr)
-water_eos.F90:subroutine PSATgeh (T, psat, dpsat_dt, ierr)
-water_eos.F90:subroutine PSAT1(T, Ps, tsp, ierr)
-water_eos.F90:subroutine wateos (t,p,dw,dwmol,dwp,dwt,hw,hwp,hwt,scale,ierr)
-water_eos.F90:subroutine wateos_noderiv (t,p,dw,dwmol,hw,scale,ierr)
-water_eos.F90:subroutine steameos (t,p,pa,dg,dgmol,dgp,dgt,hg,hgp,hgt,scale,ierr)
-water_eos.F90:subroutine COWAT (TC,PP,D,U, ierr)
-water_eos.F90:subroutine density (tc,p,d)
-water_eos.F90:subroutine nacl_den (t,p,xnacl,dnacl)
-water_eos.F90:subroutine nacl_vis (t,p,xnacl,visnacl)
-water_eos.F90:subroutine Tsat(ts,ps,t_ps,ts_guess,ierr)
-waypoint.F90:subroutine WaypointInsertInList(new_waypoint,waypoint_list)
-waypoint.F90:subroutine WaypointDeleteFromList(obsolete_waypoint,waypoint_list)
-waypoint.F90:subroutine WaypointListFillIn(option,waypoint_list)
-waypoint.F90:subroutine WaypointConvertTimes(waypoint_list,time_conversion)
-waypoint.F90:subroutine WaypointListRemoveExtraWaypnts(option,waypoint_list)
-waypoint.F90:subroutine WaypointMerge(old_waypoint,new_waypoint)
-waypoint.F90:subroutine WaypointListDestroy(waypoint_list)
-waypoint.F90:subroutine WaypointListPrint(list,option,output_option)
-waypoint.F90:subroutine WaypointPrint(waypoint,option,output_option)
-waypoint.F90:subroutine WaypointDestroy(waypoint)
-\end{verbatim}
-\end{comment}
-
 \end{document}