Reference Manual for the NUFT Flow and Transport Code, Version 2.0
Contents
1. comp lt comp name gt file lt file name gt outtimes lt t0 gt lt tl gt lt t2 gt cumulative Outputs the total instantaneous flux of a component lt comp name gt flowing into a set of elements specified as boundary elements in bct ab The name of the boundary condition lt bc name gt is the desired one in bct ab The sign convention is such that flow out of the set of elements is positive and flow into the elements is negative If the statement cumulative is present the cumulative flux is outputted instead of the instantaneous flux forcetimes outtimes lt t0 gt lt tl gt lt t2 gt Forces the model to hit specified times without necessarily outputting any information This is used to prevent the model from skipping over the times at which fluxes or boundary conditions change suddenly restart file lt file name gt outtimes lt t0 gt lt tl gt lt t2 gt Write out a restart record at the specified times Restart record can be read in as initial conditions using the rest art command Backup restarts are also written see subsection on reading restart information The state command must not be present when using this command extool range lt element range gt index range lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt variables lt var0 gt lt varl gt outtimes lt t0 gt lt tl gt lt t2 gt s a w2. out Reference Manual for the NUFT Flow and Transport Code Ver 2 0 32 UCRL MA 130651 5 Input Data Documentation Output Specifications NAME output Specify output SYNOPSIS output field file lt file name gt format lt options gt range lt element range gt index range lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt variables lt el var0 gt lt el varl gt outtimes lt t0 gt lt ti gt flux field file lt file name gt format lt options gt crange lt element range gt lt element range gt index crange lt i0 gt lt jO gt lt k0 gt lt il gt lt jl gt lt kI gt variables lt con var0 gt lt con i gt outtimes lt t0 gt lt tl gt history variable lt el var gt element lt element name gt file lt file name gt flux history variable lt con var0 gt comp flux lt comp gt lt phase gt connection lt element name gt lt element name gt index con lt i0 gt lt j0 gt lt k0 gt lt i gt lt j gt lt k gt file lt file name gt srcflux name lt src name gt comp lt comp name gt file lt file name gt outtimes lt t0 gt lt t gt lt t2 gt Reference Manual for the NUFT Flow and Transport Code Ver 2 0 UCRL MA 130651 1 33 5 Input Data Documentation Output Specifications cumulative
3. bcflux name lt bc name gt comp lt comp name gt file lt file name gt outtimes lt t0 gt lt tl gt lt ft2 gt cumulative forcetimes outtimes lt t0 gt lt tl gt lt t2 gt restart file lt file name gt outtimes lt t0 gt lt t gt lt t2 gt extool range lt element range gt index range lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt variables lt var0 gt lt varl gt outtimes lt t0 gt lt tl gt lt t2 gt file lt file name gt DESCRIPTION Specifies the writing of various output data to files Any of the preceding options can be specified none of them is required PARAMETERS field file lt file name gt format lt options gt range lt element range gt index range lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt variables lt var0 gt lt varl gt outtimes lt t0 gt lt tl gt lt t2 gt Outputs element data Reference Manual for the NUFT Flow and Transport Code Ver 2 0 34 UCRL MA 130651 5 Input Data Documentation Output Specifications flux field file lt file name gt format lt options gt crange lt elementrange gt lt element range gt index crange lt i0 gt lt j0 gt lt k0 gt lt il gt lt jl gt lt kI gt phase fluxes lt phaseO gt l
4. file lt file name gt Outputs a time history file in extool format program NOTES l outtimes lt t0 gt lt t1 gt lt t2 gt canbe replaced by either of the following Reference Manual for the NUFT Flow and Transport Code Ver 2 0 36 UCRL MA 130651 5 Input Data Documentation Output Specifications a outtimes which means all times b triggers wake lt state var gt range lt el name gt lt op gt lt val gt cond lt state var gt range lt el name gt lt op gt lt val gt wake lt state var gt range lt el name gt lt op gt lt val gt cond lt state var gt range lt el name gt lt op gt lt val gt which checks to see at every time step if any of the triggers goes off A trigger goes off if the condition v lt op gt lt val gt is true for the wake field where v is the value of the state variable lt state var gt at the elements with names in the range lt el name gt If this condition is true the corresponding condition for the cond field is checked if true then trigger goes off and output occurs Triggers only go off once format lt options gt lt options gt can be any of following list or by list list values and element names contsac format list list values and element names by set list values as a lisp vector n vl v2 vn by x list x coord and value by y list y coord and
5. print NR iter off print qsrc off print be off print log off print all terms off print eqtpar off print timepar off print srctab off print bctab off print rocktab off print fprop off print ifdgrid off print dt state off print conv state off Reference Manual for the NUFT Flow and Transport Code Ver 2 0 UCRL MA 130651 output input data output pcg convergence information output material balance output matrix output accumulation output accumulation coefficients output internal fluxes output internal flux coefficients output solution at end of each time step output solution between NR iterations output changes between NR iterations output NR iteration nnumber to stderr output source terms output be terms turn on printing to a log file output values of terms output eqtpar structure output time step data output src tables output be tables output rock tables output fluid properties output grid data output time step restriction output NR convergence restriction 38 5 Input Data Documentation Specifying Initial Conditions 5 5 Specifying Initial Conditions NAME state Set initial conditions for primary variables SYNOPSIS state lt state var name gt lt method gt lt data gt lt state var name gt lt method gt lt data gt NOTES This command must be left out when reading initial data from a restart file using the restart command Exampl
6. Narasimhan and Witherspoon 1978 Spatial discretization results in a system of ordinary differential equations of the form Be fut c where u is the solution vector and f is a vector valued function A first order implicit in time scheme Richtmyer and Morton 1967 is used to discretize the balance equations for modules with combined flow and contaminant transport For modules where flow and transport are solved sequentially the flow equations are solved using the implicit in time method and the transport equations can be solved either implicitly or explicitly in time depending on the user s choice When Eq 1 is solved using the implicit in time method the resulting system of equations that must be solved at each time step is nonlinear if f is nonlinear Fou u a Area 1 0 2 where superscripts represent the time level B 2 Newton Raphson Iteration The nonlinear system of Eq 2 is of the form F u 0 3 The Newton Raphson iterative method is used to solve the equations JM U u F u 4 where the matrix oF Ju 5 u a 5 Reference Manual for the NUFT Flow and Transport Code Ver 2 0 53 UCRL MA 130651 Appendix B Numerical Algorithms Used is the Jacobian of the function F evaluated at the n th iterate U Note that Eq 4 can be viewed as a system of linear equations Ax b 6 where A Ju 7 K U U 8 b Ftu 9 B 3 Solution of System of Linear Equations
7. The code currently has two different options for solving the system of linear equations banded gaussian elimination and preconditioned conjugate gradient methods B 3 1 Banded Gaussian Elimination First for convenience Eq 4 is rewritten in the matrix form Ax b 10 where A Avs is an n Xn matrix It is well known that in many problems the matrix A is banded i e Ai 0 for li j gt n where nb is the matrix half bandwidth If nb lt lt n it is advantageous to perform the gaussian elimination only on the elements within the band This band becomes more or less filled with non zero elements as the elimination proceeds Problems where A is banded include the case where the problem domain is discretized by a rectangular mesh and the elements are ordered either rowwise or columnwise B 3 2 Orthomin Preconditioned Conjugate Gradient For the description of the orthomin algorithm and the preconditioning options see Vinsome 1976 and Behie et al 1980 B 4 Automatic Time Stepping The time stepping algorithm seeks to control the maximum change in the solution vector from one time step to the next This control can be accomplished by estimating the time step for the solution to change by a specified amount based on the solution change that ocurred in the previous two time steps During an iteration if the change in solution from the previous time step is too large a re estimation is performed and the time step is started ov
8. e The units of the angles in the cyl ind option are in degrees Reference Manual for the NUFT Flow and Transport Code Ver 2 0 19 UCRL MA 130651 5 Input Data Documentation Mesh Generation Parameters NAME mesh file Specify name of mesh file SYNOPSIS mesh file lt file gt DESCRIPTION The user can set up a grid either by using the genmsh option or by generating a mesh file outside the program and then reading the mesh file into the NUFT model The genmsh option can only produce grids that are rectangular or cylindrical The advantage of a mesh file is that the user can write a program to generate the user s own grid taking full advantage of the generality of the integrated finite difference method The format of the mesh file is described in Appendix A PARAMETERS lt file gt name of mesh file Reference Manual for the NUFT Flow and Transport Code Ver 2 0 20 UCRL MA 130651 5 Input Data Documentation Mesh Generation Parameters NAME grav factor Set gravity modification factor optional including gravity orientation optional SYNOPSIS grav factor lt factor gt DESCRIPTION The user can optionally multiply the gravity vector in the model by this factor If the mesh file option is used this factor is multiplied in addition to the beta factor read from the mesh file By setting the factor to zero gravity may be turned off By setting this factor to the cosine of the angle of inclination
9. backup restarts Default value is 10m i e 10 minutes Reference Manual for the NUFT Flow and Transport Code Ver 2 0 40 UCRL MA 130651 5 6 Setting Rock Properties NAME rocktab Set rock properties SYNOPSIS rocktab lt rock type name gt lt rock type name gt DESCRIPTION Sets rock properties for each rock type UCRL MA 130651 5 Input Data Documentation Setting Rock Properties PARAMETERS lt rock type name gt the name of the rock type Reference Manual for the NUFT Flow and Transport Code Ver 2 0 4 5 Input Data Documentation Setting Source Terms 5 7 Setting Source Terms NAME srctab Set source terms SYNOPSIS srctab compflux lt comp name gt range lt elem range gt lt elem range gt table lt flux table gt enthalpy lt enthalpy table gt compf lux phaseflux lt phase gt name lt phaseflux name gt range lt elem range gt lt elem range gt table lt phase flux table gt setcomp lt comp name gt table lt conc table gt following only for thermal models enthalpy lt enthalpy table gt lt comp name gt internal lt comp name gt phaseflux Reference Manual for the NUFT Flow and Transport Code Ver 2 0 42 UCRL MA 130651 5 Input Data Documentation Setting Source Terms DESCRIPTION Specifies the component flux into an element or range of elements through a table of source fluxes at sp
10. included not to mention the fact that the parentheses will not match in the input file Include package statement The include pkg package statement is of the form include pkg lt file name gt Reference Manual for the NUFT Flow and Transport Code Ver 2 0 6 UCRL MA 130651 2 The Syntax of the Input Data This statement is identical to the include statement except that it includes a file from the subdirectory that contains the NUFT executable rather than a file from the current working directory The main purpose of the include package statement is to include a package of predefined input parameters that comes with the NUFT software distribution Macro commands Macro commands start with the character There are three commands available define ifdef and ifndef The following command defines a macro variable define lt variable gt Currently a variable cannot be defined to be any particular value it is used in conjunction with the other macro commands The statements within ifdef lt variable gt will be read as part of the input stream if lt variable gt is defined by the define command However the statements within i1fndef lt variable gt will not be placed as input if lt variable gt is not defined The define statements must be in the same parenthesis level as for example bctab genmsh etc The ifdef and ifndef commands can be placed anywhere except that the body of sta
11. lt file ext gt Write out minimal geometry information about the grid to file with file extension non log By default flow areas in the radial direction for cylindrical coordinates are calculated using the logarithmic formula 1 A me ri 1 Arp A Az In ri ri If the non log flag is present flow areas are calculated as A ri Ari 2 A0Az wrap around If lt coord type gt is set to cyl ind and the angles in the y angular direction sum to 360 the elements at j 1 are adjacent to corresponding elements at j ny where ny is the number of subdivisions in the y direction When this option is present the model will make connections between these elements This option is valid only for lt coord type gt set to cylind Default is no wrap around Note that the wrap around option will increase the bandwidth of the matrix when using the direct solution option or the comb option of the preconditioned conjugate gradient method and therefore will increase cpu time for these methods NOTES e Indices start from 1 e Coordinates of grid blocks sides start from zero and are incremented by corresponding values in dax dy and daz ag e The first grid block center in x direction has x lt dx0 gt 2 where lt dx0 gt is the first number in dx e If coordinate type is cylind the first coord x is radial distance the second y is angle and third z is longitudinal to central axis
12. lt j gt lt k gt denote the i j and k indices The material type lt mat type gt is defined in rocktab Thesymbolsnx ny and nz can be used anywhere in place of numbers where an index is required The model interprets these to mean the number of subdivisions in the x y and z directions respectively isot dir This parameter is optional It affects the choice of the permeability or hydraulic conductivity parameter See the documentation of the permeability parameters KO K1 and K2 in subsequent text This parameter should not be present for models where isotropic permeability is desired isot lt num gt lt dir gt lt l0 gt lt II gt lt j0 gt lt jl gt lt k0 gt lt kI gt lt num gt lt dir gt lt i0 gt lt II gt lt j0 gt lt jl gt lt k0 gt lt kI gt sets isot 0 1 2 in x y z directions respectively default is isot 0 for all elements The parameter isot selects which of the permeability or hydraulic conductivity values KO K1 K2 set in rocktab are used for the particular element volfac lt num gt lt i0 gt lt il gt lt jO gt lt jl gt lt k0 gt lt kI gt lt num gt lt i0 gt lt il gt lt jO gt lt jl gt lt k0 gt lt kl gt sets volume modifying factor Multiplies the volume of the specified elements by lt num gt Reference Manual for the NUFT Flow and Transport Code Ver 2 0 17 UCRL MA 130651 5 Input Data Documentation Mesh Generation Parame
13. rock type gt lt volume gt lt xc gt lt yc gt lt zc gt lt el name gt lt rock type gt lt volume gt lt xc gt lt yc gt lt zc gt Send Scon lt el nameO gt lt el namel gt lt isot gt lt LO gt lt LI gt lt A gt lt beta gt lt el nameO gt lt el namel gt lt isot gt lt LO gt lt LI gt lt A gt lt beta gt Send Second Form The second form uses element numbers to specify connections Seleme lt el num gt lt el name gt lt rock type gt lt volume gt lt el num gt lt el name gt lt rock type gt lt volume gt Send Sconne lt mp0 gt lt mpI gt lt isot gt lt LO gt lt LI gt lt A gt lt beta gt lt mp0 gt lt mpI gt lt isot gt lt LO gt lt LI gt lt A gt lt beta gt Send lt el name gt element name word lt rock type gt rock type of element word lt volume gt volume of element real lt xc gt lt ye gt lt zc gt coordinates of element centroid Reference Manual for the NUFT Flow and Transport Code Ver 2 0 51 UCRL MA 130651 lt el nameO gt lt el namel gt lt isot gt lt LO gt lt LI gt where lt A gt lt beta gt lt el num gt lt mp0 gt lt mpl gt Appendix A Format of the Mesh File specifies a connection with positive flow going from element lt el name0 gt to lt el namel gt word value of 0 1 or 2 referring to which conductivity KO K1 orK2 in rocktab is used for this connection integer len
14. Code Ver 2 0 5 UCRL MA 130651 2 The Syntax of the Input Data Include statement The include statement is of the form include lt file name gt It is used to insert the contents of the file with the name lt file name gt into the input file The file must lie in the working directory under which NUFT is being run It can only be used to replace a complete list 1 e must be either a collection of data delimited by a closed set of parentheses or a single data item such as a number or string For example if the file datal inc contains field format list range variables Sl file ext S1 outtimes 0 70m 102m 222m 287m 342m 23h and the file data2 inc contains the single entry 200m then the following input data output include datal inc forcetimes outtimes include data2 inc 201m will be interpreted by the model as equivalent to output field format list range variables S1 file ext S1 outtimes 0 70m 102m 222m 287m 342m 23h forcetimes outtimes 200m 201m The following is an example of an error Suppose the file file inc contains outtimes 0 70m 102m 222m and the input file as the data item output field format list range variables S1 file ext S1 include file inc 287m 342m 23h forcetimes outtimes 200m 201m file ext S1 This is an error because only complete lists or a single entry can be
15. RAMETERS lt file name gt string name of the restart file created by the option OULPUT i ai 2 BESTAAT e 2 42 20 e lt restart time gt real Time used to search in the restart file the first restart record with time lt restart time gt will be read in The initial time of the simulation run is set by t ime and overwrites the time read in through the restart file If t ime is not present the initial of the run is set to the time read in NOTES Restart filess are created from a previous run using the rest art option in the output command Restart Backup The model will periodically write out restart records so that the model can be restarted in case of system failure The model alternately writes out to two restart files named lt prefix gt reO and lt prefix gt rel where lt prefix gt is set by out put prefix Each file contains a single record previous records are overwritten Two files instead of a single one are used to prevent losing a record if the system fails during a write The user must check the two files to see which is the most recent The model writes to a file at periodic intervals based on the wall clock time backup lt option gt optional lt option gt word If set to on the model will periodically write backup restarts If set to of f the model will not do backups Default is on backup period lt backup time gt optional lt backup time gt t real Wall clock time period for model to perform
16. RAMETERS time method Valid values are fully implicit or explicit default value model specific Reference Manual for the NUFT Flow and Transport Code Ver 2 0 28 UCRL MA 130651 5 Input Data Documentation Parameters for Numerical Methods NAME upstream weighting Set upstream weighting SYNOPSIS upstream weighting lt weight gt DESCRIPTION sets upstream weighting To calculate the advective flux cV of a component between two connected elements the model will use the weighting c ac L a C own based on the weighting factor w where a wL wL 1 w L Where L refers to flow lengths the subscript up refers to upstream value and the subscript down to downstream value The default is w 1 which is full upstream weighting PARAMETERS lt weight gt weighting factor usually between 0 and 1 inclusive default 1 0 Reference Manual for the NUFT Flow and Transport Code Ver 2 0 29 UCRL MA 130651 NAME 5 Input Data Documentation Parameters for Numerical Methods flux correction flux correct options Set parameters SYNOPSIS flux correc controlling flux correction scheme tion lt word gt flux correct DESCRIPTION t options method lt word gt iter lt integer gt By default the model uses complete upstream weighting of mobilities to numerically calculate the advective flux between two elements see upst ream weighting for changing the amount of upstream weig
17. UCRL MA 130651 Reference Manual for the NUFT Flow and Transport Code Version 2 0 John J Nitao April 1998 DISCLAIMER This document was prepared as an account of work sponsored by an agency of the United States Government Neither the United States Government nor the University of California nor any of their employees makes any warranty express or implied or assumes any legal liability or responsibility for the accuracy completeness or usefulness of any information apparatus product or process disclosed or represents that its use would not infringe privately owned rights Reference herein to any specific commercial product process or service by trade name trademark manufacturer or otherwise does not necessarily constitute or imply its endorsement recommendation or favoring by the United States Government or the University of California The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or the University of California and shall not be used for advertising or product endorsement purposes UCRL MA 130651 Reference Manual for the NUFT Flow and Transport Code Version 2 0 John J Nitao Earth and Environmental Sciences Lawrence Livermore National Laboratory April 1998 YMP9804051 Work performed under the auspices of the U S Department of Energy by Lawrence Livermore National Laboratory under Contract W 7405 Eng 48 This work is supporte
18. ault is 0 Note that the D4 ordering is generalized meaning that it also works when connections between elements are nonstandard with respect to the standard i j k lattice north number of orthogonalizations performed in the orthomin PCG method toler convergence tolerance for the PCG method The convergence criteria is that the norm of the residual vector be less than toler times the norm of the initial residual vector The mean square norm is used 1 n llr l Y rD Chm itermax maximum number of PCG iterations If exceeded the time step size will be cut in half and the time step will be started over direct specifies which of the balance equations are solved directly in the combinative method used only for the preconditioning option comb This is needed only for comb preconditioning method Parameters are a list of lt integer gt s one for each balance equation A nonzero value will cause the linear equations for that balance equation to be solved directly by gaussian elimination ilu degree degree of fill in for ILU decomposition Degree 0 equals no fill in Reference Manual for the NUFT Flow and Transport Code Ver 2 0 27 UCRL MA 130651 5 Input Data Documentation Parameters for Numerical Methods NAME time method Specify the time discretization method SYNOPSIS time method lt string gt DESCRIPTION This parameter specifies whether to use either a fully implicit or fully explicit discretization in time PA
19. ct models are imbedded in a single code to utilize a common set of utility routines and input file format Currently the code runs on the Unix and DOS operating systems Versions have been successfully compiled and tested for IBM PC compatibles Cray Unicos and the following workstations Sun Hewlett Packard IBM Risc 6000 Silicon Graphics DEC Alpha Each set of related models is called a module and has its own user s manual that documents any particular features and input data specific to that module This reference manual for NUFT documents the general numerical algorithms used and gives the documentation of the input to the model common to all or most modules including options not described in the user s manual for each module The following modules are available e wUCSAT unconfined and confined saturated flow model e US1P single phase unsaturated flow Richard s equation e US1C single component contaminant transport e USNT NP phase NC component with thermal option It is recommended that new users of NUFT read the user s manual User s Manual for US1 Module of the NUFT Code Version 2 0 and User s Manual for USNT Module of the NUFT Code Version 2 0 before reading this reference manual An integrated finite difference spatial discretization is used to solve the balance equations The resulting nonlinear equation is solved at each time by the Newton Raphson method Options for solution of the lin
20. d i e if NR convergence has not been reached and the NR iteration is greater than this number the time step size is cut back by one half and the time step is started over default value 8 Go on to next time step if this many NR iterations have been reached regardless of whether the NR convergence criteria are met default value 1000000000 Maximum number of times in a given time step that the time step has to be started over again due to lack of NR convergence If exceeded the program will print an error message and then stop default value 100 Reference Manual for the NUFT Flow and Transport Code Ver 2 0 25 UCRL MA 130651 5 Input Data Documentation Parameters for Numerical Methods NAME linear solver pcg parameters Set parameters for linear solver SYNOPSIS linear solver lt word gt pcg parameters precond lt word gt north lt integer gt toler lt real gt itermax lt integer gt direct lt integer gt lt integer gt ilu degree lt integer gt DESCRIPTION These parameters are for the solution of linear system of equations that needs to be solved in each iteration of the Newton Raphson method Example pcg parameters precond comb north 10 toler 1 e 4 itermax 30 direct 1 0 PARAMETERS linear solver Sets the method used to solve the system of linear equations in the Newton Raphson method Valid values are lublkbnd standard ordered constant band
21. d by Yucca Mountain Site Characterization Project LLNL Contents PAGING TATE TIES to E A E T E E E E dus nates EE ii Vig SEKOT E LENTOS 48 64 E E T BEE SE EE I Bee 1 2 The Syntax Of the Input Datas vicrccdiseccccsascescasevsieneiedvsveravensrateassackeaa ai e e i baatens 3 3 How to Read the Input Documentation 00 0 ce eecceessecesceceenceceeneecesneecsceeceeeecseeeecsteeeeeaeers 8 4 Basic Blements or th Input Fil ssereni eestor anlar e enh ietenas aarti tude A EEES 11 5e Input Data Docume mal one manoi Siete laid aa eee ee teats a lewee 13 5 1 Mesh Generation Par aimeters sa teaeicet set ioty ic wees Nowe ented aol yas c ina Novi aiedadee toad ee 14 5 2 Time Stepping Parameters Aesi cccusenbucotdejevcauratedes E a E S 22 5 3 Parameters for Numerical Methods sssesseeeseseesseseeesesrersreseseresreseseresressesseesresseesess 24 5 4 Output SpecificatioiS canran a o E a T i 32 5 5 Specifying Initial Conditions si sciis idccesseacaacadaysceds seceaatans saedissaden ss desedanaseetadevandeenesneeeass 39 5 6 Setting Rock Properties sicjssicsscca ciancccetesaccasvaasuscntvat seca e raii e iaaio 41 Se Setin Source TEIS 475143 sake E E vee E E E ae ana ease eae 42 5 8 Specifying Boundary Conditions sesesssessseseesseesseesseessereseeessseessresseesseesseeessseesseese 45 59 Oth r PUTS en kentad e g t a e ot ses e Ea aa 48 6 Running Flow and Transport Sequentially sssnssenssessseessseeesseesseesseesseresseeesseess
22. e respective phase within the element instead of specifying through a table of concentrations and enthalpies Reference Manual for the NUFT Flow and Transport Code Ver 2 0 44 UCRL MA 130651 5 Input Data Documentation Specifying Boundary Conditions 5 8 Specifying Boundary Conditions NAME bctab Set boundary conditions SYNOPSIS bctab lt bc name gt range lt elem range gt lt elem range gt tables lt primary var gt lt var table gt lt primary var gt lt var table gt factor lt comp name gt lt comp factor table gt lt comp name gt lt comp factor table gt Jas phasefactor lt phase name gt lt phase factor table gt lt phase name gt lt phase factor table gt lt bc name gt lt bc name gt range lt elem range gt lt elem range gt clamped factor lt comp name gt lt factor table gt lt comp name gt lt factor table gt phasefactor Reference Manual for the NUFT Flow and Transport Code Ver 2 0 UCRL MA 130651 45 5 Input Data Documentation Specifying Boundary Conditions lt phase name gt lt phase factor table gt lt phase name gt lt phase factor table gt PARAMETERS lt bc name gt word Name of the boundary condition Each boundary condition has a distinct name used for identification by output options lt elem range gt pattern string Range of elements that will have the boundary cond
23. e components of the vector pointing downward in the direction of the gravity vector The program will internally normalize the vector to unity Setting the components all to zero will turn off gravity in the model The vector is always with respect to a rectangular coordinate system X Y Z For a rectangular mesh the coordinate system coincides with the rectangular coordinate system x y z of the mesh If the mesh is cylindrical the vector is with respect to a coordinate system X Y Z where X is the axis defined by 0 0 z 0 Y is the axis defined by 0 90 z 0 and the axis Z is defined by r 0 dx lt numx O gt lt numx l gt dy lt numy 0 gt lt numy I gt dz lt numz O gt lt numz I gt sets the mesh subdivisions in the x y and z coordinate directions Numbers that are repeated can be abbreviated for example 3 5 0 would stand for three repeats of the numeral 5 1 e 5 0 5 0 5 0 Reference Manual for the NUFT Flow and Transport Code Ver 2 0 16 UCRL MA 130651 5 Input Data Documentation Mesh Generation Parameters mat lt el name prefix gt lt mat type gt lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt lt el name prefix gt lt mat type gt lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt sets material property name of each element The element names will be of the form lt el name prefix gt lt i gt lt j gt lt k gt where lt i gt
24. ear equations at each iteration are direct banded solution and preconditioned conjugate gradient method with various preconditioning schemes The model can solve one two or three dimensional problems Future plans include incorporation of capillary hysteresis nonorthogonal mesh discretization finite elements and nonlinear solid sorption isotherms The first stage of code verification with one dimensional problems has been completed Lee et al 1993 and further verification efforts were completed in 1998 The distinct models in the code employ a common set of utility routines and input file format The various models are essentially isolated from each other hence future models can be added without affecting existing models This also allows for ease in code maintenance and incorporation of future enhancements Global variables in the code are virtually nonexistent The code is written principally in the C language Input data is in the form of that used by the lisp Reference Manual for the NUFT Flow and Transport Code Ver 2 0 1 UCRL MA 130651 1 Introduction language An internal Lisp interpreter for the Scheme dialect of Lisp is part of the simulator whose purpose is to read the input data file and the internal data files containing default input data values It also performs data checking Each module has its own user s manual documenting the data input specific to each module Non module specific input are also given in the u
25. ecified points in time NOTES Linear interpolation is used for time intervals between the table values Positive flux is flux into an element negative flux is out of an element PARAMETERS lt comp name gt word Name of the component model specific which will be forced out or into the element s lt elem range gt pattern string Range of elements that will have the source term flux specified by the flux table lt flux table gt table Component mass flux table of the form lt t0 gt lt q0 gt lt tl gt lt qI gt where the time values are given by lt t0 gt lt t gt which are of data type t real and the mass flux values are lt q0 gt lt ql gt which are of data type real and are in units of kg sec except that us 1p model uses volumetric flux m s See Section 6 for an important note lt phase gt name Name of the phase lt phaseflux name gt name Name of the phase flux set This is used by output options lt phase flux table gt list of reals Table of mass fluxes of the phase that are of the form lt t0 gt lt q0 gt lt tl gt lt qI gt where the time values are given by lt t0 gt lt t1 gt which are of data type r real and the mass flux at these times are lt g0 gt lt ql gt which are of data type real and are in units of kg sec Linear interpolation is used for values between the time values The last time must be greater than the end time of the run lt conc
26. eesseesseeesseee 49 T2 Referentes eee BEG Reade a a a a A a oa Sed erase A AE AO EER aN 50 Appendix A Format of the Mesh File s ssnssessesssesessseesseesssssseesssressseessersseesseessseessseesseesseesset 56 Appendix B Numerical Algorithms Used eeccceescecescecesneeceeecececeeceeeeceeceeeseeeecseeeeenseeeens 58 Reference Manual for the NUFT Flow and Transport Code Ver 2 0 i UCRL MA 130651 Acknowledgments The author wishes to thank the following organizations for supporting the documentation and verification of the NUFT code Waterways Experimental Station of the U S Army Corps of Engineers the Environmental Restoration Division at the Lawrence Livermore National Laboratory LLNL the DOD DOE Strategic Environmental Research and Development Program SERDP and the DOE Yucca Mountain Project The initial concepts of the code were developed under the LLNL Institutional Research and Development program Preparation of this manual was made possible by the administrative assistance of Adrienne F Ridolfi and the editorial assistance of Karen L Lew Reference Manual for the NUFT Flow and Transport Code Ver 2 0 il UCRL MA 130651 1 Introduction 1 Introduction NUFT Nonisothermal Unsaturated Saturated Flow and Transport model is a suite of multi phase multicomponent models for numerical solution of non isothermal flow and transport in porous media with application to subsurface contaminant transport problems These distin
27. er This method also controls to some extent the time discretization error Reference Manual for the NUFT Flow and Transport Code Ver 2 0 54 UCRL MA 130651 Appendix B Numerical Algorithms Used The method is now described in more detail Let u be the i th component of the solution vector at the current iteration of the Newton Raphson method and du be equal to u minus the i th component of the solution vector at the end of the previous time step Now let 6u be the maximum allowed change in the solution The new reference time step is defined as t by ie 1 w Ou max nis W OU nay OU Here w is a damping factor Grabowski et al 1979 that is chosen between 0 to 1 to prevent the time step from changing too rapidly A value of 0 8 is used The value of is adjusted to stay within 0 5 to 4 0 times the time step size taken in the previous time step If the reference time step is less than the current time step because the solution changed too much the current time step is replaced by 0 8 times the reference and the Newton Raphson is restarted The factor 0 8 is there to allow for some margin to prevent an excess of restarts If the equations are solved using an explicit in time method the time step is restricted so that the Courant Friedrichs Levy criteria Richtmyer and Morton 1967 is satisfied Reference Manual for the NUFT Flow and Transport Code Ver 2 0 J3 UCRL MA 130651
28. es lt state var name gt by key lt elem range gt lt value gt lt elem range gt lt value gt lt state var name gt by set lt vector gt where lt vector gt lt n gt lt v0 gt lt vl gt and lt n gt is number of components the lt n gt field is optional Here and are actual characters and do not represent delimiters of optional parameters lt state var name gt by xtable lt table gt lt state var name gt by ytable lt table gt or lt state var name gt by ztable lt table gt where lt table gt lt z0 gt lt val0 gt lt zI gt lt vall gt isa table of values with respect to the appropriate x y or z coordinate NOTES 1 A state variable can appear more than once to overwrite values set by previous specifications For example values for all elements can be set by by xt able or by set and then touched up using by key 2 The program will terminate if the primary variables have not been set for each of the elements Reference Manual for the NUFT Flow and Transport Code Ver 2 0 39 UCRL MA 130651 5 Input Data Documentation Specifying Initial Conditions NAME read restart Read restart record SYNOPSIS read restart file lt file name gt time lt restart time gt DESCRIPTION Sets initial conditions for primary variables by reading in a restart record from a file instead of using state PA
29. gths of the parts of the connection that lie in the first and second elements that define the connection respectively real flow area of a connection real cosine of the angle of vertical inclination of the connection real the element number starting from 0 must be consecutive integer in eleme used primarily for convenience by the user in associating connections with the elements they connect when the eleme and Sconne options are used specifies a flow connection with positive flow going from lt mp0 gt to lt mpl gt integer The advantage of the first format is that connections are easily identified by looking at the element names that they connect especially if the names are chosen in a convenient manner The disadvantage is that more initial set up time is needed by the model to associate the element names with the element numbers that will be used during the simulation For use with more than 4000 elements the second format is recommended Reference Manual for the NUFT Flow and Transport Code Ver 2 0 52 UCRL MA 130651 Appendix B Numerical Algorithms Used Appendix B Numerical Algorithms Used B 1 Numerical Discretization NUFT solves balance equations see for example Bear and Bachmat 1991 which are partial differential equations whose specific form depends on the particular NUFT module being used The balance equations are discretized in space using the integrated finite difference method see Edwards 1972
30. hting An alternative method is to use the flux correction scheme of Smolarkiewicz 1983 which is a modification of the upstream weighting If flux correction is set to on the method of Smolarkiewicz is used with three iterations The number of iterations can be changed by setting parameters in flux correct options An upstream modified harmonic averaging method can also be used instead o PARAMETERS f the Smolarkiewicz flux correction can be set to either on or of f to turn on flux correction on or off UCRL MA 130651 method choice of flux correction method smolark flux correction using Smolarkiewicz s method harmonic flux correction using harmonic averaging iter number of iterations for flux correction Using more than two iterations for the harmonic method can lead to spatial oscillations in the solution Using value of 1 for the harmonic appears to give the same results as does the Smolarkiewicz method Reference Manual for the NUFT Flow and Transport Code Ver 2 0 30 5 Input Data Documentation Parameters for Numerical Methods NAME title Set run title SYNOPSIS title lt string gt DESCRIPTION This input parameter specifies the run title which is placed at the top of output files Example title Run 3A hydrological study Reference Manual for the NUFT Flow and Transport Code Ver 2 0 31 UCRL MA 130651 5 Input Data Documentation Output Specifications 5 4 Output Specifications NAME output f
31. ile output prefix output ext Specify names of the various output files SYNOPSIS output file lt string gt output prefix lt string gt output ext lt string gt DESCRIPTION The model will place its output into various files At least one main output file and possibly several auxillary files will be generated by the output option described in this section The user has two possibilities for specifying the names of these files 1 separately name each file using the out put file parameter to name the main output file and the file parameter in output to name the auxilliary files 2 more conveniently have all files use the same prefix e g the run name and use different suffixes for each file e g out pg T If the latter method is used the prefix is set using output prefix and the suffix of the main output file is set using output ext The suffix for the names of the auxilliary files is set using file ext described in this section on the data unit output PARAMETERS output file name of main output file output prefix All output files including those written by the output data field will have this prefix this is usually used to specify a single run name where all output files start with this name default prefix of input file name output ext Instead of specifying the output file one can specify the suffix of the output file default
32. isot dir isot lt num gt lt num gt volfac lt num gt lt num gt areafac lt dir gt lt I0 gt lt I gt lt j0 gt lt jl gt lt k0 gt lt kI gt lt dir gt lt I0 gt lt I gt lt jO gt lt jl gt lt k0 gt lt kI gt lt I0 gt lt II gt lt j0 gt lt i0 gt lt il gt lt j0 gt lt num gt lt dir gt lt IO gt lt II gt lt num gt lt dir gt lt IO gt lt I gt ped write mesh lt file name gt write grid lt file name gt write gdef lt file name gt lt jl gt lt jl gt lt jO gt lt j0 gt lt k0 gt lt kl gt lt k0 gt lt kl gt lt jl gt lt k0 gt lt kl gt lt jl gt lt k0 gt lt kI gt Reference Manual for the NUFT Flow and Transport Code Ver 2 0 14 UCRL MA 130651 5 Input Data Documentation Mesh Generation Parameters gdef ext lt file ext gt non log wrap around Reference Manual for the NUFT Flow and Transport Code Ver 2 0 15 UCRL MA 130651 5 Input Data Documentation Mesh Generation Parameters NAME mesh file Allow user to easily generate a regular rectangular or cylindrical mesch for more specific meshes see the mesh file option PARAMETERS coord lt coord type gt set type of coordinate system lt coord type gt coordinate system type options are rect cylind down lt numx gt lt numy gt lt numz gt sets th
33. ition lt primary var gt word Name of the primary variable model specific that is being specified by the associated table lt var table gt table Table of primary variable values of form lt t0 gt lt var0 gt lt tl gt lt varI gt where the time values lt 10 gt lt ti gt are of data type f real and the entries lt var0 gt lt varl gt are the corresponding values of the primary variable that is being specified See Section 6 for an important note Primary variable values are calculated from the table using linear interpolation factor This data unit is optional and is used to modify the component mass fluxes by a factor that can depend on time and that is set by a table One use of this option is to turn off a component flux coming out of or into a boundary element at certain time intervals or at all times Note that several different components can be specified each having its own time dependent factor Tables for all of the components must be present the components are model specific Leaving the factor data unit out is equivalent to specifying a modification factor of 1 0 for all time phasefactor This data unit is optional and is used to modify the phase fluxes by a factor that can depend on time and that is set by a table lt comp name gt word Name of the component flux that will have its flux modified model specific lt phase name gt word Name of the phase that will have its flux modified mode
34. its own set of input data units in the same input data file Data units that are common to both models can be placed in a common data unit called common which holds data units used by both the flow and transport models If a data unit appears in both the common data unit and the particular unit belonging to the model the one in common takes precedence General Form for Running Flow and Transport Sequentially common title outputfile output prefix output ext meshfile genmsh time tstop lt flow model name gt GLE n gt we ee dtmax stepmax CSE ate ii ay Ss rocktab output Sp 4 lt 7 srcetab L bctab lt transport model name gt CLE And bs aah dtmax stepmax state a rocktab OuUtpUb 2 40 e k srctab e e ap J betab x 9 J phaseprop compprop Reference Manual for the NUFT Flow and Transport Code Ver 2 0 49 UCRL MA 130651 7 References 7 References Bear J and Y Bachmat Introduction to Modeling of Transport Phenomena in Porous Media Kluwer Acad Publishers 1991 Behie A and P K Vinsome Block iterative methods for fully implicit reservoir simulation Soc Petroleum Engineers paper 9303 1980 Edwards A L TRUMP a computer program for transient and steady state temperature distributio
35. l specific lt comp factor table gt table Table of modification factors for component fluxes Reference Manual for the NUFT Flow and Transport Code Ver 2 0 46 UCRL MA 130651 5 Input Data Documentation Specifying Boundary Conditions It is of the form lt t0 gt lt facO gt lt tl gt lt facI gt where the time values lt 10 gt lt ti gt are of data type f real and the entries lt facO gt lt facl gt are the corresponding modification factors See Section 6 for an important note Modification factors are calculated from the table using linear interpolation lt phase factor table gt table Table of modification factors multiplying all component fluxes in the corresponding phase given by lt phase name gt format is analogous to lt comp factor table gt clamped Keeps the primary variables for these elements as set in st ate fixed in time NOTES The data factor is optional if not present factors will be unity Currently the model may in some cases choose time steps so large that it overshoots sharp changes in a time table This may be a serious problem if for example one wishes to model a flux that is turned off suddenly A solution is to use the forcetimes command in output this forces the model to hit specified times in this case the times at which the boundary condition changes suddenly The model will abort unless the last time value in table is greater than or equal to the endi
36. ng time of the simulation as set by t stop Reference Manual for the NUFT Flow and Transport Code Ver 2 0 47 UCRL MA 130651 5 Input Data Documentation Other Options 5 9 Other Options NAME element prefix delimiter element indices separator Set format of element names SYNOPSIS element prefix delimiter lt prefix sep gt element indices separator lt ind sep gt DESCRIPTION Changes the format of element names created by genmsh NOTES The genmsh command names the element according to the general format lt elem prefix gt lt i gt lt j gt lt k gt where lt I gt lt j gt lt k gt denote the i j and k indices of the element and lt elem prefix gt is set by the mat command inside genmsh These commands allow the user to change the separators and by the single character in the strings lt prefix sep gt and lt ind sep gt respectively Reference Manual for the NUFT Flow and Transport Code Ver 2 0 48 UCRL MA 130651 6 Running Flow and Transport Sequentially 6 Running Flow and Transport Sequentially In some modules such as the us1c module the flow of the fluid phases is first calculated at the beginning of each step and then the transport of contaminants is performed using the resulting flow field Other modules such as usnt solve for flow and transport simultaneously When the flow and transport models are solved separately each model has
37. ns in multidimensional systems Springfield VA National Tech Information Service 1972 Grabowski J W P K Vinsome R C Lin A Behie and B Rubin A fully implicit general purpose finite difference thermal model for in situ combustion and steam Soc Petroleum Engineers paper 8396 1979 Lee K A Kulshrestha and J Nitao Interim Report on Verification and Benchmark Testing of the NUFT Computer Code Livermore CA Lawrence Livermore National Laboratory UCRL ID 113521 1993 Narasimhan T N and P A Witherspoon An integrated finite difference method for analyzing fluid flow in porous media Water Resour Res 14 255 261 1978 Richtmyer R D and K W Morto Difference Methods for Initial Value Problems New Y ork NY Interscience Pub 1967 Smolarkiewicz P K A fully multidimensional positive definite advection transport algorithm with small implicit diffusion J Computational Physics 54 325 1984 Vinsome P K W Orthomin an iterative method for solving sparse sets of simultaneous linear equations Soc Petroleum Engineers paper 5729 1976 Reference Manual for the NUFT Flow and Transport Code Ver 2 0 50 UCRL MA 130651 Appendix A Format of the Mesh File Appendix A Format of the Mesh File The mesh file is free format and can be either of two forms First Form The first form uses element names to specify the connections between two elements Selc lt el name gt lt
38. nths y years If no unit designator is present seconds is assumed Examples 20 0 20 seconds 23 1s 23 1 seconds 45e4M 45e4 months There must be no spaces between the number and the unit designator e A word a sequence of nonblank visible characters A word can be a variable or may be used in the same way as a string except that it cannot have internal blanks The model treats the words and strings as being distinct data types the correct one as specified in the documentation is required e A pattern string a special type of a string with the two unix shell type wild characters and so that a pattern string can represent an entire class of strings that matches the string pattern The character in a pattern matches any sequence of characters Hence the pattern matches all strings The character in a pattern matches any single character Hence the pattern matches all strings with exactly one character Other Examples The pattern ex matches all strings that begin with the characters ex The pattern ex b2 z matches all strings that begin with ex that are followed by any number including zero of strings that are then followed by the string b2 and that end with the string z The pattern r2 xay matches all strings that begin with r2 followed by a single character and that are then followed by the characters xay Reference Manual for the NUFT Flow and Transport
39. ocation of any unmatching parentheses Example porosity 0 2 file name input data par 0 1 0 3 0 6 This example sets three different variables It sets the variable porosity to the numeric value 0 2 the variable file name to the string input data and the variable par to a list of three numeric values 0 1 0 3 0 6 Example rocktab silt porosity 0 3 Kx 1 e 4 Ky 1 e 4 Kz 1 e 4 sand porosity 0 2 Kx l e 2 Ky 0 0 Kz 0 0 clay porosity 0 4 Kx l e 6 Ky 0 0 Kz 0 0 rocktab This example shows how a data unit sets the variable rockt ab to a list of data units using the alternate form Comment Character Semi colons in the input file serve as comment characters That is all characters on a given line after a semicolon are ignored by the program Using comments is a good way for the user to annotate an input file Using two semicolons instead of a single one is a good way to make sure that comments stand out Example porosity 0 2 this is how we set the value of porosity to 0 2 Reference Manual for the NUFT Flow and Transport Code Ver 2 0 3 UCRL MA 130651 2 The Syntax of the Input Data Units All quantities are in MKS units i e meters kilogram seconds Thus hydraulic conductivities are in meters second and head is in meters see Table 1 Unitless quantities such as saturation porosity and concentrations are always fractional i e between 0 and 1 inclusive not pe
40. pecification CELME yc Oye ni initial time tstop ending time dt initial time step dtmax j maximum time step stepmax maximum no of time steps read restart read from restart file state j set initial conditions rocktab 7 Ss0il property type grav factor factor multiplying gravity vector output a 2 output specification srctab s source tables octab boundary condition tables Recall that the denote subsequent data items that are to be explained later and that all of the input line past a semicolon is not read by the program but is for placing comments into the input file The above data units do not have to occur in any particular order The data entry lt name of model gt refers to the name of the model that is being used For example uslp refers to the single phase unsaturated flow model Note that the use of the square brackets around grav factor output srctab and bctab denote that these data units are optional More optional data items will be described in subsequent text but the ones shown above are the most likely to be used Initial conditions are set either using read restart or state One but not both of these initial conditions must be present The preceding applies to NUFT modules that solve for flow and transport simultaneously Some NUFT modules have the option of solving flow and
41. rcentages Table1 Table of Units Used in Input to Models length meters m mass kilograms kg time seconds s temperature centigrade C area m volume m mass density kg m molar density mole m permeability m hydraulic conductivity m s flow velocity m s force Newton Nt kg m s pressure Pascals Pa Nt m head m energy Joule J Nt m specific energy J kg mass flux kg s molar flux mole s volumetric flux m s energy flux Watts W J s thermal conductivity W m C dynamic viscosity molecular diffusivity Nt s m kg m s 10 centipoise m s t model can accept other time units by the use of unit designators Legal Data Types Following are descriptions of valid data types e A string any sequence of visible characters delimited by double quotes for example he Lor there run3 B test 2 Note that spaces and parentheses are allowed in a string e An integer number for example 11 Reference Manual for the NUFT Flow and Transport Code Ver 2 0 4 UCRL MA 130651 2 The Syntax of the Input Data e A real number that is fixed or floating point for example 1 23 4 5e7 or 900 257 Note that D or d exponents in the manner of FORTRAN are not allowed e A time number that is a real number but that has the following unit designators as the last letter to denote units of time This type of number is used to specify a time S seconds m minutes h hours d days M mo
42. real gt values one for each type of quantity in the solution vector For example for a model with saturation and pressure as the primary variables in that order the following reltolerdt S 0 5 P 0 2 would seek to adjust the time step such that the saturation does not change more than 10 nor the pressure more than 20 relative to the previous time step values The model will use the larger of the two time steps calculated from the tolerdt andthe reltolerdt values See the specific model documentation for specific details and default values minimum time step default 0 0 Reference Manual for the NUFT Flow and Transport Code Ver 2 0 23 UCRL MA 130651 5 Input Data Documentation Parameters for Numerical Methods 5 3 Parameters for Numerical Methods NAME tolerconv reltolerconv itermax iterbreak cutbackmax Set parameters controlling Newton Raphson iteration SYNOPSIS tolerconv lt real gt lt real gt reltolerconv lt real gt lt real gt itermax lt integer gt iterbreak lt integer gt cutbackmax lt integer gt DESCRIPTION Parameters controlling Newton Raphson iteration see Appendix B for description PARAMETERS tolerconv reltolerconv Maximum tolerance for change in components of solution vector from one Newton Raphson NR iteration to the next during a time step for NR convergence criteria to be satisfied The data parameters are of the form of lt
43. relative to the vertical downward direction assumed when creating the mesh file one can change the orientation of the model without rereading the mesh file When using the genmsh option one can do the same thing through the down vector The default value is unity PARAMETERS lt factor gt real number multiplying gravitational acceleration vector default 1 0 Reference Manual for the NUFT Flow and Transport Code Ver 2 0 21 UCRL MA 130651 5 Input Data Documentation Time Stepping Parameters 5 2 Time Stepping Parameters NAME time tstop dt dtmax stepmax Set automatic time stepping parameters SYNOPSIS time lt treal gt tstop lt t real gt dt lt t real gt dtmax lt t real gt stepmax lt integer gt DESCRIPTION These input parameters are related to the automatic determination of the time step size Except for stepmax their values are lt t real gt 1 e time real The time stepping algorithm that is used is described in Appendix B These parameters are required Section 5 2 2 describes optional parameters related to the automatic time stepping and Newton Raphson iteration PARAMETERS time initial simulation time tstop simulation stopping time dt initial time step dtmax maximum time step allowed stepmax maximum number of time steps that if exceeded will halt the run NOTES The initial simulation time step overrides the time read in from a restart file if the restart command i
44. rence Manual for the NUFT Flow and Transport Code Ver 2 0 12 UCRL MA 130651 5 Input Data Documentation 5 Input Data Documentation The items in the input data file are classified in the following categories Mesh Generation Parameters genmsh mesh file Time Stepping and Numerical Solution Parameters time lt gt ESTOP 2 x 4i AG re Ss dtmax stepmax Output Specification CIELE goa te OuEpUE vo ar Specification of Initial Conditions state read restart Rock Property Specification rocktab Source Term Specification SPECA a a ae Boundary Condition Specification octab Other options upstream weighting include Reference Manual for the NUFT Flow and Transport Code Ver 2 0 13 UCRL MA 130651 5 Input Data Documentation Mesh Generation Parameters 5 1 Mesh Generation Parameters NAME genmsh Internally generate a rectangular or cylindrical grid system SYNOPSIS genmsh coord lt coord type gt down lt num gt lt num gt lt num gt dx lt numx 0 gt lt numx I gt dy lt numy 0 gt lt numy I gt dz lt numz O gt lt numz I gt mat lt el name prefix gt lt mat type gt lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt lt el name prefix gt lt mat type gt lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt
45. s present If the t ime command is not present the time read in from the restart file will be used Reference Manual for the NUFT Flow and Transport Code Ver 2 0 22 UCRL MA 130651 NAME 5 Input Data Documentation Time Stepping Parameters tolerdt reltolerdt dtmin Set automatic time stepping parameters optional SYNOPSIS tolerdt lt real gt lt real gt reltolerdt lt real gt lt real gt dtmin lt treal gt DESCRIPTION These input parameters are related to the automatic determination of the time step size at each time step as generated by the time stepping algorithm The algorithm seeks to control maximum changes between the components of the solution vector from the current time step to the next The algorithm used is described in Appendix B 4 PARAMETERS tolerdt reltolerdt dtmin maximum tolerance for change in components of solution vector from one time step to the next The data parameters are in the form lt variable gt lt real gt values one for each type of quantity in the solution vector For example for a model with saturation and pressure in Pascals as the primary variables would have the form tolerdt S 0 5 P 1 e5 See the specific model documentation for specific details and the default values maximum relative tolerance for change in components of solution vector from one time step to the next The data parameters are of the form of lt variable gt lt
46. ser s manuals but with only the most commonly used input options covered This reference manual describes the options for the non module specific data input in more detail and also describes the general numerical algorithms used Reference Manual for the NUFT Flow and Transport Code Ver 2 0 2 UCRL MA 130651 2 The Syntax of the Input Data 2 The Syntax of the Input Data For each simulation run NUFT requires a text file to specify the input parameters e g the grid definition and the hydrologic and fluid properties This section describes the syntax of this file The file format is free format i e it does not matter what column the data is in nor does it matter if data is continued past the current line or lines Input consists of lists of data blocks or data units Each data unit starts with a left parenthesis and ends with a right parenthesis A data unit is of the following general form lt name gt lt data gt lt data gt where lt name gt refers to the input variable that is being set or specified lt data gt are items that are real numbers integer numbers time real numbers strings pattern strings words or other data units or list s of data items The different data types are defined later in this section An alternate form for a data unit is lt name gt lt data gt lt data gt lt name gt An advantage of this form is that the model can more reliably tell the user the exact l
47. t phasel gt comp fluxes lt comp0 gt lt phaseO gt lt compl gt lt phasel gt outtimes lt t0 gt lt ti gt lt t2 gt Outputs flux output data history variable lt var name gt element lt element name gt file lt file name gt Specifies output of element variable vs time flux history phase flux lt phase gt comp flux lt comp gt lt phase gt connection lt element name gt lt element name gt index con lt i0 gt lt j0 gt lt k0 gt lt il gt lt jl gt lt kI gt file lt file name gt Specifies output of flux variable vs time srcflux name lt src name gt comp lt comp name gt file lt file name gt outtimes lt t0 gt lt tl gt lt t2 gt s a w cumulative Outputs the total instantaneous flux of a component lt comp name gt due to a source term set in srctab The name of the source term lt src name gt is the desired one in srctab The sign convention is such that flow out of the problem domain is positive and flow out of the domain is negative If the statement cumulative is present the cumulative flux is outputted instead of the instantaneous flux Note that cumulative fluxes are reset to O at the beginning of a restart Reference Manual for the NUFT Flow and Transport Code Ver 2 0 35 UCRL MA 130651 5 Input Data Documentation Output Specifications ocflux name lt bc name gt
48. table gt list of reals Table of mole or mass fraction concentrations of the components within the phase stream the table is of the form lt t0 gt lt x0 gt lt tl gt lt xI gt where the time values are given by lt t0 gt lt t gt which are of data type t real and the concentrations are lt x0 gt lt xl gt which are of datatype real An alternative is to specify that the component concentrations used for the flux are those of element itself this is done by placing the command lt comp gt internal instead of lt comp gt table lt conc table gt Concentrations are in mass fraction if Reference Manual for the NUFT Flow and Transport Code Ver 2 0 43 UCRL MA 130651 5 Input Data Documentation Setting Source Terms input mass fraction on is present Otherwise concentrations are in mole fraction lt enthalpy table gt list of reals Table of specific enthalpies J kg of the component The table is of the form lt t0 gt lt h0 gt lt tl gt lt hI gt where the time values are given by lt t0 gt lt tl gt which are of data type t real and the enthalpies at these times are lt hO gt lt hl gt which are of data type real and have units of Joules kg Linear interpolation is used for values between the time values The last time must be greater than the end time of the run internal Calculate component and energy fluxes based on concentrations and enthalphies in th
49. tements in the conditional commands must be complete lists i e parentheses match inside the macro command Currently the macro commands only work inside an input set for a module or inside common Reference Manual for the NUFT Flow and Transport Code Ver 2 0 7 UCRL MA 130651 3 How to Read the Input Documentation 3 How to Read the Input Documentation The documentation of the input data to the code is written with special symbols that are not actually part of the data input but that are used as convenient shorthand to mean certain things Following is a list of special symbols that are used e Any word starting with the symbol lt and ending with gt e The symbols 2 48 Ge a ee a The meaning of these symbols is given as follows e Any italized word starting with the character lt and ending with the character gt represents data as described in the previous section and will be called a data token or token for short is an abbreviation that means that more data items follow but they are not specified at this point further explanation of the required missing data items will follow e means that data items inside are optional for example xyz lt real gt means that the input value of variable xyz is optional e represents a logical exclusive or of two sets of data items for example xyz lt real gt abc lt real gt means that the user must specify either the variable x
50. ters areafac lt num gt lt dir gt lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt lt num gt lt dir gt lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt sets area modifying factor lt dir gt valid options x y or Z dir x will mult the area between block i j k and i 1 j k dir y will mult the area between block i j k and 1 j 1 k dir z will mult the area between block i j k and 1 j k 1 write mesh lt file name gt write out mesh information using con and elc format write grid lt file name gt write out mesh information using freegrid format write gdef lt file name gt write out minimal geometry information about the grid to file the format of the grid definition file is Sgdef Stype lt word gt mesh type specifiedin coord Snx lt real gt no of subdivisions in x direction Sny lt real gt no of subdivisions in y direction Snz lt real gt no of subdivisions in z direction Sorder lt word gt ordering of elements e g XYZ YZX Or ZXY dx subdivisions in first coordinate lt real gt lt real gt Sdy subdivisions in second coordinate lt real gt lt real gt Sdz subdivisions in third coordinate lt real gt lt real gt Line breaks are treated as significant in this format Reference Manual for the NUFT Flow and Transport Code Ver 2 0 18 UCRL MA 130651 5 Input Data Documentation Mesh Generation Parameters gdef ext
51. transport sequentially That is the code first solves for the flow of phases and then the transport equation for the contaminant s is solved at Reference Manual for the NUFT Flow and Transport Code Ver 2 0 Il UCRL MA 130651 4 Basic Elements of the Input File each major time cycle in an alternating fashion If transport takes place at a much shorter time scale than does flow the transport may take several time steps in a single major time cycle The form used when flow and transport are solved sequentially is as follows common title outputfile output prefix output ext meshfile genmsh time ESCO 2 a lt name of flow model gt AE w a a dtmax stepmax state wv rocktab C ODEBUE a 4 2 J sretab i petab am ia ay lt name of transport model gt Gt 2 a lt lt dtmax stepmax State si w g rocktab E outp t es a a sretab l Ab tabs ic 2 ey Note that the flow model and transport model each has its own initial and maximum time steps and other data Any input data that is common to both models are placed in the common data unit Any of the items in the common data unit can also appear in the data unit of the particular model but they will be overridden by any specification that appears in the common data unit Refe
52. value by z list z coord and value by xyz list x y z coordinates and values by ijk list i j k index and value by xtable format compatible with st ate using by xtable method user needs to comment out output header by ytable format compatible with st ate using by ytable method user needs to comment out output header by ztable format compatible with st ate using by ztable method user needs to comment out output header tabular multicolumn format contour format readable by the nview program for MS DOS 1 In all options except extool option if file or file ext is missing it will write to output file 2 All extool options must write to a single file Only the file name of the firstextool data block is read file name of the rest are ignored if present 3 file lt file name gt gt can be replaced by file ext lt file name suffix gt gt if the field output prefix has been set the output file name is then the suffix appended to the output prefix 4 i j K indices start from 1 and go to nx ny or nz respectively Reference Manual for the NUFT Flow and Transport Code Ver 2 0 37 UCRL MA 130651 5 Input Data Documentation Output Specifications OPTIONAL OUTPUT INFORMATION print input on print pcg off print mat bal off print matrix off print accum off print accum coefs off print flux off print flux coefs off print sol off print sol NR off print dsol off
53. variable gt lt real gt values one for each type of quantity in the solution vector For example a model with saturation and pressure in Pascals as the primary variables in that order would have the form tolerconv S 0 5 P 1 e5 See the specific model documentation for specific details and the default values Numbers that are repeated can be abbreviated for example 3 0 1 would stand for three repeats of the numeral 0 1 e 0 1 0 1 0 1 Maximum relative tolerance for change in components of solution vector from one NR iteration to the next for NR convergence The data parameters are of the form of a list of nonnegative lt real gt values one for each type of quantity in the solution vector For example for a model with saturation and pressure as the primary variables in that order the following reltolerconv S 0 5 P 0 2 would specify that NR convergence criteria is met if the saturation does not change more than 10 and if the pressure changes no more than 20 relative to the previous NR iteration values The convergence criteria of the model are satisfied if one or both of the tolerconv and Reference Manual for the NUFT Flow and Transport Code Ver 2 0 24 UCRL MA 130651 itermax iterbreak cutbackmax 5 Input Data Documentation Parameters for Numerical Methods reltolerconv criteria are satisfied See the specific model documentation for details and default values Maximum NR iterations If exceede
54. width block banded gaussian elimination default vband variable bandwidth elimination with reverse cuthill mckee bandwidth minimization d4vband d4 ordered variable bandwidth elimination pcg orthomin preconditioned conjugate gradient method default value b1kbnd pcg parameters Parameters for preconditioned conjugate gradient PCG method precond Type of preconditioning method used Options dkr first degree incomplete ILU ilu incomplete ILU decomposition with variable fill in d4 incomplete ILU with d4 ordering with variable fill in comb combinative method Reference Manual for the NUFT Flow and Transport Code Ver 2 0 26 UCRL MA 130651 5 Input Data Documentation Parameters for Numerical Methods bgs block gauss seidel method none no preconditioning The recommended option for problems with linear or nearly linear equations e g ucsat is pcg parameters precond bgs toler 1 e 3 itermax 500 north 20 For problems with intermediate nonlinearity e g uslp usnt the incomplete ilu of degree O no fill in with generalized D4 ordering is recommended pcg parameters precond d4 toler 1 e 3 itermax 200 north 15 For problems with severe nonlinearities e g usnt with phase changes or highly nonlinear characteristic curves pcg parameters precond d4 toler 1 e 3 itermax 200 north 15 ilu degree 1 The degree of incomplete LU decomposition is set by ilu degree to 1 Recall that the def
55. yz or abc but not both xyz lt real gt abc lt real gt means that the user has the option of either specifying xyz orabc e denotes a grouping of data items usually used in conjunction with for example xyz lt real gt abc lt real gt ijk lt integer gt means that the user must either specify xyz or specify both abc and ijk In the input documentation the following data tokens have special meanings lt string gt a string lt integer gt an integer number lt real gt a real number lt t real gt a time real number the last character is alphabetic and denotes the units of time lt word gt a symbolic word lt pattern gt a pattern string Reference Manual for the NUFT Flow and Transport Code Ver 2 0 amp UCRL MA 130651 3 How to Read the Input Documentation These data types are described in Section 2 of this reference manual Reference Manual for the NUFT Flow and Transport Code Ver 2 0 9 UCRL MA 130651 4 Basic Elements of the Input File 4 Basic Elements of the Input File Before going further the user should have read the previous sections explaining the abbreviations and special symbols used in this input documentation General Form of Input Data lt name of model gt title jj run title outputfile output prefix output ext output file name meshfile genmsh mesh s
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