Reference Manual for the NUFT Flow and Transport Code
Contents
1. 30 title 30 output file 31 output 32 output flow field 36 5 7 Specifying Initial Conditions 37 state 37 5 8 Reading Restart Information 38 read restart 38 5 9 Setting Rock Properties 39 NUFT Reference Manual DRAFT March 20 1996 1 CONTENTS rocktab 2 2 39 5 10 Setting Source Terms 2 2 40 srctab 2 40 5 11 Specifying Boundary Conditions 42 betab 2 42 5 12 Other Options 45 element prefix 45 NOTES 46 6 1 Notes Table Time Values 46 Running Flow and Transport Sequentially 47 References 48 Format of the Mesh File 49 B Numerical Algorithms Used 51 B 1 Numerical Discretization 51 B 2 Newton Raphson Iteration 51 B 3 Solution of System of Linear Equations2. 51 B 3 1 Banded Gaussian Elimination 52 B 3 2 Orthomin Preconditioned Conjugate Gradient 52 BA Automatic Time Stepping 52 NUFT Reference Manual DRAFT March 20 1996 2 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 distinct models are imbedded in a single code in order 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 success fully compiled and tested for IBM PC compatibles Cray Unicos and the following workstations Sun Hewlett Packward IBM Risc 6000 Silicon Graphics DEC Alpha Each set of related mod els is called a module and has its own user s manual which documents any particular features and input data specific to that module The NUFT Reference Manual Nitao 1993 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 Available modules are e UCSAT unconfined and confined saturated flow model e US1P single phase unsaturate
3. 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 0 gt lt t gt lt 12 gt outputs element data 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 j0 gt lt k0 gt lt il gt lt jl gt lt kI gt 1 phase fluxes lt phase0 gt lt phasel gt comp fluxes lt comp0 gt lt phase0 gt lt compl gt lt phasel gt Couttimes lt i gt lt t gt lt i2 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 NUFT Reference Manual DRAFT March 20 1996 33 5 6 OUTPUT SPECIFICATION output comp lt comp name gt file lt file name gt outtimes lt t0 gt lt H gt lt 185 gt cumulative outputs the total instantaneous flux of a component lt comp name gt
4. Reference Manual for the NUFT Flow and Transport Code Version 1 0 John J Nitao Earth Sciences Department Lawrence Livermore National Laboratory date March 20 1996 time 12 00 AM file ref tex CONTENTS Contents 1 Introduction 2 3 2 The Syntax of the Input Data 5 3 How to Read the Input Documentation 10 4 Basic Elements of the Input File 11 5 Input Data Documentation 14 5 1 Mesh Generation Parameters 15 genmsh 15 mesh file 19 grav factor 20 5 2 Time Stepping Parameters 21 time 21 Other Parameters 22 5 3 Parameters for Numerical Methods 23 Newton Raphson Iteration 23 Linear Equation Solution 25 Time Step Method 27 5 4 Parameters for Numerical Methods 28 Upstream Weighting 28 5 5 Parameters for Numerical Methods 29 Flux Correction Schemes 29 5 6 Output Specification
5. lt and ending with the character gt repre sents data as described in the previous section and will be called a data token or token for short 2 is an abbreviation that means that more data items follow but are not specified at this point further explanation of the required missing data items will follow 3 means that data items inside are optional for example xyz lt real gt means that the input value of variable xyz is optional 4 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 xyz or abc but not both xyz lt real gt abc lt real gt means that the user has the option of either specifying xyz or abc or 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 alternatively the user must specify both abe 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 These data types are described in a previous section NUFT Reference Manual D
6. lt k gt where lt i gt lt j gt lt k gt denote the i j and k indices The material type lt mat type gt is defined in rocktab The symbols nx ny and nz can be used anywhere in place of a number 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 Affects the choice of the permeability or hydraulic conductivity parameter See the documentation of the permeability parameters KO K1 and K2 below This parameter should not be present for models where isotropic permeability is desired Cisot 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 NUFT Reference Manual DRAFT March 20 1996 16 5 1 MESH GENERATION PARAMETERS genmsh 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 j0 gt lt j gt lt k0 gt lt k1 gt lt num gt lt i0 gt lt il gt lt j0 gt lt j gt lt k0 gt lt k1 gt sets volume modifying factor Multiplies the volume of the specified elements by lt num gt areafac lt num gt lt dir gt
7. 325 1984 Vinsome P K W Orthomin an iterative method for solving sparse sets of simultaneous linear equations Soc Petroleum Engineers paper 5729 1976 NUFT Reference Manual DRAFT March 20 1996 48 APPENDIX A FORMAT OF THE MESH FILE 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 el lt el name gt lt rock type gt lt volume gt lt el name gt lt rock type gt lt volume gt end con Y lt el name0 gt lt el namel gt lt isot gt lt L0 gt lt LI gt lt A gt lt beta gt Y lt el name0 gt lt el namel gt lt isot gt lt L0 gt lt LI gt lt A gt lt beta gt end Second Form The second form uses element numbers to specify connections eleme h lt el num gt lt el name gt lt rock type gt lt volume gt h lt el num gt lt el name gt lt rock type gt lt volume gt end conne lt mp0 gt lt mpl gt lt isot gt lt L0 gt lt LI gt lt A gt lt beta gt lt mp0 gt lt mpl gt lt isot gt lt L0 gt lt LI gt lt A gt lt beta gt end lt el name gt lt rock type gt lt volume gt lt el name0 gt lt el namel gt lt isot gt lt L0 gt lt LI gt where lt A gt lt beta gt lt el num gt lt mp0 gt lt mpi gt element name word rock type of element word volume of element
8. 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 but it is used in conjunction with the other macro commands The statements within ifdef lt variable gt will be placed as part of the input stream if lt variable gt is defined by the define command whereas the statements within ifndef 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 statements 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 NUFT Reference Manual DRAFT March 20 1996 9 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 which are not actually part of the data input but are used as a convenient short hand to mean certain things The following is a list of special symbols that are used 1 any word starting with the symbol lt and ending with gt 2 the symbols The meaning of these symbols is given as follows 1 Any italized word starting with the character
9. initial conditions using the restart 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 10 gt lt il gt lt j0 gt lt j1 gt lt k0 gt lt k1 gt variables lt var0 gt lt vari gt outtimes lt 0 gt lt t gt lt 12 gt file lt file name gt outputs a time history file in extool format program NOTES 1 outtimes lt t0 gt lt ti gt lt t2 gt can be replaced by either of a outtimes which means all times b triggers NUFT Reference Manual DRAFT March 20 1996 34 5 6 OUTPUT SPECIFICATION output 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 iff 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 then the corresponding condition for the cond field is checked if true then trigger goes off and
10. lt i gt lt il gt lt j0 gt lt j1 gt lt k0 gt lt k1 gt lt num gt lt dir gt lt i gt lt il gt lt j0 gt lt j1 gt lt k0 gt lt k1 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 1 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 k and ij k 1 write mesh lt file name gt write out con and el write grid lt file name gt write out freegrid if two files are same will write to same file write gdef lt file name gt write out minimal geometry information about the grid to file the format of the grid definition file is gdef type lt word gt mesh type specified in coord nx lt real gt no of subdivisions in x direction ny lt real gt no of subdivisions in y direction nz lt real gt no of subdivisions in z direction order lt word gt ordering of elements e g xyZ YZX or zxy dx subdivisions in first coordinate lt real gt lt real gt dy subdivisions in second coordinate lt real gt NUFT Reference Manual DRAFT March 20 1996 17 5 1 MESH GENERATION PARAMETERS genmsh lt real gt dz subdivisions in third coordinate lt real gt lt real gt Line breaks are treated as significant in this format gdef ext lt file ext gt write out minimal geometry information about the grid to file with file ext
11. nor does it matter if the 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 which 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 location 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 1 e 2 Ky 0 0 Kz 0 0 clay porosity 0 4 Kx 1 e 6 Ky 0 0 Kz 0 0 rocktab This example shows how a data unit which sets the variable rocktab to a list of data units Comment Character Semi colons in the input
12. real 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 or K2 in rocktab is used for this connection integer lengths of the part of the connection that lies in the first and second elements that defines 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 conne options are used specifies a flow connection with positive flow going from lt mp0 gt to lt mp1 gt integer NUFT Reference Manual DRAFT March 20 1996 49 APPENDIX A FORMAT OF THE MESH FILE 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 setup time is needed by the model to associate the element names with the element numbers that will be used during the simulation For greater than 4000 elements the second format is recommended NUFT Reference Manual DRAFT March 20 1996 50 APPENDIX B NUMERICAL ALGORITHMS USED B Numerical Algorithms Used B 1 Numerical Discretization NUF
13. 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 Jis present then the cumulative flux is outputted instead of the instantaneous flux Note that cumulative fluxes are reset to zero at the beginning of a restart bcflux name lt bc name gt comp lt comp name gt file lt file name gt outtimes lt 0 gt lt t gt lt 12 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 betab The name of the boundary condition lt bc name gt is the desired one in betab 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 then the cumulative flux is outputted instead of the instantaneous flux forcetimes outtimes lt 0 gt lt t gt lt 12 gt forces the model to hit specified times without necessarily outputting any informa tion 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 0 gt lt t gt lt 12 gt write out a restart record at the specified times Restart record can be read in as
14. evaluated at the n th iterate u Note that 4 can be viewed as a system of linear equations Ax b 6 where A J u D N ZOO X Uni Un b F u PS oO B 3 Solution of System of Linear Equations The code has currently two different options for solving the system of linear equations 4 banded gaussian elimination and preconditioned conjugate gradient methods NUFT Reference Manual DRAFT March 20 1996 51 APPENDIX B NUMERICAL ALGORITHMS USED B 3 1 Banded Gaussian Elimination First for convenience let us rewrite 4 in the matrix form Ax b 10 where A A is an n x n matrix It is well known that in many problems the matrix A is banded i e Aj 0 for i j gt np where nb is the matrix half bandwidth If nb lt n then 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
15. file lt file gt DESCRIPTION The user can set up a grid either by using the genmsh or by generating a mesh file outside of the program and then by reading the mesh file into the NUFT model The genmsh option can only produce grids that are either 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 NUFT Reference Manual DRAFT March 20 1996 19 5 1 MESH GENERATION PARAMETERS grav factor NAME grav factor set gravity modification factor optional including gravity orientation optional SYNOPSIS grav factor lt factor gt DESCRIPTION The user can optionally mutiply 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 to see what its effect is By setting this factor to the cosine of the angle of inclination 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 by setting the input parameter down The default value is unity PARAME
16. 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 started over This method also controls to some extent the time discretization error We now describe the method in more detail Let u be the i th component of the solution vector at the current iteration of the Newton Raphson method and fu be equal to u minus the z th component of the solution vector at the end of the previous time step Now let ui mag be the maximum allowed change in the solution We define the new reference time step t by se CLEMO max 7 w ui mae ou 11 Here w is a damping factor Grabowski et al 1979 that is chosen between 0 to 1 in order to prevent the time step from changing too rapidly We used a value of 0 8 The value of t 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 then 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 too many restarts If the equations are solved using an explicit in time method the time step i
17. RAFT March 20 1996 10 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 run title outputfile output prefix output ext output file name meshfile genmsh mesh specification time initial time tstop ending time dt initial time step dtmax maximum time step stepmax maximum no of time steps read restart read from restart file state set initial conditions rocktab soil property type grav factor factor multiplying gravity vector output output specification srctab 3 source tables bctab boundary condition tables Recall that the denote subsequent data items which 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 the above or 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 us1p refers to the single phase unsaturated flow model Note that the use of the square brackets around grav factor output
18. T solves balance equations see for example Bear and Bachmat 1991 which are partial differential equations whose specific form depends the particular NUFT module that is being used The balance equations are discretized in space using the integrated finite difference method see Edwards 1972 Narasimhan and Witherspoon 1978 Spatial discretization results in a system of ordinary differential equations of the form u ot where u is the solution vector and f is a vector valued function f u t 1 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 is 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 1 is solved using the implicit in time method the resulting system of equations which must be solved at each time step are non linear if f is non linear F u t Wirth _ ut _ At Ful th 4 1 0 2 where superscripts represent the time level B 2 Newton Raphson Iteration The non linear system of equations 2 is of the form F u 0 3 The Newton Raphson iterative method is used to solve the equations J un un 1 un Fun 4 where the matrix _ tar Hoa 6 is the Jacobian of the function F
19. TERS lt factor gt real number multiplying gravitational acceleration vector default 1 0 NUFT Reference Manual DRAFT March 20 1996 20 5 2 TIME STEPPING PARAMETERS time NAME time tstop dt dtmax stepmax set automatic time stepping parameters SYNOPSIS time lt t real 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 i e time real The time stepping algorithm that is used is described in Appendix B 4 These parameters are required Subsection 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 if exceeded the run will stop NOTES The initial simulation time step overrides the time read in from a restart file if the restart command is present If the time command is not present then the time read in from the restart file will be used NUFT Reference Manual DRAFT March 20 1996 21 5 2 TIMESTEPPING PARAMETERS tolerdt NAME toler SYNOPSIS dt reltolerdt dt min set automatic time stepping parameters optional tolerdt lt real gt lt real gt reltolerdt lt real gt
20. ar name gt lt method gt lt data gt DESCRIPTION sets initial conditions for primary variables NOTES This command must be left out when reading initial data from a restart file using the restart command examples of lt method gt lt state var name gt by key lt elem range gt lt value gt lt elem range gt lt value gt lt stale var name gt by set lt vector gt where lt vector gt H lt n gt lt v0 gt lt vI gt and lt n gt is no of components and the lt n gt field is optional here and Jare actual characters and do not represent delimiters of optional parameters lt state var name gt by xtable lt table gt lt stale var name gt by ytable lt table gt or lt state var name gt by ztable lt table gt where lt table gt lt 20 gt lt val0 gt lt 2 1 gt lt valf gt is a 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 specifi cations for example values for all elements can be set by by xtable or by set and then touched up using by key 2 The program will terminate if a primary variable has not been set for all of the elements NUFT Reference Manual DRAFT March 20 1996 37 5 8 SPECIFYING INITIAL CONDITIONS read restart NAME read restart read restart record SYNOPSIS read restart file lt file
21. atches 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 patter matches all strings with exactly one character Other Examples 1 The pattern ex matches all strings that begin with the characters ex 2 The pattern ex b2 z matches all strings that begin with ex followed by any number including zero of strings which are then followed by the string b2 and which end with the string z 3 The pattern r2 xay matches all strings that begin with r2 followed by a single character and then followed by the characters xay NUFT Reference Manual DRAFT March 20 1996 7 2 INPUT DATA SYNTAX Include statement The include statement is of the form include lt file name gt It is used to place the contents of the file with the name lt file name gt into the input file The file must le in the working directory under which NUFT is being run It can only be used to replace a complete list i e must be either a collection of data which is delimited by a closed sets of parentheses or a single data item such as a number or string For example suppose the file datal inc contains field format list range variables S1 file ext S1 outtimes O 70m 102m 222m 287m 342m 23h and the file data2 inc contains the single entry 200m with the file data3
22. calculated at the beginning of each step and then the transport of contaminants is performed using the resulting the 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 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 then the one in common takes precedence General Form for Running Flow and Transport Sequentially common title outputfile output prefix output ext meshfile Cgenmsh time tstop lt flow model name gt dt dtmax stepmax state rocktab output srctab bctab lt transport model name gt dt dtmax stepmax state rocktab output srctab bctab phaseprop compprop NUFT Reference Manual DRAFT March 20 1996 47 REFERENCES 8 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 reser
23. d flow Richard s equation e US1C single component contaminant transport e USNT NP phase NC component with thermal option An integrated finite difference spatial discretization is used to solve the balance equations The resulting non linear equation is solved at each time by the Newton Raphson method Options for solution of the linear 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 incor poration of capillary hysteresis non orthogonal mesh discretization finite elements non linear solid sorption isotherms and chemical reactions The first stage of code verification with one dimensional problems has been completed Lee et al 1993 and further verification efforts are planned The distinct models in the code utilize a common set of utility routines and input file format The various models are essentially isolated from each other and hence future models can be added without affecting existing models This also allows for easy maintenance and future enhancements Global variables in the code are virtually non existent The code is written principally in the C language Input data is in the form of that used by the lisp language An internal lisp interpreter for the Scheme dialect of lisp is part of the simulator whose purpose is to read the input data fil
24. d4 incomplete ILU with d4 ordering with variable fill in comb combinative method bgs block gauss seidel method none no preconditioning The recommended option for problems with linear or nearly linear equations eg 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 0 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 non linear characteristic curves NUFT Reference Manual DRAFT March 20 1996 25 5 3 PARAMETERS FOR NUMERICAL METHODS linear solver 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 one Recall that the default is zero Another available option for problems where D4 ordering is not appropriate pcg parameters precond ilu toler 1 e 5 itermax 100 north 15 Note that the d4 ordering is generalized meaning that it also works when connections between elements are non standard with respect to the standard 1 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 n
25. e and the internal data files containing default input data values It also performs data checking This manual is self contained and describes a minimal set of the most commonly used input parameters necessary for the use of this module The NUFT reference manual Nitao 1995 contains generic input options common to all of most of the modules It also contains further input options not given in this manual 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 user s manual 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 NUFT Reference Manual DRAFT March 20 1996 3 1 INTRODUCTION acknowledegments The author wishes to thank the management of the Environmental Restoration Division at the Lawrence Livermore National Laboratory LLNL for supporting the documentation and verification of the NUFT code The basic concepts of the code was developed under the funding of the LLNL Institutional Research and Development program NUFT Reference Manual DRAFT March 20 1996 4 2 INPUT DATA SYNTAX 2 The Syntax of the Input Data This section describes the syntax of the input data The input data file format is in free format i e it does not matter what column the data is in
26. e ext S1 The following is an example of an error Suppose the file file inc contains the following 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 included not to mention the fact that the parentheses will not match in the input file NUFT Reference Manual DRAFT March 20 1996 13 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 tstop dt dtmax stepmax Output Specification title output Specification of Initial Conditions state read restart Rock Property Specification rocktab Source Term Specification srctab Boundary Condition Specification bctab Other options upstream weighting include NUFT Reference Manual DRAFT March 20 1996 14 5 1 MESH GENERATION PARAMETERS genmsh 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 l
27. eference Manual DRAFT March 20 1996 41 5 11 SPECIFYING BOUNDARY CONDITIONS bctab 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 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 lt phase name gt lt phase factor table gt lt phase name gt lt phase factor table gt DESCRIPTION purpose set boundary conditions PARAMETERS lt bc name gt word name of the boundary condition Each boundary condition has a distinct name used for identification in diagnostic output lt elem range gt pattern string NUFT Reference Manual DRAFT March 20 1996 42 5 11 SPECIFYING BOUNDARY CONDITIONS bctab range of elements which will have the boundary condition lt primary var gt word the 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 l
28. ension non log by default flow areas in the radial direction for cylindrical coordinates are calculated using the logarithmic formula 1 A 7 Ari 1 Ar AOAz In r ri 1 If the non log flag is present flow areas are calculated as A r Ar 2 ACAz wrap around if lt coord type gt is set to cylind 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 band width of the matrix when using the direct solution option or the comb option of the preconditioned conjugate gradient method and therefore increase cpu time NOTE indices start from 1 internally the program converts them to start at 0 coords of blocks start from zero and are incremented by corresponding values in dx dy and dz If type is cylind then the first coord x is radial distance the second y is angle and third z is longitudinal to central axis The units of the angles in the cylind option are in degrees NUFT Reference Manual DRAFT March 20 1996 18 5 1 MESH GENERATION PARAMETERS mesh file NAME mesh file specify name of mesh file SYNOPSIS mesh
29. ents of the vector pointing downward in the direction of the gravity vector The program will internally normalize the vector to unity Setting the components to all 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 a 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 4 90 z 0 and the axis Z is defined by r 0 lt numz gt lt numy gt lt numz gt x y and z components of downward vector lt numz 0 gt lt numz 1 gt lt numy 0 gt lt numy 1 gt lt numz 0 gt lt numz 1 gt sets mesh divisions lt numz 0 gt lt numa 1 gt lt numy 0 gt lt numy 1 gt lt numz 0 gt lt numz gt 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 that is 5 0 5 0 5 0 lt el name prefix gt lt mat type gt lt wU gt lt il gt lt j0 gt lt jl gt lt k0 gt lt k1 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 prefir gt lt i gt lt j gt
30. et to off the model will not do backups Default is on backup period lt backup lime gt optional lt backup time gt t real wall clock time period for model to perform backup restarts Default value is 10m i e 10 minutes NUFT Reference Manual DRAFT March 20 1996 38 5 9 SETTING ROCK PROPERTIES rocktab NAME rocktab sets rock properties SYNOPSIS rocktab lt rock type name gt porosity lt real gt lt rock type name gt DESCRIPTION sets rock properties for each rock type the rock type of each element is contained in the mesh file PARAMETERS lt rock type name gt the name of the rock type porosity lt real gt porosity NUFT Reference Manual DRAFT March 20 1996 39 5 10 SETTING SOURCE TERMS srctab NAME srctab set source terms SYNOPSIS srctab compflux lt comp name gt range lt elem range gt lt elem range gt table lt flux lable gt enthalpy lt enthalpy table gt compflux phaseflux lt phase gt name lt phaseflux name gt range lt elem range gt lt elem range gt table lt phase flur 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 DESCRIPTION specifies the component flux into an element or range of elements through a table
31. file saturations and flux used by transport program file file name to hold flow field information Optional Output Information print input on print pcg off print mat bal off print matrix off print accum off output input data output peg convergence info output material balance output matrix output accumulation print accum coefs off output accumulation coefs print flux off print flux coefs off print sol off print sol NR off print dsol off print NR iter off print qsre off print bc 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 output internal fluxes output internal flux coefs output solution at end of each time step output solution between NR iterations output changes between NR iterations output NR iteration no to stderr output source terms output be terms turns on printing to a log file output values of terms output eqtpar structure output time step data output src tables output bc tables output rock tables output fluid properties output grid data output time step restriction output NR convergence restriction NUFT Reference Manual DRAFT March 20 1996 36 5 7 SPECIFYING INITIAL CONDITIONS state SYNOPSIS state lt state var name gt lt method gt lt data gt lt state v
32. 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 his input file Using two semicolons instead of a single one is a good way to make sure that comments standout Example porosity 0 2 this is how we set the value of porosity to 0 2 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 Unitless quantities such NUFT Reference Manual DRAFT March 20 1996 5 2 INPUT DATA SYNTAX Table 1 Table of Units used in Input to Models length mass timet temperature area volume mass density molar density permeability hydraulic conductivity flow velocity force pressure head energy specific energy mass flux molar flux volumetric flux energy flux thermal conductivity dynamic viscosity molecular diffusivity meters m kilograms kg seconds s centigrade C m2 m3 kg m mole m3 m2 m s m s Newton Nt kg m s Pascals Pa Nt m m Joule J Nt m J kg kg s mole s m3 s Watts W J s W m C Nt s m kg m s 1 centipoise m s fmodel can accept other time units using unit designators NUFT Reference Manual DRAFT March 20 1996 2 INPUT DATA SYNTAX as saturation porosity and concentrations are always fractional i e between 0 t
33. has to be started over again due to lack of NR convergence If exceeded the program will print and error message and then stop default value 100 NUFT Reference Manual DRAFT March 20 1996 24 5 3 PARAMETERS FOR NUMERICAL METHODS linear solver NAME linear solver pcg parameters SYNOPSIS linear solver lt word gt peg 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 width block banded gaussian elimination default vband variable band width elimination with reverse cuthill mckee bandwidth minimization d4vband d4 ordered variable bandwidth elimination pcg orthomin preconditioned conjugate gradient method default value blkbnd 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
34. ime steps calculated from the tolerdt and the reltolerdt values See the specific model documentation for specific details and default values dtmin minimum time step default 0 0 NUFT Reference Manual DRAFT March 20 1996 22 5 3 PARAMETERS FOR NUMERICAL METHODS tolerconv NAME tolerconv reltolerconv itermax iterbreak cutbackmax set parameters control ling 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 subsection B 2 for description PARAMETERS tolerconv 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 a list of non negative 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 in that order would have the form tolerconv 0 5 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 that is 0 1 0 1 0 1 reltolerconv maximum relative tolerance for change in comp
35. inc containing the string SI Then the following input data output include datat inc forcetimes outtimes include data2 inc 201m will be interpreted by the model as begin equivalent to output field format list range variables S1 file ext S1 outtimes O 70m 102m 222m 287m 342m 23h forcetimes outtimes 200m 201m file ext S1 The following is an example of an error Suppose the file file inc contains the following outtimes 0 70m 102m 222m and the input file as the data item output field format list range variables S1 file ext S1 NUFT Reference Manual DRAFT March 20 1996 8 2 INPUT DATA SYNTAX 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 included not to mention the fact that the parentheses will not match in the input file Include package statement The include package statement is of the form include pkg lt file name gt This statment is identical to the include statement except that it includes a file from the subdirectory which contains the NUFT executable instead from the current working directory The main purpose is to include a package of pre defined input parameters which comes with the NUFT software distribution Macro commands Macro commands start with the character 1 There are three commands available
36. l will use the weighting C ACup 1 eaown based on the weighting factor w where a wLup wLup 1 w Laown where L refers to flow lengths the supscript up refers to upstream value and 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 NUFT Reference Manual DRAFT March 20 1996 28 5 5 PARAMETERS FOR NUMERICAL METHODS flux correction NAME flux correction flux correct options set parameters controlling flux correction scheme SYNOPSIS flux correction lt word gt flux correct options method lt word gt iter lt integer gt DESCRIPTION The model by default uses complete upstream weighting of mobilities to numerically cal culate the advective flux between two elements see upstream weighting for changing the amount of upstream weighting An alternative method is to use the flux correc tion scheme of Smolarkiewicz 1983 which is a modification of the upstream weight ing If flux correction is set to on then 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 of the Smolarkiewicz PARAMETERS flux correction can be set to either on or off to turn on flux correction on or off method choice of flux correc
37. lt real gt dtmin lt t real 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 that is used is described in Appendix B 4 PARAMETERS tolerdt maximum tolerance for change in components of solution vector from one time step to the next The data parameters are of the form of a list of non negative 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 in that order would have the form tolerdt 0 5 1 65 See the specific model documentation for specific details and the default values reltolerdt 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 a list of non negative 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 reltolerdt 0 1 0 2 would seek to adjust the time step such that the saturation does not change more than 10 and the pressure more than 20 relative to the previous time step values The model will use the larger of the two t
38. ment prefix delimiter lt prefix sep gt element indices separator lt ind sep gt DESCRIPTION change the format of element names created by genmsh NOTES The genmsh command names the element according to the general format lt elem prefir gt lt 1i 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 prefiz gt is set by the mat command inside of genmsh These commands allows the user to change the separators and by the single character in the strings lt prefiz sep gt and lt ind sep gt respectively NUFT Reference Manual DRAFT March 20 1996 45 6 1 OTHER OPTIONS 6 NOTES Currently the model may in some cases choose time steps which are so large that it overshoots sharp changes in a time table This may be a serious problem if for example we want to model a flux that is turned off suddenly A solution is to use the forcetimes command in output which forces the model to hit specified times in this case the times at which the boundary condition changes suddenly The last time value in table must be greater than or equal to the ending time of the simulation as set by tstop or the model will abort NUFT Reference Manual DRAFT March 20 1996 46 7 RUNNING FLOW AND TRANSPORT SEQUENTIALLY 7 Running Flow and Transport Sequentially In some modules such as the us module the flow of the fluid phases is first
39. method is have all files having the same prefix e g the run name and have different suffixes for each file e g out pg T etc If this 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 are 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 see will have this prefix this is usually used to specify a single run name where all output files start with this name output ext instead of specifying the output file one can specify the prefix of the output file NUFT Reference Manual DRAFT March 20 1996 31 5 6 OUTPUT SPECIFICATION output NAME output specifies output SYNOPSIS output field file lt file name gt format lt options gt range lt element range gt index range lt i gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt variables lt el var0 gt lt el vari gt outtimes lt 10 gt lt li 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 j0 gt lt k0 gt lt tl gt lt j1 gt lt k1 gt variables lt con var0 gt lt con va
40. name gt time lt restart time gt DESCRIPTION sets initial conditions for primary variables by reading in a restart record from a file PARAMETERS lt file name gt string name of the restart file created by the option output restart 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 time and overwrites the time read in through the restart file If time is not present the initial of the run is set to the time read in NOTES Restart records are created from a previous run using the restart option in the output command Restart Backup The model will periodically write out restart records so that the model can be restart in case of system failure The model alternately writes out to two restart files named lt prefir gt re0 and lt prefix gt rel where lt prefiz gt is set by output prefix Each file contains a single record previous records are overwritten The reason for using two files instead of a single one is to prevent losing a record if the system fails during a write The user must check the two files to see which has the record with the largest time 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 then the model will periodically write backup restarts If s
41. near interpolation is used for values between the time values The last time must be greater than the end time of the run lt conc table gt list of reals Table of mole fraction concentrations of the components withing the phase stream The table is of the form lt t0 gt lt 20 gt lt t gt lt I gt where the time values are given by lt t0 gt lt gt which are of data type t real and the concentrations are lt x0 gt lt x1 gt which are of data type real An alternative is to specify the component concentrations used for the flux of applied to each respective element as that within the element itself which is done by placing the command lt comp gt internal instead of lt comp gt table lt conc table gt lt enthalpy table gt list of reals Table of specific molar enthalpies of the component The table is of the form lt t0 gt lt h0 gt lt t gt lt hI gt where the time values are given by lt t0 gt lt t gt which are of data type t real and the enthalpy at these times are lt h0 gt lt h1 gt which are of data type real and have units of Joules mole 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 the respective phase within the element instead of specifying through a table of concentrations and enthalpies NUFT R
42. o 1 inclusive not percentages Legal Data Types We now describe the following valid data types 1 A string is any sequence of visible characters delimited by double quotes for example hello there run3 B test 2 Note that spaces and parentheses are allowed in a string 2 An integer number for example 11 3 A real number that is fixed or floating point For example 1 23 4 5e7 or 900 2E7 Note that D or d exponents in the manner of FORTRAN are not allowed 4 A time number which is a real number but with with the following unit designators as the last letter in order to denote units of time As you may have guessed this type of number is used whenever we want to specify a time seconds minutes hours days months years lt zarga If no unit designator is present then seconds is assumed Examples 20 0 20 seconds 23 18 23 1 seconds 45e4M 45e4 months There must be no spaces between the number and the unit designator 5 A word is a sequence of non blank visible characters A word can be a variable or may be used in the same way as a string except that it can not 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 6 A pattern string is 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 m
43. of source fluxes at specified 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 ele ment s NUFT Reference Manual DRAFT March 20 1996 40 5 10 SETTING SOURCE TERMS srctab lt elem range gt pattern string range of elements that will have the source term flux specified by the flux table lt fluz table gt table component mass flux table of the form lt t0 gt lt q0 gt lt ti 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 qi gt which are of data type real and are in units of kg sec except that USIP model is volumetric flux m s See subsection regarding an important note lt phase gt name Name of the phase lt phaseflux name gt name Name of the phase flux set Used when refering to this set within 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 ti 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 at these times are lt g0 gt lt qi gt which are of data type real and are in units of kg sec Li
44. onents of solution vector from one NR iteration to the next for NR convergence The data parameters are of the form of a list of non negative 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 0 1 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 is satisfied if one or both of the tolerconv and reltolerconv criteria are satisfied See the specific model documentation for specific details and default values Numbers that are repeated can be abbreviated for example 3 0 1 would stand for three repeats of the numeral 0 1 that is 0 1 0 4 0 1 itermax maximum NR iterations If exceeded i e if NR convergence has not been reached and the NR iterations is greater than this number the time step size is cutback by one half and the time step is started over again default value 8 iterbreak go on to next time step if this many NR iterations has been reached regardless of whether the NR convergence criteria are met default value 1000000000 cutbackmax NUFT Reference Manual DRAFT March 20 1996 23 5 3 PARAMETERS FOR NUMERICAL METHODS tolerconv maximum number of times in a given time step that the time step
45. orm of the initial residual vector The mean square norm is used n 1 Ie Dr i 1 itermax maximum number of PCG iterations If exceeded the time step size will be cut back in half and the time step started over direct specifies which of the balance equations are solved directly in the combinative method preconditioning option comb Needed only for comb preconditioning method Parameters are a list of lt integer gt s one for each balance equation A non zero value will cause the linear equations for that balance equation to e solved directly by gaussian elimination ilu degree degree of fill in for ILU decomposition Degree zero equals no fill in NUFT Reference Manual DRAFT March 20 1996 26 5 3 PARAMETERS FOR NUMERICAL METHODS linear solver 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 PARAMETERS time method Valid values are fully implicit or explicit default value model specific NUFT Reference Manual DRAFT March 20 1996 27 5 4 PARAMETERS FOR NUMERICAL METHODS upstream weighting 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 mode
46. output occurs triggers only go off once 2 format lt options gt lt options gt can be any of following list or by list list values and element names contsac format by set list values as a lisp vector n v1 v2 vn by x list x coord and value by y list y coord and value by z list z coord dd valuarbiexijghd value by xtabl rmat compatible with state using by xtable method user needs to comment out output header by ytabl rmat compatible with state using by ytable method user needs to comment out output header by ztabl rmat compatible with state using by ztable method user needs to comment out output header tabular multi column format contour format readable by the nview program for MS DOS 3 in all option except extool option if file or file ext is missing then will write to output file 4 all extool options must write to a single file only the file name of the first extool data block is read file name of the rest are ignored if present 5 file lt file name gt can be replaced by file ext lt file name suffiz gt if the field output prefix in the has been set the output file name is then the suffix appended to the output prefix 6 1 J k indices start from 1 and go to nx ny or nz resp NUFT Reference Manual DRAFT March 20 1996 35 5 6 OUTPUT SPECIFICATION output flow field output flow field file lt string gt states S1 fluxes liquid specifies output of flow field
47. ps as well as 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 will be overridden by any specification that appears in the common data unit Include statement Input can be read from another file and placed into the input file using the include statement The include statement is of the form include lt file name gt It is used to place the contents of the file with the name lt file name gt into the input file It can only be used to replace a complete list i e must be either a collection of data which is delimited by a closed sets of parentheses or a single data item such as a number or string For example suppose the file datal inc contains field format list range variables S1 file ext S1 outtimes O 70m 102m 222m 287m 342m 23h and the file data2 inc contains the single entry 200m with the file data3 inc containing the string SI Then the following input data NUFT Reference Manual DRAFT March 20 1996 12 4 BASIC ELEMENTS OF THE INPUT FILE output include datai inc forcetimes outtimes include data2 inc 201m will be interpreted by the model as begin equivalent to output field format list range variables S1 file ext S1 outtimes O 70m 102m 222m 287m 342m 23h forcetimes outtimes 200m 201m fil
48. ri gt outtimes lt i0 gt lt ti 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 10 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 ti gt lt i2 gt cumulative bcflux name lt bc name gt comp lt comp name gt file lt file name gt outtimes lt t0 gt lt ti gt lt i2 gt cumulative forcetimes outtimes lt t0 gt lt ti gt lt i2 gt restart file lt file name gt NUFT Reference Manual DRAFT March 20 1996 32 5 6 OUTPUT SPECIFICATION output outtimes lt t0 gt lt ti gt lt 12 gt extool range lt element range gt index range lt 10 gt lt il gt lt j0 gt lt j1 gt lt k0 gt lt k1 gt variables lt var0 gt lt vari gt outtimes lt 0 gt lt t gt lt 12 gt file lt file name gt DESCRIPTION specifies the writing of various output data to files Any of the above options can be specified none of them is required PARAMETERS field file lt file name gt format lt options gt
49. s restricted so that the Courant Friedrichs Levy criteria Richtmyer and Morton 1967 is satisfied NUFT Reference Manual DRAFT March 20 1996 52
50. srctab and bctab denote that these data units are optional There are more optional data items which will be described later but the above ones are the most likely to be used Initial conditions are set either using read restart or state One but not both of them must be present The above applies to NUFT modules that solve for flow and transport simultaneously Some NUFT modules have the option of solving flow and 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 each major time cycle in an alternating fashion The transport may take several time steps in a single major time cycle if transport takes place at a much shorter time scale than flow The form that is used when flow and transport is solved sequentially common title outputfile output prefix output ext meshfile genmsh time tstop lt name of flow model gt dt NUFT Reference Manual DRAFT March 20 1996 11 4 BASIC ELEMENTS OF THE INPUT FILE dtmax stepmax state rocktab output srctab bctab lt name of transport model gt dt dtmax stepmax state rocktab output srctab bctab Note that the flow and transport models each have their own initial and maximum time ste
51. t numz 0 gt lt numxz 1 gt dy lt numy 0 gt lt numy 1 gt dz lt numz 0 gt lt numz 1 gt mat lt el name prefiz gt lt mat type gt lt i0 gt lt tl gt lt j0 gt lt jl gt lt k0 gt lt ki gt lt el name prefiz gt lt mat type gt lt i gt lt il gt lt j0 gt lt jl gt lt k0 gt lt k gt isot dir isot 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 i gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kl gt volfac lt num gt lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt lt num gt lt i0 gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kI gt areafac lt num gt lt dir gt lt i gt lt il gt lt j0 gt lt jl gt lt k0 gt lt kl 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 write mesh lt file name gt write grid lt file name gt write gdef lt file name gt gdef ext lt file ert gt non log wrap around m m m mmaa ee DESCRIPTION put description here PARAMETERS coord lt coord type gt set type of coordinate system lt coord type gt coordinate system type options are rect cylind NUFT Reference Manual DRAFT March 20 1996 15 5 1 MESH GENERATION PARAMETERS genmsh down lt numr gt lt numy gt lt numz gt dx dy dz mat sets the the compon
52. t td gt lt var0 gt lt tl gt lt vari gt where the time values lt t0 gt lt t1 gt are of data type t real and the entries lt var0 gt lt vari gt are the corresponding values of the primary variable that is being specified See subsection regarding 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 which can depend on time and is set by a table One use of this option is to turn off a component flux coming out or into a boundary element at certain time intervals or at all times Note that several different components can be specified each with 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 mass fluxes by a factor which can depend on time and is set by a table lt comp name gt word name of the component flux which will have its flux modified model specific lt phase name gt word name of the phase which will have its flux modified model specific lt comp factor table gt table table of modification factors for component fluxes form lt l0 gt lt fac0 gt lt li gt lt facI gt where the time values lt t0 gt lt
53. t1 gt are of data type t real and the entries lt fac0 gt lt faci gt are the corresponding modification factors See subsection regarding 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 state 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 which are so large that it overshoots sharp changes in a time table This may be a serious problem if for example we want to model a flux that is turned off suddenly A solution is to use the forcetimes NUFT Reference Manual DRAFT March 20 1996 43 5 11 SPECIFYING BOUNDARY CONDITIONS bctab command in output which forces the model to hit specified times in this case the times at which the boundary condition changes suddenly The last time value in table must be greater than or equal to the ending time of the simulation as set by tstop or the model will abort NUFT Reference Manual DRAFT March 20 1996 44 5 12 OTHER OPTIONS element prefix NAME element prefix delimiter element indices separator set format of element names SYNOPSIS ele
54. tion method smolark flux correction using Smolarkiewicz s method harmonic flux correction using harmonic averaging iter Number of iterations for flux correction Using greater than two iterations for the harmonic method can lead to spatial oscillations in the solution Using value of one for the harmonic appears to give the same results as for the Smolarkiewicz method NUFT Reference Manual DRAFT March 20 1996 29 5 6 OUTPUT SPECIFICATION title 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 NUFT Reference Manual DRAFT March 20 1996 30 5 6 OUTPUT SPECIFICATION output file NAME output file output prefix output ext specifies 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 There will be at least one main output file and possibly several auxilliary files generated by the output option described in this section There are several possibilities on how the user can specify the names of these files One possibility is to separately name each file using the output file parameter to name the main output file and the file parameter in output to name the auxilliary files Another more convenient
55. voir simulation Soc Petroleum Engineers paper 9303 1980 Edwards A L TRUMP a computer program for transient and steady state temperature dis tributions in multidimensional systems National Tech Information Service Springfield VA 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 Lawrence Livermore National Laboratory Report 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 Nitao J J User s Manual for the USIP and US1C Modules of the NUFT Code Lawrence Livermore National Laboratory Rep 1995 Nitao J J User s Manual for the UCSAT Module of the NUFT Code Lawrence Livermore National Laboratory Rep 1995 Nitao J J User s Manual for the USNT Module of the NUFT Code Lawrence Livermore National Laboratory Rep 1995 Richtmyer R D and K W Morton Difference Methods for Initial Value Problems Interscience Pub N Y 1967 Smolarkiewicz P K A fully multidimensional positive definite advection transport algorithm with small implicit diffusion Journal of Computational Physics 54
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