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POLYMIN 2005 3. DESIGNING A MODEL Grid Definition & Boundary Conditions POLYMIN currently supports a 1D or 2D domain discretized using triangular elements. With triangular elements, the grid can be unstructured, the connectivity (incidence) information is provided in the meshtria.txt file. The grid is generated either with the Flonet (Fnpcg) model, or by Hydrus. In either case, the grid is imported into POLYMIN using the meshtria.txt file. The element incidence array, which defines the global node numbers connected to each element, is stored in the array in(l,i) where l is the global element number, and i (=1,2,3) is the local element node number. Two examples are provided here to clarify the grid generation procedure. Note these examples are for demonstration purposes only, and would not be of sufficient resolution for a practical application since the Peclet and Courant criteria would be violated under most situations. Transport boundary conditions can be 1 st , 2 nd or 3 rd type (Table 3, Fig. 3.). The default is 2 nd type, zero-gradient. The bdy.txt file is divided into 2 sections: top and bottom boundary nodes. Currently, the model is restricted to a fixed oxygen concentration across the top, and a zero-gradient oxygen boundary at the bottom (the O2 conc. Can also be fixed to zero across the bottom boundary nodes using lo2fix=.true.. For the aqueous components, the top boundary nodes can be either first or thirdtype, depending on the value of kcauchy. The grid numbering is shown in Fig. 4 (for the case of a rectangular grid subdivided into triangles, as created by FLONET). 22
POLYMIN 2005 Table 3. Summary of transport boundary conditions available in POLYMIN. Boundary Type Definition First / Dirichlet c = c 0 Fixed concentration boundary (e.g. a large, wellmixed source) Second / Neumann ∂c = 0 ∂n Zero-concentration gradient (e.g. outflow or impermeable boundary). Third / Cauchy q0 0 ∂c = vc - D θc ∂ x i Dispersive flux boundary (e.g. source with known influx q 0 and concentration c 0 ). 23
Page 1 and 2: POLYMIN Version 3.0 2D REACTIVE MAS
Page 3 and 4: POLYMIN 2005 TABLE OF CONTENTS page
Page 5 and 6: POLYMIN 2005 1. INTRODUCTION 1.1 Ov
Page 7 and 8: POLYMIN 2005 1.3 Software Support I
Page 9 and 10: POLYMIN 2005 where S k is the solid
Page 11 and 12: POLYMIN 2005 model involves three s
Page 13 and 14: POLYMIN 2005 The three basic mathem
Page 15 and 16: POLYMIN 2005 Solution Strategy POLY
Page 17 and 18: POLYMIN 2005 Discretization Criteri
Page 19 and 20: POLYMIN 2005 2.3 Primary Variables
Page 21: POLYMIN 2005 2.5 Input/Output File
Page 25 and 26: POLYMIN 2005 4. SAMPLE DATA SET The
Page 27 and 28: POLYMIN 2005 Input options 1.0 0.5
Page 29 and 30: POLYMIN 2005 Data Block 1 0 0 0 ;IS
Page 31 and 32: POLYMIN 2005 Tolerance and relative
Page 33 and 34: POLYMIN 2005 Background aqueous che
Page 35 and 36: POLYMIN 2005 Input File: Bkgrndpoly
Page 37 and 38: POLYMIN 2005 5. STEP BY STEP INSTRU
Page 39 and 40: POLYMIN 2005 6. TIPS AND TECHNIQUES
Page 41 and 42: POLYMIN 2005 8. REFERENCES Aachib,
Page 43 and 44: POLYMIN 2005 Molson, J.W., Fala, O.
Page 45 and 46: POLYMIN 2005 Example 1: Geochemical
Page 47 and 48: POLYMIN 2005 Bkgrndpoly.min (from E
Page 49 and 50: POLYMIN 2005 Input Data file for Ex
Page 51: POLYMIN 2005 500 1.386E-03 ;NA " 41

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