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fix(mtlistfile): fix reading MT3D budget (#1899)
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* fix character span reading tkstp with a regex match
* skip particle information reading GW-Mass Budget

Co-authored-by: Ralf Junghanns <ralf@junghanns.it>
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@rabbl @wpbonelli
2 people authored and wpbonelli committed Aug 25, 2023
1 parent ee92091 commit 2222245
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Showing 3 changed files with 374 additions and 4 deletions.
4 changes: 4 additions & 0 deletions autotest/test_listbudget.py
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Expand Up @@ -123,6 +123,10 @@ def test_mtlist(example_data_path):
mt = MtListBudget(mt_dir / "mcomp.list")
df_gw, df_sw = mt.parse(forgive=False, diff=False, start_datetime=None)

mt_dir = example_data_path / "mt3d_test"
mt = MtListBudget(mt_dir / "mt3d_with_adv.list")
df_gw, df_sw = mt.parse(forgive=False, diff=False, start_datetime=None)

mt_dir = example_data_path / "mt3d_test"
mt = MtListBudget(mt_dir / "CrnkNic.mt3d.list")
df_gw, df_sw = mt.parse(forgive=False, diff=True, start_datetime=None)
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330 changes: 330 additions & 0 deletions examples/data/mt3d_test/mt3d_with_adv.list
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@@ -0,0 +1,330 @@
LISTING FILE: mt.list
UNIT 16

OPENING mt3d_link.ftl
FILE TYPE:FTL UNIT 10

OPENING mt.btn
FILE TYPE:BTN UNIT 31

OPENING mt.adv
FILE TYPE:ADV UNIT 32

OPENING mt.dsp
FILE TYPE:DSP UNIT 33

OPENING mt.gcg
FILE TYPE:GCG UNIT 35

OPENING mt.ssm
FILE TYPE:SSM UNIT 34

OPENING mt.rct
FILE TYPE:RCT UNIT 36

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ +
+ MT3DMS +
+ A Modular 3D Multi-Species Transport Model +
+ For Simulation of Advection, Dispersion and Chemical Reactions +
+ of Contaminants in Groundwater Systems +
+ +
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

-----
| M T | ## BTN for MT3DMS, generated by Flopy.
| 3 D | ##
-----
THE TRANSPORT MODEL CONSISTS OF 1 LAYER(S) 31 ROW(S) 31 COLUMN(S)
NUMBER OF STRESS PERIOD(S) FOR TRANSPORT SIMULATION = 1
NUMBER OF ALL COMPONENTS INCLUDED IN SIMULATION = 1
NUMBER OF MOBILE COMPONENTS INCLUDED IN SIMULATION = 1
UNIT FOR TIME IS D ; UNIT FOR LENGTH IS M ; UNIT FOR MASS IS KG
OPTIONAL PACKAGES INCLUDED IN CURRENT SIMULATION:
o ADV ON UNIT 32
o DSP ON UNIT 33
o SSM ON UNIT 34
o RCT ON UNIT 36
o GCG ON UNIT 35

BTN5 -- BASIC TRANSPORT PACKAGE, VERSION 5, FEBRUARY 2010, INPUT READ FROM UNIT 31
15500 ELEMENTS OF THE X ARRAY USED BY THE BTN PACKAGE
962 ELEMENTS OF THE IX ARRAY USED BY THE BTN PACKAGE

FMI5 -- FLOW MODEL INTERFACE PACKAGE, VERSION 5, FEBRUARY 2010, INPUT READ FROM UNIT 10
FLOW MODEL IS STEADY-STATE

ADV5 -- ADVECTION PACKAGE, VERSION 5, FEBRUARY 2010, INPUT READ FROM UNIT 32
ADVECTION IS SOLVED WITH THE HYBRID [MOC]/[MMOC] SCHEME
COURANT NUMBER ALLOWED IN SOLVING THE ADVECTION TERM = 0.750
MAXIMUM NUMBER OF MOVING PARTICLES ALLOWED = 800000
3200000 ELEMENTS OF THE X ARRAY USED BY THE ADV PACKAGE
1600961 ELEMENTS OF THE IX ARRAY USED BY THE ADV PACKAGE

DSP5 -- DISPERSION PACKAGE, VERSION 5, FEBRUARY 2010, INPUT READ FROM UNIT 33
10573 ELEMENTS OF THE X ARRAY USED BY THE DSP PACKAGE
0 ELEMENTS OF THE IX ARRAY USED BY THE DSP PACKAGE

SSM5 -- SINK & SOURCE MIXING PACKAGE, VERSION 5, FEBRUARY 2010, INPUT READ FROM UNIT 34
HEADER LINE OF THE SSM PACKAGE INPUT FILE:
T F F F F F F F F F F F F F F F
MAJOR STRESS COMPONENTS PRESENT IN THE FLOW MODEL:
o WELL [WEL]
MAXIMUM NUMBER OF POINT SINKS/SOURCES = 121
1573 ELEMENTS OF THE X ARRAY USED BY THE SSM PACKAGE
0 ELEMENTS OF THE IX ARRAY BY THE SSM PACKAGE

RCT5 -- CHEMICAL REACTION PACKAGE, VERSION 5, FEBRUARY 2010, INPUT READ FROM UNIT 36
NO SORPTION [OR DUAL-DOMAIN MODEL] IS SIMULATED
NO FIRST-ORDER RATE REACTION IS SIMULATED
REACTION COEFFICIENTS ASSIGNED CELL-BY-CELL
INITIAL SORBED/IMMOBILE PHASE CONCENTRATION ASSIGNED BY DEFAULT
0 ELEMENTS OF THE X ARRAY USED BY THE RCT PACKAGE
0 ELEMENTS OF THE IX ARRAY USED BY THE RCT PACKAGE

GCG5 -- GENERALIZED CONJUGATE GRADIENT SOLVER PACKAGE, VERSION 5, FEBRUARY 2010 INPUT READ FROM UNIT 35
MAXIMUM OF 1 OUTER ITERATIONS
AND 50 INNER ITERATIONS ALLOWED FOR CLOSURE
THE PRECONDITIONING TYPE SELECTED IS MODIFIED INCOMPLETE CHOLESKY (MIC).
DISPERSION CROSS TERMS LUMPED INTO RIGHT-HAND-SIDE
21192 ELEMENTS OF THE X ARRAY USED BY THE GCG PACKAGE
150 ELEMENTS OF THE IX ARRAY USED BY THE GCG PACKAGE

..........................................
ELEMENTS OF THE X ARRAY USED = 3248839
ELEMENTS OF THE IX ARRAY USED = 1602074
..........................................

LAYER NUMBER AQUIFER TYPE
------------ ------------
1 0

WIDTH ALONG ROWS (DELR) READ ON UNIT 31 USING FORMAT: " (31E15.6) "
-----------------------------------------------------------------------------

WIDTH ALONG COLS (DELC) READ ON UNIT 31 USING FORMAT: " (31E15.6) "
-----------------------------------------------------------------------------
TOP ELEV. OF 1ST LAYER = 10.00000

CELL THICKNESS (DZ) FOR LAYER 1 READ ON UNIT 31 USING FORMAT: " (31E15.6) "
------------------------------------------------------------------------------------------
POROSITY = 0.3000000 FOR LAYER 1
CONCN. BOUNDARY ARRAY = 1 FOR LAYER 1
INITIAL CONC.: COMP. 01 = 0.000000 FOR LAYER 1

VALUE INDICATING INACTIVE CONCENTRATION CELLS = 0.1000000E+31
MINIMUM SATURATED THICKNESS [THKMIN] ALLOWED = 0.0100 OF TOTAL CELL THICKNESS


OUTPUT CONTROL OPTIONS
----------------------

DO NOT PRINT CELL CONCENTRATION
DO NOT PRINT PARTICLE NUMBER IN EACH CELL
DO NOT PRINT RETARDATION FACTOR
DO NOT PRINT DISPERSION COEFFICIENT
SAVE DISSOLVED PHASE CONCENTRATIONS IN UNFORMATTED FILES [MT3Dnnn.UCN]
FOR EACH SPECIES ON UNITS 201 AND ABOVE

NUMBER OF TIMES AT WHICH SIMULATION RESULTS ARE SAVED = 0

NUMBER OF OBSERVATION POINTS = 0

SAVE ONE-LINE SUMMARY OF MASS BUDGETS IN FILES [MT3Dnnn.MAS]
FOR EACH SPECIES ON UNITS 601 AND ABOVE, EVERY 1 TRANSPORT STEPS

MAXIMUM LENGTH ALONG THE X (J) AXIS = 311.0040
MAXIMUM LENGTH ALONG THE Y (I) AXIS = 313.7939
MAXIMUM LENGTH ALONG THE Z (K) AXIS = 1.000000


ADVECTION SOLUTION OPTIONS
--------------------------

ADVECTION IS SOLVED WITH THE HYBRID [MOC]/[MMOC] SCHEME
COURANT NUMBER ALLOWED IN SOLVING THE ADVECTION TERM = 0.750
MAXIMUM NUMBER OF MOVING PARTICLES ALLOWED = 800000
METHOD FOR PARTICLE TRACKING IS [MIXED ORDER]
CONCENTRATION WEIGHTING FACTOR [WD] = 0.500
THE CONCENTRATION GRADIENT CONSIDERED NEGLIGIBLE [DCEPS] = 0.1000000E-04
INITIAL PARTICLES ARE PLACED ON 2 VERTICAL PLANE(S) WITHIN CELL BLOCK
PARTICLE NUMBER PER CELL IF DCCELL =< DCEPS = 10
PARTICLE NUMBER PER CELL IF DCCELL > DCEPS = 40
MINIMUM PARTICLE NUMBER ALLOWD PER CELL = 5
MAXIMUM PARTICLE NUMBER ALLOWD PER CELL = 80
MULTIPLIER OF PARTICLE NUMBER AT SOURCE = 1.00
SCHEME FOR CONCENTRATION INTERPOLATION IS [LINEAR]
PARTICLES FOR APPROXIMATING A SINK CELL IN THE [MMOC] SCHEME
ARE PLACED RANDOMLY WITHIN CELL BLOCK
NUMBER OF PARTICLES USED TO APPROXIMATE A SINK CELL IN THE [MMOC] SCHEME = 15
CRITICAL CONCENTRATION GRADIENT USED IN THE "HMOC" SCHEME [DCHMOC] = 0.1000E-03
THE "MOC" SOLUTION IS USED WHEN DCCELL > DCHMOC
THE "MMOC" SOLUTION IS USED WHEN DCCELL =< DCHMOC


DISPERSION INPUT PARAMETERS
---------------------------

LONG. DISPERSIVITY (AL) = 0.1000000E-01 FOR LAYER 1
H. TRANS./LONG. DISP. = 0.1000000
V. TRANS./LONG. DISP. = 0.1000000E-01
DIFFUSION COEFFICIENT = 0.1000000E-08


SORPTION AND 1ST/0TH ORDER REACTION PARAMETERS
----------------------------------------------




SOLUTION BY THE GENERALIZED CONJUGATE GRADIENT METHOD
-----------------------------------------------------
MAXIMUM OUTER ITERATIONS ALLOWED FOR CLOSURE = 1
MAXIMUM INNER ITERATIONS ALLOWED FOR CLOSURE = 50
PRECONDITIONING TYPE SELECTED = 3
ACCELERATION PARAMETER = 1.0000
CONCENTRATION CHANGE CRITERION FOR CLOSURE = 0.10000E-04
GCG CONCENTRATION CHANGE PRINTOUT INTERVAL = 999


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
STRESS PERIOD NO. 001
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


LENGTH OF CURRENT STRESS PERIOD = 26.00000
NUMBER OF TIME STEPS FOR CURRENT STRESS PERIOD = 1
TIME STEP MULTIPLIER USED IN FLOW SOLUTION = 1.000000

***Type of Transport Simulation is TRANSIENT

USER-SPECIFIED TRANSPORT STEPSIZE = 0.000000 D
MAXIMUM NUMBER OF TRANSPORT STEPS ALLOWED IN ONE FLOW TIME STEP = 50000
MULTIPLIER FOR SUCCESSIVE TRANSPORT STEPS [USED IN IMPLICIT SCHEMES] = 1.000
MAXIMUM TRANSPORT STEP SIZE [USED IN IMPLICIT SCHEMES] = 0.000000 D

NO LAYER ROW COLUMN CONCENTRATION TYPE COMPONENT
1 1 16 16 50.00000 WELL 1


================================================
TIME STEP NO. 001
================================================

FROM TIME = 0.0000 TO 26.000


"THKSAT " FLOW TERMS FOR TIME STEP 1, STRESS PERIOD 1 READ UNFORMATTED ON UNIT 10
--------------------------------------------------------------------------------------------

"QXX " FLOW TERMS FOR TIME STEP 1, STRESS PERIOD 1 READ UNFORMATTED ON UNIT 10
--------------------------------------------------------------------------------------------

"QYY " FLOW TERMS FOR TIME STEP 1, STRESS PERIOD 1 READ UNFORMATTED ON UNIT 10
--------------------------------------------------------------------------------------------

MAXIMUM STEPSIZE DURING WHICH ANY PARTICLE CANNOT MOVE MORE THAN ONE CELL
= 1.666 (WHEN MIN. R.F.=1) AT K= 1, I= 16, J= 15

MAXIMUM STEPSIZE WHICH MEETS STABILITY CRITERION OF THE ADVECTION TERM
(FOR PURE FINITE-DIFFERENCE OPTION, MIXELM=0)
= 0.6094 (WHEN MIN. R.F.=1) AT K= 1, I= 16, J= 16

"CNH " FLOW TERMS FOR TIME STEP 1, STRESS PERIOD 1 READ UNFORMATTED ON UNIT 10
--------------------------------------------------------------------------------------------

"WEL " FLOW TERMS FOR TIME STEP 1, STRESS PERIOD 1 READ UNFORMATTED ON UNIT 10
--------------------------------------------------------------------------------------------


TOTAL NUMBER OF POINT SOURCES/SINKS PRESENT IN THE FLOW MODEL = 121

MAXIMUM STEPSIZE WHICH MEETS STABILITY CRITERION OF THE SINK & SOURCE TERM
= 0.3047 (WHEN MIN. R.F.=1) AT K= 1, I= 16, J= 16

MAXIMUM STEPSIZE WHICH MEETS STABILITY CRITERION OF THE DISPERSION TERM
= 307.1 (WHEN MIN. R.F.=1) AT K= 1, I= 16, J= 16


1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 1 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 2 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 3 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 4 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 5 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 6 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 7 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 8 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 9 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 10 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 11 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 12 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 13 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 14 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 15 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 16 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 17 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 18 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 19 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 20 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
1 CALLS TO GCG PACKAGE FOR TRANSPORT TIME STEP 21 IN FLOW TIME STEP 1 STRESS PERIOD 1
2 TOTAL ITERATIONS
MAXIMUM CONCENTRATION CHANGES FOR EACH ITERATION:
MAX. CHANGE LAYER,ROW,COL MAX. CHANGE LAYER,ROW,COL MAX. CHANGE LAYER,ROW,COL MAX. CHANGE LAYER,ROW,COL MAX. CHANGE LAYER,ROW,COL
------------------------------------------------------------------------------------------------------------------------------------
0.1276E-03 ( 1, 14, 12) 0.7523E-36 ( 1, 3, 30)



>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>FOR COMPONENT NO. 01<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


-------------------------------------------
TRANSPORT STEP NO. 21
-------------------------------------------

TOTAL ELAPSED TIME SINCE BEGINNING OF SIMULATION = 26.00000 D
.....................................................................

TOTAL PARTICLES USED IN THE CURRENT STEP = 4264
PARTICLES ADDED AT BEGINNING OF THE STEP = 256
PARTICLES REMOVED AT END OF LAST STEP = 0

CUMMULATIVE MASS BUDGETS AT END OF TRANSPORT STEP 21, TIME STEP 1, STRESS PERIOD 1
------------------------------------------------------------------------------------------

IN OUT
---------------- ----------------
CONSTANT CONCENTRATION: 0.000000 0.000000
CONSTANT HEAD: 0.000000 -0.1140626E-09
WELLS: 130000.0 0.000000
1ST/0TH ORDER REACTION: 0.000000 0.000000
MASS STORAGE (SOLUTE): 43.12313 -122520.2
---------------------------------------------------------------------------
[TOTAL]: 130043.1 KG -122520.2 KG

NET (IN - OUT): 7522.922
DISCREPANCY (PERCENT): 5.957257
-----
| M T |
| 3 D | END OF MODEL OUTPUT
-----

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