feat(PRT): introduce Particle Tracking (PRT) model #1389

wpbonelli · 2023-10-07T02:37:10Z

Status

At this time PRT supports particle tracking on all DIS and some but not all DISV grids

Outstanding issues include

DISV cells containing adjacent parallel faces are not properly handled and may cause crashes, this includes quad-refined grids as well as DISV grids generated by FloPy's voronoi module

Support is planned but not yet implemented for

configurable particle mass
local mass conservation — conserved between cells but not yet guaranteed at the subcell level
exchanging particles between models
DISU grids (longer term)
solving models in parallel (longer term)

Integration

When this merges a preliminary version of PRT will become available on the nightly build but will be excluded from official releases.

Miscellaneous info

Docs/dfns and tests make up about half the changeset, the rest is fortran source.

PRT's primary author is @aprovost-usgs. Some code is adapted from MODPATH and originally due to @dwpolloc-usgs.

wpbonelli · 2023-12-22T16:22:11Z

Squashed the branch to make rebasing with IDM easier. Commit history is backed up on my fork if needed. Recent changes are mostly non-functional and include

refactor tracking method hierarchy
refactor cell/cell definition hierarchy, factor out base cell type
refactor prp: simplify time offset support, rename referencetime -> releasetime, check release coord/cell correspondence and elevation, cleanup particle init/release logic
refactor TrackModule to support arbitrary # of track files
remove trackingmodel, extend explicitmodel directly
don't set conc on gwfprt exchange until implemented/tested
deduplicate logic in Method types, use dis%get_polyverts()
move coord transform routines to GeomUtil, remove UtilMisc
use ExpandArray interface, remove allocate_as_needed utils
use arrays for canonical velocity components, vertices, etc
introduce mod_offset function, remove *_wrap routines
remove rotate function, replace rotate() with matmuls
remove some unused utility routines
minor cleanup in MIP pkg
ifort compatibility tweaks
add scipy to environment.yml
rebase with latest IDM changes
add unit tests for math/geom utils
add integration tests: drape, voronoi grid

wpbonelli · 2023-12-28T17:44:58Z

outdated

@mjr-deltares

Do you have any ideas on this? https://github.com/MODFLOW-USGS/modflow6/actions/runs/7343758410/job/19994783536?pr=1389#step:15:392

I'm stumped. PRT doesn't touch PETSc and it doesn't reproduce on ubuntu 22.04 locally. Tried clearing caches, no luck

resolved with meson update

src/Solution/ParticleTracker/MethodCellTernary.f90

Co-authored-by: Alden Provost <[email protected]>

langevin-usgs

Looks great.

langevin-usgs · 2024-02-23T16:52:40Z

doc/mf6io/mf6ivar/dfn/sln-pts.dfn

@@ -0,0 +1,178 @@
+# --------------------- sln pts options ---------------------


We might revisit these settings. Not sure all are needed for a particle solver.

langevin-usgs · 2024-02-23T16:53:43Z

doc/mf6io/mf6ivar/examples/prt-fmi-example.dat

@@ -0,0 +1,8 @@
+BEGIN OPTIONS
+  FLOW_IMBALANCE_CORRECTION


Just an FYI that this option probably shouldn't apply to particle tracking models.

langevin-usgs · 2024-02-23T16:56:15Z

doc/mf6io/mf6ivar/tex/gwf-drn-desc.tex

@@ -45,9 +45,9 @@

 \item \textcolor{blue}{\texttt{elev}---is the elevation of the drain. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.}

-\item \textcolor{blue}{\texttt{cond}---is the hydraulic conductance of the interface between the aquifer and the drain. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value. COND values must be greater than or equal to zero. The program will terminate with an error if any COND value is less than zero.}


Looks like this change resulted from a merge (a recent change on develop). Not a problem since this file is generated from mf6ivar.py.

langevin-usgs · 2024-02-23T16:58:38Z

doc/mf6io/mf6ivar/tex/prt-nam-desc.tex

+\item \textbf{Block: OPTIONS}
+
+\begin{description}
+\item \texttt{list}---is name of the listing file to create for this PRT model.  If not specified, then the name of the list file will be the basename of the PRT model name file and the '.lst' extension.  For example, if the PRT name file is called ``my.model.nam'' then the list file will be called ``my.model.lst''.


These should be latex double quotes?

Ok. Should we update this in *-nam.dfn for the other models too? Maybe in separate PR?

If it's like that elsewhere, then maybe we are okay for now.

wpbonelli force-pushed the PRT branch from 98f84de to ed0f689 Compare October 7, 2023 17:09

wpbonelli force-pushed the PRT branch from 0c44a71 to 2b62852 Compare October 20, 2023 00:56

wpbonelli force-pushed the PRT branch from 2b62852 to 307e661 Compare October 29, 2023 20:23

rhugman mentioned this pull request Nov 9, 2023

PRT with quadtree and voronoi grids #1434

Closed

wpbonelli force-pushed the PRT branch 2 times, most recently from 0235ba7 to 636aa5d Compare November 20, 2023 19:10

wpbonelli force-pushed the PRT branch 3 times, most recently from 55bb648 to d5c593f Compare November 29, 2023 02:37

wpbonelli force-pushed the PRT branch 3 times, most recently from 840b0db to eac7285 Compare December 13, 2023 02:04

wpbonelli mentioned this pull request Dec 13, 2023

feat(GeomUtil): add geometric transformation routines #1499

Merged

wpbonelli force-pushed the PRT branch 4 times, most recently from c1067bf to 4f59888 Compare December 18, 2023 14:13

wpbonelli added the enhancement label Dec 19, 2023

wpbonelli force-pushed the PRT branch from 4f59888 to 3487570 Compare December 22, 2023 16:15

wpbonelli mentioned this pull request Dec 22, 2023

Add PRT support modflowpy/flopy#1753

Merged

wpbonelli force-pushed the PRT branch from 30002af to 060ecaa Compare December 27, 2023 21:53

wpbonelli force-pushed the PRT branch 3 times, most recently from e5f9cb6 to 39fe521 Compare December 31, 2023 02:21

wpbonelli added this to the 6.5.0 milestone Jan 10, 2024

wpbonelli force-pushed the PRT branch from 39fe521 to 0223071 Compare January 11, 2024 14:15

wpbonelli force-pushed the PRT branch 2 times, most recently from c10b0b8 to a221361 Compare January 24, 2024 21:58

wpbonelli force-pushed the PRT branch 4 times, most recently from 54aa9bf to 5f5eb37 Compare January 31, 2024 02:01

wpbonelli force-pushed the PRT branch 3 times, most recently from 1a2382e to b790db4 Compare February 9, 2024 03:24

jdhughes-usgs reviewed Feb 9, 2024

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src/Solution/ParticleTracker/MethodCellTernary.f90 Outdated Show resolved Hide resolved

wpbonelli force-pushed the PRT branch 2 times, most recently from 133e313 to d01846c Compare February 10, 2024 00:46

wpbonelli changed the title ~~feat(PRT): add particle tracking model~~ feat(PRT): introduce Particle Tracking (PRT) model Feb 19, 2024

wpbonelli force-pushed the PRT branch 2 times, most recently from 92510ed to cc0a70f Compare February 19, 2024 19:44

wpbonelli marked this pull request as ready for review February 19, 2024 23:18

wpbonelli force-pushed the PRT branch 4 times, most recently from 0564733 to 259a6d0 Compare February 23, 2024 02:38

feat(PRT): add particle tracking model

e7315bd

Co-authored-by: Alden Provost <[email protected]>

wpbonelli force-pushed the PRT branch from 259a6d0 to e7315bd Compare February 23, 2024 02:51

wpbonelli added 3 commits February 23, 2024 08:19

skip voronoi test case causing FPE in mac CI for now

e4c414f

remove edits from README

c97c9d3

cleanup src/meson.build and unit tests

07e8143

wpbonelli requested review from jdhughes-usgs, langevin-usgs and aprovost-usgs February 23, 2024 16:18

langevin-usgs approved these changes Feb 23, 2024

View reviewed changes

wpbonelli merged commit 61b0883 into MODFLOW-USGS:develop Feb 23, 2024
15 checks passed

This was referenced Feb 26, 2024

feat(timeselect): add module/type for time selections #1590

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feat: fortran styling script #1608

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feat(PRT): introduce Particle Tracking (PRT) model #1389

feat(PRT): introduce Particle Tracking (PRT) model #1389

wpbonelli commented Oct 7, 2023 •

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langevin-usgs Feb 23, 2024

		@@ -0,0 +1,178 @@
		# --------------------- sln pts options ---------------------

		@@ -45,9 +45,9 @@

		\item \textcolor{blue}{\texttt{elev}---is the elevation of the drain. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value.}

		\item \textcolor{blue}{\texttt{cond}---is the hydraulic conductance of the interface between the aquifer and the drain. If the Options block includes a TIMESERIESFILE entry (see the ``Time-Variable Input'' section), values can be obtained from a time series by entering the time-series name in place of a numeric value. COND values must be greater than or equal to zero. The program will terminate with an error if any COND value is less than zero.}

feat(PRT): introduce Particle Tracking (PRT) model #1389

feat(PRT): introduce Particle Tracking (PRT) model #1389

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wpbonelli commented Oct 7, 2023 • edited Loading

Status

Integration

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