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arkode-fullrhs #293

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arkode-fullrhs #293

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59f7c25
Removed requirement that fullrhs be supplied by the ARKODE time-stepp…
drreynolds Jun 26, 2023
6b06271
Converted multiple ARKODE examples to use Lagrange interpolation modu…
drreynolds Jun 26, 2023
c8aee7d
Updated ARKODE to only allocate 'fn' if necessary
drreynolds Jun 26, 2023
6c3efa2
Updated documentation to reflect optional nature of fullrhs function
drreynolds Jun 26, 2023
ebe06b3
Updated .out files with new results from CI
drreynolds Jun 26, 2023
c7fbf45
update answers submodule commit
gardner48 Jul 11, 2023
d631c81
Update output from Jenkins test machine
gardner48 Jul 11, 2023
6398647
Apply suggestions from code review
drreynolds Jul 12, 2023
7161d29
Merge remote-tracking branch 'origin/develop' into feature/arkode-ful…
balos1 Jul 25, 2023
97a069b
bump answers
balos1 Jul 25, 2023
d8a5031
combine call_fullrhs_start and call_fullrhs_end verification blocks
balos1 Jul 25, 2023
68f341b
update sprkstep
balos1 Jul 25, 2023
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9 changes: 9 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -30,6 +30,15 @@ Updated the F2003 utility routines `SUNDIALSFileOpen` and `SUNDIALSFileClose`
to support user specification of `stdout` and `stderr` strings for the output
file names.

Updated main ARKODE infrastructure so that the time-stepping module `fullrhs` routine,
and the `MRIStepInnerFullRhsFn` for MRIStep are optional. These may still be
required based on integrator usage, including: use of the internal initial time step
size selection algorithm, use of the Hermite interpolation module, use of temporal
root-finding, use of the now-deprecated "bootstrap" predictor method (see
`MRIStepSetPredictorMethod` and `ARKStepSetPredictorMethod`). When `fullrhs`
is not in fact required, one vector of ARKODE storage (the size of the IVP solution)
is left unallocated.

## Changes to SUNDIALS in release 6.5.1

Added the functions `ARKStepClearStopTime`, `ERKStepClearStopTime`,
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9 changes: 9 additions & 0 deletions doc/arkode/guide/source/Introduction.rst
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Expand Up @@ -163,6 +163,15 @@ Updated the F2003 utility routines :c:func:`SUNDIALSFileOpen` and :c:func:`SUNDI
to support user specification of ``stdout`` and ``stderr`` strings for the output
file names.

Updated main ARKODE infrastructure so that the time-stepping module `fullrhs` routine,
and the :c:type:`MRIStepInnerFullRhsFn` for MRIStep are optional. These may still be
required based on integrator usage, including: use of the internal initial time step
size selection algorithm, use of the Hermite interpolation module, use of temporal
root-finding, use of the now-deprecated "bootstrap" predictor method (see
:c:func:`MRIStepSetPredictorMethod` and :c:func:`ARKStepSetPredictorMethod`). When
`fullrhs` is not in fact required, one vector of ARKODE storage (the size of the IVP
solution) is left unallocated.

Changes in v5.5.1
-----------------

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19 changes: 15 additions & 4 deletions ...ode/guide/source/Usage/MRIStep_c_interface/Custom_Inner_Stepper/Description.rst
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Expand Up @@ -366,6 +366,12 @@ member functions:
* ``examples/arkode/CXX_parallel/ark_diffusion_reaction_p.cpp``


Optional Member Functions
"""""""""""""""""""""""""

An :c:type:`MRIStepInnerStepper` *may* provide implementations of any of the
following member functions:

.. c:type:: int (*MRIStepInnerFullRhsFn)(MRIStepInnerStepper stepper, realtype t, N_Vector v, N_Vector f, int mode)

This function computes the full right-hand side function of the inner (fast)
Expand Down Expand Up @@ -393,11 +399,16 @@ member functions:
**Example codes:**
* ``examples/arkode/CXX_parallel/ark_diffusion_reaction_p.cpp``

Optional Member Functions
"""""""""""""""""""""""""
.. note::

This function will instead be required by MRIStep if: the Hermite interpolation
module is used, the user requests temporal root-finding, or the user requests the
now-deprecated "bootstrap" predictor method (see :c:func:`MRIStepSetPredictorMethod`).
drreynolds marked this conversation as resolved.
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.. versionchanged:: 5.6.0

This function was made optional

An :c:type:`MRIStepInnerStepper` *may* provide implementations of any of the
following member functions:

.. c:type:: int (*MRIStepInnerResetFn)(MRIStepInnerStepper stepper, realtype tR, N_Vector vR)

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2 changes: 2 additions & 0 deletions examples/arkode/C_serial/ark_analytic.c
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Expand Up @@ -110,6 +110,8 @@ int main()
if (check_flag(&flag, "ARKStepSetUserData", 1)) return 1;
flag = ARKStepSStolerances(arkode_mem, reltol, abstol); /* Specify tolerances */
if (check_flag(&flag, "ARKStepSStolerances", 1)) return 1;
flag = ARKStepSetInterpolantType(arkode_mem, ARK_INTERP_LAGRANGE); /* Lagrange interpolant */
if (check_flag(&flag, "ARKStepSetInterpolantType", 1)) return 1;

/* Initialize dense matrix data structure and solver */
A = SUNDenseMatrix(NEQ, NEQ, ctx);
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2 changes: 2 additions & 0 deletions examples/arkode/C_serial/ark_analytic_mels.c
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Expand Up @@ -110,6 +110,8 @@ int main()
if (check_retval(&retval, "ARKStepSetUserData", 1)) return 1;
retval = ARKStepSStolerances(arkode_mem, reltol, abstol); /* Specify tolerances */
if (check_retval(&retval, "ARKStepSStolerances", 1)) return 1;
retval = ARKStepSetInterpolantType(arkode_mem, ARK_INTERP_LAGRANGE); /* Lagrange interpolant */
if (check_retval(&retval, "ARKStepSetInterpolantType", 1)) return 1;

/* Initialize custom matrix-embedded linear solver */
LS = MatrixEmbeddedLS(arkode_mem, ctx);
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4 changes: 4 additions & 0 deletions examples/arkode/C_serial/ark_analytic_nonlin.c
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Expand Up @@ -92,6 +92,10 @@ int main()
flag = ERKStepSStolerances(arkode_mem, reltol, abstol);
if (check_flag(&flag, "ERKStepSStolerances", 1)) return 1;

/* Set Lagrange interpolation module */
flag = ERKStepSetInterpolantType(arkode_mem, ARK_INTERP_LAGRANGE);
if (check_flag(&flag, "ERKStepSetInterpolantType", 1)) return 1;

/* Open output stream for results, output comment line */
UFID = fopen("solution.txt","w");
fprintf(UFID,"# t u\n");
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10 changes: 5 additions & 5 deletions examples/arkode/C_serial/ark_analytic_nonlin.out
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Expand Up @@ -6,15 +6,15 @@ Analytical ODE test problem:
t u
---------------------
1.000000 0.916291
2.000000 1.609437
3.000000 2.140066
4.000000 2.564949
2.000000 1.609435
3.000000 2.140064
4.000000 2.564948
5.000000 2.917770
6.000000 3.218876
7.000000 3.481240
7.000000 3.481239
8.000000 3.713572
9.000000 3.921973
10.000000 4.110874
10.000000 4.110873
---------------------

Final Statistics:
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2 changes: 2 additions & 0 deletions examples/arkode/C_serial/ark_brusselator1D.c
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Expand Up @@ -207,6 +207,8 @@ int main()
if (check_flag(&flag, "ARKStepSetUserData", 1)) return 1;
flag = ARKStepSStolerances(arkode_mem, reltol, abstol); /* Specify tolerances */
if (check_flag(&flag, "ARKStepSStolerances", 1)) return 1;
flag = ARKStepSetInterpolantType(arkode_mem, ARK_INTERP_LAGRANGE); /* Lagrange interpolant */
if (check_flag(&flag, "ARKStepSetInterpolantType", 1)) return 1;

/* Initialize band matrix data structure and solver -- A will be factored, so set smu to ml+mu */
A = SUNBandMatrix(NEQ, 4, 4, ctx);
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148 changes: 74 additions & 74 deletions examples/arkode/C_serial/ark_brusselator1D.out
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Expand Up @@ -8,105 +8,105 @@
t ||u||_rms ||v||_rms ||w||_rms
----------------------------------------------
0.100000 0.673914 3.377329 1.999987
0.200000 0.684316 3.356619 1.999987
0.200000 0.684316 3.356619 1.999986
0.300000 0.695306 3.334633 1.999986
0.400000 0.706918 3.311313 1.999986
0.500000 0.719185 3.286601 1.999986
0.500000 0.719184 3.286601 1.999986
0.600000 0.732137 3.260442 1.999986
0.700000 0.745798 3.232787 1.999985
0.800000 0.760185 3.203596 1.999985
0.900000 0.775303 3.172839 1.999985
1.000000 0.791135 3.140510 1.999984
1.100000 0.807648 3.106624 1.999984
1.200000 0.824771 3.071233 1.999984
1.300000 0.842402 3.034426 1.999983
1.400000 0.860384 2.996350 1.999983
1.500000 0.878514 2.957206 1.999983
1.600000 0.896525 2.917266 1.999982
1.700000 0.914089 2.876873 1.999982
1.800000 0.930823 2.836438 1.999982
1.900000 0.946292 2.796446 1.999982
2.000000 0.960033 2.757430 1.999981
2.100000 0.971576 2.719962 1.999981
2.200000 0.980475 2.684623 1.999981
2.300000 0.986338 2.651980 1.999981
2.400000 0.988852 2.622560 1.999981
2.500000 0.987815 2.596818 1.999981
2.600000 0.983141 2.575128 1.999981
2.700000 0.974858 2.557766 1.999981
2.800000 0.963114 2.544903 1.999981
2.900000 0.948154 2.536611 1.999981
3.000000 0.930299 2.532868 1.999982
3.100000 0.909930 2.533567 1.999982
3.200000 0.887464 2.538529 1.999983
3.300000 0.863335 2.547515 1.999983
3.400000 0.837978 2.560241 1.999983
3.500000 0.811818 2.576391 1.999984
3.600000 0.785255 2.595624 1.999984
3.700000 0.758659 2.617587 1.999985
3.800000 0.732363 2.641922 1.999986
3.900000 0.706662 2.668274 1.999986
4.000000 0.681809 2.696300 1.999986
4.100000 0.658012 2.725670 1.999987
4.200000 0.635435 2.756075 1.999987
4.300000 0.614205 2.787228 1.999988
4.400000 0.594404 2.818869 1.999988
4.500000 0.576082 2.850764 1.999989
4.600000 0.559255 2.882710 1.999989
4.700000 0.543909 2.914529 1.999989
0.700000 0.745795 3.232790 1.999985
0.800000 0.760184 3.203596 1.999985
0.900000 0.775294 3.172847 1.999985
1.000000 0.791132 3.140513 1.999984
1.100000 0.807633 3.106639 1.999984
1.200000 0.824765 3.071240 1.999984
1.300000 0.842379 3.034451 1.999983
1.400000 0.860372 2.996364 1.999983
1.500000 0.878491 2.957234 1.999983
1.600000 0.896508 2.917287 1.999982
1.700000 0.914081 2.876882 1.999982
1.800000 0.930808 2.836460 1.999982
1.900000 0.946289 2.796453 1.999982
2.000000 0.960031 2.757436 1.999981
2.100000 0.971579 2.719968 1.999981
2.200000 0.980482 2.684622 1.999981
2.300000 0.986339 2.651980 1.999981
2.400000 0.988870 2.622549 1.999981
2.500000 0.987832 2.596806 1.999981
2.600000 0.983142 2.575126 1.999981
2.700000 0.974875 2.557749 1.999981
2.800000 0.963129 2.544887 1.999981
2.900000 0.948160 2.536604 1.999981
3.000000 0.930300 2.532868 1.999982
3.100000 0.909935 2.533559 1.999982
3.200000 0.887466 2.538521 1.999983
3.300000 0.863335 2.547510 1.999983
3.400000 0.837978 2.560240 1.999983
3.500000 0.811817 2.576389 1.999984
3.600000 0.785252 2.595623 1.999984
3.700000 0.758655 2.617587 1.999985
3.800000 0.732361 2.641922 1.999986
3.900000 0.706662 2.668275 1.999986
4.000000 0.681805 2.696302 1.999986
4.100000 0.658007 2.725673 1.999987
4.200000 0.635432 2.756077 1.999987
4.300000 0.614204 2.787229 1.999988
4.400000 0.594402 2.818871 1.999988
4.500000 0.576079 2.850768 1.999989
4.600000 0.559252 2.882713 1.999989
4.700000 0.543908 2.914530 1.999989
4.800000 0.530011 2.946071 1.999990
4.900000 0.517506 2.977209 1.999990
5.000000 0.506326 3.007843 1.999990
5.100000 0.496394 3.037889 1.999990
5.200000 0.487626 3.067283 1.999990
5.300000 0.479935 3.095976 1.999991
5.400000 0.473237 3.123932 1.999991
5.500000 0.467445 3.151125 1.999991
4.900000 0.517504 2.977212 1.999990
5.000000 0.506325 3.007845 1.999990
5.100000 0.496393 3.037890 1.999990
5.200000 0.487625 3.067283 1.999990
5.300000 0.479935 3.095977 1.999991
5.400000 0.473237 3.123933 1.999991
5.500000 0.467446 3.151126 1.999991
5.600000 0.462480 3.177540 1.999991
5.700000 0.458264 3.203165 1.999991
5.800000 0.454726 3.227997 1.999991
5.900000 0.451800 3.252035 1.999991
5.800000 0.454726 3.227998 1.999991
5.900000 0.451800 3.252036 1.999991
6.000000 0.449425 3.275283 1.999991
6.100000 0.447546 3.297744 1.999991
6.200000 0.446115 3.319428 1.999991
6.300000 0.445086 3.340340 1.999991
6.400000 0.444419 3.360491 1.999991
6.400000 0.444419 3.360492 1.999991
6.500000 0.444079 3.379890 1.999991
6.600000 0.444034 3.398547 1.999991
6.600000 0.444034 3.398546 1.999991
6.700000 0.444257 3.416470 1.999991
6.800000 0.444722 3.433669 1.999991
6.800000 0.444723 3.433669 1.999991
6.900000 0.445409 3.450154 1.999991
7.000000 0.446297 3.465934 1.999991
7.100000 0.447370 3.481018 1.999991
7.100000 0.447371 3.481018 1.999991
7.200000 0.448614 3.495414 1.999991
7.300000 0.450016 3.509131 1.999991
7.300000 0.450017 3.509131 1.999991
7.400000 0.451564 3.522176 1.999991
7.500000 0.453249 3.534557 1.999991
7.500000 0.453250 3.534556 1.999991
7.600000 0.455064 3.546280 1.999991
7.700000 0.457000 3.557353 1.999991
7.700000 0.457001 3.557353 1.999991
7.800000 0.459052 3.567781 1.999991
7.900000 0.461216 3.577571 1.999991
8.000000 0.463486 3.586728 1.999991
8.100000 0.465860 3.595257 1.999991
8.200000 0.468335 3.603162 1.999991
8.300000 0.470909 3.610447 1.999991
8.300000 0.470910 3.610447 1.999991
8.400000 0.473582 3.617116 1.999991
8.500000 0.476352 3.623171 1.999991
8.600000 0.479220 3.628616 1.999991
8.500000 0.476353 3.623170 1.999991
8.600000 0.479221 3.628615 1.999991
8.700000 0.482186 3.633451 1.999991
8.800000 0.485250 3.637679 1.999990
8.900000 0.488416 3.641299 1.999990
9.000000 0.491684 3.644311 1.999990
9.100000 0.495058 3.646715 1.999990
9.200000 0.498540 3.648509 1.999990
9.300000 0.502134 3.649691 1.999990
9.400000 0.505844 3.650257 1.999990
9.500000 0.509675 3.650202 1.999990
8.800000 0.485252 3.637677 1.999990
8.900000 0.488417 3.641297 1.999990
9.000000 0.491685 3.644311 1.999990
9.100000 0.495059 3.646713 1.999990
9.200000 0.498541 3.648507 1.999990
9.300000 0.502134 3.649690 1.999990
9.400000 0.505845 3.650254 1.999990
9.500000 0.509676 3.650199 1.999990
9.600000 0.513632 3.649521 1.999990
9.700000 0.517722 3.648209 1.999990
9.800000 0.521951 3.646257 1.999990
9.900000 0.526326 3.643656 1.999990
10.000000 0.530857 3.640396 1.999990
9.700000 0.517724 3.648206 1.999990
9.800000 0.521953 3.646253 1.999990
9.900000 0.526327 3.643655 1.999990
10.000000 0.530859 3.640391 1.999990
----------------------------------------------

Final Solver Statistics:
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8 changes: 8 additions & 0 deletions examples/arkode/C_serial/ark_brusselator1D_imexmri.c
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Expand Up @@ -512,6 +512,10 @@ int main(int argc, char *argv[])
retval = ARKStepSetFixedStep(inner_arkode_mem, hf);
if (check_retval(&retval, "ARKStepSetFixedStep", 1)) return 1;

/* Set Lagrange interpolation type */
retval = ARKStepSetInterpolantType(inner_arkode_mem, ARK_INTERP_LAGRANGE);
if (check_retval(&retval, "ARKStepSetInterpolantType", 1)) return 1;

/* Create inner stepper */
retval = ARKStepCreateMRIStepInnerStepper(inner_arkode_mem,
&inner_stepper);
Expand Down Expand Up @@ -648,6 +652,10 @@ int main(int argc, char *argv[])
retval = MRIStepSetMaxNumSteps(arkode_mem, 1000000);
if (check_retval(&retval, "MRIStepSetMaxNumSteps", 1)) return 1;

/* Set Lagrange interpolation type */
retval = MRIStepSetInterpolantType(arkode_mem, ARK_INTERP_LAGRANGE);
if (check_retval(&retval, "MRIStepSetInterpolantType", 1)) return 1;

/*
* Integrate ODE
*/
Expand Down
2 changes: 1 addition & 1 deletion examples/arkode/C_serial/ark_brusselator1D_imexmri_0_0.001.out
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Expand Up @@ -30,7 +30,7 @@
Final Solver Statistics:
Slow Steps: nsts = 10001
Fast Steps: nstf = 120012
Total RHS evals: Fs = 30004, Ff = 994988
Total RHS evals: Fs = 30003, Ff = 864973
Fast Newton iters = 504937
Fast Newton conv fails = 0
Fast Jacobian evals = 2308
2 changes: 1 addition & 1 deletion examples/arkode/C_serial/ark_brusselator1D_imexmri_2_0.001.out
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Expand Up @@ -30,7 +30,7 @@
Final Solver Statistics:
Slow Steps: nsts = 10001
Fast Steps: nstf = 120012
Total RHS evals: Fs = 68887, Ff = 400041
Total RHS evals: Fs = 68886, Ff = 360036
Slow Newton iters = 38883
Slow Newton conv fails = 0
Slow Jacobian evals = 501
2 changes: 1 addition & 1 deletion examples/arkode/C_serial/ark_brusselator1D_imexmri_3_0.001.out
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Expand Up @@ -30,7 +30,7 @@
Final Solver Statistics:
Slow Steps: nsts = 10001
Fast Steps: nstf = 120012
Total RHS evals: Fs = 68887, Ff = 1000128
Total RHS evals: Fs = 68886, Ff = 840111
Slow Newton iters = 38883
Slow Newton conv fails = 0
Slow Jacobian evals = 501
Expand Down
2 changes: 1 addition & 1 deletion examples/arkode/C_serial/ark_brusselator1D_imexmri_4_0.001.out
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Expand Up @@ -30,7 +30,7 @@
Final Solver Statistics:
Slow Steps: nsts = 10001
Fast Steps: nstf = 110011
Total RHS evals: Fse = 40005, Fsi = 78888, Ff = 370038
Total RHS evals: Fse = 40004, Fsi = 78887, Ff = 330033
Slow Newton iters = 38883
Slow Newton conv fails = 0
Slow Jacobian evals = 501
2 changes: 1 addition & 1 deletion examples/arkode/C_serial/ark_brusselator1D_imexmri_5_0.001.out
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Expand Up @@ -30,7 +30,7 @@
Final Solver Statistics:
Slow Steps: nsts = 10001
Fast Steps: nstf = 110011
Total RHS evals: Fse = 40005, Fsi = 78888, Ff = 1174341
Total RHS evals: Fse = 40004, Fsi = 78887, Ff = 1024325
Slow Newton iters = 38883
Slow Newton conv fails = 0
Slow Jacobian evals = 501
Expand Down
2 changes: 1 addition & 1 deletion examples/arkode/C_serial/ark_brusselator1D_imexmri_6_0.001.out
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Expand Up @@ -30,7 +30,7 @@
Final Solver Statistics:
Slow Steps: nsts = 10001
Fast Steps: nstf = 130013
Total RHS evals: Fse = 60007, Fsi = 118894, Ff = 580059
Total RHS evals: Fse = 60006, Fsi = 118893, Ff = 520052
Slow Newton iters = 58887
Slow Newton conv fails = 0
Slow Jacobian evals = 501
2 changes: 1 addition & 1 deletion examples/arkode/C_serial/ark_brusselator1D_imexmri_7_0.001.out
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Expand Up @@ -30,7 +30,7 @@
Final Solver Statistics:
Slow Steps: nsts = 10001
Fast Steps: nstf = 130013
Total RHS evals: Fse = 60007, Fsi = 118894, Ff = 1946003
Total RHS evals: Fse = 60006, Fsi = 118893, Ff = 1885996
Slow Newton iters = 58887
Slow Newton conv fails = 0
Slow Jacobian evals = 501
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2 changes: 2 additions & 0 deletions examples/arkode/C_serial/ark_brusselator1D_klu.c
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Expand Up @@ -226,6 +226,8 @@ int main()
if (check_flag(&flag, "ARKStepSetUserData", 1)) return 1;
flag = ARKStepSStolerances(arkode_mem, reltol, abstol); /* Specify tolerances */
if (check_flag(&flag, "ARKStepSStolerances", 1)) return 1;
flag = ARKStepSetInterpolantType(arkode_mem, ARK_INTERP_LAGRANGE); /* Lagrange interpolation */
if (check_flag(&flag, "ARKStepSetInterpolantType", 1)) return 1;

/* Initialize sparse matrix data structure and KLU solver */
NNZ = 5*NEQ;
Expand Down
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