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894 Implement dynamic optimization #895

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merged 398 commits into from
May 17, 2024
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390ad56
fix issue of missing temnplate parameter
Oct 12, 2023
cf7ef75
fix issue of missing temnplate parameter
Oct 12, 2023
2e85e2d
fix issue of missing temnplate parameter
Oct 12, 2023
84b3c0d
fix issue of missing temnplate parameter
Oct 12, 2023
c373fa5
fix issue of missing temnplate parameter
Oct 12, 2023
47a97c1
fix issue of missing temnplate parameter
Oct 12, 2023
3a3d410
sync with upstream
Oct 16, 2023
66f04a7
Merge remote-tracking branch 'upstream/main'
Oct 16, 2023
4a3905c
Merge branch 'DLR-SC:main' into main
hannemann-tamas Oct 16, 2023
f826957
fix issue with check_constraints
Oct 16, 2023
3b4c945
progress in templatizing integrator
Oct 16, 2023
027b943
progress in templatizing integrators
Oct 17, 2023
b9917e4
some progress in templatizing integrators
Oct 17, 2023
03df1c8
some progress in templatizing integrators
Oct 17, 2023
cd0b839
compare algorithmic differentiation with finite differences
Oct 17, 2023
18d292f
fix issue with clang-6.0 on CI machines
Oct 18, 2023
3259c26
start creation of opttimization problem
Oct 23, 2023
ddc80d9
some progress in TNLP
Oct 24, 2023
11d1be7
dynamic optimization of sEAIR works
Oct 25, 2023
0fae6b2
change tolerance in consistencyStochasticMobility from 1e-8 to 1e-7
Oct 26, 2023
ea30f69
revert change from last submit
Oct 30, 2023
4654aef
switch of memilio logging
Oct 30, 2023
082f833
work on merge conflicts
Jan 15, 2024
ec20531
templatizing
Jan 15, 2024
2049ce6
add template paremeter FP to set_nodes()
Jan 15, 2024
3a61ad3
templatizing advance and IntegratorCore
Jan 15, 2024
21c83e6
add template parameter FP to CompartmentModel
Jan 15, 2024
7787eee
add template parameter FP
Jan 15, 2024
073620b
insert template parameter FP and move function definitions into header
Jan 16, 2024
4b31b53
insert template parameter FP and move function definitions into header
Jan 16, 2024
91e9c54
insert template parameter FP and move function definitions into header
Jan 16, 2024
3ada59c
insert template parameter FP and move function definitions into header
Jan 16, 2024
8019f93
insert template parameter FP and move function definitions into header
Jan 16, 2024
f00f40f
insert template parameter FP and move function definitions into header
Jan 16, 2024
9887606
insert template parameter FP and move function definitions into header
Jan 16, 2024
d3f7c57
insert template parameter FP and move function definitions into header
Jan 16, 2024
942ddd2
insert template parameter FP and move function definitions into header
Jan 16, 2024
a6e3d44
cleanup unused includes
Jan 16, 2024
cfd017b
Insert template parameter FP
Jan 16, 2024
55d7d3d
insert FP as template parameter
Jan 16, 2024
7df8181
add FP as template parameter
Jan 18, 2024
2571d6b
remove body (is already in header)
Jan 22, 2024
c8376b2
add template parameter FP
Jan 22, 2024
c559979
add FP as template parameter
Jan 22, 2024
dd67a80
improve doc
Jan 22, 2024
d1520b1
insert FP as template parameter for floating point types
Jan 22, 2024
0aac280
insert FP as template parameter for floating point types
Jan 22, 2024
a2c7b47
insert FP as template parameter for floating point types
Jan 22, 2024
2fbac93
fix issue with template parameter FP in mio::Populations
Jan 24, 2024
63cbaf1
fix issue with call of get_flat_flow_index
Jan 24, 2024
fcac539
fix issue with template parameter FP in mio::Populations
Jan 24, 2024
db2d605
replace std::abs by std::fabs
Jan 24, 2024
24fa38e
set CMAKE_OSX_DEPLOYMENT_TARGET to avoid spurious linker warnings
Jan 24, 2024
9064ad1
Change return type of integrator::advance to use FP template parameter
Jan 24, 2024
627f7b6
fix issue with model.parameters.set()
Jan 24, 2024
5b56f7d
do not include unused headers
Jan 24, 2024
db2c4e1
fix issue with get_flat_flow_index
Jan 24, 2024
babdbfc
some progress in templatizing FP parameter
Jan 24, 2024
9de51ee
fix issue with missing template parameter FP
Jan 25, 2024
6a508b6
fix issue with template parameter FP
Jan 25, 2024
d115699
fix issue with template parameter FP
Jan 25, 2024
99d42f9
fix issue with template parameter FP
Jan 25, 2024
f7197fa
fix issue with template parameter FP
Jan 25, 2024
b15acce
merge with upstream
Jan 25, 2024
8872e2b
clenaup unsused includes
Jan 25, 2024
e6f6969
fix issues related to template parameter FP
Jan 25, 2024
4aa9d27
fix issues related to template parameter FP
Jan 25, 2024
941fc01
merge with upstream
Jan 25, 2024
14ecb8e
merge with upstream
Jan 25, 2024
9d1d7ab
merge with upstream
Jan 25, 2024
353cc65
merge with upstream
Jan 25, 2024
8e80c67
merge with upstream
Jan 25, 2024
788fb94
merge with upstream
Jan 25, 2024
272c0c2
merge with upstream
Jan 25, 2024
45db0ee
merge with upstream
Jan 25, 2024
6376ff1
merge with upstream
Jan 25, 2024
bc0d8dc
some progress in merge with upstream
Jan 25, 2024
604953f
some progress in merge with upstream
Jan 25, 2024
2fc6f12
merge with upstream
Jan 25, 2024
b529ef0
merge with upstream
Jan 25, 2024
246f126
merge with upstream
Jan 25, 2024
b9cdb2b
merge with upstream
Jan 25, 2024
b17717e
merge with upstream
Jan 25, 2024
aef3367
solve issues related to template parameter FP
Jan 25, 2024
4add09c
solve issues related to template parameter FP
Jan 25, 2024
9cf6a5b
solve issues related to template parameter FP
Jan 25, 2024
aebc39e
solve issues related to template parameter FP
Jan 25, 2024
32063b7
solve issues related to template parameter FP
Jan 25, 2024
5f626e4
solve issues related to template parameter FP
Jan 25, 2024
d6d684f
solve issues related to template parameter FP
Jan 25, 2024
c978521
solve issues related to template parameter FP
Jan 25, 2024
4d0c8dd
merge with upstream
Jan 25, 2024
9cfa914
merge with upstream
Jan 25, 2024
6597950
fix issue with missing template parameter FP in rhs of is_compartment…
Feb 1, 2024
ee8b2ad
fix issue with selection of correct overload of mio::oscecir::get_inf…
Feb 1, 2024
f3dc6ac
fixx name resolution of Model in constructor of Simulation
Feb 1, 2024
c0960b4
fix issue with template instantiation related to template parameter FP
Feb 1, 2024
35fa487
Merge remote-tracking branch 'upstream/main'
Feb 5, 2024
acf20ee
fix issue with template parameter FP
Feb 5, 2024
7845725
fix issue related to template paraameter FP
Feb 5, 2024
39925bb
format
HenrZu Feb 5, 2024
41a3b8e
link .clang-format into source directory (required by QtCreator)
Feb 5, 2024
487316d
add CMakeList.txt.user to be ignored
Feb 5, 2024
f6093ed
exclude .F-files (Fortran) from test coverage
Feb 6, 2024
e62c2d0
cleanup
Feb 6, 2024
0b62a97
quick and dirty implmentation of output
Feb 8, 2024
ecea8fd
cleanup unused parameters
Feb 8, 2024
d74c84e
cleanup unused parameters
Feb 15, 2024
44a305f
merge with upstream
Feb 15, 2024
262e22e
increase tolerance of ASSERT_NEAR by a factor of 20 in ModelTestOdeS…
Feb 15, 2024
da87399
check for APPLE before setting CMAKE_OSX_DEPLOYMENT_TARGET
Feb 15, 2024
e8d689a
used ScalarType as default template parameter
Feb 15, 2024
0db0a5c
add option MEMILIO_ENABLE_OPTIMIZATION, default OFF
Feb 19, 2024
aea8543
apply clang-format
Feb 19, 2024
d59c478
sync with upstream
Feb 19, 2024
88e79e8
use FP consistently as first template parameter
Feb 19, 2024
06377c6
progress in recovering abm
Feb 19, 2024
0b0f7a2
make abm template free
Feb 19, 2024
4872bfe
Solve issues related to template parameter FP
Feb 19, 2024
d0383cc
cleanup
Feb 19, 2024
52b36ea
fix issues related to template parameter FP
Feb 19, 2024
5c437f9
fix issues with missing template parameter
Feb 20, 2024
961794b
remove exclude Fortran files from code coverage to test CI machines
Feb 20, 2024
d38423c
remove exclude Fortran files from code coverage to test CI machines
Feb 20, 2024
75f60f6
Exclude Fortran files from code coverage to test CI machines
Feb 20, 2024
e7ad0e4
rename SEIAR related examples
Feb 20, 2024
0cc47f2
Enable optimization on Linux by default
Feb 20, 2024
7439223
adapt copyright and comments
Feb 20, 2024
27e65aa
MEMILIO_ENABLE_OPTIMIZATION is OFF by default
Feb 20, 2024
9826a86
Clenaup unused header file ad.hpp
Feb 20, 2024
31fcf96
remove code the was commented out
Feb 20, 2024
c2eded3
correct type in doxygen comment
Feb 20, 2024
fe747ac
Merge remote-tracking branch 'upstream/main'
Feb 26, 2024
0ea7e42
cleanup
Feb 26, 2024
40d1928
ScalarType default for template parameter FP
Feb 26, 2024
ee16a21
comments and renaming
Feb 26, 2024
6376f56
renaming
Feb 26, 2024
4aadf73
add some comments
Feb 26, 2024
bfb6add
cleanup
Feb 26, 2024
8b6efa5
cleanup
Feb 26, 2024
7061821
cleanup
Feb 26, 2024
c7e4f6b
improve readability
Feb 26, 2024
402fdcc
improve readability
Feb 26, 2024
4b641ad
Merge remote-tracking branch 'upstream/main'
Feb 27, 2024
1eb2ea7
cleanup
Feb 28, 2024
357c239
cleanup
Feb 28, 2024
ca2c744
cleanup
Feb 28, 2024
a702929
cleanup
Feb 28, 2024
29b6897
rm build-
Feb 28, 2024
bde3418
add comment
Feb 28, 2024
243230b
merge with upstream
Mar 6, 2024
5f84629
towards testing
Mar 14, 2024
78b3d88
cleanup time_series_to_file.h
Mar 14, 2024
2b5335d
merge with upstream
Mar 14, 2024
b3687cc
merge with upstream
Mar 14, 2024
110269b
add missing template argument
Mar 14, 2024
11774d3
merge with upstream
Mar 18, 2024
10cacf1
Merge remote-tracking branch 'upstream/main'
Mar 18, 2024
ca5ccce
Merge remote-tracking branch 'upstream/main'
Mar 20, 2024
e923ec7
merge with upstream
Mar 27, 2024
dabf5c0
Merge branch 'main' into main
mknaranja Apr 2, 2024
2aaac6c
add FP parameter to SDE models
reneSchm Apr 2, 2024
5955d06
manually merge OdeIntegrator::advance
reneSchm Apr 2, 2024
48fd63c
re-add using declarations.
reneSchm Apr 2, 2024
5216e43
merge with upstream
Apr 3, 2024
b47924d
merge with upstream
Apr 3, 2024
08a4275
consistently use ScalarType in SDE models
reneSchm Apr 3, 2024
e4ef234
add a "Vector" template alias
reneSchm Apr 5, 2024
d7e5acf
merge with upstream
Apr 5, 2024
cceb53e
move arguments for template ControlledStepper
reneSchm Apr 5, 2024
495a1eb
add is_fsal_stepper back
reneSchm Apr 5, 2024
a1bc1a2
prepare and add test
Apr 8, 2024
120264c
fix issue with python bindings
Apr 8, 2024
6939994
Merge remote-tracking branch 'scicompmod/main'
reneSchm Apr 19, 2024
f69d66c
add data/analyze_result.h where needed
reneSchm Apr 19, 2024
acdc52c
add another data/analyze_result.h
reneSchm Apr 19, 2024
ff96e36
towards fixing pycode/memilio-generation
Apr 26, 2024
aab73fe
run pre-commit
reneSchm Apr 26, 2024
93aba79
include adapt_rk.h
Apr 26, 2024
57e8e95
add whitespace to fix tests
reneSchm Apr 26, 2024
5e66c16
cleanup
Apr 26, 2024
e99d9fd
exclude ad lib from code coverage
mknaranja Apr 26, 2024
daeb96a
improve and update doc
May 2, 2024
194abe7
improve comments
May 2, 2024
1b7a940
use FP instead of double in EulerStep
May 2, 2024
cfbd9fd
remove usage of ad::value()
May 2, 2024
fdcc267
use mio::RKIntegratorCore<> instead of mio::RKIntegratorCore<double>
May 2, 2024
efdd0d8
cleanup double comment
May 2, 2024
1024234
Eliminate FP und use default template argument instead
May 2, 2024
d6bd010
corrected path to exclude ad from codecov
lenaploetzke May 2, 2024
1b5a7a1
Merge remote-tracking branch 'scicompmod/main'
reneSchm May 2, 2024
149334d
post merge cleanup. includes, comments, formatting
reneSchm May 2, 2024
f5b1590
Merge branch 'main' of github.com:hannemann-tamas/memilio-rh
reneSchm May 2, 2024
894de1c
mark two more args as unused (used only in assert)
reneSchm May 2, 2024
ef1fb3a
remove unused save_result_result
reneSchm May 2, 2024
de2a353
include spdlog through logging.h
reneSchm May 3, 2024
a14e743
do not overwrite moving average
reneSchm May 3, 2024
dfadaa5
tests odeseair
HenrZu May 3, 2024
3d564ac
fix ad::value(a1_y)
May 3, 2024
71bf835
remove OSX_DEPLOYMENT_TARGET statement
May 3, 2024
8994f45
added test for ad
lenaploetzke May 3, 2024
ca91466
disabled warning no longer necessary
lenaploetzke May 3, 2024
9ba3b03
model with absolute numbers
HenrZu May 6, 2024
00f9c82
pop instead of y
HenrZu May 6, 2024
f40c996
cleanup
hannemann-tamas May 6, 2024
dd1a09a
improve doc
hannemann-tamas May 6, 2024
3a5938f
Merge branch 'main' of github.com:hannemann-tamas/memilio-rh
hannemann-tamas May 6, 2024
fc76605
Remove objective function from SEAIR model and use absolute values in…
hannemann-tamas May 6, 2024
4e97eb8
changed order of infectionstates
lenaploetzke May 6, 2024
e32bde4
improve comments
hannemann-tamas May 6, 2024
efbc9b6
Merge branch 'main' of github.com:hannemann-tamas/memilio-rh
hannemann-tamas May 6, 2024
3ce7e62
Apply suggestions from code review
mknaranja May 6, 2024
20dd5b4
fix minor typo
hannemann-tamas May 6, 2024
f663cf2
Merge branch 'main' of github.com:hannemann-tamas/memilio-rh
hannemann-tamas May 6, 2024
6c3f5dd
included reviewers comments
lenaploetzke May 6, 2024
af8e4cc
improve doc
hannemann-tamas May 6, 2024
1895a62
link memilio to AD example in order solve compilation erros on Apple
hannemann-tamas May 6, 2024
07af16e
renamed parameters
lenaploetzke May 6, 2024
702a057
resolved error
lenaploetzke May 7, 2024
460669f
update Readme + FlowChart
HenrZu May 7, 2024
0c0ed84
improve comments
hannemann-tamas May 7, 2024
b5cffbe
included reviewers comments
lenaploetzke May 7, 2024
383520e
improve comments
hannemann-tamas May 7, 2024
7318b79
Merge branch 'main' of github.com:hannemann-tamas/memilio-rh
hannemann-tamas May 7, 2024
e6819db
added test ad with oseair
lenaploetzke May 7, 2024
ca3ea21
included reviewers comments
lenaploetzke May 8, 2024
85069cc
changed location of content of ad_spdlog_formatter.h
lenaploetzke May 8, 2024
3b5d60f
removed fmod where not necessary
lenaploetzke May 8, 2024
1e276f8
added check_constraints for parameters and test
lenaploetzke May 8, 2024
2aa7bc8
[ci skip] added documentation of ad_seair test
lenaploetzke May 8, 2024
a35c9d1
some comments
hannemann-tamas May 12, 2024
03b522a
improve doc
hannemann-tamas May 13, 2024
a1f06d5
Replace SFINAE for migration edge stochastic
mknaranja May 13, 2024
261447c
improve doc
hannemann-tamas May 13, 2024
67b8fdf
remove cast in get_initial_values.
reneSchm May 13, 2024
b70de01
function pointer cast
mknaranja May 13, 2024
96c3be7
Merge branch 'main' of github.com:hannemann-tamas/memilio-rh
mknaranja May 13, 2024
5c24a2a
grammar
mknaranja May 13, 2024
c5d1cdc
rm ignored Deprecation warning
lenaploetzke May 13, 2024
be5b98e
removed unneeded operator
lenaploetzke May 13, 2024
e215f97
use fixed size array for state
hannemann-tamas May 13, 2024
6599c48
use fixed size array for state
hannemann-tamas May 13, 2024
37896a1
change order of template arguments in write_graph
hannemann-tamas May 13, 2024
2d89868
use fixed-size array in harmonic_oscillator
hannemann-tamas May 13, 2024
d995562
fix benchmarks
HenrZu May 13, 2024
be389b5
update model eq seir, benchmark seir eqs
HenrZu May 13, 2024
c38a151
[ci skip] some fixes benchmarks + pop in model eq
HenrZu May 13, 2024
7087ec5
[ci skip] directly use base in constructor benchmark
HenrZu May 14, 2024
e37d8e1
Apply suggestions from code review
lenaploetzke May 15, 2024
e2bfbe6
Merge remote-tracking branch 'scicompmod/main'
reneSchm May 17, 2024
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6 changes: 5 additions & 1 deletion .github/actions/linux-build/action.yml
Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,10 @@ inputs:
description: "Enable Multithreading with OpenMP (ON or OFF, default OFF). If ON, adds `-omp` to the name of the artifact."
required: false
default: "OFF"
enable-optimization:
description: "Enable optimization with Ipopt (ON or OFF, default ON)"
required: false
default: "ON"
runs:
using: "composite"
steps:
Expand Down Expand Up @@ -89,7 +93,7 @@ runs:
exit 1
fi
mkdir -p build && cd build
cmake -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_BUILD_TESTS=${{ inputs.build-tests }} -DMEMILIO_BUILD_BENCHMARKS=${{ inputs.build-benchmarks }} -DMEMILIO_TEST_COVERAGE=${{ inputs.coverage }} -DMEMILIO_SANITIZE_ADDRESS=${{ inputs.sanitize-addr }} -DMEMILIO_SANITIZE_UNDEFINED=${{ inputs.sanitize-ub }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DMEMILIO_ENABLE_OPENMP=${{ inputs.openmp }} ..
cmake -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_BUILD_TESTS=${{ inputs.build-tests }} -DMEMILIO_BUILD_BENCHMARKS=${{ inputs.build-benchmarks }} -DMEMILIO_ENABLE_IPOPT=${{ inputs.enable-optimization }} -DMEMILIO_TEST_COVERAGE=${{ inputs.coverage }} -DMEMILIO_SANITIZE_ADDRESS=${{ inputs.sanitize-addr }} -DMEMILIO_SANITIZE_UNDEFINED=${{ inputs.sanitize-ub }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DMEMILIO_ENABLE_OPENMP=${{ inputs.openmp }} ..
make -j4
- name: create build dir archive
shell: bash
Expand Down
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