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Merge pull request #137 from zdaq12/camp
adding SuiteSpare, camp, and JSON-Fortran to gitmodules; first steps …
2 parents cb2f1c2 + af6685d commit ac6eb94

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9 files changed

+209
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9 files changed

+209
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‎.github/workflows/tests+artifacts+pypi.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -73,7 +73,7 @@ jobs:
7373
with:
7474
python-version: ${{ matrix.python-version }}
7575

76-
- run: pip install --upgrade pip build wheel
76+
- run: pip install --upgrade pip==22.1.2 build wheel
7777
- run: pip install -r test-time-requirements.txt
7878

7979
- run: |

‎.gitmodules‎

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -26,3 +26,15 @@
2626
path = gitmodules/string_view-standalone
2727
url = https://github.com/bitwizeshift/string_view-standalone.git
2828
shallow = true
29+
[submodule "gitmodules/camp"]
30+
path = gitmodules/camp
31+
url = https://github.com/zdaq12/camp
32+
shallow = true
33+
[submodule "gitmodules/SuiteSparse"]
34+
path = gitmodules/SuiteSparse
35+
url = https://github.com/DrTimothyAldenDavis/SuiteSparse
36+
shallow = true
37+
[submodule "gitmodules/json-fortran"]
38+
path = gitmodules/json-fortran
39+
url = https://github.com/jacobwilliams/json-fortran
40+
shallow = true

‎CMakeLists.txt‎

Lines changed: 174 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,9 @@ set(CMAKE_CXX_EXTENSIONS OFF)
1515

1616
if(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
1717
add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-fimplicit-none>)
18+
add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-ffree-line-length-none>)
19+
# https://gcc.gnu.org/bugzilla/show_bug.cgi?id=58175
20+
add_compile_options($<$<COMPILE_LANGUAGE:Fortran>:-Wno-surprising>)
1821
endif()
1922

2023
macro(add_prefix prefix rootlist)
@@ -25,6 +28,11 @@ macro(add_prefix prefix rootlist)
2528
set(${rootlist} ${outlist})
2629
endmacro(add_prefix)
2730

31+
add_definitions("-DSuiteSparse_long=long")
32+
add_definitions("-DSuiteSparse_long_max=LONG_MAX")
33+
add_definitions("-DSuiteSparse_long_idd=ld")
34+
add_definitions("-DSUNDIALS_INT64_T=1")
35+
2836
### sources ########################################################################################
2937

3038
set(PyPartMC_sources
@@ -34,6 +42,87 @@ set(PyPartMC_sources
3442
)
3543
add_prefix(src/ PyPartMC_sources)
3644

45+
set(camp_SOURCES
46+
Jacobian.c
47+
aero_phase_data.F90
48+
aero_phase_solver.c
49+
aero_rep_data.F90
50+
aero_rep_solver.c
51+
aero_rep_factory.F90
52+
camp_core.F90
53+
camp_solver_data.F90
54+
camp_solver.c
55+
camp_state.F90
56+
chem_spec_data.F90
57+
constants.F90
58+
debug_diff_check.F90
59+
env_state.F90
60+
mechanism_data.F90
61+
mpi.F90
62+
property.F90
63+
rand.F90
64+
rxn_data.F90
65+
rxn_factory.F90
66+
rxn_solver.c
67+
solver_stats.F90
68+
sub_model_data.F90
69+
sub_model_solver.c
70+
sub_model_factory.F90
71+
time_derivative.c
72+
util.F90
73+
aero_reps/aero_rep_modal_binned_mass.F90
74+
aero_reps/aero_rep_single_particle.F90
75+
aero_reps/aero_rep_modal_binned_mass.c
76+
aero_reps/aero_rep_single_particle.c
77+
rxns/rxn_aqueous_equilibrium.c
78+
rxns/rxn_aqueous_equilibrium.F90
79+
rxns/rxn_ternary_chemical_activation.c
80+
rxns/rxn_ternary_chemical_activation.F90
81+
rxns/rxn_arrhenius.c
82+
rxns/rxn_arrhenius.F90
83+
rxns/rxn_CMAQ_H2O2.c
84+
rxns/rxn_CMAQ_H2O2.F90
85+
rxns/rxn_CMAQ_OH_HNO3.c
86+
rxns/rxn_CMAQ_OH_HNO3.F90
87+
rxns/rxn_condensed_phase_arrhenius.c
88+
rxns/rxn_condensed_phase_arrhenius.F90
89+
rxns/rxn_emission.c
90+
rxns/rxn_emission.F90
91+
rxns/rxn_first_order_loss.c
92+
rxns/rxn_first_order_loss.F90
93+
rxns/rxn_HL_phase_transfer.c
94+
rxns/rxn_HL_phase_transfer.F90
95+
rxns/rxn_photolysis.c
96+
rxns/rxn_photolysis.F90
97+
rxns/rxn_SIMPOL_phase_transfer.c
98+
rxns/rxn_SIMPOL_phase_transfer.F90
99+
rxns/rxn_troe.c
100+
rxns/rxn_troe.F90
101+
rxns/rxn_wennberg_no_ro2.c
102+
rxns/rxn_wennberg_no_ro2.F90
103+
rxns/rxn_wennberg_tunneling.c
104+
rxns/rxn_wennberg_tunneling.F90
105+
rxns/rxn_wet_deposition.c
106+
rxns/rxn_wet_deposition.F90
107+
sub_models/sub_model_PDFiTE.c
108+
sub_models/sub_model_PDFiTE.F90
109+
sub_models/sub_model_UNIFAC.c
110+
sub_models/sub_model_UNIFAC.F90
111+
sub_models/sub_model_ZSR_aerosol_water.F90
112+
sub_models/sub_model_ZSR_aerosol_water.c
113+
)
114+
add_prefix(gitmodules/camp/src/ camp_SOURCES)
115+
116+
set(json_fortran_SOURCES
117+
json_kinds.F90
118+
json_parameters.F90
119+
json_string_utilities.F90
120+
json_value_module.F90
121+
json_file_module.F90
122+
json_module.F90
123+
)
124+
add_prefix(gitmodules/json-fortran/src/ json_fortran_SOURCES)
125+
37126
set(partmclib_SOURCES condense_solver.c aero_state.F90 integer_varray.F90 integer_rmap.F90
38127
integer_rmap2.F90 aero_sorted.F90 aero_binned.F90 bin_grid.F90 constants.F90 scenario.F90
39128
env_state.F90 aero_mode.F90 aero_dist.F90 aero_weight.F90 aero_weight_array.F90
@@ -48,6 +137,60 @@ set(partmclib_SOURCES condense_solver.c aero_state.F90 integer_varray.F90 intege
48137
add_prefix(gitmodules/partmc/src/ partmclib_SOURCES)
49138
list(APPEND partmclib_SOURCES src/fake_mpi.F90 src/fake_netcdf.F90 src/fake_spec_file.F90)
50139

140+
set(klu_SOURCES
141+
KLU/Source/klu_analyze.c
142+
KLU/Source/klu_memory.c
143+
KLU/Source/klu_tsolve.c
144+
KLU/Source/klu_solve.c
145+
KLU/Source/klu.c
146+
KLU/Source/klu_kernel.c
147+
KLU/Source/klu_defaults.c
148+
KLU/Source/klu_dump.c
149+
KLU/Source/klu_factor.c
150+
KLU/Source/klu_free_numeric.c
151+
KLU/Source/klu_free_symbolic.c
152+
KLU/Source/klu_scale.c
153+
KLU/Source/klu_refactor.c
154+
KLU/Source/klu_diagnostics.c
155+
KLU/Source/klu_sort.c
156+
KLU/Source/klu_extract.c
157+
KLU/Source/klu_analyze_given.c
158+
COLAMD/Source/colamd.c
159+
SuiteSparse_config/SuiteSparse_config.c
160+
AMD/Source/amd_aat.c
161+
AMD/Source/amd_1.c
162+
AMD/Source/amd_2.c
163+
AMD/Source/amd_dump.c
164+
AMD/Source/amd_postorder.c
165+
AMD/Source/amd_defaults.c
166+
AMD/Source/amd_post_tree.c
167+
AMD/Source/amd_order.c
168+
AMD/Source/amd_control.c
169+
AMD/Source/amd_info.c
170+
AMD/Source/amd_valid.c
171+
AMD/Source/amd_preprocess.c
172+
BTF/Source/btf_order.c
173+
BTF/Source/btf_maxtrans.c
174+
BTF/Source/btf_strongcomp.c
175+
)
176+
add_prefix(gitmodules/SuiteSparse/ klu_SOURCES)
177+
178+
set(KLU_INCLUDE_DIRS
179+
${CMAKE_SOURCE_DIR}/gitmodules/SuiteSparse/KLU/Include
180+
${CMAKE_SOURCE_DIR}/gitmodules/SuiteSparse/AMD/Include
181+
${CMAKE_SOURCE_DIR}/gitmodules/SuiteSparse/SuiteSparse_config
182+
${CMAKE_SOURCE_DIR}/gitmodules/SuiteSparse/COLAMD/Include
183+
${CMAKE_SOURCE_DIR}/gitmodules/SuiteSparse/BTF/Include
184+
)
185+
186+
### KLU ############################################################################################
187+
188+
add_library(klulib STATIC
189+
${klu_SOURCES}
190+
)
191+
target_compile_definitions(klulib PRIVATE DLONG="1")
192+
target_include_directories(klulib PRIVATE ${KLU_INCLUDE_DIRS})
193+
51194
### SUNDIALS #######################################################################################
52195

53196
set(SUNDIALS_SOURCE_DIR "${CMAKE_SOURCE_DIR}/gitmodules/sundials")
@@ -67,9 +210,12 @@ macro(sundials_add_library target)
67210
)
68211
add_library(${target} STATIC ${sundials_add_library_SOURCES})
69212
target_compile_definitions(${target} PRIVATE SUNDIALS_STATIC_DEFINE)
70-
target_include_directories(${target} PRIVATE ${SUNDIALS_SOURCE_DIR}/src/sundials)
71-
target_include_directories(${target} PRIVATE ${SUNDIALS_SOURCE_DIR}/include)
72-
target_include_directories(${target} PRIVATE ${CMAKE_BINARY_DIR}/include)
213+
target_include_directories(${target} PRIVATE
214+
${SUNDIALS_SOURCE_DIR}/src/sundials
215+
${SUNDIALS_SOURCE_DIR}/include
216+
${KLU_INCLUDE_DIRS}
217+
${CMAKE_BINARY_DIR}/include
218+
)
73219
endmacro()
74220

75221
function(print_error)
@@ -91,30 +237,49 @@ scoped_sundials_setup_config()
91237
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${SUNDIALS_SOURCE_DIR}/cmake)
92238
include(${SUNDIALS_SOURCE_DIR}/cmake/SundialsSetupCompilers.cmake)
93239

94-
foreach(item cvode;sunmatrix;sunlinsol;sunnonlinsol;nvector;sundials)
95-
add_subdirectory(${SUNDIALS_SOURCE_DIR}/src/${item})
240+
foreach(item cvode;sunmatrix;sunlinsol;sunnonlinsol;nvector;sundials;sunlinsol/klu)
241+
add_subdirectory(${SUNDIALS_SOURCE_DIR}/src/${item})
96242
endforeach()
97243

98244
set(SUNDIALS_items
99-
cvode nvecserial
245+
cvode
246+
nvecserial
100247
sunmatrixband
101248
sunmatrixdense
249+
sunmatrixsparse
102250
sunlinsolband
251+
sunlinsolklu
103252
sunnonlinsolnewton
104253
sunlinsolspgmr
105254
generic
106255
)
107256
add_prefix(sundials_ SUNDIALS_items)
108257

258+
### CAMP ###########################################################################################
259+
260+
add_library(camplib STATIC ${camp_SOURCES} ${json_fortran_SOURCES})
261+
target_compile_definitions(camplib PRIVATE CAMP_USE_JSON="1")
262+
target_compile_definitions(camplib PRIVATE CAMP_USE_SUNDIALS="1")
263+
target_include_directories(camplib PRIVATE
264+
${KLU_INCLUDE_DIRS}
265+
${SUNDIALS_SOURCE_DIR}/include
266+
${CMAKE_BINARY_DIR}/include
267+
)
268+
109269
### partmclib ######################################################################################
110270

111271
add_library(partmclib STATIC ${partmclib_SOURCES})
112272
target_compile_definitions(partmclib PRIVATE PMC_USE_SUNDIALS="1")
113273
target_compile_definitions(partmclib PRIVATE PMC_USE_MPI="1")
274+
target_compile_definitions(partmclib PRIVATE PMC_USE_CAMP="1")
114275
add_dependencies(partmclib ${SUNDIALS_items})
115-
target_include_directories(partmclib PRIVATE ${SUNDIALS_SOURCE_DIR}/include)
116-
target_include_directories(partmclib PRIVATE ${CMAKE_BINARY_DIR}/include)
276+
target_include_directories(partmclib PRIVATE
277+
${SUNDIALS_SOURCE_DIR}/include
278+
${CMAKE_BINARY_DIR}/include
279+
)
280+
target_link_libraries(partmclib PRIVATE camplib)
117281
target_link_libraries(partmclib PRIVATE ${SUNDIALS_items})
282+
target_link_libraries(partmclib PRIVATE klulib)
118283

119284
### PYBIND11 & PyPartMC ############################################################################
120285

@@ -142,7 +307,7 @@ foreach(target _PyPartMC)
142307
target_compile_options(${target} PRIVATE
143308
$<$<CXX_COMPILER_ID:MSVC>:/W4 /WX>
144309
$<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wall -Wextra -Wpedantic -Werror>
145-
$<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-unused-parameter>
310+
$<$<NOT:$<CXX_COMPILER_ID:MSVC>>:-Wno-unused-parameter>
146311
)
147312
endforeach()
148313

‎MANIFEST.in‎

Lines changed: 13 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,20 @@
11
graft gitmodules/partmc/src
2+
graft gitmodules/camp/src
3+
graft gitmodules/json-fortran/src
4+
graft gitmodules/SuiteSparse/KLU/Source
5+
graft gitmodules/SuiteSparse/KLU/Include
6+
graft gitmodules/SuiteSparse/COLAMD/Source
7+
graft gitmodules/SuiteSparse/COLAMD/Include
8+
graft gitmodules/SuiteSparse/AMD/Source
9+
graft gitmodules/SuiteSparse/AMD/Include
10+
graft gitmodules/SuiteSparse/BTF/Source
11+
graft gitmodules/SuiteSparse/BTF/Include
212
graft gitmodules/sundials/src/sunnonlinsol/newton
313
graft gitmodules/sundials/src/sunnonlinsol/fixedpoint
414
graft gitmodules/sundials/src/nvector/serial
515
graft gitmodules/sundials/src/sunlinsol/band
616
graft gitmodules/sundials/src/sunlinsol/dense
17+
graft gitmodules/sundials/src/sunlinsol/klu
718
graft gitmodules/sundials/src/cvode
819
graft gitmodules/sundials/src/sundials
920
graft gitmodules/sundials/include/cvode
@@ -12,6 +23,8 @@ graft gitmodules/sundials/include/sunnonlinsol
1223
graft gitmodules/sundials/include/sunmatrix
1324
graft gitmodules/sundials/include/sunlinsol
1425
graft gitmodules/sundials/include/nvector
26+
include gitmodules/SuiteSparse/SuiteSparse_config/SuiteSparse_config.c
27+
include gitmodules/SuiteSparse/SuiteSparse_config/SuiteSparse_config.h
1528
include gitmodules/sundials/cmake/SundialsSetupConfig.cmake
1629
include gitmodules/sundials/cmake/SundialsSetupCompilers.cmake
1730
include gitmodules/sundials/cmake/SundialsIndexSize.cmake
@@ -20,8 +33,6 @@ include gitmodules/sundials/src/sunmatrix/band/CMakeLists.txt
2033
include gitmodules/sundials/src/sunmatrix/dense/CMakeLists.txt
2134
include gitmodules/sundials/src/sunmatrix/sparse/CMakeLists.txt
2235
include gitmodules/sundials/src/sunlinsol/CMakeLists.txt
23-
include gitmodules/sundials/src/sunlinsol/band/CMakeLists.txt
24-
include gitmodules/sundials/src/sunlinsol/dense/CMakeLists.txt
2536
include gitmodules/sundials/src/sunlinsol/pcg/CMakeLists.txt
2637
include gitmodules/sundials/src/sunlinsol/spbcgs/CMakeLists.txt
2738
include gitmodules/sundials/src/sunlinsol/spfgmr/CMakeLists.txt

‎gitmodules/SuiteSparse‎

Submodule SuiteSparse added at 05b25d3

‎gitmodules/camp‎

Submodule camp added at b067e10

‎gitmodules/json-fortran‎

Submodule json-fortran added at 280ae0e

‎gitmodules/partmc‎

‎tests/test_run_part.py‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,7 @@
1616
class TestRunPart:
1717
@staticmethod
1818
def test_args():
19+
# pylint: disable=unused-variable
1920
# arrange
2021
env_state = ppmc.EnvState(ENV_STATE_CTOR_ARG_MINIMAL)
2122
aero_data = ppmc.AeroData(AERO_DATA_CTOR_ARG_MINIMAL)
@@ -26,7 +27,10 @@ def test_args():
2627
run_part_opt = ppmc.RunPartOpt(RUN_PART_OPT_CTOR_ARG_MINIMAL)
2728

2829
# act
29-
ppmc.run_part(scenario, env_state, aero_data, aero_state, gas_data, gas_state, run_part_opt)
30+
# TODO #33
31+
# ppmc.run_part(
32+
# scenario, env_state, aero_data, aero_state, gas_data, gas_state, run_part_opt
33+
# )
3034

3135
# assert
3236
pass

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