Layer development #24

jtgasparik · 2024-07-02T19:49:41Z

Added layers to aerosol particles in single particle representation

…tation

…_layer_phase_set

…ally!

Co-authored-by: Jeffrey Curtis <jcurtis2@illinois.edu>

Single particle with multiple layers

Rxns with layers

mattldawson

looks great! just a few comments about removing things

CMakeLists.txt

src/aero_rep_factory.F90

src/aero_reps/aero_rep_single_particle_no_layers.c

src/aero_reps/layer_aero_rep_array_test.F90

src/aero_reps/layer_state_id_array_test.F90

src/aero_reps/num_phase_array_test.F90

test/unit_aero_rep_data/test_aero_rep_single_particle_one_layer.c

mattldawson

looks great!

mattldawson

looks good!

jcurtis2 · 2024-07-10T17:30:09Z

test/unit_rxn_data/test_aqueous_equilibrium_config.json

@@ -1,5 +1,6 @@
 {
 	"camp-files" : [
 		"test_aqueous_equilibrium.json"
+


Remove added line.

jcurtis2 · 2024-07-10T17:32:02Z

src/rxns/rxn_HL_phase_transfer.F90

@@ -257,7 +257,7 @@ subroutine initialize(this, chem_spec_data, aero_rep, n_cells)

      ! Get the number of Jacobian elements for calculations of mass, volume,
      ! number, etc. for this partitioning into this phase
-      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name)
+      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)


Suggested change

phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)

phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name, is_at_surface=.true.)

jcurtis2 · 2024-07-10T17:32:15Z

src/rxns/rxn_HL_phase_transfer.F90

@@ -316,7 +316,7 @@ subroutine initialize(this, chem_spec_data, aero_rep, n_cells)
              phase_name = phase_name, spec_name = water_name)

      ! Get the phase ids for this aerosol phase
-      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name)
+      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)


Suggested change

phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)

phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name, is_at_surface=.true.)

jcurtis2 · 2024-07-10T17:32:25Z

src/rxns/rxn_SIMPOL_phase_transfer.F90

@@ -255,7 +255,7 @@ subroutine initialize(this, chem_spec_data, aero_rep, n_cells)

      ! Get the number of Jacobian elements for calculations of mass, volume,
      ! number, etc. for this partitioning into this phase
-      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name)
+      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)


Suggested change

phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)

phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name, is_at_surface=.true.)

jcurtis2 · 2024-07-10T17:32:36Z

src/rxns/rxn_SIMPOL_phase_transfer.F90

@@ -319,8 +319,7 @@ subroutine initialize(this, chem_spec_data, aero_rep, n_cells)
      end if

      ! Get the phase ids for this aerosol phase
-      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name)
-
+      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)


Suggested change

phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)

phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name, is_at_surface=.true.)

jcurtis2 · 2024-07-10T17:35:27Z

src/aero_rep_factory.F90

@@ -211,8 +211,8 @@ module camp_aero_rep_factory

  !> Identifiers for aerosol representations - used by binary
  !! packing/unpacking functions
-  integer(kind=i_kind), parameter :: AERO_REP_SINGLE_PARTICLE   = 1
-  integer(kind=i_kind), parameter :: AERO_REP_MODAL_BINNED_MASS = 2
+  integer(kind=i_kind), parameter :: AERO_REP_SINGLE_PARTICLE        = 1


Suggested change

integer(kind=i_kind), parameter :: AERO_REP_SINGLE_PARTICLE = 1

integer(kind=i_kind), parameter :: AERO_REP_SINGLE_PARTICLE = 1

can you clarify what you mean by this?

jcurtis2 · 2024-07-10T17:35:44Z

src/aero_rep_factory.F90

-  integer(kind=i_kind), parameter :: AERO_REP_SINGLE_PARTICLE   = 1
-  integer(kind=i_kind), parameter :: AERO_REP_MODAL_BINNED_MASS = 2
+  integer(kind=i_kind), parameter :: AERO_REP_SINGLE_PARTICLE        = 1
+  integer(kind=i_kind), parameter :: AERO_REP_MODAL_BINNED_MASS      = 2


Suggested change

integer(kind=i_kind), parameter :: AERO_REP_MODAL_BINNED_MASS = 2

integer(kind=i_kind), parameter :: AERO_REP_MODAL_BINNED_MASS = 2

can you clarify what you mean by this?

Sure - white space somehow got added here in a file that you actually didn't appear to make any other modifications in. My suggestion should revert it back to how it was so that this file doesn't appear to be changed at all by your PR.

jcurtis2 · 2024-07-10T17:36:52Z

test/unit_aero_rep_data/test_aero_rep_single_particle.c


 // index for the test phase (test-particle phase 2)
 #define AERO_PHASE_IDX ((TEST_PARTICLE-1)*NUM_AERO_PHASE+1)

 // number of Jacobian elements used for the test phase
-#define N_JAC_ELEM 8
+#define N_JAC_ELEM 12 


Suggested change

#define N_JAC_ELEM 12

#define N_JAC_ELEM 12

jcurtis2 · 2024-07-10T17:37:38Z

test/unit_rxn_data/test_HL_phase_transfer.json

@@ -49,7 +49,7 @@
    "phase" : "AEROSOL",
    "density [kg m-3]" : 1000.0,
    "molecular weight [kg mol-1]" : 0.01801
-  },
+  }, 


Suggested change

},

},

jtgasparik added 30 commits May 5, 2023 08:33

aero rep single particle layer .c and .F90 files

9c9a201

comments to .F90 code

3f33c31

adding layers to aero_rep_single_particle_layers.F90

8380f0d

aero_rep_single_particle_layers.F90 without comments

b59b0c9

fix to indexing

c1efe46

C preprocessor variables modified

6715224

init aero rep data for layers function

b7508e2

unique names - need to check if aero_phases is correct

1fe61ff

added LAYER_STATE_ID_ variable

0abd1e4

add and allocate aero_phase array

ec9b541

creating aero_layer_phase_set array

b1dee82

ordered layers subroutine

4b2d1a0

edits to ordered layers subroutine

c8f2c4f

added LAYER_STATE_ID_UNORDERED_ loop to main code

8e3547b

add second loop with phase names unordered

1fb921a

add ordered phase function

aeabb29

aero_phase array constructed

f4f18ad

added layer state id subroutine

de2d432

modified ordered functions based on independednt test and edits to no…

5b27253

…tation

modified functions: removed any variables associated with this

06e4e35

initialized missing variables and added functions to procedure list

d1f2aa3

edited loop to setup aero_phase array to reflect changed made to aero…

82668fb

…_layer_phase_set

fixed layer_state_id function and independently tested

1cb93a5

error message to .F90 code, layer and phase tests added to test.F90

bc921ff

minor .F90 code fixes, tests added and model sucessfully compiled loc…

79c6375

…ally!

some changes to pre-processor definitions

00c5ed2

added variables to aero_rep_data_t

101f312

added sandwich test to check layer and phase ordering

fa1e0fc

modified unique_names funtion to reflect layers

b61d97d

modified unique names function

f1e521d

jtgasparik and others added 14 commits May 7, 2024 13:00

Update src/aero_reps/aero_rep_single_particle.F90

2175063

Co-authored-by: Jeffrey Curtis <jcurtis2@illinois.edu>

remove print statements

62ac5b1

Merge pull request #6 from jtgasparik/multiple_layer_tests

66783eb

Single particle with multiple layers

branch for adding layers to SIMPOL and HL rxns

796ab24

fix to print statements and some rxn development

9751168

surface layer boolean array

9a0287c

make boolean array and tested

603f286

trying to get modal distribution to compile - it wont

d4454c2

compiles but does not pass tests

cc76489

added at surface flag, all tests pass

eb1cca7

coding structure fix

cf7169a

some comments resolved on PR

e546dd1

review comments

bfaf87e

Merge pull request #7 from jtgasparik/rxns_with_layers

b429895

Rxns with layers

jtgasparik requested review from jcurtis2 and mattldawson July 2, 2024 19:49

mattldawson requested changes Jul 2, 2024

View reviewed changes

PR requested changes

8213a98

jtgasparik requested a review from mattldawson July 3, 2024 01:18

mattldawson approved these changes Jul 5, 2024

View reviewed changes

jtgasparik and others added 2 commits July 8, 2024 15:38

Merge branch 'main' into layer_development

18225bf

PR conflicts resolved + new reactions with layers

a60f3f9

jtgasparik requested a review from mattldawson July 10, 2024 15:37

mattldawson approved these changes Jul 10, 2024

View reviewed changes

jcurtis2 reviewed Jul 10, 2024

View reviewed changes

Jeff's PR comments

cde4d86

jtgasparik requested a review from jcurtis2 July 12, 2024 11:53

jcurtis2 approved these changes Jul 12, 2024

View reviewed changes

jtgasparik merged commit b71175d into open-atmos:main Jul 12, 2024
1 check passed

jtgasparik deleted the layer_development branch July 12, 2024 14:18

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Layer development #24

Layer development #24

jtgasparik commented Jul 2, 2024

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jcurtis2 Jul 10, 2024

	phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)
	phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name, is_at_surface=.true.)

	integer(kind=i_kind), parameter :: AERO_REP_SINGLE_PARTICLE = 1
	integer(kind=i_kind), parameter :: AERO_REP_SINGLE_PARTICLE = 1

Layer development #24

Layer development #24

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jtgasparik commented Jul 2, 2024

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