Merge branch 'main' into compathelper/new_version/2022-10-31-13-44-28…

…-704-03345107033

.github/workflows/AutomatedGPUTests.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: self-hosted
     strategy:
       matrix:
-        julia-version: ['1.6.0', '1.7.0']
+        julia-version: ['1.7.3','1.8.2']
 
     steps:
       - uses: actions/checkout@v2

.github/workflows/AutomatedTests.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: ['1.6.0', '1.7.0']
+        julia-version: ['1.7.3','1.8.2']
         os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:

.gitignore

@@ -24,5 +24,4 @@ test/precompile
 wigner_values_sparse.jld
 wigner_values.jld
 *.pyc
-*.dat
-*.hdf.nc4
+*.hdf.nc4

.zenodo.json

@@ -0,0 +1,27 @@
+{
+    "description": "vSmartMOM.jl is an end-to-end modular software suite for vectorized atmospheric radiative transfer calculations, based on the Matrix Operator Method.", 
+    "license": "other-open", 
+    "title": "vSmartMOM.jl: an Open-Source Julia Package for Atmospheric Radiative Transfer and Remote Sensing Tools",
+    "version": "v1.0.1", 
+    "upload_type": "software", 
+    "publication_date": "2022-11-28", 
+    "creators": [
+        {
+            "orcid": "0000-0003-0142-7367",
+            "affiliation": "California Institute of Technology",
+            "name": "Jeyaram, Rupesh"
+        },
+        {
+            "orcid": "0000-0003-0754-9154",
+            "affiliation": "NASA Jet Propulsion Laboratory",
+            "name": "Sanghavi, Suniti"
+        },
+        {
+            "orcid": "0000-0002-0546-5857",
+            "affiliation": "California Institute of Technology",
+            "name": "Frankenberg, Christian"
+        }
+    ], 
+    "access_right": "open", 
+    "keywords": ["Radiative Transfer", "Atmosphere", "Remote Sensing", "Absorption", "Scattering"]
+}

Project.toml

@@ -1,11 +1,13 @@
 name = "vSmartMOM"
 uuid = "7ba11eeb-0a61-4a04-a413-bf612cc2007e"
 authors = ["Rupesh Jeyaram <rjeyaram@caltech.edu> and contributors"]
-version = "0.5.0"
+version = "1.0.1"
 
 [deps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 CUDAKernels = "72cfdca4-0801-4ab0-bf6a-d52aa10adc57"
+CanopyOptics = "a18e34a6-5dbe-4f38-a44b-e5141852e7a7"
+ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
 DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DiffResults = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"
@@ -19,47 +21,60 @@ JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
+NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9"
-NetCDF_jll = "7243133f-43d8-5620-bbf4-c2c921802cf3"
+OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
+OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Polynomials = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
+QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
+UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
+UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+UnitfulEquivalences = "da9c4bc3-91c8-4f02-8a40-6b990d2a7e0c"
+WignerSymbols = "9f57e263-0b3d-5e2e-b1be-24f2bb48858b"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]
-CUDA = "3"
+CUDA = "3, 4"
 CUDAKernels = "0.2, 0.3"
-DataInterpolations = "3.6"
+
+DataInterpolations = "3.6, 4"
+DelimitedFiles = "1"
 DiffResults = "1.0"
 Distributions = "0.23, 0.24, 0.25"
 DocStringExtensions = "0.8, 0.9"
-FastGaussQuadrature = "0.4"
 ForwardDiff = "0.10"
+FastGaussQuadrature = "0.4, 0.5"
+
 InstrumentOperator = "0.1"
-Interpolations = "0.12, 0.13"
+Interpolations = "0.12, 0.13, 0.14"
 JLD2 = "0.1, 0.2, 0.3, 0.4"
 JSON = "0.21"
-KernelAbstractions = "0.6, 0.7"
-NCDatasets = "0.11"
-NNlib = "0.8"
+
+
+KernelAbstractions = "0.8, 0.9"
+NCDatasets = "0.11, 0.12"
+NNlib = "0.8, 0.9"
 NetCDF = "0.10, 0.11"
-NetCDF_jll = "400.701.400 - 400.702.400"
 Parameters = "0.12"
-Polynomials = "2"
+Polynomials = "2, 3"
 ProgressMeter = "1.3"
 SpecialFunctions = "2"
 StaticArrays = "1.2"
-StatsBase = "0.33"
+StatsBase = "0.33, 0.34"
 TimerOutputs = "0.5"
 YAML = "0.4"
-julia = "1.6, 1.7"
+julia = "1.7, 1.8"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -99,6 +99,4 @@ This project is being developed in the Christian Frankenberg and Paul Wennberg l
 
 ## Copyright Notice
 
-Apache 2.0 License
-
-Copyright 2022, by the California Institute of Technology. ALL RIGHTS RESERVED. United States Government Sponsorship acknowledged. Any commercial use must be negotiated with the Office of Technology Transfer at the California Institute of Technology. This software may be subject to U.S. export control laws. By accepting this software, the user agrees to comply with all applicable U.S. export laws and regulations. User has the responsibility to obtain export licenses, or other export authority as may be required before exporting such information to foreign countries or providing access to foreign persons.
+Apache 2.0 License; Copyright 2022, by the California Institute of Technology. United States Government Sponsorship acknowledged.

docs/src/pages/Absorption/Example.md

@@ -41,10 +41,12 @@ model_interp = make_interpolation_model(hitran_data, Voigt(), ν_grid, pressures
 ## STEP 3: Calculate the absorption cross section with the created model
 ## 
 
+# NOTE: Please replace the "model_*" in the following lines with whichever model option you prefer from Step 2
+
 # You can specify the wavelength grid, pressure, and temperature. 
 profile = absorption_cross_section(model_*, 6000:0.01:6400, 1000.1, 296.1)
 
 # You can obtain the derivatives of the cross-section by setting the autodiff parameter to true: 
-profile, derivs = absorption_cross_section(model, 6000:0.01:6400, 1000.1, 296.1, autodiff=true);
+profile, derivs = absorption_cross_section(model_*, 6000:0.01:6400, 1000.1, 296.1, autodiff=true);
 
 ```

docs/src/pages/tutorials/Tutorial_Scattering.jl

@@ -22,19 +22,19 @@ using Plots
 # Now, we define the aerosol size distribution and properties. We only support univariate
 # aerosols for now, but will add multivariate aerosols soon (we can use mixture models easily). 
 
-μ     = 0.3;             ## Log-normal median radius [μm]
-σ     = 2.0;             ## Log-normal stddev of radius
+rₘ    = 0.3;             ## median radius [μm]
+σ     = 2.0;             ## geometric stddev of radius
 nᵣ    = 1.3;             ## Real part of refractive index
 nᵢ    = 0.0;             ## Imag part of refractive index (sign changed, use only + here)
 r_max = 30.0;            ## Maximum radius [μm]
 nquad_radius  = 2500;    ## Number of quadrature points for integrating of size dist.
 
-## Create a Size Distribution (using Julia's Distributions package)
-size_distribution = LogNormal(log(μ), log(σ));
+## Create a Size Distribution (using Julia's Distributions package), note we have to take the natural log here
+size_distribution = LogNormal(log(rₘ), log(σ));
 
 #----------------------------------------------------------------------------
 
-# Create the aerosol
+# Create the aerosol with distribution and refractive index 
 aero = Aerosol(size_distribution, nᵣ, nᵢ)
 #----------------------------------------------------------------------------
 

myfile.txt

@@ -0,0 +1 @@
+0.523599    1.308997   0.000000     0.816923    -1.0000000.523599    1.308997   0.000000     0.816923    -1.000000

src/Absorption/compute_absorption_cross_section.jl

@@ -56,8 +56,10 @@ function compute_absorption_cross_section(
     grid_min, grid_max = wavelength_flag ? (nm_per_m /grid_max, nm_per_m/grid_min) : (grid_min, grid_max)
 
     # Interpolators from grid bounds to index values
-    grid_idx_interp_low  = LinearInterpolation(grid, 1:1:length(grid), extrapolation_bc=1)
-    grid_idx_interp_high = LinearInterpolation(grid, 1:1:length(grid), extrapolation_bc=length(grid))
+    if length(grid)>1
+        grid_idx_interp_low  = LinearInterpolation(grid, 1:1:length(grid), extrapolation_bc=1)
+        grid_idx_interp_high = LinearInterpolation(grid, 1:1:length(grid), extrapolation_bc=length(grid))
+    end
 
     # Temporary storage array for output of qoft!. Compiler/speed issues when returning value in qoft
     rate = zeros(eltype(temperature), 1)
@@ -99,13 +101,18 @@ function compute_absorption_cross_section(
 
             end
 
-            # Calculate index range that this ν impacts
-            ind_start = Int64(round(grid_idx_interp_low(ν - wing_cutoff)))
-            ind_stop  = Int64(round(grid_idx_interp_high(ν + wing_cutoff)))
-
-            # Create views from the result and grid arrays
-            result_view   = view(result, ind_start:ind_stop);
-            grid_view     = view(grid, ind_start:ind_stop);
+            if length(grid)>1
+                # Calculate index range that this ν impacts
+                ind_start = Int64(round(grid_idx_interp_low(ν - wing_cutoff)))
+                ind_stop  = Int64(round(grid_idx_interp_high(ν + wing_cutoff)))
+
+                # Create views from the result and grid arrays
+                result_view   = view(result, ind_start:ind_stop);
+                grid_view     = view(grid, ind_start:ind_stop);
+            else
+                result_view   = view(result, 1);
+                grid_view     = view(grid, 1);
+            end
 
             # Kernel for performing the lineshape calculation
             kernel! = line_shape!(device)

src/Absorption/make_model_helpers.jl

@@ -160,7 +160,10 @@ function make_interpolation_model(
     end
 
     # Perform the interpolation
-    itp = interpolate(cs_matrix, BSpline(Cubic(Line(OnGrid()))))
+    # BSpline(Cubic(Line(OnGrid())))
+    # BSpline(Quadratic(Line(OnGrid())))
+
+    itp = interpolate(cs_matrix,  (BSpline(Linear()),BSpline(Quadratic(Line(OnGrid()))),BSpline(Quadratic(Line(OnGrid())))))
 
     # Get the molecule and isotope numbers from the HitranTable
     mol = absco.mol