moving to new photolysis cross sections

Nicholaswogan · Sep 26, 2024 · afc1246 · afc1246
1 parent 0ca9109
commit afc1246
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Showing 21 changed files with 615 additions and 456 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,26 +2,8 @@
 .ipynb_checkpoints
 __pycache__
 *.so
-*.o
-Photo.run
-*.mod
+data
 build
-*.a
-a.out
-test.run
-*.dSYM
-.vscode
 
 
-src/Stringifor
-build_dir
-src/dependencies/lib
-src/dependencies/include
-src/dependencies/examples
-src/dependencies/cmake
-src/dependencies/modules
-
-julia_wrap_photochem.ipynb
-random.ipynb
-
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,6 +1,8 @@
 cmake_minimum_required(VERSION "3.14")
 cmake_policy(SET CMP0148 OLD)
-project(Photochem LANGUAGES Fortran C VERSION "0.5.6")
+
+project(Photochem LANGUAGES Fortran C VERSION "0.6.0")
+set(PHOTOCHEM_CLIMA_DATA_VERSION "0.2.0")
 
 include(FortranCInterface)
 FortranCInterface_VERIFY()

diff --git a/photochem/__init__.py b/photochem/__init__.py
@@ -2,6 +2,6 @@
 os.environ['OMP_NUM_THREADS'] = '1'
 
 from ._photochem import EvoAtmosphere, Atmosphere, PhotoException, __version__
+from photochem_clima_data import DATA_DIR
 
-zahnle_earth = os.path.dirname(os.path.realpath(__file__))+ \
-                '/data/reaction_mechanisms/zahnle_earth.yaml'
+zahnle_earth = DATA_DIR+'/reaction_mechanisms/zahnle_earth.yaml'
diff --git a/photochem/cython/Atmosphere.pyx b/photochem/cython/Atmosphere.pyx
@@ -50,7 +50,7 @@ cdef class Atmosphere:
     self._init_called = True
 
     if data_dir == None:
-      data_dir_ = os.path.dirname(os.path.realpath(__file__))+'/data'
+      data_dir_ = photochem_clima_data.DATA_DIR
     else:
       data_dir_ = data_dir
 

diff --git a/photochem/cython/EvoAtmosphere.pyx b/photochem/cython/EvoAtmosphere.pyx
@@ -51,7 +51,7 @@ cdef class EvoAtmosphere:
     self._init_called = True
 
     if data_dir == None:
-      data_dir_ = os.path.dirname(os.path.realpath(__file__))+'/data'
+      data_dir_ = photochem_clima_data.DATA_DIR
     else:
       data_dir_ = data_dir
 

diff --git a/photochem/cython/_photochem.pyx b/photochem/cython/_photochem.pyx
@@ -6,6 +6,7 @@ from cpython.object cimport PyObject_GenericSetAttr
 import numpy as np
 import ctypes as ct
 import os
+import photochem_clima_data
 
 DEF S_STR_LEN = 20;
 DEF M_STR_LEN = 100;

diff --git a/photochem/equilibrate.py b/photochem/equilibrate.py
@@ -1,7 +1,7 @@
 from ._equilibrate import ChemEquiAnalysis, EquilibrateException
 from ._equilibrate import __version__
 from .utils._format import FormatReactions_main, yaml, Loader, MyDumper
-import os
+from photochem_clima_data import DATA_DIR
 
 def generate_zahnle_earth_thermo(outfile='zahnle_earth_thermo.yaml'):
     """Generates a thermodynamic file for equilibrium solving that includes
@@ -13,7 +13,7 @@ def generate_zahnle_earth_thermo(outfile='zahnle_earth_thermo.yaml'):
         Name of the output file, by default 'zahnle_earth_thermo.yaml'
     """    
 
-    rx_folder = os.path.dirname(os.path.realpath(__file__))+'/data/reaction_mechanisms/'
+    rx_folder = DATA_DIR+'/reaction_mechanisms/'
 
     with open(rx_folder+'zahnle_earth.yaml','r') as f:
         dat = yaml.load(f, Loader=Loader)

diff --git a/src/dependencies/CMakeLists.txt b/src/dependencies/CMakeLists.txt
@@ -1,9 +1,9 @@
 
 CPMAddPackage(
   NAME futils
-  VERSION 0.1.11
+  VERSION 0.1.14
   GITHUB_REPOSITORY "Nicholaswogan/futils"
-  GIT_TAG "v0.1.11"
+  GIT_TAG "v0.1.14"
   EXCLUDE_FROM_ALL ON
 )
 
@@ -49,15 +49,15 @@ CPMAddPackage(
 
 CPMAddPackage(
   NAME clima 
-  VERSION 0.4.6
+  VERSION 0.5.0
   OPTIONS 
     "BUILD_EXECUTABLE OFF"
     "BUILD_WITH_OPENMP ${BUILD_WITH_OPENMP}"
     "SKBUILD ${SKBUILD}"
     "BUILD_PYTHON_CLIMA ${BUILD_PYTHON_PHOTOCHEM}"
     "PYTHON_CLIMA_DESTINATION photochem"
   GITHUB_REPOSITORY "Nicholaswogan/clima"
-  GIT_TAG "v0.4.6"
+  GIT_TAG "v0.5.0"
   EXCLUDE_FROM_ALL OFF
 )
 

diff --git a/src/evoatmosphere/photochem_evoatmosphere_rhs_climate.f90 b/src/evoatmosphere/photochem_evoatmosphere_rhs_climate.f90
@@ -153,7 +153,7 @@ function equilibrium_climate_equation(self, d, err) result(F_in)
     if (allocated(err)) return
 
     ! do raditative transfer
-    call self%rad%radiate(d%T_surf, d%T, d%P, d%densities, self%var%dz, d%pdensities, d%radii, err)
+    call self%rad%radiate(d%T_surf, d%T, d%P, d%densities, self%var%dz, d%pdensities, d%radii, err=err)
     if (allocated(err)) return
 
     ! compute the energy going into the atmosphere

diff --git a/src/input/photochem_input_after_read.f90 b/src/input/photochem_input_after_read.f90
@@ -221,25 +221,12 @@ module subroutine interp2xsdata(dat, var, err)
 
     character(:), allocatable, intent(out) :: err
 
-    integer :: i, j, k
-    real(dp) :: val(1), T_temp(1)
+    integer :: i, k
 
+    ! No temperature dependence, so we just copy over
     do k = 1, dat%nw
       do i = 1,dat%kj
-        if (dat%xs_data(i)%n_temps > 1) then
-          do j = 1,var%nz
-            T_temp(1) = var%temperature(j)
-
-            call interp(1, dat%xs_data(i)%n_temps, T_temp, dat%xs_data(i)%xs_temps, &
-                        log10(abs(dat%xs_data(i)%xs(:,k))+smaller_real), val)
-
-            var%xs_x_qy(j,i,k) = 10.0_dp**val(1)
-          enddo
-        else
-          do j = 1,var%nz
-            var%xs_x_qy(j,i,k) = abs(dat%xs_data(i)%xs(1,k))+smaller_real
-          enddo
-        endif
+        var%xs_x_qy(:,i,k) = abs(dat%photolysis_xs(i,k))+smaller_real
       enddo
     enddo