slight modifications to distributed volcanism to ensure we aren't trying to write beyond the bounds of an array

Author: Nicholaswogan

PhotochemPy/PhotochemPy.py

@@ -406,8 +406,10 @@ def set_surfflux(self,spec,flx):
                 raise PhotochemError('Only long-lived species can have boundary conditions')
         except ValueError:
             raise PhotochemError('species not in the model')
-        if self.vars.lbound[ind] == 2 or self.vars.lbound[ind] == 3:
+        if self.vars.lbound[ind] == 2:
             self.vars.sgflux[ind] = flx
+        elif self.vars.lbound[ind] == 3:
+            self.vars.distflux[ind] = flx
         else:
             print('mbound set to',self.vars.lbound[ind],'so the flux will not change')
 

README.md

@@ -1,6 +1,6 @@
 
 # PhotochemPy [![Memcheck](https://img.shields.io/badge/memcheck-clean-green.svg?style=flat)]() [![Build Status](https://travis-ci.com/Nicholaswogan/PhotochemPy.svg?branch=main)](https://travis-ci.com/Nicholaswogan/PhotochemPy)
-PhotochemPy is a photochemical model of rocky planet's atmospheres. Given inputs, like the stellar UV flux, the atmospheric temperature structure, etc., this code will find the steady-state chemical composition of an atmosphere, or evolve atmospheres through time.
+PhotochemPy is a photochemical model of planet's atmospheres. Given inputs, like the stellar UV flux, the atmospheric temperature structure, etc., this code will find the steady-state chemical composition of an atmosphere, or evolve atmospheres through time.
 
 <!-- [![Documentation Status](https://readthedocs.org/projects/photochempy/badge/?version=latest)](https://photochempy.readthedocs.io/en/latest/?badge=latest) -->
 
@@ -9,22 +9,22 @@ PhotochemPy is a Python wrapper to Fortran source code. This makes the code very
 ## Installation
 
 **Requirements:**
-To install PhotochemPy, you must have the following installed on your system.
+- MacOS or any Linux OS.
 - `Python` (>3.6.0) with the `numpy` package. I suggest using [anaconda](https://www.anaconda.com/) to install these regardless of your operating system.
-- A Fortran and C compiler. I suggest the GNU compiler collection, version >9 (includes `gfortran`, `gcc`, etc.). If you are using a Mac, install it with Homebrew: `brew install gcc`. For other operating systems [follow this GNU installation guide](https://gcc.gnu.org/install/binaries.html).
+- A Fortran and C compiler (any should work). I suggest the GNU compiler collection (includes `gfortran`, `gcc`, etc.). If you are using a Mac, install it with Homebrew: `brew install gcc`.
 
 **Python Module:** After satisfying the requirements, then follow these setups to install PhotochemPy
 
 - Clone or download the github repository [`https://github.com/Nicholaswogan/PhotochemPy`](https://github.com/Nicholaswogan/PhotochemPy)
 - Navigate to the root directory of PhotochemPy, then install with `python -m pip install .`
 
-**Fortran source:** If you prefer to use the code exclusively in Fortran, that is OK too. You can build `libphotochem` with CMake. Download or clone this respository, then from the root directory of the repository run
+**Fortran library:** If you prefer to use the code exclusively in Fortran, that is OK too. You can build `libphotochem` with CMake. Download or clone this respository, then from the root directory of the repository run
 
 ```sh
 mkdir build
 cd build
 cmake ..
-make -j # -j builds in parallel
+make -j
 ```
 
 ## Examples/Tutorial

setup.py

@@ -9,7 +9,7 @@
     name="PhotochemPy",
     packages=['PhotochemPy'],
     python_requires='>3.6.0',
-    version="0.2.4",
+    version="0.2.5",
     license="MIT",
     install_requires=['numpy<=1.20','scipy'],
     author='Nicholas Wogan',

src/integrate.f90

@@ -447,8 +447,8 @@ subroutine integrate(nsteps,converged,err)
 !     height index (-1 given the staggered grid)
 !     the 1 in the second postion tells minloc to return a scalar
           jdisth=minloc(Z,1, Z .ge. disth)-1
-          if (disth.lt.z(1)) then
-            jdisth = 1
+          if (jdisth < 2) then
+            jdisth = 2
           endif
 
           ZTOP=Z(jdisth)-Z(1)

src/right_hand_side.f90

@@ -410,6 +410,9 @@ subroutine right_hand_side(usol_flat,rhs,neq, err)
 !     height index (-1 given the staggered grid)
 !     the 1 in the second postion tells minloc to return a scalar
         jdisth=minloc(Z,1, Z .ge. disth)-1
+        if (jdisth < 2) then
+          jdisth = 2
+        endif
 
         ZTOP=Z(jdisth)-Z(1)
         ZTOP1=Z(jdisth)+0.5*DZ(jdistH)