ABC Simulator

.github/workflows/cont_int.yml

@@ -25,18 +25,7 @@ jobs:
       run: |
         export PYTHONPATH=$PYTHONPATH:$(pwd)
         conda activate t3_env
-        cd ..
-        git clone https://github.com/ReactionMechanismGenerator/ARC
-        cd ARC
-        export PYTHONPATH=$PYTHONPATH:$(pwd)
-        cd ..
-        git clone https://github.com/ReactionMechanismGenerator/RMG-Py
-        cd RMG-Py
-        export PYTHONPATH=$PYTHONPATH:$(pwd)
-        make
-        cd ..
-        git clone https://github.com/ReactionMechanismGenerator/RMG-database
-        cd T3
+        make install
         echo $(pwd)
         conda list
 

Makefile

@@ -4,6 +4,16 @@
 #
 ################################################################################
 
+install:
+	bash devtools/install_arc.sh
+	bash devtools/install_pyrms.sh
+
+install-arc:
+	bash devtools/install_arc.sh
+
+install-pyrms:
+	bash devtools/install_pyrms.sh
+
 test:
 	pytest -ra -vv
 

devtools/install_RMS_v032.jl

@@ -0,0 +1,3 @@
+# Install RMS v0.3.2
+import Pkg
+Pkg.add(Pkg.PackageSpec(url="https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl", rev="v0.3.2"))

devtools/install_arc.sh

@@ -0,0 +1,23 @@
+# Temporarily change directory to $HOME to install software
+pushd .
+
+cd ..
+# RMG-database
+git clone https://github.com/ReactionMechanismGenerator/RMG-database
+# RMG-Py
+git clone https://github.com/ReactionMechanismGenerator/RMG-Py
+cd RMG-Py
+export PYTHONPATH=$PYTHONPATH:$(pwd)
+echo "export PYTHONPATH=$PYTHONPATH:$(pwd)" >> ~/.bashrc
+# compile RMG
+make
+
+cd ..
+# ARC
+git clone https://github.com/ReactionMechanismGenerator/ARC
+cd ARC
+export PYTHONPATH=$PYTHONPATH:$(pwd)
+echo "export PYTHONPATH=$PYTHONPATH:$(pwd)" >> ~/.bashrc
+
+# Restore original directory
+popd || exit

devtools/install_pycall.jl

@@ -0,0 +1,3 @@
+# Install PyCall
+import Pkg
+Pkg.add("PyCall")

devtools/install_pyrms.sh

@@ -0,0 +1,21 @@
+# check that Python and Julia are being accessed from the t3_env
+echo checking which python...
+which python
+echo checking which julia...
+which julia
+
+echo linking python-jl to python...
+ln -sfn $(which python-jl) $(which python)
+
+echo installing PyCall...
+julia devtools/install_pycall.jl
+
+echo installing pyrms, RMS, and all required Julia packages...
+python -c "import pyrms; pyrms.install()"
+
+# the above line installs RMS v0.2.1
+# v0.3.2 is needed to use the latest SA features
+# once there is a functional package for v0.3.2, 
+# the line below can be deleted since pyrms.install() will pull the latest version
+echo installing RMS v0.3.2...
+julia devtools/install_RMS_v032.jl

docs/how_to.md

@@ -147,7 +147,15 @@ all_args (bool, optional):
 
 ## Writing simulation adapters
 
-Coming soon!
+T3 implements many common choices to simulate a chemical mechanism, such as using constant TP, UV,
+or HP batch reactors. To create a custom simulator for your needs, first add a new file to `T3/t3/simulate/`,
+which contains the new simulate adapter. The new class must inherit from the abstract adapter class in
+`T3/t3/simulate/adapter.py` and should implement the following methods: `set_up()`, `simulate()`, `get_sa_coefficients()`,
+and `get_idt_by_T()`. All simulate adapters must accept the same arguments; the currently implemented
+Cantera, RMG, and RMS adapters provide examples. Finally, register the adapter at the bottom of the file,
+and initialize the simulator by importing it in `T3/t3/simulate/__init__.py`. A more detailed coding example
+can be found in the tutorials section. Adding a test to `T3/tests/test_simulate_adapters/` is also recommended.
+We welcome pull-requests to incorporate new simulate adapters.
 
 
 ## Pre-QM, or: T3's iteration 0