docs update

README.md

@@ -57,7 +57,7 @@ The image can be downloaded via:
 docker pull ghcr.io/wacl-york/atchem2:1.2.2
 ```
 
-When running the container, changes to the model (e.g. those made to configurations, constraints and mechanisms) should be in a folder that matches the AtChem2 directory structure. This folder is then mounted as a volume to the container with the name `/data_transfer/`. The mechanism to use is provided as a positional argument to the image and must be stored in `mcm`.
+When running the container, changes to the model (e.g. those made to configurations, constraints and mechanisms) should be in a folder that matches the AtChem2 directory structure. This folder is then mounted as a volume to the container with the name `/data_transfer/`. The mechanism to use is provided as a positional argument to the image e.g. `./model/my_mech.fac`.
 
 #### Example host file structure:
 ```

docker/entrypoint.sh

@@ -21,7 +21,7 @@
 # First it copies the /atchem/ directory that is created during the build to 
 # the home directory of the user running the container. This is for
 # compatibility with singularity, where the user running the container is not
-# root, and therfore cannot modify the model files in place. 
+# root, and therefore cannot modify the model files in place. 
 #
 # Next it moves the user configuration from /data_transfer/ and copies it into
 # the ~/atchem/ directory. This /data_transfer/ directory is created when the

docker/install.sh

@@ -24,7 +24,7 @@
 # and install_openlibm.sh) to install additional dependancies required to build
 # the model.
 # 
-# Next it produces the Makefile from the skeleton, and ammends the dependancy 
+# Next it produces the Makefile from the skeleton, and amends the dependancy 
 # paths.
 # 
 # Finally it does some housekeeping, updating the build_atchem2.sh to be able