added citations

Author: mkphuthi

paper.md

@@ -62,7 +62,7 @@ different languages to change from one type of atomistic potential or atomic
 structure to another. This leads to poor reproducibility and inefficient
 transfer of code from one researcher to the next. In addition, there exists a
 zoo of tools and packages for atomic simulation with more being developed every
-day `[@walsh_open_2024]`. There is however no unifying framework that can
+day [@walsh_open_2024]. There is however no unifying framework that can
 encompass all these tools without significant software development effort.
 Significant effort should not be necessary because while the source of the
 fundamental outputs of atomistic potentials such as energy, forces etc. may
@@ -81,15 +81,15 @@ can be easily added to the library of provided asimmodules and iterated on.
 This will allow the community to develop a robust set of shareable simulation
 protocols. The flexibility of ASIMTools allows integration of any kind of
 simulation tools such as the heavily used Atomic Simulation Environment
-`[@larsen_atomic_2017]` pymatgen `[@ong_python_2013]`, LAMMPS
-`[@thompson_lammps_2022]` etc. with examples provided. With the asimmodules
+[@larsen_atomic_2017] pymatgen [@ong_python_2013], LAMMPS
+[@thompson_lammps_2022] etc. with examples provided. With the asimmodules
 defined, users only need to provide a set of inputs in the form of yaml files
 that define the parameters used for each simulation and are therefore a
 concrete record of used parameters. 
 
 # State of the Field
 There exist a number of popular workflow tools for atomistic simulations such
-as Aiida `[@huber_aiida_2020]`, Fireworks `[@jain_fireworks_2015]` and many
+as Aiida [@huber_aiida_2020], Fireworks [@jain_fireworks_2015] and many
 more. These tools provide frameworks for constructing complex workflows with
 different underlying principles. Some managers enforce strict rules that ensure
 that data obeys FAIR principles and emphasizes data provenance and
@@ -101,7 +101,7 @@ work in ASIMTools and with a few extra steps, the protocol can be made to
 support an arbitrary calculator and input structure.
 
 In some workflow managers, such as Atomic Simulation Recipes
-`[@gjerding_atomic_2021]`, once workflows are built, it can often be difficult
+[@gjerding_atomic_2021], once workflows are built, it can often be difficult
 to quickly change and iterate over key parameters such as the choice of
 atomistic calculator or structure as they are intrinsically built into the
 code. This is particularly challenging in an age where machine learning models