fixup: readme example paths and citation order

README.md

@@ -117,15 +117,15 @@ Examples which only include mechanics and fracture are with `examples/mechanics`
 The first example is an elastic wave propagating through a cube from an initial Gaussian radial displacement profile from [1]. Assuming the build paths above, the example can be run with:
 
 ```
-./CabanaPD/build/install/bin/ElasticWave CabanaPD/examples/inputs/elastic_wave.json
+./CabanaPD/build/install/bin/ElasticWave CabanaPD/examples/mechanics/inputs/elastic_wave.json
 ```
 
 The second example is the Kalthoff-Winkler experiment [2], where an impactor
 causes crack propagation at an angle from two pre-notches on a steel plate. The
 example can be run with:
 
 ```
-./CabanaPD/build/install/bin/KalthoffWinkler CabanaPD/examples/inputs/kalthoff_winkler.json
+./CabanaPD/build/install/bin/KalthoffWinkler CabanaPD/examples/mechanics/inputs/kalthoff_winkler.json
 ```
 
 The third example is crack branching in a pre-notched soda-lime glass plate due to traction loading [3]. The example can be run with:
@@ -134,7 +134,7 @@ The third example is crack branching in a pre-notched soda-lime glass plate due
 ./CabanaPD/build/install/bin/CrackBranching CabanaPD/examples/mechanics/inputs/crack_branching.json
 ```
 
-The fourth example is a fragmenting cylinder due to internal pressure [6]. The example can be run with:
+The fourth example is a fragmenting cylinder due to internal pressure [4]. The example can be run with:
 
 ```
 ./CabanaPD/build/install/bin/FragmentingCylinder CabanaPD/examples/mechanics/inputs/fragmenting_cylinder.json
@@ -143,13 +143,13 @@ The fourth example is a fragmenting cylinder due to internal pressure [6]. The e
 ### Thermomechanics
 Examples which demonstrate temperature-dependent mechanics and fracture are with `examples/thermomechanics`.
 
-The first example is thermoelastic deformation in a homogeneous plate due to linear thermal loading [4]. The example can be run with:
+The first example is thermoelastic deformation in a homogeneous plate due to linear thermal loading [5]. The example can be run with:
 
 ```
 ./CabanaPD/build/install/bin/ThermalDeformation CabanaPD/examples/thermomechanics/thermal_deformation.json
 ```
 
-The second example is crack initiation and propagation in an alumina ceramic plate due to a thermal shock caused by water quenching [5]. The example can be run with:
+The second example is crack initiation and propagation in an alumina ceramic plate due to a thermal shock caused by water quenching [6]. The example can be run with:
 
 ```
 ./CabanaPD/build/install/bin/ThermalCrack CabanaPD/examples/thermomechanics/thermal_crack.json
@@ -169,11 +169,11 @@ Kunze, and L.W. Meyer, eds., Vol 1, DGM Informationsgesellschaft Verlag (1988)
 
 [3] F. Bobaru and G. Zhang, Why do cracks branch? A peridynamic investigation of dynamic brittle fracture, International Journal of Fracture 196 (2015): 59–98.
 
-[4] D. He, D. Huang, and D. Jiang, Modeling and studies of fracture in functionally graded materials under thermal shock loading using peridynamics, Theoretical and Applied Fracture Mechanics 111 (2021): 102852.
+[4] D.J. Littlewood, M.L. Parks, J.T. Foster, J.A. Mitchell, and P. Diehl, The peridigm meshfree peridynamics code, Journal of Peridynamics and Nonlocal Modeling 6 (2024): 118–148.  
 
-[5] C.P. Jiang, X.F. Wu, J. Li, F. Song, Y.F. Shao, X.H. Xu, and P. Yan, A study of the mechanism of formation and numerical simulations of crack patterns in ceramics subjected to thermal shock, Acta Materialia 60 (2012): 4540–4550.
+[5] D. He, D. Huang, and D. Jiang, Modeling and studies of fracture in functionally graded materials under thermal shock loading using peridynamics, Theoretical and Applied Fracture Mechanics 111 (2021): 102852.
 
-[6] D.J. Littlewood, M.L. Parks, J.T. Foster, J.A. Mitchell, and P. Diehl, The peridigm meshfree peridynamics code, Journal of Peridynamics and Nonlocal Modeling 6 (2024): 118–148.  
+[6] C.P. Jiang, X.F. Wu, J. Li, F. Song, Y.F. Shao, X.H. Xu, and P. Yan, A study of the mechanism of formation and numerical simulations of crack patterns in ceramics subjected to thermal shock, Acta Materialia 60 (2012): 4540–4550.
 
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