code review fixes

data/lammps_input_example.lammps

@@ -16,7 +16,7 @@ mass 1 28.0855
 group Si type 1
 
 pair_style sw
-pair_coeff * * ../Si.sw Si
+pair_coeff * * data/si.sw Si
 
 velocity   all create ${T} 62177
 

data/run_lammps_example.sh

@@ -3,4 +3,4 @@
 TEMPERATURE=300
 BOX_SIZE=1
 
-lmp < data/lammps_input_example -v STEP 10 -v T $TEMPERATURE -v S $BOX_SIZE
+lmp < data/lammps_input_example.lammps -v STEP 10 -v T $TEMPERATURE -v S $BOX_SIZE

data/si.sw

@@ -0,0 +1,22 @@
+# Stillinger-Weber parameters for various elements and mixtures
+# multiple entries can be added to this file, LAMMPS reads the ones it needs
+# these entries are in LAMMPS "metal" units:
+#   epsilon = eV; sigma = Angstroms
+#   other quantities are unitless
+
+# format of a single entry (one or more lines):
+#   element 1, element 2, element 3, 
+#   epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
+
+# Here are the original parameters in metal units, for Silicon from:
+#
+# Stillinger and Weber,  Phys. Rev. B, v. 31, p. 5262, (1985)
+#
+# Parameters for 'dia' Si
+Si Si Si 2.1683  2.0951  1.80  21.0  1.20  -0.333333333333
+         7.049556277  0.6022245584  4.0  0.0 0.0
+#
+# Parameters for amorphous Si  with the modified SW potential
+#(R. L. C. Vink, G. T. Barkema, W. F. van der Weg et N. Mousseau, A semi-empirical potential for amorphous silicon, J. Non-Cryst. Sol. 282, 248-255 (2001))
+#Si Si Si 1.64833  2.0951  1.80  31.5  1.20  -0.333333333333
+#         7.049556277  0.6022245584  4.0  0.0 0.0