completed lj parameter set and compute functions for melt example

examples/python/lj-melt-potential.py

@@ -4,25 +4,32 @@ class LAMMPSLJCutPotential(object):
 
     def __init__(self):
         self.pmap=dict()
-        # coefficients: epsilon, sigma
-        self.coeff = {'lj'  : {'lj'  : (1.0,1.0),
-                               'NULL': (0.0,1.0)},
-                      'NULL': {'lj'  : (0.0,1.0),
-                               'NULL': (0.0,1.0)}}
+        # set coeffs: eps, sig, 48*eps*sig**12, 24*eps*sig**6,
+        #                        4*eps*sig**12,  4*eps*sig**6
+        self.coeff = {'lj'  : {'lj'  : (1.0,1.0,48.0,24.0,4.0,4.0),
+                               'NULL': (0.0,1.0, 0.0, 0.0,0.0,0.0)},
+                      'NULL': {'lj'  : (0.0,1.0, 0.0, 0.0,0.0,0.0),
+                               'NULL': (0.0,1.0, 0.0, 0.0,0.0,0.0)}}
 
-    def map_coeff(self,type,name):
+    def map_coeff(self,name,type):
         if self.coeff.has_key(name):
-           print("map type %d to name %s" % (type,name))
            self.pmap[type] = name
         else:
-           print("cannot match atom type",name)
+           raise Exception("cannot match atom type %s" % name)
 
-    def compute_force(self,r,itype,jtype,factor_lj):
-        return 0.0
+    def compute_force(self,rsq,itype,jtype):
+        r2inv  = 1.0/rsq
+        r6inv  = r2inv*r2inv*r2inv
+        lj1 = self.coeff[self.pmap[itype]][self.pmap[jtype]][2]
+        lj2 = self.coeff[self.pmap[itype]][self.pmap[jtype]][3]
+        return (r6inv * (lj1*r6inv - lj2))
 
-    def compute_energy(self,r,itype,jtype,factor_lj):
-        return 0.0
+    def compute_energy(self,rsq,itype,jtype):
+        r2inv  = 1.0/rsq
+        r6inv  = r2inv*r2inv*r2inv
+        lj3 = self.coeff[self.pmap[itype]][self.pmap[jtype]][4]
+        lj4 = self.coeff[self.pmap[itype]][self.pmap[jtype]][5]
+        return (r6inv * (lj3*r6inv - lj4))
 
 lammps_pair_style = LAMMPSLJCutPotential()
-print ("lj-melt potential file loaded")