Committer: ckloss <ckloss@fluid38.(none)>

On branch master
 Initial commit for lpp, version 2011-10-11

examples/group_energy.py

@@ -0,0 +1,107 @@
+# compute pairwise energy between 2 groups of atoms
+
+# Syntax: group_energy.py data.file dump.file1 dump.file2 ...
+# Author: Paul Crozier (Sandia)
+
+# return distance sq between 2 atoms with PBC
+
+def distance(box,x1,y1,z1,x2,y2,z2):
+  
+  delx = x2 - x1
+  dely = y2 - y1
+  delz = z2 - z1
+  
+  xprd = box[3] - box[0]
+  yprd = box[4] - box[1]
+  zprd = box[5] - box[2]
+
+  if abs(delx) > 0.5*xprd:
+    if delx < 0.0:
+      delx += xprd
+    else:
+      delx -= xprd
+  if abs(dely) > 0.5*yprd:
+    if dely < 0.0:
+      dely += yprd
+    else:
+      dely -= yprd
+  if abs(delz) > 0.5*zprd:
+    if delz < 0.0:
+      delz += zprd
+    else:
+      delz -= zprd
+      
+  distsq = delx*delx + dely*dely + delz*delz
+  return distsq
+
+# main script
+
+if len(argv) < 3:
+  raise StandardError,"group_energy.py data.file dump.file1 dump.file2 ..."
+
+dt = data(argv[1])				# data file
+q = dt.get("Atoms",4)
+
+files = ' '.join(argv[2:])		        # dump files
+d = dump(files,0)
+d.map(1,"id",2,"type",3,"x",4,"y",5,"z")
+
+p = pair("lj/charmm/coul/charmm")
+p.coeff(dt)
+
+cut1 = 8.0                                      # potential cutoffs
+cut2 = 10.0
+cut3 = 8.0
+cut4 = 10.0
+p.init(cut1,cut2,cut3,cut4)
+
+maxcut = cut1
+if cut2 > maxcut: maxcut = cut2
+if cut3 > maxcut: maxcut = cut3
+if cut4 > maxcut: maxcut = cut4
+maxcut_sq = maxcut*maxcut
+
+while 1:
+  time = d.next()
+  if time < 0: break
+  d.unscale(time)
+
+  box = (d.snaps[0].xlo,d.snaps[0].ylo,d.snaps[0].zlo,
+         d.snaps[0].xhi,d.snaps[0].yhi,d.snaps[0].zhi)
+  d.aselect.all(time)
+  d.aselect.test("$id >= 14306 and $id <= 14516",time)          # 1st group
+  id1,type1,x1,y1,z1 = d.vecs(time,"id","type","x","y","z")
+  d.aselect.all(time)                                           # 2nd group
+  d.aselect.test("$id >= 1 and $id <= 7243 or $id >= 7274 and $id <= 14283",
+                 time)
+  id2,type2,x2,y2,z2 = d.vecs(time,"id","type","x","y","z")
+  id1 = map(int,id1)
+  id2 = map(int,id2)
+  type1 = map(int,type1)
+  type2 = map(int,type2)
+  n1 = len(type1)
+  n2 = len(type2)
+  for i in xrange(n1): 
+    id1[i] -= 1
+    type1[i] -= 1
+  for i in xrange(n2): 
+    id2[i] -= 1
+    type2[i] -= 1
+
+  e_coul_sum = 0.0
+  e_vdwl_sum = 0.0
+  for i in xrange(n1):
+    typei = type1[i]
+    qi = q[id1[i]]
+    for j in xrange(n2):
+      rsq = distance(box,x1[i],y1[i],z1[i],x2[j],y2[j],z2[j])
+      if rsq < maxcut_sq:
+        eng_coul,eng_vdwl = p.single(rsq,typei,type2[j],qi,q[id2[j]])
+        e_coul_sum += eng_coul     
+        e_vdwl_sum += eng_vdwl    
+  print "eng_coul = %g at timestep %d" % (e_coul_sum,time)
+  print "eng_vdwl = %g at timestep %d" % (e_vdwl_sum,time)
+
+  d.tselect.none()
+  d.tselect.one(time)
+  d.delete()