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