Commit cb6d8a38 by Francois Gygi

### modified to first fold atoms into the WS cell


git-svn-id: http://qboxcode.org/svn/qb/trunk@1416 cba15fb0-1239-40c8-b417-11db7ca47a34
parent 82b152b6
 ... @@ -12,6 +12,26 @@ hlist = [] ... @@ -12,6 +12,26 @@ hlist = [] def distance(a,b,sx,sy,sz): def distance(a,b,sx,sy,sz): return math.sqrt((a[3]-b[3]-sx)**2+(a[4]-b[4]-sy)**2+(a[5]-b[5]-sz)**2) return math.sqrt((a[3]-b[3]-sx)**2+(a[4]-b[4]-sy)**2+(a[5]-b[5]-sz)**2) def fold_in_ws(atom): x = atom[3] y = atom[4] z = atom[5] while x > 0.5*a_cell + 1.e-5: x -= a_cell while x < -0.5*a_cell - 1.e-5: x += a_cell while y > 0.5*b_cell + 1.e-5: y -= b_cell while y < -0.5*b_cell - 1.e-5: y += b_cell while z > 0.5*c_cell + 1.e-5: z -= c_cell while z < -0.5*c_cell - 1.e-5: z += c_cell atom[3] = x atom[4] = y atom[5] = z f = open(sys.argv[1]) f = open(sys.argv[1]) for line in f: for line in f: l = line.split() l = line.split() ... @@ -27,6 +47,11 @@ for line in f: ... @@ -27,6 +47,11 @@ for line in f: elif ( l[0] == "atom" ) & ( l[2] == "hydrogen" ): elif ( l[0] == "atom" ) & ( l[2] == "hydrogen" ): hlist.append([l[0],l[1],l[2],float(l[3]),float(l[4]),float(l[5])]) hlist.append([l[0],l[1],l[2],float(l[3]),float(l[4]),float(l[5])]) for o in olist: fold_in_ws(o) for h in hlist: fold_in_ws(h) for h in hlist: for h in hlist: # find nearest oxygen atom in olist # find nearest oxygen atom in olist mindist = 1.e10 mindist = 1.e10 ... ...
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