def Potential(Psi, Ecut):
Ecut = Ecut / har2wave
V = CH5pot.mycalcpot(Psi.coords, N_0)
V_orig = np.array(V)
cuts = len(Ecut)
for i in range(cuts):
ind = np.argwhere(V_orig < Ecut[i])
Psi.V[i, :] = np.array(V)
Psi.V[i, ind] = Ecut[i]
Psi.Diff[i, :] = V_orig - Psi.V[i, :]
return Psi
def get_pot(coords):
V = CH5pot.mycalcpot(coords, len(coords))
return V
def V(whereUat): #-----------our potential function
v = np.zeros(len(whereUat))
emin = -40.65276470207075
v = CH5pot.mycalcpot(whereUat, len(whereUat))
v = np.array(v)
return v # must return a 1D numpy array
if timestep % 500 == 0:
print vref, ", ", timestep, ", ", len(whereUat)
# Descendant Weighting #
if timestep % 500 == 50 and timestep > 4000:
for i in whereUfrom:
ancestorPile.append(ancestors[i])
timestep += 1
ancestorPile = np.array(ancestorPile)
b = 0
convert = 0.52917725
v = np.zeros(len(ancestorPile))
v = CH5pot.mycalcpot(ancestorPile, len(ancestorPile))
# for item in ancestors: #-----------for jmol xyz file
# if mox == 1:
# fileXYZ.write("6\n")
# fileXYZ.write("CH5+ coordinates %f" % v[b])
# fileXYZ.write("%i\n" % b)
# fileXYZ.write("C %f %f %f\n" % (item[0,0]*convert, item[0,1]*convert, item[0,2]*convert))
# fileXYZ.write("H %f %f %f\n" % (item[1,0]*convert, item[1,1]*convert, item[1,2]*convert))
# fileXYZ.write("H %f %f %f\n" % (item[2,0]*convert, item[2,1]*convert, item[2,2]*convert))
# fileXYZ.write("H %f %f %f\n" % (item[3,0]*convert, item[3,1]*convert, item[3,2]*convert))
# fileXYZ.write("H %f %f %f\n" % (item[4,0]*convert, item[4,1]*convert, item[4,2]*convert))
# fileXYZ.write("H %f %f %f\n\n" % (item[5,0]*convert, item[5,1]*convert, item[5,2]*convert))
# b+=1
# else:
# print "6\n"
def Potential(Psi):
V = CH5pot.mycalcpot(Psi.coords, N_0)
Psi.V = np.array(V)
return Psi
convref = conavg(conpotentials, trueweights, n0)
energies.append(convref)
conpvalues = pcalc(conpotentials, convref, dtau)
trueweights = trueweights * conpvalues
conwalkers, trueweights = conFate(conwalkers, trueweights)
# Descendant Weighting #
# if timestep%500 == 50 and timestep > 4000:
# for i in whereUfrom:
# ancestorPile.append(ancestors[i])
timestep += 1
convert = 0.52917725
v = np.zeros(len(conwalkers))
v = CH5pot.mycalcpot(conwalkers, len(conwalkers))
b = 0
for item in conwalkers: # for jmol xyz file
if mox == 1:
fileXYZ.write("6\n")
fileXYZ.write("weight/potential/Bvalue %f %f %f" %
(trueweights[b], v[b], Bvalues[b]))
fileXYZ.write("%i\n" % b)
fileXYZ.write(
"C %f %f %f\n" %
(item[0, 0] * convert, item[0, 1] * convert, item[0, 2] * convert))
fileXYZ.write(
"H %f %f %f\n" %
(item[1, 0] * convert, item[1, 1] * convert, item[1, 2] * convert))
fileXYZ.write(
"H %f %f %f\n" %
def Potential(grid):
V = CH5pot.mycalcpot(grid, len(grid[:, 0, 0]))
V_final = np.diag(np.array(V))
return V_final
struct2 = np.array([[-0.000298856, -0.000017412, -0.000141136],
[1.022099482, 0.000046092, -0.361081497],
[0.000552766, 0.471961633, 1.102712489],
[-0.000044126, -0.471802245, 1.102854612],
[-0.606229037, -0.878215253, -0.263411220],
[-0.606365863, 0.878027160, -0.263097351]])*ang2bohr
struct3 = np.array([[-0.000110479, 0.000019746, 0.204885798],
[0.000032256, 0.000040871, -0.957945282],
[0.950920625, -0.000050787, 0.731398902],
[-0.950992179, -0.000020046, 0.731563788],
[0.000089457, -1.002878334, -0.339811499],
[0.000060320, 1.002888551, -0.339901698]])*ang2bohr
min_en = CH5pot.mycalcpot(np.array([coords_initial_min]*3), 3)*har2wave
a = CH5pot.mycalcpot(np.array([struct1]*3), 3)*har2wave
cs_en = CH5pot.mycalcpot(np.array([coords_initial_cs]*3), 3)*har2wave
b = CH5pot.mycalcpot(np.array([struct2]*3), 3)*har2wave
c2v_en = CH5pot.mycalcpot(np.array([coords_initial_c2v]*3), 3)*har2wave
c = CH5pot.mycalcpot(np.array([struct3]*3), 3)*har2wave
def grid(a, b, N, CH, coords_initial):
spacing = np.linspace(a, b, num=N)
if CH == 1:
new_coords = CoordinateSet(coords_initial, system=CartesianCoordinates3D)
new_coords = new_coords.convert(ZMatrixCoordinates, ordering=([[0, 0, 0, 0], [1, 0, 0, 0], [2, 0, 1, 0], [3, 0, 1, 2], [4, 0, 1, 2], [5, 0, 1, 2]]))
new_coords = new_coords.convert(CartesianCoordinates3D).coords
print(new_coords[1, 0]/ang2bohr)
[-5.4640011799588715E-017, -0.8923685824271653, 2.083855680290835],
[-1.145620108130841, -1.659539840225091, -0.4971351597887673],
[-1.145620108130841, 1.659539840225091, -0.4971351597887673]])
F = np.zeros((18, 18))
Ffirst = np.zeros(18)
row = 0
col = 0
track = 0
for z in xrange(0, N):
for y in xrange(0, 3):
shift = np.zeros((6, 3))
shift[z][y] = delta
shiftarr = [beg + shift, beg - shift]
Vfirst = CH5pot.mycalcpot(shiftarr, len(shiftarr))
Ffirst[track] = (1 / (2 * delta)) * (Vfirst[0] - Vfirst[1])
track += 1
for i in xrange(0, N):
for j in xrange(0, 3):
shift1 = np.zeros((6, 3))
shift1[i][j] = delta
for k in xrange(0, N):
for m in xrange(0, 3):
shift2 = np.zeros((6, 3))
shift2[k][m] = delta
shiftarray = [
def pot(Psi):
V = np.array(CH5pot.mycalcpot(Psi.coords, len(Psi.coords)))
Psi.V = V
return Psi