def getDemEnergies(self):
reshapedcoords = np.reshape(self.coords, (len(self.coords) // 3, 3, 3))
listenergies = h2o_pot.calc_hoh_pot(reshapedcoords,
len(self.coords) // 3)
self.energies = np.add.reduceat(
listenergies, np.arange(0, len(listenergies),
self.watersperwalker))
def getDemEnergies(coords):
reshapedcoords = np.reshape(coords, (len(coords) // 3, 3, 3))
listenergies = h2o_pot.calc_hoh_pot(reshapedcoords,
len(coords) // 3)
energies = np.add.reduceat(listenergies,
np.arange(0, len(listenergies), 2))
return energies
def getDemEnergies(coords,watersperwalker):
#check
#################
reshapedcoords = np.reshape(coords, (len(coords) // 3, 3, 3))
# listenergies = h2o_pot.calc_hoh_pot(reshapedcoords, len(coords) // 3)
if TryUncorrPot==True:
listenergies = h2o_uncorr_pot.calc_hoh_pot(reshapedcoords, len(coords) // 3)
else:
listenergies = h2o_pot.calc_hoh_pot(reshapedcoords, len(coords) // 3)
#numwalkersx18x3
#hex_pot.getpot(coords)
energies = np.add.reduceat(listenergies, np.arange(0, len(listenergies), watersperwalker))
return energies
def getDemEnergies(coords):
# energies=[]
#
# for a in np.arange(0,len(coords[:,0])/3):
#
# a=int(a*3)
# walkercoords=[]
# walkercoords.append(coords[a])
# walkercoords.append(coords[a+1])
# walkercoords.append(coords[a+2])
# # walkercoords.append([0,0,0])
# # walkercoords.append([1,0,0])
# # walkercoords.append([0,0,2])
# energies.append(h2o_pot.calc_hoh_pot([walkercoords],1))
reshapedcoords = np.reshape(coords, (len(coords) // 3, 3, 3))
energies = h2o_pot.calc_hoh_pot(reshapedcoords, len(coords) // 3)
return energies
def getDemEnergies(coords):
reshapedcoords = np.reshape(coords, (len(coords) // 3, 3, 3))
energies = h2o_pot.calc_hoh_pot(reshapedcoords, len(coords) // 3)
return energies
def doPropMakeHist(path, mer, identity):
timesteps = [1, 10]
for i in timesteps:
fullpath = path + f"/{i}/"
npzFilePaths = glob.glob(os.path.join(fullpath, '*.npz'))
for file in np.arange(0, 1):
# data=np.load(file)
# coords=data['coords']
coords, weights = concatenatenpz(fullpath)
initialcage = [[0.80559297, 1.82637417, 0.19044583],
[1.64546268, 1.33062728, 0.20230004],
[1.03131975, 2.74531261, 0.3303837],
[-0.86971419, -0.05280485, 1.64663647],
[-0.40947453, 0.75209702, 1.37618396],
[-1.70683682, -0.02424652, 1.15831962],
[0.65167739, -1.73597316, 0.2335045],
[0.05821864, -1.2362209, 0.84210027],
[0.569203, -2.6591634, 0.4706903],
[-0.51396268, 0.08861126, -1.76674358],
[-0.09074241, 0.82334616, -1.30525568],
[-0.09916254, -0.6895166, -1.37517223],
[2.81742948, -0.01780752, 0.18363679],
[2.20422291, -0.77223806, 0.20893524],
[3.38891525, -0.17263024, -0.5686021],
[-2.86669414, -0.14282213, -0.31653989],
[-2.17356321, -0.01889467, -0.98894102],
[-3.61843908, 0.36974668, -0.61083718]]
icoords = np.array(initialcage * (len(coords) // 18)) / 0.529177
# diffcoords=coords-icoords
reshapedcoords = np.reshape(coords, (len(coords) // (mer * 3),
(mer * 3), 3))
if mer == 6:
initialenergies = hex_pot.getpot(
reshapedcoords) / 627.5094740631 / (4.5563e-6)
elif mer == 1:
initialenergies = h2o_pot.calc_hoh_pot(
reshapedcoords,
len(coords) // 3) / (4.5563e-6)
# energies = np.add.reduceat(listenergies, np.arange(0, len(listenergies), 1))
# print(listenergies)
if mer == 6:
for atom in np.arange(0, len(coords) / 18):
actualcoord = atom * 18
countmove = 0
if atom % 10000 == 0:
print('10000')
for actualatom in np.arange(0, 3):
if countmove == 0:
# Oxygen
m = 15.9994 * amutoelectron
# elif countmove %3 == 1:
else:
# Hydrogen
m = 1.00794 * amutoelectron
# elif countmove %3 == 2:
# # Deuterium
# m = 2.014102 * amutoelectron
sigma = np.sqrt(i / m)
randomCoord = np.zeros((3))
for coordinate in np.arange(0, 3):
randomCoord[coordinate] += np.random.normal(
0, sigma)
coords[int(actualcoord + actualatom)] += randomCoord
countmove += 1
if mer == 1:
countmove = 0
for atom in np.arange(0, len(coords)):
countmove += 1
if countmove % 3 == 0:
# Oxygen
m = 15.9994 * amutoelectron
# elif countmove %3 == 1:
else:
# Hydrogen
m = 1.00794 * amutoelectron
# elif countmove %3 == 2:
# # Deuterium
# m = 2.014102 * amutoelectron
sigma = np.sqrt(i / m)
randomCoord = np.zeros((3))
for coordinate in np.arange(0, 3):
randomCoord[coordinate] += np.random.normal(0, sigma)
coords[atom] += randomCoord
reshapedcoords = np.reshape(coords, (len(coords) // (mer * 3),
(mer * 3), 3))
if mer == 6:
finalenergies = hex_pot.getpot(
reshapedcoords) / 627.5094740631 / (4.5563e-6)
elif mer == 1:
finalenergies = h2o_pot.calc_hoh_pot(
reshapedcoords,
len(coords) // 3) / (4.5563e-6)
diffenergies = finalenergies - initialenergies
print(np.average(diffenergies))
amp, xx = np.histogram(diffenergies,
range=(-5000, 5000),
bins=100,
density=True)
#
xx = 0.5 * (xx[1:] + xx[:-1])
if mer == 6:
plt.plot(xx, amp, label=f'{identity} Frozen Hex with dtau={i}')
elif mer == 1:
plt.plot(xx, amp, label=f'H2O with dtau={i}')
plt.xlabel("Efinal-Einitial(cm-1)")
plt.ylabel("Count")
plt.title(f'All Wavefunctions')
# plt.show()
plt.legend()
if mer == 6:
plt.savefig(f'Results/{identity}{i}.png')
elif mer == 1:
plt.savefig(f'Results/H2O{i}.png')
# plt.clf()
if mer == 1 and i == 10:
print('hi')
mer = 6
data = np.load('PotExpl/HOH/cage/walkers_20000.npz')
coords = data['coords'] / 0.529177
weights = data['weights']
initialenergies = hex_pot.getpot(coords) / 627.5094740631 / (
4.5563e-6) / 6
print(np.average(initialenergies, weights=weights))
# exit()
print(data)
coords = np.reshape(coords, (len(coords) * 18, 3))
countmove = 0
for atom in np.arange(0, len(coords)):
if countmove % 3 == 0:
# Oxygen
m = 15.9994 * amutoelectron
# elif countmove %3 == 1:
else:
# Hydrogen
m = 1.00794 * amutoelectron
# elif countmove %3 == 2:
# # Deuterium
# m = 2.014102 * amutoelectron
sigma = np.sqrt(i / m)
randomCoord = np.zeros((3))
for coordinate in np.arange(0, 3):
randomCoord[coordinate] += np.random.normal(0, sigma)
coords[atom] += randomCoord
countmove += 1
reshapedcoords = np.reshape(coords, (len(coords) // (6 * 3),
(6 * 3), 3))
finalenergies = hex_pot.getpot(
reshapedcoords) / 627.5094740631 / (4.5563e-6) / 6
print(np.average(finalenergies))
diffenergies = finalenergies - initialenergies
print(np.average(diffenergies))
amp, xx = np.histogram(diffenergies,
range=(-5000, 5000),
bins=100,
density=True)
#
xx = 0.5 * (xx[1:] + xx[:-1])
plt.plot(xx, amp, label=f'Hex with dtau=10')
plt.xlabel("Efinal-Einitial(cm-1)")
plt.ylabel("Count")
plt.title(f'All Wavefunctions')
# plt.show()
plt.legend()
plt.savefig(f'Results/Hex.png')
def water_pot(cds):
return calc_hoh_pot(cds, len(cds))