def test_glosim_molecules():
is_pass = True
# check if the same molecules give global similarity of around 1
from ase.collections import g2
myAlphas, myBetas = soaplite.genBasis.getBasisFunc(10.0, 5)
for molname in g2.names:
atoms = molecule(molname)
local_a = soaplite.get_soap_structure(atoms,
myAlphas,
myBetas,
rCut=10.0,
NradBas=5,
Lmax=5,
crossOver=True)
envkernel = compute_envkernel(local_a, local_a)
glosim = rematch_entry(envkernel, gamma=0.01)
if (0.99 < glosim < 1.01):
pass
else:
is_pass = False
# check randomly a few combinations of molecules, just for no errors
all_atomtypes = [1, 6, 7, 8]
for molname1 in g2.names:
for molname2 in g2.names:
if np.random.rand(1, 1) < 0.99:
continue
atoms1 = molecule(molname1)
atoms2 = molecule(molname2)
local_a = soaplite.get_soap_structure(atoms1,
myAlphas,
myBetas,
rCut=10.0,
NradBas=5,
Lmax=5,
crossOver=True,
all_atomtypes=all_atomtypes)
local_b = soaplite.get_soap_structure(atoms2,
myAlphas,
myBetas,
rCut=10.0,
NradBas=5,
Lmax=5,
crossOver=True,
all_atomtypes=all_atomtypes)
envkernel = compute_envkernel(local_a, local_b)
glosim = rematch_entry(envkernel, gamma=0.01)
#print(glosim)
return is_pass
from soaplite import get_soap_structure
from soaplite import getBasisFunc
from ase.build import molecule
atoms = molecule('CO2')
a,b = getBasisFunc(5.0, 10)
x = get_soap_structure(atoms, a, b)
print(x.shape)
print(x)
start = time.time()
x = soaplite.get_soap_locals(atoms,
Hpos,
myAlphas,
myBetas,
rCut=10.0,
NradBas=5,
Lmax=5,
crossOver=True)
endTime = time.time()
totalTime = endTime - start
print("Soap ran in seconds:", totalTime)
np.savetxt('au40cu40H.txt', x)
#-------------- run local chemical environments on each atom ----------------
start = time.time()
y = soaplite.get_soap_structure(atoms,
myAlphas,
myBetas,
rCut=10.0,
NradBas=5,
Lmax=5,
crossOver=True)
endTime = time.time()
totalTime = endTime - start
print("Soap ran in seconds:", totalTime)
np.savetxt('structure_test.txt', y)
#------------ Check Results in *txt files --------------------------------
#------------ Make sure that rCut and N_max are the same across all calculations
0.95 * (1 + math.cos(76 / 180 * math.pi)),
0.95 * math.sin(76 / 180 * math.pi), 0.0
]],
symbols=["H", "O", "H"],
)
# Test the GTO basis
myAlphas, myBetas = genBasis.getBasisFunc(10.0, 5)
atoms = orig_atoms.copy()
features = soaplite.get_soap_structure(atoms,
myAlphas,
myBetas,
rCut=10.0,
nMax=5,
Lmax=9,
crossOver=True)
for rotation in ['x', 'y', 'z']:
# print("rotating in", rotation)
atoms.rotate(45, rotation)
rot_features = soaplite.get_soap_structure(atoms,
myAlphas,
myBetas,
rCut=10.0,
nMax=5,
rCut=10.0,
nMax=5,
Lmax=6,
crossOver=True,
eta=1.5)
endTime = time.time()
totalTime = endTime - start
print("Soap ran in seconds:", totalTime)
np.savetxt('au40cu40H.txt', x)
#-------------- run local chemical environments on each atom ----------------
start = time.time()
y = soaplite.get_soap_structure(atoms,
myAlphas,
myBetas,
rCut=10.0,
nMax=5,
Lmax=6,
crossOver=True,
eta=1.5)
endTime = time.time()
totalTime = endTime - start
print("Soap ran in seconds:", totalTime)
np.savetxt('structure_test.txt', y)
#-------------- one point----------------
Hpos = [[0, 0, 0]]
atoms = ase.io.read("onePoint.xyz")
start = time.time()
y = soaplite.get_soap_locals(atoms,
Hpos,
myAlphas,
import soaplite
import datetime
import ase
import numpy as np
from soaplite import genBasis
from numpy import genfromtxt
import time
x = []
#-------------- Define Structure ------------------------------------
for i in range(2,13):
myAlphas, myBetas = genBasis.getBasisFunc(5.0, i) # input:(rCut, NradBas)
atoms1 = ase.io.read("Structs/h2o.xyz")
atoms2 = ase.io.read('Structs/h2oDiff.xyz')
#-------------- set Basis Function (rCut--soft, N_max) Environment ----------------
#-------------- run local chemical environments on each atom ----------------
#start = time.time()
y1 = soaplite.get_soap_structure(atoms1, myAlphas, myBetas, rCut=5.0, NradBas=i, Lmax=9,crossOver=True)
y2 = soaplite.get_soap_structure(atoms2, myAlphas, myBetas, rCut=5.0, NradBas=i, Lmax=9,crossOver=True)
#endTime = time.time()
#totalTime = endTime - start
print(np.sum((y1 - y2)**2, axis=1)[2])
#print("Soap ran in seconds:", totalTime)
#np.savetxt('structure_test.txt',y)
#------------ Check Results in *txt files --------------------------------
#------------ Make sure that rCut and N_max are the same across all calculations
my_alphas, my_betas = getBasisFunc(r_cut, n_max)
#--------- Get local chemical environments for each defined position -----------
x = get_soap_locals(atoms,
hpos,
my_alphas,
my_betas,
rCut=r_cut,
NradBas=n_max,
Lmax=l_max,
crossOver=True)
xs = get_soap_structure(atoms,
my_alphas,
my_betas,
rCut=r_cut,
NradBas=n_max,
Lmax=l_max,
crossOver=True)
# xps = get_periodic_soap_structure(atoms,
#
# my_alphas,
# my_betas,
# rCut=r_cut,
# NradBas=n_max,
# Lmax=l_max,
# crossOver=True)
# xp = get_periodic_soap_locals(atoms,
# hpos,
# my_alphas,
# my_betas,
#print(glosim)
return is_pass
if __name__ == "__main__":
print("Start")
myAlphas, myBetas = soaplite.genBasis.getBasisFunc(
10.0, 5) # input:(rCut, NradBas)
A = molecule('H2O')
B = molecule('H2O2')
local_a = soaplite.get_soap_structure(A,
myAlphas,
myBetas,
rCut=10.0,
NradBas=5,
Lmax=5,
crossOver=True)
local_b = soaplite.get_soap_structure(B,
myAlphas,
myBetas,
rCut=10.0,
NradBas=5,
Lmax=5,
crossOver=True)
envkernel = compute_envkernel(local_a, local_b)
glosim = rematch_entry(envkernel, gamma=0.01)
atoms = ase.io.read("Structs/au40cu40.xyz")
#-------------- Define Position of Local Environment ----------------
#Hpos = [[1.0,2.0,3.0],[4.0,5.0,6.0],[7.0,8.0,9.0],[10.0,11.0,12.0]]
#Hpos = genfromtxt('Structs/mos2H.xyz').tolist()
Hpos = genfromtxt('Structs/au40cu40H.dat').tolist()
#-------------- set Basis Function (rCut--soft, N_max) Environment ----------------
myAlphas, myBetas = genBasis.getBasisFunc(10.0, 5)
print("hello")
#-------------- run local chemical environments on each atom ----------------
features = soaplite.get_soap_structure(atoms,
myAlphas,
myBetas,
rCut=10.0,
NradBas=5,
Lmax=9,
crossOver=True)
orig_atoms = atoms.copy()
# rotation check
for rotation in ['x', 'y', 'z']:
print("rotating in", rotation)
atoms.rotate(45, rotation)
rot_features = soaplite.get_soap_structure(atoms,
myAlphas,
myBetas,
rCut=10.0,
NradBas=5,
Lmax=9,
crossOver=True)