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Add 2+MB Kernel #241

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Oct 1, 2020
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Add 2+MB Kernel #241

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503b938
Add two+mb kernels
stevetorr Sep 14, 2020
b3bbf74
Black on mc and sc
stevetorr Sep 14, 2020
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289 changes: 285 additions & 4 deletions flare/kernels/mc_simple.py
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Original file line number Diff line number Diff line change
Expand Up @@ -622,6 +622,277 @@ def two_plus_three_efs_self(
return two_e + three_e, two_f + three_f, two_s + three_s


# -----------------------------------------------------------------------------
# two plus many body kernels
# -----------------------------------------------------------------------------


def two_plus_many_body_mc(
env1: AtomicEnvironment,
env2: AtomicEnvironment,
d1: int,
d2: int,
hyps,
cutoffs,
cutoff_func=cf.quadratic_cutoff,
):
"""2+many body kernel.

Args:
env1 (AtomicEnvironment): First local environment.
env2 (AtomicEnvironment): Second local environment.
d1 (int): Force component of the first environment.
d2 (int): Force component of the second environment.
hyps (np.ndarray): Hyperparameters of the kernel function (sig2b, ls2b,
sigmb, lsmb, sig_n).
cutoffs (np.ndarray): Two-element array containing the 2- and many-body
cutoffs.
cutoff_func (Callable): Cutoff function of the kernel.

Return:
float: Value of the 2+3+many-body kernel.
"""

sig2 = hyps[0]
ls2 = hyps[1]
sigm = hyps[2]
lsm = hyps[3]

r_cut_2 = cutoffs[0]

two_term = two_body_mc_jit(
env1.bond_array_2,
env1.ctype,
env1.etypes,
env2.bond_array_2,
env2.ctype,
env2.etypes,
d1,
d2,
sig2,
ls2,
r_cut_2,
cutoff_func,
)

many_term = many_body_mc_jit(
env1.q_array,
env2.q_array,
env1.q_neigh_array,
env2.q_neigh_array,
env1.q_neigh_grads,
env2.q_neigh_grads,
env1.ctype,
env2.ctype,
env1.etypes_mb,
env2.etypes_mb,
env1.unique_species,
env2.unique_species,
d1,
d2,
sigm,
lsm,
)

return two_term + many_term


def two_plus_many_body_mc_grad(
env1: AtomicEnvironment,
env2: AtomicEnvironment,
d1: int,
d2: int,
hyps,
cutoffs,
cutoff_func=cf.quadratic_cutoff,
):
"""2+many-body single-element kernel between two force components.

Args:
env1 (AtomicEnvironment): First local environment.
env2 (AtomicEnvironment): Second local environment.
d1 (int): Force component of the first environment.
d2 (int): Force component of the second environment.
hyps (np.ndarray): Hyperparameters of the kernel function (sig1, ls1,
sig2, ls2, sig3, ls3, sig_n).
cutoffs (np.ndarray): Two-element array containing the 2- and 3-body
cutoffs.
cutoff_func (Callable): Cutoff function of the kernel.

Return:
float: Value of the 2+3+many-body kernel.
"""

sig2 = hyps[0]
ls2 = hyps[1]
sigm = hyps[2]
lsm = hyps[3]

r_cut_2 = cutoffs[0]

kern2, grad2 = two_body_mc_grad_jit(
env1.bond_array_2,
env1.ctype,
env1.etypes,
env2.bond_array_2,
env2.ctype,
env2.etypes,
d1,
d2,
sig2,
ls2,
r_cut_2,
cutoff_func,
)

kern_many, gradm = many_body_mc_grad_jit(
env1.q_array,
env2.q_array,
env1.q_neigh_array,
env2.q_neigh_array,
env1.q_neigh_grads,
env2.q_neigh_grads,
env1.ctype,
env2.ctype,
env1.etypes_mb,
env2.etypes_mb,
env1.unique_species,
env2.unique_species,
d1,
d2,
sigm,
lsm,
)

return kern2 + kern_many, np.hstack([grad2, gradm])


def two_plus_many_body_mc_force_en(
env1: AtomicEnvironment,
env2: AtomicEnvironment,
d1: int,
hyps,
cutoffs,
cutoff_func=cf.quadratic_cutoff,
):
"""2+many-body multi-element kernel between two force and energy
components.

Args:
env1 (AtomicEnvironment): First local environment.
env2 (AtomicEnvironment): Second local environment.
d1 (int): Force component of the first environment.
hyps (np.ndarray): Hyperparameters of the kernel function (sig1, ls1,
sig2, ls2, sig3, ls3, sig_n).
cutoffs (np.ndarray): Two-element array containing the 2- and 3-body
cutoffs.
cutoff_func (Callable): Cutoff function of the kernel.

Return:
float: Value of the 2+3+many-body kernel.
"""

sig2 = hyps[0]
ls2 = hyps[1]
sigm = hyps[2]
lsm = hyps[3]

r_cut_2 = cutoffs[0]

two_term = (
two_body_mc_force_en_jit(
env1.bond_array_2,
env1.ctype,
env1.etypes,
env2.bond_array_2,
env2.ctype,
env2.etypes,
d1,
sig2,
ls2,
r_cut_2,
cutoff_func,
)
/ 2
)

many_term = many_body_mc_force_en_jit(
env1.q_array,
env2.q_array,
env1.q_neigh_array,
env1.q_neigh_grads,
env1.ctype,
env2.ctype,
env1.etypes_mb,
env1.unique_species,
env2.unique_species,
d1,
sigm,
lsm,
)

return two_term + many_term


def two_plus_many_body_mc_en(
env1: AtomicEnvironment,
env2: AtomicEnvironment,
hyps,
cutoffs,
cutoff_func=cf.quadratic_cutoff,
):
"""2+3+many-body single-element energy kernel.

Args:
env1 (AtomicEnvironment): First local environment.
env2 (AtomicEnvironment): Second local environment.
hyps (np.ndarray): Hyperparameters of the kernel function (sig2b ls2b,
sigmb, lsmb, sig_n).
cutoffs (np.ndarray): Two-element array containing the 2- and 3-body
cutoffs.
cutoff_func (Callable): Cutoff function of the kernel.

Return:
float: Value of the 2+3+many-body kernel.
"""

sig2 = hyps[0]
ls2 = hyps[1]
sigm = hyps[2]
lsm = hyps[3]

r_cut_2 = cutoffs[0]

two_term = (
two_body_mc_en_jit(
env1.bond_array_2,
env1.ctype,
env1.etypes,
env2.bond_array_2,
env2.ctype,
env2.etypes,
sig2,
ls2,
r_cut_2,
cutoff_func,
)
/ 4
)

many_term = many_body_mc_en_jit(
env1.q_array,
env2.q_array,
env1.ctype,
env2.ctype,
env1.unique_species,
env2.unique_species,
sigm,
lsm,
)

return two_term + many_term


# -----------------------------------------------------------------------------
# two plus three plus many body kernels
# -----------------------------------------------------------------------------
Expand Down Expand Up @@ -662,7 +933,6 @@ def two_plus_three_plus_many_body_mc(

r_cut_2 = cutoffs[0]
r_cut_3 = cutoffs[1]
r_cut_m = cutoffs[2]

two_term = two_body_mc_jit(
env1.bond_array_2,
Expand Down Expand Up @@ -757,7 +1027,6 @@ def two_plus_three_plus_many_body_mc_grad(

r_cut_2 = cutoffs[0]
r_cut_3 = cutoffs[1]
r_cut_m = cutoffs[2]

kern2, grad2 = two_body_mc_grad_jit(
env1.bond_array_2,
Expand Down Expand Up @@ -4068,7 +4337,6 @@ def many_body_mc_jit(
d2 (int): Force component of the second environment.
sig (float): many-body signal variance hyperparameter.
ls (float): many-body length scale hyperparameter.
r_cut (float): many-body cutoff radius.
cutoff_func (Callable): Cutoff function.

Return:
Expand Down Expand Up @@ -4209,7 +4477,6 @@ def many_body_mc_grad_jit(
list(set(species1).intersection(set(species2))), dtype=np.int8
)


for s in useful_species:
s1 = np.where(species1 == s)[0][0]
s2 = np.where(species2 == s)[0][0]
Expand Down Expand Up @@ -4452,4 +4719,18 @@ def many_body_mc_en_jit(q_array_1, q_array_2, c1, c2, species1, species2, sig, l
"2+3+many_efs_energy": "not implemented",
"2+3+many_efs_force": "not implemented",
"2+3+many_efs_self": "not implemented",
"two_plus_many_body": two_plus_many_body_mc,
"two_plus_many_body_grad": two_plus_many_body_mc_grad,
"two_plus_many_body_en": two_plus_many_body_mc_en,
"two_plus_many_body_force_en": two_plus_many_body_mc_force_en,
"two_plus_many_body_efs_self": "not implemented",
"two_plus_many_body_efs_force": "not implemented",
"two_plus_many_body_efs_energy": "not implemented",
"2+many": two_plus_many_body_mc,
"2+many_grad": two_plus_many_body_mc_grad,
"2+many_en": two_plus_many_body_mc_en,
"2+many_force_en": two_plus_many_body_mc_force_en,
"2+many_efs_self": "not implemented",
"2+many_efs_force": "not implemented",
"2+many_efs_energy": "not implemented",
}
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