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Added method of storing the manipulator history for MCMC. Closes #7 #8

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Added method of storing the manipulator history for MCMC. Closes #7 #8

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14 changes: 10 additions & 4 deletions GBOpt/GBMinimizer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@

import math
import shutil
import sys
import uuid
from collections.abc import Callable
from time import time
Expand Down Expand Up @@ -32,21 +31,25 @@ def mutate(self, local_random: np.random.default_rng, GB: GBMaker, manipulator:
:param GBManipulator: GBManipulator object to perform the mutation on.
:return: Atom positions after the mutation."""
choice_key = local_random.choice(self.choices_keys)
mutation = None
match choice_key:
case "insert_atoms":
new_system = manipulator.insert_atoms(
method="grid", num_to_insert=1)
mutation = "add1"

case "remove_atoms":
new_system = manipulator.remove_atoms(num_to_remove=1)
mutation = "remove1"

case "translate_right_grain":
dz = (GB.z_dim / GB.repeat_factor[1]
) * local_random.uniform(0, 1)
dy = (GB.z_dim / GB.repeat_factor[0]
) * local_random.uniform(0, 1)
new_system = manipulator.translate_right_grain(dy=dy, dz=dz)
return new_system
mutation = f"shift{dy:.8f}dy{dz:.8f}dz"
return mutation, new_system


class MonteCarloMinimizer:
Expand All @@ -66,7 +69,8 @@ def __init__(self, GB: GBMaker, gb_energy_func: Callable, choices: list, seed=ti
self.manipulator = GBManipulator(self.GB)
self.mutator = Mutator(choices, self.manipulator)
self.accepted_idx = [0] # Initial guess is accepted by definition
self.__operation_list__ = ["START"]
# The list of mutators, and whether or not they were accepted
self.operation_list = [["START", True]]
self.local_random = np.random.default_rng(seed)
self.manipulator.rng = self.local_random
self.GBE_vals = []
Expand Down Expand Up @@ -109,7 +113,7 @@ def run_MC(self, E_accept: float = 1e-1, max_steps: int = 50, E_tol: float = 1e-
prev_gbe = self.GBE_vals[-1]

# Generate a random mutation on the current GB atom structure
new_system = self.mutator.mutate(
mutation, new_system = self.mutator.mutate(
self.local_random, self.GB, self.manipulator)

# Evaluate the energy of this new structure and append it to the GBE values list
Expand All @@ -126,6 +130,7 @@ def run_MC(self, E_accept: float = 1e-1, max_steps: int = 50, E_tol: float = 1e-
0, 1) <= math.exp(-(new_gbe - prev_gbe) / T)

if accepted:
self.operation_list.append([mutation, True])
# Generate a new GB manipulator using the new structure from the dump file
self.manipulator = GBManipulator(
dump_file_name,
Expand All @@ -150,6 +155,7 @@ def run_MC(self, E_accept: float = 1e-1, max_steps: int = 50, E_tol: float = 1e-
break
min_gbe = new_gbe
else:
self.operation_list.append([mutation, False])
rejection_count += 1
# If too many structures are rejected back-to-back, we prematurely stop the MC iterations since we are stuck
if rejection_count > max_rejections:
Expand Down