<commit_before>import sys
import numpy as np
import datetime
import time
from typing import List
import copy
import multiprocessing as mp
import concurrent.futures
from flare import struc, gp, env, qe_util, md, output


class ActiveGp:
    def __init__(self, position_list, force_list, species, cell,
                 gp: gp.GaussianProcess,
                 std_tolerance_factor: float = 1, par: bool=False,
                 init_atoms: List[int]=None,
                 calculate_energy=False, output_name='otf_run.out',
                 max_atoms_added=1, freeze_hyps=10, no_cpus=1):

        self.position_list = position_list
        self.force_list = force_list
        self.species = species
        self.cell = cell
        self.gp = gp
        self.std_tolerance = std_tolerance_factor
        self.dft_step = True
        self.freeze_hyps = freeze_hyps

        self.dt = 'N/A'
        self.number_of_steps = 'N/A'
        self.temperature = 'N/A'
        self.KE = 'N/A'
        self.velocities = 'N/A'

        positions = position_list[0]
        self.structure = struc.Structure(cell=cell, species=species,
                                         positions=positions)

        self.noa = self.structure.positions.shape[0]
        self.atom_list = list(range(self.noa))
        self.curr_step = 0

        self.max_atoms_added = max_atoms_added

        # initialize local energies
        if calculate_energy:
            self.local_energies = np.zeros(self.noa)<commit_msg>add dummy variables to fix output error<commit_after>import sys
import numpy as np
import datetime
import time
from typing import List
import copy
import multiprocessing as mp
import concurrent.futures
from flare import struc, gp, env, qe_util, md, output


class ActiveGp:
    def __init__(self, position_list, force_list, species, cell,
                 gp: gp.GaussianProcess,
                 std_tolerance_factor: float = 1, par: bool=False,
                 init_atoms: List[int]=None,
                 calculate_energy=False, output_name='otf_run.out',
                 max_atoms_added=1, freeze_hyps=10, no_cpus=1):

        self.position_list = position_list
        self.force_list = force_list
        self.species = species
        self.cell = cell
        self.gp = gp
        self.std_tolerance = std_tolerance_factor
        self.dft_step = True
        self.freeze_hyps = freeze_hyps

        positions = position_list[0]
        self.structure = struc.Structure(cell=cell, species=species,
                                         positions=positions)

        self.noa = self.structure.positions.shape[0]
        self.atom_list = list(range(self.noa))
        self.curr_step = 0

        self.dt = 1.0
        self.number_of_steps = 100
        self.temperature = 1.0
        self.KE = 1.0
        self.velocities = np.zeros((self.noa, 3))

        self.max_atoms_added = max_atoms_added

        # initialize local energies
        if calculate_energy:
            self.local_energies = np.zeros(self.noa)
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