SYMBOL INDEX (169 symbols across 17 files)

FILE: scripts/sgdml_dataset_from_aims.py
  function read_reference_data (line 36) | def read_reference_data(f):  # noqa C901

FILE: scripts/sgdml_dataset_from_extxyz.py
  function read_nonstd_ext_xyz (line 46) | def read_nonstd_ext_xyz(f):
  function extract_info_from_extxyz (line 95) | def extract_info_from_extxyz(file_path):

FILE: scripts/sgdml_dataset_from_ipi.py
  function raw_input_float (line 36) | def raw_input_float(prompt):
  function read_concat_xyz (line 45) | def read_concat_xyz(f):
  function read_out_file (line 79) | def read_out_file(f, col):

FILE: setup.py
  function get_property (line 7) | def get_property(property, package):

FILE: sgdml/__init__.py
  class ColoredFormatter (line 45) | class ColoredFormatter(logging.Formatter):
    method __init__ (line 65) | def __init__(self, msg, use_color=True):
    method format (line 70) | def format(self, record):
  class ColoredLogger (line 95) | class ColoredLogger(logging.Logger):
    method __init__ (line 96) | def __init__(self, name):
    method done (line 117) | def done(self, msg, *args, **kwargs):

FILE: sgdml/cli.py
  class AssistantError (line 77) | class AssistantError(Exception):
  function _print_splash (line 81) | def _print_splash(max_memory, max_processes, use_torch):
  function _check_update (line 146) | def _check_update():
  function _print_billboard (line 168) | def _print_billboard():
  function _print_dataset_properties (line 223) | def _print_dataset_properties(dataset, title_str='Dataset properties'):
  function _print_task_properties_reduced (line 325) | def _print_task_properties_reduced(
  function _print_task_properties (line 349) | def _print_task_properties(task, title_str='Task properties'):
  function _print_model_properties (line 427) | def _print_model_properties(model, title_str='Model properties'):
  function _print_next_step (line 558) | def _print_next_step(
  function all (line 612) | def all(
  function create (line 745) | def create(  # noqa: C901
  function train (line 946) | def train(
  function _batch (line 1164) | def _batch(iterable, n=1):
  function _online_err (line 1170) | def _online_err(err, size, n, mae_n_sum, rmse_n_sum):
  function resume (line 1183) | def resume(
  function validate (line 1288) | def validate(
  function test (line 1327) | def test(
  function select (line 1797) | def select(model_dir, overwrite, model_file=None, command=None, **kwargs...
  function show (line 1940) | def show(file, command=None, **kwargs):
  function reset (line 1955) | def reset(command=None, **kwargs):
  function main (line 1979) | def main():

FILE: sgdml/get.py
  function download (line 44) | def download(command, file_name):
  function main (line 71) | def main():

FILE: sgdml/intf/ase_calc.py
  class SGDMLCalculator (line 37) | class SGDMLCalculator(Calculator):
    method __init__ (line 41) | def __init__(
    method calculate (line 93) | def calculate(self, atoms=None, *args, **kwargs):

FILE: sgdml/predict.py
  function share_array (line 65) | def share_array(arr_np):
  function _predict_wkr (line 84) | def _predict_wkr(
  class GDMLPredict (line 248) | class GDMLPredict(object):
    method __init__ (line 249) | def __init__(
    method __del__ (line 465) | def __del__(self):
    method set_R_desc (line 510) | def set_R_desc(self, R_desc):
    method set_R_d_desc (line 526) | def set_R_d_desc(self, R_d_desc):
    method set_alphas (line 551) | def set_alphas(self, alphas_F, alphas_E=None):
    method _set_num_workers (line 603) | def _set_num_workers(
    method _set_chunk_size (line 658) | def _set_chunk_size(self, chunk_size=None):
    method _set_batch_size (line 689) | def _set_batch_size(self, batch_size=None):  # deprecated
    method _set_bulk_mp (line 717) | def _set_bulk_mp(self, bulk_mp=False):
    method set_opt_num_workers_and_batch_size_fast (line 745) | def set_opt_num_workers_and_batch_size_fast(self, n_bulk=1, n_reps=1):...
    method prepare_parallel (line 770) | def prepare_parallel(
    method _save_cached_bmark_result (line 1044) | def _save_cached_bmark_result(self, n_bulk, num_workers, chunk_size, b...
    method _load_cached_bmark_result (line 1076) | def _load_cached_bmark_result(self, n_bulk):
    method get_GPU_batch (line 1129) | def get_GPU_batch(self):
    method predict (line 1146) | def predict(self, R=None, return_E=True):

FILE: sgdml/solvers/analytic.py
  class Analytic (line 37) | class Analytic(object):
    method __init__ (line 38) | def __init__(self, gdml_train, desc, callback=None):
    method solve (line 49) | def solve(self, task, R_desc, R_d_desc, tril_perms_lin, y):
    method est_memory_requirement (line 154) | def est_memory_requirement(n_train, n_atoms):

FILE: sgdml/solvers/iterative.py
  class CGRestartException (line 56) | class CGRestartException(Exception):
  class Iterative (line 60) | class Iterative(object):
    method __init__ (line 61) | def __init__(
    method _init_precon_operator (line 83) | def _init_precon_operator(
    method _init_kernel_operator (line 144) | def _init_kernel_operator(
    method _nystroem_cholesky_factor (line 208) | def _nystroem_cholesky_factor(
    method _lev_scores (line 353) | def _lev_scores(
    method inducing_pts_from_lev_scores (line 401) | def inducing_pts_from_lev_scores(self, lev_scores, N):
    method _cho_factor_stable (line 414) | def _cho_factor_stable(self, M, pre_reg=False, eps_mag_max=1):
    method solve (line 473) | def solve(
    method max_n_inducing_pts (line 828) | def max_n_inducing_pts(n_train, n_atoms, max_memory_bytes):
    method est_memory_requirement (line 847) | def est_memory_requirement(n_train, n_inducing_pts, n_atoms):

FILE: sgdml/torchtools.py
  function _next_batch_size (line 52) | def _next_batch_size(n_total, batch_size):
  class GDMLTorchAssemble (line 61) | class GDMLTorchAssemble(nn.Module):
    method __init__ (line 67) | def __init__(
    method _forward (line 110) | def _forward(
    method forward (line 343) | def forward(self, J_indx):
  class GDMLTorchPredict (line 395) | class GDMLTorchPredict(nn.Module):
    method __init__ (line 401) | def __init__(
    method get_n_perm_batches (line 595) | def get_n_perm_batches(self):
    method set_n_perm_batches (line 600) | def set_n_perm_batches(self, n_perm_batches):
    method apply_perms_to_obj (line 618) | def apply_perms_to_obj(self, xs, perm_idxs=None):
    method remove_perms_from_obj (line 631) | def remove_perms_from_obj(self, xs):
    method uncache_perms (line 637) | def uncache_perms(self):
    method cache_perms (line 651) | def cache_perms(self):
    method est_mem_requirement (line 667) | def est_mem_requirement(self, return_min=False):
    method set_R_d_desc (line 728) | def set_R_d_desc(self, R_d_desc):
    method set_alphas (line 760) | def set_alphas(self, alphas, alphas_E=None):
    method _forward (line 877) | def _forward(self, Rs_or_train_idxs, return_E=True):
    method forward (line 1048) | def forward(self, Rs_or_train_idxs, return_E=True):

FILE: sgdml/train.py
  function _share_array (line 75) | def _share_array(arr_np, typecode_or_type):
  function _assemble_kernel_mat_wkr (line 97) | def _assemble_kernel_mat_wkr(
  class GDMLTrain (line 305) | class GDMLTrain(object):
    method __init__ (line 306) | def __init__(self, max_memory=None, max_processes=None, use_torch=False):
    method __del__ (line 363) | def __del__(self):
    method create_task (line 370) | def create_task(
    method create_task_from_model (line 649) | def create_task_from_model(self, model, dataset):
    method create_model (line 727) | def create_model(
    method train (line 836) | def train(  # noqa: C901
    method _recov_int_const (line 1090) | def _recov_int_const(
    method _assemble_kernel_mat (line 1260) | def _assemble_kernel_mat(
    method draw_strat_sample (line 1537) | def draw_strat_sample(self, T, n, excl_idxs=None):

FILE: sgdml/utils/desc.py
  function _pbc_diff (line 44) | def _pbc_diff(diffs, lat_and_inv, use_torch=False):
  function _pdist (line 80) | def _pdist(r, lat_and_inv=None):
  function _squareform (line 113) | def _squareform(vec_or_mat):
  function _r_to_desc (line 139) | def _r_to_desc(r, pdist):
  function _r_to_d_desc (line 166) | def _r_to_d_desc(r, pdist, lat_and_inv=None):
  function _from_r (line 208) | def _from_r(r, lat_and_inv=None):
  class Desc (line 242) | class Desc(object):
    method __init__ (line 244) | def __init__(self, n_atoms, max_processes=None):
    method from_R (line 288) | def from_R(self, R, lat_and_inv=None, max_processes=None, callback=None):
    method d_desc_dot_vec (line 368) | def d_desc_dot_vec(self, R_d_desc, vecs, overwrite_vecs=False):
    method vec_dot_d_desc (line 388) | def vec_dot_d_desc(self, R_d_desc, vecs, out=None):
    method d_desc_from_comp (line 422) | def d_desc_from_comp(self, R_d_desc, out=None):
    method d_desc_to_comp (line 473) | def d_desc_to_comp(self, R_d_desc):
    method perm (line 510) | def perm(perm):

FILE: sgdml/utils/io.py
  function z_str_to_z (line 154) | def z_str_to_z(z_str):
  function z_to_z_str (line 158) | def z_to_z_str(z):
  function train_dir_name (line 162) | def train_dir_name(dataset, n_train, use_sym, use_E, use_E_cstr):
  function task_file_name (line 183) | def task_file_name(task):
  function model_file_name (line 192) | def model_file_name(task_or_model, is_extended=False):
  function dataset_md5 (line 208) | def dataset_md5(dataset):
  function read_xyz (line 238) | def read_xyz(file_path):
  function write_geometry (line 264) | def write_geometry(filename, r, z, comment_str=''):
  function generate_xyz_str (line 278) | def generate_xyz_str(r, z, e=None, f=None, lattice=None):
  function lattice_vec_to_par (line 303) | def lattice_vec_to_par(lat):
  function is_file_type (line 327) | def is_file_type(arg, type):
  function filter_file_type (line 414) | def filter_file_type(dir, type, md5_match=None):
  function is_valid_file_type (line 464) | def is_valid_file_type(arg_in):
  function is_dir_with_file_type (line 514) | def is_dir_with_file_type(arg, type, or_file=False):
  function is_task_dir_resumeable (line 572) | def is_task_dir_resumeable(
  function is_strict_pos_int (line 642) | def is_strict_pos_int(arg):
  function parse_list_or_range (line 667) | def parse_list_or_range(arg):

FILE: sgdml/utils/perm.py
  function share_array (line 48) | def share_array(arr_np, typecode):
  function _bipartite_match_wkr (line 53) | def _bipartite_match_wkr(i, n_train, same_z_cost):
  function bipartite_match (line 90) | def bipartite_match(R, z, lat_and_inv=None, max_processes=None, callback...
  function sync_perm_mat (line 238) | def sync_perm_mat(match_perms_all, match_cost, n_atoms, callback=None):
  function to_cycles (line 263) | def to_cycles(perm):
  function salvage_subgroup (line 289) | def salvage_subgroup(perms):
  function complete_sym_group (line 344) | def complete_sym_group(
  function find_perms (line 384) | def find_perms(R, z, lat_and_inv=None, callback=None, max_processes=None):
  function find_extra_perms (line 415) | def find_extra_perms(R, z, lat_and_inv=None, callback=None, max_processe...
  function find_frags (line 527) | def find_frags(r, z, lat_and_inv=None):
  function find_frag_perms (line 564) | def find_frag_perms(R, z, lat_and_inv=None, callback=None, max_processes...
  function _frag_perm_to_perm (line 759) | def _frag_perm_to_perm(n_atoms, frag_idxs, frag_perms):
  function find_perms_in_frag (line 774) | def find_perms_in_frag(R, z, frag_idxs, lat_and_inv=None, max_processes=...
  function find_perms_via_alignment (line 790) | def find_perms_via_alignment(
  function find_perms_via_reflection (line 917) | def find_perms_via_reflection(
  function print_perm_colors (line 967) | def print_perm_colors(perm, pts, plane_3idxs=None):
  function inv_perm (line 1035) | def inv_perm(perm):

FILE: sgdml/utils/ui.py
  function yes_or_no (line 39) | def yes_or_no(question):
  function callback (line 61) | def callback(
  function sec_callback (line 150) | def sec_callback(
  function color_str (line 189) | def color_str(str, fore_color=WHITE, back_color=BLACK, bold=False):
  function blink_str (line 203) | def blink_str(str):
  function unicode_str (line 208) | def unicode_str(s):
  function gen_memory_str (line 218) | def gen_memory_str(bytes):
  function gen_lattice_str (line 232) | def gen_lattice_str(lat):
  function str_plen (line 244) | def str_plen(str):
  function wrap_str (line 265) | def wrap_str(str, width=MAX_PRINT_WIDTH - LOG_LEVELNAME_WIDTH):
  function indent_str (line 297) | def indent_str(str, indent):
  function wrap_indent_str (line 318) | def wrap_indent_str(label, str, width=MAX_PRINT_WIDTH - LOG_LEVELNAME_WI...
  function merge_col_str (line 346) | def merge_col_str(
  function gen_mat_str (line 378) | def gen_mat_str(mat):
  function gen_range_str (line 434) | def gen_range_str(min, max):
  function print_step_title (line 457) | def print_step_title(title_str, sec_title_str='', underscore=True):
  function print_two_column_str (line 474) | def print_two_column_str(str, sec_str=''):
  function print_lattice (line 489) | def print_lattice(lat=None, inset=False):