Source code for pymatgen.command_line.critic2_caller

This module implements an interface to the critic2 Bader analysis code.

For most Bader analysis purposes, users are referred to
pymatgen.command_line.bader_caller instead, this module is for advanced
usage requiring identification of critical points in the charge density.

This module depends on a compiled critic2 executable available in the path.
Please follow the instructions at
to compile.

New users are *strongly* encouraged to read the critic2 manual first.

In brief,
* critic2 searches for critical points in charge density
* a critical point can be one of four types: nucleus, bond, ring
or cage
* it does this by seeding locations for likely critical points
and then searching in these regions
* there are two lists of critical points in the output, a list
of non-equivalent points (with in-depth information about the
field at those points), and a full list of points generated
by the appropriate symmetry operations
* connectivity between these points is also provided when
appropriate (e.g. the two nucleus critical points linked to
 a bond critical point)
* critic2 can do many other things besides

If you use this module, please cite the following:

A. Otero-de-la-Roza, E. R. Johnson and V. Luaña,
Comput. Phys. Commun. 185, 1007-1018 (2014)

A. Otero-de-la-Roza, M. A. Blanco, A. Martín Pendás and
V. Luaña, Comput. Phys. Commun. 180, 157–166 (2009)

import os
import subprocess
import warnings
import numpy as np
import glob

from scipy.spatial import KDTree
from import Chgcar, VolumetricData
from import Potcar
from pymatgen.analysis.graphs import StructureGraph
from pymatgen.core.periodic_table import DummySpecie
from monty.os.path import which
from import requires
from monty.json import MSONable
from monty.serialization import loadfn
from monty.tempfile import ScratchDir
from enum import Enum

import logging

logger = logging.getLogger(__name__)

__author__ = "Matthew Horton"
__maintainer__ = "Matthew Horton"
__email__ = ""
__status__ = "Production"
__date__ = "July 2017"

[docs]class Critic2Caller: """ Class to call critic2 and store standard output for further processing. """ @requires( which("critic2"), "Critic2Caller requires the executable critic to be in the path. " "Please follow the instructions at", ) def __init__( self, structure, chgcar=None, chgcar_ref=None, user_input_settings=None, write_cml=False, write_json=True, zpsp=None, ): """ Run Critic2 in automatic mode on a supplied structure, charge density (chgcar) and reference charge density (chgcar_ref). The reason for a separate reference field is that in VASP, the CHGCAR charge density only contains valence electrons and may be missing substantial charge at nuclei leading to misleading results. Thus, a reference field is commonly constructed from the sum of AECCAR0 and AECCAR2 which is the total charge density, but then the valence charge density is used for the final analysis. If chgcar_ref is not supplied, chgcar will be used as the reference field. If chgcar is not supplied, the promolecular charge density will be used as the reference field -- this can often still give useful results if only topological information is wanted. User settings is a dictionary that can contain: * GRADEPS, float (field units), gradient norm threshold * CPEPS, float (Bohr units in crystals), minimum distance between critical points for them to be equivalent * NUCEPS, same as CPEPS but specifically for nucleus critical points (critic2 default is depedent on grid dimensions) * NUCEPSH, same as NUCEPS but specifically for hydrogen nuclei since associated charge density can be significantly displaced from hydrogen nucleus * EPSDEGEN, float (field units), discard critical point if any element of the diagonal of the Hessian is below this value, useful for discarding points in vacuum regions * DISCARD, float (field units), discard critical points with field value below this value, useful for discarding points in vacuum regions * SEED, list of strings, strategies for seeding points, default is ['WS 1', 'PAIR 10'] which seeds critical points by sub-dividing the Wigner-Seitz cell and between every atom pair closer than 10 Bohr, see critic2 manual for more options :param structure: Structure to analyze :param chgcar: Charge density to use for analysis. If None, will use promolecular density. Should be a Chgcar object or path (string). :param chgcar_ref: Reference charge density. If None, will use chgcar as reference. Should be a Chgcar object or path (string). :param user_input_settings (dict): as explained above :param write_cml (bool): Useful for debug, if True will write all critical points to a file 'table.cml' in the working directory useful for visualization :param write_json (bool): Whether to write out critical points and YT json. YT integration will be performed with this setting. :param zpsp (dict): Dict of element/symbol name to number of electrons (ZVAL in VASP pseudopotential), with which to properly augment core regions and calculate charge transfer. Optional. """ settings = {"CPEPS": 0.1, "SEED": ["WS", "PAIR DIST 10"]} if user_input_settings: settings.update(user_input_settings) # Load crystal structure input_script = ["crystal POSCAR"] # Load data to use as reference field if chgcar_ref: input_script += ["load ref.CHGCAR id chg_ref", "reference chg_ref"] # Load data to use for analysis if chgcar: input_script += ["load int.CHGCAR id chg_int", "integrable chg_int"] if zpsp: zpsp_str = " zpsp " + " ".join( ["{} {}".format(symbol, int(zval)) for symbol, zval in zpsp.items()] ) input_script[-2] += zpsp_str # Command to run automatic analysis auto = "auto " for k, v in settings.items(): if isinstance(v, list): for item in v: auto += "{} {} ".format(k, item) else: auto += "{} {} ".format(k, v) input_script += [auto] if write_cml: input_script += ["cpreport ../table.cml cell border graph"] if write_json: input_script += ["cpreport cpreport.json"] if write_json and chgcar: # requires gridded data to work input_script += ["yt"] input_script += ["yt JSON yt.json"] input_script = "\n".join(input_script) with ScratchDir(".") as temp_dir: os.chdir(temp_dir) with open("input_script.cri", "w") as f: f.write(input_script)"POSCAR") if chgcar and isinstance(chgcar, VolumetricData): chgcar.write_file("int.CHGCAR") elif chgcar: os.symlink(chgcar, "int.CHGCAR") if chgcar_ref and isinstance(chgcar_ref, VolumetricData): chgcar_ref.write_file("ref.CHGCAR") elif chgcar_ref: os.symlink(chgcar_ref, "ref.CHGCAR") args = ["critic2", "input_script.cri"] rs = subprocess.Popen( args, stdout=subprocess.PIPE, stdin=subprocess.PIPE, close_fds=True ) stdout, stderr = rs.communicate() stdout = stdout.decode() if stderr: stderr = stderr.decode() warnings.warn(stderr) if rs.returncode != 0: raise RuntimeError( "critic2 exited with return code {}: {}".format( rs.returncode, stdout ) ) self._stdout = stdout self._stderr = stderr if os.path.exists("cpreport.json"): cpreport = loadfn("cpreport.json") else: cpreport = None if os.path.exists("yt.json"): yt = loadfn("yt.json") else: yt = None self.output = Critic2Analysis( structure, stdout=stdout, stderr=stderr, cpreport=cpreport, yt=yt, zpsp=zpsp, )
[docs] @classmethod def from_path(cls, path, suffix="", zpsp=None): """ Convenience method to run critic2 analysis on a folder containing typical VASP output files. This method will: 1. Look for files CHGCAR, AECAR0, AECAR2, POTCAR or their gzipped counterparts. 2. If AECCAR* files are present, constructs a temporary reference file as AECCAR0 + AECCAR2. 3. Runs critic2 analysis twice: once for charge, and a second time for the charge difference (magnetization density). :param path: path to folder to search in :param suffix: specific suffix to look for (e.g. '.relax1' for 'CHGCAR.relax1.gz') :param zpsp: manually specify ZPSP if POTCAR not present :return: """ def _get_filepath(filename, warning, path=path, suffix=suffix): paths = glob.glob(os.path.join(path, filename + suffix + "*")) if not paths: warnings.warn(warning) return None if len(paths) > 1: # using reverse=True because, if multiple files are present, # they likely have suffixes 'static', 'relax', 'relax2', etc. # and this would give 'static' over 'relax2' over 'relax' # however, better to use 'suffix' kwarg to avoid this! paths.sort(reverse=True) warnings.warn( "Multiple files detected, using {}".format(os.path.basename(path)) ) path = paths[0] return path chgcar_path = _get_filepath("CHGCAR", "Could not find CHGCAR!") chgcar = Chgcar.from_file(chgcar_path) chgcar_ref = None if not zpsp: potcar_path = _get_filepath( "POTCAR", "Could not find POTCAR, will not be able to calculate charge transfer.", ) if potcar_path: potcar = Potcar.from_file(potcar_path) zpsp = {p.element: p.zval for p in potcar} if not zpsp: # try and get reference "all-electron-like" charge density if zpsp not present aeccar0_path = _get_filepath( "AECCAR0", "Could not find AECCAR0, interpret Bader results with caution.", ) aeccar0 = Chgcar.from_file(aeccar0_path) if aeccar0_path else None aeccar2_path = _get_filepath( "AECCAR2", "Could not find AECCAR2, interpret Bader results with caution.", ) aeccar2 = Chgcar.from_file(aeccar2_path) if aeccar2_path else None chgcar_ref = aeccar0.linear_add(aeccar2) if (aeccar0 and aeccar2) else None return cls(chgcar.structure, chgcar, chgcar_ref, zpsp=zpsp)
[docs]class CriticalPointType(Enum): """ Enum type for the different varieties of critical point. """ nucleus = "nucleus" # (3, -3) bond = "bond" # (3, -1) ring = "ring" # (3, 1) cage = "cage" # (3, 3) nnattr = "nnattr" # (3, -3), non-nuclear attractor
[docs]class CriticalPoint(MSONable): """ Access information about a critical point and the field values at that point. """ def __init__( self, index, type, frac_coords, point_group, multiplicity, field, field_gradient, coords=None, field_hessian=None, ): """ Class to characterise a critical point from a topological analysis of electron charge density. Note this class is usually associated with a Structure, so has information on multiplicity/point group symmetry. :param index: index of point :param type: type of point, given as a string :param coords: Cartesian co-ordinates in Angstroms :param frac_coords: fractional co-ordinates :param point_group: point group associated with critical point :param multiplicity: number of equivalent critical points :param field: value of field at point (f) :param field_gradient: gradient of field at point (grad f) :param field_hessian: hessian of field at point (del^2 f) """ self.index = index self._type = type self.coords = coords self.frac_coords = frac_coords self.point_group = point_group self.multiplicity = multiplicity self.field = field self.field_gradient = field_gradient self.field_hessian = field_hessian @property def type(self): """ Returns: Instance of CriticalPointType """ return CriticalPointType(self._type) def __str__(self): return "Critical Point: {} ({})".format(, self.frac_coords) @property def laplacian(self): """ Returns: The Laplacian of the field at the critical point """ return np.trace(self.field_hessian) @property def ellipticity(self): """ Most meaningful for bond critical points, can be physically interpreted as e.g. degree of pi-bonding in organic molecules. Consult literature for more information. Returns: The ellpiticity of the field at the critical point """ eig, _ = np.linalg.eig(self.field_hessian) eig.sort() return eig[0] / eig[1] - 1
[docs]class Critic2Analysis(MSONable): """ Class to process the standard output from critic2 into pymatgen-compatible objects. """ def __init__( self, structure, stdout=None, stderr=None, cpreport=None, yt=None, zpsp=None ): """ This class is used to store results from the Critic2Caller. To explore the bond graph, use the "structure_graph" method, which returns a user-friendly StructureGraph class with bonding information. By default, this returns a StructureGraph with edge weights as bond lengths, but can optionally return a graph with edge weights as any property supported by the `CriticalPoint` class, such as bond ellipticity. This class also provides an interface to explore just the non-symmetrically-equivalent critical points via the `critical_points` attribute, and also all critical points (via nodes dict) and connections between them (via edges dict). The user should be familiar with critic2 before trying to understand these. Indexes of nucleus critical points in the nodes dict are the same as the corresponding sites in structure, with indices of other critical points arbitrarily assigned. Only one of (stdout, cpreport) required, with cpreport preferred since this is a new, native JSON output from critic2. :param structure: associated Structure :param stdout: stdout from running critic2 in automatic mode :param stderr: stderr from running critic2 in automatic mode :param cpreport: json output from CPREPORT command :param yt: json output from YT command :param zpsp (dict): Dict of element/symbol name to number of electrons (ZVAL in VASP pseudopotential), with which to calculate charge transfer. Optional. """ self.structure = structure self._stdout = stdout self._stderr = stderr self._cpreport = cpreport self._yt = yt self._zpsp = zpsp self.nodes = {} self.edges = {} if yt: self.structure = self._annotate_structure_with_yt(yt, structure, zpsp) if cpreport: self._parse_cpreport(cpreport) elif stdout: self._parse_stdout(stdout) else: raise ValueError("One of cpreport or stdout required.") self._remap_indices()
[docs] def structure_graph(self, include_critical_points=("bond", "ring", "cage")): """ A StructureGraph object describing bonding information in the crystal. Args: include_critical_points: add DummySpecie for the critical points themselves, a list of "nucleus", "bond", "ring", "cage", set to None to disable Returns: a StructureGraph """ structure = self.structure.copy() point_idx_to_struct_idx = {} if include_critical_points: # atoms themselves don't have field information # so set to 0 for prop in ("ellipticity", "laplacian", "field"): structure.add_site_property(prop, [0] * len(structure)) for idx, node in self.nodes.items(): cp = self.critical_points[node["unique_idx"]] if cp.type.value in include_critical_points: specie = DummySpecie( "X{}cp".format(cp.type.value[0]), oxidation_state=None ) structure.append( specie, node["frac_coords"], properties={ "ellipticity": cp.ellipticity, "laplacian": cp.laplacian, "field": cp.field, }, ) point_idx_to_struct_idx[idx] = len(structure) - 1 edge_weight = "bond_length" edge_weight_units = "Å" sg = StructureGraph.with_empty_graph( structure, name="bonds", edge_weight_name=edge_weight, edge_weight_units=edge_weight_units, ) edges = self.edges.copy() idx_to_delete = [] # check for duplicate bonds for idx, edge in edges.items(): unique_idx = self.nodes[idx]["unique_idx"] # only check edges representing bonds, not rings if self.critical_points[unique_idx].type == if idx not in idx_to_delete: for idx2, edge2 in edges.items(): if idx != idx2 and edge == edge2: idx_to_delete.append(idx2) warnings.warn( "Duplicate edge detected, try re-running " "critic2 with custom parameters to fix this. " "Mostly harmless unless user is also " "interested in rings/cages." ) logger.debug( "Duplicate edge between points {} (unique point {})" "and {} ({}).".format( idx, self.nodes[idx]["unique_idx"], idx2, self.nodes[idx2]["unique_idx"], ) ) # and remove any duplicate bonds present for idx in idx_to_delete: del edges[idx] for idx, edge in edges.items(): unique_idx = self.nodes[idx]["unique_idx"] # only add edges representing bonds, not rings if self.critical_points[unique_idx].type == from_idx = edge["from_idx"] to_idx = edge["to_idx"] # have to also check bond is between nuclei if non-nuclear # attractors not in structure skip_bond = False if include_critical_points and "nnattr" not in include_critical_points: from_type = self.critical_points[ self.nodes[from_idx]["unique_idx"] ].type to_type = self.critical_points[ self.nodes[from_idx]["unique_idx"] ].type skip_bond = (from_type != CriticalPointType.nucleus) or ( to_type != CriticalPointType.nucleus ) if not skip_bond: from_lvec = edge["from_lvec"] to_lvec = edge["to_lvec"] relative_lvec = np.subtract(to_lvec, from_lvec) # for edge case of including nnattrs in bonding graph when other critical # points also included, indices may get mixed struct_from_idx = point_idx_to_struct_idx.get(from_idx, from_idx) struct_to_idx = point_idx_to_struct_idx.get(to_idx, to_idx) weight = self.structure.get_distance( struct_from_idx, struct_to_idx, jimage=relative_lvec ) crit_point = self.critical_points[unique_idx] edge_properties = { "field": crit_point.field, "laplacian": crit_point.laplacian, "ellipticity": crit_point.ellipticity, "frac_coords": self.nodes[idx]["frac_coords"], } sg.add_edge( struct_from_idx, struct_to_idx, from_jimage=from_lvec, to_jimage=to_lvec, weight=weight, edge_properties=edge_properties, ) return sg
[docs] def get_critical_point_for_site(self, n): """ Args: n: Site index n Returns: A CriticalPoint instance """ return self.critical_points[self.nodes[n]["unique_idx"]]
[docs] def get_volume_and_charge_for_site(self, n): """ Args: n: Site index n Returns: A dict containing "volume" and "charge" keys, or None if YT integration not performed """ if not self._node_values: return None return self._node_values[n]
def _parse_cpreport(self, cpreport): def get_type(signature: int, is_nucleus: bool): if signature == 3: return "cage" elif signature == 1: return "ring" elif signature == -1: return "bond" elif signature == -3: if is_nucleus: return "nucleus" else: return "nnattr" bohr_to_angstrom = 0.529177 self.critical_points = [ CriticalPoint( p["id"] - 1, get_type(p["signature"], p["is_nucleus"]), p["fractional_coordinates"], p["point_group"], p["multiplicity"], p["field"], p["gradient"], coords=[x * bohr_to_angstrom for x in p["cartesian_coordinates"]] if cpreport["units"] == "bohr" else None, field_hessian=p["hessian"], ) for p in cpreport["critical_points"]["nonequivalent_cps"] ] for idx, p in enumerate(cpreport["critical_points"]["cell_cps"]): self._add_node( idx=p["id"] - 1, unique_idx=p["nonequivalent_id"] - 1, frac_coords=p["fractional_coordinates"], ) if "attractors" in p: self._add_edge( idx=p["id"] - 1, from_idx=int(p["attractors"][0]["cell_id"]) - 1, from_lvec=p["attractors"][0]["lvec"], to_idx=int(p["attractors"][1]["cell_id"]) - 1, to_lvec=p["attractors"][1]["lvec"], ) def _remap_indices(self): """ Re-maps indices on self.nodes and self.edges such that node indices match that of structure, and then sorts self.nodes by index. """ # Order of nuclei provided by critic2 doesn't # necessarily match order of sites in Structure. # This is because critic2 performs a symmetrization step. # We perform a mapping from one to the other, # and re-index all nodes accordingly. node_mapping = {} # critic2_index:structure_index # ensure frac coords are in [0,1] range frac_coords = np.array(self.structure.frac_coords) % 1 kd = KDTree(frac_coords) node_mapping = {} for idx, node in self.nodes.items(): if ( self.critical_points[node["unique_idx"]].type == CriticalPointType.nucleus ): node_mapping[idx] = kd.query(node["frac_coords"])[1] if len(node_mapping) != len(self.structure): warnings.warn( "Check that all sites in input structure ({}) have " "been detected by critic2 ({}).".format( len(self.structure), len(node_mapping) ) ) self.nodes = { node_mapping.get(idx, idx): node for idx, node in self.nodes.items() } for edge in self.edges.values(): edge["from_idx"] = node_mapping.get(edge["from_idx"], edge["from_idx"]) edge["to_idx"] = node_mapping.get(edge["to_idx"], edge["to_idx"]) @staticmethod def _annotate_structure_with_yt(yt, structure, zpsp): volume_idx = None charge_idx = None for prop in yt["integration"]["properties"]: if prop["label"] == "Volume": volume_idx = prop["id"] - 1 # 1-indexed, change to 0 elif prop["label"] == "$chg_int": charge_idx = prop["id"] - 1 def get_volume_and_charge(nonequiv_idx): attractor = yt["integration"]["attractors"][nonequiv_idx - 1] if attractor["id"] != nonequiv_idx: raise ValueError( "List of attractors may be un-ordered (wanted id={}): {}".format( nonequiv_idx, attractor ) ) return ( attractor["integrals"][volume_idx], attractor["integrals"][charge_idx], ) volumes = [] charges = [] charge_transfer = [] for idx, site in enumerate(yt["structure"]["cell_atoms"]): if not np.allclose( structure[idx].frac_coords, site["fractional_coordinates"] ): raise IndexError( "Site in structure doesn't seem to match site in YT integration:\n{}\n{}".format( structure[idx], site ) ) volume, charge = get_volume_and_charge(site["nonequivalent_id"]) volumes.append(volume) charges.append(charge) if zpsp: if structure[idx].species_string in zpsp: charge_transfer.append(charge - zpsp[structure[idx].species_string]) else: raise ValueError( "ZPSP argument does not seem compatible with species in structure ({}): {}".format( structure[idx].species_string, zpsp ) ) structure = structure.copy() structure.add_site_property("bader_volume", volumes) structure.add_site_property("bader_charge", charges) if zpsp: if len(charge_transfer) != len(charges): warnings.warn( "Something went wrong calculating charge transfer: {}".format( charge_transfer ) ) else: structure.add_site_property("bader_charge_transfer", charge_transfer) return structure def _parse_stdout(self, stdout): warnings.warn( "Parsing critic2 standard output is deprecated and will not be maintained, " "please use the native JSON output in future." ) stdout = stdout.split("\n") # NOTE WE ARE USING 0-BASED INDEXING: # This is different from critic2 which # uses 1-based indexing, so all parsed # indices have 1 subtracted. # Parsing happens in two stages: # 1. We construct a list of unique critical points # (i.e. non-equivalent by the symmetry of the crystal) # and the properties of the field at those points # 2. We construct a list of nodes and edges describing # all critical points in the crystal # Steps 1. and 2. are essentially independent, except # that the critical points in 2. have a pointer to their # associated unique critical point in 1. so that more # information on that point can be retrieved if necessary. unique_critical_points = [] # parse unique critical points for i, line in enumerate(stdout): if "mult name f |grad| lap" in line: start_i = i + 1 elif "* Analysis of system bonds" in line: end_i = i - 2 # if start_i and end_i haven't been found, we # need to re-evaluate assumptions in this parser! for i, line in enumerate(stdout): if i >= start_i and i <= end_i: l = line.replace("(", "").replace(")", "").split() unique_idx = int(l[0]) - 1 point_group = l[1] # type = l[2] # type from definition of critical point e.g. (3, -3) critical_point_type = l[3] # type from name, e.g. nucleus frac_coords = [float(l[4]), float(l[5]), float(l[6])] multiplicity = float(l[7]) # name = float(l[8]) field = float(l[9]) field_gradient = float(l[10]) # laplacian = float(l[11]) point = CriticalPoint( unique_idx, critical_point_type, frac_coords, point_group, multiplicity, field, field_gradient, ) unique_critical_points.append(point) for i, line in enumerate(stdout): if "+ Critical point no." in line: unique_idx = int(line.split()[4]) - 1 elif "Hessian:" in line: l1 = list(map(float, stdout[i + 1].split())) l2 = list(map(float, stdout[i + 2].split())) l3 = list(map(float, stdout[i + 3].split())) hessian = [ [l1[0], l1[1], l1[2]], [l2[0], l2[1], l2[2]], [l3[0], l3[1], l3[2]], ] unique_critical_points[unique_idx].field_hessian = hessian self.critical_points = unique_critical_points # parse graph connecting critical points for i, line in enumerate(stdout): if "#cp ncp typ position " in line: start_i = i + 1 elif "* Attractor connectivity matrix" in line: end_i = i - 2 # if start_i and end_i haven't been found, we # need to re-evaluate assumptions in this parser! for i, line in enumerate(stdout): if i >= start_i and i <= end_i: l = line.replace("(", "").replace(")", "").split() idx = int(l[0]) - 1 unique_idx = int(l[1]) - 1 frac_coords = [float(l[3]), float(l[4]), float(l[5])] self._add_node(idx, unique_idx, frac_coords) if len(l) > 6: from_idx = int(l[6]) - 1 to_idx = int(l[10]) - 1 self._add_edge( idx, from_idx=from_idx, from_lvec=(int(l[7]), int(l[8]), int(l[9])), to_idx=to_idx, to_lvec=(int(l[11]), int(l[12]), int(l[13])), ) def _add_node(self, idx, unique_idx, frac_coords): """ Add information about a node describing a critical point. :param idx: index :param unique_idx: index of unique CriticalPoint, used to look up more information of point (field etc.) :param frac_coord: fractional co-ordinates of point :return: """ self.nodes[idx] = {"unique_idx": unique_idx, "frac_coords": frac_coords} def _add_edge(self, idx, from_idx, from_lvec, to_idx, to_lvec): """ Add information about an edge linking two critical points. This actually describes two edges: from_idx ------ idx ------ to_idx However, in practice, from_idx and to_idx will typically be atom nuclei, with the center node (idx) referring to a bond critical point. Thus, it will be more convenient to model this as a single edge linking nuclei with the properties of the bond critical point stored as an edge attribute. :param idx: index of node :param from_idx: from index of node :param from_lvec: vector of lattice image the from node is in as tuple of ints :param to_idx: to index of node :param to_lvec: vector of lattice image the to node is in as tuple of ints :return: """ self.edges[idx] = { "from_idx": from_idx, "from_lvec": from_lvec, "to_idx": to_idx, "to_lvec": to_lvec, }