Source code for ase.calculators.lammpsrun

"""ASE calculator for the LAMMPS classical MD code"""
# (2011/03/29)
# Copyright (C) 2009 - 2011 Joerg Meyer,
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# Lesser General Public License for more details.
# You should have received a copy of the GNU Lesser General Public
# License along with this file; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301
# USA or see <>.

import os
import shlex
import shutil
import subprocess
import warnings
from re import IGNORECASE
from re import compile as re_compile
from tempfile import NamedTemporaryFile, mkdtemp
from tempfile import mktemp as uns_mktemp
from threading import Thread
from typing import Any, Dict

import numpy as np

from ase.calculators.calculator import Calculator, all_changes
from ase.calculators.lammps import (CALCULATION_END_MARK, Prism, convert,
from import atomic_masses, chemical_symbols
from import write_lammps_data
from import read_lammps_dump

__all__ = ["LAMMPS"]

[docs]class LAMMPS(Calculator): """LAMMPS ( calculator The environment variable :envvar:`ASE_LAMMPSRUN_COMMAND` must be defined to tell ASE how to call a LAMMPS binary. This should contain the path to the lammps binary, or more generally, a command line possibly also including an MPI-launcher command. For example (in a Bourne-shell compatible environment): .. code-block:: bash export ASE_LAMMPSRUN_COMMAND=/path/to/lmp_binary or possibly something similar to .. code-block:: bash export ASE_LAMMPSRUN_COMMAND="/path/to/mpirun --np 4 lmp_binary" Parameters ---------- files : list[str] List of files needed by LAMMPS. Typically a list of potential files. parameters : dict[str, Any] Dictionary of settings to be passed into the input file for calculation. specorder : list[str] Within LAAMPS, atoms are identified by an integer value starting from 1. This variable allows the user to define the order of the indices assigned to the atoms in the calculation, with the default if not given being alphabetical keep_tmp_files : bool, default: False Retain any temporary files created. Mostly useful for debugging. tmp_dir : str, default: None path/dirname (default None -> create automatically). Explicitly control where the calculator object should create its files. Using this option implies 'keep_tmp_files=True'. no_data_file : bool, default: False Controls whether an explicit data file will be used for feeding atom coordinates into lammps. Enable it to lessen the pressure on the (tmp) file system. THIS OPTION MIGHT BE UNRELIABLE FOR CERTAIN CORNER CASES (however, if it fails, you will notice...). keep_alive : bool, default: True When using LAMMPS as a spawned subprocess, keep the subprocess alive (but idling when unused) along with the calculator object. always_triclinic : bool, default: False Force LAMMPS to treat the cell as tilted, even if the cell is not tilted, by printing ``xy``, ``xz``, ``yz`` in the data file. reduce_cell : bool, default: False If True, reduce cell to have shorter lattice vectors. write_velocities : bool, default: False If True, forward ASE velocities to LAMMPS. verbose: bool, default: False If True, print additional debugging output to STDOUT. Examples -------- Provided that the respective potential file is in the working directory, one can simply run (note that LAMMPS needs to be compiled to work with EAM potentials) :: from ase import Atom, Atoms from import bulk from ase.calculators.lammpsrun import LAMMPS parameters = {'pair_style': 'eam/alloy', 'pair_coeff': ['* * NiAlH_jea.eam.alloy H Ni']} files = ['NiAlH_jea.eam.alloy'] Ni = bulk('Ni', cubic=True) H = Atom('H', position=Ni.cell.diagonal()/2) NiH = Ni + H lammps = LAMMPS(parameters=parameters, files=files) NiH.calc = lammps print("Energy ", NiH.get_potential_energy()) """ name = "lammpsrun" implemented_properties = ["energy", "free_energy", "forces", "stress", "energies"] # parameters to choose options in LAMMPSRUN ase_parameters: Dict[str, Any] = dict( specorder=None, atorder=True, always_triclinic=False, reduce_cell=False, keep_alive=True, keep_tmp_files=False, no_data_file=False, tmp_dir=None, files=[], # usually contains potential parameters verbose=False, write_velocities=False, binary_dump=True, # bool - use binary dump files (full # precision but long long ids are casted to # double) lammps_options="-echo log -screen none -log /dev/stdout", trajectory_out=None, # file object, if is not None the # trajectory will be saved in it ) # parameters forwarded to LAMMPS lammps_parameters = dict( boundary=None, # bounadry conditions styles units="metal", # str - Which units used; some potentials # require certain units atom_style="atomic", special_bonds=None, # potential informations pair_style="lj/cut 2.5", pair_coeff=["* * 1 1"], masses=None, pair_modify=None, # variables controlling the output thermo_args=[ "step", "temp", "press", "cpu", "pxx", "pyy", "pzz", "pxy", "pxz", "pyz", "ke", "pe", "etotal", "vol", "lx", "ly", "lz", "atoms", ], dump_properties=["id", "type", "x", "y", "z", "vx", "vy", "vz", "fx", "fy", "fz", ], dump_period=1, # period of system snapshot saving (in MD steps) ) default_parameters = dict(ase_parameters, **lammps_parameters) def __init__(self, label="lammps", **kwargs): super().__init__(label=label, **kwargs) self.prism = None self.calls = 0 self.forces = None # thermo_content contains data "written by" thermo_style. # It is a list of dictionaries, each dict (one for each line # printed by thermo_style) contains a mapping between each # custom_thermo_args-argument and the corresponding # value as printed by lammps. thermo_content will be # re-populated by the read_log method. self.thermo_content = [] if self.parameters['tmp_dir'] is not None: # If tmp_dir is pointing somewhere, don't remove stuff! self.parameters['keep_tmp_files'] = True self._lmp_handle = None # To handle the lmp process if self.parameters['tmp_dir'] is None: self.parameters['tmp_dir'] = mkdtemp(prefix="LAMMPS-") else: self.parameters['tmp_dir'] = os.path.realpath( self.parameters['tmp_dir']) if not os.path.isdir(self.parameters['tmp_dir']): os.mkdir(self.parameters['tmp_dir'], 0o755) for f in self.parameters['files']: shutil.copy( f, os.path.join(self.parameters['tmp_dir'], os.path.basename(f))) def get_lammps_command(self): cmd = self.parameters.get('command') if cmd is None: from ase.config import cfg envvar = f'ASE_{}_COMMAND' cmd = cfg.get(envvar) if cmd is None: # TODO deprecate and remove guesswork cmd = 'lammps' opts = self.parameters.get('lammps_options') if opts is not None: cmd = f'{cmd} {opts}' return cmd def clean(self, force=False): self._lmp_end() if not self.parameters['keep_tmp_files'] or force: shutil.rmtree(self.parameters['tmp_dir']) def check_state(self, atoms, tol=1.0e-10): # Transforming the unit cell to conform to LAMMPS' convention for # orientation (c.f. # results in some precision loss, so we use bit larger tolerance than # machine precision here. Note that there can also be precision loss # related to how many significant digits are specified for things in # the LAMMPS input file. return Calculator.check_state(self, atoms, tol) def calculate(self, atoms=None, properties=None, system_changes=None): if properties is None: properties = self.implemented_properties if system_changes is None: system_changes = all_changes Calculator.calculate(self, atoms, properties, system_changes) def _lmp_alive(self): # Return True if this calculator is currently handling a running # lammps process return self._lmp_handle and not isinstance( self._lmp_handle.poll(), int ) def _lmp_end(self): # Close lammps input and wait for lammps to end. Return process # return value if self._lmp_alive(): # !TODO: handle lammps error codes try: self._lmp_handle.communicate(timeout=5) except subprocess.TimeoutExpired: self._lmp_handle.kill() self._lmp_handle.communicate() err = self._lmp_handle.poll() assert err is not None return err def set_missing_parameters(self): """Verify that all necessary variables are set. """ symbols = self.atoms.get_chemical_symbols() # If unspecified default to atom types in alphabetic order if not self.parameters.get('specorder'): self.parameters['specorder'] = sorted(set(symbols)) # !TODO: handle cases were setting masses actual lead to errors if not self.parameters.get('masses'): self.parameters['masses'] = [] for type_id, specie in enumerate(self.parameters['specorder']): mass = atomic_masses[chemical_symbols.index(specie)] self.parameters['masses'] += [ f"{type_id + 1:d} {mass:f}" ] # set boundary condtions if not self.parameters.get('boundary'): b_str = " ".join(["fp"[int(x)] for x in self.atoms.pbc]) self.parameters['boundary'] = b_str def run(self, set_atoms=False): # !TODO: split this function """Method which explicitly runs LAMMPS.""" pbc = self.atoms.get_pbc() if all(pbc): cell = self.atoms.get_cell() elif not any(pbc): # large enough cell for non-periodic calculation - # LAMMPS shrink-wraps automatically via input command # "periodic s s s" # below cell = 2 * np.max(np.abs(self.atoms.get_positions())) * np.eye(3) else: warnings.warn( "semi-periodic ASE cell detected - translation " + "to proper LAMMPS input cell might fail" ) cell = self.atoms.get_cell() self.prism = Prism(cell) self.set_missing_parameters() self.calls += 1 # change into subdirectory for LAMMPS calculations tempdir = self.parameters['tmp_dir'] # setup file names for LAMMPS calculation label = f"{self.label}{self.calls:>06}" lammps_in = uns_mktemp( prefix="in_" + label, dir=tempdir ) lammps_log = uns_mktemp( prefix="log_" + label, dir=tempdir ) lammps_trj_fd = NamedTemporaryFile( prefix="trj_" + label, suffix=(".bin" if self.parameters['binary_dump'] else ""), dir=tempdir, delete=(not self.parameters['keep_tmp_files']), ) lammps_trj = if self.parameters['no_data_file']: lammps_data = None else: lammps_data_fd = NamedTemporaryFile( prefix="data_" + label, dir=tempdir, delete=(not self.parameters['keep_tmp_files']), mode='w', encoding='ascii' ) write_lammps_data( lammps_data_fd, self.atoms, specorder=self.parameters['specorder'], force_skew=self.parameters['always_triclinic'], reduce_cell=self.parameters['reduce_cell'], velocities=self.parameters['write_velocities'], prismobj=self.prism, units=self.parameters['units'], atom_style=self.parameters['atom_style'], ) lammps_data = lammps_data_fd.flush() # see to it that LAMMPS is started if not self._lmp_alive(): command = self.get_lammps_command() # Attempt to (re)start lammps self._lmp_handle = subprocess.Popen( shlex.split(command, posix=( == "posix")), stdin=subprocess.PIPE, stdout=subprocess.PIPE, encoding='ascii', ) lmp_handle = self._lmp_handle # Create thread reading lammps stdout (for reference, if requested, # also create lammps_log, although it is never used) if self.parameters['keep_tmp_files']: lammps_log_fd = open(lammps_log, "w") fd = SpecialTee(lmp_handle.stdout, lammps_log_fd) else: fd = lmp_handle.stdout thr_read_log = Thread(target=self.read_lammps_log, args=(fd,)) thr_read_log.start() # write LAMMPS input (for reference, also create the file lammps_in, # although it is never used) if self.parameters['keep_tmp_files']: lammps_in_fd = open(lammps_in, "w") fd = SpecialTee(lmp_handle.stdin, lammps_in_fd) else: fd = lmp_handle.stdin write_lammps_in( lammps_in=fd, parameters=self.parameters, atoms=self.atoms, prismobj=self.prism, lammps_trj=lammps_trj, lammps_data=lammps_data, ) if self.parameters['keep_tmp_files']: lammps_in_fd.close() # Wait for log output to be read (i.e., for LAMMPS to finish) # and close the log file if there is one thr_read_log.join() if self.parameters['keep_tmp_files']: lammps_log_fd.close() if not self.parameters['keep_alive']: self._lmp_end() exitcode = lmp_handle.poll() if exitcode and exitcode != 0: raise RuntimeError( "LAMMPS exited in {} with exit code: {}." "".format(tempdir, exitcode) ) # A few sanity checks if len(self.thermo_content) == 0: raise RuntimeError("Failed to retrieve any thermo_style-output") if int(self.thermo_content[-1]["atoms"]) != len(self.atoms): # This obviously shouldn't happen, but if prism.fold_...() fails, # it could raise RuntimeError("Atoms have gone missing") trj_atoms = read_lammps_dump( infileobj=lammps_trj, order=self.parameters['atorder'], index=-1, prismobj=self.prism, specorder=self.parameters['specorder'], ) if set_atoms: self.atoms = trj_atoms.copy() self.forces = trj_atoms.get_forces() # !TODO: trj_atoms is only the last snapshot of the system; Is it # desirable to save also the inbetween steps? if self.parameters['trajectory_out'] is not None: # !TODO: is it advisable to create here temporary atoms-objects self.trajectory_out.write(trj_atoms) tc = self.thermo_content[-1] self.results["energy"] = convert( tc["pe"], "energy", self.parameters["units"], "ASE" ) self.results["free_energy"] = self.results["energy"] self.results['forces'] = convert(self.forces.copy(), 'force', self.parameters['units'], 'ASE') stress = np.array( [-tc[i] for i in ("pxx", "pyy", "pzz", "pyz", "pxz", "pxy")] ) # We need to apply the Lammps rotation stuff to the stress: xx, yy, zz, yz, xz, xy = stress stress_tensor = np.array([[xx, xy, xz], [xy, yy, yz], [xz, yz, zz]]) stress_atoms = self.prism.tensor2_to_ase(stress_tensor) stress_atoms = stress_atoms[[0, 1, 2, 1, 0, 0], [0, 1, 2, 2, 2, 1]] stress = stress_atoms self.results["stress"] = convert( stress, "pressure", self.parameters["units"], "ASE" ) lammps_trj_fd.close() if not self.parameters['no_data_file']: lammps_data_fd.close() def __enter__(self): return self def __exit__(self, *args): self._lmp_end() def read_lammps_log(self, fileobj): # !TODO: somehow communicate 'thermo_content' explicitly """Method which reads a LAMMPS output log file.""" # read_log depends on that the first (three) thermo_style custom args # can be capitalized and matched against the log output. I.e. # don't use e.g. 'ke' or 'cpu' which are labeled KinEng and CPU. mark_re = r"^\s*" + r"\s+".join( [x.capitalize() for x in self.parameters['thermo_args'][0:3]] ) _custom_thermo_mark = re_compile(mark_re) # !TODO: regex-magic necessary? # Match something which can be converted to a float f_re = r"([+-]?(?:(?:\d+(?:\.\d*)?|\.\d+)(?:e[+-]?\d+)?|nan|inf))" n_args = len(self.parameters["thermo_args"]) # Create a re matching exactly N white space separated floatish things _custom_thermo_re = re_compile( r"^\s*" + r"\s+".join([f_re] * n_args) + r"\s*$", flags=IGNORECASE ) thermo_content = [] line = fileobj.readline() while line and line.strip() != CALCULATION_END_MARK: # check error if 'ERROR:' in line: raise RuntimeError(f'LAMMPS exits with error message: {line}') # get thermo output if _custom_thermo_mark.match(line): while True: line = fileobj.readline() if 'WARNING:' in line: continue bool_match = _custom_thermo_re.match(line) if not bool_match: break # create a dictionary between each of the # thermo_style args and it's corresponding value thermo_content.append( dict( zip( self.parameters['thermo_args'], map(float, bool_match.groups()), ) ) ) else: line = fileobj.readline() self.thermo_content = thermo_content
class SpecialTee: """A special purpose, with limited applicability, tee-like thing. A subset of stuff read from, or written to, orig_fd, is also written to out_fd. It is used by the lammps calculator for creating file-logs of stuff read from, or written to, stdin and stdout, respectively. """ def __init__(self, orig_fd, out_fd): self._orig_fd = orig_fd self._out_fd = out_fd = def write(self, data): self._orig_fd.write(data) self._out_fd.write(data) self.flush() def read(self, *args, **kwargs): data =*args, **kwargs) self._out_fd.write(data) return data def readline(self, *args, **kwargs): data = self._orig_fd.readline(*args, **kwargs) self._out_fd.write(data) return data def readlines(self, *args, **kwargs): data = self._orig_fd.readlines(*args, **kwargs) self._out_fd.write("".join(data)) return data def flush(self): self._orig_fd.flush() self._out_fd.flush()