Source code for pyiron.sphinx.interactive

# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.

import numpy as np
import os
import scipy.constants
import subprocess
import warnings
import time
from pyiron.sphinx.base import SphinxBase, Group
from pyiron.atomistics.job.interactive import GenericInteractive, GenericInteractiveOutput

BOHR_TO_ANGSTROM = (
    scipy.constants.physical_constants["Bohr radius"][0] / scipy.constants.angstrom
)
HARTREE_TO_EV = scipy.constants.physical_constants["Hartree energy in eV"][0]
HARTREE_OVER_BOHR_TO_EV_OVER_ANGSTROM = HARTREE_TO_EV / BOHR_TO_ANGSTROM

__author__ = "Osamu Waseda, Jan Janssen"
__copyright__ = (
    "Copyright 2020, Max-Planck-Institut für Eisenforschung GmbH - "
    "Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "Jan Janssen"
__email__ = "janssen@mpie.de"
__status__ = "development"
__date__ = "Sep 1, 2017"


[docs]class SphinxInteractive(SphinxBase, GenericInteractive): def __init__(self, project, job_name): super(SphinxInteractive, self).__init__(project, job_name) self.output = SphinxOutput(job=self) self._interactive_write_input_files = True self._interactive_library_read = None self._interactive_fetch_completed = True self._coarse_run = False @property def structure(self): return GenericInteractive.structure.fget(self) @structure.setter def structure(self, structure): GenericInteractive.structure.fset(self, structure)
[docs] def get_structure(self, iteration_step=-1, wrap_atoms=True): return GenericInteractive.get_structure( self, iteration_step=iteration_step, wrap_atoms=wrap_atoms )
[docs] def interactive_energy_tot_getter(self): return self.interactive_energy_pot_getter()
[docs] def interactive_energy_pot_getter(self): self._interactive_pipe_write("get energy") return float(self._interactive_library_read.readline()) * HARTREE_TO_EV
[docs] def interactive_forces_getter(self): self._interactive_pipe_write("get forces") ff = [] for _ in range(len(self.structure)): line = self._interactive_library_read.readline().split() ff.append( [ float(line[i]) * HARTREE_OVER_BOHR_TO_EV_OVER_ANGSTROM for i in range(3) ] ) ff = np.array(ff)[self.id_spx_to_pyi] return ff
@property def coarse_run(self): if "CoarseRun" in self.input: self._coarse_run = self.input["CoarseRun"] return self._coarse_run @coarse_run.setter def coarse_run(self, value): if not isinstance(value, bool): raise ValueError('coarse_run has to be a boolean') self._coarse_run = value self.input["CoarseRun"] = self._coarse_run
[docs] def interactive_cells_getter(self): self._interactive_pipe_write("get cell") cc = [] for _ in range(3): line = self._interactive_library_read.readline().split() cc.append([float(line[i]) * BOHR_TO_ANGSTROM for i in range(3)]) return np.array(cc)
[docs] def interactive_positions_getter(self): self._interactive_pipe_write("get structure") xx = [] for _ in range(len(self.structure)): line = self._interactive_library_read.readline().split() xx.append([float(line[i]) * BOHR_TO_ANGSTROM for i in range(3)]) xx = np.array(xx)[self.id_spx_to_pyi] return xx
[docs] def interactive_positions_setter(self, positions): self._interactive_pipe_write("set structure") positions = positions[self.id_pyi_to_spx] positions = np.reshape(positions, 3 * len(self.structure)) / BOHR_TO_ANGSTROM self._interactive_pipe_write(positions.tolist())
[docs] def interactive_spins_getter(self): self._logger.debug("get spins - start ...") self._interactive_pipe_write("get atomspin") mm = [] for _ in range(len(self.structure)): line = self._interactive_library_read.readline().split() mm.append(float(line[0])) mm = np.array(mm)[self.id_spx_to_pyi] # self.interactive_cache['atom_spins'].append(mm) self._logger.debug("get spins - done.") return mm
[docs] def interactive_spin_constraints_setter(self, spins): if self._generic_input["fix_spin_constraint"]: self._logger.debug("set spin constraints - start ...") self._spin_constraint_enabled = True self._interactive_pipe_write("set spinconstraint") spins = np.array(spins)[self.id_pyi_to_spx] self._spin_constraints = np.array(spins) self._interactive_pipe_write(spins.tolist()) # self.interactive_cache['atom_spin_constraints'].append(spins) self._logger.debug("set spin constraints - done.") else: warnings.warn("Spin constraint not set -> set fix_spin_constraint = True")
[docs] def interactive_spin_constraints_getter(self): return self._spin_constraints
# return self.interactive_cache['atom_spin_constraints'][-1]
[docs] def interactive_magnetic_forces_getter(self): if self._generic_input["fix_spin_constraint"]: self._interactive_pipe_write("get nu") nn = [] for _ in range(len(self.structure)): line = self._interactive_library_read.readline().split() nn.append(HARTREE_TO_EV * float(line[0])) nn = np.array(nn)[self.id_spx_to_pyi] return nn else: return None
[docs] def interactive_initialize_interface(self): self.server.threads = self.input["THREADS"] if self.executable.executable_path == "": self.status.aborted = True raise ValueError("No executable set!") if self.server.cores == 1 or not self.executable.mpi: out = subprocess.Popen( str(self.executable), cwd=self.project_hdf5.working_directory, shell=True, stderr=subprocess.STDOUT, universal_newlines=True, ) else: out = subprocess.Popen( [ self.executable.executable_path, str(self.server.cores), str(self.server.threads), ], cwd=self.project_hdf5.working_directory, shell=False, stderr=subprocess.STDOUT, universal_newlines=True, ) while not self._interactive_pipes_initialized: time.sleep(1) self._logger.debug("open interactive interface!") self._interactive_library = open( os.path.join(self.working_directory, "sxctrl"), "w" ) self._interactive_library_read = open( os.path.join(self.working_directory, "sxres"), "r" ) self._logger.debug("interactive interface is opened!") if ( np.all(self.structure.get_initial_magnetic_moments() == None) and "atom_spins" in self.interactive_cache.keys() ): del self.interactive_cache["atom_spins"] if self._generic_input["fix_spin_constraint"]: self.interactive_spin_constraints_setter( self._structure_current.get_initial_magnetic_moments() ) else: if "magnetic_forces" in self.interactive_cache.keys(): del self.interactive_cache["magnetic_forces"] if "atom_spin_constraints" in self.interactive_cache.keys(): del self.interactive_cache["atom_spin_constraints"] if len(self.restart_file_list) > 0: self._logger.debug("restarting; interactive run - start ...") self._interactive_pipe_write("run restart") self.interactive_fetch()
def _output_interactive_to_generic(self): with self.project_hdf5.open("output") as h5: if "interactive" in h5.list_groups(): for key in ["positions", "cells", "indices", "cells", "forces"]: h5["generic/" + key] = h5["interactive/" + key] with self.project_hdf5.open("input") as hdf5_input: with hdf5_input.open("generic") as hdf5_generic: if "dft" not in hdf5_generic.list_groups(): hdf5_generic.create_group("dft") with hdf5_generic.open("dft") as hdf5_dft: if ( "atom_spin_constraints" in h5["interactive"].list_nodes() ): hdf5_dft["atom_spin_constraints"] = h5[ "interactive/atom_spin_constraints" ]
[docs] def collect_output(self, force_update=False): super(SphinxInteractive, self).collect_output(force_update=force_update) self._output_interactive_to_generic()
[docs] def interactive_close(self): if self.interactive_is_activated(): self._interactive_pipe_write("end") self._interactive_library.close() self._interactive_library_read.close() self.status.collect = True if self["energy.dat"] is not None: self.run() self._output_interactive_to_generic() super(SphinxInteractive, self).interactive_close()
[docs] def calc_minimize( self, electronic_steps=None, ionic_steps=None, max_iter=None, pressure=None, algorithm=None, retain_charge_density=False, retain_electrostatic_potential=False, ionic_energy=None, ionic_forces=None, volume_only=False, ): if ( self.server.run_mode.interactive or self.server.run_mode.interactive_non_modal ): raise NotImplementedError( "calc_minimize() is not implemented for the interactive mode use calc_static()!" ) else: super(SphinxInteractive, self).calc_minimize( electronic_steps=electronic_steps, ionic_steps=ionic_steps, max_iter=max_iter, pressure=pressure, algorithm=algorithm, retain_charge_density=retain_charge_density, retain_electrostatic_potential=retain_electrostatic_potential, ionic_energy=ionic_energy, ionic_forces=ionic_forces, volume_only=volume_only, )
[docs] def run_if_interactive(self): super(SphinxInteractive, self).run_if_interactive() self._logger.debug("interactive run - start ...") if self.coarse_run: self._interactive_pipe_write("run coarseelectronicminimization") else: self._interactive_pipe_write("run electronicminimization") self.interactive_fetch()
[docs] def run_if_interactive_non_modal(self): if not self._interactive_fetch_completed: print("Warning: interactive_fetch being effectuated") self.interactive_fetch() super(SphinxInteractive, self).run_if_interactive() self._logger.debug("interactive run - start ...") if self.coarse_run: self._interactive_pipe_write("run coarseelectronicminimization") else: self._interactive_pipe_write("run electronicminimization") self._interactive_fetch_completed = False
[docs] def interactive_fetch(self): if ( self._interactive_fetch_completed and self.server.run_mode.interactive_non_modal ): print("First run and then fetch") else: self.interactive_collect() self._logger.debug("interactive run - done")
@property def _interactive_pipes_initialized(self): return os.path.exists( os.path.join(self.working_directory, "sxctrl") ) and os.path.exists(os.path.join(self.working_directory, "sxres")) def _interactive_pipe_write(self, line): if isinstance(line, str) or isinstance(line, int) or isinstance(line, float): self._interactive_library.write(str(line) + "\n") self._interactive_library.flush() elif isinstance(line, list): for subline in line: self._interactive_pipe_write(subline) else: raise TypeError("only lists, strings and numbers are supported!") def _interactive_pipe_read(self): return self._interactive_library_read.readline()
[docs] def calc_static( self, electronic_steps=400, blockSize=8, dSpinMoment=1e-8, algorithm=None, retain_charge_density=False, retain_electrostatic_potential=False, ): """ Function to setup the hamiltonian to perform static SCF DFT runs Args: retain_electrostatic_potential: retain_charge_density: algorithm: electronic_steps (int): maximum number of electronic steps, which can be used to achieve convergence """ super(SphinxInteractive, self).calc_static( electronic_steps=electronic_steps, algorithm=algorithm, retain_charge_density=retain_charge_density, retain_electrostatic_potential=retain_electrostatic_potential, )
[docs] def load_main_group(self): main_group = Group() if ( self.server.run_mode.interactive or self.server.run_mode.interactive_non_modal ): commands = Group([ { "id": '"restart"', "scfDiag": self.get_scf_group( maxSteps=10, keepRhoFixed=True, dEnergy=1.0e-4 ) }, { "id": '"coarseelectronicminimization"', "scfDiag": self.get_scf_group( dEnergy=1000*self.input["Ediff"] / HARTREE_TO_EV ), }, { "id": '"electronicminimization"', "scfDiag": self.get_scf_group(), } ]) self.input.sphinx.main.extControl = Group() self.input.sphinx.main.extControl.set_group('bornOppenheimer') self.input.sphinx.main.extControl.bornOppenheimer = commands else: super(SphinxInteractive, self).load_main_group()
[docs]class SphinxOutput(GenericInteractiveOutput): def __init__(self, job): super(SphinxOutput, self).__init__(job)
[docs] def check_band_occupancy(self, plot=True): """ Check whether there are still empty bands available. args: plot (bool): plots occupancy of the last step returns: True if there are still empty bands """ import matplotlib.pylab as plt elec_dict = self._job['output/generic/dft']['n_valence'] if elec_dict is None: raise AssertionError('Number of electrons not parsed') n_elec = np.sum([elec_dict[k] for k in self._job.structure.get_chemical_symbols()]) n_elec = int(np.ceil(n_elec/2)) bands = self._job['output/generic/dft/bands_occ'][-1] bands = bands.reshape(-1, bands.shape[-1]) max_occ = np.sum(bands>0, axis=-1).max() n_bands = bands.shape[-1] if plot: xticks = np.arange(1, n_bands+1) plt.xlabel('Electron number') plt.ylabel('Occupancy') if n_bands<20: plt.xticks(xticks) plt.axvline(n_elec, label='#electrons: {}'.format(n_elec)) plt.axvline(max_occ, color='red', label='Max occupancy: {}'.format(max_occ)) plt.axvline(n_bands, color='green', label='Number of bands: {}'.format(n_bands)) plt.plot(xticks, bands.T, 'x', color='black') plt.legend() if max_occ < n_bands: return True else: return False
[docs]class SphinxInt2(SphinxInteractive): def __init__(self, project, job_name): warnings.warn("Please use SphinxInt instead of SphinxInt2") super(SphinxInt2, self).__init__(project=project, job_name=job_name)