sxextoptint.py

# 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 subprocess
import os
import time
import posixpath
import warnings
from pyiron.base.settings.generic import Settings
from pyiron.base.generic.parameters import GenericParameters
from pyiron.atomistics.job.interactivewrapper import (
    InteractiveWrapper,
    ReferenceJobOutput,
)
from pyiron.atomistics.job.interactive import InteractiveInterface
from pyiron.base.job.executable import Executable
from pyiron.sphinx.base import InputWriter

__author__ = "Jan Janssen, Osamu Waseda"
__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, 2018"


s = Settings()


class SxExtOpt(InteractiveInterface):
    def __init__(
        self,
        structure,
        working_directory=None,
        maxDist=5,
        ionic_steps=1000,
        ionic_energy=1.0e-3,
        ionic_forces=1.0e-2,
        max_step_length=1.0e-1,
        soft_mode_damping=1,
        executable=None,
        ssa=False,
    ):
        super().__init__()
        self.__name__ = "SxExtOpt"
        if working_directory is None:
            warnings.warn("WARNING: working_directory not set; current folder is used")
            working_directory = os.getcwd()
        self._interactive_library = None
        self._interactive_library_read = None
        self.working_directory = working_directory
        if executable is None:
            executable = Executable(
                path_binary_codes=s._configuration["resource_paths"],
                codename="SxExtOptInteractive",
                module=self.__module__.split(".")[1],
                overwrite_nt_flag=False,
            ).executable_path
        self._start_process(
            structure=structure,
            executable=executable,
            maxDist=maxDist,
            ionic_steps=ionic_steps,
            ionic_energy=ionic_energy,
            ionic_forces=ionic_forces,
            max_step_length=max_step_length,
            soft_mode_damping=soft_mode_damping,
            selective_dynamics="selective_dynamics" in structure._tag_list.keys(),
            ssa=ssa,
        )
        self._cell = structure.cell
        if ssa:
            self._elements = structure.get_parent_symbols()
        else:
            magmom = structure.get_initial_magnetic_moments()
            magmom[magmom!=None] = np.round(magmom[magmom!=None], decimals=1)
            magmom = np.char.mod('%s', magmom)
            self._elements = np.char.add(structure.get_parent_symbols(), magmom)
            self._elements = np.char.replace(self._elements, '-', 'm')
            self._elements = np.char.replace(self._elements, '.', 'p')
        self._positions = structure.positions
        self._converged = False

    def _start_process(
        self,
        structure,
        executable,
        maxDist=5,
        ionic_steps=1000,
        ionic_energy=1.0e-3,
        ionic_forces=1.0e-2,
        max_step_length=1.0e-1,
        soft_mode_damping=1,
        selective_dynamics=False,
        ssa=False,
    ):
        if selective_dynamics:
            input_writer_obj = InputWriter()
            input_writer_obj.structure = structure
            if ssa:
                input_writer_obj.structure.set_initial_magnetic_moments(len(structure)*[None])
            input_writer_obj.write_structure(
                file_name="structure.sx",
                cwd=self.working_directory,
                structure_str=None,
                symmetry_enabled=True,
                keep_angstrom=True,
            )
        self._write_input(
            working_directory=self.working_directory,
            maxDist=maxDist,
            ionic_steps=ionic_steps,
            ionic_energy=ionic_energy,
            ionic_forces=ionic_forces,
            max_step_length=max_step_length,
            soft_mode_damping=soft_mode_damping,
            selective_dynamics=selective_dynamics,
        )

        shell = os.name == "nt"
        try:
            with open(
                posixpath.join(self.working_directory, "out.txt"), mode="w"
            ) as f_out:
                with open(
                    posixpath.join(self.working_directory, "error.txt"), mode="w"
                ) as f_err:
                    self._process = subprocess.Popen(
                        [executable],
                        cwd=self.working_directory,
                        shell=shell,
                        stdout=f_out,
                        stderr=f_err,
                        universal_newlines=True,
                    )
        except subprocess.CalledProcessError as e:
            raise ValueError("run_job.py crashed")
        while not self._interactive_pipes_initialized(self.working_directory):
            time.sleep(1)
        self._interactive_initialize_interface()

    @staticmethod
    def _write_input(
        working_directory,
        maxDist=5,
        ionic_steps=1000,
        ionic_energy=1.0e-3,
        ionic_forces=1.0e-2,
        max_step_length=1.0e-1,
        soft_mode_damping=1,
        selective_dynamics=False,
    ):
        with open(os.path.join(working_directory, "optim.sx"), "w") as f:
            content = (
                "main { ricQN { ric { maxDist = %f; withAngles; } maxSteps = %i; dEnergy = %f; dF = %f; maxStepLength = %f; softModeDamping = %f;}}"
                % (
                    maxDist,
                    ionic_steps,
                    ionic_energy,
                    ionic_forces,
                    max_step_length,
                    soft_mode_damping,
                )
            )
            if selective_dynamics:
                content += "structure { include <structure.sx>; }"
            f.write(content)

    @staticmethod
    def _interactive_pipes_initialized(working_directory):
        return os.path.exists(
            os.path.join(working_directory, "control")
        ) and os.path.exists(os.path.join(working_directory, "response"))

    def _interactive_write_line(self, line):
        self._interactive_library.write("%s\n" % line)
        self._interactive_library.flush()

    def _interactive_initialize_interface(self):
        self._interactive_library_read = open(
            os.path.join(self.working_directory, "control"), "r"
        )
        self._interactive_library = open(
            os.path.join(self.working_directory, "response"), "w"
        )

    def interactive_close(self):
        if self.interactive_is_activated():
            self._interactive_library.close()
            self._interactive_library_read.close()
            self._delete_named_pipes(working_directory=self.working_directory)

    @staticmethod 
    def _delete_named_pipes(working_directory):
        for file in ["control", "response"]:
            file_path = posixpath.join(working_directory, file)
            if os.path.exists(file_path):
                os.remove(file_path)

    def interactive_is_activated(self):
        if self._interactive_library is None:
            return False
        else:
            return True

    def _write_cell(self, cell):
        for c in cell:
            self._interactive_write_line("%.16f %.16f %.16f" % (c[0], c[1], c[2]))

    def _write_number_of_atoms(self, count):
        self._interactive_write_line("%s" % (count))

    def _write_positions(self, positions, elements):
        for pos, el in zip(positions, elements):
            self._interactive_write_line(
                "%.16f %.16f %.16f %s" % (pos[0], pos[1], pos[2], str(el))
            )

    def _write_energy(self):
        self._interactive_write_line("0")

    def _write_forces(self, forces):
        for f in forces:
            self._interactive_write_line("%.16f %.16f %.16f" % (f[0], f[1], f[2]))

    def _read_positions(self, count):
        return [
            [float(c) for c in self._interactive_library_read.readline().split()]
            for i in range(count)
        ]

    def set_forces(self, forces):
        line = self._interactive_library_read.readline().split()
        if len(line) == 0 or line[0] == "end":
            print("Ending calculation")
            self._converged = True
        elif line[0] == "get":
            if line[1] == "cell":
                self._write_cell(cell=self._cell)
            elif line[1] == "natoms":
                self._write_number_of_atoms(count=len(self._positions))
            elif line[1] == "positions":
                self._write_positions(
                    positions=self._positions, elements=self._elements
                )
            elif line[1] == "energy":
                self._write_energy()
            elif line[1] == "forces":
                self._write_forces(forces=forces)
            else:
                raise ValueError("Unknown command:", line)
            self.set_forces(forces)
        elif line[0] == "run":
            self.set_forces(forces)
        elif line[0] == "set":
            if line[1] == "positions":
                self._positions = np.array(self._read_positions(count=len(forces)))
            else:
                raise ValueError("Unknown command:", line)
        else:
            raise ValueError("Unknown command:", line)

    def get_positions(self):
        return self._positions

    def end(self):
        while not self.converged:
            self.set_forces(np.zeros_like(self._positions))

    @property
    def converged(self):
        return self._converged

    def __del__(self):
        self.end()
        if self.interactive_is_activated():
            self.interactive_close()
        else:
            self._delete_named_pipes(working_directory=self.working_directory)


class SxExtOptInteractive(InteractiveWrapper):
    def __init__(self, project, job_name):
        super(SxExtOptInteractive, self).__init__(project, job_name)
        self.__name__ = "SxExtOptInteractive"
        self.__version__ = (
            None
        )  # Reset the version number to the executable is set automatically
        self._executable_activate()
        self.input = Input()
        self.output = SxExtOptOutput(job=self)
        self._interactive_interface = None
        self._interactive_number_of_steps = 0
        self._coarse_run = False

    def set_input_to_read_only(self):
        """
        This function enforces read-only mode for the input classes, but it has to be implement in the individual
        classes.
        """
        super(SxExtOptInteractive, self).set_input_to_read_only()
        self.input.read_only = True

    def write_input(self):
        pass

    def run_static(self):
        """
        The run if modal function is called by run to execute the simulation, while waiting for the output. For this we
        use subprocess.check_output()
        """
        self._create_working_directory()
        self._interactive_interface = SxExtOpt(
            structure=self.ref_job.structure,
            working_directory=self.working_directory,
            maxDist=int(self.input["maxDist"]),
            ionic_steps=int(self.input["ionic_steps"]),
            ionic_energy=float(self.input["ionic_energy"]),
            ionic_forces=float(self.input["ionic_forces"]),
            max_step_length=float(self.input["max_step_length"]),
            soft_mode_damping=float(self.input["soft_mode_damping"]),
            executable=self.executable.executable_path,
            ssa=self.input['ssa'],
        )
        try:
            self._coarse_run = self.ref_job.coarse_run
        except AttributeError:
            pass
        self.status.running = True
        self._logger.info("job status: %s", self.status)
        new_positions = self.ref_job.structure.positions
        self.ref_job_initialize()
        while (
            self._interactive_number_of_steps < self.input["ionic_steps"]
            and not self._interactive_interface.converged
        ):
            str_temp = self.ref_job.structure
            str_temp.positions = new_positions
            self.ref_job.structure = str_temp
            if self.ref_job.server.run_mode.interactive:
                self._logger.debug("SxExtOpt: step start!")
                self.ref_job.run()
                if (
                    self._coarse_run
                    and np.max(np.linalg.norm(self.get_forces(), axis=-1), axis=-1)
                    < self.input["ionic_forces"]
                ):
                    self._coarse_run = False
                    self.ref_job.coarse_run = False
                    self.ref_job.run()
                self._logger.debug("SxExtOpt: step finished!")
            else:
                self.ref_job.run(run_again=True)
                if (
                    self._coarse_run
                    and np.max(np.linalg.norm(self.get_forces(), axis=-1), axis=-1)
                    < self.input["ionic_forces"]
                ):
                    self._coarse_run = False
                    self.ref_job.coarse_run = False
                    self.ref_job.run(run_again=True)
            self._interactive_interface.set_forces(forces=self.get_forces())
            new_positions = self._interactive_interface.get_positions()
            self._interactive_number_of_steps += 1
        self.status.collect = True
        if self.ref_job.server.run_mode.interactive:
            self.ref_job.interactive_close()
        self._interactive_interface.interactive_close()
        self.run()

    def get_forces(self):
        ff = np.array(self.ref_job.output.forces[-1])
        if hasattr(self.ref_job.structure, "selective_dynamics"):
            ff[np.array(self.ref_job.structure.selective_dynamics) == False] = 0
            return ff
        return ff

    def convergence_check(self):
        """
        Validate the convergence of the calculation.

        Returns:
             (bool): If the calculation is converged
        """
        if self._interactive_number_of_steps < self.input["ionic_steps"]:
            return True
        else:
            return False


class Input(GenericParameters):
    """
    class to control the generic input for a Sphinx calculation.

    Args:
        input_file_name (str): name of the input file
        table_name (str): name of the GenericParameters table
    """

    def __init__(self, input_file_name=None, table_name="input"):
        super(Input, self).__init__(
            input_file_name=input_file_name,
            table_name=table_name,
            comment_char="//",
            separator_char="=",
            end_value_char=";",
        )

    def load_default(self):
        """
        Loads the default file content
        """
        file_content = (
            "ionic_steps = 1000 // maximum number of ionic steps\n"
            "ionic_energy = 1.0e-3\n"
            "ionic_forces = 1.0e-2\n"
            "maxDist = 5 // maximum possible distance for considering neighbors\n"
            "max_step_length = 1.0e-1 // maximum displacement at each step\n"
            "ssa = False // ignore different magnetic moment values when internal symmetries are considered\n"
            "soft_mode_damping = 1.0 // Tikhonov damper\n"
        )
        self.load_string(file_content)


class SxExtOptOutput(ReferenceJobOutput):
    def __init__(self, job):
        super(SxExtOptOutput, self).__init__(job=job)