geooptparser.py

from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.baseclasses import MainHierarchicalParser
from commonmatcher import CommonMatcher
import cp2kparser.generic.configurationreading
import cp2kparser.generic.csvparsing
from nomadcore.caching_backend import CachingLevel
import logging
import ase.io
import numpy as np
import math
logger = logging.getLogger("nomad")


#===============================================================================
class CP2KGeoOptParser(MainHierarchicalParser):
    """Used to parse the CP2K calculation with run types:
        -GEO_OPT/GEOMETRY_OPTIMIZATION
    """
    def __init__(self, file_path, parser_context):
        """
        """
        super(CP2KGeoOptParser, self).__init__(file_path, parser_context)
        self.setup_common_matcher(CommonMatcher(parser_context))
        self.traj_iterator = None

        #=======================================================================
        # Cached values
        self.cache_service.add_cache_object("number_of_frames_in_sequence", 0)
        self.cache_service.add_cache_object("frame_sequence_potential_energy", [])

        #=======================================================================
        # Cache levels
        self.caching_level_for_metaname.update({
            'x_cp2k_optimization_energy': CachingLevel.ForwardAndCache,
            'x_cp2k_section_geometry_optimization_step': CachingLevel.ForwardAndCache,
            'x_cp2k_section_quickstep_calculation': CachingLevel.ForwardAndCache,
            'x_cp2k_section_geometry_optimization': CachingLevel.ForwardAndCache,
            'x_cp2k_section_geometry_optimization_energy_reevaluation': CachingLevel.ForwardAndCache,
        })

        #=======================================================================
        # SimpleMatchers
        self.geo_opt = SM(
            " ***                     STARTING GEOMETRY OPTIMIZATION                      ***".replace("*", "\*"),
            sections=["section_frame_sequence", "x_cp2k_section_geometry_optimization"],
            subMatchers=[
                SM( " ***                           CONJUGATE GRADIENTS                           ***".replace("*", "\*"),
                    adHoc=self.adHoc_conjugate_gradient(),
                    otherMetaInfo=["geometry_optimization_method"],
                ),
                SM( " ***                                   BFGS                                  ***".replace("*", "\*"),
                    adHoc=self.adHoc_bfgs(),
                    otherMetaInfo=["geometry_optimization_method"],
                ),
                SM( " ***                                 L-BFGS                                  ***".replace("*", "\*"),
                    adHoc=self.adHoc_bfgs(),
                    otherMetaInfo=["geometry_optimization_method"],
                ),
                # SM( "",
                    # forwardMatch=True,
                    # sections=["section_single_configuration_calculation", "section_system", "x_cp2k_section_geometry_optimization_step"],
                    # subMatchers=[
                        # self.cm.quickstep_calculation(),
                        # SM( " --------  Informations at step"),
                        # SM( "  Optimization Method        =\s+(?P<x_cp2k_optimization_method>{})".format(self.cm.regex_word)),
                        # SM( "  Total Energy               =\s+(?P<x_cp2k_optimization_energy__hartree>{})".format(self.cm.regex_f),
                            # otherMetaInfo=["frame_sequence_potential_energy"]
                        # ),
                    # ],
                    # otherMetaInfo=["atom_positions"],
                    # adHoc=self.adHoc_step(),
                # ),
                SM( " OPTIMIZATION STEP:",
                    endReStr="  Conv. in RMS gradients     =",
                    name="geooptstep",
                    repeats=True,
                    sections=["section_system"],
                    subMatchers=[
                        SM( "",
                            forwardMatch=True,
                            sections=["x_cp2k_section_geometry_optimization_step"],
                            otherMetaInfo=[
                                "atom_positions",
                            ],
                            subMatchers=[
                                # SM( "",
                                    # forwardMatch=True,
                                    # endReStr=" ***                 MNBRACK - NUMBER OF ENERGY EVALUATIONS :\s+{}\s+***".replace("*", "\*").format(self.cm.regex_i),
                                    # subMatchers=[
                                        # SM(" SCF WAVEFUNCTION OPTIMIZATION",
                                            # forwardMatch=True,
                                            # repeats=True,
                                            # subMatchers=[
                                                # self.cm.quickstep_calculation(),
                                            # ]
                                        # )
                                    # ]
                                # ),
                                # SM( "",
                                    # forwardMatch=True,
                                    # endReStr=" ***                 BRENT   - NUMBER OF ENERGY EVALUATIONS :\s+{}\s+***".replace("*", "\*").format(self.cm.regex_i),
                                    # subMatchers=[
                                        # SM(" SCF WAVEFUNCTION OPTIMIZATION",
                                            # forwardMatch=True,
                                            # repeats=True,
                                            # subMatchers=[
                                                # self.cm.quickstep_calculation(),
                                            # ]
                                        # )
                                    # ]
                                # ),
                                SM( " --------  Informations at step"),
                                SM( "  Optimization Method        =\s+(?P<x_cp2k_optimization_method>{})".format(self.cm.regex_word)),
                                SM( "  Total Energy               =\s+(?P<x_cp2k_optimization_energy__hartree>{})".format(self.cm.regex_f),
                                    otherMetaInfo=["frame_sequence_potential_energy"]
                                ),
                                SM( "  Real energy change         =\s+(?P<x_cp2k_optimization_energy_change__hartree>{})".format(self.cm.regex_f)),
                                SM( "  Decrease in energy         =\s+(?P<x_cp2k_optimization_energy_decrease>{})".format(self.cm.regex_word)),
                                SM( "  Used time                  =\s+(?P<x_cp2k_optimization_used_time>{})".format(self.cm.regex_f)),
                                SM( "  Max. step size             =\s+(?P<x_cp2k_optimization_max_step_size__bohr>{})".format(self.cm.regex_f)),
                                SM( "  Conv. limit for step size  =\s+(?P<x_cp2k_optimization_step_size_convergence_limit__bohr>{})".format(self.cm.regex_f),
                                    otherMetaInfo=["geometry_optimization_geometry_change"]
                                ),
                                SM( "  Convergence in step size   =\s+(?P<x_cp2k_optimization_step_size_convergence>{})".format(self.cm.regex_word)),
                                SM( "  RMS step size              =\s+(?P<x_cp2k_optimization_rms_step_size__bohr>{})".format(self.cm.regex_f)),
                                SM( "  Convergence in RMS step    =\s+(?P<x_cp2k_optimization_rms_step_size_convergence>{})".format(self.cm.regex_word)),
                                SM( "  Max. gradient              =\s+(?P<x_cp2k_optimization_max_gradient__bohr_1hartree>{})".format(self.cm.regex_f)),
                                SM( "  Conv. limit for gradients  =\s+(?P<x_cp2k_optimization_gradient_convergence_limit__bohr_1hartree>{})".format(self.cm.regex_f),
                                    otherMetaInfo=["geometry_optimization_threshold_force"]
                                ),
                                SM( "  Conv. for gradients        =\s+(?P<x_cp2k_optimization_max_gradient_convergence>{})".format(self.cm.regex_word)),
                                SM( "  RMS gradient               =\s+(?P<x_cp2k_optimization_rms_gradient__bohr_1hartree>{})".format(self.cm.regex_f)),
                                SM( "  Conv. in RMS gradients     =\s+(?P<x_cp2k_optimization_rms_gradient_convergence>{})".format(self.cm.regex_word)),
                            ],
                            adHoc=self.adHoc_step()
                        ),
                    ]
                ),
                SM( " ***                    GEOMETRY OPTIMIZATION COMPLETED                      ***".replace("*", "\*"),
                    adHoc=self.adHoc_geo_opt_converged(),
                    otherMetaInfo=["geometry_optimization_converged"]
                ),
                SM( "                    Reevaluating energy at the minimum",
                    sections=["x_cp2k_section_geometry_optimization_energy_reevaluation", "section_system"],
                    subMatchers=[
                        self.cm.quickstep_calculation(),
                    ],
                    adHoc=self.adHoc_step()
                ),
            ],
        )

        # Compose root matcher according to the run type. This way the
        # unnecessary regex parsers will not be compiled and searched. Saves
        # computational time.
        self.root_matcher = SM("",
            forwardMatch=True,
            sections=["section_run", "section_sampling_method"],
            subMatchers=[
                SM( "",
                    forwardMatch=True,
                    sections=["section_method"],
                    subMatchers=[
                        self.cm.header(),
                        self.cm.quickstep_header(),
                    ],
                ),
                self.geo_opt
            ]
        )

    #===========================================================================
    # onClose triggers
    def onClose_x_cp2k_section_geometry_optimization(self, backend, gIndex, section):

        # Get the re-evaluated energy and add it to frame_sequence_potential_energy
        reeval = section["x_cp2k_section_geometry_optimization_energy_reevaluation"][0]
        quickstep = reeval["x_cp2k_section_quickstep_calculation"][0]
        energy = quickstep["x_cp2k_energy_total"]
        self.cache_service["frame_sequence_potential_energy"].append(energy[0])

        self.cache_service.push_value("number_of_frames_in_sequence")
        self.cache_service.push_array_values("frame_sequence_potential_energy")

        opt_section = section["x_cp2k_section_geometry_optimization_step"]
        if opt_section is not None:
            opt_section = opt_section[-1]
            geo_limit = opt_section["x_cp2k_optimization_step_size_convergence_limit"]
            if geo_limit is not None:
                self.backend.addValue("geometry_optimization_geometry_change", geo_limit[0])
            force_limit = opt_section["x_cp2k_optimization_gradient_convergence_limit"]
            if force_limit is not None:
                self.backend.addValue("geometry_optimization_threshold_force", force_limit[0])

    def onClose_section_sampling_method(self, backend, gIndex, section):
        self.backend.addValue("sampling_method", "geometry_optimization")

    def onClose_x_cp2k_section_geometry_optimization_step(self, backend, gIndex, section):
        energy = section["x_cp2k_optimization_energy"]
        if energy is not None:
            self.cache_service["frame_sequence_potential_energy"].append(energy[0])

    def onClose_section_method(self, backend, gIndex, section):
        traj_file = self.file_service.get_file_by_id("trajectory")
        traj_format = self.cache_service["trajectory_format"]
        if traj_format is not None and traj_file is not None:

            # Use special parsing for CP2K pdb files because they don't follow the proper syntax
            if traj_format == "PDB":
                self.traj_iterator = cp2kparser.generic.csvparsing.iread(traj_file, columns=[3, 4, 5], start="CRYST", end="END")
            else:
                try:
                    self.traj_iterator = cp2kparser.generic.configurationreading.iread(traj_file)
                except ValueError:
                    pass

    #===========================================================================
    # adHoc functions
    def adHoc_geo_opt_converged(self):
        """Called when the geometry optimization converged.
        """
        def wrapper(parser):
            parser.backend.addValue("geometry_optimization_converged", True)
        return wrapper

    def adHoc_geo_opt_not_converged(self):
        """Called when the geometry optimization did not converge.
        """
        def wrapper(parser):
            parser.backend.addValue("geometry_optimization_converged", False)
        return wrapper

    def adHoc_conjugate_gradient(self):
        """Called when conjugate gradient method is used.
        """
        def wrapper(parser):
            parser.backend.addValue("geometry_optimization_method", "conjugate_gradient")
        return wrapper

    def adHoc_bfgs(self):
        """Called when conjugate gradient method is used.
        """
        def wrapper(parser):
            parser.backend.addValue("geometry_optimization_method", "bfgs")
        return wrapper

    def adHoc_step(self):
        """Called when all the step information has been retrieved from the
        output file. Here further information is gathered from external files.
        """
        def wrapper(parser):
            self.cache_service["number_of_frames_in_sequence"] += 1

            # Get the next position from the trajectory file
            if self.traj_iterator is not None:
                # pos = next(self.traj_iterator)
                # self.cache_service["atom_positions"] = pos
                try:
                    pos = next(self.traj_iterator)
                except StopIteration:
                    logger.error("Could not get the next geometries from an external file. It seems that the number of optimization steps in the CP2K outpufile doesn't match the number of steps found in the external trajectory file.")
                else:
                    self.cache_service["atom_positions"] = pos

        return wrapper

    def adHoc_setup_traj_file(self):
        def wrapper(parser):
            pass
        return wrapper

    def debug(self):
        def wrapper(parser):
            print "FOUND"
        return wrapper