Source code for abipy.abio.outputs

"""
Objects used to extract and plot results from output files in text format.
"""
import os
import numpy as np
import pandas as pd

from collections import OrderedDict
from io import StringIO
from monty.string import is_string, marquee
from monty.functools import lazy_property
from monty.termcolor import cprint
from pymatgen.core.units import bohr_to_ang
from abipy.core.symmetries import AbinitSpaceGroup
from abipy.core.structure import Structure, dataframes_from_structures
from abipy.core.kpoints import has_timrev_from_kptopt
from abipy.core.mixins import TextFile, AbinitNcFile, NotebookWriter
from abipy.abio.inputs import GEOVARS
from abipy.abio.timer import AbinitTimerParser
from abipy.abio.robots import Robot
from abipy.flowtk import EventsParser, NetcdfReader, GroundStateScfCycle, D2DEScfCycle


[docs]class AbinitTextFile(TextFile): """ Base class for the ABINIT main output files and log files. """ @property def events(self): """ List of ABINIT events reported in the file. """ # Parse the file the first time the property is accessed or when mtime is changed. stat = os.stat(self.filepath) if stat.st_mtime != self._last_mtime or not hasattr(self, "_events"): self._events = EventsParser().parse(self.filepath) return self._events
[docs] def get_timer(self): """ Timer data. """ timer = AbinitTimerParser() timer.parse(self.filepath) return timer
[docs]class AbinitLogFile(AbinitTextFile, NotebookWriter): """ Class representing the Abinit log file. .. rubric:: Inheritance Diagram .. inheritance-diagram:: AbinitLogFile """
[docs] def to_string(self, verbose=0): return str(self.events)
[docs] def plot(self, **kwargs): """Empty placeholder.""" return None
[docs] def yield_figs(self, **kwargs): # pragma: no cover """ This function *generates* a predefined list of matplotlib figures with minimal input from the user. """ yield None
[docs] def write_notebook(self, nbpath=None): """ Write a jupyter_ notebook to ``nbpath``. If nbpath is None, a temporay file in the current working directory is created. Return path to the notebook. """ nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None) nb.cells.extend([ nbv.new_code_cell("abilog = abilab.abiopen('%s')" % self.filepath), nbv.new_code_cell("print(abilog.events)"), ]) return self._write_nb_nbpath(nb, nbpath)
[docs]class AbinitOutputFile(AbinitTextFile, NotebookWriter): """ Class representing the main Abinit output file. .. rubric:: Inheritance Diagram .. inheritance-diagram:: AbinitOutputFile """ # TODO: Extract number of errors and warnings. def __init__(self, filepath): super().__init__(filepath) self.debug_level = 0 self._parse() def _parse(self): """ header: String with the input variables footer: String with the output variables datasets: Dictionary mapping dataset index to list of strings. """ # Get code version and find magic line signaling that the output file is completed. self.version, self.run_completed = None, False self.overall_cputime, self.overall_walltime = 0.0, 0.0 self.proc0_cputime, self.proc0_walltime = 0.0, 0.0 with open(self.filepath) as fh: for line in fh: if self.version is None and line.startswith(".Version"): self.version = line.split()[1] if line.startswith("- Proc."): #- Proc. 0 individual time (sec): cpu= 25.5 wall= 26.1 tokens = line.split() self.proc0_walltime = float(tokens[-1]) self.proc0_cputime = float(tokens[-3]) if line.startswith("+Overall time"): #+Overall time at end (sec) : cpu= 25.5 wall= 26.1 tokens = line.split() self.overall_cputime = float(tokens[-3]) self.overall_walltime = float(tokens[-1]) if " Calculation completed." in line: self.run_completed = True # Parse header to get important dimensions and variables self.header, self.footer, self.datasets = [], [], OrderedDict() where = "in_header" with open(self.filepath, "rt") as fh: for line in fh: if "== DATASET" in line: # Save dataset number # == DATASET 1 ================================================================== where = int(line.replace("=", "").split()[-1]) assert where not in self.datasets self.datasets[where] = [] elif "== END DATASET(S) " in line: where = "in_footer" if where == "in_header": self.header.append(line) elif where == "in_footer": self.footer.append(line) else: # dataset number --> lines self.datasets[where].append(line) self.header = "".join(self.header) if self.debug_level: print("header:\n", self.header) # Output files produced in dryrun_mode contain the following line: # abinit : before driver, prtvol=0, debugging mode => will skip driver self.dryrun_mode = "debugging mode => will skip driver" in self.header #print("dryrun_mode:", self.dryrun_mode) #if " jdtset " in self.header: raise NotImplementedError("jdtset is not supported") #if " udtset " in self.header: raise NotImplementedError("udtset is not supported") self.ndtset = len(self.datasets) if not self.datasets: #raise NotImplementedError("Empty dataset sections.") self.ndtset = 1 self.datasets[1] = "Empty dataset" for key, data in self.datasets.items(): if self.debug_level: print("data") self.datasets[key] = "".join(data) if self.debug_level: print(self.datasets[key]) self.footer = "".join(self.footer) if self.debug_level: print("footer:\n", self.footer) self.initial_vars_global, self.initial_vars_dataset = self._parse_variables("header") self.final_vars_global, self.final_vars_dataset = None, None if self.run_completed: if self.dryrun_mode: # footer is not present. Copy values from header. self.final_vars_global, self.final_vars_dataset = self.initial_vars_global, self.initial_vars_dataset else: self.final_vars_global, self.final_vars_dataset = self._parse_variables("footer") def _parse_variables(self, what): vars_global = OrderedDict() vars_dataset = OrderedDict([(k, OrderedDict()) for k in self.datasets.keys()]) #print("keys", vars_dataset.keys()) lines = getattr(self, what).splitlines() if what == "header": magic_start = " -outvars: echo values of preprocessed input variables --------" elif what == "footer": magic_start = " -outvars: echo values of variables after computation --------" else: raise ValueError("Invalid value for what: `%s`" % str(what)) magic_stop = "================================================================================" # Select relevant portion with variables. for i, line in enumerate(lines): if magic_start in line: break else: raise ValueError("Cannot find magic_start line: `%s`\nPerhaps this is not an Abinit output file!" % magic_start) lines = lines[i+1:] for i, line in enumerate(lines): if magic_stop in line: break else: raise ValueError("Cannot find magic_stop line: `%s`\nPerhaps this is not an Abinit output file!" % magic_stop) lines = lines[:i] # Parse data. Assume format: # timopt -1 # tnons 0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000 # 0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000 def get_dtindex_key_value(line): tokens = line.split() s, value = tokens[0], " ".join(tokens[1:]) l = [] for i, c in enumerate(s[::-1]): if c.isalpha(): key = s[:len(s)-i] break l.append(c) else: raise ValueError("Cannot find dataset index in token: %s\n" % s) #print(line, "\n", l) dtindex = None if l: l.reverse() dtindex = int("".join(l)) return dtindex, key, value # (varname, dtindex), [line1, line2 ...] stack_var, stack_lines = None, [] def pop_stack(): if stack_lines: key, dtidx = stack_var value = " ".join(stack_lines) if dtidx is None: vars_global[key] = value else: vars_dataset[dtidx][key] = value for line in lines: if not line: continue # Ignore first char line = line[1:].lstrip().rstrip() if not line: continue #print("line", line) if line[0].isalpha(): pop_stack() stack_lines = [] dtidx, key, value = get_dtindex_key_value(line) stack_var = (key, dtidx) stack_lines.append(value) else: stack_lines.append(line) pop_stack() return vars_global, vars_dataset def _get_structures(self, what): if what == "header": vars_global, vars_dataset = self.initial_vars_global, self.initial_vars_dataset elif what == "footer": vars_global, vars_dataset = self.final_vars_global, self.final_vars_dataset else: raise ValueError("Invalid value for what: `%s`" % str(what)) #print("global", vars_global["acell"]) from abipy.abio.abivars import is_abiunit inigeo = {k: vars_global[k] for k in GEOVARS if k in vars_global} spgvars = ("spgroup", "symrel", "tnons", "symafm") spgd_global = {k: vars_global[k] for k in spgvars if k in vars_global} global_kptopt = vars_global.get("kptopt", 1) structures = [] for i in self.datasets: # This code breaks down if there are conflicting GEOVARS in globals and dataset. d = inigeo.copy() d.update({k: vars_dataset[i][k] for k in GEOVARS if k in vars_dataset[i]}) for key, value in d.items(): # Must handle possible unit. fact = 1.0 tokens = [t.lower() for t in value.split()] if is_abiunit(tokens[-1]): tokens, unit = tokens[:-1], tokens[-1] if unit in ("angstr", "angstrom", "angstroms"): fact = 1.0 / bohr_to_ang elif unit in ("bohr", "bohrs", "au"): fact = 1.0 else: raise ValueError("Don't know how to handle unit: %s" % unit) s = " ".join(tokens) dtype = np.float if key not in ("ntypat", "typat", "natom") else np.int try: #print(key, s) value = np.fromstring(s, sep=" ", dtype=dtype) #print(key, value) if fact != 1.0: value *= fact # Do not change integer arrays e.g typat! d[key] = value except ValueError as exc: print(key, s) raise exc if "rprim" not in d and "angdeg" not in d: d["rprim"] = np.eye(3) if "natom" in d and d["natom"] == 1 and all(k not in d for k in ("xred", "xcart", "xangst")): d["xred"] = np.zeros(3) #print(d) abistr = Structure.from_abivars(d) # Extract Abinit spacegroup. spgd = spgd_global.copy() spgd.update({k: vars_dataset[i][k] for k in spgvars if k in vars_dataset[i]}) spgid = int(spgd.get("spgroup", 0)) if "symrel" not in spgd: symrel = np.reshape(np.eye(3, 3, dtype=np.int), (1, 3, 3)) spgd["symrel"] = " ".join((str(i) for i in symrel.flatten())) else: symrel = np.reshape(np.array([int(n) for n in spgd["symrel"].split()], dtype=np.int), (-1, 3, 3)) nsym = len(symrel) assert nsym == spgd.get("nsym", nsym) #; print(symrel.shape) if "tnons" in spgd: tnons = np.reshape(np.array([float(t) for t in spgd["tnons"].split()], dtype=np.float), (nsym, 3)) else: tnons = np.zeros((nsym, 3)) if "symafm" in spgd: symafm = np.array([int(n) for n in spgd["symafm"].split()], dtype=np.int) symafm.shape = (nsym,) else: symafm = np.ones(nsym, dtype=np.int) try: has_timerev = has_timrev_from_kptopt(vars_dataset[i].get("kptopt", global_kptopt)) abi_spacegroup = AbinitSpaceGroup(spgid, symrel, tnons, symafm, has_timerev, inord="C") abistr.set_abi_spacegroup(abi_spacegroup) except Exception as exc: print("Cannot build AbinitSpaceGroup from the variables reported in file!\n", str(exc)) structures.append(abistr) return structures
[docs] @lazy_property def initial_structures(self): """List of initial |Structure|.""" return self._get_structures("header")
@property def has_same_initial_structures(self): """True if all initial structures are equal.""" return all(self.initial_structures[0] == s for s in self.initial_structures)
[docs] @lazy_property def final_structures(self): """List of final |Structure|.""" if self.run_completed: return self._get_structures("footer") else: cprint("Cannot extract final structures from file.\n %s" % self.filepath, "red") return []
[docs] @lazy_property def initial_structure(self): """ The |Structure| defined in the output file. If the input file contains multiple datasets **AND** the datasets have different structures, this property returns None. In this case, one has to access the structure of the individual datasets. For example: self.initial_structures[0] gives the structure of the first dataset. """ if not self.has_same_initial_structures: print("Datasets have different structures. Returning None. Use initial_structures[0]") return None return self.initial_structures[0]
@property def has_same_final_structures(self): """True if all initial structures are equal.""" return all(self.final_structures[0] == s for s in self.final_structures)
[docs] @lazy_property def final_structure(self): """ The |Structure| defined in the output file. If the input file contains multiple datasets **AND** the datasets have different structures, this property returns None. In this case, one has to access the structure of the individual datasets. For example: self.final_structures[0] gives the structure of the first dataset. """ if not self.has_same_final_structures: print("Datasets have different structures. Returning None. Use final_structures[0]") return None return self.final_structures[0]
[docs] def diff_datasets(self, dt_list1, dt_list2, with_params=True, differ="html", dryrun=False): """ Compare datasets """ if not isinstance(dt_list1, (list, tuple)): dt_list1 = [dt_list1] if not isinstance(dt_list2, (list, tuple)): dt_list2 = [dt_list2] dt_lists = [dt_list1, dt_list2] import tempfile tmp_names = [] for i in range(2): _, tmpname = tempfile.mkstemp(text=True) tmp_names.append(tmpname) with open(tmpname, "wt") as fh: if with_params: fh.write(self.header) for idt in dt_lists[i]: fh.write(self.datasets[idt]) if with_params: fh.write(self.footer) if differ == "html": from abipy.tools.devtools import HtmlDiff diff = HtmlDiff(tmp_names) if dryrun: return diff else: return diff.open_browser() else: cmd = "%s %s %s" % (differ, tmp_names[0], tmp_names[1]) if dryrun: return cmd else: return os.system(cmd)
def __str__(self): return self.to_string()
[docs] def to_string(self, verbose=0): """String representation.""" lines = ["ndtset: %d, completed: %s" % (self.ndtset, self.run_completed)] app = lines.append # Different cases depending whether final structures are available # and whether structures are equivalent. if self.run_completed: if self.has_same_final_structures: if self.initial_structure != self.final_structure: # Structural relaxation. df = dataframes_from_structures([self.initial_structure, self.final_structure], index=["initial", "final"]) app("Lattice parameters:") app(str(df.lattice)) app("Atomic coordinates:") app(str(df.coords)) else: # initial == final. Print final structure. app(self.final_structure.to_string(verbose=verbose)) else: # Final structures are not available. if self.has_same_initial_structures: app(self.initial_structure.to_string(verbose=verbose)) else: df = dataframes_from_structures(self.initial_structures, index=[i+1 for i in range(self.ndtset)]) app("Lattice parameters:") app(str(df.lattice)) app("Atomic coordinates:") app(str(df.coords)) # Print dataframe with dimensions. df = self.get_dims_spginfo_dataframe(verbose=verbose) from abipy.tools.printing import print_dataframe strio = StringIO() print_dataframe(df, file=strio) strio.seek(0) app("") app(marquee("Dimensions of calculation", mark="=")) app("".join(strio)) return "\n".join(lines)
[docs] def get_dims_spginfo_dataframe(self, verbose=0): """ Parse the section with the dimensions of the calculation. Return Dataframe. """ dims_dataset, spginfo_dataset = self.get_dims_spginfo_dataset(verbose=verbose) rows = [] for dtind, dims in dims_dataset.items(): d = OrderedDict() d["dataset"] = dtind d.update(dims) d.update(spginfo_dataset[dtind]) rows.append(d) df = pd.DataFrame(rows, columns=list(rows[0].keys()) if rows else None) df = df.set_index('dataset') return df
[docs] def get_dims_spginfo_dataset(self, verbose=0): """ Parse the section with the dimensions of the calculation. Return dictionaries Args: verbose: Verbosity level. Return: (dims_dataset, spginfo_dataset) where dims_dataset[i] is an OrderedDict with the dimensions of dataset `i` spginfo_dataset[i] is a dictionary with space group information. """ # If single dataset, we have to parse # # Symmetries : space group Fd -3 m (#227); Bravais cF (face-center cubic) # ================================================================================ # Values of the parameters that define the memory need of the present run # intxc = 0 ionmov = 0 iscf = 7 lmnmax = 6 # lnmax = 6 mgfft = 18 mpssoang = 3 mqgrid = 3001 # natom = 2 nloc_mem = 1 nspden = 1 nspinor = 1 # nsppol = 1 nsym = 48 n1xccc = 2501 ntypat = 1 # occopt = 1 xclevel = 2 # - mband = 8 mffmem = 1 mkmem = 29 # mpw = 202 nfft = 5832 nkpt = 29 # ================================================================================ # P This job should need less than 3.389 Mbytes of memory. # Rough estimation (10% accuracy) of disk space for files : # _ WF disk file : 0.717 Mbytes ; DEN or POT disk file : 0.046 Mbytes. # ================================================================================ # If multi datasets we have to parse: # DATASET 2 : space group F-4 3 m (#216); Bravais cF (face-center cubic) # ================================================================================ # Values of the parameters that define the memory need for DATASET 2. # intxc = 0 ionmov = 0 iscf = 7 lmnmax = 2 # lnmax = 2 mgfft = 12 mpssoang = 3 mqgrid = 3001 # natom = 2 nloc_mem = 1 nspden = 1 nspinor = 1 # nsppol = 1 nsym = 24 n1xccc = 2501 ntypat = 2 # occopt = 1 xclevel = 1 # - mband = 10 mffmem = 1 mkmem = 2 # mpw = 69 nfft = 1728 nkpt = 2 # ================================================================================ # P This job should need less than 1.331 Mbytes of memory. # Rough estimation (10% accuracy) of disk space for files : # _ WF disk file : 0.023 Mbytes ; DEN or POT disk file : 0.015 Mbytes. # ================================================================================ magic = "Values of the parameters that define the memory need" memory_pre = "P This job should need less than" magic_exit = "------------- Echo of variables that govern the present computation" filesizes_pre = "_ WF disk file :" #verbose = 1 def parse_spgline(line): """Parse the line with space group info, return dict.""" # Could use regular expressions ... i = line.find("space group") spg_str, brav_str = line[i:].replace("space group", "").split(";") toks = spg_str.split() return { "spg_symbol": "".join(toks[:-1]), "spg_number": int(toks[-1].replace("(", "").replace(")", "").replace("#", "")), "bravais": brav_str.strip(), } from abipy.tools.numtools import grouper dims_dataset, spginfo_dataset = OrderedDict(), OrderedDict() inblock = 0 with open(self.filepath, "rt") as fh: for line in fh: line = line.strip() if verbose > 1: print("inblock:", inblock, " at line:", line) if line.startswith(magic_exit): break if (not line or line.startswith("===") or line.startswith("---") #or line.startswith("P") or line.startswith("Rough estimation") or line.startswith("PAW method is used")): continue if line.startswith("DATASET") or line.startswith("Symmetries :"): # Get dataset index, parse space group and lattice info, init new dims dict. inblock = 1 if line.startswith("Symmetries :"): # No multidataset dtindex = 1 else: tokens = line.split() dtindex = int(tokens[1]) dims_dataset[dtindex] = dims = OrderedDict() spginfo_dataset[dtindex] = parse_spgline(line) continue if inblock == 1 and line.startswith(magic): inblock = 2 continue if inblock == 2: # Lines with data. if line.startswith("For the susceptibility"): continue if line.startswith(memory_pre): dims["mem_per_proc_mb"] = float(line.replace(memory_pre, "").split()[0]) elif line.startswith(filesizes_pre): tokens = line.split() mbpos = [i - 1 for i, t in enumerate(tokens) if t.startswith("Mbytes")] assert len(mbpos) == 2 dims["wfk_size_mb"] = float(tokens[mbpos[0]]) dims["denpot_size_mb"] = float(tokens[mbpos[1]]) elif line.startswith("Pmy_natom="): dims.update(my_natom=int(line.replace("Pmy_natom=", "").strip())) #print("my_natom", dims["my_natom"]) else: if line and line[0] == "-": line = line[1:] tokens = grouper(2, line.replace("=", "").split()) if verbose > 1: print("tokens:", tokens) dims.update([(t[0], int(t[1])) for t in tokens]) return dims_dataset, spginfo_dataset
[docs] def next_gs_scf_cycle(self): """ Return the next :class:`GroundStateScfCycle` in the file. None if not found. """ return GroundStateScfCycle.from_stream(self)
[docs] def get_all_gs_scf_cycles(self): """Return list of :class:`GroundStateScfCycle` objects. Empty list if no entry is found.""" # NOTE: get_all should not used with next because of the call to self.seek(0) # The API should be refactored cycles = [] self.seek(0) while True: cycle = self.next_gs_scf_cycle() if cycle is None: break cycles.append(cycle) self.seek(0) return cycles
[docs] def next_d2de_scf_cycle(self): """ Return :class:`D2DEScfCycle` with information on the DFPT iterations. None if not found. """ return D2DEScfCycle.from_stream(self)
[docs] def get_all_d2de_scf_cycles(self): """Return list of :class:`D2DEScfCycle` objects. Empty list if no entry is found.""" cycles = [] self.seek(0) while True: cycle = self.next_d2de_scf_cycle() if cycle is None: break cycles.append(cycle) return cycles
[docs] def plot(self, tight_layout=True, with_timer=False, show=True): """ Plot GS/DFPT SCF cycles and timer data found in the output file. Args: with_timer: True if timer section should be plotted """ from abipy.tools.plotting import MplExpose with MplExpose(slide_mode=False, slide_timeout=5.0) as e: e(self.yield_figs(tight_layout=tight_layout, with_timer=with_timer))
# TODO: Use header and vars to understand if we have SCF/DFPT/Relaxation
[docs] def yield_figs(self, **kwargs): # pragma: no cover """ This function *generates* a predefined list of matplotlib figures with minimal input from the user. """ tight_layout = kwargs.pop("tight_layout", False) with_timer = kwargs.pop("with_timer", True) for icycle, cycle in enumerate(self.get_all_gs_scf_cycles()): yield cycle.plot(title="SCF cycle #%d" % icycle, tight_layout=tight_layout, show=False) for icycle, cycle in enumerate(self.get_all_d2de_scf_cycles()): yield cycle.plot(title="DFPT cycle #%d" % icycle, tight_layout=tight_layout, show=False) if with_timer: self.seek(0) try: yield self.get_timer().plot_all(tight_layout=tight_layout, show=False) except Exception: print("Abinit output files does not contain timopt data")
[docs] def compare_gs_scf_cycles(self, others, show=True): """ Produce and returns a list of matplotlib_ figure comparing the GS self-consistent cycle in self with the ones in others. Args: others: list of :class:`AbinitOutputFile` objects or strings with paths to output files. show: True to diplay plots. """ # Open file here if we receive a string. Files will be closed before returning close_files = [] for i, other in enumerate(others): if is_string(other): others[i] = self.__class__.from_file(other) close_files.append(i) fig, figures = None, [] while True: cycle = self.next_gs_scf_cycle() if cycle is None: break fig = cycle.plot(show=False) for i, other in enumerate(others): other_cycle = other.next_gs_scf_cycle() if other_cycle is None: break last = (i == len(others) - 1) fig = other_cycle.plot(ax_list=fig.axes, show=show and last) if last: fig.tight_layout() figures.append(fig) self.seek(0) for other in others: other.seek(0) if close_files: for i in close_files: others[i].close() return figures
[docs] def compare_d2de_scf_cycles(self, others, show=True): """ Produce and returns a matplotlib_ figure comparing the DFPT self-consistent cycle in self with the ones in others. Args: others: list of :class:`AbinitOutputFile` objects or strings with paths to output files. show: True to diplay plots. """ # Open file here if we receive a string. Files will be closed before returning close_files = [] for i, other in enumerate(others): if is_string(other): others[i] = self.__class__.from_file(other) close_files.append(i) fig, figures = None, [] while True: cycle = self.next_d2de_scf_cycle() if cycle is None: break fig = cycle.plot(show=False) for i, other in enumerate(others): other_cycle = other.next_d2de_scf_cycle() if other_cycle is None: break last = (i == len(others) - 1) fig = other_cycle.plot(ax_list=fig.axes, show=show and last) if last: fig.tight_layout() figures.append(fig) self.seek(0) for other in others: other.seek(0) if close_files: for i in close_files: others[i].close() return figures
[docs] def get_panel(self): """ Build panel with widgets to interact with the Abinit output file either in a notebook or in panel app. """ from abipy.panels.outputs import AbinitOutputFilePanel return AbinitOutputFilePanel(self).get_panel()
[docs] def write_notebook(self, nbpath=None): """ Write a jupyter_ notebook to nbpath. If ``nbpath`` is None, a temporay file in the current working directory is created. Return path to the notebook. """ nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None) nb.cells.extend([ nbv.new_code_cell("abo = abilab.abiopen('%s')" % self.filepath), nbv.new_code_cell("print(abo.events)"), nbv.new_code_cell("abo.plot()"), ]) return self._write_nb_nbpath(nb, nbpath)
[docs]def validate_output_parser(abitests_dir=None, output_files=None): # pragma: no cover """ Validate/test Abinit output parser. Args: dirpath: Abinit tests directory. output_files: List of Abinit output files. Return: Exit code. """ def is_abinit_output(path): """ True if path is one of the output files used in the Abinit Test suite. """ if not path.endswith(".abo"): return False if not path.endswith(".out"): return False with open(path, "rt") as fh: for i, line in enumerate(fh): if i == 1: return line.rstrip().lower().endswith("abinit") return False # Files are collected in paths. paths = [] if abitests_dir is not None: print("Analyzing directory %s for input files" % abitests_dir) for dirpath, dirnames, filenames in os.walk(abitests_dir): for fname in filenames: path = os.path.join(dirpath, fname) if is_abinit_output(path): paths.append(path) if output_files is not None: print("Analyzing files:", str(output_files)) for arg in output_files: if is_abinit_output(arg): paths.append(arg) nfiles = len(paths) if nfiles == 0: cprint("Empty list of input files.", "red") return 0 print("Found %d Abinit output files" % len(paths)) errpaths = [] for path in paths: print(path + ": ", end="") try: out = AbinitOutputFile.from_file(path) s = out.to_string(verbose=2) assert out.run_completed cprint("OK", "green") except Exception as exc: if not isinstance(exc, NotImplementedError): cprint("FAILED", "red") errpaths.append(path) import traceback print(traceback.format_exc()) #print("[%s]: Exception:\n%s" % (path, str(exc))) #with open(path, "rt") as fh: # print(10*"=" + "Input File" + 10*"=") # print(fh.read()) # print() else: cprint("NOTIMPLEMENTED", "magenta") if errpaths: cprint("failed: %d/%d [%.1f%%]" % (len(errpaths), nfiles, 100 * len(errpaths)/nfiles), "red") for i, epath in enumerate(errpaths): cprint("[%d] %s" % (i, epath), "red") else: cprint("All input files successfully parsed!", "green") return len(errpaths)
[docs]class AboRobot(Robot): """ This robot analyzes the results contained in multiple Abinit output files. Can compare dimensions, SCF cycles, analyze timers. .. rubric:: Inheritance Diagram .. inheritance-diagram:: AboRobot """ EXT = "abo"
[docs] def get_dims_dataframe(self, with_time=True, index=None): """ Build and return |pandas-DataFrame| with the dimensions of the calculation. Args: with_time: True if walltime and cputime should be added index: Index of the dataframe. Use relative paths of files if None. """ rows, my_index = [], [] for i, abo in enumerate(self.abifiles): try: dims_dataset, spg_dataset = abo.get_dims_spginfo_dataset() except Exception as exc: cprint("Exception while trying to get dimensions from %s\n%s" % (abo.relpath, str(exc)), "yellow") continue for dtindex, dims in dims_dataset.items(): dims = dims.copy() dims.update({"dtset": dtindex}) # Add walltime and cputime in seconds if with_time: dims.update(OrderedDict([(k, getattr(abo, k)) for k in ("overall_cputime", "proc0_cputime", "overall_walltime", "proc0_walltime")])) rows.append(dims) my_index.append(abo.relpath if index is None else index[i]) return pd.DataFrame(rows, index=my_index, columns=list(rows[0].keys()))
[docs] def get_dataframe(self, with_geo=True, with_dims=True, abspath=False, funcs=None): """ Return a |pandas-DataFrame| with the most important results and the filenames as index. Args: with_geo: True if structure info should be added to the dataframe with_dims: True if dimensions should be added abspath: True if paths in index should be absolute. Default: Relative to getcwd(). funcs: Function or list of functions to execute to add more data to the DataFrame. Each function receives a |GsrFile| object and returns a tuple (key, value) where key is a string with the name of column and value is the value to be inserted. """ rows, row_names = [], [] for label, abo in self.items(): row_names.append(label) d = OrderedDict() if with_dims: dims_dataset, spg_dataset = abo.get_dims_spginfo_dataset() if len(dims_dataset) > 1: cprint("Multiple datasets are not supported. ARGH!", "yellow") d.update(dims_dataset[1]) # Add info on structure. if with_geo and abo.run_completed: d.update(abo.final_structure.get_dict4pandas(with_spglib=True)) # Execute functions if funcs is not None: d.update(self._exec_funcs(funcs, abo)) rows.append(d) row_names = row_names if not abspath else self._to_relpaths(row_names) return pd.DataFrame(rows, index=row_names, columns=list(rows[0].keys()))
[docs] def get_time_dataframe(self): """ Return a |pandas-DataFrame| with the wall-time, cpu time in seconds and the filenames as index. """ rows, row_names = [], [] for label, abo in self.items(): row_names.append(label) d = OrderedDict([(k, getattr(abo, k)) for k in ("overall_cputime", "proc0_cputime", "overall_walltime", "proc0_walltime")]) rows.append(d) return pd.DataFrame(rows, index=row_names, columns=list(rows[0].keys()))
# TODO #def gridplot_timer(self)
[docs] def yield_figs(self, **kwargs): # pragma: no cover """ This function *generates* a predefined list of matplotlib figures with minimal input from the user. """ yield None
[docs] def write_notebook(self, nbpath=None): """ Write a jupyter_ notebook to nbpath. If nbpath is None, a temporay file in the current working directory is created. Return path to the notebook. """ nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None) args = [(l, f.filepath) for l, f in self.items()] nb.cells.extend([ #nbv.new_markdown_cell("# This is a markdown cell"), nbv.new_code_cell("robot = abilab.AboRobot(*%s)\nrobot.trim_paths()\nrobot" % str(args)), nbv.new_code_cell("# robot.get_dims_dataframe()"), nbv.new_code_cell("robot.get_dataframe()"), ]) # Mixins nb.cells.extend(self.get_baserobot_code_cells()) return self._write_nb_nbpath(nb, nbpath)
[docs]class OutNcFile(AbinitNcFile): """ Class representing the _OUT.nc file containing the dataset results produced at the end of the run. The netcdf variables can be accessed via instance attribute e.g. ``outfile.ecut``. Provides integration with ipython_. """ # TODO: This object is deprecated def __init__(self, filepath): super().__init__(filepath) self.reader = NetcdfReader(filepath) self._varscache = {k: None for k in self.reader.rootgrp.variables} def __dir__(self): """Ipython integration.""" return sorted(list(self._varscache.keys())) def __getattribute__(self, name): try: return super().__getattribute__(name) except AttributeError: # Look in self._varscache varscache = super().__getattribute__("_varscache") if name not in varscache: raise AttributeError("Cannot find attribute %s" % name) reader = super().__getattribute__("reader") if varscache[name] is None: varscache[name] = reader.read_value(name) return varscache[name]
[docs] @lazy_property def params(self): """:class:`OrderedDict` with parameters that might be subject to convergence studies.""" return {}
[docs] def close(self): """Close the file.""" self.reader.close()
[docs] def get_allvars(self): """ Read all netcdf_ variables present in the file. Return dictionary varname --> value """ for k, v in self._varscache.items(): if v is not None: continue self._varscache[k] = self.reader.read_value(k) return self._varscache