mirror of https://github.com/abinit/abipy.git
Add output parser for abinit dimensions
This commit is contained in:
Matteo Giantomassi
parent
a6c1143771
commit
89645d377a
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@ -414,6 +414,7 @@ class AbinitOutputFile(AbinitTextFile, NotebookWriter):
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return self.to_string()
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def to_string(self, verbose=0):
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"""String representation."""
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lines = ["ndtset: %d, completed: %s" % (self.ndtset, self.run_completed)]
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app = lines.append
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@ -446,6 +447,119 @@ class AbinitOutputFile(AbinitTextFile, NotebookWriter):
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return "\n".join(lines)
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def get_dims_spginfo_dataset(self, verbose=0):
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"""
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Parse the section with the dimensions of the calculation.
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Args:
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verbose: Verbosity level.
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Return: (dims_dataset, spginfo_dataset)
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where dims_dataset[i] is an OrderedDict with the dimensions of dataset `i`
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spginfo_dataset[i] is a dictionary with space group information.
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"""
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# If single dataset, we have to parse
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#
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# Symmetries : space group Fd -3 m (#227); Bravais cF (face-center cubic)
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# ================================================================================
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# Values of the parameters that define the memory need of the present run
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# intxc = 0 ionmov = 0 iscf = 7 lmnmax = 6
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# lnmax = 6 mgfft = 18 mpssoang = 3 mqgrid = 3001
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# natom = 2 nloc_mem = 1 nspden = 1 nspinor = 1
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# nsppol = 1 nsym = 48 n1xccc = 2501 ntypat = 1
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# occopt = 1 xclevel = 2
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# - mband = 8 mffmem = 1 mkmem = 29
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# mpw = 202 nfft = 5832 nkpt = 29
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# ================================================================================
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# P This job should need less than 3.389 Mbytes of memory.
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# Rough estimation (10% accuracy) of disk space for files :
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# _ WF disk file : 0.717 Mbytes ; DEN or POT disk file : 0.046 Mbytes.
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# ================================================================================
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# If multi datasets we have to parse:
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# DATASET 2 : space group F-4 3 m (#216); Bravais cF (face-center cubic)
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# ================================================================================
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# Values of the parameters that define the memory need for DATASET 2.
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# intxc = 0 ionmov = 0 iscf = 7 lmnmax = 2
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# lnmax = 2 mgfft = 12 mpssoang = 3 mqgrid = 3001
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# natom = 2 nloc_mem = 1 nspden = 1 nspinor = 1
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# nsppol = 1 nsym = 24 n1xccc = 2501 ntypat = 2
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# occopt = 1 xclevel = 1
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# - mband = 10 mffmem = 1 mkmem = 2
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# mpw = 69 nfft = 1728 nkpt = 2
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# ================================================================================
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# P This job should need less than 1.331 Mbytes of memory.
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# Rough estimation (10% accuracy) of disk space for files :
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# _ WF disk file : 0.023 Mbytes ; DEN or POT disk file : 0.015 Mbytes.
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# ================================================================================
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magic = "Values of the parameters that define the memory need"
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memory_pre = "P This job should need less than"
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magic_exit = "------------- Echo of variables that govern the present computation"
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filesizes_pre = "_ WF disk file :"
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def parse_spgline(line):
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"""Parse the line with space group info, return dict."""
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# Could use regular expressions ...
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i = line.find("space group")
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spg_str, brav_str = line[i:].replace("space group", "").split(";")
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toks = spg_str.split()
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return {
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"spg_symbol": "".join(toks[:-1]),
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"spg_number": int(toks[-1].replace("(", "").replace(")", "").replace("#", "")),
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"bravais": brav_str.strip(),
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}
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from abipy.tools.numtools import grouper
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dims_dataset, spginfo_dataset = OrderedDict(), OrderedDict()
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inblock = 0
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with open(self.filepath, "rt") as fh:
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for line in fh:
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line = line.strip()
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if line.startswith(magic_exit):
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break
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if not line or line.startswith("===") or line.startswith("---") or line.startswith("Rough estimation"):
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continue
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if verbose: print("inblock:", inblock, " at line:", line)
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if line.startswith("DATASET") or line.startswith("Symmetries :"):
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# Get dataset index, parse space group and lattice info, init new dims dict.
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inblock = 1
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if line.startswith("Symmetries :"):
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# No multidataset
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dtindex = 1
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else:
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tokens = line.split()
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dtindex = int(tokens[1])
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dims_dataset[dtindex] = dims = OrderedDict()
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spginfo_dataset[dtindex] = parse_spgline(line)
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continue
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if inblock == 1 and line.startswith(magic):
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inblock = 2
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continue
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if inblock == 2:
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# Lines with data.
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if line.startswith(memory_pre):
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dims["mem_per_proc_mb"] = float(line.replace(memory_pre, "").split()[0])
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elif line.startswith(filesizes_pre):
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tokens = line.split()
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mbpos = [i - 1 for i, t in enumerate(tokens) if t.startswith("Mbytes")]
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assert len(mbpos) == 2
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dims["wfk_size_mb"] = float(tokens[mbpos[0]])
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dims["denpot_size_mb"] = float(tokens[mbpos[1]])
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else:
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if line and line[0] == "-": line = line[1:]
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tokens = grouper(2, line.replace("=", "").split())
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if verbose: print("tokens:", tokens)
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dims.update([(t[0], int(t[1])) for t in tokens])
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return dims_dataset, spginfo_dataset
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def next_gs_scf_cycle(self):
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"""
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Return the next :class:`GroundStateScfCycle` in the file. None if not found.
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@ -30,7 +30,6 @@ class AbinitOutputTest(AbipyTest):
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with AbinitOutputFile(abo_path) as abo:
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repr(abo); str(abo)
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assert abo.to_string(verbose=2)
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assert abo.version == "8.0.6"
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assert abo.run_completed
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assert not abo.dryrun_mode
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@ -43,6 +42,25 @@ class AbinitOutputTest(AbipyTest):
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assert abo.initial_structure == abo.final_structure
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abo.diff_datasets(1, 2, dryrun=True)
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# Test the parsing of dimension and spginfo
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dims_dataset, spginfo_dataset = abo.get_dims_spginfo_dataset()
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assert len(dims_dataset) == 2 and list(dims_dataset.keys()) == [1, 2]
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dims1 = dims_dataset[1]
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assert dims1["iscf"] == 7
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assert dims1["nfft"] == 5832
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self.assert_almost_equal(dims1["mem_per_proc_mb"], 3.045)
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self.assert_almost_equal(dims1["wfk_size_mb"], 0.717)
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self.assert_almost_equal(dims1["denpot_size_mb"], 0.046)
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assert spginfo_dataset[1]["spg_symbol"] == "Fd-3m"
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assert spginfo_dataset[1]["spg_number"] == 227
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assert spginfo_dataset[1]["bravais"] == "Bravais cF (face-center cubic)"
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dims2 = dims_dataset[2]
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assert dims2["iscf"] == -2
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assert dims2["n1xccc"] == 2501
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self.assert_almost_equal(dims2["mem_per_proc_mb"], 1.901)
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self.assert_almost_equal(dims2["wfk_size_mb"], 0.340)
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self.assert_almost_equal(dims2["denpot_size_mb"], 0.046)
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print(abo.events)
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gs_cycle = abo.next_gs_scf_cycle()
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assert gs_cycle is not None
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@ -107,6 +125,20 @@ class AbinitOutputTest(AbipyTest):
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assert abo.initial_structure.abi_spacegroup is not None
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# This to test get_dims_spginfo_dataset with one dataset.
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dims_dataset, spg_dataset = abo.get_dims_spginfo_dataset()
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assert len(dims_dataset) == 1
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dims = dims_dataset[1]
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assert dims["nsppol"] == 1
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assert dims["nsym"] == 48
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assert dims["nkpt"] == 29
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self.assert_almost_equal(dims["mem_per_proc_mb"], 3.389)
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self.assert_almost_equal(dims["wfk_size_mb"], 0.717)
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self.assert_almost_equal(dims["denpot_size_mb"], 0.046)
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assert spg_dataset[1]["spg_symbol"] == "Fd-3m"
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assert spg_dataset[1]["spg_number"] == 227
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assert spg_dataset[1]["bravais"] == "Bravais cF (face-center cubic)"
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def test_all_outputs_in_tests(self):
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"""
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Try to parse all Abinit output files inside the Abinit `tests` directory.
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@ -92,7 +92,7 @@ class A2f(object):
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# TODO: Add ElectronDos
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app("Isotropic lambda: %.3f" % (self.lambda_iso))
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app("Omega_log: %s [eV], %s [K]" % (self.omega_log, self.omega_log * abu.eV_to_K))
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for mustar in (0.1, 0.2):
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for mustar in (0.1, 0.12, 0.2):
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app("\tFor mustar %s: McMillan Tc: %s [K]" % (mustar, self.get_mcmillan_tc(mustar)))
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if verbose:
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@ -114,20 +114,15 @@ class A2f(object):
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"""
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#return 270 / abu.eV_to_K
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iw = self.iw0 + 1
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#iw = self.iw0 + 100
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wmesh, a2fw = self.mesh[iw:], self.values[iw:]
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#wmesh = wmesh * units.eV_to_Ha
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#wmesh = wmesh * abu.eV_to_THz
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#ax, fig, plt = get_ax_fig_plt(ax=None)
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#ax.plot(wmesh, a2fw / wmesh * np.log(wmesh))
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#plt.show()
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integral = simps(a2fw / wmesh * np.log(wmesh), x=wmesh)
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#return np.exp(2.0 / self.lambda_iso * integral) * units.Ha_to_eV
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#return np.exp(2.0 / self.lambda_iso * integral) / abu.eV_to_THz
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return np.exp(2.0 / self.lambda_iso * integral) #/ abu.eV_to_THz
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fw = a2fw / wmesh * np.log(wmesh)
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integral = simps(fw, x=wmesh)
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return np.exp(1.0 / self.lambda_iso * integral)
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def get_moment(self, n, spin=None, cumulative=False):
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r"""
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@ -166,6 +161,9 @@ class A2f(object):
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def get_mcmillan_tc(self, mustar):
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"""
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Computes the critical temperature with the McMillan equation and the input mustar.
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Return:
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Tc in Kelvin degrees
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"""
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tc = (self.omega_log / 1.2) * \
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np.exp(-1.04 * (1.0 + self.lambda_iso) / (self.lambda_iso - mustar * (1.0 + 0.62 * self.lambda_iso)))
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@ -173,7 +171,11 @@ class A2f(object):
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def get_mustar_from_tc(self, tc):
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"""
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Return the value of mustar that gives the critical temperature tc in K in the McMillan equation.
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Return the value of mustar that gives the critical temperature `tc` in the McMillan equation.
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Args:
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tc:
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Critical temperature in Kelvin
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"""
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l = self.lambda_iso
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num = l + (1.04 * (1 + l) / np.log(1.2 * abu.kb_eVK * tc / self.omega_log))
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@ -383,6 +385,7 @@ class A2f(object):
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Returns:
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`matplotlib` figure
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"""
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# TODO start and stop to avoid singularity in Mc Tc
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mustar_values = np.linspace(start, stop, num=num)
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tc_vals = [self.get_mcmillan_tc(mustar) for mustar in mustar_values]
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@ -426,7 +429,6 @@ class A2Ftr(object):
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raise ValueError("Cannot find zero in energy mesh")
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# TODO Change name.
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class EphFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter):
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"""
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@ -471,9 +473,10 @@ class EphFile(AbinitNcFile, Has_Structure, Has_ElectronBands, NotebookWriter):
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app("")
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# E-PH section
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app(marquee("E-PH calculation", mark="="))
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app(self.a2f_qcoarse.to_string(title="A2f coarse:", verbose=verbose))
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app("Has transport a2Ftr(w): %s" % self.has_a2ftr)
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app(self.a2f_qcoarse.to_string(title="A2f(w) on the ab-initio q-mesh:", verbose=verbose))
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app("")
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app(self.a2f_qintp.to_string(title="A2f interpolated:", verbose=verbose))
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app(self.a2f_qintp.to_string(title="A2f(w) interpolated on the dense q-mesh:", verbose=verbose))
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return "\n".join(lines)
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@ -327,6 +327,55 @@ def flow_compare_hist(flow, nids=None, with_spglib=False, verbose=0,
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return df
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def flow_get_dims_dataframe(flow, nids=None, printout=False, with_colors=False):
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"""
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Analyze output files produced by Abinit tasks. Print pandas DataFrame with dimensions.
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Args:
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nids: List of node identifiers. By defaults all nodes are shown
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printout: True to print dataframe.
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with_colors: True if task status should be colored.
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"""
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abo_paths, index, status, abo_relpaths, task_classes = [], [], [], [], []
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for task in flow.iflat_tasks(nids=nids):
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if task.status not in (flow.S_OK, flow.S_RUN): continue
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#if not task.is_abinit_task: continue
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abo_paths.append(task.output_file.path)
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index.append(task.pos_str)
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status.append(task.status.colored if with_colors else str(task.status))
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abo_relpaths.append(os.path.relpath(task.output_file.relpath))
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task_classes.append(task.__class__.__name__)
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if not abo_paths: return
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# Get dimensions from output files.
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rows = []
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for p in abo_paths:
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print(p)
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with abilab.AbinitOutputFile(p) as abo:
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try:
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dims_dataset, spg_dataset = abo.get_dims_spginfo_dataset()
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except Exception as exc:
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cprint("Exception while trying to get dimensions from %s\n%s" % (p, str(exc)), "yellow")
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continue
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rows.append(dims_dataset[1])
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import pandas as pd
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df = pd.DataFrame(rows, index=index, columns=list(rows[0].keys()))
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# Add columns to the dataframe.
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status = [str(s) for s in status]
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df["task_class"] = task_classes
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df["relpath"] = abo_relpaths
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df["status"] = status
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if printout:
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abilab.print_dataframe(df, title="Table with Abinit dimensions:\n")
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return df
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def flow_compare_abivars(flow, varnames, nids=None, wslice=None, printout=False, with_colors=False):
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"""
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Print the input of the tasks to the given stream.
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@ -527,8 +576,9 @@ Usage example:
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abirun.py [FLOWDIR] abivars -vn ecut,nband => Print table with these input variables.
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abirun.py [FLOWDIR] structures => Compare input/output structures of the tasks.
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abirun.py [FLOWDIR] ebands => Print table with electronic properties.
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abirun.py [FLOWDIR] hist => Print table with last iteratin in hist files.
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abirun.py [FLOWDIR] hist => Print table with last iteration in hist files.
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abirun.py [FLOWDIR] cycles => Print SCF cycles extracted from the output of the tasks.
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abirun.py [FLOWDIR] dims => Print table with dimensions extracted from the output of the tasks.
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abirun.py [FLOWDIR] inspect => Call matplotlib to inspect the tasks
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abirun.py [FLOWDIR] tail => Use unix tail to follow the main output files of the flow.
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abirun.py [FLOWDIR] deps => Show task dependencies.
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@ -669,7 +719,7 @@ def get_parser(with_epilog=False):
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# Subparser for scheduler command.
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p_scheduler = subparsers.add_parser('scheduler', parents=[copts_parser],
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help="Run all tasks with a Python scheduler. Requires scheduler.yml.")
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help="Run all tasks with a Python scheduler. Requires scheduler.yml either in $PWD or ~/.abinit/abipy.")
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p_scheduler.add_argument('-w', '--weeks', default=0, type=int, help="Number of weeks to wait.")
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p_scheduler.add_argument('-d', '--days', default=0, type=int, help="Number of days to wait.")
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p_scheduler.add_argument('-hs', '--hours', default=0, type=int, help="Number of hours to wait.")
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@ -697,7 +747,7 @@ def get_parser(with_epilog=False):
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# Subparser for cancel command.
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p_cancel = subparsers.add_parser('cancel', parents=[copts_parser, flow_selector_parser],
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help="Cancel the tasks in the queue. Not available if qtype == shell.")
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help="Cancel the tasks in the queue. Not available if qtype is shell.")
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p_cancel.add_argument("-r", "--rmtree", action="store_true", default=False, help="Remove flow directory.")
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# Subparser for restart command.
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@ -783,6 +833,10 @@ Specify the files to open. Possible choices:
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p_cycles = subparsers.add_parser('cycles', parents=[copts_parser, flow_selector_parser],
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help="Print SCF cycles extracted from the output of the tasks.")
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# Subparser for dims.
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p_dims = subparsers.add_parser('dims', parents=[copts_parser, flow_selector_parser],
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help="Print table with dimensions extracted from the output of the tasks.")
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# Subparser for inspect.
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p_inspect = subparsers.add_parser('inspect', parents=[copts_parser, flow_selector_parser],
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help="Call matplotlib to inspect the tasks (execute task.inspect method)")
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@ -1294,6 +1348,10 @@ def main():
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print(cycle)
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print()
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elif options.command == "dims":
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flow_get_dims_dataframe(flow, nids=selected_nids(flow, options),
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printout=True, with_colors=not options.no_colors)
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elif options.command == "inspect":
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tasks = flow.select_tasks(nids=options.nids, wslice=options.wslice)
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@ -95,6 +95,20 @@ def iflat(iterables):
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yield it
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def grouper(n, iterable, fillvalue=None):
|
||||
"""
|
||||
>>> assert grouper(3, "ABCDEFG", "x") == ["ABC", "DEF" "Gxx"]
|
||||
"""
|
||||
# https://stackoverflow.com/questions/434287/what-is-the-most-pythonic-way-to-iterate-over-a-list-in-chunks/434411#434411
|
||||
try:
|
||||
from itertools import zip_longest
|
||||
except ImportError:
|
||||
from itertools import izip_longest as zip_longest
|
||||
|
||||
args = [iter(iterable)] * n
|
||||
return list(zip_longest(fillvalue=fillvalue, *args))
|
||||
|
||||
|
||||
#########################################################################################
|
||||
# Sorting and ordering
|
||||
#########################################################################################
|
||||
|
|
|
|||
|
|
@ -347,7 +347,7 @@ class TestAbirun(ScriptTest):
|
|||
# Test abirun commands requiring a flow (no submission)
|
||||
for command in ["status", "debug", "debug_reset", "deps", "inputs", "corrections", "events",
|
||||
"history", "handlers", "cancel", "tail", "inspect", "structures", "ebands", "hist",
|
||||
"cycles", "tricky",]:
|
||||
"cycles", "dims", "tricky",]:
|
||||
r = env.run(self.script, flowdir, command, self.loglevel, self.verbose, *no_logo_colors,
|
||||
expect_stderr=self.expect_stderr)
|
||||
assert r.returncode == 0
|
||||
|
|
|
|||
Loading…
Reference in New Issue