Source code for ase.calculators.fleur

"""This module defines an ASE interface to FLAPW code FLEUR.

http://www.flapw.de
"""

import os

from subprocess import Popen, PIPE

import re

import numpy as np

from ase.units import Hartree, Bohr
from ase.calculators.calculator import PropertyNotImplementedError

class FLEUR:
    """Class for doing FLEUR calculations.

    In order to use fleur one has to define the following environment
    variables:

    FLEUR_INPGEN path to the input generator (inpgen.x) of fleur

    FLEUR path to the fleur executable. Note that fleur uses different
    executable for real and complex cases (systems with/without inversion
    symmetry), so FLEUR must point to the correct executable.

    The initialize_density step can be performed in parallel
    only if run on one compute node. FLEUR_SERIAL is used for this step.

    It is probable that user needs to tune manually the input file before
    the actual calculation, so in addition to the standard
    get_potential_energy function this class defines the following utility
    functions:

    write_inp
        generate the input file *inp*
    initialize_density
        creates the initial density after possible manual edits of *inp*
    calculate
        convergence the total energy. With fleur, one specifies always
        only the number of SCF-iterations so this function launches
        the executable several times and monitors the convergence.
    relax
        Uses fleur's internal algorithm for structure
        optimization. Requires that the proper optimization parameters
        (atoms to optimize etc.) are specified by hand in *inp*

    """
    def __init__(self, xc='LDA', kpts=None, nbands=None, convergence=None,
                 width=None, kmax=None, mixer=None, maxiter=None,
                 maxrelax=20, workdir=None, equivatoms=True, rmt=None,
                 lenergy=None):

        """Construct FLEUR-calculator object.

        Parameters
        ==========
        xc: str
            Exchange-correlation functional. Must be one of LDA, PBE,
            RPBE.
        kpts: list of three int
            Monkhost-Pack sampling.
        nbands: int
            Number of bands. (not used at the moment)
        convergence: dictionary
            Convergence parameters (currently only energy in eV)
            {'energy' : float}
        width: float
            Fermi-distribution width in eV.
        kmax: float
            Plane wave cutoff in a.u. If kmax is set then:
            gmax = 3.0 * kmax
            gmaxxc = int(2.5 * kmax * 10)/10. (from set_inp.f)
        mixer: dictionary
            Mixing parameters imix, alpha, spinf
            {'imix' : int, 'alpha' : float, 'spinf' : float}
        maxiter: int
            Maximum number of SCF iterations (name in the code: itmax)
        maxrelax: int
            Maximum number of relaxation steps
        workdir: str
            Working directory for the calculation
        equivatoms: bool
            If False: generate inequivalent atoms (default is True).
            Setting to False allows one for example to calculate spin-polarized dimers.
            See http://www.flapw.de/pm/index.php?n=User-Documentation.InputFileForTheInputGenerator.
        rmt: dictionary
            rmt values in Angstrom., e.g: {'O': 1.1 * Bohr, 'N': -0.1}
            Negative number with respect to the rmt set by FLEUR.
        lenergy: float
            Lower energy in eV. Default -1.8 * Hartree.
        """

        self.xc = xc
        self.kpts = kpts
        self.nbands = nbands
        self.width = width
        self.kmax = kmax
        self.itmax_step_default = 9 # SCF steps per run (default)
        self.itmax_step = 5 # SCF steps per run
        assert self.itmax_step_default <= 9
        assert self.itmax_step <= self.itmax_step_default
        self.itmax_default = 40
        if maxiter is None:
            self.itmax = self.itmax_default
        else:
            self.itmax = maxiter
        self.maxrelax = maxrelax
        self.mixer = mixer

        if convergence:
            self.convergence = convergence
            self.convergence['energy'] /= Hartree
        else:
            self.convergence = {'energy' : 0.0001}

        self.start_dir = None
        self.workdir = workdir
        if self.workdir:
            self.start_dir = os.getcwd()
            if not os.path.isdir(workdir):
                os.mkdir(workdir)
        else:
            self.workdir = '.'
            self.start_dir = '.'

        self.equivatoms = equivatoms

        self.rmt = rmt
        self.lenergy = lenergy

        self.converged = False

    def run_executable(self, mode='fleur', executable='FLEUR'):

        assert executable in ['FLEUR', 'FLEUR_SERIAL']

        executable_use = executable
        if executable == 'FLEUR_SERIAL' and not os.environ.get(executable, ''):
            executable_use = 'FLEUR' # use FLEUR if FLEUR_SERIAL not set
        try:
            code_exe = os.environ[executable_use]
        except KeyError:
            raise RuntimeError('Please set ' + executable_use)
        p = Popen(code_exe, shell=True, stdin=PIPE, stdout=PIPE,
                  stderr=PIPE)
        stat = p.wait()
        out = p.stdout.read()
        err = p.stderr.read()
        print(mode, ': stat= ', stat, ' out= ', out, ' err=', err)
        # special handling of exit status from density generation and regular fleur.x
        if mode in ['density']:
            if '!' in err:
                os.chdir(self.start_dir)
                raise RuntimeError(executable_use + ' exited with a code %s' % err)
        else:
            if stat != 0:
                os.chdir(self.start_dir)
                raise RuntimeError(executable_use + ' exited with a code %d' % stat)


    def update(self, atoms):
        """Update a FLEUR calculation."""

        if (not self.converged or
            len(self.numbers) != len(atoms) or
            (self.numbers != atoms.get_atomic_numbers()).any()):
            self.initialize(atoms)
            self.calculate(atoms)
        elif ((self.positions != atoms.get_positions()).any() or
              (self.pbc != atoms.get_pbc()).any() or
              (self.cell != atoms.get_cell()).any()):
            self.converged = False
            self.initialize(atoms)
            self.calculate(atoms)

    def initialize(self, atoms):
        """Create an input file inp and generate starting density."""

        self.converged = False
        self.initialize_inp(atoms)
        self.initialize_density(atoms)

    def initialize_inp(self, atoms):
        """Create a inp file"""
        os.chdir(self.workdir)

        self.numbers = atoms.get_atomic_numbers().copy()
        self.positions = atoms.get_positions().copy()
        self.cell = atoms.get_cell().copy()
        self.pbc = atoms.get_pbc().copy()

        # create the input
        self.write_inp(atoms)

        os.chdir(self.start_dir)

[docs] def initialize_density(self, atoms): """Creates a new starting density.""" os.chdir(self.workdir) # remove possible conflicting files files2remove = ['cdn1', 'fl7para', 'stars', 'wkf2', 'enpara', 'kpts', 'broyd', 'broyd.7', 'tmat', 'tmas'] if 0: # avoid STOP bzone3 error by keeping the kpts file files2remove.remove('kpts') for f in files2remove: if os.path.isfile(f): os.remove(f) # generate the starting density os.system("sed -i -e 's/strho=./strho=T/' inp") self.run_executable(mode='density', executable='FLEUR_SERIAL') os.system("sed -i -e 's/strho=./strho=F/' inp") os.chdir(self.start_dir) # generate spin-polarized density # http://www.flapw.de/pm/index.php?n=User-Documentation.Magnetism if atoms.get_initial_magnetic_moments().sum() > 0.0: os.chdir(self.workdir) # generate cdnc file (1 SCF step: swsp=F - non-magnetic) os.system("sed -i -e 's/itmax=.*,maxiter/itmax= 1,maxiter/' inp") self.run_executable(mode='cdnc', executable='FLEUR') sedline = "'s/itmax=.*,maxiter/itmax= '" sedline += str(self.itmax_step_default) + "',maxiter/'" os.system("sed -i -e " + sedline + " inp") # generate spin polarized density (swsp=T) os.system("sed -i -e 's/swsp=./swsp=T/' inp") self.run_executable(mode='swsp', executable='FLEUR_SERIAL') # restore swsp=F os.system("sed -i -e 's/swsp=./swsp=F/' inp") os.chdir(self.start_dir)
def get_potential_energy(self, atoms, force_consistent=False): self.update(atoms) if force_consistent: return self.efree * Hartree else: # Energy extrapolated to zero Kelvin: return (self.etotal + self.efree) / 2 * Hartree def get_number_of_iterations(self, atoms): self.update(atoms) return self.niter def get_forces(self, atoms): self.update(atoms) # electronic structure is converged, so let's calculate forces: # TODO return np.array((0.0, 0.0, 0.0)) def get_stress(self, atoms): raise PropertyNotImplementedError def get_dipole_moment(self, atoms): """Returns total dipole moment of the system.""" raise PropertyNotImplementedError
[docs] def calculate(self, atoms): """Converge a FLEUR calculation to self-consistency. Input files should be generated before calling this function FLEUR performs always fixed number of SCF steps. This function reduces the number of iterations gradually, however, a minimum of five SCF steps is always performed. """ os.chdir(self.workdir) self.niter = 0 out = '' err = '' while not self.converged: if self.niter > self.itmax: os.chdir(self.start_dir) raise RuntimeError('FLEUR failed to convergence in %d iterations' % self.itmax) self.run_executable(mode='fleur', executable='FLEUR') # catenate new output with the old one os.system('cat out >> out.old') self.read() self.check_convergence() if os.path.exists('out.old'): os.rename('out.old', 'out') # After convergence clean up broyd* files os.system('rm -f broyd*') os.chdir(self.start_dir) return out, err
[docs] def relax(self, atoms): """Currently, user has to manually define relaxation parameters (atoms to relax, relaxation directions, etc.) in inp file before calling this function.""" nrelax = 0 relaxed = False while not relaxed: # Calculate electronic structure self.calculate(atoms) # Calculate the Pulay forces os.system("sed -i -e 's/l_f=./l_f=T/' inp") while True: self.converged = False out, err = self.calculate(atoms) if 'GEO new' in err: os.chdir(self.workdir) os.rename('inp_new', 'inp') os.chdir(self.start_dir) break if 'GEO: Des woas' in err: relaxed = True break nrelax += 1 # save the out and cdn1 files os.system('cp out out_%d' % nrelax) os.system('cp cdn1 cdn1_%d' % nrelax) if nrelax > self.maxrelax: os.chdir(self.start_dir) raise RuntimeError('Failed to relax in %d iterations' % self.maxrelax) self.converged = False
[docs] def write_inp(self, atoms): """Write the *inp* input file of FLEUR. First, the information from Atoms is written to the simple input file and the actual input file *inp* is then generated with the FLEUR input generator. The location of input generator is specified in the environment variable FLEUR_INPGEN. Finally, the *inp* file is modified according to the arguments of the FLEUR calculator object. """ fh = open('inp_simple', 'w') fh.write('FLEUR input generated with ASE\n') fh.write('\n') if atoms.pbc[2]: film = 'f' else: film = 't' fh.write('&input film=%s /' % film) fh.write('\n') for vec in atoms.get_cell(): fh.write(' ') for el in vec: fh.write(' %21.16f' % (el/Bohr)) fh.write('\n') fh.write(' %21.16f\n' % 1.0) fh.write(' %21.16f %21.16f %21.16f\n' % (1.0, 1.0, 1.0)) fh.write('\n') natoms = len(atoms) fh.write(' %6d\n' % natoms) positions = atoms.get_scaled_positions() if not atoms.pbc[2]: # in film calculations z position has to be in absolute # coordinates and symmetrical cart_pos = atoms.get_positions() cart_pos[:, 2] -= atoms.get_cell()[2, 2]/2.0 positions[:, 2] = cart_pos[:, 2] / Bohr atomic_numbers = atoms.get_atomic_numbers() for n, (Z, pos) in enumerate(zip(atomic_numbers, positions)): if self.equivatoms: fh.write('%3d' % Z) else: # generate inequivalent atoms, by using non-integer Z # (only the integer part will be used as Z of the atom) # see http://www.flapw.de/pm/index.php?n=User-Documentation.InputFileForTheInputGenerator fh.write('%3d.%04d' % (Z, n)) # MDTMP don't think one can calculate more that 10**4 atoms for el in pos: fh.write(' %21.16f' % el) fh.write('\n') # avoid "STOP read_record: ERROR reading input" fh.write('&end /') fh.close() try: inpgen = os.environ['FLEUR_INPGEN'] except KeyError: raise RuntimeError('Please set FLEUR_INPGEN') # rename the previous inp if it exists if os.path.isfile('inp'): os.rename('inp', 'inp.bak') os.system('%s -old < inp_simple' % inpgen) # read the whole inp-file for possible modifications fh = open('inp', 'r') lines = fh.readlines() fh.close() window_ln = -1 for ln, line in enumerate(lines): # XC potential if line.startswith('pbe'): if self.xc == 'PBE': pass elif self.xc == 'RPBE': lines[ln] = 'rpbe non-relativi\n' elif self.xc == 'LDA': lines[ln] = 'mjw non-relativic\n' del lines[ln+1] else: raise RuntimeError('XC-functional %s is not supported' % self.xc) if line.startswith('Window'): # few things are set around this line window_ln = ln # kmax if self.kmax and ln == window_ln: line = '%10.5f\n' % self.kmax lines[ln+2] = line # lower energy if self.lenergy is not None and ln == window_ln: l0 = lines[ln+1].split()[0] l = lines[ln+1].replace(l0, '%8.5f' % (self.lenergy / Hartree)) lines[ln+1] = l # gmax cutoff for PW-expansion of potential & density ( > 2*kmax) # gmaxxc cutoff for PW-expansion of XC-potential ( > 2*kmax, < gmax) if self.kmax and line.startswith('vchk'): gmax = 3. * self.kmax line = ' %10.6f %10.6f\n' % (gmax, int(2.5 * self.kmax * 10)/10.) lines[ln-1] = line # Fermi width if self.width and line.startswith('gauss'): line = 'gauss=F %7.5ftria=F\n' % (self.width / Hartree) lines[ln] = line # kpts if self.kpts and line.startswith('nkpt'): line = 'nkpt= nx=%2d,ny=%2d,nz=%2d\n' % (self.kpts[0], self.kpts[1], self.kpts[2]) lines[ln] = line # itmax if self.itmax < self.itmax_step_default and line.startswith('itmax'): # decrease number of SCF steps; increasing is done by 'while not self.converged:' lsplit = line.split(',') if lsplit[0].find('itmax') != -1: lsplit[0] = 'itmax=' + ('%2d' % self.itmax) lines[ln] = ",".join(lsplit) # Mixing if self.mixer and line.startswith('itmax'): imix = self.mixer['imix'] alpha = self.mixer['alpha'] spinf = self.mixer['spinf'] line_end = 'imix=%2d,alpha=%6.2f,spinf=%6.2f\n' % (imix, alpha, spinf) line = line[:21] + line_end lines[ln] = line # jspins and swsp if atoms.get_initial_magnetic_moments().sum() > 0.0: assert not self.equivatoms, 'equivatoms currently not allowed in magnetic systems' if line.find('jspins=1') != -1: lines[ln] = line.replace('jspins=1', 'jspins=2') if line.startswith('swsp=F'): # setting initial magnetic moments for all atom types lines[ln] = 'swsp=F' for m in atoms.get_initial_magnetic_moments(): lines[ln] += (' %5.2f' % m) lines[ln] += '\n' # inpgen produces incorrect symbol 'J' for Iodine if line.startswith(' J 53'): lines[ln] = lines[ln].replace(' J 53', ' I 53') # rmt if self.rmt is not None: for s in list(set(atoms.get_chemical_symbols())): # unique if s in self.rmt: # set the requested rmt for ln, line in enumerate(lines): ls = line.split() if len(ls) == 7 and ls[0].strip() == s: rorig = ls[5].strip() if self.rmt[s] < 0.0: r = float(rorig) + self.rmt[s] / Bohr else: r = self.rmt[s] / Bohr print(s, rorig, r) lines[ln] = lines[ln].replace(rorig, ("%.6f" % r)) # write everything back to inp fh = open('inp', 'w') for line in lines: fh.write(line) fh.close()
def read(self): """Read results from FLEUR's text-output file `out`.""" lines = open('out', 'r').readlines() # total energies self.total_energies = [] pat = re.compile(r'(.*total energy=)(\s)*([-0-9.]*)') for line in lines: m = pat.match(line) if m: self.total_energies.append(float(m.group(3))) self.etotal = self.total_energies[-1] # free_energies self.free_energies = [] pat = re.compile(r'(.*free energy=)(\s)*([-0-9.]*)') for line in lines: m = pat.match(line) if m: self.free_energies.append(float(m.group(3))) self.efree = self.free_energies[-1] # TODO forces, charge density difference... def check_convergence(self): """Check the convergence of calculation""" energy_error = np.ptp(self.total_energies[-3:]) self.converged = energy_error < self.convergence['energy'] # TODO check charge convergence # reduce the itmax in inp lines = open('inp', 'r').readlines() pat = re.compile('(itmax=)([ 0-9]*)') fh = open('inp', 'w') for line in lines: m = pat.match(line) if m: itmax = int(m.group(2)) self.niter += itmax itmax_new = itmax // 2 itmax = max(self.itmax_step, itmax_new) line = 'itmax=%2d' % itmax + line[8:] fh.write(line) fh.close()