Chimie Théorique » QMX

#!/usr//bin/env python

# lammps.py (2011/02/22)

# An ASE calculator for the LAMMPS classical MD code available from

#       http://lammps.sandia.gov/

# The environment variable LAMMPS_COMMAND must be defined to point to the LAMMPS binary.

#

# Copyright (C) 2009 - 2011 Joerg Meyer, joerg.meyer@ch.tum.de

#

# This library is free software; you can redistribute it and/or

# modify it under the terms of the GNU Lesser General Public

# License as published by the Free Software Foundation; either

# version 2.1 of the License, or (at your option) any later version.

#

# This library is distributed in the hope that it will be useful,

# but WITHOUT ANY WARRANTY; without even the implied warranty of

# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU

# Lesser General Public License for more details.

#

# You should have received a copy of the GNU Lesser General Public

# License along with this file; if not, write to the Free Software

# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA

# or see <http://www.gnu.org/licenses/>.

import os

import shutil

import time

import math

import decimal as dec

import numpy as np

from ase import Atoms

from ase.parallel import paropen

class LAMMPS:

    def __init__(self, label="lammps", dir="LAMMPS", parameters={}, files=[], always_triclinic=False):

        self.label = label

        self.dir = dir

        self.parameters = parameters

        self.files = files

        self.always_triclinic = always_triclinic

        self.calls = 0

        self.potential_energy = None

        self.forces = None

        if os.path.isdir(self.dir):

            if (os.listdir(self.dir) == []):

                os.rmdir(self.dir)

            else:

                os.rename(self.dir, self.dir + ".bak-" + time.strftime("%Y%m%d-%H%M%S"))

        os.mkdir(self.dir, 0755)

        for f in files:

            shutil.copy(f, os.path.join(self.dir, f))

    def clean(self, force=False):

        if os.path.isdir(self.dir):

            files_in_dir = os.listdir(self.dir)

            files_copied = self.files

            if (len(files_in_dir) == 0):

                os.rmdir(self.dir)

            elif (set(files_in_dir).issubset(set(files_copied)) or force):

                shutil.rmtree(self.dir)

    def get_potential_energy(self, atoms):

        self.update(atoms)

        return self.potential_energy

    def get_forces(self, atoms):

        self.update(atoms)

        return self.forces.copy()

    def get_stress(self, atoms):

        raise NotImplementedError

    def update(self, atoms):

        # TODO: check if (re-)calculation is necessary

        self.calculate(atoms)

    def calculate(self, atoms):

        self.atoms = atoms.copy()

        self.run()

    def run(self):

        """Method which explicitely runs LAMMPS."""

        self.calls += 1

        # set LAMMPS command from environment variable

        if os.environ.has_key('LAMMPS_COMMAND'):

            lammps_command = os.path.abspath(os.environ['LAMMPS_COMMAND'])

        else:

            self.clean()

            raise RuntimeError('Please set LAMMPS_COMMAND environment variable')

        if os.environ.has_key('LAMMPS_OPTIONS'):

            lammps_options = os.environ['LAMMPS_OPTIONS']

        else:

            lammps_options = "-echo log -screen none"

        # change into subdirectory for LAMMPS calculations

        cwd = os.getcwd()

        os.chdir(self.dir)

        # setup file names for LAMMPS calculation

        label = "%s-%06d" % (self.label, self.calls)

        lammps_data = "data." + label

        lammps_in = "in." + label

        lammps_trj = label + ".lammpstrj"

        lammps_log = label + ".log"

        # write LAMMPS input files

        self.write_lammps_data(lammps_data=lammps_data)

        self.write_lammps_in(lammps_in=lammps_in, lammps_data=lammps_data, lammps_trj=lammps_trj, parameters=self.parameters)

        # run LAMMPS

        # TODO: check for successful completion (based on output files?!) of LAMMPS call...

        exitcode = os.system("%s %s -in %s -log %s" % (lammps_command, lammps_options, lammps_in, lammps_log))

        if exitcode != 0:

            cwd = os.getcwd()

            raise RuntimeError("LAMMPS exited in %s with exit code: %d.  " % (cwd,exitcode))

        # read LAMMPS output files

        self.read_lammps_log(lammps_log=lammps_log)

        self.read_lammps_trj(lammps_trj=lammps_trj)

        # change back to previous working directory

        os.chdir(cwd)

    def write_lammps_data(self, lammps_data=None):

        """Method which writes a LAMMPS data file with atomic structure."""

        if (lammps_data == None):

            lammps_data = "data." + self.label

        write_lammps(lammps_data, self.atoms, force_skew=self.always_triclinic)

    def write_lammps_in(self, lammps_in=None, lammps_data=None, lammps_trj=None, parameters={}):

        """Method which writes a LAMMPS in file with run parameters and settings."""

        if (lammps_in == None):

            lammps_in = "in." + self.label

        if (lammps_data == None):

            lammps_data = "data." + self.label

        if (lammps_trj == None):

            lammps_trj = self.label + ".lammpstrj"

        f = paropen(lammps_in, 'w')

        f.write("# " + f.name + " (written by ASE) \n")

        f.write("\n")

        f.write("### variables \n")

        f.write("variable data_file index \"%s\" \n" % lammps_data)

        f.write("variable dump_file index \"%s\" \n" % lammps_trj)

        f.write("\n\n")

        pbc = self.atoms.get_pbc()

        f.write("### simulation box \n")

        f.write("units metal \n")

        if ("boundary" in parameters):

            f.write("boundary %s \n" % parameters["boundary"])

        else:

            f.write("boundary %c %c %c \n" % tuple('sp'[x] for x in pbc))

        f.write("atom_modify sort 0 0.0 \n")

        for key in ("neighbor" ,"newton"):

            if key in parameters:

                f.write("%s %s \n" % (key, parameters[key]))

        f.write("\n")

        f.write("read_data ${data_file} \n")

        f.write("\n\n")

        f.write("### interactions \n")

        if ( ("pair_style" in parameters) and ("pair_coeff" in parameters) ):

            pair_style = parameters["pair_style"]

            f.write("pair_style %s \n" % pair_style)

            for pair_coeff in parameters["pair_coeff"]:

                f.write("pair_coeff %s \n" % pair_coeff)

            if "mass" in parameters:

                for mass in parameters["mass"]:

                    f.write("mass %s \n" % mass)

        else:

            # simple default parameters that should always make the LAMMPS calculation run

            #    pair_style         lj/cut 2.5

            #    pair_coeff         * * 1 1

            #    mass           * 1.0        else:

            f.write("pair_style lj/cut 2.5 \n")

            f.write("pair_coeff * * 1 1 \n")

            f.write("mass * 1.0 \n")

        f.write("\n")

        f.write("### run \n")

        f.write("fix fix_nve all nve \n")

        f.write("\n")

        f.write("dump dump_all all custom 1 ${dump_file} id type x y z vx vy vz fx fy fz \n")

        f.write("\n")

        f.write("thermo_style custom step temp ke pe etotal cpu \n")

        f.write("thermo_modify format 1 %4d format 2 %9.3f format 3 %20.6f format 4 %20.6f format 5 %20.6f format 6 %9.3f \n")

        f.write("thermo 1 \n")

        f.write("\n")

        if ("minimize" in parameters):

            f.write("minimize %s \n" % parameters["minimize"])

        if ("run" in parameters):

            f.write("run %s \n" % parameters["run"])

        if not ( ("minimize" in parameters) or ("run" in parameters) ):

            f.write("run 0 \n")

        f.close()

    def read_lammps_log(self, lammps_log=None):

        """Method which reads a LAMMPS output log file."""

        if (lammps_log == None):

            lammps_log = self.label + ".log"

        epot = 0.0

        f = paropen(lammps_log, 'r')

        while True:

            line = f.readline()

            if not line:

                break

            # get potential energy of first step (if more are done)

            if "PotEng" in line:

                i = line.split().index("PotEng")

                line = f.readline()

                epot = float(line.split()[i])

        f.close()

#        print epot

        self.potential_energy = epot

    def read_lammps_trj(self, lammps_trj=None, set_atoms=False):

        """Method which reads a LAMMPS dump file."""

        if (lammps_trj == None):

            lammps_trj = self.label + ".lammpstrj"

        f = paropen(lammps_trj, 'r')

        while True:

            line = f.readline()

            if not line:

                break

            #TODO: extend to proper dealing with multiple steps in one trajectory file

            if "ITEM: TIMESTEP" in line:

                n_atoms = 0

                lo = [] ; hi = [] ; tilt = []

                id = [] ; type = []

                positions = [] ; velocities = [] ; forces = []

            if "ITEM: NUMBER OF ATOMS" in line:

                line = f.readline()

                n_atoms = int(line.split()[0])

            if "ITEM: BOX BOUNDS" in line:

                # save labels behind "ITEM: BOX BOUNDS" in triclinic case (>=lammps-7Jul09)

                tilt_items = line.split()[3:]

                for i in range(3):

                    line = f.readline()

                    fields = line.split()

                    lo.append(float(fields[0]))

                    hi.append(float(fields[1]))

                    if (len(fields) >= 3):

                        tilt.append(float(fields[2]))

            if "ITEM: ATOMS" in line:

                # (reliably) identify values by labels behind "ITEM: ATOMS" - requires >=lammps-7Jul09

                # create corresponding index dictionary before iterating over atoms to (hopefully) speed up lookups...

                atom_attributes = {}

                for (i, x) in enumerate(line.split()[2:]):

                    atom_attributes[x] = i

                for n in range(n_atoms):

                    line = f.readline()

                    fields = line.split()

                    id.append( int(fields[atom_attributes['id']]) )

                    type.append( int(fields[atom_attributes['type']]) )

                    positions.append( [ float(fields[atom_attributes[x]]) for x in ['x', 'y', 'z'] ] )

                    velocities.append( [ float(fields[atom_attributes[x]]) for x in ['vx', 'vy', 'vz'] ] )

                    forces.append( [ float(fields[atom_attributes[x]]) for x in ['fx', 'fy', 'fz'] ] )

        f.close()

        # determine cell tilt (triclinic case!)

        if (len(tilt) >= 3):

            # for >=lammps-7Jul09 use labels behind "ITEM: BOX BOUNDS" to assign tilt (vector) elements ...

            if (len(tilt_items) >= 3):

                xy = tilt[tilt_items.index('xy')]

                xz = tilt[tilt_items.index('xz')]

                yz = tilt[tilt_items.index('yz')]

            # ... otherwise assume default order in 3rd column (if the latter was present)

            else:

                xy = tilt[0]

                xz = tilt[1]

                yz = tilt[2]

        else:

            xy = xz = yz = 0

        xhilo = (hi[0] - lo[0]) - xy - xz

        yhilo = (hi[1] - lo[1]) - yz

        zhilo = (hi[2] - lo[2])

        # The simulation box bounds are included in each snapshot and if the box is triclinic (non-orthogonal),

        # then the tilt factors are also printed; see the region prism command for a description of tilt factors.

        # For triclinic boxes the box bounds themselves (first 2 quantities on each line) are a true "bounding box"

        # around the simulation domain, which means they include the effect of any tilt.

        # [ http://lammps.sandia.gov/doc/dump.html , lammps-7Jul09 ]

        #

        # This *should* extract the lattice vectors that LAMMPS uses from the true "bounding box" printed in the dump file

        # It might fail in some cases (negative tilts?!) due to the MIN / MAX construction of these box corners:

        #

        #        void Domain::set_global_box()

        #        [...]

        #          if (triclinic) {

        #            [...]

        #            boxlo_bound[0] = MIN(boxlo[0],boxlo[0]+xy);

        #            boxlo_bound[0] = MIN(boxlo_bound[0],boxlo_bound[0]+xz);

        #            boxlo_bound[1] = MIN(boxlo[1],boxlo[1]+yz);

        #            boxlo_bound[2] = boxlo[2];

        #

        #            boxhi_bound[0] = MAX(boxhi[0],boxhi[0]+xy);

        #            boxhi_bound[0] = MAX(boxhi_bound[0],boxhi_bound[0]+xz);

        #            boxhi_bound[1] = MAX(boxhi[1],boxhi[1]+yz);

        #            boxhi_bound[2] = boxhi[2];

        #          }

        # [ lammps-7Jul09/src/domain.cpp ]

        #

        cell = [[xhilo,0,0],[xy,yhilo,0],[xz,yz,zhilo]]

#       print n_atoms

#       print lo

#       print hi

#       print id

#       print type

#       print positions

#       print velocities

#       print forces

        # assume that LAMMPS does not reorder atoms internally

#        print np.array(positions)

#        print self.atoms.get_positions()

#        print np.array(positions) - self.atoms.get_positions()

        cell_atoms = np.array(cell)

        type_atoms = np.array(type)

#      velocities_atoms = np.array(velocities)

        positions_atoms = np.array(positions)

        forces_atoms = np.array(forces)

        if self.atoms:

            cell_atoms = self.atoms.get_cell()

            rotation_lammps2ase = np.dot(np.linalg.inv(np.array(cell)), cell_atoms)

#           print "rotation_lammps2ase:"

#           print rotation_lammps2ase

#           print np.transpose(rotation_lammps2ase)

#           print np.linalg.det(rotation_lammps2ase)                                            # check for orthogonality of matrix 'rotation'

#           print np.dot(rotation_lammps2ase, np.transpose(rotation_lammps2ase))                # check for orthogonality of matrix 'rotation'

            type_atoms = self.atoms.get_atomic_numbers()

            positions_atoms = np.array( [np.dot(np.array(r), rotation_lammps2ase) for r in positions] )

            velocities_atoms = np.array( [np.dot(np.array(v), rotation_lammps2ase) for v in velocities] )

            forces_atoms = np.array( [np.dot(np.array(f), rotation_lammps2ase) for f in forces] )

        if (set_atoms):

            # assume periodic boundary conditions here (like also below in write_lammps) <- TODO:?!

            self.atoms = Atoms(type_atoms, positions=positions_atoms, cell=cell_atoms, pbc=True)

        self.forces = forces_atoms

# could perhaps go into io.lammps in the future...

#from ase.parallel import paropen

def write_lammps(fileobj, atoms, force_skew=False):

    """Method which writes atomic structure data to a LAMMPS data file."""

    if isinstance(fileobj, file):

        f = fileobj

    elif isinstance(fileobj, str):

        f = paropen(fileobj, 'w')

    else :

        raise TypeError('fileobj is not of type file or str!')

    if isinstance(atoms, list):

        if len(atoms) > 1:

            raise ValueError('Can only write one configuration to a lammps data file!')

        atoms = atoms[0]

    f.write(f.name + " (written by ASE) \n\n")

    symbols = atoms.get_chemical_symbols()

    n_atoms = len(symbols)

    f.write("%d \t atoms \n" % n_atoms)

    # Uniqify 'symbols' list and sort to a new list 'species'.

    # Sorting is important in case of multi-component systems:

    # This way it is assured that LAMMPS atom types are always

    # assigned predictively according to the alphabetic order

    # of the species present in the current system.

    # (Hence e.g. the mapping in interaction statements for alloy

    #  potentials depending on the order of the elements in the

    #  external potential can also be safely adjusted accordingly.)

    species = sorted(list(set(symbols)))

    n_atom_types = len(species)

    f.write("%d \t atom types \n" % n_atom_types)

    ### cell -> bounding box for LAMMPS

    ## A) simple version

    # - For orthogonal cells which are properly aligned with the reference coordinate system only.

#    cell = atoms.get_cell()

#    lo = [0.0, 0.0, 0.0]

#    hi = sum(cell[0:3])

#    f.write("%15.8f %15.8f \t xlo xhi \n" % (lo[0], hi[0]))

#    f.write("%15.8f %15.8f \t ylo yhi \n" % (lo[1], hi[1]))

#    f.write("%15.8f %15.8f \t zlo zhi \n" % (lo[2], hi[2]))

#    f.write("\n\n")

    ## B) convert to (perhaps) triclinic cells in LAMMPS

    # B.1) calculate lengths of and angles between cell vectors

    #     (conventional crystallographic nomenclature)

    cell = atoms.get_cell()

    a = np.linalg.norm(cell[0])

    b = np.linalg.norm(cell[1])

    c = np.linalg.norm(cell[2])

    alpha = np.arccos( np.vdot(cell[1], cell[2]) / (b * c) )

    beta = np.arccos( np.vdot(cell[0], cell[2]) / (a * c) )

    gamma = np.arccos( np.vdot(cell[0], cell[1]) / (a * b) )

#    print [a, b, c]

#    print map(np.degrees, [alpha, beta, gamma])

    # B.2) construct bounding box edges and skew vector of

    #     corresponding (perhaps rotated!) LAMMPS cell

    # http://lammps.sandia.gov/doc/read_data.html :

    #         a_LAMMPS = (xhi-xlo,0,0); b_LAMMPS = (xy,yhi-ylo,0); c_LAMMPS = (xz,yz,zhi-zlo)

    xlo = ylo = zlo = 0.0

    # this choice of origin simplifies things:

    #         a_LAMMPS = (xhi,0,0); b_LAMMPS = (xy,yhi,0); c_LAMMPS = (xz,yz,zhi)

    xhi = a                        # a_LAMMPS

    xy = np.cos(gamma) * b        # b_LAMMPS

    yhi = np.sin(gamma) * b

    xz = np.cos(beta) * c        # c_LAMMPS

    yz = ( b * c * np.cos(alpha) - xy * xz ) / yhi

    zhi = np.sqrt( c**2 - xz**2 - yz**2 )

    # B.3) obtain rotation of original cell with respect to LAMMPS cell

    #     to properly tranform the atoms contained within (see below!)

    # IMPORTANT: use same convention as in cell of ASE atoms object, i.e.

    #            cell vectors are ROW VECTORS in numpy array

    cell_lammps = np.array([[xhi-xlo,0,0],[xy,yhi-ylo,0],[xz,yz,zhi-zlo]])

#    a_lammps = np.linalg.norm(cell_lammps[0])

#    b_lammps = np.linalg.norm(cell_lammps[1])

#    c_lammps = np.linalg.norm(cell_lammps[2])

#    alpha_lammps = np.arccos( np.vdot(cell_lammps[1], cell_lammps[2]) / (b_lammps * c_lammps) )

#    beta_lammps = np.arccos( np.vdot(cell_lammps[0], cell_lammps[2]) / (a_lammps * c_lammps) )

#    gamma_lammps = np.arccos( np.vdot(cell_lammps[0], cell_lammps[1]) / (a_lammps * b_lammps) )

#    print [a_lammps, b_lammps, c_lammps]

#    print map(np.degrees, [alpha_lammps, beta_lammps, gamma_lammps])

    # IMPORTANT: need vector-(rotation-)matrix product (instead of matrix-vector product) here,

    #            cell vectors are ROW VECTORS (also see above)

    rotation = np.dot(np.linalg.inv(cell), cell_lammps)

#    print rotation

#    print np.transpose(rotation)

#    print np.linalg.det(rotation)                                # check for orthogonality of matrix 'rotation'

#    print np.dot(rotation, np.transpose(rotation))                # check for orthogonality of matrix 'rotation'

#    print np.dot(rotation, cell[0])

#    print np.dot(rotation, cell[1])

#    print np.dot(rotation, cell[2])

    # B.4.1) write bounding box edges

    f.write("%15.8f %15.8f \t\t\t xlo xhi \n" % (xlo, xhi))

    f.write("%15.8f %15.8f \t\t\t ylo yhi \n" % (ylo, yhi))

    f.write("%15.8f %15.8f \t\t\t zlo zhi \n" % (zlo, zhi))

    # B.4.2) sanitize and write skew vector (if necessary)

    # The too simple version

    #    f.write("%20.10f %20.10f %20.10f \t xy xz yz \n" % (xy, xz, yz))

    # can make LAMMPS (easily) reject the definition of a triclinic box because

    #        a) skew vector components calculated above are outside the respective ranges

    #           which LAMMPS expects as described here

    #                http://lammps.sandia.gov/doc/read_data.html

    #           and coded here

    #                domain.cpp -> Domain::set_initial_box()

    #         b) rounding up in the skew vector output can make the result violate those

    #      ranges for purely numeric reasons (perhaps even more frequent problem than a)

    #      and definitely more stupid!)

    # More elaborate solution addressing the issues described above:

    # -> a):

    # Fold back skew vector components calculated above to equivalent ones complying with

    # what LAMMPS expects (see references above) and describing another ("less skewed")

    # unit cell for the same lattice:

    #                t -> t_folded in [-period/2, +period/2]

    def fold_skew_dec(t, period) :

        t_dec = dec.Decimal(repr(t))

        period_dec = dec.Decimal(repr(period))

        # dec.ROUND_HALF_DOWN leaves all t in [-period/2, +period/2] unchanged whereas

        # dec.ROUND_HALF_UP does the same for all t in (-period/2, +period/2) but

        # swaps the boundary values:

        #        t=-period/2 -> t_folded=+period/2

        #        t=+period/2 -> t_folded=-period/2

        t_folded_dec = t_dec - period_dec * (t_dec/period_dec).to_integral_value(dec.ROUND_HALF_DOWN)

        return t_folded_dec

    skew_folded_dec = [ fold_skew_dec(xy, xhi-xlo), fold_skew_dec(xz, xhi-xlo), fold_skew_dec(yz, yhi-ylo) ]

    # -> b):

    # This should be kept in sync with the accuracy used for writing the bounding box edges above

    prec_dec = dec.Decimal('1E-8')

    # Make sure to always round down and hence avoid numerical problems with skew vector in LAMMPS.

    skew_folded_and_rounded_dec = [ d.quantize(prec_dec, dec.ROUND_DOWN) for d in skew_folded_dec ]

    # Do not write zero skew vector.

    # (I.e. calculate orthogonal cell with LAMMPS in that case!)

    has_skew = any( [not d.is_zero() for d in skew_folded_and_rounded_dec] )

    if force_skew or has_skew:

        f.write( "%15s %15s %15s \t xy xz yz \n" % tuple( str(d) for d in skew_folded_and_rounded_dec ) )

    f.write("\n\n")

    ### atoms

    ## A) simple version

    # - For orthogonal cells which are properly aligned with the reference coordinate system only.

#    f.write("Atoms \n\n")

#    for i, (x, y, z) in enumerate(atoms.get_positions()):

#        s = species.index(symbols[i]) + 1

#        f.write("%6d %3d %22.15f %22.15f %22.15f \n" % (i+1, s, x, y, z))

    ## B) convert to (perhaps) triclinic cells in LAMMPS:

    # - Apply rotation determined above for this case.

    # - Lattice translation in case of a folded skew vector above should not be necessary,

    #   since the resulting (perhaps) new unit cell does describe the same lattice.

    #   Therefore the (rotated) atoms are still at correct lattice sites, only some of them

    #   probably are outside of that new unit cell, which LAMMPS can hopefully deal with.

    f.write("Atoms \n\n")

    for i, r in enumerate(atoms.get_positions()):

        s = species.index(symbols[i]) + 1

        [x, y, z] = np.dot(r, rotation)

#        print r, [x, y, z]

        f.write("%6d %3d %22.15f %22.15f %22.15f \n" % (i+1, s, x, y, z))

    f.close()

if __name__ == "__main__":

    pair_style = "eam"

    Pd_eam_file = "Pd_u3.eam"

    pair_coeff = [ "* * " + Pd_eam_file ]

    parameters = { "pair_style" : pair_style, "pair_coeff" : pair_coeff }

    files = [ Pd_eam_file ]

    calc = LAMMPS(parameters=parameters, files=files)

    from ase import Atoms

    a0 = 3.93

    b0 = a0 / 2.0

    if True:

        bulk = Atoms(['Pd']*4,

                     positions=[(0,0,0),(b0,b0,0),(b0,0,b0),(0,b0,b0)],

                     cell=[a0]*3,

                     pbc=True)

        # test get_forces

        print "forces for a = %f" % a0

        print calc.get_forces(bulk)

        # single points for various lattice constants

        bulk.set_calculator(calc)

        for n in range(-5,5,1):

            a = a0 * (1 + n/100.0)

            bulk.set_cell([a]*3)

            print "a : %f , total energy : %f" % (a, bulk.get_potential_energy())

#    calc.clean(force=True)

    calc.clean()