Source code for kvazar.core.airebo

# -*- coding: utf-8 -*-
import numpy

from mm import MM
from params import airebo_parm
from params import consts
from lib import libairebo

TRUE_NAME = {'Carbon' : 'C', 'Hydrogen' : 'H', 'C': 'C', 'H' : 'H'}

class REBOMessage(object):
    def __init__(self, a, b, full_links, num_full_links, NC, NH):
        self.a = a
        self.b = b
        self.full_links = full_links
        self.num_full_links = num_full_links
        self.NC = NC
        self.NH = NH

def b_cast_airebo(comm, struct, parm, a, b):
    procid = comm.Get_rank()
    for sender in xrange(comm.Get_size()):
        msg = None
        if (sender == procid):
            fl = struct.full_links[a:b]
            nfl = struct.num_full_links[a:b]
            nc = parm['NC_full'][a:b]
            nh = parm['NH_full'][a:b]
            msg = REBOMessage(a, b, fl, nfl, nc, nh)

        msg = comm.bcast(msg, root = sender)

        if (sender != procid):
            ia, ib = msg.a, msg.b

            struct.full_links[ia : ib] = msg.full_links
            struct.num_full_links[ia : ib] = msg.num_full_links
            parm['NC_full'][ia : ib] = msg.NC
            parm['NH_full'][ia : ib] = msg.NH

class AIREBOException(Exception):
    def __init__(self, message):
        super(AIREBOException, self).__init__(message)

[docs]class AIREBO(MM): """ This class is the successor of class MM Constructor of class AIREBO: Args: struct(structure): nanostructure ff_params(list): list of names of potentials functions """ def __init__(self, struct, ff_params, comm = None): if not ff_params: ff_params = ["u_rebo", "u_tors", "u_lj"] self.parm = airebo_parm.getAIREBO_parm() self.parm["atypes"] = ["C", "H"] self.parm['use_tors'] = "u_tors" in ff_params self.parm['use_lj'] = "u_lj" in ff_params super(AIREBO, self).__init__(struct, libairebo, ff_params, self.parm) self.update_neighbours(0, self.struct.n_atoms) fc = self.forces def nforces(f, a, b): fc(f, a, b) self.update_neighbours(a, b) if comm: b_cast_airebo(comm, self.struct, self.parm, a, b) self.forces = nforces
[docs] def preprocessing(self, struct): """ It corrects atom type and atom boxnames, group them and find out. Masses is taken from parameters. """ struct = self.struct atypes = self.parm["atypes"] if not hasattr(struct, "atom_types"): struct.atom_types = numpy.zeros(struct.n_atoms, numpy.int32) calc_mass = False if not hasattr(struct, "mass"): calc_mass = True struct.mass = numpy.zeros(struct.n_atoms, numpy.float) if hasattr(struct, "atom_names"): for i, name in enumerate(struct.atom_names): if name in atypes: struct.atom_types[i] = atypes.index(name) if calc_mass: struct.mass[i] = consts.ATOM_MASS[TRUE_NAME[name]] else: if name in TRUE_NAME: struct.atom_types[i] = atypes.index(TRUE_NAME[name]) if calc_mass: struct.mass[i] = consts.ATOM_MASS[TRUE_NAME[name]] else: raise AIREBOException("Wrong atom type name %s" % name) else: raise AIREBOException("Error: didn't find attribute 'atom_names' for object of structure.") self.parm['NC_full'] = numpy.zeros(struct.n_atoms, numpy.float) self.parm['NH_full'] = numpy.zeros(struct.n_atoms, numpy.float) self.g = lambda costh, Nij, ati, : libairebo.g(costh, Nij, ati, self.parm["G_coefs"]) self.P = lambda x, y, ati, atj : libairebo.bicubic_spline(x, y, ati, atj, self.parm["P_coefs"]) self.F = lambda x, y, z, ati, atj : libairebo.tricubic_spline(x, y, z, ati, atj, self.parm["F_coefs"]) self.T = lambda x, y, z, ati, atj : libairebo.tricubic_spline(x, y, z, ati, atj, self.parm["T_coefs"]) self.update_neighbours = lambda a, b : libairebo.update_neighbours(self.struct.__dict__, self.parm, a, b) return True
[docs] def init_cutoff(self, r_in, r_out, cutoff_neighbours): """ Args: r_in(float): internal cutoff radius r_out(float): external cutoff radius cutoff_neighbours(list): list of neighbours get into the field with r_out radius """ self.parm["use_cutoff"] = True self.parm["cutoff_r"] = r_in self.parm["cutoff_d"] = r_out - r_in self.update_cutoff(cutoff_neighbours)
[docs] def update_cutoff(self, cutoff_neighbours): """ Updates list of neighbours in cutoff area Args: cutoff_neighbours(list): list of neighbours """ self.struct.cutoff_neighbours = map(list, map(set, cutoff_neighbours))