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build/lib.linux-x86_64-3.6/pymbd/__init__.py

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+from .pymbd import *
+from .lib import mbd as lib
+from .lib import mbd_math as lib_math
+from .lib import mbd_repulsion as lib_coul

build/lib.linux-x86_64-3.6/pymbd/pymbd.py

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+# This Source Code Form is subject to the terms of the Mozilla Public
+# License, v. 2.0. If a copy of the MPL was not distributed with this
+# file, You can obtain one at http://mozilla.org/MPL/2.0/.
+import json
+import sys
+import numpy as np
+
+from .lib import mbd as _mbd
+from .vdw_param import vdw_param as free_atom_db
+
+try:
+    from mpi4py import MPI
+    ntasks = MPI.COMM_WORLD.Get_size()
+    myid = MPI.COMM_WORLD.Get_rank()
+except ImportError:
+    ntasks = 1
+    myid = 0
+
+_mbd.my_task = myid
+_mbd.n_tasks = ntasks
+
+bohr = _mbd.bohr
+
+
+def get_free_atom_data(species):
+    return list(map(
+        list,
+        zip(*[
+            (at['alpha_0'], at['C6'], at['R_vdw']) for at in
+            [free_atom_db[sp] for sp in species]
+        ])
+    ))
+
+
+def printout(s, each=False):
+    if each or myid == 0:
+        sys.stdout.write('{}\n'.format(s))
+
+
+def printerr(s, each=False):
+    if each or myid == 0:
+        sys.stderr.write('{}\n'.format(s))
+
+
+def get_damping(xc):
+    return dict(zip(['ts_d', 'ts_s_r', 'mbd_scs_a', 'mbd_ts_a',
+                     'mbd_ts_erf_beta', 'mbd_ts_fermi_beta', 'mbd_rsscs_a',
+                     'mbd_rsscs_beta'],
+                    _mbd.get_damping_parameters(xc)))
+
+
+def scale_hirsh(hirsh, alpha, C6, R_vdw):
+    hirsh = np.array(hirsh)
+    return [np.array(q)*hirsh**factor
+            for q, factor in zip([alpha, C6, R_vdw], [1, 2, 1/3])]
+
+
+def mbd_rsscs(
+        coords, species, volumes, beta, lattice=None, k_grid=None, supercell=None, vacuum=None,
+        custom_params=None, get_spectrum=False
+):
+    _mbd.param_vacuum_axis = [False]*3 if vacuum is None else vacuum
+    mode = 'P' if ntasks > 1 else ''
+    params = get_free_atom_data(species)
+    if custom_params:
+        for i, specie in enumerate(species):
+            if specie in custom_params:
+                for j, paramname in enumerate(['alpha_0', 'C6', 'R_vdw']):
+                    params[j][i] = custom_params[specie][paramname]
+    alpha_0, C6, R_vdw = scale_hirsh(volumes, *params)
+    if lattice is not None:
+        mode += 'C'
+    alpha_scs_dyn = _mbd.run_scs(
+        mode, 'fermi,dip,gg', coords,
+        _mbd.alpha_dynamic_ts_all('C', _mbd.n_grid_omega, alpha_0, c6=C6),
+        unit_cell=lattice,
+        r_vdw=R_vdw, beta=beta, a=6.
+    )
+    C6_scs = _mbd.get_c6_from_alpha(alpha_scs_dyn)
+    R_vdw_scs = R_vdw*(alpha_scs_dyn[0]/alpha_0)**(1/3)
+    if get_spectrum:
+        mode += 'EV'
+    if k_grid is not None:
+        mode = mode.replace('C', 'R')
+        k_grid = _mbd.make_k_grid(_mbd.make_g_grid(*k_grid), lattice)
+        ene, *spectrum = _mbd.get_reciprocal_mbd_energy(
+            mode, 'fermi,dip', coords,
+            alpha_scs_dyn[0],
+            _mbd.omega_eff(C6_scs, alpha_scs_dyn[0]),
+            k_grid,
+            unit_cell=lattice,
+            r_vdw=R_vdw_scs, beta=beta, a=6.
+        )
+    elif supercell is not None:
+        ene, *spectrum = _mbd.get_supercell_mbd_energy(
+            mode, 'fermi,dip', coords,
+            alpha_scs_dyn[0],
+            _mbd.omega_eff(C6_scs, alpha_scs_dyn[0]),
+            unit_cell=lattice,
+            supercell=supercell,
+            r_vdw=R_vdw_scs, beta=beta, a=6.
+        )
+    else:
+        ene, *spectrum = _mbd.get_single_mbd_energy(
+            mode, 'fermi,dip', coords,
+            alpha_scs_dyn[0],
+            _mbd.omega_eff(C6_scs, alpha_scs_dyn[0]),
+            r_vdw=R_vdw_scs, beta=beta, a=6.
+        )
+    if get_spectrum:
+        return (ene, *spectrum)
+    return ene
+
+
+def mbd_rsscs_deriv(
+        coords, species, volumes, beta, lattice=None, k_grid=None, supercell=None,
+        delta=1e-4
+):
+    forces = np.zeros(coords.shape)
+    for i_atom in range(coords.shape[0]):
+        for i_xyz in range(3):
+            ene = []
+            for step in [-1, 1]:
+                coords_diff = coords.copy()
+                coords_diff[i_atom, i_xyz] += step*delta
+                ene.append(mbd_rsscs(
+                    coords_diff, species, volumes, beta, lattice, k_grid, supercell
+                ))
+            forces[i_atom, i_xyz] = -(ene[1]-ene[0])/(2*delta)
+    if lattice is None:
+        return forces
+    stress = np.zeros((3, 3))
+    for i_xyz in range(3):
+        for j_xyz in range(3):
+            ene = []
+            for step in [-1, 1]:
+                strain = np.eye(3)
+                strain[i_xyz, j_xyz] += step*delta
+                coords_diff = coords.dot(strain)
+                lattice_diff = lattice.dot(strain)
+                ene.append(mbd_rsscs(
+                    coords_diff, species, volumes, beta, lattice_diff, k_grid, supercell
+                ))
+            stress[i_xyz, j_xyz] = -(ene[1]-ene[0])/(2*delta)
+    return forces, stress
+
+
+def mbd_coul(coords, species, volumes, beta, lattice=None, k_grid=None,
+             supercell=None, vacuum=None, custom_params=None):
+    mode = 'P'
+    _mbd.param_vacuum_axis = [False]*3 if vacuum is None else vacuum
+    mode = 'P' if ntasks > 1 else ''
+    params = get_free_atom_data(species)
+    alpha_0, C6, R_vdw = scale_hirsh(volumes, *params)
+    alpha_scs_dyn = _mbd.run_scs(
+        mode, 'fermi,dip,gg', coords,
+        _mbd.alpha_dynamic_ts_all('C', _mbd.n_grid_omega, alpha_0, c6=C6),
+        unit_cell=lattice,
+        r_vdw=R_vdw, beta=beta, a=6.
+    )
+    C6_scs = _mbd.get_c6_from_alpha(alpha_scs_dyn)
+    R_vdw_scs = R_vdw*(alpha_scs_dyn[0]/alpha_0)**(1/3)
+    ene = _mbd.get_single_mbd_energy(
+        mode, 'fermi,dip', coords,
+        alpha_scs_dyn[0],
+        _mbd.omega_eff(C6_scs, alpha_scs_dyn[0]),
+        r_vdw=R_vdw_scs, beta=beta, a=6.
+    )[0]
+    return ene
+
+
+class ArrayEncoder(json.JSONEncoder):
+    def default(self, obj):
+        try:
+            return obj.tolist()
+        except AttributeError:
+            return super().default(obj)

build/lib.linux-x86_64-3.6/pymbd/tests.py

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+import numpy as np
+from numpy import sqrt
+import unittest
+
+import pymbd
+
+
+class TestFreqGrid(unittest.TestCase):
+    pass
+
+
+for n in range(15, 40, 5):
+    def test(self, n=n):
+        grid1 = -pymbd.lib.gauss_legendre(n)[0]
+        grid2 = np.polynomial.legendre.leggauss(n)[0]
+        self.assertAlmostEqual(0, np.linalg.norm(grid1-grid2), 8)
+    if n > 25:
+        test = unittest.expectedFailure(test)
+    setattr(TestFreqGrid, 'test_frequency_grid_{}'.format(n), test)
+
+
+class TestMBD(unittest.TestCase):
+    def setUp(self):
+        pymbd.lib.init_grid(15)
+
+    def test_argon_dimer(self):
+        ene = pymbd.mbd_rsscs(
+            [[0, 0, 0], [4.0/pymbd.bohr, 0, 0]],
+            ['Ar', 'Ar'],
+            [1., 1.],
+            0.83
+        )
+        self.assertAlmostEqual(ene, -0.0002462647623815428, 10)
+
+    def tearDown(self):
+        pymbd.lib.destroy_grid()
+
+
+class TestCoulomb(unittest.TestCase):
+    def test_basic(self):
+        a = 1/sqrt(2)
+        C = np.array([
+            [ 0,  0, -a,  0, -a,  0],  # noqa
+            [ 0,  a,  0,  a,  0,  0],  # noqa
+            [-a,  0,  0,  0,  0, -a],  # noqa
+            [ 0,  0,  a,  0, -a,  0],  # noqa
+            [ 0, -a,  0,  a,  0,  0],  # noqa
+            [-a,  0,  0,  0,  0,  a],  # noqa
+        ], dtype=float)
+        coords = [[0, 0, 0], [0, 0, 1.1]]
+        n = len(coords)
+        e1, eatt, erep = pymbd.lib_coul.fullcoulomb(
+            C, coords, n*[1], n*[1], 3*n*[2], n*[2]
+        )
+        self.assertAlmostEqual(e1, -0.058346493647401076, 10)
+        self.assertAlmostEqual(eatt, 1.767623829681647, 10)
+        self.assertAlmostEqual(erep, 0.800186426943337, 10)

build/lib.linux-x86_64-3.6/pymbd/vdw_param.py

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+# Any copyright is dedicated to the Public Domain.
+# http://creativecommons.org/publicdomain/zero/1.0/
+
+vdw_param = {
+    "H": {"alpha_0": 4.5, "C6": 6.5, "R_vdw": 3.1},
+    "He": {"alpha_0": 1.38, "C6": 1.46, "R_vdw": 2.65},
+    "Li": {"alpha_0": 164.2, "C6": 1387., "R_vdw": 4.16},
+    "Be": {"alpha_0": 38., "C6": 214., "R_vdw": 4.17},
+    "B": {"alpha_0": 21., "C6": 99.5, "R_vdw": 3.89},
+    "C": {"alpha_0": 12., "C6": 46.6, "R_vdw": 3.59},
+    "N": {"alpha_0": 7.4, "C6": 24.2, "R_vdw": 3.34},
+    "O": {"alpha_0": 5.4, "C6": 15.6, "R_vdw": 3.19},
+    "F": {"alpha_0": 3.8, "C6": 9.52, "R_vdw": 3.04},
+    "Ne": {"alpha_0": 2.67, "C6": 6.38, "R_vdw": 2.91},
+    "Na": {"alpha_0": 13.6, "C6": 69.3, "R_vdw": 1.63},
+    "Mg": {"alpha_0": 71., "C6": 627., "R_vdw": 4.27},
+    "Al": {"alpha_0": 60., "C6": 528., "R_vdw": 4.33},
+    "Si": {"alpha_0": 37., "C6": 305., "R_vdw": 4.2},
+    "P": {"alpha_0": 25., "C6": 185., "R_vdw": 4.01},
+    "S": {"alpha_0": 19.6, "C6": 134., "R_vdw": 3.86},
+    "Cl": {"alpha_0": 15., "C6": 94.6, "R_vdw": 3.71},
+    "Ar": {"alpha_0": 11.1, "C6": 64.3, "R_vdw": 3.55},
+    "K": {"alpha_0": 292.9, "C6": 3897., "R_vdw": 3.71},
+    "Ca": {"alpha_0": 160., "C6": 2221., "R_vdw": 4.65},
+    "Sc": {"alpha_0": 120., "C6": 1383., "R_vdw": 4.59},
+    "Ti": {"alpha_0": 98., "C6": 1044., "R_vdw": 4.51},
+    "V": {"alpha_0": 84., "C6": 832., "R_vdw": 4.44},
+    "Cr": {"alpha_0": 78., "C6": 602., "R_vdw": 3.99},
+    "Mn": {"alpha_0": 63., "C6": 552., "R_vdw": 3.97},
+    "Fe": {"alpha_0": 56., "C6": 482., "R_vdw": 4.23},
+    "Co": {"alpha_0": 50., "C6": 408., "R_vdw": 4.18},
+    "Ni": {"alpha_0": 48., "C6": 373., "R_vdw": 3.82},
+    "Cu": {"alpha_0": 42., "C6": 253., "R_vdw": 3.76},
+    "Zn": {"alpha_0": 40., "C6": 284., "R_vdw": 4.02},
+    "Ga": {"alpha_0": 60., "C6": 498., "R_vdw": 4.19},
+    "Ge": {"alpha_0": 41., "C6": 354., "R_vdw": 4.2},
+    "As": {"alpha_0": 29., "C6": 246., "R_vdw": 4.11},
+    "Se": {"alpha_0": 25., "C6": 210., "R_vdw": 4.04},
+    "Br": {"alpha_0": 20., "C6": 162., "R_vdw": 3.93},
+    "Kr": {"alpha_0": 16.8, "C6": 129.6, "R_vdw": 3.82},
+    "Rb": {"alpha_0": 319.2, "C6": 4691., "R_vdw": 3.72},
+    "Sr": {"alpha_0": 199., "C6": 3170., "R_vdw": 4.54},
+    "Y": {"alpha_0": 126.7370, "C6": 1968.580, "R_vdw": 4.81510},
+    "Zr": {"alpha_0": 119.97, "C6": 1677.91, "R_vdw": 4.53},
+    "Nb": {"alpha_0": 101.603, "C6": 1263.61, "R_vdw": 4.2365},
+    "Mo": {"alpha_0": 88.4225785, "C6": 1028.73, "R_vdw": 4.099},
+    "Tc": {"alpha_0": 80.083, "C6": 1390.87, "R_vdw": 4.076},
+    "Ru": {"alpha_0": 65.8950, "C6": 609.754, "R_vdw": 3.99530},
+    "Rh": {"alpha_0": 56.1, "C6": 469.0, "R_vdw": 3.95},
+    "Pd": {"alpha_0": 23.68, "C6": 157.5, "R_vdw": 3.66},
+    "Ag": {"alpha_0": 50.6, "C6": 339., "R_vdw": 3.82},
+    "Cd": {"alpha_0": 39.7, "C6": 452.0, "R_vdw": 3.99},
+    "In": {"alpha_0": 70.22, "C6": 707.046, "R_vdw": 4.23198},
+    "Sn": {"alpha_0": 55.95, "C6": 587.417, "R_vdw": 4.303},
+    "Sb": {"alpha_0": 43.67197, "C6": 459.322, "R_vdw": 4.276},
+    "Te": {"alpha_0": 37.65, "C6": 396.0, "R_vdw": 4.22},
+    "I": {"alpha_0": 35., "C6": 385., "R_vdw": 4.17},
+    "Xe": {"alpha_0": 27.3, "C6": 285.9, "R_vdw": 4.08},
+    "Cs": {"alpha_0": 427.12, "C6": 6582.08, "R_vdw": 3.78},
+    "Ba": {"alpha_0": 275.0, "C6": 5727.0, "R_vdw": 4.77},
+    "Hf": {"alpha_0": 99.52, "C6": 1274.8, "R_vdw": 4.21},
+    "Ta": {"alpha_0": 82.53, "C6": 1019.92, "R_vdw": 4.15},
+    "W": {"alpha_0": 71.041, "C6": 847.93, "R_vdw": 4.08},
+    "Re": {"alpha_0": 63.04, "C6": 710.2, "R_vdw": 4.02},
+    "Os": {"alpha_0": 55.055, "C6": 596.67, "R_vdw": 3.84},
+    "Ir": {"alpha_0": 42.51, "C6": 359.1, "R_vdw": 4.00},
+    "Pt": {"alpha_0": 39.68, "C6": 347.1, "R_vdw": 3.92},
+    "Au": {"alpha_0": 36.5, "C6": 298.0, "R_vdw": 3.86},
+    "Hg": {"alpha_0": 33.9, "C6": 392.0, "R_vdw": 3.98},
+    "Tl": {"alpha_0": 69.92, "C6": 717.44, "R_vdw": 3.91},
+    "Pb": {"alpha_0": 61.8, "C6": 697.0, "R_vdw": 4.31},
+    "Bi": {"alpha_0": 49.02, "C6": 571.0, "R_vdw": 4.32},
+    "Po": {"alpha_0": 45.013, "C6": 530.92, "R_vdw": 4.097},
+    "At": {"alpha_0": 38.93, "C6": 457.53, "R_vdw": 4.07},
+    "Rn": {"alpha_0": 33.54, "C6": 390.63, "R_vdw": 4.23}
+}

build/lib.linux-x86_64-3.7/pymbd/__init__.py

@@ -0,0 +1,4 @@
+from .pymbd import *
+from .lib import mbd as lib
+from .lib import mbd_math as lib_math
+from .lib import mbd_repulsion as lib_coul