def hc1_complete_cell():
"""HC1 completed cell"""
cell = Mol(rf.read_pos(_in_data("hc1_complete_cell.xyz")))
vectors = np.array([[12.1199998856, 0.0, 0.0], [0.0, 10.2849998474, 0.0],
[-5.4720203118, 0.0, 11.2441994632]])
cell.vectors = vectors
return cell
def run(self, atoms):
"""
Write a DFTB .gen file and return a subprocess.Popen
Parameters
----------
atoms : list of Atom objects
Atoms to be calculated with DFTB+
Returns
-------
proc : subprocess.Popen object
the object should have a .wait() method
"""
dftb_path = os.path.join(self.here, self.calc_name)
os.chdir(dftb_path)
mol = Mol(atoms)
region_2_file = "r2.xyz"
if os.path.exists(region_2_file):
mol_r2 = rf.mol_from_file(region_2_file)
mol += mol_r2
mol.write_xyz("geom.xyz")
subprocess.call("xyz2gen geom.xyz", shell=True)
# Run DFTB+
proc = subprocess.Popen("dftb+ > dftb_out", shell=True)
os.chdir(self.here)
return proc
def read_points(in_name):
"""
Read point charges from an in-house Ewald.c output.
The modified version of Ewald.c is needed. The extension is .pts-cry
Parameters
----------
in_name : str
Name of the file to read
Returns
-------
points : Mol object
Point charges in the file. They have element "point"
"""
with open(in_name) as pts_file:
pts_content = pts_file.readlines()
# store point charges here
points = Mol([])
for line in pts_content:
xIn, yIn, zIn, qIn = map(float, line.split())
point = Atom("point", xIn, yIn, zIn, qIn)
points.append(point)
return points
def test_fit_benz_clust_shell(benz_clust_char):
sample_point = Atom("", 0, 0, 0)
sample_point2 = Atom("", 0.1, 0, 0)
sample_point.es = 0
sample_point2.es = 0
fixed_atoms = benz_clust_char.select(0)
var_atoms = Mol([i for i in benz_clust_char if i not in fixed_atoms])
fi.fit_points(var_atoms, fixed_atoms, Mol([sample_point, sample_point2]))
return
def read_cube(in_file):
"""
Read a cube file and return a Mol and a CubeGrid object
Parameters
----------
in_file : str
Input file name
Returns
-------
out_mol : Mol object
The atoms in the cube file
out_cub : CubeGrid object
The grid in the cube file where all distances are in Angstrom
"""
vectors = np.zeros((3, 3))
xyz_nums = [0, 0, 0]
values = []
out_mol = Mol([])
ind = 0
natoms = 0
with open(in_file) as lines:
for line in lines:
if ind == 2:
natoms = int(line.split()[0])
origin = np.array([float(i)
for i in line.split()[1:]]) / pt.bohrconv
if ind == 3:
xyz_nums[0] = int(line.split()[0])
vectors[0] = np.array([float(i) for i in line.split()[1:]
]) / pt.bohrconv
if ind == 4:
xyz_nums[1] = int(line.split()[0])
vectors[1] = np.array([float(i) for i in line.split()[1:]
]) / pt.bohrconv
if ind == 5:
xyz_nums[2] = int(line.split()[0])
vectors[2] = np.array([float(i) for i in line.split()[1:]
]) / pt.bohrconv
out_cub = CubeGrid(vectors, xyz_nums[0], xyz_nums[1],
xyz_nums[2], origin)
out_cub.set_grid_coord()
if 6 <= ind < (6 + natoms):
line_s = line.split()
new_atom = Atom()
new_atom.elem = per.num_to_elem(int(line_s[0]))
new_atom.set_pos([float(i) / pt.bohrconv for i in line_s[2:]])
out_mol.append(new_atom)
if ind >= (6 + natoms):
values.extend([float(i) for i in line.split()])
ind += 1
values_arr = np.array(values)
out_cub.grid[:, 3] = values_arr
return out_cub, out_mol
def test():
from fromage.utils.atom import Atom
from fromage.utils.mol import Mol
mol_a = Mol([Atom("C", 1)])
mol_b = Mol([Atom("C", 2)])
mol_c = Mol([Atom("C", 3)])
mol_d = Mol([Atom("C", 4)])
lis = [mol_a, mol_b, mol_c, mol_d]
print(all_dimers(lis))
def test_same_atoms_as():
mol_a_lis = [Atom("C", 1., 0., 0.), Atom("H", 1., 1., 1.)]
mol_b_lis = [Atom("H", 1., 1., 1.), Atom("C", 1., 0., 0.)]
mol_c_lis = [Atom("C", 1., 0., 0.), Atom("C", 1., 1., 1.)]
mol_a = Mol(mol_a_lis)
mol_b = Mol(mol_b_lis)
mol_c = Mol(mol_c_lis)
assert mol_a.same_atoms_as(mol_b) == True
assert mol_a.same_atoms_as(mol_c) == False
def test_fit_to_pot(benz_pot_cub, benz_clust_char):
print(benz_pot_cub.grid)
sample_point = Atom("", 0, 0, 0)
sample_point.es = 0.17671
print(benz_clust_char.es_pot([0, 0, 0]))
fixed_atoms = benz_clust_char.select(0)
var_atoms = Mol([i for i in benz_clust_char if i not in fixed_atoms])
fi.fit_points(var_atoms, fixed_atoms, Mol([sample_point]))
out_clust = var_atoms + fixed_atoms
print(out_clust.es_pot([0, 0, 0]))
return
def test_fit_benz_clust(benz_clust_char):
sample_point = Atom("", 0, 0, 0)
sample_point2 = Atom("", 0.1, 0, 0)
sample_point.es = 0
sample_point2.es = 0
fi.fit_points(benz_clust_char, None, Mol([sample_point, sample_point2]))
return
def fit_points(var_points, samples, fix_points=None):
"""
Return a new set of point charges that matches the potential at points
Parameters
----------
var_points : Mol object
Point charges to be fitted
samples : list of Mol objects or just one Mol object
Sampling points each with an associated electrostatic potential
fix_points : Mol object
Point charges to remain in place
Returns
-------
out_points : Mol object
The points at their same position but with optimised charge value
"""
if fix_points is None:
fix_points = Mol([])
coeffs = coeff_mat(var_points, samples)
deps = dep_var(var_points, fix_points, samples)
res = np.linalg.lstsq(coeffs, deps, rcond=None)
print("RMSD: " + str(np.sqrt(np.sum(res[3]) / len(samples))))
print(res[1:])
fitting = res[0]
print(fitting[0:6])
var_points.change_charges(var_points.charges() + fitting)
return var_points
def mol_from_gauss(in_name, pop="ESP"):
"""
Read Mol from a Gaussian log file
Include the requested charges.
Parameters
----------
in_name : str
Name of the file to read
pop : str, optional
Type of charges requested
Returns
-------
out_mol : Mol object
The atoms in the Gaussian log file, along with their charge
"""
atoms = read_g_pos(in_name)
charges = read_g_char(in_name, pop=pop)[0]
for i, char in enumerate(charges):
atoms[i].q = char
out_mol = Mol(atoms)
return out_mol
def mol_from_file(in_name, bonding='', vectors=np.zeros((3, 3))):
"""
Return a Mol object from a file
Parameters
----------
in_name : str
Name of the file to read
bonding : str
A string determining the type of bonding in the molecule. Something like
'dis0.2' or '-13cov'
vectors : 3 x 3 np array
The unit cell vectors if pertinent
Returns
-------
atom_step : Mol object
The atomic positions in the file
"""
mol = Mol(read_pos(in_name))
mol.vectors = vectors
mol.set_bonding_str(bonding)
return mol
def test_sample(benz_pot_cub, benz_cell):
pts = fi.shell_region(benz_pot_cub.grid, benz_cell, 0.2, 0.7)
out_mol = Mol([])
for point in pts:
out_mol.append(Atom("point", point[0], point[1], point[2]))
def hc1_quad():
"""HC1 quadrimer"""
out_mo = Mol(rf.read_pos(_in_data("hc1_quad.xyz")))
return out_mo
def h2o_dimer_mol(at_list):
"""Water dimer Mol object"""
out_mo = Mol(at_list)
return out_mo
def c_o():
"""CO Mol object"""
c_at = Atom("C", 0.0, 0.0, 0.0)
o_at = Atom("O", 1.0, 0.0, 0.0)
out_mol = Mol([c_at, o_at])
return out_mol
def h2o_dimer(at_list):
"""Return a water dimer Mol object"""
out_mo = Mol(at_list)
return out_mo
def test_add(h2o_dimer, newat):
"""Addition is implemented"""
new_mol = h2o_dimer + Mol(newat)
assert len(new_mol) == 7
def c_o():
c_at = Atom("C", 0.0, 0.0, 0.0)
o_at = Atom("O", 1.0, 0.0, 0.0)
out_mol = Mol([c_at, o_at])
return out_mol
def empty_mol():
return Mol([])
def hc1_quad():
"""Return a HC1 quadrimer"""
out_mo = Mol(rf.read_pos("hc1_quad.xyz"))
return out_mo
def empty_mol():
"""Empty Mol object"""
return Mol([])
def test_init():
"""The Mol object is initialised correctly"""
mo = Mol(at_list())
assert isinstance(mo, Mol)