def test_read():
ff = ForceField.open(cwd + '/files/TEAM_IL.ppf', cwd + '/files/SPCE.ppf')
assert len(ff.atom_types) == 65
c_4pp = ff.atom_types.get('c_4pp')
assert c_4pp.charge == 0
assert c_4pp.eqt_vdw == c_4pp.name
assert c_4pp.eqt_q_inc == c_4pp.name
assert c_4pp.eqt_bond == 'c_4'
assert c_4pp.eqt_ang_c == 'c_4'
assert c_4pp.eqt_ang_s == 'c_4'
assert c_4pp.eqt_dih_c == 'c_4'
assert c_4pp.eqt_dih_s == 'c_4'
assert c_4pp.eqt_imp_c == 'c_4'
assert c_4pp.eqt_imp_s == 'c_4'
assert c_4pp.version == '0.25'
c_3_ = ff.atom_types.get('c_3-')
assert c_3_.charge == -1
assert c_3_.version == '0.1'
o_1_t = ff.atom_types.get('o_1-t')
assert o_1_t.charge == -0.3333
binc = ff.bci_terms.get('c_35an2,h_1')
assert binc.type1 == 'c_35an2'
assert binc.type2 == 'h_1'
assert binc.version == '0.16'
assert binc.value == -0.22
vdw = ff.vdw_terms.get('b_4-,b_4-')
assert vdw.type1 == 'b_4-'
assert vdw.type2 == 'b_4-'
assert pytest.approx(vdw.epsilon / 4.184, abs=1E-6) == 0.05
assert pytest.approx(vdw.sigma * 2**(1 / 6) * 10, abs=1E-6) == 3.8
assert vdw.version == '0.36'
vdw = ff.pairwise_vdw_terms.get('o_2,o_2w')
assert vdw.type1 == 'o_2'
assert vdw.type2 == 'o_2w'
assert pytest.approx(vdw.epsilon / 4.184, abs=1E-6) == 0.22936
assert pytest.approx(vdw.sigma * 2**(1 / 6) * 10, abs=1E-6) == 3.44671
assert vdw.version == None
bond = ff.bond_terms.get('c_2n,n_2-')
assert bond.type1 == 'c_2n'
assert bond.type2 == 'n_2-'
assert pytest.approx(bond.length * 10, abs=1E-6) == 1.276
assert pytest.approx(bond.k / 4.184 / 100, abs=1E-6) == 487.36
assert bond.version == '0.3'
angle = ff.angle_terms.get('c_3a,c_3a,h_1')
assert angle.type1 == 'c_3a'
assert angle.type2 == 'c_3a'
assert angle.type3 == 'h_1'
assert pytest.approx(angle.theta, abs=1E-6) == 118.916
assert pytest.approx(angle.k / 4.184, abs=1E-6) == 43.8769
assert angle.version == '0.1'
dihedral = ff.dihedral_terms.get('*,c_4,c_4,*')
assert dihedral.type1 == '*'
assert dihedral.type2 == 'c_4'
assert dihedral.type3 == 'c_4'
assert dihedral.type4 == '*'
para1 = dihedral.parameters[0]
assert pytest.approx(para1.k / 4.184, abs=1E-6) == 0.6214
assert para1.n == 1
assert para1.phi == 0.0
para2 = dihedral.parameters[1]
assert pytest.approx(para2.k / 4.184, abs=1E-6) == 0.0507
assert para2.n == 2
assert para2.phi == 180.0
para0 = dihedral.parameters[2]
assert pytest.approx(para0.k / 4.184, abs=1E-6) == 0.0688
assert para0.n == 3
assert para0.phi == 0.0
assert dihedral.version == '0.12'
improper = ff.improper_terms.get('c_3o,o_1,*,*')
assert pytest.approx(improper.k / 4.184, abs=1E-6) == 18
assert improper.version == '0.21'
assert len(ff.polarizable_terms) == 0
def test_write():
ff = ForceField.open(cwd + '/files/CLP.ff', cwd + '/files/CLPol-alpha.ff')
tmp = os.path.join(tmpdir, 'out-CLP.ppf')
Ppf.save_to(ff, tmp)
assert filecmp.cmp(tmp, cwd + '/files/baselines/out-CLP.ppf')
c_4h3 [CX4;H3] 0
HierarchicalTree
h_1
c_4
c_4h2
c_4h3
'''
typer = ZftTyper(io.StringIO(definition))
butane = Molecule.from_smiles('CCCC butane')
typer.type_molecule(butane)
# Load force field parameters from ZFP file
ff = ForceField.open('alkane.zfp')
# Initialize a topology with periodic boundary condition
# For now, it contains only one butane molecule
top = Topology([butane], cell=UnitCell([3, 3, 3]))
# Assign atomic charges based on the charge parameters in the force field
top.assign_charge_from_ff(ff)
# Call Packmol to build a configuration containing 100 butane molecules
packmol = Packmol(r'/path/of/packmol')
top.scale_with_packmol([100], packmol=packmol)
# Associate force field parameters to the topology
# And then export input files for simulation engines
system = System(top, ff)