def test_lmp_write_skew():
Mol = Molecule()
Mol.setFmt('angstrom')
Mol.setCellDim(1)
Mol.setVec(((5, 0, 0), (1, 5, 0), (2, 3, 5)))
Mol.newAtom('Na', (0, 0, 0))
p = newParam('lmp')
f = StringIO()
lammpsData.writer(Mol, f, p)
print(f.getvalue())
target = "\n"\
"1 atoms\n"\
"1 atom types\n"\
"\n"\
" 0.0000 5.0000 xlo xhi\n"\
" 0.0000 5.0000 ylo yhi\n"\
" 0.0000 5.0000 zlo zhi\n"\
" 1.0000 2.0000 3.0000 xy xz yz\n"\
"\n"\
"Masses\n"\
"\n"\
"1 22.9900 #Na\n"\
"\n"\
"Atoms # atomic\n"\
"\n"\
"1 1 0.0000 0.0000 0.0000\n"\
"\n"
assert f.getvalue() == target
Mol.setVec(((5, 3, 2), (0, 5, 1), (0, 0, 5)))
try:
lammpsData.writer(Mol, f, p)
except ValueError:
assert True
except:
assert False
else:
assert False
def test_lmp_write_proper():
Mol = Molecule()
Mol.setFmt('angstrom')
Mol.setCellDim(1)
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.newAtom('Na', (0.0, 0.0, 0.0), charge=1.)
Mol.newAtom('Na', (2.5, 2.5, 0.0), charge=1.)
Mol.newAtom('Na', (0.0, 2.5, 2.5), charge=1.)
Mol.newAtom('Na', (2.5, 0.0, 2.5), charge=1.)
Mol.newAtom('Cl', (0.0, 2.5, 0.0), charge=-1.)
Mol.newAtom('Cl', (2.5, 0.0, 0.0), charge=-1.)
Mol.newAtom('Cl', (0.0, 0.0, 2.5), charge=-1.)
Mol.newAtom('Cl', (2.5, 2.5, 2.5), charge=-1.)
p = newParam('lmp')
p['atom_style'] = 'full'
p['bonds'] = True
p['angles'] = True
p['dihedrals'] = True
p['impropers'] = True
head = "\n"\
"8 atoms\n"\
"2 atom types\n"\
"12 bonds\n"\
"1 bond types\n"\
"#1 Cl Na\n"\
"24 angles\n"\
"2 angle types\n"\
"#1 Cl Na Cl\n"\
"#2 Na Cl Na\n"\
"48 dihedrals\n"\
"1 dihedral types\n"\
"#1 Cl Na Cl Na\n"\
"8 impropers\n"\
"2 improper types\n"\
"#1 Cl Na Na Na\n"\
"#2 Na Cl Cl Cl\n"\
"\n"\
" 0.0000 5.0000 xlo xhi\n"\
" 0.0000 5.0000 ylo yhi\n"\
" 0.0000 5.0000 zlo zhi\n"\
"\n"\
"Masses\n"\
"\n"\
"1 22.9900 #Na\n"\
"2 35.4530 #Cl\n"\
"\n"
tail = "\nBonds\n\n"\
"1 1 1 5\n2 1 1 6\n3 1 1 7\n4 1 2 5\n5 1 2 6\n"\
"6 1 2 8\n7 1 3 5\n8 1 3 7\n9 1 3 8\n10 1 4 6\n"\
"11 1 4 7\n12 1 4 8\n"\
"\nAngles\n\n"\
"1 1 5 1 6\n2 1 5 1 7\n3 2 1 5 2\n4 2 1 5 3\n"\
"5 1 6 1 7\n6 2 1 6 2\n7 2 1 6 4\n8 2 1 7 3\n"\
"9 2 1 7 4\n10 1 5 2 6\n11 1 5 2 8\n12 2 2 5 3\n"\
"13 1 6 2 8\n14 2 2 6 4\n15 2 2 8 3\n16 2 2 8 4\n"\
"17 1 5 3 7\n18 1 5 3 8\n19 1 7 3 8\n20 2 3 7 4\n"\
"21 2 3 8 4\n22 1 6 4 7\n23 1 6 4 8\n24 1 7 4 8\n"\
"\nDihedrals\n\n"\
"1 1 6 1 5 2\n2 1 6 1 5 3\n3 1 5 1 6 2\n4 1 5 1 6 4\n"\
"5 1 7 1 5 2\n6 1 7 1 5 3\n7 1 5 1 7 3\n8 1 5 1 7 4\n"\
"9 1 1 5 2 6\n10 1 1 5 2 8\n11 1 1 5 3 7\n12 1 1 5 3 8\n"\
"13 1 7 1 6 2\n14 1 7 1 6 4\n15 1 6 1 7 3\n16 1 6 1 7 4\n"\
"17 1 1 6 2 5\n18 1 1 6 2 8\n19 1 1 6 4 7\n20 1 1 6 4 8\n"\
"21 1 1 7 3 5\n22 1 1 7 3 8\n23 1 1 7 4 6\n24 1 1 7 4 8\n"\
"25 1 6 2 5 3\n26 1 5 2 6 4\n27 1 8 2 5 3\n28 1 5 2 8 3\n"\
"29 1 5 2 8 4\n30 1 2 5 3 7\n31 1 2 5 3 8\n32 1 8 2 6 4\n"\
"33 1 6 2 8 3\n34 1 6 2 8 4\n35 1 2 6 4 7\n36 1 2 6 4 8\n"\
"37 1 2 8 3 5\n38 1 2 8 3 7\n39 1 2 8 4 6\n40 1 2 8 4 7\n"\
"41 1 5 3 7 4\n42 1 5 3 8 4\n43 1 8 3 7 4\n44 1 7 3 8 4\n"\
"45 1 3 7 4 6\n46 1 3 7 4 8\n47 1 3 8 4 6\n48 1 3 8 4 7\n"\
"\nImpropers\n\n"\
"1 2 1 5 6 7\n2 2 2 5 6 8\n3 2 3 5 7 8\n4 2 4 6 7 8\n"\
"5 1 5 1 2 3\n6 1 6 1 2 4\n7 1 7 1 3 4\n8 1 8 2 3 4\n"\
"\n"
atoms = "Atoms # full\n"\
"\n"\
"1 1 1 1.0000 0.0000 0.0000 0.0000\n"\
"2 1 1 1.0000 2.5000 2.5000 0.0000\n"\
"3 1 1 1.0000 0.0000 2.5000 2.5000\n"\
"4 1 1 1.0000 2.5000 0.0000 2.5000\n"\
"5 1 2 -1.0000 0.0000 2.5000 0.0000\n"\
"6 1 2 -1.0000 2.5000 0.0000 0.0000\n"\
"7 1 2 -1.0000 0.0000 0.0000 2.5000\n"\
"8 1 2 -1.0000 2.5000 2.5000 2.5000\n"
f = StringIO()
lammpsData.writer(Mol, f, p)
target = head + atoms + tail
assert f.getvalue() == target