def test_json(self):
f1 = MagresFile(open(os.path.join(DATA_DIR, "ethanol", "ethanol-nmr.magres")))
json = f1.as_json()
f2 = MagresFile.load_json(json)
self.assertEqual(f1.data_dict, f2.data_dict)
def __init__(self, magres_file=None):
"""
Load new .magres format file into dictionary structure.
"""
if type(magres_file) == MagresFile:
self.magres_file = magres_file
else:
self.magres_file = MagresFile(magres_file)
def test_nmr_new(self):
f = MagresFile(open(os.path.join(DATA_DIR, "ethanol", "ethanol-nmr-new.magres")))
self.assertTrue("calculation" in f.data_dict)
self.assertTrue("atoms" in f.data_dict)
self.assertTrue("magres" in f.data_dict)
self.assertTrue("lattice" in f.data_dict["atoms"])
self.assertTrue("units" in f.data_dict["atoms"])
self.assertTrue("atom" in f.data_dict["atoms"])
self.assertTrue("units" in f.data_dict["magres"])
self.assertTrue("efg" in f.data_dict["magres"])
self.assertTrue("ms" in f.data_dict["magres"])
num_atoms = len(f.data_dict['atoms']['atom'])
self.assertTrue(len(f.data_dict['magres']['efg']), num_atoms)
self.assertTrue(len(f.data_dict['magres']['ms']), num_atoms)
def test_full_isc(self):
magres_files = [
MagresFile(open(os.path.join(DATA_DIR, "ethanol", f)))
for f in os.listdir(os.path.join(DATA_DIR, "ethanol"))
if f.startswith('ethanol-jc')
]
self.assertEqual(len(magres_files), 9)
atoms = MagresAtoms.load_magres(magres_files)
for atom in atoms:
self.assertTrue(hasattr(atom, "isc"))
self.assertEqual(len(atoms.isc), len(atoms) * (len(atoms) - 1))
# Check every atom has couplings to every other atom
for atom in atoms:
self.assertEqual(len(atom.isc), len(atoms) - 1)
#!/usr/bin/python
import sys
from numpy.linalg import det
from magres.format import MagresFile, BadVersion
from magres.atoms import MagresAtoms
from magres.utils import find_all_magres
magres_files = []
for f in find_all_magres(sys.argv[1]):
try:
magres_files.append(MagresFile(f))
except BadVersion:
continue
s1 = sys.argv[2]
i1 = int(sys.argv[3])
s2 = sys.argv[4]
i2 = int(sys.argv[5])
tensor = 'isc'
if len(sys.argv) >= 7:
tensor = sys.argv[6]
atoms = MagresAtoms.load_magres(magres_files)
atom1 = atoms.get_species(s1, i1)
atom2 = atoms.get_species(s2, i2)
if tensor == "isc_spin_total":
K1 = atom1.isc_fc[atom2].K + atom1.isc_spin[atom2].K
K2 = atom2.isc_fc[atom1].K + atom2.isc_spin[atom1].K
def test_badversion(self):
with self.assertRaises(BadVersion):
f = MagresFile(open(os.path.join(DATA_DIR, "noversion.magres")))
with self.assertRaises(BadVersion):
f = MagresFile(open(os.path.join(DATA_DIR, "badversion.magres")))
#!/usr/bin/python
"""
Merge several magres files into one.
"""
import sys
from magres.format import MagresFile
if __name__ == "__main__":
magres_file_paths = sys.argv[1:]
magres_files = [
MagresFile(magres_file_path) for magres_file_path in magres_file_paths
]
merged_magres_file = MagresFile.merge(magres_files)
print str(merged_magres_file)
from __future__ import print_function
from magres.format import MagresFile
import sys
magres_file = MagresFile(sys.argv[1])
atoms = magres_file.as_ase()
print(atoms)
for atom in atoms:
print(atom.symbol, atom.tag, atom.position)
class AtomsTest(unittest.TestCase):
cubic = MagresFile.load_json(
'{"atoms": {"units": [["atom", "Angstrom"], ["lattice", "Angstrom"]], "lattice": [[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]], "atom": [{"index": 1, "position": [0.0, 0.0, 0.0], "species": "H", "label": "H"}]}}'
)
orthorhombic = MagresFile.load_json(
'{"atoms": {"units": [["atom", "Angstrom"], ["lattice", "Angstrom"]], "lattice": [[[1.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]]], "atom": [{"index": 1, "position": [0.0, 0.0, 0.0], "species": "H", "label": "H"}]}}'
)
species = MagresFile.load_json(
'{"atoms": {"units": [["atom", "Angstrom"], ["lattice", "Angstrom"]], "lattice": [[[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]], "atom": [{"index": 1, "position": [0.0, 0.0, 0.0], "species": "H", "label": "H"},{"index": 1, "position": [0.0, 0.0, 1.0], "species": "C", "label": "C1"},{"index": 1, "position": [0.0, 0.0, 2.0], "species": "C", "label": "C2"}]}}'
)
def test_within_cubic(self):
atoms = MagresAtoms.load_magres(self.cubic)
self.assertEquals(len(atoms), 1)
p = atoms[0].position
self.assertEquals(len(atoms.within(p, 1.0)), 7)
num_within_3 = 0
for atom in atoms.within(atoms[0], 5.0):
if atom.dist(atoms[0]) <= 3.0:
num_within_3 += 1
self.assertEquals(len(atoms.within(p, 3.0)), num_within_3)
self.assertEquals(len(atoms.within(p, 5.0).within(p, 2.0)),
len(atoms.within(p, 2.0).within(p, 5.0)))
def test_within_orthorhombic(self):
atoms = MagresAtoms.load_magres(self.orthorhombic)
self.assertEquals(len(atoms), 1)
p = atoms[0].position
self.assertEquals(len(atoms.within(p, 1.0)), 3)
num_within_3 = 0
for atom in atoms.within(p, 10.0):
if atom.dist(atoms[0]) <= 3.0:
num_within_3 += 1
self.assertEquals(len(atoms.within(p, 3.0)), num_within_3)
self.assertEquals(len(atoms.within(p, 5.0).within(p, 2.0)),
len(atoms.within(p, 2.0).within(p, 5.0)))
def test_species(self):
atoms = MagresAtoms.load_magres(self.species)
self.assertEquals(len(atoms), 3)
self.assertEquals(len(atoms.species('H')), 1)
self.assertEquals(len(atoms.species('C')), 2)
def test_labels(self):
atoms = MagresAtoms.load_magres(self.species)
self.assertEquals(len(atoms), 3)
self.assertEquals(len(atoms.label('H')), 1)
self.assertEquals(len(atoms.label('C')), 0)
self.assertEquals(len(atoms.label('C1')), 1)
self.assertEquals(len(atoms.label('C2')), 1)
#!python """ Merge several magres files into one. """ import sys from magres.format import MagresFile if __name__ == "__main__": magres_file_paths = sys.argv[1:] magres_files = [MagresFile(magres_file_path) for magres_file_path in magres_file_paths] merged_magres_file = MagresFile.merge(magres_files) print str(merged_magres_file)
import sys
from magres.format import MagresFile
from magres.utils import find_all_magres
from magres.atoms import MagresAtoms
magres_files = [MagresFile(f) for f in find_all_magres(sys.argv[1])]
atoms = MagresAtoms.load_magres(magres_files)
coupling_atom = atoms.get_species('C', 1)
# Set a bunch of arbitrary references for the magnetic shielding
atoms.set_reference('H', 100.0)
atoms.set_reference('C', 55.0)
atoms.set_reference('O', -2.0)
for atom in atoms:
print atom, atom.efg.Cq, atom.ms.iso, atom.isc[coupling_atom].J_iso
