def test_isc(self):
atoms = MagresAtoms.load_magres(
os.path.join(DATA_DIR, "ethanol-isc.magres"))
self.assertTrue(hasattr(atoms.C2, "isc"))
self.assertTrue(hasattr(atoms.C2, "isc_orbital_p"))
self.assertTrue(hasattr(atoms.C2, "isc_orbital_d"))
self.assertTrue(hasattr(atoms.C2, "isc_spin"))
self.assertTrue(hasattr(atoms.C2, "isc_fc"))
self.assertEqual(len(atoms.C2.isc), len(atoms) - 1)
perturb_atom = atoms.get('C', 2)
for isc in atoms.C2.isc:
self.assertEqual(isc.atom1, perturb_atom)
self.assertEqual(isc.K_iso, numpy.trace(isc.K) / 3.0)
# Check that the principal components are ordered by the Haeberlen convention
for isc in atoms.C2.isc:
self.assertTrue(
abs(isc.K_evals[2] - isc.K_iso) >= abs(isc.K_evals[0] -
isc.K_iso))
self.assertTrue(
abs(isc.K_evals[0] - isc.K_iso) >= abs(isc.K_evals[1] -
isc.K_iso))
def test(self):
from magres.atoms import MagresAtoms
atoms = MagresAtoms.load_magres(
os.path.join(DATA_DIR, 'ethanol-all.magres'))
self.assertEqual(len(atoms), 9)
for atom in atoms:
"{} {}".format(atom, atom.ms.iso)
atoms.species('H').set_reference(10.0)
for atom in atoms.species('H'):
"{} {}".format(atom, atom.ms.cs)
for atom in atoms.within(atoms.C1, 2.0):
"{} {}".format(atom, atom.ms.iso, atom.ms.aniso)
self.assertEqual(len(atoms.species('H').ms.iso), 6)
self.assertAlmostEqual(mean(atoms.C1.bonded.species('H').ms.iso),
29.9838078506)
self.assertAlmostEqual(mean(atoms.C2.bonded.species('H').ms.iso),
28.7851386496)
self.assertAlmostEqual(mean(atoms.O1.bonded.species('H').ms.iso),
31.9849757497)
self.assertEqual(atoms.C1.ms.sigma.shape, (3, 3))
self.assertEqual(len(atoms.C1.ms.evecs), 3)
self.assertEqual(len(atoms.C1.ms.evals), 3)
def test_efg(self):
atoms = MagresAtoms.load_magres(
os.path.join(DATA_DIR, "ethanol/ethanol-nmr.magres"))
self.assertTrue(hasattr(atoms, "efg"))
self.assertEqual(len(atoms.efg), 9)
# Check that the EFGs are traceless
for efg in atoms.efg:
self.assertTrue(numpy.trace(efg.V) / 3.0 < 1e-12)
# Check that the principal components are ordered by the Haeberlen convention
# |Vzz| >= |Vxx| >= |Vyy|
for efg in atoms.efg:
self.assertTrue(abs(efg.evals[2]) >= abs(efg.evals[0]))
self.assertTrue(abs(efg.evals[0]) >= abs(efg.evals[1]))
# Check that eta is positive and <=1 (Cq can be positive or negative)
# eta = (Vxx - Vyy)/Vzz, 0 <= eta <= 1
for efg in atoms.efg:
self.assertTrue((efg.evals[1] - efg.evals[0]) / efg.evals[2] >= 0)
self.assertTrue((efg.evals[1] - efg.evals[0]) / efg.evals[2] <= 1)
self.assertTrue(efg.eta >= 0)
self.assertTrue(efg.eta <= 1)
def test(self):
from magres.atoms import MagresAtoms
atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, 'ethanol-all.magres'))
self.assertEqual(len(atoms), 9)
for atom in atoms:
"{} {}".format(atom, atom.ms.iso)
atoms.species('H').set_reference(10.0)
for atom in atoms.species('H'):
"{} {}".format(atom, atom.ms.cs)
for atom in atoms.within(atoms.C1, 2.0):
"{} {}".format(atom, atom.ms.iso, atom.ms.aniso)
self.assertEqual(len(atoms.species('H').ms.iso), 6)
self.assertAlmostEqual(mean(atoms.C1.bonded.species('H').ms.iso), 29.9838078506)
self.assertAlmostEqual(mean(atoms.C2.bonded.species('H').ms.iso), 28.7851386496)
self.assertAlmostEqual(mean(atoms.O1.bonded.species('H').ms.iso), 31.9849757497)
self.assertEqual(atoms.C1.ms.sigma.shape, (3, 3))
self.assertEqual(len(atoms.C1.ms.evecs), 3)
self.assertEqual(len(atoms.C1.ms.evals), 3)
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)
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)
def test_angles(self): atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, "angles/angles1.magres")) self.assertTrue(allclose(atoms.angle(atoms.C1, atoms.C2, atoms.C4, degrees=True), 45.0)) self.assertTrue(allclose(atoms.angle(atoms.C1, atoms.C2, atoms.C6, degrees=True), 90.0)) self.assertTrue(allclose(atoms.angle(atoms.C2, atoms.C1, atoms.C4), math.pi/2.0)) self.assertTrue(allclose(atoms.angle(atoms.C2, atoms.C1, atoms.C6), math.pi/4.0))
def test_nmr(self):
"""
Check that the magnetic shielding tensors are being loaded.
"""
atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, "ethanol/ethanol-nmr.magres"))
self.assertTrue(hasattr(atoms, "ms"))
self.assertEqual(len(atoms.ms), 9)
def test_angles_boundary(self):
atoms = MagresAtoms.load_magres(
os.path.join(DATA_DIR, "angles/angles1.magres"))
self.assertTrue(
allclose(atoms.angle(atoms.C2, atoms.C1, atoms.C3, degrees=True),
180.0))
self.assertTrue(
allclose(atoms.angle(atoms.C6, atoms.C1, atoms.C9, degrees=True),
90.0))
def test_dihedral5(self):
atoms = MagresAtoms.load_magres(
os.path.join(DATA_DIR, "angles/dihedral5.magres"))
self.assertTrue(
allclose(
atoms.dihedral(atoms.C1,
atoms.C2,
atoms.C3,
atoms.C4,
degrees=True), 45.0))
def test_replace_isc(self):
atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, "ethanol-isc.magres"))
atoms.C2.isc[0].K
with self.assertRaises(Exception):
atoms.C2.isc[0].K = numpy.array([1,2,3])
orig_iso = atoms.C2.isc[0].K_iso
new_K = atoms.C2.isc[0].K * 2.0
atoms.C2.isc[0].K = new_K
self.assertEqual(atoms.C2.isc[0].K_iso, orig_iso * 2.0)
def test_angles(self):
atoms = MagresAtoms.load_magres(
os.path.join(DATA_DIR, "angles/angles1.magres"))
self.assertTrue(
allclose(atoms.angle(atoms.C1, atoms.C2, atoms.C4, degrees=True),
45.0))
self.assertTrue(
allclose(atoms.angle(atoms.C1, atoms.C2, atoms.C6, degrees=True),
90.0))
self.assertTrue(
allclose(atoms.angle(atoms.C2, atoms.C1, atoms.C4), math.pi / 2.0))
self.assertTrue(
allclose(atoms.angle(atoms.C2, atoms.C1, atoms.C6), math.pi / 4.0))
def test_replace_isc(self):
atoms = MagresAtoms.load_magres(
os.path.join(DATA_DIR, "ethanol-isc.magres"))
atoms.C2.isc[0].K
with self.assertRaises(Exception):
atoms.C2.isc[0].K = numpy.array([1, 2, 3])
orig_iso = atoms.C2.isc[0].K_iso
new_K = atoms.C2.isc[0].K * 2.0
atoms.C2.isc[0].K = new_K
self.assertEqual(atoms.C2.isc[0].K_iso, orig_iso * 2.0)
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)
def test_efg(self):
atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, "ethanol/ethanol-nmr.magres"))
self.assertTrue(hasattr(atoms, "efg"))
self.assertEqual(len(atoms.efg), 9)
# Check that the EFGs are traceless
for efg in atoms.efg:
self.assertTrue(numpy.trace(efg.V)/3.0 < 1e-12)
# Check that the principal components are ordered by the Haeberlen convention
# |Vzz| >= |Vxx| >= |Vyy|
for efg in atoms.efg:
self.assertTrue(abs(efg.evals[2]) >= abs(efg.evals[0]))
self.assertTrue(abs(efg.evals[0]) >= abs(efg.evals[1]))
def test_replace_efg(self):
"""
Check that we can replace the tensor on an atom.
"""
atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, "ethanol/ethanol-nmr.magres"))
with self.assertRaises(Exception):
atoms.C1.efg.V = numpy.array([1,2,3])
orig_Cq = atoms.C1.efg.Cq
new_V = atoms.C1.efg.V * 2.0
atoms.C1.efg.V = new_V
self.assertEqual(atoms.C1.efg.Cq, orig_Cq * 2.0)
def test_replace_nmr(self):
"""
Check that we can replace the tensor on an atom.
"""
atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, "ethanol/ethanol-nmr.magres"))
with self.assertRaises(Exception):
atoms.C1.ms.sigma = numpy.array([1, 2, 3])
orig_iso = atoms.C1.ms.iso
new_sigma = atoms.C1.ms.sigma * 2.0
atoms.C1.ms.sigma = new_sigma
self.assertEqual(atoms.C1.ms.iso, orig_iso * 2.0)
def test_within_orthorhombic(self):
atoms = MagresAtoms.load_magres(self.orthorhombic)
self.assertEqual(len(atoms), 1)
p = atoms[0].position
self.assertEqual(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.assertEqual(len(atoms.within(p, 3.0)), num_within_3)
self.assertEqual(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_replace_efg(self):
"""
Check that we can replace the tensor on an atom.
"""
atoms = MagresAtoms.load_magres(
os.path.join(DATA_DIR, "ethanol/ethanol-nmr.magres"))
with self.assertRaises(Exception):
atoms.C1.efg.V = numpy.array([1, 2, 3])
orig_Cq = atoms.C1.efg.Cq
new_V = atoms.C1.efg.V * 2.0
atoms.C1.efg.V = new_V
self.assertEqual(atoms.C1.efg.Cq, orig_Cq * 2.0)
def test_nmr(self):
atoms = MagresAtoms.load_magres(
os.path.join(DATA_DIR, "ethanol/ethanol-nmr.magres"))
self.assertTrue(hasattr(atoms, "ms"))
self.assertTrue(hasattr(atoms, "efg"))
self.assertEqual(len(atoms.efg), 9)
self.assertEqual(len(atoms.ms), 9)
# Check that the EFGs are traceless
for efg in atoms.efg:
self.assertTrue(numpy.trace(efg.V) / 3.0 < 1e-12)
# Check that the principal components are ordered by the Haeberlen convention
# |Vzz| >= |Vxx| >= |Vyy|
for efg in atoms.efg:
self.assertTrue(abs(efg.evals[2]) >= abs(efg.evals[0]))
self.assertTrue(abs(efg.evals[0]) >= abs(efg.evals[1]))
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)
def test_isc(self):
atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, "ethanol-isc.magres"))
self.assertTrue(hasattr(atoms.C2, "isc"))
self.assertTrue(hasattr(atoms.C2, "isc_orbital_p"))
self.assertTrue(hasattr(atoms.C2, "isc_orbital_d"))
self.assertTrue(hasattr(atoms.C2, "isc_spin"))
self.assertTrue(hasattr(atoms.C2, "isc_fc"))
self.assertEqual(len(atoms.C2.isc), len(atoms)-1)
perturb_atom = atoms.get('C', 2)
for isc in atoms.C2.isc:
self.assertEqual(isc.atom1, perturb_atom)
self.assertEqual(isc.K_iso, numpy.trace(isc.K)/3.0)
# Check that the principal components are ordered by the Haeberlen convention
for isc in atoms.C2.isc:
self.assertTrue(abs(isc.K_evals[2] - isc.K_iso) >= abs(isc.K_evals[0] - isc.K_iso))
self.assertTrue(abs(isc.K_evals[0] - isc.K_iso) >= abs(isc.K_evals[1] - isc.K_iso))
def test_efg(self):
atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, "ethanol/ethanol-nmr.magres"))
self.assertTrue(hasattr(atoms, "efg"))
self.assertEqual(len(atoms.efg), 9)
# Check that the EFGs are traceless
for efg in atoms.efg:
self.assertTrue(numpy.trace(efg.V) / 3.0 < 1e-12)
# Check that the principal components are ordered by the Haeberlen convention
# |Vzz| >= |Vxx| >= |Vyy|
for efg in atoms.efg:
self.assertTrue(abs(efg.evals[2]) >= abs(efg.evals[0]))
self.assertTrue(abs(efg.evals[0]) >= abs(efg.evals[1]))
# Check that eta is positive and <=1 (Cq can be positive or negative)
# eta = (Vxx - Vyy)/Vzz, 0 <= eta <= 1
for efg in atoms.efg:
self.assertTrue((efg.evals[1] - efg.evals[0]) / efg.evals[2] >= 0)
self.assertTrue((efg.evals[1] - efg.evals[0]) / efg.evals[2] <= 1)
self.assertTrue(efg.eta >= 0)
self.assertTrue(efg.eta <= 1)
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
else:
K1 = getattr(atom1, tensor)[atom2].K
K2 = getattr(atom2, tensor)[atom1].K
#K1 = getattr(atom1, tensor)[atom2].K
#K2 = getattr(atom2, tensor)[atom1].K
atoms_filter_str = a.atoms
if atoms_filter_str:
atoms_filter = parse_atom_list(atoms_filter_str)
else:
atoms_filter = lambda x: True
tensors = ['ms']
lines = []
print "# Number\tAtom\tIso\tAniso\tAsym\tPath"
if os.path.isfile(a.source_dir):
magres_atoms = [MagresAtoms.load_magres(a.source_dir)]
else:
magres_atoms = load_all_magres(a.source_dir)
isos = {}
for iso_ in a.iso:
num = re.findall('([0-9]+)', iso_)[0]
sym = re.findall('([A-Za-z]+)', iso_)[0]
isos[sym] = int(num)
for i, atoms in enumerate(magres_atoms):
num = get_numeric(atoms.magres_file.path)
for s, iso in isos.items():
# -*- coding: utf-8 -*- # ============================================================================= # Copyright (C) 2015 Christian Fernandez # Laboratoire Catalyse et Spectrochimie, Caen, France. # [email protected] # # This software is governed by the CeCILL-B license under French law # and abiding by the rules of distribution of free software. # You can use, modify and/ or redistribute the software under # the terms of the CeCILL-B license as circulated by CEA, CNRS and INRIA # at the following URL "http://www.cecill.info". # # See Licence.txt in the main directory # ============================================================================= """Short description. A longer description. """ from __future__ import print_function from magres.atoms import MagresAtoms, MagresAtomsView ethanol_atoms = MagresAtoms.load_magres('../samples/ethanol-all.magres') ethanol_atoms.calculate_bonds()
else:
atoms_filter = lambda x: True
tensors = [
'efg',
] # 'efg_local', 'efg_nonlocal']
lines = []
if a.numbers:
print("# Number\tAtom\tCq\tEta\tPath")
else:
print("# Atom\tCq\tEta\tPath")
if os.path.isfile(a.source):
magres_atoms = [MagresAtoms.load_magres(a.source)]
else:
magres_atoms = load_all_magres(a.source)
for i, atoms in enumerate(magres_atoms):
num = get_numeric(atoms.magres_file.path)
if num:
idx = num
else:
idx = [i]
for atom in atoms:
if atoms_filter(atom) and \
hasattr(atom, 'efg'):
"""
Script for extracting NMR shielding values
from .magres files generated by CASTEP
Generates line plot of all shifts
Comment out H or C as necessary
"""
from magres.atoms import MagresAtoms
import matplotlib.pyplot as plt
import numpy as np
import csv
atoms = MagresAtoms.load_magres(
'./spectra_processing/1,2-dichlorobenzene/free/12_dichlorobenzene_free.magres'
) #add path to magres file
nucleus = 'h'
save_csv = './spectra_processing/1,2-dichlorobenzene/free/H_shifts.csv'
shifts = []
shift_labels = []
# Extracts Atoms
C = atoms.species('C')
#I = np.linspace(1, 1, len(C))
H = atoms.species('H')
#I = np.linspace(1, 1, len(H))
# Extracts isotopic magnetic shielding and references shifts
for atom in H:
import sys
import math
import numpy
from magres.atoms import MagresAtoms
# Load T1Si0.magres sample into an atoms structure
atoms = MagresAtoms.load_magres("samples/T1Si0.magres")
atomAl15 = atoms.get_species('Al', 15)
for atom in atoms.species('Al'):
if atom == atomAl15:
continue
Vzz = atom.efg.evecs[2]
dr = atom.position - atomAl15.position
Vzz_dr_ang = math.acos(numpy.dot(Vzz, dr) / math.sqrt(numpy.dot(dr,dr) * numpy.dot(Vzz,Vzz)))
print atom, atom.efg.Cq, Vzz_dr_ang
from __future__ import print_function
import sys
from magres.atoms import MagresAtoms
# Load ethanol-jc.magres sample into an atoms structure
atoms = MagresAtoms.load_magres("../samples/ethanol-jc.magres")
# For fun, set all the hydrogens to be tritium
for atom in atoms.species('H'):
atom.isotope = 3
# Set all the carbons to be 12C (won't work!)
try:
for atom in atoms.species('C'):
atom.isotope = 12
except ValueError as e:
print("Error changing C isotopes:", e, file=sys.stderr)
# Loop over and print out coupling symbol, distance between atoms, isotropic coupling, anisotropic coupling and
# asymmetry
for isc in atoms.isc:
print(isc.atom1, isc.atom2, isc.dist, isc.J_iso, isc.J_aniso, isc.J_eta)
def test_angles_boundary(self): atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, "angles/angles1.magres")) self.assertTrue(allclose(atoms.angle(atoms.C2, atoms.C1, atoms.C3, degrees=True), 180.0)) self.assertTrue(allclose(atoms.angle(atoms.C6, atoms.C1, atoms.C9, degrees=True), 90.0))
#!python
from __future__ import print_function
import sys
from numpy import mean
from magres.atoms import MagresAtoms
# Load the magres files
out_atoms = MagresAtoms.load_magres(sys.argv[1])
atomss = [MagresAtoms.load_magres(f) for f in sys.argv[1:]]
for atom in out_atoms:
other_atoms = [atoms.species(atom.species)[atom.index - 1] for atoms in atomss]
atom.magres_atom['position'] = mean([atom_.position for atom_ in other_atoms], 0).tolist()
if hasattr(atom, 'ms'):
atom.ms.magres_ms['sigma'] = mean([atom_.ms.sigma for atom_ in other_atoms], 0).tolist()
if hasattr(atom, 'efg'):
atom.efg.magres_efg['V'] = mean([atom_.efg.V for atom_ in other_atoms], 0).tolist()
print(out_atoms.magres_file)
def test_labels(self):
atoms = MagresAtoms.load_magres(self.species)
def test_dihedral5(self):
atoms = MagresAtoms.load_magres(os.path.join(DATA_DIR, "angles/dihedral5.magres"))
self.assertTrue(allclose(atoms.dihedral(atoms.C1, atoms.C2, atoms.C3, atoms.C4, degrees=True), 45.0))
def test_labels(self):
atoms = MagresAtoms.load_magres(self.species)
def test_species(self):
atoms = MagresAtoms.load_magres(self.species)
self.assertEqual(len(atoms), 3)
self.assertEqual(len(atoms.species("H")), 1)
self.assertEqual(len(atoms.species("C")), 2)
#!python
from __future__ import print_function
import sys
from numpy import mean
from magres.atoms import MagresAtoms
# Load the magres files
out_atoms = MagresAtoms.load_magres(sys.argv[1])
atomss = [MagresAtoms.load_magres(f) for f in sys.argv[1:]]
for atom in out_atoms:
other_atoms = [
atoms.species(atom.species)[atom.index - 1] for atoms in atomss
]
atom.magres_atom['position'] = mean(
[atom_.position for atom_ in other_atoms], 0).tolist()
if hasattr(atom, 'ms'):
atom.ms.magres_ms['sigma'] = mean(
[atom_.ms.sigma for atom_ in other_atoms], 0).tolist()
if hasattr(atom, 'efg'):
atom.efg.magres_efg['V'] = mean([atom_.efg.V for atom_ in other_atoms],
0).tolist()
print(out_atoms.magres_file)
from magres.atoms import MagresAtoms
atoms = MagresAtoms.load_magres('samples/simple.magres')
print atoms[0].position
Catoms = atoms.species('C')
print "1"
for atom in Catoms.within(atoms[0], 1.0):
print atom, atom.position
print "5"
for atom in Catoms.within(atoms[0], 3.0):
print atom, atom.position
print "5-1"
for atom in Catoms.within(atoms[0], 3.0).within(atoms[0], 1.0):
print atom, atom.position
print "1-5"
for atom in Catoms.within(atoms[0], 1.0).within(atoms[0], 3.0):
print atom, atom.position
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)
from __future__ import print_function
import sys
import math
import numpy
from magres.atoms import MagresAtoms
# Load T1Si0.magres sample into an atoms structure
atoms = MagresAtoms.load_magres("../samples/T1Si0.magres")
atomAl15 = atoms.get("Al", 15)
for atom in atoms.species("Al"):
if atom == atomAl15:
continue
Vzz = atom.efg.evecs[2]
dr = atom.position - atomAl15.position
Vzz_dr_ang = math.acos(numpy.dot(Vzz, dr) / math.sqrt(numpy.dot(dr, dr) * numpy.dot(Vzz, Vzz)))
print(atom, atom.efg.Cq, Vzz_dr_ang)
import sys
from magres.atoms import MagresAtoms
atoms = MagresAtoms.load_magres("samples/ethanol-nmr.magres")
for atom in atoms:
print atom, atom.ms.iso, atom.ms.aniso, atom.ms.zeta, atom.ms.eta, atom.ms.span, atom.ms.skew, atom.ms.evals[0], atom.ms.evals[1], atom.ms.evals[2]
from __future__ import print_function
from magres.atoms import MagresAtoms
atoms = MagresAtoms.load_magres('../samples/simple.magres')
print(atoms[0].position)
Catoms = atoms.species('C')
print("1")
for atom in Catoms.within(atoms[0], 1.0):
print(atom, atom.position)
print("5")
for atom in Catoms.within(atoms[0], 3.0):
print(atom, atom.position)
print("5-1")
for atom in Catoms.within(atoms[0], 3.0).within(atoms[0], 1.0):
print(atom, atom.position)
print("1-5")
for atom in Catoms.within(atoms[0], 1.0).within(atoms[0], 3.0):
print(atom, atom.position)
#!python
import sys
from magres.atoms import MagresAtoms
file = sys.argv[1]
atoms = MagresAtoms.load_magres(file)
print "# Principle components of sigma (magnetic shielding, unreferenced) tensor"
for atom in atoms:
pcs = atom.ms.evals
print ", ".join(
map(str, [atom.species, atom.index, pcs[0], pcs[1], pcs[2]]))
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
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)
