# Save the results to a hdf5 file
main_output(mult, outputname=npz_fid, otype='native', ftype='numpy')
# Reset the `orbkit.multiple_files` module
try:
from importlib import reload # >= Python3.4
except ImportError:
try:
from imp import reload # <= Python3.3
except ImportError:
pass # Python2.X
# Read in the results
mult = main_read(npz_fid,gname='multi')
t.append(time())
# Perform a standard orbkit computation
mult.construct_qc() # Construct the qc_info class for every structure
r = 0 # Index to be calculated
outputname = 'nacl_r%d' % r # Specifies the name of the output file
display('Running orbkit for the structure %d' % r)
import orbkit
# Initialize orbkit with default parameters and options
orbkit.init(reset_display=False)
# Set some options
from orbkit.read.high_level import main_read from orbkit.output.high_level import main_output from orbkit.grid import set_grid, get_shape from orbkit.test.tools import equal from orbkit.qcinfo import QCinfo from orbkit import options import os, inspect, tempfile, numpy options.quiet = True tests_home = os.path.dirname(inspect.getfile(inspect.currentframe())) folder = os.path.join(tests_home, '../outputs_for_testing') filepath = os.path.join(folder, 'NaCl_molden_files.tar.gz') qc_old = main_read(filepath) tests_home = tempfile.gettempdir() filepath = os.path.join(tests_home, 'tmp.npz') main_output(qc_old, outputname=filepath, otype='native', ftype='numpy') qc_new = main_read(filepath) equal(qc_old, qc_new) os.remove(filepath) # Test restart from standard npz data output set_grid(0, 0, 0, is_vector=False) main_output(numpy.zeros(get_shape()), qc=qc_old, outputname=filepath) qc_new = main_read(filepath)
from orbkit.read.high_level import main_read
from orbkit.test.tools import equal
from orbkit.qcinfo import QCinfo
import numpy
from orbkit import options
import os, inspect
options.quiet = True
tests_home = os.path.dirname(inspect.getfile(inspect.currentframe()))
folder = os.path.join(tests_home, '../outputs_for_testing/gamess')
filepath = os.path.join(folder, 'formaldehyde.log')
qc = main_read(filepath, all_mo=True)
item = qc.mo_spec.get_coeffs()
for i in range(item.shape[0]):
item[i] = numpy.zeros(item.shape[1]) + i
qc.mo_spec.set_coeffs(item)
equal(qc.mo_spec.get_coeffs(), item)
item = qc.mo_spec.get_occ()
qc.mo_spec.set_occ(item)
equal(qc.mo_spec.get_occ(), item)
item = qc.mo_spec.get_eig()
qc.mo_spec.set_eig(item)
equal(qc.mo_spec.get_eig(), item)
item = qc.mo_spec.get_sym()
qc.mo_spec.set_sym(item)
import os, shutil, inspect, tempfile, numpy from orbkit.read.high_level import main_read from orbkit.output.high_level import main_output from orbkit.grid import set_grid, get_shape from orbkit.test.tools import equal from orbkit.qcinfo import QCinfo from orbkit import options options.quiet = True tests_home = os.path.dirname(inspect.getfile(inspect.currentframe())) folder = os.path.join(tests_home, '../outputs_for_testing') filepath = os.path.join(folder, 'NaCl_molden_files.tar.gz') qc_old = main_read(filepath) test_dir = tempfile.mkdtemp() testfile = os.path.join(test_dir, 'tmp.hdf5') main_output(qc_old, outputname=testfile, otype='native', ftype='hdf5') qc_new = main_read(testfile) equal(qc_old, qc_new) # Test restart from standard HDF5 data output set_grid(0, 0, 0, is_vector=False) main_output(numpy.zeros(get_shape()), qc=qc_old, outputname=testfile) qc_new = main_read(filepath)