def add_zma_inp():
""" Add the zma input files using geo inputs
"""
cnf_managers = fs.iterate_managers(PFX, ['REACTION', 'THEORY', 'TRANSITION STATE'],
'CONFORMER')
for cnf_fs in cnf_managers:
if cnf_fs is not None:
print()
for locs in cnf_fs[-1].existing():
cnf_path = cnf_fs[-1].path(locs)
# zma_fs = fs.manager(cnf_path, 'ZMATRIX')
if cnf_fs[-1].file.geometry_input.exists(locs):
inp_str = cnf_fs[-1].file.geometry_input.read(locs)
print('FOUND INPUT')
print(cnf_fs[-1].path(locs))
break
for locs in cnf_fs[-1].existing():
cnf_path = cnf_fs[-1].path(locs)
zma_fs = fs.manager(cnf_path, 'ZMATRIX')
zma_path = zma_fs[-1].path([0])
if not zma_fs[-1].file.geometry_input.exists([0]):
print('WRITING INPUT')
print(zma_path)
# zma_fs = fs.manager(cnf_path, 'ZMATRIX')
zma_fs[-1].file.geometry_input.write(inp_str, [0])
else:
print('INPUT GOOD')
print(zma_path)
def add_ene_to_sp():
""" Add the energy files
"""
ini = ['SPECIES', 'THEORY']
# saddle = bool('REACTION' in ini)
# managers = fs.iterate_managers(
# PFX, ini, 'CONFORMER'
# )
managers = fs.iterate_managers(
PFX, ['SPECIES'], 'THEORY'
)
for thy_fs in managers:
if thy_fs is not None:
for thy_locs in thy_fs[-1].existing():
thy_path = thy_fs[-1].path(thy_locs)
print('thy', thy_path)
cnf_fs = fs.conformer(thy_path)
for cnf_locs in cnf_fs[-1].existing():
cnf_path = cnf_fs[-1].path(cnf_locs)
print('cnf', cnf_path)
sp_locs = fs.iterate_locators(cnf_path, ['SINGLE POINT'])
sp_lst = list(sp_locs)
print('thy_locs', thy_locs)
print('sp_locs', sp_lst)
if sp_lst:
if (thy_locs,) not in sp_lst:
if cnf_fs[-1].file.energy.exists(cnf_locs):
print('ADD SP FILES')
sp_fs = fs.single_point(cnf_path)
sp_fs[-1].create(thy_locs)
inp_str = cnf_fs[-1].file.geometry_input.read(cnf_locs)
ene = cnf_fs[-1].file.energy.read(cnf_locs)
sp_fs[-1].file.input.write(inp_str, thy_locs)
sp_fs[-1].file.energy.write(ene, thy_locs)
else:
print('NEED SP FILE')
else:
print('ADD SP DIR AND FILES')
sp_fs = fs.single_point(cnf_path)
sp_fs[-1].create(thy_locs)
inp_str = cnf_fs[-1].file.geometry_input.read(cnf_locs)
ene = cnf_fs[-1].file.energy.read(cnf_locs)
sp_fs[-1].file.input.write(inp_str, thy_locs)
sp_fs[-1].file.energy.write(ene, thy_locs)
def example6():
"""
Example 6: Iterate over CSCANS managers
"""
for scn_fs in fs.iterate_managers(
PFX,
['REACTION', 'THEORY', 'TRANSITION STATE', 'CONFORMER', 'ZMATRIX'],
'CSCAN'):
if scn_fs[0].exists():
print(scn_fs[0].path())
# Note that the following loops all do the same thing
# Combined loop over scan coordinates, coordinate values, and
# constraints
for locs in scn_fs[-1].existing():
print(locs)
print()
# Loop over all directories for a given set of scan coordinates
for root_locs in scn_fs[1].existing():
print('root: {}'.format(root_locs))
for locs in scn_fs[3].existing(root_locs):
print(locs)
print()
# Loop over all directories for a given set of scan coordinates and
# values
for root_locs in scn_fs[2].existing():
print('root: {}'.format(root_locs))
for locs in scn_fs[3].existing(root_locs):
print(locs)
print()
# Completely split out the loop
for root_locs1 in scn_fs[1].existing():
print('root1: {}'.format(root_locs1))
for root_locs2 in scn_fs[2].existing(root_locs1):
print('root2: {}'.format(root_locs2))
for locs in scn_fs[3].existing(root_locs2):
print(locs)
print()
def example5():
"""
Example 5: Iterate over CONFORMER managers under SPECIES/THEORY paths
"""
for cnf_fs in fs.iterate_managers(PFX, ['SPECIES', 'THEORY'], 'CONFORMER'):
print(cnf_fs[0].path())
# If it has an energy file, print the value
for locs in cnf_fs[-1].existing():
path = cnf_fs[-1].path(locs)
print(path)
# ene = cnf_fs[-1].file.energy.read(locs)
# print(ene)
print()
def check_zma_for_trans():
""" Check zma for trans files
"""
zma_managers = fs.iterate_managers(PFX, ['REACTION', 'THEORY', 'TRANSITION STATE',
'CONFORMER'], 'ZMATRIX')
BAD = 0
for zma_fs in zma_managers:
zma_path = zma_fs[-1].path([0])
print(zma_path)
if zma_fs is not None:
if zma_fs[-1].file.transformation.exists([0]):
print('GOOD')
else:
print('NO TRANS')
BAD += 1
else:
print('zma none')
print()
print('\nBAD CNT', BAD)
def add_ene_yaml():
""" Add the energy files
"""
ini = ['SPECIES', 'THEORY']
# saddle = bool('REACTION' in ini)
# managers = fs.iterate_managers(
# PFX, ini, 'CONFORMER'
# )
managers = fs.iterate_managers(
PFX, ['SPECIES', 'THEORY'], 'CONFORMER')
for cnf_fs in managers:
for cnf_locs in cnf_fs[-1].existing():
cnf_path = cnf_fs[-1].path(cnf_locs)
sp_fs = fs.single_point(cnf_path)
sp_locs = fs.iterate_locators(cnf_path, ['SINGLE POINT'])
for locs in sp_locs:
sp_fs = fs.single_point(cnf_path)
if not sp_fs[-1].file.info.exists(locs):
print('BAD')
def add_zma_trans():
""" Add the zma input files using geo inputs
"""
cnf_managers = fs.iterate_managers(PFX, ['REACTION', 'THEORY', 'TRANSITION STATE'],
'CONFORMER')
for cnf_fs in cnf_managers:
if cnf_fs is not None:
print()
gra = None
for locs in cnf_fs[-1].existing():
cnf_path = cnf_fs[-1].path(locs)
zma_fs = fs.manager(cnf_path, 'ZMATRIX')
zma_path = zma_fs[-1].path([0])
# if zma_fs[-1].file.transformation.exists([0]):
# tra = zma_fs[-1].file.transformation.read([0])
# print('FOUND TRA')
# print(zma_path)
# break
if zma_fs[-1].file.reactant_graph.exists([0]):
gra = zma_fs[-1].file.reactant_graph.read([0])
print('FOUND GRAPH')
print(zma_fs[-1].path([0]))
break
print('---')
print()
for locs in cnf_fs[-1].existing():
cnf_path = cnf_fs[-1].path(locs)
zma_fs = fs.manager(cnf_path, 'ZMATRIX')
zma_path = zma_fs[-1].path([0])
# if not zma_fs[-1].file.transformation.exists([0]):
if not zma_fs[-1].file.reactant_graph.exists([0]):
print('WRITING GRA AT CONF')
print(zma_path)
zma_fs = fs.manager(cnf_path, 'ZMATRIX')
# zma_fs[-1].file.transformation.write(tra, [0])
zma_fs[-1].file.reactant_graph.write(gra, [0])
else:
print('GRA GOOD')
print(zma_path)
if locs_lst:
geos = [fs_[-1].file.geometry.read(locs) for locs in locs_lst]
traj = []
for geo, locs in zip(geos, locs_lst):
comment = '{}'.format(locs[0])
traj.append((comment, geo))
traj_path = fs_[0].file.trajectory.path()
print("Updating trajectory file at {}".format(traj_path))
fs_[0].file.trajectory.write(traj)
# First, write them in the CONFORMER layer
for cnf_fs in itertools.chain(
fs.iterate_managers(SAVE_PFX, ['SPECIES', 'THEORY'], 'CONFORMER'),
fs.iterate_managers(SAVE_PFX,
['REACTION', 'THEORY', 'TRANSITION STATE'],
'CONFORMER')):
write_sorted_trajectory_file(cnf_fs)
# Then write them in the SYMMETRY layer
for sym_fs in itertools.chain(
fs.iterate_managers(SAVE_PFX, ['SPECIES', 'THEORY', 'CONFORMER'],
'SYMMETRY'),
fs.iterate_managers(
SAVE_PFX, ['REACTION', 'THEORY', 'TRANSITION STATE', 'CONFORMER'],
'SYMMETRY')):
write_trajectory_file(sym_fs)
# zma = zma_df.read(cnf_locs)
#
# zma_fs = fs.manager(cnf_path, 'ZMATRIX')
#
# zma_fs[-1].file.zmatrix.write(zma, [0])
#
# zma_path = zma_fs[-1].path([0])
#
# # # Now that we've written the z-matrix to the new location, we can
# # # remove the old one
# # zma_df.removable = True
# # zma_df.remove(cnf_locs)
# Lastly, write the zmatrix files for the z-matrix guess
for zma_fs in itertools.chain(
fs.iterate_managers(SAVE_PFX, ['REACTION', 'THEORY'], 'ZMATRIX')):
if zma_fs[-1].exists([0]):
path = zma_fs[-1].path([0])
print(path)
scan_fs = fs.manager(path, 'SCAN')
scan_locs_lst = sorted(scan_fs[-1].existing())
if scan_locs_lst:
scan_locs = scan_locs_lst[0]
scan_path = scan_fs[-1].path(scan_locs)
print(scan_locs)
zma = scan_fs[-1].file.zmatrix.read(scan_locs)
def write_freqs():
""" write the harm freqs using ProjRot
"""
# Build tmp dir to run ProjRot
prefix = tempfile.mkdtemp()
print(prefix)
start_path = os.getcwd()
# ini = ['REACTION', 'THEORY', 'TRANSITION STATE']
ini = ['SPECIES', 'THEORY']
saddle = bool('REACTION' in ini)
managers = fs.iterate_managers(
PFX, ini, 'CONFORMER'
)
bad_path = []
for cnf_fs in managers:
# print(cnf_fs[-1].existing())
for locs in cnf_fs[-1].existing():
cnf_path = cnf_fs[-1].path(locs)
print(cnf_path)
if cnf_fs[-1].file.hessian.exists(locs):
print('RUNNING HESS')
# Read the info
geom = cnf_fs[-1].file.geometry.read(locs)
# grad = cnf_fs[-1].file.gradient.read(locs)
grad = []
hess = cnf_fs[-1].file.hessian.read(locs)
# Write the ProjRot input file
inp_str = projrot_io.writer.rpht_input(
[geom], [grad], [hess], rotors_str='')
in_path = os.path.join(prefix, 'RPHt_input_data.dat')
with open(in_path, 'w') as proj_file:
proj_file.write(inp_str)
os.chdir(prefix)
subprocess.check_call(['RPHt.exe'])
os.chdir(start_path)
# Read the harmonic frequencies
out_path = os.path.join(prefix, 'RTproj_freq.dat')
with open(out_path, 'r') as proj_file:
out_str = proj_file.read()
freqs, imag = projrot_io.reader.rpht_output(
out_str)
# Combine freqs
if saddle:
if len(imag) == 1:
wfreqs = freqs + [-1.0*x for x in imag]
else:
wfreqs = []
bad_path.append(cnf_path)
print('bad_freqs')
print(freqs)
print(imag)
else:
if len(imag) == 0:
wfreqs = freqs
else:
wfreqs = []
bad_path.append(cnf_path)
print('bad_freqs')
print(freqs)
print(imag)
# Write the freqs
if wfreqs:
print('FREQS GOOD')
print(wfreqs)
cnf_fs[-1].file.harmonic_frequencies.write(sorted(wfreqs), locs)
""" demonstrates use of the safemode setting
"""
import autofile
from autofile import fs
autofile.turn_off_safemode()
PFX = '/lcrc/project/PACC/AutoMech/data/save/'
print(autofile.safemode_is_on())
for zma_fs in fs.iterate_managers(
PFX, ['REACTION', 'THEORY', 'TRANSITION STATE', 'CONFORMER'],
'ZMATRIX'):
print(zma_fs[0].path())
rct_smis = list((automol.inchi.smiles(ich) for ich in rct_ichs))
prd_smis = list((automol.inchi.smiles(ich) for ich in prd_ichs))
# print('ichs')
# print(rct_ichs)
# print(prd_ichs)
# print('smi')
# print(list((automol.inchi.smiles(ich) for ich in rct_ichs)))
# print(list((automol.inchi.smiles(ich) for ich in prd_ichs)))
# Get one z-matrix for this reaction, if there is one
rxn_path = RXN_FS[-1].path(rxn_locs)
zma_fs = next(
fs.iterate_managers(rxn_path,
['THEORY', 'TRANSITION STATE', 'CONFORMER'],
'ZMATRIX'), None)
if zma_fs is not None:
zma_path = zma_fs[-1].path([0])
# print([rct_ichs, prd_ichs])
print(zma_path)
if zma_fs[-1].file.zmatrix.exists([0]):
# Read out the z-matrix
ts_zma = zma_fs[-1].file.zmatrix.read([0])
# Note that the keys in rct_gras and prd_gras at this point are
# arbitrary. The following work determines the transformation and
# the reactant graph *in terms of the z-matrix keys*.
# Attempt to determine the transformation in the forward direction
""" A script to wipe out all cscan directories
"""
import itertools
from autofile import fs
RUN_PFX = '/lcrc/project/PACC/AutoMech/data/run/'
SAVE_PFX = '/lcrc/project/PACC/AutoMech/data/save/'
for sca_fs in itertools.chain(
fs.iterate_managers(RUN_PFX,
['SPECIES', 'THEORY', 'CONFORMER', 'ZMATRIX'],
'CSCAN'),
fs.iterate_managers(SAVE_PFX,
['SPECIES', 'THEORY', 'CONFORMER', 'ZMATRIX'],
'CSCAN'),
fs.iterate_managers(
RUN_PFX,
['REACTION', 'THEORY', 'TRANSITION STATE', 'CONFORMER', 'ZMATRIX'],
'CSCAN'),
fs.iterate_managers(
SAVE_PFX,
['REACTION', 'THEORY', 'TRANSITION STATE', 'CONFORMER', 'ZMATRIX'],
'CSCAN')):
if sca_fs[0].exists():
print(sca_fs[0].path())
sca_fs[0].removable = True
sca_fs[0].remove()
print('removing...')
