def scan(prefix):
""" construct the scan filesystem
layers:
- trunk (specifiers: [])
- branch (specifiers: [coo_names])
- leaf (specifiers: [coo_names, coo_vals])
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
trunk_ds = dir_.scan_trunk(prefix)
branch_ds = dir_.scan_branch(prefix, root_ds=trunk_ds)
leaf_ds = dir_.scan_leaf(prefix, root_ds=branch_ds)
vma_dfile = file_.vmatrix(FilePrefix.SCAN)
trunk_ds.add_data_files({FileAttributeName.VMATRIX: vma_dfile})
inf_dfile = file_.information(FilePrefix.SCAN, function=info.scan_branch)
traj_dfile = file_.trajectory(FilePrefix.SCAN)
branch_ds.add_data_files({
FileAttributeName.INFO: inf_dfile,
FileAttributeName.TRAJ: traj_dfile
})
geom_inf_dfile = file_.information(FilePrefix.GEOM, function=info.run)
grad_inf_dfile = file_.information(FilePrefix.GRAD, function=info.run)
hess_inf_dfile = file_.information(FilePrefix.HESS, function=info.run)
geom_inp_dfile = file_.input_file(FilePrefix.GEOM)
grad_inp_dfile = file_.input_file(FilePrefix.GRAD)
hess_inp_dfile = file_.input_file(FilePrefix.HESS)
ene_dfile = file_.energy(FilePrefix.GEOM)
geom_dfile = file_.geometry(FilePrefix.GEOM)
zmat_dfile = file_.zmatrix(FilePrefix.GEOM)
grad_dfile = file_.gradient(FilePrefix.GRAD)
hess_dfile = file_.hessian(FilePrefix.HESS)
hfreq_dfile = file_.harmonic_frequencies(FilePrefix.HESS)
leaf_ds.add_data_files({
FileAttributeName.GEOM_INFO: geom_inf_dfile,
FileAttributeName.GRAD_INFO: grad_inf_dfile,
FileAttributeName.HESS_INFO: hess_inf_dfile,
FileAttributeName.GEOM_INPUT: geom_inp_dfile,
FileAttributeName.GRAD_INPUT: grad_inp_dfile,
FileAttributeName.HESS_INPUT: hess_inp_dfile,
FileAttributeName.ENERGY: ene_dfile,
FileAttributeName.GEOM: geom_dfile,
FileAttributeName.ZMAT: zmat_dfile,
FileAttributeName.GRAD: grad_dfile,
FileAttributeName.HESS: hess_dfile,
FileAttributeName.HFREQ: hfreq_dfile
})
dir_fs = model.FileSystem({
SeriesAttributeName.TRUNK: trunk_ds,
SeriesAttributeName.BRANCH: branch_ds,
SeriesAttributeName.BRANCH1: branch_ds,
SeriesAttributeName.LEAF: leaf_ds
})
return dir_fs
def run(prefix):
""" construct the run filesystem [trunk/leaf]
layers:
- trunk (specifiers: [])
- leaf (specifiers: [job])
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
trunk_ds = dir_.run_trunk(prefix)
leaf_ds = dir_.run_leaf(prefix, root_ds=trunk_ds)
inf_dfile = file_.information(FilePrefix.RUN, function=info.run)
inp_dfile = file_.input_file(FilePrefix.RUN)
out_dfile = file_.output_file(FilePrefix.RUN)
trunk_ds.add_data_files({FileAttributeName.INFO: inf_dfile})
leaf_ds.add_data_files({
FileAttributeName.INFO: inf_dfile,
FileAttributeName.INPUT: inp_dfile,
FileAttributeName.OUTPUT: out_dfile
})
dir_fs = model.FileSystem({
SeriesAttributeName.TRUNK: trunk_ds,
SeriesAttributeName.LEAF: leaf_ds
})
return dir_fs
def direction(prefix):
""" filesystem object for reaction direction
layers:
- leaf (specifiers: [forw])
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
leaf_ds = dir_.direction_leaf(prefix)
inf_dfile = file_.information(FilePrefix.GEOM, function=info.run)
inp_dfile = file_.input_file(FilePrefix.GEOM)
ene_dfile = file_.energy(FilePrefix.GEOM)
geom_dfile = file_.geometry(FilePrefix.GEOM)
zmat_dfile = file_.zmatrix(FilePrefix.GEOM)
leaf_ds.add_data_files({
FileAttributeName.GEOM_INPUT: inp_dfile,
FileAttributeName.GEOM_INFO: inf_dfile,
FileAttributeName.ENERGY: ene_dfile,
FileAttributeName.GEOM: geom_dfile,
FileAttributeName.ZMAT: zmat_dfile
})
dir_fs = model.FileSystem({SeriesAttributeName.LEAF: leaf_ds})
return dir_fs
def high_spin(prefix):
""" construct the high-spin, single-point filesystem [trunk/leaf]
layers:
- trunk (specifiers: [])
- leaf (specifiers: [method, basis, orb_restricted])
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
trunk_ds = dir_.high_spin_trunk(prefix)
leaf_ds = dir_.high_spin_leaf(prefix, root_ds=trunk_ds)
inp_dfile = file_.input_file(FilePrefix.HS)
inf_dfile = file_.information(FilePrefix.HS, function=info.run)
ene_dfile = file_.energy(FilePrefix.HS)
leaf_ds.add_data_files({
FileAttributeName.INFO: inf_dfile,
FileAttributeName.INPUT: inp_dfile,
FileAttributeName.ENERGY: ene_dfile
})
dir_fs = model.FileSystem({
SeriesAttributeName.TRUNK: trunk_ds,
SeriesAttributeName.LEAF: leaf_ds
})
return dir_fs
def energy_transfer(prefix):
""" construct the energy transfer filesystem [trunk/leaf]
layers:
- trunk (specifiers: [])
- branch (specifiers: [ich, chg, mul])
- leaf (specifiers: [method, basis, orb_restricted])
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
trunk_ds = dir_.energy_transfer_trunk(prefix)
branch_ds = dir_.energy_transfer_branch(prefix, root_ds=trunk_ds)
leaf_ds = dir_.energy_transfer_leaf(prefix, root_ds=branch_ds)
# inp_dfile = file_.input_file(FilePrefix.LJ)
inf_dfile = file_.information(FilePrefix.LJ, function=info.lennard_jones)
ene_dfile = file_.energy(FilePrefix.LJ)
eps_dfile = file_.lennard_jones_epsilon(FilePrefix.LJ)
sig_dfile = file_.lennard_jones_sigma(FilePrefix.LJ)
traj_dfile = file_.trajectory(FilePrefix.LJ)
trunk_ds.add_data_files({FileAttributeName.INFO: inf_dfile})
leaf_ds.add_data_files({
# FileAttributeName.INFO: inf_dfile,
# FileAttributeName.INPUT: inp_dfile,
FileAttributeName.ENERGY:
ene_dfile,
FileAttributeName.LJ_EPS:
eps_dfile,
FileAttributeName.LJ_SIG:
sig_dfile,
FileAttributeName.TRAJ:
traj_dfile
})
dir_fs = model.FileSystem({
SeriesAttributeName.TRUNK: trunk_ds,
SeriesAttributeName.BRANCH: branch_ds,
SeriesAttributeName.BRANCH1: branch_ds,
SeriesAttributeName.LEAF: leaf_ds
})
return dir_fs
def subrun(prefix):
""" construct the subrun filesystem [leaf]
layers:
- leaf (specifiers: [macro_idx, micro_idx])
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
leaf_ds = dir_.subrun_leaf(prefix)
inf_dfile = file_.information(FilePrefix.RUN, function=info.run)
inp_dfile = file_.input_file(FilePrefix.RUN)
out_dfile = file_.output_file(FilePrefix.RUN)
leaf_ds.add_data_files({
FileAttributeName.INFO: inf_dfile,
FileAttributeName.INPUT: inp_dfile,
FileAttributeName.OUTPUT: out_dfile
})
dir_fs = model.FileSystem({SeriesAttributeName.LEAF: leaf_ds})
return dir_fs
def conformer(prefix):
""" construct the conformer filesystem [trunk/leaf]
layers:
- trunk (specifiers: [])
- leaf (specifiers: [cid])
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
trunk_ds = dir_.conformer_trunk(prefix)
leaf_ds = dir_.conformer_leaf(prefix, root_ds=trunk_ds)
min_ene_dfile = file_.energy(FilePrefix.MIN)
vma_dfile = file_.vmatrix(FilePrefix.CONF)
inf_dfile = file_.information(FilePrefix.CONF,
function=info.conformer_trunk)
traj_dfile = file_.trajectory(FilePrefix.CONF)
trunk_ds.add_data_files({
FileAttributeName.VMATRIX: vma_dfile,
FileAttributeName.INFO: inf_dfile,
FileAttributeName.ENERGY: min_ene_dfile,
FileAttributeName.TRAJ: traj_dfile
})
geom_inf_dfile = file_.information(FilePrefix.GEOM, function=info.run)
grad_inf_dfile = file_.information(FilePrefix.GRAD, function=info.run)
hess_inf_dfile = file_.information(FilePrefix.HESS, function=info.run)
geom_inp_dfile = file_.input_file(FilePrefix.GEOM)
grad_inp_dfile = file_.input_file(FilePrefix.GRAD)
hess_inp_dfile = file_.input_file(FilePrefix.HESS)
ene_dfile = file_.energy(FilePrefix.GEOM)
geom_dfile = file_.geometry(FilePrefix.GEOM)
zmat_dfile = file_.zmatrix(FilePrefix.GEOM)
grad_dfile = file_.gradient(FilePrefix.GRAD)
hess_dfile = file_.hessian(FilePrefix.HESS)
hfreq_dfile = file_.harmonic_frequencies(FilePrefix.HESS)
vpt2_inf_dfile = file_.information(FilePrefix.VPT2,
function=info.vpt2_trunk)
vpt2_inp_dfile = file_.input_file(FilePrefix.VPT2)
anhfreq_dfile = file_.anharmonic_frequencies(FilePrefix.VPT2)
anhzpve_dfile = file_.anharmonic_zpve(FilePrefix.VPT2)
xmat_dfile = file_.anharmonicity_matrix(FilePrefix.VPT2)
vibrot_mat_dfile = file_.vibro_rot_alpha_matrix(FilePrefix.VPT2)
centrif_dist_dfile = file_.quartic_centrifugal_dist_consts(FilePrefix.VPT2)
leaf_ds.add_data_files({
FileAttributeName.GEOM_INFO: geom_inf_dfile,
FileAttributeName.GRAD_INFO: grad_inf_dfile,
FileAttributeName.HESS_INFO: hess_inf_dfile,
FileAttributeName.GEOM_INPUT: geom_inp_dfile,
FileAttributeName.GRAD_INPUT: grad_inp_dfile,
FileAttributeName.HESS_INPUT: hess_inp_dfile,
FileAttributeName.ENERGY: ene_dfile,
FileAttributeName.GEOM: geom_dfile,
FileAttributeName.ZMAT: zmat_dfile,
FileAttributeName.GRAD: grad_dfile,
FileAttributeName.HESS: hess_dfile,
FileAttributeName.HFREQ: hfreq_dfile,
FileAttributeName.VPT2_INFO: vpt2_inf_dfile,
FileAttributeName.VPT2_INPUT: vpt2_inp_dfile,
FileAttributeName.ANHFREQ: anhfreq_dfile,
FileAttributeName.ANHZPVE: anhzpve_dfile,
FileAttributeName.XMAT: xmat_dfile,
FileAttributeName.VIBROT_MAX: vibrot_mat_dfile,
FileAttributeName.CENTIF_DIST: centrif_dist_dfile
})
dir_fs = model.FileSystem({
SeriesAttributeName.TRUNK: trunk_ds,
SeriesAttributeName.LEAF: leaf_ds
})
return dir_fs