def energy_transfer(prefix):
""" construct the energy transfer filesystem (3 layers)
locators:
0 - []
files:
- info
1 - [ich, chg, mul]
(no files)
2 - [ich, chg, mul, method, basis, orb_type]
files:
- energy
- lennard_jones_epsilon
- lennard_jones_sigma
- trajectory
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
trunk_ds = data_series.energy_transfer_trunk(prefix)
branch_ds = data_series.energy_transfer_branch(prefix, root_ds=trunk_ds)
leaf_ds = data_series.energy_transfer_leaf(prefix, root_ds=branch_ds)
# inp_dfile = data_files.input_file(_FilePrefix.LJ)
inf_dfile = data_files.information(_FilePrefix.LJ,
function=info_objects.lennard_jones)
ene_dfile = data_files.energy(_FilePrefix.LJ)
eps_dfile = data_files.lennard_jones_epsilon(_FilePrefix.LJ)
sig_dfile = data_files.lennard_jones_sigma(_FilePrefix.LJ)
traj_dfile = data_files.trajectory(_FilePrefix.LJ)
trunk_ds.add_data_files({_FileAttributeName.INFO: inf_dfile})
leaf_ds.add_data_files({
_FileAttributeName.ENERGY: ene_dfile,
_FileAttributeName.LJ_EPS: eps_dfile,
_FileAttributeName.LJ_SIG: sig_dfile,
_FileAttributeName.TRAJ: traj_dfile
})
return (trunk_ds, branch_ds, leaf_ds)
def symmetry(prefix):
""" Create a symmetry-conformer file system manager for a given path.
Layers:
[0] The "trunk" layer.
Specifiers:
[]
Files:
- trajectory
Generated by :meth:`autofile.schema.data_series.symmetry_trunk`
[1] The "leaf" layer.
Specifiers:
[Conformer ID]
Files:
- geometry
Generated by :meth:`autofile.schema.data_series.conformer_leaf`
:param prefix: Path to where the file system will be created
:type prefix: str
:returns: A tuple of DataSeries objects. Each item in this tuple manages a
different layer in the file system, as described above.
"""
trunk_ds = data_series.symmetry_trunk(prefix)
leaf_ds = data_series.conformer_leaf(prefix, root_ds=trunk_ds)
traj_dfile = data_files.trajectory(_FilePrefix.CONF)
geom_dfile = data_files.geometry(_FilePrefix.GEOM)
trunk_ds.add_data_files({
FileAttributeName.TRAJ: traj_dfile})
leaf_ds.add_data_files({
FileAttributeName.GEOM: geom_dfile})
return (trunk_ds, leaf_ds)
def tau(prefix):
""" construct the tau filesystem (2 layers)
locators:
0 - []
files:
- vmatrix
- info
- trajectory
0 - [tid]
files:
- geometry_info
- gradient_info
- hessian_info
- geometry_input
- gradient_input
- hessian_input
- energy
- geometry
- zmatrix
- gradient
- hessian
- harmonic_frequencies
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
trunk_ds = data_series.tau_trunk(prefix)
leaf_ds = data_series.tau_leaf(prefix, root_ds=trunk_ds)
vma_dfile = data_files.vmatrix(_FilePrefix.TAU)
inf_dfile = data_files.information(_FilePrefix.TAU,
function=info_objects.tau_trunk)
traj_dfile = data_files.trajectory(_FilePrefix.TAU)
trunk_ds.add_data_files({
_FileAttributeName.VMATRIX: vma_dfile,
_FileAttributeName.INFO: inf_dfile,
_FileAttributeName.TRAJ: traj_dfile
})
geom_inf_dfile = data_files.information(_FilePrefix.GEOM,
function=info_objects.run)
grad_inf_dfile = data_files.information(_FilePrefix.GRAD,
function=info_objects.run)
hess_inf_dfile = data_files.information(_FilePrefix.HESS,
function=info_objects.run)
geom_inp_dfile = data_files.input_file(_FilePrefix.GEOM)
grad_inp_dfile = data_files.input_file(_FilePrefix.GRAD)
hess_inp_dfile = data_files.input_file(_FilePrefix.HESS)
ene_dfile = data_files.energy(_FilePrefix.GEOM)
geom_dfile = data_files.geometry(_FilePrefix.GEOM)
zmat_dfile = data_files.zmatrix(_FilePrefix.GEOM)
grad_dfile = data_files.gradient(_FilePrefix.GRAD)
hess_dfile = data_files.hessian(_FilePrefix.HESS)
hfreq_dfile = data_files.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
})
geom_inf_jobj = json_objects.information(_FilePrefix.GEOM,
function=info_objects.run)
grad_inf_jobj = json_objects.information(_FilePrefix.GRAD,
function=info_objects.run)
hess_inf_jobj = json_objects.information(_FilePrefix.HESS,
function=info_objects.run)
geom_inp_jobj = json_objects.input_file(_FilePrefix.GEOM)
grad_inp_jobj = json_objects.input_file(_FilePrefix.GRAD)
hess_inp_jobj = json_objects.input_file(_FilePrefix.HESS)
ene_jobj = json_objects.energy(_FilePrefix.GEOM)
geom_jobj = json_objects.geometry(_FilePrefix.GEOM)
zmat_jobj = json_objects.zmatrix(_FilePrefix.GEOM)
grad_jobj = json_objects.gradient(_FilePrefix.GRAD)
hess_jobj = json_objects.hessian(_FilePrefix.HESS)
hfreq_jobj = json_objects.harmonic_frequencies(_FilePrefix.HESS)
leaf_ds.add_json_entries({
_JSONAttributeName.GEOM_INFO: geom_inf_jobj,
_JSONAttributeName.GRAD_INFO: grad_inf_jobj,
_JSONAttributeName.HESS_INFO: hess_inf_jobj,
_JSONAttributeName.GEOM_INPUT: geom_inp_jobj,
_JSONAttributeName.GRAD_INPUT: grad_inp_jobj,
_JSONAttributeName.HESS_INPUT: hess_inp_jobj,
_JSONAttributeName.ENERGY: ene_jobj,
_JSONAttributeName.GEOM: geom_jobj,
_JSONAttributeName.ZMAT: zmat_jobj,
_JSONAttributeName.GRAD: grad_jobj,
_JSONAttributeName.HESS: hess_jobj,
_JSONAttributeName.HFREQ: hfreq_jobj
})
return (trunk_ds, leaf_ds)
def cscan(prefix):
""" Create a constrained scan (c-scan) file system manager for a given path.
Layers:
[0] The c-scan "trunk" layer.
Specifiers:
[]
(no files)
Generated by :meth:`autofile.schema.data_series.cscan_trunk`
[1] The first c-scan "branch" layer.
Specifiers:
[Constraints]
Files:
- info
- trajectory
Generated by :meth:`autofile.schema.data_series.cscan_branch1`
[2] The second c-scan "branch" layer.
Specifiers:
[Constraints, Scan Coordinate Names]
(no files)
Generated by :meth:`autofile.schema.data_series.cscan_branch2`
[3] The c-scan "leaf" layer.
Specifiers:
[Constraints, Scan Coordinate Names, Scan Coordinate Values]
Files:
- geometry_info
- gradient_info
- hessian_info
- geometry_input
- gradient_input
- hessian_input
- energy
- geometry
- zmatrix
- gradient
- hessian
- harmonic_frequencies
Generated by :meth:`autofile.schema.data_series.cscan_leaf`
:param prefix: Path to where the file system will be created
:type prefix: str
:returns: A tuple of DataSeries objects. Each item in this tuple manages a
different layer in the file system, as described above.
"""
trunk_ds = data_series.cscan_trunk(prefix)
branch1_ds = data_series.cscan_branch1(prefix, root_ds=trunk_ds)
branch2_ds = data_series.cscan_branch2(prefix, root_ds=branch1_ds)
leaf_ds = data_series.cscan_leaf(prefix, root_ds=branch2_ds)
inf_dfile = data_files.information(_FilePrefix.SCAN,
function=info_objects.scan_branch)
traj_dfile = data_files.trajectory(_FilePrefix.SCAN)
branch1_ds.add_data_files({
_FileAttributeName.INFO: inf_dfile,
_FileAttributeName.TRAJ: traj_dfile
})
geom_inf_dfile = data_files.information(_FilePrefix.GEOM,
function=info_objects.run)
grad_inf_dfile = data_files.information(_FilePrefix.GRAD,
function=info_objects.run)
hess_inf_dfile = data_files.information(_FilePrefix.HESS,
function=info_objects.run)
geom_inp_dfile = data_files.input_file(_FilePrefix.GEOM)
grad_inp_dfile = data_files.input_file(_FilePrefix.GRAD)
hess_inp_dfile = data_files.input_file(_FilePrefix.HESS)
ene_dfile = data_files.energy(_FilePrefix.GEOM)
geom_dfile = data_files.geometry(_FilePrefix.GEOM)
zmat_dfile = data_files.zmatrix(_FilePrefix.GEOM)
grad_dfile = data_files.gradient(_FilePrefix.GRAD)
hess_dfile = data_files.hessian(_FilePrefix.HESS)
hfreq_dfile = data_files.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
})
return (trunk_ds, branch1_ds, branch2_ds, leaf_ds)
def scan(prefix):
""" construct the scan filesystem (3 layers)
three layers with the following locators:
0 - []
files:
- vmatrix
1 - [coo_names]
files:
- info
- trajectory
2 - [coo_names, coo_vals]
files:
- geometry_info
- gradient_info
- hessian_info
- irc_info
- geometry_input
- gradient_input
- hessian_input
- irc_input
- energy
- geometry
- zmatrix
- gradient
- hessian
- harmonic_frequencies
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
trunk_ds = data_series.scan_trunk(prefix)
branch_ds = data_series.scan_branch(prefix, root_ds=trunk_ds)
leaf_ds = data_series.scan_leaf(prefix, root_ds=branch_ds)
vma_dfile = data_files.vmatrix(_FilePrefix.SCAN)
trunk_ds.add_data_files({_FileAttributeName.VMATRIX: vma_dfile})
inf_dfile = data_files.information(_FilePrefix.SCAN,
function=info_objects.scan_branch)
traj_dfile = data_files.trajectory(_FilePrefix.SCAN)
branch_ds.add_data_files({
_FileAttributeName.INFO: inf_dfile,
_FileAttributeName.TRAJ: traj_dfile
})
# Need an irc file in the branch!
# Need an run irc file in the forward and backward direction
geom_inf_dfile = data_files.information(_FilePrefix.GEOM,
function=info_objects.run)
grad_inf_dfile = data_files.information(_FilePrefix.GRAD,
function=info_objects.run)
hess_inf_dfile = data_files.information(_FilePrefix.HESS,
function=info_objects.run)
irc_inf_dfile = data_files.information(_FilePrefix.IRC,
function=info_objects.run)
geom_inp_dfile = data_files.input_file(_FilePrefix.GEOM)
grad_inp_dfile = data_files.input_file(_FilePrefix.GRAD)
hess_inp_dfile = data_files.input_file(_FilePrefix.HESS)
irc_inp_dfile = data_files.input_file(_FilePrefix.IRC)
ene_dfile = data_files.energy(_FilePrefix.GEOM)
geom_dfile = data_files.geometry(_FilePrefix.GEOM)
zmat_dfile = data_files.zmatrix(_FilePrefix.GEOM)
grad_dfile = data_files.gradient(_FilePrefix.GRAD)
hess_dfile = data_files.hessian(_FilePrefix.HESS)
hfreq_dfile = data_files.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.IRC_INFO: irc_inf_dfile,
_FileAttributeName.GEOM_INPUT: geom_inp_dfile,
_FileAttributeName.GRAD_INPUT: grad_inp_dfile,
_FileAttributeName.HESS_INPUT: hess_inp_dfile,
_FileAttributeName.IRC_INPUT: irc_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
})
return (trunk_ds, branch_ds, leaf_ds)
def conformer(prefix):
""" Create a conformer file system manager for a given path.
Layers:
[0] The "trunk" layer.
Specifiers:
[]
Files:
- info
- energy
- trajectory
Generated by :meth:`autofile.schema.data_series.conformer_trunk`
[1] The "leaf" layer.
Specifiers:
[Conformer ID]
Files:
- geometry_info
- gradient_info
- hessian_info
- geometry_input
- gradient_input
- hessian_input
- energy
- geometry
- gradient
- hessian
- harmonic_frequencies
- vpt2_info
- vpt2_input
- anharmonic_frequencies
- anharmonic_zpve
- anharmonicity_matrix
- vibro_rot_alpha_matrix
- quartic_centrifugal_dist_consts
Generated by :meth:`autofile.schema.data_series.conformer_leaf`
:param prefix: Path to where the file system will be created
:type prefix: str
:returns: A tuple of DataSeries objects. Each item in this tuple manages a
different layer in the file system, as described above.
"""
trunk_ds = data_series.conformer_trunk(prefix)
leaf_ds = data_series.conformer_leaf(prefix, root_ds=trunk_ds)
min_ene_dfile = data_files.energy(_FilePrefix.MIN)
inf_dfile = data_files.information(_FilePrefix.CONF,
function=info_objects.conformer_trunk)
traj_dfile = data_files.trajectory(_FilePrefix.CONF)
trunk_ds.add_data_files({
_FileAttributeName.INFO: inf_dfile,
_FileAttributeName.ENERGY: min_ene_dfile,
_FileAttributeName.TRAJ: traj_dfile
})
geom_inf_dfile = data_files.information(_FilePrefix.GEOM,
function=info_objects.run)
grad_inf_dfile = data_files.information(_FilePrefix.GRAD,
function=info_objects.run)
hess_inf_dfile = data_files.information(_FilePrefix.HESS,
function=info_objects.run)
# need addl vpt2 info file, one for job status and other for fermi
vpt2_inf_dfile = data_files.information(_FilePrefix.VPT2,
function=info_objects.vpt2)
geom_inp_dfile = data_files.input_file(_FilePrefix.GEOM)
grad_inp_dfile = data_files.input_file(_FilePrefix.GRAD)
hess_inp_dfile = data_files.input_file(_FilePrefix.HESS)
vpt2_inp_dfile = data_files.input_file(_FilePrefix.VPT2)
ene_dfile = data_files.energy(_FilePrefix.GEOM)
geom_dfile = data_files.geometry(_FilePrefix.GEOM)
grad_dfile = data_files.gradient(_FilePrefix.GRAD)
hess_dfile = data_files.hessian(_FilePrefix.HESS)
hfreq_dfile = data_files.harmonic_frequencies(_FilePrefix.HESS)
anhfreq_dfile = data_files.anharmonic_frequencies(_FilePrefix.VPT2)
anhzpve_dfile = data_files.anharmonic_zpve(_FilePrefix.VPT2)
xmat_dfile = data_files.anharmonicity_matrix(_FilePrefix.VPT2)
vibrot_mat_dfile = data_files.vibro_rot_alpha_matrix(_FilePrefix.VPT2)
centrif_dist_dfile = data_files.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.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
})
return (trunk_ds, leaf_ds)
def conformer(prefix):
""" Create a conformer file system manager for a given path.
Layers:
[0] The "trunk" layer.
Specifiers:
[]
Generated by :meth:`autofile.schema.data_series.conformer_trunk`
[1] The "branch" layer.
Specifiers:
[Ring ID]
Files:
- info
- energy
- trajectory
Generated by :meth:`autofile.schema.data_series.conformer_branch`
[2] The "leaf" layer.
Specifiers:
[Conformer ID]
Files:
- geometry_info
- gradient_info
- hessian_info
- geometry_input
- gradient_input
- hessian_input
- geometry
- gradient
- hessian
- harmonic_frequencies
- vpt2_info
- vpt2_input
- anharmonic_frequencies
- anharmonic_zpve
- anharmonicity_matrix
- vibro_rot_alpha_matrix
- quartic_centrifugal_dist_consts
- cubic_force_constants
- quartic_force_constants
- dipole_moment
- polarizability
Generated by :meth:`autofile.schema.data_series.conformer_leaf`
:param prefix: Path to where the file system will be created
:type prefix: str
:returns: A tuple of DataSeries objects. Each item in this tuple manages a
different layer in the file system, as described above.
"""
trunk_ds = data_series.conformer_trunk(prefix)
branch_ds = data_series.conformer_branch(prefix, root_ds=trunk_ds)
leaf_ds = data_series.conformer_leaf(prefix, root_ds=branch_ds)
# Trunk Files
inf_dfile = data_files.information(_FilePrefix.RSAMP,
function=info_objects.conformer_trunk)
traj_dfile = data_files.trajectory(_FilePrefix.CONF)
trunk_ds.add_data_files({
FileAttributeName.INFO: inf_dfile,
FileAttributeName.TRAJ: traj_dfile
})
# Branch Files
inf2_dfile = data_files.information(_FilePrefix.CSAMP,
function=info_objects.conformer_branch)
traj2_dfile = data_files.trajectory(_FilePrefix.CONF)
branch_ds.add_data_files({
FileAttributeName.INFO: inf2_dfile,
FileAttributeName.TRAJ: traj2_dfile
})
# Leaf files
geom_inf_dfile = data_files.information(_FilePrefix.GEOM,
function=info_objects.run)
grad_inf_dfile = data_files.information(_FilePrefix.GRAD,
function=info_objects.run)
hess_inf_dfile = data_files.information(_FilePrefix.HESS,
function=info_objects.run)
vpt2_inf_dfile = data_files.information(_FilePrefix.VPT2,
function=info_objects.vpt2)
geom_inp_dfile = data_files.input_file(_FilePrefix.GEOM)
grad_inp_dfile = data_files.input_file(_FilePrefix.GRAD)
hess_inp_dfile = data_files.input_file(_FilePrefix.HESS)
vpt2_inp_dfile = data_files.input_file(_FilePrefix.VPT2)
geom_dfile = data_files.geometry(_FilePrefix.GEOM)
grad_dfile = data_files.gradient(_FilePrefix.GRAD)
hess_dfile = data_files.hessian(_FilePrefix.HESS)
hfreq_dfile = data_files.harmonic_frequencies(_FilePrefix.HESS)
anhfreq_dfile = data_files.anharmonic_frequencies(_FilePrefix.VPT2)
anhzpve_dfile = data_files.anharmonic_zpve(_FilePrefix.VPT2)
xmat_dfile = data_files.anharmonicity_matrix(_FilePrefix.VPT2)
vibrot_mat_dfile = data_files.vibro_rot_alpha_matrix(_FilePrefix.VPT2)
centrif_dist_dfile = data_files.quartic_centrifugal_dist_consts(
_FilePrefix.VPT2)
cubic_fc_dfile = data_files.cubic_force_constants(_FilePrefix.FC)
quartic_fc_dfile = data_files.quartic_force_constants(_FilePrefix.FC)
dip_mom_dfile = data_files.dipole_moment(_FilePrefix.GEOM)
polar_dfile = data_files.polarizability(_FilePrefix.GEOM)
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.GEOM: geom_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,
FileAttributeName.CUBIC_FC: cubic_fc_dfile,
FileAttributeName.QUARTIC_FC: quartic_fc_dfile,
FileAttributeName.DIP_MOM: dip_mom_dfile,
FileAttributeName.POLAR: polar_dfile
})
return (trunk_ds, branch_ds, leaf_ds)