def theory(prefix):
""" construct the theory filesystem (1 layer)
locators:
0 - [method, basis, orb_type]
files:
- energy
- geometry
- hessian
- zmatrix
- instability trajectory
- instability reactant_graph
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
leaf_ds = data_series.theory_leaf(prefix)
geom_dfile = data_files.geometry(_FilePrefix.GEOM)
ene_dfile = data_files.energy(_FilePrefix.GEOM)
zmat_dfile = data_files.zmatrix(_FilePrefix.GEOM)
hess_dfile = data_files.hessian(_FilePrefix.HESS)
graph_dfile = data_files.graph(_FilePrefix.INSTAB)
trans_dfile = data_files.transformation(_FilePrefix.INSTAB)
leaf_ds.add_data_files({
_FileAttributeName.ENERGY: ene_dfile,
_FileAttributeName.GEOM: geom_dfile,
_FileAttributeName.HESS: hess_dfile,
_FileAttributeName.ZMAT: zmat_dfile,
_FileAttributeName.REACTANT_GRAPH: graph_dfile,
_FileAttributeName.TRANS: trans_dfile
})
return (leaf_ds, )
def transition_state(prefix):
""" construct the ts filesystem (1 layer)
locators:
0 - []
files:
- energy
- geometry
- zmatrix
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
trunk_ds = data_series.transition_state_trunk(prefix)
geom_dfile = data_files.geometry(_FilePrefix.GEOM)
ene_dfile = data_files.energy(_FilePrefix.GEOM)
zmat_dfile = data_files.zmatrix(_FilePrefix.GEOM)
vmat_dfile = data_files.vmatrix(_FilePrefix.GEOM)
trunk_ds.add_data_files({
_FileAttributeName.ENERGY: ene_dfile,
_FileAttributeName.GEOM: geom_dfile,
_FileAttributeName.ZMAT: zmat_dfile,
_FileAttributeName.VMATRIX: vmat_dfile
})
return (trunk_ds, )
def zmatrix(prefix):
""" Create a z-matrix file system manager for a given path.
Layers:
[0] The zmatrix "trunk" layer.
Specifiers:
[]
(no files)
Generated by :meth:`autofile.schema.data_series.zmatrix_trunk`
[1] The zmatrix "leaf" layer.
Specifiers:
[Z-Matrix Number]
Files:
-
Generated by :meth:`autofile.schema.data_series.zmatrix_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.zmatrix_trunk(prefix)
leaf_ds = data_series.zmatrix_leaf(prefix, root_ds=trunk_ds)
zmat_inf_dfile = data_files.information(_FilePrefix.ZMAT,
function=info_objects.run)
zmat_inp_dfile = data_files.input_file(_FilePrefix.ZMAT)
inf_dfile = data_files.information(_FilePrefix.CONF,
function=info_objects.conformer_trunk)
zmat_dfile = data_files.zmatrix(_FilePrefix.ZMAT)
vma_dfile = data_files.vmatrix(_FilePrefix.ZMAT)
graph_dfile = data_files.graph(_FilePrefix.ZMAT)
trans_dfile = data_files.transformation(_FilePrefix.ZMAT)
leaf_ds.add_data_files({
_FileAttributeName.GEOM_INFO: zmat_inf_dfile,
_FileAttributeName.TORS_INFO: inf_dfile,
_FileAttributeName.GEOM_INPUT: zmat_inp_dfile,
_FileAttributeName.ZMAT: zmat_dfile,
_FileAttributeName.VMATRIX: vma_dfile,
_FileAttributeName.REACTANT_GRAPH: graph_dfile,
_FileAttributeName.TRANS: trans_dfile
})
return (trunk_ds, leaf_ds)
def zmatrix(prefix):
""" Create a z-matrix file system manager for a given path.
Layers:
[0] The zmatrix "trunk" layer.
Specifiers:
[]
(no files)
Generated by :meth:`autofile.schema.data_series.zmatrix_trunk`
[1] The zmatrix "leaf" layer.
Specifiers:
[Z-Matrix Number]
Files:
-
Generated by :meth:`autofile.schema.data_series.zmatrix_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.zmatrix_trunk(prefix)
leaf_ds = data_series.zmatrix_leaf(prefix, root_ds=trunk_ds)
instab_inf_dfile = data_files.instability(_FilePrefix.INSTAB)
zmat_inf_dfile = data_files.information(_FilePrefix.ZMAT,
function=info_objects.run)
zmat_inp_dfile = data_files.input_file(_FilePrefix.ZMAT)
tors_dfile = data_files.torsions(_FilePrefix.ZMAT)
rtors_dfile = data_files.ring_torsions(_FilePrefix.ZMAT)
zmat_dfile = data_files.zmatrix(_FilePrefix.ZMAT)
reac_dfile = data_files.reaction(_FilePrefix.ZMAT)
leaf_ds.add_data_files({
FileAttributeName.INSTAB: instab_inf_dfile,
FileAttributeName.GEOM_INFO: zmat_inf_dfile,
FileAttributeName.TORS: tors_dfile,
FileAttributeName.RTORS: rtors_dfile,
FileAttributeName.GEOM_INPUT: zmat_inp_dfile,
FileAttributeName.ZMAT: zmat_dfile,
FileAttributeName.REAC: reac_dfile
})
return (trunk_ds, leaf_ds)
def run(prefix):
""" construct the run filesystem (2 layers)
locators:
0 - []
files:
- info
1 - [job]
files:
- info
- input
- output
- geometry
- zmatrix
:param prefix: sets the path where this filesystem will sit
:type prefix: str
"""
trunk_ds = data_series.run_trunk(prefix)
leaf_ds = data_series.run_leaf(prefix, root_ds=trunk_ds)
inf_dfile = data_files.information(_FilePrefix.RUN,
function=info_objects.run)
inp_dfile = data_files.input_file(_FilePrefix.RUN)
out_dfile = data_files.output_file(_FilePrefix.RUN)
geom_dfile = data_files.geometry(_FilePrefix.GEOM)
zmat_dfile = data_files.zmatrix(_FilePrefix.ZMAT)
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,
_FileAttributeName.GEOM: geom_dfile,
_FileAttributeName.ZMAT: zmat_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)