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quasar yaml script
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Ajay Panyala
parent
ac7e8856a5
commit
e490cabc78
1 changed files with 325 additions and 0 deletions
325
contrib/quasar/extract_yaml.py
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325
contrib/quasar/extract_yaml.py
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emitter_yaml = False
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emitter_ruamel = False
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import sys
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try:
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try:
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import ruamel.yaml as ruamel
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except ImportError:
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import ruamel_yaml as ruamel
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emitter_ruamel = True
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except ImportError:
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import yaml
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emitter_yaml = True
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preamble="""
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"$schema": https://microsoft.com/qchem-0.1.schema.json
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"""
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def extract_fields():
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data = {} #yaml.load(initial_input)
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data['format'] = {'version' : '0.1'}
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data['bibliography'] = [{'url' : 'https://www.nwchem-sw.org'}]
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data['generator'] = {'source' : 'nwchem',
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'version' : '6.8'}
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coulomb_repulsion = None
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scf_energy = None
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scf_energy_offset = None
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energy_offset = None
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one_electron_integrals = None
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two_electron_integrals = None
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n_electrons_alpha = None
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n_electrons_beta = None
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n_orbitals = None
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reader_mode = ""
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for line in sys.stdin.readlines():
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ln = line.strip()
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ln_segments = ln.split()
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if len(ln) == 0 or ln[0]=="#": #blank or comment line
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continue
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if reader_mode=="":
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if ln == "============================== echo of input deck ==============================":
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reader_mode = "input_deck"
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elif ln_segments[:2] == ["enrep_tce", "="]:
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coulomb_repulsion = {
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'units' : 'hartree',
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'value' : float(ln_segments[2])
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}
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elif ln_segments[:2] == ["EHF(total)", "="]:
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scf_energy = {
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'units' : 'hartree',
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'value' : float(ln_segments[2])
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}
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elif ln_segments[:3] == ["Shift", "(HFtot-HFA)", "="]:
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scf_energy_offset = {
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'units' : 'hartree',
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'value' : float(ln_segments[3])
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}
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energy_offset = {
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'units' : 'hartree',
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'value' : float(ln_segments[3])
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}
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elif ln == "begin_one_electron_integrals":
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reader_mode = "one_electron_integrals"
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one_electron_integrals = {
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'units' : 'hartree',
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'format' : 'sparse',
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'values' : []
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}
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elif ln == "begin_two_electron_integrals":
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reader_mode = "two_electron_integrals"
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two_electron_integrals = {
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'units' : 'hartree',
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'format' : 'sparse',
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'index_convention' : 'mulliken',
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'values' : []
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}
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elif ln_segments[0] == "q_ele_a":
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assert len(ln_segments) == 2
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n_electrons_alpha = int(ln_segments[1])
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elif ln_segments[0] == "q_ele_b":
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assert len(ln_segments) == 2
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n_electrons_beta = int(ln_segments[1])
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elif ln_segments[0] == "q_orb":
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assert len(ln_segments) == 2
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n_orbitals = int(ln_segments[1])
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elif reader_mode == "input_deck":
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if ln == "================================================================================":
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reader_mode = ""
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elif ln_segments[0:2]== ["geometry", "units"]:
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reader_mode = "input_geometry"
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assert len(ln_segments) == 3
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geometry = {'coordinate_system': 'cartesian'}
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geometry['units'] = ln_segments[2]
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elif ln == "basis":
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reader_mode = "input_basis"
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elif reader_mode=="input_geometry":
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if ln=="end":
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reader_mode = "input_deck"
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elif ln_segments[0] == "symmetry":
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assert len(ln_segments) == 2
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geometry['symmetry'] = ln_segments[1]
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else: #atom description line
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assert len(ln_segments) == 4
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if not 'atoms' in geometry:
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geometry['atoms'] = []
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geometry['atoms'] += [{"name":ln_segments[0],
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"coords":
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[float(ln_segments[1]), float(ln_segments[2]), float(ln_segments[3])]}]
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elif reader_mode == "input_basis":
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if ln == "end":
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reader_mode = "input_deck"
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else:
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assert len(ln_segments) == 3
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assert ln_segments[1] == "library"
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basis_set = {}
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basis_set['name'] = ln_segments[2]
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basis_set['type'] = 'gaussian'
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elif reader_mode == "one_electron_integrals":
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if ln == "end_one_electron_integrals":
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reader_mode = ""
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else:
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assert len(ln_segments) == 3
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one_electron_integrals['values'] += [[
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int(ln_segments[0]),
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int(ln_segments[1]),
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float(ln_segments[2])
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]]
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elif reader_mode == "two_electron_integrals":
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if ln == "end_two_electron_integrals":
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reader_mode = ""
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else:
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assert len(ln_segments) == 5
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two_electron_integrals['values'] += [[
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int(ln_segments[0]),
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int(ln_segments[1]),
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int(ln_segments[2]),
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int(ln_segments[3]),
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float(ln_segments[4])
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]]
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fci_energy = {"units" : "hartree", "value" : 0.0, "upper":0.0, "lower":0.0}
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assert one_electron_integrals is not None, "one_electron_integrals is missing from NWChem output. Required to extract YAML"
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assert two_electron_integrals is not None, "two_electron_integrals is missing from NWChem output. Required to extract YAML"
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assert geometry is not None, "geometry information is missing from NWChem output. Required to extract YAML"
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assert basis_set is not None, "basis_set is missing from NWChem output. Required to extract YAML"
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assert coulomb_repulsion is not None, "coulomb_repulsion is missing from NWChem output. Required to extract YAML"
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assert scf_energy is not None, "scf_energy is missing from NWChem output. Required to extract YAML"
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assert scf_energy_offset is not None, "scf_energy_offset is missing from NWChem output. Required to extract YAML"
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assert energy_offset is not None, "energy_offset is missing from NWChem output. Required to extract YAML"
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assert fci_energy is not None, "fci_energy is missing from NWChem output. Required to extract YAML"
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assert n_orbitals is not None, "n_orbitals is missing from NWChem output. Required to extract YAML"
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assert n_electrons_alpha is not None, "n_electrons_alpha is missing from NWChem output. Required to extract YAML"
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assert n_electrons_beta is not None, "n_electrons_beta is missing from NWChem output. Required to extract YAML"
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hamiltonian = {'one_electron_integrals' : one_electron_integrals,
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'two_electron_integrals' : two_electron_integrals}
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integral_sets = [{"metadata": { 'molecule_name' : 'unknown'},
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"geometry":geometry,
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"basis_set":basis_set,
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"coulomb_repulsion" : coulomb_repulsion,
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"scf_energy" : scf_energy,
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"scf_energy_offset" : scf_energy_offset,
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"energy_offset" : energy_offset,
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"fci_energy" : fci_energy,
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"hamiltonian" : hamiltonian,
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"n_orbitals" : n_orbitals,
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"n_electrons" : n_electrons_alpha + n_electrons_beta }]
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data['integral_sets'] = integral_sets
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return data
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def emitter_ruamel_func():
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yaml = ruamel.YAML(typ="safe")
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#yaml.default_flow_style = False
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print(preamble)
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data = extract_fields()
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yaml.dump(data, sys.stdout)
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def emitter_yaml_func():
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print(preamble)
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data = extract_fields()
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print(yaml.dump(data, default_flow_style=False))
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# def emitter_yaml_func():
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# print(preamble)
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# yformat = {"version" : "0.1"}
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# generator = {"source" : "nwchem",
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# "version" : "6.8"}
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# bibliography = [ {"url" : "https://www.nwchem-sw.org"}] # "doi": "10.1016/j.cpc.2010.04.018"}
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# geometry = { "coordinate_system": "cartesian"}
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# basis_set = {"type" : "gaussian"}
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# metadata = {"molecule" : "unknown"}
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# coulomb_repulsion = {"units" : "hartree"}
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# scf_energy = {"units" : "hartree"}
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# scf_energy_offset = {"units" : "hartree"}
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# energy_offset = {"units" : "hartree"}
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# fci_energy = {"units" : "hartree", "value" : 0.0, "upper":0.0, "lower":0.0}
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# hamiltonian = {}
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# one_electron_integrals = {"units" : "hartree",
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# "format" : "sparse",
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# "values" : []}
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# two_electron_integrals = {"units" : "hartree",
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# "format" : "sparse",
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# "index_convention": "mulliken",
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# "values" : []}
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# n_orbitals = 0
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# n_electrons = None
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# reader_mode = ""
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# for line in sys.stdin.readlines():
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# ln = line.strip()
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# ln_segments = ln.split()
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# if len(ln) == 0 or ln[0]=="#": #blank or comment line
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# continue
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# if reader_mode=="":
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# if ln == "============================== echo of input deck ==============================":
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# reader_mode = "input_deck"
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# elif ln_segments[:2] == ["enrep_tce", "="]:
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# coulomb_repulsion["value"] = float(ln_segments[2])
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# elif ln_segments[:2] == ["EHF(total)", "="]:
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# scf_energy["value"] = float(ln_segments[2])
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# elif ln_segments[:3] == ["Shift", "(HFtot-HFA)", "="]:
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# scf_energy_offset["value"] = float(ln_segments[3])
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# energy_offset["value"] = float(ln_segments[3])
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# elif ln == "begin_one_electron_integrals":
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# reader_mode = "one_electron_integrals"
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# elif ln == "begin_two_electron_integrals":
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# reader_mode = "two_electron_integrals"
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# elif ln_segments[0] == "q_ele_a":
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# assert len(ln_segments) == 2
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# if n_electrons is None:
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# n_electrons = int(ln_segments[1])
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# else:
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# n_electrons += int(ln_segments[1])
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# elif ln_segments[0] == "q_ele_b":
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# assert len(ln_segments) == 2
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# if n_electrons is None:
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# n_electrons = int(ln_segments[1])
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# else:
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# n_electrons += int(ln_segments[1])
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# elif ln_segments[0] == "q_orb":
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# assert len(ln_segments) == 2
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# n_orbitals = int(ln_segments[1])
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# elif reader_mode == "input_deck":
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# if ln == "================================================================================":
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# reader_mode = ""
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# elif ln_segments[0:2]== ["geometry", "units"]:
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# reader_mode = "input_geometry"
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# assert len(ln_segments) == 3
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# geometry["units"] = ln_segments[2]
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# #geometry["symmetry"] = ln.split()[1]
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# elif ln == "basis":
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# reader_mode = "input_basis"
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# elif reader_mode=="input_geometry":
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# if ln=="end":
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# reader_mode = "input_deck"
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# elif ln_segments[0] == "symmetry":
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# assert len(ln_segments) == 2
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# geometry["symmetry"] = ln_segments[1]
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# else: #atom description line
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# assert len(ln_segments) == 4
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# if not "atoms" in geometry:
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# geometry["atoms"] = []
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# geometry["atoms"] += [{"name":ln_segments[0], "coords":
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# [float(ln_segments[1]), float(ln_segments[2]), float(ln_segments[3])]}]
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# elif reader_mode == "input_basis":
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# if ln == "end":
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# reader_mode = "input_deck"
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# else:
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# assert len(ln_segments) == 3
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# assert ln_segments[1] == "library"
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# basis_set["name"] = ln_segments[2]
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# elif reader_mode == "one_electron_integrals":
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# if ln == "end_one_electron_integrals":
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# reader_mode = ""
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# else:
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# assert len(ln_segments) == 3
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# one_electron_integrals["values"] += [[
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# int(ln_segments[0]),
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# int(ln_segments[1]),
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# float(ln_segments[2])
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# ]]
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# elif reader_mode == "two_electron_integrals":
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# if ln == "end_two_electron_integrals":
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# reader_mode = ""
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# else:
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# assert len(ln_segments) == 5
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# two_electron_integrals["values"] += [[
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# int(ln_segments[0]),
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# int(ln_segments[1]),
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# int(ln_segments[2]),
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# int(ln_segments[3]),
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# float(ln_segments[4])
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# ]]
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# hamiltonian["one_electron_integrals"] = one_electron_integrals
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# hamiltonian["two_electron_integrals"] = two_electron_integrals
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# output = {"format" : yformat,
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# "generator" : generator,
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# "bibliography" : bibliography,
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# "integral_sets":
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# [{"metadata":metadata,
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# "geometry":geometry,
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# "basis_set":basis_set,
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# "coulomb_repulsion" : coulomb_repulsion,
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# "scf_energy" : scf_energy,
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# "scf_energy_offset" : scf_energy_offset,
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# "energy_offset" : energy_offset,
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# "fci_energy" : fci_energy,
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# "hamiltonian" : hamiltonian,
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# "n_orbitals" : n_orbitals,
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# "n_electrons" : n_electrons }]}
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# print(yaml.dump(output, default_flow_style=False))
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def main():
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assert emitter_yaml or emitter_ruamel, "Extraction failed: could not import YAML or RUAMEL packages."
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if emitter_yaml:
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emitter_yaml_func()
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elif emitter_ruamel:
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emitter_ruamel_func()
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else:
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assert False #unreachable code
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if __name__ == "__main__":
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main()
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