disp: propagate dispersion citations

psi4/driver/procrouting/dft_funcs/dict_builder.py

@@ -71,7 +71,7 @@
      "dispersion":  {          definition of dispersion corrections
                "type": "",       dispersion type - "d2", "d3zero", "d3bj" etc., see empirical_dispersion.py
              "params": {},       parameters for the dispersion correction
-           "citation": "",       special reference for the dispersion correction, appended to output
+           "citation": "",       special reference for the dispersion correction parameters, appended to output
     },
 }
 """
@@ -122,8 +122,7 @@ def get_functional_aliases(functional_dict):
     # if the parent functional is already dispersion corrected, skip to next
     if "dispersion" in dict_functionals[functional_name]:
         disp = dict_functionals[functional_name]['dispersion']
-        dashcoeff_supplement[disp['type']]['definitions'][functional_name] = disp['params']
-        # TODO still needs citation
+        dashcoeff_supplement[disp['type']]['definitions'][functional_name] = disp
         # this is to "bless" dft_funcs dispersion definitions
         continue
 
@@ -134,13 +133,8 @@ def get_functional_aliases(functional_dict):
             if dispersion_functional.lower() in functional_aliases:
                 func = copy.deepcopy(dict_functionals[functional_name])
                 func["name"] += "-" + resolved_dispersion_level
-                func["dispersion"] = dict()
-
-                # we need to pop the citation as the EmpiricalDispersion class only expects dashparams
-                if "citation" in intf_dftd3.dashcoeff[resolved_dispersion_level]['definitions'][dispersion_functional]:
-                    func["dispersion"]["citation"] = intf_dftd3.dashcoeff[resolved_dispersion_level]['definitions'][dispersion_functional].pop("citation")
+                func["dispersion"] = copy.deepcopy(intf_dftd3.dashcoeff[resolved_dispersion_level]['definitions'][dispersion_functional])
                 func["dispersion"]["type"] = resolved_dispersion_level
-                func["dispersion"]["params"] = intf_dftd3.dashcoeff[resolved_dispersion_level]['definitions'][dispersion_functional]
 
                 # this ensures that M06-2X-D3, M06-2X-D3ZERO, M062X-D3 or M062X-D3ZERO
                 #   all point to the same method (M06-2X-D3ZERO)
@@ -202,6 +196,28 @@ def check_consistency(func_dictionary):
         raise ValidationError(
             "SCF: Libxc parameters requested for an exchange functional not defined as a component of %s." % (name))
 
+    # 3) checks would be caught at runtime or involve only formatting.
+    #    included here to preempt driver definition problems, if specific fctl not in tests.
+    # 3a) check formatting for citation
+    if "citation" in func_dictionary:
+        cit = func_dictionary["citation"]
+        if cit and not (cit.startswith('    ') and cit.endswith('\n')):
+            raise ValidationError("SCF: All citations should have the form '    A. Student, B. Prof, J. Goodstuff Vol, Page, Year\n', not : {}".format(cit))
+    if "dispersion" in func_dictionary:
+        disp = func_dictionary["dispersion"]
+    # 3b) check dispersion type present and known
+        if "type" not in disp or disp["type"] not in _dispersion_aliases:
+            raise ValidationError("SCF: Dispersion type ({}) should be among ({})".format(disp['type'], _dispersion_aliases.keys()))
+    # 3c) check dispersion params complete
+        allowed_params = sorted(intf_dftd3.dashcoeff[_dispersion_aliases[disp["type"]]]["default"].keys())
+        if "params" not in disp or sorted(disp["params"].keys()) != allowed_params:
+            raise ValidationError("SCF: Dispersion params ({}) must include all ({})".format(list(disp['params'].keys()), allowed_params))
+    # 3d) check formatting for dispersion citation
+        if "citation" in disp:
+            cit = disp["citation"]
+            if cit and not (cit.startswith('    ') and cit.endswith('\n')):
+                raise ValidationError("SCF: All citations should have the form '    A. Student, B. Prof, J. Goodstuff Vol, Page, Year\n', not : {}".format(cit))
+
 
 def build_superfunctional_from_dictionary(func_dictionary, npoints, deriv, restricted):
     """

psi4/driver/procrouting/dft_funcs/dict_gga_funcs.py

@@ -166,8 +166,8 @@
         "GGA_C_P86": {}
     },
     "citation":
-    '   A. D. Becke, Phys. Rev. A, 38, 3098-3100, 1988\n' + \
-    '   J. P. Perdew, Phys. Rev. B, 33, 8822, 1986\n',
+    '    A. D. Becke, Phys. Rev. A, 38, 3098-3100, 1988\n' + \
+    '    J. P. Perdew, Phys. Rev. B, 33, 8822, 1986\n',
     "description":
     '    BP86 GGA Exchange-Correlation Functional\n',
 })

psi4/driver/procrouting/dft_funcs/dict_mgga_funcs.py

@@ -146,7 +146,7 @@
         "MGGA_C_TPSS": {}
     },
     "description": '    TPSS Meta-GGA XC Functional\n',
-    "citation": '   J. Tao, et al., Phys. Rev. Lett., 91, 146401, 2003\n',
+    "citation": '    J. Tao, et al., Phys. Rev. Lett., 91, 146401, 2003\n',
 })
 
 funcs.append({
@@ -158,7 +158,7 @@
         "MGGA_C_REVTPSS": {}
     },
     "description": '    revised TPSS Meta-GGA XC Functional\n',
-    "citation": '   J. Sun  et. al., Phys. Rev. B, 84, 035117, 2011\n',
+    "citation": '    J. Sun  et. al., Phys. Rev. B, 84, 035117, 2011\n',
 })
 
 funcs.append({
@@ -170,7 +170,7 @@
         "MGGA_C_PKZB": {}
     },
     "description": '    PKZB Meta-GGA XC Functional\n',
-    "citation": '   J.P. Perdew, S. Kurth, A. Zupan, P. Blaha, Phys. Rev. Lett. 82, 2544, 1999\n',
+    "citation": '    J.P. Perdew, S. Kurth, A. Zupan, P. Blaha, Phys. Rev. Lett. 82, 2544, 1999\n',
 })
 
 funcs.append({

psi4/driver/procrouting/dft_funcs/dict_xc_funcs.py

@@ -37,9 +37,9 @@
 funcs.append({"name": "TETER93"        , "xc_functionals": {"LDA_XC_TETER93"            : {}}})
 funcs.append({"name": "ZLP"            , "xc_functionals": {"LDA_XC_ZLP"                : {}}})
 funcs.append({"name": "KSDT"           , "xc_functionals": {"LDA_XC_KSDT"               : {}}})
-funcs.append({"name": "OPBE-D"         , "xc_functionals": {"GGA_XC_OPBE_D"             : {}}, "dispersion": {"type": "d2", "params": {'s6': 1.0,  'alpha6': 20.0, 'sr6': 1.15}, "citation": '    L. Goerigk, S. Grimme, J. Chem. Theory. Comput. 6, 107-126, 2010'}})
-funcs.append({"name": "OPWLYP-D"       , "xc_functionals": {"GGA_XC_OPWLYP_D"           : {}}, "dispersion": {"type": "d2", "params": {'s6': 1.0,  'alpha6': 20.0, 'sr6': 1.15}, "citation": '    L. Goerigk, S. Grimme, J. Chem. Theory. Comput. 6, 107-126, 2010'}})
-funcs.append({"name": "OBLYP-D"        , "xc_functionals": {"GGA_XC_OBLYP_D"            : {}}, "dispersion": {"type": "d2", "params": {'s6': 1.0,  'alpha6': 20.0, 'sr6': 1.15}, "citation": '    L. Goerigk, S. Grimme, J. Chem. Theory. Comput. 6, 107-126, 2010'}})
+funcs.append({"name": "OPBE-D"         , "xc_functionals": {"GGA_XC_OPBE_D"             : {}}, "dispersion": {"type": "d2", "params": {'s6': 1.0,  'alpha6': 20.0, 'sr6': 1.15}, "citation": '    L. Goerigk, S. Grimme, J. Chem. Theory. Comput. 6, 107-126, 2010\n'}, 'alias': ['OPBE-D2']})
+funcs.append({"name": "OPWLYP-D"       , "xc_functionals": {"GGA_XC_OPWLYP_D"           : {}}, "dispersion": {"type": "d2", "params": {'s6': 1.0,  'alpha6': 20.0, 'sr6': 1.15}, "citation": '    L. Goerigk, S. Grimme, J. Chem. Theory. Comput. 6, 107-126, 2010\n'}, 'alias': ['OPWLYP-D2']})
+funcs.append({"name": "OBLYP-D"        , "xc_functionals": {"GGA_XC_OBLYP_D"            : {}}, "dispersion": {"type": "d2", "params": {'s6': 1.0,  'alpha6': 20.0, 'sr6': 1.15}, "citation": '    L. Goerigk, S. Grimme, J. Chem. Theory. Comput. 6, 107-126, 2010\n'}, 'alias': ['OBLYP-D2']})
 funcs.append({"name": "HCTH407P"       , "xc_functionals": {"GGA_XC_HCTH_407P"          : {}}})
 funcs.append({"name": "HCTHP76"        , "xc_functionals": {"GGA_XC_HCTH_P76"           : {}}})
 funcs.append({"name": "HCTHP14"        , "xc_functionals": {"GGA_XC_HCTH_P14"           : {}}})
@@ -135,7 +135,7 @@
 funcs.append({"name": "revTPSSh"       , "xc_functionals": {"HYB_MGGA_XC_REVTPSSH"      : {}}})
 funcs.append({"name": "wB97M-V"        , "xc_functionals": {"HYB_MGGA_XC_WB97M_V"       : {}}, "alias": ["WB97MV"]})
 funcs.append({"name": "ZLP"            , "xc_functionals": {"MGGA_XC_ZLP"               : {}}})
-funcs.append({"name": "OTPSS-D"        , "xc_functionals": {"MGGA_XC_OTPSS_D"           : {}}, "dispersion": {"type": "d2", "params": {'s6': 1.0,  'alpha6': 20.0, 'sr6': 1.15}, "citation": '    L. Goerigk, S. Grimme, J. Chem. Theory. Comput. 6, 107-126, 2010'}})
+funcs.append({"name": "OTPSS-D"        , "xc_functionals": {"MGGA_XC_OTPSS_D"           : {}}, "dispersion": {"type": "d2", "params": {'s6': 1.0,  'alpha6': 20.0, 'sr6': 1.15}, "citation": '    L. Goerigk, S. Grimme, J. Chem. Theory. Comput. 6, 107-126, 2010\n'}, 'alias': ['OTPSS-D2']})
 funcs.append({"name": "TPSSLYP1W"      , "xc_functionals": {"MGGA_XC_TPSSLYP1W"         : {}}})
 funcs.append({"name": "B97M-V"         , "xc_functionals": {"MGGA_XC_B97M_V"            : {}}})
 funcs.append({"name": "B5050LYP"       , "xc_functionals": {"HYB_GGA_XC_B5050LYP"       : {}}})

psi4/driver/procrouting/empirical_dispersion.py

@@ -71,6 +71,10 @@ class EmpiricalDispersion(object):
     dashlevel_citation : str
         Literature reference for dispersion `dashlevel` in general,
         *not necessarily* for `dashparams`.
+    dashparams_citation : str
+        Literature reference for dispersion parameters, if `dashparams`
+        corresponds to a defined, named, untweaked "functional-dashlevel"
+        set with a citation. Otherwise, empty string.
     dashcoeff_supplement : dict
         See description in `qcdb.intf_dftd3.dashparam.from_arrays`. Used
         here to "bless" the dispersion definitions attached
@@ -127,6 +131,7 @@ def __init__(self, name_hint=None, level_hint=None, param_tweaks=None, **kwargs)
         self.description = intf_dftd3.dashcoeff[self.dashlevel]['description']
         self.ordered_params = intf_dftd3.dashcoeff[self.dashlevel]['default'].keys()
         self.dashlevel_citation = intf_dftd3.dashcoeff[self.dashlevel]['citation']
+        self.dashparams_citation = resolved['dashparams_citation']
 
         engine = kwargs.pop('engine', None)
         if engine is None:
@@ -140,38 +145,22 @@ def __init__(self, name_hint=None, level_hint=None, param_tweaks=None, **kwargs)
         if self.engine == 'libdisp':
             self.disp = core.Dispersion.build(self.dashlevel, **resolved['dashparams'])
 
-    #    # 5) Override parameters from user input
-    #    # 5a) pop citation if present
-    #    if "citation" in kwargs:
-    #        custom_citation = kwargs.pop("citation")
-    #    else:
-    #        custom_citation = False
-
-    #    if len(kwargs):
-    #        raise Exception("The following parameters in empirical_dispersion.py were not understood for %s dispersion type: %s" %
-    #                        (dtype, ', '.join(kwargs.keys())))
-
-    #    # 6) Process citations
-    #    # 6a) Set default citations for method
-    #    self.description = intf_dftd3.dashcoeff[self.dtype[1:]]['description']
-    #    # 6b) add custom citations if available
-    #    if custom_citation:
-    #        self.citation += "\n    Parametrisation from: \n" + custom_citation
-
     def print_out(self):
         """Format dispersion parameters of `self` for output file."""
 
-        core.print_out("   => %s: Empirical Dispersion <=\n\n" % self.fctldash.upper())
-        core.print_out(self.description + "\n")
-
-        # TODO core.print_out(self.citation + "\n\n")
-
-        if self.engine == 'nl':
-            return
-
+        text = []
+        text.append("   => %s: Empirical Dispersion <=" % (self.fctldash.upper() if self.fctldash.upper() else 'Custom'))
+        text.append('')
+        text.append(self.description)
+        text.append(self.dashlevel_citation.rstrip())
+        if self.dashparams_citation:
+            text.append("    Parametrisation from:{}".format(self.dashparams_citation.rstrip()))
+        text.append('')
         for op in self.ordered_params:
-            core.print_out("    %6s = %14.6f\n" % (op, self.dashparams[op]))
-        core.print_out("\n")
+            text.append("    %6s = %14.6f" % (op, self.dashparams[op]))
+        text.append('\n')
+
+        core.print_out('\n'.join(text))
 
     def compute_energy(self, molecule):
         """Compute dispersion energy based on engine, dispersion level, and parameters in `self`.

psi4/driver/procrouting/proc.py

@@ -1016,17 +1016,18 @@ def scf_wavefunction_factory(name, ref_wfn, reference, **kwargs):
 
     if disp_type:
         if isinstance(name, dict):
+            # user dft_functional={} spec - type for lookup, dict val for param defs,
+            #   name & citation discarded so only param matches to existing defs will print labels
             wfn._disp_functor = empirical_dispersion.EmpiricalDispersion(
                 name_hint='',
                 level_hint=disp_type["type"],
-                citation=disp_type["citation"],
                 param_tweaks=disp_type["params"],
                 engine=kwargs.get('engine', None))
         else:
+            # dft/*functionals.py spec - name & type for lookup, option val for param tweaks
             wfn._disp_functor = empirical_dispersion.EmpiricalDispersion(
                 name_hint=superfunc.name(),
                 level_hint=disp_type["type"],
-                citation=disp_type["citation"],
                 param_tweaks=modified_disp_params,
                 engine=kwargs.get('engine', None))
 
@@ -1035,12 +1036,12 @@ def scf_wavefunction_factory(name, ref_wfn, reference, **kwargs):
         #   ever again sighted, make an issue so this code can accommodate.
 
         wfn._disp_functor.print_out()
-        if (disp_type["type"] == 'nl'):
+        if disp_type["type"] == 'nl':
             del wfn._disp_functor
 
     # Set the DF basis sets
-    if ("DF" in core.get_global_option("SCF_TYPE")) or \
-       (core.get_option("SCF", "DF_SCF_GUESS") and (core.get_global_option("SCF_TYPE") == "DIRECT")):
+    if (("DF" in core.get_global_option("SCF_TYPE")) or
+            (core.get_option("SCF", "DF_SCF_GUESS") and (core.get_global_option("SCF_TYPE") == "DIRECT"))):
         aux_basis = core.BasisSet.build(wfn.molecule(), "DF_BASIS_SCF",
                                         core.get_option("SCF", "DF_BASIS_SCF"),
                                         "JKFIT", core.get_global_option('BASIS'),